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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 BGRSLV02-1 and BGRSLV02-2


NT-BGRSLV02-1,NT-BGRSLV02-2:
  • TAF15-BGRSLV02-RS293
  • FUS-BGRSLV02-RS293
  • U2AF1-BGRSLV02-RS293
  • ZC3H8-BGRSLV02-RS293
  • ZRANB2-BGRSLV02-RS293
  • DDX59-BGRSLV02-RS293
  • NR5A2-BGRSLV02-RS293
  • BMI1-BGRSLV02-RS293
  • MNAT1-BGRSLV02-RS293
  • ZIC3-BGRSLV02-RS293
  • PHF11-BGRSLV02-RS293
  • ZNF22-BGRSLV02-RS293
  • ZFP37-BGRSLV02-RS293
  • TTF2-BGRSLV02-RS293
  • ZNF800-BGRSLV02-RS293
  • ZNHIT3-BGRSLV02-RS293
  • TRIP4-BGRSLV02-RS293
  • RNF20-BGRSLV02-RS293
  • ZCCHC7-BGRSLV02-RS293
  • DZIP3-BGRSLV02-RS293
  • ZC3H18-BGRSLV02-RS293
  • CNOT4-BGRSLV02-RS293




    • Experiment Information (Status: Submitted)
    BGRSLV02-1BGRSLV02-2
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSLV02-1BGRSLV02-2
    transduction_Date12/5/2212/5/22
    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
    ID82388239




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSLV02-1BGRSLV02-2
    Sample_IDBGRSLV02-1BGRSLV02-2
    Sample Name
    Sample NameNT-BGRSLV02-1NT-BGRSLV02-2
    RBPnon-targetnon-target
    Cell_LineRibo-STAMP-293TRibo-STAMP-293T
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1129811299




    Library-Prep Information
    BGRSLV02-1BGRSLV02-2
    Sample #12
    Sample NameNT-BGRSLV02-1NT-BGRSLV02-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-02-072023-02-07
    Lib_IDLib-230207Lib-230207
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp278285
    Peak_Molarity39.1074.20
    libSampleQC_DNA_WellDNA_Library_set57/set1/A7.pngDNA_Library_set57/set1/B7.png
    RIN9.99.9
    libSample_RNA_WellRNA_Library_set57/set1/A1.pngRNA_Library_set57/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-02-072023-02-07
    Sample_IDBGRSLV02-1BGRSLV02-2
    RBPNTNT
    Batch_IDBGRSLV02BGRSLV02
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID34623463




    Sequencing Information
    BGRSLV02-1BGRSLV02-2
    Sample_IDBGRSLV02-1BGRSLV02-2
    Sample NameNT-BGRSLV02-1NT-BGRSLV02-2
    Pool IDPool-230207Pool-230207
    LocalServer_folderset57set57
    total_reads54,301,54829,900,216
    total_aligned_reads46,272,90926,342,371
    unique_aligned_reads41,689,61324,388,661
    percent_uniqueAligned0.767740.81567
    correlation_replicates0.9880420.988042
    spikein_reads34,00812,848
    percent_spikeins0.000630.00043
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID23332334




    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-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set57/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2333NovaSeq6000100paired-ended1ENCORE28224
    NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set57/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2333NovaSeq6000100paired-ended2ENCORE28270
    NT-BGRSLV02-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2333GRCh38V40NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE211513
    NT-BGRSLV02-1_Signal.Unique.strand+.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2333GRCh38V40NT-BGRSLV02-1/Aligned.sortedByCoord.out.bamENCORE211559
    NT-BGRSLV02-1_Signal.Unique.strand-.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2333GRCh38V40NT-BGRSLV02-1/Aligned.sortedByCoord.out.bamENCORE211605
    NT-BGRSLV02-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2333GRCh38V40NT-BGRSLV02-1/Aligned.sortedByCoord.out.bamENCORE211651
    NT-BGRSLV02-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2333GRCh38V40NT-BGRSLV02-1/Aligned.sortedByCoord.out.bamENCORE211697
    NT-BGRSLV02-1_quant.sfENCODE_DATA/set57/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2333GRCh38V40NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE211743
    NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set57/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2334NovaSeq6000100paired-ended1ENCORE28225
    NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set57/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2334NovaSeq6000100paired-ended2ENCORE28271
    NT-BGRSLV02-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2334GRCh38V40NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE211514
    NT-BGRSLV02-2_Signal.Unique.strand+.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2334GRCh38V40NT-BGRSLV02-2/Aligned.sortedByCoord.out.bamENCORE211560
    NT-BGRSLV02-2_Signal.Unique.strand-.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2334GRCh38V40NT-BGRSLV02-2/Aligned.sortedByCoord.out.bamENCORE211606
    NT-BGRSLV02-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2334GRCh38V40NT-BGRSLV02-2/Aligned.sortedByCoord.out.bamENCORE211652
    NT-BGRSLV02-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2334GRCh38V40NT-BGRSLV02-2/Aligned.sortedByCoord.out.bamENCORE211698
    NT-BGRSLV02-2_quant.sfENCODE_DATA/set57/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2334GRCh38V40NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE211744