non-target      shRNA in Ribo-STAMP-293T      Control: NT-BGRSDLV02-1,NT-BGRSDLV02-2

General Information

List KD experiments controlled by BGRSDLV02-1 and BGRSDLV02-2


NT-BGRSDLV02-1,NT-BGRSDLV02-2:
  • APEX2-BGRSDLV02-RS293
  • BRCA1-BGRSDLV02-RS293
  • CISD1-BGRSDLV02-RS293
  • CNBP-BGRSDLV02-RS293
  • CTCF-BGRSDLV02-RS293
  • G2E3-BGRSDLV02-RS293
  • GTF3C4-BGRSDLV02-RS293
  • IGHMBP2-BGRSDLV02-RS293
  • LIN28B-BGRSDLV02-RS293
  • MAZ-BGRSDLV02-RS293
  • PHF7-BGRSDLV02-RS293
  • RBM5-BGRSDLV02-RS293
  • ZMAT3-BGRSDLV02-RS293
  • ZMAT5-BGRSDLV02-RS293
  • ZNF277-BGRSDLV02-RS293
  • ZNF317-BGRSDLV02-RS293
  • CISD2-BGRSDLV02-RS293
  • ZNF473-BGRSDLV02-RS293
  • NT-BGRSDLV02-RSD293RBP




    • Experiment Information (Status: Released)
    BGRSDLV02-1BGRSDLV02-2
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSDLV02-1BGRSDLV02-2
    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
    ID1126011261




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSDLV02-1BGRSDLV02-2
    Sample_IDBGRSDLV02-1BGRSDLV02-2
    Sample Name
    Sample NameNT-BGRSDLV02-1NT-BGRSDLV02-2
    RBPnon-targetnon-target
    Cell_LineDOX-RS293DOX-RS293
    Exp UID
    StatusReleasedReleased
    Status_date2025-02-132025-02-13
    ProjectENCORE2ENCORE2
    Note
    ID1232012321




    Library-Prep Information
    BGRSDLV02-1BGRSDLV02-2
    Sample #12
    Sample NameNT-BGRSDLV02-1NT-BGRSDLV02-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-09-262023-09-26
    Lib_IDLib-230926Lib-230926
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp287297
    Peak_Molarity30.2047.30
    libSampleQC_DNA_WellDNA_Library_set65/set1/A1.pngDNA_Library_set65/set1/B1.png
    RIN9.910.0
    libSample_RNA_WellRNA_Library_set65/set1/A1.pngRNA_Library_set65/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-09-272023-09-27
    Sample_IDBGRSDLV02-1BGRSDLV02-2
    RBPNTNT
    Batch_IDBGRSDLV02BGRSDLV02
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID39223923




    Sequencing Information
    BGRSDLV02-1BGRSDLV02-2
    Sample_IDBGRSDLV02-1BGRSDLV02-2
    Sample NameNT-BGRSDLV02-1NT-BGRSDLV02-2
    Pool IDPool-231003Pool-231003
    LocalServer_folderset65set65
    total_reads47,600,44028,707,806
    total_aligned_reads36,814,23324,116,724
    unique_aligned_reads34,043,84222,420,140
    percent_uniqueAligned0.715200.78098
    correlation_replicates0.9956790.995679
    spikein_reads32,3046,490
    percent_spikeins0.000680.00023
    original_ReadLength100100
    QC_StatusSubmittedSubmitted
    ID26692670




    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-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2669NovaSeq6000100paired-ended1ENCORE28782
    NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2669NovaSeq6000100paired-ended2ENCORE28858
    NT-BGRSDLV02-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2669GRCh38V40NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29347
    NT-BGRSDLV02-1_Signal.Unique.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2669GRCh38V40NT-BGRSDLV02-1/Aligned.sortedByCoord.out.bamENCORE29423
    NT-BGRSDLV02-1_Signal.Unique.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2669GRCh38V40NT-BGRSDLV02-1/Aligned.sortedByCoord.out.bamENCORE29499
    NT-BGRSDLV02-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2669GRCh38V40NT-BGRSDLV02-1/Aligned.sortedByCoord.out.bamENCORE29575
    NT-BGRSDLV02-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2669GRCh38V40NT-BGRSDLV02-1/Aligned.sortedByCoord.out.bamENCORE29651
    NT-BGRSDLV02-1_quant.sfENCODE_DATA/set65/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2669GRCh38V40NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29727
    NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2670NovaSeq6000100paired-ended1ENCORE28783
    NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set65/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2670NovaSeq6000100paired-ended2ENCORE28859
    NT-BGRSDLV02-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2670GRCh38V40NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29348
    NT-BGRSDLV02-2_Signal.Unique.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2670GRCh38V40NT-BGRSDLV02-2/Aligned.sortedByCoord.out.bamENCORE29424
    NT-BGRSDLV02-2_Signal.Unique.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2670GRCh38V40NT-BGRSDLV02-2/Aligned.sortedByCoord.out.bamENCORE29500
    NT-BGRSDLV02-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2670GRCh38V40NT-BGRSDLV02-2/Aligned.sortedByCoord.out.bamENCORE29576
    NT-BGRSDLV02-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2670GRCh38V40NT-BGRSDLV02-2/Aligned.sortedByCoord.out.bamENCORE29652
    NT-BGRSDLV02-2_quant.sfENCODE_DATA/set65/salmon_ENCORE2_file_linkstranscript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2670GRCh38V40NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE29728