non-target      CRISPR in K562      Control: NT-BGKcLV19

General Information

List KD experiments controlled by BGKcLV19-1 and BGKcLV19-2


NT-BGKcLV19-1,NT-BGKcLV19-2:
  • CIZ1-BGKcLV19-K562
  • MDM2-BGKcLV19-K562
  • MORC2-BGKcLV19-K562
  • NCL-BGKcLV19-K562
  • NSUN5-BGKcLV19-K562
  • RBM19-BGKcLV19-K562
  • RNF187-BGKcLV19-K562
  • RYBP-BGKcLV19-K562
  • SMAD5-BGKcLV19-K562
  • SMYD3-BGKcLV19-K562
  • TAF9-BGKcLV19-K562




    • Experiment Information (Status: Released)
    BGKcLV19-1BGKcLV19-2
    idx671672
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV19-1BGKcLV19-2
    transduction_Date11/6/1911/6/19
    daysDay 6Day 6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc05600
    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_date09/24/2009/24/20
    repeat_library
    Note
    ID47914792




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV19-1BGKcLV19-2
    Sample_IDBGKcLV19-1BGKcLV19-2
    Sample Name
    Sample NameNT-BGKcLV19-1NT-BGKcLV19-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusReleasedReleased
    Status_date2021-03-182021-03-18
    ProjectENCODE4ENCODE4
    Note
    ID56935694




    Library-Prep Information
    BGKcLV19-1BGKcLV19-2
    Sample #78
    Sample NameNT-BGKcLV19-1NT-BGKcLV19-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2020-09-242020-09-24
    Lib_IDLib-200924Lib-200924
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp324309
    Peak_Molarity76.1093.00
    libSampleQC_DNA_WellDNA_Library_set45/set1/A1.pngDNA_Library_set45/set1/B1.png
    RIN9.79.6
    libSample_RNA_WellRNA_Library_set45/set1/A1.pngRNA_Library_set45/set1/B1.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2020-09-222020-09-22
    Sample_IDBGKcLV19-1BGKcLV19-2
    RBPNTNT
    Batch_IDBGKcLV19BGKcLV19
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID781782




    Sequencing Information
    BGKcLV19-1BGKcLV19-2
    Sample_IDBGKcLV19-1BGKcLV19-2
    Sample NameNT-BGKcLV19-1NT-BGKcLV19-2
    Pool IDPool-200928Pool-200928
    LocalServer_folderset45_Kset45_K
    total_reads190,731,61493,534,026
    total_aligned_reads164,847,18687,369,382
    unique_aligned_reads150,111,06479,863,984
    percent_uniqueAligned0.787030.85385
    correlation_replicates0.9941100.994110
    spikein_reads253,56478,976
    percent_spikeins0.001330.00084
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID412413




    Data Submission Information
    BGKcLV19-1BGKcLV19-1BGKcLV19-1BGKcLV19-1BGKcLV19-1BGKcLV19-2BGKcLV19-2BGKcLV19-2BGKcLV19-2
    ENCODE_aliasbrenton-graveley:NT-BGKcLV19brenton-graveley:NT-BGKcLV19-1brenton-graveley:L-NT-BGKcLV19-1brenton-graveley:NT-BGKcLV19-1_S1_R1_001.fastq.gzbrenton-graveley:NT-BGKcLV19-1_S1_R2_001.fastq.gzbrenton-graveley:NT-BGKcLV19-2brenton-graveley:L-NT-BGKcLV19-2brenton-graveley:NT-BGKcLV19-2_S2_R1_001.fastq.gzbrenton-graveley:NT-BGKcLV19-2_S2_R2_001.fastq.gz
    ENCODE_accessionENCSR978MMZENCBS878GWRENCLB907KRTENCFF788BNIENCFF559SIVENCBS866YOWENCLB483FFLENCFF443VVTENCFF772ZYG
    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_IDBGKcLV19-1BGKcLV19-1BGKcLV19-1BGKcLV19-1BGKcLV19-1BGKcLV19-2BGKcLV19-2BGKcLV19-2BGKcLV19-2
    Sample NameNT-BGKcLV19-1NT-BGKcLV19-1NT-BGKcLV19-1NT-BGKcLV19-1NT-BGKcLV19-1NT-BGKcLV19-2NT-BGKcLV19-2NT-BGKcLV19-2NT-BGKcLV19-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-18
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV45K_biosample_protocolLV45K_library_protocolLV45K_biosample_protocolLV45K_library_protocol
    protocol_URLNT-BGKcLV19-1.pdfL-NT-BGKcLV19-1.pdfNT-BGKcLV19-2.pdfL-NT-BGKcLV19-2.pdf
    ID209021352205227523452136220622762346




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGKcLV19-1_S1_R1_001.fastq.gzENCODE_DATA/set45_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab412NovaSeq6000100paired-ended1ENCODE41236
    NT-BGKcLV19-1_S1_R2_001.fastq.gzENCODE_DATA/set45_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab412NovaSeq6000100paired-ended2ENCODE41286
    NT-BGKcLV19-1_quant.sfENCODE_DATA/set45_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab412GRCh38V40NT-BGKcLV19-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV19-1_S1_R2_001.filtered.trimmed.paired.fastq.gzENCORE225229
    NT-BGKcLV19-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab412GRCh38V40NT-BGKcLV19-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV19-1_S1_R2_001.filtered.trimmed.paired.fastq.gzENCORE227183
    NT-BGKcLV19-1_Signal.Unique.strand+.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab412GRCh38V40NT-BGKcLV19-1/Aligned.sortedByCoord.out.bamENCORE227233
    NT-BGKcLV19-1_Signal.Unique.strand-.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab412GRCh38V40NT-BGKcLV19-1/Aligned.sortedByCoord.out.bamENCORE227283
    NT-BGKcLV19-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab412GRCh38V40NT-BGKcLV19-1/Aligned.sortedByCoord.out.bamENCORE227333
    NT-BGKcLV19-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab412GRCh38V40NT-BGKcLV19-1/Aligned.sortedByCoord.out.bamENCORE227383
    NT-BGKcLV19-2_S2_R1_001.fastq.gzENCODE_DATA/set45_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab413NovaSeq6000100paired-ended1ENCODE41237
    NT-BGKcLV19-2_S2_R2_001.fastq.gzENCODE_DATA/set45_K/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab413NovaSeq6000100paired-ended2ENCODE41287
    NT-BGKcLV19-2_quant.sfENCODE_DATA/set45_K/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab413GRCh38V40NT-BGKcLV19-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV19-2_S2_R2_001.filtered.trimmed.paired.fastq.gzENCORE225230
    NT-BGKcLV19-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab413GRCh38V40NT-BGKcLV19-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV19-2_S2_R2_001.filtered.trimmed.paired.fastq.gzENCORE227184
    NT-BGKcLV19-2_Signal.Unique.strand+.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab413GRCh38V40NT-BGKcLV19-2/Aligned.sortedByCoord.out.bamENCORE227234
    NT-BGKcLV19-2_Signal.Unique.strand-.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab413GRCh38V40NT-BGKcLV19-2/Aligned.sortedByCoord.out.bamENCORE227284
    NT-BGKcLV19-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab413GRCh38V40NT-BGKcLV19-2/Aligned.sortedByCoord.out.bamENCORE227334
    NT-BGKcLV19-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab413GRCh38V40NT-BGKcLV19-2/Aligned.sortedByCoord.out.bamENCORE227384