non-target      CRISPR in HepG2      Control: NT-BGHcLV14

General Information

List KD experiments controlled by BGHcLV14-1 and BGHcLV14-2


NT-BGHcLV14-1,NT-BGHcLV14-2:
  • APEX1-BGHcLV14-HepG2
  • ELAVL1-BGHcLV14-HepG2
  • GSK3A-BGHcLV14-HepG2
  • KPNB1-BGHcLV14-HepG2
  • PARP1-BGHcLV14-HepG2




    • Experiment Information (Status: Released)
    BGHcLV14-1BGHcLV14-2
    idx356357
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGHcLV14-1BGHcLV14-2
    transduction_Date12/5/1812/5/18
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc04485
    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
    ID65016502




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV14-1BGHcLV14-2
    Sample_IDBGHcLV14-1BGHcLV14-2
    Sample NameNT-BGHcLV14-1NT-BGHcLV14-2
    Sample NameNT-BGHcLV14-1NT-BGHcLV14-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusReleasedReleased
    Status_date2020-11-062020-11-06
    ProjectENCODE4ENCODE4
    Note
    ID29772978




    Library-Prep Information
    BGHcLV14-1BGHcLV14-2
    Sample #7172
    Sample NameNT-BGHcLV14-1NT-BGHcLV14-2
    Sample_Name_Alias
    Index Well PositionG09H09
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2019-03-182019-03-18
    Lib_IDLib-190318Lib-190318
    Tecan_Location2-G12-H1
    Tecan68.5954.67
    Tecan_date2019-03-182019-03-18
    Size_bp285272
    Peak_Molarity54.0045.80
    libSampleQC_DNA_WellDNA_Library_set42/set1/G9.pngDNA_Library_set42/set1/H9.png
    RIN9.89.7
    libSample_RNA_WellRNA_Library_set42/set1/G9.pngRNA_Library_set42/set1/H9.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-03-182019-03-18
    Sample_IDBGHcLV14-1BGHcLV14-2
    RBPNTNT
    Batch_IDBGHcLV14BGHcLV14
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID7172




    Sequencing Information
    BGHcLV14-1BGHcLV14-2
    Sample_IDBGHcLV14-1BGHcLV14-2
    Sample NameNT-BGHcLV14-1NT-BGHcLV14-2
    Pool IDPool-190423Pool-190423
    LocalServer_folderset42set42
    total_reads78,576,44466,007,134
    total_aligned_reads72,926,50060,735,116
    unique_aligned_reads68,634,62657,168,050
    percent_uniqueAligned0.873480.86609
    correlation_replicates0.9967150.996715
    spikein_reads58,29272,250
    percent_spikeins0.000740.00109
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID4344




    Data Submission Information
    BGHcLV14-1BGHcLV14-1BGHcLV14-1BGHcLV14-1BGHcLV14-1BGHcLV14-2BGHcLV14-2BGHcLV14-2BGHcLV14-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV14brenton-graveley:NT-BGHcLV14-1brenton-graveley:L-NT-BGHcLV14-1brenton-graveley:NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV14-2brenton-graveley:L-NT-BGHcLV14-2brenton-graveley:NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR750CPTENCBS223NPXENCLB070DWEENCFF337JPHENCFF383JILENCBS363HBBENCLB215INHENCFF520TTSENCFF665ECK
    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_IDBGHcLV14-1BGHcLV14-1BGHcLV14-1BGHcLV14-1BGHcLV14-1BGHcLV14-2BGHcLV14-2BGHcLV14-2BGHcLV14-2
    Sample NameNT-BGHcLV14-1NT-BGHcLV14-1NT-BGHcLV14-1NT-BGHcLV14-1NT-BGHcLV14-1NT-BGHcLV14-2NT-BGHcLV14-2NT-BGHcLV14-2NT-BGHcLV14-2
    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-BGHcLV14-1.pdfL-NT-BGHcLV14-1.pdfNT-BGHcLV14-2.pdfL-NT-BGHcLV14-2.pdf
    ID75981389599310758148969941076




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab43NovaSeq6000100paired-ended1ENCODE4375
    NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab43NovaSeq6000100paired-ended2ENCODE4457
    NT-BGHcLV14-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab43GRCh38V40NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223714
    NT-BGHcLV14-1_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab43GRCh38V40NT-BGHcLV14-1/Aligned.sortedByCoord.out.bamENCORE223796
    NT-BGHcLV14-1_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab43GRCh38V40NT-BGHcLV14-1/Aligned.sortedByCoord.out.bamENCORE223878
    NT-BGHcLV14-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab43GRCh38V40NT-BGHcLV14-1/Aligned.sortedByCoord.out.bamENCORE223960
    NT-BGHcLV14-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab43GRCh38V40NT-BGHcLV14-1/Aligned.sortedByCoord.out.bamENCORE224042
    NT-BGHcLV14-1_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab43GRCh38V40NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224124
    NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab44NovaSeq6000100paired-ended1ENCODE4376
    NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab44NovaSeq6000100paired-ended2ENCODE4458
    NT-BGHcLV14-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab44GRCh38V40NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223715
    NT-BGHcLV14-2_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab44GRCh38V40NT-BGHcLV14-2/Aligned.sortedByCoord.out.bamENCORE223797
    NT-BGHcLV14-2_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab44GRCh38V40NT-BGHcLV14-2/Aligned.sortedByCoord.out.bamENCORE223879
    NT-BGHcLV14-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab44GRCh38V40NT-BGHcLV14-2/Aligned.sortedByCoord.out.bamENCORE223961
    NT-BGHcLV14-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab44GRCh38V40NT-BGHcLV14-2/Aligned.sortedByCoord.out.bamENCORE224043
    NT-BGHcLV14-2_quant.sfENCODE_DATA/set42/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab44GRCh38V40NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224125