non-target      CRISPR in K562      Control: NT-BGKcLV23

General Information

List KD experiments controlled by BGKcLV23-1 and BGKcLV23-2


NT-BGKcLV23-1,NT-BGKcLV23-2:
  • ADAT3-BGKcLV23-K562
  • ALKBH1-BGKcLV23-K562
  • APTX-BGKcLV23-K562
  • BARD1-BGKcLV23-K562
  • BRIX1-BGKcLV23-K562
  • CACTIN-BGKcLV23-K562
  • CNOT2-BGKcLV23-K562
  • DDX43-BGKcLV23-K562
  • EIF6-BGKcLV23-K562
  • ELAC2-BGKcLV23-K562
  • LARS-BGKcLV23-K562
  • METTL1-BGKcLV23-K562
  • METTL3-BGKcLV23-K562
  • PRPF3-BGKcLV23-K562
  • SNRPC-BGKcLV23-K562
  • WBP11-BGKcLV23-K562




    • Experiment Information (Status: Released)
    BGKcLV23-1BGKcLV23-2
    idx787788
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV23-1BGKcLV23-2
    transduction_Date9/17/209/17/20
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc02944
    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_date11/24/2011/24/20
    repeat_library
    Note
    ID49074908




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV23-1BGKcLV23-2
    Sample_IDBGKcLV23-1BGKcLV23-2
    Sample Name
    Sample NameNT-BGKcLV23-1NT-BGKcLV23-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2021-06-022021-06-02
    ProjectENCODE4ENCODE4
    Note
    ID74297430




    Library-Prep Information
    BGKcLV23-1BGKcLV23-2
    Sample #3132
    Sample NameNT-BGKcLV23-1NT-BGKcLV23-2
    Sample_Name_Alias
    Index Well PositionG04H04
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2020-11-242020-11-24
    Lib_IDLib-201124Lib-201124
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp288291
    Peak_Molarity140.00144.00
    libSampleQC_DNA_WellDNA_Library_set46/set1/G4.pngDNA_Library_set46/set1/H4.png
    RIN8.79.0
    libSample_RNA_WellRNA_Library_set46/set3/A12.pngRNA_Library_set46/set3/B12.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2020-12-042020-12-04
    Sample_IDBGKcLV23-1BGKcLV23-2
    RBPNTNT
    Batch_IDBGKcLV23BGKcLV23
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID14061407




    Sequencing Information
    BGKcLV23-1BGKcLV23-2
    Sample_IDBGKcLV23-1BGKcLV23-2
    Sample NameNT-BGKcLV23-1NT-BGKcLV23-2
    Pool IDPool-201204Pool-201204
    LocalServer_folderset46_Kset46_K
    total_reads104,252,644110,900,752
    total_aligned_reads95,890,31298,639,996
    unique_aligned_reads87,530,92089,895,666
    percent_uniqueAligned0.839600.81060
    correlation_replicates0.9990330.999033
    spikein_reads51,42247,890
    percent_spikeins0.000490.00043
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID512513




    Data Submission Information
    BGKcLV23-1BGKcLV23-1BGKcLV23-1BGKcLV23-1BGKcLV23-1BGKcLV23-2BGKcLV23-2BGKcLV23-2BGKcLV23-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV23brenton-graveley:NT-BGKcLV23-1brenton-graveley:L-NT-BGKcLV23-1brenton-graveley:NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV23-2brenton-graveley:L-NT-BGKcLV23-2brenton-graveley:NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR877JEMENCBS794DDLENCLB592NRNENCFF805HMTENCFF848HCLENCBS571XPDENCLB891XEOENCFF659QXGENCFF267XLI
    object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2biosamplelibraryfile_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-seq
    Sample_IDBGKcLV23-1BGKcLV23-1BGKcLV23-1BGKcLV23-1BGKcLV23-1BGKcLV23-2BGKcLV23-2BGKcLV23-2BGKcLV23-2
    Sample NameNT-BGKcLV23-1NT-BGKcLV23-1NT-BGKcLV23-1NT-BGKcLV23-1NT-BGKcLV23-1NT-BGKcLV23-2NT-BGKcLV23-2NT-BGKcLV23-2NT-BGKcLV23-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2021-06-022021-06-022021-06-022021-06-022021-06-022021-06-022021-06-022021-06-022021-06-02
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV46K_biosample_protocolLV46K_library_protocolLV46K_biosample_protocolLV46K_library_protocol
    protocol_URLNT-BGKcLV23-1.pdfL-NT-BGKcLV23-1.pdfNT-BGKcLV23-2.pdfL-NT-BGKcLV23-2.pdf
    ID241024572521261526492458252226162650




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set46_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab512NovaSeq6000100paired-ended1ENCODE41404
    NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set46_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab512NovaSeq6000100paired-ended2ENCODE41468
    NT-BGKcLV23-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab512GRCh38V40NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225307
    NT-BGKcLV23-1_quant.sfENCODE_DATA/set46_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab512GRCh38V40NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225341
    NT-BGKcLV23-1_Signal.Unique.strand+.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab512GRCh38V40NT-BGKcLV23-1/Aligned.sortedByCoord.out.bamENCORE226145
    NT-BGKcLV23-1_Signal.Unique.strand-.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab512GRCh38V40NT-BGKcLV23-1/Aligned.sortedByCoord.out.bamENCORE226179
    NT-BGKcLV23-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab512GRCh38V40NT-BGKcLV23-1/Aligned.sortedByCoord.out.bamENCORE226213
    NT-BGKcLV23-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab512GRCh38V40NT-BGKcLV23-1/Aligned.sortedByCoord.out.bamENCORE226247
    NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set46_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab513NovaSeq6000100paired-ended1ENCODE41405
    NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set46_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab513NovaSeq6000100paired-ended2ENCODE41469
    NT-BGKcLV23-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab513GRCh38V40NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225308
    NT-BGKcLV23-2_quant.sfENCODE_DATA/set46_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab513GRCh38V40NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225342
    NT-BGKcLV23-2_Signal.Unique.strand+.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab513GRCh38V40NT-BGKcLV23-2/Aligned.sortedByCoord.out.bamENCORE226146
    NT-BGKcLV23-2_Signal.Unique.strand-.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab513GRCh38V40NT-BGKcLV23-2/Aligned.sortedByCoord.out.bamENCORE226180
    NT-BGKcLV23-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab513GRCh38V40NT-BGKcLV23-2/Aligned.sortedByCoord.out.bamENCORE226214
    NT-BGKcLV23-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab513GRCh38V40NT-BGKcLV23-2/Aligned.sortedByCoord.out.bamENCORE226248