ENCORE eCLIP:4204

Experiment Information (Status: Released)

	4204-control	4204
Exp_UID	4204	4204
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR964KMC	ENCSR038CCV
ENCODE_alias	gene-yeo:4204-control	gene-yeo:4204
RBP	SNRPD3	SNRPD3
Cell_Line	HepG2	HepG2
Batch	batch21	batch21
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB860WEE	ENCAB860WEE
Antibody	A303-954A	A303-954A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.542907	1.542907
rescue_GRCh38	1.294410	1.294410
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	545	546

Replicate Information


Rep_UID	4204_01	4204_02	4204_INPUT1	4204_INPUT2
Exp UID	4204	4204	4204	4204
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	HepG2_080316	HepG2_111019	HepG2_080316	HepG2_111019
Biosample_ENCODE_Accession	ENCBS133LVQ	ENCBS766GPS	ENCBS133LVQ	ENCBS766GPS
Biosample_ENCODE_Alias	gene-yeo:HepG2_080316	gene-yeo:HepG2_111019	gene-yeo:HepG2_080316	gene-yeo:HepG2_111019
Cell_Line	HepG2	HepG2	HepG2	HepG2
Culture_Start_Date	2016-08-03	2019-10-23	2016-08-03	2019-10-23
Culture_End_Date	2016-08-29	2019-11-10	2016-08-29	2019-11-10
Passage	3	3	3	3

QC Stats

Experiment QC

	4204-control	4204
Self_consistency_hg38	1.542907	1.542907
rescue_GRCh38	1.294410	1.294410

Replicate QC


Rep_UID	4204_01	4204_02	4204_INPUT1	4204_INPUT2
eCT	15.90	13.60	7.20	7.30
Usable_reads	1287576	2871423	2342713	4059902
Entropy_hg38	5.380838	1.010030

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4204_01	4204_02	4204_INPUT1	4204_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	TAATCTTA	GTACTGAC	AGGCGAAG	CAGGACGT
i7_barcode	TAATGCGC	TAATGCGC	TAATGCGC	TAATGCGC

Sequencing Information


Rep_UID	4204_01	4204_02	4204_INPUT1	4204_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
4204_CLIP1_R_S47_L003_R1_001.fastq.gz	4204_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4204_CLIP2_R_S49_L003_R1_001.fastq.gz	4204_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4204_IN1_R_S46_L003_R1_001.fastq.gz	4204_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4204_IN2_R_S48_L003_R1_001.fastq.gz	4204_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4204_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4204_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4204_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4204_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4204_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4204_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4204_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4204_CLIP1_rep1.vs.4204_CLIP2_rep2.sorted.nh.bb	4204_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4204_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4204_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4204_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4204_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4204_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4204_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4204_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4204_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4204_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4204_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4204_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4204_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4204_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4204_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4204_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4204_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch21.4204_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4204_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:4204-control	ENCSR964KMC	experiment	eCLIP	4204-SNRPD3-HepG2-control	Released	ENCODE4
gene-yeo:4204	ENCSR038CCV	experiment	eCLIP	4204-SNRPD3-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4204_01	ENCLB477ZKX	library	eCLIP	4204_01	Released	ENCODE4
gene-yeo:L-HepG2_111019-4204_02	ENCLB526NXE	library	eCLIP	4204_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4204_INPUT1	ENCLB948UZV	library	eCLIP	4204_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_111019-4204_INPUT2	ENCLB707YGU	library	eCLIP	4204_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4204_CLIP1_R_S47_L003_R1_001.fastq.gz	ENCFF785ZMY	file_fastq	eCLIP	4204_01	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF542QXR	file_bam	eCLIP	4204_01	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF629SHO	file_bam	eCLIP	4204_01	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF783WOG	file_bw	eCLIP	4204_01	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF212VAB	file_bw	eCLIP	4204_01	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF952SDT	file_quantifications	eCLIP	4204_01	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF153RMQ	file_bed	eCLIP	4204_01	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF042KRM	file_bb	eCLIP	4204_01	Released	ENCODE4
gene-yeo:4204_CLIP2_R_S49_L003_R1_001.fastq.gz	ENCFF944MVA	file_fastq	eCLIP	4204_02	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF841OKZ	file_bam	eCLIP	4204_02	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF115GUR	file_bam	eCLIP	4204_02	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF279JMN	file_bw	eCLIP	4204_02	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF180AHI	file_bw	eCLIP	4204_02	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF968CKY	file_quantifications	eCLIP	4204_02	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF892UUA	file_bed	eCLIP	4204_02	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF269BRS	file_bb	eCLIP	4204_02	Released	ENCODE4
gene-yeo:4204_IN1_R_S46_L003_R1_001.fastq.gz	ENCFF712CKW	file_fastq	eCLIP	4204_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF248NIT	file_bam	eCLIP	4204_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF854AYS	file_bam	eCLIP	4204_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF220MTB	file_bw	eCLIP	4204_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF278XKF	file_bw	eCLIP	4204_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF307WIB	file_quantifications	eCLIP	4204_INPUT1	Released	ENCODE4
gene-yeo:4204_IN2_R_S48_L003_R1_001.fastq.gz	ENCFF737CAK	file_fastq	eCLIP	4204_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF856PMD	file_bam	eCLIP	4204_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF464QPB	file_bam	eCLIP	4204_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF934RHB	file_bw	eCLIP	4204_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF361FDG	file_bw	eCLIP	4204_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch21.4204_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF086PWZ	file_quantifications	eCLIP	4204_INPUT2	Released	ENCODE4