ENCORE eCLIP:726

Experiment Information (Status: Released)

	726	726-control
Exp_UID	726	726
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR539BEV	ENCSR042RCU
ENCODE_alias	gene-yeo:726	gene-yeo:726-control
RBP	UPF1	UPF1
Cell_Line	HepG2	HepG2
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB730BOO	ENCAB730BOO
Antibody	RN108PW	RN108PW
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	418	473

Replicate Information


Rep_UID	726_01	726_02	726_INPUT
Exp UID	726	726	726
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB822FCH	ENCLB368JMW	ENCLB265CMC
ENCODE_alias	gene-yeo:726_01	gene-yeo:726_02	gene-yeo:726_INPUT
Biosample Name	HepG2_012016	HepG2_102015	HepG2_012016
Biosample_ENCODE_Accession	ENCBS074YUC	ENCBS575NGC	ENCBS074YUC
Biosample_ENCODE_Alias	gene-yeo:HepG2_012016	gene-yeo:HepG2_102015	gene-yeo:HepG2_012016
Cell_Line	HepG2	HepG2	HepG2
Culture_Start_Date	2016-01-20	2015-10-20	2016-01-20
Culture_End_Date	2016-02-17	2015-11-17	2016-02-17
Passage	4	4	4

QC Stats

Experiment QC

	726	726-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	726_01	726_02	726_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	726_01	726_02	726_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	A01	C01	none
inline_barcode_2	B06	D08fixed	none
i5_barcode	503	503	504
i7_barcode	703	703	704

Sequencing Information


Rep_UID	726_01	726_02	726_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
726_01_UPF1.R1.fastq.gz	726_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
726_01_UPF1.R2.fastq.gz	726_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
726_02_UPF1.R1.fastq.gz	726_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
726_02_UPF1.R2.fastq.gz	726_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
726_INPUT_UPF1.R1.fastq.gz	726_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
726_INPUT_UPF1.R2.fastq.gz	726_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly
GRCh38/726.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	726	final_peaks	peaks	eCLIP	GRCh38
GRCh38_726_01_UPF1.merged.bam	726_01	bam	alignments	eCLIP	GRCh38
GRCh38_726_01_UPF1.merged.r2.norm.neg.bw	726_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_726_01_UPF1.merged.r2.norm.pos.bw	726_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/726_01.basedon_726_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	726_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/726_01.basedon_726_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	726_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_726_02_UPF1.merged.bam	726_02	bam	alignments	eCLIP	GRCh38
GRCh38_726_02_UPF1.merged.r2.norm.neg.bw	726_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_726_02_UPF1.merged.r2.norm.pos.bw	726_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/726_02.basedon_726_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	726_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/726_02.basedon_726_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	726_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_726_INPUT_S45_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	726_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_726_INPUT_S45_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	726_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_726_INPUT_S45_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	726_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly
726.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	726	final_peaks	peaks	eCLIP	hg19
726_01_UPF1.merged.bam	726_01	bam	alignments	eCLIP	hg19
726_01_UPF1.merged.r2.norm.neg.bw	726_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
726_01_UPF1.merged.r2.norm.pos.bw	726_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
726_01.basedon_726_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	726_01	bed_eCLIP	peaks	eCLIP	hg19
726_01.basedon_726_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	726_01	bigBed_eCLIP	peaks	eCLIP	hg19
726_02_UPF1.merged.bam	726_02	bam	alignments	eCLIP	hg19
726_02_UPF1.merged.r2.norm.neg.bw	726_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
726_02_UPF1.merged.r2.norm.pos.bw	726_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
726_02.basedon_726_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	726_02	bed_eCLIP	peaks	eCLIP	hg19
726_02.basedon_726_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	726_02	bigBed_eCLIP	peaks	eCLIP	hg19
726_INPUT_S45_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	726_INPUT	bam	alignments	eCLIP	hg19
726_INPUT_S45_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	726_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
726_INPUT_S45_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	726_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=726)