ENCORE eCLIP:670

AQR eCLIP in K562

Experiment Information (Status: Released)

	670	670-control
Exp_UID	670	670
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR606BPV	ENCSR952RGL
ENCODE_alias	gene-yeo:670	gene-yeo:670-control
RBP	AQR	AQR
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB609IGM	ENCAB609IGM
Antibody	A302-547A	A302-547A
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	397	452

Replicate Information


Rep_UID	670_01	670_02	670_INPUT
Exp UID	670	670	670
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB734VED	ENCLB086LMP	ENCLB859DBB
ENCODE_alias	gene-yeo:670_01	gene-yeo:670_02	gene-yeo:670_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

	670	670-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	670_01	670_02	670_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	670_01	670_02	670_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	502	502	501
i7_barcode	706	706	705

Sequencing Information


Rep_UID	670_01	670_02	670_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
670_01_AQR.R1.fastq.gz	670_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
670_01_AQR.R2.fastq.gz	670_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
670_02_AQR.R1.fastq.gz	670_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
670_02_AQR.R2.fastq.gz	670_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
670_INPUT_AQR.R1.fastq.gz	670_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
670_INPUT_AQR.R2.fastq.gz	670_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/670.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	670	final_peaks	peaks	eCLIP	GRCh38
GRCh38_670_01_AQR.merged.bam	670_01	bam	alignments	eCLIP	GRCh38
GRCh38_670_01_AQR.merged.r2.norm.neg.bw	670_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_670_01_AQR.merged.r2.norm.pos.bw	670_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/670_01.basedon_670_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	670_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/670_01.basedon_670_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	670_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_670_02_AQR.merged.bam	670_02	bam	alignments	eCLIP	GRCh38
GRCh38_670_02_AQR.merged.r2.norm.neg.bw	670_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_670_02_AQR.merged.r2.norm.pos.bw	670_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/670_02.basedon_670_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	670_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/670_02.basedon_670_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	670_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_670_INPUT_S62_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	670_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_670_INPUT_S62_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	670_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_670_INPUT_S62_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	670_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
670.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	670	final_peaks	peaks	eCLIP	hg19
670_01_AQR.merged.bam	670_01	bam	alignments	eCLIP	hg19
670_01_AQR.merged.r2.norm.neg.bw	670_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
670_01_AQR.merged.r2.norm.pos.bw	670_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
670_01.basedon_670_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	670_01	bed_eCLIP	peaks	eCLIP	hg19
670_01.basedon_670_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	670_01	bigBed_eCLIP	peaks	eCLIP	hg19
670_02_AQR.merged.bam	670_02	bam	alignments	eCLIP	hg19
670_02_AQR.merged.r2.norm.neg.bw	670_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
670_02_AQR.merged.r2.norm.pos.bw	670_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
670_02.basedon_670_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	670_02	bed_eCLIP	peaks	eCLIP	hg19
670_02.basedon_670_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	670_02	bigBed_eCLIP	peaks	eCLIP	hg19
670_INPUT_S62_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	670_INPUT	bam	alignments	eCLIP	hg19
670_INPUT_S62_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	670_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
670_INPUT_S62_L006_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	670_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:4044_CLIP1_rep1.vs.4044_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF566LNK	file_finalPeaks	eCLIP	4044	Released	ENCODE4
gene-yeo:4221_CLIP1_rep1.vs.4221_CLIP2_rep2.sorted.nh.bb	ENCFF393LHT	file_finalPeaks_bb	eCLIP	4044	Released	ENCODE4
gene-yeo:4040_CLIP1_rep1.vs.4040_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF390NMJ	file_finalPeaks	eCLIP	4040	Released	ENCODE4
gene-yeo:4223_CLIP1_rep1.vs.4223_CLIP2_rep2.sorted.nh.bb	ENCFF195YXF	file_finalPeaks_bb	eCLIP	4040	Released	ENCODE4