DDX6 RNA-Seq in HepG2

General Information


RBP	DDX6
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX6-BGHLV12-HepG2
ENCODE_series_ID	ENCSR983ZKO
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR147ZBD
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	DDX6-BGHLV12-17
Rep2	DDX6-BGHLV12-18
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	88.7
Rep2_qPCR	94.3
Rep1_WB	95.4
Rep2_WB	94.4
Antibody Cat#	A300-460A
Antibody Lot#	A300-460A
Antibody DCC ID	ENCAB348UON
Status	Released
Project	ENCODE3
ID	333

Experiment Information (Status: Released)

	BGHLV12-17	BGHLV12-18
idx	17	18
TRCN#_or_BGC#	TRCN0000074696	TRCN0000074696
shRNA_or_gRNA_sequence	CTGATCTGTTTACCCGAGGTA	CTGATCTGTTTACCCGAGGTA
PAM
Name	DDX6	DDX6
Sample_ID	BGHLV12-17	BGHLV12-18
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	DDX6	DDX6
qPCR_result	88.7	94.3
Ave_qPCR	91.5
RT-qPCR_primer-F	TACCACAGCGAGCCTGTAGA
RT-qPCR_primer-R	TGTCACAGATCCAAACGAGC
protein_conc	3670	3369
WB_result	95.4	94.4
Ave_WB	94.9
WB_DONE_date	2/22/2016
MW	54kDa	WES
IP	1	1
antibody_Cat#	A300-460A	A300-460A
Antibody DCC ID	ENCAB348UON	ENCAB348UON
submitted_to_DCC_date	3/8/2016
Rep1_TPM	8.6	0
Rep2_TPM	8	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2064	2065

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX6	Product_ID: A300-460A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX6-human

Experiment Status

	BGHLV12-17	BGHLV12-18
Sample_ID	BGHLV12-17	BGHLV12-18
Sample Name	DDX6-BGHLV12-17	DDX6-BGHLV12-18
Sample Name	DDX6-BGHLV12-17	DDX6-BGHLV12-18
RBP	DDX6	DDX6
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	380	381

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-17	BGHLV12-18
Sample #
Sample Name	DDX6-BGHLV12-17	DDX6-BGHLV12-18
Sample_Name_Alias	DDX6-BGHLV12-17	DDX6-BGHLV12-18
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set1/C2.png	DNA_Library_LV12/set1/D2.png
RIN	9.0	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/C2.png	RNA_Library_LV12/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-17	BGHLV12-18
RBP	DDX6	DDX6
Batch_ID	BGHLV12	BGHLV12
WB_result	95.400	94.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2002	2003

Sequencing Information

	BGHLV12-17	BGHLV12-18
Sample_ID	BGHLV12-17	BGHLV12-18
Sample Name	DDX6-BGHLV12-17	DDX6-BGHLV12-18
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	72,510,000	77,600,000
total_aligned_reads	64,717,226	70,506,708
unique_aligned_reads	61,526,386	67,065,422
percent_uniqueAligned	0.84852	0.86425
correlation_replicates	0.969997	0.969997
spikein_reads	654,934	578,144
percent_spikeins	0.00903	0.00745
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	702	703

Data Submission Information

	BGHLV12-17	BGHLV12-17
ENCODE_alias	brenton-graveley:DDX6-BGHLV12	brenton-graveley:DDX6-BGHLV12-HepG2
ENCODE_accession	ENCSR147ZBD	ENCSR983ZKO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-17	BGHLV12-17
Sample Name	DDX6-BGHLV12-17	DDX6-BGHLV12-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2739	6662

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
DDX6-BGHLV12-17_GGCTAC_L002_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	702	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12759
DDX6-BGHLV12-17_GGCTAC_L002_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	702	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12828
DDX6-BGHLV12-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	702					GRCh38	V40	DDX6-BGHLV12-17_GGCTAC_L002_R1_001.fastq.gz,DDX6-BGHLV12-17_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	12898
DDX6-BGHLV12-17_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	702					GRCh38	V40	DDX6-BGHLV12-17/Aligned.sortedByCoord.out.bam		ENCORE2	12968
DDX6-BGHLV12-17_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	702					GRCh38	V40	DDX6-BGHLV12-17/Aligned.sortedByCoord.out.bam		ENCORE2	13038
DDX6-BGHLV12-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	702					GRCh38	V40	DDX6-BGHLV12-17/Aligned.sortedByCoord.out.bam		ENCORE2	13108
DDX6-BGHLV12-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	702					GRCh38	V40	DDX6-BGHLV12-17/Aligned.sortedByCoord.out.bam		ENCORE2	13178
DDX6-BGHLV12-17_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	702					GRCh38	V40	DDX6-BGHLV12-17_GGCTAC_L002_R1_001.fastq.gz,DDX6-BGHLV12-17_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	13248
DDX6-BGHLV12-18_CTTGTA_L002_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	703	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12760
DDX6-BGHLV12-18_CTTGTA_L002_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	703	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12829
DDX6-BGHLV12-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	703					GRCh38	V40	DDX6-BGHLV12-18_CTTGTA_L002_R1_001.fastq.gz,DDX6-BGHLV12-18_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	12899
DDX6-BGHLV12-18_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	703					GRCh38	V40	DDX6-BGHLV12-18/Aligned.sortedByCoord.out.bam		ENCORE2	12969
DDX6-BGHLV12-18_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	703					GRCh38	V40	DDX6-BGHLV12-18/Aligned.sortedByCoord.out.bam		ENCORE2	13039
DDX6-BGHLV12-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	703					GRCh38	V40	DDX6-BGHLV12-18/Aligned.sortedByCoord.out.bam		ENCORE2	13109
DDX6-BGHLV12-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	703					GRCh38	V40	DDX6-BGHLV12-18/Aligned.sortedByCoord.out.bam		ENCORE2	13179
DDX6-BGHLV12-18_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	703					GRCh38	V40	DDX6-BGHLV12-18_CTTGTA_L002_R1_001.fastq.gz,DDX6-BGHLV12-18_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	13249