ENCORE eCLIP:4139

Experiment Information (Status: Released)

	4139-control	4139
Exp_UID	4139	4139
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR790SPV	ENCSR168VUE
ENCODE_alias	gene-yeo:4139-control	gene-yeo:4139
RBP	MORC2	MORC2
Cell_Line	K562	K562
Batch	batch22	batch22
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB179RUB	ENCAB179RUB
Antibody	PA5-51172	PA5-51172
Lot_num	UF2796314	UF2796314
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	1.069307	1.069307
rescue_GRCh38	2.043142	2.043142
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	527	528

Replicate Information


Rep_UID	4139_01	4139_02	4139_INPUT1	4139_INPUT2
Exp UID	4139	4139	4139	4139
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_081815	K562_102015	K562_081815	K562_102015
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-10-20	2015-08-18	2015-10-20
Culture_End_Date	2015-09-08	2015-11-17	2015-09-08	2015-11-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4139-control	4139
Self_consistency_hg38	1.069307	1.069307
rescue_GRCh38	2.043142	2.043142

Replicate QC


Rep_UID	4139_01	4139_02	4139_INPUT1	4139_INPUT2
eCT	14.20	13.60	10.30	8.30
Usable_reads	4036638	4175347	5601834	5648919
Entropy_hg38	0.145959	0.133288

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4139_01	4139_02	4139_INPUT1	4139_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	AGGCGAAG	AGGCGAAG	CCTATCCT	CCTATCCT
i7_barcode	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4139_01	4139_02	4139_INPUT1	4139_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
4139_CLIP1_S112_L007_R1_001.fastq.gz	4139_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4139_CLIP2_R_S115_L007_R1_001.fastq.gz	4139_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4139_IN1_S111_L007_R1_001.fastq.gz	4139_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4139_IN2_S113_L007_R1_001.fastq.gz	4139_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4139_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4139_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4139_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4139_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4139_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4139_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4139_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4139_CLIP1_rep1.vs.4139_CLIP2_rep2.sorted.nh.bb	4139_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4139_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4139_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4139_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4139_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4139_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4139_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4139_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4139_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4139_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4139_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4139_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4139_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4139_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4139_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4139_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4139_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch22.4139_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4139_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:4139-control	ENCSR790SPV	experiment	eCLIP	4139-MORC2-K562-control	Released	ENCODE4
gene-yeo:4139	ENCSR168VUE	experiment	eCLIP	4139-MORC2-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4139_01	ENCLB079TTR	library	eCLIP	4139_01	Released	ENCODE4
gene-yeo:L-K562_102015-4139_02	ENCLB543ZUO	library	eCLIP	4139_02	Released	ENCODE4
gene-yeo:L-K562_081815-4139_INPUT1	ENCLB534XBO	library	eCLIP	4139_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4139_INPUT2	ENCLB384AYR	library	eCLIP	4139_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4139_CLIP1_S112_L007_R1_001.fastq.gz	ENCFF470SFI	file_fastq	eCLIP	4139_01	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF669UWF	file_bam	eCLIP	4139_01	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF695ABL	file_bam	eCLIP	4139_01	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF363SQA	file_bw	eCLIP	4139_01	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF765TNA	file_bw	eCLIP	4139_01	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF683DXB	file_quantifications	eCLIP	4139_01	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF112HAC	file_bed	eCLIP	4139_01	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF078ORO	file_bb	eCLIP	4139_01	Released	ENCODE4
gene-yeo:4139_CLIP2_R_S115_L007_R1_001.fastq.gz	ENCFF456NCY	file_fastq	eCLIP	4139_02	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF200RUC	file_bam	eCLIP	4139_02	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF463FPE	file_bam	eCLIP	4139_02	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF474DAP	file_bw	eCLIP	4139_02	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF449SZR	file_bw	eCLIP	4139_02	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF164EHM	file_quantifications	eCLIP	4139_02	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF899XIV	file_bed	eCLIP	4139_02	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF045XQA	file_bb	eCLIP	4139_02	Released	ENCODE4
gene-yeo:4139_IN1_S111_L007_R1_001.fastq.gz	ENCFF810VLQ	file_fastq	eCLIP	4139_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF247OTF	file_bam	eCLIP	4139_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF982GVP	file_bam	eCLIP	4139_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF963HDK	file_bw	eCLIP	4139_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF346BWH	file_bw	eCLIP	4139_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF395GWB	file_quantifications	eCLIP	4139_INPUT1	Released	ENCODE4
gene-yeo:4139_IN2_S113_L007_R1_001.fastq.gz	ENCFF217VLB	file_fastq	eCLIP	4139_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF639WLH	file_bam	eCLIP	4139_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF504PCS	file_bam	eCLIP	4139_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF799OXT	file_bw	eCLIP	4139_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF127JVO	file_bw	eCLIP	4139_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch22.4139_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF631XNP	file_quantifications	eCLIP	4139_INPUT2	Released	ENCODE4