ENCORE eCLIP:729

Experiment Information (Status: Released)

	729	729-control
Exp_UID	729	729
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR735HOK	ENCSR700UGT
ENCODE_alias	gene-yeo:729	gene-yeo:729-control
RBP	YBX3	YBX3
Cell_Line	HepG2	HepG2
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB021IRD	ENCAB021IRD
Antibody	A303-070A	A303-070A
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	419	474

Replicate Information


Rep_UID	729_01	729_02	729_INPUT
Exp UID	729	729	729
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB360MWN	ENCLB563IDV	ENCLB053AXU
ENCODE_alias	gene-yeo:729_01	gene-yeo:729_02	gene-yeo:729_INPUT
Biosample Name	HepG2_102015	HepG2_012016	HepG2_102015
Biosample_ENCODE_Accession	ENCBS575NGC	ENCBS074YUC	ENCBS575NGC
Biosample_ENCODE_Alias	gene-yeo:HepG2_102015	gene-yeo:HepG2_012016	gene-yeo:HepG2_102015
Cell_Line	HepG2	HepG2	HepG2
Culture_Start_Date	2015-10-20	2016-01-20	2015-10-20
Culture_End_Date	2015-11-17	2016-02-17	2015-11-17
Passage	4	4	4

QC Stats

Experiment QC

	729	729-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	729_01	729_02	729_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	729_01	729_02	729_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	A04	A03	none
inline_barcode_2	F05	G07	none
i5_barcode	504	504	503
i7_barcode	702	702	701

Sequencing Information


Rep_UID	729_01	729_02	729_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
729_01_YBX3.R1.fastq.gz	729_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
729_01_YBX3.R2.fastq.gz	729_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
729_02_YBX3.R1.fastq.gz	729_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
729_02_YBX3.R2.fastq.gz	729_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
729_INPUT_YBX3.R1.fastq.gz	729_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
729_INPUT_YBX3.R2.fastq.gz	729_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly
GRCh38/729.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	729	final_peaks	peaks	eCLIP	GRCh38
GRCh38_729_01_YBX3.merged.bam	729_01	bam	alignments	eCLIP	GRCh38
GRCh38_729_01_YBX3.merged.r2.norm.neg.bw	729_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_729_01_YBX3.merged.r2.norm.pos.bw	729_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/729_01.basedon_729_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	729_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/729_01.basedon_729_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	729_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_729_02_YBX3.merged.bam	729_02	bam	alignments	eCLIP	GRCh38
GRCh38_729_02_YBX3.merged.r2.norm.neg.bw	729_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_729_02_YBX3.merged.r2.norm.pos.bw	729_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/729_02.basedon_729_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	729_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/729_02.basedon_729_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	729_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_729_INPUT_S65_L007_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	729_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_729_INPUT_S65_L007_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	729_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_729_INPUT_S65_L007_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	729_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly
729.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	729	final_peaks	peaks	eCLIP	hg19
729_01_YBX3.merged.bam	729_01	bam	alignments	eCLIP	hg19
729_01_YBX3.merged.r2.norm.neg.bw	729_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
729_01_YBX3.merged.r2.norm.pos.bw	729_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
729_01.basedon_729_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	729_01	bed_eCLIP	peaks	eCLIP	hg19
729_01.basedon_729_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	729_01	bigBed_eCLIP	peaks	eCLIP	hg19
729_02_YBX3.merged.bam	729_02	bam	alignments	eCLIP	hg19
729_02_YBX3.merged.r2.norm.neg.bw	729_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
729_02_YBX3.merged.r2.norm.pos.bw	729_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
729_02.basedon_729_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	729_02	bed_eCLIP	peaks	eCLIP	hg19
729_02.basedon_729_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	729_02	bigBed_eCLIP	peaks	eCLIP	hg19
729_INPUT_S65_L007_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	729_INPUT	bam	alignments	eCLIP	hg19
729_INPUT_S65_L007_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	729_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
729_INPUT_S65_L007_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	729_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=729)