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non-target RNA-Seq in 293T



non-target      shRNA in 293T      Control:

General Information

List KD experiments controlled by BG293LV05-1 and BG293LV05-2


NT-BG293LV05-1,NT-BG293LV05-2:
  • CPSF6-BG293LV05-WT293
  • HNRNPF-BG293LV05-WT293
  • PPP1CA-BG293LV05-WT293
  • DZIP3-BG293LV05-WT293
  • LSM1-BG293LV05-WT293
  • YTHDF1-BG293LV05-WT293
  • LSM10-BG293LV05-WT293
  • PCBP1-BG293LV05-WT293
  • PRPF4-BG293LV05-WT293
  • HNRNPH2-BG293LV05-WT293
  • YWHAG-BG293LV05-WT293
  • AHNAK-BG293LV05-WT293
  • ZMAT3-BG293LV05-WT293
  • STAU2-BG293LV05-WT293
  • MBNL2-BG293LV05-WT293
  • TPD52L2-BG293LV05-WT293
  • RBM42-BG293LV05-WT293
  • RPS19BP1-BG293LV05-WT293
  • WDR6-BG293LV05-WT293
  • SMNDC1-BG293LV05-WT293
  • EIF4H-BG293LV05-WT293




    • Experiment Information (Status: Submitting)
    BG293LV05-1BG293LV05-2
    idx00
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenonnon
    Sample_IDBG293LV05-1BG293LV05-2
    transduction_Date12/18/2312/18/23
    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
    ID99739974




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BG293LV05-1BG293LV05-2
    Sample_IDBG293LV05-1BG293LV05-2
    Sample Name
    Sample NameNT-BG293LV05-1NT-BG293LV05-2
    RBPnon-targetnon-target
    Cell_Line293T293T
    Exp UID
    StatusSubmittingSubmitting
    Status_date2024-05-072024-05-07
    ProjectENCORE2ENCORE2
    Note
    ID1283412835




    Library-Prep Information
    BG293LV05-1BG293LV05-2
    Sample #12
    Sample NameNT-BG293LV05-1NT-BG293LV05-2
    Sample_Name_Alias
    Index Well PositionA07B07
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2024-01-162024-01-16
    Lib_IDLib-240116Lib-240116
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp283286
    Peak_Molarity66.2045.30
    libSampleQC_DNA_WellDNA_Library_set69/set1/A1.pngDNA_Library_set69/set1/B1.png
    RIN9.99.9
    libSample_RNA_WellRNA_Library_set69/set1/A6.pngRNA_Library_set69/set1/B6.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2024-01-192024-01-19
    Sample_IDBG293LV05-1BG293LV05-2
    RBPNTNT
    Batch_IDBG293LV05BG293LV05
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID41824183




    Sequencing Information
    BG293LV05-1BG293LV05-2
    Sample_IDBG293LV05-1BG293LV05-2
    Sample NameNT-BG293LV05-1NT-BG293LV05-2
    Pool IDPool-240119Pool-240119
    LocalServer_folderset69set69
    total_reads16,488,53716,409,952
    total_aligned_reads12,870,07913,607,134
    unique_aligned_reads11,915,60812,642,653
    percent_uniqueAligned0.722660.77043
    correlation_replicates0.9923890.992389
    spikein_reads4,9081,322
    percent_spikeins0.000300.00008
    original_ReadLength101101
    QC_StatusSubmittingSubmitting
    ID29012902




    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-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2901NovaSeq6000100paired-ended1ENCORE228511
    NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2901NovaSeq6000100paired-ended2ENCORE228555
    NT-BG293LV05-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2901GRCh38V40NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE228599
    NT-BG293LV05-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2901GRCh38V40NT-BG293LV05-1/Aligned.sortedByCoord.out.bamENCORE228643
    NT-BG293LV05-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2901GRCh38V40NT-BG293LV05-1/Aligned.sortedByCoord.out.bamENCORE228687
    NT-BG293LV05-1_Signal.Unique.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2901GRCh38V40NT-BG293LV05-1/Aligned.sortedByCoord.out.bamENCORE228731
    NT-BG293LV05-1_Signal.Unique.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2901GRCh38V40NT-BG293LV05-1/Aligned.sortedByCoord.out.bamENCORE228775
    NT-BG293LV05-1_quant.sfENCODE_DATA/set69/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2901GRCh38V40NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE228819
    NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2902NovaSeq6000100paired-ended1ENCORE228512
    NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set69/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2902NovaSeq6000100paired-ended2ENCORE228556
    NT-BG293LV05-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2902GRCh38V40NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228600
    NT-BG293LV05-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2902GRCh38V40NT-BG293LV05-2/Aligned.sortedByCoord.out.bamENCORE228644
    NT-BG293LV05-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2902GRCh38V40NT-BG293LV05-2/Aligned.sortedByCoord.out.bamENCORE228688
    NT-BG293LV05-2_Signal.Unique.strand-.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2902GRCh38V40NT-BG293LV05-2/Aligned.sortedByCoord.out.bamENCORE228732
    NT-BG293LV05-2_Signal.Unique.strand+.bwENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2902GRCh38V40NT-BG293LV05-2/Aligned.sortedByCoord.out.bamENCORE228776
    NT-BG293LV05-2_quant.sfENCODE_DATA/set69/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2902GRCh38V40NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE228820