DDX1 RNA-Seq in K562

General Information


RBP	DDX1
Cell_Line	K562
Method	shRNA
Exp_Name	DDX1-BGKLV24-K562
ENCODE_series_ID	ENCSR181LUC
Batch_ID	BGKLV24
Pool ID	Pool-150615
Local_Set_Name	set24
ENCODE_KD_Exp_ID	ENCSR208GPE
ENCODE_CN_Exp_ID	ENCSR667PLJ
Rep1	DDX1_BGKLV24_13_17604
Rep2	DDX1_BGKLV24_14_17605
CN1	non-target_BGKLV24_1_17594
CN2	non-target_BGKLV24_2_17595
Rep1_qPCR	89.8
Rep2_qPCR	90.5
Rep1_WB	77.3
Rep2_WB	75.0
Antibody Cat#	GTX105205
Antibody Lot#	GTX105205
Antibody DCC ID	ENCAB297EGB
Status	Released
Project	ENCODE3
ID	559

Experiment Information (Status: Released)

	BGKLV24-13	BGKLV24-13	BGKLV24-14	BGKLV24-14
idx	350	0	351	0
TRCN#_or_BGC#	TRCN0000050500	TRCN0000050500	TRCN0000050500	TRCN0000050500
shRNA_or_gRNA_sequence	CCGGGCAATCAAGGAACATAA	CCGGGCAATCAAGGAACATAA	CCGGGCAATCAAGGAACATAA	CCGGGCAATCAAGGAACATAA
PAM
Name	DDX1	DDX1	DDX1	DDX1
Sample_ID	BGKLV24-13	BGKLV24-13	BGKLV24-14	BGKLV24-14
transduction_Date	2/27/2015	2/27/2015	2/27/2015	2/27/2015
days
RBP_name	DDX1	DDX1	DDX1	DDX1
qPCR_result	89.8	89.8	90.5	90.5
Ave_qPCR	90.2	90.2
RT-qPCR_primer-F	CATGGTGACAGAAAGCCTCA	CATGGTGACAGAAAGCCTCA
RT-qPCR_primer-R	AGCAGCTACATCTGTGCAAATC	AGCAGCTACATCTGTGCAAATC
protein_conc	3240	3240	3416	3416
WB_result	77.3	61.6	75.0	64.7
Ave_WB	76.1	63.1
WB_DONE_date	5/19/2015	3/27/2019		WES
MW	82kDa	82kDa
IP	1		1
antibody_Cat#	GTX105205	703141	GTX105205	703141
Antibody DCC ID	ENCAB297EGB	ENCAB741VRO	ENCAB297EGB
submitted_to_DCC_date	8/6/2015	4/17/2019
Rep1_TPM	191.965914	0	0	0
Rep2_TPM	104.283174	0	0	0
Action
Library_start_date	5/22/2015		5/22/2015
repeat_library
Note
ID	397	399	398	400

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
DDX1	Product_ID: 703141 Lot_ID: None Source: Thermo Fisher Target Name: DDX1-human

Experiment Status

	BGKLV24-13	BGKLV24-14
Sample_ID	BGKLV24-13	BGKLV24-14
Sample Name	DDX1_BGKLV24_13_17604	DDX1_BGKLV24_14_17605
Sample Name	DDX1_BGKLV24_13_17604	DDX1_BGKLV24_14_17605
RBP	DDX1	DDX1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	856	857

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-13	BGKLV24-14
Sample #
Sample Name	DDX1-BGKLV24-13	DDX1-BGKLV24-14
Sample_Name_Alias	DDX1_BGKLV24_13_17604	DDX1_BGKLV24_14_17605
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-05-22
Lib_ID	Lib-150522	Lib-150522
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/D2.png	DNA_Library_LV21-24/set1/E2.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/A2.png	RNA_Library_LV20-22-24/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-13	BGKLV24-14
RBP	DDX1	DDX1
Batch_ID	BGKLV24	BGKLV24
WB_result	77.300	75.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2544	2545

Sequencing Information

	BGKLV24-13	BGKLV24-14
Sample_ID	BGKLV24-13	BGKLV24-14
Sample Name	DDX1_BGKLV24_13_17604	DDX1_BGKLV24_14_17605
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set24	set24
total_reads	34,920,000	39,540,000
total_aligned_reads	32,537,102	37,044,572
unique_aligned_reads	29,796,548	34,051,222
percent_uniqueAligned	0.85328	0.86118
correlation_replicates	0.966062	0.966062
spikein_reads	147,290	188,878
percent_spikeins	0.00422	0.00478
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1078	1079

Data Submission Information

	BGKLV24-13	BGKLV24-13
ENCODE_alias	brenton-graveley:DDX1_BGKLV24	brenton-graveley:DDX1-BGKLV24-K562
ENCODE_accession	ENCSR208GPE	ENCSR181LUC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-13	BGKLV24-13
Sample Name	DDX1_BGKLV24_13_17604	DDX1_BGKLV24_13_17604
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2979	6638

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_BGKLV24_13_17604_TTAGGC_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1078	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17190
DDX1_BGKLV24_13_17604_TTAGGC_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1078	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17226
DDX1_BGKLV24_13_17604_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1078					GRCh38	V40	DDX1_BGKLV24_13_17604_TTAGGC_L006_R1_001.fastq.gz,DDX1_BGKLV24_13_17604_TTAGGC_L006_R2_001.fastq.gz		ENCORE2	17262
DDX1_BGKLV24_13_17604_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1078					GRCh38	V40	DDX1_BGKLV24_13_17604/Aligned.sortedByCoord.out.bam		ENCORE2	17298
DDX1_BGKLV24_13_17604_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1078					GRCh38	V40	DDX1_BGKLV24_13_17604/Aligned.sortedByCoord.out.bam		ENCORE2	17334
DDX1_BGKLV24_13_17604_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1078					GRCh38	V40	DDX1_BGKLV24_13_17604/Aligned.sortedByCoord.out.bam		ENCORE2	17370
DDX1_BGKLV24_13_17604_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1078					GRCh38	V40	DDX1_BGKLV24_13_17604/Aligned.sortedByCoord.out.bam		ENCORE2	17406
DDX1_BGKLV24_13_17604_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1078					GRCh38	V40	DDX1_BGKLV24_13_17604_TTAGGC_L006_R1_001.fastq.gz,DDX1_BGKLV24_13_17604_TTAGGC_L006_R2_001.fastq.gz		ENCORE2	17442
DDX1_BGKLV24_14_17605_TGACCA_L006_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1079	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE3	17191
DDX1_BGKLV24_14_17605_TGACCA_L006_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1079	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE3	17227
DDX1_BGKLV24_14_17605_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1079					GRCh38	V40	DDX1_BGKLV24_14_17605_TGACCA_L006_R1_001.fastq.gz,DDX1_BGKLV24_14_17605_TGACCA_L006_R2_001.fastq.gz		ENCORE2	17263
DDX1_BGKLV24_14_17605_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1079					GRCh38	V40	DDX1_BGKLV24_14_17605/Aligned.sortedByCoord.out.bam		ENCORE2	17299
DDX1_BGKLV24_14_17605_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1079					GRCh38	V40	DDX1_BGKLV24_14_17605/Aligned.sortedByCoord.out.bam		ENCORE2	17335
DDX1_BGKLV24_14_17605_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1079					GRCh38	V40	DDX1_BGKLV24_14_17605/Aligned.sortedByCoord.out.bam		ENCORE2	17371
DDX1_BGKLV24_14_17605_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1079					GRCh38	V40	DDX1_BGKLV24_14_17605/Aligned.sortedByCoord.out.bam		ENCORE2	17407
DDX1_BGKLV24_14_17605_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1079					GRCh38	V40	DDX1_BGKLV24_14_17605_TGACCA_L006_R1_001.fastq.gz,DDX1_BGKLV24_14_17605_TGACCA_L006_R2_001.fastq.gz		ENCORE2	17443