ENCORE eCLIP:4221

Experiment Information (Status: Released)

	4221-control	4221
Exp_UID	4221	4221
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR932CJI	ENCSR539DEW
ENCODE_alias	gene-yeo:4221-control	gene-yeo:4221
RBP	TIAL1	TIAL1
Cell_Line	K562	K562
Batch	batch26	batch26
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB050ZSG	ENCAB050ZSG
Antibody	RN059PW	RN059PW
Lot_num	001	001
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.612332	1.612332
rescue_GRCh38	2.550543	2.550543
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	499	500

Replicate Information


Rep_UID	4221_01	4221_02	4221_INPUT1	4221_INPUT2
Exp UID	4221	4221	4221	4221
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

	4221-control	4221
Self_consistency_hg38	1.612332	1.612332
rescue_GRCh38	2.550543	2.550543

Replicate QC


Rep_UID	4221_01	4221_02	4221_INPUT1	4221_INPUT2
eCT	7.40	7.80	5.90	5.90
Usable_reads	10670006	12627632	3234324	5750189
Entropy_hg38	0.401172	0.418549

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4221_01	4221_02	4221_INPUT1	4221_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	GGCTCTGA	GGCTCTGA	CCTATCCT	CCTATCCT
i7_barcode	ATTCAGAA	GAATTCGT	ATTCAGAA	GAATTCGT

Sequencing Information


Rep_UID	4221_01	4221_02	4221_INPUT1	4221_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
4221_clip1_S64_L008_R1_001.fastq.gz	4221_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4221_clip2_S66_L008_R1_001.fastq.gz	4221_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4221_input1_S63_L008_R1_001.fastq.gz	4221_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4221_input2_S65_L008_R1_001.fastq.gz	4221_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4221_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4221_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4221_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4221_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4221_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4221_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4221_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4221_CLIP1_rep1.vs.4221_CLIP2_rep2.sorted.nh.bb	4221_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4221_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4221_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4221_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4221_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4221_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4221_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4221_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4221_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4221_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4221_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4221_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4221_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4221_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4221_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4221_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4221_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch26.4221_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4221_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:4221-control	ENCSR932CJI	experiment	eCLIP	4221-TIAL1-K562-control	Released	ENCODE4
gene-yeo:4221	ENCSR539DEW	experiment	eCLIP	4221-TIAL1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4221_01	ENCLB604HLH	library	eCLIP	4221_01	Released	ENCODE4
gene-yeo:L-K562_102015-4221_02	ENCLB846EUR	library	eCLIP	4221_02	Released	ENCODE4
gene-yeo:L-K562_081815-4221_INPUT1	ENCLB039RJE	library	eCLIP	4221_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4221_INPUT2	ENCLB188UMW	library	eCLIP	4221_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4221_clip1_S64_L008_R1_001.fastq.gz	ENCFF846ROY	file_fastq	eCLIP	4221_01	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF077EYK	file_bam	eCLIP	4221_01	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF197WPO	file_bam	eCLIP	4221_01	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF794VGM	file_bw	eCLIP	4221_01	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF531EDH	file_bw	eCLIP	4221_01	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF635YZV	file_quantifications	eCLIP	4221_01	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF886RMI	file_bed	eCLIP	4221_01	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF825APS	file_bb	eCLIP	4221_01	Released	ENCODE4
gene-yeo:4221_clip2_S66_L008_R1_001.fastq.gz	ENCFF460CNR	file_fastq	eCLIP	4221_02	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF071RPR	file_bam	eCLIP	4221_02	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF832PGP	file_bam	eCLIP	4221_02	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF353RRW	file_bw	eCLIP	4221_02	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF505NET	file_bw	eCLIP	4221_02	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF476OGU	file_quantifications	eCLIP	4221_02	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF845VVL	file_bed	eCLIP	4221_02	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF327SWS	file_bb	eCLIP	4221_02	Released	ENCODE4
gene-yeo:4221_input1_S63_L008_R1_001.fastq.gz	ENCFF856YWX	file_fastq	eCLIP	4221_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF667HNE	file_bam	eCLIP	4221_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF844PKV	file_bam	eCLIP	4221_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF979JFN	file_bw	eCLIP	4221_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF316WOW	file_bw	eCLIP	4221_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF316CZN	file_quantifications	eCLIP	4221_INPUT1	Released	ENCODE4
gene-yeo:4221_input2_S65_L008_R1_001.fastq.gz	ENCFF170NDE	file_fastq	eCLIP	4221_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF873ZHQ	file_bam	eCLIP	4221_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF977VQI	file_bam	eCLIP	4221_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF053HUP	file_bw	eCLIP	4221_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF746GSQ	file_bw	eCLIP	4221_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch26.4221_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF908IMA	file_quantifications	eCLIP	4221_INPUT2	Released	ENCODE4