ENCORE eCLIP:4014

Experiment Information (Status: Released)

	4014-control	4014
Exp_UID	4014	4014
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR720EEM	ENCSR720BJU
ENCODE_alias	gene-yeo:4014-control	gene-yeo:4014
RBP	TARDBP	TARDBP
Cell_Line	K562	K562
Batch	batch10	batch10
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	1.264717	1.264717
rescue_GRCh38	1.417901	1.417901
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	605	606

Replicate Information


Rep_UID	4014_01	4014_02	4014_INPUT1	4014_INPUT2
Exp UID	4014	4014	4014	4014
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_111915	K562_072016	K562_111915	K562_072016
Biosample_ENCODE_Accession	ENCBS344MAK	ENCBS177POD	ENCBS344MAK	ENCBS177POD
Biosample_ENCODE_Alias	gene-yeo:K562_111915	gene-yeo:K562_072016	gene-yeo:K562_111915	gene-yeo:K562_072016
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-11-19	2016-07-20	2015-11-19	2016-07-20
Culture_End_Date	2015-12-11	2016-08-15	2015-12-11	2016-08-15
Passage	4	5	4	5

QC Stats

Experiment QC

	4014-control	4014
Self_consistency_hg38	1.264717	1.264717
rescue_GRCh38	1.417901	1.417901

Replicate QC


Rep_UID	4014_01	4014_02	4014_INPUT1	4014_INPUT2
eCT	14.60	12.20	3.80	2.50
Usable_reads	1631471	1563386	1998863	2217175
Entropy_hg38	3.142164	2.310249

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4014_01	4014_02	4014_INPUT1	4014_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	ATTACTCG	TCCGGAGA	ATTACTCG	TCCGGAGA

Sequencing Information


Rep_UID	4014_01	4014_02	4014_INPUT1	4014_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
4014_CLIP1_S2_L006_R1_001.fastq.gz	4014_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4014_CLIP2_S4_L006_R1_001.fastq.gz	4014_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4014_INPUT1_S1_L006_R1_001.fastq.gz	4014_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4014_INPUT2_S3_L006_R1_001.fastq.gz	4014_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4014_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4014_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4014_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4014_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4014_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4014_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4014_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4014_CLIP1_rep1.vs.4014_CLIP2_rep2.sorted.nh.bb	4014_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4014_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4014_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4014_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4014_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4014_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4014_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4014_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4014_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4014_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4014_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4014_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4014_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4014_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4014_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4014_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4014_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch10.4014_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4014_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:4014-control	ENCSR720EEM	experiment	eCLIP	4014-TARDBP-K562-control	Released	ENCODE4
gene-yeo:4014	ENCSR720BJU	experiment	eCLIP	4014-TARDBP-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4014_01	ENCLB043YOF	library	eCLIP	4014_01	Released	ENCODE4
gene-yeo:L-K562_072016-4014_02	ENCLB661XWS	library	eCLIP	4014_02	Released	ENCODE4
gene-yeo:L-K562_111915-4014_INPUT1	ENCLB933YGK	library	eCLIP	4014_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4014_INPUT2	ENCLB403SOD	library	eCLIP	4014_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4014_CLIP1_S2_L006_R1_001.fastq.gz	ENCFF673VEJ	file_fastq	eCLIP	4014_01	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF946DDI	file_bam	eCLIP	4014_01	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF862SNV	file_bam	eCLIP	4014_01	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF003HLV	file_bw	eCLIP	4014_01	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF848FSN	file_bw	eCLIP	4014_01	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF909NAM	file_quantifications	eCLIP	4014_01	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF381KTD	file_bed	eCLIP	4014_01	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF164XWU	file_bb	eCLIP	4014_01	Released	ENCODE4
gene-yeo:4014_CLIP2_S4_L006_R1_001.fastq.gz	ENCFF679SNJ	file_fastq	eCLIP	4014_02	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF198BGK	file_bam	eCLIP	4014_02	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF748KMS	file_bam	eCLIP	4014_02	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF518YAZ	file_bw	eCLIP	4014_02	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF214TBL	file_bw	eCLIP	4014_02	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF195OTD	file_quantifications	eCLIP	4014_02	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF265XPM	file_bed	eCLIP	4014_02	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF720KXG	file_bb	eCLIP	4014_02	Released	ENCODE4
gene-yeo:4014_INPUT1_S1_L006_R1_001.fastq.gz	ENCFF110DXI	file_fastq	eCLIP	4014_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF826CFH	file_bam	eCLIP	4014_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF913CBD	file_bam	eCLIP	4014_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF147BIG	file_bw	eCLIP	4014_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF507BMI	file_bw	eCLIP	4014_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF870HUC	file_quantifications	eCLIP	4014_INPUT1	Released	ENCODE4
gene-yeo:4014_INPUT2_S3_L006_R1_001.fastq.gz	ENCFF706SRG	file_fastq	eCLIP	4014_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF949DIB	file_bam	eCLIP	4014_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF667EQF	file_bam	eCLIP	4014_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF491HBA	file_bw	eCLIP	4014_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF629HXN	file_bw	eCLIP	4014_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch10.4014_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF179SNI	file_quantifications	eCLIP	4014_INPUT2	Released	ENCODE4