title: Ileal biopsy, J10114

description:
RISK_80
Ileal biopsy from Male CD patient aged 8.83333333333333 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10238

status: Public on Aug 21 2019

type: SRA

city: Cincinnati

first: Yael

last: Haberman

address: 3333 Burnet Av

country: USA

institute: CCHMC

description:
RISK_100
Ileal biopsy from Male CD patient aged 9.58333333333333 years at diagnosis with L3 location and Paris age A1a

library_source: transcriptomic

data_processing:
Sequencing was peformed on the Illumina HiSeq 2000
Reads were quantified using kallisto with  Gencode v23 as the reference genome, with transcripts per million as the output.
Genome_build: Gencode v23
Supplementary_files_format_and_content: Tab delimited file with gene symbol and FPKMs

molecule: total RNA

organism: Homo sapiens

source_name: Ileal biopsy

extract_protocol:
Ileal biopsies were obtained at diagnostic colonoscopies and stored in RNALater at -80.  RNA was isolated using Qiagen AllPrep RNA/DNA MiniKiet.
Poly-A-RNA selection, fragmentation, cDNA synthesis, adaptor ligation, and library preparation were performed using TruSeq RNA Sample preparation (Illumina)

tag: diagnosis

value: CD

tag: location

tag: gender

value: Male

tag: agedxyrs

tag: paris age

tag: tissue

value: Ileal biopsy


title: Ileal biopsy, J10136

description:
RISK_76
Ileal biopsy from Female CD patient aged 8.66666666666667 years at diagnosis with L3 location and Paris age A1a

value: Female


title: Ileal biopsy, J10170

description:
RISK_92
Ileal biopsy from Male CD patient aged 9.25 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10120

description:
RISK_73
Ileal biopsy from Female CD patient aged 8.5 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0759]

city: london

first: Tamsyn

middle: Ruth

last: Derrick

address: keppel street

country: United Kingdom

institute: london school of hygiene and tropical medicine

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49738_TCAGGA

data_processing:
Libraries were shipped to Lexogen GmbH for quality control and sequencing on two lanes of an Illumina HiSeq (Illumina).
Bam files were converted to FastQ using Picard and FastQ files were uploaded to BlueBee Genomics Platform (BlueBee).
FastQ files were trimmed and quality filtered using the default BlueBee Integrated QuantSeq FWD workflow.
Bbduk was used to trim low-quality tails, adapter contamination and polyA read-through, reads were aligned to human genome version GRCh38.77 using STAR Aligner and reads were counted using HTSeq-count with kit-specific options.
Read count data were downloaded from BlueBee and imported to R (www.R-project.org) for analysis. Read count data were analysed for differential expression using DEseq2. Genes were retained in the analysis that had a read count of 10 or more in 48 or more samples (n=11424). The DEseq2 package internally corrects for library size and a plot of the Cook’s distance between samples revealed no sample outliers (data not shown) therefore no samples were excluded from the analyses.
Genome_build: human genome version GRCh38.77
Supplementary_files_format_and_content: Matrix of HUGO gene names against sample names, with a read count for each.

extract_protocol:
Swabs from the tarsal conjunctiva were collected at baseline and at one, six and twelve months post-surgery. A sterile polyester swab (Puritan) was passed across the conjunctival surface four times, with a quarter-turn on each pass. Swabs were stored in RNAlater (Thermo Fisher Scientific) at 4°C overnight and then long-term at -80°C. RNA and DNA were extracted from swabs using Norgen RNA/DNA purification kit (Norgen Biotek) following manufacturer’s instructions.
Library preparation was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH, Austria), following the manufacturer’s instructions.
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina

value: Conjunctival epithelium


title: Ileal biopsy, J10055

description:
RISK_72
Ileal biopsy from Male CD patient aged 8.41666666666667 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0962]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49739_ATTGGT


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0609]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49735_AATCCG


title: Ileal biopsy, J10026

description:
RISK_71
Ileal biopsy from Male CD patient aged 8.41666666666667 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0733]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49737_ACTCTT


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0370]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49697_GGCCAA


title: Ileal biopsy, J10118

description:
RISK_86
Ileal biopsy from Female CD patient aged 8.91666666666667 years at diagnosis with L1 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0465]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49740_CTCATA


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0689]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49736_GTGTAG


title: Ileal biopsy, J10369

description:
RISK_68
Ileal biopsy from Male CD patient aged 8 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10288

description:
RISK_74
Ileal biopsy from Female CD patient aged 8.58333333333333 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10097

description:
RISK_93
Ileal biopsy from Male CD patient aged 9.25 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10014

description:
RISK_67
Ileal biopsy from Male CD patient aged 7.91666666666667 years at diagnosis with L1 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0310]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49696_CAGGAC


title: Ileal biopsy, J10129

description:
RISK_89
Ileal biopsy from Male CD patient aged 9.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0281]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49695_GGAGGT


title: Ileal biopsy, J10386

description:
RISK_65
Ileal biopsy from Male CD patient aged 7.66666666666667 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10240

description:
RISK_64
Ileal biopsy from Male CD patient aged 7.58333333333333 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0165]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49693_TTCAGC


title: Ileal biopsy, J10051

description:
RISK_66
Ileal biopsy from Male CD patient aged 7.91666666666667 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10286

description:
RISK_63
Ileal biopsy from Male CD patient aged 7.33333333333333 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10057

description:
RISK_77
Ileal biopsy from Male CD patient aged 8.75 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0184]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49694_CAATGC


title: Ileal biopsy, J10380

description:
RISK_69
Ileal biopsy from Male CD patient aged 8.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, 1 month post trichiasis surgery [B_1_T1_DT0096]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49692_GAACTA


title: Ileal biopsy, J10371

description:
RISK_62
Ileal biopsy from Male CD patient aged 7.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0962]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49745_ATATCC

source_name: Doxycycline-arm, Poor outcome, Baseline


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0759]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49744_TAGGCT


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0733]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49743_TTCCGC


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0689]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49742_GGTATA


title: Ileal biopsy, J10209

description:
RISK_58
Ileal biopsy from Male CD patient aged 6.25 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0609]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49741_CCTGCT


title: Ileal biopsy, J10370

description:
RISK_57
Ileal biopsy from Female CD patient aged 6.16666666666667 years at diagnosis with L3 location and Paris age A1a


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0465]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49734_CTAGTC


title: Ileal biopsy, J10315

description:
RISK_60
Ileal biopsy from Male CD patient aged 6.5 years at diagnosis with L3 location and Paris age A1a


title: Ileal biopsy, J10079

description:
RISK_52
Ileal biopsy from Male CD patient aged 15.9166666666667 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0370]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49691_TACCTT


title: Ileal biopsy, J10357

description:
RISK_47
Ileal biopsy from Male CD patient aged 15.4166666666667 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0310]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49690_AAGCTC


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0281]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49689_CACTAA


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0184]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49688_TGGCGA


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0165]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49687_AACCGA


title: Ileal biopsy, J10178

description:
RISK_41
Ileal biopsy from Male CD patient aged 14.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10197

description:
RISK_48
Ileal biopsy from Male CD patient aged 15.75 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10095

description:
RISK_42
Ileal biopsy from Male CD patient aged 14.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0987]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49727_ATGGCG


title: Doxycycline-arm, Poor outcome, Baseline [B_1_T0_DT0096]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49686_AACAAG


title: Ileal biopsy, J10231

description:
RISK_40
Ileal biopsy from Male CD patient aged 14.75 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10348

description:
RISK_39
Ileal biopsy from Female CD patient aged 14.25 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10291

description:
RISK_38
Ileal biopsy from Female CD patient aged 14.1666666666667 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0646]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49725_AGACCA


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0670]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49726_GCTCGA


title: Ileal biopsy, J10344

description:
RISK_34
Ileal biopsy from Male CD patient aged 13.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10174

description:
RISK_32
Ileal biopsy from Male CD patient aged 13.5833333333333 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10175

description:
RISK_30
Ileal biopsy from Male CD patient aged 12.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0613]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49723_TGACAC


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0625]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49724_ACAGAT


title: Ileal biopsy, J10347

description:
RISK_23
Ileal biopsy from Male CD patient aged 11.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0549]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49722_TATGTC


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0405]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49685_AAGTGG


title: Ileal biopsy, J10359

description:
RISK_56
Ileal biopsy from Male CD patient aged 16.9166666666667 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10169

description:
RISK_51
Ileal biopsy from Male CD patient aged 15.8333333333333 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10362

description:
RISK_18
Ileal biopsy from Male CD patient aged 10.6666666666667 years at diagnosis with L2 location and Paris age A1b


title: Ileal biopsy, J10278

description:
RISK_14
Ileal biopsy from Male CD patient aged 10.4166666666667 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0326]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49683_CGATCT


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0318]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49682_GCGAAT


title: Ileal biopsy, J10201

description:
RISK_11
Ileal biopsy from Female CD patient aged 9.5 years at diagnosis with L2 location and Paris age A1a


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0016]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49680_GAAGTG


title: Ileal biopsy, J10123

description:
RISK_10
Ileal biopsy from Female CD patient aged 9.16666666666667 years at diagnosis with L2 location and Paris age A1a


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0133]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49681_AGAATC


title: Ileal biopsy, J10352

description:
RISK_1
Ileal biopsy from Male CD patient aged 6.58333333333333 years at diagnosis with L2 location and Paris age A1a


title: Ileal biopsy, J10327

description:
RISK_5
Ileal biopsy from Female CD patient aged 8 years at diagnosis with L2 location and Paris age A1a


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0646]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49731_GTAGAA

source_name: Doxycycline-arm, Good outcome, Baseline


title: Red light treated phyAB rep2

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

country: China

institute: Shanghai  University

description: Col-phyAB 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR 10 whole genome using bowtie0.12.5  with parameters default
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al,Nature methods 2008.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 1h red light treated 4.5d phyAB seedlings

growth_protocol: All seeds were surface sterilized and plated on the 1/2MS media with 1% sucrose, cold stratified for three days before treated for 12 hours of white light and 21 hours to induce germination. Seeds were incubated at 22℃ in the dark for 4day and then seedings were treated with 1h red light (50 µmole/s2/m2) or further incubated in the dark.

extract_protocol: Total RNA was isolated

treatment_protocol: Col, phyB and phyAB seedlings were used for RNA-seq analysis

tag: ecotype

value: Col

tag: genotype/variation

value: phyAB mutant

value: Seedlings

tag: age

tag: treatment

value: 1h red light


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0613]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49729_TCGTTC


title: Red light treated phyAB rep1

description: Col-phyAB 1


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0670]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49732_AGTACT


title: Doxycycline-arm, Good outcome, 1 month post trichiasis surgery [B_0_T1_DT0374]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49684_CATCTA


title: Ileal biopsy, J10033

description:
RISK_27
Ileal biopsy from Male CD patient aged 12.5833333333333 years at diagnosis with L2 location and Paris age A1b


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0549]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49728_TGCACG


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0625]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49730_ACACGC


title: Red light treated phyB rep2

description: Col-phyB 2

source_name: 1h red light treated 4.5d phyB seedlings

value: phyB mutant


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0405]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49679_CCGACC


title: Red light treated phyB rep1

description: Col-phyB 1


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0374]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49678_CGCCTG


title: Dard treated Col rep2

description: Col-Dark 2

source_name: Dark grown 4.5d WT seedlings

value: WT

value: darkness


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0318]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49676_TGGATT


title: Dard treated Col rep1

description: Col-Dark 1


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0326]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49677_GCAGCC


title: Red light treated Col rep1

description: Col-RL 1

source_name: 1h red light treated 4.5d WT seedlings


title: Red light treated Col rep2

description: Col-RL 2


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0987]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49733_GCATGG


title: scRNA-Seq Non-Responder

city: Boston

first: Mohammad

last: Rashidian

state: MA

address: 1  Blackfan Circle, Karp Research Lab building

institute: Boston Children's Hospital

description:
PolyA RNA
Single cell RNA-Seq

data_processing:
Fastq files were obtained with using "cellranger mkfastq" (Cell Ranger 1.1.0 from 10x Genomics).
Demultiplexing, mapping and gene counting were performed with "cellranger count", Cell Ranger 1.1.0 from 10x Genomics. Mapping was done against the refdata-cellranger-mm10-1.2 (November 16, 2016).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: filtered_gene_bc_matrices text output files from Cell Ranger count.

organism: Mus musculus

source_name: CD45+ immune cells from tumors

extract_protocol:
Tumors were excised and CD45+ immune cells were isolated by FACS, and submitted for single cell RNAseq analysis.
Cells were processed using the 10X Genomics Chromium Controller with the Single Cell 3ʹ v3 Reagent Kit, according to manufacturer’s directions. Briefly, a target number of cells per library was roughly achieved by loading 1.6 times the target number of cells in suspension, along with barcoded beads and partitioning oil, into the Chromium Controller, in order to create GEMs (Gel Beads in Emulsion). The Chromium Controller combines individual cells, first strand master mix, and gel beads (GEMs) containing barcoded oligonucleotides into single-cell droplets for first strand cDNA synthesis, so that each cell is marked with its own unique barcode during reverse transcription. After first strand synthesis is complete, the emulsion is dissolved and the cDNA is pooled for bulk processing as a single sample. The sample is fragmented, end-repaired, A-tailed and ligated with universal adapters. A second sample barcode is then added during the PCR step, allowing for unique library identification. The end result is a single library representing one cell suspension, containing data for each individual cell.

treatment_protocol: MC38-GFP+ adenocarcinoma (from Dr. A. Sharpe) was used for all experiments. Cells were cultured in vitro in DMEM supplemented with 10% FBS. Animals were inoculated with 50,000 MC38-GFP+ cells, subcutaneous, below the right shoulder, and were treated with a sub-optimal dose of anti-PD-1 antibody as explained in detail in the manuscript. Responder and nonresponder tumors were excised and cancer cells and CD45+ immune cells were sorted, and submitted separately for bulk RNAseq analysis (tumor cells), and single cell RNAseq analysis (immune cells).

tag: strain

tag: tumor cells injected

value: MC38 adenocarcinoma

value: anti-PD-1 antibody

tag: response to treatment

value: Non responder

tag: cell type

value: CD45+ immune cells from tumors


title: scRNA-Seq Responder

description:
PolyA RNA
Single cell RNA-Seq

value: Responder


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0016]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49674_AGGCAT


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0452]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49721_GACATC


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0443]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49720_GAGTCC


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0403]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49719_ACGTCT


title: Responder Rep2

description:
PolyA RNA
Stranded (reverse) RNA-Seq

data_processing:
Reads were mapped to the canonical mouse genome, release mm10, with STAR (PMID: 23104886), using an annotation file from ENSEMBL GRCm38.91.
Reads were assigned to genes with FeatureCounts (PMID: 24227677) using -s 2 and the same gtf file used in the mapping.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.featureCounts.txt: Tab-delimited text files containing gene counts.

source_name: Tumor cells

extract_protocol:
Tumors were excised and cancer cells were isolated.
KAPA HyperPrep mRNA: Libraries were prepared for RNA-Seq using KAPA Biosystems KAPA mRNA HyperPrep Kit, according to manufacturer’s directions. Briefly, total RNA (0.1-1 ug) is enriched for polyadenylated sequences using oligo-dT magnetic bead capture. The enriched mRNA fraction is then fragmented, and first-strand cDNA is generated using random primers. Strand specificity is achieved during second-strand cDNA synthesis by replacing dTTP with dUTP, which quenches the second strand during amplification. The resulting cDNA is A-Tailed and ligated with indexed adapters. Finally, the library is amplified using a DNA Polymerase which cannot incorporate past dUTPs, effectively quenching the second strand during PCR.

value: Tumor cells


title: Non Responder Rep2

description:
PolyA RNA
Stranded (reverse) RNA-Seq


title: Non Responder Rep1

description:
PolyA RNA
Stranded (reverse) RNA-Seq

treatment_protocol: MC38-GFP+ adenocarcinoma (from Dr. A. Sharpe) was used for all experiments. Cells were cultured in vitro in DMEM supplemented with 10% FBS.  Animals were inoculated with 50,000 MC38-GFP+ cells, subcutaneous, below the right shoulder, and were treated with a sub-optimal dose of anti-PD-1 antibody as explained in detail in the manuscript. Responder and nonresponder tumors were excised and cancer cells and CD45+ immune cells were sorted, and submitted separately for bulk RNAseq analysis (tumor cells), and single cell RNAseq analysis (immune cells).


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0335]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49718_GTCAGG


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0216]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49717_CTCCAT


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0200]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49716_CCGCAA


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0161]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49671_CAGCGT


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0190]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49673_TCTTAA


title: Doxycycline-arm, Good outcome, Baseline [B_0_T0_DT0133]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49675_ACCTAC


title: OIL2F: Cohort2 Oil

city: Columbus

first: Craig

middle: Joseph

last: Burd

state: OH

address: 460 W. 12th Ave. Rm 920 BRT

department: Molecular Genetics

institute: The Ohio State University

data_processing:
Alignment to mm10 mouse genome using the STAR read aligner.
Read counts were generated using featureCounts and normalized in DESeq2.
Genes with sum of less than 10 reads across all samples were removed.
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated text files with normalized read counts

source_name: Mammary gland

extract_protocol:
Fibroblasts were isolated from mammary glands by rapid plating following enzymatic digestion of the tissue.   RNA was purified from fibroblast via Zyme RNA/DNA miniprep kit.
standard illumina library prep

treatment_protocol: pregnant mothers were exposed via ip injection to 25 ug/kg bw BPA or oil control daily from embryonic day 8.5 to 18.5.

value: Primary mammary fibroblasts

value: 12 weeks of age primary cells

value: Oil exposed (control)


title: OIL1F: Cohort1 Oil


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0157]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49670_CACACT

value: Conjunctival epithelium


title: BPA2F: Cohort2 BPA

value: BPA expossed


title: BPA1F: Cohort1 BPA


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0134]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49669_ACGTCG


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0116]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49668_AGTTGA


title: LD_DiI.rs_4

city: Bethesda

first: Anton

last: Schulmann

state: Maryland (MD)

address: 35 Convent Dr

institute: NIH/NIMH

data_processing:
Truseq adapter trimming (cutadapt version 1.16, with options --trim-n -n 3 -m 40)
Alignment to mouse genome (STAR, version 2.5.3a, using ENCODE options for long RNAseq, see manual 3.2.2)
Counting unique exon-mapping reads per gene (featurecounts, version 1.52, using gencode M13 annotation)
Filtering (only genes with TPM>5 in at least 3 samples)
Genome_build: mm10
Supplementary_files_format_and_content: read counts per gene

source_name: thalamic projection neurons

extract_protocol:
Retrogradely labelled cells were collected as previously described (Hempel et al., Nat Protoc 2007; (Hempel et al., Nat Protoc 2007, PMID 18007629; Sugino et al., eLife 2019, PMID 30977723). Coronal slices (200-300 μm) were cut and incubated for 1 hour with pronases and neural activity blockers in artificial cerebrospinal fluid (ACSF). Thalamic areas were then microdissected and the tissue dissociated. Fluorescent neurons were manually sorted, washed, aspirated into a small volume and lysed with 47 μL XB lysis buffer (PicoPure, Thermo Fisher), incubated for 5 min at 42ºC and stored at -80ºC.
Upon thawing, total RNA was extracted using the PicoPure kit (KIT0204, Thermo Fisher) and External RNA Controls Consortium (ERCC) spike-ins added at 1: 10^5 dilution. cDNA was synthesized and amplified using the Ovation RNA-seq v2 kit (NuGEN), yielding 4-8 µg of cDNA, and sheared using a Covaris E220 sonicator. Libraries were generated using the Ovation rapid DR multiplexing kit (NuGEN), quantified by qPCR using Kapa Library Quantification for Illumina (KK4854, Kapa Biosystems), and sequenced on a HiSeq 2500 flow cell (Illumina).

value: LD

tag: striatumics


title: AV_DiI.rs_6

value: AV


title: AV_DiI.rs_7


title: AV_DiI.rs_8


title: Responder Rep1

description:
PolyA RNA
Stranded (reverse) RNA-Seq


title: LD_DiI.rs_5


title: PO_DiI.s1_7

value: PO


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0452]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49715_ATGAAC

source_name: Placebo-arm, Poor outcome, Baseline


title: PO_DiI.s1_5


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0443]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49714_ATACTG


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0216]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49711_CGTCGC


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0335]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49712_TGTGCA


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0403]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49713_ACCGTG


title: PO_DiI.s1_6


title: VB_DiI.s1_4

value: VB


title: Placebo-arm, Poor outcome, 1 month post trichiasis surgery [A_1_T1_DT0183]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49672_TGCTAT


title: VB_DiI.s1_2


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0200]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49710_TTCGAG


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0190]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49667_CCAATT


title: VB_DiI.s1_1


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0183]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49666_CTCTCG


title: LP_DiI.v1_9

value: LP


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0161]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49665_GTTACC


title: LP_DiI.v1_8


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0134]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49663_GCGCTG


title: LP_DiI.v1_6


title: LP_DiI.v1_7


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0157]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49664_CAAGCA


title: Placebo-arm, Poor outcome, Baseline [A_1_T0_DT0116]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49662_ACAACG


title: LP_DiI.v1_3


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0817]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49701_GATTGT


title: LP_DiI.v1_4


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0890]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49702_ATAAGA


title: LP_DiI.v1_5


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0960]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49703_GCCACA


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0703]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49700_AATGAA


title: LGd_DiI.v1_5

value: LGd


title: VB_DiI.s1_3


title: LGd_DiI.v1_3


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0496]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49661_CGCGGA


title: LGd_DiI.v1_4


title: LGd_DiI.v1_2


title: LGd_DiI.v1_1


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0456]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49660_GATCAC


title: PO_DiI.s1_4


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0386]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49659_CAGATG


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0381]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49658_AACGCC


title: PO_DiI.s1_2


title: PO_DiI.s1_1


title: PO_DiI.s1_3


title: VPMpc_DiI.ins_6

value: VPMpc


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0351]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49657_CGGTTA


title: VPMpc_DiI.ins_5


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0960]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49709_TCGAGG

source_name: Placebo-arm, Good outcome, Baseline


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0317]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49656_GAACCT


title: VPMpc_DiI.ins_4


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0586]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49699_TTAACT


title: VPMpc_DiI.ins_3


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0890]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49708_AGATAG


title: Placebo-arm, Good outcome, 1 month post trichiasis surgery [A_0_T1_DT0540]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49704_CCTAAG


title: LD_DiI.rs_2


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0586]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49705_GGCTGC


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0540]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49698_AATAGC


title: LD_DiI.rs_3


title: LD_DiI.rs_1


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0817]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49707_GTGCCA


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0496]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49655_CGCAAC


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0456]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49654_TAATCG


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0381]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49652_CGAAGG


title: MD_DiI.orb_5

value: MD


title: MD_DiI.orb_4


title: MD_DiI.orb_6


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0351]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49651_CGTGAT


title: MD_DiI.orb_2


title: MD_DiI.orb_1


title: VPMpc_DiI.ins_2


title: VPMpc_DiI.ins_1


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0703]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
1_49706_ACCAGT


title: Cd12.ICI.3

city: Blacksburg

first: Mathew

last: Bloomfield

state: VA

address: 1015 Life Science Circle

department: Biological Sciences

institute: Virginia Tech

data_processing:
Illumina HiSeq 2500 reads were trimmed for quality control in Trimmomatic v.0.33.
Read quality was checked for each sample using FastQC v.0.11.7.
High-quality reads were then imported into Samtools  v.1.5 for alignment into BAM files.
BAM files were imported into the Gopher RNA-Seq pipeline (module version 1.6)  and RPKM counts were calculated and counts were processed and mapped to the human genome hg38 (archive-2015-08-14-08-18-15).
RPKM values were log2-transformed with an offset value of 1.0. The aligner used was HISAT2 v.2.1.0.  Cufflinks v.2.2.1 was used to assemble transcripts, estimate their abundances, and test for differential expression in RNA-Seq samples.
Genome_build: hg38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw count expression values for each sample

source_name: treated with ICI-182,780 for 24 hr

growth_protocol: MCF7, Cd7, and Cd12 cells were grown at 37C (5% CO2) in DMEM. media supplemented with 10% FBS and 1% P/S.  Cd7 and Cd12 cells were generated from single cell clones after 6 months of continuous cadmium exposure at 100 nM.

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Life Technologies) and columns from the Direct-zol RNA MiniPrep kit (Zymo Research Corporation, Irvine, CA) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were either mock-treated or 100 nM ICI-182,780 was added for 24 hours.

value: breast cancer

value: epithelial

tag: disease

value: adenocarcinoma


title: Cd12.ICI.1


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0317]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49650_ACATTA


title: Cd12.ICI.2


title: LP_DiI.v1_2


title: LP_DiI.v1_1


title: RE_DiI.cg_8

value: RE


title: Cd12.3

source_name: mock-treated


title: Cd12.1


title: Cd7.ICI.3


title: Cd7.ICI.2


title: RE_DiI.cg_6


title: Cd7.ICI.1


title: RE_DiI.cg_7


title: MD_DiI.orb_3


title: Placebo-arm, Good outcome, Baseline [A_0_T0_DT0386]

description:
A conjunctival swab (Puritan, USA) was taken from the left upper tarsal conjunctiva of each participant. Swabs were stored in RNAlater (Ambion, Life technologies) at -80°C. Total RNA was extracted using Norgen RNA/DNA purification kits.
In vivo
6_49653_AAGACA


title: RE_DiI.cg_5


title: AM_AAV.cg_1

value: AM


title: AV_DiI.rs_5


title: Cd7.1


title: Cd7.2


title: AV_DiI.rs_4


title: MCF7.ICI.3


title: AV_DiI.rs_3


title: AV_DiI.rs_1


title: IAD_DiI.cg_3

value: IAD


title: MCF7.ICI.1


title: MCF7.3


title: MCF7.ICI.2


title: IAD_DiI.cg_2


title: IAD_DiI.cg_1


title: AD_DiI.rs_4

value: AD


title: MCF7.1


title: MCF7.2


title: NOR_46_FW_2445

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Non-Frail white woman

data_processing:
Illumina RTA software (Version number 1.18.66) was used to process the images and generate base-calls to perform the primary analysis. The FASTQ file was then used for sequence input for alignment to the human genome NCBI build v38 using TopHat version 2.21
Transcripts were assembled using Cufflinks version 2.2.1, Cuffmerge version 2.2.1 and differential gene expression was determined using Cuffdiff version 2.2.1.
Significance was determined using the q-value (FDR adjusted p-value using Benjamini-Hochberg correction for multiple-testing) less than 0.05 and also log2 fold change > 0.58 or < -0.58.
Genome_build: NCBI build v38

source_name: PBMCs

growth_protocol: Fasting blood samples are obtained from participants in the morning and collected in 8-ml Vacutainer® heparinized vials (BD, Franklin Lakes, NJ).  Peripheral blood mononuclear cells were isolated within 3 hours of phlebotomy as detailed previously. After isolation, PBMCs are aliquoted and stored at -80oC.

extract_protocol:
Total RNA was isolated using TRIzol® (Life Technologies) according to the manufacturer’s instructions with the addition of a DNase treatment and overnight precipitation. Samples were resuspended in 20 µl RNase-free water and frozen at -80°C until further use.
Libraries were prepared with the TruSeq stranded total RNA with Ribo-Zero Gold kit (RS-122-2301). The libraries were multiplexed into 4 plex per pool and sequenced on Illumina HiSeq 2500 and the associated Illumina RTA software (Version number 1.18.66) was used to process the images and generate base-calls to perform the primary analysis.

tag: frailty status

value: Non-Frail

tag: race

value: White

tag: Sex

value: Female


title: AD_DiI.rs_3


title: Cd7.3


title: FRA_47_MA_2346

description: Frail African American man

value: Frail

value: African American

value: Male


title: AD_DiI.rs_2


title: AD_DiI.rs_1


title: FRA_48_FW_1614

description: Frail white woman


title: NOR_48_FW_1291

description: Non-Frail white woman


title: RE_DiI.cg_4


title: AM_DiI.cg_4


title: FRA_49_MW_1194

description: Frail white man


title: Cd12.2


title: AM_DiI.cg_3


title: FRA_46_MW_1176

description: Frail white man


title: NOR_48_MW_1345

description: Non-Frail white man


title: AV_DiI.rs_2

value: AV


title: FRA_49_FW_992

description: Frail white woman


title: RE_DiI.cg_3


title: NOR_48_MW_990

description: Non-Frail white man


title: NOR_48_MA_766

description: Non-Frail African American man


title: CM_DiI.st_1

value: CM


title: CM_DiI.st_2


title: FRA_49_MA_673

description: Frail African American man


title: VA_DiI.m1_8

value: VA


title: NOR_46_MA_288

description: Non-Frail African American man


title: VA_DiI.m1_7


title: VL_DiI.m1_5

value: VL


title: VL_DiI.m1_6


title: VL_DiI.m1_4


title: VL_DiI.m1_3


title: VM_DiI.m1_6

value: VM


title: VM_DiI.m1_5


title: VA_DiI.m1_6


title: FRA_45_FA_377

description: Frail African American woman


title: VM_DiI.m1_4


title: CRISPRko-Peak-UNT-C

city: Kansas City

first: Scott

middle: T

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
Read Alignment: 20 bases immediately following 'CACCG' matched to library reference file
Differential Abundance: MAGeCK
Genome_build: N/A
Supplementary_files_format_and_content: TXT files are raw read counts from amplicon sequencing for each sample

molecule: genomic DNA

source_name: human renal adenocarcinoma cells (769P)

extract_protocol:
Column purification of gDNA
sgRNA libraries were designed to target p53-regulated genes (Gene Library) or p53 binding sites (Peak Library).  Both libraries were cloned into lentiGuide-Puro (Addgene #52963).
Amplicon sequencing - To determine the abundance of individual sgRNAs within the libraries the sgRNA sequences were directly amplified from pDNA/gDNA and the resulting amplicons were sequenced.

value: human renal adenocarcinoma cells (769P)

tag: library type

value: Peak Library

value: Late Time Point - Untreated


title: CRISPRko-Peak-DOXO-B

value: Late Time Point - 250nM Doxorubicin


title: CRISPRko-Peak-DOXO-A


title: CRISPRko-Peak-DOXO-C


title: CRISPRko-Peak-UNT-B


title: CRISPRko-Peak-ETP-C

value: Early Time Point


title: CRISPRko-Peak-UNT-A


title: CM_DiI.st_3


title: RE_DiI.cg_2

value: RE


title: FRA_46_FA_336

description: Non-Frail African American woman


title: CRISPRko-Peak-ETP-B


title: CRISPRko-Peak-ETP-A


title: RE_DiI.cg_1


title: NOR_49_FA_28

description: Non-Frail African American woman

value: Non-Frail


title: CRISPRi-Peak-DOXO-C


title: SPA_AAV.st_4

value: SPA


title: SPA_AAV.st_3


title: CRISPRi-Peak-DOXO-A


title: CRISPRi-Peak-UNT-C


title: VM_DiI.m1_3


title: SPA_AAV.st_1


title: CRISPRi-Peak-UNT-B


title: VA_DiI.m1_5


title: VA_DiI.m1_4


title: AM_DiI.cg_2

value: AM


title: CRISPRi-Peak-UNT-A


title: CRISPRi-Peak-ETP-C


title: VM_DiI.m1_2


title: CRISPRi-Peak-ETP-B


title: VM_DiI.m1_1


title: CRISPRi-Peak-DOXO-B


title: CRISPRko-Gene-DOXO-C

value: Gene Library


title: VA_DiI.m1_3


title: CRISPRi-Peak-ETP-A


title: VL_DiI.m1_2


title: CRISPRko-Gene-UNT-C


title: AM_DiI.cg_1


title: VA_DiI.m1_2


title: CRISPRko-Gene-DOXO-A


title: VL_DiI.m1_1


title: PF_AAV.st_4

value: PF


title: CRISPRko-Gene-UNT-B


title: VA_DiI.m1_1


title: PF_AAV.st_3


title: CRISPRko-Gene-UNT-A


title: PF_AAV.st_2


title: CRISPRko-Gene-ETP-B


title: CRISPRko-Gene-ETP-C


title: PF_AAV.st_1


title: CRISPRko-Gene-ETP-A


title: HRP8

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

description:
e_cig_exposure_htseq_gene.txt
e_cig_exposure_htseq_gene.txt
e_cig_exposure_e-cig_2_ppm_vs_control_full_DESeq2_results.txt

data_processing:
STAR was used to align sequencing reads to the hg38 reference genome
HTSeq was used to quantify transcript levels corresponding to the hg38 reference genome
DESeq2 was used to perform differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Space-delimited text files include mapped read values per gene for each sample that passed QC (e_cig_exposure_htseq_gene.txt) and transcript-based differential expression results for pairs of samples that passed QC for the Diacetyl vs. vehicle, Pentanedione vs. vehicle and e-cig  vs vehicle comparisons (e_cig_exposure_Diacetyl_25_ppm_vs_control_full_DESeq2_results.txt, e_cig_exposure_Pentanedione_100_ppm_vs_control_full_DESeq2_results.txt and e_cig_exposure_e-cig_2_ppm_vs_control_full_DESeq2_results.txt respectively).
Supplementary_files_format_and_content: e_cig_exposure_htseq_gene.txt :Estimates of mapped reads to reference genes for each sample.
Supplementary_files_format_and_content: e_cig_exposure_Diacetyl_25_ppm_vs_control_full_DESeq2_results.txt :Differential expression results for Diacetyl (25 ppm) vs. vehicle control samples.
Supplementary_files_format_and_content: e_cig_exposure_e-cig_2_ppm_vs_control_full_DESeq2_results.txt :Differential expression results for e-cig smoke solution (2 ppm) vs. vehicle control samples.
Supplementary_files_format_and_content: e_cig_exposure_Pentanedione_100_ppm_vs_control_full_DESeq2_results.txt :Differential expression results for Pentanedione (100 ppm) vs. vehicle control samples.

source_name: Bronchial Epithelium

extract_protocol:
Total RNA was extracted using the miRNAeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
PrepX RNA-seq for Illumina Library kit (Takara Bio, USA)

treatment_protocol: Human bronchial epithelial cells were exposed to vehicle control, diacetyl (25 ppm), pentanedione (100 ppm) or e-cig smoke solution with 2 ppm diacetyl for 24 hrs

tag: donor

value: Bronchial Epithelium


title: CRISPRko-Gene-DOXO-B


title: CL_AAV.st_2

value: CL


title: HRP7


title: CL_AAV.st_1


title: CM_AAV.st_4

value: CM


title: HRP4

description:
e_cig_exposure_htseq_gene.txt
e_cig_exposure_htseq_gene.txt
e_cig_exposure_Diacetyl_25_ppm_vs_control_full_DESeq2_results.txt


title: HRP3


title: HRP2

description:
e_cig_exposure_htseq_gene.txt
e_cig_exposure_htseq_gene.txt
e_cig_exposure_Diacetyl_25_ppm_vs_control_full_DESeq2_results.txt
e_cig_exposure_Pentanedione_100_ppm_vs_control_full_DESeq2_results.txt
e_cig_exposure_e-cig_2_ppm_vs_control_full_DESeq2_results.txt

value: control


title: PCN_AAV.st_3

value: PCN


title: HRP1


title: NOR_47_FA_228

description: Non-Frail African American woman

value: African American

value: Female


title: CM_AAV.st_3


title: PCN_AAV.st_2


title: MS2-Control_1

city: Strasbourg

first: Isabelle

last: Caldelari

address: rue René Descartes

country: France

institute: CNRS

description: MS2 affinity purified RNA

data_processing:
Basecalling pipeline: 1. HiSeq Control Software 2.2.38; 2. RTA 1.18.61.0; 3. CASAVA-1.8.2
Adapter sequences and poor quality reads removed with Trimmomatic
Reads alignement on the HG001 genome (GenBank assembly accession: GCA_001900185.1) using BOWTIE2 (very sensitive end-to-end protocol with maximum 4 mismatches allowed).
Reads per feature counted with HTseq. The protocol chosen is interception non-empty, with reverse strand interpretation.
Differential analysis with DEseq2 (n=2)
Genome_build: GCA_001900185.1
Supplementary_files_format_and_content: tab-delimited text file including Fold changes and P-values.

organism: Staphylococcus aureus

source_name: Bacterial cells

growth_protocol: Bacteria were grown in Brain Heart Infusion (BHI) medium until late exponential phase of growth (6h). Erythromycin at 10 ug/ml final concentration was added to the medium for plasmid selection.

extract_protocol:
Bacterial cells were resuspended in lysis Buffer (20 mM Tris-HCl pH 8, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and broken using the FastPrep apparatus. Crude extract were loaded on a MS2-MBP coated column and purified by affinity chromatography. Eluted RNA were extracted with phenol:chloroform:isoamylalcohol prior to RNAseq analysis.
DNase I (0.1 U/ml) treatment was performed 1h at 37°C. The reactions mixtures were then purified by phenol/chloroform/isoamylalcohol and subsequent ethanol precipitation. RNA pellets were re-suspended in sterile milliQ water. RNA quality and quantity assessments were performed on Agilent Nano Chip on the Bioanalyzer 2100. RNAs were then treated to deplete abundant rRNAs (Ribozero), and the cDNA libraries were performed using the Random Hexamer approach and sequenced by Fasteris (Switzerland). The standard protocol used is the “TruSeq Stranded mRNA” which is based on the TruSeq Illumina kit and which preserves the information about the orientation of the transcripts and produces reads of 125 nts, which map on the complementary strand. The libraries were sequenced using Illumina Hi-Seq 2500 with High-Output (HO) mode using a V4 chemistry sequencing kit (Illumina).

value: HG001 delta_rsaC

tag: plasmid

value: pCN51-P3 MS2


title: CM_AAV.st_1


title: PCN_AAV.st_1


title: MS2-Control_2

description: MS2 affinity purified RNA


title: MS2-RsaC_2

description: MS2 affinity purified RNA

value: pCN51-P3 MS2-RsaC544


title: CL_AAV.st_4


title: CL_AAV.st_3


title: MS2-RsaC_1

description: MS2 affinity purified RNA


title: HRP5

description:
e_cig_exposure_htseq_gene.txt
e_cig_exposure_htseq_gene.txt
e_cig_exposure_Pentanedione_100_ppm_vs_control_full_DESeq2_results.txt

tag: tissue


title: HRP6


title: IMD_AAV.st_4

value: IMD


title: PCN_AAV.st_4


title: HEPS_AND1_AF4MLL_MLLAF4_Sample3_Rep3

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

description:
Single cell RNA-seq
processed data file: HTSeq_counts.txt

data_processing:
RNA-seq reads were aligned to hg19 using STAR (version 2.4.2a) with parameters (--outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HTSeq_counts.txt: HT-Seq counts / gene counts.

source_name: Human embryonic stem cells

extract_protocol:
HEPs were FACS-purified from day 15 EBs of EV or MA4-A4M expressing cells into individual wells of a 96-well PCR plate containing lysis buffer (0.2% Triton-X100 and 2.3 U of SUPERase-In RNase Inhibitor; Ambion).
Three independent replicates (50 cells/replicate) per condition were analyzed.
RNA/cDNA was obtained and amplified as per the SMARTSEQ2 protocol.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were sequenced on the Illumina HiSeq 4000 platform.
Libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit.

value: Hemato-endothelial precursors

tag: day


title: HEPS_AND1_AF4MLL_MLLAF4_Sample3_Rep2


title: KidneyFFPE_CTRL_Patient 1

type: RNA

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

hyb_protocol: Labeled cRNA was then hybridized for 17 hours at 65°C on Agilent-029297 Human miRNA Microarray 8x15K slides, Release 14.0 (Agilent Technologies, Santa Clara, CA). After hybridization, the slides were washed according to manufacturer's protocols.

scan_protocol: The slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies).

data_processing:
Data extraction was performed using Agilent Feature Extraction software. The values in the matrix are log2 transformed.
A p-value cut-off of 0.05 and a fold-change cut-off of 2 were applied to identify differentially expressed miRNAs able to discriminate between the study groups.

source_name: Human FFPE kidney histologically normal

label_protocol: Labeled cRNA was generated using the Low Input Quick Amp Labeling (LIQA) kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: For each sample, total RNA, including miRNAs, was extracted from 8 formalin-fixed, paraffin-embedded (FFPE) sections with a 5µm thickness using the miRNeasy FFPE Kit (Qiagen) according to manufacturer's instructions. To ensure the complete elimination of genomic DNA, a DNase digestion step was also included. Following purification, RNA concentration and purity were assessed using NanoDrop ND-1000 Spectrophotometer (Thermo).

tag: disease state

value: normal control

value: kidney

tag: gender

value: female

tag: proteinuria (g/24h)


title: KidneyFFPE_CTRL_Patient 2

value: male

tag: age


title: IMD_AAV.st_2


title: KidneyFFPE_MN_Patient 5

hyb_protocol: Labeled cRNA was then hybridized for 17 hours at 65°C on Human miRNA Microarray8x15K slides, Release 14.0, (Agilent Technologies, Santa Clara, CA). After hybridization the slides were washed according to manufacturer’s protocols.

source_name: Human FFPE kidney showing MN lesions

extract_protocol: For each sample, total RNA, including miRNAs, was extracted from 8 formalin-fixed, paraffin-embedded sections with a 5µm thickness using the miRNeasy FFPE Kit (Qiagen) according to manufacturer’s instructions. To ensure the complete elimination of genomic DNA, a DNase digestion step was also included. Following purification, RNA concentration and purity were assessed using NanoDrop ND-1000 Spectrophotometer (Thermo).

value: Male


title: KidneyFFPE_MN_Patient 6


title: KidneyFFPE_MN_Patient 4


title: HEPS_AND1_AF4MLL_MLLAF4_Sample3_Rep1

tag: treatment


title: CM_AAV.st_2


title: IMD_AAV.st_1


title: KidneyFFPE_MN_Patient 3


title: HEPS_AND1_MLLAF4_Sample3_Rep3


title: KidneyFFPE_MN_Patient 1


title: KidneyFFPE_MN_Patient 2


title: HEPS_AND1_MLLAF4_Sample3_Rep2


title: KidneyFFPE_DN_Patient 6

source_name: Human FFPE kidney showing Kimmestiel-Wilson lesions (type 2 diabetic nephropathy)

value: type 2 diabetes with diabetic nephropathy


title: HEPS_AND1_MLLAF4_Sample3_Rep1


title: KidneyFFPE_DN_Patient 5


title: IMD_AAV.st_3


title: PVT_AAV.st_2

value: PVT


title: KidneyFFPE_DN_Patient 4


title: KidneyFFPE_DN_Patient 3


title: PVT_AAV.st_1


title: KidneyFFPE_DN_Patient 2


title: HEPS_AND1_AF4MLL_Sample3_Rep3


title: KidneyFFPE_DN_Patient 1


title: KidneyFFPE_CTRL_Patient 4


title: KO_Cyclic_Pressure

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

description:
KO_Cyclic_NT_16
16_GAGATTCC_L00*

data_processing:
Base calling performed using CASAVA 1.8
Quality control on fastq files was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment and junction mapping to mouse genome GRCm38/mm10 performed using Tophat2 and Bowtie2 (Trapnell et. Al. Genome Biology, 2013)
Transcript quantitation, normalization and differential expression testing performed using Cufflinks ((Trapnell et. al. 2012 Nature Protocols)
Data analysis and visualization performed in R, using packages cummeRbund (http://compbio.mit.edu/cummeRbund/) and pheatmap (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of normalized FPKM between samples

molecule: polyA RNA

source_name: Bone marrow derived macrophages from Piezo fl/fl, LysM Cre+ (ΔLysM) mice

growth_protocol: Experimental groups of mice were obtained by crossing homozygous Piezo1fl/fl; homozygous Cre-negative to homozygous Piezo1fl/fl; heterozygous Cre-positive mice, which would theoretically produce an equal number of Cre-negative and Cre-positive mice. All experiments were performed using littermate control, cohoused mice. Mice were sacrificed and hind legs were removed and placed in conical tubes containing 5% FCS DMEM media (Gibco). Muscle was removed from tibia and femur bones and the ends of bones were cut off. Using a 27½ gauge needle, 10 mL of sterile DMEM media supplemented with 10% FBS, pen/strep, and L-glutamine was passed through the bone. Cells were pelleted and plated with mouse MCSF (50 ng/mL) (BioLegend). Following 4 days of incubation, supernatant was removed and plated in a new dish. Cells were again incubated in media with mouse MCSF for 3 more days. Dishes were then washed 3 times with sterile PBS to remove unadhered cells. BMDMs were gently scraped off the dish, pelleted, counted, and seeded in new plates for experimentation.

extract_protocol:
BMDMs were plated at 1-2x106 cells per well on a flat bottom non-adherent 12-well plates. Following treatment, cells were washed once with PBS, and gently dislodged from the plate with PBS. Cells were pelleted and then processed using Qiagen RNeasy Mini Plus Kit (Qiagen) using the manufacturer’s protocol. RNA quantity was assayed using a NanoDrop Microvolume Spectrophotometer (Thermo).
mRNA for RNAseq analysis was purified using PolyA+ selection and processed by the Yale Center for Genome Analysis using standard methodology using Illumina TruSeq mRNA-Seq Sample Prep Kits, library quality and concentration assayed using a Bioanalyzer, RNA was sequenced on a Illumina HiSeq 2500 with 75bp pair-ended reads.

treatment_protocol: All pressure chamber experiments used a custom-built pressure chamber bioreactor built from the lab of Dr. James Warnock. The chamber computational board was connected to a laptop running custom software designed and coded on LabVIEW. The air intake valve was connected to a regulated gas tank containing 5% CO2 balanced in air (21% O2, 79% N2), except in the case of hypoxia synergy studies, where a gas tank containing 2% O2, rather than 21% O2, was substituted. The chamber was placed inside a tissue culture chamber to allow temperatures to reach 37°C. The program parameters were set such that the air intake valve would be open for 0.6s, then the exhaust valve would be opened for 0.4s at a sampling rate of 10 samples per second. The regulator on the gas tank was adjusted such that the amplitude of cyclical hydrostatic pressure was approximately 15mmHg, and adjustments were made constantly throughout the experiments to maintain this amplitude. For static pressure control experiments, both the air intake and exhaust valve were opened, and the regulator was adjusted such that the pressure within the chamber reached the lower parameter achieved in the corresponding cyclical hydrostatic pressure experiment, unless otherwise noted.

tag: strain background

tag: genotype/variation

value: Piezo fl/fl, LysM Cre+ (Piezo1{delta}LysM)

tag: tissue/cell type

value: Bone marrow derived macrophages

value: Cyclic Pressure in pressure chamber for 6 hours


title: WT_Cyclic_Pressure

description:
WT_Cyclic_NT_15
15_CGCTCATT_L00*

source_name: Bone marrow derived macrophages from Piezo fl/fl mice

value: Piezo1 fl/fl


title: HEPS_AND1_AF4MLL_Sample3_Rep2

tag: cell type


title: KO_Static_Pressure

description:
KO_Static_NT_12
12_TCCGGAGA_L00*

value: Static Pressure in pressure chamber for 6 hours


title: HEPS_AND1_AF4MLL_Sample3_Rep1


title: KidneyFFPE_CTRL_Patient 3


title: PVT_AAV.st_3

tag: striatumics


title: HEPS_AND1_Neo_Sample3_Rep3

value: Control


title: HEPS_AND1_Neo_Sample3_Rep2


title: ESC_Hybrid_KO2_H3K9me3_ChIP

city: Cambridge

first: Hui

last: Shi

address: Downing Street

department: Department of Physiology, Development and Neuroscience

institute: University of Cambridge

description:
Illumina HiSeq 2000 platform
ESC_Hybrid_ZFP57_PEAKS.bed

data_processing:
Raw ChIP-seq fastq were first quality checked with FastQC (version 0.11.5), followed by adapter and base quality trimming with TrimGalore (version 0.2.7).  Reads post-QC were aligned using BWA (v0.6.2).
Potential PCR duplicates were removed with Picard tools (“MarkDuplicates” function)
Peaks were called on mapped data using MACS2 (version 2.1.0) with broad peak option using only uniquely aligned reads (MAPQ>10)
For RNA-seq, reads post-QC were aligned with STAR (v2.5.2, --alignEndsType EndToEnd --outFilterMultimapNmax 300 --outSAMmultNmax 1 --outMultimapperOrder Random)
Genome_build: mm10
Supplementary_files_format_and_content: .bw : bigWig file, .bed : bed file containing ChIP-seq peaks for ZFP57, ESC_RNA-Seq_FPKM.txt : normalised gene expression

source_name: ES cells (maternal zygotic ZFP57 mutants)

growth_protocol: Morula stage embryos were collected at E2.5 and cultured for 2 days in KSOM with inhibitors of Erk and Gsk3 (2i) signaling pathways (PD0325901 and CHIR99021). The trophectoderm was then removed using complement immunosurgery and used for genotyping. The inner cell mass was cultured in N2B27 media supplemented with 2i and LIF until establishment of stable ES cell cultures. Each ES cell line was characterized by staining for alkaline phosphatase activity and expression of Oct-4 (SantaCruz, sc8628) and SSEA1 (Millipore, MAB4301) markers. Finally, each newly established line was karyotyped and screened for mycoplasma contamination prior to use in downstream experiments. ES cells were cultured under 2i/LIF conditions up to a maximum of 15 passages, matching the passage number for WT and KO cells for each experiment.

extract_protocol:
DNA was extracted using tale lysis buffer (50mM Tris-Cl pH8.5; 5mM EDTA; 200mM Nacl; 0.25% SDS) and 1 µg/ml Proteinase K for 1 hr. The mixture was purified with phenol/chloroform extraction and precipitated with isopropanol.
Paired-end libraries were prepared and sequenced in 100bp reads run according to Illumina instructions.

tag: strain

value: C57BL/6J X 129aa hybrid

value: ES cells

tag: genotype

value: ZFP57 KO (maternal & zygotic)

tag: antibody


title: HEPS_AND1_AF4MLL_MLLAF4_Sample2_Rep3

value: Hemato-endothelial precursors


title: HEPS_AND1_Neo_Sample3_Rep1


title: T1

city: Changchun

first: Xianlu

last: Zeng

address: No. 5268, Renmin Avenue

institute: Northeast Normal University

description: 32D clone 3 cells transfected with CXCR2

data_processing:
Library construction and sequencing on an Illumina HiSeq 2500 instrument
Bowtie2 v2.2.3 was used for building the genome index
Clean data was then aligned to the reference genome using HISAT2 v2.1.0
Gene expression levels were quantified using a software package called FPKM
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates
Genome_build: Mus musculus. GRCm38. 89
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample.

growth_protocol: 32D clone 3 cells were maintained in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 10% mouse interleukin(IL)-3 culture supplement.

extract_protocol:
The cellular RNA was extracted using Trizol reagent followed by a genomic DNA elimination step. RNA purity was checked using the kaiaoK5500® Spectrophotometer. RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 32D clone 3 cells transfected with PEGP-N1(an empty vector) or CXCR2 were cultured in complete medium supplemented with CXCL1 (50 ng/mL) and CXCL2 (50 ng/mL) for 4 h

value: bone marrow

tag: cell line

value: 32D clone 3


title: ESC_Hybrid_KO1_H3K9me3_ChIP

tag: Sex


title: C3

description: 32D clone 3 cells transfected with an empty vector

tag: tissue


title: ESC_Hybrid_WT_H3K9me3_ChIP

source_name: ES cells

value: WT


title: ESC2_KO_ZFP57_ChIP

description:
Illumina HiSeq 2000 platform
ESC_ZFP57_PEAKS.bed

source_name: ES cells (zygotic mutants)

value: ZFP57 KO (zygotic)

value: male


title: ESC1_KO_ZFP57_ChIP


title: Apical sample 2

city: Heidelberg

first: Megan

last: Stanifer

address: INF 344

country: Germany

institute: Heidelberg University Hospital

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background correction using negative control probes and quantile normalization using negative and positive control probes. After normalization control probes are removed. Preprocessing was done with neqc function in R/Bioconductor package limma

source_name: colon carcinoma cells

label_protocol: Standard Illumina label protocol

growth_protocol: T84 cells were seeded onto transwell inserts and allowed to polarize for 5-7 days. When TEER reached 1000 Ohm/cm2 cells were considered polarized.

extract_protocol: 24 hours post-infection RNA was extracted using RNA extraction kit from Machery Nagel as per manufacturers protocol. 1ug of RNA was sent for analysis.

treatment_protocol: Polarized cells were left non-infected (mock), or infected from either the apical (A) or basolateral (B) side. Infection was allowed to proceed for 24 hours.

value: T84 cells

tag: membrane

value: Apical


title: HEPS_AND1_AF4MLL_MLLAF4_Sample2_Rep2

tag: day


title: HEPS_AND1_AF4MLL_MLLAF4_Sample2_Rep1


title: Basolateral sample 2

description: replicate 2

value: Basolateral


title: mock sample 3

description: replicate 3

value: mock


title: C1

source_name: 32D clone 3 cells transfected with an empty vector


title: ESC_Hybrid_INPUT_H3K9me3_ChIP

extract_protocol:
DNA was extracted using tale lysis buffer (50mM Tris-Cl pH8.5; 5mM EDTA; 200mM Nacl; 0.25% SDS) and 1 µg/ml Proteinase K for 1 hr. The mixture was purified with phenol/chloroform extraction and precipitated with isopropanol.
Paired-end libraries were prepared and sequenced in 125bp reads run according to Illumina instructions.

value: mixture of WT and ZFP57 KO (maternal & zygotic)

value: none (input)


title: ESC3_WT_ZFP57_ChIP


title: Basolateral

description: replicate 1


title: mock sample 2

description: replicate 2


title: WT_Static_Pressure

description:
WT_Static_NT_8
8_ATTACTCG_L00*

value: Piezo1 fl/fl

value: Bone marrow derived macrophages

value: Static Pressure in pressure chamber for 6 hours


title: ESC2_WT_ZFP57_ChIP

value: ES cells


title: ESC1_WT_ZFP57_ChIP


title: mock

description: replicate 1


title: GCTfh_3_KO

city: La Jolla

first: Li-Fan

last: Lu

state: CA

address: 9500 Gilman Dr., NSB 5314

institute: University of California, San Diego

description: total RNA (including small RNAs)

data_processing:
Reads from all libraries were mapped to the mouse genome (mm9) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values from all experiments and gene annotation information for RefSeq transcripts

source_name: T-DKO GC-Tfh cells

extract_protocol:
total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted CD44-CD4+ naive T cells (Tn), CD44+PSGL1hiCXCR5-CD4+ T cells (Th1), CD44+PSGL1intCXCR5+CD4+ T cells (Tfh) and CD44+PSGL1loCXCR5+CD4+ T cells (GC-Tfh) isolated from indicated mice
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

value: T cell-specific miR-23~27~24 family KO

value: CD44+PSGL1loCXCR5+CD4+ T cells


title: HEPS_AND1_MLLAF4_Sample2_Rep3

value: Hemato-endothelial precursors


title: GCTfh_2_KO

description: total RNA (including small RNAs)


title: T3

source_name: 32D clone 3 cells transfected with CXCR2

value: bone marrow

value: 32D clone 3


title: CD4 ASC KO Stimulated 1  AntiCD3/CD28

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: CD4 ASC KO Stimulated 1  AntiCD3/CD28

data_processing:
FASTQ files were mapped to the mouse genome mm10 using Salmon based on the annotations from GENCODE vM16.
Bioconductor package tximport was used to process the Salmon output to generate TPM data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab delimited file contains TPM for each sample together with Ensembl gene id, name and type.

source_name: CD4 T cells

growth_protocol: Cell were grown in Complete RPMI medium suppleented with Pen/Strep, 10% FBS and HEPES.

extract_protocol:
Total RNA was extracted following the double extraction protocol. RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen). All mouse RNAs were analyzed on Agilent Bioanalyzer (Agilent) for quality assessment with RNA Integrity Number (RIN) range from 6.6-9.4 and median RIN 8.05.
cDNA libraries were prepared using 1 ng of total RNA and 1 ul of a 1:100,000 dilution of ERCC RNA Spike in Controls (Ambion Thermo Fisher Scientific) using SMARTSeq v2 protocol [1] except for the following modifications: 1. Use of 20 µM TSO, 2. Use of 250 pg of cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina). The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip GX system (Perkin Elmer). All samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (21 samples/lane).

treatment_protocol: Cells were treated with 5ug/mL anti-CD3 and 2ug/mL anti-CD28 antibodies for 12h.

tag: stimulation

value: Anti CD3/CD28

value: ASC KO


title: CD4 ASC KO Stimulated 3  AntiCD3/CD28

description: CD4 ASC KO Stimulated 3  AntiCD3/CD28


title: HEPS_AND1_MLLAF4_Sample2_Rep2


title: GCTfh_1_KO

description: total RNA (including small RNAs)


title: CD4 WT Stimulated 3 AntiCD3/CD28

description: CD4 WT Stimulated 3 AntiCD3/CD28

value: Wildtype


title: HEPS_AND1_MLLAF4_Sample2_Rep1


title: CD4 WT Stimulated 1 AntiCD3/CD28

description: CD4 WT Stimulated 1 AntiCD3/CD28


title: Apical

description: replicate 1

value: T84 cells

value: Apical


title: GCTfh_3_WT

description: total RNA (including small RNAs)

source_name: WT GC-Tfh cells

value: WT


title: RNA seq E10.5 WT1Cre #3158 lineage labelled

city: Edinburgh

first: Timothy

middle: James

last: Kendall

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

description: Lineage labelling induced at E10.5 in WT1CreERT2;Ai14 animals by injection of tamoxifen. Livers harvested for cell isolation from uninjured animals after weaning.

data_processing:
Reads were aligned to mm9 (mm10) using TopHat2 (v2.0.3) Kim et al Genome Biology 14:R36 (2013)
Differential expression was called using Cufflinks (2.0.1) Trapnell et al Nature Protocols 7, 562–578 (2012) and by DESeq2 Love et al Genome Biology 15:550 (2014)
differential_expression_high_13_04_2016.csv: log2 fold change in gene expression (mm9)
differential_expression_low_13_04_2016.csv: log2 fold change in gene expression (mm9)
differential_expression_minus_plus_04_10_2016.csv: log2 fold change in gene expression (mm10)
FPKM_GFP_high.tsv: FPKM values for control and deletion for all genes
FPKM_GFP_low.tsv: FPKM values for control and deletion for all genes
FPKM_minus_plus.tsv: FPKM values for minus and plus conditions for all genes

source_name: Quiescent hepatic stellate cells

extract_protocol:
Hepatic stellate cells were isolated from livers by density centrifugation and subpopulations sorted by flow cytometry into RLT with beta-mercaptoethanol. Total RNA was isolated using Qiagen RNeasy columns following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Quiescent hepatic stellate cells

tag: rfp status

value: Positive

tag: gfp status

tag: injury

value: Uninjured

tag: gender

value: Male


title: RNA seq E10.5 WT1Cre #3197 lineage labelled


title: RNA seq E10.5 WT1Cre #3158 unlabelled

value: Negative


title: RNA seq E10.5 WT1Cre #3153 unlabelled


title: RNA seq E10.5 WT1Cre #3197 unlabelled


title: HEPS_AND1_AF4MLL_Sample2_Rep2

tag: treatment


title: CD4 ASC KO Stimulated 2  AntiCD3/CD28

description: CD4 ASC KO Stimulated 2  AntiCD3/CD28


title: HEPS_AND1_AF4MLL_Sample2_Rep1


title: RNA seq E10.5 WT1Cre #3153 lineage labelled


title: HEPS_AND1_AF4MLL_Sample2_Rep3


title: GCTfh_2_WT

description: total RNA (including small RNAs)

tag: genotype/variation


title: RNA seq PDGFRbCre;WT1_fl_GFP;Ai14 deleted, GFP high #610

description: Adult animals injured for 8 weeks with intraperitoneal injection of carbon tetrachloride

source_name: Activated hepatic stellate cells

tag: cell type

value: Activated hepatic stellate cells

value: High

value: Chronic CCl4


title: GCTfh_1_WT

description: total RNA (including small RNAs)

value: CD44+PSGL1loCXCR5+CD4+ T cells


title: HEPS_AND1_Neo_Sample2_Rep3

source_name: Human embryonic stem cells

value: Hemato-endothelial precursors

value: Control


title: RNA seq PDGFRbCre;WT1_fl_GFP;Ai14 deleted, GFP high #569


title: Tfh_3_KO

description: total RNA (including small RNAs)

source_name: T-DKO Tfh cells

value: T cell-specific miR-23~27~24 family KO

value: CD44+PSGL1intCXCR5+CD4+ T cells


title: HEPS_AND1_Neo_Sample2_Rep2


title: RNA seq PDGFRbCre;WT1_+_GFP;Ai14 control, GFP high #1802


title: RNA seq PDGFRbCre;WT1_+_GFP;Ai14 control, GFP high #1268


title: RNA seq PDGFRbCre;WT1_+_GFP;Ai14 control, GFP high #1804


title: Tfh_1_KO

description: total RNA (including small RNAs)


title: HEPS_AND1_Neo_Sample2_Rep1


title: RNA seq PDGFRbCre;WT1_fl_GFP;Ai14 deleted, GFP low #734

value: Low


title: Tfh_3_WT

description: total RNA (including small RNAs)

source_name: WT Tfh cells


title: SPA_AAV.st_2

source_name: thalamic projection neurons

extract_protocol:
Retrogradely labelled cells were collected as previously described (Hempel et al., Nat Protoc 2007; (Hempel et al., Nat Protoc 2007, PMID 18007629; Sugino et al., eLife 2019, PMID 30977723). Coronal slices (200-300 μm) were cut and incubated for 1 hour with pronases and neural activity blockers in artificial cerebrospinal fluid (ACSF). Thalamic areas were then microdissected and the tissue dissociated. Fluorescent neurons were manually sorted, washed, aspirated into a small volume and lysed with 47 μL XB lysis buffer (PicoPure, Thermo Fisher), incubated for 5 min at 42ºC and stored at -80ºC.
Upon thawing, total RNA was extracted using the PicoPure kit (KIT0204, Thermo Fisher) and External RNA Controls Consortium (ERCC) spike-ins added at 1: 10^5 dilution. cDNA was synthesized and amplified using the Ovation RNA-seq v2 kit (NuGEN), yielding 4-8 µg of cDNA, and sheared using a Covaris E220 sonicator. Libraries were generated using the Ovation rapid DR multiplexing kit (NuGEN), quantified by qPCR using Kapa Library Quantification for Illumina (KK4854, Kapa Biosystems), and sequenced on a HiSeq 2500 flow cell (Illumina).

value: SPA

tag: striatumics


title: RNA seq PDGFRbCre;WT1_fl_GFP;Ai14 deleted, GFP low #610

tag: strain


title: HEPS_AND1_AF4MLL_MLLAF4_Sample1_Rep3


title: RNA seq PDGFRbCre;WT1_+_GFP;Ai14 control, GFP low #1268/1802

tag: genotype


title: Tfh_2_WT

description: total RNA (including small RNAs)


title: RNA seq PDGFRbCre;WT1_+_GFP;Ai14 control, GFP low #1804


title: RNA seq PDGFRbCre;WT1_fl_GFP;Ai14 deleted, GFP high #734


title: HEPS_AND1_AF4MLL_MLLAF4_Sample1_Rep2


title: Tfh_1_WT

description: total RNA (including small RNAs)


title: Tfh_2_KO

description: total RNA (including small RNAs)


title: Th1_3_KO

description: total RNA (including small RNAs)

source_name: T-DKO Th1 cells

value: CD44+PSGL1hiCXCR5-CD4+ T cells


title: HEPS_AND1_MLLAF4_Sample1_Rep3


title: HEPS_AND1_AF4MLL_MLLAF4_Sample1_Rep1


title: Th1_2_KO

description: total RNA (including small RNAs)


title: HEPS_AND1_MLLAF4_Sample1_Rep2


title: HEPS_AND1_MLLAF4_Sample1_Rep1


title: Th1_1_KO

description: total RNA (including small RNAs)


title: Th1_2_WT

description: total RNA (including small RNAs)

source_name: WT Th1 cells

value: WT


title: 72 hpf, periderm, replicate B

city: Los Angeles

first: Shawn

middle: J.

last: Cokus

address: UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East

institute: UCLA

data_processing:
Demultiplexing: single mismatch to expected 7-mers, only keeping PF=1 spots
Adapter, low quality base trimming: CutAdapt 1.8.1 (-m 21 --trim-n --max-n=2 -q 10,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC), then only keeping reads >=47 nt long and only keeping the first 47 nt of those reads
Alignment: STAR 2.5.3a (to genome and transcriptome, single pass mode with known junctions), retaining multiple locations for non-uniquely aligning reads (see paper or BAMs for parameters)
Quantification: Salmon patched 0.10.2 (--numGibbsSamples=1000 --thinningFactor=25 --useVBOpt --libType=U --fldMean=200 --fldSD=200 --rangeFactorizationBins=4 --minAssignedFrags=1 --seqBias --noBiasLengthThreshold), with 1,000 Gibbs samples per experiment
Statistics: see paper; similar to R Bioconductor Sleuth (with Wasabi as importer), but elaborated and with some DESeq2 features incorporated
Genome_build: Ensembl release 92 top-level reference Zebrafish genome (GRCz11 chr1..25 + MT + 847/120 KN/KZ scaffolds) + PhiX, and associated Ensembl genebuild annotations/models
Supplementary_files_format_and_content: GZIP-TAR-Salmon files: GZIP-compressed TAR archives of Salmon transcript quantification output filesystem trees. Supplementary file: Microsoft Excel workbook in XLSX format, with multiple worksheets, containing a comprehensive collection of analysis input data, intermediate steps, and statistical outputs (see column headers as well as Methods and Supplemental methods of the associated journal publication).

organism: Danio rerio

source_name: FACS-isolated periderm from whole embryos

growth_protocol: Zebrafish were maintained in 28.5 C and pH 7.5 fish water. Adults were kept in a 14-hour light / 10-hour dark cycle.

extract_protocol:
Dechorionated embryos were transferred into 1.5 ml tubes and rinsed with Ca2+-free Ringer’s solution for 15 min. During this incubation, yolk was removed by gently pipetting embryos through a 200 µl tip (with the end cut off) three to five times. Yolk-free embryos were transferred into a 35 mm petri dish with 5 ml of 0.25% Trypsin-EDTA. Embryos were incubated at 28.5 °C and homogenized with a 200 µl tip every 10 min until most cells were dissociated (20 to 50 min). 55 µl 100 mM CaCl2 and 550 µl FCS were added to stop digestion. Dissociated cells were transferred into a 15 ml tube and centrifuged at 300 g for 5 min at 15 °C. Cells were rinsed once with 10 ml suspension solution (colorless Leibovitz medium L-15 with 0.3 g/L glutamine, 0.8 mM CaCl2, Pen 50U/ml, Strep 0.05 mg/ml, and 1% FCS). Dissociated cells were resuspended in suspension solution to ~10^7 cells/ml and immediately proceeded to cell sorting at the UCLA Broad Stem Cell Research Center Flow Cytometry Core. BD FACS ARIA II SORP instruments sorted cells, using a 488 nm laser for GFP detection and a 561 nm laser for RFP (dsRed) detection.
Sorted cells in suspension solution were immediately lysed using the Qiagen RNeasy kit. Lysis was completed within two hours of dissociating cells. Total RNA was isolated following the Qiagen RNeasy kit and stored at –80 °C. Quality of all samples was assayed with an Agilent Bioanalyzer, and only samples with RNA Integrity Number > 8 were used for creating sequencing libraries. Poly-A bead-purified RNA-Seq libraries were prepared with the Illumina TruSeq RNA Library Prep Kit.

treatment_protocol: Transgenic embryos without further treatment

value: AB+TU

tag: developmental stage

value: 72 hpf

value: FACS periderm

value: pooled male and female

tag: biomaterial provider

value: Fang Wang (CSUDH)

tag: birth location

value: UCLA


title: 72 hpf, periderm, replicate A

tag: tissue

tag: Sex


title: HEPS_AND1_AF4MLL_Sample1_Rep3

city: Shanghai

tag: day


title: 72 hpf, basal cells, replicate B

source_name: FACS-isolated basal cells from whole embryos

value: FACS basal cells


title: HEPS_AND1_AF4MLL_Sample1_Rep2


title: Th1_3_WT

description: total RNA (including small RNAs)


title: 72 hpf, basal cells, replicate A


title: 72 hpf, nonskin2, replicate B

source_name: FACS-isolated nonskin cells from whole embryos

value: FACS nonskin2