APOBEC3C      eCLIP in K562

Experiment Information (Status: Released)
374374-control
Exp_UID374374
RBPARK_Exp_name
ENCODE_ACCESSIONENCSR739VVTENCSR382QLC
ENCODE_aliasgene-yeo:374gene-yeo:374-control
RBPAPOBEC3CAPOBEC3C
Cell_LineK562K562
Batch
Exp_typeeCLIPcontrol
ENCODE_Antibody_IDENCAB529HWMENCAB529HWM
AntibodyGTX102164GTX102164
Lot_num4096840968
crosslinking_methodultraviolet irradiationultraviolet irradiation
queried_RNP_size_range175-300175-300
Self_consistency_hg38
rescue_GRCh38
StatusReleasedReleased
ProjectENCODE4ENCODE4
ID380435




Replicate Information
Rep_UID374_01374_02374_INPUT
Exp UID374374374
Replicate_typerep1rep2control
ENCODE_ACCESSIONENCLB669EPIENCLB769DQYENCLB308KEY
ENCODE_aliasgene-yeo:374_01gene-yeo:374_02gene-yeo:374_INPUT
Biosample NameK562_022315K562_040915K562_022315
Biosample_ENCODE_AccessionENCBS831COVENCBS931MQOENCBS831COV
Biosample_ENCODE_Aliasgene-yeo:K562_022315gene-yeo:K562_040915gene-yeo:K562_022315
Cell_LineK562K562K562
Culture_Start_Date2015-02-232015-04-092015-02-23
Culture_End_Date2015-03-202015-05-082015-03-20
Passage656




QC Stats
Experiment QC
374374-control
Self_consistency_hg38
rescue_GRCh38


Replicate QC
Rep_UID374_01374_02374_INPUT
eCT
Usable_reads
Entropy_hg38




Library-Prep Information
Rep_UID374_01374_02374_INPUT
library_size_selection_methodagarose gel extractionagarose gel extractionagarose gel extraction
strand_specificityreversereversereverse
inline_barcode_1A01C01none
inline_barcode_2B06D08fixednone
i5_barcode506506506
i7_barcode706706705




Sequencing Information
Rep_UID374_01374_02374_INPUT
seq_read_typepaired-endedpaired-endedpaired-ended
read_length505050
machine
flowcell
lane




File Information

FASTQ

file_nameSample IDfile_formatoutput_typerun_typepaired_endread_lengthplatformassay_type
374_01_4000_APOBEC3C.R1.fastq.gz374_01fastqreadspaired-ended150HiSeq4000eCLIP
374_01_4000_APOBEC3C.R2.fastq.gz374_01fastqreadspaired-ended250HiSeq4000eCLIP
374_02_APOBEC3C.R1.fastq.gz374_02fastqreadspaired-ended150HiSeq4000eCLIP
374_02_APOBEC3C.R2.fastq.gz374_02fastqreadspaired-ended250HiSeq4000eCLIP
374_INPUT_APOBEC3C.R1.fastq.gz374_INPUTfastqreadspaired-ended150HiSeq4000eCLIP
374_INPUT_APOBEC3C.R2.fastq.gz374_INPUTfastqreadspaired-ended250HiSeq4000eCLIP


GRCh38

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
GRCh38/374x4000fix.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz374final_peakspeakseCLIPGRCh38
GRCh38_374_01_4000_APOBEC3C.merged.bam374_01bamalignmentseCLIPGRCh38
GRCh38_374_01_4000_APOBEC3C.merged.r2.norm.neg.bw374_01bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_374_01_4000_APOBEC3C.merged.r2.norm.pos.bw374_01bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/374x4000fix_01.basedon_374x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz374_01bed_eCLIPpeakseCLIPGRCh38
GRCh38/374x4000fix_01.basedon_374x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb374_01bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_374_02_APOBEC3C.merged.bam374_02bamalignmentseCLIPGRCh38
GRCh38_374_02_APOBEC3C.merged.r2.norm.neg.bw374_02bigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_374_02_APOBEC3C.merged.r2.norm.pos.bw374_02bigWig+uniqueplus strand signal of unique readseCLIPGRCh38
GRCh38/374x4000fix_02.basedon_374x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz374_02bed_eCLIPpeakseCLIPGRCh38
GRCh38/374x4000fix_02.basedon_374x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb374_02bigBed_eCLIPpeakseCLIPGRCh38
GRCh38_374_INPUT_ATTCAGAA-TAATCTTA_L005_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam374_INPUTbamalignmentseCLIPGRCh38
GRCh38_374_INPUT_ATTCAGAA-TAATCTTA_L005_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw374_INPUTbigWig-uniqueminus strand signal of unique readseCLIPGRCh38
GRCh38_374_INPUT_ATTCAGAA-TAATCTTA_L005_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw374_INPUTbigWig+uniqueplus strand signal of unique readseCLIPGRCh38


hg19

file_nameSample IDfile_formatoutput_typeassay_typeassemblygenome_annotationNote
374x4000fix.01v02.IDR.out.0102merged.bed.blacklist_removed.bed.narrowPeak.encode.bed.gz374final_peakspeakseCLIPhg19
374_01_4000_APOBEC3C.merged.bam374_01bamalignmentseCLIPhg19
374_01_4000_APOBEC3C.merged.r2.norm.neg.bw374_01bigWig-uniqueminus strand signal of unique readseCLIPhg19
374_01_4000_APOBEC3C.merged.r2.norm.pos.bw374_01bigWig+uniqueplus strand signal of unique readseCLIPhg19
374x4000fix_01.basedon_374x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz374_01bed_eCLIPpeakseCLIPhg19
374x4000fix_01.basedon_374x4000fix_01.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb374_01bigBed_eCLIPpeakseCLIPhg19
374_02_APOBEC3C.merged.bam374_02bamalignmentseCLIPhg19
374_02_APOBEC3C.merged.r2.norm.neg.bw374_02bigWig-uniqueminus strand signal of unique readseCLIPhg19
374_02_APOBEC3C.merged.r2.norm.pos.bw374_02bigWig+uniqueplus strand signal of unique readseCLIPhg19
374x4000fix_02.basedon_374x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.encode.bed.gz374_02bed_eCLIPpeakseCLIPhg19
374x4000fix_02.basedon_374x4000fix_02.peaks.l2inputnormnew.bed.compressed.bed.narrowPeak.bed.bb374_02bigBed_eCLIPpeakseCLIPhg19
374_INPUT_ATTCAGAA-TAATCTTA_L005_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.bam374_INPUTbamalignmentseCLIPhg19
374_INPUT_ATTCAGAA-TAATCTTA_L005_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.neg.bw374_INPUTbigWig-uniqueminus strand signal of unique readseCLIPhg19
374_INPUT_ATTCAGAA-TAATCTTA_L005_R1.unassigned.adapterTrim.round2.rmRep.rmDup.sorted.r2.norm.pos.bw374_INPUTbigWig+uniqueplus strand signal of unique readseCLIPhg19






Data Submission Information

Files

ENCODE_aliasENCODE_accessionobject_typeassay_typeSample_IDStatusProject
gene-yeo:4132_CLIP1_rep1.vs.4132_CLIP2_rep2.sorted.nh.narrowPeak.gzENCFF781BNSfile_finalPeakseCLIP4132ReleasedENCODE4
gene-yeo:4117_CLIP1_rep1.vs.4117_CLIP2_rep2.sorted.nh.bbENCFF708EKAfile_finalPeaks_bbeCLIP4132ReleasedENCODE4