ENCORE eCLIP:4158

Experiment Information (Status: Released)

	4158-control	4158
Exp_UID	4158	4158
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR237DZX	ENCSR145KZO
ENCODE_alias	gene-yeo:4158-control	gene-yeo:4158
RBP	CACTIN	CACTIN
Cell_Line	K562	K562
Batch	batch20	batch20
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB389VTI	ENCAB389VTI
Antibody	A303-349A	A303-349A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.687755	1.687755
rescue_GRCh38	3.400932	3.400932
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	549	550

Replicate Information


Rep_UID	4158_01	4158_02	4158_INPUT1	4158_INPUT2
Exp UID	4158	4158	4158	4158
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_081815	K562_080316	K562_081815	K562_080316
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS839QBD	ENCBS175JIH	ENCBS839QBD
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_080316	gene-yeo:K562_081815	gene-yeo:K562_080316
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-08-18	2016-08-03	2015-08-18	2016-08-03
Culture_End_Date	2015-09-08	2016-08-29	2015-09-08	2016-08-29
Passage	5	3	5	3

QC Stats

Experiment QC

	4158-control	4158
Self_consistency_hg38	1.687755	1.687755
rescue_GRCh38	3.400932	3.400932

Replicate QC


Rep_UID	4158_01	4158_02	4158_INPUT1	4158_INPUT2
eCT	12.70	12.90	7.50	9.10
Usable_reads	2306360	3126537	4061307	2993556
Entropy_hg38	0.657987	0.109791

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4158_01	4158_02	4158_INPUT1	4158_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	GGCTCTGA	TATAGCCT	CCTATCCT
i7_barcode	GAGATTCC	GAGATTCC	GAGATTCC	GAGATTCC

Sequencing Information


Rep_UID	4158_01	4158_02	4158_INPUT1	4158_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
4158_CLIP1_S10_L001_R1_001.fastq.gz	4158_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4158_CLIP2_S12_L001_R1_001.fastq.gz	4158_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4158_IN1_S9_L001_R1_001.fastq.gz	4158_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4158_IN2_S11_L001_R1_001.fastq.gz	4158_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4158_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4158_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4158_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4158_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4158_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4158_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4158_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4158_CLIP1_rep1.vs.4158_CLIP2_rep2.sorted.nh.bb	4158_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4158_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4158_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4158_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4158_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4158_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4158_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4158_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4158_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4158_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4158_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4158_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4158_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4158_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4158_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4158_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4158_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch20.4158_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4158_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:4158-control	ENCSR237DZX	experiment	eCLIP	4158-CACTIN-K562-control	Released	ENCODE4
gene-yeo:4158	ENCSR145KZO	experiment	eCLIP	4158-CACTIN-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4158_01	ENCLB867WUE	library	eCLIP	4158_01	Released	ENCODE4
gene-yeo:L-K562_080316-4158_02	ENCLB437IAC	library	eCLIP	4158_02	Released	ENCODE4
gene-yeo:L-K562_081815-4158_INPUT1	ENCLB616MSV	library	eCLIP	4158_INPUT1	Released	ENCODE4
gene-yeo:L-K562_080316-4158_INPUT2	ENCLB993CBZ	library	eCLIP	4158_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4158_CLIP1_S10_L001_R1_001.fastq.gz	ENCFF203HUB	file_fastq	eCLIP	4158_01	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF895IWQ	file_bam	eCLIP	4158_01	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF276OBL	file_bam	eCLIP	4158_01	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF413SSC	file_bw	eCLIP	4158_01	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF679AJG	file_bw	eCLIP	4158_01	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF104ANG	file_quantifications	eCLIP	4158_01	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF621NXT	file_bed	eCLIP	4158_01	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF247EBM	file_bb	eCLIP	4158_01	Released	ENCODE4
gene-yeo:4158_CLIP2_S12_L001_R1_001.fastq.gz	ENCFF853WAD	file_fastq	eCLIP	4158_02	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF281FDO	file_bam	eCLIP	4158_02	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF146IAV	file_bam	eCLIP	4158_02	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF462NON	file_bw	eCLIP	4158_02	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF518UKT	file_bw	eCLIP	4158_02	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF585TKB	file_quantifications	eCLIP	4158_02	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF799HPA	file_bed	eCLIP	4158_02	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF653UZE	file_bb	eCLIP	4158_02	Released	ENCODE4
gene-yeo:4158_IN1_S9_L001_R1_001.fastq.gz	ENCFF887URI	file_fastq	eCLIP	4158_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF034CRE	file_bam	eCLIP	4158_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF978LQT	file_bam	eCLIP	4158_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF026FTX	file_bw	eCLIP	4158_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF370MNC	file_bw	eCLIP	4158_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF364OYW	file_quantifications	eCLIP	4158_INPUT1	Released	ENCODE4
gene-yeo:4158_IN2_S11_L001_R1_001.fastq.gz	ENCFF915TEL	file_fastq	eCLIP	4158_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF238QRE	file_bam	eCLIP	4158_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF006RSX	file_bam	eCLIP	4158_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF220DED	file_bw	eCLIP	4158_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF944PRC	file_bw	eCLIP	4158_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch20.4158_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF883SDQ	file_quantifications	eCLIP	4158_INPUT2	Released	ENCODE4