title: delta-goxR (after oxygen limitation) rep 3

data_processing:
Read processing and strand-specific mapping to the G. oxydans 621H reference genome (NC_006672.1-NC_006677.1) was carried out with the CLC Genomics Workbench (Qiagen, Aarhus, Denmark).
Empirical analysis of differential gene expression for three biological replicates was performed with EdgeR
Genome_build: NC_006672.1-NC_006677.1
Supplementary_files_format_and_content: Results of differential gene expression analysis with edgeR as tab limited text file.
Supplementary_files_format_and_content: EdgeR result matrix with fold change values, p-values and absolute measurements for every gene per sample

source_name: delta-goxR (after oxygen limitation)

growth_protocol: G. oxydans 621H and mutant strains were cultivated in mannitol medium containing 220 mM (4% w/v) mannitol, 5 g l-1 yeast extract, 2.5 g l-1 MgSO4 x 7 H20, 1 g l-1 (NH4)2SO4 and 1 g l-1 KH2PO4. The initial pH value of the medium was 6.0. G. oxydans possesses a natural resistance towards cefoxitin; as a precaution to prevent bacterial contaminations, cefoxitin was added to the media at a concentration of 50 μg ml-1. Precultures were grown in baffled shaking flasks at 30°C and 140 rpm. Main cultures were cultivated in 250 ml of the same medium in a bioreactor system (DASGIP, Jülich, Germany) composed of four 400-ml vessels, each equipped with electrodes for measuring the dissolved oxygen concentration (DO) and the pH. The system enabled these two parameters to be kept constant. The carbon dioxide concentration in the exhaust gas was measured continuously by an infrared spectrometer and the oxygen concentration by a zirconium dioxide sensor. The oxygen availability was kept constant at 15% DO by mixing air, O2 and N2. Calibration was performed by gassing with air (100% DO) and 100% N2 (0% DO). Anaerobic conditions were achieved by gassing with 100% N2. The agitation speed was kept constant at 900 rpm. Controlling and recording of all data as well as calculation of oxygen transfer rates (OTR) and CO2 transfer rates (CTR) was carried out by the “Fedbatch Pro” software (DASGIP, Jülich, Germany). For oxygen limitation experiments, the bacteria were first cultivated at 15% DO to an optical density at 600 nm (OD600) of 2.5 and then the culture was supplied with a gas mixture composed of 2% O2/98% N2

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen, Hilden, Germany) and quality-checked using the Agilent Tape station 2200 (Agilent Technologies, Waldbronn, Germany) with the RNA ScreenTape according to the manufacturer´s instructions.
To remove rRNA of all samples, the RiboMinus Transcriptome Isolation Kit for Yeast and Bacteria (Invitrogen, Carlsbad, USA) was used. rRNA-depleted RNA was precipitated with ethanol overnight at -20°C. The pellet was dissolved in 7 µl nuclease-free water. Successful depletion was verified with the Tape Station using Agilent´s High Sensitivity RNA ScreenTape. Sequencing libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Frankfurt, Germany) following the protocol for rRNA-depleted RNA using 11 cycles for PCR amplification of adaptor-ligated DNA. For quantification of the final cDNA libraries, the KAPA library quantification Kit from KapaBiosystems (Roche, Unterhaching, Germany) was used following the manufacturer´s instructions. The qPCR itself was conducted on a qTOWER 2.2 (Analytik Jena, Jena, Germany).

value: delta-hsdR delta-goxR


title: Salluit S2B DNA

status: Public on Mar 11 2021

type: genomic

city: Tachikawa-shi,

first: Shu-Kuan

last: Wong

state: Tokyo

address: 10-3, Midori-cho,

country: Japan

institute: National Polar Research Institute

description: Low Arctic: Salluit

hyb_protocol: Each dried and labelled DNA sample was resuspended in 42 µL of hybridization solution. This solution consisted of 1 x HI-RPM hybridization buffer, 1 x comparative genome hybridization blocking agent, 0.05 µg・µL-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). The solution was later denatured by remaining at 95 ℃ for 3 min. To remove the bubbles created during the denaturation process, the conditions were maintained at 37 ℃ for 30 min. The hybridizations were carried out at 67 ℃ for 24 h

scan_protocol: The scanned images of the GeoChip hybridizations were obtained and converted by means of the Agilent Feature Extraction 11.5 software (Agilent Technologies, California, USA)

data_processing: The signal intensities, used as a proxy of abundances, were quantified and processed based on previous pipelines48 as follows: (i) removing probes with a signal-to-noise ratio of less than 2.0; (ii) normalizing the signal intensity of each probe by dividing the total signal intensity of a sample and multiplying by a constant

molecule: genomic DNA

organism: soil metagenome

source_name: Soil

label_protocol: The DNA from each sample (500 ng) was labelled with the fluorescent dye Cy-3 by random priming.

growth_protocol: Samples collected directly from the environment

extract_protocol: Total DNA and RNA were extracted from each soil sample using ZymoBIOMICS DNA & RNA kit. The total RNA extracted were subjected to DNAse I treatment and cDNA was generated from the RNA template using SuperScript IV First-Strand Synthesis System for RT-PCR according to the manufacturer’s instruction.

treatment_protocol: Soil samples were collected using a sterile scoop and placed into a 5 mL sampling tube containing RNAlater Stabilization Solution

tag: source material

value: Environmental soil

tag: location

value: low Arctic region of Salluit

tag: molecule subtype

value: Genomic DNA


title: Salluit S3A DNA

description: Low Arctic: Salluit


title: Salluit S2A DNA

description: Low Arctic: Salluit


title: WG17019_B01-W21

type: SRA

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
single cell
GGTATTCAAGAAG

library_source: transcriptomic

data_processing:
Reads flagged as invalid by the Illumina HiSeq control software were discarded. In the remaining reads, any 3′ bases with a quality score of B were removed. If any of the six UMI bases in the 5' end had a Phred score <17 the read was discarded, else the UMI was cut away and saved. The following three bases had to be G for the read to be kept. These, as well as any additional up to totally nine (presumably template-switch derived) G:s were cut away. Reads were discarded if the remaining transcript-derived sequence ended in a poly(A) sequence leaving <25 bases, or if the remaining sequence consisted of fewer than six non-A bases or a dinucleotide repeat with fewer than six other bases at either end. The reads were sorted by the well, as defined by the combined two index read barcodes.
Alignment was performed using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings. Reads with no alignments were realigned against an artificial chromosome, containing all possible splice junctions arising from the exons defined by the UCSC transcript models. The coordinates of aligned splice junctions were translated back to the corresponding genomic positions.
For expression level calculation, the exons of each locus with several transcript variants were merged to a combined model representing total expression of the locus. To account for incomplete cap site knowledge, the 5′ ends of all models were extended by 100 bases, but not beyond the 3′ end of any upstream nearby exon of another gene of the same orientation.
The annotation step was performed separately for each well. For each genomic position and strand combination the number of reads in each UMI was counted. Any multiread that mapped to some repeat outside exons was assigned randomly as one of these repeats and did not contribute to the transcript corresponding to the exon. Else, if the multiread mapped to some exon, and not to any repeat outside exons, it was assigned to the exon where it was closest to the transcript model 5′ end. If it had no exon mapping, it was assigned randomly at one of the mappings. The total number of molecules at each mapping position was determined by the number of distinct UMIs observed. Any UMI represented by only a single read was excluded, in order to reduce false molecules due to PCR and sequencing errors. The raw UMI count was corrected for the UMI collision probability.
Genome_build: rheMac8
Supplementary_files_format_and_content: Processed data consists of a UMI count matrix, where rows are geneIDs and columns cellIDs, and an annotation text file where rows are CellIDs and columns the annotations

molecule: total RNA

organism: Macaca mulatta

source_name: dorsal root ganglion

extract_protocol:
Extracted DRGs were cut once longitudinally (along the nerve) followed by chopping into ~0.5 mm slices. Samples were enzymatically treated for 1 h at 37°C with triturating every 15 min. The resulting cell suspension was then run through 100 µm cell-strainers. 1 ml of 10% Optiprep was loaded under the cell suspension solution using a gel loading tip and centrifugated at 200g for 6 min with a low break. Supernatant was discarded, the cell pellet resuspended and run through a 10 µm strainer. The strainer was rinsed twice and cells were then collected by flushing the filter twice. The cells were kept on ice for 15-20 min, centrifuged for 3 min  at 100 g and resuspended in 900 µl of filtered NMDG-SC/B27/12% optiprep and dispensed immediately into a WaferGen9600 Chip.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: dorsal root ganglion

tag: cell type

value: injured cell

tag: gender

value: Female

tag: age

value: 4 years 8 months


title: delta-goxR (after oxygen limitation) rep 2

city: Jülich

first: Angela

last: Kranz

state: NRW

address: Wilhelm-Johnen-Strasse

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

organism: Gluconobacter oxydans

tag: strain

tag: genotype


title: Salluit S1B DNA

description: Low Arctic: Salluit


title: WG17019_B01-W15

description:
single cell
GGTATTCAACCTG


title: delta-goxR (after oxygen limitation) rep 1


title: WG17019_B01-W14

description:
single cell
GGTATTCAACCAT


title: WG17019_B01-W13

description:
single cell
GGTATTCAACAGA


title: Parental strain (after oxygen limitation) rep 2

value: delta-hsdR


title: Parental strain (after oxygen limitation) rep 3


title: Parental strain (after oxygen limitation) rep 1


title: WG17019_B01-W16

description:
single cell
GGTATTCAACGAC


title: WG17019_B01-W12

description:
single cell
GGTATTCAAATGC


title: WG17019_B01-W11

description:
single cell
GGTATTCAAAGTC


title: At_T_R3_24h

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

country: China

institute: Huazhong Agricultural University

description: processed data file: merged_counts_Ath.txt

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to A. thaliana (TAIR10), C. hirsuta (http://chi.mpipz.mpg.de/), C. rubella (Phytozome 10), E. salsugineum (Phytozome10) or individual A. thalianna accession genomes corrected for SNPs usingTopHat2 (v2.1.1) with following parameters: --read-mismatches 10 --read-gap-length 10 --read-edit-dist 20 --read-realign-edit-dist 0  --min-anchor 5 --splice-mismatches 2 --min-intron-length 30 --max-intron-length 10000 --max-insertion-length 20 --max-deletion-length 20 --num-threads 10 --max-multihits 10 --coverage-search --library-type fr-firststrand --segment-mismatches 3 --min-segment-intron 30 --max-segment-intron 10000 --min-coverage-intron 30 --max-coverage-intron 10000 --b2-very-sensitive
reads per gene were counted using HtSeq (v 0.6.0) with default parameters
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0

extract_protocol:
seedlings were flash frozen in liquid nitrogen and RNA was extracted using peqGOLD TriFast reagent
library preparation was performed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: Eleven-day-old seedlings were transferred from ½ MS-Agar to 24-well plates each with 1.6 ml of ½ MS-Medium 24 h prior to treatments. Five to ten seedlings were transferred per well. For the flg22 treatment 800 µl of 3 µM flg22 solution was added to the medium containing the seedlings resulting in a final concentration of 1 µM flg22. For mock treatments 800 µl 1/2 MS medium was added to the wells. Three well were combined to create one sample.

value: seedling

value: 12 day old

tag: treatment

tag: timepoint

tag: replicate


title: At_M_R3_24h

value: mock


title: WG17019_B01-W10

description:
single cell
GGTATTCAAAGGA


title: Salluit S1A DNA

description: Low Arctic: Salluit


title: WG17019_B01-W09

description:
single cell
GGTATTCAAAGCG


title: At_M_R3_9h


title: At_T_R3_1h


title: At_T_R3_9h


title: At_M_R3_1h


title: WG17019_B01-W08

description:
single cell
GGTATTCAAACGG


title: WG17019_B01-W07

description:
single cell
GGTATTCAAACCT

value: ambiguous


title: WG17019_B01-W05

description:
single cell
GGTATTCAAACAC


title: At_T_R2_24h


title: WG17019_B01-W04

description:
single cell
GGTATTCAAAACC


title: At_M_R2_24h


title: WG17019_B01-W03

description:
single cell
GGTATTCAATCCA


title: WG17019_A01-W14

description:
single cell
ATTAGACGACGAC


title: At_M_R2_9h


title: At_T_R2_1h


title: Root of Cd plus GSH-treated Brassica napus, biological replicate 1

type: RNA

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description:
GSH_Cd1
Brassica napus L.

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were quantified with Factor Analysis for Robust Microarray Summarization (FARMS), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

label: biotin

organism: Brassica napus

source_name: Root of Brassica napus, treated with Cd plus GSH for 2 days

label_protocol: Biotinylated cRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Seeds of oilseed rape (Brassica napus L. cv. Nourin No.16, Kaneko Seed Co. Ltd., Gumma, Japan) were germinated in submerged vermiculite. The solution used for the bottom flooding is a nutrient solution for hydroponics. This solution is containing 0.5 mM NH4H2PO4, 3.0 mM KNO3,  2.0 mM Ca(NO3)2, 1.0 mM MgSO4, 90 µM Na2EDTA (ethylenediamine-N, N, N’, N’-tetra acetic acid disodium), 90 µM FeSO4, 22.5 µM H3BO3, 10 µM MnSO4, 0.1 µM (NH4)6Mo7O24, 0.35 µM ZnCl2, 0.20 µM CuCl2 [Soil Sci. Plant Nutr. 54 (2008) 118–127.]. The pH of this solution was adjusted to 5.5 using KOH solution. After one week, plants were transferred to hydroponic culture condition in 3 L plastic containers (6 plants per one container) with 2 L of Hoagland solution and aeration. The Nutrient solution was freshly replaced once a week. 2 – 3 week old seedlings were used for each experiment.

extract_protocol: Total RNA was isolated using an RNeasy Plant kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Plants were cultivated in 10 µM CdCl2-containing hydroponics solution with or without 100 mM GSH (glutathione, reduced form) for 2 days.

tag: cultivar

value: Nourin No.16

value: root

tag: growth stage

value: 4 weeks after germination

value: Cd plus GSH for 2 days


title: Root of Cd plus GSH-treated Brassica napus, biological replicate 3

description:
GSH_Cd3
Brassica napus L.


title: At_T_R2_9h


title: WG17019_A01-W13

description:
single cell
ATTAGACGACAGA


title: Root of control (treated with Cd only) Brassica napus, biological replicate 3

description:
C_Cd3
Brassica napus L.

source_name: Root of Brassica napus, treated with Cd only for 2 days

value: Cd only for 2 days


title: WG17019_A01-W10

description:
single cell
ATTAGACGAATGC


title: genomic DNA from monocytes UM1157

city: Cleveland

first: Katherine

middle: Rose

last: Dobbs

state: OH

address: 10900 Euclid Ave.

country: USA

institute: Case Western Reserve University

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM1157

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan System using standard recommended Illumina scanner setting

data_processing: Bioconductor/R minfi pipeline  v1.28.14

label: Cy5 and Cy3

organism: Homo sapiens

source_name: monocytes UM1157

label_protocol: Standard Illumina protocol

extract_protocol:
Monocytes were freshly isolated from whole blood via negative selection using the RosetteSep Human Monocyte Enrichment Cocktail (Stemcell Technologies, 15068) according to standard instructions.
Genomic DNA was extracted and purified from monocyte samples using Qiagen DNeasy Kit according to standard instructions.

tag: Sex

value: Male

tag: sample type

value: monocyte

tag: group

value: ChildUM

tag: plasmodium falciparum infection status

value: acute uncomplicated malaria


title: genomic DNA from monocytes UM295

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM295

source_name: monocytes UM295


title: At_T_R1_24h


title: Root of Cd plus GSH-treated Brassica napus, biological replicate 2

description:
GSH_Cd2
Brassica napus L.


title: WG17019_B01-W01

description:
single cell
ATTAGACGACGCT

value: dorsal root ganglion


title: Root of control (treated with Cd only) Brassica napus, biological replicate 1

description:
C_Cd1
Brassica napus L.


title: WG17019_A01-W09

description:
single cell
ATTAGACGAAGCG

value: Female


title: genomic DNA from monocytes UM293

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM293

source_name: monocytes UM293


title: genomic DNA from monocytes UM297

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM297

source_name: monocytes UM297


title: genomic DNA from monocytes UM300

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM300

source_name: monocytes UM300


title: CD8 SEA-stimulated, donor11

city: Homburg

first: Eva

middle: C

last: Schwarz

address: Geb. 48

department: Biophysics

institute: Saarland University

description: gene expression in NK cells untouched

hyb_protocol: A total of 600 ng labeled cRNA was then fragmented and hybridized for 17 h at 10 rpmand 65 °Cwith the use of the Gene Expression and Hybridization Kit (Agilent, #5188-5242).

scan_protocol: Slides were scanned on an Agilent Microarray Scanner.

data_processing: Using the Agilent Feature Extraction Software the raw values from the scanned image files were extracted. In a next step, the R software was used to normalize the data (quantile normalization) and to perform a log2 transformation.

source_name: peripheral blood

label_protocol: cDNA was transcribed into cRNA and labeled with Cyanine 3-CTP

growth_protocol: PBMC were isolated from Leukocyte reduction system (LRS) chambers, CD8+ T-cells or NK cells were bead-isolated

extract_protocol: Purity and integrity of the input template RNA were assessed using a Nanodrop-1000 and an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Assay Kit (Agilent, #5067-1511).

treatment_protocol: CD8+ T cells were stimulated with SEA or anti-CD3/CD28 beads

value: PBMC isolated from LRS chambers

value: NK cells untouched


title: At_T_R1_9h

value: seedling


title: genomic DNA from monocytes US3

description:
monocytes from healthy US adult
US3

source_name: monocytes US3

value: USadult

value: uninfected


title: genomic DNA from monocytes UM299

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM299

source_name: monocytes UM299


title: genomic DNA from monocytes UM294

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM294

source_name: monocytes UM294


title: genomic DNA from monocytes US2

description:
monocytes from healthy US adult
US2

source_name: monocytes US2


title: genomic DNA from monocytes US5

description:
monocytes from healthy US adult
US5

source_name: monocytes US5


title: genomic DNA from monocytes US4

description:
monocytes from healthy US adult
US4

source_name: monocytes US4


title: genomic DNA from monocytes US8

description:
monocytes from healthy US adult
US8

source_name: monocytes US8


title: At_M_R1_24h

value: 12 day old

value: mock


title: At_M_R2_1h


title: genomic DNA from monocytes C1157

description:
monocytes from healthy Kenyan child
C1157

source_name: monocytes C1157

value: ChildRec


title: WG17019_A01-W01

description:
single cell
ATTAGACGATCCA

source_name: dorsal root ganglion

value: 4 years 8 months


title: At_T_R1_1h

source_name: Arabidopsis thaliana Col-0


title: At_M_R1_9h


title: At_M_R1_1h


title: genomic DNA from monocytes US1

description:
monocytes from healthy US adult
US1

source_name: monocytes US1


title: genomic DNA from monocytes US6

description:
monocytes from healthy US adult
US6

source_name: monocytes US6


title: WG17019_A01-W06

description:
single cell
ATTAGACGAACGG

value: ambiguous


title: WG17019_A01-W02

description:
single cell
ATTAGACGAAACC


title: genomic DNA from monocytes C1189

description:
monocytes from healthy Kenyan child
C1189

source_name: monocytes C1189


title: genomic DNA from monocytes C300

description:
monocytes from healthy Kenyan child
C300

source_name: monocytes C300

value: subclinical parasitemia


title: CD8 SEA-stimulated, donor10

description: gene expression in NK cells untouched


title: Hh77 Rep 2 X77_1

city: Athens

first: Holly

last: McQueary

state: GA

address: 120 E Green St

department: Genetics

institute: University of Georgia

description:
Heterozygous Ancestor Line 77
X77_1

data_processing:
Raw reads were processed by the Georgia Genomics and Bioinformatics Core to remove sequencing adapters and demultiplex samples.
Quality control was performed using FastQC version 1.8.0_20 with default parameters (available at www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low-quality bases were trimmed using Trimgalore version 0.4.4 using -phred 33, -q 20 (available at www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
RNA sequences were aligned to the Saccharomyces cerevisiae reference genome (UCSC version sacCer3, available at support.illumina.com/sequencing/sequencing_software/igenome.html) and transcripts were annotated using Tophat v. 2.1.1 with -i 10 -I 10000 (Trapnell et al. 2012).
Cufflinks v. 2.2.1 was used to assemble sample transcriptomes using default parameters (Trapnell et al. 2012) and Cuffnorm v. 2.2.1 was used with default parameters to normalize reads.
Differential expression was determined using Cuffdiff v. 2.2.1 with default parameters, and raw read counts were found using HTseq v. 0.6.1pl (Python v. 2.7.8) (Anders et al. 2015).
Finally, we used Samtools v. 1.3.1 to convert .sam files into .bam files and sort the resulting .bam files (Li et al. 2009). Bash scripts for genome assembly and annotation can be found at https://github.com/hollygene/Dosage_Compensation/tree/master/src/bash_scripts.
To compare chromosome-level changes in gene expression across strains, Cuffnorm v. 2.2.1  (Trapnell et al. 2012) was used to calculate FPKM (fragments per kilobase per million reads) for each RNAseq data set.
A custom bash script was then generated to join the FPKM values for each strain with the gene annotations file, convert the resulting file into a .csv formatted file, remove mitochondrial sequences (as we were not interested in mitochondrial gene expression), and change the chromosome names from Roman numerals to numbers (script can be found at https://github.com/hollygene/Dosage_Compensation/blob/master/src/bash_scripts/old/DC_workflow_April2017.sh).
All analyses were done in RStudio (Team 2013). R scripts for data analysis are available at https://github.com/hollygene/Dosage_Compensation/tree/master/src/R/scripts/Final_Scripts_Used.
Raw read counts obtained from Htseq-count were used as input for DESeq2 (Love et al. 2014; Anders et al. 2015).
Genome_build: UCSC version sacCer3, available at support.illumina.com/sequencing/sequencing_software/igenome.html
Supplementary_files_format_and_content: .csv: FPKM values for each replicate from Cuffnorm; .txt: read counts files from htseqCount

organism: Saccharomyces cerevisiae

source_name: Heterozygous Ancestor

growth_protocol: In both, an ancestral strain was copied into multiple MA lines, which were then maintained separately for ~2000 cell generations (G) (2063 generations in the homozygous ancestor lines and 2108 in the heterozygous ancestor lines) via single-colony transfer every 48 hours ( 1 hour) for 100 transfers on solid YPD (1% yeast extract, 2% peptone, 2% glucose, 2% agarose) medium.

extract_protocol:
For obtaining RNA, each line was pulled onto solid YPD and allowed to grow for two days at 30C, and then three individual colonies (biological replicates) were used to inoculate three 3ml liquid YPD cultures (no agarose) of each line. Liquid cultures were incubated on a rotator at 30C for 24 hours, before being diluted into 50ml YPD and allowed to grow on a shaker at 30C for 6 hours. Optical density (OD) measurements were taken to ensure all cultures were in the same log growth phase. Cells were then pelleted, and RNA was extracted from each replicate using the MasterPure Yeast RNA Purification Kit (Epicentre). Integrity, concentration, and quality of RNA samples were assessed using a Qubit (Thermo Fisher Scientific).
Libraries were prepared using the Illumina Stranded RNAseq Kit and were sequenced at the Georgia Genomics and Bioinformatics Core (https://dna.uga.edu/) on the Illumina NextSeq (75 cycles) single end 75bp reads High Output flow cell. Samples were multiplexed and split across two sequencing lanes.

treatment_protocol: The two diploid ancestral strains differed in their origin and degree of heterozygosity.

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106

tag: ploidy

value: Trisomy XII


title: Hh77 Rep 3 X77_2

description:
Heterozygous Ancestor Line 77
X77_2


title: genomic DNA from monocytes C299

description:
monocytes from healthy Kenyan child
C299

source_name: monocytes C299

value: Male

value: monocyte


title: genomic DNA from monocytes UM1189

description:
monocytes from Kenyan child with acute uncopmlicated malaria
UM1189

source_name: monocytes UM1189

value: ChildUM

value: acute uncomplicated malaria


title: CD8 bead-stimulated, donor11

description: gene expression in CD8, bead-stimulated

source_name: peripheral blood

value: PBMC isolated from LRS chambers

value: CD8, bead-stimulated


title: Hh77 Rep 1 X77_0

description:
Heterozygous Ancestor Line 77
X77_0


title: genomic DNA from monocytes US7

description:
monocytes from healthy US adult
US7

source_name: monocytes US7

value: Female


title: Hh76 Rep 3 X76_2

description:
Heterozygous Ancestor Line 76
X76_2

value: Trisomy IX, Partial X, Trisomy XIV


title: CD8 untouched, donor11

description: gene expression in CD8 untouched

value: CD8 untouched


title: Mouse3 Wnt3a

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

data_processing:
Quality Control of fastq files: FASTQC v0.11.7
Trimming: trimmomatic v0.36
Alignment: STAR v2.6.0
Indexing: samtools v1.9
Gene quantification: HTSeq-count v0.11.1
Differential expression: DESeq2 v1.24.0
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files containing DESeq22 output and 2 counts tables (FPKM, and raw counts)

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Whole bone marrows were seeded in DMEM (1g/L glucose) containing 10ng/mL mCSF. Media was replenished every other day and used on day 7.

extract_protocol:
Media was removed and RNA isolated using Trizol reagent and the ZymoResearch miniprep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
Single read RNA sequencing was performed using the Illumina HiSeq 2500

treatment_protocol: Cells were treated with DMEM (1g/L glucose) containing 100ng/mL Wnt3a, 100pg/mL IL4 or their combination for 16 hours. Untreated cells were used as controls.

value: 100ng/mL Wnt3a


title: Mouse3 IL4

value: 100pg/mL IL4


title: Mouse3 Wnt3a+IL4

value: 100ng/mL Wnt3a+ 100pg/mL IL4


title: genomic DNA from monocytes C297

description:
monocytes from healthy Kenyan child
C297

source_name: monocytes C297

value: ChildRec


title: CD8 untouched, donor10

description: gene expression in CD8 untouched


title: Root of control (treated with Cd only) Brassica napus, biological replicate 2

description:
C_Cd2
Brassica napus L.

source_name: Root of Brassica napus, treated with Cd only for 2 days

value: Nourin No.16

value: root

value: 4 weeks after germination

value: Cd only for 2 days


title: Mouse3 Untreated


title: Hh76 Rep 1 X76_0

description:
Heterozygous Ancestor Line 76
X76_0

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106


title: Mouse2 Wnt3a+IL4


title: Hh61 Rep 3 X61_2

description:
Heterozygous Ancestor Line 61
X61_2

value: Trisomy VII


title: Mouse2 IL4


title: genomic DNA from monocytes C295

description:
monocytes from healthy Kenyan child
C295

source_name: monocytes C295

value: Male

value: monocyte

value: uninfected


title: genomic DNA from monocytes C293

description:
monocytes from healthy Kenyan child
C293

source_name: monocytes C293


title: Hh61 Rep 2 X61_1

description:
Heterozygous Ancestor Line 61
X61_1


title: NK cells, donor11

description: gene expression in NK untouched

value: PBMC isolated from LRS chambers

value: NK untouched


title: Mouse2 Wnt3a

value: Female


title: Hh61 Rep 1 X61_0

description:
Heterozygous Ancestor Line 61
X61_0


title: NK cells, donor10

description: gene expression in NK untouched


title: Mouse2 Untreated


title: Hh76 Rep 2 X76_1

description:
Heterozygous Ancestor Line 76
X76_1

value: Trisomy IX, Partial X, Trisomy XIV


title: genomic DNA from monocytes C294

description:
monocytes from healthy Kenyan child
C294

source_name: monocytes C294

value: subclinical parasitemia


title: Mouse1 Wnt3a+IL4


title: Hh59 Rep 3 X59_2

description:
Heterozygous Ancestor Line 59
X59_2


title: CD8 bead-stimulated, donor4

description: gene expression in CD8, bead-stimulated

value: CD8, bead-stimulated


title: Mouse1 IL4

value: 100pg/mL IL4


title: CD8 bead-stimulated, donor8

description: gene expression in CD8, bead-stimulated


title: Hh59 Rep 2 X59_1

description:
Heterozygous Ancestor Line 59
X59_1


title: CD8 bead-stimulated, donor3

description: gene expression in CD8, bead-stimulated


title: NK cells IL-2 stimulated, donor8

description: gene expression in NK cells, IL-2 stimulated

value: NK cells, IL-2 stimulated


title: CD8 bead-stimulated, donor2

description: gene expression in CD8, bead-stimulated


title: Hh49 Rep 3 X49_2

description:
Heterozygous Ancestor Line 49
X49_2

value: Trisomy V


title: Hh59 Rep 1 X59_0

description:
Heterozygous Ancestor Line 59
X59_0


title: NK cells, donor8

description: gene expression in NK cells untouched

value: NK cells untouched


title: Mouse1 Wnt3a

value: 100ng/mL Wnt3a


title: CD8 SEA-stimulated, donor8

description: gene expression in CD8, SEA stimulated

value: CD8, SEA stimulated


title: Hh49 Rep 2 X49_1

description:
Heterozygous Ancestor Line 49
X49_1

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106


title: genomic DNA from monocytes A8

description:
monocytes from healthy Kenyan adult
A8

source_name: monocytes A8

value: Adult


title: CD8 bead-stimulated, donor10

description: gene expression in CD8, bead-stimulated


title: CD8 untouched, donor8

description: gene expression in CD8 untouched

value: CD8 untouched


title: genomic DNA from monocytes A4

description:
monocytes from healthy Kenyan adult
A4

source_name: monocytes A4

value: monocyte


title: Hh49 Rep 1 X49_0

description:
Heterozygous Ancestor Line 49
X49_0


title: Hh18 Rep 3 X18_2

description:
Heterozygous Ancestor Line 18
X18_2

value: Trisomy I


title: NK cells, donor4

description: gene expression in NK cells - IL-2 stimulated

value: PBMC isolated from LRS chambers

value: NK cells - IL-2 stimulated


title: ATAC-seq_P3 Lung CD45-depleted

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

library_source: genomic

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.  Genome_build: mm10 or hGRC38
Genome_build: mm10 or hGRC38
Supplementary_files_format_and_content: H5 matrix: contains the UMI counts per feature (gene or peak). BAM:  alignment data. Singlecell: file is the Cellranger Cell annotation file. Fragments: a  BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay.

source_name: P3 Atac

extract_protocol: Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al.

value: wild type

value: lung

value: female


title: genomic DNA from monocytes A5

description:
monocytes from healthy Kenyan adult
A5

source_name: monocytes A5

value: Male

value: uninfected


title: P42 Lung CD45-depleted


title: NK cells IL-2 stimulated, donor4

description: gene expression in NK cells untouched


title: Mouse1 Untreated

value: Female


title: Control7

city: Houston

first: FENG

last: WANG

state: TX

address: 1881 East Road

institute: UT MD Anderson Cancer Center

description: Control

hyb_protocol: DNA methylation analysis was performed using Illumina’s Infinium MethylationEPIC assay (EPIC) according to the manufacturer’s protocol.

data_processing: Data analysis was conducted using the ChAMP algorithm.

source_name: Bone Marrow

label_protocol: not provided

extract_protocol: Genomic DNA was extracted from bone marrow mononuclear cells using an Autopure extractor (QIAGEN/Gentra, Valencia, CA).

tag: patient diagnosis

value: AML

tag: idh1/2 genotype

value: wildtype

value: Bone Marrow

value: Control

tag: treated with


title: Hh18 Rep 2 X18_1

description:
Heterozygous Ancestor Line 18
X18_1

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106


title: Control8

description: Control

scan_protocol: DNA methylation analysis was performed using Illumina’s Infinium MethylationEPIC assay (EPIC) according to the manufacturer’s protocol.

tag: tissue


title: P15 Lung CD45-depleted

tag: age


title: genomic DNA from monocytes A1

description:
monocytes from healthy Kenyan adult
A1

source_name: monocytes A1

value: Adult


title: CD8 untouched, donor4

description: gene expression in CD8, SEA stimulated

tag: cell type

value: CD8, SEA stimulated


title: Control3

description: Control


title: Hh11 Rep 3 X11_2

description:
Heterozygous Ancestor Line 11
X11_2

source_name: Heterozygous Ancestor

tag: strain

tag: genotype

value: Monosomy I, Trisomy XV


title: Control5

description: Control

tag: timepoint


title: P7 Lung CD45-depleted


title: P3 Lung CD45-depleted


title: genomic DNA from monocytes A3

description:
monocytes from healthy Kenyan adult
A3

source_name: monocytes A3

value: monocyte


title: Hh11 Rep 2 X11_1

description:
Heterozygous Ancestor Line 11
X11_1


title: NK cells IL-2 stimulated, donor3

value: PBMC isolated from LRS chambers

tag: treatment


title: NK cells, donor3

description: gene expression in NK cells untouched

value: NK cells untouched


title: Control2

description: Control


title: Hh18 Rep 1 X18_0

description:
Heterozygous Ancestor Line 18
X18_0

value: Trisomy I


title: genomic DNA from monocytes A2

description:
monocytes from healthy Kenyan adult
A2

source_name: monocytes A2


title: Control4

description: Control


title: CD8 SEA-stimulated, donor3

description: gene expression in CD8, SEA stimulated

source_name: peripheral blood


title: CD8 SEA-stimulated, donor4

description: gene expression in NK cells untouched


title: Hh11 Rep 1 X11_0

description:
Heterozygous Ancestor Line 11
X11_0


title: genomic DNA from monocytes A6

description:
monocytes from healthy Kenyan adult
A6

source_name: monocytes A6


title: E12.5 Lung

value: wild type

value: lung


title: Control1

description: Control


title: 974025_RES

description: Response

value: IDH1/IDH2 mutant

value: RES

value: IDH inhibitors (IDHi)


title: Hh9 Rep 3 X9_2

description:
Heterozygous Ancestor Line 9
X9_2

value: euploid


title: E17.5 Lung

value: female


title: 757509_BL

description: Baseline

value: AML

value: Bone Marrow

value: BL


title: 8505C DHT treated

city: Udine

first: Giuseppe

last: Damante

address: via chiusaforte, E

department: Medical Area

country: Italy

institute: University of Udine

data_processing:
Bcl2Fastq version 2.20 in the Illumina pipeline was used for processing the raw data (format conversion and de-multiplexing)
adapter sequences were masked with Cutadapt2 version 1.11 from raw fastq data and the ERNE software was used to remove lower quality bases and adapters
assembly and quantitation of full-length transcripts representing multiple spliced variants for each gene locus was performed using the Stringtie tool
Genome_build: hg38

source_name: 8505C DHT treated

growth_protocol: SW1736 and 8505C cells, derived from ATC, were grown in RPMI-1640 medium supplemented with 10% FBS, 2 mM L-glutamine and 50 mg/ml gentamicin, in a humidified incubator (5% CO2, 95% air, at 37°C).

extract_protocol:
RNA of SW1736 and 8505C cells, treated with vehicle (DMSO) or DHT was extracted using a RNeasy Mini kit according to the manufacturer's instructions.  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the Universal Plus mRNA-Seq kit, according to the manufacturer'instructions

treatment_protocol: SW1736 and 8505C cells were treated with vehicle (DMSO) or DHT 1.5uM for 24h.

tag: cell line

value: Anaplastic thyroid cancer (ATC)

value: DHT 1.5uM


title: genomic DNA from monocytes A7

description:
monocytes from healthy Kenyan adult
A7

source_name: monocytes A7

value: Female

value: Adult

value: uninfected


title: Control6

description: Control

value: wildtype

value: Control


title: 8505C DMSO treated

source_name: 8505C DMSO treated

value: vehicle (DMSO)


title: SW1736 DHT treated

source_name: SW1736 DHT treated


title: Hh9 Rep 1 X9_0

description:
Heterozygous Ancestor Line 9
X9_0

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106


title: Hh8 Rep 3 X8_2

description:
Heterozygous Ancestor Line 8
X8_2

value: Tetrasomy XVI


title: NK cells IL-2 stimulated, donor2

value: PBMC isolated from LRS chambers

value: NK cells untouched


title: NK cells, donor2

description: gene expression in NK cells untouched

value: CD8, SEA stimulated


title: SW1736 DMSO treated

source_name: SW1736 DMSO treated


title: CD8 SEA-stimulated, donor2

description: gene expression in CD8, SEA stimulated

value: CD8, bead-stimulated


title: sh-E4F1_3

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the 6pb index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 26, based on Ensembl version 88
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

molecule: polyA RNA

source_name: U2OS expressing shRNA against E4F1

growth_protocol: U2OS in DMEM 10% FBS

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA HyperPrep PolyA

treatment_protocol: 24h infection with shRNA + 48h puro selection

tag: knockdown

value: E4F1 shRNA


title: Hh8 Rep 2 X8_1

description:
Heterozygous Ancestor Line 8
X8_1


title: Hh8 Rep 1 X8_0

description:
Heterozygous Ancestor Line 8
X8_0


title: CD8 untouched, donor2

description: gene expression in CD8 untouched

value: CD8 untouched


title: sh-E4F1_2


title: Hh7 Rep 3 X7_2

description:
Heterozygous Ancestor Line 7
X7_2

value: Trisomy I


title: sh-E4F1_1


title: CD8 untouched, donor3

description: gene expression in CD8 untouched


title: 4259035_BL

description: Baseline

value: AML

value: IDH1/IDH2 mutant

value: Bone Marrow

value: BL

value: IDH inhibitors (IDHi)


title: sh-CT_3

source_name: U2OS expressing scramble shRNA

value: ctrl shRNA


title: Hh7 Rep 1 X7_0

description:
Heterozygous Ancestor Line 7
X7_0


title: CD8 bead-stimulated, donor9

description: gene expression in CD8, bead-stimulated


title: Hh7 Rep 2 X7_1

description:
Heterozygous Ancestor Line 7
X7_1


title: CD8 SEA-stimulated, donor9

description: gene expression in CD8, SEA stimulated


title: sh-CT_2


title: CD8 untouched, donor9

description: gene expression in CD8 untouched


title: 4235533_BL

description: Baseline


title: Hh9 Rep 2 X9_1

description:
Heterozygous Ancestor Line 9
X9_1

value: euploid


title: NK cells, donor9

description: gene expression in NK cells untouched


title: 4259035_NR

description: Nonresponse

value: NR


title: 4235533_NR

description: Nonresponse


title: Hh5 Rep 2 X5_1

description:
Heterozygous Ancestor Line 5
X5_1

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106


title: CD8 SEA-stimulated, donor7

description: gene expression in CD8, SEA stimulated


title: E15.5 Lung

value: wild type

value: lung

tag: Sex

value: female


title: IF: n-6/n-3 LCPUFA pool placenta - female

city: Freising-Weihenstephan

first: Bernhard

middle: L

last: Bader

address: Gregor-Mendel Straße 2

department: Clinical Nutritional Unit - ZIEL-Research Center for Nutrition and Food Sciences

institute: Technische Universität München

description: n-6/n-3 LCPUFA intervention

data_processing:
Data were read out by the SDS (Sequence Detection System) Software v2.4. Statistical calculations were conducted in R (version 2.11.1). Log fold changes were calculated as following using the term [Cq (IG) – Cq (CG)] and normalized with a cyclic LOESS procedure, separately for microRNAs analyzed on plate A and plate B. For the calculation of putative differentially expressed microRNAs an adaptive cut-off was determined by polynomial quantile regression (quadratic model).
MicroRNAs with a log (FC) below the 0.05 or above the 0.95 quantile of the cut-off were regarded as suitable targets for further validation.

label: TaqMan® probes

source_name: female offspring

label_protocol: 350 ng of total RNA containing small RNA was conducted with TaqMan® MicroRNA Reverse Transcription Kit using Megaplex™ RT primer. Obtained cDNA was reverse-transcribed with TaqMan® PreAmp Primers and TaqMan® PreAmp Master Mix for twelve cycles, and analyzed with the TaqMan® Array Human Micro RNA A+B Cards Set v3.0 and TaqMan® Universal PCR Master Mix, No AmpErase® UNG on the 7900HT Fast Real-Time PCR System to assess the profile of 754 human microRNAs including endogenous and negative controls. All reagents and kits applied were obtained from Applied Biosystems (Darmstadt, Germany)

growth_protocol: Both groups were advised to follow a healthy diet during pregnancy. The women in the intervention group were additionally advised to decrease their dietary n-6/n-3 LCPUFA ratio to about 3:1 by reducingarachidonic acid intake to 50 - 90 mg per day decreasing meat products and were instructed to take a daily n-3 LCPUFA supplement (1020 mg DHA and 180 mg EPA). The offspring were born by vaginal delivery and considered as appropriate for gestational age (10th - 90th percentile of birth weight). For subsequent analyses, data from study participants and their offspring (female, n = 21; male, n = 20), including placenta data, were divided into the control group (Con, n=20) and the n-3 LCPUFA intervention group (N3, n=21).

extract_protocol: For extraction of total RNA or total RNA containing small RNA from placental tissue, the trizol method was combined with the midi RNeasy Kit (Qiagen, Hilden, Germany) or the mirPremier® microRNA isolation Kit (Sigma-Aldrich, Taufkirchen, Germany), respectively. For each placenta, the four-quadrant tissue samples were first homogenized separately in TRIzol® Reagent (Invitrogen, Darmstadt, Germany) and afterwards pooled in equal parts for extraction.

treatment_protocol: Placenta samples were dissected from four quadrants according to a standardized sampling protoco. The chorionic villous portion of each placenta, obtained by removing maternal basal and fetal chorionic plates was immediately snap-frozen.

tag: gender

value: term placenta - villous fraction


title: Hh5 Rep 1 X5_0

description:
Heterozygous Ancestor Line 5
X5_0


title: sh-CT_1


title: Hh5 Rep 3 X5_2

description:
Heterozygous Ancestor Line 5
X5_2


title: 2620771_BL

description: Baseline


title: NK cells, donor7

description: gene expression in NK cells untouched

value: PBMC isolated from LRS chambers

value: NK cells untouched


title: CF: Control pool placenta - female

description: control


title: CD8 bead-stimulated, donor7

description: gene expression in CD8, bead-stimulated

value: CD8, bead-stimulated


title: Hh4 Rep 3 X4_2

description:
Heterozygous Ancestor Line 4
X4_2

value: Trisomy V


title: Hh4 Rep 2 X4_1

description:
Heterozygous Ancestor Line 4
X4_1


title: Visudyne

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: Cortical microglia was sorted from the brains of 3 mice

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline with force_counts set to 2000. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes .  Additionally, a compressed csv file containing a matrix with raw UMI counts from both samples, merged by gene symbols.

source_name: Brain cortex

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

treatment_protocol: Injection of Visudyne (5 uL) alone (control), or injection of Visudyne (5 uL) followed by 5 steps of transcranial photoconversion (meningeal lymphatic vessel ablation)

tag: genotype/variation

value: 5xFAD hemizygous

value: microglia

value: 5.5 months

value: Male

value: Visudyne (5 uL)


title: Hh4 Rep 1 X4_0

description:
Heterozygous Ancestor Line 4
X4_0


title: Hh3 Rep 3 X3_2

description:
Heterozygous Ancestor Line 3
X3_2


title: NK cells, donor6

description: gene expression in NK cells untouched


title: Hh3 Rep 2 X3_1

description:
Heterozygous Ancestor Line 3
X3_1


title: CD8 SEA-stimulated, donor6

description: gene expression in CD8, SEA stimulated

value: CD8, SEA stimulated


title: CD8 bead-stimulated, donor6

description: gene expression in CD8, bead-stimulated


title: 2616045_BL

description: Baseline

value: AML

value: IDH1/IDH2 mutant

value: Bone Marrow

value: BL

value: IDH inhibitors (IDHi)


title: 2498789_NR

description: Nonresponse

value: NR


title: Hh3 Rep 1 X3_0

description:
Heterozygous Ancestor Line 3
X3_0

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106

value: euploid


title: NK cells, donor5

description: gene expression in NK cells untouched

value: PBMC isolated from LRS chambers

value: NK cells untouched


title: Visudyne/photoconversion

value: Visudyne (5 uL) followed by 5 steps of transcranial photoconversion using a 689-nm-wavelength non-thermal red light


title: Hh2 Rep 3 X2_2

description:
Heterozygous Ancestor Line 2
X2_2


title: 2512641_BL

description: Baseline


title: CD8 bead-stimulated, donor5

description: gene expression in CD8, bead-stimulated

value: CD8, bead-stimulated


title: Hh2 Rep 2 X2_1

description:
Heterozygous Ancestor Line 2
X2_1


title: CD8 untouched, donor7

description: gene expression in CD8 untouched

value: CD8 untouched


title: 4128869_BL

description: Baseline


title: 2620771_RES

description: Response

value: RES


title: CD8 untouched, donor6

description: gene expression in CD8 untouched


title: Hh2 Rep 1 X2_0

description:
Heterozygous Ancestor Line 2
X2_0


title: 2480485_NR

description: Nonresponse


title: CD8 untouched, donor5

description: gene expression in CD8 untouched


title: Hh1 Rep 3 X1_2

description:
Heterozygous Ancestor Line 1
X1_2


title: 2583919_BL

description: Baseline


title: NK cells, donor1

description: gene expression in NK cells untouched


title: 2480485_BL

description: Baseline


title: Hh1 Rep 1 X1_0

description:
Heterozygous Ancestor Line 1
X1_0


title: 2502699_BL

description: Baseline


title: CD8 SEA-stimulated, donor1

description: gene expression in CD8, SEA stimulated


title: CD8 bead-stimulated, donor1

description: gene expression in CD8, bead-stimulated


title: 2432389_RES

description: Response


title: CD8 untouched, donor1

description: gene expression in CD8 untouched


title: Cochlea-scATACseq-Base

city: Ann Arbor

first: Joerg

last: Waldhaus

state: MI

address: Medical Sciences I Building, Rm. 5315A, 1150 West Medical Center Drive

department: Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute

institute: University of Michigan

description: single-nuclei chromatin accessibility data

data_processing:
Sequencing reads were demultiplexed and aligned against the mm10 mouse genome reference using 10X CellRanger v3.0.0 for scRNA-seq samples
Sequencing reads were demultiplexed and aligned against the mm10 mouse genome reference using 10X CellRangerATAC v1.1.0 for scATAC-seq samples. The .bam files were used calculate the coverage for each fixed bin (5kb) across the whole genome.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices (with gene expression counts) were generated by CellRanger (v3.0.0) software for scRNA-seq samples and CellRangerATAC (v1.1.0) for scATAC-seq samples

source_name: Cochlear

extract_protocol:
Organs of Corti were dissected, dissociated and flow sorted for dtTomato and GFP expression. Next cells were loaded on 10X Genomics chip for scRNA-seq and scATAC-seq library preparation following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

value: Fgfr3-iCre, Ai14, Atoh1-GFP

value: 200mg/kg Tamoxifen at P0

value: Organ of Corti

tag: compartment

value: Base

tag: developmental stage

value: post natal day 2


title: Cochlea-scATACseq-Apex

value: Apex


title: 2450523_BL

description: Baseline

source_name: Bone Marrow

tag: patient diagnosis

value: AML

value: IDH1/IDH2 mutant

value: Bone Marrow

value: BL


title: Cochlea-scRNAseq-Base

description: single-nuclei gene expression data


title: 2463247_BL

description: Baseline

tag: idh1/2 genotype

value: IDH inhibitors (IDHi)


title: HH152 Rep 3 X152_2

description:
Homozygous Ancestor Line 152
X152_2

source_name: Homozygous ancestor

value: S288C derivative

tag: ploidy

value: Trisomy I, Trisomy VII


title: Hh Ancestor Rep 1 GC_Anc_0

description:
Heterozygous Ancestor
GC_Anc_0

source_name: Heterozygous Ancestor

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106

value: euploid


title: VATN24_4

city: Chongqing

first: Min-Dian

last: Li

address: 30 Gaotanyan Main Street

department: Cardiology

institute: Southwest Hospital, Third Military Medical University (Army Medical University)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Gene expression levels were quantified by featureCounts v1.5.0-p3 (Liao et al., 2014), and represented as transcript per million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: adult female visceral adipose tissue

growth_protocol: Special pathogen-free (SPF) mice were purchased from Hunan SJT Laboratory Animal Co. and housed in a SPF barrier facility. C57BL/6J female mice at 7 weeks of age were grouped housed, and entrained to a 12h light:12h dark cycle with normal chow food and water ad libitum for 7 days before assigned to daytime-restricted feeding (DRF) and nighttime-restricted feeding (NRF) groups for additional 7 days.

extract_protocol:
Heart and visceral adipose tissue were removed, flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ml USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

treatment_protocol: Animals were subjected to daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF) for 7 days

value: adult

value: female

tag: tissue

value: visceral adipose tissue

value: 9 weeks

tag: dietary regimen

value: NRF

tag: zeitgeber time in hours


title: HH152 Rep 2 X152_1

description:
Homozygous Ancestor Line 152
X152_1

tag: strain


title: VATN24_3

tag: age


title: 2463247_RES

description: Response

tag: timepoint

value: RES

tag: treated with


title: HH152 Rep 1 X152_0

description:
Homozygous Ancestor Line 152
X152_0

tag: genotype


title: 2432389_BL

description: Baseline


title: 2419959_RES

description: Response


title: 2430935_BL

description: Baseline


title: 2419959_BL

description: Baseline


title: Hh1 Rep 2 X1_1

description:
Heterozygous Ancestor Line 1
X1_1


title: VATN24_2


title: VATN24_1


title: HH123 Rep 2 X123_1

description:
Homozygous Ancestor Line 123
X123_1

value: Trisomy V


title: 2412147_RES

description: Response


title: HH123 Rep 1 X123_0

description:
Homozygous Ancestor Line 123
X123_0


title: 2382431_BL

description: Baseline


title: VATN20_3


title: VATN20_2


title: HH119 Rep 2 SC119_1

description:
Homozygous Ancestor Line 119
SC119_1

value: Trisomy IX


title: HH119 Rep 3 SC119_2

description:
Homozygous Ancestor Line 119
SC119_2


title: 2370759_BL

description: Baseline

value: AML


title: 2410163_RES

description: Response

value: IDH1/IDH2 mutant


title: 2382431_NR

description: Nonresponse

value: Bone Marrow

value: NR


title: HH119 Rep 1 SC119_0

description:
Homozygous Ancestor Line 119
SC119_0


title: 2498789_BL

description: Baseline

value: BL

value: IDH inhibitors (IDHi)


title: CD8 SEA-stimulated, donor5

description: gene expression in CD8, SEA stimulated

tag: cell type

value: PBMC isolated from LRS chambers

tag: treatment

value: CD8, SEA stimulated


title: VATN16_4

tag: Sex


title: VATN20_1


title: Hh Ancestor Rep 2 GC_Anc_1

description:
Heterozygous Ancestor
GC_Anc_1

value: Mating between NCYC 3631, which is a Matalpha derivative of YPS606 (an oak strain from Pennsylvania, USA), and NCYC3596, a Mata derivative of DBPVG1106

value: euploid


title: HH117 Rep 3 X117_2

description:
Homozygous Ancestor Line 117
X117_2

value: S288C derivative


title: 2383235_BL

description: Baseline


title: VATN16_3

value: adult

value: female

value: visceral adipose tissue


title: Hh Ancestor Rep 3 GC_Anc_2

description:
Heterozygous Ancestor
GC_Anc_2


title: 2394529_BL

description: Baseline


title: HH117 Rep 2 X117_1

description:
Homozygous Ancestor Line 117
X117_1


title: 2370233_NR

description: Nonresponse


title: VATN16_2

value: 9 weeks

value: NRF


title: HH117 Rep 1 X117_0

description:
Homozygous Ancestor Line 117
X117_0

value: Trisomy V


title: Cochlea-scRNAseq-Apex

description: single-nuclei gene expression data

value: Fgfr3-iCre, Ai14, Atoh1-GFP

value: 200mg/kg Tamoxifen at P0

value: Organ of Corti

value: Apex

value: post natal day 2


title: VATN16_1


title: VATN12_3


title: HH115 Rep 2 X115_1

description:
Homozygous Ancestor Line 115
X115_1


title: VATN12_4


title: Visudyne/photoconversion+mAdu Sample 16

description:
Visudyne/photoconversion+mAdu
RNA was isolated from the brains of 3 mice.
vph_adu.tar.gz

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline with force_counts set to 2000. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Mouse brain meninges

growth_protocol: not applicable

treatment_protocol: Injection of Visudyne (5 uL) alone (control), or injection of Visudyne (5 uL) followed by 5 steps of transcranial photoconversion (meningeal lymphatic vessel ablation). Each combined with injection of either mIgG or mAdu.

value: 4 months

tag: gender

value: male


title: HH115 Rep 1 X115_0

description:
Homozygous Ancestor Line 115
X115_0


title: VATN20_4


title: 2366711_NR

description: Nonresponse

value: AML

value: IDH1/IDH2 mutant

value: Bone Marrow

value: NR

value: IDH inhibitors (IDHi)


title: HH115 Rep 3 X115_2

description:
Homozygous Ancestor Line 115
X115_2

value: S288C derivative

value: euploid


title: HH112 Rep 3 X112_2

description:
Homozygous Ancestor Line 112
X112_2

value: Trisomy XVI


title: VATN12_2

value: adult

value: female

value: visceral adipose tissue

value: 9 weeks

value: NRF


title: Visudyne/photoconversion+mAdu Sample 15


title: VATN12_1


title: Visudyne/photoconversion+mAdu Sample 13


title: Visudyne/photoconversion+mAdu Sample 14


title: VATN08_4


title: 2370233_BL

description: Baseline

value: BL


title: 2366711_BL

description: Baseline


title: HH112 Rep 1 X112_0

description:
Homozygous Ancestor Line 112
X112_0


title: HH123 Rep 3 X123_2

description:
Homozygous Ancestor Line 123
X123_2

value: Trisomy V


title: HH112 Rep 2 X112_1

description:
Homozygous Ancestor Line 112
X112_1


title: VATN08_3


title: VATN08_2


title: HH108 Rep 2 SC108_1

description:
Homozygous Ancestor Line 108
SC108_1

value: Trisomy VIII, Monosomy IX


title: Visudyne/photoconversion+mIgG Sample 12

description:
Visudyne/photoconversion+mIgG
RNA was isolated from the brains of 3 mice.
vph_igg.tar.gz

value: 4 months

value: male


title: HH108 Rep 3 SC108_2

description:
Homozygous Ancestor Line 108
SC108_2


title: 2361767_BL

description: Baseline

value: AML

value: IDH1/IDH2 mutant


title: VATN04_4


title: VATN08_1


title: HH108 Rep 1 SC108_0

description:
Homozygous Ancestor Line 108
SC108_0


title: 2361361_NR

description: Nonresponse

value: Bone Marrow

value: NR


title: 2361361_BL

description: Baseline

value: IDH inhibitors (IDHi)


title: Visudyne/photoconversion+mIgG Sample 9


title: 2297941_RES

description: Response

value: RES


title: Visudyne/photoconversion+mIgG Sample 10


title: 2361405_RES

description: Response


title: Visudyne/photoconversion+mIgG Sample 11


title: VATN04_2


title: 2337831_BL

description: Baseline


title: 2297625_BL

description: Baseline


title: 2361405_BL

description: Baseline


title: Visudyne+mAdu Sample 8

description:
Visudyne+mAdu
RNA was isolated from the brains of 3 mice.
v_adu.tar.gz


title: HH88 Rep 3 SC088_2

description:
Homozygous Ancestor Line 88
SC088_2

value: S288C derivative

value: Trisomy IX


title: VATN04_1

value: adult

value: female


title: VATN04_3

value: visceral adipose tissue

value: 9 weeks


title: HH50 Rep 3 X50_2

description:
Homozygous Ancestor Line 50
X50_2

value: euploid


title: HH88 Rep 2 SC088_1

description:
Homozygous Ancestor Line 88
SC088_1


title: 2410163_BL

description: Baseline

value: BL


title: 2297625_RES

description: Response


title: 2295595_BL

description: Baseline


title: VATN00_4

value: NRF


title: Visudyne+mAdu Sample 7

value: 4 months


title: 2295595_RES

description: Response


title: 2292915_NR

description: Nonresponse


title: 2296723_BL

description: Baseline


title: 2292915_BL

description: Baseline


title: Visudyne+mAdu Sample 5

value: male


title: Visudyne+mIgG Sample 4

description:
Visudyne+mIgG
RNA was isolated from the brains of 3 mice.
v_igg.tar.gz


title: 2292873_RES

description: Response

value: AML


title: HH29 Rep 3 X29_2

description:
Homozygous Ancestor Line 29
X29_2

value: Monosomy IX


title: VATN00_2


title: Visudyne+mIgG Sample 2


title: HH50 Rep 1 X50_0

description:
Homozygous Ancestor Line 50
X50_0


title: Visudyne+mIgG Sample 3


title: 2307799_RES

description: Response

value: IDH1/IDH2 mutant

value: Bone Marrow


title: Visudyne+mAdu Sample 6


title: HH50 Rep 2 X50_1

description:
Homozygous Ancestor Line 50
X50_1


title: 2292873_BL

description: Baseline

value: IDH inhibitors (IDHi)


title: HH29 Rep 2 X29_1

description:
Homozygous Ancestor Line 29
X29_1


title: VATN00_1


title: 2283265_NR

description: Nonresponse

value: NR


title: Visudyne+mIgG Sample 1


title: 2283265_BL

description: Baseline


title: VATD24_4

value: DRF


title: VATN00_3


title: HH29 Rep 1 X29_0

description:
Homozygous Ancestor Line 29
X29_0

value: S288C derivative


title: 2281469_BL

description: Baseline


title: HH28 Rep 3 SC028_2

description:
Homozygous Ancestor Line 28
SC028_2


title: mVEGF-C+mAdu Sample 15

description:
mVEGF-C+mAdu
RNA was isolated from the brains of 3 mice.
vegfc_adu.tar.gz

treatment_protocol: Injection of AAV1-CMV-eGFP (control), or injection of AAV1-CMV-mVEGF-C. Each combined with injection of either mIgG or mAdu.

value: 22-26 months

value: APPswe


title: 2281469_RES

description: Response

value: RES


title: mVEGF-C+mAdu Sample 14


title: VATD24_2

value: adult

value: female

value: visceral adipose tissue

value: 9 weeks


title: HH88 Rep 1 SC088_0

description:
Homozygous Ancestor Line 88
SC088_0

value: Trisomy IX


title: VATD24_1


title: HH28 Rep 1 SC028_0

description:
Homozygous Ancestor Line 28
SC028_0

value: euploid


title: mVEGF-C+mAdu Sample 13

value: male


title: mVEGF-C+mAdu Sample 16


title: eGFP+mAdu Sample 12

description:
eGFP+mAdu
RNA was isolated from the brains of 3 mice.
gfp_adu.tar.gz


title: HH28 Rep 2 SC028_1

description:
Homozygous Ancestor Line 28
SC028_1


title: VATD20_4


title: eGFP+mAdu Sample 11


title: HH15 Rep 3 SC015_2

description:
Homozygous Ancestor Line 15
SC015_2


title: VATD20_2


title: HH15 Rep 2 SC015_1

description:
Homozygous Ancestor Line 15
SC015_1


title: VATD20_3


title: VATD24_3


title: eGFP+mAdu Sample 10


title: HH11 Rep 3 SC011_2

description:
Homozygous Ancestor Line 11
SC011_2


title: VATD16_4


title: mVEGF-C+mIgG Sample 8

description:
mVEGF-C+mIgG
RNA was isolated from the brains of 3 mice.
vegfc_igg.tar.gz


title: eGFP+mAdu Sample 9


title: VATD16_3


title: HH15 Rep 1 SC015_0

description:
Homozygous Ancestor Line 15
SC015_0


title: HH11 Rep 2 SC011_1

description:
Homozygous Ancestor Line 11
SC011_1


title: HH11 Rep 1 SC011_0

description:
Homozygous Ancestor Line 11
SC011_0


title: mVEGF-C+mIgG Sample 7


title: HH9 Rep 3 SC009_2

description:
Homozygous Ancestor Line 9
SC009_2

value: Trisomy XIV


title: mVEGF-C+mIgG Sample 6


title: HH9 Rep 2 SC009_1

description:
Homozygous Ancestor Line 9
SC009_1


title: mVEGF-C+mIgG Sample 5


title: eGFP+mIgG Sample 4

description:
eGFP+mIgG
RNA was isolated from the brains of 3 mice.
gfp_igg.tar.gz


title: 2260553_BL

description: Baseline

value: AML

value: IDH1/IDH2 mutant

value: BL


title: HH9 Rep 1 SC009_0

description:
Homozygous Ancestor Line 9
SC009_0


title: VATD16_1


title: VATD12_3


title: VATD16_2


title: VATD20_1


title: 2264727_NR

description: Nonresponse

value: Bone Marrow

value: NR

value: IDH inhibitors (IDHi)


title: 2260671_RES

description: Response


title: HH8 Rep 3 SC008_2

description:
Homozygous Ancestor Line 8
SC008_2

value: S288C derivative


title: VATD12_4

value: DRF


title: 2247707_RES

description: Response

value: RES


title: 2263055_BL

description: Baseline


title: eGFP+mIgG Sample 3

value: 22-26 months

value: APPswe


title: VATD12_2

value: adult

value: female

value: visceral adipose tissue


title: 2280935_BL

description: Baseline


title: eGFP+mIgG Sample 2


title: VATD12_1

value: 9 weeks


title: eGFP+mIgG Sample 1

value: male


title: HH8 Rep 1 SC008_0

description:
Homozygous Ancestor Line 8
SC008_0

value: euploid


title: VATD08_4


title: HH8 Rep 2 SC008_1

description:
Homozygous Ancestor Line 8
SC008_1


title: mVEGF-C+mAdu Sample 12

description:
mVEGF-C+mAdu
RNA was isolated from brain tissue from one mouse.
Sample 12

data_processing:
Reads were assessed for quality using FastQC.
Reads were trimmed using Trimgalore to remove adapter sequences and low quality bases
Trimmed reads were mapped to mm10 reference genome using STAR
Gene counts were generated with Subread featurecounts
Raw counts were then filtered using EdgeR filtering to remove outliers
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing gene x count matrix for all samples

extract_protocol:
RNA was extracted using Arcturus PicoPure kit (Thermo Fisher)
All RNA sample processing (including linear RNA amplification and cDNA library generation) and RNA-seq was performed by HudsonAlpha Genomic Services Laboratory


title: HH7 Rep 3 SC007_2

description:
Homozygous Ancestor Line 7
SC007_2


title: VATD08_3


title: HH7 Rep 2 SC007_1

description:
Homozygous Ancestor Line 7
SC007_1


title: mVEGF-C+mAdu Sample 11

description:
mVEGF-C+mAdu
RNA was isolated from brain tissue from one mouse.
Sample 11


title: mVEGF-C+mAdu Sample 10

description:
mVEGF-C+mAdu
RNA was isolated from brain tissue from one mouse.
Sample 10


title: VATD08_1


title: HH5 Rep 3 SC005_2

description:
Homozygous Ancestor Line 5
SC005_2


title: VATD04_4


title: HH5 Rep 2 SC005_1

description:
Homozygous Ancestor Line 5
SC005_1


title: mVEGF-C+mIgG Sample 9

description:
mVEGF-C+mIgG
RNA was isolated from brain tissue from one mouse.
Sample 9


title: 2246061_RES

description: Response

value: AML


title: 2244043_RES

description: Response

value: IDH1/IDH2 mutant


title: mVEGF-C+mIgG Sample 8

description:
mVEGF-C+mIgG
RNA was isolated from brain tissue from one mouse.
Sample 8


title: HH7 Rep 1 SC007_0

description:
Homozygous Ancestor Line 7
SC007_0


title: 2246709_BL

description: Baseline

value: BL


title: VATD04_3


title: 2247707_BL

description: Baseline

value: Bone Marrow


title: HH4 Rep 3 SC004_2

description:
Homozygous Ancestor Line 4
SC004_2


title: VATD04_1


title: HH5 Rep 1 SC005_0

description:
Homozygous Ancestor Line 5
SC005_0


title: VATD04_2


title: 2222935_BL

description: Baseline


title: mVEGF-C+mIgG Sample 7

description:
mVEGF-C+mIgG
RNA was isolated from brain tissue from one mouse.
Sample 7


title: HH4 Rep 2 SC004_1

description:
Homozygous Ancestor Line 4
SC004_1


title: eGFP+mAdu Sample 5

description:
eGFP+mAdu
RNA was isolated from brain tissue from one mouse.
Sample 5


title: VATD00_3


title: 2244043_BL

description: Baseline


title: 2221709_RES

description: Response


title: 2210551_NR

description: Nonresponse

value: NR


title: VATD00_2


title: 2246061_BL

description: Baseline

value: IDH inhibitors (IDHi)


title: HH3 Rep 3 SC003_2

description:
Homozygous Ancestor Line 3
SC003_2

value: S288C derivative


title: VATD00_4

value: DRF


title: eGFP+mAdu Sample 4

description:
eGFP+mAdu
RNA was isolated from brain tissue from one mouse.
Sample 4


title: eGFP+mIgG Sample 3

description:
eGFP+mIgG
RNA was isolated from brain tissue from one mouse.
Sample 3


title: 2219711_BL

description: Baseline


title: 2163337_RES

description: Response

value: RES


title: HH4 Rep 1 SC004_0

description:
Homozygous Ancestor Line 4
SC004_0


title: eGFP+mAdu Sample 6

description:
eGFP+mAdu
RNA was isolated from brain tissue from one mouse.
Sample 6

value: 22-26 months


title: VATD08_2


title: 2152641_NR

description: Nonresponse


title: VATD00_1


title: eGFP+mIgG Sample 1

description:
eGFP+mIgG
RNA was isolated from brain tissue from one mouse.
Sample 1

value: APPswe


title: HrtN24_4

source_name: adult female heart

value: adult

value: heart

value: NRF


title: HH3 Rep 1 SC003_0

description:
Homozygous Ancestor Line 3
SC003_0


title: 2151503_BL

description: Baseline


title: 2163337_BL

description: Baseline


title: 2152641_BL

description: Baseline


title: HrtN24_3

value: female

value: 9 weeks


title: 2150901_NR

description: Nonresponse


title: HH2 Rep 2 SC002_1

description:
Homozygous Ancestor Line 3
SC002_1

value: euploid


title: HrtN24_2


title: 2151503_NR

description: Nonresponse

value: AML


title: Baicalein treated N2 animals, Independent Trial 2

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

country: Spain

institute: University of Murcia

description: Gene expression data from baicalein treated animals

hyb_protocol: 3.75 µg of fragmented and biotinylated ss-cDNA were included in the hybridization mix, using the GenAtlas Hybridization, Wash and Stain kit for WT Array Strips (Affymetrix, P/N 901667) according to the recommendations of the manufacturer. The resulting preparations were hybridized to GeneChip® C. elegans Gene 1.1 ST Array Strip (Affymetrix, 902157) with 26 unique sequences of each transcript. After applying hybridization (spike controls) and labeling tests it was observed that the 20 chips had fulfilled the quality criteria.

scan_protocol: GeneAtlas Microarray System from Affymetrix

data_processing: After scanning, microarrays data were processed using Affymetrix Expression Command Console (Affymetrix) and all samples were within bounds for hybridization and labeling tests. Three independent RNA samples were employed. Samples from worms treated with baicalein were grouped as “treatment” and worms with DMSO exposition were grouped as “control”. Data analysis was then performed with RMA (Robust Multiarray Average) allowing raw intensity values to be background corrected, log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.

label: BIOTIN-STREPTAVIDIN

organism: Caenorhabditis elegans

source_name: C. elegans treated with baicalein (100 uM)

label_protocol: Ss-cDNA was synthetized from 3.5 ng of each sample using the GeneChip WT Pico Reagent kit (Affymetrix, P/N 703262). The amount and quality of ss-cDNA were checked by Nanodrop and Bioanalyzer. ss-cDNA targets were cleaned up, and after fragmentation and terminal labelling with biotin

growth_protocol: N2 worm  were syncronized using the bleaching protocol, from adultworms maintained in standart NGM agar plates at 20 ºC

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions, followed by a purification using  PureLink TM RNA Mini Kit from Invitrogen

treatment_protocol: 16-18 hours after haching L1 larvae were treated with 100 uM of baicalein, or DMSO (0.4%) as control in S. medium for 48 hours at 20 ºC

value: Whole animal

value: Wild-type N2

value: 3 days after hacht, young adults

value: 100 uM of baicalein


title: HH2 Rep 1 SC002_0

description:
Homozygous Ancestor Line 2
SC002_0


title: Baicalein treated N2 animals, Independent Trial 1


title: HrtN24_1


title: HH1 Rep 3 SC001_0

description:
Homozygous Ancestor Line 1
SC001_0


title: 2150901_BL

description: Baseline

value: IDH1/IDH2 mutant

value: Bone Marrow

value: BL

value: IDH inhibitors (IDHi)


title: HH2 Rep 3 SC002_2

description:
Homozygous Ancestor Line 4
SC002_2

value: S288C derivative


title: HrtN20_4


title: HH1 Rep 2 SC001_2

description:
Homozygous Ancestor Line 1
SC001_2


title: HH3 Rep 2 SC003_1

description:
Homozygous Ancestor Line 3
SC003_1


title: 2010157_NR

description: Nonresponse

value: NR


title: 1956615_BL

description: Baseline


title: DMSO control N2 animals, Independent Trial 2

description: Gene expression data from DMSO (0.4%)  control animals

source_name: C. elegans treated with DMSO (0.4 %)


title: DMSO control N2 animals, Independent Trial 1


title: eGFP+mIgG Sample 2

description:
eGFP+mIgG
RNA was isolated from brain tissue from one mouse.
Sample 2

value: 22-26 months

value: APPswe

value: male


title: 2010157_BL

description: Baseline


title: 1850651_BL

description: Baseline


title: HrtN20_3

value: adult

value: female

value: heart

value: NRF


title: 2210551_BL

description: Baseline

value: AML


title: Water treated N2 animals, Independent Trial 2

description: Gene expression data from water (non treated) animals

source_name: C. elegans water

value: Whole animal

value: Wild-type N2

value: water


title: Water treated N2 animals, Independent Trial 1

value: 3 days after hacht, young adults


title: HH Ancestor Run 2 Rep 1 MA_Anc_0

description:
Homozygous Ancestor Second Seq Run
MA_Anc_0

value: euploid


title: cldnb

city: Kansas City

first: Tatjana

last: Piotrowski

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed and aligned to version 11 of the zebrafish genome (GRCz11) using the Cell Ranger (version 3.0.0) pipeline from 10x genomics using the default settings.
Genome_build: danRer11
Supplementary_files_format_and_content: h5 files contain UMI counts for each cell

organism: Danio rerio

source_name: zebrafish epithelial cells

extract_protocol:
GFP+ cells isolated by FACS from 5 dpf cldnb:lyn-EGFP zebrafish embryos
Droplet based scRNA-seq: Standard 10x genomics scRNA-seq protocol using v3 chemistry

value: epithelial cells


title: 2264225_BL

description: Baseline

value: IDH1/IDH2 mutant

value: Bone Marrow

value: BL

value: IDH inhibitors (IDHi)


title: Ch_M_R3_24h

description: processed data file: merged_counts_Chi.txt

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to A. thaliana (TAIR10), C. hirsuta (http://chi.mpipz.mpg.de/), C. rubella (Phytozome 10), E. salsugineum (Phytozome10) or individual A. thalianna accession genomes corrected for SNPs usingTopHat2 (v2.1.1) with following parameters: --read-mismatches 10 --read-gap-length 10 --read-edit-dist 20 --read-realign-edit-dist 0  --min-anchor 5 --splice-mismatches 2 --min-intron-length 30 --max-intron-length 10000 --max-insertion-length 20 --max-deletion-length 20 --num-threads 10 --max-multihits 10 --coverage-search --library-type fr-firststrand --segment-mismatches 3 --min-segment-intron 30 --max-segment-intron 10000 --min-coverage-intron 30 --max-coverage-intron 10000 --b2-very-sensitive
reads per gene were counted using HtSeq (v 0.6.0) with default parameters
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Cardamine hirsuta

source_name: Cardamine hirsuta Ox

extract_protocol:
seedlings were flash frozen in liquid nitrogen and RNA was extracted using peqGOLD TriFast reagent
library preparation was performed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

value: seedling

value: 12 day old

value: mock

tag: replicate


title: No0_T_r3

description: processed data file: merged_counts_No0.txt

source_name: Arabidopsis thaliana No-0


title: HH1 Rep 1 SC001_1

description:
Homozygous Ancestor Line 1
SC001_1

value: S288C derivative


title: HH Ancestor Run 2 Rep 2 MA_Anc_2

description:
Homozygous Ancestor Second Seq Run
MA_Anc_2


title: HrtN20_1

tag: developmental stage

value: adult

value: female

value: heart

value: 9 weeks


title: No0_M_r3


title: 2219711_NR

description: Nonresponse

tag: patient diagnosis

value: AML

value: NR


title: Ch_M_R3_9h


title: Ch_T_R3_9h


title: HrtN16_4

value: NRF


title: HH Ancestor Run 1 Rep 3 SCA1_2

description:
Homozygous Ancestor First Seq Run
SCA1_2

value: euploid


title: 1825001_BL

description: Baseline

tag: idh1/2 genotype


title: 1825001_RES

description: Response

value: RES


title: Ch_T_R3_24h


title: HH Ancestor Run 1 Rep 2 SCA1_1

description:
Homozygous Ancestor First Seq Run
SCA1_1

tag: ploidy


title: 1794247_RES

description: Response

value: IDH1/IDH2 mutant

tag: tissue


title: HrtN16_3

tag: dietary regimen


title: 1794247_BL

description: Baseline

value: Bone Marrow


title: 1873085_BL

description: Baseline

value: BL


title: 1446307_BL

description: Baseline

value: IDH inhibitors (IDHi)


title: Kon_T_r3

description: processed data file: merged_counts_Kon.txt

source_name: Arabidopsis thaliana Kon

value: seedling


title: 1799723_BL

description: Baseline


title: HH Ancestor Run 1 Rep 1 SCA1_0

description:
Homozygous Ancestor First Seq Run
SCA1_0


title: Kon_M_r3

value: 12 day old


title: 1799723_RES

description: Response


title: HrtN16_1

tag: zeitgeber time in hours


title: Ch_T_R2_24h


title: Ch_T_R3_1h


title: MH86_ZT48

city: Beijing

first: Zhen

last: Zhu

address: No.1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

description:
mRNA profiling
AllSamples_FPKM.txt

data_processing:
Illumina GA Pipeline version 1.5 was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then filtered into clean reads.
The expression levels of each gene were quantified by calculated expected number of fragments per kilobase of transcript per millions fragments sequenced (FPKM) using Cuffdiff 2
The mRNA-Seq clean reads were aligned to the gene models in MSU Rice Genome Annotation release 7.0 using TopHat 2.
The gene expression level was calculated by using fragments per kilobase transcriptome per million mapped reads (FPKM) method, with unique position matched reads.
Genome_build: MSU Rice Genome Annotation release 7.0
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa

source_name: Flag leaves

growth_protocol: Super-hybrid rice LY2186 and its parental lines, sterile line SE21s and restorer line MH86 were planted in the field under the same environmental conditions. Flag leaf  samples were collected at grain-filling stage during 17 serial time points (circadian clock ZT0~ZT48, 3h interval). The samples were collected, frozen in liquid nitrogen and stored at –80 °C for total RNA extraction.

extract_protocol:
Total RNAs were extracted from the collected flag leaf at grain-filling stage of hybrid rice and its parents using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol.
Strand-specific transcriptome libraries were constructed using TruSeq® Stranded RNA LT Kit (Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

tag: strain

value: Flag leaves

value: Grain-filling stage


title: HrtN20_2

value: adult

tag: age


title: Kn0_T_r3

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

description: processed data file: merged_counts_Kn0.txt

source_name: Arabidopsis thaliana Kn-0

tag: timepoint


title: HrtN16_2

value: female


title: Kn0_M_r3

value: mock


title: Ch_M_R3_1h


title: HrtN12_4

value: heart

value: 9 weeks


title: HrtN12_2


title: MH86_ZT39

description:
mRNA profiling
AllSamples_FPKM.txt


title: Gy0_M_r3

description: processed data file: merged_counts_Gy0.txt

source_name: Arabidopsis thaliana Gy-0


title: HrtN12_3


title: Ch_M_R2_24h


title: MH86_ZT36

description:
mRNA profiling
AllSamples_FPKM.txt


title: MH86_ZT42

description:
mRNA profiling
AllSamples_FPKM.txt


title: MH86_ZT45

description:
mRNA profiling
AllSamples_FPKM.txt


title: Gy-0_T_r3


title: Can0_T_r3

description: processed data file: merged_counts_Can0.txt

source_name: Arabidopsis thaliana Can-0


title: MH86_ZT33

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtN08_4


title: Can0_M_r3


title: Ch_T_R2_9h


title: Ch_M_R2_9h


title: HrtN08_3


title: HrtN12_1


title: No0_M_r2


title: No0_T_r2


title: Ch_M_R1_24h


title: Ch_T_R1_9h


title: Ch_T_R1_1h


title: MH86_ZT24

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtN04_4


title: HrtN04_1


title: Kon_M_r2


title: Kn0_T_r2


title: Ch_M_R1_1h


title: HrtN00_4


title: Gy-0_T_r2


title: Apc Rac1b tumour 4

city: Edinburgh

first: Kevin

last: Myant

address: Crewe Road

country: United Kingdom

institute: MRC Institute of Genetics and Molecular Medicine

description: Small intestinal tumour from Apcfl/+ Rac1bfl/fl mouse

data_processing:
Transcript abundances were quantified using Kallisto 0.45 (Bray, 2016)  from a transcriptome index compiled from coding and non-coding cDNA sequences defined in Ensembl 95
Differential expression was called using DESeq2 (Love, 2014) at the gene level after importing estimated counts per transcript from Kallisto using tximport (Soneson, 2015).
Supplementary_files_format_and_content: tsv

source_name: Apc Rac1b tumour

growth_protocol: VilCreERT2 Apcfl/+ and VilCreERT2 Apcfl/+ Rac1bfl/fl mice were induced with 80mg/kg tamoxifen and aged until signs of intestinal tumourigenesis were apparent. Mice were culled and tumours harvested and stored in RNAlater.

extract_protocol:
RNA was extracted using RNAeasy kit (Qiagen).
Libraries were prepared from mRNA

value: Small intestinal tumour

value: Apcfl/+ Rac1bfl/fl


title: MH86_ZT12

description:
mRNA profiling
AllSamples_FPKM.txt


title: Apc Rac1b tumour 3


title: Apc Rac1b tumour 1


title: Can0_M_r2


title: HrtN00_1

value: NRF


title: MH86_ZT0

description:
mRNA profiling
AllSamples_FPKM.txt


title: Apc tumour 4

description: Small intestinal tumour from Apcfl/+ mouse

source_name: Apc tumour

value: Apcfl/+ Rac1b+/+


title: No0_T_r1


title: Ch_M_R2_1h


title: LY2186_ZT48

description:
mRNA profiling
AllSamples_FPKM.txt


title: Ch_T_R2_1h


title: Apc tumour 2


title: MH86_ZT30

description:
mRNA profiling
AllSamples_FPKM.txt


title: Ch_T_R1_24h


title: MH86_ZT27

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtN08_1


title: MH86_ZT21

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtN04_3


title: Ch_M_R1_9h


title: MH86_ZT18

description:
mRNA profiling
AllSamples_FPKM.txt


title: Kon_T_r2


title: HrtN04_2


title: MH86_ZT15

description:
mRNA profiling
AllSamples_FPKM.txt


title: Kn0_M_r2


title: Apc tumour 1


title: MH86_ZT9

description:
mRNA profiling
AllSamples_FPKM.txt


title: Gy0_M_r2


title: HrtN00_3


title: LY2186_ZT42

description:
mRNA profiling
AllSamples_FPKM.txt


title: MH86_ZT6

description:
mRNA profiling
AllSamples_FPKM.txt


title: Apc Rac1b tumour 2


title: HrtN00_2


title: MH86_ZT3

description:
mRNA profiling
AllSamples_FPKM.txt


title: Can0_T_r2


title: HrtN08_2


title: HrtD24_4

value: DRF


title: HrtD24_3


title: Apc tumour 3


title: LY2186_ZT39

description:
mRNA profiling
AllSamples_FPKM.txt


title: LY2186_ZT45

description:
mRNA profiling
AllSamples_FPKM.txt


title: Kon_T_r1


title: No0_M_r1


title: Kn0_M_r1


title: HrtD24_2


title: MAZRKO_effector repl1

city: Vienna

first: Shinya

last: Sakaguchi

address: Lazarettgasse 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

description: sequencing was done in 1 lane

data_processing:
Base calls were performed using the Illumina Realtime Analysis software.
STAR version 2.5.2b (with default parameters´) was used to align the reads to the mouse reference genome mm10
The number of uniquely mapped reads associated with each gene, according to RefSeq gene annotation, was counted using the Subread version 1.5.0.
The count data were normalized using the trimmed mean of M-values method implemented in the edgeR R-package (Bioconductor version 3.2).
Normalized data was exported as RPKM values provided by edgeR package.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: tab-delimited text file includes normalized RPKM values for each sample

source_name: lymphocyte

growth_protocol: Sorted naïve CD8+ T cells were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of recombinant human interleukin 2 (rhIL-2, 20 U/ml). Thereafter, cells were split 1:2 to 3 every two days and placed in fresh T cell medium containing rhIL-2 (100 U/ml). Six days after stimulation cells were harvested for total RNA isolation.

extract_protocol:
Total RNA was isolated with RNaeasy kit (Qiagen) combined with DNase I digestion in the extraction columns.
RNA-seq libraries were prepared using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina).

value: Effector CD8-positive T cell


title: Kon_M_r1


title: Kn0_T_r1


title: HrtD20_4


title: HrtD24_1


title: Gy0_M_r1


title: LY2186_ZT33

description:
mRNA profiling
AllSamples_FPKM.txt


title: Gy-0_T_r1


title: LY2186_ZT36

description:
mRNA profiling
AllSamples_FPKM.txt


title: MAZRKO_effector repl2

description: sequencing was done in 1 lane


title: HrtD16_4


title: LY2186_ZT27

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD20_1


title: HrtD20_2


title: Can0_T_r1


title: Can0_M_r1


title: MAZRKO_effector repl3

description: sequencing was done in 1 lane


title: WT_effector repl2

description: sequencing was done in 1 lane

value: WT


title: WT_effector repl1

description: sequencing was done in 1 lane


title: LY2186_ZT24

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD20_3


title: WT_effector repl3

description: sequencing was done in 1 lane


title: LY2186_ZT21

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD16_3


title: RUNX3KO_effector repl3

description: sequencing was done in 1 lane


title: Es_T_R3_24h

description: processed data file: merged_counts_Esa.txt

organism: Eutrema salsugineum

source_name: Eutrema salsugineum Shandong


title: HrtD16_2


title: Es_M_R3_24h


title: RUNX3KO_effector repl2

description: sequencing was done in 1 lane


title: LY2186_ZT30

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD12_3


title: HrtD12_4


title: MAZRKO_RUNX3KO_effector repl2

description: sequencing was done in 1 lane


title: HrtD12_2


title: RUNX3KO_effector repl1

description: sequencing was done in 1 lane


title: Es_T_R3_9h


title: LY2186_ZT12

description:
mRNA profiling
AllSamples_FPKM.txt


title: LY2186_ZT15

description:
mRNA profiling
AllSamples_FPKM.txt


title: MAZRKO_RUNX3KO_effector repl3

description: sequencing was done in 1 lane


title: LY2186_ZT6

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD16_1


title: Es_M_R3_1h


title: MAZRKO_RUNX3KO_effector repl1

description: sequencing was done in 1 lane


title: Es_T_R2_24h


title: HrtD08_4


title: LY2186_ZT0

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD12_1


title: Es_T_R3_1h


title: LY2186_ZT3

description:
mRNA profiling
AllSamples_FPKM.txt


title: LY2186_ZT18

description:
mRNA profiling
AllSamples_FPKM.txt


title: SE21s_ZT48

description:
mRNA profiling
AllSamples_FPKM.txt


title: LY2186_ZT9

description:
mRNA profiling
AllSamples_FPKM.txt


title: Es_T_R2_9h


title: HrtD08_3


title: Es_M_R3_9h


title: Es_M_R2_9h


title: HrtD08_2


title: HrtD08_1


title: SE21s_ZT45

description:
mRNA profiling
AllSamples_FPKM.txt


title: SE21s_ZT42

description:
mRNA profiling
AllSamples_FPKM.txt


title: Es_T_R2_1h


title: HrtD04_4


title: Es_M_R2_1h


title: SE21s_ZT39

description:
mRNA profiling
AllSamples_FPKM.txt


title: SE21s_ZT36

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD04_2


title: Es_M_R1_24h


title: Es_M_R2_24h


title: Es_T_R1_24h


title: HrtD04_3


title: HrtD04_1


title: SE21s_ZT30

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD00_4


title: Es_T_R1_9h


title: SE21s_ZT27

description:
mRNA profiling
AllSamples_FPKM.txt


title: Es_M_R1_9h


title: HrtD00_3


title: SE21s_ZT24

description:
mRNA profiling
AllSamples_FPKM.txt


title: SE21s_ZT21

description:
mRNA profiling
AllSamples_FPKM.txt


title: Es_T_R1_1h


title: SE21s_ZT33

description:
mRNA profiling
AllSamples_FPKM.txt


title: HrtD00_2


title: HrtD00_1


title: 5xFAD 3

description:
RNA was isolated from LECs sorted from a pool of 10 mouse brain meninges
mouse_wt_vs_5xfad_norm_counts (SL357718)

data_processing:
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Filtered reads were trimmed using Trimmomatic to remove adapter sequences and low quality bases
Transcript-level abundances were calculated using Salmon.
Transcript-level abundances were summarized into gene-level counts with tximport.
Raw counts were then filtered to remove genes without at least  5 counts in at least 3 samples,  as well as genes with standard deviations of log transformed counts greater than 2 between replicates
The filtered raw counts were then normalized with DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: processed data files are csv files containing gene x count matrices of the DEseq2 normalized counts.

source_name: Mouse brain meninges

tag: genotype/variation

value: 5xFAD hemizygous

tag: celltype

value: meningeal lymphatic endothelial cells

value: 6 months

value: male