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non-target RNA-Seq in HepG2



non-target      CRISPR in HepG2      Control:

General Information

List KD experiments controlled by BGHcLV41-1 and BGHcLV41-2


NT-BGHcLV41-1,NT-BGHcLV41-2:
  • BCLAF1-BGHcLV41-HepG2
  • DYNC1I2-BGHcLV41-HepG2
  • EEF2K-BGHcLV41-HepG2
  • EFL1-BGHcLV41-HepG2
  • EIF3E-BGHcLV41-HepG2
  • EIF3J-BGHcLV41-HepG2
  • EIF3K-BGHcLV41-HepG2
  • EIF5B-BGHcLV41-HepG2
  • EML4-BGHcLV41-HepG2
  • EXOSC9-BGHcLV41-HepG2
  • FAM98A-BGHcLV41-HepG2
  • FDPS-BGHcLV41-HepG2
  • FEN1-BGHcLV41-HepG2
  • FKBP3-BGHcLV41-HepG2
  • IARS-BGHcLV41-HepG2
  • MARS-BGHcLV41-HepG2
  • PABPN1-BGHcLV41-HepG2
  • SRP72-BGHcLV41-HepG2
  • TARS-BGHcLV41-HepG2

    • NT-BGHcLV41-1B,NT-BGHcLV41-2B:
  • EIF2B5-BGHcLV41-HepG2
  • EPB41L2-BGHcLV41-HepG2




    • Experiment Information (Status: Submitting)
    BGHcLV41-1BGHcLV41-2
    idx12681269
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon- targetnon- target
    Sample_IDBGHcLV41-1BGHcLV41-2
    transduction_Date1/12/241/12/24
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc02333
    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_date
    repeat_library
    Note
    ID74597460




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV41-1BGHcLV41-1BGHcLV41-2BGHcLV41-2
    Sample_IDBGHcLV41-1BGHcLV41-1BGHcLV41-2BGHcLV41-2
    Sample Name
    Sample NameNT-BGHcLV41-1NT-BGHcLV41-1BNT-BGHcLV41-2NT-BGHcLV41-2B
    RBPnon-targetnon-targetnon-targetnon-target
    Cell_LineHepG2HepG2HepG2HepG2
    Exp UID
    StatusSubmittingSubmittingSubmittingSubmitting
    Status_date2024-09-202024-09-202024-09-202024-09-20
    ProjectENCORE2ENCORE2ENCORE2ENCORE2
    Note
    ID12948133041294913305




    Library-Prep Information
    BGHcLV41-1BGHcLV41-1BGHcLV41-2BGHcLV41-2
    Sample #1122
    Sample NameNT-BGHcLV41-1NT-BGHcLV41-1BNT-BGHcLV41-2NT-BGHcLV41-2B
    Sample_Name_Alias
    Index Well PositionA01A01B01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96IDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2024-03-012024-08-222024-03-012024-08-22
    Lib_IDLib-240301Lib-240822Lib-240301Lib-240822
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp299278308288
    Peak_Molarity80.6053.7081.1082.50
    libSampleQC_DNA_WellDNA_Library_set70/set1/A1.pngDNA_Library_set70/set2/A9.pngDNA_Library_set70/set1/B1.pngDNA_Library_set70/set2/B9.png
    RIN9.49.49.49.4
    libSample_RNA_WellRNA_Library_set70/set1/E6.pngRNA_Library_set70/set1/E6.pngRNA_Library_set70/set1/F6.pngRNA_Library_set70/set1/F6.png
    SampleQC_methodTapeStation_2022TapeStation_2022TapeStation_2022TapeStation_2022
    SampleQC_date2024-03-142024-08-222024-03-142024-08-22
    Sample_IDBGHcLV41-1BGHcLV41-1BGHcLV41-2BGHcLV41-2
    RBPNTNTNTNT
    Batch_IDBGHcLV41BGHcLV41BGHcLV41BGHcLV41
    WB_result0.0000.0000.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNATruSeq mRNATruSeq mRNA
    Repeat_Library_SuffixBB
    Lib_StatusSendToSequenceSendToSequenceSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2ENCORE2ENCORE2
    ID4226441842274419




    Sequencing Information
    BGHcLV41-1BGHcLV41-1BGHcLV41-2BGHcLV41-2
    Sample_IDBGHcLV41-1BGHcLV41-1BGHcLV41-2BGHcLV41-2
    Sample NameNT-BGHcLV41-1NT-BGHcLV41-1BNT-BGHcLV41-2NT-BGHcLV41-2B
    Pool IDPool-240314Pool-240822Pool-240314Pool-240822
    LocalServer_folderset70set70set70set70
    total_reads54,419,19083,369,13029,688,36264,262,304
    total_aligned_reads46,459,35970,590,13424,965,12053,687,439
    unique_aligned_reads43,780,90166,200,78323,574,81250,403,434
    percent_uniqueAligned0.804510.794070.794080.78434
    correlation_replicates0.9985490.9987480.9985490.998748
    spikein_reads10,312191,4461,990162,880
    percent_spikeins0.000190.002300.000070.00253
    original_ReadLength151100151100
    QC_StatusSubmittingSubmittingSubmittingSubmitting
    ID2945298929462990




    Data Submission Information
    DCC submission information was not avaliable




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV41-1B_S1_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set70/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2989NovaSeq6000100paired-ended1ENCORE228933
    NT-BGHcLV41-1B_S1_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set70/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2989NovaSeq6000100paired-ended2ENCORE228979
    NT-BGHcLV41-1B_Aligned.sortedByCoord.out.bamENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2989GRCh38V40NT-BGHcLV41-1B_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-1B_S1_R2_001.filtered.trimmed.paired.fastq.gzENCORE229025
    NT-BGHcLV41-1B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2989GRCh38V40NT-BGHcLV41-1B/Aligned.sortedByCoord.out.bamENCORE229071
    NT-BGHcLV41-1B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2989GRCh38V40NT-BGHcLV41-1B/Aligned.sortedByCoord.out.bamENCORE229117
    NT-BGHcLV41-1B_Signal.Unique.strand-.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2989GRCh38V40NT-BGHcLV41-1B/Aligned.sortedByCoord.out.bamENCORE229163
    NT-BGHcLV41-1B_Signal.Unique.strand+.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2989GRCh38V40NT-BGHcLV41-1B/Aligned.sortedByCoord.out.bamENCORE229209
    NT-BGHcLV41-1B_quant.sfENCODE_DATA/set70/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2989GRCh38V40NT-BGHcLV41-1B_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-1B_S1_R2_001.filtered.trimmed.paired.fastq.gzENCORE229255
    NT-BGHcLV41-2B_S2_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set70/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2990NovaSeq6000100paired-ended1ENCORE228935
    NT-BGHcLV41-2B_S2_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set70/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2990NovaSeq6000100paired-ended2ENCORE228981
    NT-BGHcLV41-2B_Aligned.sortedByCoord.out.bamENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2990GRCh38V40NT-BGHcLV41-2B_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-2B_S2_R2_001.filtered.trimmed.paired.fastq.gzENCORE229027
    NT-BGHcLV41-2B_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2990GRCh38V40NT-BGHcLV41-2B/Aligned.sortedByCoord.out.bamENCORE229073
    NT-BGHcLV41-2B_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2990GRCh38V40NT-BGHcLV41-2B/Aligned.sortedByCoord.out.bamENCORE229119
    NT-BGHcLV41-2B_Signal.Unique.strand-.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2990GRCh38V40NT-BGHcLV41-2B/Aligned.sortedByCoord.out.bamENCORE229165
    NT-BGHcLV41-2B_Signal.Unique.strand+.bwENCODE_DATA/set70/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2990GRCh38V40NT-BGHcLV41-2B/Aligned.sortedByCoord.out.bamENCORE229211
    NT-BGHcLV41-2B_quant.sfENCODE_DATA/set70/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2990GRCh38V40NT-BGHcLV41-2B_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV41-2B_S2_R2_001.filtered.trimmed.paired.fastq.gzENCORE229257