non-target      CRISPR in HepG2      Control: NT-BGHcLV20

General Information

List KD experiments controlled by BGHcLV20-1 and BGHcLV20-2


NT-BGHcLV20-1,NT-BGHcLV20-2:
  • CIZ1-BGHcLV20-HepG2
  • DNMT3B-BGHcLV20-HepG2
  • MORC2-BGHcLV20-HepG2
  • RBM19-BGHcLV20-HepG2
  • RNF187-BGHcLV20-HepG2
  • RPS25-BGHcLV20-HepG2
  • RYBP-BGHcLV20-HepG2
  • SMYD3-BGHcLV20-HepG2
  • TAF9-BGHcLV20-HepG2




    • Experiment Information (Status: Released)
    BGHcLV20-1BGHcLV20-2
    idx551552
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGHcLV20-1BGHcLV20-2
    transduction_Date12/10/1912/10/19
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc06186
    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
    ID67066707




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV20-1BGHcLV20-2
    Sample_IDBGHcLV20-1BGHcLV20-2
    Sample Name
    Sample NameNT-BGHcLV20-1NT-BGHcLV20-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusReleasedReleased
    Status_date2021-03-182021-03-18
    ProjectENCODE4ENCODE4
    Note
    ID58075808




    Library-Prep Information
    BGHcLV20-1BGHcLV20-2
    Sample #5758
    Sample NameNT-BGHcLV20-1NT-BGHcLV20-2
    Sample_Name_Alias
    Index Well PositionC07D07
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2020-09-242020-09-24
    Lib_IDLib-200924Lib-200924
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp313310
    Peak_Molarity120.0099.60
    libSampleQC_DNA_WellDNA_Library_set45/set1/C7.pngDNA_Library_set45/set1/D7.png
    RIN9.59.6
    libSample_RNA_WellRNA_Library_set45/set2/H10.pngRNA_Library_set45/set2/A11.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2020-09-222020-09-22
    Sample_IDBGHcLV20-1BGHcLV20-2
    RBPNTNT
    Batch_IDBGHcLV20BGHcLV20
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID831832




    Sequencing Information
    BGHcLV20-1BGHcLV20-2
    Sample_IDBGHcLV20-1BGHcLV20-2
    Sample NameNT-BGHcLV20-1NT-BGHcLV20-2
    Pool IDPool-200928Pool-200928
    LocalServer_folderset45_Hset45_H
    total_reads124,911,85089,825,650
    total_aligned_reads111,947,60486,877,090
    unique_aligned_reads105,531,54882,014,298
    percent_uniqueAligned0.844850.91304
    correlation_replicates0.9936780.993678
    spikein_reads65,41234,352
    percent_spikeins0.000520.00038
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID462463




    Data Submission Information
    BGHcLV20-1BGHcLV20-1BGHcLV20-1BGHcLV20-1BGHcLV20-1BGHcLV20-2BGHcLV20-2BGHcLV20-2BGHcLV20-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV20brenton-graveley:NT-BGHcLV20-1brenton-graveley:L-NT-BGHcLV20-1brenton-graveley:NT-BGHcLV20-1_S51_R1_001.fastq.gzbrenton-graveley:NT-BGHcLV20-1_S51_R2_001.fastq.gzbrenton-graveley:NT-BGHcLV20-2brenton-graveley:L-NT-BGHcLV20-2brenton-graveley:NT-BGHcLV20-2_S52_R1_001.fastq.gzbrenton-graveley:NT-BGHcLV20-2_S52_R2_001.fastq.gz
    ENCODE_accessionENCSR306EWEENCBS989SEXENCLB952MTZENCFF141NOEENCFF096NVCENCBS217OPSENCLB768VNUENCFF520IZBENCFF922CIA
    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_IDBGHcLV20-1BGHcLV20-1BGHcLV20-1BGHcLV20-1BGHcLV20-1BGHcLV20-2BGHcLV20-2BGHcLV20-2BGHcLV20-2
    Sample NameNT-BGHcLV20-1NT-BGHcLV20-1NT-BGHcLV20-1NT-BGHcLV20-1NT-BGHcLV20-1NT-BGHcLV20-2NT-BGHcLV20-2NT-BGHcLV20-2NT-BGHcLV20-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-182021-03-18
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV45H_biosample_protocolLV45H_library_protocolLV45H_biosample_protocolLV45H_library_protocol
    protocol_URLNT-BGHcLV20-1.pdfL-NT-BGHcLV20-1.pdfNT-BGHcLV20-2.pdfL-NT-BGHcLV20-2.pdf
    ID208021152185225523252116218622562326




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV20-1_S51_R1_001.fastq.gzENCODE_DATA/set45_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab462NovaSeq6000100paired-ended1ENCODE41314
    NT-BGHcLV20-1_S51_R2_001.fastq.gzENCODE_DATA/set45_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab462NovaSeq6000100paired-ended2ENCODE41334
    NT-BGHcLV20-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab462GRCh38V40NT-BGHcLV20-1_S51_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV20-1_S51_R2_001.filtered.trimmed.paired.fastq.gzENCORE224855
    NT-BGHcLV20-1_quant.sfENCODE_DATA/set45_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab462GRCh38V40NT-BGHcLV20-1_S51_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV20-1_S51_R2_001.filtered.trimmed.paired.fastq.gzENCORE224875
    NT-BGHcLV20-1_Signal.Unique.strand+.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab462GRCh38V40NT-BGHcLV20-1/Aligned.sortedByCoord.out.bamENCORE225925
    NT-BGHcLV20-1_Signal.Unique.strand-.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab462GRCh38V40NT-BGHcLV20-1/Aligned.sortedByCoord.out.bamENCORE225945
    NT-BGHcLV20-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab462GRCh38V40NT-BGHcLV20-1/Aligned.sortedByCoord.out.bamENCORE225965
    NT-BGHcLV20-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab462GRCh38V40NT-BGHcLV20-1/Aligned.sortedByCoord.out.bamENCORE225985
    NT-BGHcLV20-2_S52_R1_001.fastq.gzENCODE_DATA/set45_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab463NovaSeq6000100paired-ended1ENCODE41315
    NT-BGHcLV20-2_S52_R2_001.fastq.gzENCODE_DATA/set45_H/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab463NovaSeq6000100paired-ended2ENCODE41335
    NT-BGHcLV20-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab463GRCh38V40NT-BGHcLV20-2_S52_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV20-2_S52_R2_001.filtered.trimmed.paired.fastq.gzENCORE224856
    NT-BGHcLV20-2_quant.sfENCODE_DATA/set45_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab463GRCh38V40NT-BGHcLV20-2_S52_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV20-2_S52_R2_001.filtered.trimmed.paired.fastq.gzENCORE224876
    NT-BGHcLV20-2_Signal.Unique.strand+.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab463GRCh38V40NT-BGHcLV20-2/Aligned.sortedByCoord.out.bamENCORE225926
    NT-BGHcLV20-2_Signal.Unique.strand-.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab463GRCh38V40NT-BGHcLV20-2/Aligned.sortedByCoord.out.bamENCORE225946
    NT-BGHcLV20-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab463GRCh38V40NT-BGHcLV20-2/Aligned.sortedByCoord.out.bamENCORE225966
    NT-BGHcLV20-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab463GRCh38V40NT-BGHcLV20-2/Aligned.sortedByCoord.out.bamENCORE225986