DDX59 RNA-Seq in HepG2

General Information


RBP	DDX59
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX59-BGHLV18-HepG2
ENCODE_series_ID
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR067AUG
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	DDX59_BGHLV18_3
Rep2	DDX59_BGHLV18_4
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	59.2
Rep2_qPCR	65.0
Rep1_WB	27.1
Rep2_WB	39.3
Antibody Cat#	A303-028A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB112HZS
Status	Archived
Project	ENCODE3
ID	444

Experiment Information (Status: Released)

	BGHLV18-3	BGHLV18-4
idx	303	304
TRCN#_or_BGC#	TRCN0000050908	TRCN0000050908
shRNA_or_gRNA_sequence	CCCATTCAAATGCAGATGATT	CCCATTCAAATGCAGATGATT
PAM
Name	DDX59	DDX59
Sample_ID	BGHLV18-3	BGHLV18-4
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	DDX59	DDX59
qPCR_result	59.2	65.0
Ave_qPCR	62.1
RT-qPCR_primer-F	ctctgtggtgtaaagattgtgg
RT-qPCR_primer-R	caagcacttgttgttgaaaacc
protein_conc	4635	4465
WB_result	27.1	39.3
Ave_WB	33.2
WB_DONE_date	2/22/2016
MW	69kDa	WES
IP	1IP	1IP
antibody_Cat#	A303-028A	A303-028A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	4.3	0
Rep2_TPM	3.5	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2368	2369

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV18-3	BGHLV18-4
Sample_ID	BGHLV18-3	BGHLV18-4
Sample Name	DDX59_BGHLV18_3	DDX59_BGHLV18_4
Sample Name	DDX59_BGHLV18_3	DDX59_BGHLV18_4
RBP	DDX59	DDX59
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	616	617

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-3	BGHLV18-4
Sample #
Sample Name	DDX59-BGHLV18-3	DDX59-BGHLV18-4
Sample_Name_Alias	DDX59_BGHLV18_3	DDX59_BGHLV18_4
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C1.png	DNA_Library_LV18-19/set1/D1.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A8.png	RNA_Library_LV16-17-18/set1/B8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-3	BGHLV18-4
RBP	DDX59	DDX59
Batch_ID	BGHLV18	BGHLV18
WB_result	27.100	39.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2300	2301

Sequencing Information

	BGHLV18-3	BGHLV18-4
Sample_ID	BGHLV18-3	BGHLV18-4
Sample Name	DDX59_BGHLV18_3	DDX59_BGHLV18_4
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	27,740,000	45,040,000
total_aligned_reads	25,436,832	41,612,864
unique_aligned_reads	23,999,312	39,284,718
percent_uniqueAligned	0.86515	0.87222
correlation_replicates	0.997965	0.997965
spikein_reads	89,750	117,130
percent_spikeins	0.00324	0.00260
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	942	943

Data Submission Information

	BGHLV18-3
ENCODE_alias	brenton-graveley:DDX59_BGHLV18
ENCODE_accession	ENCSR067AUG
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV18-3
Sample Name	DDX59_BGHLV18_3
Selected	Yes
Status	Released
Status_Date	2014-12-08
Project	ENCODE3

protocol_URL
ID	2825

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
DDX59_BGHLV18_3_TTAGGC_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	942	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14790
DDX59_BGHLV18_3_TTAGGC_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	942	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14828
DDX59_BGHLV18_3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	942					GRCh38	V40	DDX59_BGHLV18_3_TTAGGC_L008_R1_001.fastq.gz,DDX59_BGHLV18_3_TTAGGC_L008_R2_001.fastq.gz		ENCORE2	14866
DDX59_BGHLV18_3_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	942					GRCh38	V40	DDX59_BGHLV18_3/Aligned.sortedByCoord.out.bam		ENCORE2	14904
DDX59_BGHLV18_3_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	942					GRCh38	V40	DDX59_BGHLV18_3/Aligned.sortedByCoord.out.bam		ENCORE2	14942
DDX59_BGHLV18_3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	942					GRCh38	V40	DDX59_BGHLV18_3/Aligned.sortedByCoord.out.bam		ENCORE2	14980
DDX59_BGHLV18_3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	942					GRCh38	V40	DDX59_BGHLV18_3/Aligned.sortedByCoord.out.bam		ENCORE2	15018
DDX59_BGHLV18_3_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	942					GRCh38	V40	DDX59_BGHLV18_3_TTAGGC_L008_R1_001.fastq.gz,DDX59_BGHLV18_3_TTAGGC_L008_R2_001.fastq.gz		ENCORE2	15056
DDX59_BGHLV18_4_TGACCA_L008_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	943	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14791
DDX59_BGHLV18_4_TGACCA_L008_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	943	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14829
DDX59_BGHLV18_4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	943					GRCh38	V40	DDX59_BGHLV18_4_TGACCA_L008_R1_001.fastq.gz,DDX59_BGHLV18_4_TGACCA_L008_R2_001.fastq.gz		ENCORE2	14867
DDX59_BGHLV18_4_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	943					GRCh38	V40	DDX59_BGHLV18_4/Aligned.sortedByCoord.out.bam		ENCORE2	14905
DDX59_BGHLV18_4_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	943					GRCh38	V40	DDX59_BGHLV18_4/Aligned.sortedByCoord.out.bam		ENCORE2	14943
DDX59_BGHLV18_4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	943					GRCh38	V40	DDX59_BGHLV18_4/Aligned.sortedByCoord.out.bam		ENCORE2	14981
DDX59_BGHLV18_4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	943					GRCh38	V40	DDX59_BGHLV18_4/Aligned.sortedByCoord.out.bam		ENCORE2	15019
DDX59_BGHLV18_4_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	943					GRCh38	V40	DDX59_BGHLV18_4_TGACCA_L008_R1_001.fastq.gz,DDX59_BGHLV18_4_TGACCA_L008_R2_001.fastq.gz		ENCORE2	15057