non-target      CRISPR in HepG2      Control: NT-BGHcLV12

General Information

List KD experiments controlled by BGHcLV12-1 and BGHcLV12-2


NT-BGHcLV12-1,NT-BGHcLV12-2:
  • ANXA2-BGHcLV12-HepG2
  • CIRBP-BGHcLV12-HepG2
  • DDX51-BGHcLV12-HepG2
  • GLRX3-BGHcLV12-HepG2
  • MAK16-BGHcLV12-HepG2
  • PPP1R8-BGHcLV12-HepG2
  • SRPK2-BGHcLV12-HepG2
  • WDR43-BGHcLV12-HepG2




    • Experiment Information (Status: Released)
    BGHcLV12-1BGHcLV12-2
    idx261262
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Name
    Sample_IDBGHcLV12-1BGHcLV12-2
    transduction_Date8/17/188/17/18
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc04588
    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_date03/13/1903/13/19
    repeat_library
    Note
    ID84528453




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV12-1BGHcLV12-2
    Sample_IDBGHcLV12-1BGHcLV12-2
    Sample NameNT-BGHcLV12-1NT-BGHcLV12-2
    Sample NameNT-BGHcLV12-1NT-BGHcLV12-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusReleasedReleased
    Status_date2020-11-062020-11-06
    ProjectENCODE4ENCODE4
    Note
    ID28012802




    Library-Prep Information
    BGHcLV12-1BGHcLV12-2
    Sample #3132
    Sample NameNT-BGHcLV12-1NT-BGHcLV12-2
    Sample_Name_Alias
    Index Well PositionG04H04
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2019-03-132019-03-13
    Lib_IDLib-190313Lib-190313
    Tecan_Location2-G22-H2
    Tecan65.9036.80
    Tecan_date2019-03-132019-03-13
    Size_bp291301
    Peak_Molarity51.5048.90
    libSampleQC_DNA_WellDNA_Library_set42/set2/C1.pngDNA_Library_set42/set1/H4.png
    RIN10.09.9
    libSample_RNA_WellRNA_Library_set42/set1/G4.pngRNA_Library_set42/set1/H4.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-03-132019-03-13
    Sample_IDBGHcLV12-1BGHcLV12-2
    RBPNTNT
    Batch_IDBGHcLV12BGHcLV12
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID3132




    Sequencing Information
    BGHcLV12-1BGHcLV12-2
    Sample_IDBGHcLV12-1BGHcLV12-2
    Sample NameNT-BGHcLV12-1NT-BGHcLV12-2
    Pool IDPool-190423Pool-190423
    LocalServer_folderset42set42
    total_reads39,996,12452,696,814
    total_aligned_reads38,470,85451,160,436
    unique_aligned_reads36,288,77648,355,548
    percent_uniqueAligned0.907310.91762
    correlation_replicates0.9973120.997312
    spikein_reads46,88263,076
    percent_spikeins0.001170.00120
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID4142




    Data Submission Information
    BGHcLV12-1BGHcLV12-1BGHcLV12-1BGHcLV12-1BGHcLV12-1BGHcLV12-2BGHcLV12-2BGHcLV12-2BGHcLV12-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV12brenton-graveley:NT-BGHcLV12-1brenton-graveley:L-NT-BGHcLV12-1brenton-graveley:NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV12-2brenton-graveley:L-NT-BGHcLV12-2brenton-graveley:NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR827PIIENCBS421MNKENCLB117DULENCFF066NRAENCFF404YUJENCBS372ZCCENCLB975ZEYENCFF748HIIENCFF791KFP
    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_IDBGHcLV12-1BGHcLV12-1BGHcLV12-1BGHcLV12-1BGHcLV12-1BGHcLV12-2BGHcLV12-2BGHcLV12-2BGHcLV12-2
    Sample NameNT-BGHcLV12-1NT-BGHcLV12-1NT-BGHcLV12-1NT-BGHcLV12-1NT-BGHcLV12-1NT-BGHcLV12-2NT-BGHcLV12-2NT-BGHcLV12-2NT-BGHcLV12-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-202020-11-20
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV42_biosample_protocolLV42_library_protocolLV42_biosample_protocolLV42_library_protocol
    protocol_URLNT-BGHcLV12-1.pdfL-NT-BGHcLV12-1.pdfNT-BGHcLV12-2.pdfL-NT-BGHcLV12-2.pdf
    ID75179787999110737988809921074




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab41NovaSeq6000100paired-ended1ENCODE4373
    NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab41NovaSeq6000100paired-ended2ENCODE4455
    NT-BGHcLV12-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab41GRCh38V40NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223712
    NT-BGHcLV12-1_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab41GRCh38V40NT-BGHcLV12-1/Aligned.sortedByCoord.out.bamENCORE223794
    NT-BGHcLV12-1_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab41GRCh38V40NT-BGHcLV12-1/Aligned.sortedByCoord.out.bamENCORE223876
    NT-BGHcLV12-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab41GRCh38V40NT-BGHcLV12-1/Aligned.sortedByCoord.out.bamENCORE223958
    NT-BGHcLV12-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab41GRCh38V40NT-BGHcLV12-1/Aligned.sortedByCoord.out.bamENCORE224040
    NT-BGHcLV12-1_quant.sfENCODE_DATA/set42/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab41GRCh38V40NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224122
    NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab42NovaSeq6000100paired-ended1ENCODE4374
    NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set42/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab42NovaSeq6000100paired-ended2ENCODE4456
    NT-BGHcLV12-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab42GRCh38V40NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE223713
    NT-BGHcLV12-2_Signal.Unique.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab42GRCh38V40NT-BGHcLV12-2/Aligned.sortedByCoord.out.bamENCORE223795
    NT-BGHcLV12-2_Signal.Unique.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab42GRCh38V40NT-BGHcLV12-2/Aligned.sortedByCoord.out.bamENCORE223877
    NT-BGHcLV12-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab42GRCh38V40NT-BGHcLV12-2/Aligned.sortedByCoord.out.bamENCORE223959
    NT-BGHcLV12-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab42GRCh38V40NT-BGHcLV12-2/Aligned.sortedByCoord.out.bamENCORE224041
    NT-BGHcLV12-2_quant.sfENCODE_DATA/set42/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab42GRCh38V40NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE224123