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non-target RNA-Seq in K562



non-target      CRISPR in K562      Control:

General Information

List KD experiments controlled by BGKcLV38-1 and BGKcLV38-2


NT-BGKcLV38-1,NT-BGKcLV38-2:
  • DHX15-BGKcLV38-K562
  • DHX33-BGKcLV38-K562
  • DHX9-BGKcLV38-K562
  • DNAJC1-BGKcLV38-K562
  • DNAJC2-BGKcLV38-K562
  • DYNC1I2-BGKcLV38-K562
  • DYNC1LI1-BGKcLV38-K562
  • EEF1G-BGKcLV38-K562
  • EEF2K-BGKcLV38-K562
  • EFL1-BGKcLV38-K562
  • EIF2B4-BGKcLV38-K562
  • EIF2B5-BGKcLV38-K562
  • EIF2D-BGKcLV38-K562
  • EIF3B-BGKcLV38-K562
  • EIF3J-BGKcLV38-K562
  • EIF3L-BGKcLV38-K562
  • EIF3M-BGKcLV38-K562
  • EIF4ENIF1-BGKcLV38-K562




    • Experiment Information (Status: Submitting)
    BGKcLV38-1BGKcLV38-2
    idx14181419
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon-targetnon-target
    Sample_IDBGKcLV38-1BGKcLV38-2
    transduction_Date10/18/2210/18/22
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc02951
    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
    ID55805581




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGKcLV38-1BGKcLV38-2
    Sample_IDBGKcLV38-1BGKcLV38-2
    Sample Name
    Sample NameNT-BGKcLV38-1NT-BGKcLV38-2
    RBPnon-targetnon-target
    Cell_LineK562K562
    Exp UID
    StatusSubmittingSubmitting
    Status_date2023-04-142023-04-14
    ProjectENCORE2ENCORE2
    Note
    ID1101611017




    Library-Prep Information
    BGKcLV38-1BGKcLV38-2
    Sample #5152
    Sample NameNT-BGKcLV38-1NT-BGKcLV38-2
    Sample_Name_Alias
    Index Well PositionA08B08
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-01-192023-01-19
    Lib_IDLib-230119Lib-230119
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp301319
    Peak_Molarity35.7046.60
    libSampleQC_DNA_WellDNA_Library_set54-56/set2/A8.pngDNA_Library_set54-56/set2/B8.png
    RIN9.99.8
    libSample_RNA_WellRNA_Library_set54-56/set1/C7.pngRNA_Library_set54-56/set1/D7.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-01-272023-01-27
    Sample_IDBGKcLV38-1BGKcLV38-2
    RBPNTNT
    Batch_IDBGKcLV38BGKcLV38
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID34223423




    Sequencing Information
    BGKcLV38-1BGKcLV38-2
    Sample_IDBGKcLV38-1BGKcLV38-2
    Sample NameNT-BGKcLV38-1NT-BGKcLV38-2
    Pool IDPool-230127CPool-230127C
    LocalServer_folderset56set56
    total_reads83,768,27342,003,538
    total_aligned_reads74,091,12538,772,991
    unique_aligned_reads68,821,49335,933,991
    percent_uniqueAligned0.821570.85550
    correlation_replicates0.9967220.996722
    spikein_reads67,38619,996
    percent_spikeins0.000800.00048
    original_ReadLength101101
    QC_StatusSubmittingSubmitting
    ID22952296




    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-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set56/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2295NovaSeq6000100paired-ended1ENCORE28338
    NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set56/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2295NovaSeq6000100paired-ended2ENCORE28376
    NT-BGKcLV38-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2295GRCh38V40NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE216990
    NT-BGKcLV38-1_Signal.Unique.strand+.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2295GRCh38V40NT-BGKcLV38-1/Aligned.sortedByCoord.out.bamENCORE217028
    NT-BGKcLV38-1_Signal.Unique.strand-.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2295GRCh38V40NT-BGKcLV38-1/Aligned.sortedByCoord.out.bamENCORE217066
    NT-BGKcLV38-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2295GRCh38V40NT-BGKcLV38-1/Aligned.sortedByCoord.out.bamENCORE217104
    NT-BGKcLV38-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2295GRCh38V40NT-BGKcLV38-1/Aligned.sortedByCoord.out.bamENCORE217142
    NT-BGKcLV38-1_quant.sfENCODE_DATA/set56/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2295GRCh38V40NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE217180
    NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set56/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2296NovaSeq6000100paired-ended1ENCORE28339
    NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set56/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2296NovaSeq6000100paired-ended2ENCORE28377
    NT-BGKcLV38-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2296GRCh38V40NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE216991
    NT-BGKcLV38-2_Signal.Unique.strand+.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2296GRCh38V40NT-BGKcLV38-2/Aligned.sortedByCoord.out.bamENCORE217029
    NT-BGKcLV38-2_Signal.Unique.strand-.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2296GRCh38V40NT-BGKcLV38-2/Aligned.sortedByCoord.out.bamENCORE217067
    NT-BGKcLV38-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2296GRCh38V40NT-BGKcLV38-2/Aligned.sortedByCoord.out.bamENCORE217105
    NT-BGKcLV38-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2296GRCh38V40NT-BGKcLV38-2/Aligned.sortedByCoord.out.bamENCORE217143
    NT-BGKcLV38-2_quant.sfENCODE_DATA/set56/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2296GRCh38V40NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gzENCORE217181