ENCORE eCLIP:4040

Experiment Information (Status: Released)

	4040-control	4040
Exp_UID	4040	4040
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR237YKY	ENCSR448GXJ
ENCODE_alias	gene-yeo:4040-control	gene-yeo:4040
RBP	GARS	GARS
Cell_Line	K562	K562
Batch	batch11a	batch11a
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB009SWM	ENCAB009SWM
Antibody	MA5-26714	MA5-26714
Lot_num	UA2693064	UA2693064
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.464567	1.464567
rescue_GRCh38	1.629310	1.629310
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	599	600

Replicate Information


Rep_UID	4040_01	4040_02	4040_INPUT1	4040_INPUT2
Exp UID	4040	4040	4040	4040
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_111915	K562_072016	K562_111915	K562_072016
Biosample_ENCODE_Accession	ENCBS344MAK	ENCBS177POD	ENCBS344MAK	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_111915	gene-yeo:K562_072016	gene-yeo:K562_111915	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-11-19	2016-07-20	2015-11-19	2016-07-20
Culture_End_Date	2015-12-11	2016-08-15	2015-12-11	2016-08-15
Passage	4	5	4	5

QC Stats

Experiment QC

	4040-control	4040
Self_consistency_hg38	1.464567	1.464567
rescue_GRCh38	1.629310	1.629310

Replicate QC


Rep_UID	4040_01	4040_02	4040_INPUT1	4040_INPUT2
eCT	14.40	14.10	3.70	5.30
Usable_reads	649210	1542898	3471163	1731728
Entropy_hg38	2.376552	1.368248

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4040_01	4040_02	4040_INPUT1	4040_INPUT2
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse	reverse
inline_barcode_1
inline_barcode_2
i5_barcode	ATAGAGGC	ATAGAGGC	TATAGCCT	TATAGCCT
i7_barcode	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4040_01	4040_02	4040_INPUT1	4040_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	HiSeq4000	HiSeq4000	HiSeq4000	HiSeq4000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4040_CLIP1_S14_L001_R1_001.fastq.gz	4040_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4040_CLIP2_S16_L001_R1_001.fastq.gz	4040_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4040_INPUT1_S13_L001_R1_001.fastq.gz	4040_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4040_INPUT2_S15_L001_R1_001.fastq.gz	4040_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4040_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4040_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4040_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4040_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4040_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4040_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4040_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4040_CLIP1_rep1.vs.4040_CLIP2_rep2.sorted.nh.bb	4040_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4040_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4040_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4040_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4040_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4040_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4040_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4040_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4040_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4040_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4040_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4040_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4040_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4040_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4040_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4040_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4040_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4040_INPUT2	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29

Data Submission Information

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4040-control	ENCSR237YKY	experiment	eCLIP	4040-GARS-K562-control	Released	ENCODE4
gene-yeo:4040	ENCSR448GXJ	experiment	eCLIP	4040-GARS-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4040_01	ENCLB630NXD	library	eCLIP	4040_01	Released	ENCODE4
gene-yeo:L-K562_072016-4040_02	ENCLB505WYK	library	eCLIP	4040_02	Released	ENCODE4
gene-yeo:L-K562_111915-4040_INPUT1	ENCLB335WMG	library	eCLIP	4040_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4040_INPUT2	ENCLB542ZZE	library	eCLIP	4040_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4040_CLIP1_S14_L001_R1_001.fastq.gz	ENCFF530TJP	file_fastq	eCLIP	4040_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF212MXS	file_bam	eCLIP	4040_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF548HWJ	file_bam	eCLIP	4040_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF293RPW	file_bw	eCLIP	4040_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF358EEW	file_bw	eCLIP	4040_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF673SBQ	file_quantifications	eCLIP	4040_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF223VLH	file_bed	eCLIP	4040_01	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF129LEK	file_bb	eCLIP	4040_01	Released	ENCODE4
gene-yeo:4040_CLIP2_S16_L001_R1_001.fastq.gz	ENCFF432GIZ	file_fastq	eCLIP	4040_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF221NHT	file_bam	eCLIP	4040_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF852FHN	file_bam	eCLIP	4040_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF945JTL	file_bw	eCLIP	4040_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF039LSL	file_bw	eCLIP	4040_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF751AFU	file_quantifications	eCLIP	4040_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF371VBO	file_bed	eCLIP	4040_02	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF597FSD	file_bb	eCLIP	4040_02	Released	ENCODE4
gene-yeo:4040_INPUT1_S13_L001_R1_001.fastq.gz	ENCFF079TBA	file_fastq	eCLIP	4040_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF889BQF	file_bam	eCLIP	4040_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF327VVV	file_bam	eCLIP	4040_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF721YFF	file_bw	eCLIP	4040_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF868CLZ	file_bw	eCLIP	4040_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF257FTC	file_quantifications	eCLIP	4040_INPUT1	Released	ENCODE4
gene-yeo:4040_INPUT2_S15_L001_R1_001.fastq.gz	ENCFF226DPF	file_fastq	eCLIP	4040_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF154VSV	file_bam	eCLIP	4040_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF807OEK	file_bam	eCLIP	4040_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF823OSZ	file_bw	eCLIP	4040_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF312PYQ	file_bw	eCLIP	4040_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch11a.4040_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF018JTQ	file_quantifications	eCLIP	4040_INPUT2	Released	ENCODE4