ENCORE eCLIP:4138

Experiment Information (Status: Released)

	4138-control	4138
Exp_UID	4138	4138
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR724YPP	ENCSR311SHM
ENCODE_alias	gene-yeo:4138-control	gene-yeo:4138
RBP	EIF3A	EIF3A
Cell_Line	K562	K562
Batch	batch23	batch23
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB543LFV	ENCAB543LFV
Antibody	3411S	3411S
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.683093	1.683093
rescue_GRCh38	1.433304	1.433304
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	519	520

Replicate Information


Rep_UID	4138_01	4138_02	4138_INPUT1	4138_INPUT2
Exp UID	4138	4138	4138	4138
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_081815	K562_102015	K562_081815	K562_102015
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-10-20	2015-08-18	2015-10-20
Culture_End_Date	2015-09-08	2015-11-17	2015-09-08	2015-11-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4138-control	4138
Self_consistency_hg38	1.683093	1.683093
rescue_GRCh38	1.433304	1.433304

Replicate QC


Rep_UID	4138_01	4138_02	4138_INPUT1	4138_INPUT2
eCT	9.00	9.20	7.80	8.30
Usable_reads	2631502	3504648	4020182	8113763
Entropy_hg38	2.719089	2.857692

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4138_01	4138_02	4138_INPUT1	4138_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	AGGCGAAG	AGGCGAAG	GGCTCTGA	GGCTCTGA
i7_barcode	ATTCAGAA	GAATTCGT	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4138_01	4138_02	4138_INPUT1	4138_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
4138_CLIP1_S10_L001_R1_001.fastq.gz	4138_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4138_CLIP2_S12_L001_R1_001.fastq.gz	4138_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4138_INPUT1_S9_L001_R1_001.fastq.gz	4138_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4138_INPUT2_S11_L001_R1_001.fastq.gz	4138_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4138_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4138_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4138_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4138_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4138_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4138_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4138_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4138_CLIP1_rep1.vs.4138_CLIP2_rep2.sorted.nh.bb	4138_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4138_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4138_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4138_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4138_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4138_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4138_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4138_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4138_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4138_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4138_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4138_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4138_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4138_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4138_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4138_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4138_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4138_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4138_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:4138-control	ENCSR724YPP	experiment	eCLIP	4138-EIF3A-K562-control	Released	ENCODE4
gene-yeo:4138	ENCSR311SHM	experiment	eCLIP	4138-EIF3A-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4138_01	ENCLB846DVA	library	eCLIP	4138_01	Released	ENCODE4
gene-yeo:L-K562_102015-4138_02	ENCLB571HVI	library	eCLIP	4138_02	Released	ENCODE4
gene-yeo:L-K562_081815-4138_INPUT1	ENCLB151SQY	library	eCLIP	4138_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4138_INPUT2	ENCLB883VTV	library	eCLIP	4138_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4138_CLIP1_S10_L001_R1_001.fastq.gz	ENCFF242KYF	file_fastq	eCLIP	4138_01	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF582JEX	file_bam	eCLIP	4138_01	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF931JWU	file_bam	eCLIP	4138_01	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF198TJR	file_bw	eCLIP	4138_01	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF845EOP	file_bw	eCLIP	4138_01	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF298FFE	file_quantifications	eCLIP	4138_01	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF121XVR	file_bed	eCLIP	4138_01	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF105XPO	file_bb	eCLIP	4138_01	Released	ENCODE4
gene-yeo:4138_CLIP2_S12_L001_R1_001.fastq.gz	ENCFF541MEL	file_fastq	eCLIP	4138_02	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF456WQV	file_bam	eCLIP	4138_02	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF409BXG	file_bam	eCLIP	4138_02	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF489MOM	file_bw	eCLIP	4138_02	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF994XFR	file_bw	eCLIP	4138_02	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF213JSU	file_quantifications	eCLIP	4138_02	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF376QYK	file_bed	eCLIP	4138_02	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF304SLY	file_bb	eCLIP	4138_02	Released	ENCODE4
gene-yeo:4138_INPUT1_S9_L001_R1_001.fastq.gz	ENCFF610PPR	file_fastq	eCLIP	4138_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF553TQW	file_bam	eCLIP	4138_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF868WRL	file_bam	eCLIP	4138_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF965NRR	file_bw	eCLIP	4138_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF470FLS	file_bw	eCLIP	4138_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF528EZO	file_quantifications	eCLIP	4138_INPUT1	Released	ENCODE4
gene-yeo:4138_INPUT2_S11_L001_R1_001.fastq.gz	ENCFF829NNW	file_fastq	eCLIP	4138_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF210WOW	file_bam	eCLIP	4138_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF260ILL	file_bam	eCLIP	4138_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF831MIN	file_bw	eCLIP	4138_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF525XJR	file_bw	eCLIP	4138_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4138_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF386AAM	file_quantifications	eCLIP	4138_INPUT2	Released	ENCODE4