ENCORE eCLIP:642

DDX52 eCLIP in HepG2

Experiment Information (Status: Released)

	642	642-control
Exp_UID	642	642
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR970FEW	ENCSR991LWQ
ENCODE_alias	gene-yeo:642	gene-yeo:642-control
RBP	DDX52	DDX52
Cell_Line	HepG2	HepG2
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB607JMR	ENCAB607JMR
Antibody	A303-054A	A303-054A
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	391	446

Replicate Information


Rep_UID	642_01	642_02	642_INPUT
Exp UID	642	642	642
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB219RTK	ENCLB041ILA	ENCLB018RGO
ENCODE_alias	gene-yeo:642_01	gene-yeo:642_02	gene-yeo:642_INPUT
Biosample Name	HepG2_091615	HepG2_012016	HepG2_091615
Biosample_ENCODE_Accession	ENCBS621TAB	ENCBS074YUC	ENCBS621TAB
Biosample_ENCODE_Alias	gene-yeo:HepG2_091615	gene-yeo:HepG2_012016	gene-yeo:HepG2_091615
Cell_Line	HepG2	HepG2	HepG2
Culture_Start_Date	2015-09-16	2016-01-20	2015-09-16
Culture_End_Date	2015-10-09	2016-02-17	2015-10-09
Passage	3	4	3

QC Stats

Experiment QC

	642	642-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	642_01	642_02	642_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	642_01	642_02	642_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	502	502	501
i7_barcode	704	704	703

Sequencing Information


Rep_UID	642_01	642_02	642_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
642_01_DDX52.R1.fastq.gz	642_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
642_01_DDX52.R2.fastq.gz	642_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
642_02_DDX52.R1.fastq.gz	642_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
642_02_DDX52.R2.fastq.gz	642_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
642_INPUT_DDX52.R1.fastq.gz	642_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
642_INPUT_DDX52.R2.fastq.gz	642_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/642.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	642	final_peaks	peaks	eCLIP	GRCh38
GRCh38_642_01_DDX52.merged.bam	642_01	bam	alignments	eCLIP	GRCh38
GRCh38_642_01_DDX52.merged.r2.norm.neg.bw	642_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_642_01_DDX52.merged.r2.norm.pos.bw	642_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/642_01.basedon_642_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	642_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/642_01.basedon_642_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	642_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_642_02_DDX52.merged.bam	642_02	bam	alignments	eCLIP	GRCh38
GRCh38_642_02_DDX52.merged.r2.norm.neg.bw	642_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_642_02_DDX52.merged.r2.norm.pos.bw	642_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/642_02.basedon_642_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	642_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/642_02.basedon_642_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	642_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_642_INPUT_S113_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	642_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_642_INPUT_S113_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	642_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_642_INPUT_S113_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	642_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
642.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	642	final_peaks	peaks	eCLIP	hg19
642_01_DDX52.merged.bam	642_01	bam	alignments	eCLIP	hg19
642_01_DDX52.merged.r2.norm.neg.bw	642_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
642_01_DDX52.merged.r2.norm.pos.bw	642_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
642_01.basedon_642_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	642_01	bed_eCLIP	peaks	eCLIP	hg19
642_01.basedon_642_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	642_01	bigBed_eCLIP	peaks	eCLIP	hg19
642_02_DDX52.merged.bam	642_02	bam	alignments	eCLIP	hg19
642_02_DDX52.merged.r2.norm.neg.bw	642_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
642_02_DDX52.merged.r2.norm.pos.bw	642_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
642_02.basedon_642_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	642_02	bed_eCLIP	peaks	eCLIP	hg19
642_02.basedon_642_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	642_02	bigBed_eCLIP	peaks	eCLIP	hg19
642_INPUT_S113_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	642_INPUT	bam	alignments	eCLIP	hg19
642_INPUT_S113_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	642_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
642_INPUT_S113_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	642_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:4030_CLIP1_rep1.vs.4030_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF630KXK	file_finalPeaks	eCLIP	4030	Released	ENCODE4
gene-yeo:4187_CLIP1_rep1.vs.4187_CLIP2_rep2.sorted.nh.bb	ENCFF920ZFE	file_finalPeaks_bb	eCLIP	4030	Released	ENCODE4
gene-yeo:4036_CLIP1_rep1.vs.4036_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF136CWQ	file_finalPeaks	eCLIP	4036	Released	ENCODE4
gene-yeo:4190_CLIP1_rep1.vs.4190_CLIP2_rep2.sorted.nh.bb	ENCFF493YOB	file_finalPeaks_bb	eCLIP	4036	Released	ENCODE4