DDX52 RNA-Seq in HepG2

General Information


RBP	DDX52
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX52-BGHLV16-HepG2
ENCODE_series_ID	ENCSR544DKQ
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR913ZWR
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	DDX52_BGHLV16_13
Rep2	DDX52_BGHLV16_14
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	57.9
Rep2_qPCR	57.6
Rep1_WB	36.0
Rep2_WB	31.2
Antibody Cat#	A303-054A
Antibody Lot#	A303-054A
Antibody DCC ID	ENCAB607JMR
Status	Released
Project	ENCODE3
ID	414

Experiment Information (Status: Released)

	BGHLV16-13	BGHLV16-14
idx	181	182
TRCN#_or_BGC#	TRCN0000052106	TRCN0000052106
shRNA_or_gRNA_sequence	GCCAATCCAAATGCAAGCCAT	GCCAATCCAAATGCAAGCCAT
PAM
Name	DDX52_06	DDX52_06
Sample_ID	BGHLV16-13	BGHLV16-14
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	DDX52	DDX52
qPCR_result	57.9	57.6
Ave_qPCR	57.8
RT-qPCR_primer-F	ttccggaaagttggagaatc
RT-qPCR_primer-R	caattgggtcaggaagatcg
protein_conc	3319	3277
WB_result	36.0	31.2
Ave_WB	33.6
WB_DONE_date	2/23/2015
MW	67kDa
IP	1	1
antibody_Cat#	A303-054A	A303-054A
Antibody DCC ID	ENCAB607JMR	ENCAB607JMR
submitted_to_DCC_date	4/2/2015
Rep1_TPM	7.5	0
Rep2_TPM	8.3	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2246	2247

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

	BGHLV16-13	BGHLV16-14
Sample_ID	BGHLV16-13	BGHLV16-14
Sample Name	DDX52_BGHLV16_13	DDX52_BGHLV16_14
Sample Name	DDX52_BGHLV16_13	DDX52_BGHLV16_14
RBP	DDX52	DDX52
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	552	553

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-13	BGHLV16-14
Sample #
Sample Name	DDX52-BGHLV16-13	DDX52-BGHLV16-14
Sample_Name_Alias	DDX52_BGHLV16_13	DDX52_BGHLV16_14
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/C6.png	DNA_Library_LV16-17/set1/D6.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A12.png	RNA_Library_LV13-14-16/set1/B12.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-13	BGHLV16-14
RBP	DDX52	DDX52
Batch_ID	BGHLV16	BGHLV16
WB_result	36.000	31.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2236	2237

Sequencing Information

	BGHLV16-13	BGHLV16-14
Sample_ID	BGHLV16-13	BGHLV16-14
Sample Name	DDX52_BGHLV16_13	DDX52_BGHLV16_14
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	47,120,000	53,190,000
total_aligned_reads	42,308,216	47,093,782
unique_aligned_reads	39,885,002	44,433,528
percent_uniqueAligned	0.84646	0.83537
correlation_replicates	0.998676	0.998676
spikein_reads	68,534	46,888
percent_spikeins	0.00145	0.00088
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	878	879

Data Submission Information

	BGHLV16-13	BGHLV16-13
ENCODE_alias	brenton-graveley:DDX52_BGHLV16	brenton-graveley:DDX52-BGHLV16-HepG2
ENCODE_accession	ENCSR913ZWR	ENCSR544DKQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-13	BGHLV16-13
Sample Name	DDX52_BGHLV16_13	DDX52_BGHLV16_13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2844	6657

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_BGHLV16_13_TTAGGC_L006_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	878	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14278
DDX52_BGHLV16_13_TTAGGC_L006_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	878	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14304
DDX52_BGHLV16_13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	878					GRCh38	V40	DDX52_BGHLV16_13_TTAGGC_L006_R1_001.fastq.gz,DDX52_BGHLV16_13_TTAGGC_L006_R2_001.fastq.gz		ENCORE2	14330
DDX52_BGHLV16_13_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	878					GRCh38	V40	DDX52_BGHLV16_13/Aligned.sortedByCoord.out.bam		ENCORE2	14356
DDX52_BGHLV16_13_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	878					GRCh38	V40	DDX52_BGHLV16_13/Aligned.sortedByCoord.out.bam		ENCORE2	14382
DDX52_BGHLV16_13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	878					GRCh38	V40	DDX52_BGHLV16_13/Aligned.sortedByCoord.out.bam		ENCORE2	14408
DDX52_BGHLV16_13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	878					GRCh38	V40	DDX52_BGHLV16_13/Aligned.sortedByCoord.out.bam		ENCORE2	14434
DDX52_BGHLV16_13_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	878					GRCh38	V40	DDX52_BGHLV16_13_TTAGGC_L006_R1_001.fastq.gz,DDX52_BGHLV16_13_TTAGGC_L006_R2_001.fastq.gz		ENCORE2	14460
DDX52_BGHLV16_14_TGACCA_L006_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	879	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14279
DDX52_BGHLV16_14_TGACCA_L006_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	879	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14305
DDX52_BGHLV16_14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	879					GRCh38	V40	DDX52_BGHLV16_14_TGACCA_L006_R1_001.fastq.gz,DDX52_BGHLV16_14_TGACCA_L006_R2_001.fastq.gz		ENCORE2	14331
DDX52_BGHLV16_14_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	879					GRCh38	V40	DDX52_BGHLV16_14/Aligned.sortedByCoord.out.bam		ENCORE2	14357
DDX52_BGHLV16_14_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	879					GRCh38	V40	DDX52_BGHLV16_14/Aligned.sortedByCoord.out.bam		ENCORE2	14383
DDX52_BGHLV16_14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	879					GRCh38	V40	DDX52_BGHLV16_14/Aligned.sortedByCoord.out.bam		ENCORE2	14409
DDX52_BGHLV16_14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	879					GRCh38	V40	DDX52_BGHLV16_14/Aligned.sortedByCoord.out.bam		ENCORE2	14435
DDX52_BGHLV16_14_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	879					GRCh38	V40	DDX52_BGHLV16_14_TGACCA_L006_R1_001.fastq.gz,DDX52_BGHLV16_14_TGACCA_L006_R2_001.fastq.gz		ENCORE2	14461