ENCORE eCLIP:4231

Experiment Information (Status: Released)

	4231-control	4231
Exp_UID	4231	4231
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR561QXJ	ENCSR293FWY
ENCODE_alias	gene-yeo:4231-control	gene-yeo:4231
RBP	DDX1	DDX1
Cell_Line	K562	K562
Batch	batch25	batch25
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB741VRO	ENCAB741VRO
Antibody	703141	703141
Lot_num	Unknown	Unknown
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.835938	1.835938
rescue_GRCh38	1.523575	1.523575
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	501	502

Replicate Information


Rep_UID	4231_01	4231_02	4231_INPUT1	4231_INPUT2
Exp UID	4231	4231	4231	4231
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_102015	K562_091615	K562_102015	K562_091615
Biosample_ENCODE_Accession	ENCBS592SHU	ENCBS505ILK	ENCBS592SHU	ENCBS505ILK
Biosample_ENCODE_Alias	gene-yeo:K562_102015	gene-yeo:K562_091615	gene-yeo:K562_102015	gene-yeo:K562_091615
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-10-20	2015-09-16	2015-10-20	2015-09-16
Culture_End_Date	2015-11-17	2015-10-14	2015-11-17	2015-10-14
Passage	5	4	5	4

QC Stats

Experiment QC

	4231-control	4231
Self_consistency_hg38	1.835938	1.835938
rescue_GRCh38	1.523575	1.523575

Replicate QC


Rep_UID	4231_01	4231_02	4231_INPUT1	4231_INPUT2
eCT	14.50	14.00	8.10	7.20
Usable_reads	3238945	4451577	3289241	4912817
Entropy_hg38	0.344413	0.382805

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4231_01	4231_02	4231_INPUT1	4231_INPUT2
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse	reverse
inline_barcode_1
inline_barcode_2
i5_barcode	GTACTGAC	GTACTGAC	CAGGACGT	CAGGACGT
i7_barcode	ATTCAGAA	GAATTCGT	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4231_01	4231_02	4231_INPUT1	4231_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	HiSeq4000	HiSeq4000	HiSeq4000	HiSeq4000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4231_CLIP1_S99_L007_R1_001.fastq.gz	4231_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4231_CLIP2_S101_L007_R1_001.fastq.gz	4231_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4231_INPUT1_S98_L007_R1_001.fastq.gz	4231_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4231_INPUT2_S100_L007_R1_001.fastq.gz	4231_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4231_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4231_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4231_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4231_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4231_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4231_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4231_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4231_CLIP1_rep1.vs.4231_CLIP2_rep2.sorted.nh.bb	4231_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4231_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4231_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4231_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4231_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4231_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4231_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4231_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4231_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4231_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4231_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4231_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4231_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4231_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4231_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4231_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4231_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch25.4231_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4231_INPUT2	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29

Data Submission Information

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4231-control	ENCSR561QXJ	experiment	eCLIP	4231-DDX1-K562-control	Released	ENCODE4
gene-yeo:4231	ENCSR293FWY	experiment	eCLIP	4231-DDX1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_102015-4231_01	ENCLB899EWW	library	eCLIP	4231_01	Released	ENCODE4
gene-yeo:L-K562_091615-4231_02	ENCLB569OYB	library	eCLIP	4231_02	Released	ENCODE4
gene-yeo:L-K562_102015-4231_INPUT1	ENCLB826VGA	library	eCLIP	4231_INPUT1	Released	ENCODE4
gene-yeo:L-K562_091615-4231_INPUT2	ENCLB873ZDL	library	eCLIP	4231_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4231_CLIP1_S99_L007_R1_001.fastq.gz	ENCFF926UWX	file_fastq	eCLIP	4231_01	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF171YQS	file_bam	eCLIP	4231_01	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF184QVM	file_bam	eCLIP	4231_01	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF037YQK	file_bw	eCLIP	4231_01	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF490IGM	file_bw	eCLIP	4231_01	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF878QES	file_quantifications	eCLIP	4231_01	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF535FFL	file_bed	eCLIP	4231_01	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF619DGS	file_bb	eCLIP	4231_01	Released	ENCODE4
gene-yeo:4231_CLIP2_S101_L007_R1_001.fastq.gz	ENCFF507WKA	file_fastq	eCLIP	4231_02	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF483TEX	file_bam	eCLIP	4231_02	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF484APP	file_bam	eCLIP	4231_02	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF790WYG	file_bw	eCLIP	4231_02	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF788XWZ	file_bw	eCLIP	4231_02	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF597KCH	file_quantifications	eCLIP	4231_02	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF494PHH	file_bed	eCLIP	4231_02	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF776LMZ	file_bb	eCLIP	4231_02	Released	ENCODE4
gene-yeo:4231_INPUT1_S98_L007_R1_001.fastq.gz	ENCFF207BBK	file_fastq	eCLIP	4231_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF200JWN	file_bam	eCLIP	4231_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF469LIC	file_bam	eCLIP	4231_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF730QUL	file_bw	eCLIP	4231_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF696JPM	file_bw	eCLIP	4231_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF869EFK	file_quantifications	eCLIP	4231_INPUT1	Released	ENCODE4
gene-yeo:4231_INPUT2_S100_L007_R1_001.fastq.gz	ENCFF920MUN	file_fastq	eCLIP	4231_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF882DPK	file_bam	eCLIP	4231_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF809EQN	file_bam	eCLIP	4231_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF789HTG	file_bw	eCLIP	4231_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF260CPG	file_bw	eCLIP	4231_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch25.4231_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF294IPX	file_quantifications	eCLIP	4231_INPUT2	Released	ENCODE4