ENCORE eCLIP:593

STAU2 eCLIP in HepG2

Experiment Information (Status: Released)

	593	593-control
Exp_UID	593	593
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR979EWD	ENCSR701QEP
ENCODE_alias	gene-yeo:593	gene-yeo:593-control
RBP	STAU2	STAU2
Cell_Line	HepG2	HepG2
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB995HZA	ENCAB995HZA
Antibody	RN013P	RN013P
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	388	443

Replicate Information


Rep_UID	593_01	593_02	593_INPUT
Exp UID	593	593	593
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB676TYH	ENCLB539UCR	ENCLB696RTY
ENCODE_alias	gene-yeo:593_01	gene-yeo:593_02	gene-yeo:593_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

	593	593-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	593_01	593_02	593_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	593_01	593_02	593_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	503	503	504
i7_barcode	706	706	705

Sequencing Information


Rep_UID	593_01	593_02	593_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
593_01_STAU2.R1.fastq.gz	593_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
593_01_STAU2.R2.fastq.gz	593_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
593_02_STAU2.R1.fastq.gz	593_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
593_02_STAU2.R2.fastq.gz	593_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
593_INPUT_STAU2.R1.fastq.gz	593_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
593_INPUT_STAU2.R2.fastq.gz	593_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/593.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	593	final_peaks	peaks	eCLIP	GRCh38
GRCh38_593_01_STAU2.merged.bam	593_01	bam	alignments	eCLIP	GRCh38
GRCh38_593_01_STAU2.merged.r2.norm.neg.bw	593_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_593_01_STAU2.merged.r2.norm.pos.bw	593_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/593_01.basedon_593_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	593_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/593_01.basedon_593_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	593_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_593_02_STAU2.merged.bam	593_02	bam	alignments	eCLIP	GRCh38
GRCh38_593_02_STAU2.merged.r2.norm.neg.bw	593_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_593_02_STAU2.merged.r2.norm.pos.bw	593_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/593_02.basedon_593_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	593_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/593_02.basedon_593_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	593_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_593_INPUT_S16_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	593_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_593_INPUT_S16_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	593_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_593_INPUT_S16_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	593_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
593.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	593	final_peaks	peaks	eCLIP	hg19
593_01_STAU2.merged.bam	593_01	bam	alignments	eCLIP	hg19
593_01_STAU2.merged.r2.norm.neg.bw	593_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
593_01_STAU2.merged.r2.norm.pos.bw	593_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
593_01.basedon_593_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	593_01	bed_eCLIP	peaks	eCLIP	hg19
593_01.basedon_593_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	593_01	bigBed_eCLIP	peaks	eCLIP	hg19
593_02_STAU2.merged.bam	593_02	bam	alignments	eCLIP	hg19
593_02_STAU2.merged.r2.norm.neg.bw	593_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
593_02_STAU2.merged.r2.norm.pos.bw	593_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
593_02.basedon_593_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	593_02	bed_eCLIP	peaks	eCLIP	hg19
593_02.basedon_593_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	593_02	bigBed_eCLIP	peaks	eCLIP	hg19
593_INPUT_S16_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	593_INPUT	bam	alignments	eCLIP	hg19
593_INPUT_S16_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	593_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
593_INPUT_S16_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	593_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:4028_CLIP1_rep1.vs.4028_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF283WLS	file_finalPeaks	eCLIP	4028	Released	ENCODE4
gene-yeo:4160_CLIP1_rep1.vs.4160_CLIP2_rep2.sorted.nh.bb	ENCFF879CAU	file_finalPeaks_bb	eCLIP	4028	Released	ENCODE4