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non-target RNA-Seq in 293T



non-target      shRNA in 293T      Control:

General Information

List KD experiments controlled by BG293LV02-1 and BG293LV02-2


NT-BG293LV02-1,NT-BG293LV02-2:
  • CNOT2-BG293LV02-WT293
  • CNOT4-BG293LV02-WT293
  • CPSF6-BG293LV02-WT293
  • CSTF2T-BG293LV02-WT293
  • EIF4B-BG293LV02-WT293
  • FUBP1-BG293LV02-WT293
  • GRB2-BG293LV02-WT293
  • GTSF1-BG293LV02-WT293
  • LGALS1-BG293LV02-WT293
  • LGALS3-BG293LV02-WT293
  • LUC7L-BG293LV02-WT293
  • MBNL1-BG293LV02-WT293
  • NGRN-BG293LV02-WT293
  • PARN-BG293LV02-WT293
  • PRPF40A-BG293LV02-WT293
  • RBM10-BG293LV02-WT293
  • RBM14-BG293LV02-WT293
  • RBM22-BG293LV02-WT293
  • SNRPA-BG293LV02-WT293
  • TIAL1-BG293LV02-WT293
  • ZRANB2-BG293LV02-WT293




    • Experiment Information (Status: Revoked)
    BG293LV02-1BG293LV02-2
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    NameNON-TARGETNON-TARGET
    Sample_IDBG293LV02-1BG293LV02-2
    transduction_Date3/20/233/20/23
    daysD4D4
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc00
    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
    ID97969797




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BG293LV02-1BG293LV02-2
    Sample_IDBG293LV02-1BG293LV02-2
    Sample Name
    Sample NameNT-BG293LV02-1NT-BG293LV02-2
    RBPnon-targetnon-target
    Cell_Line293T293T
    Exp UID
    StatusRevokedRevoked
    Status_date2023-09-202023-09-20
    ProjectENCORE2ENCORE2
    Note
    ID1155811559




    Library-Prep Information
    BG293LV02-1BG293LV02-2
    Sample #12
    Sample NameNT-BG293LV02-1NT-BG293LV02-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-04-122023-04-12
    Lib_IDLib-230412Lib-230412
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp288283
    Peak_Molarity30.0068.30
    libSampleQC_DNA_WellDNA_Library_set60-62/set2/A1.pngDNA_Library_set60-62/set2/B1.png
    RIN9.69.7
    libSample_RNA_WellRNA_Library_set60-62/set1/A1.pngRNA_Library_set60-62/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-04-172023-04-17
    Sample_IDBG293LV02-1BG293LV02-2
    RBPNTNT
    Batch_IDBG293LV02BG293LV02
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID35883589




    Sequencing Information
    BG293LV02-1BG293LV02-2
    Sample_IDBG293LV02-1BG293LV02-2
    Sample NameNT-BG293LV02-1NT-BG293LV02-2
    Pool IDPool-230417Pool-230417
    LocalServer_folderset60set60
    total_reads45,478,05056,377,208
    total_aligned_reads35,728,19447,206,934
    unique_aligned_reads33,231,81144,180,123
    percent_uniqueAligned0.730720.78365
    correlation_replicates0.9938680.993868
    spikein_reads348,918194,584
    percent_spikeins0.007670.00345
    original_ReadLength101101
    QC_StatusSubmittingSubmitting
    ID24592460




    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-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set60/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2459NovaSeq6000100paired-ended1ENCORE27988
    NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set60/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2459NovaSeq6000100paired-ended2ENCORE28032
    NT-BG293LV02-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2459GRCh38V40NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE210781
    NT-BG293LV02-1_Signal.Unique.strand+.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2459GRCh38V40NT-BG293LV02-1/Aligned.sortedByCoord.out.bamENCORE210825
    NT-BG293LV02-1_Signal.Unique.strand-.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2459GRCh38V40NT-BG293LV02-1/Aligned.sortedByCoord.out.bamENCORE210869
    NT-BG293LV02-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2459GRCh38V40NT-BG293LV02-1/Aligned.sortedByCoord.out.bamENCORE210913
    NT-BG293LV02-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2459GRCh38V40NT-BG293LV02-1/Aligned.sortedByCoord.out.bamENCORE210957
    NT-BG293LV02-1_quant.sfENCODE_DATA/set60/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2459GRCh38V40NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE211001
    NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set60/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2460NovaSeq6000100paired-ended1ENCORE27989
    NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set60/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2460NovaSeq6000100paired-ended2ENCORE28033
    NT-BG293LV02-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2460GRCh38V40NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE210782
    NT-BG293LV02-2_Signal.Unique.strand+.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2460GRCh38V40NT-BG293LV02-2/Aligned.sortedByCoord.out.bamENCORE210826
    NT-BG293LV02-2_Signal.Unique.strand-.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2460GRCh38V40NT-BG293LV02-2/Aligned.sortedByCoord.out.bamENCORE210870
    NT-BG293LV02-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2460GRCh38V40NT-BG293LV02-2/Aligned.sortedByCoord.out.bamENCORE210914
    NT-BG293LV02-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2460GRCh38V40NT-BG293LV02-2/Aligned.sortedByCoord.out.bamENCORE210958
    NT-BG293LV02-2_quant.sfENCODE_DATA/set60/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2460GRCh38V40NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE211002