DDX3X RNA-Seq in HepG2

General Information


RBP	DDX3X
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX3X-BGHLV12-HepG2
ENCODE_series_ID	ENCSR279BOZ
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR637JLM
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	DDX3X-BGHLV12-15
Rep2	DDX3X-BGHLV12-16
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	85.0
Rep2_qPCR	78.2
Rep1_WB	95.7
Rep2_WB	94.3
Antibody Cat#	A300-474A
Antibody Lot#	A300-474A
Antibody DCC ID	ENCAB173JTT
Status	Released
Project	ENCODE3
ID	332

Experiment Information (Status: Released)

	BGHLV12-15	BGHLV12-16
idx	15	16
TRCN#_or_BGC#	TRCN0000000003	TRCN0000000003
shRNA_or_gRNA_sequence	CGTAGAATAGTCGAACAAGAT	CGTAGAATAGTCGAACAAGAT
PAM
Name	DDX3X	DDX3X
Sample_ID	BGHLV12-15	BGHLV12-16
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	DDX3X	DDX3X
qPCR_result	85.0	78.2
Ave_qPCR	81.6
RT-qPCR_primer-F	gccactccaggacgtctagt
RT-qPCR_primer-R	atccaacatccgatcagctt
protein_conc	1338	2579
WB_result	95.7	94.3
Ave_WB	95.0
WB_DONE_date	1/22/2016
MW	73kDa	wes
IP	1	1
antibody_Cat#	A300-474A	A300-474A
Antibody DCC ID	ENCAB173JTT	ENCAB173JTT
submitted_to_DCC_date	3/8/2016
Rep1_TPM	69.3	0
Rep2_TPM	73.6	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2062	2063

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX3X	Product_ID: A300-474A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX3X-human

Experiment Status

	BGHLV12-15	BGHLV12-16
Sample_ID	BGHLV12-15	BGHLV12-16
Sample Name	DDX3X-BGHLV12-15	DDX3X-BGHLV12-16
Sample Name	DDX3X-BGHLV12-15	DDX3X-BGHLV12-16
RBP	DDX3X	DDX3X
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	378	379

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-15	BGHLV12-16
Sample #
Sample Name	DDX3X-BGHLV12-15	DDX3X-BGHLV12-16
Sample_Name_Alias	DDX3X-BGHLV12-15	DDX3X-BGHLV12-16
Index Well Position	S09	S10
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/A2.png	DNA_Library_LV12/set1/B2.png
RIN	9.1	9.2
libSample_RNA_Well	RNA_Library_LV12/set1/A2.png	RNA_Library_LV12/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-15	BGHLV12-16
RBP	DDX3X	DDX3X
Batch_ID	BGHLV12	BGHLV12
WB_result	95.700	94.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2000	2001

Sequencing Information

	BGHLV12-15	BGHLV12-16
Sample_ID	BGHLV12-15	BGHLV12-16
Sample Name	DDX3X-BGHLV12-15	DDX3X-BGHLV12-16
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	71,150,000	76,280,000
total_aligned_reads	65,794,064	69,726,042
unique_aligned_reads	62,779,740	66,425,620
percent_uniqueAligned	0.88236	0.87081
correlation_replicates	0.997557	0.997557
spikein_reads	643,302	496,726
percent_spikeins	0.00904	0.00651
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	700	701

Data Submission Information

	BGHLV12-15	BGHLV12-15
ENCODE_alias	brenton-graveley:DDX3X-BGHLV12	brenton-graveley:DDX3X-BGHLV12-HepG2
ENCODE_accession	ENCSR637JLM	ENCSR279BOZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-15	BGHLV12-15
Sample Name	DDX3X-BGHLV12-15	DDX3X-BGHLV12-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2738	6651

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
DDX3X-BGHLV12-15_GATCAG_L002_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	700	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12757
DDX3X-BGHLV12-15_GATCAG_L002_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	700	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12826
DDX3X-BGHLV12-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	700					GRCh38	V40	DDX3X-BGHLV12-15_GATCAG_L002_R1_001.fastq.gz,DDX3X-BGHLV12-15_GATCAG_L002_R2_001.fastq.gz		ENCORE2	12896
DDX3X-BGHLV12-15_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	700					GRCh38	V40	DDX3X-BGHLV12-15/Aligned.sortedByCoord.out.bam		ENCORE2	12966
DDX3X-BGHLV12-15_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	700					GRCh38	V40	DDX3X-BGHLV12-15/Aligned.sortedByCoord.out.bam		ENCORE2	13036
DDX3X-BGHLV12-15_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	700					GRCh38	V40	DDX3X-BGHLV12-15/Aligned.sortedByCoord.out.bam		ENCORE2	13106
DDX3X-BGHLV12-15_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	700					GRCh38	V40	DDX3X-BGHLV12-15/Aligned.sortedByCoord.out.bam		ENCORE2	13176
DDX3X-BGHLV12-15_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	700					GRCh38	V40	DDX3X-BGHLV12-15_GATCAG_L002_R1_001.fastq.gz,DDX3X-BGHLV12-15_GATCAG_L002_R2_001.fastq.gz		ENCORE2	13246
DDX3X-BGHLV12-16_TAGCTT_L002_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	701	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12758
DDX3X-BGHLV12-16_TAGCTT_L002_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	701	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12827
DDX3X-BGHLV12-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	701					GRCh38	V40	DDX3X-BGHLV12-16_TAGCTT_L002_R1_001.fastq.gz,DDX3X-BGHLV12-16_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	12897
DDX3X-BGHLV12-16_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	701					GRCh38	V40	DDX3X-BGHLV12-16/Aligned.sortedByCoord.out.bam		ENCORE2	12967
DDX3X-BGHLV12-16_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	701					GRCh38	V40	DDX3X-BGHLV12-16/Aligned.sortedByCoord.out.bam		ENCORE2	13037
DDX3X-BGHLV12-16_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	701					GRCh38	V40	DDX3X-BGHLV12-16/Aligned.sortedByCoord.out.bam		ENCORE2	13107
DDX3X-BGHLV12-16_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	701					GRCh38	V40	DDX3X-BGHLV12-16/Aligned.sortedByCoord.out.bam		ENCORE2	13177
DDX3X-BGHLV12-16_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	701					GRCh38	V40	DDX3X-BGHLV12-16_TAGCTT_L002_R1_001.fastq.gz,DDX3X-BGHLV12-16_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	13247