ENCORE eCLIP:4028

Experiment Information (Status: Released)

	4028-control	4028
Exp_UID	4028	4028
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR937QWU	ENCSR256NCI
ENCODE_alias	gene-yeo:4028-control	gene-yeo:4028
RBP	APEX1	APEX1
Cell_Line	K562	K562
Batch	batch16	batch16
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB328DHC	ENCAB328DHC
Antibody	MA1-440	MA1-440
Lot_num	TB260470	TB260470
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.651786	1.651786
rescue_GRCh38	1.960265	1.960265
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	571	572

Replicate Information


Rep_UID	4028_01	4028_02	4028_INPUT1	4028_INPUT2
Exp UID	4028	4028	4028	4028
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

	4028-control	4028
Self_consistency_hg38	1.651786	1.651786
rescue_GRCh38	1.960265	1.960265

Replicate QC


Rep_UID	4028_01	4028_02	4028_INPUT1	4028_INPUT2
eCT	18.90	13.20	6.70	3.90
Usable_reads	802200	1016182	1905544	2463925
Entropy_hg38	0.383120	0.212254

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4028_01	4028_02	4028_INPUT1	4028_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	ATAGAGGC	TATAGCCT	TATAGCCT
i7_barcode	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4028_01	4028_02	4028_INPUT1	4028_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	NovaSeq6000	NovaSeq6000	NovaSeq6000	NovaSeq6000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4028_CLIP1_S40_L002_R1_001.fastq.gz	4028_01	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4028_CLIP2_S42_L002_R1_001.fastq.gz	4028_02	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4028_INPUT1_S39_L002_R1_001.fastq.gz	4028_INPUT1	fastq	reads	single-ended	101	NovaSeq6000	eCLIP
4028_INPUT2_S41_L002_R1_001.fastq.gz	4028_INPUT2	fastq	reads	single-ended	101	NovaSeq6000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4028_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4028_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4028_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4028_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4028_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4028_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4028_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4028_CLIP1_rep1.vs.4028_CLIP2_rep2.sorted.nh.bb	4028_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4028_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4028_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4028_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4028_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4028_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4028_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4028_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4028_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4028_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4028_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4028_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4028_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4028_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4028_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4028_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4028_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch16.4028_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4028_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:4028-control	ENCSR937QWU	experiment	eCLIP	4028-APEX1-K562-control	Released	ENCODE4
gene-yeo:4028	ENCSR256NCI	experiment	eCLIP	4028-APEX1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_111915-4028_01	ENCLB838QKG	library	eCLIP	4028_01	Released	ENCODE4
gene-yeo:L-K562_072016-4028_02	ENCLB421YPG	library	eCLIP	4028_02	Released	ENCODE4
gene-yeo:L-K562_111915-4028_INPUT1	ENCLB075BPY	library	eCLIP	4028_INPUT1	Released	ENCODE4
gene-yeo:L-K562_072016-4028_INPUT2	ENCLB676JLI	library	eCLIP	4028_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4028_CLIP1_S40_L002_R1_001.fastq.gz	ENCFF785OLO	file_fastq	eCLIP	4028_01	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF229VXP	file_bam	eCLIP	4028_01	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF111VDP	file_bam	eCLIP	4028_01	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF808VYJ	file_bw	eCLIP	4028_01	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF785VGC	file_bw	eCLIP	4028_01	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF674OZZ	file_quantifications	eCLIP	4028_01	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF815YXB	file_bed	eCLIP	4028_01	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF726TGL	file_bb	eCLIP	4028_01	Released	ENCODE4
gene-yeo:4028_CLIP2_S42_L002_R1_001.fastq.gz	ENCFF495VVD	file_fastq	eCLIP	4028_02	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF055GIW	file_bam	eCLIP	4028_02	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF504OBG	file_bam	eCLIP	4028_02	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF842TZP	file_bw	eCLIP	4028_02	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF934PME	file_bw	eCLIP	4028_02	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF129GFV	file_quantifications	eCLIP	4028_02	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF143NZE	file_bed	eCLIP	4028_02	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF825GIW	file_bb	eCLIP	4028_02	Released	ENCODE4
gene-yeo:4028_INPUT1_S39_L002_R1_001.fastq.gz	ENCFF795YNY	file_fastq	eCLIP	4028_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF749JIC	file_bam	eCLIP	4028_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF599OGU	file_bam	eCLIP	4028_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF163KEB	file_bw	eCLIP	4028_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF545HII	file_bw	eCLIP	4028_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF861UYY	file_quantifications	eCLIP	4028_INPUT1	Released	ENCODE4
gene-yeo:4028_INPUT2_S41_L002_R1_001.fastq.gz	ENCFF904EOE	file_fastq	eCLIP	4028_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF914DVJ	file_bam	eCLIP	4028_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF216GUI	file_bam	eCLIP	4028_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF987DCJ	file_bw	eCLIP	4028_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF433CNZ	file_bw	eCLIP	4028_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch16.4028_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF270XZA	file_quantifications	eCLIP	4028_INPUT2	Released	ENCODE4