ENCORE eCLIP:4225

Experiment Information (Status: Released)

	4225-control	4225
Exp_UID	4225	4225
RBPARK_Exp_name
ENCODE_ACCESSION	ENCSR181YHI	ENCSR498DQS
ENCODE_alias	gene-yeo:4225-control	gene-yeo:4225
RBP	METTL1	METTL1
Cell_Line	K562	K562
Batch	batch24	batch24
Exp_type	control	eCLIP
ENCODE_Antibody_ID	ENCAB061GXO	ENCAB061GXO
Antibody	PA5-80810	PA5-80810
Lot_num	UL2893376	UL2893376
crosslinking_method	ultraviolet irradiation	ultraviolet irradiation
queried_RNP_size_range	175-300	175-300
Self_consistency_hg38	2.195822	2.195822
rescue_GRCh38	3.421488	3.421488
Status	Released	Released
Project	ENCODE4	ENCODE4
ID	509	510

Replicate Information


Rep_UID	4225_01	4225_02	4225_INPUT1	4225_INPUT2
Exp UID	4225	4225	4225	4225
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

	4225-control	4225
Self_consistency_hg38	2.195822	2.195822
rescue_GRCh38	3.421488	3.421488

Replicate QC


Rep_UID	4225_01	4225_02	4225_INPUT1	4225_INPUT2
eCT	14.30	12.60	6.80	7.70
Usable_reads	7176877	8346139	5345105	2641711
Entropy_hg38	0.379874	0.202840

Library-Prep
Sequencing

Library-Prep Information


Rep_UID	4225_01	4225_02	4225_INPUT1	4225_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	TATAGCCT	TATAGCCT
i7_barcode	CTGAAGCT	TAATGCGC	CTGAAGCT	TAATGCGC

Sequencing Information


Rep_UID	4225_01	4225_02	4225_INPUT1	4225_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
4225_CLIP1_S91_L006_R1_001.fastq.gz	4225_01	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4225_CLIP2_S93_L006_R1_001.fastq.gz	4225_02	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4225_INPUT1_S90_L006_R1_001.fastq.gz	4225_INPUT1	fastq	reads	single-ended	75	HiSeq4000	eCLIP
4225_INPUT2_S92_L006_R1_001.fastq.gz	4225_INPUT2	fastq	reads	single-ended	75	HiSeq4000	eCLIP

GRCh38

file_name	Sample ID	file_format	output_type	assay_type	assembly	genome_annotation
encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4225_01	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4225_01	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4225_01	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4225_01	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4225_01	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4225_01	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4225_01	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
4225_CLIP1_rep1.vs.4225_CLIP2_rep2.sorted.nh.bb	4225_01	final_peaks_bb	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	4225_02	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4225_02	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4225_02	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4225_02	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	4225_02	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	4225_02	bed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	4225_02	bigBed_eCLIP	peaks	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4225_INPUT1	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4225_INPUT1	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4225_INPUT1	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4225_INPUT1	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4225_INPUT1	transcript_quantification	transcript quantifications	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	4225_INPUT2	unfiltered_bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	4225_INPUT2	bam	alignments	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	4225_INPUT2	bigWig-unique	minus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	4225_INPUT2	bigWig+unique	plus strand signal of unique reads	eCLIP	GRCh38	Gencode29
encode4_batch24.4225_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	4225_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:4225-control	ENCSR181YHI	experiment	eCLIP	4225-METTL1-K562-control	Released	ENCODE4
gene-yeo:4225	ENCSR498DQS	experiment	eCLIP	4225-METTL1-K562-eCLIP	Released	ENCODE4
gene-yeo:L-K562_081815-4225_01	ENCLB607OMB	library	eCLIP	4225_01	Released	ENCODE4
gene-yeo:L-K562_102015-4225_02	ENCLB547OYJ	library	eCLIP	4225_02	Released	ENCODE4
gene-yeo:L-K562_081815-4225_INPUT1	ENCLB641DVY	library	eCLIP	4225_INPUT1	Released	ENCODE4
gene-yeo:L-K562_102015-4225_INPUT2	ENCLB411WSR	library	eCLIP	4225_INPUT2	Released	ENCODE4

Files

ENCODE_alias	ENCODE_accession	object_type	assay_type	Sample_ID	Status	Project
gene-yeo:4225_CLIP1_S91_L006_R1_001.fastq.gz	ENCFF924RUW	file_fastq	eCLIP	4225_01	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF170CLJ	file_bam	eCLIP	4225_01	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF923EBZ	file_bam	eCLIP	4225_01	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF116STD	file_bw	eCLIP	4225_01	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF990ODU	file_bw	eCLIP	4225_01	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF104HUS	file_quantifications	eCLIP	4225_01	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF075MZV	file_bed	eCLIP	4225_01	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF044GUK	file_bb	eCLIP	4225_01	Released	ENCODE4
gene-yeo:4225_CLIP2_S93_L006_R1_001.fastq.gz	ENCFF459PMF	file_fastq	eCLIP	4225_02	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.bam	ENCFF558ZVR	file_bam	eCLIP	4225_02	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF163QHZ	file_bam	eCLIP	4225_02	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF046STR	file_bw	eCLIP	4225_02	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF320TZU	file_bw	eCLIP	4225_02	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_CLIP.umi.r1.fqTrTr.sorted.fq.barcode1.parsed	ENCFF925WPG	file_quantifications	eCLIP	4225_02	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.narrowPeak.gz	ENCFF618DYL	file_bed	eCLIP	4225_02	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_CLIP.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.sorted.blacklist-removed.nh.bb	ENCFF244WSF	file_bb	eCLIP	4225_02	Released	ENCODE4
gene-yeo:4225_INPUT1_S90_L006_R1_001.fastq.gz	ENCFF808IYM	file_fastq	eCLIP	4225_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF469ERM	file_bam	eCLIP	4225_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF949MNH	file_bam	eCLIP	4225_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF272ZLL	file_bw	eCLIP	4225_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF101PKK	file_bw	eCLIP	4225_INPUT1	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP1_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF897IAO	file_quantifications	eCLIP	4225_INPUT1	Released	ENCODE4
gene-yeo:4225_INPUT2_S92_L006_R1_001.fastq.gz	ENCFF851DJV	file_fastq	eCLIP	4225_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.bam	ENCFF963VEL	file_bam	eCLIP	4225_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.bam	ENCFF287AFU	file_bam	eCLIP	4225_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.neg.bw	ENCFF757RWQ	file_bw	eCLIP	4225_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_INPUT.umi.r1.fq.genome-mappedSoSo.rmDupSo.norm.pos.bw	ENCFF245FTM	file_bw	eCLIP	4225_INPUT2	Released	ENCODE4
gene-yeo:encode4_batch24.4225_CLIP2_INPUT.umi.r1.fqTrTr.sorted.fq.input.parsed	ENCFF439HQO	file_quantifications	eCLIP	4225_INPUT2	Released	ENCODE4