non-target      CRISPR in HepG2      Control: NT-BGHcLV29-B

General Information

List KD experiments controlled by BGHcLV29-1 and BGHcLV29-2


NT-BGHcLV29-1,NT-BGHcLV29-2:
  • ARHGEF2-BGHcLV29-HepG2
  • ATP5A1-BGHcLV29-HepG2
  • CDK9-BGHcLV29-HepG2
  • CDV3-BGHcLV29-HepG2
  • CHCHD3-BGHcLV29-HepG2
  • CLNS1A-BGHcLV29-HepG2
  • CLTC-BGHcLV29-HepG2
  • CMTR1-BGHcLV29-HepG2
  • CNDP2-BGHcLV29-HepG2
  • CPSF2-BGHcLV29-HepG2
  • CPSF3-BGHcLV29-HepG2
  • CPSF7-BGHcLV29-HepG2
  • CSDE1-BGHcLV29-HepG2
  • CSTF3-BGHcLV29-HepG2
  • CTTN-BGHcLV29-HepG2
  • DARS-BGHcLV29-HepG2
  • DBNL-BGHcLV29-HepG2
  • DCPS-BGHcLV29-HepG2
  • DCTN2-BGHcLV29-HepG2
  • DDX18-BGHcLV29-HepG2

    • NT-BGHcLV29-1B,NT-BGHcLV29-2B:
  • ATXN2L-BGHcLV29-HepG2




    • Experiment Information (Status: Released)
    BGHcLV29-1BGHcLV29-2
    idx832833
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGHcLV29-1BGHcLV29-2
    transduction_Date7/207/20
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc05129
    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_date11/5/2111/5/21
    repeat_library
    Note
    ID70057006




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2
    Sample_IDBGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2
    Sample Name
    Sample NameNT-BGHcLV29-1NT-BGHcLV29-1BNT-BGHcLV29-2NT-BGHcLV29-2B
    RBPnon-targetnon-targetnon-targetnon-target
    Cell_LineHepG2HepG2HepG2HepG2
    Exp UID
    StatusReleasedReleasedReleasedReleased
    Status_date2022-02-112022-02-112022-02-112022-02-11
    ProjectENCODE4ENCODE4ENCODE4ENCODE4
    Note
    ID997310285997410286




    Library-Prep Information
    BGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2
    Sample #1324
    Sample NameNT-BGHcLV29-1NT-BGHcLV29-1BNT-BGHcLV29-2NT-BGHcLV29-2B
    Sample_Name_Alias
    Index Well PositionA01A11B01B11
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96IDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2021-11-012021-11-152021-11-012021-11-15
    Lib_IDLib-211101Lib-211115Lib-211101Lib-211115
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp301270297266
    Peak_Molarity39.8037.7036.8042.40
    libSampleQC_DNA_WellDNA_Library_set50/set1/A1.pngDNA_Library_set50/set1/A1.pngDNA_Library_set50/set1/B1.pngDNA_Library_set50/set1/B1.png
    RIN9.59.58.98.9
    libSample_RNA_WellRNA_Library_set50/set1/A7.pngRNA_Library_set50/set1/A7.pngRNA_Library_set50/set1/B7.pngRNA_Library_set50/set1/B7.png
    SampleQC_methodTapeStationTapeStationTapeStationTapeStation
    SampleQC_date2021-11-172021-11-172021-11-172021-11-17
    Sample_IDBGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2
    RBPNTNTNTNT
    Batch_IDBGHcLV29BGHcLV29BGHcLV29BGHcLV29
    WB_result0.0000.0000.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
    Repeat_Library_SuffixBB
    Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4ENCODE4ENCODE4
    ID3088317630893177




    Sequencing Information
    BGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2
    Sample_IDBGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2
    Sample NameNT-BGHcLV29-1NT-BGHcLV29-1BNT-BGHcLV29-2NT-BGHcLV29-2B
    Pool IDPool-211117Pool-211117Pool-211117Pool-211117
    LocalServer_folderset50_Hset50_Hset50_Hset50_H
    total_reads77,247,20072,241,97256,163,02843,961,096
    total_aligned_reads70,255,56259,380,08850,391,05836,021,104
    unique_aligned_reads66,301,32455,743,86247,525,00033,812,642
    percent_uniqueAligned0.858300.771630.846200.76915
    correlation_replicates0.9898110.9893010.9898110.989301
    spikein_reads14,46011,27013,2125,672
    percent_spikeins0.000190.000160.000240.00013
    original_ReadLength101101101101
    QC_StatusSubmittedSubmittedSubmittedSubmitted
    ID1871191518721916




    Data Submission Information
    BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV29brenton-graveley:NT-BGHcLV29-1brenton-graveley:L-NT-BGHcLV29-1brenton-graveley:NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV29-Bbrenton-graveley:L-NT-BGHcLV29-1Bbrenton-graveley:NT-BGHcLV29-1B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV29-1B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV29-2brenton-graveley:L-NT-BGHcLV29-2brenton-graveley:NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:L-NT-BGHcLV29-2Bbrenton-graveley:NT-BGHcLV29-2B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV29-2B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR462MFNENCBS125VHWENCLB242TCTENCFF940FEGENCFF109JZUENCSR248WTRENCLB997LJNENCFF451YIMENCFF755AWNENCBS692PXQENCLB969TMOENCFF499IBJENCFF098RBGENCLB816QOSENCFF232LIWENCFF568BCW
    object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2experimentlibraryfile_fastq1file_fastq2biosamplelibraryfile_fastq1file_fastq2libraryfile_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-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_IDBGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-1BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2BGHcLV29-2
    Sample NameNT-BGHcLV29-1NT-BGHcLV29-1NT-BGHcLV29-1NT-BGHcLV29-1NT-BGHcLV29-1NT-BGHcLV29-1BNT-BGHcLV29-1BNT-BGHcLV29-1BNT-BGHcLV29-1BNT-BGHcLV29-2NT-BGHcLV29-2NT-BGHcLV29-2NT-BGHcLV29-2NT-BGHcLV29-2BNT-BGHcLV29-2BNT-BGHcLV29-2B
    SelectedYesYesYesYesYesYesYesYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-112022-02-11
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV50H_biosample_protocolLV50H_library_protocolLV50H_library_protocolLV50H_biosample_protocolLV50H_library_protocolLV50H_library_protocol
    protocol_URLNT-BGHcLV29-1.pdfL-NT-BGHcLV29-1.pdfL-NT-BGHcLV29-1B.pdfNT-BGHcLV29-2.pdfL-NT-BGHcLV29-2.pdfL-NT-BGHcLV29-2B.pdf
    ID5843587959516023609565556561656365645880595260246096656265656566




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV29-1B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1915NovaSeq6000100paired-ended1ENCODE418972
    NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1871NovaSeq6000100paired-ended1ENCODE418973
    NT-BGHcLV29-1B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1915NovaSeq6000100paired-ended2ENCODE418976
    NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1871NovaSeq6000100paired-ended2ENCODE418977
    NT-BGHcLV29-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1871GRCh38V40NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE218980
    NT-BGHcLV29-1B_Aligned.sortedByCoord.out.bamENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1915GRCh38V40NT-BGHcLV29-1B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-1B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE218981
    NT-BGHcLV29-1B_Signal.Unique.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1915GRCh38V40NT-BGHcLV29-1B/Aligned.sortedByCoord.out.bamENCORE219026
    NT-BGHcLV29-1_Signal.Unique.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1871GRCh38V40NT-BGHcLV29-1/Aligned.sortedByCoord.out.bamENCORE219027
    NT-BGHcLV29-1B_Signal.Unique.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1915GRCh38V40NT-BGHcLV29-1B/Aligned.sortedByCoord.out.bamENCORE219072
    NT-BGHcLV29-1_Signal.Unique.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1871GRCh38V40NT-BGHcLV29-1/Aligned.sortedByCoord.out.bamENCORE219073
    NT-BGHcLV29-1B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1915GRCh38V40NT-BGHcLV29-1B/Aligned.sortedByCoord.out.bamENCORE219118
    NT-BGHcLV29-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1871GRCh38V40NT-BGHcLV29-1/Aligned.sortedByCoord.out.bamENCORE219119
    NT-BGHcLV29-1B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1915GRCh38V40NT-BGHcLV29-1B/Aligned.sortedByCoord.out.bamENCORE219164
    NT-BGHcLV29-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1871GRCh38V40NT-BGHcLV29-1/Aligned.sortedByCoord.out.bamENCORE219165
    NT-BGHcLV29-1B_quant.sfENCODE_DATA/set50_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1915GRCh38V40NT-BGHcLV29-1B_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-1B_S43_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE219210
    NT-BGHcLV29-1_quant.sfENCODE_DATA/set50_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1871GRCh38V40NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE219211
    NT-BGHcLV29-2B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1916NovaSeq6000100paired-ended1ENCODE418974
    NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1872NovaSeq6000100paired-ended1ENCODE418975
    NT-BGHcLV29-2B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1916NovaSeq6000100paired-ended2ENCODE418978
    NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set50_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab1872NovaSeq6000100paired-ended2ENCODE418979
    NT-BGHcLV29-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1872GRCh38V40NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE218982
    NT-BGHcLV29-2B_Aligned.sortedByCoord.out.bamENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1916GRCh38V40NT-BGHcLV29-2B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE218983
    NT-BGHcLV29-2B_Signal.Unique.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1916GRCh38V40NT-BGHcLV29-2B/Aligned.sortedByCoord.out.bamENCORE219028
    NT-BGHcLV29-2_Signal.Unique.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1872GRCh38V40NT-BGHcLV29-2/Aligned.sortedByCoord.out.bamENCORE219029
    NT-BGHcLV29-2B_Signal.Unique.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1916GRCh38V40NT-BGHcLV29-2B/Aligned.sortedByCoord.out.bamENCORE219074
    NT-BGHcLV29-2_Signal.Unique.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1872GRCh38V40NT-BGHcLV29-2/Aligned.sortedByCoord.out.bamENCORE219075
    NT-BGHcLV29-2B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1916GRCh38V40NT-BGHcLV29-2B/Aligned.sortedByCoord.out.bamENCORE219120
    NT-BGHcLV29-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1872GRCh38V40NT-BGHcLV29-2/Aligned.sortedByCoord.out.bamENCORE219121
    NT-BGHcLV29-2B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1916GRCh38V40NT-BGHcLV29-2B/Aligned.sortedByCoord.out.bamENCORE219166
    NT-BGHcLV29-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1872GRCh38V40NT-BGHcLV29-2/Aligned.sortedByCoord.out.bamENCORE219167
    NT-BGHcLV29-2B_quant.sfENCODE_DATA/set50_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1916GRCh38V40NT-BGHcLV29-2B_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2B_S44_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE219212
    NT-BGHcLV29-2_quant.sfENCODE_DATA/set50_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1872GRCh38V40NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE219213