non-target      shRNA in K562      Control: non-target_BGKLV13

General Information

List KD experiments controlled by BGKLV13-1 and BGKLV13-2


NT-BGKLV13-1,NT-BGKLV13-2 (alias:NT_BGKLV13_1,NT_BGKLV13_2):
  • HLTF-BGKLV13-K562
  • EXOSC9-BGKLV13-K562
  • PRPF6-BGKLV13-K562
  • ZRANB2-BGKLV13-K562
  • AATF-BGKLV13-K562
  • SMNDC1-BGKLV13-K562
  • RTF1-BGKLV13-K562
  • XRCC6-BGKLV13-K562
  • NFX1-BGKLV13-K562
  • XRCC5-BGKLV13-K562
  • DAZAP1-BGKLV13-K562
  • GTF2F1-BGKLV13-K562
  • SUB1-BGKLV13-K562
  • CSTF2T-BGKLV13-K562
  • SRSF4-BGKLV13-K562

    • NT-BGKLV13-1B,NT-BGKLV13-2B (alias:non-target_BGKLV13_73,non-target_BGKLV13_74):
  • FUS-BGKLV13-K562
  • FASTKD2-BGKLV13-K562
  • SLTM-BGKLV13-K562
  • SND1-BGKLV13-K562
  • RPS10-BGKLV13-K562
  • RPS3-BGKLV13-K562
  • SSB-BGKLV13-K562
  • AGO1-BGKLV13-K562
  • EIF3G-BGKLV13-K562




    • Experiment Information (Status: Released)
    BGKLV13-1BGKLV13-2
    idx134135
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGKLV13-1BGKLV13-2
    transduction_Date6/13/20146/13/2014
    days
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc20881933
    WB_result
    Ave_WB
    WB_DONE_date
    MW
    IP
    antibody_Cat#
    Antibody DCC ID
    submitted_to_DCC_date
    Rep1_TPM00
    Rep2_TPM00
    Action
    Library_start_date7/27/20147/27/2014
    repeat_library
    Note
    ID149150




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKLV13-1BGKLV13-1BGKLV13-2BGKLV13-2
    Sample_IDBGKLV13-1BGKLV13-1BGKLV13-2BGKLV13-2
    Sample Namenon-target_BGKLV13_73NT_BGKLV13_1non-target_BGKLV13_74NT_BGKLV13_2
    Sample Namenon-target_BGKLV13_73NT_BGKLV13_1non-target_BGKLV13_74NT_BGKLV13_2
    RBPnon-targetnon-targetnon-targetnon-target
    Cell_LineK562K562K562K562
    Exp UID
    StatusReleasedReleasedReleasedReleased
    Status_date2014-10-292014-10-292014-10-292014-10-29
    ProjectENCODE3ENCODE3ENCODE3ENCODE3
    Note
    ID460462461463




    Library-Prep Information
    BGKLV13-1BGKLV13-1BGKLV13-2BGKLV13-2
    Sample #
    Sample NameNT-BGKLV13-1NT-BGKLV13-1BNT-BGKLV13-2NT-BGKLV13-2B
    Sample_Name_AliasNT_BGKLV13_1non-target_BGKLV13_73NT_BGKLV13_2non-target_BGKLV13_74
    Index Well PositionS01S09S02S10
    Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
    LibPrep_date2014-07-272014-07-302014-07-272014-07-30
    Lib_IDLib-140727Lib-140730Lib-140727Lib-140730
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp
    Peak_Molarity
    libSampleQC_DNA_WellDNA_Library_LV13-14/set1/B1.pngDNA_Library_LV13-14/set1/B5.pngDNA_Library_LV13-14/set1/C1.pngDNA_Library_LV13-14/set1/C5.png
    RIN9.59.49.39.3
    libSample_RNA_WellRNA_Library_LV12/set1/E9.pngRNA_Library_LV13-14-16/set1/E1.pngRNA_Library_LV12/set1/F9.pngRNA_Library_LV13-14-16/set1/F1.png
    SampleQC_methodTapeStationTapeStationTapeStationTapeStation
    SampleQC_date
    Sample_IDBGKLV13-1BGKLV13-1BGKLV13-2BGKLV13-2
    RBPNTNTNTNT
    Batch_IDBGKLV13BGKLV13BGKLV13BGKLV13
    WB_result0.0000.0000.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
    Repeat_Library_SuffixBB
    Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequence
    ProjectENCODE3ENCODE3ENCODE3ENCODE3
    ID2120215221212153




    Sequencing Information
    BGKLV13-1BGKLV13-2
    Sample_IDBGKLV13-1BGKLV13-2
    Sample NameNT_BGKLV13_1NT_BGKLV13_2
    Pool IDPool-140901Pool-140901
    LocalServer_folderset13set13
    total_reads44,420,00047,050,000
    total_aligned_reads40,856,27042,354,028
    unique_aligned_reads37,657,58038,935,816
    percent_uniqueAligned0.847760.82754
    correlation_replicates0.9917180.991718
    spikein_reads131,240108,620
    percent_spikeins0.002950.00231
    original_ReadLength100100
    QC_StatusSubmittedSubmitted
    ID762763




    Data Submission Information
    BGKLV13-1
    ENCODE_aliasbrenton-graveley:NT_BGKLV13
    ENCODE_accessionENCSR815CVQ
    object_typeexperiment
    assay_typeknockdown followed by RNA-seq
    Sample_IDBGKLV13-1
    Sample NameNT_BGKLV13_1
    SelectedYes
    StatusReleased
    Status_Date2014-10-15
    ProjectENCODE3
    protocol_URL
    ID2780




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab762HiSeq2000100paired-ended1ENCODE313390
    NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab762HiSeq2000100paired-ended2ENCODE313442
    NT_BGKLV13_1_Aligned.sortedByCoord.out.bamENCODE_DATA/set13/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab762GRCh38V40NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gzENCORE213494
    NT_BGKLV13_1_Signal.Unique.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab762GRCh38V40NT_BGKLV13_1/Aligned.sortedByCoord.out.bamENCORE213546
    NT_BGKLV13_1_Signal.Unique.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab762GRCh38V40NT_BGKLV13_1/Aligned.sortedByCoord.out.bamENCORE213598
    NT_BGKLV13_1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab762GRCh38V40NT_BGKLV13_1/Aligned.sortedByCoord.out.bamENCORE213650
    NT_BGKLV13_1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab762GRCh38V40NT_BGKLV13_1/Aligned.sortedByCoord.out.bamENCORE213702
    NT_BGKLV13_1_quant.sfENCODE_DATA/set13/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab762GRCh38V40NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gzENCORE213754
    NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab763HiSeq2000100paired-ended1ENCODE313391
    NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gzENCODE_DATA/set13/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab763HiSeq2000100paired-ended2ENCODE313443
    NT_BGKLV13_2_Aligned.sortedByCoord.out.bamENCODE_DATA/set13/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab763GRCh38V40NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gzENCORE213495
    NT_BGKLV13_2_Signal.Unique.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab763GRCh38V40NT_BGKLV13_2/Aligned.sortedByCoord.out.bamENCORE213547
    NT_BGKLV13_2_Signal.Unique.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab763GRCh38V40NT_BGKLV13_2/Aligned.sortedByCoord.out.bamENCORE213599
    NT_BGKLV13_2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab763GRCh38V40NT_BGKLV13_2/Aligned.sortedByCoord.out.bamENCORE213651
    NT_BGKLV13_2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set13/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab763GRCh38V40NT_BGKLV13_2/Aligned.sortedByCoord.out.bamENCORE213703
    NT_BGKLV13_2_quant.sfENCODE_DATA/set13/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab763GRCh38V40NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gzENCORE213755