ENCORE eCLIP:416

WRN eCLIP in K562

Experiment Information (Status: Released)

	416	416-control
Exp_UID	416	416
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR038JME	ENCSR925ZRV
ENCODE_alias	gene-yeo:416	gene-yeo:416-control
RBP	WRN	WRN
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB362RRM	ENCAB362RRM
Antibody	GTX101081	GTX101081
Lot_num	39812	39812
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38
rescue_GRCh38
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	382	437

Replicate Information


Rep_UID	416_01	416_02	416_INPUT
Exp UID	416	416	416
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB827QDN	ENCLB233CTD	ENCLB915LFT
ENCODE_alias	gene-yeo:416_01	gene-yeo:416_02	gene-yeo:416_INPUT
Biosample Name	K562_040915	K562_051215	K562_040915
Biosample_ENCODE_Accession	ENCBS931MQO	ENCBS489LOC	ENCBS931MQO
Biosample_ENCODE_Alias	gene-yeo:K562_040915	gene-yeo:K562_051215	gene-yeo:K562_040915
Cell_Line	K562	K562	K562
Culture_Start_Date	2015-04-09	2015-05-12	2015-04-09
Culture_End_Date	2015-05-08	2015-06-11	2015-05-08
Passage	5	4	5

QC Stats

Experiment QC

	416	416-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	416_01	416_02	416_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	416_01	416_02	416_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	A01	C01	none
inline_barcode_2	B06	D08fixed	none
i5_barcode	504	504	505
i7_barcode	703	703	704

Sequencing Information


Rep_UID	416_01	416_02	416_INPUT
seq_read_type	paired-ended	paired-ended	paired-ended
read_length	50	50	50
machine
flowcell
lane

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	paired_end	read_length	platform	assay_type
416_01_WRN.R1.fastq.gz	416_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
416_01_WRN.R2.fastq.gz	416_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
416_02_WRN.R1.fastq.gz	416_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
416_02_WRN.R2.fastq.gz	416_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
416_INPUT_WRN.R1.fastq.gz	416_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
416_INPUT_WRN.R2.fastq.gz	416_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/416.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	416	final_peaks	peaks	eCLIP	GRCh38
GRCh38_416_01_WRN.merged.bam	416_01	bam	alignments	eCLIP	GRCh38
GRCh38_416_01_WRN.merged.r2.norm.neg.bw	416_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_416_01_WRN.merged.r2.norm.pos.bw	416_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/416_01.basedon_416_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	416_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/416_01.basedon_416_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	416_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_416_02_WRN.merged.bam	416_02	bam	alignments	eCLIP	GRCh38
GRCh38_416_02_WRN.merged.r2.norm.neg.bw	416_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_416_02_WRN.merged.r2.norm.pos.bw	416_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/416_02.basedon_416_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	416_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/416_02.basedon_416_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	416_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_416_INPUT_S54_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	416_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_416_INPUT_S54_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	416_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_416_INPUT_S54_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	416_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
416.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	416	final_peaks	peaks	eCLIP	hg19
416_01_WRN.merged.bam	416_01	bam	alignments	eCLIP	hg19
416_01_WRN.merged.r2.norm.neg.bw	416_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
416_01_WRN.merged.r2.norm.pos.bw	416_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
416_01.basedon_416_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	416_01	bed_eCLIP	peaks	eCLIP	hg19
416_01.basedon_416_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	416_01	bigBed_eCLIP	peaks	eCLIP	hg19
416_02_WRN.merged.bam	416_02	bam	alignments	eCLIP	hg19
416_02_WRN.merged.r2.norm.neg.bw	416_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
416_02_WRN.merged.r2.norm.pos.bw	416_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
416_02.basedon_416_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	416_02	bed_eCLIP	peaks	eCLIP	hg19
416_02.basedon_416_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	416_02	bigBed_eCLIP	peaks	eCLIP	hg19
416_INPUT_S54_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	416_INPUT	bam	alignments	eCLIP	hg19
416_INPUT_S54_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	416_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
416_INPUT_S54_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	416_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19

Data Submission Information

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4004_CLIP1_rep1.vs.4004_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF950EYJ	file_finalPeaks	eCLIP	4004	Released	ENCODE4
gene-yeo:4138_CLIP1_rep1.vs.4138_CLIP2_rep2.sorted.nh.bb	ENCFF864DDW	file_finalPeaks_bb	eCLIP	4004	Released	ENCODE4