non-target      shRNA in K562      Control: NT-BGKLV38-D

General Information

List KD experiments controlled by BGKLV38-1 and BGKLV38-2


NT-BGKLV38-1C,NT-BGKLV38-2C:
  • ABT1-BGKLV38-K562
  • FUBP1-BGKLV38-K562
  • NUP35-BGKLV38-K562
  • PRPF4-BGKLV38-K562
  • XPO1-BGKLV38-K562
  • XRN1-BGKLV38-K562

    • NT-BGKLV38-1,NT-BGKLV38-2 (alias:NT_BGKLV38-1,NT_BGKLV38-2):
  • AQR-BGKLV38-K562
  • AUH-BGKLV38-K562
  • WRN-BGKLV38-K562
  • ZC3H8-BGKLV38-K562

    • NT-BGKLV38-1B,NT-BGKLV38-2B (alias:NT-BGKLV38-1B,NT-BGKLV38-2B):
  • UTP3-BGKLV38-K562_A

    • NT-BGKLV38-1D,NT-BGKLV38-2D:
  • UTP3-BGKLV38-K562




    • Experiment Information (Status: Released)
    BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2
    idx772924773925
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target-D12non-targetnon-target-D12
    Sample_IDBGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2
    transduction_Date9/15/169/15/169/15/169/15/16
    days
    RBP_namenon-targetnon-targetnon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc0023882718
    WB_result
    Ave_WB
    WB_DONE_date
    MW
    IP
    antibody_Cat#
    Antibody DCC ID
    submitted_to_DCC_date
    Rep1_TPM0000
    Rep2_TPM0000
    Action
    Library_start_date11/3/1611/3/16
    repeat_library05/11/1705/11/17
    Note
    ID86510238661024




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    Sample_IDBGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    Sample NameNT-BGKLV38-1CNT_BGKLV38-1NT-BGKLV38-1BNT-BGKLV38-2CNT_BGKLV38-2NT-BGKLV38-2B
    Sample NameNT-BGKLV38-1CNT_BGKLV38-1NT-BGKLV38-1BNT-BGKLV38-1DNT-BGKLV38-2CNT_BGKLV38-2NT-BGKLV38-2BNT-BGKLV38-2D
    RBPnon-targetnon-targetnon-targetnon-targetnon-targetnon-targetnon-targetnon-target
    Cell_LineK562K562K562K562K562K562K562K562
    Exp UID
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_date2021-03-182016-12-122017-11-202022-03-072021-03-182016-12-122017-11-202022-03-07
    ProjectENCODE4ENCODE3ENCODE3ENCODE4ENCODE4ENCODE3ENCODE3ENCODE4
    Note
    ID11013091341104471111310134210448




    Library-Prep Information
    BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    Sample #55675668
    Sample NameNT-BGKLV38-1CNT-BGKLV38-1NT-BGKLV38-1BNT-BGKLV38-1DNT-BGKLV38-2CNT-BGKLV38-2NT-BGKLV38-2BNT-BGKLV38-2D
    Sample_Name_AliasNT_BGKLV38-1NT-BGKLV38-1BNT_BGKLV38-2NT-BGKLV38-2B
    Index Well PositionS09S09S11S11S10S10S12S12
    Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
    LibPrep_date2018-01-022016-11-032017-05-112018-11-192018-01-022016-11-032017-05-112018-11-19
    Lib_IDLib-180102Lib-161103Lib-170511Lib-181119Lib-180102Lib-161103Lib-170511Lib-181119
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp279292278293
    Peak_Molarity9.9956.5011.0058.50
    libSampleQC_DNA_WellDNA_Library_set40/set1/A9.pngDNA_Library_LV37-38/set1/A5.pngDNA_Library_set39/set2/C6.pngDNA_Library_set41/set1/C8.pngDNA_Library_set40/set1/B9.pngDNA_Library_LV37-38/set1/B5.pngDNA_Library_set39/set2/D6.pngDNA_Library_set41/set1/D8.png
    RIN9.79.79.79.79.29.29.29.2
    libSample_RNA_WellRNA_Library_LV37_38/set2/E2.pngRNA_Library_LV37_38/set2/E2.pngRNA_Library_LV37_38/set2/E2.pngRNA_Library_LV37_38/set2/E2.pngRNA_Library_LV37_38/set1/B3.pngRNA_Library_LV37_38/set1/B3.pngRNA_Library_LV37_38/set1/B3.pngRNA_Library_LV37_38/set1/B3.png
    SampleQC_methodTapeStationTapeStationTapeStationTapeStation
    SampleQC_date2018-01-022022-03-012018-01-022022-03-01
    Sample_IDBGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    RBPNTNTNTNTNTNTNTNT
    Batch_IDBGKLV38BGKLV38BGKLV38BGKLV38BGKLV38BGKLV38BGKLV38BGKLV38
    WB_result0.0000.0000.0000.0000.0000.0000.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
    Repeat_Library_SuffixCBDCBD
    Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequenceSendToSequenceSendToSequenceSendToSequenceSendToSequence
    ProjectENCODE4ENCODE3ENCODE3ENCODE4ENCODE4ENCODE3ENCODE3ENCODE4
    ID978299830383244979299930393245




    Sequencing Information
    BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    Sample_IDBGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    Sample NameNT-BGKLV38-1CNT_BGKLV38-1NT-BGKLV38-1BNT-BGKLV38-1DNT-BGKLV38-2CNT_BGKLV38-2NT-BGKLV38-2BNT-BGKLV38-2D
    Pool IDPool-180109Pool-161129Pool-170911Pool-181119Pool-180109Pool-161129Pool-170911Pool-181119
    LocalServer_folderset40_Kset38set39_Kset41_spikeinsset40_Kset38set39_Kset41_spikeins
    total_reads44,057,730103,000,00084,494,51242,242,40659,084,21089,064,52871,931,01639,589,168
    total_aligned_reads32,236,44894,526,24475,498,39841,336,51644,943,11883,786,60664,086,29038,582,864
    unique_aligned_reads29,443,18486,349,50068,690,20437,520,68840,906,18476,508,45658,681,11835,233,288
    percent_uniqueAligned0.668290.838340.812950.888220.692340.859020.815800.88997
    correlation_replicates0.9936020.9964840.9968230.9967900.9936020.9964840.9968230.996790
    spikein_reads12,466210,8921871,36012,076223,3862064,718
    percent_spikeins0.000280.002050.001690.000200.002510.00163
    original_ReadLength100100100100100100100100
    QC_StatusSubmittedSubmittedSubmittedSubmittedSubmittedSubmittedSubmittedSubmitted
    ID381164716931957382164816941958




    Data Submission Information
    BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    ENCODE_aliasbrenton-graveley:NT-BGKLV38-Cbrenton-graveley:NT_BGKLV38-1brenton-graveley:L-NT-BGKLV38-1Cbrenton-graveley:NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gzbrenton-graveley:NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gzbrenton-graveley:NT_BGKLV38brenton-graveley:NT-BGKLV38-Bbrenton-graveley:NT-BGKLV38-Dbrenton-graveley:L-NT-BGKLV38-1Dbrenton-graveley:NT_BGKLV38-2brenton-graveley:L-NT-BGKLV38-2Cbrenton-graveley:NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gzbrenton-graveley:NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gzbrenton-graveley:L-NT-BGKLV38-2D
    ENCODE_accessionENCSR260BQCENCBS800AVHENCLB341NEHENCFF475HIXENCFF860QVJENCSR718EWLENCSR024FOFENCSR655JYCENCLB037RHFENCBS458BDUENCLB911HYZENCFF687PMRENCFF204IKWENCLB169DYG
    object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2experimentexperimentexperimentlibrarybiosamplelibraryfile_fastq1file_fastq2library
    assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seq
    Sample_IDBGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-1BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2BGKLV38-2
    Sample NameNT-BGKLV38-1CNT_BGKLV38-1NT-BGKLV38-1CNT-BGKLV38-1CNT-BGKLV38-1CNT_BGKLV38-1NT-BGKLV38-1BNT-BGKLV38-1DNT-BGKLV38-1DNT_BGKLV38-2NT-BGKLV38-2CNT-BGKLV38-2CNT-BGKLV38-2CNT-BGKLV38-2D
    SelectedYesYesYesYesYesYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2022-03-072019-03-132022-03-072022-03-072022-03-072022-03-072022-03-072022-03-072022-03-072019-03-132022-03-072022-03-072022-03-072022-03-07
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE3ENCODE3ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV38_biosample_protocol_WESLV40_library_protocolLV41_library_protocol_spikeinsLV38_biosample_protocol_WESLV40_library_protocolLV41_library_protocol_spikeins
    protocol_URLNT_BGKLV38-1.pdfL-NT-BGKLV38-1C.pdfL-NT-BGKLV38-1D.pdfNT_BGKLV38-2.pdfL-NT-BGKLV38-2C.pdfL-NT-BGKLV38-2D.pdf
    ID14461490154616611694319432107376739314911547166216957394




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gzENCODE_DATA/set40_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab381HiSeq2500100paired-ended1ENCODE4744
    NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gzENCODE_DATA/set40_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab381HiSeq2500100paired-ended2ENCODE4787
    NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gzENCODE_DATA/set38/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1647HiSeq2500100paired-ended1ENCODE322178
    NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gzENCODE_DATA/set38/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1647HiSeq2500100paired-ended2ENCODE322190
    NT_BGKLV38-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set38/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1647GRCh38V40NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gzENCORE222202
    NT_BGKLV38-1_Signal.Unique.strand+.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1647GRCh38V40NT_BGKLV38-1/Aligned.sortedByCoord.out.bamENCORE222214
    NT_BGKLV38-1_Signal.Unique.strand-.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1647GRCh38V40NT_BGKLV38-1/Aligned.sortedByCoord.out.bamENCORE222226
    NT_BGKLV38-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1647GRCh38V40NT_BGKLV38-1/Aligned.sortedByCoord.out.bamENCORE222238
    NT_BGKLV38-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1647GRCh38V40NT_BGKLV38-1/Aligned.sortedByCoord.out.bamENCORE222250
    NT_BGKLV38-1_quant.sfENCODE_DATA/set38/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1647GRCh38V40NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gzENCORE222262
    NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R1.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1693HiSeq2500100paired-ended1ENCODE322474
    NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R2.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1693HiSeq2500100paired-ended2ENCODE322510
    NT-BGKLV38-1B_Aligned.sortedByCoord.out.bamENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1693GRCh38V40NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R1.fastq.gz,NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R2.fastq.gzENCORE222546
    NT-BGKLV38-1B_Signal.Unique.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1693GRCh38V40NT-BGKLV38-1B/Aligned.sortedByCoord.out.bamENCORE222582
    NT-BGKLV38-1B_Signal.Unique.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1693GRCh38V40NT-BGKLV38-1B/Aligned.sortedByCoord.out.bamENCORE222618
    NT-BGKLV38-1B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1693GRCh38V40NT-BGKLV38-1B/Aligned.sortedByCoord.out.bamENCORE222654
    NT-BGKLV38-1B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1693GRCh38V40NT-BGKLV38-1B/Aligned.sortedByCoord.out.bamENCORE222690
    NT-BGKLV38-1B_quant.sfENCODE_DATA/set39_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1693GRCh38V40NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R1.fastq.gz,NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R2.fastq.gzENCORE222726
    NT-BGKLV38-1C_Aligned.sortedByCoord.out.bamENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab381GRCh38V40NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gzENCORE223486
    NT-BGKLV38-1C_Signal.Unique.strand+.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab381GRCh38V40NT-BGKLV38-1C/Aligned.sortedByCoord.out.bamENCORE223520
    NT-BGKLV38-1C_Signal.Unique.strand-.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab381GRCh38V40NT-BGKLV38-1C/Aligned.sortedByCoord.out.bamENCORE223554
    NT-BGKLV38-1C_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab381GRCh38V40NT-BGKLV38-1C/Aligned.sortedByCoord.out.bamENCORE223588
    NT-BGKLV38-1C_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab381GRCh38V40NT-BGKLV38-1C/Aligned.sortedByCoord.out.bamENCORE223622
    NT-BGKLV38-1C_quant.sfENCODE_DATA/set40_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab381GRCh38V40NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gzENCORE223656
    NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41_spikeins/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1957HiSeq2500100paired-ended1ENCORE227419
    NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41_spikeins/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1957HiSeq2500100paired-ended2ENCORE227447
    NT-BGKLV38-1D_Aligned.sortedByCoord.out.bamENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1957GRCh38V40NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227475
    NT-BGKLV38-1D_Signal.Unique.strand+.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1957GRCh38V40NT-BGKLV38-1D/Aligned.sortedByCoord.out.bamENCORE227503
    NT-BGKLV38-1D_Signal.Unique.strand-.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1957GRCh38V40NT-BGKLV38-1D/Aligned.sortedByCoord.out.bamENCORE227531
    NT-BGKLV38-1D_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1957GRCh38V40NT-BGKLV38-1D/Aligned.sortedByCoord.out.bamENCORE227559
    NT-BGKLV38-1D_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1957GRCh38V40NT-BGKLV38-1D/Aligned.sortedByCoord.out.bamENCORE227587
    NT-BGKLV38-1D_quant.sfENCODE_DATA/set41_spikeins/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1957GRCh38V40NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227615
    NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gzENCODE_DATA/set40_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab382HiSeq2500100paired-ended1ENCODE4745
    NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gzENCODE_DATA/set40_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab382HiSeq2500100paired-ended2ENCODE4788
    NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gzENCODE_DATA/set38/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1648HiSeq2500100paired-ended1ENCODE322179
    NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gzENCODE_DATA/set38/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1648HiSeq2500100paired-ended2ENCODE322191
    NT_BGKLV38-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set38/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1648GRCh38V40NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gzENCORE222203
    NT_BGKLV38-2_Signal.Unique.strand+.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1648GRCh38V40NT_BGKLV38-2/Aligned.sortedByCoord.out.bamENCORE222215
    NT_BGKLV38-2_Signal.Unique.strand-.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1648GRCh38V40NT_BGKLV38-2/Aligned.sortedByCoord.out.bamENCORE222227
    NT_BGKLV38-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1648GRCh38V40NT_BGKLV38-2/Aligned.sortedByCoord.out.bamENCORE222239
    NT_BGKLV38-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set38/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1648GRCh38V40NT_BGKLV38-2/Aligned.sortedByCoord.out.bamENCORE222251
    NT_BGKLV38-2_quant.sfENCODE_DATA/set38/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1648GRCh38V40NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gzENCORE222263
    NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R1.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1694HiSeq2500100paired-ended1ENCODE322475
    NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R2.fastq.gzENCODE_DATA/set39_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1694HiSeq2500100paired-ended2ENCODE322511
    NT-BGKLV38-2B_Aligned.sortedByCoord.out.bamENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1694GRCh38V40NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R1.fastq.gz,NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R2.fastq.gzENCORE222547
    NT-BGKLV38-2B_Signal.Unique.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1694GRCh38V40NT-BGKLV38-2B/Aligned.sortedByCoord.out.bamENCORE222583
    NT-BGKLV38-2B_Signal.Unique.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1694GRCh38V40NT-BGKLV38-2B/Aligned.sortedByCoord.out.bamENCORE222619
    NT-BGKLV38-2B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1694GRCh38V40NT-BGKLV38-2B/Aligned.sortedByCoord.out.bamENCORE222655
    NT-BGKLV38-2B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set39_K/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1694GRCh38V40NT-BGKLV38-2B/Aligned.sortedByCoord.out.bamENCORE222691
    NT-BGKLV38-2B_quant.sfENCODE_DATA/set39_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1694GRCh38V40NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R1.fastq.gz,NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R2.fastq.gzENCORE222727
    NT-BGKLV38-2C_Aligned.sortedByCoord.out.bamENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab382GRCh38V40NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gzENCORE223487
    NT-BGKLV38-2C_Signal.Unique.strand+.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab382GRCh38V40NT-BGKLV38-2C/Aligned.sortedByCoord.out.bamENCORE223521
    NT-BGKLV38-2C_Signal.Unique.strand-.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab382GRCh38V40NT-BGKLV38-2C/Aligned.sortedByCoord.out.bamENCORE223555
    NT-BGKLV38-2C_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab382GRCh38V40NT-BGKLV38-2C/Aligned.sortedByCoord.out.bamENCORE223589
    NT-BGKLV38-2C_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set40_K/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab382GRCh38V40NT-BGKLV38-2C/Aligned.sortedByCoord.out.bamENCORE223623
    NT-BGKLV38-2C_quant.sfENCODE_DATA/set40_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab382GRCh38V40NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gzENCORE223657
    NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41_spikeins/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1958HiSeq2500100paired-ended1ENCORE227420
    NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41_spikeins/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1958HiSeq2500100paired-ended2ENCORE227448
    NT-BGKLV38-2D_Aligned.sortedByCoord.out.bamENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1958GRCh38V40NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227476
    NT-BGKLV38-2D_Signal.Unique.strand+.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1958GRCh38V40NT-BGKLV38-2D/Aligned.sortedByCoord.out.bamENCORE227504
    NT-BGKLV38-2D_Signal.Unique.strand-.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1958GRCh38V40NT-BGKLV38-2D/Aligned.sortedByCoord.out.bamENCORE227532
    NT-BGKLV38-2D_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1958GRCh38V40NT-BGKLV38-2D/Aligned.sortedByCoord.out.bamENCORE227560
    NT-BGKLV38-2D_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1958GRCh38V40NT-BGKLV38-2D/Aligned.sortedByCoord.out.bamENCORE227588
    NT-BGKLV38-2D_quant.sfENCODE_DATA/set41_spikeins/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1958GRCh38V40NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227616