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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 BGRSDLV04-3dox and BGRSDLV04-4dox


NT-BGRSDLV04-3dox,NT-BGRSDLV04-4dox:
  • U2AF1-BGRSDLV04-RSD293
  • DDX59-BGRSDLV04-RSD293
  • DZIP3-BGRSDLV04-RSD293
  • RBM10-BGRSDLV04-RSD293
  • SNRNP48-BGRSDLV04-RSD293
  • ZNF22-BGRSDLV04-RSD293
  • ZNF302-BGRSDLV04-RSD293
  • ZNF593-BGRSDLV04-RSD293
  • ZNF706-BGRSDLV04-RSD293
  • ZNF800-BGRSDLV04-RSD293
  • TEX13A-BGRSDLV04-RSD293
  • TRIM55-BGRSDLV04-RSD293
  • CPSF4L-BGRSDLV04-RSD293
  • TEX13A-BGRSDLV04-RSD293_2
  • TRIM55-BGRSDLV04-RSD293_2




    • Experiment Information (Status: Submitted)
    BGRSDLV04-3doxBGRSDLV04-4dox
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSDLV04-3doxBGRSDLV04-4dox
    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
    ID93679368




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSDLV04-3doxBGRSDLV04-4dox
    Sample_IDBGRSDLV04-3doxBGRSDLV04-4dox
    Sample Name
    Sample NameNT-BGRSDLV04-3doxNT-BGRSDLV04-4dox
    RBPnon-targetnon-target
    Cell_LineDOX-RS293DOX-RS293
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1264812649




    Library-Prep Information
    BGRSDLV04-3doxBGRSDLV04-4dox
    Sample #34
    Sample NameNT-BGRSDLV04-3doxNT-BGRSDLV04-4dox
    Sample_Name_Alias
    Index Well PositionC01D01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-11-142023-11-14
    Lib_IDLib-231114Lib-231114
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp289289
    Peak_Molarity30.9058.60
    libSampleQC_DNA_WellDNA_Library_set68/set1/C1.pngDNA_Library_set68/set1/D1.png
    RIN10.010.0
    libSample_RNA_WellRNA_Library_set68/set1/C1.pngRNA_Library_set68/set1/D1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-11-162023-11-16
    Sample_IDBGRSDLV04-3doxBGRSDLV04-4dox
    RBPNTNT
    Batch_IDBGRSDLV04BGRSDLV04
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID40764077




    Sequencing Information
    BGRSDLV04-3doxBGRSDLV04-4dox
    Sample_IDBGRSDLV04-3doxBGRSDLV04-4dox
    Sample NameNT-BGRSDLV04-3doxNT-BGRSDLV04-4dox
    Pool IDPool-231116Pool-231116
    LocalServer_folderset68set68
    total_reads35,444,59338,239,429
    total_aligned_reads28,642,31832,014,671
    unique_aligned_reads26,623,71029,942,555
    percent_uniqueAligned0.751140.78303
    correlation_replicates0.9985030.998503
    spikein_reads10,5486,656
    percent_spikeins0.000300.00017
    original_ReadLength151151
    QC_StatusSubmittedSubmitted
    ID28392840




    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-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2839NovaSeq6000100paired-ended1ENCORE227643
    NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2839NovaSeq6000100paired-ended1ENCORE227707
    NT-BGRSDLV04-3dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2839GRCh38V40NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE227771
    NT-BGRSDLV04-3dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2839GRCh38V40NT-BGRSDLV04-3dox/Aligned.sortedByCoord.out.bamENCORE227835
    NT-BGRSDLV04-3dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2839GRCh38V40NT-BGRSDLV04-3dox/Aligned.sortedByCoord.out.bamENCORE227899
    NT-BGRSDLV04-3dox_Signal.Unique.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2839GRCh38V40NT-BGRSDLV04-3dox/Aligned.sortedByCoord.out.bamENCORE227963
    NT-BGRSDLV04-3dox_Signal.Unique.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2839GRCh38V40NT-BGRSDLV04-3dox/Aligned.sortedByCoord.out.bamENCORE228027
    NT-BGRSDLV04-3dox_quant.sfENCODE_DATA/set68/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2839GRCh38V40NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE228091
    NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2840NovaSeq6000100paired-ended1ENCORE227644
    NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set68/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2840NovaSeq6000100paired-ended1ENCORE227708
    NT-BGRSDLV04-4dox_Aligned.sortedByCoord.out.bamENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2840GRCh38V40NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE227772
    NT-BGRSDLV04-4dox_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2840GRCh38V40NT-BGRSDLV04-4dox/Aligned.sortedByCoord.out.bamENCORE227836
    NT-BGRSDLV04-4dox_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2840GRCh38V40NT-BGRSDLV04-4dox/Aligned.sortedByCoord.out.bamENCORE227900
    NT-BGRSDLV04-4dox_Signal.Unique.strand-.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2840GRCh38V40NT-BGRSDLV04-4dox/Aligned.sortedByCoord.out.bamENCORE227964
    NT-BGRSDLV04-4dox_Signal.Unique.strand+.bwENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2840GRCh38V40NT-BGRSDLV04-4dox/Aligned.sortedByCoord.out.bamENCORE228028
    NT-BGRSDLV04-4dox_quant.sfENCODE_DATA/set68/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2840GRCh38V40NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gzENCORE228092