non-target      CRISPR in K562      Control: NT-BGKcLV13

General Information

List KD experiments controlled by BGKcLV13-1 and BGKcLV13-2


NT-BGKcLV13-1,NT-BGKcLV13-2:
  • APEX1-BGKcLV13-K562
  • DNMT1-BGKcLV13-K562
  • EIF2AK2-BGKcLV13-K562
  • ELAVL1-BGKcLV13-K562
  • GSK3A-BGKcLV13-K562
  • KPNB1-BGKcLV13-K562
  • PARP1-BGKcLV13-K562
  • POLR2A-BGKcLV13-K562
  • PSMA1-BGKcLV13-K562
  • RPS6-BGKcLV13-K562




    • Experiment Information (Status: Released)
    BGKcLV13-1BGKcLV13-2
    idx446447
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Name
    Sample_IDBGKcLV13-1BGKcLV13-2
    transduction_Date11/28/1811/28/18
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc03062
    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_date03/18/1903/18/19
    repeat_library
    Note
    ID45504551




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV13-1BGKcLV13-2
    Sample_IDBGKcLV13-1BGKcLV13-2
    Sample NameNT-BGKcLV13-1NT-BGKcLV13-2
    Sample NameNT-BGKcLV13-1NT-BGKcLV13-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2020-11-062020-11-06
    ProjectENCODE4ENCODE4
    Note
    ID28952896




    Library-Prep Information
    BGKcLV13-1BGKcLV13-2
    Sample #4950
    Sample NameNT-BGKcLV13-1NT-BGKcLV13-2
    Sample_Name_Alias
    Index Well PositionA07B07
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2019-03-182019-03-18
    Lib_IDLib-190318Lib-190318
    Tecan_Location1-A11-B1
    Tecan59.1341.29
    Tecan_date2019-03-182019-03-18
    Size_bp300292
    Peak_Molarity38.0033.20
    libSampleQC_DNA_WellDNA_Library_set42/set1/A7.pngDNA_Library_set42/set1/B7.png
    RIN9.49.7
    libSample_RNA_WellRNA_Library_set42/set1/A7.pngRNA_Library_set42/set1/B7.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-03-182019-03-18
    Sample_IDBGKcLV13-1BGKcLV13-2
    RBPNTNT
    Batch_IDBGKcLV13BGKcLV13
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID4950




    Sequencing Information
    BGKcLV13-1BGKcLV13-2
    Sample_IDBGKcLV13-1BGKcLV13-2
    Sample NameNT-BGKcLV13-1NT-BGKcLV13-2
    Pool IDPool-190423Pool-190423
    LocalServer_folderset42set42
    total_reads75,615,03865,434,430
    total_aligned_reads73,012,05863,234,174
    unique_aligned_reads66,648,59457,780,188
    percent_uniqueAligned0.881420.88302
    correlation_replicates0.9873200.987320
    spikein_reads69,57840,850
    percent_spikeins0.000920.00062
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID4748




    Data Submission Information
    BGKcLV13-1BGKcLV13-1BGKcLV13-1BGKcLV13-1BGKcLV13-1BGKcLV13-2BGKcLV13-2BGKcLV13-2BGKcLV13-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV13brenton-graveley:NT-BGKcLV13-1brenton-graveley:L-NT-BGKcLV13-1brenton-graveley:NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV13-2brenton-graveley:L-NT-BGKcLV13-2brenton-graveley:NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR712CQCENCBS323JXUENCLB232BMIENCFF778OLXENCFF509GGAENCBS160IFAENCLB640GFHENCFF048VADENCFF584EBM
    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_IDBGKcLV13-1BGKcLV13-1BGKcLV13-1BGKcLV13-1BGKcLV13-1BGKcLV13-2BGKcLV13-2BGKcLV13-2BGKcLV13-2
    Sample NameNT-BGKcLV13-1NT-BGKcLV13-1NT-BGKcLV13-1NT-BGKcLV13-1NT-BGKcLV13-1NT-BGKcLV13-2NT-BGKcLV13-2NT-BGKcLV13-2NT-BGKcLV13-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-20
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV42_biosample_protocolLV42_library_protocolLV42_biosample_protocolLV42_library_protocol
    protocol_URLNT-BGKcLV13-1.pdfL-NT-BGKcLV13-1.pdfNT-BGKcLV13-2.pdfL-NT-BGKcLV13-2.pdf
    ID78185793999710798589409981080




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab47NovaSeq6000100paired-ended1ENCODE4379
    NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab47NovaSeq6000100paired-ended2ENCODE4461
    NT-BGKcLV13-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab47GRCh38V40NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223718
    NT-BGKcLV13-1_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab47GRCh38V40NT-BGKcLV13-1/Aligned.sortedByCoord.out.bamENCORE223800
    NT-BGKcLV13-1_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab47GRCh38V40NT-BGKcLV13-1/Aligned.sortedByCoord.out.bamENCORE223882
    NT-BGKcLV13-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab47GRCh38V40NT-BGKcLV13-1/Aligned.sortedByCoord.out.bamENCORE223964
    NT-BGKcLV13-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab47GRCh38V40NT-BGKcLV13-1/Aligned.sortedByCoord.out.bamENCORE224046
    NT-BGKcLV13-1_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab47GRCh38V40NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224128
    NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab48NovaSeq6000100paired-ended1ENCODE4380
    NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab48NovaSeq6000100paired-ended2ENCODE4462
    NT-BGKcLV13-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab48GRCh38V40NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223719
    NT-BGKcLV13-2_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab48GRCh38V40NT-BGKcLV13-2/Aligned.sortedByCoord.out.bamENCORE223801
    NT-BGKcLV13-2_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab48GRCh38V40NT-BGKcLV13-2/Aligned.sortedByCoord.out.bamENCORE223883
    NT-BGKcLV13-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab48GRCh38V40NT-BGKcLV13-2/Aligned.sortedByCoord.out.bamENCORE223965
    NT-BGKcLV13-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab48GRCh38V40NT-BGKcLV13-2/Aligned.sortedByCoord.out.bamENCORE224047
    NT-BGKcLV13-2_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab48GRCh38V40NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224129