ENCORE eCLIP:690

Experiment Information (Status: Released)

	690	690-control
Exp_UID	690	690
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR308YNT	ENCSR832DWW
ENCODE_alias	gene-yeo:690	gene-yeo:690-control
RBP	PUM1	PUM1
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB744LEE	ENCAB744LEE
Antibody	A302-576A	A302-576A
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	404	459

Replicate Information


Rep_UID	690_01	690_02	690_INPUT
Exp UID	690	690	690
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB428AQN	ENCLB554ZYW	ENCLB406IPB
ENCODE_alias	gene-yeo:690_01	gene-yeo:690_02	gene-yeo:690_INPUT
Biosample Name	K562_012016	K562_091615	K562_012016
Biosample_ENCODE_Accession	ENCBS039CVO	ENCBS505ILK	ENCBS039CVO
Biosample_ENCODE_Alias	gene-yeo:K562_012016	gene-yeo:K562_091615	gene-yeo:K562_012016
Cell_Line	K562	K562	K562
Culture_Start_Date	2016-01-20	2015-09-16	2016-01-20
Culture_End_Date	2016-02-17	2015-10-14	2016-02-17
Passage	5	4	5

QC Stats

Experiment QC

	690	690-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	690_01	690_02	690_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	690_01	690_02	690_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	503	503	504
i7_barcode	704	704	703

Sequencing Information


Rep_UID	690_01	690_02	690_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
690_01_PUM1.R1.fastq.gz	690_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
690_01_PUM1.R2.fastq.gz	690_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
690_02_PUM1.R1.fastq.gz	690_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
690_02_PUM1.R2.fastq.gz	690_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
690_INPUT_PUM1.R1.fastq.gz	690_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
690_INPUT_PUM1.R2.fastq.gz	690_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly
GRCh38/690.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	690	final_peaks	peaks	eCLIP	GRCh38
GRCh38_690_01_PUM1.merged.bam	690_01	bam	alignments	eCLIP	GRCh38
GRCh38_690_01_PUM1.merged.r2.norm.neg.bw	690_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_690_01_PUM1.merged.r2.norm.pos.bw	690_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/690_01.basedon_690_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	690_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/690_01.basedon_690_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	690_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_690_02_PUM1.merged.bam	690_02	bam	alignments	eCLIP	GRCh38
GRCh38_690_02_PUM1.merged.r2.norm.neg.bw	690_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_690_02_PUM1.merged.r2.norm.pos.bw	690_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/690_02.basedon_690_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	690_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/690_02.basedon_690_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	690_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_690_INPUT_S1_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	690_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_690_INPUT_S1_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	690_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_690_INPUT_S1_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	690_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly
690.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	690	final_peaks	peaks	eCLIP	hg19
690_01_PUM1.merged.bam	690_01	bam	alignments	eCLIP	hg19
690_01_PUM1.merged.r2.norm.neg.bw	690_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
690_01_PUM1.merged.r2.norm.pos.bw	690_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
690_01.basedon_690_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	690_01	bed_eCLIP	peaks	eCLIP	hg19
690_01.basedon_690_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	690_01	bigBed_eCLIP	peaks	eCLIP	hg19
690_02_PUM1.merged.bam	690_02	bam	alignments	eCLIP	hg19
690_02_PUM1.merged.r2.norm.neg.bw	690_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
690_02_PUM1.merged.r2.norm.pos.bw	690_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
690_02.basedon_690_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	690_02	bed_eCLIP	peaks	eCLIP	hg19
690_02.basedon_690_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	690_02	bigBed_eCLIP	peaks	eCLIP	hg19
690_INPUT_S1_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	690_INPUT	bam	alignments	eCLIP	hg19
690_INPUT_S1_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	690_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
690_INPUT_S1_L003_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	690_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19

Data Submission Information No DCC registered objects are available for eCLIP experiment (Exp_UID=690)