title: OM_EI_321

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
After sequencing, reads were aligned against the mm10 transcriptome and genome (UCSC) in StrandNGS software (v4.0; Strand Life Sciences). Parameters for alignment and filtering included: adapter trimming, fixed 2-bp trim from 5′ and 2 bp from 3′ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum 5% gap, and trimming of 3′ ends with Q < 30. Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in the forward orientation, as previously (8).
Binary alignment map (BAM) files were exported from StrandNGS software for further analysis. The Rsubread package (13) was used to quantify the read counts using the featureCount command. Normalization and differential expression calling was then performed using edgeR (14) with the quasi-likelihood pipeline (15). Differentially expressed genes (DEGs) (GLM QLF<0.1, |FC|>1.25) were identified for each of the comparisons (YF v YM, OF v OM, OF v YF, OM v YM) as well as the interaction term.
DEGs were uploaded to Ingenuity Pathway Analysis software (IPA; Qiagen) to assess the biological significance of differential expression. Heatmaps of DEGs and pathway activation z-scores were made using Morpheus software (https://software.broadinstitute.org/morpheus).
Volcano plots were made in R using the EnhancedVolcano package. Upset plots were created using the UpSetR package. Gene set enrichment analysis (GSEA) was run using GSEA v4.1.0 (16). For the differential transcript analysis of the Cdkn2a gene, StrandNGS software was used for quantitation.
Assembly: Mm10
Supplementary files format and content: Xlsx files containg the gene expression (CPM) for all detected genes in each sample

source_name: hippocampus

extract_protocol:
For CD11b-MACS: Hippocampal cells from C57BL6/N mice were pelleted at 300 x g for 10 minutes at 4°C then resuspended in 90 µL of 0.5% BSA in D-PBS and 10 µL of CD11b (Microglia) MicroBeads (#130-093-634, Miltenyi Biotec) followed by thorough mixing. The cells were then labeled by incubating with the CD11b-beads for 15 minutes at 2-8°C. After incubation, labeled cells were washed in 1 mL of 0.5% BSA in D-PBS and then centrifuged at 300 x g for 10 minutes. Cells were resuspended in 700 µL of 0.5% BSA in D-PBS. 200 µL of the cell suspension was reserved as the CD11b-MACS Input for flow cytometric and RNA-Seq analyses. The remaining 500 µL was processed on the autoMACS Pro Separator (#130-092-545, Miltenyi Biotec). After priming the autoMACS instrument, the sample and collection tubes were placed in a cold Chill5 tube rack (#130-092-951, Miltenyi Biotec), collecting both positive and negative fractions. The double-positive selection (Posseld) program was used to elute highly pure CD11b+ cells.
For Cx3cr1-TRAP: Hippocampal tissue was isolated from Cx3cr1-NuTRAP mice of both sexes at 6 and 22 mo (n=5-7/sex/age). The hippocampi from both hemispheres were minced into small pieces and homogenized in 100 µL ice-cold TRAP homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1 mM DTT; 100 μg/ml cycloheximide [#C4859-1ML, Millipore Sigma]; 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor [#10777019; Thermo Fisher Scientific]; 1× complete EDTA-free Protease Inhibitor Cocktail [#11836170001; Millipore Sigma] with a Kimble pellet pestle mixer [#749540-0000; DWK Life Sciences), as previously described (7, 8). Volume was brought up to 1.5 mL with TRAP homogenization buffer. Homogenates were centrifuged at 12,000 × g for 10 min at 4°C. After centrifugation, 100 μL of the cleared supernatant was saved as TRAP Input. The remaining supernatant was incubated with 5 μg/μL of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for 1 hour. A volume of 50 µL per sample of Protein G Dynabeads (#10003D; Thermo Fisher Scientific) was washed three times in 1-mL ice-cold low-salt wash buffer (50 mM Tris, pH 7.5; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 100 μg/ml cycloheximide; 1 mM DTT) and then resuspended in the original volume of low salt wash buffer. 50 µL of washed beads were added to each cleared homogenate and incubated at 4°C with end-over-end rotation overnight. Following overnight incubation, the beads and GFP-bound polysomes were washed three times with 0.5 mL of high-salt wash buffer (50 mM Tris, pH 7.5; 12 mM MgCl2; 300 mM KCl; 1% NP-40; 100 μg/mL cycloheximide; 2 mM DTT) using a magnetic stand for separation. After the last wash, 350 μL of Buffer RLT (Qiagen) was supplemented with 3.5 μl of 2-β mercaptoethanol (#444203, Millipore Sigma) and added to the washed beads. Samples were incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated, and the supernatant (Positive Fraction) was transferred to a new tube. RNA was isolated using the RNeasy Mini kit (#74104, QIAGEN) according to the manufacturer’s instructions. RNA was quantified with a Nanodrop Onec spectrophotometer (#ND-ONEC-W, Thermo Fisher Scientific), and its quality was assessed by HSRNA ScreenTape (#5067-5579, Agilent Technologies) with a 4150 Tapestation analyzer (#G2992AA, Agilent Technologies).
RNA was isolated using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions.
Directional RNA-Seq libraries were made according to the manufacturer’s protocol from 5-100 ng RNA. Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (#NEBE7490L, New England Biolabs) and then processed using NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L, New England Biolabs) for the creation of cDNA libraries. Library sizing was performed with HSD1000 ScreenTape (#5067-5584, Agilent Technologies) and quantified by Qubit dsDNA HS Assay Kit (#Q32851, ThermoFisher Scientific) on a Qubit 4 Fluorometer (#Q33226, ThermoFisher Scientific). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NovaSeq 6000 system (SP PE50bp, S4 PE150).

value: hippocampus

value: male

value: microglia

value: Cx3cr1-cre/ERT(+/-); NuTRAP(flox/wt)

tag: age

value: 22-25 months-old

tag: isolation technique


title: control 2

status: Public on Aug 18 2023

type: SRA

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

country: USA

institute: NYU Grossman School of Medicine

library_source: transcriptomic

data_processing:
NovaSeq 6000 System (RTA Version 3.4.4)
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Bone and bone marrow

extract_protocol:
Cells were isolated from the tibia and femur and crushed once, using mortar and pestle, then cut into small pieces with scissors. The tissue was subjected to three rounds of enzymatic digestion with 0.2%collagenaseat 37°C under agitation for 30min each. Cells were filtered through a 70-μm strainer and centrifuged at 1500 rpm for 5 minutes at 4°C.  Red blood cells were lysed using NH4Cl (StemCell Technologies, Vancouver, Canada) for 10 min on ice, washed with staining media (HBSS (Thermo Fisher Scientific, Waltham, MA, USA) containing 2% fetal bovine serum (Life Technologies: 10437-028), 1% HEPES (10 mM) (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Thermo Fisher Scientific) and resuspended in HBSS for subsequent analyses
RNA was isolated from cells using RNeasy Kit (Qiagen, Germantown, MD, USA) according to manufacturer’s instruction
RNA-seq, Low input RNA (10 pg) library prep (SMARTer or Nugen method)

tag: tissue

value: Bone and bone marrow

tag: cell type

value: LEPR+CD45-CD31-TER-119- skeletal stem cells

tag: genotype

value: Ncstnfl/fl

tag: treatment


title: ovary_H_RNA2_rep2

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

data_processing:
Sequencing reads were pseudoaligned to the Drosophila melanogaster transcriptome using Kallisto v0.46.1 with parameter --rf-stranded
Estimated transcript counts were summarised per gene in R v4.0.1 using the tximport package v1.16.1 with parameter type="kallisto"
Differential expression analysis was conducted in R v4.0.1 using the DESeq2 package v1.28.1
Genome_build: Drosophila_melanogaster.BDGP6.22.cdna.all.fa
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in head
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in fat body
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in ovary

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Drosophila melanogaster were maintained under standard conditions. See the publication for further details.

extract_protocol:
Drosophila melanogaster females were flash-frozen in liquid nitrogen and stored at -80oC. Females were then defrosted and the head, fat body (abdomen minus gut and ovaries) and ovaries were dissected out (over dry ice), pooled into groups of 11 or 12 within each treatment and sub-group, then flash-frozen in liquid nitrogen, and stored at -80oC. Each sample (tissue pooled from 11 or 12 individuals) was then ground in liquid nitrogen using a micropestle with the resulting powder resuspended in Tri-reagent (Sigma-Aldrich, UK). RNA was extracted using the Direct-zolTM RNA extraction kit (Zymo Research, USA) according to the manufacturer's protocol. An additional DNase treatment was performed using TurboTM DNA-free kit (Thermo Fisher Scientific, UK), according to the manufacturer's protocol.
Illumina TruSeq stranded mRNA-seq libraries constructed by Edinburgh Genomics (Edinburgh, UK)

treatment_protocol: Drosophila melanogaster larvae were reared on either 100% sugar-yeast-agar (SYA) (medium-quality diet (M) treatment) or 120% SYA (high-quality diet (H) treatment).

value: ovary

value: high (H), larval diet of 120% sugar-yeast-agar (SYA)

tag: time point

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died

tag: biological replicate

value: biological replicate 2


title: ovary_H_RNA2_rep1

value: biological replicate 1


title: foam cells SARSCov2 infected timepoint 2 [Foam-cells-Donor-2-2-hpi_S8]

first: Dr. Chiara

last: Giannarelli

address: 435 E 30th St

department: Cardiology

institute: NYU Langone Health

description: RNA bulk sequencing

data_processing:
Quality control of RNA-seq data was performed using FastQC2 v.0.11.7, a final report was generated for each FASTQ file to
assess general sequencing quality.
Following that the raw reads were aligned
using STAR v.2.6.1d with hg38 as the reference genome. The gene-level expression counts were
computed with featureCounts function in the Subread package (v.1.6.3; parameters: -g gene_id -s 2)
using the human gene annotations from Gencode release 33.
Assembly: hg38 concatenated with SARS-CoV-2 Washington isolate (WA1/2020) genome
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample

organism: Homo sapiens

source_name: foam cell

growth_protocol: Human primary monocytes derived from peripheral blood mononuclear cells (PBMCs) were obtained (StemCell Technologies, Cat. #200-0167) and maintained in DMEM culture media (Corning, Cat. #10-013-CV) supplemented with 10% FBS, 2 mM L-glutamine, 100 U ml−1 penicillin–streptomycin in a humidified 37°C, 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent and Direct-zol RNA Microprep Kits following the manufacturer’s instructions.
For human primary macrophage and foam cellin-vitroexperiments, library preparation was performed byPolyA capture and ligation-based addition of adapters and indexeswith Illumina Stranded mRNA Preparation and Ligation.

treatment_protocol:
Monocytes were plated and differentiated to macrophages in the presence of 20 nM human macrophage-colony stimulating factor (M-CSF) for 5 days. Macrophages were first treated with ox-LDL at final concentration of 10 μg/mL for 1 hour before infection
Cells were cultured with SARS-CoV-2 virus (USA-WA1/2020 strain) at MOI 0.1 in infection media with 2% FBS.  Mock infected cells were used as controls.

value: foam cell

value: SARS-CoV-2 infection


title: OM_EI_320

molecule: polyA RNA

tag: Sex


title: foam cells SARSCov2 infected timepoint 8 [Foam-cells-Donor-2-8-hpi-1_S17]

description: RNA bulk sequencing


title: ovary_M_RNA2_rep3

value: medium (M), larval diet of 100% sugar-yeast-agar (SYA)

value: biological replicate 3


title: foam cells SARSCov2 infected timepoint 8 [Foam-cells-Donor-2-8-hpi-2_S18]

description: RNA bulk sequencing


title: OM_EI_319

value: hippocampus


title: Macrophage not infected timepoint 0 [Primary-mac-Donor-1-0hpi_S1]

description: RNA bulk sequencing

source_name: macrophage

value: macrophage

value: not infected


title: Wildtype, DRG, Injured

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Department of Brain Sciences

country: South Korea

institute: DGIST

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts

source_name: Dorsal root ganglion(DRG)

extract_protocol:
For CSDE1-IP or HA-IP sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-CSDE1 or anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using Rneasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB109))

value: Dorsal root ganglion(DRG)

tag: strain

value: Wild type

tag: developmental stage

value: adult

value: Sciatic nerve injury, 72hr

tag: in vivo_viral_gene_delivery

tag: in vitro_viral_gene_delivery

tag: ip antibody

tag: molecule subtype

value: CSDE1-IP product, RNA


title: OM_EI_204

value: male

value: microglia

value: Cx3cr1-cre/ERT(+/-); NuTRAP(flox/wt)

value: 22-25 months-old


title: ovary_M_RNA2_rep2

value: ovary

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died

value: biological replicate 2


title: ovary_M_RNA2_rep1

value: medium (M), larval diet of 100% sugar-yeast-agar (SYA)

value: biological replicate 1


title: foam cells SARSCov2 infected timepoint 2 [Foam-cells-Donor-2-2-hpi-2_S12]

description: RNA bulk sequencing

value: foam cell

value: SARS-CoV-2 infection


title: OM_EI_203

value: hippocampus


title: Macrophage SARSCov2 infected timepoint 48 [Primary-mac-Donor-1-2-dpi_S25]

description: RNA bulk sequencing

value: macrophage


title: Macrophage SARSCov2 infected timepoint 24 [Primary-mac-Donor-1-1-dpi_S19]

description: RNA bulk sequencing


title: ovary_H_RNA1_rep2

value: high (H), larval diet of 120% sugar-yeast-agar (SYA)

value: RNA 1 (RNA_1), after 10% of the members of the cohort had died


title: ovary_H_RNA1_rep4

value: biological replicate 4


title: OF_EI_400

value: female


title: Macrophage SARSCov2 infected timepoint 2 [Primary-mac-Donor-1-2-hpi_S7]

description: RNA bulk sequencing


title: ovary_H_RNA1_rep1


title: Macrophage not infected timepoint 0 [Primary-mac-Donor-2-0hpi-1_S2]

description: RNA bulk sequencing

value: not infected


title: Macrophage SARSCov2 infected timepoint 8 [Primary-mac-Donor-1-8-hpi_S9]

description: RNA bulk sequencing


title: ovary_M_RNA1_rep3

value: biological replicate 3


title: ovary_M_RNA1_rep2


title: OF_EI_325

value: microglia

value: Cx3cr1-cre/ERT(+/-); NuTRAP(flox/wt)


title: OF_EI_382

value: 22-25 months-old


title: Macrophage not infected timepoint 0 [Primary-mac-Donor-2-0hpi-2_S3]

description: RNA bulk sequencing


title: OF_EI_324


title: OF_EI_210


title: ovary_M_RNA1_rep1

value: ovary


title: head_H_RNA2_rep4

source_name: head

value: head

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died


title: OF_EI_383


title: OF_EI_209


title: head_H_RNA2_rep3


title: Macrophage SARSCov2 infected timepoint 24 [Primary-mac-Donor-2-1-dpi-2_S21]

description: RNA bulk sequencing


title: YM_EI_1445

value: male

value: 5-6 months-old


title: head_H_RNA2_rep1

value: biological replicate 1


title: Macrophage SARSCov2 infected timepoint 48 [Primary-mac-Donor-2-2-dpi-1_S26]

description: RNA bulk sequencing

value: SARS-CoV-2 infection


title: head_M_RNA2_rep3

value: medium (M), larval diet of 100% sugar-yeast-agar (SYA)


title: YM_EI_1438

value: hippocampus


title: Macrophage SARSCov2 infected timepoint 48 [Primary-mac-Donor-2-2-dpi-2_S27]

description: RNA bulk sequencing

value: macrophage


title: Macrophage SARSCov2 infected timepoint 2 [Primary-mac-Donor-2-2-hpi-1_S8]

description: RNA bulk sequencing


title: YM_EI_1437


title: head_M_RNA2_rep2

value: biological replicate 2


title: Macrophage SARSCov2 infected timepoint 2 [Primary-mac-Donor-2-2-hpi-2_S9]

description: RNA bulk sequencing


title: Macrophage SARSCov2 infected timepoint 24 [Primary-mac-Donor-2-1-dpi-1_S20]

description: RNA bulk sequencing


title: head_M_RNA2_rep1


title: Macrophage SARSCov2 infected timepoint 8 [Primary-mac-Donor-2-8-hpi-1_S14]

description: RNA bulk sequencing


title: YM_EI_1436


title: head_H_RNA1_rep3

value: high (H), larval diet of 120% sugar-yeast-agar (SYA)

value: RNA 1 (RNA_1), after 10% of the members of the cohort had died


title: denervated_ileum_day4 IR #1

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

description:
SAM24413537
B6 mice treated with 6-OHDA ip. , followed by 12 gy IR and take down at indicated timepoint

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing and single cell 3' gene counting were performed using 10X Cell Ranger.
Reads were aligned to GRCm38 mouse reference assembly.
Quality control was performed using an outlier-based approach; outliers were defined as cells with counts/detected genes below or with percentage mitochondrial reads over three times the median absolute deviations (MAD), and were excluded for further analysis.
Per-gene UMI counts were normalized by the total number of transcripts per cell, scaled by the median number of transcripts across all cells and log-transformed for downstream analysis.
Our data was generated in multiple batches (days). For each batch, we performed quality control, normalization and variance modelling steps, and then applied a mutual nearest neighbor (MNN) correction to merge all batches.
Assembly: GRCm38
Supplementary files format and content: csv, count matrix

source_name: Intestinal cells

extract_protocol:
Mouse ileum (5cm from the cecum) was removed; fat was trimmed off. Ileum was cut into 1-cm pieces, added to 10 ml Dissociation Reagent 1 [HBSS Ca2+ and Mg2+ free; 10mM HEPES; 10mM EDTA; 1.5mM DTT; 5% FBS] and incubated on ice for 20min. Samples were transferred to gentleMacs C-tube containing 10 ml Dissociation Reagent 2 [HBSS w/o; 10mM HEPES; 10mM EDTA; 5% FBS] and incubated on ice for 1hr, followed by 1min spin at 100rpm on gentleMacs dissociateor (Miltenyi Biotec). Samples were washed 2x in RPMI, followed by pelleting at 100g in a swing bucket at 4 °C. After the last spin, samples were resuspended in RPMI. To better preserve epithelial cells, samples were separated by free-floating villi chucks and undissociated piece (containing crypts and mesenchymal tissue). The undissociated pieces were picked out and placed in a new C-tube containing 2.5mL digestion buffer w/ collagenase [HBSS, 10mM HEPES, 5% FBS, 0.8 mg/ml dispase, 0.2 mg/ml Collagenase P; 0.1 mg/ml DNAse]. The villi chucks were spun again at 100g, and resuspended in 2.5mL digestion buffer w/o collagenase [HBSS, 10mM HEPES, 5% FBS, 0.8 mg/ml dispase, 0.1 mg/ml DNAse]. Both tissue segments were incubated in 37°C water bath for 5min, followed by 1 min spin at 100rpm on gentleMacs dissociateor. Two portions of samples were combined again, washed by RPMI, passed through 100um filter, spun at 300g to pellet single cell and resuspended in PBS + 3% FBS. Cells were filtered with 40um filter and counted right before 10x chromium chip loading.
Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library reagent kit v3.1 following manufacturer’s guide (10x Genomics). Cell density and viability of single-cell suspension were determined by Vi-CELL XR cell counter (Beckman Coulter) or by manual counting using a hemocytometer. We loaded ~10,000 cells on each chip. cDNAs and libraries were prepared following the manufacturer’s user guide (10x Genomics). Libraries were profiled by Tapestation D1000 kit (Agilent) and quantified using IQubit HS dsDNA kit (Invitrogen). Each library was sequenced in one lane of HiSeq4000 (Illumina) following the manufacturer’s sequencing specification (10x Genomics).
Chromium Single Cell 3’ Library reagent kit v3.1

treatment_protocol: Mice were placed into an "irradiator pie”, unrestrained and able to comfortably move about within the compartment. Small holes were in the plexiglass to allow air exchange. A plexiglass lid was placed onto the pie, and the assembled pie was placed on a metal turntable inside the shielded irradiator chamber. The turntable rotated the pie(s) at a slow, steady speed to ensure that all animals in the pie receive a uniform dose. Mice were returned to their home cage after exposure and took down at indicated time points to isolate ileum cells for sequencing. For denervation, 6-Hydroxydopamine (6-OHDA; Sigma, 162957) was dissolved in 0.1% l-ascorbic acid (Sigma, 255564) in sterile PBS. This solution was injected i.p. at a concentration of 80 mg/kg body weight on three consecutive days; iR was performed two days post the last i.p. treatment.

value: Intestine

value: 6-OHDA treated + 12gy IR

tag: mouse strain


title: denervated_ileum_day0 IR #2

description:
SAM24413536
B6 mice treated with 6-OHDA ip.

value: 6-OHDA treated


title: YF_EI_1444

value: female

value: microglia

value: Cx3cr1-cre/ERT(+/-); NuTRAP(flox/wt)


title: Macrophage SARSCov2 infected timepoint 8 [Primary-mac-Donor-2-8-hpi-2_S15]

description: RNA bulk sequencing


title: head_H_RNA1_rep2

value: head


title: YF_EI_1442


title: head_H_RNA1_rep1


title: ileum_day 7 IR #2

description:
SAM24412585
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: 12gy IR

value: day 7


title: YM_EI_1439

value: male

value: 5-6 months-old


title: ileum_day 4 IR #2

description:
SAM24412584
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: day 4


title: 22097-0008

city: Tübingen

first: Ali

last: El-Ayoubi

address: otfried müller straße 27

country: Germany

institute: Hertie Institute for Clinical Brain Research

data_processing:
Raw data were imported into the CLC Genomics Workbench  v.21.0.5. Failed reads are indicated by a flag within the quality score header information inside the *.fastq file, specifying whether or not a read has passed the sequencer-inherent  quality filters. These were removed from the data set during data import.
Assembly: The Homo sapiens GRCh38 reference genome was downloaded from NCBI and used as reference sequence.
Supplementary files format and content: The *.fastq-files were quality controlled in CLC Genomics WoThe *.fastq-files were quality controlled in CLC Genomics Workbench. A detailed graphical QC report for the whole sample set is provided as file 22097_QC/22097_Sequencing_QC_trimmed.pdf
Supplementary files format and content: all_trimmed (TE).xlsx

source_name: LX-2mCherry FR/TK

growth_protocol: All cell lines were cultivated in DMEM containing 2% fetal calf serum (FCS), 1% glutamine and 1% penicillin/streptomycin

extract_protocol:
Total RNA from 2.5 million human cells per sample were isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. An on-column DNase digestion step was included in the RNA isolation protocol. The elution volume was 50 μl.
Library preparation was performed with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® UltraTM II Directional mRNA kit .  Adapter-ligated fragments were amplified during a 8-cycle PCR reaction. Universal Human Reference RNA (UHR) was simultaneously processed as internal positive control (PosC), but discarded after successful library validation.

tag: cell line

value: LX-2mCherry FR/TK

value: Hepatic Stellate cells

value: Fast Running/ TK transduced

value: No treatment


title: 22097-0009


title: head_M_RNA1_rep3

value: medium (M), larval diet of 100% sugar-yeast-agar (SYA)

value: RNA 1 (RNA_1), after 10% of the members of the cohort had died

value: biological replicate 3


title: denervated_ileum_day4IR #2

description:
SAM24413538
B6 mice treated with 6-OHDA ip. , followed by 12 gy IR and take down at indicated timepoint

value: Intestine

value: 6-OHDA treated + 12gy IR


title: YF_EI_1441

value: hippocampus

value: female

value: microglia

tag: age


title: 22097-0007


title: head_M_RNA1_rep2

value: head

value: biological replicate 2


title: YF_EI_1440

value: Cx3cr1-cre/ERT(+/-); NuTRAP(flox/wt)

tag: isolation technique


title: head_M_RNA1_rep1

tag: tissue

value: biological replicate 1


title: ileum_day 3 IR #2

description:
SAM24412583
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: 12gy IR

value: day 3


title: 22097-0006

source_name: LX-2mCherry FR

value: LX-2mCherry FR

tag: cell type

value: Hepatic Stellate cells

value: WT/ Fast Running


title: ileum_day 0 IR #3

description:
SAM24412581
B6 mice without treatment

value: No treatment

value: day 0


title: ileum_day 2 IR #2

description:
SAM24412582
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: day 2


title: OM5

value: male

tag: genotype

value: 22-25 months-old


title: denervated_ileum_day0 IR #1

description:
SAM24413535
B6 mice treated with 6-OHDA ip.

value: Intestine

tag: treatment

value: 6-OHDA treated


title: fatbody_H_RNA2_rep3

source_name: fat body

value: fat body

value: high (H), larval diet of 120% sugar-yeast-agar (SYA)

tag: time point

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died

value: biological replicate 3


title: OM4

value: hippocampus

value: microglia


title: 22097-0005


title: 22097-0004


title: YF_EI_1443

value: female

value: Cx3cr1-cre/ERT(+/-); NuTRAP(flox/wt)

value: 5-6 months-old


title: OM3


title: ileum_day 1 IR #2

description:
SAM24409464
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: 12gy IR

value: day 1


title: ileum_day 0 IR #2

description:
SAM24409463
B6 mice without treatment

value: No treatment

value: day 0


title: 22097-0003

source_name: LX-2mCherry PAR

value: LX-2mCherry PAR

value: Hepatic Stellate cells

value: WT


title: fatbody_H_RNA2_rep1

tag: biological replicate

value: biological replicate 1


title: OM2

tag: Sex

value: male

value: 22-25 months-old


title: 22097-0002


title: fatbody_M_RNA2_rep3

value: fat body

value: medium (M), larval diet of 100% sugar-yeast-agar (SYA)

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died


title: ileum_day 7 IR #1

description:
SAM24406845
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: Intestine

value: day 7


title: ileum_day 4 IR #1

description:
SAM24406844
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: day 4


title: 22097-0001


title: fatbody_M_RNA2_rep2

value: biological replicate 2


title: OM1

value: hippocampus

value: microglia


title: OF4

value: female


title: PBMC TCR library for Donor5

city: Oslo

first: Benedicte

middle: Alexandra

last: Lie

address: Kirkeveien 166

department: Department of Medical Genetics

country: Norway

institute: University Of Oslo

data_processing:
CellRanger v.3.1.0
Assembly: refdata-cellranger-vdj-GRCh38-alts-emsebl-5.0.0  (10x Genomics)
Supplementary files format and content: filtered_contig_annotation.csv files from Cellranger
Library strategy: scAIRRseq

source_name: Blood

extract_protocol:
mRNA was harvested using 10x Genomics 5' V(D)J kit (v1 Chemistry) following manufacturer's protocol (10x Genomics protocol CG000186, RevD).
RNA libraries were prepared using 10x Genomics 5' V(D)J kit (v1 Chemistry) with enrichement of TCR- and BCR-specific segments following manufacturer's protocol (10x Genomics protocol CG000186, RevD).

value: Blood

value: 13.5 months

value: Male

tag: tcr or_bcr

value: TCR

tag: enrichment

value: PBMC isolation by LymphoPrep (Abott)


title: CD45-depleted TCR library for Donor 5

source_name: Thymus

value: Thymus

value: Optiprep (Abott) density gradient + CD45 depletion by magnetic beads (STEMcell Technologies)


title: OF3

value: 22-25 months-old


title: APC enriched TCR library for Donor 5

value: Optiprep (Abott) density gradient


title: fatbody_H_RNA2_rep2

value: fat body

value: high (H), larval diet of 120% sugar-yeast-agar (SYA)

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died


title: ileum_day 1 IR #1

description:
SAM24406841
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: Intestine

value: 12gy IR

value: day 1


title: OF2

value: hippocampus

value: microglia


title: ileum_day 2 IR #1

description:
SAM24406842
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: day 2


title: fatbody_H_RNA1_rep4

value: RNA 1 (RNA_1), after 10% of the members of the cohort had died

value: biological replicate 4


title: OF1

value: female


title: Unenriched TCR library for Donor 5

value: 13.5 months

value: Male

value: TCR


title: fatbody_H_RNA1_rep1

value: biological replicate 1


title: fatbody_M_RNA1_rep3

value: medium (M), larval diet of 100% sugar-yeast-agar (SYA)

value: biological replicate 3


title: PBMC TCR library for Donor 4

value: Blood

value: 1.6 months

value: Female

value: PBMC isolation by LymphoPrep (Abott)


title: DD_RNAm688_1372

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
Alignment and gene count by STAR (version 2.6.0b).
Gene annotation used GENCODE M19 (Ensembl 94).
Differential expression analysis carried out in R (3.5.1) using Bioconductor package DESeq2.
Assembly: GRCm38
Supplementary files format and content: DD_RNAm_raw_count.txt: Tab-delimited data matrix of normalized gene counts.

source_name: breast adenocarcinoma

growth_protocol: Spontaneous breast tumors.

extract_protocol:
Flash frozen tissue was pulverized and homogenized in TRIzol RNA isolation reagent (Invitrogen). RNA was then purified based on manufacturer protocol.
Barcoded, Illumina compatible, strand-specific total RNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina).

treatment_protocol: Breast tumors were treated with AAV on day 0, 3, 8 and tumors were harvested once animals reached euthanasia criteria.

value: breast tumor

value: K14-Cre, Trp53wm-R172H/fl and Rosa26LSL CAS9-P2A-EGFP/+


title: YM3

value: hippocampus

value: male

value: microglia

value: 5-6 months-old


title: YM4


title: ileum_day 3 IR #1

description:
SAM24406843
B6 mice treated with 12 gy IR and take down at indicated timepoints

value: Intestine

value: 12gy IR

value: day 3


title: CD45-depleted TCR library for Donor 4

value: Thymus

value: TCR

value: Optiprep (Abott) density gradient + CD45 depletion by magnetic beads (STEMcell Technologies)


title: DD_RNAm_1284T1


title: APC enriched TCR library for Donor 4

value: Optiprep (Abott) density gradient


title: DD_RNAm_1284T2


title: fatbody_M_RNA2_rep1

value: fat body

value: medium (M), larval diet of 100% sugar-yeast-agar (SYA)

value: RNA 2 (RNA_2), after 60% of the members of the cohort had died

value: biological replicate 1


title: fatbody_M_RNA1_rep1

value: RNA 1 (RNA_1), after 10% of the members of the cohort had died


title: fatbody_M_RNA1_rep2

value: biological replicate 2


title: YM1

value: hippocampus


title: DD_RNAm_1283

value: breast tumor

value: K14-Cre, Trp53wm-R172H/fl and Rosa26LSL CAS9-P2A-EGFP/+


title: Unenriched TCR library for Donor 4

value: 1.6 months

value: Female


title: fatbody_H_RNA1_rep2

value: high (H), larval diet of 120% sugar-yeast-agar (SYA)


title: YF4

value: female

value: microglia

value: 5-6 months-old


title: ileum_day 0 IR #1

description:
SAM24406840
B6 mice without treatment

value: Intestine

value: No treatment

value: day 0


title: PBMC TCR library for Donor 3

value: Blood

value: 9 months

value: TCR

value: PBMC isolation by LymphoPrep (Abott)


title: YF3


title: DD_RNAm_1096


title: CD45-depleted TCR library for Donor 3

value: Thymus

value: Optiprep (Abott) density gradient + CD45 depletion by magnetic beads (STEMcell Technologies)


title: DD_RNAm_687

value: breast tumor

value: AAV-Control


title: APC enriched TCR library for Donor 3

value: Optiprep (Abott) density gradient


title: YF1

value: hippocampus


title: DD_RNAm_2041

value: K14-Cre, Trp53wm-R172H/fl and Rosa26LSL CAS9-P2A-EGFP/+


title: Mouse 3 LT-HSCs CD61 Low

city: Groningen

first: Leonid

last: Bystrykh

email: l.bystrykh@umcg.nl, l.bystrykh@rug.nl

address: Ant.Deusinglaan 1

department: ERIBA

country: Netherlands

institute: UMCG

data_processing:
fastq files checked with multiqc
mapping with STAR 2.7 to mouse M21 genome
tab files reads per gene (unstranded) used for differential expressionb analysis (DE)
edgeR package (Bioconductor) used for DE
Assembly: M.musculus gencode M21
Supplementary files format and content: row counts in .tsv and .tab files

source_name: LT-HSC

extract_protocol:
RNA isolation:  RNA isolation using RNeasy Plus Micro Kit (Quiagen) cDNA conversion was done using SMART-Seq v4 Ultra low input RNA kit for sequencing (TAKARA Bio, 4ng total RNA was used).
Library preparation: Kit used for library preparation: Nextera XT DNA Library Prep, preparation was performed according to the protocol. 1ng of amplified cDNA was used and the remaining volume was supplemented with EB buffer. A 0.6x bead cleanup was performed. Samples were eluted in 14μl EB. Tagmentation was used for primer attachment

treatment_protocol: Sample sorting: 22-24 month Old male mice were used for the isolation of the hematopoietic stem cells (LT-HSCs). The LT-HSCs were sorted for the following markers: Lin-, Sca1+, cKit+, CD48-, CD150+. Each pool of LT-HSC was divided on LT-HSCs CD61High and 3 samples CD61Low as follows: LT-HSC CD61High : top 10% of LT-HSC,  LT-HSC CD61Low : bottom 10% of LT-HSC population. In both cases 5,000 LT-HSC cells were sorted into 5uL of RLT Plus buffer.

value: LT-HSC

tag: strain

value: WT


title: Unenriched TCR library for Donor 3

value: Female


title: PBMC TCR library for Donor 2

value: 2.5 months

value: Male


title: DD_RNAm_1089


title: Mouse 2 LT-HSCs CD61 Low


title: infected_Cacnes42_mouse_scRNAseq

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
This study compared scRNA-seq data from 3 samples: 1- mice infected with C. acnes with plasmid ("Cacnes61"), 2 - mice infected with C. acnes without plasmid ("Cacnes42"), and 3 -  non-infection control  ("RCM"). Data for RCM and Cacnes 61 were previously uploaded to GEO at GSE193584 (O'Neill and Liggins et al, 2022 PMID: 35171653). Raw data for Cacnes42 and processed data comparing all 3 samples are uploaded here.
The 10X Genomics Cell Ranger version 3.0.1 software pipeline with default parameters was used to perform sample demultiplexing, barcode processing, alignment to the mm10 reference genome, and single-cell gene counting. Data were further filtered, processed and analyzed using the Seurat R toolkit version 3 (Butler et al, 2018 PMID: 29608179, Stuart et al, 2019 PMID: 31178118). Filtering of initial data involved selecting cells with > 100 features and < 10% mitochondrial genes. Data were normalized and scaled and variable genes identified using the function scTransform(). Principal components (PCs) were calculated from these variable genes using RunPCA() and the top 30 PCs were used for downstream analysis. Clusters were identified using FindNeighbors() then FindClusters() with argument resolution = 2.0. Nonlinear dimensionality reduction and visualization was performed with UMAP (Becht et al, 2019 PMID: 30531897) using the RunUMAP() function. Marker genes for each cluster were determined using FindAllMarkers() with parameters only.pos = TRUE, min.pct = 0.25, and thresh.use = 0.25. Clusters were assigned to cell types “Myeloid”, “Fibroblast”, “Lymphocyte”, “Keratinocyte”, “Endothelial”, “Melanocyte”, “Mast”, “Adipocyte”, and “Sm_Muscle” based on marker genes. 14 out of the original 53 clusters were annotated as fibroblasts and underwent additional quality control. In brief, a new Seurat object was generated using only the cells in these clusters with their corresponding raw counts, followed by normalization, scaling, clustering and dimensionality reduction as described above, resulting in 15 fibroblast clusters with FindClusters() resolution argument = 0.6. Clusters with high expression of leukocyte, keratinocyte, and adipocyte marker genes as well as cell cycle genes were excluded. A final Seurat object was created from the remaining cells and their raw counts with a final iteration of normalization, scaling, clustering and dimensionality reduction, resulting in 12 fibroblast clusters with FindClusters() resolution argument = 0.6.  Marker genes were identified on the three groups with FindAllMarkers() with parameter only.pos = TRUE and thresh.use = 0.25. Gene ontology analysis was performed on marker genes using Metascape (Tripathi et al 2015, PMID: 26651948).
Assembly: mm10
Supplementary files format and content: Comma-separated values files

source_name: skin

extract_protocol:
All animal experiments were approved by the University of California, San Diego (UCSD), Institutional Animal Care and Use Committee (#S09074). For single cell RNA-Seq analysis of mouse skin, the upper back skin of SKH-1 mice were intradermally infected with 1 x 107 CFU of C. acnes or RCM control for 3 days. Skin samples were collected from 6 mm punch biopsies and immediately placed on ice. In total, 3 biopsies were pooled per condition (infected or non-infected) for single cell generation. Single cell suspensions were generated by cutting skin into small pieces using a scalpel followed by digestion in Hanks Balanced Salt Solution (HBSS) (ThermoFisher, #14175095) supplemented with 20 mg/ml Bovine Serum Albumin (BSA), 1X Antibiotic-Antimycotic (ThermoFisher, #15240062), 50 U/ml DNAse I (Sigma, #04716728001), 0.1 mg/ml Liberase (Sigma, #05401020001), 20 mM HEPES (ThermoFisher, #15630080), 2 mM sodium pyruvate (ThermoFisher, #11360070) and 1 mg/ml Collagenase Type IV (ThermoFisher, 17104019). Tissue dissociation was carried out by a 2 h ice-cold incubation in the digestion buffer followed by 45 min incubation at 37°C shaking at 200 rpm. Enzymatic dissociation was terminated by addition of 5 mM EDTA and 10% Fetal Bovine Serum (FBS). Digests were filtered twice through a 40 μm filter, then incubated in red blood cell lysis buffer followed by removal of dead cell using MACS Dead Cell Removal Kit (Milteny Biotek) for downstream applications in 10X Genomics Chromium platform.
Single cell suspensions were loaded onto the 10X Genomics Chromium Controller instrument to generate single cell GEMs. GEM-RT and library construction were performed following the 10X Genomics Protocol.

value: skin

value: wild-type

value: intradermally infected with C acnes


title: CD45-depleted TCR library for Donor 2

value: TCR


title: bladder tissue (28 days after spinal cord injury) rep3

city: Beijing

first: Jimeng

last: Ruan

address: No. 45 Changchun Street, Xuanwu District

country: China

institute: Xuanwu Hospital Capital Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the rn6 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: bladder

extract_protocol:
Total RNA was extracted from bladder tissues using TRIzol and quantified using a spectrophotometer. Ribosomal RNA was depleted from total RNA using a RiboMinus kit. RNA-Seq was conducted using a HiSeq 4000 Sequencing System with a paired-end 150 bp.RNA-seq libraries were constructed using the Illumina TruSeq protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder

value: Wistar

value: post natal 10–12 weeks

tag: time

value: Day 28

value: suprasacral spinal cord injured


title: Testes,Srsf2cKO-2, P10 [RNA-seq]

first: Wenlong

last: Lei

state: 北京

address: 北京市朝阳区北辰西路1号院5号

institute: 中国科学院

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to mm9 using HISAT2
Differential expressed analysis were performed by DESeq2
Alternative splicing were identified by rMAST
Assembly: mm9
Supplementary files format and content: bigwig

source_name: testes

extract_protocol:
One Total RNA was extracted from whole testes using TRNzol Universal Reagent (cat. # DP424, Tiangen, China) according to the manufacturer’s instructions. The quality of RNA samples was examined by NanoDrop 2000&8000 and Agilent 2100 Bioanalyzer，Agilent RNA 6000 Nano Kit. The high-quality RNAs were used to prepare the libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Total testes samples were used from P10 Srsf2WT and Srsf2cKO male mice according to three individual collections.

value: testes

value: male


title: APC enriched TCR library for Donor 2

value: Thymus

value: Optiprep (Abott) density gradient


title: DD_RNAm_1142T3

value: breast tumor

value: K14-Cre, Trp53wm-R172H/fl and Rosa26LSL CAS9-P2A-EGFP/+


title: Mouse 1 LT-HSCs CD61 Low

value: LT-HSC

value: WT


title: YM2

source_name: hippocampus

value: hippocampus

value: microglia

value: 5-6 months-old


title: Mouse 2 LT-HSCs CD61 High


title: Mouse 3 LT-HSCs CD61 High


title: Unenriched TCR library for Donor 2

value: 2.5 months

value: Male

value: TCR


title: Testes,Srsf2WT-3, P10 [RNA-seq]

address: 北京市朝阳区北辰西路1号院5号


title: bladder tissue (28 days after spinal cord injury) rep2

value: bladder

value: Wistar

value: post natal 10–12 weeks


title: Testes,Srsf2WT-2, P10 [RNA-seq]

address: 北京市朝阳区北辰西路1号院5号

value: testes


title: PBMC TCR library for Donor 1

value: Blood

value: 7 days

value: PBMC isolation by LymphoPrep (Abott)


title: bladder tissue (14 days after spinal cord injury) rep3

value: Day 14

value: suprasacral spinal cord injured


title: middle-aged 3

data_processing:
RNA sequencing was performed utilizing the high output, paired-end reads with the Illumina HiSeq. 2500 System.
bcl2fastq Conversion software (v1.8.4)
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
Tibial and femoral SSPCs were isolated by centrifugation. Bone marrow was resuspended in growth media (GM) [DMEM containing 10% FBS and 1% penicillin/streptomycin;  and then plated in 150cm2 tissue- culture flasks. Media changed the following day and then every two days. All cellular assays were performed with SSPCs at passage one from at least three different mice and young and middle-aged SSPCs subjected to RNA-sequencing.
Libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: middle-aged

value: SSPC


title: Testes,Srsf2WT-1, P10 [RNA-seq]

address: 北京市朝阳区北辰西路1号院5号

value: male

value: WT


title: Testes,Srsf2cKO-3, P10 [RNA-seq]

address: 北京市朝阳区北辰西路1号院5号


title: bladder tissue (14 days after spinal cord injury) rep2


title: CD45-depleted TCR library for Donor 1

value: Thymus

value: Optiprep (Abott) density gradient + CD45 depletion by magnetic beads (STEMcell Technologies)


title: middle-aged 1


title: Liver high-fat diet ERRa KO biol rep 4

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

data_processing:
Raw data (raw reads) of FASTQ format were processed through fastp to remove reads containing adapter and poly-N  sequences and reads with low quality.
Paired-end clean reads were aligned to the  Mus musculus reference genome GRCm38/mm10 using the Spliced Transcripts Alignment to a Reference (STAR) software version 2.5 (mismatch = 2).
HTSeq version 0.6.1 (-m union) was used to count the read numbers mapped of each gene. Then, FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including the read count values for all 16 samples
Supplementary files format and content: tab-delimited text file including the fpkm values for all 16 samples

source_name: Liver

extract_protocol:
Total RNA was extracted from frozen liver using a RNeasy Mini Kit (QIAGEN).
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® UltraTM RNA  Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: WT and ERRa KO mice on a C57BL/6N genetic background fed either a chow or high-fat diet (HFD) for 15 weeks initiated from 6 weeks of age.

value: Liver

value: ERRa KO (Esrra KO)

value: 15-week high-fat diet


title: bladder tissue (14 days after spinal cord injury) rep1

value: bladder

value: Wistar

value: post natal 10–12 weeks


title: APC enriched TCR library for Donor 1

value: 7 days

value: Male

value: TCR

value: Optiprep (Abott) density gradient


title: Testes,Srsf2cKO-1, P10 [RNA-seq]

address: 北京市朝阳区北辰西路1号院5号

value: testes


title: bladder tissue (7 days after spinal cord injury) rep3

value: Day 7

value: suprasacral spinal cord injured


title: Unenriched TCR library for Donor 1


title: Liver high-fat diet ERRa KO biol rep 3

value: male


title: young 3

value: Bone marrow

value: young

value: SSPC


title: Liver high-fat diet ERRa KO biol rep 2

value: Liver


title: young 2


title: bladder tissue (28 days after spinal cord injury) rep1

value: Day 28


title: young 1


title: Liver high-fat diet ERRa KO biol rep 1

value: ERRa KO (Esrra KO)

value: 15-week high-fat diet


title: bladder tissue (7 days after spinal cord injury) rep1

value: bladder

value: Wistar


title: T30B_NP24_rep3

city: Poznań

first: Joanna

last: Wesoly

address: Uniwersytetu Poznańskiego 6

country: Poland

institute: Adam Mickiewicz University

data_processing:
Sequencing quality was verified using fastqc
Sequence reads were mapped to GRCh38 using STAR
Read counts were obtained with featureCounts and DGE was performed with DESeq2 package. Only significantly differentially expressed genes (DGE) (p-value < 0.01, -2<FC>2) were used for GO analysis
Assembly: hg38
Supplementary files format and content: csv file including raw counts  for each sample

growth_protocol: HEk293 cells were maintained in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using Trizol and Qiagen MinElute RNA kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries
The sequencing libraries were prepared with NEBNext Ultra RNA II Library Kit for Illumina (NewEngland Biolabs) following manufacturer's protocol

treatment_protocol: Cells were transfected with X-tremeGENE HP DNA Transfection Reagent (Roche) at a ratio of 1 μg plasmid per 2 μl X-tremeGENE HP DNA Transfection Reagent. Cells were harvested/observed under confocal microscope 24-48h after transfection

value: human kidney (embryonic)

tag: transfection


title: bladder tissue (7 days after spinal cord injury) rep2

value: post natal 10–12 weeks


title: T30B_NP5_rep1


title: T30B_NP17_rep2


title: bladder tissue (normal control) rep3

value: Day 0

value: normal control


title: Liver high-fat diet WT biol rep 4

value: WT

value: 15-week chow diet


title: ATAC-Seq middle-aged 2

data_processing:
ATACseq differential chromatin detection analysis was performed for three lanes of a paired-end 50 Illumina HiSeq. 2500 run
bcl2fastq Conversion software (v1.8.4)
Alignment, duplicate reads removal, generating genome browser tracks and calling peaks were all done by using the sns/atac pipeline (https://igordot.github.io/sns/routes/atac.html)
Assembly: mm10
Supplementary files format and content: normalized bigWig (rpkm), narrowPeak

extract_protocol:
Tibial and femoral SSPCs were isolated by centrifugation. Bone marrow was resuspended in growth media (GM) [DMEM containing 10% FBS and 1% penicillin/streptomycin;  and then plated in 150cm2 tissue- culture flasks. Media changed the following day and then every two days. All cellular assays were performed with SSPCs at passage one from at least three different mice and young and middle-aged SSPCs subjected to ATAC-sequencing.
Libraries were prepared for sequencing using standard Illumina protocols

value: middle-aged


title: Liver high-fat diet WT biol rep 3

value: male


title: ATAC-Seq middle-aged 3

value: Bone marrow


title: bladder tissue (normal control) rep2


title: Liver high-fat diet WT biol rep 2


title: ATAC-Seq middle-aged 1


title: T72_NP28_rep2


title: bladder tissue (normal control) rep1


title: middle-aged 2


title: Liver high-fat diet WT biol rep 1


title: ATAC-Seq young 3

value: young


title: ATAC-Seq young 2

value: SSPC


title: T116_NP26_rep3


title: salivary glands (E13.5),  300 ng/ml of BMP-2, rep3

city: Shinagawa

first: Atsushi

last: Yamada

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

country: Japan

institute: Showa University

data_processing:
DNBSEQ-G400  Zebra Call v2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v 2.9.
Trimmed sequence reads were mapped to GrCM39 using HISAT2 v2.2.0 .
Read count extraction and normalization were performed using featureCounts v2.6.0 .
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: salivary glands (E13.5)

extract_protocol:
RNA was harvested using the NucleoSpin RNA Plus XS kit.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module MGIEasy RNA Directional Library Prep Set v2.0.

value: salivary glands (E13.5)

value: wild type

value: 300 ng/ml of BMP-2


title: Liver chow diet ERRa KO biol rep 4

value: Liver

value: ERRa KO (Esrra KO)

value: 15-week high-fat diet


title: salivary glands (E13.5),  300 ng/ml of BMP-2, rep2


title: T116_NP16_rep2

value: human kidney (embryonic)


title: Liver chow diet ERRa KO biol rep 3


title: ATAC-Seq young 1


title: salivary glands (E13.5),  300 ng/ml of BMP-2, rep1


title: Testes,IgG-2, P10 [LACE-seq]

address: 北京市朝阳区北辰西路1号院5号

data_processing:
library strategy: linear amplification of complementary DNA ends and sequencing (LACE-seq)
The adapter sequences and poly(A) tails at the 3′ end of raw reads were removed using Cutadapt (v.1.15) with two parameters: -f fastq -q 30,0 -a ATCTCGTATGCCGTCTTCTGCTT -m 18 --max-n 0.25 --trim-n., and -f fastq -a A{15} -m 18 -n 2.
Clean reads were first aligned to mouse pre-rRNA using Bowtie, and the remaining unmapped reads were then aligned to the mouse (mm9) reference genome.
For LACE-seq data mapping, two mismatches were allowed (Bowtie parameters: -v 2 -m 10 --best -strata; -v 2 -k 10 --best -strata).
Peaks were identified by Piranha with parameters: -s -b 20 -p 0.01. peaks without IgG signal were selected for further usage.
For motif analysis, LACE-seq peaks/clusters were first extended 30 nt to 5′ upstream, and overrepresented hexamers in the extended sequences were identified . The consensus motifs were generated from the top-10 enriched hexamers using WebLogo.
Assembly: mm9
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Testes were resuspended in PBS and manually picked under a microscope using needles.
The LACE-seq library was single-end sequenced using Illumina HiSeq 2500 at Novogene. The step-by-step protocol for LACE-seq is provided at Nature Protocol Exchange.

value: testes


title: T116_NP7_rep1


title: Liver chow diet ERRa KO biol rep 2


title: salivary glands  (E13.5),  0 ng/ml of BMP-2,  rep3

value: 0 ng/ml of BMP-2


title: Testes,IgG-1, P10 [LACE-seq]

address: 北京市朝阳区北辰西路1号院5号


title: Liver chow diet ERRa KO biol rep 1


title: T207_NP12_rep2


title: salivary glands (E13.5),  0 ng/ml of BMP-2, rep2


title: Testes,Srsf2-2, P10 [LACE-seq]

address: 北京市朝阳区北辰西路1号院5号


title: salivary glands (E13.5),  0 ng/ml of BMP-2, rep1


title: Liver chow diet WT biol rep 4


title: T72_NP13_rep1


title: T207_NP3_rep1


title: Testes,Srsf2-1, P10 [LACE-seq]

address: 北京市朝阳区北辰西路1号院5号


title: Liver chow diet WT biol rep 3


title: T213_NP25_rep2


title: Liver endothelial cells at embryonic stage

city: Kanazawa

first: Tomohiro

last: Iba

state: Ishikawa

address: 13-1, Takara-machi

institute: Kanazawa University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Seurat (v4.1.1) for downstream single cell analysis.
Assembly: mm10
Supplementary files format and content: Matrix files

source_name: liver

extract_protocol:
Fluorescence-activated cell sorting (FACS)-purified liver ECs were processed using the Chromium Single Cell 3’ Kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the standard protocol.
Chromium Single Cell 3’ Kit v3.1 (10X Genomics, Pleasanton, CA)

value: liver

tag: developmental stage

value: Embryonic

value: Endothelial cells


title: T213_NP18_rep1


title: Liver chow diet WT biol rep 1

value: WT

value: 15-week chow diet


title: Liver chow diet WT biol rep 2

value: male


title: FGF2  48h replicate2

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt -1.9.1
Reads were aligned and quantified using RSEM-1.3.0/STAR-2.5.2
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited file containing matrix table with raw gene counts for every gene and every sample

source_name: Embryonic stem cells

growth_protocol: mES cells were grown in 2iLIF media

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Mini Kit as per manufacturer's instructions
Libraries were constructed using a KAPA mRNA HyperPrep Kit.

treatment_protocol: mES cells were stimulated with NB27+100ng/ml FGF2 for 24hrs or 48hrs

value: R1 mouse embryonic stem cells

tag: treatment length


title: SP_H3.R1

city: 上海

first: Zishuo

last: Fang

state: 上海

address: 沪城环路999号

institute: Shanghai Ocean University

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
The reads were reassembled using StringTie. Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile. SNP and INDEL were called using samtools and bcftools, and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates and predicts the effects of variants on genes (such as amino acid changes).
Assembly: mm10
Supplementary files format and content: tab-delimited text files inculde RPKM values for each Sample

organism: Micropterus salmoides

source_name: whole body

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

value: whole body


title: FGF2  48h replicate3


title: SP_H2.R1


title: FGF2 48h replicate1


title: Fbxw7_LKO_Liver_ERRa_ChIP

library_source: genomic

data_processing:
ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic v0.36.
Paired-end cleaned reads were mapped to the mouse reference genome (mm10) using BWA-MEM v0.7.12 with default parameters.
Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1.
Peaks were called using MACS2 software suite v2.1.1.20160309 at an an FDR alpha < 0.05 followed by subsequent filtering to FDR < 0.001 using sequenced libraries of input DNA as control. Peaks in mitochondrial chromosome and scaffold regions were removed.
Peak annotations were performed using the annotatePeaks.pl command from HOMER software suite v4.11.1.
Assembly: mm10
Supplementary files format and content: bigwig (.bw) files for each sample
Supplementary files format and content: tab-delimited text files of annotated ERRa peaks for both flox and Fbxw7 LKO 24h-fasted mice using respective inputs as controls

molecule: genomic DNA

extract_protocol:
Livers were crosslinked with 1% formaldehyde for 12 minutes followed by sonication (200-500 bp enrichment). Each ChIP-seq sample consisted of a pool of three independent ChIP samples each prepared using 2 mouse livers.
ChIP DNA libraries were prepared using the NEB Ultra II DNA library preparation kit according to Illumina recommendations.

treatment_protocol: Flox and liver-specific Fbxw7 KO (Fbxw7 LKO) on a C57BL/6J background were fasted 24h prior to liver isolation.

value: Fbxw7 liver-specific KO (LKO)

value: Fasted 24h

tag: chip antibody

value: ERRa (Abcam, Cat# ab76228)


title: FGF2 24h replicate3


title: T207_NP29_rep3

tag: cell line


title: pcDNA_NP1_rep1

value: pcDNA


title: Fbxw7_LKO_Liver_input

value: Liver


title: pcDNA_NP21_rep3


title: pcDNA_NP19_rep2


title: SP_L2.R1


title: flox_Liver_ERRa_ChIP

value: floxed Fbxw7 (WT)


title: SP_H1.R1


title: cont_NP30_rep2

value: human kidney (embryonic)


title: flox_Liver_input


title: SP_L1.R1


title: NME6_KO_rep1

status: Public on Aug 17 2023

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

institute: Université de Sherbrooke

data_processing:
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of transcript abundance and processing levels (custom scripts available at https://github.com/churchmanlab)
Assembly: GRCh38
Supplementary files format and content: *_polyA_estimates.tsv: poly(A) tail length estimated by nanopolish
Supplementary files format and content: *_read_processing_status.txt: 5' and 3' ends processing status for each mitochondrial read
Library strategy: Direct RNA nanopore sequencing

extract_protocol:
total RNA Trizol extraction
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)

value: NME6 sgRNA


title: PREPL_KO_rep1

value: PREPL sgRNA


title: NT_rep2

value: non-targeting sgRNA


title: SP_L3.R1


title: Sp_3dpf_2_scRNAseq

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

country: Italy

institute: Stazione Zoologica Anton Dohrn

data_processing:
Fastq reads were aligned to S. purpuratus genome version 3.1 using Cell Ranger 3.0.2 (10x Genomics).
Cell Ranger output files for all the replicates were used in Seurat v3.0.2 R package.
Genes transcribed in less than three cells and cells with less than 200 transcribed genes were excluded.
Datasets were normalized and variable genes were found using vst method with maximum 2000 variable features.
Data was integration was performded using anchors between the six different objects.
Data was scaled and principal component (PCA) analysis was performed. Sharing Nearest Neighbor (SNN) was computed with 20 dimensions (resolution 1.0). UMAP was used to perform clustering dimensionality reduction..
Cluster markers were found using the genes that are detected in at least 0.01 fraction of min.pct cells in the two clusters.
Subclustering analysis was performed by selecting a cell type family of interest and performing similar analysis as described above
Assembly: S. purpuratus genome 3.1
Supplementary files format and content: R Seurat object

organism: Strongylocentrotus purpuratus

source_name: dissociated 3dpf pluteus larvae

growth_protocol: AdultStrongylocentrotus purpuratus were kept in circulating seawater aquaria at Stazione Zoologica Anton Dohrn in Naples. Spawning was induced by vigorous shaking of adult animals. Embryos and larvae were cultured at 15 °C in filtered Mediterranean Sea water diluted 9:1 with deionized water.

extract_protocol:
Larvae were collected using a 40 μm Nitex mesh filter and spun down at 500 g for 5 min. Sea water was removed and larvae were resuspended in Ca2+ Mg2+-free artificial sea water, then spun down at 500 g for 5 min and resuspended in dissociation buffer (1 M glycine and 0.02 M EDTA in Ca2+ Mg2+-free artificial sea water). Larvae were incubated for 10 min on ice and dissociated gently via pipette aspiration every 2 min. Dissociated cells were spun down at 700 g for 5 min and washed several times with Ca2+ Mg2+-free artificial sea water.
Single cell cDNA libraries were prepared using the Chromium Single Cell 3’ Reagent Kit, Chemistry v2 and v3.
Libraries were indexed, multiplexed and sequenced on Illumina NextSeq 500 to generate paired end reads.

value: 3dpf pluteus cells

value: 3dpf pluteus larva

tag: sample type

value: single cell RNA-seq


title: Sp_3dpf_1_scRNAseq


title: Sp_3dpf_1a_scRNAseq


title: FGF2 24h replicate2


title: PREPL_KO_rep2


title: NME6_KO_rep2


title: NeuroD1ST_H3K4me3

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

data_processing:
library strategy: CUT&Tag
Sequencing data were mapped using bowtie2 (version 2.2.5) to mouse genome GRCm38 primary assembly. PCR duplicates were not removed.
Reads were filtered for those with quality mapping higher than 2 with samtools (version 1.3.1).
Only fragments with mapped pairs on the same chromosome and fragment length lower than 1000 bp were kept.
Peaks were called with SEACR 1.3. using stringent mode and edevelopmental stage relevant IgG control sample as background.
Assembly: GRCm38.p6 (Ensembl)
Supplementary files format and content: bigWig files generated from bam files using bamCoverage from deeptools (version 3.5.1), CPM (counts per milion) normalized.

source_name: Pancreas

growth_protocol: Cre/loxP system was used to delete Neurod1 from embryonic (E15.5) pancreatic cells with active Neurod1 promoter. TdTomato was used as Cre-activity reporter in this model.

extract_protocol:
The pancreata microdissected from E15.5 embryos were directly trypsinized and prepared for FACS. Briefly, tissue was dissociated using 0.05% trypsin/0.53 mM EDTA at 37°C for 5 min. Digestion was stopped by adding the FACS buffer (2% FBS and 10 mM EGTA in PBS), and cells were then 1x washed by FACS buffer. Finally, cell suspensions were filtered through 40 μm nylon mesh and immediately tdTomato+ cells were sorted using a flow cytometer (BD FACSAriaTM Fusion), through a 100 μm nozzle in 20 psi, operated with BD FACSDiva™ Software. Freshly FACS-sorted tdTomato+ pancreatic endocrine cells were captured by Concanavalin A-coated magnetic beads to facilitate subsequent washing steps. Spike-in (SNAP-CUTANA™ K-MetStat Panel, EpiCypher, 19-1002) was added to the immobilized nuclei in dilution 1:250.  CUT&Tag validated primary antibodies anti-H3K4me3, anti-H3K27me3, normal rabbit IgG negative control, and anti-rabbit secondary antibody were used. Binding of pAG-Tn5 (EpiCypher,15-1017, 2.5μL/reaction) was at RT for 60 min followed by tagmentation. To stop tagmentation and solubilize DNA fragments, 1.67 μL 0.5M EDTA, 0.5 μL 10% SDS and 0.42 μL 20 mg/mL Proteinase K (20mg/mL) was added to each sample. Samples were incubated for 1 hr at 55°C to digest (and reverse cross-links), followed by DNA precipitation and purification. DNA was dissolved in 22 μL of 1 mM Tris-HCl pH 8, 0.1 mM EDTA buffer and utilized as template for library generation with Universal i5 Primer and Uniquely Barcoded i7 Primers for Illumina.
21 μL DNA + 2 μL of 10 μM Universal or barcoded i5 primer + 2 μL of 10 μM uniquely barcoded i7 primer (using a different barcode for each sample) and 25 μL non-hot start CUTANA® High Fidelity 2x PCR Master Mix (EpiCypher, 15-1017) was added to each thin-wall 0.2 ml PCR tube. Library was amplified under CUT&Tag-specific PCR cycling parameters: a)5 min at 58°C; b) 5 min at 72°C; c) 45 sec at 98°C; d) 15 sec at 98°C; e) 10 sec at 60°C; f) 1 min 72°C. Steps "d-e" were repeated 25-27 times. DNA cleanup was performed using 1.3x AMPure beads (Beckman Coulter, A63880). Each purified DNA library for Illumina sequencing was tested on Agilent High Sensitivity DNA Chip. MiSeqReagent Kit v3 (150-cycle) was used for sequencing.

tag: tissue

value: Pancreas

value: endocrine cells

tag: cut&tag-validated antibody


title: NeuroD1ST_H3K27me3

tag: cell type

tag: genotype


title: Sp_3dpf_4_scRNAseq


title: Dusp1(-/-) derived Macrophage replicate 2 LPS and dexamethasone Stimulated 4 hour

type: RNA

city: Birmingham

first: John

middle: Daniel

last: O'Neil

address: Queen Elizabeth Hospital

department: Immunity and Infection

institute: University of Birmingham

description: hybridized onto SurePrint G3 Mouse GE 8x60K slides

scan_protocol: Scanned using a G2505C scanner (Agilent Technologies).

data_processing: Agilent Feature Extraction Software (10.7.3.1) using default parameters using the Cy3 colour only

source_name: Bone Marrow M-CSF dervied Macrophage

label_protocol: Total RNA was converted to labelled cRNA with Cy3 or Cy5 respectively using the Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technologies).

growth_protocol: Bone Marrow differentiated using 100ng/mL M-CSF for 5 days

extract_protocol: Total RNA was isolated using QIAGEN RNA isolation kit and ZYMO RNA concentrator kit following manufacturer's instructions

treatment_protocol: Cells were either left untreated or stimulated with 10ng/ml LPS for 1-4 hours, or 10ng/ml LPS plus 100nM dexamethasone for 4 hours, prior to RNA isolation.

tag: genotype/variation

value: Dusp1(-/-) derived macrophage

tag: treatment

value: Cells were stimulated with 10ng/mL LPS and 100nM dexamethasone for 4 hours prior to RNA isolation

tag: replicate


title: Sp_3dpf_3_scRNAseq


title: Dusp1(-/-) x Zfp36aa/aa derived Macrophage replicate 2 LPS and dexamethasone Stimulated 4 hour

hyb_protocol: hybridized onto SurePrint G3 Mouse GE 8x60K slides

value: Dusp1(-/-) x Zfp36aa/aa derived macrophage


title: Wild Type derived Macrophage replicate 3 LPS and dexamethasone Stimulated 4 hour

value: wild type derived macrophage


title: Dusp1(-/-) x Zfp36aa/aa derived Macrophage replicate 1 LPS and dexamethasone Stimulated 4 hour


title: Sp_3dpf_2b_scRNAseq


title: Dusp1(-/-) derived Macrophage replicate 3 LPS and dexamethasone Stimulated 4 hour


title: Control_H3K27me3


title: Wild Type derived Macrophage replicate 1 LPS and dexamethasone Stimulated 4 hour


title: FGF2 24h replicate1

value: R1 mouse embryonic stem cells


title: Dusp1(-/-) x Zfp36aa/aa derived Macrophage replicate 3 LPS and dexamethasone Stimulated 4 hour


title: Wild Type derived Macrophage replicate 2 LPS and dexamethasone Stimulated 4 hour


title: IgG_control

value: Neurod1loxP/+; Neurod1Cre/+; TdTomatoloxP/+ & Neurod1loxP/loxP; Neurod1Cre/+; TdTomatoloxP/+

value: IgG


title: RNA-seq_hES_rep2_re-analyzed

city: Worcester

first: René

last: Maehr

state: MA

address: 368 Plantation St

department: Program in Molecular Medicine/Diabetes Center of Excellence

institute: UMass Medical School

data_processing:
Base calling: fastq files were obtained from Illumina Basespace under default parameters.
Alignment and quantification: The samples were aligned and counts were obtained using the encode pipeline https://github.com/ENCODE-DCC/rna-seq-pipeline/tree/1.2.3
Differential expression analysis: Pairwise differential expression was performed with default parameters in Deseq2. This an other downstream analyses for the manuscript were performed in R/python as described in the methods of the manuscript
Assembly: hg38
Supplementary files format and content: tab-delimited text files per sample with RSEM transcipt quantification containing TPM, FPKM counts

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen, 15596-018) according to the manufacturer’s instructions. For quantitative PCR analysis, 1 μg of total RNA was reverse-transcribed using SuperScript III First-Strand Synthesis System (Thermo, 18080051).
Bulk RNA-sequencing library preparation was performed following a published protocol {Zhang:2012kc}. Briefly, 4 μg of total RNA was depleted of ribosomal RNA using Ribo-Zero rRNA Removal Kit (Epicentre, MRZH116) and then converted to cDNA. Final sequencing libraries were generated using dUTP (Thermo, R0133) incorporation and uracil-N-glycosylase (NEB, M0280) treatment to generate strand-specific RNA-seq libraries. The final libraries were sequenced at paired-end on a Hi-Seq2000 platform.

value: hESC


title: RNA-seq_hDE_rep2_re-analyzed

value: hDE


title: cont_NP20_rep1

value: human kidney (embryonic)


title: RNA-seq_hES_rep1_re-analyzed


title: RNA-seq_hPFE_rep2

value: hPFE


title: hAFE_Input

data_processing:
Base calling: fastq files were obtained from Illumina Basespace under default parameters.
Alignment, Peak-calling and signal generation: Samples were aligned, peaks were called and the bigwig files were generated using the pipeline from https://github.com/ENCODE-DCC/chip-seq-pipeline2/tree/v1.6.1
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak files from the encode pipeline for each sample (except for Input sample)

extract_protocol:
Approximately 3-5 million cells were used for each histone ChIPseq experiment. Cells were cross-linked with 1% formaldehyde for 10 minutes, followed by quenching with 125mM glycine for 4-5 minutes and washed for twice with PBS. The cell pellet was lysed in cell lysis buffer (20mM Tris-HCl, pH8, 85mM KCl, 0.5% NP-40) supplemented with 1x protease inhibitor cocktail (Roche, 11836170001) on ice for 20 minutes then pelleted at 5000rpm for 10 minutes. The pellet was resuspended in sonication buffer (10mM Tris pH7.5, 1% NP-40, 0.5% sodium deoxycholate and 0.1% SDS) with 1x protease inhibitor cocktail and incubated for 10 minutes at 4oC. In order to achieve 200-700nt DNA fragmentation range, nuclei were sonicated (Bronson sonifier model 250 with the following conditions: Amplitude = 15%, Time interval = 3 min (total of 8-12min) and pulse ON/OFF = 0.7sec/1.3sec). Chromatin was pre-cleared with Dynabeads Protein A (Invitrogen, 10002D) for 1 hour and incubated with antibody overnight at 4C. On the following day, 30-40ul of Dynabeads Protein A were added to the chromatin and antibody mix for 2-3 hours and then the captured immuno-complexes were washed as follows – 1x low-salt buffer, 1x High-salt buffer, 1x LiCl salt buffer and 1x TE. And the washed immuno-complexes were eluted in ChIP-DNA elution buffer (10mM TriHcl pH8, 100mM NaCl, 20mM EDTA and 1% SDS) for 20 minutes, reverse cross-linked overnight at 65C, followed by proteinase K treatment (Invitrogen, 25530-049), RNase A (Thermo Fischer Scientific, ENO531) treatment and Phenol:Chloroform:isoamyl alcohol extraction.
The illumina library construction steps were carried out with 5-10ng of purified ChIP’ed DNA. During the library construction, PCR purification was performed after every step using Qiagen kit (QIAquick PCR purification 28104 or QIAquick gel extraction 28706). The library reaction steps with ChIP’ed DNA as follows: 1.) End-repair - T4 PNK (NEB, M0201L), Klenow fragment (NEB, M0210S), T4 DNA Polymerase (NEB, M0203L) and dNTP mix (Thermo Fischer Scientific, 18427013) incubated at RT for 45min, 2.) 3’ end A-base addition - 3’ -> 5’ exo- Klenow fragment (NEB, M0212L) and dATP (NEB, N0440S) incubated at 37oC for 30min, 3.) Adapter ligation - T4 DNA ligase (NEB, M0202M) and illumina adapters incubated at 16C overnight and 4.) PCR amplification - 2x PfU Ultra Hotstart master mix (Agilent, 600850-51) for 10-14 cycles. The amplified libraries were size selected for 200-450nt on 2% Agarose E-gel (Thermo Fischer Scientific, G402002).

value: hAFE


title: Zfp36aa/aa  derived Macrophage replicate 1 LPS and dexamethasone Stimulated 4 hour

value: Zfp36 mutant (aa/aa) macrophage


title: NT_rep1

value: non-targeting sgRNA


title: hES_H3K27ac_rep1_re-analyzed


title: hES_H3K4me2_rep1


title: Mouse 1  LT-HSCs CD61 High

data_processing:
fastq files checked with multiqc
mapping with STAR 2.7 to mouse M21 genome
tab files reads per gene (unstranded) used for differential expressionb analysis (DE)
edgeR package (Bioconductor) used for DE
Assembly: M.musculus gencode M21
Supplementary files format and content: row counts in .tsv and .tab files

extract_protocol:
RNA isolation:  RNA isolation using RNeasy Plus Micro Kit (Quiagen) cDNA conversion was done using SMART-Seq v4 Ultra low input RNA kit for sequencing (TAKARA Bio, 4ng total RNA was used).
Library preparation: Kit used for library preparation: Nextera XT DNA Library Prep, preparation was performed according to the protocol. 1ng of amplified cDNA was used and the remaining volume was supplemented with EB buffer. A 0.6x bead cleanup was performed. Samples were eluted in 14μl EB. Tagmentation was used for primer attachment

value: LT-HSC

value: WT


title: Zfp36aa/aa  derived Macrophage replicate 3 LPS and dexamethasone Stimulated 4 hour


title: NME6KO_RNAseq_Rep2

city: Boston

first: Nicholas

middle: J

last: Kramer

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Data were processed to generate synthesis (TPMs for ribosome footprints) or RNA abundance (TPMs for total RNA-seq) according to the pipeline: https://github.com/churchmanlab/human-mitoribosome-profiling
Assembly: hg38
Supplementary files format and content: TPMs for mitoribosome footprints and total RNA

extract_protocol:
Cells were lysed in extraction buffers for mitoribosome profiling or total RNA-seq according to PMID: 35945592
Ribosome footprints were isolated after RNAseI digestion and ultracentrifugation (PMID: 35945592). Total RNA or purified ribosome footprints were prepared for sequencing according to library prep protocols in PMID: 35945592

value: NME6 KO


title: Zfp36aa/aa  derived Macrophage replicate 2 LPS and dexamethasone Stimulated 4 hour


title: NME6KO_MitoRP_Rep1

data_processing:
Data were processed to generate synthesis (TPMs for ribosome footprints) or RNA abundance (TPMs for total RNA-seq) according to the pipeline: https://github.com/churchmanlab/human-mitoribosome-profiling
Assembly: hg38
Supplementary files format and content: TPMs for mitoribosome footprints and total RNA
Library strategy: Ribo-seq


title: WT_RNAseq_Rep1

value: control non-targeting sgRNA


title: Control_H3K4me3

value: Pancreas

value: endocrine cells


title: HTO_Hashtag_R342_DMSO, scRNAseq

city: MARSEILLE

first: MADACI

last: LAMIA

address: Parc Scientifique de Luminy case 928 163, avenue de Luminy

country: France

institute: INSERM/TAGC

description: UPN73-78_DMSO, scRNAseq

library_source: other

data_processing:
The preparation of libraries for sequencing is performed using the NextSeq 500/550 high Output v2 kit protocol (75 cycles, Illumina) . Libraries are denatured in NaOH and mixed in the HT1 buffer (Illumina) to be loaded on the flow cell at 1.8 pM. The libraries are sequenced on a NextSeq 500 with the following parameters: 28 cycles for Read 1, 8 cycles for Index i7 and 91 cycles for Read 2.
Data processing, alignment, gene quantification and QA/QC: The sequencing data was analyzed using the Cell Ranger Pipeline (version 6.0.2) to perform quality control, the mkfastq to sample demultiplexing, barcode processing, alignment and single cell 3’ gene counting was performed using the cellranger count. Samples were demultiplexed with bcl2fastq based on the 8-bq sample index, 10-bp UMI tags, and the 16-bp GemCode barcode. The 55-bp-long read 2 containing cDNA sequence was aligned using cell Ranger version 3.0.0 and 3.1.0.
Normalization and correlation of gene expression levels : Each sample was normalized separately using "log-normalization" of the Seurat object. To analyze the correlation between the different samples, a first Seurat filter was applied to keep the genes detected in at least 3 cells and to keep the cells that have at least 200 UMI
PCA and tSNE analysis for cell clustering and classification, and data visualization:  The Cell Ranger count and aggr pipelines were used to run secondary analysis. Before clustering the cells, Principal Component Analysis (PCA) was run on the normalized, log-transformed, centered, and scaled gene-barcodes matrix to reduce the number of feature (gene) dimensions. After running PCA, t-distributed Stochastic Neighbor Embedding (t-SNE) was run to visualize cells in 2-D space. Clustering is then run to group cells together that have similar expression profiles, based on their projection into PCA space. Two clustering methods were performed: graph-based and k-means.  For multiplexed samples, HTO data are processed using the “cite-seq count, v1.4.3” tool ( https://hoohm.github.io/CITE-seq-Count/ & https://zenodo.org/record/2590196). The results are read using the Seurat "Read10X" tool (https://satijalab.org/seurat/articles/hashing_vignette.html ). Only common cell barcodes from the HTO (from cite-seq count) and mRNA (from cellranger) data are retained. These barcodes represent the cells detected by cellranger and for which an HTO was assigned. Finally, the HTO arrays are normalized using the Log-Ratio Centered (CLR) method.
Assembly: GRCh38-2020-A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: peripheral blood

extract_protocol:
Human Peripheral Blood Mononuclear Cells (PBMCs) used in this study are obtained after consent from AML patients. PBMCs were isolated from peripheral blood after centrifugation to separate them from plasma and other peripheral blood components using ficoll-Hystopaque density gradient centrifugation. After the separation of PBMCs from whole blood, the cells were preserved using : Cryopreservation that consists of freezing the cells at -80°C or in liquid nitrogen at -195.79°C for a long period using freezing medium (90% FBS and 10% DMSO), the second method to preserve the cell is the cell fixation using the pre-chiled methanol before storage at -80°C . . Cryopreserved cells in liquid nitrogen were thawed at 37°C. Cells were rinsed with RPMI 1640 medium to remove the DMSO-containing freezing medium. To enrich the samples with live cells, dead cells were removed using the Dead Cell Removal Kit. Before starting cell labeling, a 50-μL aliquot containing 1,000,000 cells suspended in a Cell Staining Buffer (CSB) with >95% viability was prepared for each sample. The antibodies used for labeling were TotalSeq -A0251(HTO1) and -A0252 (HTO2) antibody-oligo (Biolegend). Next, we proceeded to the labeling step. For this, 1μg HTO is added to each cell suspension. The two labeled samples are then incubated for 30 minutes at 4°C. The cells then undergo 3 successive washes with 3.5 mL of CSB and centrifugation at 400 g for 5 minutes at 5°C. Finally, the cells are resuspended at a concentration of 1.106 cells/mL in PBS. To rehydrate methanol-fixed PBMCs, the cells were thawed from -80°C to 4°C and incubated for 5 minutes. After incubation, the cells were centrifuged at 1000 g for 5 minutes, and the methanol was carefully removed. The resulting cell pellet was then resuspended in a rehydration buffer containing 3x SSC buffer, 0.04% BSA, 1mM DTT, and 0.2 U/µl RNase inhibitor. Finally, the cell concentration was determined by counting the cells using the LUNA FL cell counter. This rehydration process allows for the preparation of viable and well-dispersed PBMCs for downstream analyses.
Library was performed according to the manufacter’s instructions Chromium Next Gem Single Cell 3' Reagent Kits v3.1 with Feature Barcoding technology for Cell Surface Protein (for the cryoconserved cells), and and the user guide single cell 3’ v3 protocol, 10x Genomics (for fixed cells). Briefly, PBMCs labeled with/without HTOs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: disease state

value: acute myeloid leukemia (AML)

value: Peripheral Blood Mononuclear Cells

value: peripheral blood

tag: Sex

value: pooled male and female

tag: age

tag: library type

value: HTO

tag: antibodies/tags

value: B2M/TotalSeq A0251-A0252

value: DMSO cryopreservation


title: UPN78_R378_fixed 12 months, scRNAseq

description: UPN78_fixed 12 months, scRNAseq

value: male

value: mRNA

value: methanol fixation  for 12 months


title: mRNA_Hashtag_R342_DMSO, scRNAseq

description: UPN73-78_DMSO, scRNAseq


title: UPN73_R372_fixed 18 months, scRNAseq

description: UPN73_fixed 18 months, scRNAseq

value: methanol fixation  for 18 months


title: RNA-seq_hPFE_rep1

value: hPFE


title: Dusp1(-/-) derived Macrophage replicate 1 LPS and dexamethasone Stimulated 4 hour

tag: strain

value: Dusp1(-/-) derived macrophage

value: Cells were stimulated with 10ng/mL LPS and 100nM dexamethasone for 4 hours prior to RNA isolation


title: HeLa_WT_TASOR_CT_rep2

city: New York

first: Zhiguo

last: Zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.
Library strategy: CUT&TAG

source_name: HeLa

growth_protocol: Mouse E14 ES cells (a gift from Dr. Thomas Fazzio, University of Massachusetts Medical School, Worcester, MA) were cultured in DMEM (Corning) medium supplemented with 15% (vol/vol) fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen), 1 mM sodium pyruvate (Cellgro), 2 mM L-glutamine (Cellgro), 1% MEM non-essential amino acids (Invitrogen), 55 µM β-Mercaptoethanol (Sigma), 10 ng/mL mouse leukemia inhibitory factor (mLIF) on gelatin-coated dishes in a 37°C incubator with a humidified, 5% CO2 atmosphere. HeLa and HEK 293T cells were cultured in DMEM medium supplemented with 10% (vol/vol) FBS and 1% penicillin/streptomycin. Primary mouse B cells were isolated from the spleen of 1-month old wild-type C57BL6 mice. B cells were activated and cultured as in Tubbs, A. et al. (2018).

extract_protocol:
eSPAN in mESC, mouse B cells and HeLa  cells were performed exactly as previously described (Li et al., 2020).GRO-seq (global run-on sequencing) was performed as previous described (Barbieri, E. et al., 2020).
GRO-seq libraries were prepared and deep sequencing was performed by Columbia University Genome Center. For CUT&TAG, CUT&RUN and eSPAN libraries, the supernatants were purified with ChIP DNA concentrator columns and library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end sequencing on Illumina NextSeq 500 platforms at Columbia University Genome Center.

tag: experiments

value: WT

value: Anti-TASOR

tag: antibody vendor

value: GeneTex

tag: antibody catalog#


title: RNA-seq_hAFE_rep1

tag: cell line

value: hAFE


title: RNA-seq_hDE_rep1_re-analyzed

value: hDE


title: HeLa_WT_MPP8_CT_rep2

tag: chip antibody

value: Proteintech


title: RNA-seq_hAFE_rep2


title: HeLa_WT_MPP8_CT_rep1


title: hPFE_H3K4me2_rep1


title: HeLa_WT_MPP8_eSPAN_rep3

data_processing:
Raw reads were trimmed to remove sequencing adaptors and low-quality reads using Trim Galore (version 0.6.7) with default parameters.
Sequence reads were mapped back to the mouse reference genome (mm10) or human reference genome (hg19) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis. Sequence alignment map files including uniquely mapped and multi-mapped reads were transformed into BAM files using SAMtools. GRO-seq reads were mapped using STAR.
Coverage for each base pair of the mouse  or human genome was computed using genomeCoverageBed from BEDTools (version 2.29.2) and normalized to library size (reads-per-million; RPM).
The consistent paired-end reads mapped to the Watson (W) and Crick (C) strands of the reference genome were separated by BEDTools bamtobed function (Quinlan and Hall, 2010) and in-house Perl programs. The bias of each bin was computed from these separated Watson and Crick reads within 5kb window size using the formula Bias = (W−C)/(W+C) across the whole genome.
Read count on gene body or promoters were calculated by FeatureCount. Differential genes/TEs and log fold change were calculated by edgeR.
Assembly: mm10, hg19
Supplementary files format and content: bigwig files were generated using UCSC bedGraphToBigWig (version 359), scores (RPM) represent the normalization reads density. Read density (RPM) on plus strand, minus strand were also calculated seperately.
Library strategy: eSPAN


title: hPFE_H3K27ac_rep1


title: HeLa_WT_MPP8_eSPAN_rep2


title: hAFE_H3K27ac_rep1


title: hDE_H3K4me2_rep1


title: hDE_H3K27ac_rep1


title: Scr1_OffDiag_LowRight_T14

description: library transduced cells screen day14_COX1_COX4_PopD rep1

data_processing:
sgRNA abundance and enrichment analysis using both MAGeCK and casTLE software comparing sorted vs unsorted cells
Assembly: sgRNA library (see PubMed 28474669)
Supplementary files format and content: csv files of differential representation of sgRNAs collapsed to gene level
Library strategy: sgRNA barcode sequencing

extract_protocol:
Genomic DNA extraction using QIAamp DNA Blood Maxi Kit from methanol fixed, FACS sorted cells
PCR based library construction for Illumina sequencing

treatment_protocol: sgRNA library transduced K562-Cas9 cells, methanol fixed, and FACS stained for COX1 and COX4

value: Cas9 stable expression

value: genome-wide sgRNA library transduced

tag: cell population


title: Scr2_OffDiag_LowRight_T14

description: library transduced cells screen day14_COX1_COX4_PopD rep2


title: Scr2_OffDiag_UpLeft_T14

description: library transduced cells screen day14_COX1_COX4_PopC rep2


title: NME6KO_RNAseq_Rep1

value: NME6 KO


title: NME6KO_MitoRP_Rep2


title: HeLa_MPP8KD1_H3K9me3_eSPAN_rep2

value: Zhang Lab


title: Scr2_Unsorted_T10

description: library transduced cells screen day10_unsorted rep2


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Gelding - SUN_DANCER

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Horse_60K_2016_01_22 021322 GE 8x60K (AMID 081421) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 081421_D_F_20160126). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 6 out of 45 microarrays. At this step, 42126 spots out of 62976 were selected.  The mean signal of the 16 first samples and 29 last ones were subtracted to individuals signals to correct the batch effect of the 2 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 30265 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Equus caballus

source_name: Whole blood

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Venous blood (10 ml) was collected from 51 horses using EDTA tubes (BD Vacutainer®). In order to stabilized intracellular RNA, 0.8 ml of venous blood was transferred in a tube containing 0.8 ml of Lysis Buffer DL (Macherey-Nagel, Düren, Germany). After homogenization, the samples were maintained at -20°C until RNA extraction. Total RNA was extracted using the NucleoSpin® RNA Blood kit (Macherey-Nagel, Düren, Germany). The manufacturer’s protocol was modified to obtained sufficient ARN quantities for the Microarray gene expression analyses: extraction was carried out from 1.6 ml of the mix blood and Lysis Buffer DL. Twenty µl of proteinase K was then added to complete blood lysis. To adjust RNA binding conditions, 0.8 ml of 70% ethanol was added. The following steps were not modified, except the elution that was carried out with 40 µl of RNase free water. Total RNA quality was assessed using RNA Pico chips on a Bioanalyser 2100 (Agilent, Boeblingen, Germany) and and its concentration was measured on a Nano Drop One Spectrophotometer (ThermoScientific, Illkirch, France).

tag: alert

tag: welfare score

tag: horse type

value: Gelding

tag: animal

tag: washbatch


title: WT_RNAseq_Rep2

tag: genotype

value: control non-targeting sgRNA


title: Whole blood - Ag.0_Al.H_Ap.L_St.0 - Gelding - TAXUS_D_ENGANDOU


title: Whole blood - Ag.H_Al.0_Ap.0_St.0 - Gelding - ONIX_DU_HAMEAU

tag: agressiveness


title: hAFE_H3K4me2_rep1

tag: cell type


title: WT_MitoRP_Rep2


title: WT_MitoRP_Rep1


title: Whole blood - Ag.0_Al.0_Ap.L_St.0 - Gelding - VIF_DU_LOUVET

tag: unresponsiveness


title: HeLa_WT_TASOR_CT_rep1


title: UPN73_R378_fixed 18 months, scRNAseq

description: UPN73_fixed 18 months, scRNAseq

tag: disease state

value: acute myeloid leukemia (AML)

value: Peripheral Blood Mononuclear Cells

tag: tissue

value: peripheral blood

tag: Sex

value: male

tag: age

tag: library type

value: mRNA

tag: antibodies/tags

tag: treatment


title: HeLa_WT_TASOR_eSPAN_rep3

tag: experiments

value: WT

tag: chip antibody

tag: antibody vendor

tag: antibody catalog#


title: Whole blood - Ag.0_Al.0_Ap.H_St.H - Gelding - CRACK_DE_SISSE

tag: welfare score

tag: horse type

tag: animal


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Mare - CHAPKA_DE_LA_LIE

tag: alert

value: Mare

tag: washbatch


title: HeLa_TASORKD2_H3K9me3_eSPAN_rep2

tag: genotype

value: TASORKD


title: Scr1_T0

description: library transduced cells screen day0 rep1

tag: cell line

tag: cell population


title: Whole blood - Ag.0_Al.H_Ap.0_St.0 - Stallion - QLASSIK_SAINT_CLAIR

tag: unresponsiveness

value: Stallion


title: HeLa_TASORKD1_H3K9me3_eSPAN_rep2


title: HeLa_MPP8KD2_H3K9me3_eSPAN_rep2


title: HeLa_WT_TASOR_eSPAN_rep2

value: Anti-TASOR

value: GeneTex


title: Whole blood - Ag.L_Al.L_Ap.0_St.L - Gelding - RAMSES_DU_FIGUIER


title: Scr1_OffDiag_UpLeft_T14

description: library transduced cells screen day14_COX1_COX4_PopC rep1

value: Cas9 stable expression