DDX59      CRISPR in K562      Control: NT-BGKcLV08

General Information
RBPDDX59
Cell_LineK562
MethodCRISPR
Exp_NameDDX59-BGKcLV08-K562
ENCODE_series_IDENCSR732SBG
Batch_IDBGKcLV08
Pool IDPool-180901
Local_Set_Nameset41
ENCODE_KD_Exp_IDENCSR126UCL
ENCODE_CN_Exp_IDENCSR015KGT
Rep1DDX59-BGKcLV08-23
Rep2DDX59-BGKcLV08-24
CN1NT-BGKcLV08-1
CN2NT-BGKcLV08-2
Rep1_qPCR48.2
Rep2_qPCR57.9
Rep1_WB76.0
Rep2_WB76.0
Antibody Cat#A303-028A
Antibody Lot#A303-028A
Antibody DCC IDENCAB112HZS
StatusReleased
ProjectENCODE4
ID202




Experiment Information (Status: Released)
BGKcLV08-23BGKcLV08-24
idx248249
TRCN#_or_BGC#BGC#0000114BGC#0000114
shRNA_or_gRNA_sequenceGGGGTGCTCTTTGTAGACATGGGGTGCTCTTTGTAGACAT
PAMAGGAGG
NameDDX59-74FDDX59-74F
Sample_IDBGKcLV08-23BGKcLV08-24
transduction_Date3/8/183/8/18
daysDay 6Day 6
RBP_nameDDX59DDX59
qPCR_result48.257.9
Ave_qPCR53.1
RT-qPCR_primer-Fctctgtggtgtaaagattgtgg
RT-qPCR_primer-Rcaagcacttgttgttgaaaacc
protein_conc34983384
WB_result76.076.0
Ave_WB76.0
WB_DONE_date3/9/18wes
MW69kDa
IP1IP1IP
antibody_Cat#A303-028AA303-028A
Antibody DCC IDENCAB112HZS
submitted_to_DCC_date9/6/18
Rep1_TPM4.10
Rep2_TPM5.30
ActionReadyReady
Library_start_date7/26/187/26/18
repeat_library
Note
ID43484349




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
DDX59Product_ID: A303-028A
Lot_ID: 1
Source: Bethyl Labs
Target Name: DDX59-human
HepG2_Bethyl_A303-028A_1_DDX59.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using DDX59 specific antibody. Lane 1 is 1% of twenty million whole cell lysate input and lane 2 is 25% of IP enrichment using rabbit normal IgG (lanes under 'IgG'). Lane 3 is 1% of twenty million whole cell lysate input and lane 4 is 10% IP enrichment using rabbit polyclonal anti-DDX59 antibody (lanes under 'DDX59').
DDX59-HEPG2.png<br>Caption: Western blot following shRNA against DDX59 in HepG2 whole cell lysate using DDX59 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against DDX59.DDX59 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
DDX59-K562-CRISPR.png<br>Caption: Western blot following CRISPR against DDX59 in K562 whole cell lysate using DDX59 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against DDX59.DDX59 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.




Experiment Status
BGKcLV08-23BGKcLV08-24
Sample_IDBGKcLV08-23BGKcLV08-24
Sample Name
Sample NameDDX59-BGKcLV08-23DDX59-BGKcLV08-24
RBPDDX59DDX59
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2020-11-062020-11-06
ProjectENCODE4ENCODE4
Note
ID61756176




Library-Prep Information
BGKcLV08-23BGKcLV08-24
Sample #1112
Sample NameDDX59-BGKcLV08-23DDX59-BGKcLV08-24
Sample_Name_Alias
Index Well PositionC02D02
Index_tableIDT_UniqueDualIndex_96IDT_UniqueDualIndex_96
LibPrep_date2018-10-012018-10-01
Lib_IDLib-181001Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp279274
Peak_Molarity57.3052.90
libSampleQC_DNA_WellDNA_Library_set41/set2/C2.pngDNA_Library_set41/set2/D2.png
RIN9.49.7
libSample_RNA_WellRNA_Library_set41/set1/C2.pngRNA_Library_set41/set1/D2.png
SampleQC_methodTapeStationTapeStation
SampleQC_date2018-07-272018-07-27
Sample_IDBGKcLV08-23BGKcLV08-24
RBPDDX59DDX59
Batch_IDBGKcLV08BGKcLV08
WB_result76.00076.000
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE4ENCODE4
ID861862




Sequencing Information
BGKcLV08-23BGKcLV08-24
Sample_IDBGKcLV08-23BGKcLV08-24
Sample NameDDX59-BGKcLV08-23DDX59-BGKcLV08-24
Pool IDPool-180901Pool-180901
LocalServer_folderset41set41
total_reads136,987,736156,936,706
total_aligned_reads132,555,214152,462,410
unique_aligned_reads118,645,214136,593,898
percent_uniqueAligned0.866100.87038
correlation_replicates0.9931580.993158
spikein_reads266,242341,666
percent_spikeins0.001940.00218
original_ReadLength150150
QC_StatusSubmittedSubmitted
ID267268




Data Submission Information
BGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-24BGKcLV08-24BGKcLV08-24BGKcLV08-24
ENCODE_aliasbrenton-graveley:DDX59-BGKcLV08brenton-graveley:DDX59-BGKcLV08-23brenton-graveley:L-DDX59-BGKcLV08-23brenton-graveley:DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:DDX59-BGKcLV08-K562brenton-graveley:DDX59-BGKcLV08-24brenton-graveley:L-DDX59-BGKcLV08-24brenton-graveley:DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzbrenton-graveley:DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accessionENCSR126UCLENCBS625ITQENCLB127TLRENCFF316XTDENCFF168LQDENCSR732SBGENCBS040AYWENCLB051IYRENCFF700QFGENCFF423CBO
object_typeexperimentbiosamplelibraryfile_fastq1file_fastq2gene_silencing_seriesbiosamplelibraryfile_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-seqknockdown followed by RNA-seq
Sample_IDBGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-23BGKcLV08-24BGKcLV08-24BGKcLV08-24BGKcLV08-24
Sample NameDDX59-BGKcLV08-23DDX59-BGKcLV08-23DDX59-BGKcLV08-23DDX59-BGKcLV08-23DDX59-BGKcLV08-23DDX59-BGKcLV08-23DDX59-BGKcLV08-24DDX59-BGKcLV08-24DDX59-BGKcLV08-24DDX59-BGKcLV08-24
SelectedYesYesYesYesYesYesYesYesYesYes
StatusReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleasedReleased
Status_Date2020-11-202020-11-202020-11-202020-11-202020-11-202022-03-022020-11-202020-11-202020-11-202020-11-20
ProjectENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4ENCODE4
LV41_biosample_protocolLV41_library_protocolLV41_biosample_protocolLV41_library_protocol
protocol_URLDDX59-BGKcLV08-23.pdfL-DDX59-BGKcLV08-23.pdfDDX59-BGKcLV08-24.pdfL-DDX59-BGKcLV08-24.pdf
ID1123116612361306137671841167123713071377




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab267NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE4513
DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab267NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE4583
DDX59-BGKcLV08-23_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab267GRCh38V40DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226751
DDX59-BGKcLV08-23_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab267GRCh38V40DDX59-BGKcLV08-23/Aligned.sortedByCoord.out.bamENCORE226821
DDX59-BGKcLV08-23_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab267GRCh38V40DDX59-BGKcLV08-23/Aligned.sortedByCoord.out.bamENCORE226891
DDX59-BGKcLV08-23_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab267GRCh38V40DDX59-BGKcLV08-23/Aligned.sortedByCoord.out.bamENCORE226961
DDX59-BGKcLV08-23_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab267GRCh38V40DDX59-BGKcLV08-23/Aligned.sortedByCoord.out.bamENCORE227031
DDX59-BGKcLV08-23_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab267GRCh38V40DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGKcLV08-23_TCTCTACT+CGCGGTTC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227101
DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab268NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gzENCODE4514
DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE_DATA/set41/fastq_trimmedfastqreadsknockdown followed by RNA-seqGraveley Lab268NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCODE4584
DDX59-BGKcLV08-24_Aligned.sortedByCoord.out.bamENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab268GRCh38V40DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE226752
DDX59-BGKcLV08-24_Signal.Unique.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab268GRCh38V40DDX59-BGKcLV08-24/Aligned.sortedByCoord.out.bamENCORE226822
DDX59-BGKcLV08-24_Signal.Unique.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab268GRCh38V40DDX59-BGKcLV08-24/Aligned.sortedByCoord.out.bamENCORE226892
DDX59-BGKcLV08-24_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab268GRCh38V40DDX59-BGKcLV08-24/Aligned.sortedByCoord.out.bamENCORE226962
DDX59-BGKcLV08-24_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab268GRCh38V40DDX59-BGKcLV08-24/Aligned.sortedByCoord.out.bamENCORE227032
DDX59-BGKcLV08-24_quant.sfENCODE_DATA/set41/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab268GRCh38V40DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,DDX59-BGKcLV08-24_CTCTCGTC+TATAACCT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gzENCORE227102