title: ExFig_4c_PDCD1_site2_subs_AS_PE2_TL17nt

description: Amplified from the human PDCD1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm40_rep2

status: Public on Oct 23 2021

type: SRA

city: Beijing

first: Hao

last: Wu

address: HaiDian, Beijing

department: Peking University

country: China

institute: Peking University

description: Amplified from the human EMX1 locus

library_source: genomic

data_processing:
Removed-adapter reads were aligned to corresponding amplicon reference with BWA MEM algorithm (v0.7.17-r1188).
After alignment, mapped reads were sorted by positions and converted into mpileup format with samtools (v1.10).
Targeted amplicon sequencing data was analyzed using the published toolkit CRlSPResso2 (v2.0.45).
Graphpad prism 9 was used to analyze the data.
Sanger sequencing data was analyzed using the Snapgene.
The.mpileup files were converted into.bmat files by Python scripts of "Detect-Seq" pipeline (http://detect-seq.com/).
Potential off-target sites were predicted using Cas-OFFinder (V2.4).
Genome_build: WT amplicon sequences were used as WT amplicon genome references, HDR amplicon sequences were used as HDR (insertion and deletion) amplicon references.
Supplementary_files_format_and_content: MPILEUP format: mutation information.

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured and maintained at 37 °C in DMEM medium plus additional 10% FBS. For HCT116 cells, they were maintained in RPMI medium supplementing with 10% FBS.

extract_protocol:
Genomic DNA was extracted with CWBIO universal genomic DNA kit (CWbiotech, CW2298M) following the manufacturer’s protocol.
Genomic sites to be identified were amplified from genomic DNA samples and sequenced on the Illumina NovaSeq platform.
Targeted amplicon based high throughput sequencing

treatment_protocol: Plasmid transfections into HEK293T or HCT116 cells were conducted with lipofectamine 2000 as the manufacturer’s instructions.

tag: cell type

value: human embryonic kidney 293 cells

tag: treatment

value: transfected with HOPE vectors for 72 h

tag: cell line

value: HEK293T cells


title: Ex_Fig_3e_EMX1subs_S_tm26_rep1

description: Amplified from the human EMX1 locus

value: transfected with PE2 vectors for 72 h


title: ExFig_4c_PDCD1_site2_subs_HOPE_sTL10nt_asTL17nt

description: Amplified from the human PDCD1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm40_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm44_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm26_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm40_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm33_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm45_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm26_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_HOPE_tm33_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm26_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm45_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm34_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm34_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_S_tm43_rep2

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm40_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3e_EMX1subs_AS_tm26_rep1

description: Amplified from the human EMX1 locus


title: Ex_Fig_3d_EMX1site2del_S_tm38_rep3

description: Amplified from the human EMX1site2 locus


title: Ex_Fig_3d_EMX1site2del_S_tm32_rep3


title: Ex_Fig_3d_EMX1site2del_HOPE_tm38_rep3


title: Ex_Fig_3d_EMX1site2del_HOPE_tm42_rep3


title: Ex_Fig_3d_EMX1site2del_AS_tm43_rep3


title: Ex_Fig_3d_EMX1site2del_AS_tm37_rep3


title: Ex_Fig_3d_EMX1site2del_S_tm42_rep2


title: Ex_Fig_3d_EMX1site2del_S_tm38_rep2


title: Ex_Fig_3d_EMX1site2del_S_tm32_rep2


title: Ex_Fig_3d_EMX1site2del_AS_tm34_rep3


title: Ex_Fig_3d_EMX1site2del_HOPE_tm32_rep2


title: Ex_Fig_3d_EMX1site2del_HOPE_tm38_rep2


title: Ex_Fig_3d_EMX1site2del_AS_tm37_rep2


title: Ex_Fig_3d_EMX1site2del_S_tm32_rep1


title: Ex_Fig_3d_EMX1site2del_HOPE_tm42_rep1


title: Ex_Fig_3d_EMX1site2del_AS_tm43_rep2


title: Ex_Fig_3d_EMX1site2del_S_tm38_rep1


title: Ex_Fig_3d_EMX1site2del_AS_tm34_rep2


title: Ex_Fig_3d_EMX1site2del_AS_tm43_rep1


title: Ex_Fig_3d_EMX1site2del_AS_tm34_rep1


title: Ex_Fig_3d_EMX1site2del_AS_tm37_rep1


title: Ex_Fig_3c_ABE21del_S_tm45_rep3

description: Amplified from the human ABEsite21 locus


title: Ex_Fig_3d_EMX1site2del_S_tm42_rep3


title: Ex_Fig_3d_EMX1site2del_HOPE_tm32_rep1


title: Ex_Fig_3c_ABE21del_S_tm42_rep3


title: Ex_Fig_3d_EMX1site2del_HOPE_tm32_rep3


title: Ex_Fig_3c_ABE21del_S_tm34_rep3


title: Ex_Fig_3c_ABE21del_S_tm28_rep3


title: Ex_Fig_3d_EMX1site2del_HOPE_tm42_rep2


title: Ex_Fig_3c_ABE21del_HOPE_tm42_rep3


title: Ex_Fig_3c_ABE21del_HOPE_tm34_rep3


title: Ex_Fig_3c_ABE21del_HOPE_tm45_rep3


title: Ex_Fig_3c_ABE21del_AS_tm45_rep3


title: Ex_Fig_3c_ABE21del_AS_tm34_rep3


title: Ex_Fig_3c_ABE21del_AS_tm40_rep3


title: Ex_Fig_3c_ABE21del_S_tm45_rep2


title: Ex_Fig_3d_EMX1site2del_HOPE_tm38_rep1


title: Ex_Fig_3c_ABE21del_S_tm42_rep2


title: Ex_Fig_3d_EMX1site2del_S_tm42_rep1


title: Ex_Fig_3c_ABE21del_S_tm34_rep2


title: Ex_Fig_3c_ABE21del_AS_tm28_rep3


title: Ex_Fig_3c_ABE21del_S_tm28_rep2


title: Ex_Fig_3c_ABE21del_HOPE_tm34_rep2


title: Ex_Fig_3c_ABE21del_HOPE_tm45_rep2


title: Ex_Fig_3c_ABE21del_HOPE_tm28_rep2


title: Ex_Fig_3c_ABE21del_AS_tm28_rep2


title: Ex_Fig_3c_ABE21del_AS_tm40_rep2


title: Ex_Fig_3c_ABE21del_S_tm45_rep1


title: Ex_Fig_3c_ABE21del_HOPE_tm45_rep1


title: Ex_Fig_3c_ABE21del_S_tm28_rep1


title: Ex_Fig_3c_ABE21del_S_tm42_rep1


title: Ex_Fig_3c_ABE21del_AS_tm34_rep2


title: Ex_Fig_3c_ABE21del_HOPE_tm28_rep1


title: Ex_Fig_3c_ABE21del_AS_tm45_rep1


title: Ex_Fig_3c_ABE21del_S_tm34_rep1


title: Ex_Fig_3c_ABE21del_AS_tm34_rep1


title: Ex_Fig_3c_ABE21del_HOPE_tm34_rep1


title: Ex_Fig_3c_ABE21del_HOPE_tm42_rep1


title: Ex_Fig_3c_ABE21del_AS_tm40_rep1


title: Ex_Fig_3c_ABE21del_HOPE_tm28_rep3


title: Ex_Fig_3b_PRNPsubs_S_tm30_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm40_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm49_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm22_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3c_ABE21del_HOPE_tm42_rep2


title: Ex_Fig_3b_PRNPsubs_S_tm34_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3c_ABE21del_AS_tm45_rep2


title: Ex_Fig_3b_PRNPsubs_HOPE_tm40_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm34_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm49_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm22_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm30_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm45_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm40_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm34_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm30_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm22_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm44_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm49_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3c_ABE21del_AS_tm28_rep1


title: Ex_Fig_3b_PRNPsubs_HOPE_tm44_rep3

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm30_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm34_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm44_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm44_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm22_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm40_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm49_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm34_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm40_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm49_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm30_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm45_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm34_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm22_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm49_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm40_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm44_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm49_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm40_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm49_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm22_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm40_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm34_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_S_tm30_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm22_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm30_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm44_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_HOPE_tm22_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm40_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm49_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm45_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm47_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3b_PRNPsubs_AS_tm22_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm34_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3b_PRNPsubs_AS_tm30_rep2

description: Amplified from the human PRNP locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm42_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm38_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm30_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm18_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm24_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm42_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm47_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm30_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3b_PRNPsubs_S_tm34_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm55_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm55_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm24_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm42_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm38_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm18_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3b_PRNPsubs_AS_tm30_rep1

description: Amplified from the human PRNP locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm38_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm47_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm54_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm18_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm30_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm24_rep3

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm38_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm47_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm55_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm42_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm18_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm30_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm24_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm42_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm47_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm54_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm38_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm18_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm24_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm55_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm30_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm47_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm42_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm30_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm18_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm24_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm54_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm42_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm38_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm55_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm24_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm18_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm47_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm30_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm24_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm42_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm18_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm30_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm38_rep2

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm55_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm18_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm30_rep1

description: Amplified from the human HEK3 locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_7_rep3

description: Amplified from the human FANCF locus

value: transfected with PE3 vectors for 72 h


title: Ex_Fig_3a_HEK3_FlagIns_HOPE_tm38_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm38_rep1

description: Amplified from the human HEK3 locus


title: Ex_Fig_3a_HEK3_FlagIns_S_tm47_rep1

description: Amplified from the human HEK3 locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_5_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_10_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_8_rep3

description: Amplified from the human FANCF locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm47_rep1

description: Amplified from the human HEK3 locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_6_rep3

description: Amplified from the human FANCF locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm42_rep1

description: Amplified from the human HEK3 locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_10_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_3_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_4_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_8_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_6_rep2

description: Amplified from the human FANCF locus


title: Ex_Fig_3a_HEK3_FlagIns_AS_tm24_rep1

description: Amplified from the human HEK3 locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_7_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_4_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_5_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_1_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_3_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_2_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_6_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_10_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_7_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_8_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_5_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_3_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_2_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_2_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_4_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis2_2_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis2_2_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis2_1_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_1_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_10_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis2_2_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis3_1_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis2_1_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_7_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_6_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_5_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_8_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_2_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_3_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_4_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_1_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_8_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_4_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_7_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_3_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_5_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_6_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_10_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_PE3_subs_AS_mis2_1_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_1_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_2_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_8_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_4_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_5_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_1_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_7_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_10_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_3_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_2_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis3_6_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis2_2_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis2_2_rep1

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis2_1_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis2_1_rep2

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis2_1_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_17_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_15_rep3

description: Amplified from the human FANCF locus


title: Fig_6b_FANCF_HOPE_subs_AS_mis2_2_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_14_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_13_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_12_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_16_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_10_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_8_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_5_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_6_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_2_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_9_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_3_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_4_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_1_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_16_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_12_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_13_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_11_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_17_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_9_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_10_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_15_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_14_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_5_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_6_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_4_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_3_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_8_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_7_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_7_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_11_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_2_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_1_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_15_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_16_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_10_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_7_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_9_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_12_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_8_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_13_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_11_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_5_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_6_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_4_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_2_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_1_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis2_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_3_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_ontarget_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_17_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis2_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis2_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_15_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_14_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_PE3_subs_S_mis3_14_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_9_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_16_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_7_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_10_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_12_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_11_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_13_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_8_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_6_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_16_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_15_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_4_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_3_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_17_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_1_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_2_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_5_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_10_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_13_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_17_rep3

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_11_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_6_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_5_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_14_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_7_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_12_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_1_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_4_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_16_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_15_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_3_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_2_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_14_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_8_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_9_rep2

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_17_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_11_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_12_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_6_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_5_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_8_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_3_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis2_rep2

description: Amplified from the human FANCF locus


title: Fig_5e_HEK3_ins_cor_PE3_rep2

description: Amplified from the human HEK3 locus

source_name: HCT116 cells

value: human colorectal carcinoma cells

value: HCT116 cells


title: Fig_6a_FANCF_HOPE_subs_S_mis3_4_rep1

description: Amplified from the human FANCF locus


title: Fig_5e_HEK3_ins_cor_PE3_rep1

description: Amplified from the human HEK3 locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_2_rep1

description: Amplified from the human FANCF locus


title: Fig_5e_HEK3_ins_HOPE_rep2

description: Amplified from the human HEK3 locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_1_rep1

description: Amplified from the human FANCF locus


title: Fig_5e_HEK3_ins_S_PE2_rep2

description: Amplified from the human HEK3 locus


title: Fig_5d_HEK5_del_HOPE_rep3

description: Amplified from the human HEK5 locus


title: Fig_5e_HEK3_ins_S_PE2_rep1

description: Amplified from the human HEK3 locus


title: Fig_5e_HEK3_ins_HOPE_rep1

description: Amplified from the human HEK3 locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_10_rep1

description: Amplified from the human FANCF locus


title: Fig_5d_HEK5_del_HOPE_rep2

description: Amplified from the human HEK5 locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_13_rep1

description: Amplified from the human FANCF locus


title: Fig_5d_HEK5_del_AS_PE2_rep3

description: Amplified from the human HEK5 locus


title: Fig_5e_HEK3_ins_cor_PE3_rep3

description: Amplified from the human HEK3 locus


title: Fig_5d_HEK5_del_HOPE_rep1

description: Amplified from the human HEK5 locus


title: Fig_6a_FANCF_HOPE_subs_S_mis2_rep3

description: Amplified from the human FANCF locus


title: Fig_5d_HEK5_del_cor_PE3_rep3

description: Amplified from the human HEK5 locus


title: Fig_5e_HEK3_ins_S_PE2_rep3

description: Amplified from the human HEK3 locus


title: Fig_5e_HEK3_ins_HOPE_rep3

description: Amplified from the human HEK3 locus


title: Fig_5d_HEK5_del_cor_PE3_rep1

description: Amplified from the human HEK5 locus


title: Fig_5d_HEK5_del_S_PE2_rep2

description: Amplified from the human HEK5 locus


title: Fig_5d_HEK5_del_cor_PE3_rep2

description: Amplified from the human HEK5 locus


title: Fig_6a_FANCF_HOPE_subs_S_mis2_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_9_rep1

description: Amplified from the human FANCF locus


title: Fig_6a_FANCF_HOPE_subs_S_mis3_7_rep1

description: Amplified from the human FANCF locus


title: Fig_5d_HEK5_del_S_PE2_rep1

description: Amplified from the human HEK5 locus


title: Fig_5d_HEK5_del_AS_PE2_rep2

description: Amplified from the human HEK5 locus


title: Fig_5c_EMX1site2_del_HOPE_rep3


title: Fig_5d_HEK5_del_AS_PE2_rep1

description: Amplified from the human HEK5 locus


title: Fig_5d_HEK5_del_S_PE2_rep3

description: Amplified from the human HEK5 locus


title: Fig_5c_EMX1site2_del_cor_PE3_rep2


title: Fig_5c_EMX1site2_del_HOPE_rep1


title: Fig_5c_EMX1site2_del_cor_PE3_rep3


title: Fig_5c_EMX1site2_del_AS_PE2_rep2


title: Fig_5c_EMX1site2_del_HOPE_rep2


title: Fig_5c_EMX1site2_del_AS_PE2_rep3


title: Fig_5c_EMX1site2_del_AS_PE2_rep1


title: Fig_5c_EMX1site2_del_S_PE2_rep2


title: Fig_5b_PDCD1_subs_cor_PE3_rep3

description: Amplified from the human PDCD1 locus


title: Fig_5b_PDCD1_subs_HOPE_rep3

description: Amplified from the human PDCD1 locus


title: Fig_5b_PDCD1_subs_HOPE_rep2

description: Amplified from the human PDCD1 locus


title: Fig_5b_PDCD1_subs_AS_PE2_rep3

description: Amplified from the human PDCD1 locus


title: Fig_5b_PDCD1_subs_AS_PE2_rep1

description: Amplified from the human PDCD1 locus


title: Fig_5b_PDCD1_subs_S_PE2_rep2

description: Amplified from the human PDCD1 locus


title: Fig_5b_PDCD1_subs_S_PE2_rep3

description: Amplified from the human PDCD1 locus


title: Fig_5c_EMX1site2_del_cor_PE3_rep1


title: Fig_5a_FANCF_subs_opti_PE3_rep3

description: Amplified from the human FANCF locus


title: Fig_5b_PDCD1_subs_S_PE2_rep1

description: Amplified from the human PDCD1 locus


title: Fig_5a_FANCF_subs_opti_PE3_rep2

description: Amplified from the human FANCF locus


title: Fig_5a_FANCF_subs_cor_PE3_rep3

description: Amplified from the human FANCF locus


title: Fig_5a_FANCF_subs_opti_PE3_rep1

description: Amplified from the human FANCF locus


title: Fig_5a_FANCF_subs_cor_PE3_rep1

description: Amplified from the human FANCF locus


title: Fig_5c_EMX1site2_del_S_PE2_rep3


title: Fig_5a_FANCF_subs_cor_PE3_rep2

description: Amplified from the human FANCF locus


title: Fig_5a_FANCF_subs_HOPE_rep3

description: Amplified from the human FANCF locus


title: Fig_5a_FANCF_subs_S_PE2_rep1

description: Amplified from the human FANCF locus


title: Fig_5b_PDCD1_subs_cor_PE3_rep2

description: Amplified from the human PDCD1 locus


title: Fig_4g_EMX1site2_del_cor_PE3_rep3


title: Fig_5b_PDCD1_subs_cor_PE3_rep1

description: Amplified from the human PDCD1 locus


title: Fig_5a_FANCF_subs_S_PE2_rep2

description: Amplified from the human FANCF locus


title: Fig_5c_EMX1site2_del_S_PE2_rep1


title: Fig_5b_PDCD1_subs_HOPE_rep1

description: Amplified from the human PDCD1 locus


title: Fig_5a_FANCF_subs_HOPE_rep1

description: Amplified from the human FANCF locus


title: Fig_4g_EMX1site2_del_cor_PE3_rep2


title: Fig_4g_EMX1site2_del_cor_PE3_rep1


title: Fig_4g_EMX1site2_del_HOPE_rep3


title: Fig_4g_EMX1site2_del_HOPE_rep2


title: CoV2 4

city: Atlanta

first: Mehul

last: Suthar

state: GA

address: 2015 Uppergate Dr

department: Department of Pediatrics

country: USA

institute: Emory University School of Medicine

library_source: transcriptomic

data_processing:
Base-calling done at  RTA v3.4.4
cellranger mkfastq used to demultiplex raw base call (BCL) files generated by Illumina sequencer into FASTQ files
cellranger count used to perform alignment, filtering, barcode counting, and UMI counting (provided BAM files and processed count matrices)
Genome_build: Mouse reference, mm10 (GENCODE vM23/Ensembl 98)
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing only cellular barcodes in MEX format produced from cellranger count

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
GEMS were captured on a 10x Chromium Controller using the Chromium NextGEM Single Cell Gel bead kit according to manufacturer's instruction
Chromium NextGEM Single Cell 5′ Library, according to manufacturer's instructions.

tag: tissue

value: lung

tag: timepoint

value: Day 4 p.i.

tag: age

value: 10 weeks of age


title: Fig_4g_EMX1site2_del_HOPE_rep1


title: Fig_5b_PDCD1_subs_AS_PE2_rep2

description: Amplified from the human PDCD1 locus


title: CoV2 2


title: CoV2 3


title: Fig_5a_FANCF_subs_HOPE_rep2

description: Amplified from the human FANCF locus


title: Fig_5a_FANCF_subs_S_PE2_rep3

description: Amplified from the human FANCF locus


title: Fig_4g_EMX1site2_del_AS_PE2_rep1


title: Fig_4g_EMX1site2_del_AS_PE2_rep2


title: Mock 3

value: PBS (uninfected)


title: CoV2 1


title: Mock 2


title: Mock 4


title: Fig_4g_EMX1site2_del_S_PE2_rep3


title: Fig_4g_EMX1site2_del_S_PE2_rep2


title: Fig_4f_ABEsite21_del_cor_PE3_rep3


title: Fig_4f_ABEsite21_del_cor_PE3_rep2


title: Fig_4f_ABEsite21_del_cor_PE3_rep1


title: SC266

city: Providence

first: Bess

last: Frost

state: RI

address: 185 Meeting St

institute: Center for Alzheimer’s Disease Research, Brown University

data_processing:
Sequenced reads were trimmed with trimmomatic and alligned to the mouse mm10 genome using STAR. Counts were then generated with TEtranscripts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with Deseq2 normalized transposon expression counts for every sample.

molecule: polyA RNA

source_name: Spinal Cord_Control

extract_protocol:
Qiagen RNeasy Mini kit
Illumina Truseq  150 bp paired-end stranded reads

tag: sample type

value: Total Spinal Cord Lysate

tag: mouse model

value: Control

value: 4 months


title: SC265


title: SC261

source_name: Spinal Cord_PS19


title: Fig_4f_ABEsite21_del_HOPE_rep3


title: SC259


title: Fig_4f_ABEsite21_del_HOPE_rep1


title: SC260


title: Fig_4f_ABEsite21_del_HOPE_rep2


title: SC258


title: Fig_4g_EMX1site2_del_AS_PE2_rep3


title: Fig_4f_ABEsite21_del_AS_PE2_rep3


title: SC257


title: Fig_4f_ABEsite21_del_AS_PE2_rep2


title: SC255


title: Mock 1


title: Fig_4f_ABEsite21_del_AS_PE2_rep1


title: Fig_4g_EMX1site2_del_S_PE2_rep1


title: Fig_4f_ABEsite21_del_S_PE2_rep1


title: Fig_4f_ABEsite21_del_S_PE2_rep3


title: SC190

value: 9 months


title: SC191


title: SC264


title: Fig_4f_ABEsite21_del_S_PE2_rep2


title: Fig_4e_PDCD1_del_cor_PE3_rep3

description: Amplified from the human PDCD1 locus


title: SC193


title: SC185


title: SC189


title: Fig_4e_PDCD1_del_HOPE_rep3

description: Amplified from the human PDCD1 locus


title: Fig_4e_PDCD1_del_cor_PE3_rep1

description: Amplified from the human PDCD1 locus


title: SC184


title: Fig_4e_PDCD1_del_cor_PE3_rep2

description: Amplified from the human PDCD1 locus


title: Fig_4e_PDCD1_del_HOPE_rep1

description: Amplified from the human PDCD1 locus


title: Fig_4e_PDCD1_del_HOPE_rep2

description: Amplified from the human PDCD1 locus


title: SC156


title: SC256


title: SC180


title: SC181


title: Fig_4e_PDCD1_del_AS_PE2_rep3

description: Amplified from the human PDCD1 locus


title: Fig_4e_PDCD1_del_AS_PE2_rep2

description: Amplified from the human PDCD1 locus


title: Fig_4e_PDCD1_del_AS_PE2_rep1

description: Amplified from the human PDCD1 locus


title: SC154


title: SC140


title: SC131


title: Fig_4e_PDCD1_del_S_PE2_rep3

description: Amplified from the human PDCD1 locus


title: Fig_4e_PDCD1_del_S_PE2_rep1

description: Amplified from the human PDCD1 locus


title: 24_CoH_X31_PR8_S256 [whole lung transcriptome]

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

data_processing:
SAMPLE 1 AND 2: Sequencing reads were mapped to the mouse genome (GRCm38) using Bowtie aligner (bowtie2 version 2.3.4.1) with local mode, -L 22 and -N 1 parameters (Langmead and Salzberg, 2012). Reads were assigned to Ensembl gene models (Mus_musculus.GRCm38.87.gtf) with featureCounts of the Subread software package (version 1.5.1) (Liao et al., 2014). The reads count matrices were organized corresponding to experimental design and used for subsequent statistical analysis using the bioconductor package edgeR (version 3.24.3) (McCarthy et al., 2012; Robinson et al., 2010). The raw reads count table were normalized by using default method in the package prior to generating statistics. Multidimensional scaling was performed with edgeR using the top 500 differentially expressed genes across samples. The regression model in the edgeR package with block design and interaction model was used for statistical analysis to select the corresponding significant genes.
SAMPLE 1 ONLY: The normalized reads table of mouse blood samples were reformatted to meet the requirements for the subsequent GSEA analysis (Mootha et al., 2003; Subramanian et al., 2005). The gene lists were prepared from human vaccination data and merged into an immune geneset (c7.immune.datasets.gmt) to generate a customized geneset (c7.custom.immune.datasets.gmt) (Mootha et al., 2003; Subramanian et al., 2005). The mouse datasets originated from either SPF or dirty mouse models were computed against the customized geneset by using desktop GSEA analysis engine with default parameters except the enrichment plot generation.
Bowtie 2 mapping
FeatureCounts for reads assignment
edgeR for statistical analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: rawcounts matrix

source_name: Whole lung

extract_protocol:
SAMPLE GROUP 1: Mouse PBMCs were isolated using FicolÒ-Paque PREMIUM (Millipore Sigma) and RNA was extracted using RNeasy Micro Plus Kit (Qiagen).
SAMPLE GROUP 1: The cDNA library was prepared using strand-specific RNA-sequencing protocols.
SAMPLE GROUP 1: Samples were run on an Illumina NovaSeq (150 bp paired-end). We obtained an average of 35 million read pairs per sample.
SAMPLE GROUP 2: Whole lungs were harvested and RNA was extracted using AllPrep DNA/RNA kit (Qiagen).
SAMPLE GROUP 2: The cDNA library was prepared using strand-specific RNA-sequencing protocols.
SAMPLE GROUP 2: Samples were run on an Illumina NovaSeq (50 bp paired-end). We obtained an average of 27 million read pairs per sample.

treatment_protocol:
SAMPLE GROUP 1: Mice were vaccinated intramuscularly (i.m.) with 180 ug of 2019-2020 seasonal quadrivalent influenza vaccine (Sanofi Pasteur) with or without 25 uL AddaVax (InvivoGen).
SAMPLE GROUP 2: For IAV infections, mice were anesthetized using a weight-based dose of ketamine/xylazine delivered intraperitoneally (i.p.). Mice were vaccinated intranasally (i.n.) with 1000 PFU of X31. For challenge, mice were infected i.n. with 1000 PFU of PR8.

tag: tissue/cell type

value: Whole lung

tag: strain

tag: treatment (spf or dirty)

value: Dirty, cohoused

tag: treatment vaccination/infection

value: X31 vaccinated, PR8 challenged

tag: treatment time point

value: 2 days post challenge


title: 23_CoH_X31_PR8_S255 [whole lung transcriptome]


title: Fig_4e_PDCD1_del_S_PE2_rep2

description: Amplified from the human PDCD1 locus

value: human embryonic kidney 293 cells

value: HEK293T cells


title: Fig_4d_PDCD1_ins_cor_PE3_rep1

description: Amplified from the human PDCD1 locus

value: transfected with PE3 vectors for 72 h


title: 22_CoH_X31_PR8_S254 [whole lung transcriptome]


title: 20_CoH_X31_S264 [whole lung transcriptome]

value: X31 vaccinated

value: 31 days post vaccination


title: Fig_4d_PDCD1_ins_cor_PE3_rep3

description: Amplified from the human PDCD1 locus


title: 21_CoH_X31_PR8_S253 [whole lung transcriptome]


title: Fig_4d_PDCD1_ins_HOPE_rep3

description: Amplified from the human PDCD1 locus

value: transfected with HOPE vectors for 72 h


title: 19_CoH_X31_S252 [whole lung transcriptome]


title: Fig_4d_PDCD1_ins_cor_PE3_rep2

description: Amplified from the human PDCD1 locus


title: Fig_4d_PDCD1_ins_HOPE_rep2

description: Amplified from the human PDCD1 locus


title: 17_CoH_X31_S262 [whole lung transcriptome]


title: 18_CoH_X31_S263 [whole lung transcriptome]


title: SC155


title: Fig_4d_PDCD1_ins_AS_PE2_rep3

description: Amplified from the human PDCD1 locus

value: transfected with PE2 vectors for 72 h


title: Fig_4d_PDCD1_ins_AS_PE2_rep2

description: Amplified from the human PDCD1 locus


title: Fig_4d_PDCD1_ins_AS_PE2_rep1

description: Amplified from the human PDCD1 locus


title: 15_CoH_Naive_S261 [whole lung transcriptome]

value: Naïve


title: Fig_4d_PDCD1_ins_S_PE2_rep3

description: Amplified from the human PDCD1 locus


title: 14_CoH_Naive_S251 [whole lung transcriptome]


title: 13_CoH_Naive_S266 [whole lung transcriptome]


title: Fig_4d_PDCD1_ins_S_PE2_rep2

description: Amplified from the human PDCD1 locus


title: 12_SPF_X31_PR8_S250 [whole lung transcriptome]

value: SPF


title: 11_SPF_X31_PR8_S249 [whole lung transcriptome]


title: Fig_4c_HEK3_ins_opti_PE3_rep3

description: Amplified from the human HEK3 locus


title: Fig_4c_HEK3_ins_opti_PE3_rep2

description: Amplified from the human HEK3 locus


title: Fig_4d_PDCD1_ins_S_PE2_rep1

description: Amplified from the human PDCD1 locus


title: 10_SPF_X31_PR8_S248 [whole lung transcriptome]


title: Fig_4c_HEK3_ins_opti_PE3_rep1

description: Amplified from the human HEK3 locus


title: Fig_4d_PDCD1_ins_HOPE_rep1

description: Amplified from the human PDCD1 locus


title: 9_SPF_X31_PR8_S247 [whole lung transcriptome]


title: 16_CoH_Naive_S267 [whole lung transcriptome]


title: 7_SPF_X31_S260 [whole lung transcriptome]


title: 4_SPF_Naive_S258 [whole lung transcriptome]


title: 5_SPF_X31_S246 [whole lung transcriptome]


title: Fig_4c_HEK3_ins_cor_PE3_rep3

description: Amplified from the human HEK3 locus


title: Fig_4c_HEK3_ins_HOPE_rep3

description: Amplified from the human HEK3 locus


title: Fig_4c_HEK3_ins_cor_PE3_rep2

description: Amplified from the human HEK3 locus


title: Fig_4c_HEK3_ins_cor_PE3_rep1

description: Amplified from the human HEK3 locus


title: Fig_4c_HEK3_ins_HOPE_rep2

description: Amplified from the human HEK3 locus


title: 3_SPF_Naive_S257 [whole lung transcriptome]


title: 2_SPF_Naive_S245 [whole lung transcriptome]


title: Fig_4c_HEK3_ins_S_PE2_rep3

description: Amplified from the human HEK3 locus


title: Fig_4c_HEK3_ins_HOPE_rep1

description: Amplified from the human HEK3 locus


title: 26_CoH_72_Naive_S78 [PBMC vaccine transcriptome]

source_name: PBMC

value: PBMC

value: 72 hours


title: 1_SPF_Naive_S244 [whole lung transcriptome]


title: Fig_4c_HEK3_ins_S_PE2_rep2

description: Amplified from the human HEK3 locus


title: Fig_4c_HEK3_ins_S_PE2_rep1

description: Amplified from the human HEK3 locus


title: 8_SPF_X31_S265 [whole lung transcriptome]


title: 26_CoH_24_Naive_S52 [PBMC vaccine transcriptome]

value: 24 hours


title: KO3

city: NY

first: Yoshinobu

last: Nakayama

state: NY

address: 160 Convent Ave

institute: City College of New York

data_processing:
The trimmed reads were mapped to the mus musculus GRCm38 reference genome available on ENSEMBL using STAR ultrafast universal RNA-seq aligner.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The differential expression analysis was performed by DESeq2
The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample

source_name: ARRDC4 knock-out by CRISPR-Cas9

growth_protocol: In vivo tissues

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep kit, according to the manufacturer’s instructions.

value: heart

tag: background strain

tag: genotype

value: ARRDC4 knock-out


title: KO2


title: 6_SPF_X31_S259 [whole lung transcriptome]

value: Whole lung


title: WT2

source_name: ARRDC4 WT

value: wild-type


title: Fig_3&Ex_Fig_2__EMX1_subs_opti_PE3

description: Amplified from the human EMX1 locus


title: 26_CoH_0_Naive_S26 [PBMC vaccine transcriptome]

value: Dirty, cohoused


title: 25_CoH_72_Naive_S77 [PBMC vaccine transcriptome]


title: WT1


title: 25_CoH_0_Naive_S25 [PBMC vaccine transcriptome]


title: Fig_2f_EMX1_subs_opti_PE3_rep3

description: Amplified from the human EMX1 locus

value: human embryonic kidney 293 cells


title: RAS_3_CEBPB

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: ChIP-seq

data_processing:
Fastq files were quality checked using FastQC [Babraham Institute, Simon Andrews], trimmed using cutadapt 2.0 [https://doi.org/10.14806/ej.17.1.200]
Reads were aligned with bowtie2 [Langmead and Salzberg 2012, Nature Methods] using default parameters and samtools [Li et al. 2009, Bioinformatics] was used for selecting only uniquely mapping reads and removing duplicates.
Alignment files corresponding to multiple lanes were merged using samtools [Li et al. 2009, Bioinformatics].
Peak calling was performed using macs2 [Zhang et al 2008, Genome Biology] in two stages, one with default parameters and one with insert sizes calculated using ChIPQC [Caroll et al. Frontiers in Genetics and R Bioconductor].
BigWig files were obtained by using THOR [Alhoff et al. 2016, Nucleic Acids Research] which performs input subtraction and library normalisation, as well as differential binding analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: IMR90 cells

growth_protocol: IMR90 cells (ATCC) were cultured in DMEM supplemented with 10% FBS. Cells were maintained in physiological 5% O2.

extract_protocol:
Fixed cells were lysed and sonicated to generate 200-400 bp chromatin fragments before immunoprecipitation.
Libraries were prepared using the NEBnext ultra II DNA-library prep kit for Illumina (E7645) according to manufacturers instructions except that size selection was performed during the final bead purification step using SPRIselect beads (B23319, Beckman Coulter)

treatment_protocol: For RIS samples,IMR90 ER:HRAS(G12V) cells were treated for 6 days with 100nM 4OHT.

tag: passage

value: pLNCX2 ER:HRAS G12V

value: 4OHT (6 days)

value: pQCXIN-i N1ICD

tag: antibody

value: C/EBPb (C-19, Santa Cruz,sc-150)


title: RAS_1_CEBPB

description: ChIP-seq


title: Fig_2f_EMX1_subs_opti_PE3_rep2

description: Amplified from the human EMX1 locus

tag: cell type

value: transfected with PE3 vectors for 72 h

value: HEK293T cells


title: 25_CoH_24_Naive_S51 [PBMC vaccine transcriptome]

value: Naïve


title: InputRAS

description: ChIP-seq


title: Fig_3&Ex_Fig_2__EMX1_subs_PE2

description: Amplified from the human EMX1 locus

tag: treatment

value: transfected with PE2 vectors for 72 h


title: WT3


title: RAS_2_CEBPB

description: ChIP-seq


title: Ctrl_3_CEBPB

description: ChIP-seq


title: KO1


title: Fig_2f_EMX1_subs_opti_PE3_rep1

description: Amplified from the human EMX1 locus

tag: cell line


title: InputCTRL

description: ChIP-seq


title: 24_CoH_24_Naive_S50 [PBMC vaccine transcriptome]

value: PBMC


title: Ctrl_2_CEBPB

description: ChIP-seq


title: Fig_3&Ex_Fig_2__EMX1_subs_HOPE_PAM_in_14nt

description: Amplified from the human EMX1 locus

value: transfected with HOPE vectors for 72 h


title: Fig_2f_EMX1_subs_HOPE_PAM_in_41nt_rep3

description: Amplified from the human EMX1 locus


title: 24_CoH_0_Naive_S24 [PBMC vaccine transcriptome]


title: 24_CoH_72_Naive_S76 [PBMC vaccine transcriptome]

value: 72 hours


title: Cohort2_642X_0_TET

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
Cohort2_642X_0_TET
Cohort2.vsn.normalised.csv

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform, with 6 samples pooled per lane.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the human GRCh38 genome assembly including ERCC spike-ins using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.45.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count quantitation file was generated by counting reads using Rsubread, normalisation with RUVseq package (k = 3, with model.matrix ~d$sex +d$group) followed by vsd normalisation using ‘varianceStabilzingTransformation’ within DESeq2 package. Row names are Ensembl_IDs, with each sample included as columns.

source_name: TET

extract_protocol:
PBMCs were isolated at the Babraham Institute by density gradient centrifugation and cryopreserved in liquid nitrogen. Before sorting, ~10-30 million PBMC cells were thawed in culture media and rested for 2 hours at 37 degrees C, after which influenza HLADR tetramers (TET)added along with a panel of cell surface antibodies. Live CD3+ CD4+ CD45RA- TET+ cells were sorted on a BD Aria Fusion sorter directly into 1x lysis buffer as per the SmartseqV4 Ultra low input RNA kit for sequencing from Takara Clontech. Cells from day 7 after vaccination (cTfhTet) were also sorted on the basis of expressing PD1 and CXCR5 markers.
cDNA was prepared directly from cells (40-1000 max) lysed in 1x lysis buffer, and amplified acccording to the protocol for the SmartseqV4 Ultra low input RNA kit for sequencing from Takara Clontech. Between 16 and 18 PCR cycles were used for each sample, depending on cell input. Quality of cDNA was confirmed using an Agilent Bioanalyser.
Libraries were generated from amplified cDNA using the NexteraXTDNA library preparation kit from Illumina, with nexteraXT indexes. Library quantitatation was performed using Agilent Bioanalyser, KAPA qPCR and Qubit High-sensitivity kits.

value: TET

tag: group

tag: cohort

tag: pid

tag: day

value: OLD

tag: Sex

value: M

tag: lane

tag: cells

tag: bleed


title: Ctrl_1_CEBPB

description: ChIP-seq


title: Fig_2f_EMX1_subs_HOPE_PAM_in_41nt_rep2

description: Amplified from the human EMX1 locus


title: Cohort2_630J_0_TET

description:
Cohort2_630J_0_TET
Cohort2.vsn.normalised.csv

value: YOUNG


title: 23_CoH_72_V_A_S75 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain

tag: treatment (spf or dirty)

value: Dirty, cohoused

tag: treatment vaccination/infection

value: 2019-2020 seasonal quadrivalent influenza vaccine + Adjuvant


title: MTB 6h ex

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 and bowtie2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue < =0.01
Genome_build: GRCh38, BCG NC_012207.1,MTB NZ_CP013475.1

organism: Mycobacterium tuberculosis M1458

source_name: MTB, extracellular

extract_protocol:
For pathogens and the second biological replicates of THP-1, 1.5μg of total RNA was used for RNA-seq library preparation. rRNA was removed from total RNA using Ribo-Zero rRNA Removal Kit. Ribo-Zero RNAs were iron fragmented at 85℃. First-strand cDNA was synthesized with random primers harboring adaptor sequence, the randomized hexamer and Terminal-Tagging oligo cDNA using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (epicentre). The cDNAs were then purified and amplified. PCR products corresponding to 150-350 bps were purified by 12% PAGE gel, quantified and stored at -80℃ until used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and BCG were first sequenced with illumina GAIIx system for 33 nt single-end sequencing by ABlife. Inc (Wuhan, China). MTB were applied to Hiseq 2000 system for 101 nt pair-end sequencing by Majorbio. Inc (Shanghai, China). The second biological replicates of THP-1 were applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China).For the first biological replicates of THP-1, total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis. For each sample, 5μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80℃ until used for sequencing. For high-throughput sequencing, the first biological replicates of THP-1 were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: MTB, extracellular

tag: agent

value: Mycobacterium tuberculosis M1458

tag: time

tag: library type

value: Ribo-Zero


title: Cohort2_643Y_0_TET

description:
Cohort2_643Y_0_TET
Cohort2.vsn.normalised.csv

tag: cell type

tag: genotype


title: 23_CoH_24_V_A_S49 [PBMC vaccine transcriptome]

tag: treatment time point

value: 24 hours


title: Fig_2f_EMX1_subs_HOPE_PAM_in_41nt_rep1

description: Amplified from the human EMX1 locus

value: human embryonic kidney 293 cells

tag: treatment

tag: cell line


title: MTB 24h ex


title: Cohort2_627F_0_TET

description:
Cohort2_627F_0_TET
Cohort2.vsn.normalised.csv

tag: group

tag: cohort

tag: pid

tag: day

tag: Sex

value: F


title: MTB 24h in

source_name: MTB, intracellular

value: MTB, intracellular


title: Fig_2f_EMX1_subs_HOPE_PAM_in_27nt_rep1

description: Amplified from the human EMX1 locus

value: HEK293T cells


title: MTB 6h in


title: Cohort2_651G_0_TET

description:
Cohort2_651G_0_TET
Cohort2.vsn.normalised.csv

tag: lane

tag: cells

tag: bleed


title: 22_CoH_72_V_A_S74 [PBMC vaccine transcriptome]

tag: tissue/cell type

value: PBMC

tag: strain

tag: treatment (spf or dirty)

tag: treatment vaccination/infection


title: BE organoids_miRNA_aomeilazuo

city: Shanghai

first: Hua

last: Xiong

state: 上海市

address: Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute,Shanghai, Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China

institute: Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University

description:
BE organoids exposed to periodic bile acids (400µM, pH 5.5) stimulation with omeprazole (40µM) treatment
processed data file: microRNA.txt

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: text files include RPKM values for each Sample

source_name: BE organoids exposed to periodic bile acids stimulation with omeprazole treatment

growth_protocol: Endoscopic biopsy samples of Barrett's esophagus (BE) were Cutted into small pieces，and isolated fragments of Barrett’s epithelium were embedded in Matrigel on ice (growth factor reduced, phenol red free; BD Biosciences) and seeded in 24-well plates. The Matrigel was polymerized for 10 minutes at 37℃, and 500 µL/well basal culture medium was overlaid containing growth factor combinations.

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

treatment_protocol: organoids were treated with periodic bile acids (400 µM, pH 5.5) stimulation with or without omeprazole (40 µM).

tag: tissue

value: Barrett's esophagus (BE)

tag: organoid model

value: human-derived Barrett's esophagus organoids


title: BE organoids_lncRNA_aomeilazuo

description:
BE organoids exposed to periodic bile acids (400µM, pH 5.5) stimulation with omeprazole (40µM) treatment
processed data files: lncRNA.txt, mRNA.txt


title: Fig_2f_EMX1_subs_HOPE_PAM_in_14nt_rep2

description: Amplified from the human EMX1 locus

tag: cell type

value: transfected with HOPE vectors for 72 h


title: Fig_2f_EMX1_subs_HOPE_PAM_in_14nt_rep3

description: Amplified from the human EMX1 locus

tag: treatment


title: 22_CoH_24_V_A_S48 [PBMC vaccine transcriptome]

tag: treatment time point


title: Cohort2_543P_0_TET

description:
Cohort2_543P_0_TET
Cohort2.vsn.normalised.csv

value: TET

tag: group

value: OLD

tag: genotype


title: Cohort2_622A_0_TET

description:
Cohort2_622A_0_TET
Cohort2.vsn.normalised.csv

tag: cohort

tag: pid

value: YOUNG


title: 23_CoH_0_Naive_S23 [PBMC vaccine transcriptome]

value: Dirty, cohoused

value: Naïve


title: 21_CoH_72_V_A_S73 [PBMC vaccine transcriptome]

value: 2019-2020 seasonal quadrivalent influenza vaccine + Adjuvant

value: 72 hours


title: 21_CoH_24_V_A_S47 [PBMC vaccine transcriptome]


title: 22_CoH_0_Naive_S22 [PBMC vaccine transcriptome]


title: Fig_2f_EMX1_subs_HOPE_PAM_in_27nt_rep2

description: Amplified from the human EMX1 locus

tag: cell line


title: Fig_2f_EMX1_subs_HOPE_PAM_in_27nt_rep3

description: Amplified from the human EMX1 locus


title: Cohort2_544Q_0_TET

description:
Cohort2_544Q_0_TET
Cohort2.vsn.normalised.csv

tag: day

tag: Sex

tag: lane


title: 21_CoH_0_Naive_S21 [PBMC vaccine transcriptome]

tag: tissue/cell type


title: Cohort2_594V_0_TET

description:
Cohort2_594V_0_TET
Cohort2.vsn.normalised.csv

value: M

tag: cells

tag: bleed


title: Fig_2f_EMX1_subs_S_PE2_rep1

description: Amplified from the human EMX1 locus

value: transfected with PE2 vectors for 72 h


title: Cohort2_546S_0_TET

description:
Cohort2_546S_0_TET
Cohort2.vsn.normalised.csv


title: BE organoids_miRNA_duizhao

description:
BE organoids exposed to periodic bile acids (400µM, pH 5.5) stimulation without omeprazole (40µM) treatment
processed data file: microRNA.txt

source_name: BE organoids exposed to periodic bile acids stimulation


title: Fig_2f_EMX1_subs_HOPE_PAM_in_14nt_rep1

description: Amplified from the human EMX1 locus

value: human embryonic kidney 293 cells


title: Cohort2_542N_0_TET

description:
Cohort2_542N_0_TET
Cohort2.vsn.normalised.csv

value: F


title: BE organoids_lncRNA_duizhao

description:
BE organoids exposed to periodic bile acids (400µM, pH 5.5) stimulation without omeprazole (40µM) treatment
processed data files: lncRNA.txt, mRNA.txt


title: 19_CoH_72_V_A_S71 [PBMC vaccine transcriptome]

tag: strain

tag: treatment (spf or dirty)

tag: treatment vaccination/infection


title: Fig_2f_EMX1_subs_S_PE2_rep3

description: Amplified from the human EMX1 locus

tag: cell type


title: Cohort2_559G_0_TET

description:
Cohort2_559G_0_TET
Cohort2.vsn.normalised.csv


title: Cohort2_535F_0_TET

description:
Cohort2_535F_0_TET
Cohort2.vsn.normalised.csv


title: 20_CoH_24_V_A_S46 [PBMC vaccine transcriptome]

value: 24 hours


title: Fig_2c_FANCF_subs_opti_PE3_rep3

description: Amplified from the human FANCF locus

tag: treatment

value: transfected with PE3 vectors for 72 h

value: HEK293T cells


title: 20_CoH_0_Naive_S20 [PBMC vaccine transcriptome]

value: PBMC

tag: treatment time point


title: Cohort2_501T_0_TET

description:
Cohort2_501T_0_TET
Cohort2.vsn.normalised.csv

tag: group


title: Cohort2_526W_0_TET

description:
Cohort2_526W_0_TET
Cohort2.vsn.normalised.csv

tag: genotype


title: SCL/LMO1 7114/1

type: RNA

city: Bethesda

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

hyb_protocol: Fragmentation and Hybridization was done as mentioned in manufacturer protocol to GeneChip array (GeneChip Mouse Genome 430 2.0).

scan_protocol: Array hybridization and scanning performed at: Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD 21702.

label: Biotin

source_name: non DN1/DN2 cortical T-ALL, SCL/LMO1, thymus

label_protocol: 1ug of total RNA was reverse transcribed and Biotin labelled as per manufacturer protocol.

growth_protocol: All three mouse genotypes(Wild type, Idh2R140Q/NHD13 and SCL/LMO1) were maintained from birth in mice facility.

extract_protocol: Total RNA was isolated from leukemic Idh2R140Q/NHD13 spleen, leukemic SCL/LMO1 thymi and WT thymi using TRIzol reagent following the manufacturer’s recommended protocol

tag: tissue

value: Thymus


title: Fig_2c_FANCF_subs_opti_PE3_rep2

description: Amplified from the human FANCF locus


title: 20_CoH_72_V_A_S72 [PBMC vaccine transcriptome]


title: SCL/LMO1 6883/2

data_processing: Array hybridization and scanning performed at: Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD 21702.


title: Fig_2c_FANCF_subs_opti_PE3_rep1

description: Amplified from the human FANCF locus


title: Fig_2c_FANCF_subs_HOPE_PAM_in_48nt_rep3

description: Amplified from the human FANCF locus

value: transfected with HOPE vectors for 72 h


title: 19_CoH_0_Naive_S19 [PBMC vaccine transcriptome]


title: 19_CoH_24_V_A_S45 [PBMC vaccine transcriptome]


title: SCL/LMO1 7114/3


title: 18_SPF_72_V_S70 [PBMC vaccine transcriptome]

value: 2019-2020 seasonal quadrivalent influenza vaccine


title: Fig_2c_FANCF_subs_HOPE_PAM_in_48nt_rep2

description: Amplified from the human FANCF locus


title: Fig_2c_FANCF_subs_HOPE_PAM_in_21nt_rep3

description: Amplified from the human FANCF locus


title: Cohort2_562K_0_TET

description:
Cohort2_562K_0_TET
Cohort2.vsn.normalised.csv

value: TET

tag: cohort

tag: pid


title: Cohort2_545R_7_cTfhTET

description:
Cohort2_545R_7_cTfhTET
Cohort2.vsn.normalised.csv

source_name: cTfhTET

value: cTfhTET

tag: day

value: OLD


title: Cohort2_660R_7_cTfhTET

description:
Cohort2_660R_7_cTfhTET
Cohort2.vsn.normalised.csv

tag: Sex


title: 18_CoH_0_Naive_S18 [PBMC vaccine transcriptome]

value: Dirty, cohoused

value: Naïve


title: Cohort2_594V_7_cTfhTET

description:
Cohort2_594V_7_cTfhTET
Cohort2.vsn.normalised.csv

value: YOUNG

tag: lane


title: 18_CoH_24_V_S44 [PBMC vaccine transcriptome]

tag: tissue/cell type


title: Fig_2f_EMX1_subs_S_PE2_rep2

description: Amplified from the human EMX1 locus

source_name: HEK293T cells

tag: cell line


title: Cohort2_520P_7_cTfhTET

description:
Cohort2_520P_7_cTfhTET
Cohort2.vsn.normalised.csv

tag: cells

tag: bleed


title: Cohort2_607J_7_cTfhTET

description:
Cohort2_607J_7_cTfhTET
Cohort2.vsn.normalised.csv

value: M


title: Fig_2c_FANCF_subs_HOPE_PAM_in_21nt_rep1

description: Amplified from the human FANCF locus


title: 17_CoH_72_V_S69 [PBMC vaccine transcriptome]

tag: strain

tag: treatment (spf or dirty)

value: 72 hours


title: 17_CoH_0_Naive_S17 [PBMC vaccine transcriptome]

tag: treatment vaccination/infection


title: SCL/LMO1 6466/4


title: Cohort2_622A_7_cTfhTET

description:
Cohort2_622A_7_cTfhTET
Cohort2.vsn.normalised.csv

tag: cell type


title: Cohort2_559G_7_cTfhTET

description:
Cohort2_559G_7_cTfhTET
Cohort2.vsn.normalised.csv


title: Fig_2c_FANCF_subs_HOPE_PAM_in_48nt_rep1

description: Amplified from the human FANCF locus

value: human embryonic kidney 293 cells

tag: treatment


title: Rh_TSG-6

city: Xi'an

first: min

last: wang

state: Shaanxi

address: 169 West Changle Road

institute: Fourth military medical university

description: Gene expression of treatment with Rh_TSG-6 in liver tissues.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 22.5 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 mouse Gene Expression (8*60k) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: fibrotic mice_TSG-6_liver

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with the RNAeasy Plus kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The total RNA was further purified by NucleoSpin® RNA clean-up kit （MACHEREY- NAGEL, Germany). RNA was quantified using spectrophotometer and quality was monitored with the Agilent 2100(Agilent Technologies, Santa Clara, CA).

value: male

value: liver


title: 17_CoH_24_V_S43 [PBMC vaccine transcriptome]

tag: treatment time point

value: 24 hours


title: SCL/LMO1 3767

tag: genotype


title: IDH2/NHD13 570

source_name: DN1/DN2 T-ALL, Idh2R140Q/NHD13, spleen

tag: tissue

value: Spleen


title: SCL/LMO1 6889/1


title: Fig_2c_FANCF_subs_HOPE_PAM_in_7nt_rep3

description: Amplified from the human FANCF locus

value: HEK293T cells


title: IDH2/NHD13 559


title: PBS

description: Gene expression of treatment with PBS in liver tissues.

source_name: fibrotic mice_control_liver

value: PBS


title: Fig_2c_FANCF_subs_S_PE2_rep3

description: Amplified from the human FANCF locus

value: transfected with PE2 vectors for 72 h


title: IDH2/NHD13 550


title: IDH2/NHD13 555


title: Fig_2c_FANCF_subs_HOPE_PAM_in_21nt_rep2

description: Amplified from the human FANCF locus

value: transfected with HOPE vectors for 72 h


title: 16_CoH_72_V_S68 [PBMC vaccine transcriptome]

value: PBMC

value: 2019-2020 seasonal quadrivalent influenza vaccine


title: IDH2/NHD13 531


title: IDH2/NHD13 546


title: Cohort2_562K_7_cTfhTET

description:
Cohort2_562K_7_cTfhTET
Cohort2.vsn.normalised.csv

value: cTfhTET

tag: group

tag: cohort

value: F


title: Fig_2c_FANCF_subs_HOPE_PAM_in_7nt_rep2

description: Amplified from the human FANCF locus


title: Fig_2c_FANCF_subs_HOPE_PAM_in_7nt_rep1

description: Amplified from the human FANCF locus


title: Fig_2c_FANCF_subs_S_PE2_rep2

description: Amplified from the human FANCF locus


title: Cohort2_590Q_7_cTfhTET

description:
Cohort2_590Q_7_cTfhTET
Cohort2.vsn.normalised.csv

tag: pid

tag: day


title: 15_CoH_24_V_S41 [PBMC vaccine transcriptome]

value: Dirty, cohoused


title: Fig_1f_METTL3_subs_cor_PE3_rep3

description: Amplified from the human METTL3 locus


title: Fig_2c_FANCF_subs_S_PE2_rep1

description: Amplified from the human FANCF locus


title: 15_CoH_0_Naive_S15 [PBMC vaccine transcriptome]

value: Naïve


title: 16_CoH_0_Naive_S16 [PBMC vaccine transcriptome]


title: 16_CoH_24_V_S42 [PBMC vaccine transcriptome]


title: Cohort2_543P_7_cTfhTET

description:
Cohort2_543P_7_cTfhTET
Cohort2.vsn.normalised.csv

value: OLD

tag: Sex

tag: lane


title: 15_CoH_72_V_S67 [PBMC vaccine transcriptome]

tag: tissue/cell type

value: 72 hours


title: Cohort2_665X_7_cTfhTET

description:
Cohort2_665X_7_cTfhTET
Cohort2.vsn.normalised.csv

value: YOUNG

tag: cells


title: Fig_1f_METTL3_subs_AS_PE2_rep3

description: Amplified from the human METTL3 locus

value: human embryonic kidney 293 cells

tag: cell line


title: Cohort2_544Q_7_cTfhTET

description:
Cohort2_544Q_7_cTfhTET
Cohort2.vsn.normalised.csv

value: M

tag: bleed


title: LL_8

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Filtered reads were aligned to the reference bovine genome (UMD 3.1) using Tophat 2.1.1.
The BAM alignment files generated from Tophat were sorted using Samtools (v1.4) and converted to SAM files.
The SAM files were analyzed using HTSeq-count to obtain gene read counts based on the annotation from ENSEMBL bovine genes.
Genome_build: UMD3.1
Supplementary_files_format_and_content: a text file include count number for each sample .

organism: Bos taurus

source_name: LL, Blood

extract_protocol:
Blood samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: Low milk protein yield

value: Blood


title: 14_CoH_72_V_S66 [PBMC vaccine transcriptome]

tag: strain

tag: treatment (spf or dirty)

tag: treatment vaccination/infection


title: Cohort2_517L_7_TET

description:
Cohort2_517L_7_TET
Cohort2.vsn.normalised.csv

tag: cell type

value: TET


title: Fig_1f_METTL3_subs_HOPE_rep3

description: Amplified from the human METTL3 locus

tag: treatment

value: HEK293T cells


title: Cohort2_637R_7_cTfhTET

description:
Cohort2_637R_7_cTfhTET
Cohort2.vsn.normalised.csv

tag: genotype


title: WT 627

source_name: normal, wildtype, thymus

tag: tissue

value: Thymus

value: Wild Type


title: IDH2/NHD13 526

value: Spleen


title: WT 631


title: LL_7


title: 14_CoH_0_Naive_S14 [PBMC vaccine transcriptome]

source_name: PBMC

value: PBMC

tag: treatment time point


title: WT 623


title: IDH2/NHD13 525


title: 14_CoH_24_V_S40 [PBMC vaccine transcriptome]

value: 2019-2020 seasonal quadrivalent influenza vaccine

value: 24 hours


title: Fig_1f_METTL3_subs_HOPE_rep2

description: Amplified from the human METTL3 locus

value: transfected with HOPE vectors for 72 h


title: Fig_1f_METTL3_subs_S_PE2_rep3

description: Amplified from the human METTL3 locus

value: transfected with PE2 vectors for 72 h


title: LL_6


title: 13_SPF_72_Naive_S65 [PBMC vaccine transcriptome]

value: SPF

value: Naïve


title: Cohort2_507A_7_cTfhTET

description:
Cohort2_507A_7_cTfhTET
Cohort2.vsn.normalised.csv

value: cTfhTET

tag: group

tag: cohort

tag: pid

value: YOUNG


title: 13_SPF_24_Naive_S39 [PBMC vaccine transcriptome]


title: Cohort2_557E_7_cTfhTET

description:
Cohort2_557E_7_cTfhTET
Cohort2.vsn.normalised.csv

tag: day

tag: Sex

value: M

tag: lane


title: Fig_1f_METTL3_subs_cor_PE3_rep2

description: Amplified from the human METTL3 locus

value: human embryonic kidney 293 cells

value: transfected with PE3 vectors for 72 h

tag: cell line


title: Cohort2_594V_7_TET

description:
Cohort2_594V_7_TET
Cohort2.vsn.normalised.csv

value: TET

tag: cells

tag: bleed


title: 13_SPF_0_Naive_S13 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain


title: Cohort2_517L_7_cTfhTET

description:
Cohort2_517L_7_cTfhTET
Cohort2.vsn.normalised.csv

value: OLD


title: Cohort2_542N_7_TET

description:
Cohort2_542N_7_TET
Cohort2.vsn.normalised.csv


title: LL_3

tag: phenotype

value: Low milk protein yield

value: Blood


title: Cohort2_543P_7_TET

description:
Cohort2_543P_7_TET
Cohort2.vsn.normalised.csv

tag: cell type

value: F


title: HH_8

source_name: HH, Blood

value: High milk protein yield


title: Fig_1f_METTL3_subs_S_PE2_rep2

description: Amplified from the human METTL3 locus

tag: treatment

value: HEK293T cells


title: Cohort2_546S_7_cTfhTET

description:
Cohort2_546S_7_cTfhTET
Cohort2.vsn.normalised.csv

tag: genotype


title: 11_SPF_72_Naive_S63 [PBMC vaccine transcriptome]

value: PBMC

tag: treatment (spf or dirty)

tag: treatment vaccination/infection

value: 72 hours


title: LL_4

tag: tissue


title: Fig_1f_METTL3_subs_AS_PE2_rep1

description: Amplified from the human METTL3 locus

value: transfected with PE2 vectors for 72 h


title: IDH2/NHD13 524

value: Spleen


title: Fig_1f_METTL3_subs_AS_PE2_rep2

description: Amplified from the human METTL3 locus


title: 12_SPF_72_Naive_S64 [PBMC vaccine transcriptome]

value: SPF

value: Naïve

tag: treatment time point


title: Cohort2_655L_7_TET

description:
Cohort2_655L_7_TET
Cohort2.vsn.normalised.csv

tag: group

tag: cohort

tag: pid


title: Fig_1f_METTL3_subs_cor_PE3_rep1

description: Amplified from the human METTL3 locus


title: 12_SPF_24_Naive_S38 [PBMC vaccine transcriptome]

value: 24 hours


title: LL_2


title: Fig_1f_METTL3_subs_HOPE_rep1

description: Amplified from the human METTL3 locus

value: transfected with HOPE vectors for 72 h


title: LL_5


title: 12_SPF_0_Naive_S12 [PBMC vaccine transcriptome]


title: Cohort2_590Q_7_TET

description:
Cohort2_590Q_7_TET
Cohort2.vsn.normalised.csv

tag: day

value: YOUNG

tag: Sex

tag: lane


title: Fig_1e_PDCD1_subs_cor_PE3_rep3

description: Amplified from the human PDCD1 locus

value: human embryonic kidney 293 cells

value: transfected with PE3 vectors for 72 h

tag: cell line


title: Cohort2_546S_7_TET

description:
Cohort2_546S_7_TET
Cohort2.vsn.normalised.csv

value: TET

tag: cells

tag: bleed


title: Fig_1f_METTL3_subs_S_PE2_rep1

description: Amplified from the human METTL3 locus


title: 11_SPF_24_Naive_S37 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain


title: HH_7

tag: phenotype


title: LL_1

value: Low milk protein yield


title: 10_SPF_72_V_A_S62 [PBMC vaccine transcriptome]

value: 2019-2020 seasonal quadrivalent influenza vaccine + Adjuvant

value: 72 hours post vaccination


title: Cohort2_541M_7_TET

description:
Cohort2_541M_7_TET
Cohort2.vsn.normalised.csv

tag: cell type

value: OLD

value: M

tag: genotype


title: Cohort2_568R_7_TET

description:
Cohort2_568R_7_TET
Cohort2.vsn.normalised.csv

value: F


title: HH_4

value: High milk protein yield

value: Blood


title: 10_SPF_24_V_A_S36 [PBMC vaccine transcriptome]

value: PBMC

tag: treatment (spf or dirty)

tag: treatment vaccination/infection

value: 24 hours post vaccination


title: Fig_1e_PDCD1_subs_HOPE_rep3

description: Amplified from the human PDCD1 locus

tag: treatment

value: HEK293T cells


title: Fig_1e_PDCD1_subs_cor_PE3_rep1

description: Amplified from the human PDCD1 locus


title: Cohort2_652H_7_TET

description:
Cohort2_652H_7_TET
Cohort2.vsn.normalised.csv

tag: group


title: 10_SPF_0_Naive_S10 [PBMC vaccine transcriptome]

value: SPF

value: Naïve

tag: treatment time point


title: Cohort2_520P_7_TET

description:
Cohort2_520P_7_TET
Cohort2.vsn.normalised.csv

tag: cohort

tag: pid


title: Cohort2_562K_7_TET

description:
Cohort2_562K_7_TET
Cohort2.vsn.normalised.csv

tag: day

value: YOUNG

tag: Sex


title: Fig_1e_PDCD1_subs_HOPE_rep1

description: Amplified from the human PDCD1 locus

value: human embryonic kidney 293 cells

value: transfected with HOPE vectors for 72 h

tag: cell line


title: 9_SPF_72_V_A_S61 [PBMC vaccine transcriptome]


title: 11_SPF_0_Naive_S11 [PBMC vaccine transcriptome]


title: HH_2

tag: tissue


title: Fig_1e_PDCD1_subs_HOPE_rep2

description: Amplified from the human PDCD1 locus


title: HH_6


title: HH_1


title: 9_SPF_24_V_A_S35 [PBMC vaccine transcriptome]


title: Fig_1e_PDCD1_subs_AS_PE2_rep3

description: Amplified from the human PDCD1 locus

value: transfected with PE2 vectors for 72 h


title: Cohort2_536G_7_TET

description:
Cohort2_536G_7_TET
Cohort2.vsn.normalised.csv

value: TET

tag: lane

tag: cells

tag: bleed


title: HH_5

tag: phenotype


title: Fig_1e_PDCD1_subs_cor_PE3_rep2

description: Amplified from the human PDCD1 locus

tag: cell type

value: transfected with PE3 vectors for 72 h


title: Cohort2_637R_7_TET

description:
Cohort2_637R_7_TET
Cohort2.vsn.normalised.csv

tag: genotype


title: HH_3


title: Cohort2_643Y_7_TET

description:
Cohort2_643Y_7_TET
Cohort2.vsn.normalised.csv


title: Fig_1e_PDCD1_subs_AS_PE2_rep1

description: Amplified from the human PDCD1 locus


title: 8_SPF_72_V_A_S60 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain

tag: treatment (spf or dirty)

value: 2019-2020 seasonal quadrivalent influenza vaccine + Adjuvant

value: 72 hours post vaccination


title: 8_SPF_24_V_A_S34 [PBMC vaccine transcriptome]

tag: treatment vaccination/infection


title: LB10

data_processing:
Illumina Casava1.5 software used for basecalling.
3' adapter(TTAGATCAG) trimmed with cutadapt -e 0.12 -O 6 --trimmed-only -m 15 -M 25
mapped using bowtie2 -t -N 1 -p 24
detecting different expression gene using edgeR
Genome_build: Gossypium_hirsutum_v1.1
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

organism: Gossypium hirsutum

source_name: Gossypium hirsutum 10 DPA

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at A260/A280 and A260/A230 using smartspec plus (BioRad)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 10 DPA

value: fiber


title: LB15

source_name: Gossypium hirsutum 15 DPA

value: 15 DPA


title: LB5

source_name: Gossypium hirsutum 5 DPA

value: 5 DPA


title: Cohort2_642X_7_TET

description:
Cohort2_642X_7_TET
Cohort2.vsn.normalised.csv

source_name: TET

tag: group

tag: cohort

value: OLD

value: M


title: HTO_Pool4b_SFC854

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

description: Pool of 8 experimental groups for SFC854, each marked by a different HashTagOligo

data_processing:
We used Cell Ranger pipeline (v 2.1.0) to process the sequencing data including alignment with STAR and single cell 3’ gene counting.
CITE-seq Count python tool was used to demultiplex samples by antibody hashtag.
We used the HTODemux function from Seurat to identify doublets and keep singlets (n = 20231).
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts_ProteinCodingGenes.txt tab delimited counts for all protein coding genes; Metadata.txt tab delimited metadata per cell

source_name: iPSC-microglia

growth_protocol: Two male (SFC841-03-01 (Dafinca et al.), SFC854-03-02 (Haenseler et al.)) and two female iPSC lines (SFC180-01-01 (Haenseler et al.), SFC856-03-04 (Haenseler et al.)) were used for the study. They were originally reprogrammed from healthy donors recruited through StemBANCC/Oxford Parkinson's Disease Centre (participants were recruited to this study having given signed informed consent, which included derivation of hiPSC lines from skin biopsies, Ethics Committee: National Health Service, Health Research Authority, NRES Committee South Central, Berkshire, UK [REC 10/H0505/71]), and are all listed in hPSCreg and available from EBiSC. They were differentiated to primitive macrophage precursors and subsequently skewed to microglia-like cells in monoculture according to (Haenseler et al.). Primitive macrophage precursors were plated in IBIDI dishes (IBIDI µ-Dish 35 mm, low, cat no 80136) at a starting density of 500.000 cells per IBIDI dish (approx. 125.000 cells/cm2).

extract_protocol:
Then 1ug of cell hashing antibodies was added to each of the samples. Each cell line had 8 IBIDI dishes corresponding to the 8 different treatment conditions and 8 hashing antibodies. After 30 min incubation at 4o C, cells were washed 2 times: first wash by spinning them at 600g for 5min and resuspending them in 500ml staining buffer spinning, second wash by spinning the cells at 600g 5min and resuspending them in 200ul staining buffer. Finally, cells were resuspended in 150ul PBS, filtered through a 40um cell strainer and counted.
All the treatments from a cell line were pooled together and were loaded on a 10X Chromium.  For SFC841-03-01, SFC856-03-04 and SFC180-01-01 cell line 10.000 cells per pool were loaded in one 10X Chromium lane, for SFC854-03-02 cell line 5000 cells per pool were loaded on two 10X Chromium lanes.

treatment_protocol: Cells were treated with LPS 10ng/ml and IFN-γ 10ng/ml or with PGE2 500nM for 24h or 48h in a final volume of 500ul of media per IBIDI dish. ATPγS 1mM was added for the second 24h where relevant (Fig. S1). Cells were lifted by incubating them with 200ul accutase (ThermoFisher) 3min at 37o C. Cells were then collected 2x 500ul PBS and pelleted by spinning at 600g for 5min at 4o C. Next, cells were resuspended in 100ul staining buffer (2% BSA, 0.02% PBS-Tween20) and incubated with 7ul Fc blocking reagent (Biolegend) for 10min.

tag: line

tag: files


title: 7_SPF_72_V_A_S59 [PBMC vaccine transcriptome]

value: PBMC

tag: treatment time point


title: Fig_1e_PDCD1_subs_S_PE2_rep1

description: Amplified from the human PDCD1 locus

tag: treatment

tag: cell line

value: HEK293T cells


title: Cohort2_545R_7_TET

description:
Cohort2_545R_7_TET
Cohort2.vsn.normalised.csv

tag: pid

tag: day

tag: Sex

value: F

tag: lane

tag: cells


title: Fig_1e_PDCD1_subs_S_PE2_rep2

description: Amplified from the human PDCD1 locus

tag: cell type


title: HTO_Pool4_SFC854


title: Cohort2_627F_7_TET

description:
Cohort2_627F_7_TET
Cohort2.vsn.normalised.csv

value: YOUNG

tag: bleed

tag: genotype


title: LB25

source_name: Gossypium hirsutum 20 DPA

value: 20 DPA

tag: tissue


title: Fig_1d_PRNP_subs_opti_PE3_rep3

description: Amplified from the human PRNP locus

value: human embryonic kidney 293 cells


title: 7_SPF_24_V_A_S33 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain

tag: treatment (spf or dirty)

value: SPF

tag: treatment vaccination/infection

value: 24 hours post vaccination


title: 9_SPF_0_Naive_S9 [PBMC vaccine transcriptome]

value: Naïve


title: HTO_Pool2_SFC856

description: Pool of 8 experimental groups for SFC856, each marked by a different HashTagOligo

tag: line

tag: files


title: Fig_1e_PDCD1_subs_AS_PE2_rep2

description: Amplified from the human PDCD1 locus

tag: treatment

value: transfected with PE2 vectors for 72 h


title: 7_SPF_0_Naive_S7 [PBMC vaccine transcriptome]

tag: treatment time point


title: Cohort2_501T_7_TET

description:
Cohort2_501T_7_TET
Cohort2.vsn.normalised.csv

value: TET

tag: group

tag: cohort

tag: pid


title: Fig_1d_PRNP_subs_cor_PE3_rep3

description: Amplified from the human PRNP locus

value: transfected with PE3 vectors for 72 h

tag: cell line


title: 8_SPF_0_Naive_S8 [PBMC vaccine transcriptome]


title: Cohort2_660R_7_TET

description:
Cohort2_660R_7_TET
Cohort2.vsn.normalised.csv

tag: day

tag: Sex

tag: lane

tag: cells


title: HTO_Pool1_SFC841

description: Pool of 8 experimental groups for SFC841, each marked by a different HashTagOligo


title: 6_SPF_72_V_A_S58 [PBMC vaccine transcriptome]

value: 2019-2020 seasonal quadrivalent influenza vaccine + Adjuvant

value: 72 hours post vaccination


title: Fig_1e_PDCD1_subs_S_PE2_rep3

description: Amplified from the human PDCD1 locus

tag: cell type


title: Fig_1d_PRNP_subs_HOPE_rep3

description: Amplified from the human PRNP locus

value: transfected with HOPE vectors for 72 h


title: 6_SPF_24_V_A_S32 [PBMC vaccine transcriptome]

tag: tissue/cell type


title: HTO_Pool3_SFC180

description: Pool of 8 experimental groups for SFC180, each marked by a different HashTagOligo


title: Cohort2_544Q_7_TET

description:
Cohort2_544Q_7_TET
Cohort2.vsn.normalised.csv

value: OLD

tag: bleed

tag: genotype


title: Fig_1d_PRNP_subs_AS_PE2_rep3

description: Amplified from the human PRNP locus


title: Cohort2_622A_7_TET

description:
Cohort2_622A_7_TET
Cohort2.vsn.normalised.csv


title: 6_SPF_0_Naive_S6 [PBMC vaccine transcriptome]

tag: strain

tag: treatment (spf or dirty)

tag: treatment vaccination/infection


title: GEX_SFC854_Pool4b

tag: line

value: M

tag: files


title: Fig_1d_PRNP_subs_S_PE2_rep3

description: Amplified from the human PRNP locus

tag: treatment


title: GEX_SFC854_Pool4


title: 5_SPF_24_V_S31 [PBMC vaccine transcriptome]

value: PBMC

value: 2019-2020 seasonal quadrivalent influenza vaccine

tag: treatment time point


title: Cohort2_559G_7_TET

description:
Cohort2_559G_7_TET
Cohort2.vsn.normalised.csv

tag: group

tag: cohort

tag: pid


title: 5_SPF_72_V_S57 [PBMC vaccine transcriptome]


title: Cohort2_557E_7_TET

description:
Cohort2_557E_7_TET
Cohort2.vsn.normalised.csv

tag: day

tag: Sex


title: GEX_SFC180_Pool3

value: F


title: Fig_1d_PRNP_subs_cor_PE3_rep2

description: Amplified from the human PRNP locus

tag: cell line

value: HEK293T cells


title: Cohort2_602D_7_TET

description:
Cohort2_602D_7_TET
Cohort2.vsn.normalised.csv

tag: cell type

value: YOUNG

tag: lane

tag: cells


title: Cohort2_523S_7_TET

description:
Cohort2_523S_7_TET
Cohort2.vsn.normalised.csv

tag: bleed

tag: genotype


title: 5_SPF_0_Naive_S5 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain

tag: treatment (spf or dirty)


title: GEX_SFC856_Pool2

tag: line

tag: files


title: GEX_SFC841_Pool1


title: THP-1 6h ctrl polyA

source_name: THP-1, uninfected Control

tag: tissue

tag: agent

value: uninfected Control

tag: time

tag: library type

value: polyA-capture


title: 4_SPF_72_V_S56 [PBMC vaccine transcriptome]

value: SPF

tag: treatment vaccination/infection

tag: treatment time point


title: Fig_1d_PRNP_subs_AS_PE2_rep2

description: Amplified from the human PRNP locus

value: human embryonic kidney 293 cells

tag: treatment

tag: cell line


title: Fig_1d_PRNP_subs_HOPE_rep2

description: Amplified from the human PRNP locus

tag: cell type


title: Cohort2_508B_7_TET

description:
Cohort2_508B_7_TET
Cohort2.vsn.normalised.csv

tag: group

tag: cohort

tag: pid

tag: day

tag: Sex

tag: lane

tag: cells


title: THP-1 BCG 6h polyA

source_name: THP-1, infected

value: Mycobacterium bovis BCG str. Tokyo 172


title: Cohort2_607J_7_TET

description:
Cohort2_607J_7_TET
Cohort2.vsn.normalised.csv

value: TET

tag: bleed

tag: genotype


title: THP-1 MTB 6h polyA

tag: tissue

tag: agent

value: Mycobacterium tuberculosis M1458


title: Fig_1d_PRNP_subs_S_PE2_rep2

description: Amplified from the human PRNP locus

value: transfected with PE2 vectors for 72 h


title: Cohort2_526W_7_TET

description:
Cohort2_526W_7_TET
Cohort2.vsn.normalised.csv


title: 3_SPF_72_V_S55 [PBMC vaccine transcriptome]

tag: tissue/cell type

tag: strain

tag: treatment (spf or dirty)

value: 72 hours post vaccination


title: Fig_1d_PRNP_subs_opti_PE3_rep2

description: Amplified from the human PRNP locus

tag: treatment

value: transfected with PE3 vectors for 72 h


title: 4_SPF_0_Naive_S4 [PBMC vaccine transcriptome]

tag: treatment vaccination/infection

value: Naïve

tag: treatment time point


title: Cohort1_072C_7_cTfhTET

description:
Cohort1_072C_7_cTfhTET
Cohort1.vsn.normalised.csv

source_name: cTfhTET

tag: cell type

value: cTfhTET

tag: group

value: OLD

value: M


title: THP-1 MTB 24h polyA

tag: time

tag: library type


title: THP-1 24h ctrl polyA


title: 2_SPF_72_V_S54 [PBMC vaccine transcriptome]

value: PBMC

value: 2019-2020 seasonal quadrivalent influenza vaccine


title: ATAC-seq_NIH1 Lin-CD34+ cells

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Equal molar concentrations of uniquely indexed samples were pooled together. Pooled libraries were sequenced using a NextSeq500 150-cycle flow cell (Illumina).
Reads were aligned to the mouse (mm10) or human (hg38) genomes, and peaks were called using the cellranger-atac count pipeline.
Individual samples were merged using the cellranger-atac pipeline to generate the peak-barcode matrix and TF-barcode matrix.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: A sparse matrix with the number of reads in each peak for each cell, a sparse matrix with the transcription factor (TF) activity for each cell, and a fragment file with the number of reads in each peaks for each cell

source_name: Stem and Progenitor cells from a patients with a pathogenic mutation in TERT

extract_protocol:
The scATAC Low Cell Input Nuclei Isolation protocol (10X Genomics) was used to isolate nuclei from FACS-purified cells. The trypan blue exclusion assay was performed to check for intact nuclei.
The remaining extracted nuclei were used for the consecutive steps of the scATAC-seq library preparation protocol following 10X Genomics guidelines.

value: bone marrow hematopoietic cells

value: TERT c.2110C>T


title: Cohort2_518M_7_TET

description:
Cohort2_518M_7_TET
Cohort2.vsn.normalised.csv

tag: cohort

tag: pid

tag: day

tag: Sex

value: F


title: Fig_1d_PRNP_subs_HOPE_rep1

description: Amplified from the human PRNP locus

source_name: HEK293T cells

value: transfected with HOPE vectors for 72 h

tag: cell line

value: HEK293T cells


title: Cohort2_507A_7_TET

description:
Cohort2_507A_7_TET
Cohort2.vsn.normalised.csv

value: YOUNG

tag: lane

tag: cells

tag: bleed

tag: genotype