non-target      shRNA in K562      Control: Nontarget-LV11

General Information

List KD experiments controlled by BGKLV11-1 and BGKLV11-2


NT-BGKLV11-1,NT-BGKLV11-2 (alias:Nontarget-LV11-1,nontarget-LV11-2):
  • CIRBP-BGKLV11-K562
  • DDX21-BGKLV11-K562
  • G3BP1-BGKLV11-K562
  • HNRNPK-BGKLV11-K562
  • IGF2BP1-BGKLV11-K562
  • IGF2BP2-BGKLV11-K562
  • IGF2BP3-BGKLV11-K562
  • KHSRP-BGKLV11-K562
  • MAGOH-BGKLV11-K562
  • MATR3-BGKLV11-K562
  • PCBP1-BGKLV11-K562
  • PCBP2-BGKLV11-K562
  • PTBP1-BGKLV11-K562
  • RBM22-BGKLV11-K562
  • RBM34-BGKLV11-K562
  • NELFE-BGKLV11-K562
  • SRSF1-BGKLV11-K562
  • SRSF5-BGKLV11-K562
  • SRSF7-BGKLV11-K562
  • SRSF9-BGKLV11-K562
  • TARDBP-BGKLV11-K562
  • TIA1-BGKLV11-K562
  • TRA2A-BGKLV11-K562




    • Experiment Information (Status: Released)
    BGKLV11-1BGKLV11-2
    idx7071
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGKLV11-1BGKLV11-2
    transduction_Date5/1/20145/1/2014
    days
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc02276
    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_date5/19/20145/19/2014
    repeat_library
    Note
    ID7576




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKLV11-1BGKLV11-2
    Sample_IDBGKLV11-1BGKLV11-2
    Sample NameNontarget-LV11-1nontarget-LV11-2
    Sample NameNontarget-LV11-1nontarget-LV11-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2014-09-172014-09-17
    ProjectENCODE3ENCODE3
    Note
    ID344345




    Library-Prep Information
    BGKLV11-1BGKLV11-2
    Sample #
    Sample NameNT-BGKLV11-1NT-BGKLV11-2
    Sample_Name_AliasNontarget-LV11-1nontarget-LV11-2
    Index Well PositionS01S02
    Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
    LibPrep_date2014-05-192014-05-19
    Lib_IDLib-140519Lib-140519
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp
    Peak_Molarity
    libSampleQC_DNA_WellDNA_Library_LV11/set1/B1.pngDNA_Library_LV11/set1/C1.png
    RIN9.09.2
    libSample_RNA_WellRNA_Library_LV11/set1/A1.pngRNA_Library_LV11/set1/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date
    Sample_IDBGKLV11-1BGKLV11-2
    RBPNTNT
    Batch_IDBGKLV11BGKLV11
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE3ENCODE3
    ID19661967




    Sequencing Information
    BGKLV11-1BGKLV11-2
    Sample_IDBGKLV11-1BGKLV11-2
    Sample NameNontarget-LV11-1nontarget-LV11-2
    Pool IDPool-140701Pool-140701
    LocalServer_folderset11set11
    total_reads63,410,00066,270,000
    total_aligned_reads51,526,24251,967,014
    unique_aligned_reads47,166,43847,680,576
    percent_uniqueAligned0.743830.71949
    correlation_replicates0.9968800.996880
    spikein_reads383,016531,746
    percent_spikeins0.006040.00802
    original_ReadLength100100
    QC_StatusSubmittedSubmitted
    ID666667




    Data Submission Information
    BGKLV11-1
    ENCODE_aliasbrenton-graveley:Nontarget-LV11
    ENCODE_accessionENCSR129RWD
    object_typeexperiment
    assay_typeknockdown followed by RNA-seq
    Sample_IDBGKLV11-1
    Sample NameNontarget-LV11-1
    SelectedYes
    StatusReleased
    Status_Date2014-09-08
    ProjectENCODE3
    protocol_URL
    ID2721




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab666HiSeq2000100paired-ended1ENCODE312387
    Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab666HiSeq2000100paired-ended2ENCODE312435
    Nontarget-LV11-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab666GRCh38V40Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gzENCORE212483
    Nontarget-LV11-1_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab666GRCh38V40Nontarget-LV11-1/Aligned.sortedByCoord.out.bamENCORE212531
    Nontarget-LV11-1_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab666GRCh38V40Nontarget-LV11-1/Aligned.sortedByCoord.out.bamENCORE212579
    Nontarget-LV11-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab666GRCh38V40Nontarget-LV11-1/Aligned.sortedByCoord.out.bamENCORE212627
    Nontarget-LV11-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab666GRCh38V40Nontarget-LV11-1/Aligned.sortedByCoord.out.bamENCORE212675
    Nontarget-LV11-1_quant.sfENCODE_DATA/set11/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab666GRCh38V40Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gzENCORE212723
    nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab667HiSeq2000100paired-ended1ENCODE312388
    nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCODE_DATA/set11/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab667HiSeq2000100paired-ended2ENCODE312436
    nontarget-LV11-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set11/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab667GRCh38V40nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCORE212484
    nontarget-LV11-2_Signal.Unique.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab667GRCh38V40nontarget-LV11-2/Aligned.sortedByCoord.out.bamENCORE212532
    nontarget-LV11-2_Signal.Unique.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab667GRCh38V40nontarget-LV11-2/Aligned.sortedByCoord.out.bamENCORE212580
    nontarget-LV11-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab667GRCh38V40nontarget-LV11-2/Aligned.sortedByCoord.out.bamENCORE212628
    nontarget-LV11-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set11/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab667GRCh38V40nontarget-LV11-2/Aligned.sortedByCoord.out.bamENCORE212676
    nontarget-LV11-2_quant.sfENCODE_DATA/set11/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab667GRCh38V40nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gzENCORE212724