DDX51 RNA-Seq in K562

General Information


RBP	DDX51
Cell_Line	K562
Method	shRNA
Exp_Name	DDX51-BGKLV19-K562
ENCODE_series_ID	ENCSR160QCC
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR029LGJ
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	DDX51_BGKLV19_15B
Rep2	DDX51_BGKLV19_16B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	55.6
Rep2_qPCR	62.6
Rep1_WB	86.5
Rep2_WB	84.8
Antibody Cat#	A301-089A
Antibody Lot#	A301-089A
Antibody DCC ID	ENCAB820ZVZ
Status	Released
Project	ENCODE3
ID	467

Experiment Information (Status: Released)

	BGKLV19-15	BGKLV19-16
idx	222	223
TRCN#_or_BGC#	TRCN0000050001	TRCN0000050001
shRNA_or_gRNA_sequence	GCCTAACTGTGTCAGAAGGAA	GCCTAACTGTGTCAGAAGGAA
PAM
Name	DDX51	DDX51
Sample_ID	BGKLV19-15	BGKLV19-16
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	DDX51	DDX51
qPCR_result	55.6	62.6
Ave_qPCR	59.1
RT-qPCR_primer-F	agcgacctctgtgtttctgc
RT-qPCR_primer-R	ggatgtggcagaccactctc
protein_conc	2580	2598
WB_result	86.5	84.8
Ave_WB	76.0
WB_DONE_date	2/4/2016
MW	72kd	WES
IP	1	1
antibody_Cat#	A301-089A	A301-089A
Antibody DCC ID	ENCAB820ZVZ
submitted_to_DCC_date	3/8/2016
Rep1_TPM	8.96850167	0
Rep2_TPM	7.65127423	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	241	242

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX51	Product_ID: A301-089A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX51-human

Experiment Status

	BGKLV19-15	BGKLV19-16
Sample_ID	BGKLV19-15	BGKLV19-16
Sample Name	DDX51_BGKLV19_15B	DDX51_BGKLV19_16B
Sample Name	DDX51_BGKLV19_15B	DDX51_BGKLV19_16B
RBP	DDX51	DDX51
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	664	665

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-15	BGKLV19-16
Sample #
Sample Name	DDX51-BGKLV19-15B	DDX51-BGKLV19-16B
Sample_Name_Alias	DDX51_BGKLV19_15B	DDX51_BGKLV19_16B
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E7.png	DNA_Library_LV18-19/set1/F7.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/A1.png	RNA_Library_LV19-21-24/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-15	BGKLV19-16
RBP	DDX51	DDX51
Batch_ID	BGKLV19	BGKLV19
WB_result	86.500	84.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2350	2351

Sequencing Information

	BGKLV19-15	BGKLV19-16
Sample_ID	BGKLV19-15	BGKLV19-16
Sample Name	DDX51_BGKLV19_15B	DDX51_BGKLV19_16B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	51,770,000	60,220,000
total_aligned_reads	47,131,282	55,040,998
unique_aligned_reads	42,988,820	50,411,614
percent_uniqueAligned	0.83038	0.83712
correlation_replicates	0.996804	0.996804
spikein_reads	150,758	190,164
percent_spikeins	0.00291	0.00316
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	992	993

Data Submission Information

	BGKLV19-15	BGKLV19-15
ENCODE_alias	brenton-graveley:DDX51_BGKLV19	brenton-graveley:DDX51-BGKLV19-K562
ENCODE_accession	ENCSR029LGJ	ENCSR160QCC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-15	BGKLV19-15
Sample Name	DDX51_BGKLV19_15B	DDX51_BGKLV19_15B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2881	6656

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
DDX51_BGKLV19_15B_ACAGTG_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	992	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15104
DDX51_BGKLV19_15B_ACAGTG_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	992	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15162
DDX51_BGKLV19_15B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	992					GRCh38	V40	DDX51_BGKLV19_15B_ACAGTG_L002_R1_001.fastq.gz,DDX51_BGKLV19_15B_ACAGTG_L002_R2_001.fastq.gz		ENCORE2	15220
DDX51_BGKLV19_15B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	992					GRCh38	V40	DDX51_BGKLV19_15B/Aligned.sortedByCoord.out.bam		ENCORE2	15291
DDX51_BGKLV19_15B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	992					GRCh38	V40	DDX51_BGKLV19_15B/Aligned.sortedByCoord.out.bam		ENCORE2	15349
DDX51_BGKLV19_15B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	992					GRCh38	V40	DDX51_BGKLV19_15B/Aligned.sortedByCoord.out.bam		ENCORE2	15407
DDX51_BGKLV19_15B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	992					GRCh38	V40	DDX51_BGKLV19_15B/Aligned.sortedByCoord.out.bam		ENCORE2	15465
DDX51_BGKLV19_15B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	992					GRCh38	V40	DDX51_BGKLV19_15B_ACAGTG_L002_R1_001.fastq.gz,DDX51_BGKLV19_15B_ACAGTG_L002_R2_001.fastq.gz		ENCORE2	16362
DDX51_BGKLV19_16B_GCCAAT_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	993	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15105
DDX51_BGKLV19_16B_GCCAAT_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	993	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15163
DDX51_BGKLV19_16B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	993					GRCh38	V40	DDX51_BGKLV19_16B_GCCAAT_L002_R1_001.fastq.gz,DDX51_BGKLV19_16B_GCCAAT_L002_R2_001.fastq.gz		ENCORE2	15221
DDX51_BGKLV19_16B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	993					GRCh38	V40	DDX51_BGKLV19_16B/Aligned.sortedByCoord.out.bam		ENCORE2	15292
DDX51_BGKLV19_16B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	993					GRCh38	V40	DDX51_BGKLV19_16B/Aligned.sortedByCoord.out.bam		ENCORE2	15350
DDX51_BGKLV19_16B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	993					GRCh38	V40	DDX51_BGKLV19_16B/Aligned.sortedByCoord.out.bam		ENCORE2	15408
DDX51_BGKLV19_16B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	993					GRCh38	V40	DDX51_BGKLV19_16B/Aligned.sortedByCoord.out.bam		ENCORE2	15466
DDX51_BGKLV19_16B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	993					GRCh38	V40	DDX51_BGKLV19_16B_GCCAAT_L002_R1_001.fastq.gz,DDX51_BGKLV19_16B_GCCAAT_L002_R2_001.fastq.gz		ENCORE2	16363