DDX52 RNA-Seq in K562

General Information


RBP	DDX52
Cell_Line	K562
Method	shRNA
Exp_Name	DDX52-BGKLV19-K562
ENCODE_series_ID	ENCSR040OWU
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR560RSZ
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	DDX52_BGKLV19_17B
Rep2	DDX52_BGKLV19_18B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	81.7
Rep2_qPCR	85.8
Rep1_WB	75.2
Rep2_WB	76.7
Antibody Cat#	A303-054A
Antibody Lot#	A303-054A
Antibody DCC ID	ENCAB607JMR
Status	Released
Project	ENCODE3
ID	468

Experiment Information (Status: Released)

	BGKLV19-17	BGKLV19-18
idx	224	225
TRCN#_or_BGC#	TRCN0000052106	TRCN0000052106
shRNA_or_gRNA_sequence	GCCAATCCAAATGCAAGCCAT	GCCAATCCAAATGCAAGCCAT
PAM
Name	DDX52_06	DDX52_06
Sample_ID	BGKLV19-17	BGKLV19-18
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	DDX52	DDX52
qPCR_result	81.7	85.8
Ave_qPCR	83.7
RT-qPCR_primer-F	ttccggaaagttggagaatc
RT-qPCR_primer-R	caattgggtcaggaagatcg
protein_conc	3132	3489
WB_result	75.2	76.7
Ave_WB	76.0
WB_DONE_date	2/23/2015
MW
IP	1	1
antibody_Cat#	A303-054A	A303-054A
Antibody DCC ID	ENCAB607JMR	ENCAB607JMR
submitted_to_DCC_date	4/2/2015
Rep1_TPM	14.0546136	0
Rep2_TPM	8.89623828	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	243	244

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX52	Product_ID: A303-054A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX52-human

Experiment Status

	BGKLV19-17	BGKLV19-18
Sample_ID	BGKLV19-17	BGKLV19-18
Sample Name	DDX52_BGKLV19_17B	DDX52_BGKLV19_18B
Sample Name	DDX52_BGKLV19_17B	DDX52_BGKLV19_18B
RBP	DDX52	DDX52
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	666	667

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-17	BGKLV19-18
Sample #
Sample Name	DDX52-BGKLV19-17B	DDX52-BGKLV19-18B
Sample_Name_Alias	DDX52_BGKLV19_17B	DDX52_BGKLV19_18B
Index Well Position	S07	S08
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/G7.png	DNA_Library_LV18-19/set1/H7.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C2.png	RNA_Library_LV19-21-24/set1/D2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-17	BGKLV19-18
RBP	DDX52	DDX52
Batch_ID	BGKLV19	BGKLV19
WB_result	75.200	76.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2352	2353

Sequencing Information

	BGKLV19-17	BGKLV19-18
Sample_ID	BGKLV19-17	BGKLV19-18
Sample Name	DDX52_BGKLV19_17B	DDX52_BGKLV19_18B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	48,130,000	53,620,000
total_aligned_reads	44,075,926	49,731,992
unique_aligned_reads	40,354,952	45,578,152
percent_uniqueAligned	0.83846	0.85002
correlation_replicates	0.994209	0.994209
spikein_reads	133,416	286,578
percent_spikeins	0.00277	0.00534
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	994	995

Data Submission Information

	BGKLV19-17	BGKLV19-17
ENCODE_alias	brenton-graveley:DDX52_BGKLV19	brenton-graveley:DDX52-BGKLV19-K562
ENCODE_accession	ENCSR560RSZ	ENCSR040OWU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-17	BGKLV19-17
Sample Name	DDX52_BGKLV19_17B	DDX52_BGKLV19_17B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2882	6658

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
DDX52_BGKLV19_17B_CAGATC_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	994	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15106
DDX52_BGKLV19_17B_CAGATC_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	994	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15164
DDX52_BGKLV19_17B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	994					GRCh38	V40	DDX52_BGKLV19_17B_CAGATC_L003_R1_001.fastq.gz,DDX52_BGKLV19_17B_CAGATC_L003_R2_001.fastq.gz		ENCORE2	15222
DDX52_BGKLV19_17B_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	994					GRCh38	V40	DDX52_BGKLV19_17B/Aligned.sortedByCoord.out.bam		ENCORE2	15293
DDX52_BGKLV19_17B_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	994					GRCh38	V40	DDX52_BGKLV19_17B/Aligned.sortedByCoord.out.bam		ENCORE2	15351
DDX52_BGKLV19_17B_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	994					GRCh38	V40	DDX52_BGKLV19_17B/Aligned.sortedByCoord.out.bam		ENCORE2	15409
DDX52_BGKLV19_17B_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	994					GRCh38	V40	DDX52_BGKLV19_17B/Aligned.sortedByCoord.out.bam		ENCORE2	15467
DDX52_BGKLV19_17B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	994					GRCh38	V40	DDX52_BGKLV19_17B_CAGATC_L003_R1_001.fastq.gz,DDX52_BGKLV19_17B_CAGATC_L003_R2_001.fastq.gz		ENCORE2	16364
DDX52_BGKLV19_18B_ACTTGA_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	995	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15107
DDX52_BGKLV19_18B_ACTTGA_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	995	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15165
DDX52_BGKLV19_18B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	995					GRCh38	V40	DDX52_BGKLV19_18B_ACTTGA_L003_R1_001.fastq.gz,DDX52_BGKLV19_18B_ACTTGA_L003_R2_001.fastq.gz		ENCORE2	15223
DDX52_BGKLV19_18B_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	995					GRCh38	V40	DDX52_BGKLV19_18B/Aligned.sortedByCoord.out.bam		ENCORE2	15294
DDX52_BGKLV19_18B_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	995					GRCh38	V40	DDX52_BGKLV19_18B/Aligned.sortedByCoord.out.bam		ENCORE2	15352
DDX52_BGKLV19_18B_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	995					GRCh38	V40	DDX52_BGKLV19_18B/Aligned.sortedByCoord.out.bam		ENCORE2	15410
DDX52_BGKLV19_18B_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	995					GRCh38	V40	DDX52_BGKLV19_18B/Aligned.sortedByCoord.out.bam		ENCORE2	15468
DDX52_BGKLV19_18B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	995					GRCh38	V40	DDX52_BGKLV19_18B_ACTTGA_L003_R1_001.fastq.gz,DDX52_BGKLV19_18B_ACTTGA_L003_R2_001.fastq.gz		ENCORE2	16365