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non-target RNA-Seq in K562



non-target      CRISPR in K562      Control:

General Information

List KD experiments controlled by BGKcLV35-1 and BGKcLV35-2


NT-BGKcLV35-1,NT-BGKcLV35-2:
  • ARHGEF1-BGKcLV35-K562
  • C1QBP-BGKcLV35-K562
  • CCDC47-BGKcLV35-K562
  • CSDE1-BGKcLV35-K562
  • CSTF3-BGKcLV35-K562
  • CTNND1-BGKcLV35-K562
  • DCTN2-BGKcLV35-K562
  • ROCK2-BGKcLV35-K562
  • ROR2-BGKcLV35-K562
  • RPL35A-BGKcLV35-K562
  • RPS14-BGKcLV35-K562
  • RTCB-BGKcLV35-K562




    • Experiment Information (Status: Submitting)
    BGKcLV35-1BGKcLV35-2
    idx12761277
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV35-1BGKcLV35-2
    transduction_Date4/28/224/28/22
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc03204
    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_date06/17/2206/17/22
    repeat_library
    Note
    ID54185419




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV35-1BGKcLV35-2
    Sample_IDBGKcLV35-1BGKcLV35-2
    Sample Name
    Sample NameNT-BGKcLV35-1NT-BGKcLV35-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusSubmittingSubmitting
    Status_date2023-04-142023-04-14
    ProjectENCORE2ENCORE2
    Note
    ID1085710858




    Library-Prep Information
    BGKcLV35-1BGKcLV35-2
    Sample #2324
    Sample NameNT-BGKcLV35-1NT-BGKcLV35-2
    Sample_Name_Alias
    Index Well PositionG03H03
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2022-06-172022-06-17
    Lib_IDLib-220617Lib-220617
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp275270
    Peak_Molarity24.8022.20
    libSampleQC_DNA_WellDNA_Library_set54-56/set3/G7.pngDNA_Library_set54-56/set3/H7.png
    RIN9.910.0
    libSample_RNA_WellRNA_Library_set54-56/set2/G3.pngRNA_Library_set54-56/set2/H3.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2022-06-202022-06-20
    Sample_IDBGKcLV35-1BGKcLV35-2
    RBPNTNT
    Batch_IDBGKcLV35BGKcLV35
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID33403341




    Sequencing Information
    BGKcLV35-1BGKcLV35-2
    Sample_IDBGKcLV35-1BGKcLV35-2
    Sample NameNT-BGKcLV35-1NT-BGKcLV35-2
    Pool IDPool-220720Pool-220720
    LocalServer_folderset54set54
    total_reads68,722,15261,293,956
    total_aligned_reads62,239,73454,765,730
    unique_aligned_reads57,132,48050,325,534
    percent_uniqueAligned0.831350.82105
    correlation_replicates0.9922750.992275
    spikein_reads7,52610,150
    percent_spikeins0.000110.00017
    original_ReadLength101101
    QC_StatusSubmittingSubmitting
    ID22192220




    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-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set54/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2219NovaSeq6000100paired-ended1ENCORE28502
    NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set54/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2219NovaSeq6000100paired-ended2ENCORE28552
    NT-BGKcLV35-1_Signal.Unique.strand+.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2219GRCh38V40NT-BGKcLV35-1/Aligned.sortedByCoord.out.bamENCORE217748
    NT-BGKcLV35-1_Signal.Unique.strand-.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2219GRCh38V40NT-BGKcLV35-1/Aligned.sortedByCoord.out.bamENCORE217798
    NT-BGKcLV35-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2219GRCh38V40NT-BGKcLV35-1/Aligned.sortedByCoord.out.bamENCORE217848
    NT-BGKcLV35-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2219GRCh38V40NT-BGKcLV35-1/Aligned.sortedByCoord.out.bamENCORE217898
    NT-BGKcLV35-1_quant.sfENCODE_DATA/set54/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2219GRCh38V40NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gzENCORE217948
    NT-BGKcLV35-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2219GRCh38V40NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gzENCORE229289
    NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set54/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2220NovaSeq6000100paired-ended1ENCORE28503
    NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set54/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2220NovaSeq6000100paired-ended2ENCORE28553
    NT-BGKcLV35-2_Signal.Unique.strand+.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2220GRCh38V40NT-BGKcLV35-2/Aligned.sortedByCoord.out.bamENCORE217749
    NT-BGKcLV35-2_Signal.Unique.strand-.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2220GRCh38V40NT-BGKcLV35-2/Aligned.sortedByCoord.out.bamENCORE217799
    NT-BGKcLV35-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2220GRCh38V40NT-BGKcLV35-2/Aligned.sortedByCoord.out.bamENCORE217849
    NT-BGKcLV35-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2220GRCh38V40NT-BGKcLV35-2/Aligned.sortedByCoord.out.bamENCORE217899
    NT-BGKcLV35-2_quant.sfENCODE_DATA/set54/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2220GRCh38V40NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gzENCORE217949
    NT-BGKcLV35-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2220GRCh38V40NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gzENCORE229290