ENCORE eCLIP:511

AATF eCLIP in K562

Experiment Information (Status: Released)

	511	511-control
Exp_UID	511	511
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR819XBT	ENCSR290JPJ
ENCODE_alias	gene-yeo:511	gene-yeo:511-control
RBP	AATF	AATF
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB064GNR	ENCAB064GNR
Antibody	A301-032A	A301-032A
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	384	439

Replicate Information


Rep_UID	511_01	511_02	511_INPUT
Exp UID	511	511	511
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB790TIX	ENCLB000JYH	ENCLB981SPY
ENCODE_alias	gene-yeo:511_01	gene-yeo:511_02	gene-yeo:511_INPUT
Biosample Name	K562_061215	K562_070715	K562_061215
Biosample_ENCODE_Accession	ENCBS318IMK	ENCBS517UIR	ENCBS318IMK
Biosample_ENCODE_Alias	gene-yeo:K562_061215	gene-yeo:K562_070715	gene-yeo:K562_061215
Cell_Line	K562	K562	K562
Culture_Start_Date	2015-06-12	2015-07-07	2015-06-12
Culture_End_Date	2015-06-30	2015-08-04	2015-06-30
Passage	4	5	4

QC Stats

Experiment QC

	511	511-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	511_01	511_02	511_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	511_01	511_02	511_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	701	701	702

Sequencing Information


Rep_UID	511_01	511_02	511_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
511_01_AATF.R1.fastq.gz	511_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
511_01_AATF.R2.fastq.gz	511_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
511_02_AATF.R1.fastq.gz	511_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
511_02_AATF.R2.fastq.gz	511_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
511_INPUT_AATF.R1.fastq.gz	511_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
511_INPUT_AATF.R2.fastq.gz	511_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/511.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	511	final_peaks	peaks	eCLIP	GRCh38
GRCh38_511_01_AATF.merged.bam	511_01	bam	alignments	eCLIP	GRCh38
GRCh38_511_01_AATF.merged.r2.norm.neg.bw	511_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_511_01_AATF.merged.r2.norm.pos.bw	511_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/511_01.basedon_511_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	511_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/511_01.basedon_511_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	511_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_511_02_AATF.merged.bam	511_02	bam	alignments	eCLIP	GRCh38
GRCh38_511_02_AATF.merged.r2.norm.neg.bw	511_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_511_02_AATF.merged.r2.norm.pos.bw	511_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/511_02.basedon_511_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	511_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/511_02.basedon_511_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	511_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_511_INPUT_S18_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	511_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_511_INPUT_S18_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	511_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_511_INPUT_S18_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	511_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
511.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	511	final_peaks	peaks	eCLIP	hg19
511_01_AATF.merged.bam	511_01	bam	alignments	eCLIP	hg19
511_01_AATF.merged.r2.norm.neg.bw	511_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
511_01_AATF.merged.r2.norm.pos.bw	511_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
511_01.basedon_511_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	511_01	bed_eCLIP	peaks	eCLIP	hg19
511_01.basedon_511_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	511_01	bigBed_eCLIP	peaks	eCLIP	hg19
511_02_AATF.merged.bam	511_02	bam	alignments	eCLIP	hg19
511_02_AATF.merged.r2.norm.neg.bw	511_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
511_02_AATF.merged.r2.norm.pos.bw	511_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
511_02.basedon_511_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	511_02	bed_eCLIP	peaks	eCLIP	hg19
511_02.basedon_511_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	511_02	bigBed_eCLIP	peaks	eCLIP	hg19
511_INPUT_S18_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	511_INPUT	bam	alignments	eCLIP	hg19
511_INPUT_S18_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	511_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
511_INPUT_S18_L002_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	511_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:4084_CLIP1_rep1.vs.4084_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF011XTO	file_finalPeaks	eCLIP	4084	Released	ENCODE4
gene-yeo:4142_CLIP1_rep1.vs.4142_CLIP2_rep2.sorted.nh.bb	ENCFF180QAF	file_finalPeaks_bb	eCLIP	4084	Released	ENCODE4