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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 BGRSLV04-1 and BGRSLV04-2


NT-BGRSLV04-1,NT-BGRSLV04-2:
  • BL-BGRSLV04-RS293
  • IRF2BP1-BGRSLV04-RS293
  • KDM5A-BGRSLV04-RS293
  • LYAR-BGRSLV04-RS293
  • NDUFS6-BGRSLV04-RS293
  • NUFIP1-BGRSLV04-RS293
  • PAN3-BGRSLV04-RS293
  • PCGF1-BGRSLV04-RS293
  • PHF7-BGRSLV04-RS293
  • PML-BGRSLV04-RS293
  • PRR3-BGRSLV04-RS293
  • RBM4B-BGRSLV04-RS293
  • RC3H2-BGRSLV04-RS293
  • RFFL-BGRSLV04-RS293
  • RNF41-BGRSLV04-RS293
  • UBR7-BGRSLV04-RS293
  • USP44-BGRSLV04-RS293
  • ZC3HC1-BGRSLV04-RS293




    • Experiment Information (Status: Submitted)
    BGRSLV04-1BGRSLV04-2
    idx00
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSLV04-1BGRSLV04-2
    transduction_Date2/14/232/14/23
    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
    ID83818382




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSLV04-1BGRSLV04-2
    Sample_IDBGRSLV04-1BGRSLV04-2
    Sample Name
    Sample NameNT-BGRSLV04-1NT-BGRSLV04-2
    RBPnon-targetnon-target
    Cell_LineRibo-STAMP-293TRibo-STAMP-293T
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1143811439




    Library-Prep Information
    BGRSLV04-1BGRSLV04-2
    Sample #12
    Sample NameNT-BGRSLV04-1NT-BGRSLV04-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-03-022023-03-02
    Lib_IDLib-230302Lib-230302
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp279279
    Peak_Molarity16.0039.10
    libSampleQC_DNA_WellDNA_Library_set59/set1/A7.pngDNA_Library_set59/set1/B7.png
    RIN9.89.8
    libSample_RNA_WellRNA_Library_set59/set1/A2.pngRNA_Library_set59/set1/B2.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-03-062023-03-06
    Sample_IDBGRSLV04-1BGRSLV04-2
    RBPNTNT
    Batch_IDBGRSLV04BGRSLV04
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID35503551




    Sequencing Information
    BGRSLV04-1BGRSLV04-2
    Sample_IDBGRSLV04-1BGRSLV04-2
    Sample NameNT-BGRSLV04-1NT-BGRSLV04-2
    Pool IDPool-230306Pool-230306
    LocalServer_folderset59set59
    total_reads68,268,23157,200,596
    total_aligned_reads51,000,31844,122,216
    unique_aligned_reads47,200,08840,714,681
    percent_uniqueAligned0.691390.71179
    correlation_replicates0.9948420.994842
    spikein_reads342,924279,778
    percent_spikeins0.005020.00489
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID24212422




    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-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set59/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2421NovaSeq6000100paired-ended1ENCORE28060
    NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set59/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2421NovaSeq6000100paired-ended2ENCORE28098
    NT-BGRSLV04-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2421GRCh38V40NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE211029
    NT-BGRSLV04-1_Signal.Unique.strand+.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2421GRCh38V40NT-BGRSLV04-1/Aligned.sortedByCoord.out.bamENCORE211067
    NT-BGRSLV04-1_Signal.Unique.strand-.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2421GRCh38V40NT-BGRSLV04-1/Aligned.sortedByCoord.out.bamENCORE211105
    NT-BGRSLV04-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2421GRCh38V40NT-BGRSLV04-1/Aligned.sortedByCoord.out.bamENCORE211143
    NT-BGRSLV04-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2421GRCh38V40NT-BGRSLV04-1/Aligned.sortedByCoord.out.bamENCORE211181
    NT-BGRSLV04-1_quant.sfENCODE_DATA/set59/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2421GRCh38V40NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE211219
    NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set59/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2422NovaSeq6000100paired-ended1ENCORE28061
    NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set59/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2422NovaSeq6000100paired-ended2ENCORE28099
    NT-BGRSLV04-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2422GRCh38V40NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE211030
    NT-BGRSLV04-2_Signal.Unique.strand+.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2422GRCh38V40NT-BGRSLV04-2/Aligned.sortedByCoord.out.bamENCORE211068
    NT-BGRSLV04-2_Signal.Unique.strand-.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2422GRCh38V40NT-BGRSLV04-2/Aligned.sortedByCoord.out.bamENCORE211106
    NT-BGRSLV04-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2422GRCh38V40NT-BGRSLV04-2/Aligned.sortedByCoord.out.bamENCORE211144
    NT-BGRSLV04-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2422GRCh38V40NT-BGRSLV04-2/Aligned.sortedByCoord.out.bamENCORE211182
    NT-BGRSLV04-2_quant.sfENCODE_DATA/set59/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2422GRCh38V40NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE211220