non-target      CRISPR in HepG2      Control: NT-BGHcLV10

General Information

List KD experiments controlled by BGHcLV10-1 and BGHcLV10-2


NT-BGHcLV10-1,NT-BGHcLV10-2:
  • CHD3-BGHcLV10-HepG2
  • CNOT7-BGHcLV10-HepG2
  • DDX20-BGHcLV10-HepG2
  • EIF4B-BGHcLV10-HepG2
  • NCBP1-BGHcLV10-HepG2
  • NFX1-BGHcLV10-HepG2
  • STAU2-BGHcLV10-HepG2
  • TRNAU1AP-BGHcLV10-HepG2
  • ZC3H11A-BGHcLV10-HepG2
  • ZNF106-BGHcLV10-HepG2




    • Experiment Information (Status: Released)
    BGHcLV10-1BGHcLV10-2
    idx198199
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Name
    Sample_IDBGHcLV10-1BGHcLV10-2
    transduction_Date4/27/184/27/18
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc02436
    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
    ID63416342




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV10-1BGHcLV10-2
    Sample_IDBGHcLV10-1BGHcLV10-2
    Sample Name
    Sample NameNT-BGHcLV10-1NT-BGHcLV10-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusReleasedReleased
    Status_date2020-11-062020-11-06
    ProjectENCODE4ENCODE4
    Note
    ID62896290




    Library-Prep Information
    BGHcLV10-1BGHcLV10-2
    Sample #4950
    Sample NameNT-BGHcLV10-1NT-BGHcLV10-2
    Sample_Name_Alias
    Index Well PositionE07F07
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2018-10-012018-10-01
    Lib_IDLib-181001Lib-181001
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp271274
    Peak_Molarity44.8054.20
    libSampleQC_DNA_WellDNA_Library_set41/set5/E7.pngDNA_Library_set41/set5/F7.png
    RIN9.79.7
    libSample_RNA_WellRNA_Library_set41/set1/A7.pngRNA_Library_set41/set1/B7.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2018-08-082018-08-08
    Sample_IDBGHcLV10-1BGHcLV10-2
    RBPNTNT
    Batch_IDBGHcLV10BGHcLV10
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID899900




    Sequencing Information
    BGHcLV10-1BGHcLV10-2
    Sample_IDBGHcLV10-1BGHcLV10-2
    Sample NameNT-BGHcLV10-1NT-BGHcLV10-2
    Pool IDPool-180901Pool-180901
    LocalServer_folderset41set41
    total_reads143,300,286108,205,742
    total_aligned_reads137,833,386104,787,200
    unique_aligned_reads127,991,03297,579,586
    percent_uniqueAligned0.893170.90180
    correlation_replicates0.9939110.993911
    spikein_reads234,492196,248
    percent_spikeins0.001640.00181
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID305306




    Data Submission Information
    BGHcLV10-1BGHcLV10-1BGHcLV10-1BGHcLV10-1BGHcLV10-1BGHcLV10-2BGHcLV10-2BGHcLV10-2BGHcLV10-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV10brenton-graveley:NT-BGHcLV10-1brenton-graveley:L-NT-BGHcLV10-1brenton-graveley:NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV10-2brenton-graveley:L-NT-BGHcLV10-2brenton-graveley:NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR775ZWOENCBS275IUWENCLB382WZUENCFF434NYFENCFF319SJLENCBS282MMSENCLB718PAEENCFF258LSKENCFF112JHP
    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_IDBGHcLV10-1BGHcLV10-1BGHcLV10-1BGHcLV10-1BGHcLV10-1BGHcLV10-2BGHcLV10-2BGHcLV10-2BGHcLV10-2
    Sample NameNT-BGHcLV10-1NT-BGHcLV10-1NT-BGHcLV10-1NT-BGHcLV10-1NT-BGHcLV10-1NT-BGHcLV10-2NT-BGHcLV10-2NT-BGHcLV10-2NT-BGHcLV10-2
    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-BGHcLV10-1.pdfL-NT-BGHcLV10-1.pdfNT-BGHcLV10-2.pdfL-NT-BGHcLV10-2.pdf
    ID113511901260133013941191126113311395




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab305NovaSeq6000100paired-ended1ENCODE4537
    NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab305NovaSeq6000100paired-ended2ENCODE4607
    NT-BGHcLV10-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab305GRCh38V40NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226775
    NT-BGHcLV10-1_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab305GRCh38V40NT-BGHcLV10-1/Aligned.sortedByCoord.out.bamENCORE226845
    NT-BGHcLV10-1_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab305GRCh38V40NT-BGHcLV10-1/Aligned.sortedByCoord.out.bamENCORE226915
    NT-BGHcLV10-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab305GRCh38V40NT-BGHcLV10-1/Aligned.sortedByCoord.out.bamENCORE226985
    NT-BGHcLV10-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab305GRCh38V40NT-BGHcLV10-1/Aligned.sortedByCoord.out.bamENCORE227055
    NT-BGHcLV10-1_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab305GRCh38V40NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227125
    NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab306NovaSeq6000100paired-ended1ENCODE4538
    NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab306NovaSeq6000100paired-ended2ENCODE4608
    NT-BGHcLV10-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab306GRCh38V40NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226776
    NT-BGHcLV10-2_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab306GRCh38V40NT-BGHcLV10-2/Aligned.sortedByCoord.out.bamENCORE226846
    NT-BGHcLV10-2_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab306GRCh38V40NT-BGHcLV10-2/Aligned.sortedByCoord.out.bamENCORE226916
    NT-BGHcLV10-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab306GRCh38V40NT-BGHcLV10-2/Aligned.sortedByCoord.out.bamENCORE226986
    NT-BGHcLV10-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab306GRCh38V40NT-BGHcLV10-2/Aligned.sortedByCoord.out.bamENCORE227056
    NT-BGHcLV10-2_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab306GRCh38V40NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227126