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IGVF_shendure_proximalPromoter_assignment.yaml
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IGVF_shendure_proximalPromoter_assignment.yaml
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---
!Assay
seqspec_version: 0.3.0
assay_id: lentiMPRA
name: mpra_shendure_proximal_promoter
doi: ''
date: 16 October 2024
description: Reporter library targeting candidate cis-regulatory elements genome-wide
modalities:
- dna
lib_struct: ""
library_protocol: massively parallel reporter assay (OBI:0002675)
library_kit: Custom
sequence_protocol: Illumina NextSeq 500 (EFO:0009173)
sequence_kit: NextSeq 500 Mid Output v2 Kit
sequence_spec:
- !Read
read_id: Oligo fwd
name: Forward oligo read
modality: dna
primer_id: R1_custom_primer
min_len: 146
max_len: 146
strand: pos
files:
- !File
file_id: IGVFFI7003XVUG
filename: IGVFFI7003XVUG.fastq.gz
md5: f30f12ecabf07277bb0199c907187187
filetype: fastq
filesize: 6946181066
url: https://api.data.igvf.org/sequence-files/IGVFFI7003XVUG/@@download/IGVFFI7003XVUG.fastq.gz
urltype: https
- !File
file_id: IGVFFI5231ATBS
filename: IGVFFI5231ATBS.fastq.gz
md5: b1913d3806ebf2fb4ae230003e40e6ea
filetype: fastq
filesize: 9720715570
url: https://api.data.igvf.org/sequence-files/IGVFFI5231ATBS/@@download/IGVFFI5231ATBS.fastq.gz
urltype: https
- !File
file_id: IGVFFI0921LXBF
filename: IGVFFI0921LXBF.fastq.gz
md5: e1bc1ddbbbc49d80251b3fc617822a32
filetype: fastq
filesize: 10165101536
url: https://api.data.igvf.org/sequence-files/IGVFFI0921LXBF/@@download/IGVFFI0921LXBF.fastq.gz
urltype: https
- !Read
read_id: Oligo rev
name: Reverse oligo read
modality: dna
primer_id: R3_custom_primer
min_len: 146
max_len: 146
strand: neg
files:
- !File
file_id: IGVFFI4403ENTR
filename: IGVFFI4403ENTR.fastq.gz
md5: 01e019b8b23558584b4c98a791c2a445
filetype: fastq
filesize: 7459407909
url: https://api.data.igvf.org/sequence-files/IGVFFI4403ENTR/@@download/IGVFFI4403ENTR.fastq.gz
urltype: https
- !File
file_id: IGVFFI2142OYFW
filename: IGVFFI2142OYFW.fastq.gz
md5: dbb4f3cbdb1045085b9162c2dfbb1102
filetype: fastq
filesize: 10198975067
url: https://api.data.igvf.org/sequence-files/IGVFFI2142OYFW/@@download/IGVFFI2142OYFW.fastq.gz
urltype: https
- !File
file_id: IGVFFI6807PKQA
filename: IGVFFI6807PKQA.fastq.gz
md5: 1089ed561c85b9cf89f4c4cff27bf8b2
filetype: fastq
filesize: 10295293708
url: https://api.data.igvf.org/sequence-files/IGVFFI6807PKQA/@@download/IGVFFI6807PKQA.fastq.gz
urltype: https
- !Read
read_id: BC
name: Barcode read
modality: dna
primer_id: R2_custom_primer
min_len: 15
max_len: 15
strand: pos
files:
- !File
file_id: IGVFFI8640LLIG
filename: IGVFFI8640LLIG.fastq.gz
md5: 3dc5961e711f619630f204857fbc22bd
filetype: fastq
filesize: 1252997951
url: https://api.data.igvf.org/sequence-files/IGVFFI8640LLIG/@@download/IGVFFI8640LLIG.fastq.gz
urltype: https
- !File
file_id: IGVFFI0576IRDC
filename: IGVFFI0576IRDC.fastq.gz
md5: 5a0772e39f4e22cf1db3d4c77e164d7f
filetype: fastq
filesize: 1719113872
url: https://api.data.igvf.org/sequence-files/IGVFFI0576IRDC/@@download/IGVFFI0576IRDC.fastq.gz
urltype: https
- !File
file_id: IGVFFI6354NJGB
filename: IGVFFI6354NJGB.fastq.gz
md5: fd2ea69299e807d346a36c773726e8b9
filetype: fastq
filesize: 1809729998
url: https://api.data.igvf.org/sequence-files/IGVFFI6354NJGB/@@download/IGVFFI6354NJGB.fastq.gz
urltype: https
library_spec:
- !Region
parent_id: null
region_id: dna
region_type: dna
name: primer, barcode and umi
sequence_type: joined
sequence: AATGATACGGCGACCACCGAGATCTACACXXXXXXXXXXCAGCCTGCATTTCTGCCAGGGCCCGCTCTAGACCTGCAGGAGGACCGGATCAACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAAAGTGAACACATCGCTAAGCGAAAGCTAAGGAAGCTCGACTTCCAGCTTGGCAATCCGGTACTGTCATTGCGTGAACCGACACTAGAGGGTATATAATGXXXXXXXXXXXXXXXACCGGTCGCCACCATGGTGAGCAAGGGCGAGGAGCATCTCGTATGCCGTCTTCTGCTTG
min_len: 470
max_len: 470
onlist: null
regions:
- !Region
parent_id: dna
region_id: P5
region_type: illumina_p5
name: P5
sequence_type: fixed
sequence: AATGATACGGCGACCACCGAGATCTACAC
min_len: 29
max_len: 29
onlist: null
regions: null
- !Region
parent_id: dna
region_id: i5_index
region_type: index5
name: i5_index
sequence_type: random
sequence: XXXXXXXXXX
min_len: 10
max_len: 10
onlist: null
regions: null
- !Region
parent_id: dna
region_id: linker_1
region_type: linker
name: linker_1
sequence_type: fixed
sequence: CAGCCTGCATTTCTGCCAG
min_len: 19
max_len: 19
onlist: null
regions: null
- !Region
parent_id: dna
region_id: R1_custom_primer
region_type: custom_primer
name: R1_custom_primer
sequence_type: fixed
sequence: GGCCCGCTCTAGACCTGCAGGAGGACCGGATCAACT
min_len: 36
max_len: 36
onlist: null
regions: null
- !Region
parent_id: dna
region_id: oligo
region_type: dna
name: oligo
sequence_type: onlist
sequence: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
min_len: 200
max_len: 200
onlist: !Onlist
file_id: IGVFFI2041KXFD
filename: IGVFFI2041KXFD.tsv.gz
md5: ca4f3d660dfcee1afd99c766d888ac80
filetype: tsv
filesize: 14033497
url: https://api.data.igvf.org/tabular-files/IGVFFI2041KXFD/@@download/IGVFFI2041KXFD.tsv.gz
urltype: https
regions: null
- !Region
parent_id: dna
region_id: R3_custom_primer
region_type: custom_primer
name: R3_custom_primer
sequence_type: fixed
sequence: CATTGCGTGAACCGACACTAGAGGGTATATAATG
min_len: 34
max_len: 34
onlist: null
regions: null
- !Region
parent_id: dna
region_id: linker_2
region_type: linker
name: linker_2
sequence_type: fixed
sequence: GAAGCTCGACTTCCAGCTTGGCAATCCGGTACTGT
min_len: 35
max_len: 35
onlist: null
regions: null
- !Region
parent_id: dna
region_id: R2_custom_primer
region_type: custom_primer
name: R2_custom_primer
sequence_type: fixed
sequence: GCAAAGTGAACACATCGCTAAGCGAAAGCTAAG
min_len: 33
max_len: 33
onlist: null
regions: null
- !Region
parent_id: dna
region_id: barcode
region_type: barcode
name: barcode
sequence_type: random
sequence: XXXXXXXXXXXXXXX
min_len: 15
max_len: 15
onlist: null
regions: null
- !Region
parent_id: dna
region_id: linker_3
region_type: linker
name: linker_3
sequence_type: fixed
sequence: ACCGGTCGCCACCATGGTGAGCAAGGGCGAGGAGC
min_len: 35
max_len: 35
onlist: null
regions: null
- !Region
parent_id: dna
region_id: P7
region_type: illumina_p7
name: P7
sequence_type: fixed
sequence: ATCTCGTATGCCGTCTTCTGCTTG
min_len: 24
max_len: 24
onlist: null
regions: null