non-target      CRISPR in HepG2      Control: NT-BGHcLV09

General Information

List KD experiments controlled by BGHcLV09-1 and BGHcLV09-2


NT-BGHcLV09-1,NT-BGHcLV09-2:
  • CENPI-BGHcLV09-HepG2
  • NIP7-BGHcLV09-HepG2
  • RPL23A-BGHcLV09-HepG2
  • SAFB-BGHcLV09-HepG2
  • SRSF9-BGHcLV09-HepG2




    • Experiment Information (Status: Released)
    BGHcLV09-1BGHcLV09-2
    idx163164
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon -targetnon -target
    Sample_IDBGHcLV09-1BGHcLV09-2
    transduction_Date4/20/184/20/18
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc04350
    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_date8/7/188/7/18
    repeat_library
    Note
    ID63066307




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV09-1BGHcLV09-2
    Sample_IDBGHcLV09-1BGHcLV09-2
    Sample Name
    Sample NameNT-BGHcLV09-1NT-BGHcLV09-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusReleasedReleased
    Status_date2020-11-062020-11-06
    ProjectENCODE4ENCODE4
    Note
    ID62556256




    Library-Prep Information
    BGHcLV09-1BGHcLV09-2
    Sample #3738
    Sample NameNT-BGHcLV09-1NT-BGHcLV09-2
    Sample_Name_Alias
    Index Well PositionA06B06
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2018-10-012018-10-01
    Lib_IDLib-181001Lib-181001
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp281273
    Peak_Molarity78.2044.00
    libSampleQC_DNA_WellDNA_Library_set41/set4/F10.pngDNA_Library_set41/set5/B6.png
    RIN9.79.8
    libSample_RNA_WellRNA_Library_set41/set1/E5.pngRNA_Library_set41/set1/F5.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2018-08-082018-08-08
    Sample_IDBGHcLV09-1BGHcLV09-2
    RBPNTNT
    Batch_IDBGHcLV09BGHcLV09
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID887888




    Sequencing Information
    BGHcLV09-1BGHcLV09-2
    Sample_IDBGHcLV09-1BGHcLV09-2
    Sample NameNT-BGHcLV09-1NT-BGHcLV09-2
    Pool IDPool-180901Pool-180901
    LocalServer_folderset41set41
    total_reads90,285,482178,768,458
    total_aligned_reads73,363,704172,929,812
    unique_aligned_reads68,075,726159,909,712
    percent_uniqueAligned0.754010.89451
    correlation_replicates0.9683120.968312
    spikein_reads92,054158,502
    percent_spikeins0.001020.00089
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID293294




    Data Submission Information
    BGHcLV09-1BGHcLV09-1BGHcLV09-1BGHcLV09-1BGHcLV09-1BGHcLV09-2BGHcLV09-2BGHcLV09-2BGHcLV09-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV09brenton-graveley:NT-BGHcLV09-1brenton-graveley:L-NT-BGHcLV09-1brenton-graveley:NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV09-2brenton-graveley:L-NT-BGHcLV09-2brenton-graveley:NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR300EBWENCBS205XWZENCLB549HTSENCFF019PTPENCFF522HHXENCBS271VOSENCLB497GSDENCFF197NKMENCFF476YEI
    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_IDBGHcLV09-1BGHcLV09-1BGHcLV09-1BGHcLV09-1BGHcLV09-1BGHcLV09-2BGHcLV09-2BGHcLV09-2BGHcLV09-2
    Sample NameNT-BGHcLV09-1NT-BGHcLV09-1NT-BGHcLV09-1NT-BGHcLV09-1NT-BGHcLV09-1NT-BGHcLV09-2NT-BGHcLV09-2NT-BGHcLV09-2NT-BGHcLV09-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-20
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV41_biosample_protocolLV41_library_protocolLV41_biosample_protocolLV41_library_protocol
    protocol_URLNT-BGHcLV09-1.pdfL-NT-BGHcLV09-1.pdfNT-BGHcLV09-2.pdfL-NT-BGHcLV09-2.pdf
    ID113411881258132813921189125913291393




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab293NovaSeq6000100paired-ended1ENCODE4535
    NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab293NovaSeq6000100paired-ended2ENCODE4605
    NT-BGHcLV09-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab293GRCh38V40NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226773
    NT-BGHcLV09-1_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab293GRCh38V40NT-BGHcLV09-1/Aligned.sortedByCoord.out.bamENCORE226843
    NT-BGHcLV09-1_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab293GRCh38V40NT-BGHcLV09-1/Aligned.sortedByCoord.out.bamENCORE226913
    NT-BGHcLV09-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab293GRCh38V40NT-BGHcLV09-1/Aligned.sortedByCoord.out.bamENCORE226983
    NT-BGHcLV09-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab293GRCh38V40NT-BGHcLV09-1/Aligned.sortedByCoord.out.bamENCORE227053
    NT-BGHcLV09-1_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab293GRCh38V40NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227123
    NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab294NovaSeq6000100paired-ended1ENCODE4536
    NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab294NovaSeq6000100paired-ended2ENCODE4606
    NT-BGHcLV09-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab294GRCh38V40NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226774
    NT-BGHcLV09-2_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab294GRCh38V40NT-BGHcLV09-2/Aligned.sortedByCoord.out.bamENCORE226844
    NT-BGHcLV09-2_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab294GRCh38V40NT-BGHcLV09-2/Aligned.sortedByCoord.out.bamENCORE226914
    NT-BGHcLV09-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab294GRCh38V40NT-BGHcLV09-2/Aligned.sortedByCoord.out.bamENCORE226984
    NT-BGHcLV09-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab294GRCh38V40NT-BGHcLV09-2/Aligned.sortedByCoord.out.bamENCORE227054
    NT-BGHcLV09-2_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab294GRCh38V40NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227124