DDX19B RNA-Seq in K562

General Information


RBP	DDX19B
Cell_Line	K562
Method	shRNA
Exp_Name	DDX19B-BGKLV32-K562
ENCODE_series_ID	ENCSR240WZF
Batch_ID	BGKLV32
Pool ID	Pool-160425
Local_Set_Name	set32
ENCODE_KD_Exp_ID	ENCSR281IUF
ENCODE_CN_Exp_ID	ENCSR143COQ
Rep1	DDX19B_BGKLV32-17
Rep2	DDX19B_BGKLV32-18
CN1	NT_BGKLV32-1
CN2	NT_BGKLV32-2
Rep1_qPCR	55.8
Rep2_qPCR	79.5
Rep1_WB	94.5
Rep2_WB	92.2
Antibody Cat#	A300-545A
Antibody Lot#	A300-545A
Antibody DCC ID	ENCAB890IXX
Status	Released
Project	ENCODE3
ID	707

Experiment Information (Status: Released)

	BGKLV32-17	BGKLV32-17	BGKLV32-18	BGKLV32-18
idx	616	616	617	617
TRCN#_or_BGC#	TRCN0000051129	TRCN0000051129	TRCN0000051129	TRCN0000051129
shRNA_or_gRNA_sequence	CCTGAACTGAAGCTAGCTTAT	CCTGAACTGAAGCTAGCTTAT	CCTGAACTGAAGCTAGCTTAT	CCTGAACTGAAGCTAGCTTAT
PAM
Name	DDX19B	DDX19B	DDX19B	DDX19B
Sample_ID	BGKLV32-17	BGKLV32-17	BGKLV32-18	BGKLV32-18
transduction_Date	10/1/2015	10/1/2015	10/1/2015	10/1/2015
days
RBP_name	DDX19B	DDX19B	DDX19B	DDX19B
qPCR_result	55.8	55.8	79.5	79.5
Ave_qPCR	67.7	67.7
RT-qPCR_primer-F	tgattgaacaaatgggcaaa	tgattgaacaaatgggcaaa
RT-qPCR_primer-R	ctgatcttctggcctctttcc	ctgatcttctggcctctttcc
protein_conc	2659	2659	2334	2334
WB_result	94.5	75.1	92.2	84.1
Ave_WB	93.3	79.6
WB_DONE_date	11/20/2015	6/28/22
MW	54kDa	54kDa
IP	1		1
antibody_Cat#	A300-545A	A300-546A	A300-545A	LOT # 1
Antibody DCC ID	ENCAB890IXX	ENCAB726VLQ	ENCAB890IXX
submitted_to_DCC_date	3/8/2016
Rep1_TPM	40.09750917	0	0	0
Rep2_TPM	29.35353483	0	0	0
Action
Library_start_date	3/7/2016		3/7/2016
repeat_library
Note
ID	697	699	698	700

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX19B	Product_ID: A300-545A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX19B-human
DDX19B	Product_ID: A300-546A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX19B-human

Experiment Status

	BGKLV32-17	BGKLV32-18
Sample_ID	BGKLV32-17	BGKLV32-18
Sample Name	DDX19B_BGKLV32-17	DDX19B_BGKLV32-18
Sample Name	DDX19B_BGKLV32-17	DDX19B_BGKLV32-18
RBP	DDX19B	DDX19B
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1163	1164

Library-Prep
Sequencing

Library-Prep Information

	BGKLV32-17	BGKLV32-18
Sample #
Sample Name	DDX19B-BGKLV32-17	DDX19B-BGKLV32-18
Sample_Name_Alias	DDX19B_BGKLV32-17	DDX19B_BGKLV32-18
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-07	2016-03-07
Lib_ID	Lib-160307	Lib-160307
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/E7.png	DNA_Library_LV33-34-25B-32/set1/F7.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E12.png	RNA_Library_LV29-30-31-32/set1/F12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV32-17	BGKLV32-18
RBP	DDX19B	DDX19B
Batch_ID	BGKLV32	BGKLV32
WB_result	94.500	92.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2848	2849

Sequencing Information

	BGKLV32-17	BGKLV32-18
Sample_ID	BGKLV32-17	BGKLV32-18
Sample Name	DDX19B_BGKLV32-17	DDX19B_BGKLV32-18
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set32	set32
total_reads	88,461,698	90,552,846
total_aligned_reads	75,388,566	78,064,166
unique_aligned_reads	69,112,792	71,611,626
percent_uniqueAligned	0.78127	0.79083
correlation_replicates	0.989937	0.989937
spikein_reads	273,618	264,460
percent_spikeins	0.00309	0.00292
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1497	1498

Data Submission Information

	BGKLV32-17	BGKLV32-17
ENCODE_alias	brenton-graveley:DDX19B_BGKLV32	brenton-graveley:DDX19B-BGKLV32-K562
ENCODE_accession	ENCSR281IUF	ENCSR240WZF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV32-17	BGKLV32-17
Sample Name	DDX19B_BGKLV32-17	DDX19B_BGKLV32-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3121	6640

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
DDX19B_BGKLV32-17_AGTCAA_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1497	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21196
DDX19B_BGKLV32-17_AGTCAA_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1497	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21226
DDX19B_BGKLV32-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1497					GRCh38	V40	DDX19B_BGKLV32-17_AGTCAA_L002_001.R1.fastq.gz,DDX19B_BGKLV32-17_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	21256
DDX19B_BGKLV32-17_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1497					GRCh38	V40	DDX19B_BGKLV32-17/Aligned.sortedByCoord.out.bam		ENCORE2	21286
DDX19B_BGKLV32-17_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1497					GRCh38	V40	DDX19B_BGKLV32-17/Aligned.sortedByCoord.out.bam		ENCORE2	21316
DDX19B_BGKLV32-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1497					GRCh38	V40	DDX19B_BGKLV32-17/Aligned.sortedByCoord.out.bam		ENCORE2	21346
DDX19B_BGKLV32-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1497					GRCh38	V40	DDX19B_BGKLV32-17/Aligned.sortedByCoord.out.bam		ENCORE2	21376
DDX19B_BGKLV32-17_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1497					GRCh38	V40	DDX19B_BGKLV32-17_AGTCAA_L002_001.R1.fastq.gz,DDX19B_BGKLV32-17_AGTCAA_L002_001.R2.fastq.gz		ENCORE2	21406
DDX19B_BGKLV32-18_AGTTCC_L002_001.R1.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1498	HiSeq2500	100	paired-ended	1				NT_BGKLV32-1_ATCACG_L001_001.R1.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	21197
DDX19B_BGKLV32-18_AGTTCC_L002_001.R2.fastq.gz	ENCODE_DATA/set32/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1498	HiSeq2500	100	paired-ended	2				NT_BGKLV32-1_ATCACG_L001_001.R2.fastq.gz,NT_BGKLV32-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	21227
DDX19B_BGKLV32-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1498					GRCh38	V40	DDX19B_BGKLV32-18_AGTTCC_L002_001.R1.fastq.gz,DDX19B_BGKLV32-18_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	21257
DDX19B_BGKLV32-18_Signal.Unique.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1498					GRCh38	V40	DDX19B_BGKLV32-18/Aligned.sortedByCoord.out.bam		ENCORE2	21287
DDX19B_BGKLV32-18_Signal.Unique.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1498					GRCh38	V40	DDX19B_BGKLV32-18/Aligned.sortedByCoord.out.bam		ENCORE2	21317
DDX19B_BGKLV32-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1498					GRCh38	V40	DDX19B_BGKLV32-18/Aligned.sortedByCoord.out.bam		ENCORE2	21347
DDX19B_BGKLV32-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set32/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1498					GRCh38	V40	DDX19B_BGKLV32-18/Aligned.sortedByCoord.out.bam		ENCORE2	21377
DDX19B_BGKLV32-18_quant.sf	ENCODE_DATA/set32/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1498					GRCh38	V40	DDX19B_BGKLV32-18_AGTTCC_L002_001.R1.fastq.gz,DDX19B_BGKLV32-18_AGTTCC_L002_001.R2.fastq.gz		ENCORE2	21407