ENCORE eCLIP:645

GRWD1 eCLIP in K562

Experiment Information (Status: Released)

	645	645-control
Exp_UID	645	645
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR999YGP	ENCSR251FMT
ENCODE_alias	gene-yeo:645	gene-yeo:645-control
RBP	GRWD1	GRWD1
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB573ZJV	ENCAB573ZJV
Antibody	A301-576A	A301-576A
Lot_num	1	1
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	393	448

Replicate Information


Rep_UID	645_01	645_02	645_INPUT
Exp UID	645	645	645
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB355VZJ	ENCLB813LYA	ENCLB928RJM
ENCODE_alias	gene-yeo:645_01	gene-yeo:645_02	gene-yeo:645_INPUT
Biosample Name	K562_081815	K562_091615	K562_081815
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS505ILK	ENCBS175JIH
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_091615	gene-yeo:K562_081815
Cell_Line	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-09-16	2015-08-18
Culture_End_Date	2015-09-08	2015-10-14	2015-09-08
Passage	5	4	5

QC Stats

Experiment QC

	645	645-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	645_01	645_02	645_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	645_01	645_02	645_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	A03	A04	none
inline_barcode_2	G07	F05	none
i5_barcode	504	504	503
i7_barcode	704	704	703

Sequencing Information


Rep_UID	645_01	645_02	645_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
645_01_GRWD1.R1.fastq.gz	645_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
645_01_GRWD1.R2.fastq.gz	645_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
645_02_GRWD1.R1.fastq.gz	645_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
645_02_GRWD1.R2.fastq.gz	645_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
645_INPUT_GRWD1.R1.fastq.gz	645_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
645_INPUT_GRWD1.R2.fastq.gz	645_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/645.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	645	final_peaks	peaks	eCLIP	GRCh38
GRCh38_645_01_GRWD1.merged.bam	645_01	bam	alignments	eCLIP	GRCh38
GRCh38_645_01_GRWD1.merged.r2.norm.neg.bw	645_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_645_01_GRWD1.merged.r2.norm.pos.bw	645_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/645_01.basedon_645_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	645_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/645_01.basedon_645_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	645_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_645_02_GRWD1.merged.bam	645_02	bam	alignments	eCLIP	GRCh38
GRCh38_645_02_GRWD1.merged.r2.norm.neg.bw	645_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_645_02_GRWD1.merged.r2.norm.pos.bw	645_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/645_02.basedon_645_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	645_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/645_02.basedon_645_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	645_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_645_INPUT_S55_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	645_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_645_INPUT_S55_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	645_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_645_INPUT_S55_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	645_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
645.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	645	final_peaks	peaks	eCLIP	hg19
645_01_GRWD1.merged.bam	645_01	bam	alignments	eCLIP	hg19
645_01_GRWD1.merged.r2.norm.neg.bw	645_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
645_01_GRWD1.merged.r2.norm.pos.bw	645_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
645_01.basedon_645_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	645_01	bed_eCLIP	peaks	eCLIP	hg19
645_01.basedon_645_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	645_01	bigBed_eCLIP	peaks	eCLIP	hg19
645_02_GRWD1.merged.bam	645_02	bam	alignments	eCLIP	hg19
645_02_GRWD1.merged.r2.norm.neg.bw	645_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
645_02_GRWD1.merged.r2.norm.pos.bw	645_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
645_02.basedon_645_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	645_02	bed_eCLIP	peaks	eCLIP	hg19
645_02.basedon_645_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	645_02	bigBed_eCLIP	peaks	eCLIP	hg19
645_INPUT_S55_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	645_INPUT	bam	alignments	eCLIP	hg19
645_INPUT_S55_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	645_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
645_INPUT_S55_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	645_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:4110_CLIP1_rep1.vs.4110_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF673QBV	file_finalPeaks	eCLIP	4110	Released	ENCODE4
gene-yeo:4203_CLIP1_rep1.vs.4203_CLIP2_rep2.sorted.nh.bb	ENCFF678ILF	file_finalPeaks_bb	eCLIP	4110	Released	ENCODE4
gene-yeo:4050_CLIP1_rep1.vs.4050_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF252CWU	file_finalPeaks	eCLIP	4050	Released	ENCODE4
gene-yeo:4204_CLIP1_rep1.vs.4204_CLIP2_rep2.sorted.nh.bb	ENCFF385TUC	file_finalPeaks_bb	eCLIP	4050	Released	ENCODE4