non-target      CRISPR in K562      Control: NT-BGKcLV15

General Information

List KD experiments controlled by BGKcLV15-1 and BGKcLV15-2


NT-BGKcLV15-1,NT-BGKcLV15-2:
  • CD3EAP-BGKcLV15-K562
  • DICER1-BGKcLV15-K562
  • EIF2AK1-BGKcLV15-K562
  • EIF2B3-BGKcLV15-K562
  • EIF4A3-BGKcLV15-K562
  • EIF4E-BGKcLV15-K562
  • GSK3B-BGKcLV15-K562
  • MECP2-BGKcLV15-K562
  • NPM1-BGKcLV15-K562
  • NSUN4-BGKcLV15-K562
  • ERO1L-BGKcLV15-K562
  • PTGES3-BGKcLV15-K562
  • RPL11-BGKcLV15-K562
  • RPL28-BGKcLV15-K562
  • SMAD2-BGKcLV15-K562
  • THOC1-BGKcLV15-K562
  • XRCC6-BGKcLV15-K562
  • YBX1-BGKcLV15-K562




    • Experiment Information (Status: Released)
    BGKcLV15-1BGKcLV15-2
    idx529530
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV15-1BGKcLV15-2
    transduction_Date4/2/194/2/19
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc04555
    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_date05/30/1905/30/19
    repeat_library
    Note
    ID46394640




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV15-1BGKcLV15-2
    Sample_IDBGKcLV15-1BGKcLV15-2
    Sample Name
    Sample NameNT-BGKcLV15-1NT-BGKcLV15-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2020-12-012020-12-01
    ProjectENCODE4ENCODE4
    Note
    ID53315332




    Library-Prep Information
    BGKcLV15-1BGKcLV15-2
    Sample #12
    Sample NameNT-BGKcLV15-1NT-BGKcLV15-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2020-08-302020-08-30
    Lib_IDLib-200830Lib-200830
    Tecan_Location1-A11-B1
    Tecan19.8638.86
    Tecan_date2019-12-102019-12-10
    Size_bp265266
    Peak_Molarity20.0031.60
    libSampleQC_DNA_WellDNA_Library_set43-44/set1/A1.pngDNA_Library_set43-44/set1/B1.png
    RIN9.69.6
    libSample_RNA_WellRNA_Library_set43-44/set1/A1.pngRNA_Library_set43-44/set1/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-12-112019-12-11
    Sample_IDBGKcLV15-1BGKcLV15-2
    RBPNTNT
    Batch_IDBGKcLV15BGKcLV15
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID577578




    Sequencing Information
    BGKcLV15-1BGKcLV15-2
    Sample_IDBGKcLV15-1BGKcLV15-2
    Sample NameNT-BGKcLV15-1NT-BGKcLV15-2
    Pool IDPool-200102Pool-200102
    LocalServer_folderset43_Kset43_K
    total_reads97,927,81479,339,214
    total_aligned_reads90,862,03074,539,976
    unique_aligned_reads83,275,06668,205,468
    percent_uniqueAligned0.850370.85967
    correlation_replicates0.9979820.997982
    spikein_reads69,80613,342
    percent_spikeins0.000710.00017
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID8384




    Data Submission Information
    BGKcLV15-1BGKcLV15-1BGKcLV15-1BGKcLV15-1BGKcLV15-1BGKcLV15-2BGKcLV15-2BGKcLV15-2BGKcLV15-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV15brenton-graveley:NT-BGKcLV15-1brenton-graveley:L-NT-BGKcLV15-1brenton-graveley:NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV15-2brenton-graveley:L-NT-BGKcLV15-2brenton-graveley:NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR404OHQENCBS351RNEENCLB513MBWENCFF250AJSENCFF319WJNENCBS996SVSENCLB223MFLENCFF239PORENCFF962DHI
    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_IDBGKcLV15-1BGKcLV15-1BGKcLV15-1BGKcLV15-1BGKcLV15-1BGKcLV15-2BGKcLV15-2BGKcLV15-2BGKcLV15-2
    Sample NameNT-BGKcLV15-1NT-BGKcLV15-1NT-BGKcLV15-1NT-BGKcLV15-1NT-BGKcLV15-1NT-BGKcLV15-2NT-BGKcLV15-2NT-BGKcLV15-2NT-BGKcLV15-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-18
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV43K_biosample_protocolLV43K_library_protocolLV43K_biosample_protocolLV43K_library_protocol
    protocol_URLNT-BGKcLV15-1.pdfL-NT-BGKcLV15-1.pdfNT-BGKcLV15-2.pdfL-NT-BGKcLV15-2.pdf
    ID17116280478530117281479531




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab83NovaSeq6000100paired-ended1ENCODE499
    NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab83NovaSeq6000100paired-ended2ENCODE4151
    NT-BGKcLV15-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab83GRCh38V40NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gzENCORE224390
    NT-BGKcLV15-1_Signal.Unique.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab83GRCh38V40NT-BGKcLV15-1/Aligned.sortedByCoord.out.bamENCORE224442
    NT-BGKcLV15-1_Signal.Unique.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab83GRCh38V40NT-BGKcLV15-1/Aligned.sortedByCoord.out.bamENCORE224494
    NT-BGKcLV15-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab83GRCh38V40NT-BGKcLV15-1/Aligned.sortedByCoord.out.bamENCORE224546
    NT-BGKcLV15-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab83GRCh38V40NT-BGKcLV15-1/Aligned.sortedByCoord.out.bamENCORE224598
    NT-BGKcLV15-1_quant.sfENCODE_DATA/set43_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab83GRCh38V40NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gzENCORE224650
    NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab84NovaSeq6000100paired-ended1ENCODE4100
    NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_K/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab84NovaSeq6000100paired-ended2ENCODE4152
    NT-BGKcLV15-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab84GRCh38V40NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gzENCORE224391
    NT-BGKcLV15-2_Signal.Unique.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab84GRCh38V40NT-BGKcLV15-2/Aligned.sortedByCoord.out.bamENCORE224443
    NT-BGKcLV15-2_Signal.Unique.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab84GRCh38V40NT-BGKcLV15-2/Aligned.sortedByCoord.out.bamENCORE224495
    NT-BGKcLV15-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab84GRCh38V40NT-BGKcLV15-2/Aligned.sortedByCoord.out.bamENCORE224547
    NT-BGKcLV15-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab84GRCh38V40NT-BGKcLV15-2/Aligned.sortedByCoord.out.bamENCORE224599
    NT-BGKcLV15-2_quant.sfENCODE_DATA/set43_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab84GRCh38V40NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gzENCORE224651