ENCORE eCLIP:284

DDX21 eCLIP in K562

Experiment Information (Status: Released)

	284	284-control
Exp_UID	284	284
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR040QLV	ENCSR266XXD
ENCODE_alias	gene-yeo:284	gene-yeo:284-control
RBP	DDX21	DDX21
Cell_Line	K562	K562
Batch
Exp_type	eCLIP	control
ENCODE_Antibody_ID	ENCAB315FWL	ENCAB315FWL
Antibody	RN090PW	RN090PW
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	379	434

Replicate Information


Rep_UID	284_01	284_02	284_INPUT
Exp UID	284	284	284
Replicate_type	rep1	rep2	control
ENCODE_ACCESSION	ENCLB362JGP	ENCLB886BYY	ENCLB912YUQ
ENCODE_alias	gene-yeo:284_01	gene-yeo:284_02	gene-yeo:284_INPUT
Biosample Name	K562_110314A	K562_110314B	K562_110314A
Biosample_ENCODE_Accession	ENCBS126AJR	ENCBS658KIL	ENCBS126AJR
Biosample_ENCODE_Alias	gene-yeo:K562_110314A	gene-yeo:K562_110314B	gene-yeo:K562_110314A
Cell_Line	K562	K562	K562
Culture_Start_Date	2014-10-03	2014-10-06	2014-10-03
Culture_End_Date	2014-11-03	2014-11-03	2014-11-03
Passage	6	5	6

QC Stats

Experiment QC

	284	284-control
Self_consistency_hg38
rescue_GRCh38

Replicate QC


Rep_UID	284_01	284_02	284_INPUT
eCT
Usable_reads
Entropy_hg38

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	284_01	284_02	284_INPUT
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse
inline_barcode_1	A01	A04	none
inline_barcode_2	B06	F05	none
i5_barcode	502	502	501
i7_barcode	703	703	703

Sequencing Information


Rep_UID	284_01	284_02	284_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
284_01_4000_fixed_DDX21.R1.fastq.gz	284_01	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
284_01_4000_fixed_DDX21.R2.fastq.gz	284_01	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
284_02_4000_fixed_DDX21.R1.fastq.gz	284_02	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
284_02_4000_fixed_DDX21.R2.fastq.gz	284_02	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP
284_INPUT_DDX21.R1.fastq.gz	284_INPUT	fastq	reads	paired-ended	1	50	HiSeq4000	eCLIP
284_INPUT_DDX21.R2.fastq.gz	284_INPUT	fastq	reads	paired-ended	2	50	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation	Note
GRCh38/284x4000fix.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	284	final_peaks	peaks	eCLIP	GRCh38
GRCh38_284_01_4000_fixed_DDX21.merged.bam	284_01	bam	alignments	eCLIP	GRCh38
GRCh38_284_01_4000_fixed_DDX21.merged.r2.norm.neg.bw	284_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_284_01_4000_fixed_DDX21.merged.r2.norm.pos.bw	284_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/284x4000fix_01.basedon_284x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	284_01	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/284x4000fix_01.basedon_284x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	284_01	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_284_02_4000_fixed_DDX21.merged.bam	284_02	bam	alignments	eCLIP	GRCh38
GRCh38_284_02_4000_fixed_DDX21.merged.r2.norm.neg.bw	284_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_284_02_4000_fixed_DDX21.merged.r2.norm.pos.bw	284_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38
GRCh38/284x4000fix_02.basedon_284x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	284_02	bed_eCLIP	peaks	eCLIP	GRCh38
GRCh38/284x4000fix_02.basedon_284x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	284_02	bigBed_eCLIP	peaks	eCLIP	GRCh38
GRCh38_284_INPUT_CGCTCATT-TATAGCCT_L007_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	284_INPUT	bam	alignments	eCLIP	GRCh38
GRCh38_284_INPUT_CGCTCATT-TATAGCCT_L007_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	284_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38
GRCh38_284_INPUT_CGCTCATT-TATAGCCT_L007_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	284_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
284x4000fix.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz	284	final_peaks	peaks	eCLIP	hg19
284_01_4000_fixed_DDX21.merged.bam	284_01	bam	alignments	eCLIP	hg19
284_01_4000_fixed_DDX21.merged.r2.norm.neg.bw	284_01	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
284_01_4000_fixed_DDX21.merged.r2.norm.pos.bw	284_01	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
284x4000fix_01.basedon_284x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	284_01	bed_eCLIP	peaks	eCLIP	hg19
284x4000fix_01.basedon_284x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	284_01	bigBed_eCLIP	peaks	eCLIP	hg19
284_02_4000_fixed_DDX21.merged.bam	284_02	bam	alignments	eCLIP	hg19
284_02_4000_fixed_DDX21.merged.r2.norm.neg.bw	284_02	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
284_02_4000_fixed_DDX21.merged.r2.norm.pos.bw	284_02	bigWig+unique	plus strand signal of unique reads	eCLIP	hg19
284x4000fix_02.basedon_284x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz	284_02	bed_eCLIP	peaks	eCLIP	hg19
284x4000fix_02.basedon_284x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb	284_02	bigBed_eCLIP	peaks	eCLIP	hg19
284_INPUT_CGCTCATT-TATAGCCT_L007_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam	284_INPUT	bam	alignments	eCLIP	hg19
284_INPUT_CGCTCATT-TATAGCCT_L007_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw	284_INPUT	bigWig-unique	minus strand signal of unique reads	eCLIP	hg19
284_INPUT_CGCTCATT-TATAGCCT_L007_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw	284_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:4155_CLIP1_rep1.vs.4155_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF488MWW	file_finalPeaks	eCLIP	4155	Released	ENCODE4
gene-yeo:4114_CLIP1_rep1.vs.4114_CLIP2_rep2.sorted.nh.bb	ENCFF902HNW	file_finalPeaks_bb	eCLIP	4155	Released	ENCODE4
gene-yeo:4204_CLIP1_rep1.vs.4204_CLIP2_rep2.sorted.nh.narrowPeak.gz	ENCFF977HDU	file_finalPeaks	eCLIP	4204	Released	ENCODE4
gene-yeo:4116_CLIP1_rep1.vs.4116_CLIP2_rep2.sorted.nh.bb	ENCFF550OAJ	file_finalPeaks_bb	eCLIP	4204	Released	ENCODE4