non-target      CRISPR in HepG2      Control: NT-BGHcLV16

General Information

List KD experiments controlled by BGHcLV16-1 and BGHcLV16-2


NT-BGHcLV16-1,NT-BGHcLV16-2:
  • CD3EAP-BGHcLV16-HepG2
  • DICER1-BGHcLV16-HepG2
  • EIF2B3-BGHcLV16-HepG2
  • EIF4A3-BGHcLV16-HepG2
  • EIF4E-BGHcLV16-HepG2
  • GSK3B-BGHcLV16-HepG2
  • MECP2-BGHcLV16-HepG2
  • NSUN4-BGHcLV16-HepG2
  • ERO1L-BGHcLV16-HepG2
  • PTGES3-BGHcLV16-HepG2
  • RPL11-BGHcLV16-HepG2
  • SMAD2-BGHcLV16-HepG2
  • THOC1-BGHcLV16-HepG2
  • XRCC6-BGHcLV16-HepG2
  • YBX1-BGHcLV16-HepG2




    • Experiment Information (Status: Released)
    BGHcLV16-1BGHcLV16-2
    idx429430
    TRCN#_or_BGC#BGC#0000000BGC#0000000
    shRNA_or_gRNA_sequenceCAGTCGGGCGTCATCATGATCAGTCGGGCGTCATCATGAT
    PAM
    Namenon-targetnon-target
    Sample_IDBGHcLV16-1BGHcLV16-2
    transduction_Date4/16/194/16/19
    daysD6D6
    RBP_namenon-targetnon-target
    qPCR_result
    Ave_qPCR
    RT-qPCR_primer-F
    RT-qPCR_primer-R
    protein_conc05094
    WB_result
    Ave_WB
    WB_DONE_date
    MW
    IP
    antibody_Cat#
    Antibody DCC ID
    submitted_to_DCC_date
    Rep1_TPM00
    Rep2_TPM00
    Action
    Library_start_date12/03/1912/03/19
    repeat_library
    Note
    ID65746575




    Western Blot
    Western Blot info was not avaliable




    Experiment Status
    BGHcLV16-1BGHcLV16-2
    Sample_IDBGHcLV16-1BGHcLV16-2
    Sample Name
    Sample NameNT-BGHcLV16-1NT-BGHcLV16-2
    RBPnon-targetnon-target
    Cell_LineHepG2HepG2
    Exp UID
    StatusReleasedReleased
    Status_date2020-12-012020-12-01
    ProjectENCODE4ENCODE4
    Note
    ID54095410




    Library-Prep Information
    BGHcLV16-1BGHcLV16-2
    Sample #4344
    Sample NameNT-BGHcLV16-1NT-BGHcLV16-2
    Sample_Name_Alias
    Index Well PositionG05H05
    Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
    LibPrep_date2020-08-312020-08-31
    Lib_IDLib-200831Lib-200831
    Tecan_Location1-A11-B1
    Tecan23.2034.12
    Tecan_date2019-12-102019-12-10
    Size_bp278294
    Peak_Molarity45.6033.40
    libSampleQC_DNA_WellDNA_Library_set43-44/set2/A1.pngDNA_Library_set43-44/set2/B1.png
    RIN9.99.9
    libSample_RNA_WellRNA_Library_set43-44/set1/G5.pngRNA_Library_set43-44/set1/H5.png
    SampleQC_methodTapeStationTapeStation
    SampleQC_date2019-12-132019-12-13
    Sample_IDBGHcLV16-1BGHcLV16-2
    RBPNTNT
    Batch_IDBGHcLV16BGHcLV16
    WB_result0.0000.000
    Library DescriptionTruSeq mRNATruSeq mRNA
    Repeat_Library_Suffix
    Lib_StatusSendToSequenceSendToSequence
    ProjectENCODE4ENCODE4
    ID619620




    Sequencing Information
    BGHcLV16-1BGHcLV16-2
    Sample_IDBGHcLV16-1BGHcLV16-2
    Sample NameNT-BGHcLV16-1NT-BGHcLV16-2
    Pool IDPool-200102Pool-200102
    LocalServer_folderset43_Hset43_H
    total_reads100,104,154119,240,300
    total_aligned_reads93,933,076110,012,024
    unique_aligned_reads88,190,936103,287,250
    percent_uniqueAligned0.880990.86621
    correlation_replicates0.9977080.997708
    spikein_reads192,456213,490
    percent_spikeins0.001920.00179
    original_ReadLength150150
    QC_StatusSubmittedSubmitted
    ID121122




    Data Submission Information
    BGHcLV16-1BGHcLV16-1BGHcLV16-1BGHcLV16-1BGHcLV16-1BGHcLV16-2BGHcLV16-2BGHcLV16-2BGHcLV16-2
    ENCODE_aliasbrenton-graveley:NT-BGHcLV16brenton-graveley:NT-BGHcLV16-1brenton-graveley:L-NT-BGHcLV16-1brenton-graveley:NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV16-2brenton-graveley:L-NT-BGHcLV16-2brenton-graveley:NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz
    ENCODE_accessionENCSR964HKTENCBS306SIAENCLB404GTTENCFF906ZOHENCFF930MSCENCBS804GDXENCLB441OTMENCFF788MKIENCFF990XOE
    object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2biosamplelibraryfile_fastq1file_fastq2
    assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seqknockdown followed by RNA-seq
    Sample_IDBGHcLV16-1BGHcLV16-1BGHcLV16-1BGHcLV16-1BGHcLV16-1BGHcLV16-2BGHcLV16-2BGHcLV16-2BGHcLV16-2
    Sample NameNT-BGHcLV16-1NT-BGHcLV16-1NT-BGHcLV16-1NT-BGHcLV16-1NT-BGHcLV16-1NT-BGHcLV16-2NT-BGHcLV16-2NT-BGHcLV16-2NT-BGHcLV16-2
    SelectedYesYesYesYesYesYesYesYesYes
    StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
    Status_Date2020-12-012020-12-012020-12-012020-12-012020-12-012020-12-012020-12-012020-12-012020-12-01
    ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
    LV43H_biosample_protocolLV43H_library_protocolLV43H_biosample_protocolLV43H_library_protocol
    protocol_URLNT-BGHcLV16-1.pdfL-NT-BGHcLV16-1.pdfNT-BGHcLV16-2.pdfL-NT-BGHcLV16-2.pdf
    ID18424841444685249415447




    File Information
    file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
    NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab121NovaSeq6000100paired-ended1ENCODE419
    NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab121NovaSeq6000100paired-ended2ENCODE451
    NT-BGHcLV16-1_Aligned.sortedByCoord.out.bamENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab121GRCh38V40NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gzENCORE224182
    NT-BGHcLV16-1_Signal.Unique.strand+.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab121GRCh38V40NT-BGHcLV16-1/Aligned.sortedByCoord.out.bamENCORE224214
    NT-BGHcLV16-1_Signal.Unique.strand-.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab121GRCh38V40NT-BGHcLV16-1/Aligned.sortedByCoord.out.bamENCORE224246
    NT-BGHcLV16-1_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab121GRCh38V40NT-BGHcLV16-1/Aligned.sortedByCoord.out.bamENCORE224278
    NT-BGHcLV16-1_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab121GRCh38V40NT-BGHcLV16-1/Aligned.sortedByCoord.out.bamENCORE224310
    NT-BGHcLV16-1_quant.sfENCODE_DATA/set43_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab121GRCh38V40NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gzENCORE224342
    NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab122NovaSeq6000100paired-ended1ENCODE420
    NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set43_H/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab122NovaSeq6000100paired-ended2ENCODE452
    NT-BGHcLV16-2_Aligned.sortedByCoord.out.bamENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab122GRCh38V40NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gzENCORE224183
    NT-BGHcLV16-2_Signal.Unique.strand+.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab122GRCh38V40NT-BGHcLV16-2/Aligned.sortedByCoord.out.bamENCORE224215
    NT-BGHcLV16-2_Signal.Unique.strand-.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab122GRCh38V40NT-BGHcLV16-2/Aligned.sortedByCoord.out.bamENCORE224247
    NT-BGHcLV16-2_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab122GRCh38V40NT-BGHcLV16-2/Aligned.sortedByCoord.out.bamENCORE224279
    NT-BGHcLV16-2_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab122GRCh38V40NT-BGHcLV16-2/Aligned.sortedByCoord.out.bamENCORE224311
    NT-BGHcLV16-2_quant.sfENCODE_DATA/set43_H/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab122GRCh38V40NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gzENCORE224343