ENCORE eCLIP:621

UTP18 eCLIP in HepG2

Experiment Information (Status: Released)

	621	621-control
Exp_UID	621	621
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR488JKQ	ENCSR387OVO
ENCODE_alias	gene-yeo:621	gene-yeo:621-control
RBP	UTP18	UTP18
Cell_Line	HepG2	HepG2
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB362LIJ	ENCAB362LIJ
Antibody	A301-551A	A301-551A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38
rescue_GRCh38
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	390	445

Replicate Information


Rep_UID	621_01	621_02	621_INPUT
Exp UID	621	621	621
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB890FUB	ENCLB269FBK	ENCLB180AJD
ENCODE_alias	gene-yeo:621_01	gene-yeo:621_02	gene-yeo:621_INPUT
Biosample Name	HepG2_091615	HepG2_111915	HepG2_091615
Biosample_ENCODE_Accession	ENCBS621TAB	ENCBS492SDY	ENCBS621TAB
Biosample_ENCODE_Alias	gene-yeo:HepG2_091615	gene-yeo:HepG2_111915	gene-yeo:HepG2_091615
Cell_Line	HepG2	HepG2	HepG2
Culture_Start_Date	2015-09-16	2015-11-19	2015-09-16
Culture_End_Date	2015-10-09	2015-12-10	2015-10-09
Passage	3	4	3

QC Stats

Experiment QC

	621	621-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	621_01	621_02	621_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	621_01	621_02	621_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	A04	A03	none
inline_barcode_2	F05	G07	none
i5_barcode	504	504	503
i7_barcode	706	706	705

Sequencing Information


Rep_UID	621_01	621_02	621_INPUT
seq_read_type	paired-ended	paired-ended	paired-ended
read_length	50	50	50
machine
flowcell
lane

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	paired_end	read_length	platform	assay_type
621_01_UTP18.R1.fastq.gz	621_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
621_01_UTP18.R2.fastq.gz	621_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
621_02_UTP18.R1.fastq.gz	621_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
621_02_UTP18.R2.fastq.gz	621_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
621_INPUT_UTP18.R1.fastq.gz	621_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
621_INPUT_UTP18.R2.fastq.gz	621_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/621.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	621	final_peaks	peaks	eCLIP	GRCh38
GRCh38_621_01_UTP18.merged.bam	621_01	bam	alignments	eCLIP	GRCh38
GRCh38_621_01_UTP18.merged.r2.norm.neg.bw	621_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_621_01_UTP18.merged.r2.norm.pos.bw	621_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/621_01.basedon_621_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	621_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/621_01.basedon_621_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	621_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_621_02_UTP18.merged.bam	621_02	bam	alignments	eCLIP	GRCh38
GRCh38_621_02_UTP18.merged.r2.norm.neg.bw	621_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_621_02_UTP18.merged.r2.norm.pos.bw	621_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/621_02.basedon_621_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	621_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/621_02.basedon_621_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	621_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_621_INPUT_S46_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	621_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_621_INPUT_S46_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	621_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_621_INPUT_S46_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	621_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
621.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	621	final_peaks	peaks	eCLIP	hg19
621_01_UTP18.merged.bam	621_01	bam	alignments	eCLIP	hg19
621_01_UTP18.merged.r2.norm.neg.bw	621_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
621_01_UTP18.merged.r2.norm.pos.bw	621_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
621_01.basedon_621_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	621_01	bed_eCLIP	peaks	eCLIP	hg19
621_01.basedon_621_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	621_01	bigBed_eCLIP	peaks	eCLIP	hg19
621_02_UTP18.merged.bam	621_02	bam	alignments	eCLIP	hg19
621_02_UTP18.merged.r2.norm.neg.bw	621_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
621_02_UTP18.merged.r2.norm.pos.bw	621_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
621_02.basedon_621_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	621_02	bed_eCLIP	peaks	eCLIP	hg19
621_02.basedon_621_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	621_02	bigBed_eCLIP	peaks	eCLIP	hg19
621_INPUT_S46_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	621_INPUT	bam	alignments	eCLIP	hg19
621_INPUT_S46_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	621_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
621_INPUT_S46_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	621_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19

Data Submission Information

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4083_CLIP1_rep1.vs.4083_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF792SRL	file_finalPeaks	eCLIP	4083	Released	ENCODE4
gene-yeo:4169_CLIP1_rep1.vs.4169_CLIP2_rep2.sorted.nh.bb	ENCFF017YPF	file_finalPeaks_bb	eCLIP	4083	Released	ENCODE4