ENCORE eCLIP:4110

Experiment Information (Status: Released)

	4110-control	4110
Exp_UID	4110	4110
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR265LJL	ENCSR187VEQ
ENCODE_alias	gene-yeo:4110-control	gene-yeo:4110
RBP	TARDBP	TARDBP
Cell_Line	HepG2	HepG2
Batch	batch14	batch14
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB349KOV	ENCAB349KOV
Antibody	711051	711051
Lot_num	SI259917	SI259917
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.411744	1.411744
rescue_GRCh38	1.421685	1.421685
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	585	586

Replicate Information


Rep_UID	4110_01	4110_02	4110_INPUT1	4110_INPUT2
Exp UID	4110	4110	4110	4110
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

	4110-control	4110
Self_consistency_hg38	1.411744	1.411744
rescue_GRCh38	1.421685	1.421685

Replicate QC


Rep_UID	4110_01	4110_02	4110_INPUT1	4110_INPUT2
eCT	8.20	9.00	0.40	1.90
Usable_reads	7427433	7944965	4153418	5345646
Entropy_hg38	4.914074	5.603986

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4110_01	4110_02	4110_INPUT1	4110_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	TAATCTTA	AGGCGAAG	AGGCGAAG
i7_barcode	TCCGGAGA	ATTACTCG	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4110_01	4110_02	4110_INPUT1	4110_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
4110_CLIP1_S9_L008_R1_001.fastq.gz	4110_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4110_CLIP2_S10_L008_R1_001.fastq.gz	4110_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4110_INPUT1_S11_L008_R1_001.fastq.gz	4110_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4110_INPUT2_S12_L008_R1_001.fastq.gz	4110_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4110_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4110_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4110_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4110_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4110_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4110_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4110_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4110_CLIP1_rep1.vs.4110_CLIP2_rep2.sorted.nh.bb	4110_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4110_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4110_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4110_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4110_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4110_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4110_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4110_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4110_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4110_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4110_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4110_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4110_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4110_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4110_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4110_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4110_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch14.4110_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4110_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:4110-control	ENCSR265LJL	experiment	eCLIP	4110-TARDBP-HepG2-control	Released	ENCODE4
gene-yeo:4110	ENCSR187VEQ	experiment	eCLIP	4110-TARDBP-HepG2-eCLIP	Released	ENCODE4
gene-yeo:L-HepG2_080316-4110_01	ENCLB233ERR	library	eCLIP	4110_01	Released	ENCODE4
gene-yeo:L-HepG2_062716-4110_02	ENCLB139SPG	library	eCLIP	4110_02	Released	ENCODE4
gene-yeo:L-HepG2_080316-4110_INPUT1	ENCLB168DIP	library	eCLIP	4110_INPUT1	Released	ENCODE4
gene-yeo:L-HepG2_062716-4110_INPUT2	ENCLB871TUL	library	eCLIP	4110_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4110_CLIP1_S9_L008_R1_001.fastq.gz	ENCFF137LSG	file_fastq	eCLIP	4110_01	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF174CYH	file_bam	eCLIP	4110_01	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF918MZV	file_bam	eCLIP	4110_01	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF235GOJ	file_bw	eCLIP	4110_01	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF504BRQ	file_bw	eCLIP	4110_01	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF782SZT	file_quantifications	eCLIP	4110_01	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF421FJD	file_bed	eCLIP	4110_01	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF644MXY	file_bb	eCLIP	4110_01	Released	ENCODE4
gene-yeo:4110_CLIP2_S10_L008_R1_001.fastq.gz	ENCFF868WQR	file_fastq	eCLIP	4110_02	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF958TEE	file_bam	eCLIP	4110_02	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF792QOH	file_bam	eCLIP	4110_02	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF896PLI	file_bw	eCLIP	4110_02	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF945MEA	file_bw	eCLIP	4110_02	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF432XFH	file_quantifications	eCLIP	4110_02	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF626XAA	file_bed	eCLIP	4110_02	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF992HVN	file_bb	eCLIP	4110_02	Released	ENCODE4
gene-yeo:4110_INPUT1_S11_L008_R1_001.fastq.gz	ENCFF887XEU	file_fastq	eCLIP	4110_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF351KZM	file_bam	eCLIP	4110_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF079ZVC	file_bam	eCLIP	4110_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF096ILG	file_bw	eCLIP	4110_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF460UIE	file_bw	eCLIP	4110_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF412QTJ	file_quantifications	eCLIP	4110_INPUT1	Released	ENCODE4
gene-yeo:4110_INPUT2_S12_L008_R1_001.fastq.gz	ENCFF037ICH	file_fastq	eCLIP	4110_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF527CXQ	file_bam	eCLIP	4110_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF334XQN	file_bam	eCLIP	4110_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF880IUX	file_bw	eCLIP	4110_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF013DWY	file_bw	eCLIP	4110_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch14.4110_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF471WGO	file_quantifications	eCLIP	4110_INPUT2	Released	ENCODE4