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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 BGRSDLV03-1 and BGRSDLV03-2


NT-BGRSDLV03-1,NT-BGRSDLV03-2:
  • CNOT4-BGRSDLV03-RS293
  • CPSF4-BGRSDLV03-RS293
  • ERI2-BGRSDLV03-RS293
  • FUS-BGRSDLV03-RS293
  • MBNL1-BGRSDLV03-RS293
  • RNF113A-BGRSDLV03-RS293
  • RNF14-BGRSDLV03-RS293
  • WBP4-BGRSDLV03-RS293
  • ZC3H3-BGRSDLV03-RS293
  • NT-BGRSDLV03-RSD293RBP




    • Experiment Information (Status: Submitted)
    BGRSDLV03-1BGRSDLV03-2
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSDLV03-1BGRSDLV03-2
    transduction_Date9/29/239/29/23
    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
    ID93159316




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSDLV03-1BGRSDLV03-2
    Sample_IDBGRSDLV03-1BGRSDLV03-2
    Sample Name
    Sample NameNT-BGRSDLV03-1NT-BGRSDLV03-2
    RBPnon-targetnon-target
    Cell_LineDOX-RS293DOX-RS293
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1259812599




    Library-Prep Information
    BGRSDLV03-1BGRSDLV03-2
    Sample #12
    Sample NameNT-BGRSDLV03-1NT-BGRSDLV03-2
    Sample_Name_Alias
    Index Well PositionA05B05
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-10-172023-10-17
    Lib_IDLib-231017Lib-231017
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp268271
    Peak_Molarity40.5050.00
    libSampleQC_DNA_WellDNA_Library_set66/set1/A6.pngDNA_Library_set66/set1/B6.png
    RIN9.99.9
    libSample_RNA_WellRNA_Library_set66/set1/A1.pngRNA_Library_set66/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-10-182023-10-18
    Sample_IDBGRSDLV03-1BGRSDLV03-2
    RBPNTNT
    Batch_IDBGRSDLV03BGRSDLV03
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID40344035




    Sequencing Information
    BGRSDLV03-1BGRSDLV03-2
    Sample_IDBGRSDLV03-1BGRSDLV03-2
    Sample NameNT-BGRSDLV03-1NT-BGRSDLV03-2
    Pool IDPool-231018Pool-231018
    LocalServer_folderset66set66
    total_reads20,704,44425,387,390
    total_aligned_reads16,212,67821,211,997
    unique_aligned_reads14,938,56319,491,221
    percent_uniqueAligned0.721510.76775
    correlation_replicates0.9974350.997435
    spikein_reads6,9361,698
    percent_spikeins0.000340.00007
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID27532754




    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-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2753NovaSeq6000100paired-ended1ENCORE28926
    NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2753NovaSeq6000100paired-ended2ENCORE28966
    NT-BGRSDLV03-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2753GRCh38V40NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE29006
    NT-BGRSDLV03-1_Signal.Unique.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2753GRCh38V40NT-BGRSDLV03-1/Aligned.sortedByCoord.out.bamENCORE29046
    NT-BGRSDLV03-1_Signal.Unique.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2753GRCh38V40NT-BGRSDLV03-1/Aligned.sortedByCoord.out.bamENCORE29086
    NT-BGRSDLV03-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2753GRCh38V40NT-BGRSDLV03-1/Aligned.sortedByCoord.out.bamENCORE29126
    NT-BGRSDLV03-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2753GRCh38V40NT-BGRSDLV03-1/Aligned.sortedByCoord.out.bamENCORE29166
    NT-BGRSDLV03-1_quant.sfENCODE_DATA/set66/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2753GRCh38V40NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE29206
    NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2754NovaSeq6000100paired-ended1ENCORE28927
    NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set66/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2754NovaSeq6000100paired-ended2ENCORE28967
    NT-BGRSDLV03-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2754GRCh38V40NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE29007
    NT-BGRSDLV03-2_Signal.Unique.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2754GRCh38V40NT-BGRSDLV03-2/Aligned.sortedByCoord.out.bamENCORE29047
    NT-BGRSDLV03-2_Signal.Unique.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2754GRCh38V40NT-BGRSDLV03-2/Aligned.sortedByCoord.out.bamENCORE29087
    NT-BGRSDLV03-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2754GRCh38V40NT-BGRSDLV03-2/Aligned.sortedByCoord.out.bamENCORE29127
    NT-BGRSDLV03-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2754GRCh38V40NT-BGRSDLV03-2/Aligned.sortedByCoord.out.bamENCORE29167
    NT-BGRSDLV03-2_quant.sfENCODE_DATA/set66/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2754GRCh38V40NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gzENCORE29207