Notice: Undefined offset: 1 in /website/encore_alpha/gene/index.php on line 599
non-target RNA-Seq in Ribo-STAMP-293T



non-target      shRNA in Ribo-STAMP-293T      Control:

General Information

List KD experiments controlled by BGRSLV08-1 and BGRSLV08-2


NT-BGRSLV08-1,NT-BGRSLV08-2:
  • WBP4-BGRSLV08-RS293
  • YAF2-BGRSLV08-RS293
  • ZC3H7A-BGRSLV08-RS293
  • ZCCHC24-BGRSLV08-RS293
  • ZNF184-BGRSLV08-RS293
  • ZNF354A-BGRSLV08-RS293
  • ZNF385C-BGRSLV08-RS293
  • ZNF593-BGRSLV08-RS293
  • ZNF770-BGRSLV08-RS293
  • ZXDC-BGRSLV08-RS293




    • Experiment Information (Status: Submitted)
    BGRSLV08-1BGRSLV08-2
    idx00
    TRCN#_or_BGC#SHC002SHC002
    shRNA_or_gRNA_sequenceCAACAAGATGAAGAGCACCAACAACAAGATGAAGAGCACCAA
    PAM
    Namenon-targetnon-target
    Sample_IDBGRSLV08-1BGRSLV08-2
    transduction_Date4/22/234/22/23
    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
    ID86508651




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGRSLV08-1BGRSLV08-2
    Sample_IDBGRSLV08-1BGRSLV08-2
    Sample Name
    Sample NameNT-BGRSLV08-1NT-BGRSLV08-2
    RBPnon-targetnon-target
    Cell_LineRibo-STAMP-293TRibo-STAMP-293T
    Exp UID
    StatusSubmittedSubmitted
    Status_date2024-12-032024-12-03
    ProjectENCORE2ENCORE2
    Note
    ID1177411775




    Library-Prep Information
    BGRSLV08-1BGRSLV08-2
    Sample #3940
    Sample NameNT-BGRSLV08-1NT-BGRSLV08-2
    Sample_Name_Alias
    Index Well PositionG05H05
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-05-022023-05-02
    Lib_IDLib-230502Lib-230502
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp286286
    Peak_Molarity87.6074.50
    libSampleQC_DNA_WellDNA_Library_set60-62/set4/G5.pngDNA_Library_set60-62/set4/H5.png
    RIN10.09.9
    libSample_RNA_WellRNA_Library_set60-62/set2/G5.pngRNA_Library_set60-62/set2/H5.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-05-042023-05-04
    Sample_IDBGRSLV08-1BGRSLV08-2
    RBPNTNT
    Batch_IDBGRSLV08BGRSLV08
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID37223723




    Sequencing Information
    BGRSLV08-1BGRSLV08-2
    Sample_IDBGRSLV08-1BGRSLV08-2
    Sample NameNT-BGRSLV08-1NT-BGRSLV08-2
    Pool IDPool-230504Pool-230504
    LocalServer_folderset62_Rset62_R
    total_reads22,342,57223,957,583
    total_aligned_reads18,113,10219,429,183
    unique_aligned_reads16,997,72017,922,632
    percent_uniqueAligned0.760780.74810
    correlation_replicates0.9942620.994262
    spikein_reads15,13826,914
    percent_spikeins0.000680.00112
    original_ReadLength101101
    QC_StatusSubmittedSubmitted
    ID25932594




    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-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set62_R/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2593NovaSeq6000100paired-ended1ENCORE27882
    NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set62_R/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2593NovaSeq6000100paired-ended2ENCORE27926
    NT-BGRSLV08-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2593GRCh38V40NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE210187
    NT-BGRSLV08-1_Signal.Unique.strand+.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2593GRCh38V40NT-BGRSLV08-1/Aligned.sortedByCoord.out.bamENCORE210231
    NT-BGRSLV08-1_Signal.Unique.strand-.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2593GRCh38V40NT-BGRSLV08-1/Aligned.sortedByCoord.out.bamENCORE210275
    NT-BGRSLV08-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2593GRCh38V40NT-BGRSLV08-1/Aligned.sortedByCoord.out.bamENCORE210319
    NT-BGRSLV08-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2593GRCh38V40NT-BGRSLV08-1/Aligned.sortedByCoord.out.bamENCORE210363
    NT-BGRSLV08-1_quant.sfENCODE_DATA/set62_R/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2593GRCh38V40NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE210407
    NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set62_R/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2594NovaSeq6000100paired-ended1ENCORE27883
    NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set62_R/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2594NovaSeq6000100paired-ended2ENCORE27927
    NT-BGRSLV08-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2594GRCh38V40NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE210188
    NT-BGRSLV08-2_Signal.Unique.strand+.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2594GRCh38V40NT-BGRSLV08-2/Aligned.sortedByCoord.out.bamENCORE210232
    NT-BGRSLV08-2_Signal.Unique.strand-.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2594GRCh38V40NT-BGRSLV08-2/Aligned.sortedByCoord.out.bamENCORE210276
    NT-BGRSLV08-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2594GRCh38V40NT-BGRSLV08-2/Aligned.sortedByCoord.out.bamENCORE210320
    NT-BGRSLV08-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2594GRCh38V40NT-BGRSLV08-2/Aligned.sortedByCoord.out.bamENCORE210364
    NT-BGRSLV08-2_quant.sfENCODE_DATA/set62_R/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2594GRCh38V40NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gzENCORE210408