ENCORE eCLIP:4098

Experiment Information (Status: Released)

	4098-control	4098
Exp_UID	4098	4098
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR635EEO	ENCSR270FOD
ENCODE_alias	gene-yeo:4098-control	gene-yeo:4098
RBP	FXR2	FXR2
Cell_Line	HepG2	HepG2
Batch	batch14	batch14
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB479NSE	ENCAB479NSE
Antibody	MA1-16767	MA1-16767
Lot_num	SD251451	SD251451
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.809052	2.809052
rescue_GRCh38	1.462656	1.462656
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	583	584

Replicate Information


Rep_UID	4098_01	4098_02	4098_INPUT1	4098_INPUT2
Exp UID	4098	4098	4098	4098
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_062716	HepG2_080316	HepG2_062716
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS768GCL	ENCBS133LVQ	ENCBS768GCL
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_062716	gene-yeo:HepG2_080316	gene-yeo:HepG2_062716
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2016-06-27	2016-08-03	2016-06-27
Culture_End_Date	2016-08-29	2016-07-25	2016-08-29	2016-07-25
Passage	3	3	3	3

QC Stats

Experiment QC

	4098-control	4098
Self_consistency_hg38	2.809052	2.809052
rescue_GRCh38	1.462656	1.462656

Replicate QC


Rep_UID	4098_01	4098_02	4098_INPUT1	4098_INPUT2
eCT	7.50	9.40	1.40	3.10
Usable_reads	6115091	6801933	6083511	5343158
Entropy_hg38	0.108029	0.340758

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4098_01	4098_02	4098_INPUT1	4098_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	CCTATCCT	CCTATCCT	GGCTCTGA
i7_barcode	GAGATTCC	GAGATTCC	CGCTCATT	CGCTCATT

Sequencing Information


Rep_UID	4098_01	4098_02	4098_INPUT1	4098_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
4098_CLIP1_S1_L008_R1_001.fastq.gz	4098_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4098_CLIP2_S2_L008_R1_001.fastq.gz	4098_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4098_INPUT1_S3_L008_R1_001.fastq.gz	4098_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4098_INPUT2_S4_L008_R1_001.fastq.gz	4098_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4098_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4098_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4098_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4098_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4098_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4098_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4098_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4098_CLIP1_rep1.vs.4098_CLIP2_rep2.sorted.nh.bb	4098_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4098_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4098_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4098_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4098_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4098_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4098_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4098_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4098_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4098_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4098_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4098_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4098_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4098_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4098_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4098_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4098_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4098_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4098_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:4098-control	ENCSR635EEO	experiment	eCLIP	4098-FXR2-HepG2-control	Released	ENCODE4
gene-yeo:4098	ENCSR270FOD	experiment	eCLIP	4098-FXR2-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4098_01	ENCLB797LFA	library	eCLIP	4098_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4098_02	ENCLB891LLA	library	eCLIP	4098_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4098_INPUT1	ENCLB665SAC	library	eCLIP	4098_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4098_INPUT2	ENCLB954FSM	library	eCLIP	4098_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4098_CLIP1_S1_L008_R1_001.fastq.gz	ENCFF102DWE	file_fastq	eCLIP	4098_01	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF002YMI	file_bam	eCLIP	4098_01	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF318NRI	file_bam	eCLIP	4098_01	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF468KAE	file_bw	eCLIP	4098_01	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF259WTC	file_bw	eCLIP	4098_01	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF746AVT	file_quantifications	eCLIP	4098_01	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF446KOG	file_bed	eCLIP	4098_01	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF413PHB	file_bb	eCLIP	4098_01	Released	ENCODE4
gene-yeo:4098_CLIP2_S2_L008_R1_001.fastq.gz	ENCFF762RHJ	file_fastq	eCLIP	4098_02	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF593UDA	file_bam	eCLIP	4098_02	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF449FBJ	file_bam	eCLIP	4098_02	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF678SDC	file_bw	eCLIP	4098_02	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF656PLB	file_bw	eCLIP	4098_02	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF525HRN	file_quantifications	eCLIP	4098_02	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF633YYD	file_bed	eCLIP	4098_02	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF978KMC	file_bb	eCLIP	4098_02	Released	ENCODE4
gene-yeo:4098_INPUT1_S3_L008_R1_001.fastq.gz	ENCFF687KXK	file_fastq	eCLIP	4098_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF848PLC	file_bam	eCLIP	4098_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF641BOC	file_bam	eCLIP	4098_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF242ORH	file_bw	eCLIP	4098_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF836YPH	file_bw	eCLIP	4098_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF361IJG	file_quantifications	eCLIP	4098_INPUT1	Released	ENCODE4
gene-yeo:4098_INPUT2_S4_L008_R1_001.fastq.gz	ENCFF110UCK	file_fastq	eCLIP	4098_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF977XEW	file_bam	eCLIP	4098_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF480RCM	file_bam	eCLIP	4098_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF368GAF	file_bw	eCLIP	4098_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF977PED	file_bw	eCLIP	4098_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4098_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF769ADQ	file_quantifications	eCLIP	4098_INPUT2	Released	ENCODE4