non-target      shRNA in HepG2      Control: NT_BGHLV14

General Information

List KD experiments controlled by BGHLV14-1 and BGHLV14-2


NT-BGHLV14-1,NT-BGHLV14-2 (alias:NT_BGHLV14-1_1,NT_BGHLV14-2_1):
  • AATF-BGHLV14-HepG2
  • CSTF2T-BGHLV14-HepG2
  • DAZAP1-BGHLV14-HepG2
  • DDX21-BGHLV14-HepG2
  • DDX24-BGHLV14-HepG2
  • AGO1-BGHLV14-HepG2
  • EIF3G-BGHLV14-HepG2
  • EXOSC9-BGHLV14-HepG2
  • FASTKD2-BGHLV14-HepG2

    • NT-BGHLV14-1B,NT-BGHLV14-2B (alias:NT_BGHLV14-1,NT_BGHLV14-2):
  • FUS-BGHLV14-HepG2
  • GTF2F1-BGHLV14-HepG2
  • HLTF-BGHLV14-HepG2
  • IGF2BP1-BGHLV14-HepG2
  • PCBP2-BGHLV14-HepG2
  • PRPF6-BGHLV14-HepG2
  • RAVER1-BGHLV14-HepG2
  • RBM34-BGHLV14-HepG2
  • RPS10-BGHLV14-HepG2
  • RTF1-BGHLV14-HepG2
  • SLTM-BGHLV14-HepG2
  • SMNDC1-BGHLV14-HepG2
  • SND1-BGHLV14-HepG2
  • SRSF5-BGHLV14-HepG2
  • SUB1-BGHLV14-HepG2
  • TRA2A-BGHLV14-HepG2
  • U2AF2-BGHLV14-HepG2
  • XRCC5-BGHLV14-HepG2
  • XRCC6-BGHLV14-HepG2
  • ZRANB2-BGHLV14-HepG2




    • Experiment Information (Status: Released)
    BGHLV14-1BGHLV14-2
    idx9596
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGHLV14-1BGHLV14-2
    transduction_Date7/4/20147/4/2014
    days
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc05304
    WB_result
    Ave_WB
    WB_DONE_date
    MW
    IP
    antibody_Cat#
    Antibody DCC ID
    submitted_to_DCC_date
    Rep1_TPM00
    Rep2_TPM00
    Action
    Library_start_date7/30/20147/30/2014
    repeat_library
    Note
    ID21522153




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHLV14-1BGHLV14-1BGHLV14-2BGHLV14-2
    Sample_IDBGHLV14-1BGHLV14-1BGHLV14-2BGHLV14-2
    Sample NameNT_BGHLV14-1NT_BGHLV14-1_1NT_BGHLV14-2NT_BGHLV14-2_1
    Sample NameNT_BGHLV14-1NT_BGHLV14-1_1NT_BGHLV14-2NT_BGHLV14-2_1
    RBPnon-targetnon-targetnon-targetnon-target
    Cell_LineHepG2HepG2HepG2HepG2
    Exp UID
    StatusReleasedReleasedReleasedReleased
    Status_date2014-11-042014-11-042014-11-042014-11-04
    ProjectENCODE3ENCODE3ENCODE3ENCODE3
    Note
    ID516517518519




    Library-Prep Information
    BGHLV14-1BGHLV14-1BGHLV14-2BGHLV14-2
    Sample #
    Sample NameNT-BGHLV14-1NT-BGHLV14-1BNT-BGHLV14-2NT-BGHLV14-2B
    Sample_Name_AliasNT_BGHLV14-1_1NT_BGHLV14-1NT_BGHLV14-2_1NT_BGHLV14-2
    Index Well PositionS05S01S06S02
    Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
    LibPrep_date2014-07-302014-08-122014-07-302014-08-12
    Lib_IDLib-140730Lib-140812Lib-140730Lib-140812
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp
    Peak_Molarity
    libSampleQC_DNA_WellDNA_Library_LV13-14/set1/B10.pngDNA_Library_LV13-14/set1/B10.pngDNA_Library_LV13-14/set1/C10.pngDNA_Library_LV13-14/set1/C10.png
    RIN9.49.49.59.5
    libSample_RNA_WellRNA_Library_LV13-14-16/set1/A4.pngRNA_Library_LV13-14-16/set1/A4.pngRNA_Library_LV13-14-16/set1/B4.pngRNA_Library_LV13-14-16/set1/B4.png
    SampleQC_methodTapeStationTapeStationTapeStationTapeStation
    SampleQC_date
    Sample_IDBGHLV14-1BGHLV14-1BGHLV14-2BGHLV14-2
    RBPNTNTNTNT
    Batch_IDBGHLV14BGHLV14BGHLV14BGHLV14
    WB_result0.0000.0000.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequence
    ProjectENCODE3ENCODE3ENCODE3ENCODE3
    ID2172219221732193




    Sequencing Information
    BGHLV14-1BGHLV14-2
    Sample_IDBGHLV14-1BGHLV14-2
    Sample NameNT_BGHLV14-1_1NT_BGHLV14-2_1
    Pool IDPool-140901Pool-140901
    LocalServer_folderset14set14
    total_reads37,930,00042,340,000
    total_aligned_reads34,845,29639,468,512
    unique_aligned_reads32,801,84237,186,474
    percent_uniqueAligned0.864800.87828
    correlation_replicates0.9911560.991156
    spikein_reads00
    percent_spikeins
    original_ReadLength100100
    QC_StatusSubmittedSubmitted
    ID814815




    Data Submission Information
    BGHLV14-1BGHLV14-1
    ENCODE_aliasbrenton-graveley:NT_BGHLV14_1brenton-graveley:NT_BGHLV14
    ENCODE_accessionENCSR003EKRENCSR491FOC
    object_typeexperimentexperiment
    assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
    Sample_IDBGHLV14-1BGHLV14-1
    Sample NameNT_BGHLV14-1_1NT_BGHLV14-1
    SelectedYesYes
    StatusReleasedReleased
    Status_Date2014-10-302014-10-30
    ProjectENCODE3ENCODE3
    protocol_URL
    ID27972808




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gzENCODE_DATA/set14/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab814HiSeq2000100paired-ended1ENCODE313809
    NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gzENCODE_DATA/set14/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab814HiSeq2000100paired-ended2ENCODE313871
    NT_BGHLV14-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set14/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab814GRCh38V40NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gzENCORE213933
    NT_BGHLV14-1_Signal.Unique.strand+.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab814GRCh38V40NT_BGHLV14-1/Aligned.sortedByCoord.out.bamENCORE213995
    NT_BGHLV14-1_Signal.Unique.strand-.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab814GRCh38V40NT_BGHLV14-1/Aligned.sortedByCoord.out.bamENCORE214057
    NT_BGHLV14-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab814GRCh38V40NT_BGHLV14-1/Aligned.sortedByCoord.out.bamENCORE214119
    NT_BGHLV14-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab814GRCh38V40NT_BGHLV14-1/Aligned.sortedByCoord.out.bamENCORE214181
    NT_BGHLV14-1_quant.sfENCODE_DATA/set14/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab814GRCh38V40NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gzENCORE214243
    NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gzENCODE_DATA/set14/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab815HiSeq2000100paired-ended1ENCODE313811
    NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gzENCODE_DATA/set14/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab815HiSeq2000100paired-ended2ENCODE313873
    NT_BGHLV14-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set14/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab815GRCh38V40NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gzENCORE213935
    NT_BGHLV14-2_Signal.Unique.strand+.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab815GRCh38V40NT_BGHLV14-2/Aligned.sortedByCoord.out.bamENCORE213997
    NT_BGHLV14-2_Signal.Unique.strand-.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab815GRCh38V40NT_BGHLV14-2/Aligned.sortedByCoord.out.bamENCORE214059
    NT_BGHLV14-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab815GRCh38V40NT_BGHLV14-2/Aligned.sortedByCoord.out.bamENCORE214121
    NT_BGHLV14-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set14/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab815GRCh38V40NT_BGHLV14-2/Aligned.sortedByCoord.out.bamENCORE214183
    NT_BGHLV14-2_quant.sfENCODE_DATA/set14/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab815GRCh38V40NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gzENCORE214245