ENCORE eCLIP:700

Experiment Information (Status: Released)

	700	700-control
Exp_UID	700	700
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR046JHH	ENCSR533BNK
ENCODE_alias	gene-yeo:700	gene-yeo:700-control
RBP	CPEB4	CPEB4
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB442TOR	ENCAB442TOR
Antibody	RN040PW	RN040PW
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	409	464

Replicate Information


Rep_UID	700_01	700_02	700_INPUT
Exp UID	700	700	700
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB404DZZ	ENCLB790ATE	ENCLB783FXM
ENCODE_alias	gene-yeo:700_01	gene-yeo:700_02	gene-yeo:700_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

	700	700-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	700_01	700_02	700_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	700_01	700_02	700_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	504	504	503
i7_barcode	701	701	702

Sequencing Information


Rep_UID	700_01	700_02	700_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
700_01_CPEB4.R1.fastq.gz	700_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
700_01_CPEB4.R2.fastq.gz	700_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
700_02_CPEB4.R1.fastq.gz	700_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
700_02_CPEB4.R2.fastq.gz	700_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
700_INPUT_CPEB4.R1.fastq.gz	700_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
700_INPUT_CPEB4.R2.fastq.gz	700_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly
GRCh38/700.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	700	final_peaks	peaks	eCLIP	GRCh38
GRCh38_700_01_CPEB4.merged.bam	700_01	bam	alignments	eCLIP	GRCh38
GRCh38_700_01_CPEB4.merged.r2.norm.neg.bw	700_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_700_01_CPEB4.merged.r2.norm.pos.bw	700_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/700_01.basedon_700_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	700_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/700_01.basedon_700_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	700_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_700_02_CPEB4.merged.bam	700_02	bam	alignments	eCLIP	GRCh38
GRCh38_700_02_CPEB4.merged.r2.norm.neg.bw	700_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_700_02_CPEB4.merged.r2.norm.pos.bw	700_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/700_02.basedon_700_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	700_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/700_02.basedon_700_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	700_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_700_INPUT_S4_L001_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	700_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_700_INPUT_S4_L001_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	700_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_700_INPUT_S4_L001_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	700_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly
700.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	700	final_peaks	peaks	eCLIP	hg19
700_01_CPEB4.merged.bam	700_01	bam	alignments	eCLIP	hg19
700_01_CPEB4.merged.r2.norm.neg.bw	700_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
700_01_CPEB4.merged.r2.norm.pos.bw	700_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
700_01.basedon_700_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	700_01	bed_eCLIP	peaks	eCLIP	hg19
700_01.basedon_700_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	700_01	bigBed_eCLIP	peaks	eCLIP	hg19
700_02_CPEB4.merged.bam	700_02	bam	alignments	eCLIP	hg19
700_02_CPEB4.merged.r2.norm.neg.bw	700_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
700_02_CPEB4.merged.r2.norm.pos.bw	700_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
700_02.basedon_700_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	700_02	bed_eCLIP	peaks	eCLIP	hg19
700_02.basedon_700_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	700_02	bigBed_eCLIP	peaks	eCLIP	hg19
700_INPUT_S4_L001_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	700_INPUT	bam	alignments	eCLIP	hg19
700_INPUT_S4_L001_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	700_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
700_INPUT_S4_L001_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	700_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=700)