DDX59 RNA-Seq in HepG2

General Information


RBP	DDX59
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX59-BGHLV35-HepG2
ENCODE_series_ID	ENCSR968OBA
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR598GKQ
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	DDX59_BGHLV35-15
Rep2	DDX59_BGHLV35-16
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	68.5
Rep2_qPCR	66.9
Rep1_WB	73.3
Rep2_WB	65.6
Antibody Cat#	303-028A
Antibody Lot#	303-028A
Antibody DCC ID	ENCAB112HZS
Status	Released
Project	ENCODE3
ID	732

Experiment Information (Status: Released)

	BGHLV35-15	BGHLV35-16
idx	871	872
TRCN#_or_BGC#	TRCN0000050911	TRCN0000050911
shRNA_or_gRNA_sequence	CCACAGCTTTATCGTCTGCAA	CCACAGCTTTATCGTCTGCAA
PAM
Name	DDX59	DDX59
Sample_ID	BGHLV35-15	BGHLV35-16
transduction_Date	4/29/16	4/29/16
days
RBP_name	DDX59	DDX59
qPCR_result	68.5	66.9
Ave_qPCR	67.7
RT-qPCR_primer-F	ctctgtggtgtaaagattgtgg
RT-qPCR_primer-R	caagcacttgttgttgaaaacc
protein_conc	2865	3357
WB_result	73.3	65.6
Ave_WB	69.4
WB_DONE_date	5/10/2016	WES
MW	69kDa
IP
antibody_Cat#	303-028A	303-028A
Antibody DCC ID	ENCAB112HZS	ENCAB112HZS
submitted_to_DCC_date	10/26/16
Rep1_TPM	4.3	4.3
Rep2_TPM	3.5	3.5
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	2960	2961

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX59	Product_ID: A303-028A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX59-human

Experiment Status

	BGHLV35-15	BGHLV35-16
Sample_ID	BGHLV35-15	BGHLV35-16
Sample Name	DDX59_BGHLV35-15	DDX59_BGHLV35-16
Sample Name	DDX59_BGHLV35-15	DDX59_BGHLV35-16
RBP	DDX59	DDX59
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1253	1254

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-15	BGHLV35-16
Sample #
Sample Name	DDX59-BGHLV35-15	DDX59-BGHLV35-16
Sample_Name_Alias	DDX59_BGHLV35-15	DDX59_BGHLV35-16
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set2/G1.png	DNA_Library_LV35/set2/H1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/G1.png	RNA_Library_LV35_LV36/set1/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-15	BGHLV35-16
RBP	DDX59	DDX59
Batch_ID	BGHLV35	BGHLV35
WB_result	73.300	65.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2938	2939

Sequencing Information

	BGHLV35-15	BGHLV35-16
Sample_ID	BGHLV35-15	BGHLV35-16
Sample Name	DDX59_BGHLV35-15	DDX59_BGHLV35-16
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	81,777,022	88,274,992
total_aligned_reads	64,664,754	66,865,904
unique_aligned_reads	60,723,360	62,600,136
percent_uniqueAligned	0.74255	0.70915
correlation_replicates	0.980066	0.980066
spikein_reads	115,304	125,694
percent_spikeins	0.00141	0.00142
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1587	1588

Data Submission Information

	BGHLV35-15	BGHLV35-15
ENCODE_alias	brenton-graveley:DDX59_BGHLV35	brenton-graveley:DDX59-BGHLV35-HepG2
ENCODE_accession	ENCSR598GKQ	ENCSR968OBA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-15	BGHLV35-15
Sample Name	DDX59_BGHLV35-15	DDX59_BGHLV35-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3166	6661

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_BGHLV35-15_CAGATC_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1587	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21686
DDX59_BGHLV35-15_CAGATC_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1587	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21712
DDX59_BGHLV35-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1587					GRCh38	V40	DDX59_BGHLV35-15_CAGATC_L005_001.R1.fastq.gz,DDX59_BGHLV35-15_CAGATC_L005_001.R2.fastq.gz		ENCORE2	21738
DDX59_BGHLV35-15_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1587					GRCh38	V40	DDX59_BGHLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	21764
DDX59_BGHLV35-15_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1587					GRCh38	V40	DDX59_BGHLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	21790
DDX59_BGHLV35-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1587					GRCh38	V40	DDX59_BGHLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	21816
DDX59_BGHLV35-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1587					GRCh38	V40	DDX59_BGHLV35-15/Aligned.sortedByCoord.out.bam		ENCORE2	21842
DDX59_BGHLV35-15_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1587					GRCh38	V40	DDX59_BGHLV35-15_CAGATC_L005_001.R1.fastq.gz,DDX59_BGHLV35-15_CAGATC_L005_001.R2.fastq.gz		ENCORE2	21868
DDX59_BGHLV35-16_ACTTGA_L005_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1588	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21687
DDX59_BGHLV35-16_ACTTGA_L005_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1588	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21713
DDX59_BGHLV35-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1588					GRCh38	V40	DDX59_BGHLV35-16_ACTTGA_L005_001.R1.fastq.gz,DDX59_BGHLV35-16_ACTTGA_L005_001.R2.fastq.gz		ENCORE2	21739
DDX59_BGHLV35-16_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1588					GRCh38	V40	DDX59_BGHLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	21765
DDX59_BGHLV35-16_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1588					GRCh38	V40	DDX59_BGHLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	21791
DDX59_BGHLV35-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1588					GRCh38	V40	DDX59_BGHLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	21817
DDX59_BGHLV35-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1588					GRCh38	V40	DDX59_BGHLV35-16/Aligned.sortedByCoord.out.bam		ENCORE2	21843
DDX59_BGHLV35-16_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1588					GRCh38	V40	DDX59_BGHLV35-16_ACTTGA_L005_001.R1.fastq.gz,DDX59_BGHLV35-16_ACTTGA_L005_001.R2.fastq.gz		ENCORE2	21869