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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 BGRSDLV04-1 and BGRSDLV04-2


NT-BGRSDLV04-1,NT-BGRSDLV04-2:
  • U2AF1-BGRSDLV04-RS293
  • DDX59-BGRSDLV04-RS293
  • DZIP3-BGRSDLV04-RS293
  • RBM10-BGRSDLV04-RS293
  • SNRNP48-BGRSDLV04-RS293
  • ZNF22-BGRSDLV04-RS293
  • ZNF302-BGRSDLV04-RS293
  • ZNF706-BGRSDLV04-RS293
  • ZNF800-BGRSDLV04-RS293
  • TEX13A-BGRSDLV04-RS293
  • TRIM55-BGRSDLV04-RS293
  • CPSF4L-BGRSDLV04-RS293
  • TEX13A-BGRSDLV04-RS293_2
  • TRIM55-BGRSDLV04-RS293_2
  • NT-BGRSDLV04-RSD293RBP
  • ZNF593-BGRSDLV04-RS293




    • Experiment Information (Status: Submitted)
    BGRSDLV04-1BGRSDLV04-2
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSDLV04-1BGRSDLV04-2
    transduction_Date10/16/2310/16/23
    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
    ID93659366




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSDLV04-1BGRSDLV04-2
    Sample_IDBGRSDLV04-1BGRSDLV04-2
    Sample Name
    Sample NameNT-BGRSDLV04-1NT-BGRSDLV04-2
    RBPnon-targetnon-target
    Cell_LineDOX-RS293DOX-RS293
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1264612647




    Library-Prep Information
    BGRSDLV04-1BGRSDLV04-2
    Sample #12
    Sample NameNT-BGRSDLV04-1NT-BGRSDLV04-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-11-142023-11-14
    Lib_IDLib-231114Lib-231114
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp285283
    Peak_Molarity26.3040.90
    libSampleQC_DNA_WellDNA_Library_set68/set1/A1.pngDNA_Library_set68/set1/B1.png
    RIN10.09.7
    libSample_RNA_WellRNA_Library_set68/set1/A1.pngRNA_Library_set68/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-11-162023-11-16
    Sample_IDBGRSDLV04-1BGRSDLV04-2
    RBPNTNT
    Batch_IDBGRSDLV04BGRSDLV04
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID40744075




    Sequencing Information
    BGRSDLV04-1BGRSDLV04-2
    Sample_IDBGRSDLV04-1BGRSDLV04-2
    Sample NameNT-BGRSDLV04-1NT-BGRSDLV04-2
    Pool IDPool-231116Pool-231116
    LocalServer_folderset68set68
    total_reads44,946,98630,905,689
    total_aligned_reads32,697,54425,299,873
    unique_aligned_reads30,260,33823,648,483
    percent_uniqueAligned0.673250.76518
    correlation_replicates0.9805640.980564
    spikein_reads14,10212,840
    percent_spikeins0.000310.00042
    original_ReadLength151151
    QC_StatusSubmittedSubmitted
    ID28372838




    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-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2837NovaSeq6000100paired-ended1ENCORE227641
    NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2837NovaSeq6000100paired-ended1ENCORE227705
    NT-BGRSDLV04-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2837GRCh38V40NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE227769
    NT-BGRSDLV04-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2837GRCh38V40NT-BGRSDLV04-1/Aligned.sortedByCoord.out.bamENCORE227833
    NT-BGRSDLV04-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2837GRCh38V40NT-BGRSDLV04-1/Aligned.sortedByCoord.out.bamENCORE227897
    NT-BGRSDLV04-1_Signal.Unique.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2837GRCh38V40NT-BGRSDLV04-1/Aligned.sortedByCoord.out.bamENCORE227961
    NT-BGRSDLV04-1_Signal.Unique.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2837GRCh38V40NT-BGRSDLV04-1/Aligned.sortedByCoord.out.bamENCORE228025
    NT-BGRSDLV04-1_quant.sfENCODE_DATA/set68/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2837GRCh38V40NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE228089
    NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2838NovaSeq6000100paired-ended1ENCORE227642
    NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2838NovaSeq6000100paired-ended1ENCORE227706
    NT-BGRSDLV04-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2838GRCh38V40NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE227770
    NT-BGRSDLV04-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2838GRCh38V40NT-BGRSDLV04-2/Aligned.sortedByCoord.out.bamENCORE227834
    NT-BGRSDLV04-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2838GRCh38V40NT-BGRSDLV04-2/Aligned.sortedByCoord.out.bamENCORE227898
    NT-BGRSDLV04-2_Signal.Unique.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2838GRCh38V40NT-BGRSDLV04-2/Aligned.sortedByCoord.out.bamENCORE227962
    NT-BGRSDLV04-2_Signal.Unique.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2838GRCh38V40NT-BGRSDLV04-2/Aligned.sortedByCoord.out.bamENCORE228026
    NT-BGRSDLV04-2_quant.sfENCODE_DATA/set68/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2838GRCh38V40NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE228090