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non-target RNA-Seq in K562



non-target      CRISPR in K562      Control:

General Information

List KD experiments controlled by BGKcLV40-1 and BGKcLV40-2


NT-BGKcLV40-1,NT-BGKcLV40-2:
  • BCLAF1-BGKcLV40-K562
  • DNAJA1-BGKcLV40-K562
  • EDC3-BGKcLV40-K562
  • EDF1-BGKcLV40-K562
  • EML4-BGKcLV40-K562
  • EPB41L2-BGKcLV40-K562
  • EPRS-BGKcLV40-K562
  • ERAL1-BGKcLV40-K562
  • ERP29-BGKcLV40-K562
  • EXO1-BGKcLV40-K562
  • EXOSC1-BGKcLV40-K562
  • EXOSC9-BGKcLV40-K562
  • EZH2-BGKcLV40-K562
  • F11R-BGKcLV40-K562
  • FAM98A-BGKcLV40-K562
  • FAM98B-BGKcLV40-K562
  • FDPS-BGKcLV40-K562
  • FEN1-BGKcLV40-K562
  • FKBP3-BGKcLV40-K562
  • FSCN1-BGKcLV40-K562
  • FTSJ3-BGKcLV40-K562




    • Experiment Information (Status: Submitting)
    BGKcLV40-1BGKcLV40-2
    idx14841485
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV40-1BGKcLV40-2
    transduction_Date10/31/2310/31/23
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc03160
    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
    ID56685669




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV40-1BGKcLV40-2
    Sample_IDBGKcLV40-1BGKcLV40-2
    Sample Name
    Sample NameNT-BGKcLV40-1NT-BGKcLV40-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusSubmittingSubmitting
    Status_date2024-02-162024-02-16
    ProjectENCORE2ENCORE2
    Note
    ID1275412755




    Library-Prep Information
    BGKcLV40-1BGKcLV40-2
    Sample #12
    Sample NameNT-BGKcLV40-1NT-BGKcLV40-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-12-192023-12-19
    Lib_IDLib-231219Lib-231219
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp9283
    Peak_Molarity98.6982.60
    libSampleQC_DNA_WellDNA_Library_set67/set1/A7.pngDNA_Library_set67/set1/B7.png
    RIN10.09.9
    libSample_RNA_WellRNA_Library_set67/set1/A1.pngRNA_Library_set67/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-12-262023-12-26
    Sample_IDBGKcLV40-1BGKcLV40-2
    RBPNTNT
    Batch_IDBGKcLV40BGKcLV40
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID41384139




    Sequencing Information
    BGKcLV40-1BGKcLV40-2
    Sample_IDBGKcLV40-1BGKcLV40-2
    Sample NameNT-BGKcLV40-1NT-BGKcLV40-2
    Pool IDPool-231226Pool-231226
    LocalServer_folderset67set67
    total_reads37,720,23630,500,419
    total_aligned_reads30,067,23125,225,008
    unique_aligned_reads27,615,44323,178,991
    percent_uniqueAligned0.732110.75996
    correlation_replicates0.9973360.997336
    spikein_reads5,8761,948
    percent_spikeins0.000160.00006
    original_ReadLength151151
    QC_StatusSubmittingSubmitting
    ID27932794




    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-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set67/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2793NovaSeq6000100paired-ended1ENCORE228183
    NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set67/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2793NovaSeq6000100paired-ended2ENCORE228227
    NT-BGKcLV40-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2793GRCh38V40NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE228271
    NT-BGKcLV40-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2793GRCh38V40NT-BGKcLV40-1/Aligned.sortedByCoord.out.bamENCORE228315
    NT-BGKcLV40-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2793GRCh38V40NT-BGKcLV40-1/Aligned.sortedByCoord.out.bamENCORE228359
    NT-BGKcLV40-1_Signal.Unique.strand-.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2793GRCh38V40NT-BGKcLV40-1/Aligned.sortedByCoord.out.bamENCORE228403
    NT-BGKcLV40-1_Signal.Unique.strand+.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2793GRCh38V40NT-BGKcLV40-1/Aligned.sortedByCoord.out.bamENCORE228447
    NT-BGKcLV40-1_quant.sfENCODE_DATA/set67/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2793GRCh38V40NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE228491
    NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set67/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2794NovaSeq6000100paired-ended1ENCORE228184
    NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set67/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2794NovaSeq6000100paired-ended2ENCORE228228
    NT-BGKcLV40-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2794GRCh38V40NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE228272
    NT-BGKcLV40-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2794GRCh38V40NT-BGKcLV40-2/Aligned.sortedByCoord.out.bamENCORE228316
    NT-BGKcLV40-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2794GRCh38V40NT-BGKcLV40-2/Aligned.sortedByCoord.out.bamENCORE228360
    NT-BGKcLV40-2_Signal.Unique.strand-.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2794GRCh38V40NT-BGKcLV40-2/Aligned.sortedByCoord.out.bamENCORE228404
    NT-BGKcLV40-2_Signal.Unique.strand+.bwENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2794GRCh38V40NT-BGKcLV40-2/Aligned.sortedByCoord.out.bamENCORE228448
    NT-BGKcLV40-2_quant.sfENCODE_DATA/set67/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2794GRCh38V40NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE228492