ENCORE eCLIP:716

Experiment Information (Status: Released)

	716	716-control
Exp_UID	716	716
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR440SUX	ENCSR183FVK
ENCODE_alias	gene-yeo:716	gene-yeo:716-control
RBP	MATR3	MATR3
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB789SRM	ENCAB789SRM
Antibody	ab151714	ab151714
Lot_num	GR108745-9	GR108745-9
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	414	469

Replicate Information


Rep_UID	716_01	716_02	716_INPUT
Exp UID	716	716	716
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB921YYK	ENCLB990EAA	ENCLB426AJM
ENCODE_alias	gene-yeo:716_01	gene-yeo:716_02	gene-yeo:716_INPUT
Biosample Name	K562_081815	K562_012016	K562_081815
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS039CVO	ENCBS175JIH
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_012016	gene-yeo:K562_081815
Cell_Line	K562	K562	K562
Culture_Start_Date	2015-08-18	2016-01-20	2015-08-18
Culture_End_Date	2015-09-08	2016-02-17	2015-09-08
Passage	5	5	5

QC Stats

Experiment QC

	716	716-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	716_01	716_02	716_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	716_01	716_02	716_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	705	705	706

Sequencing Information


Rep_UID	716_01	716_02	716_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
716_01_MATR3.R1.fastq.gz	716_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
716_01_MATR3.R2.fastq.gz	716_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
716_02_MATR3.R1.fastq.gz	716_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
716_02_MATR3.R2.fastq.gz	716_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
716_INPUT_MATR3.R1.fastq.gz	716_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
716_INPUT_MATR3.R2.fastq.gz	716_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly
GRCh38/716.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	716	final_peaks	peaks	eCLIP	GRCh38
GRCh38_716_01_MATR3.merged.bam	716_01	bam	alignments	eCLIP	GRCh38
GRCh38_716_01_MATR3.merged.r2.norm.neg.bw	716_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_716_01_MATR3.merged.r2.norm.pos.bw	716_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/716_01.basedon_716_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	716_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/716_01.basedon_716_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	716_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_716_02_MATR3.merged.bam	716_02	bam	alignments	eCLIP	GRCh38
GRCh38_716_02_MATR3.merged.r2.norm.neg.bw	716_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_716_02_MATR3.merged.r2.norm.pos.bw	716_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/716_02.basedon_716_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	716_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/716_02.basedon_716_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	716_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_716_INPUT_S36_L004_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	716_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_716_INPUT_S36_L004_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	716_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_716_INPUT_S36_L004_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	716_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly
716.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	716	final_peaks	peaks	eCLIP	hg19
716_01_MATR3.merged.bam	716_01	bam	alignments	eCLIP	hg19
716_01_MATR3.merged.r2.norm.neg.bw	716_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
716_01_MATR3.merged.r2.norm.pos.bw	716_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
716_01.basedon_716_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	716_01	bed_eCLIP	peaks	eCLIP	hg19
716_01.basedon_716_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	716_01	bigBed_eCLIP	peaks	eCLIP	hg19
716_02_MATR3.merged.bam	716_02	bam	alignments	eCLIP	hg19
716_02_MATR3.merged.r2.norm.neg.bw	716_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
716_02_MATR3.merged.r2.norm.pos.bw	716_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
716_02.basedon_716_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	716_02	bed_eCLIP	peaks	eCLIP	hg19
716_02.basedon_716_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	716_02	bigBed_eCLIP	peaks	eCLIP	hg19
716_INPUT_S36_L004_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	716_INPUT	bam	alignments	eCLIP	hg19
716_INPUT_S36_L004_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	716_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
716_INPUT_S36_L004_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	716_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=716)