ENCORE eCLIP:4169

Experiment Information (Status: Released)

	4169-control	4169
Exp_UID	4169	4169
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR851BGK	ENCSR491HUW
ENCODE_alias	gene-yeo:4169-control	gene-yeo:4169
RBP	MFAP1	MFAP1
Cell_Line	K562	K562
Batch	batch23	batch23
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB079FZQ	ENCAB079FZQ
Antibody	A304-647A	A304-647A
Lot_num	1	1
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.442231	2.442231
rescue_GRCh38	1.600846	1.600846
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	521	522

Replicate Information


Rep_UID	4169_01	4169_02	4169_INPUT1	4169_INPUT2
Exp UID	4169	4169	4169	4169
Replicate_type	rep1	rep2	control1	control2
ENCODE_ACCESSION
ENCODE_alias
Biosample Name	K562_081815	K562_102015	K562_081815	K562_102015
Biosample_ENCODE_Accession	ENCBS175JIH	ENCBS592SHU	ENCBS175JIH	ENCBS592SHU
Biosample_ENCODE_Alias	gene-yeo:K562_081815	gene-yeo:K562_102015	gene-yeo:K562_081815	gene-yeo:K562_102015
Cell_Line	K562	K562	K562	K562
Culture_Start_Date	2015-08-18	2015-10-20	2015-08-18	2015-10-20
Culture_End_Date	2015-09-08	2015-11-17	2015-09-08	2015-11-17
Passage	5	5	5	5

QC Stats

Experiment QC

	4169-control	4169
Self_consistency_hg38	2.442231	2.442231
rescue_GRCh38	1.600846	1.600846

Replicate QC


Rep_UID	4169_01	4169_02	4169_INPUT1	4169_INPUT2
eCT	10.60	11.60	7.40	8.30
Usable_reads	2583247	5151057	5179510	4577140
Entropy_hg38	0.944498	1.400751

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4169_01	4169_02	4169_INPUT1	4169_INPUT2
library_size_selection_method	agarose gel extraction	agarose gel extraction	agarose gel extraction	agarose gel extraction
strand_specificity	reverse	reverse	reverse	reverse
inline_barcode_1
inline_barcode_2
i5_barcode	ATAGAGGC	ATAGAGGC	GGCTCTGA	TATAGCCT
i7_barcode	CGCTCATT	GAGATTCC	CGCTCATT	GAGATTCC

Sequencing Information


Rep_UID	4169_01	4169_02	4169_INPUT1	4169_INPUT2
seq_read_type	single-ended	single-ended	single-ended	single-ended
read_length	75	75	75	75
machine	HiSeq4000	HiSeq4000	HiSeq4000	HiSeq4000
flowcell	flowcell	flowcell	flowcell	flowcell
lane	-	-	-	-

File Information

FASTQ

file_name	Sample ID	file_format	output_type	run_type	read_length	platform	assay_type
4169_CLIP1_S31_L002_R1_001.fastq.gz	4169_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4169_CLIP2_S33_L002_R1_001.fastq.gz	4169_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4169_INPUT1_S30_L002_R1_001.fastq.gz	4169_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4169_INPUT2_S32_L002_R1_001.fastq.gz	4169_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4169_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4169_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4169_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4169_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4169_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4169_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4169_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4169_CLIP1_rep1.vs.4169_CLIP2_rep2.sorted.nh.bb	4169_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4169_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4169_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4169_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4169_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4169_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4169_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4169_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4169_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4169_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4169_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4169_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4169_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4169_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4169_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4169_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4169_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch23.4169_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4169_INPUT2	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29

Data Submission Information

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4169-control	ENCSR851BGK	experiment	eCLIP	4169-MFAP1-K562-control	Released	ENCODE4
gene-yeo:4169	ENCSR491HUW	experiment	eCLIP	4169-MFAP1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4169_01	ENCLB989LCX	library	eCLIP	4169_01	Released	ENCODE4
gene-yeo:L-K562_102015-4169_02	ENCLB108GPP	library	eCLIP	4169_02	Released	ENCODE4
gene-yeo:L-K562_081815-4169_INPUT1	ENCLB041IUW	library	eCLIP	4169_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4169_INPUT2	ENCLB729JFC	library	eCLIP	4169_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4169_CLIP1_S31_L002_R1_001.fastq.gz	ENCFF350MVS	file_fastq	eCLIP	4169_01	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF766SIC	file_bam	eCLIP	4169_01	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF826KMG	file_bam	eCLIP	4169_01	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF978AXM	file_bw	eCLIP	4169_01	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF912GSP	file_bw	eCLIP	4169_01	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF686QIV	file_quantifications	eCLIP	4169_01	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF802LMK	file_bed	eCLIP	4169_01	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF947OFV	file_bb	eCLIP	4169_01	Released	ENCODE4
gene-yeo:4169_CLIP2_S33_L002_R1_001.fastq.gz	ENCFF089NUQ	file_fastq	eCLIP	4169_02	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF641FOC	file_bam	eCLIP	4169_02	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF896AIC	file_bam	eCLIP	4169_02	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF106VBQ	file_bw	eCLIP	4169_02	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF878ZNG	file_bw	eCLIP	4169_02	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF446PBQ	file_quantifications	eCLIP	4169_02	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF756NTZ	file_bed	eCLIP	4169_02	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF994SQN	file_bb	eCLIP	4169_02	Released	ENCODE4
gene-yeo:4169_INPUT1_S30_L002_R1_001.fastq.gz	ENCFF486TYS	file_fastq	eCLIP	4169_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF955BZK	file_bam	eCLIP	4169_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF435IBI	file_bam	eCLIP	4169_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF616WFF	file_bw	eCLIP	4169_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF823BUI	file_bw	eCLIP	4169_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF477RSN	file_quantifications	eCLIP	4169_INPUT1	Released	ENCODE4
gene-yeo:4169_INPUT2_S32_L002_R1_001.fastq.gz	ENCFF741LXU	file_fastq	eCLIP	4169_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF769ASE	file_bam	eCLIP	4169_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF593VTC	file_bam	eCLIP	4169_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF009IPX	file_bw	eCLIP	4169_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF521FYA	file_bw	eCLIP	4169_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch23.4169_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF729DKD	file_quantifications	eCLIP	4169_INPUT2	Released	ENCODE4