DDX3X RNA-Seq in K562

General Information


RBP	DDX3X
Cell_Line	K562
Method	shRNA
Exp_Name	DDX3X-BGKLV08-K562
ENCODE_series_ID	ENCSR782XRW
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR000KYM
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	DDX3X-LV08-15
Rep2	DDX3X-LV08-16
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	70.1
Rep2_qPCR	83.9
Rep1_WB	80.1
Rep2_WB	67.9
Antibody Cat#	A300-474A
Antibody Lot#	A300-474A
Antibody DCC ID	ENCAB173JTT
Status	Released
Project	ENCODE3
ID	284

Experiment Information (Status: Released)

	BGKLV08-15	BGKLV08-16
idx	16	17
TRCN#_or_BGC#	TRCN0000000003	TRCN0000000003
shRNA_or_gRNA_sequence	CGTAGAATAGTCGAACAAGAT	CGTAGAATAGTCGAACAAGAT
PAM
Name	DDX3X	DDX3X
Sample_ID	BGKLV08-15	BGKLV08-16
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	DDX3X	DDX3X
qPCR_result	70.1	83.9
Ave_qPCR	77.0
RT-qPCR_primer-F	gccactccaggacgtctagt
RT-qPCR_primer-R	atccaacatccgatcagctt
protein_conc	2661	3090
WB_result	80.1	67.9
Ave_WB	74.0
WB_DONE_date	7/27/2015
MW	73kDa
IP	1	1
antibody_Cat#	A300-474A	A300-474A
Antibody DCC ID	ENCAB173JTT	ENCAB173JTT
submitted_to_DCC_date	8/6/2015
Rep1_TPM	78.6664618	0
Rep2_TPM	56.5583872	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	15	16

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

	BGKLV08-15	BGKLV08-16
Sample_ID	BGKLV08-15	BGKLV08-16
Sample Name	DDX3X-LV08-15	DDX3X-LV08-16
Sample Name	DDX3X-LV08-15	DDX3X-LV08-16
RBP	DDX3X	DDX3X
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	276	277

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-15	BGKLV08-16
Sample #
Sample Name	DDX3X-BGKLV08-15	DDX3X-BGKLV08-16
Sample_Name_Alias	DDX3X-LV08-15	DDX3X-LV08-16
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set1/D2.png	DNA_Library_LV08/set1/E2.png
RIN	9.0	9.4
libSample_RNA_Well	RNA_Library_LV08/set1/G2.png	RNA_Library_LV08/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-15	BGKLV08-16
RBP	DDX3X	DDX3X
Batch_ID	BGKLV08	BGKLV08
WB_result	80.100	67.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1898	1899

Sequencing Information

	BGKLV08-15	BGKLV08-16
Sample_ID	BGKLV08-15	BGKLV08-16
Sample Name	DDX3X-LV08-15	DDX3X-LV08-16
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	45,810,000	49,100,000
total_aligned_reads	40,367,136	43,656,220
unique_aligned_reads	36,866,166	39,844,778
percent_uniqueAligned	0.80476	0.81150
correlation_replicates	0.990356	0.990356
spikein_reads	408,638	494,428
percent_spikeins	0.00892	0.01007
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	598	599

Data Submission Information

	BGKLV08-15	BGKLV08-15
ENCODE_alias	brenton-graveley:DDX3X-LV08	brenton-graveley:DDX3X-BGKLV08-K562
ENCODE_accession	ENCSR000KYM	ENCSR782XRW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-15	BGKLV08-15
Sample Name	DDX3X-LV08-15	DDX3X-LV08-15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2687	6652

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-LV08-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	598					GRCh38	V40	DDX3X-LV08-15_GGCTAC_L002_R1_001.fastq.gz,DDX3X-LV08-15_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	11983
DDX3X-LV08-15_GGCTAC_L002_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	598	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12039
DDX3X-LV08-15_GGCTAC_L002_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	598	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12095
DDX3X-LV08-15_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	598					GRCh38	V40	DDX3X-LV08-15/Aligned.sortedByCoord.out.bam		ENCORE2	12151
DDX3X-LV08-15_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	598					GRCh38	V40	DDX3X-LV08-15/Aligned.sortedByCoord.out.bam		ENCORE2	12207
DDX3X-LV08-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	598					GRCh38	V40	DDX3X-LV08-15/Aligned.sortedByCoord.out.bam		ENCORE2	12263
DDX3X-LV08-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	598					GRCh38	V40	DDX3X-LV08-15/Aligned.sortedByCoord.out.bam		ENCORE2	12319
DDX3X-LV08-15_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	598					GRCh38	V40	DDX3X-LV08-15_GGCTAC_L002_R1_001.fastq.gz,DDX3X-LV08-15_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	13318
DDX3X-LV08-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	599					GRCh38	V40	DDX3X-LV08-16_CTTGTA_L002_R1_001.fastq.gz,DDX3X-LV08-16_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	11984
DDX3X-LV08-16_CTTGTA_L002_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	599	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12040
DDX3X-LV08-16_CTTGTA_L002_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	599	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12096
DDX3X-LV08-16_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	599					GRCh38	V40	DDX3X-LV08-16/Aligned.sortedByCoord.out.bam		ENCORE2	12152
DDX3X-LV08-16_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	599					GRCh38	V40	DDX3X-LV08-16/Aligned.sortedByCoord.out.bam		ENCORE2	12208
DDX3X-LV08-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	599					GRCh38	V40	DDX3X-LV08-16/Aligned.sortedByCoord.out.bam		ENCORE2	12264
DDX3X-LV08-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	599					GRCh38	V40	DDX3X-LV08-16/Aligned.sortedByCoord.out.bam		ENCORE2	12320
DDX3X-LV08-16_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	599					GRCh38	V40	DDX3X-LV08-16_CTTGTA_L002_R1_001.fastq.gz,DDX3X-LV08-16_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	13319