non-target      CRISPR in HepG2      Control: NT-BGHcLV07

General Information

List KD experiments controlled by BGHcLV07-1 and BGHcLV07-2


NT-BGHcLV07-1B,NT-BGHcLV07-2B:
  • HNRNPH1-BGHcLV07-HepG2

    • NT-BGHcLV07-1,NT-BGHcLV07-2 (alias:NT-BGHcLV07-1,NT-BGHcLV07-2):
  • EXOSC5-BGHcLV07-HepG2
  • NOLC1-BGHcLV07-HepG2
  • RBM14-BGHcLV07-HepG2
  • SDAD1-BGHcLV07-HepG2




    • Experiment Information (Status: Released)
    BGHcLV07-1BGHcLV07-2
    idx113114
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon -targetnon -target
    Sample_IDBGHcLV07-1BGHcLV07-2
    transduction_Date6/13/176/13/17
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc04372
    WB_result
    Ave_WB
    WB_DONE_date
    MW
    IP
    antibody_Cat#
    Antibody DCC ID
    submitted_to_DCC_date
    Rep1_TPM00
    Rep2_TPM00
    ActionReadyReady
    Library_start_date8/3/178/3/17
    repeat_library
    Note
    ID62546255




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2
    Sample_IDBGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2
    Sample NameNT-BGHcLV07-1BNT-BGHcLV07-1NT-BGHcLV07-2BNT-BGHcLV07-2
    Sample NameNT-BGHcLV07-1BNT-BGHcLV07-1NT-BGHcLV07-2BNT-BGHcLV07-2
    RBPnon-targetnon-targetnon-targetnon-target
    Cell_LineHepG2HepG2HepG2HepG2
    Exp UID
    StatusReleasedReleasedReleasedReleased
    Status_date2021-03-182017-11-202021-03-182017-11-20
    ProjectENCODE4ENCODE3ENCODE4ENCODE3
    Note
    ID10213851031386




    Library-Prep Information
    BGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2
    Sample #78
    Sample NameNT-BGHcLV07-1BNT-BGHcLV07-1NT-BGHcLV07-2BNT-BGHcLV07-2
    Sample_Name_AliasNT-BGHcLV07-1NT-BGHcLV07-2
    Index Well PositionS01S07S02S08
    Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
    LibPrep_date2018-01-022017-08-032018-01-022017-08-03
    Lib_IDLib-180102Lib-170803Lib-180102Lib-170803
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp313304
    Peak_Molarity6.1112.10
    libSampleQC_DNA_WellDNA_Library_set40/set1/A8.pngDNA_Library_set39/set2/G3.pngDNA_Library_set40/set1/B8.pngDNA_Library_set39/set2/H3.png
    RIN9.69.69.79.7
    libSample_RNA_WellRNA_Library_set39/set2/A1.pngRNA_Library_set39/set2/A1.pngRNA_Library_set39/set2/B1.pngRNA_Library_set39/set2/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2018-01-022018-01-02
    Sample_IDBGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2
    RBPNTNTNTNT
    Batch_IDBGHcLV07BGHcLV07BGHcLV07BGHcLV07
    WB_result0.0000.0000.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
    Repeat_Library_SuffixBB
    Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequence
    ProjectENCODE4ENCODE3ENCODE4ENCODE3
    ID93030809313081




    Sequencing Information
    BGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2
    Sample_IDBGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2
    Sample NameNT-BGHcLV07-1BNT-BGHcLV07-1NT-BGHcLV07-2BNT-BGHcLV07-2
    Pool IDPool-180109Pool-170911Pool-180109Pool-170911
    LocalServer_folderset40_Hset39_Hset40_Hset39_H
    total_reads70,474,34040,441,96439,981,70247,425,768
    total_aligned_reads57,167,37834,505,18832,902,36641,285,206
    unique_aligned_reads53,868,34432,564,91631,082,69638,935,644
    percent_uniqueAligned0.764370.805230.777420.82098
    correlation_replicates0.9980140.9978300.9980140.997830
    spikein_reads12,06614,5125,68215,832
    percent_spikeins0.000170.000360.000140.00033
    original_ReadLength100100100100
    QC_StatusSubmittedSubmittedSubmittedSubmitted
    ID33317313341732




    Data Submission Information
    BGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2BGHcLV07-2BGHcLV07-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV07-Bbrenton-graveley:NT-BGHcLV07-1brenton-graveley:L-NT-BGHcLV07-1Bbrenton-graveley:NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gzbrenton-graveley:NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gzbrenton-graveley:NT-BGHcLV07brenton-graveley:NT-BGHcLV07-2brenton-graveley:L-NT-BGHcLV07-2Bbrenton-graveley:NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gzbrenton-graveley:NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gz
    ENCODE_accessionENCSR194SPWENCBS058XCCENCLB517HLAENCFF986FDXENCFF747HQNENCSR521WAIENCBS914MWEENCLB149TWKENCFF225GWFENCFF047GFM
    object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2experimentbiosamplelibraryfile_fastq1file_fastq2
    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-seq
    Sample_IDBGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-1BGHcLV07-2BGHcLV07-2BGHcLV07-2BGHcLV07-2
    Sample NameNT-BGHcLV07-1BNT-BGHcLV07-1BNT-BGHcLV07-1BNT-BGHcLV07-1BNT-BGHcLV07-1BNT-BGHcLV07-1NT-BGHcLV07-2BNT-BGHcLV07-2BNT-BGHcLV07-2BNT-BGHcLV07-2B
    SelectedYesYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2021-03-182021-03-182021-03-182021-03-182021-03-182017-11-152021-03-182021-03-182021-03-182021-03-18
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE3ENCODE4ENCODE4ENCODE4ENCODE4
    LV39_biosample_protocolLV40_library_protocolLV39_biosample_protocolLV40_library_protocol
    protocol_URLNT-BGHcLV07-1.pdfL-NT-BGHcLV07-1B.pdfNT-BGHcLV07-2.pdfL-NT-BGHcLV07-2B.pdf
    ID1443148415401591162832321485154115921629




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gzENCODE_DATA/set40_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab333HiSeq2500100paired-ended1ENCODE4661
    NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gzENCODE_DATA/set40_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab333HiSeq2500100paired-ended2ENCODE4703
    NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gzENCODE_DATA/set39_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1731HiSeq2500100paired-ended1ENCODE322280
    NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gzENCODE_DATA/set39_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1731HiSeq2500100paired-ended2ENCODE322304
    NT-BGHcLV07-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1731GRCh38V40NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gzENCORE222328
    NT-BGHcLV07-1_Signal.Unique.strand+.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1731GRCh38V40NT-BGHcLV07-1/Aligned.sortedByCoord.out.bamENCORE222352
    NT-BGHcLV07-1_Signal.Unique.strand-.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1731GRCh38V40NT-BGHcLV07-1/Aligned.sortedByCoord.out.bamENCORE222376
    NT-BGHcLV07-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1731GRCh38V40NT-BGHcLV07-1/Aligned.sortedByCoord.out.bamENCORE222400
    NT-BGHcLV07-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1731GRCh38V40NT-BGHcLV07-1/Aligned.sortedByCoord.out.bamENCORE222424
    NT-BGHcLV07-1_quant.sfENCODE_DATA/set39_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1731GRCh38V40NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gzENCORE222448
    NT-BGHcLV07-1B_Aligned.sortedByCoord.out.bamENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab333GRCh38V40NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gzENCORE223264
    NT-BGHcLV07-1B_Signal.Unique.strand+.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab333GRCh38V40NT-BGHcLV07-1B/Aligned.sortedByCoord.out.bamENCORE223298
    NT-BGHcLV07-1B_Signal.Unique.strand-.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab333GRCh38V40NT-BGHcLV07-1B/Aligned.sortedByCoord.out.bamENCORE223332
    NT-BGHcLV07-1B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab333GRCh38V40NT-BGHcLV07-1B/Aligned.sortedByCoord.out.bamENCORE223366
    NT-BGHcLV07-1B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab333GRCh38V40NT-BGHcLV07-1B/Aligned.sortedByCoord.out.bamENCORE223400
    NT-BGHcLV07-1B_quant.sfENCODE_DATA/set40_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab333GRCh38V40NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-1B_ATCACG_ACBYWVANXX_L003_001.R2.fastq.gzENCORE223434
    NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gzENCODE_DATA/set40_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab334HiSeq2500100paired-ended1ENCODE4662
    NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gzENCODE_DATA/set40_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab334HiSeq2500100paired-ended2ENCODE4704
    NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gzENCODE_DATA/set39_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1732HiSeq2500100paired-ended1ENCODE322281
    NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gzENCODE_DATA/set39_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1732HiSeq2500100paired-ended2ENCODE322305
    NT-BGHcLV07-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1732GRCh38V40NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gzENCORE222329
    NT-BGHcLV07-2_Signal.Unique.strand+.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1732GRCh38V40NT-BGHcLV07-2/Aligned.sortedByCoord.out.bamENCORE222353
    NT-BGHcLV07-2_Signal.Unique.strand-.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1732GRCh38V40NT-BGHcLV07-2/Aligned.sortedByCoord.out.bamENCORE222377
    NT-BGHcLV07-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1732GRCh38V40NT-BGHcLV07-2/Aligned.sortedByCoord.out.bamENCORE222401
    NT-BGHcLV07-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set39_H/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1732GRCh38V40NT-BGHcLV07-2/Aligned.sortedByCoord.out.bamENCORE222425
    NT-BGHcLV07-2_quant.sfENCODE_DATA/set39_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1732GRCh38V40NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gzENCORE222449
    NT-BGHcLV07-2B_Aligned.sortedByCoord.out.bamENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab334GRCh38V40NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gzENCORE223265
    NT-BGHcLV07-2B_Signal.Unique.strand+.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab334GRCh38V40NT-BGHcLV07-2B/Aligned.sortedByCoord.out.bamENCORE223299
    NT-BGHcLV07-2B_Signal.Unique.strand-.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab334GRCh38V40NT-BGHcLV07-2B/Aligned.sortedByCoord.out.bamENCORE223333
    NT-BGHcLV07-2B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab334GRCh38V40NT-BGHcLV07-2B/Aligned.sortedByCoord.out.bamENCORE223367
    NT-BGHcLV07-2B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set40_H/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab334GRCh38V40NT-BGHcLV07-2B/Aligned.sortedByCoord.out.bamENCORE223401
    NT-BGHcLV07-2B_quant.sfENCODE_DATA/set40_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab334GRCh38V40NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV07-2B_CGATGT_ACBYWVANXX_L003_001.R2.fastq.gzENCORE223435