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non-target RNA-Seq in HepG2



non-target      CRISPR in HepG2      Control:

General Information

List KD experiments controlled by BGHcLV36-1 and BGHcLV36-2


NT-BGHcLV36-1,NT-BGHcLV36-2:
  • PARP1-BGHcLV36-HepG2
  • RACK1-BGHcLV36-HepG2
  • SRP9-BGHcLV36-HepG2
  • SRPK1-BGHcLV36-HepG2
  • SRPRA-BGHcLV36-HepG2
  • SRPRB-BGHcLV36-HepG2
  • VARS-BGHcLV36-HepG2
  • WARS-BGHcLV36-HepG2
  • RPS15-BGHcLV36-HepG2




    • Experiment Information (Status: Submitting)
    BGHcLV36-1BGHcLV36-2
    idx11321133
    TRCN#_or_BGC#
    shRNA_or_gRNA_sequence
    PAM
    Namenon-targetnon-target
    Sample_IDBGHcLV36-1BGHcLV36-2
    transduction_Date8/2/228/2/22
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc03906
    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
    ID73137314




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV36-1BGHcLV36-2
    Sample_IDBGHcLV36-1BGHcLV36-2
    Sample Name
    Sample NameNT-BGHcLV36-1NT-BGHcLV36-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusSubmittingSubmitting
    Status_date2023-04-142023-04-14
    ProjectENCORE2ENCORE2
    Note
    ID1094110942




    Library-Prep Information
    BGHcLV36-1BGHcLV36-2
    Sample #12
    Sample NameNT-BGHcLV36-1NT-BGHcLV36-2
    Sample_Name_Alias
    Index Well PositionA01B01
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2023-01-132023-01-13
    Lib_IDLib-230113Lib-230113
    Tecan_Location
    Tecan
    Tecan_date
    Size_bp298327
    Peak_Molarity29.0054.90
    libSampleQC_DNA_WellDNA_Library_set54-56/set1/A1.pngDNA_Library_set54-56/set1/B1.png
    RIN9.99.9
    libSample_RNA_WellRNA_Library_set54-56/set1/A1.pngRNA_Library_set54-56/set1/B1.png
    SampleQC_methodTapeStation_2022TapeStation_2022
    SampleQC_date2023-01-272023-01-27
    Sample_IDBGHcLV36-1BGHcLV36-2
    RBPNTNT
    Batch_IDBGHcLV36BGHcLV36
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCORE2ENCORE2
    ID33723373




    Sequencing Information
    BGHcLV36-1BGHcLV36-2
    Sample_IDBGHcLV36-1BGHcLV36-2
    Sample NameNT-BGHcLV36-1NT-BGHcLV36-2
    Pool IDPool-230130Pool-230130
    LocalServer_folderset55set55
    total_reads70,385,54738,192,690
    total_aligned_reads64,192,90335,521,744
    unique_aligned_reads60,775,25633,627,639
    percent_uniqueAligned0.863460.88047
    correlation_replicates0.9987800.998780
    spikein_reads18,3809,988
    percent_spikeins0.000260.00026
    original_ReadLength101101
    QC_StatusSubmittingSubmitting
    ID22452246




    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-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2245NovaSeq6000100paired-ended1ENCORE28386
    NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2245NovaSeq6000100paired-ended2ENCORE28436
    NT-BGHcLV36-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2245GRCh38V40NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225627
    NT-BGHcLV36-1_Signal.Unique.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2245GRCh38V40NT-BGHcLV36-1/Aligned.sortedByCoord.out.bamENCORE225677
    NT-BGHcLV36-1_Signal.Unique.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2245GRCh38V40NT-BGHcLV36-1/Aligned.sortedByCoord.out.bamENCORE225727
    NT-BGHcLV36-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2245GRCh38V40NT-BGHcLV36-1/Aligned.sortedByCoord.out.bamENCORE225777
    NT-BGHcLV36-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2245GRCh38V40NT-BGHcLV36-1/Aligned.sortedByCoord.out.bamENCORE225827
    NT-BGHcLV36-1_quant.sfENCODE_DATA/set55/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2245GRCh38V40NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225877
    NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2246NovaSeq6000100paired-ended1ENCORE28387
    NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set55/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab2246NovaSeq6000100paired-ended2ENCORE28437
    NT-BGHcLV36-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab2246GRCh38V40NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225628
    NT-BGHcLV36-2_Signal.Unique.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2246GRCh38V40NT-BGHcLV36-2/Aligned.sortedByCoord.out.bamENCORE225678
    NT-BGHcLV36-2_Signal.Unique.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab2246GRCh38V40NT-BGHcLV36-2/Aligned.sortedByCoord.out.bamENCORE225728
    NT-BGHcLV36-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2246GRCh38V40NT-BGHcLV36-2/Aligned.sortedByCoord.out.bamENCORE225778
    NT-BGHcLV36-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab2246GRCh38V40NT-BGHcLV36-2/Aligned.sortedByCoord.out.bamENCORE225828
    NT-BGHcLV36-2_quant.sfENCODE_DATA/set55/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab2246GRCh38V40NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE225878