non-target      CRISPR in HepG2      Control: NT-BGHcLV18

General Information

List KD experiments controlled by BGHcLV18-1 and BGHcLV18-2


NT-BGHcLV18-1,NT-BGHcLV18-2:
  • BAZ1A-BGHcLV18-HepG2
  • CTCF-BGHcLV18-HepG2
  • CXXC1-BGHcLV18-HepG2
  • DDX39B-BGHcLV18-HepG2
  • DHX57-BGHcLV18-HepG2
  • DUS3L-BGHcLV18-HepG2
  • E4F1-BGHcLV18-HepG2
  • ERN1-BGHcLV18-HepG2
  • FBL-BGHcLV18-HepG2
  • GARS-BGHcLV18-HepG2
  • GEMIN2-BGHcLV18-HepG2
  • IFIT2-BGHcLV18-HepG2
  • NCL-BGHcLV18-HepG2
  • PDCD4-BGHcLV18-HepG2
  • PPP1R10-BGHcLV18-HepG2
  • PRPF39-BGHcLV18-HepG2
  • RAE1-BGHcLV18-HepG2
  • RPL28-BGHcLV18-HepG2
  • SF3A1-BGHcLV18-HepG2
  • SMAD4-BGHcLV18-HepG2
  • SMAD5-BGHcLV18-HepG2
  • SUZ12-BGHcLV18-HepG2
  • ZNF574-BGHcLV18-HepG2




    • Experiment Information (Status: Released)
    BGHcLV18-1BGHcLV18-2
    idx494495
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGHcLV18-1BGHcLV18-2
    transduction_Date8/13/198/13/19
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc04697
    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_date12/11/1912/11/19
    repeat_library
    Note
    ID66456646




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV18-1BGHcLV18-2
    Sample_IDBGHcLV18-1BGHcLV18-2
    Sample Name
    Sample NameNT-BGHcLV18-1NT-BGHcLV18-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusReleasedReleased
    Status_date2020-12-012020-12-01
    ProjectENCODE4ENCODE4
    Note
    ID56135614




    Library-Prep Information
    BGHcLV18-1BGHcLV18-2
    Sample #119120
    Sample NameNT-BGHcLV18-1NT-BGHcLV18-2
    Sample_Name_Alias
    Index Well PositionA04B04
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2020-01-022020-01-02
    Lib_IDLib-200102Lib-200102
    Tecan_Location3-C13-D1
    Tecan19.4738.88
    Tecan_date2019-12-162019-12-16
    Size_bp268278
    Peak_Molarity23.8027.90
    libSampleQC_DNA_WellDNA_Library_set43-44/set2/A5.pngDNA_Library_set43-44/set2/B5.png
    RIN9.99.7
    libSample_RNA_WellRNA_Library_set43-44/set4/E6.pngRNA_Library_set43-44/set4/F6.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-12-132019-12-13
    Sample_IDBGHcLV18-1BGHcLV18-2
    RBPNTNT
    Batch_IDBGHcLV18BGHcLV18
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID695696




    Sequencing Information
    BGHcLV18-1BGHcLV18-2
    Sample_IDBGHcLV18-1BGHcLV18-2
    Sample NameNT-BGHcLV18-1NT-BGHcLV18-2
    Pool IDPool-200103Pool-200103
    LocalServer_folderset44_Hset44_H
    total_reads174,495,124134,481,204
    total_aligned_reads163,247,848125,014,430
    unique_aligned_reads152,627,948117,002,418
    percent_uniqueAligned0.874680.87003
    correlation_replicates0.9991350.999135
    spikein_reads327,880269,022
    percent_spikeins0.001880.00200
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID201202




    Data Submission Information
    BGHcLV18-1BGHcLV18-1BGHcLV18-1BGHcLV18-1BGHcLV18-1BGHcLV18-2BGHcLV18-2BGHcLV18-2BGHcLV18-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV18brenton-graveley:NT-BGHcLV18-1brenton-graveley:L-NT-BGHcLV18-1brenton-graveley:NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV18-2brenton-graveley:L-NT-BGHcLV18-2brenton-graveley:NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR670KASENCBS876GKIENCLB922EXYENCFF500CKUENCFF550MXWENCBS742NFJENCLB502SZZENCFF078QWKENCFF003PFD
    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_IDBGHcLV18-1BGHcLV18-1BGHcLV18-1BGHcLV18-1BGHcLV18-1BGHcLV18-2BGHcLV18-2BGHcLV18-2BGHcLV18-2
    Sample NameNT-BGHcLV18-1NT-BGHcLV18-1NT-BGHcLV18-1NT-BGHcLV18-1NT-BGHcLV18-1NT-BGHcLV18-2NT-BGHcLV18-2NT-BGHcLV18-2NT-BGHcLV18-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2020-12-012020-12-012020-12-012020-12-012020-12-012020-12-012020-12-012020-12-012020-12-01
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV44H_biosample_protocolLV44H_library_protocolLV44H_biosample_protocolLV44H_library_protocol
    protocol_URLNT-BGHcLV18-1.pdfL-NT-BGHcLV18-1.pdfNT-BGHcLV18-2.pdfL-NT-BGHcLV18-2.pdf
    ID45170336586638171337587639




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set44_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab201NovaSeq6000100paired-ended1ENCODE4199
    NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set44_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab201NovaSeq6000100paired-ended2ENCODE4251
    NT-BGHcLV18-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab201GRCh38V40NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gzENCORE224919
    NT-BGHcLV18-1_Signal.Unique.strand+.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab201GRCh38V40NT-BGHcLV18-1/Aligned.sortedByCoord.out.bamENCORE224971
    NT-BGHcLV18-1_Signal.Unique.strand-.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab201GRCh38V40NT-BGHcLV18-1/Aligned.sortedByCoord.out.bamENCORE225023
    NT-BGHcLV18-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab201GRCh38V40NT-BGHcLV18-1/Aligned.sortedByCoord.out.bamENCORE225075
    NT-BGHcLV18-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab201GRCh38V40NT-BGHcLV18-1/Aligned.sortedByCoord.out.bamENCORE225127
    NT-BGHcLV18-1_quant.sfENCODE_DATA/set44_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab201GRCh38V40NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gzENCORE225179
    NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set44_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab202NovaSeq6000100paired-ended1ENCODE4200
    NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set44_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab202NovaSeq6000100paired-ended2ENCODE4252
    NT-BGHcLV18-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab202GRCh38V40NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gzENCORE224920
    NT-BGHcLV18-2_Signal.Unique.strand+.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab202GRCh38V40NT-BGHcLV18-2/Aligned.sortedByCoord.out.bamENCORE224972
    NT-BGHcLV18-2_Signal.Unique.strand-.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab202GRCh38V40NT-BGHcLV18-2/Aligned.sortedByCoord.out.bamENCORE225024
    NT-BGHcLV18-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab202GRCh38V40NT-BGHcLV18-2/Aligned.sortedByCoord.out.bamENCORE225076
    NT-BGHcLV18-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab202GRCh38V40NT-BGHcLV18-2/Aligned.sortedByCoord.out.bamENCORE225128
    NT-BGHcLV18-2_quant.sfENCODE_DATA/set44_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab202GRCh38V40NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gzENCORE225180