non-target      shRNA in K562      Control: nontarget-LV08-3531

General Information

List KD experiments controlled by BGKLV08-1 and BGKLV08-2


NT-BGKLV08-1,NT-BGKLV08-2 (alias:Nontarget-LV08-1_00003527,nontarget-LV08-2_00003527):
  • AKAP1-BGKLV08-K562
  • ASCC1-BGKLV08-K562
  • CPSF6-BGKLV08-K562
  • DDX24-BGKLV08-K562
  • DDX3X-BGKLV08-K562
  • DDX6-BGKLV08-K562
  • EIF2S1-BGKLV08-K562
  • EIF4A3-BGKLV08-K562
  • EIF4B-BGKLV08-K562
  • EWSR1-BGKLV08-K562
  • FUBP3-BGKLV08-K562
  • FXR1-BGKLV08-K562
  • FXR2-BGKLV08-K562
  • NCBP2-BGKLV08-K562

    • NT-BGKLV08-1B,NT-BGKLV08-2B (alias:Nontarget-LV08-1_00003531,nontarget-LV08-2_00003531):
  • G3BP2-BGKLV08-K562
  • PABPC4-BGKLV08-K562
  • QKI-BGKLV08-K562
  • RAVER1-BGKLV08-K562
  • RBM15-BGKLV08-K562
  • RBM25-BGKLV08-K562
  • RECQL-BGKLV08-K562
  • SF3B4-BGKLV08-K562
  • TAF15-BGKLV08-K562
  • TBRG4-BGKLV08-K562
  • U2AF1-BGKLV08-K562
  • U2AF2-BGKLV08-K562




    • Experiment Information (Status: Released)
    BGKLV08-1BGKLV08-2
    idx23
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGKLV08-1BGKLV08-2
    transduction_Date4/4/20144/4/2014
    days
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc05304
    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_date5/5/20145/5/2014
    repeat_library
    Note
    ID12




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKLV08-1BGKLV08-1BGKLV08-2BGKLV08-2
    Sample_IDBGKLV08-1BGKLV08-1BGKLV08-2BGKLV08-2
    Sample NameNontarget-LV08-1_00003527Nontarget-LV08-1_00003531nontarget-LV08-2_00003527nontarget-LV08-2_00003531
    Sample NameNontarget-LV08-1_00003527Nontarget-LV08-1_00003531nontarget-LV08-2_00003527nontarget-LV08-2_00003531
    RBPnon-targetnon-targetnon-targetnon-target
    Cell_LineK562K562K562K562
    Exp UID
    StatusReleasedReleasedReleasedReleased
    Status_date2014-09-162014-09-162014-09-162014-09-16
    ProjectENCODE3ENCODE3ENCODE3ENCODE3
    Note
    ID298299300301




    Library-Prep Information
    BGKLV08-1BGKLV08-1BGKLV08-2BGKLV08-2
    Sample #
    Sample NameNT-BGKLV08-1NT-BGKLV08-1BNT-BGKLV08-2NT-BGKLV08-2B
    Sample_Name_AliasNontarget-LV08-1_00003527Nontarget-LV08-1_00003531nontarget-LV08-2_00003527nontarget-LV08-2_00003531
    Index Well PositionS01S09S02S10
    Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
    LibPrep_date2014-05-052014-05-082014-05-052014-05-08
    Lib_IDLib-140505Lib-140508Lib-140505Lib-140508
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp
    Peak_Molarity
    libSampleQC_DNA_WellDNA_Library_LV08/set1/B1.pngDNA_Library_LV08/set4/B1.pngDNA_Library_LV08/set1/C1.pngDNA_Library_LV08/set4/C1.png
    RIN9.29.29.29.2
    libSample_RNA_WellRNA_Library_LV08/set1/A1.pngRNA_Library_LV08/set1/A1.pngRNA_Library_LV08/set1/B1.pngRNA_Library_LV08/set1/B1.png
    SampleQC_methodTapeStationTapeStationTapeStationTapeStation
    SampleQC_date
    Sample_IDBGKLV08-1BGKLV08-1BGKLV08-2BGKLV08-2
    RBPNTNTNTNT
    Batch_IDBGKLV08BGKLV08BGKLV08BGKLV08
    WB_result0.0000.0000.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
    Repeat_Library_SuffixBB
    Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequence
    ProjectENCODE3ENCODE3ENCODE3ENCODE3
    ID1918194419191945




    Sequencing Information
    BGKLV08-1BGKLV08-2
    Sample_IDBGKLV08-1BGKLV08-2
    Sample NameNontarget-LV08-1_00003527nontarget-LV08-2_00003527
    Pool IDPool-140601Pool-140601
    LocalServer_folderset10set10
    total_reads55,840,00047,680,000
    total_aligned_reads47,525,69240,999,362
    unique_aligned_reads43,479,67637,488,122
    percent_uniqueAligned0.778650.78624
    correlation_replicates0.9949400.994940
    spikein_reads470,424393,352
    percent_spikeins0.008420.00825
    original_ReadLength100100
    QC_StatusSubmittedSubmitted
    ID618619




    Data Submission Information
    BGKLV08-1BGKLV08-1
    ENCODE_aliasbrenton-graveley:Nontarget-LV08-3527brenton-graveley:nontarget-LV08-3531
    ENCODE_accessionENCSR913CAEENCSR344XID
    object_typeexperimentexperiment
    assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
    Sample_IDBGKLV08-1BGKLV08-1
    Sample NameNontarget-LV08-1_00003527Nontarget-LV08-1_00003531
    SelectedYesYes
    StatusReleasedReleased
    Status_Date2014-08-132014-08-13
    ProjectENCODE3ENCODE3
    protocol_URL
    ID26982699




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    Nontarget-LV08-1_00003527_Aligned.sortedByCoord.out.bamENCODE_DATA/set10/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab618GRCh38V40Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gzENCORE212005
    Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab618HiSeq2000100paired-ended1ENCODE312061
    Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab618HiSeq2000100paired-ended2ENCODE312117
    Nontarget-LV08-1_00003527_Signal.Unique.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab618GRCh38V40Nontarget-LV08-1_00003527/Aligned.sortedByCoord.out.bamENCORE212173
    Nontarget-LV08-1_00003527_Signal.Unique.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab618GRCh38V40Nontarget-LV08-1_00003527/Aligned.sortedByCoord.out.bamENCORE212229
    Nontarget-LV08-1_00003527_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab618GRCh38V40Nontarget-LV08-1_00003527/Aligned.sortedByCoord.out.bamENCORE212285
    Nontarget-LV08-1_00003527_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab618GRCh38V40Nontarget-LV08-1_00003527/Aligned.sortedByCoord.out.bamENCORE212341
    Nontarget-LV08-1_00003527_quant.sfENCODE_DATA/set10/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab618GRCh38V40Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gzENCORE213340
    nontarget-LV08-2_00003527_Aligned.sortedByCoord.out.bamENCODE_DATA/set10/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab619GRCh38V40nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gzENCORE212007
    nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab619HiSeq2000100paired-ended1ENCODE312063
    nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab619HiSeq2000100paired-ended2ENCODE312119
    nontarget-LV08-2_00003527_Signal.Unique.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab619GRCh38V40nontarget-LV08-2_00003527/Aligned.sortedByCoord.out.bamENCORE212175
    nontarget-LV08-2_00003527_Signal.Unique.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab619GRCh38V40nontarget-LV08-2_00003527/Aligned.sortedByCoord.out.bamENCORE212231
    nontarget-LV08-2_00003527_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab619GRCh38V40nontarget-LV08-2_00003527/Aligned.sortedByCoord.out.bamENCORE212287
    nontarget-LV08-2_00003527_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab619GRCh38V40nontarget-LV08-2_00003527/Aligned.sortedByCoord.out.bamENCORE212343
    nontarget-LV08-2_00003527_quant.sfENCODE_DATA/set10/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab619GRCh38V40nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gzENCORE213342