DDX1 RNA-Seq in HepG2

General Information


RBP	DDX1
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX1-BGHLV20-HepG2
ENCODE_series_ID	ENCSR357ZAI
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR070LJO
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	DDX1-BGHLV20-11_17712
Rep2	DDX1-BGHLV20-12_17713
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	84.7
Rep2_qPCR	76.2
Rep1_WB	82.0
Rep2_WB	72.6
Antibody Cat#	GTX105205
Antibody Lot#	GTX105205
Antibody DCC ID	ENCAB297EGB
Status	Released
Project	ENCODE3
ID	491

Experiment Information (Status: Released)

	BGHLV20-11	BGHLV20-12
idx	375	376
TRCN#_or_BGC#	TRCN0000050500	TRCN0000050500
shRNA_or_gRNA_sequence	CCGGGCAATCAAGGAACATAA	CCGGGCAATCAAGGAACATAA
PAM
Name	DDX1	DDX1
Sample_ID	BGHLV20-11	BGHLV20-12
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	DDX1	DDX1
qPCR_result	84.7	76.2
Ave_qPCR	80.5
RT-qPCR_primer-F	CATGGTGACAGAAAGCCTCA
RT-qPCR_primer-R	AGCAGCTACATCTGTGCAAATC
protein_conc	5927	5171
WB_result	82.0	72.6
Ave_WB	77.3
WB_DONE_date	5/19/2015
MW	82kDa
IP	1	1
antibody_Cat#	GTX105205	GTX105205
Antibody DCC ID	ENCAB297EGB	ENCAB297EGB
submitted_to_DCC_date	8/6/2015
Rep1_TPM	135.2	0
Rep2_TPM	101.4	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2440	2441

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX1	Product_ID: GTX105205 Lot_ID: 39904 Source: GeneTex Target Name: DDX1-human

Experiment Status

	BGHLV20-11	BGHLV20-12
Sample_ID	BGHLV20-11	BGHLV20-12
Sample Name	DDX1-BGHLV20-11_17712	DDX1-BGHLV20-12_17713
Sample Name	DDX1-BGHLV20-11_17712	DDX1-BGHLV20-12_17713
RBP	DDX1	DDX1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	712	713

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-11	BGHLV20-12
Sample #
Sample Name	DDX1-BGHLV20-11	DDX1-BGHLV20-12
Sample_Name_Alias	DDX1-BGHLV20-11_17712	DDX1-BGHLV20-12_17713
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G1.png	DNA_Library_LV20-22-23/set1/H1.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A8.png	RNA_Library_LV20-22-24/set1/B8.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-11	BGHLV20-12
RBP	DDX1	DDX1
Batch_ID	BGHLV20	BGHLV20
WB_result	82.000	72.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2398	2399

Sequencing Information

	BGHLV20-11	BGHLV20-12
Sample_ID	BGHLV20-11	BGHLV20-12
Sample Name	DDX1-BGHLV20-11_17712	DDX1-BGHLV20-12_17713
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	45,180,000	40,460,000
total_aligned_reads	40,538,818	34,182,308
unique_aligned_reads	38,460,476	32,314,472
percent_uniqueAligned	0.85127	0.79868
correlation_replicates	0.995218	0.995218
spikein_reads	198,146	155,902
percent_spikeins	0.00439	0.00385
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1166	1167

Data Submission Information

	BGHLV20-11	BGHLV20-11
ENCODE_alias	brenton-graveley:DDX1-BGHLV20	brenton-graveley:DDX1-BGHLV20-HepG2
ENCODE_accession	ENCSR070LJO	ENCSR357ZAI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-11	BGHLV20-11
Sample Name	DDX1-BGHLV20-11_17712	DDX1-BGHLV20-11_17712
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2905	6637

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
DDX1-BGHLV20-11_17712_CAGATC_L001_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1166	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15590
DDX1-BGHLV20-11_17712_CAGATC_L001_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1166	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15632
DDX1-BGHLV20-11_17712_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1166					GRCh38	V40	DDX1-BGHLV20-11_17712_CAGATC_L001_R1_001.fastq.gz,DDX1-BGHLV20-11_17712_CAGATC_L001_R2_001.fastq.gz		ENCORE2	15674
DDX1-BGHLV20-11_17712_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1166					GRCh38	V40	DDX1-BGHLV20-11_17712/Aligned.sortedByCoord.out.bam		ENCORE2	15716
DDX1-BGHLV20-11_17712_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1166					GRCh38	V40	DDX1-BGHLV20-11_17712/Aligned.sortedByCoord.out.bam		ENCORE2	15758
DDX1-BGHLV20-11_17712_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1166					GRCh38	V40	DDX1-BGHLV20-11_17712/Aligned.sortedByCoord.out.bam		ENCORE2	15800
DDX1-BGHLV20-11_17712_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1166					GRCh38	V40	DDX1-BGHLV20-11_17712/Aligned.sortedByCoord.out.bam		ENCORE2	15842
DDX1-BGHLV20-11_17712_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1166					GRCh38	V40	DDX1-BGHLV20-11_17712_CAGATC_L001_R1_001.fastq.gz,DDX1-BGHLV20-11_17712_CAGATC_L001_R2_001.fastq.gz		ENCORE2	15884
DDX1-BGHLV20-12_17713_ACTTGA_L002_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1167	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15591
DDX1-BGHLV20-12_17713_ACTTGA_L002_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1167	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15633
DDX1-BGHLV20-12_17713_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1167					GRCh38	V40	DDX1-BGHLV20-12_17713_ACTTGA_L002_R1_001.fastq.gz,DDX1-BGHLV20-12_17713_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	15675
DDX1-BGHLV20-12_17713_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1167					GRCh38	V40	DDX1-BGHLV20-12_17713/Aligned.sortedByCoord.out.bam		ENCORE2	15717
DDX1-BGHLV20-12_17713_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1167					GRCh38	V40	DDX1-BGHLV20-12_17713/Aligned.sortedByCoord.out.bam		ENCORE2	15759
DDX1-BGHLV20-12_17713_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1167					GRCh38	V40	DDX1-BGHLV20-12_17713/Aligned.sortedByCoord.out.bam		ENCORE2	15801
DDX1-BGHLV20-12_17713_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1167					GRCh38	V40	DDX1-BGHLV20-12_17713/Aligned.sortedByCoord.out.bam		ENCORE2	15843
DDX1-BGHLV20-12_17713_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1167					GRCh38	V40	DDX1-BGHLV20-12_17713_ACTTGA_L002_R1_001.fastq.gz,DDX1-BGHLV20-12_17713_ACTTGA_L002_R2_001.fastq.gz		ENCORE2	15885