DDX5 RNA-Seq in HepG2

General Information


RBP	DDX5
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX5-BGHLV30-HepG2
ENCODE_series_ID	ENCSR295JYN
Batch_ID	BGHLV30
Pool ID	Pool-160425
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR808FBR
ENCODE_CN_Exp_ID	ENCSR776SXA
Rep1	DDX5_BGHLV30-25B
Rep2	DDX5_BGHLV30-26B
CN1	NT_BGHLV30-1B
CN2	NT_BGHLV30-2B
Rep1_qPCR	66.8
Rep2_qPCR	72.7
Rep1_WB
Rep2_WB
Antibody Cat#	GTX100234
Antibody Lot#	LOT# 39274
Antibody DCC ID	ENCAB749MOE
Status	Released
Project	ENCODE3
ID	690

Experiment Information (Status: Released)

	BGHLV30-25	BGHLV30-25	BGHLV30-26	BGHLV30-26
idx	709	711	710	712
TRCN#_or_BGC#	TRCN0000001130	TRCN0000001130	TRCN0000001130	TRCN0000001130
shRNA_or_gRNA_sequence	GCTCCTATTCTGATTGCTACA	GCTCCTATTCTGATTGCTACA	GCTCCTATTCTGATTGCTACA	GCTCCTATTCTGATTGCTACA
PAM
Name	DDX5_30	DDX5_30	DDX5_30	DDX5_30
Sample_ID	BGHLV30-25	BGHLV30-25	BGHLV30-26	BGHLV30-26
transduction_Date	8/25/2015	8/25/2015	8/25/2015	8/25/2015
days
RBP_name	DDX5	DDX5	DDX5	DDX5
qPCR_result	66.8	66.8	72.7	72.7
Ave_qPCR	69.8	69.8
RT-qPCR_primer-F	cccaagttgcttcagttggt	cccaagttgcttcagttggt
RT-qPCR_primer-R	gtatctgtcccgacggtcat	gtatctgtcccgacggtcat
protein_conc	4235	4235	4564	4564
WB_result		98.5		99.4
Ave_WB	no clear band	98.9	no clear band
WB_DONE_date	9/9/2015	3/3/2016	2/26/2016, 3/3/16
MW	69kDa	69kDa	WES	FU'S
IP	1		1	Cell Signa
antibody_Cat#	GTX100234	#9877	GTX100234	#9877
Antibody DCC ID		ENCAB946VDH		ENCAB946VDH
submitted_to_DCC_date		3/8/2016
Rep1_TPM	181.9	181.9	0	0
Rep2_TPM	211.7	211.7	0	0
Action
Library_start_date		3/10/2016		3/10/2016
repeat_library
Note
ID	2796	2798	2797	2799

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX5	Product_ID: 9877 Lot_ID: 1 Source: Cell Signaling Technology Target Name: DDX5-human

Experiment Status

	BGHLV30-25	BGHLV30-26
Sample_ID	BGHLV30-25	BGHLV30-26
Sample Name	DDX5_BGHLV30-25B	DDX5_BGHLV30-26B
Sample Name	DDX5_BGHLV30-25B	DDX5_BGHLV30-26B
RBP	DDX5	DDX5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1187	1188

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-25	BGHLV30-26
Sample #
Sample Name	DDX5-BGHLV30-25B	DDX5-BGHLV30-26B
Sample_Name_Alias	DDX5_BGHLV30-25B	DDX5_BGHLV30-26B
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-10	2016-03-10
Lib_ID	Lib-160310	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV30-25B_31-1B/set1/A1.png	DNA_Library_LV33-34-25B-32/set1/D12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E5.png	RNA_Library_LV29-30-31-32/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-25	BGHLV30-26
RBP	DDX5	DDX5
Batch_ID	BGHLV30	BGHLV30
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2872	2873

Sequencing Information

	BGHLV30-25	BGHLV30-26
Sample_ID	BGHLV30-25	BGHLV30-26
Sample Name	DDX5_BGHLV30-25B	DDX5_BGHLV30-26B
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set30	set30
total_reads	79,919,584	85,761,484
total_aligned_reads	56,820,614	62,702,788
unique_aligned_reads	53,508,042	59,076,030
percent_uniqueAligned	0.66952	0.68884
correlation_replicates	0.995427	0.995427
spikein_reads	149,536	170,138
percent_spikeins	0.00187	0.00198
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1521	1522

Data Submission Information

	BGHLV30-25	BGHLV30-25
ENCODE_alias	brenton-graveley:DDX5_BGHLV30	brenton-graveley:DDX5-BGHLV30-HepG2
ENCODE_accession	ENCSR808FBR	ENCSR295JYN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-25	BGHLV30-25
Sample Name	DDX5_BGHLV30-25B	DDX5_BGHLV30-25B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3133	6655

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
DDX5_BGHLV30-25B_GTCCGC_L007_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1521	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1B_ATGTCA_L007_001.R1.fastq.gz,NT_BGHLV30-2B_CCGTCC_L007_001.R1.fastq.gz	ENCODE3	20708
DDX5_BGHLV30-25B_GTCCGC_L007_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1521	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1B_ATGTCA_L007_001.R2.fastq.gz,NT_BGHLV30-2B_CCGTCC_L007_001.R2.fastq.gz	ENCODE3	20742
DDX5_BGHLV30-25B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1521					GRCh38	V40	DDX5_BGHLV30-25B_GTCCGC_L007_001.R1.fastq.gz,DDX5_BGHLV30-25B_GTCCGC_L007_001.R2.fastq.gz		ENCORE2	20776
DDX5_BGHLV30-25B_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1521					GRCh38	V40	DDX5_BGHLV30-25B/Aligned.sortedByCoord.out.bam		ENCORE2	20810
DDX5_BGHLV30-25B_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1521					GRCh38	V40	DDX5_BGHLV30-25B/Aligned.sortedByCoord.out.bam		ENCORE2	20844
DDX5_BGHLV30-25B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1521					GRCh38	V40	DDX5_BGHLV30-25B/Aligned.sortedByCoord.out.bam		ENCORE2	20878
DDX5_BGHLV30-25B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1521					GRCh38	V40	DDX5_BGHLV30-25B/Aligned.sortedByCoord.out.bam		ENCORE2	20912
DDX5_BGHLV30-25B_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1521					GRCh38	V40	DDX5_BGHLV30-25B_GTCCGC_L007_001.R1.fastq.gz,DDX5_BGHLV30-25B_GTCCGC_L007_001.R2.fastq.gz		ENCORE2	20946
DDX5_BGHLV30-26B_GTGAAA_L007_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1522	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1B_ATGTCA_L007_001.R1.fastq.gz,NT_BGHLV30-2B_CCGTCC_L007_001.R1.fastq.gz	ENCODE3	20709
DDX5_BGHLV30-26B_GTGAAA_L007_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1522	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1B_ATGTCA_L007_001.R2.fastq.gz,NT_BGHLV30-2B_CCGTCC_L007_001.R2.fastq.gz	ENCODE3	20743
DDX5_BGHLV30-26B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1522					GRCh38	V40	DDX5_BGHLV30-26B_GTGAAA_L007_001.R1.fastq.gz,DDX5_BGHLV30-26B_GTGAAA_L007_001.R2.fastq.gz		ENCORE2	20777
DDX5_BGHLV30-26B_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1522					GRCh38	V40	DDX5_BGHLV30-26B/Aligned.sortedByCoord.out.bam		ENCORE2	20811
DDX5_BGHLV30-26B_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1522					GRCh38	V40	DDX5_BGHLV30-26B/Aligned.sortedByCoord.out.bam		ENCORE2	20845
DDX5_BGHLV30-26B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1522					GRCh38	V40	DDX5_BGHLV30-26B/Aligned.sortedByCoord.out.bam		ENCORE2	20879
DDX5_BGHLV30-26B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1522					GRCh38	V40	DDX5_BGHLV30-26B/Aligned.sortedByCoord.out.bam		ENCORE2	20913
DDX5_BGHLV30-26B_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1522					GRCh38	V40	DDX5_BGHLV30-26B_GTGAAA_L007_001.R1.fastq.gz,DDX5_BGHLV30-26B_GTGAAA_L007_001.R2.fastq.gz		ENCORE2	20947