ENCORE eCLIP:680

PHF6 eCLIP in K562

Experiment Information (Status: Released)

	680	680-control
Exp_UID	680	680
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR001KKZ	ENCSR103HDM
ENCODE_alias	gene-yeo:680	gene-yeo:680-control
RBP	PHF6	PHF6
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB411AGR	ENCAB411AGR
Antibody	A301-450A	A301-450A
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	398	453

Replicate Information


Rep_UID	680_01	680_02	680_INPUT
Exp UID	680	680	680
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB256CGZ	ENCLB248OFU	ENCLB235RVW
ENCODE_alias	gene-yeo:680_01	gene-yeo:680_02	gene-yeo:680_INPUT
Biosample Name	K562_081815	K562_091615	K562_081815
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS505ILK	ENCBS175JIH
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_091615	gene-yeo:K562_081815
Cell_Line	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-09-16	2015-08-18
Culture_End_Date	2015-09-08	2015-10-14	2015-09-08
Passage	5	4	5

QC Stats

Experiment QC

	680	680-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	680_01	680_02	680_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	680_01	680_02	680_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	X1A	X2A	none
inline_barcode_2	X1B	X2B	none
i5_barcode	506	506	505
i7_barcode	705	705	706

Sequencing Information


Rep_UID	680_01	680_02	680_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
680_01_PHF6.R1.fastq.gz	680_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
680_01_PHF6.R2.fastq.gz	680_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
680_02_PHF6.R1.fastq.gz	680_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
680_02_PHF6.R2.fastq.gz	680_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
680_INPUT_PHF6.R1.fastq.gz	680_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
680_INPUT_PHF6.R2.fastq.gz	680_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/680.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	680	final_peaks	peaks	eCLIP	GRCh38
GRCh38_680_01_PHF6.merged.bam	680_01	bam	alignments	eCLIP	GRCh38
GRCh38_680_01_PHF6.merged.r2.norm.neg.bw	680_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_680_01_PHF6.merged.r2.norm.pos.bw	680_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/680_01.basedon_680_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	680_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/680_01.basedon_680_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	680_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_680_02_PHF6.merged.bam	680_02	bam	alignments	eCLIP	GRCh38
GRCh38_680_02_PHF6.merged.r2.norm.neg.bw	680_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_680_02_PHF6.merged.r2.norm.pos.bw	680_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/680_02.basedon_680_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	680_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/680_02.basedon_680_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	680_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_680_INPUT_S87_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	680_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_680_INPUT_S87_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	680_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_680_INPUT_S87_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	680_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
680.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	680	final_peaks	peaks	eCLIP	hg19
680_01_PHF6.merged.bam	680_01	bam	alignments	eCLIP	hg19
680_01_PHF6.merged.r2.norm.neg.bw	680_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
680_01_PHF6.merged.r2.norm.pos.bw	680_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
680_01.basedon_680_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	680_01	bed_eCLIP	peaks	eCLIP	hg19
680_01.basedon_680_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	680_01	bigBed_eCLIP	peaks	eCLIP	hg19
680_02_PHF6.merged.bam	680_02	bam	alignments	eCLIP	hg19
680_02_PHF6.merged.r2.norm.neg.bw	680_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
680_02_PHF6.merged.r2.norm.pos.bw	680_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
680_02.basedon_680_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	680_02	bed_eCLIP	peaks	eCLIP	hg19
680_02.basedon_680_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	680_02	bigBed_eCLIP	peaks	eCLIP	hg19
680_INPUT_S87_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	680_INPUT	bam	alignments	eCLIP	hg19
680_INPUT_S87_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	680_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
680_INPUT_S87_L008_R1_001.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	680_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:4047_CLIP1_rep1.vs.4047_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF031CQH	file_finalPeaks	eCLIP	4047	Released	ENCODE4
gene-yeo:4224_CLIP1_rep1.vs.4224_CLIP2_rep2.sorted.nh.bb	ENCFF641FTO	file_finalPeaks_bb	eCLIP	4047	Released	ENCODE4