non-target      CRISPR in K562      Control: NT-BGKcLV28

General Information

List KD experiments controlled by BGKcLV28-1 and BGKcLV28-2


NT-BGKcLV28-1,NT-BGKcLV28-2:
  • CCT2-BGKcLV28-K562
  • CCT3-BGKcLV28-K562
  • CCT4-BGKcLV28-K562
  • CD3EAP-BGKcLV28-K562
  • CDC5L-BGKcLV28-K562
  • CDK9-BGKcLV28-K562
  • CDV3-BGKcLV28-K562
  • CHCHD3-BGKcLV28-K562
  • CLASP2-BGKcLV28-K562
  • CLNS1A-BGKcLV28-K562
  • CLTC-BGKcLV28-K562
  • CMTR1-BGKcLV28-K562
  • CNDP2-BGKcLV28-K562
  • CPSF2-BGKcLV28-K562
  • CPSF3-BGKcLV28-K562
  • CPSF7-BGKcLV28-K562
  • CSE1L-BGKcLV28-K562
  • CSNK1E-BGKcLV28-K562
  • CTTN-BGKcLV28-K562
  • CWC15-BGKcLV28-K562
  • CWF19L2-BGKcLV28-K562
  • DBNL-BGKcLV28-K562
  • DCP1A-BGKcLV28-K562
  • DCPS-BGKcLV28-K562
  • DDX10-BGKcLV28-K562
  • DDX17-BGKcLV28-K562
  • DDX18-BGKcLV28-K562
  • DDX23-BGKcLV28-K562




    • Experiment Information (Status: Released)
    BGKcLV28-1BGKcLV28-2
    idx931932
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV28-1BGKcLV28-2
    transduction_Date7/12/217/12/21
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc01748
    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_date09/23/2109/23/21
    repeat_library
    Note
    ID50655066




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV28-1BGKcLV28-2
    Sample_IDBGKcLV28-1BGKcLV28-2
    Sample Name
    Sample NameNT-BGKcLV28-1NT-BGKcLV28-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2022-01-292022-01-29
    ProjectENCODE4ENCODE4
    Note
    ID98939894




    Library-Prep Information
    BGKcLV28-1BGKcLV28-2
    Sample #12
    Sample NameNT-BGKcLV28-1NT-BGKcLV28-2
    Sample_Name_Alias
    Index Well PositionA05B05
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2021-09-212021-09-21
    Lib_IDLib-210921Lib-210921
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp365331
    Peak_Molarity99.20103.00
    libSampleQC_DNA_WellDNA_Library_set48-49/set3/A1.pngDNA_Library_set48-49/set3/B1.png
    RIN9.59.5
    libSample_RNA_WellRNA_Library_set48-49/set2/A1.pngRNA_Library_set48-49/set2/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2021-09-272021-09-27
    Sample_IDBGKcLV28-1BGKcLV28-2
    RBPNTNT
    Batch_IDBGKcLV28BGKcLV28
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID20622063




    Sequencing Information
    BGKcLV28-1BGKcLV28-2
    Sample_IDBGKcLV28-1BGKcLV28-2
    Sample NameNT-BGKcLV28-1NT-BGKcLV28-2
    Pool IDPool-210929Pool-210929
    LocalServer_folderset49set49
    total_reads88,198,33686,039,368
    total_aligned_reads81,758,39682,898,828
    unique_aligned_reads75,528,58876,456,124
    percent_uniqueAligned0.856350.88862
    correlation_replicates0.9956310.995631
    spikein_reads32,16224,856
    percent_spikeins0.000360.00029
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID18131814




    Data Submission Information
    BGKcLV28-1BGKcLV28-1BGKcLV28-1BGKcLV28-1BGKcLV28-1BGKcLV28-2BGKcLV28-2BGKcLV28-2BGKcLV28-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV28brenton-graveley:NT-BGKcLV28-1brenton-graveley:L-NT-BGKcLV28-1brenton-graveley:NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV28-2brenton-graveley:L-NT-BGKcLV28-2brenton-graveley:NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR220DTXENCBS735BVVENCLB253YLVENCFF522GAPENCFF241JYNENCBS225NCGENCLB911CEZENCFF004JQIENCFF923YTY
    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_IDBGKcLV28-1BGKcLV28-1BGKcLV28-1BGKcLV28-1BGKcLV28-1BGKcLV28-2BGKcLV28-2BGKcLV28-2BGKcLV28-2
    Sample NameNT-BGKcLV28-1NT-BGKcLV28-1NT-BGKcLV28-1NT-BGKcLV28-1NT-BGKcLV28-1NT-BGKcLV28-2NT-BGKcLV28-2NT-BGKcLV28-2NT-BGKcLV28-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2022-01-292022-01-292022-01-292022-01-292022-01-292022-01-292022-01-292022-01-292022-01-29
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV49_biosample_protocolLV49_library_protocolLV49_biosample_protocolLV49_library_protocol
    protocol_URLNT-BGKcLV28-1.pdfL-NT-BGKcLV28-1.pdfNT-BGKcLV28-2.pdfL-NT-BGKcLV28-2.pdf
    ID347135763710384439783577371138453979




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set49/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1813NovaSeq6000100paired-ended1ENCODE43988
    NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set49/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1813NovaSeq6000100paired-ended2ENCODE44046
    NT-BGKcLV28-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1813GRCh38V40NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE219270
    NT-BGKcLV28-1_Signal.Unique.strand+.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1813GRCh38V40NT-BGKcLV28-1/Aligned.sortedByCoord.out.bamENCORE219328
    NT-BGKcLV28-1_Signal.Unique.strand-.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1813GRCh38V40NT-BGKcLV28-1/Aligned.sortedByCoord.out.bamENCORE219386
    NT-BGKcLV28-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1813GRCh38V40NT-BGKcLV28-1/Aligned.sortedByCoord.out.bamENCORE219444
    NT-BGKcLV28-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1813GRCh38V40NT-BGKcLV28-1/Aligned.sortedByCoord.out.bamENCORE219502
    NT-BGKcLV28-1_quant.sfENCODE_DATA/set49/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1813GRCh38V40NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE219560
    NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set49/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1814NovaSeq6000100paired-ended1ENCODE43989
    NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set49/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1814NovaSeq6000100paired-ended2ENCODE44047
    NT-BGKcLV28-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1814GRCh38V40NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE219271
    NT-BGKcLV28-2_Signal.Unique.strand+.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1814GRCh38V40NT-BGKcLV28-2/Aligned.sortedByCoord.out.bamENCORE219329
    NT-BGKcLV28-2_Signal.Unique.strand-.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1814GRCh38V40NT-BGKcLV28-2/Aligned.sortedByCoord.out.bamENCORE219387
    NT-BGKcLV28-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1814GRCh38V40NT-BGKcLV28-2/Aligned.sortedByCoord.out.bamENCORE219445
    NT-BGKcLV28-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1814GRCh38V40NT-BGKcLV28-2/Aligned.sortedByCoord.out.bamENCORE219503
    NT-BGKcLV28-2_quant.sfENCODE_DATA/set49/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1814GRCh38V40NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE219561