ENCORE eCLIP:708

Experiment Information (Status: Released)

	708	708-control
Exp_UID	708	708
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR356ZMO	ENCSR902XTJ
ENCODE_alias	gene-yeo:708	gene-yeo:708-control
RBP	AKAP1	AKAP1
Cell_Line	HepG2	HepG2
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB496QKB	ENCAB496QKB
Antibody	A301-379A	A301-379A
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	411	466

Replicate Information


Rep_UID	708_01	708_02	708_INPUT
Exp UID	708	708	708
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB946GLU	ENCLB350JCB	ENCLB103YZP
ENCODE_alias	gene-yeo:708_01	gene-yeo:708_02	gene-yeo:708_INPUT
Biosample Name	HepG2_102015	HepG2_012016	HepG2_102015
Biosample_ENCODE_Accession	ENCBS575NGC	ENCBS074YUC	ENCBS575NGC
Biosample_ENCODE_Alias	gene-yeo:HepG2_102015	gene-yeo:HepG2_012016	gene-yeo:HepG2_102015
Cell_Line	HepG2	HepG2	HepG2
Culture_Start_Date	2015-10-20	2016-01-20	2015-10-20
Culture_End_Date	2015-11-17	2016-02-17	2015-11-17
Passage	4	4	4

QC Stats

Experiment QC

	708	708-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	708_01	708_02	708_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	708_01	708_02	708_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	506	506	505
i7_barcode	706	706	705

Sequencing Information


Rep_UID	708_01	708_02	708_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
708_01_AKAP1.R1.fastq.gz	708_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
708_01_AKAP1.R2.fastq.gz	708_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
708_02_AKAP1.R1.fastq.gz	708_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
708_02_AKAP1.R2.fastq.gz	708_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
708_INPUT_AKAP1.R1.fastq.gz	708_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
708_INPUT_AKAP1.R2.fastq.gz	708_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly
GRCh38/708.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	708	final_peaks	peaks	eCLIP	GRCh38
GRCh38_708_01_AKAP1.merged.bam	708_01	bam	alignments	eCLIP	GRCh38
GRCh38_708_01_AKAP1.merged.r2.norm.neg.bw	708_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_708_01_AKAP1.merged.r2.norm.pos.bw	708_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/708_01.basedon_708_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	708_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/708_01.basedon_708_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	708_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_708_02_AKAP1.merged.bam	708_02	bam	alignments	eCLIP	GRCh38
GRCh38_708_02_AKAP1.merged.r2.norm.neg.bw	708_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_708_02_AKAP1.merged.r2.norm.pos.bw	708_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/708_02.basedon_708_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	708_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/708_02.basedon_708_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	708_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_708_INPUT_S51_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	708_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_708_INPUT_S51_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	708_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_708_INPUT_S51_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	708_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38

hg19

file_name	Sample ID	file_format	output_type	assay_type	assembly
708.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	708	final_peaks	peaks	eCLIP	hg19
708_01_AKAP1.merged.bam	708_01	bam	alignments	eCLIP	hg19
708_01_AKAP1.merged.r2.norm.neg.bw	708_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
708_01_AKAP1.merged.r2.norm.pos.bw	708_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
708_01.basedon_708_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	708_01	bed_eCLIP	peaks	eCLIP	hg19
708_01.basedon_708_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	708_01	bigBed_eCLIP	peaks	eCLIP	hg19
708_02_AKAP1.merged.bam	708_02	bam	alignments	eCLIP	hg19
708_02_AKAP1.merged.r2.norm.neg.bw	708_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
708_02_AKAP1.merged.r2.norm.pos.bw	708_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
708_02.basedon_708_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	708_02	bed_eCLIP	peaks	eCLIP	hg19
708_02.basedon_708_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	708_02	bigBed_eCLIP	peaks	eCLIP	hg19
708_INPUT_S51_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	708_INPUT	bam	alignments	eCLIP	hg19
708_INPUT_S51_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	708_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
708_INPUT_S51_L005_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	708_INPUT	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19

Data Submission Information No DCC registered objects are available for eCLIP experiment (Exp_UID=708)