ENCORE eCLIP:740

Experiment Information (Status: Released)

	740	740-control
Exp_UID	740	740
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR906ZJF	ENCSR155XOS
ENCODE_alias	gene-yeo:740	gene-yeo:740-control
RBP	SDAD1	SDAD1
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB322LZP	ENCAB322LZP
Antibody	A304-692A	A304-692A
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	424	479

Replicate Information


Rep_UID	740_01	740_02	740_INPUT
Exp UID	740	740	740
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB811QYA	ENCLB414PJC	ENCLB466AKC
ENCODE_alias	gene-yeo:740_01	gene-yeo:740_02	gene-yeo:740_INPUT
Biosample Name	K562_091615	K562_012016	K562_091615
Biosample_ENCODE_Accession	ENCBS505ILK	ENCBS039CVO	ENCBS505ILK
Biosample_ENCODE_Alias	gene-yeo:K562_091615	gene-yeo:K562_012016	gene-yeo:K562_091615
Cell_Line	K562	K562	K562
Culture_Start_Date	2015-09-16	2016-01-20	2015-09-16
Culture_End_Date	2015-10-14	2016-02-17	2015-10-14
Passage	4	5	4

QC Stats

Experiment QC

	740	740-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	740_01	740_02	740_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	740_01	740_02	740_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	A03	A01	none
inline_barcode_2	G07	B06	none
i5_barcode	503	503	504
i7_barcode	702	702	701

Sequencing Information


Rep_UID	740_01	740_02	740_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
740_01_SDAD1.R1.fastq.gz	740_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
740_01_SDAD1.R2.fastq.gz	740_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
740_02_SDAD1.R1.fastq.gz	740_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
740_02_SDAD1.R2.fastq.gz	740_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
740_INPUT_SDAD1.R1.fastq.gz	740_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
740_INPUT_SDAD1.R2.fastq.gz	740_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly
GRCh38/740.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	740	final_peaks	peaks	eCLIP	GRCh38
GRCh38_740_01_SDAD1.merged.bam	740_01	bam	alignments	eCLIP	GRCh38
GRCh38_740_01_SDAD1.merged.r2.norm.neg.bw	740_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_740_01_SDAD1.merged.r2.norm.pos.bw	740_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/740_01.basedon_740_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	740_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/740_01.basedon_740_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	740_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_740_02_SDAD1.merged.bam	740_02	bam	alignments	eCLIP	GRCh38
GRCh38_740_02_SDAD1.merged.r2.norm.neg.bw	740_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_740_02_SDAD1.merged.r2.norm.pos.bw	740_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/740_02.basedon_740_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	740_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/740_02.basedon_740_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	740_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_740_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	740_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_740_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	740_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_740_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	740_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly
740.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	740	final_peaks	peaks	eCLIP	hg19
740_01_SDAD1.merged.bam	740_01	bam	alignments	eCLIP	hg19
740_01_SDAD1.merged.r2.norm.neg.bw	740_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
740_01_SDAD1.merged.r2.norm.pos.bw	740_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
740_01.basedon_740_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	740_01	bed_eCLIP	peaks	eCLIP	hg19
740_01.basedon_740_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	740_01	bigBed_eCLIP	peaks	eCLIP	hg19
740_02_SDAD1.merged.bam	740_02	bam	alignments	eCLIP	hg19
740_02_SDAD1.merged.r2.norm.neg.bw	740_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
740_02_SDAD1.merged.r2.norm.pos.bw	740_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
740_02.basedon_740_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	740_02	bed_eCLIP	peaks	eCLIP	hg19
740_02.basedon_740_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	740_02	bigBed_eCLIP	peaks	eCLIP	hg19
740_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	740_INPUT	bam	alignments	eCLIP	hg19
740_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	740_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
740_INPUT_S14_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	740_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=740)