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non-target RNA-Seq in Ribo-STAMP-293T



non-target      shRNA in Ribo-STAMP-293T      Control:

General Information

List KD experiments controlled by BGRSDLV02-3dox and BGRSDLV02-4dox


NT-BGRSDLV02-3dox,NT-BGRSDLV02-4dox:
  • APEX2-BGRSDLV02-RSD293
  • BRCA1-BGRSDLV02-RSD293
  • CISD1-BGRSDLV02-RSD293
  • CNBP-BGRSDLV02-RSD293
  • CTCF-BGRSDLV02-RSD293
  • G2E3-BGRSDLV02-RSD293
  • GTF3C4-BGRSDLV02-RSD293
  • IGHMBP2-BGRSDLV02-RSD293
  • LIN28B-BGRSDLV02-RSD293
  • MAZ-BGRSDLV02-RSD293
  • PHF7-BGRSDLV02-RSD293
  • RBM5-BGRSDLV02-RSD293
  • ZMAT3-BGRSDLV02-RSD293
  • ZMAT5-BGRSDLV02-RSD293
  • ZNF277-BGRSDLV02-RSD293
  • ZNF317-BGRSDLV02-RSD293
  • CISD2-BGRSDLV02-RSD293
  • ZNF473-BGRSDLV02-RSD293




    • Experiment Information (Status: Submitted)
    BGRSDLV02-3doxBGRSDLV02-4dox
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSDLV02-3doxBGRSDLV02-4dox
    transduction_Date9/15/239/15/23
    days4 days4 days
    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
    ID92149215




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSDLV02-3doxBGRSDLV02-4dox
    Sample_IDBGRSDLV02-3doxBGRSDLV02-4dox
    Sample Name
    Sample NameNT-BGRSDLV02-3doxNT-BGRSDLV02-4dox
    RBPnon-targetnon-target
    Cell_LineDOX-RS293DOX-RS293
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1232212323




    Library-Prep Information
    BGRSDLV02-3doxBGRSDLV02-4dox
    Sample #34
    Sample NameNT-BGRSDLV02-3doxNT-BGRSDLV02-4dox
    Sample_Name_Alias
    Index Well PositionC01D01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-09-262023-09-26
    Lib_IDLib-230926Lib-230926
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp290292
    Peak_Molarity33.9050.10
    libSampleQC_DNA_WellDNA_Library_set65/set1/C1.pngDNA_Library_set65/set1/D1.png
    RIN10.010.0
    libSample_RNA_WellRNA_Library_set65/set1/C1.pngRNA_Library_set65/set1/D1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-09-272023-09-27
    Sample_IDBGRSDLV02-3doxBGRSDLV02-4dox
    RBPNTNT
    Batch_IDBGRSDLV02BGRSDLV02
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID39243925




    Sequencing Information
    BGRSDLV02-3doxBGRSDLV02-4dox
    Sample_IDBGRSDLV02-3doxBGRSDLV02-4dox
    Sample NameNT-BGRSDLV02-3doxNT-BGRSDLV02-4dox
    Pool IDPool-231003Pool-231003
    LocalServer_folderset65set65
    total_reads27,148,38530,677,675
    total_aligned_reads21,952,76125,990,678
    unique_aligned_reads20,187,64624,107,366
    percent_uniqueAligned0.743600.78583
    correlation_replicates0.9925440.992544
    spikein_reads12,2128,138
    percent_spikeins0.000450.00027
    original_ReadLength100100
    QC_StatusSubmittedSubmitted
    ID26712672




    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-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2671NovaSeq6000100paired-ended1ENCORE28784
    NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2671NovaSeq6000100paired-ended2ENCORE28860
    NT-BGRSDLV02-3dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2671GRCh38V40NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29349
    NT-BGRSDLV02-3dox_Signal.Unique.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2671GRCh38V40NT-BGRSDLV02-3dox/Aligned.sortedByCoord.out.bamENCORE29425
    NT-BGRSDLV02-3dox_Signal.Unique.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2671GRCh38V40NT-BGRSDLV02-3dox/Aligned.sortedByCoord.out.bamENCORE29501
    NT-BGRSDLV02-3dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2671GRCh38V40NT-BGRSDLV02-3dox/Aligned.sortedByCoord.out.bamENCORE29577
    NT-BGRSDLV02-3dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2671GRCh38V40NT-BGRSDLV02-3dox/Aligned.sortedByCoord.out.bamENCORE29653
    NT-BGRSDLV02-3dox_quant.sfENCODE_DATA/set65/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2671GRCh38V40NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29729
    NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2672NovaSeq6000100paired-ended1ENCORE28785
    NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2672NovaSeq6000100paired-ended2ENCORE28861
    NT-BGRSDLV02-4dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2672GRCh38V40NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29350
    NT-BGRSDLV02-4dox_Signal.Unique.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2672GRCh38V40NT-BGRSDLV02-4dox/Aligned.sortedByCoord.out.bamENCORE29426
    NT-BGRSDLV02-4dox_Signal.Unique.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2672GRCh38V40NT-BGRSDLV02-4dox/Aligned.sortedByCoord.out.bamENCORE29502
    NT-BGRSDLV02-4dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2672GRCh38V40NT-BGRSDLV02-4dox/Aligned.sortedByCoord.out.bamENCORE29578
    NT-BGRSDLV02-4dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2672GRCh38V40NT-BGRSDLV02-4dox/Aligned.sortedByCoord.out.bamENCORE29654
    NT-BGRSDLV02-4dox_quant.sfENCODE_DATA/set65/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2672GRCh38V40NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29730