title: VR_SD2

city: Brookings

first: Anne

middle: Y

last: Fennell

state: South Dakota

address: North Campus Drive

department: Department of Plant Science

institute: South Dakota State University

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.3)
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.1) and prinseq-lite (v 0.20.4) (Schmieder & Edwards, 2011)
The reference genome based alignment and assembly of clean reads were performed using tuxedo pipeline (Trapnell et al., 2012). The Vitis vinifera reference genome (Genome12X, V1) was indexed using Bowtie2 (v.2.2.4).
Quality reads were aligned using tophat (v2.0.13) to the indexed reference genome and guided using gene model available for V. vinifera (V1.phase.gff3).
Mapped reads in each library were assembled into transcripts using cufflinks (v. 2.2.1).
Genome_build: V. vinifera reference genome (Genome12X, V1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Vitis riparia

source_name: BUD, short day

growth_protocol: Spur pruned ecodormant V. riparia vines 6-year-old were repotted and grown in long photoperiod (LD, 15h) at 25/20 ± 3°C day/night temperatures with 600–1400 mol m−2 s−1 photosynthetic photon flux in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) in Brookings, South Dakota (44.3 N). Grapevines were grown for 30 days post bud break reaching shoot lengths of 10-15 nodes.

extract_protocol:
Total RNA was extracted from each replicate of LD and SD buds using a modified method of (Sreekantan et al., 2010; Fennell et al., 2015).  DNA free RNA quality and quantity were verified with an Agilent (Santa Clara, CA) 2100 Bioanalyzer RNA 6000 nano chip.
RNA seq libraries for LD and SD buds transcriptome were prepared and sequenced by Illumina HiScanSQ (100 bp, single strand) at the Cornell University Institute of Biotechnology Genome Facility (Ithaca, NY, USA).

treatment_protocol: Ten vine experimental units were randomly assigned either to continued LD or short photoperiod (SD, 13h) as previously described (Fennell et al., 2015). After 28 days, three replicate bud samples for each photoperiod were harvested into separate tubes of liquid nitrogen and stored at -80C until small RNA or total RNA extraction.

tag: days of treatment

value: 28 day of Short Day photoperiod

value: V. riparia PI588259

value: bud


title: VR_SD3

status: Public on Apr 28 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: genotype

tag: tissue


title: VR_SD1


title: VR_LD3

source_name: BUD, long day

value: Continued Long Day photoperiod


title: C6S43

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

data_processing: Illumina Casava1.7 software used for basecalling.  Read quality was observed using FastQC v. 0.11.2  quality trimming was performed using FastX-Toolkit version 0.0.14 with a trimscore of 30 and a trim length of 50  Topha2t version 2.1.0 was used to align trimmed reads to the human genome with default parameters other than that 1 mismatch was allowed  The htseq-count script was used in HTSeq v 0.6.1 to count the number of reads mapping to each gene. HTSeq used Biopython v.2.7.3.  BPSC in R, version 0.99.1 was used to determine normalize genes based on library size and to identify differentially expressed genes. A Benjamini-Hochmerg FDR of 0.05 was used as the cutoff.  IPA version  Genome_build: ENSEMBL version GrCh38.p7  Supplementary_files_format_and_content: counts generated from HTSeq are provided, along with 5 rows at the end of the matrix which include information about where reads aligned in the genome, how many alignments there were for each, etc.

organism: Homo sapiens

source_name: low passage patient-derived PDAC cells

growth_protocol: All cells were maintained at 37 degrees Celsius in 5% Carbon dioxide and grown in DMEM. Patient-derived cells were only passaged up to 10 times.

extract_protocol: The C1 fluidigm instrument was used to capture single cells, extract RNA, reverse transcribe cDNA using the SMARTer system. The Nextera kit was used to prepare the library.

treatment_protocol: To transfect cells 1x10^5 cells were plated per well of a 6-well plate and allowed to attach overnight. The next day Lipofectamine RNAiMax reagent was used to transfect according to the manufacturer's protocol. After 16 hrs transfection normal growth media was added and cells recovered for 24 hr. Then the cells were place in a hypoxia chamber at 1% O2 for 24 hr prior to isolation for RNA sequencing.

tag: condition

value: Hypoxia

tag: transfection

value: Hypoxia Scrambled Control


title: WT-5-18hrs

city: Emeryville

first: John

last: Gladden

state: CA

address: 5885 Hollis Street

institute: Agile BioFoundry

data_processing:
Illumina MiSeq GenerateFASTQ protocol
Sequenced reads were trimmed and filtered using BBDuk
Trimmed and filtered reads were mapped to Rhodosporidium toruloides IFO0880 reference genome using hisat2
Mapped reads were assigned to genes using featureCounts
Genome_build: https://mycocosm.jgi.doe.gov/Rhoto_IFO0880_4/
Supplementary_files_format_and_content: a tab-delimited text file that includes counts for all samples

molecule: polyA RNA

organism: Rhodotorula toruloides

source_name: R. toruloides cells

growth_protocol: Cells were grown in synthetic defined medium + 2% glucose with starting OD of 0.1 and sampled at 18 and 48 hours of growth

extract_protocol:
Total RNA was isolated by disrupting harvested cells using an MP Biomedicals FastPrep bead beater (MP Biomedicals, Irvine, CA, USA) followed by purification using the QIAGEN RNeasy Mini kit with on-column DNase treatment following the manufacturer’s protocol.
10 ug of RNA was then used to prepare a sequencing library with the TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA, USA).

tag: strain

tag: time

value: 18 hours


title: C5S35


title: VR_LD2


title: C4S27


title: C2S11


title: VR_LD1


title: C1S3


title: B6S42


title: WT-2-18hrs


title: B5S34


title: B2S10


title: ATCC17978_1

city: Changchun

last: Sun

address: Xinmin street

country: China

institute: Jilin university

data_processing:
Sequences were mapped to the ATCC 17978 genome (accession No.cp018664.1) using Bowtie2.
Differentially expressed genes were identified using the DESeq2 package (Bioconductor)
Genes were deemed as differentially expressed if they presented a log2-fold change greater than 1 or less than −1 and P value (P-adj) was less than 0.05 in mutant strain compared to WT strain.
Genome_build: ATCC 17978
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Acinetobacter baumannii ATCC 17978

source_name: WT

growth_protocol: A. baumannii strains were grown in lysogeny broth (LB)

extract_protocol:
RNA was extracted from three biological replicates of each strain with a GeneMark Total RNA Purification Kit.
RNA libraries were prepared and sequenced with Illumina HiSeq2000 at the Beijing Genomics Institute (BGI).

value: wild type


title: abaR_3

source_name: ΔabaR

value: markerless deletion of abaR gene


title: ATCC17978_3


title: ATCC17978_2


title: abaR_1


title: abaI_abaR_2

source_name: ΔabaIR

value: markerless deletion of abaI and abaR genes


title: B1S2


title: abaI_abaR_3


title: A6S41


title: abaI_abaR_1


title: abaR_2


title: A5S33


title: A4S25


title: abaI_3

source_name: ΔabaI

value: markerless deletion of abaI gene


title: abaI_2


title: A3S17


title: B4S26


title: MTX-17

city: Oslo

first: Fatima

last: Heinicke

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: Oslo University Hospital

data_processing:
Primary base calling and quality scoring was performed using RTA v1.18.66.4 (Illumina)
demultiplexing and processing with Bcl2fastq v2.18.0.12 (Illumina)
3' adapter were trimmed using trimmomatic v0.36 with the options SE, ILLUMINACLIP=adapter.fa:2:30:7 and the following adapter sequence: AGATCGGAAGAGCACACGTCT.
Remaining reads were mapped to a miRNA reference based on miRBase v22 using bowtie v1.1.2 without allowing for mismatches and parameters --norc,  --best --strata
Reads were counted using a custom script
Genome_build: miRBase v22

source_name: CD19+ B cells

extract_protocol:
RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
NEBNext Small RNA Library Prep Set for Illumina

tag: cell type

value: CD19+ B cells

tag: disease status

value: rheumatoid arthritis patient

tag: treatment

value: methotrexate treated


title: Cmo_SR3

city: Yangling

first: zhenchao

last: yang

state: China

address: China

institute: Northwest A&F University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and Ballgown were used to perform expression level for genes by calculating FPKM.
Genome_build: Cucurbita moschata
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

organism: Cucurbita moschata

source_name: seedling, cotyledon expansion

growth_protocol: The Cucurbita moschata(Duch. ex Lam.) was provided by the Shaanxi Academy of Agricultural Sciences ((Certification number: No. 2010001 of  Shaanxi Vegetable Registration) for use in the following experiments. Seeds were sown into a 50-hole seedling plate and grown in seedling substrate , under artificial light (14 hours light at 28 ℃, 10 hours dark at 18℃). After their hypocotyl hooks had emerged and straightened and the cotyledons were fully unfolded, seedlings of uniform size were selected for use in the experiment.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the poly(A) RNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded mRNA Library Prep Kit(Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).

treatment_protocol: Far red light processing for 120 seconds

value: hypocotyl


title: Cmo_SR2


title: MTX-16


title: A1S1


title: B3S18


title: Cmo_SR1


title: abaI_1


title: MTX-18


title: MTX-15


title: Cmo_SCK2


title: MTX-12


title: ChIPseq of H3K4me3 in sunflower 13 days after anthesis developing seeds

city: Seville

first: Antonio J.

last: Moreno-Perez

address: Campus UPO. Building 4. Crta. Utrera Km 1

country: Spain

institute: Instituto de la Grasa (CSIC)

description: ChIP-seq

library_source: genomic

data_processing:
Reads were mapped using BWA-MEM software
Duplicated reads were deleted using MarkDuplicates from Picard Tools
Peak-calling was performed using MACS2
Genome_build: Sunflower 2016 (XRQ genotype)
Supplementary_files_format_and_content: Called peaks in narrowPeak format

molecule: genomic DNA

organism: Helianthus annuus

source_name: Developing seed

growth_protocol: Sunflowers grown  in growth chambers on a 25/15 ºC (day/night) cycle with a 16h photoperiod and a photon flux density of 200 umol m-2s-1. Developing seeds from sunflower plants were harvested at 13 (early fatty acid biosynthesis stage), 18 (intermediate fatty acid biosyn-thesis stage) and 28 (late fatty acid biosynthesis stage) days after anthesis (DAA

extract_protocol:
The seeds were cross-linked with 1% formaldehyde by vacuum infiltration and quenched with 0.125 M glycine. After grinding, nuclei were isolated in extraction buffer (1% Triton X-100, 0.25 M sucrose, 10 mM MgCl2, 10 mM Tris-HCl pH 8.0 and protease inhibitors). Nuclei were pelleted by centrifugation and resuspended in lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0 and 10 mM EDTA). Then, nuclei were disrupted by sonication in Bioruptor obtaining genomic fragments from 200 to 600 bp. The rest of ChIP-Seq experiment was carried out as described previously by Villar and Köhler (2010) with minor modifications. 1ug of DNA/protein complexes was inmunoprecipitated with anti-H3K4me3 antibody. After crossliked reversal and DNA purification, the ChIP DNA was quantified with the Qubit HS dsDNA kit (Invitrogen).
Illumina libraries for sequencing were generated, and the libraries were sequenced using the HiSEq Sequencing System (Illumina), following the manufacturer’s instructions.

tag: developmental stage

value: 13 DDA (days after anthesis)

value: Developing seed

tag: chip antibody


title: MTX-14


title: A2S9


title: MTX-11


title: MTX-8


title: Cmo_SCK1


title: Cmo_SCK3


title: MTX-6


title: MTX-5


title: MTX-9


title: ChIPseq of H3K4me3 in sunflower 28 days after anthesis developing seeds

description: ChIP-seq

value: 28 DDA (days after anthesis)


title: MTX-13


title: MTX-3


title: MTX-7


title: MTX-4


title: MTX-2


title: MTX-1


title: New-10

value: newly-diagnosed untreated


title: New-9


title: New-8


title: MTX-10


title: New-7


title: Female WT Hippocampus replicate 1

city: NEW YORK

first: Claire-Marie

last: Vacher

state: NY

address: 630 West 168th Street

department: Pediatrics

institute: Columbia University

data_processing:
De-multiplexed sequencing reads were generated using Illumina bcl2fastq allowing no mismatches in the index read.
The Bluebee genomics analysis platform was used for QuantSeq data analysis.
Brielfy, quality trimming of the sequencing reade was performed using BBDuk.
the trimmed reads were aligned to the mouse reerence genome (mm10) using the alignment algorithm STAR v2.5.2a.
Raw read counts per gene were summerized using HTSeq by supplementing Ensembl gene annotation (GRCm38.78).
Genome_build: mm10
Supplementary_files_format_and_content: text file with logFC, logCPM, FDR

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Cerebral cortex, hippocampus, hypothalamus and cerebellum were dissected, flash-frozen and kept at -80°C until use. Tissue homogenization and RNA extraction were performed using the mirVana Isolation kit (Thermo Fisher Scientific; #AM1560) according to the manufacturer’s instructions.
The cDNA libraries were prepared using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) as per the manufacturer’s instructions. Briefly, total RNA was reverse transcribed using oligo (dT) primers. The second cDNA strand was synthesized by random priming, in a manner that DNA polymerase is efficiently stopped when reaching the next hybridized random primer, so only the fragment closed to the 3’ end gets captured for later indexed adapter ligation and PCR amplification. The processed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto a TruSeq v2 Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

value: Hippocampus

tag: age

value: post-natal day 30

value: WT

tag: Sex

value: Female


title: Female WT Hypothalamus replicate 1

source_name: Hypothalamus

value: Hypothalamus


title: Female WT Cerebellum replicate 1

source_name: Cerebellum

value: Cerebellum


title: New-6


title: DMBA-treated Endpoint Cip2a-/- mouse mammary gland cells_rep2

city: Turku

first: Jukka

last: Westermarck

address: Tykistokatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using Star (v. 2.5.2b)
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: mouse genome mm10
Supplementary_files_format_and_content: Processed data file GeneCounts.csv is tab delimited text file containing the genewise read counts for each sample.

source_name: Mouse mammary gland cells

growth_protocol: Mammary gland tissue samples were collected by excluding lymph nodes. A-WT and A-HOZ samples were collected from untreated mice. B-WT and B-HOZ samples were collected 2 weeks after the last (6th) DMBA dosing. C-WT and C-HOZ tumor-free mammary gland samples were collected when mice were sacrificed due to DMBA-induced tumors in any tissue.

extract_protocol:
RNA was isolated using NucleoSpin RNA Mini kit for RNA purification (Macherey-Nagel)
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide

treatment_protocol: 1mg of DMBA dissolved in oil was administered by oral gavage starting when mice were 12-14 weeks old. DMBA was dosed once a week for six weeks.

value: Mouse mammary gland

tag: strain/genotype

value: 6x DMBA, samples when mouse sacrificed due to DMBA-induced tumors


title: DMBA-treated Endpoint Cip2a-/- mouse mammary gland cells_rep3


title: Female WT Cerebral cortex replicate 1

source_name: Cerebral cortex

value: Cerebral cortex


title: Male KO Cerebellum replicate 3

value: KO

value: Male


title: DMBA-treated 2we Cip2a-/- mouse mammary gland cells_rep2

value: 6x DMBA, samples 2 weeks after the last dose


title: DMBA-treated Endpoint Cip2a-/- mouse mammary gland cells_rep1


title: DMBA-treated 2we Cip2a-/- mouse mammary gland cells_rep3


title: DMBA-treated 2we Cip2a-/- mouse mammary gland cells_rep1


title: New-4

value: CD19+ B cells

value: rheumatoid arthritis patient


title: Male KO Hippocampus replicate 3


title: DMBA-treated 2we WT mouse mammary gland cells_rep2

value: C57BL/6Jx129 WT


title: DMBA-treated Endpoint WT mouse mammary gland cells_rep3


title: Male KO Hypothalamus replicate 3


title: New-5


title: DMBA-treated Endpoint WT mouse mammary gland cells_rep1


title: DMBA-treated Endpoint WT mouse mammary gland cells_rep2


title: New-3


title: DMBA-treated 2we WT mouse mammary gland cells_rep3


title: New-2


title: Control Cip2a-/- mouse mammary gland cells_rep3

value: No treatment


title: DMBA-treated 2we WT mouse mammary gland cells_rep1


title: Control Cip2a-/- mouse mammary gland cells_rep1


title: Control WT mouse mammary gland cells_rep3


title: New-1

value: newly-diagnosed untreated


title: Control WT mouse mammary gland cells_rep2


title: Male WT Hypothalamus replicate 3


title: Male WT Cerebellum replicate 3


title: HC-9

value: control

value: controls


title: Control WT mouse mammary gland cells_rep1


title: Male WT Hippocampus replicate 3

value: Hippocampus

value: post-natal day 30

value: WT


title: HC-8


title: 9_S9: Uninfected 72h replicate 3

city: Utrecht

first: Arnar Kari

last: Sigurdarson Sandholt

address: Yalelaan 2

department: IRAS

country: Netherlands

institute: Utrecht University

data_processing:
Base calling with Illumina basecaller
Reads were trimmed to get rid of adapters and low-quality parts with Trimmomatic v. 0.36, using the standard Illumina adapter library, SLIDINGWINDOW:4:20 and MINLEN:50
Reads were mapped to a merged version of the reference genomes (effectively mapping to both at the same time as if they were a single genome) with STAR v. 2.7.2b, using default settings
Reads mapping to features were counted using HTSeq v. 0.9.1, with strandedness set on reverse, i.e. -s reverse, and otherwise default settings
Read counts loaded into R and, using edgeR, each sample was CPM normalized with regards to library size and genes filtered out that had few/no reads mapping to them across samples
Genome_build: GRCg6a/Eth001
Supplementary_files_format_and_content: comma separated text files containing raw gene counts for each gene and sample, one for the chicken data and one for E. tenella
Supplementary_files_format_and_content: comma separated text files containing CPM normalized read counts for each organism, with low expressed genes across time points filtered out along with samples without chicken data, for the chicken dataset, and samples without E. tenella data, for the E. tenella dataset

organism: Gallus gallus

source_name: Chicken macrophage cell culture

growth_protocol: The immortalised chicken macrophage cell-line HD11 (Beug et al., 1979) was maintained in growth medium, i.e. RPMI 1640 (National Veterinary Institute) supplemented with 200 IU penicillin/ml, 100 µg streptomycin/ml, 2mM L glutamine, and 5% FCS. Before infection HD11 cells were trypsinised and live cells were counted by trypan blue exclusion. Cells were seeded at 5.6 x105 cells per well in flat-bottomed 6-well tissue culture plates (Nunc™, ThermoFisher Scientific) in 2 ml of growth medium and at 0.35 x105 cells per well in flat-bottomed 96-well tissue culture plates (Nunc™, ThermoFisher Scientific) in 100 µl of growth medium. Plates were incubated at 40°C, 5.2% CO2 in air at a humid atmosphere for 24 h after which the HD11 cells were approx. 50-70 % confluent in the wells. Cryopreserved E. tenella sporozoites were thawed into RPMI 1640 medium with 15% FCS, centrifuged down at 910 x g for 7 min, resuspended in growth medium and viable sporozoites were counted by trypan blue exclusion

extract_protocol:
For RNA isolation 1 ml of HD11 cell lysate in TRIzol was used and RNA was extracted using chloroform according to the TRIzol manufacturer’s protocol. The Isolated RNA was subsequently treated with DNAse (TURBO™ DNase, 2U/ul, ThermoFisher Scientific) according to the manufacturers protocol and further purified using reagents and the “RNA cleanup” protocol of the RNeasy Mini kit (Qiagen) protocol. RNA concentration and quality was then assessed using the Agilent RNA 6000 Nano kit on a 2100 Bioanalyzer Instrument (Agilent) and the RNA stored at -70°C until further analysis.
Sequencing libraries were prepared from 0.12 – 0.5 μg total RNA using the TruSeq stranded mRNA library preparation kit (Cat# RS-122-2101/2102, Illumina Inc.) including polyA selection. The library preparation was performed according to the manufacturers’ protocol (#15031047). Sequencing: HiSeq2500, paired-end 125bp read length, v4 sequencing chemistry.

treatment_protocol: At infection, 4.5 x106 sporozoites per well in 6-well plates and 0.28 x106 sporozoites per well in 96-well plates were added to the cultures aiming at a ratio of 4 sporozoites per HD11 cell. The same volume of growth medium without parasites was added to uninfected control cultures. Plates were then cultured until RNA harvest up to 72 h and for plates cultured longer than 24 h, growth medium was removed at 24 h, cultures washed with phosphate buffered saline (PBS; without Ca2+ and Mg2+ at pH 7) to remove loose sporozoites and fresh growth medium was added to the wells before culture was continued.

tag: infection status

value: Uninfected

tag: sample time post-infection [hours]

tag: chicken cell line

value: Macrophage HD-11

tag: e. tenella strain


title: Male WT Cerebral cortex replicate 3

tag: tissue

tag: genotype


title: Male KO Cerebral cortex replicate 3


title: 21_S18: Uninfected 72h replicate 2


title: Male KO Hypothalamus replicate 2

value: Hypothalamus


title: Male KO Cerebellum replicate 2

value: Cerebellum


title: 19_S16: Uninfected 48h replicate 2


title: 7_S7: Uninfected 48h replicate 3


title: 13_S12: Uninfected 48h replicate 1


title: Male KO Hippocampus replicate 2

value: KO


title: 5_S5: Uninfected 24h replicate 3


title: HC-4


title: 32_S28: Uninfected 12h replicate 3


title: Control Cip2a-/- mouse mammary gland cells_rep2

value: Mouse mammary gland


title: Male KO Cerebral cortex replicate 2

value: Cerebral cortex

value: Male


title: HC-7

value: CD19+ B cells


title: HC-3


title: HC-5


title: Male WT Cerebellum replicate 2


title: 15_S14: Uninfected 72h replicate 1


title: 31_S27: Uninfected 12h replicate 2


title: HC-6


title: 26_S22: Uninfected 2h replicate 3


title: HC-1


title: 25_S21: Uninfected 2h replicate 2


title: 11_S10: Uninfected 0h replicate 1


title: 9_S25: Uninfected 24h replicate 2


title: Male WT Hippocampus replicate 2


title: X55_EctoCx444CD4plusCD103minusCD69plus

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

data_processing:
RNA-seq data were aligned to the human genome (UCSC Human Genome Assembly, reference sequence GRCh38) using STAR (v2.4.2a), and gene expression quantification was performed using RSEM (v1.2.22). Genes with less than 13 nonzero read counts were filtered out, leaving 14,720 expressed genes for downstream analysis. Samples with less than 500,000 reads; 7,000 detected genes; and an exon rate < 50% were discarded. All libraries except one passed these quality criteria, ending up with 43 samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_countMatrix.csv

source_name: Fresh Ectocervical Tissue

extract_protocol:
250 freshly isolated cells for each sample were sorted using FACSAriaII directly into SMARTer v4 lysis reagents.
Sequencing libraries were prepared using Nextera XT DNA Library Preparation Kit. Barcoded single-cell libraries were pooled and quantified using a Qubit Fluorometer

tag: patient id

value: Donor 444

value: Ectocervix

tag: phenotype


title: 3_S19: Uninfected 24h replicate 1


title: 7_S23: Uninfected 4h replicate 2


title: 30_S26: Uninfected 12h replicate 1


title: X56_EctoCx444CD4plusCD103minusCD69minus


title: 1_S17: Uninfected 4h replicate 1


title: 5_S21: Uninfected 2h replicate 1


title: Female KO Cerebellum replicate 3

tag: strain

value: Female


title: X54_EctoCx444CD4plusCD103plusCD69plus


title: 3_S3: Uninfected 4h replicate 3


title: sop1-5 R2 Exp3

city: København N

first: Peter

last: Brodersen

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

description:
small RNA
deseqcontrast3

data_processing:
trimming with cutadapt v.2.4
mapping with STAR_2.6.0a
reads were quantified with featureCounts from subread-1.6.3 using an Araport11 GFF3 file modified to also include intergenic regions with a gene accession number as 1, 2, 3 etc.
reads were normalized and transformed with DESeq2
DESeq2 analysis was performed and the mutant vs WT results were extracted with an alpha cut-off = 0.1
Genome_build: TAIR10
Supplementary_files_format_and_content: matrix of gathered DESeq2 contrasts from each mutant genotype vs WT

organism: Arabidopsis thaliana

source_name: inflorescences

growth_protocol: seeds were surface-sterilized, plated on 1xMS agar plates and 10 DAG seedlings were transferred to soil and grown in percival growth chambers with a cycle of 16 h light (21 ºC, 70% relative humidity)/ 8 h darkness (16 ºC, 70% relative humidity)

extract_protocol:
inflorescences were collected and snap-frozen in liquid nitrogen. Total RNA was extracted with Trizol reagent according to the instructions from the manufacturer. After the RNA extraction, the RNA was treated for polysaccharides with an additional mild EtOH precipitation.
1 µg of total RNA was used as input per sample. The libraries were constructed with the NEBNext small RNA libraries preperation kit #E7300 following the protocal of the kit.
miRNA-Seq (or rather small RNA seq as you do not only sequence miRNAs)

tag: experiment


title: Female KO Hypothalamus replicate 3


title: sop1-5 R1 Exp3

description:
small RNA
deseqcontrast3


title: sop1-5 R3 Exp3

description:
small RNA
deseqcontrast3


title: 1_S1: Uninfected 0h replicate 2


title: X53_EndoCx444CD4plusCD103minusCD69minus

source_name: Fresh Endocervical Tissue

value: Endocervix


title: Female KO Hippocampus replicate 3


title: HC-2

tag: cell type

tag: disease status

value: control

value: controls


title: ski2-5 R2 Exp3

description:
small RNA
deseqcontrast3


title: ski2-5 R1 Exp3

description:
small RNA
deseqcontrast3


title: Female KO Cerebral cortex replicate 3

value: post-natal day 30


title: ski2-5 R3 Exp3

description:
small RNA
deseqcontrast3


title: X51_EndoCx444CD4plusCD103plusCD69plus


title: X52_EndoCx444CD4plusCD103minusCD69plus


title: hen2-5 R2 Exp3

description:
small RNA
deseqcontrast3


title: Male WT Cerebral cortex replicate 2

value: WT


title: Female KO Cerebellum replicate 2


title: hen2-5 R1 Exp3

description:
small RNA
deseqcontrast3


title: Col-0 WT R3 Exp3

description:
small RNA
deseqcontrast3

value: Col-0 WT


title: X50_VT444CD4plusCD103minusCD69minus

source_name: Fresh Vaginal Tract Tissue

value: Vaginal Tract


title: X49_VT444CD4plusCD103minusCD69plus


title: Col-0 WT R2 Exp3

description:
small RNA
deseqcontrast3


title: Col-0 WT R1 Exp3

description:
small RNA
deseqcontrast3


title: Female KO Hypothalamus replicate 2

value: Hypothalamus


title: Female KO Hippocampus replicate 2

value: Hippocampus


title: ski2-5 R3 Exp2

description:
small RNA
deseqcontrast2


title: X47_Bld444CD4plusCD103minusCD69plus

source_name: Fresh PBMC

value: Peripheral Blood


title: Female KO Cerebral cortex replicate 2

value: KO


title: X48_VT444CD4plusCD103plusCD69plus


title: ski2-5 R1 Exp2

description:
small RNA
deseqcontrast2


title: Male KO Cerebellum replicate 1

value: Cerebellum


title: ski2-5 R2 Exp2

description:
small RNA
deseqcontrast2


title: rrp4 R3 Exp2

description:
small RNA
deseqcontrast2


title: X46_Bld444CD4plusCD103minusCD69minus


title: X42_EctoCx443CD4plusCD103minusCD69minus

value: Donor 443


title: hen2-5 R3 Exp3

description:
small RNA
deseqcontrast3


title: rrp45a R3 Exp2

description:
small RNA
deseqcontrast2


title: rrp4 R1 Exp2

description:
small RNA
deseqcontrast2


title: rrp45a R1 Exp2

description:
small RNA
deseqcontrast2


title: rrp45a R2 Exp2

description:
small RNA
deseqcontrast2


title: Male KO Hippocampus replicate 1

value: Male


title: Male KO Hypothalamus replicate 1


title: X41_EctoCx443CD4plusCD103minusCD69plus


title: Male KO Cerebral cortex replicate 1

value: Cerebral cortex


title: pel1-2 R3 Exp2

description:
small RNA
deseqcontrast2


title: Male WT Hypothalamus replicate 2


title: pel1-2 R2 Exp2

description:
small RNA
deseqcontrast2


title: X40_EctoCx443CD4plusCD103plusCD69plus

value: Ectocervix


title: pel1-1 R1 Exp2

description:
small RNA
deseqcontrast2


title: Male WT Hypothalamus replicate 1


title: hen2-5 R3 Exp2

description:
small RNA
deseqcontrast2


title: pel1-2 R1 Exp2

description:
small RNA
deseqcontrast2


title: hen2-5 R2 Exp2

description:
small RNA
deseqcontrast2


title: rrp4 R2 Exp2

description:
small RNA
deseqcontrast2


title: Male WT Hippocampus replicate 1


title: X38_EndoCx443CD4plusCD103minusCD69plus


title: X37_EndoCx443CD4plusCD103plusCD69plus


title: Male WT Cerebral cortex replicate 1


title: Col-0 WT R2 Exp2

description:
small RNA
deseqcontrast2


title: Col-0 WT R1 Exp2

description:
small RNA
deseqcontrast2


title: hen2-5 R1 Exp2

description:
small RNA
deseqcontrast2


title: X36_VT443CD4plusCD103minusCD69minus


title: ski3-5 R1 Exp1

description:
small RNA
deseqcontrast1


title: ski2-5 R2 Exp1

description:
small RNA
deseqcontrast1


title: ski3-5 R2 Exp1

description:
small RNA
deseqcontrast1


title: Col-0 WT R3 Exp2

description:
small RNA
deseqcontrast2


title: Male WT Cerebellum replicate 1


title: X34_VT443CD4plusCD103plusCD69plus


title: Female WT Hippocampus replicate 3

value: Female


title: ski2-5 R1 Exp1

description:
small RNA
deseqcontrast1


title: cer7-3 R1 Exp1

description:
small RNA
deseqcontrast1


title: Female WT Hypothalamus replicate 3


title: Female WT Cerebral cortex replicate 3


title: Female WT Cerebellum replicate 3


title: X32_Bld443CD4plusCD103minusCD69minus


title: 20170626_B17_DW4323_S23

city: Boston

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

description: 030817B Best1 GFP

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC. (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis.
Quasimapping and quantification of raw reads was achieved using Salmon (0.8.2) with transcript information from Ensembl release 88. The same samples from different sequencing runs were aggregated at the counts level.
Genome_build: Mapped to the transcriptome - Ensembl release 88
Supplementary_files_format_and_content: nrf2_cd1_p40_raw_counts.csv - matrix table in comma separated value format (csv) with raw gene counts for every gene and every sample

source_name: cd1 RPE cells

extract_protocol:
The retina was removed and the eyecup was quickly cleaned of connective tissue and placed in RNA Protect (Qiagen, Hilden, Germany).  The supernatant was  collected and purified with a RNAeasy micro column (Qiagen) adapting the protocol introduce by Xing-Zhao Wang et al.
Purified RPE RNA was then amplified with a Ultra Low v4 kit (Clontech/Takara Bio) and libraries were prepared for sequencing using standard Illumina protocols. Samples were run on two separate sequencing runs.

treatment_protocol: Each mouse had one eye injected with AAV Best1 Nrf2 and AAV Best1 GFP, and the contralateral eye injected with AAV Best1 GFP only.  Immediately after sacrifice, the eye was enucleated and complete GFP infection was verified.

value: retinal pigment epithelial cells (RPE)

tag: treatment

tag: individual


title: X35_VT443CD4plusCD103minusCD69plus


title: Col-0 WT R2 Exp1

description:
small RNA
deseqcontrast1


title: X33_Bld443CD4plusCD103minusCD69plus


title: Col-0 WT R1 Exp1

description:
small RNA
deseqcontrast1


title: Female WT Cerebellum replicate 2

tag: age


title: 20170626_B16_DW4323_S22

description: 030817B Best1 GFP / Best1 hNrf2


title: X28_EctoCx421CD4plusCD103minusCD69minus

value: Donor 421


title: Female WT Hypothalamus replicate 2

tag: Sex


title: X27_EctoCx421CD4plusCD103minusCD69plus


title: 20170626_B14_DW4323_S20

description: 030817B Best1 GFP / Best1 hNrf2


title: 20170626_B13_DW4323_S19

description: 030817B Best1 GFP


title: 20170626_B12_DW4323_S18

description: 030817B Best1 GFP / Best1 hNrf2


title: Female WT Hippocampus replicate 2


title: cer7-3 R2 Exp1

description:
small RNA
deseqcontrast1


title: 20170626_B10_DW4323_S16

description: 030817B Best1 GFP / Best1 hNrf2


title: X26_EctoCx421CD4plusCD103plusCD69plus


title: Female WT Cerebral cortex replicate 2


title: 20170626_B11_DW4323_S17

description: 030817B Best1 GFP


title: X25_EndoCx421CD4plusCD103minusCD69minus

value: Endocervix


title: Female KO Cerebellum replicate 1

value: post-natal day 30


title: 20170626_B1_DW4323_S7

description: 030817B Best1 GFP / Best1 hNrf2


title: Female KO Hypothalamus replicate 1


title: X24_EndoCx421CD4plusCD103minusCD69plus


title: A24_40_CTL8_NRF2

description: 030817B Best1 GFP

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC. (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis.
Quasimapping and quantification of raw reads was achieved using Salmon (v0.8.1) with transcript information from Ensembl release 89. The same samples from different sequencing runs were aggregated at the counts level.
Genome_build: Mapped to the transcriptome - Ensembl release 89
Supplementary_files_format_and_content: nrf2_rd1_p40_raw_counts.csv - matrix table in comma separated value format (csv) with raw gene counts for every gene and every sample

source_name: rd1 RPE cells


title: A25_40_TRT9_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: A26_40_CTL9_NRF2

description: 030817B Best1 GFP


title: 20170626_B15_DW4323_S21

description: 030817B Best1 GFP


title: X22_VT421CD4plusCD103minusCD69minus


title: Female KO Hippocampus replicate 1


title: A22_40_CTL7_NRF2

description: 030817B Best1 GFP


title: A23_40_TRT8_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: Female KO Cerebral cortex replicate 1


title: A21_40_TRT7_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: X21_VT421CD4plusCD103minusCD69plus


title: A20_40_CTL6_NRF2

description: 030817B Best1 GFP


title: X20_VT421CD4plusCD103plusCD69plus


title: A18_40_CTL5_NRF2

description: 030817B Best1 GFP


title: A19_40_TRT6_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: 20170626_B2_DW4323_S8

description: 030817B Best1 GFP


title: A17_40_TRT5_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: X19_Bld421CD4plusCD103minusCD69plus


title: Sedentary_rep2

city: Columbus

first: Hai

last: Huang

state: OH

address: 486 Biomedical Research Tower, 460 West 12th Ave

department: Surgery

institute: The Ohio State University

data_processing:
Preliminary sequencing results (bcl files) were demultiplexed and converted to FASTQ files with CellRanger mkfastq (version 3.0).
The FASTQ files were aligned to the mm10 reference genome (GRCm38.91).
CellRanger count/aggr were applied for preliminary data analysis and generated a file that contained a barcode table, a gene table, and a gene expression matrix.
UMI count matrix was further processed using the Seurat (v3.1)
Genes expressed in ≥ 3 cells were retained. Cells with gene counts less than 200 or more than 5000 were filtered out.
The UMI count matrixes, which pass the above preliminary filtering and contain the data collected from all the samples, were provided as the processed data.
Genome_build: mm10
Supplementary_files_format_and_content: the UMI count matrix which were generated by cellranger aggr (--normalize=mapped) and passed Seurat preliminary filtering was converted into .txt file and further compressed into .gz file.

source_name: Liver Tissue

extract_protocol:
For a single-cell transcriptional profile, the liver was perfused with enzymatic solution of Collagenase, Type 1 (1 mg/ml) (Worthington-biochem) and for 10 min at 37 °C in a water bath with continuous agitation. After this treatment, the enzymatic solution was inactivated by adding DMEM-Dulbecco's Modified Eagle Medium (Gibco) with 10% fetal bovine serum (Gibco) and was immediately centrifuged at 400 g for 5 min at 4 °C. The cell suspension was filtered through a 70-μm cell strainer, subjected to discontinuous Percoll gradient separation (Sigma-Aldrich). NPCs were separated from the hepatocytes by differential centrifugation (400 rpm for 5 min). The supernatant was centrifuged again (1500 rpm for 5 min x2) to obtain NPCs.
For 10X Genomics sample processing and cDNA library construction, hepatic CD45+ cells were isolated from NPC fraction using CD45 MicroBeads (Miltenyi Biotec). Samples were prepared as outlined in the 10X Genomics Single Cell 3′v3 Reagent Kit user guide. The samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and resuspended in PBS + 0.04% BSA. Cell viability was assessed by staining with Trypan Blue (Invitrogen) and scoring on a hemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 6000 cells. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/μl) were pelleted, resuspended, recounted, and volume adjusted prior to loading onto the 10X Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcribed using a Veriti 96-well thermal cycler (Thermo Fisher). cDNA was recovered using Recovery Agent provided by the kit followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before cleaning using SPRIselect beads (Beckman). Samples were diluted 4:1 in elution buffer (Qiagen) and run on a Bioanalyzer (Agilent Technologies) to determine the cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′Reagent Kit v3(10X) user guide with appropriate modifications to the PCR cycles and based on the calculated cDNA concentration, as recommended by 10X Genomics.

tag: cell/nuclei type

value: adult hepatic CD45+ leukocytes

value: WT C57BL/6

value: stay on a staionary treadmill for 60 min/day, 5 days/week for 4 weeks

tag: hepatic injury level

value: Serum alanine aminotransferase (sALT) at Harvest 56 (U/L)


title: X18_Bld421CD4plusCD103minusCD69minus


title: A15_40_TRT4_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: A16_40_CTL4_NRF2

description: 030817B Best1 GFP


title: Sedentary_rep1

value: Serum alanine aminotransferase (sALT) at Harvest 33 (U/L)


title: Exercise_rep2

value: ran on a motorized treadmill at a speed of 12.5 m/min for 60 min/day, 5 days/week for 4 weeks

value: Serum alanine aminotransferase (sALT) at Harvest 59 (U/L)


title: X23_EndoCx421CD4plusCD103plusCD69plus


title: A14_40_CTL3_NRF2

description: 030817B Best1 GFP


title: Exercise_rep1

value: Serum alanine aminotransferase (sALT) at Harvest 26 (U/L)


title: X14_EctoCx417CD4plusCD103minusCD69plus

value: Donor 417


title: A12_40_CTL2_NRF2

description: 030817B Best1 GFP


title: A13_40_TRT3_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: A11_40_TRT2_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: X13_EctoCx417CD4plusCD103minusCD69minus


title: A10_40_CTL1_NRF2

description: 030817B Best1 GFP


title: A9_40_TRT1_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: X11_EndoCx417CD4plusCD103minusCD69plus


title: M26_20_CTL7_NRF2

description: 030817B Best1 GFP

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC. (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis.
Quasimapping and quantification of raw reads was achieved using Salmon (0.9.1) with transcript information from Ensembl release 90. The same samples from different sequencing runs were aggregated at the counts level.
Genome_build: Mapped to the transcriptome - Ensembl release 90
Supplementary_files_format_and_content: nrf2_rd1_p20_raw_counts.csv - matrix table in comma separated value format (csv) with raw gene counts for every gene and every sample


title: M25_20_TRT7_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: M24_20_CTL6_NRF2

description: 030817B Best1 GFP


title: M23_20_TRT6_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: CVSS_17

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

data_processing:
Illumina small RNA 3' adapter sequence was trimmed from the raw sequencing data using cutadapt
A minimum read length of 17 bp was specified while trimming and shorter reads were discarded.
Fastqc reports were generated before and after trimming.
ShortStack was used to map the data to mouse genome assembly mm10.
miRNA annotations were downloaded from miRBase and reads mapped to miRNAs were counted using ShortStack.
Differential exrression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file with raw counts for each sample.
Supplementary_files_format_and_content: Tab delimited files with normalized counts and DESeq2 differential expression results.

source_name: prefrontal cortex

extract_protocol:
Prefrontal cortex were removed and placed into RNAlater.  RNA was extracted using the RNeasy® Plus Universal Mini Kit .
TruSeq Small RNA Library Construction Kit

treatment_protocol: Male C57BL/6J mice were assigned to chronic variable social stress (CVSS) or control conditions.  To minimize litter effects, littermates were evenly distributed between the CVSS and control groups at weaning. CVSS mice underwent the stress protocol during adolescence (PND 25-59) as previously described (Caruso et al., 2017, 2018c, 2018b, 2018a). Following weaning mice sat undisturbed with littermates (PND 21-25). On PND 25, CVSS mice were individually housed for 3 days followed by social rehousing with 1-2 unfamiliar cage mates for 4 days. This procedure was repeated for 5 consecutive weeks. On PND 59, CVSS mice were rehoused with their original cage mates from weaning until behavioral testing or sacrifice. For control mice, cage mates remained the same from weaning to the end of the study. To equate handling between the control and CVSS conditions, each time CVSS mice were transferred to a new cage for individual or social rehousing, control mice were also moved to new cages. Following CVSS, these mice remained undisturbed (i.e. no behavioral testing) until PND 70 when they were euthanized by cervical dislocation and brains removed. A mouse brain matrix was used to obtain 1 mm slices. The PFC was punched from the slice with a blunt needle that captured both hemispheres and immediately place into RNAlater.

value: CVSS

value: male

value: prefrontal cortex

value: PND 70 (when sacrificed)


title: CVSS_9


title: M21_20_TRT5_NRF2

description: 030817B Best1 GFP / Best1 hNrf2

value: retinal pigment epithelial cells (RPE)


title: M22_20_CTL5_NRF2

description: 030817B Best1 GFP


title: CVSS_1


title: CVSS_41

value: control


title: X9_EndoCx417CD4plusCD103plusCD69plus

value: Endocervix


title: M19_20_TRT4_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: X10_EndoCx417CD4plusCD103minusCD69minus


title: CVSS_37


title: X8_VT417CD4plusCD103minusCD69plus

value: Vaginal Tract


title: CVSS_13


title: X7_VT417CD4plusCD103minusCD69minus


title: X12_EctoCx417CD4plusCD103plusCD69plus

value: Ectocervix


title: X6_VT417CD4plusCD103plusCD69plus


title: M17_20_TRT3_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: CVSS_29


title: CVSS_33


title: CVSS_5


title: X5_Bld417CD4plusCD103minusCD69plus

value: Peripheral Blood


title: M20_20_CTL4_NRF2

description: 030817B Best1 GFP


title: Torpor+radiation [18-24-F1-RAD]

city: Belfast

first: Gary

last: Hardiman

state: Antrim

address: 19 Chlorine Gardens

department: Institute for Global Food Security

country: United Kingdom

institute: Queen's University Belfast

description:
18-24-F1-RAD
DEG_torpor_with_radiation_group_zebrafish_IDs_human_IDs.txt
DEG_torpor_with_radiation_group_zebrafish_IDs_human_IDs.txt

data_processing:
Sequence quality was assessed with FastQC to identify over-represented sequences and low quality reads
Low quality reads and over-represented sequences were removed with Cutadapt
The STAR aligner was utilised to align the RNA-Seq reads to the zebrafish genome (GRCz11)
HTSeq was used to determine the number of reads per transcript
DESeq2 was used for determination of differentially expressed genes
Genome_build: zebrafish genome (GRCz11)
Supplementary_files_format_and_content: HTSeq counts, DESeq output

organism: Danio rerio

source_name: Gastrointestinal tract

extract_protocol:
Total mRNA was extracted from GIT tissues using the miRNeasy Qiagen kit (Qiagen, Hilden, Germany).
To prepare mRNA-Seq libraries the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) was utilized; 100–200 ng of total input GIT RNA was used in accordance with the manufacturer’s protocol.
High through-put sequencing was performed at the University of North Carolina-Chapel Hill High Throughput Sequencing Facility, Chapel Hill, NC and the Queens University Belfast, Genomics Core Technology Unit. RNAseq was performed on Illumina Next SEQ 500 and HiSeq4000 instruments with each mRNA library sequenced to a minimum depth of ~25 million reads.

treatment_protocol: A melatonin group (28.5- melatonin) received melatonin daily for 10 days at a concentration of 24 µM for 10 days to reduce locomotion and arousal. A reduced temperature group (18.5-Ctrl) received a reduction in ambient temperature by 10°C from 28.5°C to 18.5°C to reduce their metabolism. An induced torpor group (18.5-mel) was established with a 10°C reduction in ambient temperature and the addition of 24 µM melatonin.A radiation group was exposed to a total whole body dose of 32.68 cGy.A torpor+radiation group was also established using a cold acclimatised group with melatonin that was also subject to the radiation protocol.

tag: radiation (cgy)

tag: temperature (°c)

tag: melatonin (µm)


title: Torpor+radiation [18-24-M2-RAD]

description:
18-24-M2-RAD
DEG_torpor_with_radiation_group_zebrafish_IDs_human_IDs.txt


title: Torpor+radiation [18-24-F2-RAD]

description:
18-24-F2-RAD
DEG_torpor_with_radiation_group_zebrafish_IDs_human_IDs.txt


title: Radiation [C-M1-RAD]

description:
C-M1-RAD
Htseq_counts_radiation_group.xlsx


title: Torpor+radiation [18-24-M1-RAD]

description:
18-24-M1-RAD
DEG_torpor_with_radiation_group_zebrafish_IDs_human_IDs.txt


title: X4_Bld417CD4plusCD103minusCD69minus

tag: tissue


title: M15_20_TRT2_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: CVSS_21


title: M14_20_CTL1_NRF2

description: 030817B Best1 GFP


title: D25 aCD3aCD28_24h

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

description:
NormCounts.txt
D25_9

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adaptor contaminations were removed using cutadapt, discarding those that were shorter than 15 nt or longer than 35 nt after trimming.
Resulting reads were aligned against a collection of 2657 human, mature miRNA sequences extracted from miRBase (release 22), to obtain expression estimates with RSEM.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method), taking into acount that samples had been obtained in three batches (from three donors) and considering only 626 miRNA species for which expression was at least 1 count per million (CPM) in 3 samples.
Genome_build: miRBase22
Supplementary_files_format_and_content: TMM normalized counts per million (CPM) table, with miRNAs as rows, and samples as columns

source_name: Resting human CD4+ T cells

growth_protocol: Three independent experiments, with resting CD4+ T cells isolated from different healthy donors were performed.

extract_protocol:
Samples were lysed in QIAzol Lysis Reagent and RNA was extracted using the miRNeasy Mini Kit. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer.
200 ng of total RNA were used to generate barcoded miRNA-seq libraries using the NEBNext Multiplex SmallRNA Library Prep Set from Illumina.
The quantity and quality of the miRNA libraries were determined using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip.

treatment_protocol: Samples were collected at 0h and after antiCD3/antiCD28 or IFN I stimulation during 3h, 6h and 24h.

tag: donor

tag: time point


title: Radiation [C-F7-RAD]

description:
C-F7-RAD
Htseq_counts_radiation_group.xlsx


title: D25 aCD3aCD28_6h

description:
NormCounts.txt
D25_8


title: Radiation [C-F2-RAD]

description:
C-F2-RAD
DEG_radiation_group_zebrafish_human_IDs.txt
Htseq_counts_radiation_group.xlsx


title: M13_20_TRT1_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: M18_20_CTL3_NRF2

description: 030817B Best1 GFP


title: X39_EndoCx443CD4plusCD103minusCD69minus

tag: patient id

value: Donor 443

tag: phenotype


title: Control [C-F7-NORAD]

description:
C-F7-NORAD
Htseq_counts_control_group.xlsx


title: A26_40_CTL9_NRF2

description: 030817B Best1 GFP

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC. (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis.
Quasimapping and quantification of raw reads was achieved using Salmon (0.9.1) with transcript information from Ensembl release 91. The same samples from different sequencing runs were aggregated at the counts level.
Genome_build: Mapped to the transcriptome - Ensembl release 91
Supplementary_files_format_and_content: nrf2_rd1_all_samples_raw_counts.csv - matrix table in comma separated value format (csv) with raw gene counts for every gene and every sample


title: Control [C-F3-NORAD]

description:
C-F3-NORAD
Htseq_counts_control_group.xlsx


title: D25 IFN_24h

description:
NormCounts.txt
D25_4

value: IFN I


title: M16_20_CTL2_NRF2

description: 030817B Best1 GFP


title: CVSS_25

tag: strain


title: A25_40_TRT9_NRF2

description: 030817B Best1 GFP / Best1 hNrf2

tag: cell type


title: A23_40_TRT8_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: A24_40_CTL8_NRF2

description: 030817B Best1 GFP


title: D25 aCD3aCD28_3h

description:
NormCounts.txt
D25_7


title: A21_40_TRT7_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: A22_40_CTL7_NRF2

description: 030817B Best1 GFP


title: A20_40_CTL6_NRF2

description: 030817B Best1 GFP


title: A19_40_TRT6_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: PF_2

city: Fullerton

first: M. S.

last: Ramirez

address: 800 N. State College Blvd

institute: California State University Fullerton

data_processing:
Low-quality reads were removed using Trimmomatic v0.36
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
RNA-seq counts were deetermined using FeatureCounts
RNA-seq differential expression analysis was performed using DESeq2
Genome_build: RNA-seq reads were aligned to sequences of the whole genome of strain Acinetobacter baumannii AB5075
Supplementary_files_format_and_content: tsv file generated by DESeq2 provides gene ID, base mean reads, log2 fold-change, log2 fold-change standard error, Wald statistic, Wald test p-value, and Bonferroni Hochberg corrected p-value for the expression of each gene.

organism: Acinetobacter baumannii

source_name: LB + 4% HPF

growth_protocol: Bacteria were grown in a rotary shaker with agitation at 37oC.

extract_protocol:
Total RNA was extracted using the TRI REAGENT® Kit
Illumina RNA-seq

treatment_protocol: Bacteria were cultured in Luria-Bertani broth (LB) with or without  4 % HPF or 0.2 % HSA for 18 h. Overnight cultures were then diluted 1:10 in fresh LB broth and incubated for additional 7 h.

tag: condition

value: LB + 4% HPF

tag: biological replicate


title: HSA_2

source_name: LB + 0.2% HSA

value: LB + 0.2% HSA


title: PF_1


title: PF_3


title: HSA_1


title: HSA_3


title: LB2_3

source_name: LB

value: LB


title: A18_40_CTL5_NRF2

description: 030817B Best1 GFP

tag: treatment

tag: individual


title: Atac-seq - IM infected 4

city: Ithaca

first: Davide

last: Pisu

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description:
Atac-seq analysis of infected IM
Atac-seq
counts_in_merged_idr_peaks.tsv
cpm_in_merged_idr_peaks.tsv

data_processing:
scRNA-seq: Raw sequencing reads from each run were processed using the software CellRanger (v.3.0) from 10X for the mRNA libraries and CITE-Seq-Count (v. 1.4.3) (https://hoohm.github.io/CITE-seq-Count/ ) for the ADT and HTO libraries, to generate raw count matrices for both mRNA and proteins.  Downstream analysis of the datasets was performed in Seurat (v. 3.1.4) as previously described.(Stuart et al., 2019)  Briefly, we first filtered out cells with  < 200 unique genes/cell and with very-high mitochondrial content (> 30% mitochondrial reads), then multiplexed samples were demultiplexed using the MULTIseqDemux function in Seurat ((McGinnis et al., 2019)), doublets and empty droplets were identified and removed, and the correct identity assigned to each sample. scRNA-seq datasets for each sample were pre-processed using the regularized negative binomial regression in Seurat (regressing out both the number of counts and percentage of mitochondrial reads) (Hafemeister and Satija, 2019) and analyzed to identify myeloid cell subsets. Myeloid cell subsets from the different samples were then merged to generate an annotated object containing information from all the different datasets. Subsequently, the RNA slot (containing the raw counts) of the merged object was used as an input for Harmony, as previously described (Korsunsky et al., 2019). Briefly, raw counts were log-normalized and the first 3000 highly variable genes identified. The expression of these genes was scaled and centered, PCA was computed on the scaled expression values and data integration with Harmony was performed using both “Batch” and “Infection Status” as covariates for the murine datasets and “Batch” for the human datasets. The aligned Harmony embeddings were then used to perform graph-based cluster detection using PCs (principal components) that were identified as statistically significant by the jackstraw method. (Chung and Storey, 2015) The Louvain algorithm was used for community detection. (Blondel, 2008) We annotated clusters of cell types by reference-based and canonical marker genes analysis, as described in the text. Trajectory and pseudotime analysis was performed in Monocle (v3.0), using the SeuratWrappers package in R (v. 0.2.0) to convert the integrated Seurat object. For unbiased trajectory and pseudotime analysis of the macrophage populations in both murine and human datasets, all cells previously classified as macrophages were assigned to the same partition and trajectory/pseudotime analysis was conducted as previously described.(Qiu et al., 2017)  Pathway enrichment analysis was performed in g:Profiler, using an ordered by fold change list of genes as a query, using the g:SCS method for multiple testing correction and the Reactome database as a data source. Only pathways enriched with FDR <0.05 were considered statistically significative.
Dual RNA-seq: Data analysis for the Dual RNA-seq datasets was performed as previously described. (Pisu et al., 2020a; Pisu et al., 2020b) Briefly, low quality reads and Illumina adapters were removed using FlexBar (v. 3.4) (Roehr et al., 2017) while remaining rRNA reads were removed using Bowtie2 (-sensitive mode) (Langmead and Salzberg, 2012) and a custom GTF file. The filtered fastq files were split using Bowtie2 (–very-sensitive mode) into species-specific files using the two reference genomes, GRCm38.94 for Mus musculus and NCBI assembly GCA_00668235.1 for Mtb Erdman. Hisat2 (v. 2.1.0) (Kim et al., 2015) was then used to align Mtb reads to the M.tuberculosis transcriptome and raw read counts for each sample were obtained using HTSeq. (v. 0.11.0)(Anders et al., 2015) The raw read count matrices obtained in this study (hspx-high and hspx-low) were then combined with the matrices obtained from samples of a previous study (Mtb in AM and Mtb in IM) (Pisu et al., 2020a) to compare bacterial responses belonging to ontogeny vs activation of the host immune cell. Exploratory, visualization and differential gene expression analysis was then carried out in R using DESeq2 and APEGLM for LFC estimation, as previously described (Pisu et al., 2020a). Genes with less than 10 raw counts across all samples were excluded from downstream analysis. The protein-protein interaction network for the Mtb genes was created in Cytoscape using the String app. (v. 1.4.1) . Only high-confidence interactions (co-expression, experiments, neighborhood, co-occurrence with a score > 0.7) relative to query proteins were considered.
ATAC-seq: Paired-end sequencing reads of length 2 x 42 bp were trimmed to remove adapter sequences using cutadapt (ver. 2.5) (Martin, 2011) and quality checked using FASTQC. The reads were aligned to the mm10 (GRCm38) mouse reference genome using bwa (ver. 0.7.17) (Li and Durbin, 2009). Low quality alignments (MAPQ < 30), secondary alignments, unmapped reads and reads with unmapped mate were discarded using samtools. For reads with multiple alignments only five best alignments were retained. PCR duplicates were removed using Picard MarkDuplicates. The remaining clean alignments were analysed for fragment length distribution using the ATACseqQC R/Bioconductor library (Ou et al., 2018). Read alignments to the positive strand were shifted 4 bp downstream and alignments to the negative strand were shifted 5bp upstream to centre the reads on the transposon binding events. Subsequently, peaks were called using macs2 (ver. 2.1.1.20160309) callpeak command with the parameters “-p 0.01 --shift -75 --extsize 150 --nomodel -B --SPMR --keep-dup all --call-summits”. Fold enrichment and p-value tracks normalized to input were produced using macs2 bdgcmp command (options -m FE and -m ppois respectively). Peaks with a q-value < 0.01 were shortlisted. Peaks in the blacklisted regions specified by ENCODE project were removed. For each of the four sample groups, viz. Uninfected AM, Infected AM, Uninfected IM and Infected IM, pooled samples were generated by pooling together reads from all individual replicates of the same group. These pooled samples were also analysed in the same manner as above. Peaks called in the pooled samples were compared against peaks called in the individual samples of the same condition using irreproducible discovery rate (IDR) framework. High quality reproducible peaks were shortlisted based on IDR < 0.05. Subsequently, the IDR peaks from the four groups were merged using “bedtools merge” to generate a final set of peaks (n = 127,513). Counts of reads aligned at each peak interval in each sample was determined using summarizeOverlaps function of the GenomicAlignments R/Bioconductor package (Lawrence et al., 2013) and TMM normalized using edgeR (Robinson et al., 2010).
Genome_build: Mus Musculus: GRCm38.94 / Homo Sapiens: GRCh38.98 / M.tuberculosis: GCA_00668235.1
Supplementary_files_format_and_content: TSV files: contains raw count matrices to import in R for downstream analysis
Supplementary_files_format_and_content: CSV files: contains raw or normalized count data, they were generated from the integrated Seurat objects and contain count data from all datasets
Supplementary_files_format_and_content: RDS file: Integrated Seurat objects that contain all datasets, metadata, dimensional reductions and cluster informations described in the manuscript

source_name: Lung infected cells

extract_protocol:
AM and IM were sorted from lung single cell suspensions prepared as described previously (Pisu et al, 2020) using a BD FACSAria sorter. Cells were sorted in PBS containing 0.04% BSA and processed for ATAC-seq library preparation immediately.
FACS-sorted cells were spun down at 500g for 5 min, followed by a wash using 50 mL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and immediately after lysis, nuclei were spun at 500g for 10 min. Following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition, the sample was purified using a Qiagen MinElute kit. Then, we amplified library fragments using 1× NEB next PCR master mix and 1.25 μM of custom Nextera PCR primers using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. The libraries were purified using a Qiagen PCR cleanup kit in 20 μl. Libraries were amplified for a total of 10–13 cycles and were subjected to high-throughput sequencing using the Illumina HiSeq 2500 Sequencer (pair-end).

value: lung

tag: timepoint

value: 4 weeks

tag: disease state

value: Infected

tag: pathogen

value: BCG Pasteur


title: Atac-seq - AM infected_7

description:
Atac-seq analysis of infected AM
Atac-seq
counts_in_merged_idr_peaks.tsv
cpm_in_merged_idr_peaks.tsv


title: Atac-seq - IM infected 6


title: Atac-seq - IM uninfected 1

description:
Atac-seq analysis of uninfected IM
Atac-seq
counts_in_merged_idr_peaks.tsv
cpm_in_merged_idr_peaks.tsv

source_name: Lung uninfected cells

value: Uninfected


title: Atac-seq - IM infected 5


title: Atac-seq - AM infected_5


title: Atac-seq - AM infected_6


title: D25 IFN_3h

description:
NormCounts.txt
D25_2


title: Atac-seq - AM uninfected_3

description:
Atac-seq analysis of uninfected AM
Atac-seq
counts_in_merged_idr_peaks.tsv
cpm_in_merged_idr_peaks.tsv


title: Atac-seq - AM uninfected_2


title: D25 IFN_6h

description:
NormCounts.txt
D25_3


title: Atac-seq - IM uninfected 2


title: D22 aCD3aCD28_6h

description:
NormCounts.txt
D22_8


title: D25 t0h

description:
NormCounts.txt
D25_1


title: D22 aCD3aCD28_24h

description:
NormCounts.txt
D22_9


title: D22 IFN_24h

description:
NormCounts.txt
D22_4


title: LB1_2


title: Atac-seq - AM uninfected_1


title: D22 aCD3aCD28_3h

description:
NormCounts.txt
D22_7


title: A17_40_TRT5_NRF2

description: 030817B Best1 GFP / Best1 hNrf2

tag: age


title: WT_ctr_rep3

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

country: Germany

institute: Medizinische Fakultät Mannheim

description:
control
WT_cre_3

data_processing:
raw reads were trimmed with Trim Galore! wrapper tool (http://github.com/felixkrueger/trimgalore). High quality trimmed fastq files were mapped with STAR to mm10
Quantification performed with featureCounts from Subreads using Mouse GRM38.79 annotation from ENSEMBL as reference
Differential expression calculated with EdgeR in R
Genome_build: mm10
Supplementary_files_format_and_content: Gata4_Gata6_DEG_EdgeR_Differential_expression

source_name: isolated fibroblasts from the heart

extract_protocol: RNA was isolated from cultured cells using the NucleoSpin RNA II Kit (Macherey Nagel) according to the manufacturer's instructions

treatment_protocol: cells were infected with Ad-Cre or Ad-βGal and cultured for 48 hours

tag: genotype

value: wildtype

tag: adenovirus

value: Cre recombinase

value: 6-8 week


title: LB1_1


title: D22 IFN_6h

description:
NormCounts.txt
D22_3


title: A16_40_CTL4_NRF2

description: 030817B Best1 GFP

value: retinal pigment epithelial cells (RPE)


title: D22 t0h

description:
NormCounts.txt
D22_1


title: A15_40_TRT4_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: WT_ctr_rep2

description:
control
WT_cre_2


title: WT_ctr_rep1

description:
control
WT_cre_1


title: D21 aCD3aCD28_24h

description:
NormCounts.txt
D21_9


title: A14_40_CTL3_NRF2

description: 030817B Best1 GFP


title: D21 aCD3aCD28_6h

description:
NormCounts.txt
D21_8


title: Gata6fl-Cre_LOF_rep2

description:
Gata6 single deletion
GATA6_2


title: D21 IFN_24h

description:
NormCounts.txt
D21_4


title: Gata6fl-Cre_LOF_rep1

description:
Gata6 single deletion
GATA6_1


title: Gata6fl-Cre_LOF_rep3

description:
Gata6 single deletion
GATA6_3


title: D21 aCD3aCD28_3h

description:
NormCounts.txt
D21_7


title: D21 IFN_6h

description:
NormCounts.txt
D21_3


title: Gata4fl-Cre_LOF_rep3

description:
Gata4 single deletion
GATA4_3


title: D21 t0h

description:
NormCounts.txt
D21_1


title: Gata4fl-Cre_LOF_rep1

description:
Gata4 single deletion
GATA4_1


title: A9_40_TRT1_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: A11_40_TRT2_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: A10_40_CTL1_NRF2

description: 030817B Best1 GFP


title: Gata4fl-Cre_LOF_rep2

description:
Gata4 single deletion
GATA4_2


title: D21 IFN_3h

description:
NormCounts.txt
D21_2


title: A13_40_TRT3_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: Gata4_Gata6fl-Cre_LOF_rep3

description:
Gata4/6 double deletion
G4_G6_Cre_4

value: Gata4tm1.1Sad; Gata6tm2.1Sad


title: LPS+JQ1-treated HMC3 [LPSJQ13]

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.7.1) software based on reference genome sequence (Homo sapiens UCSC hg38) and the differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Homo sapiens UCSC hg38
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: LPS+JQ1-treated HMC3 (LPS+JQ1)

growth_protocol: HMC3 cells were grown in high-glucose Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 10 μg/ml streptomycin (Thermo Fisher Scientific, MA, USA).

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO, JQ1, LPS and LPS+JQ1

tag: cell line

value: human microglia cell line


title: Gata4_Gata6fl-Cre_LOF_rep2

description:
Gata4/6 double deletion
G4_G6_Cre_2


title: D22 IFN_3h

description:
NormCounts.txt
D22_2

tag: donor


title: Gata4_Gata6fl-Cre_LOF_rep1

description:
Gata4/6 double deletion
G4_G6_Cre_1


title: M24_20_CTL6_NRF2

first: John

description: 030817B Best1 GFP


title: M25_20_TRT7_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: M23_20_TRT6_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: LPS+JQ1-treated HMC3 [LPSJQ11]


title: Gata6fl-βGal_Ctr_rep3

description:
control
control_3

value: β-Galactosidase


title: A12_40_CTL2_NRF2

description: 030817B Best1 GFP


title: M26_20_CTL7_NRF2

description: 030817B Best1 GFP


title: LPS-treated HMC3 [LPS2]

source_name: LPS-treated HMC3 (LPS)

value: LPS


title: M22_20_CTL5_NRF2

description: 030817B Best1 GFP


title: M21_20_TRT5_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: BMDMs, IgG_Int

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9

source_name: BMDMs

growth_protocol: Mouse bone marrow cells were induced in vitro by adding 20ng/ml of M-csf in DMEM medium.

extract_protocol:
UV-RIP in BMDMs after exposed to flagellin. Cell lysates were incubated with normal rabbit IgG, NLRC4 and caspase11 antibody.RNAs were isolated from the Protein–RNA complexes with phenol-chloroform and subjected to library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 6 days of M-CSF induction, BMDMs were exposed to flagellin.

value: Bone marrow cells

value: wild type

tag: rip antibody

value: IgG


title: LPS-treated HMC3 [LPS3]


title: iCLIP Tis11b 3

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

description:
The first 7 bases of each read (included in the submitted fastq files; see above for sequence) comprise a barcode consisting of three known nucleotides used for demultiplexing, followed by four random nucleotides used for deduplication.
iCLIP_crosslink_sites_Tis11b.txt

data_processing:
Quality of all libraries was checked by FastQC (v0.11.8) and FastqScreen (v0.13.0)
For mRNA-seq, Ribo-seq and 4sU-seq: reads were trimmed for poor quality and adaptor sequences using Trim Galore (0.5.0 dev) with default parameters, then mapped to the mouse GRCm38 genome build using Hisat2 (--dta --sp 1000,1000, including known-splicesite-infile).
Mapped reads were imported into Seqmonk (v1.44.0), and raw read counts were generated for the GRCm38 v90 annotation release over mRNA features assuming opposing strand specificity (mRNA-seq and 4sU-seq), or over CDS features assuming same strand specificity.
For iCLIP datasets: fastq files were uploaded to the Genialis iMaps platform (without first demultiplexing), demultiplexed based on the first three bases, deduplicated based on their random 5' barcode (next four bases), and analysed using the iCount (v2.0.1.dev) demulitplex and analyse pipeline with default paramters to identify cross-link sites (see König et al, Nat Struct Mol Biol, 2010, DOI: 10.1038/nsmb.1838 for details). For iCLIP BRF1/2 1, where RNA from low and high molecular weight protein:RNA complexes were sequenced separately, fastq files for these were merged prior to analysis.
Cross-link sites for the three replicates for iCLIP with each antibody were then merged before calling peaks using iCount (v2.0.1.dev). These were then filtered to include only sites with FDR < 0.05, and annotated in R (using biomaRt and GenomicRanges packages) to indicate genes whose 3'UTR overlaps each site, considering only transcript isoforms with a CCDS.
Genome_build: GRCm38
Supplementary_files_format_and_content: For mRNA-seq, Ribo-seq and 4sU-seq, tab-delimited text files show gene names together with raw read counts generated over mRNA (mRNA-seq and 4sU-seq) or CDS (Ribo-seq) features for each sample. For iCLIP, position and strand of significant crosslink sites (FDR < 0.05) for merged replicates (separate file for each antibody) are shown together the number of detected crosslinks and FDR, and a comma-separated list of genes whose 3'UTR overlaps with the site, considering only isoforms with a CCDS.

source_name: Activated CD4+ T cells

growth_protocol: Naïve CD4+ T cells were isolated from pooled peripheral and mesenteric lymph nodes and spleen using the Miltenyi Biotech CD4+ CD62L+ T Cell Isolation Kit

extract_protocol:
iCLIP was performed on activated CD4+ T cell lysates as previously described (Díaz-Muñoz et al, Methods Mol Biol, 2017, DOI: 10.1007/978-1-4939-7095-7_14), using anti-BRF1/2 (Cell Signalling 2119) or anti-Tis11b (abcam ab42473) antibodies. For one sample (iCLIP BRF1/2 1), low and high molecular weight protein:RNA complexes were isolated separately for library generation, but data was pooled for analysis.
iCLIP libraries were generated as previously described (Díaz-Muñoz et al, Methods Mol Biol, 2017, DOI: 10.1007/978-1-4939-7095-7_14), and sequenced on the HiSeq 2500.

treatment_protocol: T cells were cultured in RPMI1640 containing 10% FCS RPMI media with 10% FCS, 50 µM β-mercaptoethanol, 2mM Glutamine, penicillin/streptomycin and activated by crosslinking CD3ε on 2C11 monoclonal antibody coated tissue culture wells (10µg/ml), together with the 37.51 anti-CD28 monoclonal antibody as a hybridoma supernatant or purified antibody at 10µg/ml

value: WT

tag: age of mice

value: 9-16 weeks

tag: number of mice

tag: tissue

value: Spleen, peripheral and mesenteric LN

value: CD4+ T cells

tag: iclip antibody

value: anti-Tis11b (abcam ab42473)

tag: iclip 5' barcode

value: TTCNNNN


title: BMDMs, CAS11_IP

tag: strain

tag: cell type


title: M19_20_TRT4_NRF2

description: 030817B Best1 GFP / Best1 hNrf2

tag: treatment

tag: individual


title: LPS+JQ1-treated HMC3 [LPSJQ12]


title: M20_20_CTL4_NRF2

description: 030817B Best1 GFP


title: Gata6fl-βGal_Ctr_rep2

description:
control
control_2


title: iCLIP Tis11b 2

value: CCCNNNN


title: IECs, GF

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: gene_fpkm.txt

source_name: Intestinal epithelial cells

extract_protocol:
Intestinal epithelial cells were isolated by incubating in HBSS containing 2 mM EDTA for 30 min and shaking.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestinal epithelial cells

value: germ-free

tag: infection

value: not infected


title: JQ1-treated HMC3 [JQ12]

source_name: JQ1-treated HMC3 (JQ1)


title: LPS-treated HMC3 [LPS1]


title: BMDMs, NLRC4_IP


title: M17_20_TRT3_NRF2

description: 030817B Best1 GFP / Best1 hNrf2

source_name: rd1 RPE cells

value: retinal pigment epithelial cells (RPE)


title: IECs, WT


title: Gata6fl-βGal_Ctr_rep1

description:
control
control_1

value: 6-8 week


title: IECs, ST_1

value: S. Typhimurium


title: M16_20_CTL2_NRF2

description: 030817B Best1 GFP


title: iCLIP Tis11b 1

value: AACNNNN


title: JQ1-treated HMC3 [JQ13]

value: human microglia cell line


title: iCLIP BRF1/2 3

description:
The first 7 bases of each read (included in the submitted fastq files; see above for sequence) comprise a barcode consisting of three known nucleotides used for demultiplexing, followed by four random nucleotides used for deduplication.
iCLIP_crosslink_sites_BRF1_2.txt

value: anti-BRF1/2 (Cell Signalling 2119)

value: CTTNNNN


title: BMDMs, lnc57Rik

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: lncRNA.stat.xlsx, mRNA.stat.xlsx

growth_protocol: Mouse bone marrow cells cultured in DMEM medium

extract_protocol:
Mouse bone marrow-derived macrophages were collected using cell scrapers and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse bone marrow cells were induced in vitro by adding 20ng/ml of M-csf in DMEM medium, and cells were collected after 6 days.

value: BMDMs


title: Control HMC3 [Con2]

source_name: Control HMC3 (Con)

value: DMSO


title: M15_20_TRT2_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: iCLIP BRF1/2 1 high MW

value: WT

value: 9-16 weeks

value: Spleen, peripheral and mesenteric LN

value: GGCNNNN


title: BMDMs, lnc1082


title: JQ1-treated HMC3 [JQ11]


title: Control HMC3 [Con1]


title: M13_20_TRT1_NRF2

description: 030817B Best1 GFP / Best1 hNrf2


title: BMDMs, NC

value: wild type


title: Caucasian TNBC 19

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

data_processing:
The raw sequence reads obtained as FASTQ files were trimmed using Trim Galore (v0.4.1) [http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] to remove adapter sequences and low quality reads.
After performing the quality control analysis using FastQC (v0.11.5) [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/], the trimmed reads were mapped to human genome (GRCh38/hg38) using TopHat v2.1.0.
The aligned reads were sorted via samtools (Version: 1.3.1). HTSeq-count (version 0.6.0) was used to obtain raw read counts for each annotated human gene. Differential expression analysis and read count normalization was carried out using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file include normalized read counts for each sample from DESeq.

source_name: triple negative breast cancer tumor (FFPE)

extract_protocol:
RNA were extracted from FFPE sections using Qiagen All Prep DNA/RNA FFPE Kit (cat # 80234)
RNA sequencing libraries were prepared for Illumina using manufacturer’s instructions.

tag: age in years

tag: Stage

value: Stage II

tag: race

value: Caucasian


title: Caucasian TNBC 18

value: triple negative breast cancer tumor (FFPE)


title: iCLIP BRF1/2 1 low MW

tag: genotype

value: CD4+ T cells

value: GATNNNN


title: iCLIP BRF1/2 2

value: TCTNNNN


title: M14_20_CTL1_NRF2

description: 030817B Best1 GFP

value: retinal pigment epithelial cells (RPE)

tag: age


title: 4sU-seq total Zfp36/Zfp36l1 dKO 1

extract_protocol:
4sU (Sigma, T4509) was added to a final concentration of 500μM for last hour of a 24hour culture and RNA purified with TRIzol (Invitrogen).  RNA was labelled with Biotin-HPDP (Pierce, 50mg EZ-Link Biotin-HPDP) in 100 mM Tris pH 7.4 10 mM EDTA at room temperature for 1.5 h with rotation. RNA was separated from unincorporated biotin-HPDP by Chloroform/Isoamyl-alcohol (24:1) extraction and ethanol precipitation, resuspended in TE and the labelled (nascent) and unlabelled (pre-existing) RNA was separated using Streptavidin-coated magnetic beads. Libraries were also generated from the total RNA (labelled+unlabelled) pool.
Libraries were prepared using the TruSeq stranded mRNA sample prep kit, and sequenced on the HiSeq 2000.

value: Zfp36fl/fl Zfp36l1fl/fl CD4-cre dKO

value: 10-18 weeks

tag: sex of mice

value: Mix of male/female


title: Caucasian TNBC 16


title: Control HMC3 [Con3]

tag: cell line

value: human microglia cell line


title: Ribo-seq WT4

data_processing:
Library strategy: Ribo-Seq
Basecalling was performed using the Illumina default pipeline
Raw sequencing data was demultiplexed, adaptor trimmed with Trim Galore v0.4.5 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), quality checked with FastQC v 0.11.8 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc).
Ribo-Seq reads were aligned to mouse rRNA or tRNA sequences using Bowtie v1.2.2 the reads that were not aligned were kept to alignment to reference genome.
The reads were mapped to the GRCm38/mm10 reference genome using the STAR aligner v2.5.2a. The aligner only reports uniquely mapped reads. Raw read counts over genes and CDSs were obstained by HT-Seq v0.11.2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Ensembl gene ids and raw read counts over CDSs.

source_name: Activated CD19+ B cells

growth_protocol: Fo CD19+ B cells were isolated from pooled peripheral and mesenteric lymph nodes using the negative depletion with biotin-conjugated antibodies against CD5, CD43, Mac and Ter119 followed by DynaBeads-Streptavidin   All samples are from individual female mice aged 8-11 weeks

extract_protocol:
Ribo-seq libraries were prepared using an ARTseq Ribosome Profiling Kit (Epicentre, Illumina) according to the manufacturer’s instructions
Ribo-seq libraries were prepared using an ARTseq Ribosome Profiling Kit (Epicentre, Illumina), pooled and sequenced on two lanes of Illumina HiSeq 2500.

treatment_protocol: B cells were cultured for 48 hours in RPMI-1640 containing 10% FCS, 1mM Na-pyruvate, 2mM GlutaMAX, penicillin/streptomycin, 50 µM β-mercaptoethanol and activated with 10µg/ml LPS, 10ng/ml IL4, 10ng/ml IL5

value: Peripheral and mesenteric LN

value: LN CD19+ B cells

value: Zfp36l1 (fl/fl) control

tag: Sex

value: Female


title: Ribo-seq WT5


title: Ribo-seq WT2


title: HFD_CL_BAT_rep 3

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

department: BMB

institute: University of Southern Denmark

data_processing:
RNA-sequencing (RNA-seq) (TruSeq2, Illumina) was performed according to the instructions by the manufacturer using 1µg of RNA for preparation of cDNA libraries.
Sequencing reads were mapped to the mouse genome using STAR (Dobin et al., 2013).
Tag counts were summarized at the gene level using HOMER (Heinz et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brown adipose tissue

extract_protocol:
BAT was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wildtype

tag: injection scheme

value: daily inj; CL-316,243, 1mg/kg, 9 conseq. days

tag: diet

value: 7 days HFD

value: BAT


title: HFD_CL_BAT_rep 4

tag: tissue


title: HFD_CL_BAT_rep 2


title: HFD_CL_BAT_rep 5


title: 4sU-seq total Ctrl 1

value: Zfp36fl/fl Zfp36l1fl/fl control

tag: age of mice

tag: number of mice

value: Spleen, peripheral and mesenteric LN


title: Ribo-seq WT6

tag: strain

tag: cell type


title: Ribo-seq WT1


title: Caucasian TNBC 15

value: triple negative breast cancer tumor (FFPE)

value: Stage II

value: Caucasian


title: 4sU-seq total Ctrl 2

value: 7-14 weeks

value: CD4+ T cells


title: HFD_Saline_BAT_rep 5

value: daily inj; saline, 10uL/g BW, 9 conseq. days


title: 4sU-seq total Zfp36/Zfp36l1 dKO 2

value: Zfp36fl/fl Zfp36l1fl/fl CD4-cre dKO

value: Mix of male/female


title: Caucasian TNBC 17


title: Caucasian TNBC 13


title: HFD_CL_BAT_rep 1


title: Caucasian TNBC 12


title: Caucasian TNBC 14


title: 27919_12: WT-REC-IgG RNA-seq

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: WT C57BL/6 donor CD8+ T cells in the spleen of HCT recipients given IgG treatment

data_processing:
Reads were aligned to mm10 Genome Assembly using Tophat2 with default settings
Gene expression level of UCSC known genes were quantified using HTseq-count v0.9.1
Annotaton file used was TxDb.Mmusculus.UCSC.mm10.knownGene (downloaded 8/30/2018)
Genome_build: mm10
Supplementary_files_format_and_content: text files containing raw gene level counts

source_name: T cells from Gut

growth_protocol: spleen and bone marrow cell from WT C57BL/6 mice were harvested and intravenus injection into the lethally irradiated WT BALB/C mice, then given the control IgG or anti-IL-2 mAb to the recipients every other day from day 0 to day 6 after injection, on day 7 after injection, spleen and colon were harvested from recipients,and WT C57BL/6 type CD4+ T or CD8+ T cells were purify by FACS sorting

extract_protocol:
RNA extracted by using miRNeasy mini kit (QIAGEN) ,RNA concentration was mesuared by NanoDrop 1000 (Thermo Fisher Scientific, Waltham Massachusetts, US) and RNA integrity was determined using Bioanalyzer (Agilent).
Library construction of 280 ng total RNA for each sample was made using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) (Kapa Biosystems, Wilmington, USA). and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).
Using 10 cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (Thermo Fisher Scientific). Each library was quantified using a Qubit fluorometer (Life Technologies)

treatment_protocol: the cells were freshly isolated from spleen and colon tissue by FACS sorting

value: CD8 T Cells

value: Gut

value: WT C57BL/6

tag: treatment

value: REC-IgG

tag: batch


title: 4sU-seq unlabelled Ctrl 2


title: HFD_Saline_BAT_rep 3

value: Wildtype


title: 27915_8: WT-REC-IgG RNA-seq

description: WT C57BL/6 donor CD8+ T cells in the colon of HCT recipients given IgG treatment

source_name: T cells from Spleen

value: Spleen


title: 4sU-seq unlabelled Ctrl 1

value: 10-18 weeks


title: Caucasian TNBC 11

tag: age in years


title: 4sU-seq unlabelled Zfp36/Zfp36l1 dKO 1


title: Caucasian TNBC 10

tag: Stage


title: 27914_7: WT-REC-IgG RNA-seq

description: WT C57BL/6 donor CD4+ T cells in the spleen of HCT recipients given IgG treatment

value: CD4  T Cells


title: 27913_6: WT-REC-anti-IL-2 RNA-seq

description: WT C57BL/6 donor CD8+ T cells in the colon of HCT recipients given antip-IL-2 treatment


title: HFD_Saline_BAT_rep 1

value: 7 days HFD

value: BAT


title: 4sU-seq unlabelled Zfp36/Zfp36l1 dKO 2

value: Spleen, peripheral and mesenteric LN


title: 27912_5: WT-REC-anti-IL-2 RNA-seq

description: WT C57BL/6 donor CD4+ T cells in the colon of HCT recipients given anti-IL-2 treatment


title: Caucasian TNBC 9

value: triple negative breast cancer tumor (FFPE)

value: Stage II

tag: race

value: Caucasian


title: Chow_CL_BAT_rep 5

tag: genotype

value: daily inj; CL-316,243, 1mg/kg, 9 conseq. days

value: Chow


title: 4sU-seq labelled Zfp36/Zfp36l1 dKO 1

value: Zfp36fl/fl Zfp36l1fl/fl CD4-cre dKO

value: Mix of male/female

value: CD4+ T cells


title: Caucasian TNBC 8


title: 4sU-seq labelled Ctrl 2

value: Zfp36fl/fl Zfp36l1fl/fl control

value: 7-14 weeks


title: Chow_CL_BAT_rep 4

value: Wildtype


title: HFD_Saline_BAT_rep 4

value: daily inj; saline, 10uL/g BW, 9 conseq. days


title: Caucasian TNBC 7

value: Stage III


title: 27909_2: WT-REC-anti-IL-2 RNA-seq

description: WT C57BL/6 donor CD8+ T cells in the spleen of HCT recipients given anti-IL-2 treatment

value: CD8 T Cells

value: Spleen

value: WT C57BL/6


title: 4sU-seq labelled Ctrl 1

value: 10-18 weeks

value: Spleen, peripheral and mesenteric LN


title: Ribo Zfp36/Zfp36l1 dKO 5

data_processing:
Library strategy: Ribo-seq
Quality of all libraries was checked by FastQC (v0.11.8) and FastqScreen (v0.13.0)
For mRNA-seq, Ribo-seq and 4sU-seq: reads were trimmed for poor quality and adaptor sequences using Trim Galore (0.5.0 dev) with default parameters, then mapped to the mouse GRCm38 genome build using Hisat2 (--dta --sp 1000,1000, including known-splicesite-infile).
Mapped reads were imported into Seqmonk (v1.44.0), and raw read counts were generated for the GRCm38 v90 annotation release over mRNA features assuming opposing strand specificity (mRNA-seq and 4sU-seq), or over CDS features assuming same strand specificity.
For iCLIP datasets: fastq files were uploaded to the Genialis iMaps platform (without first demultiplexing), demultiplexed based on the first three bases, deduplicated based on their random 5' barcode (next four bases), and analysed using the iCount (v2.0.1.dev) demulitplex and analyse pipeline with default paramters to identify cross-link sites (see König et al, Nat Struct Mol Biol, 2010, DOI: 10.1038/nsmb.1838 for details). For iCLIP BRF1/2 1, where RNA from low and high molecular weight protein:RNA complexes were sequenced separately, fastq files for these were merged prior to analysis.
Cross-link sites for the three replicates for iCLIP with each antibody were then merged before calling peaks using iCount (v2.0.1.dev). These were then filtered to include only sites with FDR < 0.05, and annotated in R (using biomaRt and GenomicRanges packages) to indicate genes whose 3'UTR overlaps each site, considering only transcript isoforms with a CCDS.
Genome_build: GRCm38
Supplementary_files_format_and_content: For mRNA-seq, Ribo-seq and 4sU-seq, tab-delimited text files show gene names together with raw read counts generated over mRNA (mRNA-seq and 4sU-seq) or CDS (Ribo-seq) features for each sample. For iCLIP, position and strand of significant crosslink sites (FDR < 0.05) for merged replicates (separate file for each antibody) are shown together the number of detected crosslinks and FDR, and a comma-separated list of genes whose 3'UTR overlaps with the site, considering only isoforms with a CCDS.

extract_protocol:
Ribosome-protected mRNA was isolated using the ART-seq Ribosome Profiling kit (Epicentre, Illumina), according to manufacturers instructions: cells were treated with cycloheximide (CHX, 100 µg/ml) three minutes before rapid cooling of the culturing plate, cell extract preparation and isoaltion of ribosome-protected fragments.
Libraries were prepared using the ARTseq Ribosome Profiling Kit (Epicentre, Illumina), and sequenced on the HiSeq 2000.

value: 11 weeks


title: Chow_CL_BAT_rep 2

value: BAT


title: Caucasian TNBC 6

value: triple negative breast cancer tumor (FFPE)

value: Stage II

value: Caucasian


title: Chow_CL_BAT_rep 3

value: daily inj; CL-316,243, 1mg/kg, 9 conseq. days

value: Chow


title: HFD_Saline_BAT_rep 2

value: 7 days HFD


title: 26983_12: WT-REC-anti-IL-2 RNA-seq

value: Gut


title: 27908_1: WT-REC-anti-IL-2 RNA-seq

description: WT C57BL/6 donor CD4+ T cells in the spleen of HCT recipients given anti-IL-2 treatment

value: CD4  T Cells


title: Caucasian TNBC 5


title: 26982_11: WT-REC-anti-IL-2 RNA-seq


title: 27918_11: WT-REC-IgG RNA-seq

description: WT C57BL/6 donor CD4+ T cells in the colon of HCT recipients given IgG treatment

value: REC-IgG


title: 4sU-seq labelled Zfp36/Zfp36l1 dKO 2

value: Zfp36fl/fl Zfp36l1fl/fl CD4-cre dKO

value: 7-14 weeks

value: Mix of male/female

value: CD4+ T cells


title: Ribo Zfp36/Zfp36l1 dKO 4


title: Chow_CL_BAT_rep 1

value: Wildtype


title: Ribo Zfp36/Zfp36l1 dKO 3

value: Spleen, peripheral and mesenteric LN


title: 26979_8: WT-REC-anti-IL-2 RNA-seq

value: CD8 T Cells

value: Spleen

value: WT C57BL/6


title: Chow_Saline_BAT_rep 5

value: daily inj; saline, 10uL/g BW, 9 conseq. days

value: BAT


title: Ribo Zfp36/Zfp36l1 dKO 2

value: 11-13 weeks


title: Chow_Saline_BAT_rep 4

value: Chow


title: 26978_7: WT-REC-anti-IL-2 RNA-seq


title: Caucasian TNBC 4

value: triple negative breast cancer tumor (FFPE)

value: Stage III

value: Caucasian


title: Caucasian TNBC 3


title: Caucasian TNBC 2

value: Stage II


title: 26977_6: WT-REC-IgG RNA-seq

value: Gut

value: REC-IgG


title: Caucasian TNBC 1


title: Chow_Saline_BAT_rep 3


title: Chow_Saline_BAT_rep 2


title: 26976_5: WT-REC-IgG RNA-seq

value: CD4  T Cells


title: Ribo Ctrl 5

value: Zfp36fl/fl Zfp36l1fl/fl control

value: 10 weeks

value: Male

value: CD4+ T cells


title: Ribo Ctrl 4

value: 11 weeks

value: Spleen, peripheral and mesenteric LN


title: African American TNBC 23

value: African American


title: 26973_2: WT-REC-IgG RNA-seq

value: CD8 T Cells

value: Spleen

value: WT C57BL/6


title: African American TNBC 22

value: triple negative breast cancer tumor (FFPE)


title: HFD_C-3BO_BAT_rep 5

value: 7 days HFD

value: BAT


title: Chow_Saline_BAT_rep 1

value: Wildtype

value: daily inj; saline, 10uL/g BW, 9 conseq. days

value: Chow


title: 26972_1: WT-REC-IgG RNA-seq

value: CD4  T Cells

value: REC-IgG


title: Ribo Ctrl 3

value: Zfp36fl/fl Zfp36l1fl/fl control


title: 26308_9: WT-REC-anti-IL-2 RNA-seq

value: Gut


title: Ribo Zfp36/Zfp36l1 dKO 1

value: Zfp36fl/fl Zfp36l1fl/fl CD4-cre dKO

value: 11-13 weeks

value: Mix of male/female

value: CD4+ T cells


title: African American TNBC 21

value: Stage II

value: African American


title: Ribo Ctrl 2

value: 13 weeks

value: Male

value: Spleen, peripheral and mesenteric LN


title: HFD_C-3BO_BAT_rep 3

value: 7 days HFD

value: BAT


title: African American TNBC 20

value: triple negative breast cancer tumor (FFPE)


title: mRNA Zfp36/Zfp36l1 dKO 3

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Libraries were prepared using the TruSeq stranded mRNA sample prep kit, and sequenced on the HiSeq 2000.

value: 7 weeks

value: Female


title: 26309_10: WT-REC-anti-IL-2 RNA-seq

value: CD8 T Cells

value: WT C57BL/6


title: Ribo Ctrl 1

value: Zfp36fl/fl Zfp36l1fl/fl control


title: African American TNBC 18


title: HFD_C-3BO_BAT_rep 4


title: African American TNBC 17


title: HFD_C-3BO_BAT_rep 2


title: African American TNBC 19


title: HFD_C-3BO_BAT_rep 1


title: mRNA Zfp36/Zfp36l1 dKO 2

value: Zfp36fl/fl Zfp36l1fl/fl CD4-cre dKO


title: mRNA Zfp36/Zfp36l1 dKO 1

value: 8 weeks


title: African American TNBC 16

value: Stage III


title: HFD_WT_BAT_rep 5

value: Control


title: mRNA Ctrl 3

value: Mix of male/female

value: CD4+ T cells


title: 26301_2: WT-REC-IgG RNA-seq

value: Spleen

value: REC-IgG


title: African American TNBC 15

value: African American


title: African American TNBC 14

value: Stage II


title: HFD_WT_BAT_rep 4

value: 7 days HFD

value: BAT


title: mRNA Ctrl 1

value: 7 weeks

value: Male

value: Spleen, peripheral and mesenteric LN


title: 26305_6: WT-REC-anti-IL-2 RNA-seq

value: CD8 T Cells

value: WT C57BL/6


title: HFD_WT_BAT_rep 3


title: HFD_WT_BAT_rep 2


title: African American TNBC 13

value: triple negative breast cancer tumor (FFPE)