title: mouse lineage-ckit+ cells, Dars2-KO, rep2

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

data_processing:
The sequence reads were aligned to GRCm38/M22 using STAR (v2.7.3a).
Uniquely mapped sequencing reads were assigned to Gencode M22 gene using featureCounts (v1.6.2)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include log2RPKM values for all Sample

source_name: Bone Marrow

extract_protocol:
Total RNA was isolated from WT control or Dars2-KO LK (Lineage-c-Kit+) cells using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme).
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then RNA was digested with RNase H. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. Each group was sequenced in replicates by Illumina NovaSeq 6000 with single end 150 bp read length.

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: Dars2 KO


title: BALF-MP-OM-CDH002

status: Public on Sep 25 2023

type: RNA

city: Paris

first: Nicolas

last: Huot

address: 28, rue du Dr Roux

country: France

institute: Institut Pasteur

hyb_protocol: Seventy microliters of hybridization buffer was added to the reporter code set to make a master mixture. 2,1µl of proteinase K were added. Eight microliters of this master mixture was then incubated in separate tubes with 5µl of the lysate's sample and 2 ul of the capture code set. This hybridization mixture was incubated at 65°C for 18 hours. The hybridization mixture bind to Cartridge with a NanoString Prepstation.

scan_protocol: The cartridgenCounter™ Analysis System allows then to collect image and count barcodes.

data_processing:
Raw counts were normalized to geometric mean counts of the synthetic positive controls included on the codeset. nCAAM and the geNorm algorithm was used to normalize each dataset by taking the five most stable housekeeping genes across samples and using it on all datasets.
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library.

molecule: total RNA

organism: Macaca fascicularis

source_name: Bronchoalveolar lavage fluids

label_protocol: The system uses molecular “barcodes” and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.

growth_protocol: Macrophages were isolated from BALF samples using a positive selection strategy. We employed the anti-CD64 PE-conjugated monoclonal antibody (clone 10.1, BD Bioscience, USA) for this purpose.To reveal the isolated macrophages, anti-PE microbeads from Miltenyi Biotec (USA) were utilized. These macrophages were cultured for 8h.

extract_protocol: After the incubation, the cells were resuspended in 30µl of RLT buffer with beta-mercaptoethanol (Qiagen) following the Nanostring protocols recommendation for cell Lysate (MAN-10051-05).

tag: cell type

value: CD64+ macrophages

tag: viral status

value: >221 days post infection with the Omicron BA.2 variant


title: mouse lineage-ckit+ cells, Dars2-KO, rep1

type: SRA

country: USA

library_source: transcriptomic

organism: Mus musculus

tag: tissue

tag: genotype


title: mouse lineage-ckit+ cells, Dars2-KO, rep3


title: Adult astrocytes (10-12 dpe)_biol rep1

city: Portland

first: Taylor

middle: Reagan

last: Jay

email: taylor.jay@case.edu, jayta@ohsu.edu

state: OR

address: 3181 Sam Jackson Park Rd.

department: Vollum Institute

institute: Oregon Health & Science University

library_source: other

data_processing:
Fastq files were assembled using bcl2fastq
Assembly: Drosophila melanogaster BDGP6 references genome
Supplementary files format and content: Gene read counts table with all samples compiled (.csv)
Library strategy: Ribosomal RNA depletion

molecule: other

organism: Drosophila melanogaster

source_name: RNA pulled down from tagged ribosomes in astrocytes

growth_protocol: Flies were maintained on standard corn agar food with molasses

extract_protocol:
For adult flies, heads were removed by freezing and vortexing the animals; for pupal samples, head tissue was obtained by cutting the anterior third of the pupae with a razor blade
TruSeq Stranded ribosomal reduction protocol

tag: sample type

value: mixed males and females, pooled from 200 fly heads

value: astrocytes

value: elav-Gal80, alrm-Gal4, UAS-EGFP-L10a

tag: age


title: HSCs, IRF1 KO, biol rep 3

city: Lund

first: Alexandra

last: Rundberg Nilsson

address: Klinikgatan 26

department: Experimental Hematology

country: Sweden

institute: Lund University

description:
NexteraXT
IRF1_KO_4

data_processing:
RNA Galaxy workbench 2.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!
Trimmed sequence reads were mapped to mm39.ncbiRefSeq using HISAT2
Read count extraction and normalization were performed using RNA Galaxy workbench
Assembly: mm39
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

source_name: Bone marrow

extract_protocol:
RNA was harvested using Single Cell RNA Purification Kit (Norgen Biotek Corp)
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc) following manufacturer's protocols.

tag: cell line

value: Bone marrow

value: hematopoietic stem cells

value: IRF1 KO

tag: treatment

value: untreated

tag: time

value: 8 weeks old


title: BALF-MP-WTM-CGC060

value: >221 days post infection with the wild type Wuhan strain


title: Adult astrocytes (10-12 dpe)_biol rep2

value: RNA pulled down from tagged ribosomes in astrocytes


title: BALF-MP-HC-2MK18

value: Healthy Control


title: Darier Patient 2, lesion skin biopsy

city: Lausanne

first: Emmanuella

last: Guenova-Hoetzenecker

state: Vaud

address: 49 rue Bugnon

department: Dermatology

country: Switzerland

institute: CHUV

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were subjected to demultiplexing and aligned to the human reference genome (refdata-gex-GRCh38-2020-A) using the cellranger count tool with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-separated files and matrix files.

organism: Homo sapiens

source_name: Skin

extract_protocol:
Slow-frozen skin biopsies were washed with RPMI 1640 medium (Gibco, 61870- 010), supplemented with 10% Gold FBS (PAA Laboratories, A15-151). The skin  biopsies were then minced and transferred in 1mL of Liberase (Roche,  5401119001, final concentration 0.5 mg/mL diluted with PBS without Ca and Mg)  to digest the tissues. The mixture was incubated for 1 hour at 37°C and the tube  was manually inverted every 15 minutes. Afterwards, 100 μl of 0.05% trypsin was added to the mixture and incubated at 37°C for additional 15 minutes. The tissue remnants were removed by using 70μm cell strainer. The cells were washed with  MACS buffer (PBS, 0.5% BSA and 2mM EDTA) and then stained with SYTOX Red  (ThermoFisher, S34859) and Hoechst 33342 (ThermoFisher, H3570) for cell  viability assessment. The stained cells were suspended in MACS buffer and single living cells (SYTOX Red-negative and Hoechst 33342-positive) were sorted by  FACS sorter (BD FACSAris-II SORP) at Flow Cytometry Facility of UNIL.  scRNA-seq processing
Single-cell mRNA capture and sequencing were performed immediately by the  Lausanne Genomic Technologies Facility (GTF) of UNIL using the Chromium Next  GEM Single Cell 5’ GEM kit (10x Genimics) following the manufacturer’s protocol.

value: Skin

tag: disease state

value: Darier disease

tag: individual

value: patient 2


title: mouse lineage-ckit+ cells, Dars2f/f, rep3

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: WT


title: DR2-3: Severe drought

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

country: China

institute: Shanxi Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data.
At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Index of the reference genome was built using hisat2-2.0.4 and paired-end clean reads were mapped to the reference genome. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads.
Stringtie-1.3.3b ）was used to count the read numbers mapped to each gene. And then FPKM was calculated, which expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced.
Supplementary files format and content: "lnc_transcripts.FPKM.txt" contains the FPKMs of each lncRNA
Supplementary files format and content: "lnc_transcripts.readcount.txt" contains the readcount of each lncRNA
Supplementary files format and content: "mRNA_gene.FPKM.txt" contains the FPKMs of each gene
Supplementary files format and content: "genes.readcount.txt" contains the readcount of each gene

organism: Sorghum bicolor

source_name: Leaves

extract_protocol:
According to the manufacturer’s protocol, the total RNA from all samples was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
A total of 1 μg total RNA per sample was used as input material for the lncRNA library preparation.
Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Leaves

value: Severe drought


title: DR2-2: Severe drought


title: mouse lineage-ckit+ cells, Dars2f/f, rep2


title: Adult astrocytes (1-3 dpe)_biol rep2

value: mixed males and females, pooled from 200 fly heads

value: astrocytes

value: elav-Gal80, alrm-Gal4, UAS-EGFP-L10a

value: 1-3 dpe


title: DR1-3: Mild drought

value: Mild drought


title: DR2-1: Severe drought


title: Adult astrocytes (1-3 dpe)_biol rep1


title: Pupal astrocytes (48-72hr APF)_biol rep5

value: 48-72hr APF


title: mouse lineage-ckit+ cells, Dars2f/f, rep1


title: ATF4_WT_rep4

city: Daegu

first: Jaemin

last: Lee

state: Select One

address: 333 Techno Jungang Daero, Hyeonpung-Myeon, Dalseong-Gun

department: New Biology

country: South Korea

institute: DGIST

data_processing:
Sequence reads are aligned to mm39 genome assembly using STAR (2.7.10a) --outFilterMultimapNmax 1 -- outSAMtype BAM Unsorted --outSAMattributes All --twopassMode Basic
Raw read counts are calculated by htseq-count(0.11.3) -m union -s no -a 0 -i gene_id -f bam
Assembly: mm39
Supplementary files format and content: raw read counts

source_name: pancreatic islet

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: pancreatic islet

value: 5 weeks old


title: DR1-2: Mild drought


title: ATF4_WT_rep3


title: DR1-1: Mild drought


title: Pupal astrocytes (48-72hr APF)_biol rep4

value: RNA pulled down from tagged ribosomes in astrocytes


title: ATF4_WT_rep2


title: CK-3: Normal water supply

value: Normal water supply


title: Pupal astrocytes (48-72hr APF)_biol rep3


title: Pupal astrocytes (48-72hr APF)_biol rep2


title: BALF-MP-OM-DF993

value: CD64+ macrophages

value: >221 days post infection with the Omicron BA.2 variant


title: CK-2: Normal water supply


title: ATF4_TG_rep4


title: ATF4_TG_rep3


title: ATF4_TG_rep2


title: CK-1: Normal water supply


title: Severe drought

data_processing: Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.

extract_protocol:
According to the manufacturer’s protocol, the total RNA from all samples was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: condition


title: Mild drought


title: old control gut cells  [OMC]

city: Kobe

first: Fumiaki

last: Obata

address: 2-2-3 Minatojima-minamimachi

country: Japan

institute: RIKEN BDR

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq2 (ver2.20)
Sequence data was processed using Cell Ranger 5.0.1
Assembly: Drosophila_melanogaster.BDGP6.28.dna.toplevel
Supplementary files format and content: Matrix table with raw UMI counts for every gene and every cell
Supplementary files format and content: List of cell barcodes
Supplementary files format and content: List of genes (features)

molecule: polyA RNA

source_name: old control gut cells

extract_protocol:
Guts of anesthetised adult female flies were dissected in PBS. Proventriculus and hind gut were carefully removed. The dissected midguts were placed in ice-cold Schneider’s medium (without FBS or penicillin/streptomycin). Collected midguts (100 midguts/sample) were washed briefly with PBS and transferred to a 1.5 mL eppendorf tube containing 5 mg/mL elastase/PBS solution (SIGMA, E0258). The midgut solution was incubated on a shaker at 27℃, 1,000 rpm for 25 min with pipetting (40 times) every five minutes. Pipette tips were pre-coated with the elastase solution to prevent midgut from sticking to them. The dissociation reaction was stopped by adding 400 μL of the Schneider’s medium. The cell suspension was passed through a 100 μm cell strainer. The flow through was centrifuged at 600 × g for 20 minutes and the supernatant was discarded. The cell pellet was resuspended in 100 μL of the Schneider’s medium. Cell number and viability were assessed by trypan blue staining using a hemocytometer. A single cell suspension was obtained by filtering with a 40 μm cell strainer.
Library preparation were performed with the Single Cell 3' Library & Gel Bead Kit v3.1 according to the 10X Genomics' standard protocol.

value: aged (5 weeks old)

tag: tissue/cell type

value: fruit fly midgut cells


title: old mehionine restricted gut cells  [OMR]

source_name: old mehionine restricted gut cells


title: Adult astrocytes (1-3 dpe)_biol rep3


title: Pupal astrocytes (48-72hr APF)_biol rep1


title: Well-watered

description: CK

value: Well-watered


title: RA-6

status: Public on Sep 24 2023

city: Hefei

first: Xiaoke

last: Yang

state: Anhui

address: 218 Jixi Road

department: Department of Rheumatology and Immunology

institute: The First Affiliated Hospital of Anhui Medical University

data_processing:
DESeq2(v1.36.0) software
Differential expression analysis of miRNA was performed using the DESeq2 [parameters-Q value≤ 0.05 (or FDR value≤0.001)].
The data were presented as the relative level of target miRNA expression normalized to U6.
Supplementary files format and content: excel files of miRNA expression for each Sample

source_name: plasma exosome

extract_protocol:
Ultra-centrifugation was conducted to isolate exosomes from the plasma samples，RNA in exosome was harvested using an miRNAeasy Plasma Kit (Qiagen, Germany) following manufacturer's protocols.
Library sequencing was performed with the BGISEQ-500 platform.

value: plasma exosome

value: active


title: RS-6

value: stable


title: young control gut cells [YMC]

source_name: young control gut cells

value: young (day5)


title: RS-1


title: RS-4


title: RA-4


title: ATF4_WT_rep1


title: ATF4_TG_rep1


title: RA-1


title: STXA2 60h 2

city: Sevilla

first: Manuel Jesús

last: Mallén-Ponce

state: Sevilla

address: Americo Vespucio 49

department: IBVF

country: Spain

institute: CSIC-US

data_processing:
Reads were aligned against the NCBI genome sequence for Synechocystis (NC_000911.1, NC_005229.1, NC_005230.1, NC_005231.1, and NC_005232.1) using Bowtie2
Transcript assembly and estimation of gene expression was performed using Stringtie
Assembly: Synechocystis sp. PCC 6803 (NC_000911.1, NC_005229.1, NC_005230.1, NC_005231.1 and NC_005232.1)
Supplementary files format and content: tab-delimited includes raw counts for each sample

organism: Synechocystis sp. PCC 6803

source_name: Bacteria

growth_protocol: Cells were collected before and after being  treated with arsenite

extract_protocol:
Cells were collected by centrifugation and total RNA was extracted by phenol-chloroform method. RNA samples were further purified by RNeasy MinElute Cleanup Kit (Cat No./ID: 74204).
Library construction of cDNA molecules was carried out using Illumina Kapa Stranded Total RNA with Ribo-Zero Library Preparation Kit

value: Bacteria

value: STXA2 after re-addition of arsenite (60h)


title: STXA2 48h 1

value: STXA2 after arsenite removal (48h)


title: STXA2 0h 3

value: STXA2 in the presence of arsenite (0h)


title: STXA2 48h 2


title: STXA2 72h 3

value: STXA2 after re-addition of arsenite (72h)


title: STXA2 60h 1


title: STXA2 72h 1


title: STXA2 60h 3


title: STXA2 48h 3


title: STXA2 24h 1

value: STXA2 after arsenite removal (24h)


title: STXA2 72h 2


title: STXA2 24h 2


title: STXA2 24h 3


title: STXA2 0h 2


title: WT 0h 2

value: WT

value: WT in the presence of arsenite


title: STXA2 0h 1


title: WT 0h 1


title: PAECs, hypoxia condition, rep2

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on  [MTA-1_0] Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

source_name: PAECs, hypoxia condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Cell growth was arrested by incubating in 2% serum and GS-free ECM for 6 h under normoxia, then growth-arrested cells were incubated with low-serum (5% FBS) and GS-free ECM under normoxia or hypoxia for 24 h.

extract_protocol: cDNAs of samples from normoxia and hypoxia group were hybridized to Affymetrix Clariom D human GeneChip® arrays (Affymetrix, America) according to the User Manuals. Affymetrix® Expression Console Software (version 1.2.1) was used for microarray analysis. Raw data (CEL files) were normalized at transcript level using robust multiaverage method (RMA workflow). Median summarization of transcript expressions was calculated. Gene-level data was then filtered to include only those probe sets that are in the ‘core’ metaprobe list, which represent RefSeq genes.

treatment_protocol: Pulmonary artery endothelial cells (PAECs) were exposed to normoxia condition (21% O2, 5% CO2, 74% N2) or hypoxia condition (3% O2, 5% CO2, 92% N2) (n=3 for each group).PAECs were harvested after 24 hours and performed to further analysis.

tag: stress

value: hypoxia


title: PAECs, hypoxia condition, rep3

value: Pulmonary artery endothelial cells (PAECs)


title: PAECs, normoxia condition, rep3

source_name: PAECs, normoxia condition

value: normoxia


title: PAECs, hypoxia condition, rep1


title: hCD4_ACT_HIVinf_sorted_LATENT_rep6

type: other

city: Essen

first: Hannah Sabeth

last: Sperber

state: NRW

address: Virchowstr. 171

department: Institute for transaltional HIV Research

country: Germany

institute: Essen University Hospital

description: total RNA and protein

hyb_protocol: Probe hybridization was performed according to manufacturer's protocol MAN-10066-01_Cell_Surface_Protein_Processing_from_Cell_Suspensions and MAN-10060-03_RNA_Protein_Codeset_Hybridization_Setup

scan_protocol: Data was acquired on the nCounter SPRINT profiler (NanoString Technologies).

data_processing: RNA and protein expression values were normalized and analyzed using the nSolver Analysis Software 4.0 and the add-on Advanced Analysis Software 2.0.115 (NanoString Technologies). Samples that did not pass the default control performance and quality parameters were excluded from subsequent analysis.

label: nanostring reporter probe

source_name: Blood-derived CD4+ T cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density gradient centrifugation (Corning) at 2000 rpm (~ 850 x g) at RT for 30 min, without brake. PBMCs were immediately processed to isolate CD4+ T cells by negative selection using the EasySep Human CD4+ T Cell Isolation Cocktail (StemCell Technologies) according to manufacturer’s protocol. Purified CD4+ T cells were cultured in RPMI +/+ (supplemented with 10% FBS and 1% Penicillin/Streptomycin) at 37°C, 5% CO2.

extract_protocol: Quantitative RNA and protein expression data were generated using the nCounter Vantage 3D RNA:Protein Immune Cell Profiling Assay (NanoString Technologies) and the nCounter SPRINT profiler (NanoString Technologies), comprising 770 RNA and 30 protein targets as well as positive and negative controls. 100,000 cells were used per sample, which were processed according to the manufacturer’s instructions.

treatment_protocol: Following CD4+ T cell isolation, cells were seeded at a concentration of 1x106 cells/ml and activated with αCD3/αCD28 activating beads (ThermoFisher Scientific) for 72h at a concentration of 1 bead/cell in the presence of 100 U/ml IL-2 (PeproTech) in RPMI +/+ (except for mock controls). At the day of infection, cells were spinoculated in 96-well V-bottom plates (MilliporeSigma) in 50 μl RPMI+/+ with 100 ng (HIVDFII) of p24 per 1×106 cells with 5×106 cells total per well for 2 h at 2350 rpm (1173 × g) at 37°C. After spinoculation, all cells were returned to culture in the presence of 30 U/ml IL-2. Pre-stimulated CD4+ T cells stayed in αCD3/αCD28 activating beads during spininfection and subsequent cell culture. Samples were subjected to fluorescence-activated cell sorting 4 days post infection.

value: Blood-derived CD4+ T cells


title: hCD4_ACT_HIVinf_sorted_PRODUCTIVE_rep6

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_UNINFECTED_rep6

description: total RNA and protein


title: hCD4_ACT_rep4

description: total RNA and protein


title: hCD4_untreated_rep6

description: total RNA and protein


title: hCD4_untreated_rep3

description: total RNA and protein


title: hCD4_HIVinf_rep6

description: total RNA and protein


title: hCD4_HIVinf_rep4

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_UNINFECTED_rep2

description: total RNA and protein


title: hCD4_ACT_rep6

description: total RNA and protein


title: hCD4_ACT_rep3

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_PRODUCTIVE_rep4

description: total RNA and protein


title: hCD4_ACT_rep5

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_LATENT_rep4

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_LATENT_rep5

description: total RNA and protein


title: hCD4_untreated_rep4

description: total RNA and protein


title: hCD4_untreated_rep5

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_UNINFECTED_rep4

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_PRODUCTIVE_rep5

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_UNINFECTED_rep3

description: total RNA and protein


title: PAECs, normoxia condition, rep1


title: hCD4_ACT_HIVinf_sorted_PRODUCTIVE_rep3

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_PRODUCTIVE_rep2

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_LATENT_rep3

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_LATENT_rep2

description: total RNA and protein


title: hCD4_untreated_rep2

description: total RNA and protein


title: hCD4_HIVinf_rep3

description: total RNA and protein


title: hCD4_HIVinf_rep2

description: total RNA and protein


title: CD45 KO- 1dpi from cortex [group_14_37]

city: Blacksburg

first: Michelle

last: Theus

state: VA

address: 234 Craig Drive

institute: Virginia Polytechnic Institute and State University

description:
group_14_37
raw.CD45.csv
DESeq2.normalized.CD45.csv

data_processing:
Sequence read is trimmed using trimgalore (--paired --phred33 --fastqc --illumina -q 30 --length 30)
Trimmed sequence is mapped to Mouse genome (Mus_musculus.GRCm38.99) and quantified using STAR 2.7.9a quantMode (--quantMode GeneCounts)
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: comma-separated values file includes the raw count for each sample
Supplementary files format and content: comma-separated values file includes the DESeq2 normalized count for each sample

source_name: cortex

growth_protocol: Fresh brain ipsilateral cortex were neural dissociated and subjected to CD45 and CD31 microbeads

extract_protocol:
RNA was extracted using Cholorform extraction
Illumina TruSeq Stranded mRNA HT Sample Prep Kit, enriched by 14 cycles of PCR, validated using Agilent TapeStation and quantified by qPCR

treatment_protocol: moderate CCI injury using eCCI device to the right parietal cortex

value: cortex

value: CD45 immune cells

value: Endothelial EphA4 KO

value: CCI


title: CD45 WT- 1dpi from cortex [group_15_38]

description:
group_15_38
raw.CD45.csv
DESeq2.normalized.CD45.csv


title: CD45 KO- 1dpi from cortex [group_13_36]

description:
group_13_36
raw.CD45.csv
DESeq2.normalized.CD45.csv


title: CD45 KO- 1dpi from cortex [group_12_35]

description:
group_12_35
raw.CD45.csv
DESeq2.normalized.CD45.csv


title: CD45 WT- 1dpi from cortex [group_10_33]

description:
group_10_33
raw.CD45.csv
DESeq2.normalized.CD45.csv


title: Flow through KO-- 1dpi from cortex [group_08_31]

description:
group_08_31
raw.FT.csv
DESeq2.normalized.FT.csv

value: All other cortical cells


title: Flow through KO-- 1dpi from cortex [group_06_29]

description:
group_06_29
raw.FT.csv
DESeq2.normalized.FT.csv


title: hCD4_ACT_HIVinf_sorted_UNINFECTED_rep1

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_LATENT_rep1

description: total RNA and protein


title: hCD4_ACT_HIVinf_sorted_PRODUCTIVE_rep1

description: total RNA and protein


title: PAECs, normoxia condition, rep2


title: hCD4_ACT_rep2

description: total RNA and protein


title: Flow through WT-- 1dpi from cortex [group_09_32]

description:
group_09_32
raw.FT.csv
DESeq2.normalized.FT.csv


title: CD45 KO- 1dpi from cortex [group_16_39]

description:
group_16_39
raw.CD45.csv
DESeq2.normalized.CD45.csv


title: hCD4_ACT_rep1

description: total RNA and protein


title: hCD4_untreated_rep1

description: total RNA and protein


title: CD45 WT- 1dpi from cortex [group_11_34]

description:
group_11_34
raw.CD45.csv
DESeq2.normalized.CD45.csv


title: Flow through WT-- 1dpi from cortex [group_01_24]

description:
group_01_24
raw.FT.csv
DESeq2.normalized.FT.csv


title: Flow through WT-- 1dpi from cortex [group_02_25]

description:
group_02_25
raw.FT.csv
DESeq2.normalized.FT.csv


title: Flow through WT-- 1dpi from cortex [group_03_26]

description:
group_03_26
raw.FT.csv
DESeq2.normalized.FT.csv


title: Oligodendrocyte, 0 mM Alcohol, biol rep 12

city: Austin

first: Esther

last: Melamed

state: TX

address: 1601 Trinity St bldg b

department: Department of Neurology, Dell Medical School

institute: The University of Texas at Austin

data_processing:
Reads were trimmed and filtered using cutadapt (v 1.18) to remove the illumina header and poly-A sequences (cutadapt -a AAAAAAAA -a AGATCGG -q 15 -m 25)
Trimmed and filtered reads were mapped to GRCm39 cDNA ensembl mouse transcriptome using STAR (v 020201).
Assembly: Ensembl GRCm39
Supplementary files format and content: tab-deliminated text file that contains raw counts (gene level) for each sample.

source_name: Oligodendrocyte

growth_protocol: Oligodendrocytes were isolated according to Flores-Abando, et al., 2018. In brief, the brain was removed from P5-7 C57BL6/J mice pups, and the cortices were isolated. Cortices were cut up and digested with papain before mechanical disruption to create a single cell solution. Magnetic bead sorting using a magnetic O4 antibody from Miltenyi Biotec was used to isolate immature oligodendrocytes. The cells were then plated on poly-D-lysine/Laminin-coated coverslips and differentiated in culture for three days, with the primary differentiating factor being triiodothyronine (T3).

extract_protocol:
RNA was isolated using the Qiagen RNeasy mini kit according to manufacturer's instruction. Less than or equal to 150 ng of total RNA was used for construction of the sequence libraries.
3’ TagSeq was performed by the University of Texas Genomic Sequencing and Analysis Facility, based on the protocols from Lohman BK et al. (2016) and Meyer E et al. (2011). Libraries were quantified using the Quant-it PicoGreen dsDNA assay (ThermoFisher) and pooled equally for subsequent size selection at 350-550bp on a 2% gel using the Blue Pippin (Sage Science). The final pools were checked for size and quality with the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche). Samples were then sequenced on the NovaSeq 6000 (Illumina) instrument with single-end, 100-bp reads.

treatment_protocol: After differentiation, the oligodendrocytes were then exposed to either a high concentration of ethanol (30mM), moderate concentration of ethanol (10mM) or control (0mM) for three days. A beaker of ethanol was kept in the incubator to slow down evaporation from culture dishes and alcohol concentration was measured daily to ensure steady exposure of ethanol. Control plates were kept in a separate incubator to avoid ethanol exposure.

value: Oligodendrocyte

value: 0 mM Alcohol (Control)

tag: batch


title: Oligodendrocyte, 0 mM Alcohol, biol rep 11


title: Oligodendrocyte, 0 mM Alcohol, biol rep 8


title: Oligodendrocyte, 0 mM Alcohol, biol rep 9


title: Oligodendrocyte, 0 mM Alcohol, biol rep 10


title: Flow through KO-- 1dpi from cortex [group_05_28]

description:
group_05_28
raw.FT.csv
DESeq2.normalized.FT.csv


title: hCD4_HIVinf_rep1

description: total RNA and protein


title: Flow through WT-- 1dpi from cortex [group_04_27]

description:
group_04_27
raw.FT.csv
DESeq2.normalized.FT.csv


title: Oligodendrocyte, 0 mM Alcohol, biol rep 7


title: Oligodendrocyte, 10 mM Alcohol, biol rep 5

value: 10 mM Alcohol


title: Oligodendrocyte, 10 mM Alcohol, biol rep 4


title: Oligodendrocyte, 10 mM Alcohol, biol rep 6


title: Oligodendrocyte, 10 mM Alcohol, biol rep 2


title: Oligodendrocyte, 0 mM Alcohol, biol rep 5


title: Oligodendrocyte, 10 mM Alcohol, biol rep 1


title: Oligodendrocyte, 0 mM Alcohol, biol rep 6


title: Oligodendrocyte, 10 mM Alcohol, biol rep 3


title: Oligodendrocyte, 0 mM Alcohol, biol rep 3


title: Oligodendrocyte, 30 mM Alcohol, biol rep 6

value: 30 mM Alcohol


title: Oligodendrocyte, 0 mM Alcohol, biol rep 4


title: Oligodendrocyte, 0 mM Alcohol, biol rep 2


title: Oligodendrocyte, 0 mM Alcohol, biol rep 1


title: Oligodendrocyte, 30 mM Alcohol, biol rep 4


title: Oligodendrocyte, 30 mM Alcohol, biol rep 5


title: Oligodendrocyte, 30 mM Alcohol, biol rep 3


title: huIFNAR mouse intestine, mock, 16h, rep 3

city: Guangzhou

first: Feng

last: Li

address: No.8, Huaying Road, Baiyun District.

department: Infectious Diseases Institute

institute: Guangzhou Eighth People's Hospital, Guangzhou Medical University

data_processing:
Raw reads were trimmed using trim_galore (quality limit: 25)
Trimmed reads were mapped to mm10 using HISAT2 (parameters: default)
Read count extraction and normalization were performed using featureCounts(v2.0.1)(parameters: default)
Assembly: mm10
Supplementary files format and content: E5vE2-1-counts-formal: tab-delimited text files include raw counts for each sample (blood)
Supplementary files format and content: E5vE2-2-counts-formal: tab-delimited text files include raw counts for each sample (liver)
Supplementary files format and content: E5vE2-3-counts-formal: tab-delimited text files include raw counts for each sample (spleen)
Supplementary files format and content: E5vE2-4-counts-formal: tab-delimited text files include raw counts for each sample (lung)
Supplementary files format and content: E5vE2-5-counts-formal: tab-delimited text files include raw counts for each sample (kidney)
Supplementary files format and content: E5vE2-6-counts-formal: tab-delimited text files include raw counts for each sample (heart)
Supplementary files format and content: E5vE2-7-counts-formal: tab-delimited text files include raw counts for each sample (muscle)
Supplementary files format and content: E5vE2-8-counts-formal: tab-delimited text files include raw counts for each sample (intestine)
Supplementary files format and content: E5vE2-9-counts-formal: tab-delimited text files include raw counts for each sample (brain)

source_name: Intestine

extract_protocol:
Total RNA was extracted from tissues using RNeasy with DNase treatment (Qiagen).
RNA libraries for RNA-Seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina(NR604-01) following manufacturer's protocols.

treatment_protocol: At 16h after subcutaneous inoculation of human PEG-IFN (ug/mouse, 200 ul), tissues were collected.

value: Intestine

value: physiological saline solution


title: Oligodendrocyte, 30 mM Alcohol, biol rep 2


title: huIFNAR mouse brain, mock, 16h, rep 3

source_name: Brain

value: Brain


title: Oligodendrocyte, 30 mM Alcohol, biol rep 1


title: huIFNAR mouse muscle, mock, 16h, rep 3

source_name: Muscle

value: Muscle


title: huIFNAR mouse heart, mock, 16h, rep 3

source_name: Heart

value: Heart


title: huIFNAR mouse kidney, mock, 16h, rep 3

source_name: Kidney

value: Kidney


title: huIFNAR mouse lung, mock, 16h, rep 3

source_name: Lung

value: Lung


title: huIFNAR mouse blood, mock, 16h, rep 3

source_name: Blood

value: Blood


title: huIFNAR mouse liver, mock, 16h, rep 3

source_name: Liver

value: Liver


title: huIFNAR mouse brain, mock, 16h, rep 2


title: huIFNAR mouse heart, mock, 16h, rep 2


title: huIFNAR mouse muscle, mock, 16h, rep 2


title: huIFNAR mouse kidney, mock, 16h, rep 2


title: huIFNAR mouse intestine, mock, 16h, rep 2


title: huIFNAR mouse spleen, mock, 16h, rep 2

source_name: Spleen

value: Spleen


title: huIFNAR mouse liver, mock, 16h, rep 2


title: huIFNAR mouse lung, mock, 16h, rep 2


title: huIFNAR mouse kidney, mock, 16h, rep 1


title: huIFNAR mouse spleen, mock, 16h, rep 1


title: huIFNAR mouse intestine, mock, 16h, rep 1


title: huIFNAR mouse liver, mock, 16h, rep 1


title: huIFNAR mouse blood, mock, 16h, rep 2


title: huIFNAR mouse blood, mock, 16h, rep 1


title: huIFNAR mouse brain, mock, 16h, rep 1


title: huIFNAR mouse lung, mock, 16h, rep 1


title: huIFNAR mouse spleen, mock, 16h, rep 3


title: huIFNAR mouse intestine, Human Peg-IFNα2 treatment, 16h, rep 3

value: Human Peg-IFNα2


title: Con-sEV C3

city: Xi'an

last: Fu

state: Shaanxi

address: Changle Xi Road 169

institute: Fourth Military Medical University

data_processing:
The raw reads obtained from Illumina HiSeqTM 2500 sequencing were first filtered by removing junctions at both ends of the reads, removing reads with fragment length <17nt and low-quality reads to obtain high-quality data (clean reads).
The clean reads were compared with the reference genome to obtain a genome-wide reads distribution map, and the clean reads were annotated with ncRNA classification.
Expression of the identified miRNAs was analyzed.
The identified miRNAs were subjected to expression quantification, miRNA expression clustering, and miRNA differential expression analysis among samples.
Assembly: rn6
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: RPKM values for each sample

organism: Rattus norvegicus

source_name: small extracellular vesicles

growth_protocol: Male 6–8-week-old Sprague-Dawley rats were obtained and maintained under controlled settings (12h/12h light/dark cycle) and fed a recommended chow with ad libitum access to water.

extract_protocol:
Total RNAs were extracted from sEV purified from 2 ml of rat plasma using TRIZOL (Invitrogen, Carlsbad, CA) per the manufacturer’s protocol.
Both 3' and 5' adaptors were added to each end, respectively, followed by reverse transcription and PCR amplification. The PCR products derived from the 18- to 30- nucleotide RNA molecules were purified by electrophoresis and sequenced using the Illumina HiSeq 2500 platform.

treatment_protocol: Streptozotocin (STZ, Sigma-Aldrich), at a dosage of 65 mg/kg, was administered intraperitoneally to fasting rats to cause diabetes. One week after STZ injection, experimental animals with fasting glucose levels >11.1 mmol/L were determined to develop diabetes.

value: small extracellular vesicles

value: Sprague-Dawley

value: WT

value: control rats


title: huIFNAR mouse muscle, Human Peg-IFNα2 treatment, 16h, rep 3


title: huIFNAR mouse brain, Human Peg-IFNα2 treatment, 16h, rep 3


title: DM-sEV DM2

value: 8-week diabetic rats


title: DM-sEV DM3


title: huIFNAR mouse kidney, Human Peg-IFNα2 treatment, 16h, rep 3


title: Con-sEV C1


title: huIFNAR mouse lung, Human Peg-IFNα2 treatment, 16h, rep 3


title: huIFNAR mouse heart, Human Peg-IFNα2 treatment, 16h, rep 3


title: huIFNAR mouse muscle, mock, 16h, rep 1


title: RNA-seq_miR630_2

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue <=0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa Cells

growth_protocol: The human cervical cancer cell line HeLa was obtained from the American Type Culture Collection (Manassas, VA) and the cell was maintained as a monolayer in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS，Sijiqing Biological Engineering Materials Co., Hangzhou, China) at 37°C in the presence of 5% CO2-balanced air.

extract_protocol:
For each sample, 5μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation.
Purified mRNAs were iron fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80℃ until used for sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacture’s instructions and applied to Illumina NextSeq500 or Illumina Hiseq X Ten system with 150x2 paired-end type (ABLife Inc., Wuhan, China).

treatment_protocol: Full-length human HIF-3α cDNA was cloned into a Pcmv-ORF-flag-his expression vector . The fidelity of the construction vector was confirmed by sequencing. Transfection was performed with lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) 24 h after cell seeding. Lentiviral constructs containing up-regulating miR-630 (LV-hsa-mir-630), inhibiting miR-630 (LV-hsa-mir-630-inhibitor) and the negative control lenti-vector (LV-Negative Control) were designed and provided by Genechem lnc. (Shanghai, China). 60–70% confluent HeLa cell was infected with three lentivirus at multiplicity of infection (MOI) of 10 with enhanced infection solution (ENI.S) according to the manufacturer’s protocol. 10 hours post-infection, viruses were replaced by complete DMEM and 48 hours post-infection, three stably infected cells (LV-hsa-mir-630, LV-hsa-mir-630-inhibitor, LV-Negative Control) were selected by complete DMEM with 2 g/ ml puromycin (Sigma, German). The expression level of miR-630 in the stable transformants were identified by qRT-PCR.

value: HeLa

value: Cervical cancer cells

value: MiR-630 overexpression with lentiviral constructs


title: RNA-seq_miR630_1


title: huIFNAR mouse spleen, Human Peg-IFNα2 treatment, 16h, rep 3


title: huIFNAR mouse heart, mock, 16h, rep 1

value: physiological saline solution


title: Con-sEV C2


title: HPC GPR107 KO cells, HG, Day 5, rep3

first: Haisheng

last: Zhou

address: 69 Meishan Rd.

institute: Anhui medical university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Homo sapiens（ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Homo sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: kidney

value: HPC

value: podocytes

value: GPR107 knock out

value: gene expression


title: RNA-seq_Vect_2

value: negative control lenti-vector


title: HPC GPR107 KO cells, HG, Day 5, rep1


title: huIFNAR mouse liver, Human Peg-IFNα2 treatment, 16h, rep 3

value: Liver


title: HPC cells, HG, Day 5, rep3


title: SKMEL28 shp16, heavy polysome fraction, rep2

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file includes raw counts for all samples
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

source_name: cell line

growth_protocol: SKMEL28 cells were cultured in DMEM + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)
Next generation sequencing was performed at Novogene using a NovaSeq 6000 Sequencing System  (Illumina)

treatment_protocol: Cells were transduced with lentivirus expressing shRNA targeting GFP (shCont) or p16 (shp16) and selected for 3 days with 1ug/ml puromycin.

value: cell line

value: melanoma

value: p16 knockdown


title: SKMEL28 shp16, heavy polysome fraction, rep3


title: HPC GPR107 KO cells, HG, Day 5, rep2


title: huIFNAR mouse blood, Human Peg-IFNα2 treatment, 16h, rep 3

value: Blood

value: Human Peg-IFNα2


title: DM-sEV DM1

value: small extracellular vesicles

value: Sprague-Dawley

value: WT

value: 8-week diabetic rats


title: HPC cells, HG, Day 5, rep2


title: huIFNAR mouse intestine, Human Peg-IFNα2 treatment, 16h, rep 2

value: Intestine


title: SKMEL28 shp16, heavy polysome fraction, rep1


title: huIFNAR mouse brain, Human Peg-IFNα2 treatment, 16h, rep 2

value: Brain


title: SKMEL28 shp16, light polysome fraction, rep3


title: RNA-seq_Vect_1

value: HeLa

value: Cervical cancer cells


title: HPC cells, HG, Day 5, rep1

value: kidney

value: HPC

value: podocytes


title: HIF3a_input_1

library_source: genomic

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
MACS version 1.4.2 was used to peakcalling
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak for each group.

molecule: genomic DNA

source_name: HeLa cell

extract_protocol:
The suspension was sonicated to generate DNA fragments of 200-500bp, centrifuged for 10 min at 12,000 g, and the supernatant was directly used for immunoprecipitation.
For each immunoprecipitation, 1000μL cell extracts were incubated with HIF3A antibody (orb101652, Biobyt, China) overnight at 4 ℃. The immunoprecipitates were further incubated with protein A Dynabeads for 3h at 4 ℃. After applying to magnet and removing the supernatants, the beads were sequentially washed with lysis buffer, high-salt buffer (250 mM Tris 7.4, 750 mM NaCl, 10 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5 deoxycholate), and PNK buffer (50 mM Tris, 20 mM EGTA and 0.5% NP-40) for two times, respectively. The immunoprecipitates were eluted from the beads with elution buffer (50 nM Tris 8.0, 10 mM EDTA and 1% SDS) and reverse cross-linked by overnight incubation at 65 ℃. After sequential RNase A and proteinase K treatment, DNA fragments were purified by phenol extraction and ethanol precipitation.
To generate libraries for high-throughput sequencing, purified DNA fragments were end-repaired, adenylated, ligated to adaptors and PCR amplified for 12 cycles. The PCR products corresponding to 300-500 bps were gel purified, quantified and stored at -80 ℃ until used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacture’s instructions and applied to Illumina X-Ten system with 150x2 paired-end type by Novogene.

treatment_protocol: Total cell extracts were prepared from 2 x 10e7 formaldehyde fixed cells resuspended in 1 mL lysis buffer containing 50 mM Tris 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5% deoxycholate.

tag: chip antibody


title: SKMEL28 shp16, light polysome fraction, rep2

tag: cell type


title: HIF3a_input_2


title: huIFNAR mouse muscle, Human Peg-IFNα2 treatment, 16h, rep 2

value: Muscle


title: SKMEL28 shp16, light polysome fraction, rep1

value: cell line


title: BEAS-2B, Input

city: Yanji

first: Guang

middle: hai

last: Yan

address: gongyuan road 977

institute: yanbian university

data_processing:
Basecalling was performed using CASAVA version 1.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Reads were aligned to the hg19 genome assembly using Hisat version 2.2.1
Peaks were called uing MACS v2.2.7 with the significance cut-off q-value <=0.05
Assembly: hg19
Supplementary files format and content: bigWig files contain treat pileup read per million (RPM) normalized in bigWig format

extract_protocol:
The BEAS-2B cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA.
The ChIP DNA was purified by QIAquick PCR Purification Kit (Cat. 28104; QIAGEN) following the manufacturer’s protocol.  The ChIP DNA library preparation was performed by using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (Cat. E7645S; NEB).  Paired-end sequencing was performed with Illumina NovaSeq platform.

value: Human bronchial epithelium, normal


title: BEAS-2B, HA


title: SKMEL28 shGFP,heavy polysome fraction, rep3

value: melanoma

value: Control knockdown


title: AlHendy_Human_UI-41_F_SC.6_092420_Walker [F.SC_S13]

city: Chicago

first: Qiwei

address: 909 S. Wolcott Ave

department: Surgery

institute: University of Illinois at Chicago

description: processed data file: AlHendy.combined.RNA-Seq.10072020.featureCounts-genes.geo.txt

data_processing:
Reads were mapped to the UCSC human reference genome hg38 using HISAT2.
featureCounts was used to evaluate gene expression level as read counts
edgeR was used to determine significantly changed genes, with significance achieved for fdr<0.05
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

growth_protocol: Human myometrial Stro1+/CD44+ SCs were growth in pre-coated cell culture flasks in regular DMEM/F12 media supplemented with 12% FBS and 1% antibiotics. Cells were incubated under hypoxic conditions at 37°C, 2% O2, and 5% CO2.

extract_protocol: The RNeasy RNA isolation kit (Qiagen, Valencia, CA) was used to isolated RNA for RNA-seq analysis

treatment_protocol: FACS was used to isolate human myometrial SCs using Stro1/CD44 antibodies

value: Human myometrial SCs isolated from uterine fibroids

tag: group


title: AlHendy_Human_UI-41_MyoF_SC.5_092420_Walker [MyoF.SC_S14]

value: Human myometrial SCs isolated from myometrium adjacent to fibroids


title: HIF3a_IP_2

value: anti-HIF3a, orb101652, Biobyt


title: HIF3a_IP_1


title: AlHendy_Human_UI-36_MyoN_SC.1_092420_Walker [MyoN.SC_S15]

value: Human myometrial SCs isolated from myometrium without fibroids


title: SKMEL28 shGFP,heavy polysome fraction, rep2

tag: tissue


title: huIFNAR mouse lung, Human Peg-IFNα2 treatment, 16h, rep 2

value: Lung

value: Human Peg-IFNα2


title: AlHendy_Human_UI-34_MyoF_SC.3_092420_Walker [MyoF.SC_S11]


title: SKMEL28 shGFP,heavy polysome fraction, rep1

tag: genotype


title: huIFNAR mouse spleen, Human Peg-IFNα2 treatment, 16h, rep 2

value: Spleen


title: AlHendy_Human_UI-34_F_SC.4_092420_Walker [F.SC_S10]


title: HeLa cells, QKO (ORP9KO / GRAMD1 TKO), biol rep 1

city: Singapore

first: Yasunori

last: Saheki

state: Singapore

address: 11 Mandalay road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nangyang Technological University

data_processing:
Obtained data were cleaned and aligned to reference genome via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) was used to estimate gene and isoform expression levels from the pair-end clean data
DESeq2 Bioconductor package was used to perform differential expression analysis
The estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were set <0.05 to detect differential expressed ones.
Assembly: GRCh38.p13
Supplementary files format and content: xls file includes fpkm values for each sample
Supplementary files format and content: xls files include Gene Differential Expression analysis in comparison to WT control

source_name: HeLa

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

extract_protocol:
RNA was harvested using Rneasy min plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries
mRNA isolation was performed using Oligo(dT) beads, and the mRNA fragmentation was performed using divalent cations and high temperature. First strand cDNA and the second-strand cDNA were synthesized using random primers. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated

value: HeLa

value: cervical carcinoma, epithelial

value: QKO (ORP9 KO / GRAMD1 TKO)


title: SKMEL28 shGFP, light polysome fraction, rep3


title: AlHendy_Human_510_MyoN_SC.2_092420_Walker [MyoN.SC_S12]


title: HeLa cells, QKO (ORP9KO / GRAMD1 TKO), biol rep 3


title: HeLa cells, ORP9 KO, biol rep 3

value: ORP9 KO


title: huIFNAR mouse liver, Human Peg-IFNα2 treatment, 16h, rep 2

value: Liver


title: huIFNAR mouse blood, Human Peg-IFNα2 treatment, 16h, rep 2

value: Blood


title: huIFNAR mouse kidney, Human Peg-IFNα2 treatment, 16h, rep 2

value: Kidney


title: huIFNAR mouse heart, Human Peg-IFNα2 treatment, 16h, rep 2

value: Heart


title: miRNA-seq_vacant_2

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG; end2:GATCGTCGGACTGTAGAACTCTGAAC) trimmed with fastx_clipper
discovering novel miRNAs using miRDeep2, then predicting miRNA target gene using miRanda
Mapping of clean reads on the reference genome using bowtie -v 1
edgeR was used to detect differentially expressed miRNAs
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene TPM values for each Sample

extract_protocol:
A total of 3μg of total RNA was used for small RNA cDNA library preparation with Balancer NGS Library Preparation Kit for small/microRNA (GnomeGen) following manufacture's instruction.
Briefly, RNAs were ligated to 3' and 5' adaptor sequentially and reverse transcribed to cDNA and then PCR amplified. Whole library was applied to 10% native PAGE gel electrophoresis and ba nds corresponding to microRNA insertion were cut and eluted. After ethanol precipitation and washing, the purified small RNA libraries were quantified and stored at -80 ℃ before sequencing
For high-throughput sequencing, the libraries were prepared following the manufacture’s instructions and applied to illumina NextSeq 500 system with 150x2 paired-end type (ABLife Inc., Wuhan, China).

treatment_protocol: Full-length human HIF-3α cDNA was cloned into a Pcmv-ORF-flag-his expression vector and HIF-1α was cloned into a pBabe-puro-HA expression vector (TranSheepBio, Shanghai, China). The fidelity of the construction vector was confirmed by sequencing. Transfection was performed with lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) 24 h after cell seeding.

value: Cervical cancer cells

value: Empty vector

tag: rna population

value: cytoplasmic RNA(16~30 nt)


title: HeLa cells, ORP9 KO, biol rep 2


title: huIFNAR mouse brain, Human Peg-IFNα2 treatment, 16h, rep 1

value: Brain


title: miRNA-seq_HIF_3a_2

value: HIF-3alpha overexpression with Pcmv-ORF-flag-his expression vector


title: HeLa cells, GRAMD1 TKO, biol rep 3

value: GRAMD1 TKO


title: miRNA-seq_vacant_1


title: HeLa cells, ORP9 KO, biol rep 1


title: SKMEL28 shp16, total mRNA, rep3

value: cell line

value: melanoma

value: p16 knockdown


title: SKMEL28 shp16, total mRNA, rep2


title: SKMEL28 shGFP, light polysome fraction, rep2

value: Control knockdown


title: SKMEL28 shGFP, light polysome fraction, rep1


title: miRNA-seq_HIF_3a_1

value: HeLa


title: huIFNAR mouse intestine, Human Peg-IFNα2 treatment, 16h, rep 1

value: Intestine

value: Human Peg-IFNα2


title: huIFNAR mouse muscle, Human Peg-IFNα2 treatment, 16h, rep 1

value: Muscle


title: miRNA-seq_HIF_1a_2

value: HIF-1alpha overexpression with pBabe-puro-HA expression vector


title: hCD4_ACT_HIVinf_sorted_UNINFECTED_rep5

description: total RNA and protein

source_name: Blood-derived CD4+ T cells

value: Blood-derived CD4+ T cells


title: huIFNAR mouse heart, Human Peg-IFNα2 treatment, 16h, rep 1

value: Heart


title: SKMEL28 shp16, total mRNA, rep1


title: HeLa cells, GRAMD1 TKO, biol rep 2

value: cervical carcinoma, epithelial


title: HeLa cells, WT, biol rep 3

value: WT


title: HeLa cells, GRAMD1 TKO, biol rep 1


title: huIFNAR mouse kidney, Human Peg-IFNα2 treatment, 16h, rep 1

value: Kidney


title: SKMEL28 shGFP, total mRNA, rep3


title: HeLa cells, QKO (ORP9KO / GRAMD1 TKO), biol rep 2

value: QKO (ORP9 KO / GRAMD1 TKO)


title: SKMEL28 shGFP, total mRNA, rep2


title: miRNA-seq_HIF_1a_1

value: Cervical cancer cells

value: cytoplasmic RNA(16~30 nt)


title: huIFNAR mouse lung, Human Peg-IFNα2 treatment, 16h, rep 1

value: Lung


title: RNA-seq_vacant_2

value: Empty vector


title: HeLa cells, WT, biol rep 2


title: SKMEL28 shGFP, total mRNA, rep1

value: cell line

value: melanoma


title: RNA-seq_vacant_1

value: HeLa


title: HeLa cells, WT, biol rep 1


title: RNA-seq_HIF_3alpha_2

value: HIF-3alpha overexpression with Pcmv-ORF-flag-his expression vector


title: FD4

first: Han

last: Xueya

address: 10 Xitoutiao Street, Fengtai District, Beijing

institute: Capital Medical University

data_processing:
Image processing and base recognition were performed using Solexa pipeline software (Illumina, version 1.8).
The RNA sequencing reads were aligned to the human reference genome GRCh37 (also known as hg19) using HISAT2 (version 2.1.0) with default parameters.
The normalized expression value, fragments per kilobase of transcript per million mapped reads (FPKM), was calculated for each gene using StringTie (version 1.3.3).
FPKM at the gene level and transcript level were calculated using Ballgown (version  2.10.0). Differentially expressed genes with a fold change≥1.5, p-value ≤ 0.05 and FPKM≥0.5 were screened and retained in groups.
Gene Set Enrichment Analysis (GSEA) for the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis was analysed using GSEA (version 2.2.4).
Assembly: GRCh37
Supplementary files format and content: The Express file format is xlsx, which analyses the expression of gene and transcript; the Diff_express file format is xlsx, which analyses all differentially expressed genes /transcripts and differentially expressed genes /transcripts; the Pathway_Report file format includes doc, pdf, png, html, xls, txt, which analyses the upregulated and downregulated pathways of differentially expressed genes; the GO_Report file format includes doc, pdf, png, html, xls, txt, which analyses the upregulated and downregulated  differentially expressed genes; the Plots file format includes pdf, png, txt, which analyses differentially expressed genes; the GSEA file format includes pdf, png, xls, html, which analyses differentially expressed genes in biological processes, cellular components,molecular functions and KEGG pathway.

source_name: adipose tissue

growth_protocol: hASCs from lean donors (body mass index, BMI<24k/m2) and obese donors (BMI>30 kg/m2) were separately cultured. Briefly, hASCs were plated  on collagen I-coated dishes and cultured in DMEM/F-12 (Invitrogen, Grand Island, NY, USA)supplemented with 10% foetal bovine serum (FBS) (Gibco, Rockville, MD, USA), 100 U/ml penicillin and 100 µg/ml streptomycin (Invitrogen) at 37°C with 5% CO2. Once the cells reached 90% confluence, these cells were harvested.

extract_protocol:
RNA was harvested using Trizol reagent and the KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1-2 ug of total RNA for the construction of sequencing libraries.
Approximately 1-2 µg of total RNA isolated from each independent biological sample was processed with a Ribo-Zero Magnetic Gold kit (Epicentre Biotechnologies) to reduce ribosomal RNA abundance. Sequencing libraries were then constructed using the KAPA Stranded RNA-Seq Library Prep kit (Illumina). The quality of the constructed sequencing libraries was analysed using an Agilent 2100 Bioanalyzer. Quantitative real-time PCR was performed to quantify the sequencing libraries, and the mixed different sample libraries were sequenced using an Illumina HiSeq 6000 platform.

value: adipose tissue

value: adipose tissue derived stem cell

value: obese


title: Microglia, PSNPs, 24h, rep2

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

institute: Chung-Ang

data_processing:
Raw sequencing data were processed using Illumina bcl2fastq conversion tool to generate FASTQ files
Sequences were aligned to mRatBN7.2 genome to gene expression count using New Tuxedo Protocol's default settings
Gene expression level of Refseq coding genes were quantified using Ballgown tool which inspect the distribution of abundance estimates.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Primary cultured microglia

growth_protocol: Cultures were suspended in Dulbecco’s modified Eagle’s medium/nutrient mixture F12 (DMEM F12, Thermo Fisher Scientific, MA, USA) supplemented with 10% fetal bovine serum (FBS, Youngin, Korea), 100 μg/mL streptomycin, and 100 U/mL penicillin (Thermo Fisher Scientific) and grown at 37 °C with 5% CO2 in a humidified chamber for seven days. To harvest microglia, confluent co-cultures were incubated for 1 h at 250 rpm on an orbital shaker at 37°C and detached microglia was collected by centrifuge for 2 min at 1200 rpm

extract_protocol:
Total RNA was isolated from Rat Primary cells using Direct-Zol™ RNA microprep kit (Zymo research, CA, USA) according to the manufacturer’s protocol.
1000 ng of total RNA was processed to mRNA enrichment using NEBNext Poly(A) mRNA magnetic isolation module (New England BioLabs, MA, USA) and followed by fragmentation, cDNA synthesis, and library preparation with unique dual index using NEBNext Ultra II RNA library prep kit (New England BioLabs) according to the manufacturer’s manual.

treatment_protocol: To collect CM, 8 x 105 of microglia was seeded and the medium was changed to a 1mL of fresh one, which was collected after an additional 24 hours incubation with IR-813 or PSNPs. CM was filtered with Whatman Puradisc 25 syringe filters (Merck) and immediately applied to hippocampal neurons.

value: Primary cultured microglia

value: PSNPs


title: huIFNAR mouse blood, Human Peg-IFNα2 treatment, 16h, rep 1

value: Blood

value: Human Peg-IFNα2


title: Microglia, PSNPs, 24h, rep3


title: FD3


title: RNA-seq_HIF_3alpha_1


title: Microglia, PSNPs, 24h, rep1


title: FD23


title: Microglia, IR-813, 24h, rep3


title: UI-32-MyoF-SC_S2

source_name: Human myometrium

growth_protocol: Human myometrial Stro1+/CD44+ SCs were grown in pre-coated cell culture flasks in regular DMEM/F12 media supplemented with 12% FBS and 1% antibiotics. Cells were incubated under hypoxic conditions at 37°C, 2% O2, and 5% CO2.

value: Human myometrial SCs isolated from myometrium adjacent to fibroids

value: MyoF-SC


title: UI-32-F-SC_S1

source_name: Human uterine fibroid

value: Human myometrial SCs isolated from uterine fibroids

value: F-SC


title: UI-30-MyoF-SC_S4


title: FD19


title: Liver, A475_NC

city: Jinan

first: Zixiang

last: Wang

state: Shandong

address: No.44 Wenhuaxi Road

department: Cheeloo College of Medicine

institute: Shandong University

data_processing:
The adaptor sequences and low-quality reads were removed with Trim Galore (version 0.6.1), and the quality of the clean reads was checked with FastQC (version 0.11.9).
Clean reads were mapped to the mouse genome (mm10) with HISAT2 and visualized in IGV.
Duplicated reads were removed with Picard.
Gene expression was quantified with featureCounts.
Differential expression was analyzed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
RNA was extracted with TRIzol method.
The sequencing library was constructed with the NEB Next Ultra RNA Library Prep Kit for Illumina.
High-throughput sequencing of the RNA libraries was performed on a NovaSeq 6000 using the PE150 sequencing strategy (Novogene).

treatment_protocol: 5-week-old Usp39-HKO and control littermates (n=4) were fasted for 16 hours and anesthetized.

value: Liver

value: WT

tag: Sex

value: male


title: FD16


title: huIFNAR mouse spleen, Human Peg-IFNα2 treatment, 16h, rep 1

value: Spleen


title: FD21


title: UI-30-F-SC_S3


title: UI-28-MyoN-SC_S9

value: Human myometrial SCs isolated from myometrium without fibroids

value: MyoN-SC


title: FD10

value: adipose tissue


title: Liver, A471_HKO


title: Liver, A473_NC


title: Liver, A474_HKO


title: Liver, A472_NC


title: UI-18-MyoF-SC_S6


title: R14

value: adipose tissue derived stem cell

value: lean


title: Liver, A469_HKO


title: Microglia, IR-813, 24h, rep2

value: Primary cultured microglia


title: Liver, A468_NC


title: Microglia, IR-813, 24h, rep1


title: 514-MyoN-SC_S8


title: 518-MyoN-SC_S7


title: IP, RIP, AML12

data_processing:
The adaptor sequences and low-quality reads were removed with Trim Galore (version 0.6.1), and the quality of the clean reads was checked with FastQC (version 0.11.9).
rRNA sequences were removed with bowtie (version 1.2.3).
Clean reads were mapped to the mouse genome (mm10) with HISAT2 and visualized in IGV.
Usp39 binding peaks were identified with Piranha (-p 0.001 -z 100) and annotated with R package clusterProfiler.
De novo motif analysis was conducted with HOMER.
Assembly: mm10
Supplementary files format and content: Processed Usp39 binding peaks and genes table (except for Input sample).

growth_protocol: AML12 cells were cultured in DMEM-F12 medium with ITS liquid medium supplement (Sigma), and 40 ng/m dexamethasone.

extract_protocol:
RNA was extracted with Spin Column RNA Cleanup & Concentration Kit (Qiagen)
The sequencing library was constructed with the NEB Next Ultra RNA Library Prep Kit for Illumina.
High-throughput sequencing of the RIP libraries was performed on a NovaSeq 6000 using the PE150 sequencing strategy (Novogene).

treatment_protocol: AML12 cells were transfected with a doxycycline-induced FLAG-Usp39 expression vector. After 72 h of doxycycline induction, the cells were cross-linked with paraformaldehyde for 5 min and nuclear pellets were isolated and incubated with anti-FLAG magnetic beads (MBL, M185-11) at 4 °C overnight.

tag: cell line

value: Normal mouse hepatocytes

tag: rip antibody

value: anti-FLAG magnetic beads (MBL, M185-11)


title: R12


title: WT mouse, Human Peg-IFNα2 treatment, 15 weeks, 3 mice pooled, rep 2

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software )
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Intrahepatic lymphocyte cell isolation was done by enzymatic digestion. Briefly, the liver was minced into 0.5-mm3 pieces in digestion buffer (RMPI 1640 + 5%FBS + 20ng/ml DNase I + 0.5mg/mL Collagenase D), and enzymatically digested with 37C_m_LIDK_1 by gentleMACS. Liver homogenates were passed through a 70-µm cell strainer and then centrifuged at 300rpm for 5 min. Resuspend the pellet in 5 ml of 40% Percoll and centrifuge at 2000rpm for 20 min without brake. After the supernatant was removed, the pelleted cells were suspended in RBS lysis buffer and incubated on ice for 5 min to lyse red blood cells. After washing twice with PBS, the cell pellets were re-suspended in PBS (containing 0.04%BSA).
DNBelab C Series High-throughput Single-Cell RNA Library (MGI, #940-000047-00) was utilized for scRNA-seq library preparation.

value: hepatic immune cells

tag: treatment

value: Human Peg-IFNα3


title: huIFNAR mouse, Human Peg-IFNα2 treatment, 15 weeks, 3 mice pooled, rep 2

value: Human Peg-IFNα5


title: huIFNAR mouse, mock, 15 weeks, 3 mice pooled, rep 2

value: physiological saline solution


title: Input, RIP, AML12


title: huIFNAR mouse, mock, 15 weeks, 2 mice pooled, rep 1


title: WT mouse, Human Peg-IFNα2 treatment, 15 weeks, 3 mice pooled, rep 1

value: Human Peg-IFNα2


title: Liver, A470_HKO

value: Liver


title: S6.R1

status: Public on Sep 23 2023

city: Seoul

first: Woo Young

last: Kwon

address: Yonsei-ro 50

department: Department of Surgery

institute: Severance hospital

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2
The read count data were processed based on quantile normalization method using EdgeR within R
Gene classification was based on searches done by DAVID and Medline databases
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Human pancreas

extract_protocol:
Total RNA was isolated using Trizol reagent.
The construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit

tag: cell line origin

value: Human pancreas


title: S9.R1


title: huIFNAR mouse, Human Peg-IFNα2 treatment, 15 weeks, 3 mice pooled, rep 1

value: Human Peg-IFNα4


title: Wet-AMD.R1


title: S7.R1


title: S5.R1


title: UI-18-F-SC_S5

last: Yang

value: Human myometrial SCs isolated from uterine fibroids

value: F-SC


title: S8.R1


title: S2.R1


title: FD1

value: obese


title: S12.R1


title: R13

value: adipose tissue


title: S13.R1


title: S11.R1


title: S1.R1


title: S10.R1


title: 201


title: 200


title: 199


title: 198


title: 197


title: 196


title: 193


title: 194


title: 192


title: 191


title: S4.R1


title: 190


title: 189


title: 187


title: 188


title: 186


title: 184


title: 178


title: 179


title: 177


title: 176


title: 175


title: lesionalskinRNA-PSO5-pretreatment

city: Linz

first: Susanne

last: Kimeswenger

address: Krankenhausstraße 5

department: Department of Dermatology and Venerology

country: Austria

institute: Johannes Kepler University Linz

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Data was nomalized by using all housekeeping genes from the panel with an average count higher than 100 and with less than 35 % coefficient of variance.

label: not provided

source_name: lesional skin bunch biopsy

label_protocol: not provided

extract_protocol: 3-mm biopsies of patients’ lesional skin and controls’ normal skin were kept at  80 °C in RNAlater® (Invitrogen). After thawing, biopsies were mechanically disrupted using a TissueLyser II and 5-mm Stainless Steel Beads (Qiagen). RNA was isolated using Monarch Total Miniprep Kit (New England Biolabs) according to the manufacturer’s protocol.

value: PSO

value: lesional skin bunch biopsy


title: 174


title: 195


title: lesionalskinRNA-PSO1-pretreatment


title: normalskinRNA-HC8-notreatment

source_name: normal skin bunch biopsy

value: HC

value: normal skin bunch biopsy


title: lesionalskinRNA-DAR1-posttreatment


title: normalskinRNA-HC3-notreatment


title: 172


title: 170


title: lesionalskinRNA-DAR2-posttreatment


title: 168


title: lesionalskinRNA-DAR7-pretreatment

value: DAR


title: lesionalskinRNA-DAR5-pretreatment


title: 180


title: 166


title: lesionalskinRNA-DAR4-pretreatment


title: 165


title: B6xPWK_MPac_atac_rep2

first: Jing

last: He

state: Beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

department: School of Medicine

institute: Tsinghua University

data_processing:
For Hi-C samples: Hi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb or 10Kb bin size was used for compartment calling and a 40Kb bin size was used for TAD calling. The raw contact counts are normalized with iterative correction.
For RNA-Seq samples: Paired-end reads of RNA-seq libraries were quality confirmed by FastQC and then mapped to mm9 by Hisat2. Duplicated and multiple hit reads were discarded using SAMtools. The gene expression level was calculated by Python package HTSeq using the annotation file from the Gencode database. Only uniquely mapped reads were kept for raw counts matrix building.
For ATAC-Seq samples: Paired-end reads of ATAC-seq libraries were quality confirmed by FastQC and then mapped to mm9 by Hisat2. SAMtools was used for removing duplicates and multiple hit reads. Deeptools function bamCoverage was used for generates a bigwig coverage track.
Assembly: mm9
Supplementary files format and content: .hic files contain chromosomal contacts at different resolutions for each sisHi-C sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: bigwig files contain open chromatin regions for each ATAC-Seq sample

source_name: testis

extract_protocol:
FPGC, FLep, FZyg, FPac and FDip were isolated from ovaries of E11.5, E13.5, E15.5, E17.5 and E19.5 B6xPWK F1 female mice. For SGA, MLep, MZyg, MPac and MDip, we separated them from testes of 7dpp, 9dpp, 11dpp, 17dpp and 29dpp B6xPWK F1 male mice.
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification; RNA-Seq and ATAC-Seq libraries were constructed using TruSeq

value: testis

tag: Stage

value: pachytene spermatocyte

value: germ cells

value: FACS isolated


title: lesionalskinRNA-DAR1-pretreatment


title: Chronic infection without CNS pathology (CP-)-EVs-4

city: Baltimore

first: Kenneth

middle: W.

last: Witwer

state: MD

address: 733 N. Broadway

department: Department of Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description:
Yiyao8_EV_combined
EVs15

data_processing:
Raw reads were first trimmed from polyA-tails using cutadapt software, and the PCR duplicates were removed by collapsing identical sequences with seqkit. De-duplicated reads were trimmed from the 5'-UMI sequences and size-selected using cutadapt software.
Trimmed and size-selected (>15 nt) readswere aligned to custom-curated hg38 reference transcriptomes using Bowtie,allowing 1 mismatch tolerance (-v 1 option) as follows.
First, reads were mapped to RNA species with low sequence complexity and/or high repeat number:rRNA,tRNA,RN7S,snRNA,snoRNA, scaRNA,vault RNA, RNY, and mitochondrial chromosome (mtRNA).Unmapped reads were aligned sequentially tomature miRNA,pre-miRNA, protein-coding mRNA transcripts (mRNA), and long non-coding RNAs (lncRNAs).Unmapped reads were aligned to the remaining transcriptome (otherncRNAs: mostly pseudogenes and non-protein-coding parts of mRNAs). Finally, all remaining unmapped reads were aligned to the human genome reference (rest hg38) corresponding to introns and intergenic regions.
Assembly: Hg38
Supplementary files format and content: Excel file contains all mapped reads

organism: Macaca nemestrina

source_name: Brain

extract_protocol:
bdEVs were separated from frozen occipital cortex tissues using our published protocol with minor modifications (Huang et al., 2022a, 2022b, 2020). Before extraction, a small (∼50 mg) piece of tissue was stored at –80°C for later RNA extraction from brain homogenate (BH).  bdEV RNAs were extracted by adding Trizol LS (Thermo Fisher 10296028) to 100 μL bdEV resuspension. After phase separation, RNAs were purified by miRNeasy Mini Kit solutions (Qiagen217004) and Zymo-Spin I Columns (Zymo ResearchC1003–50) according to the manufacturer's instructions.  BH RNA was extracted by adding Trizol (Thermo Fisher15596018) and homogenizing tissues with Lysing Matrix D (MP Biomedicals116913100) in a benchtop homogenizer (FastPrep-24, MP Biomedicals) at 4.0 m/s for 20 seconds. After homogenization, the supernatant was collected, and RNA was isolated by miRNeasy Mini Kit solutions (Qiagen217004) and Zymo-Spin IIICG Columns (Zymo Research C1006-50-G) following the manufacturer's instructions.
RNA was resuspended in 40 μL Rnase-free water, and 8 µl was used for small RNA libraries construction by the D-Plex Small RNA-seq Kit (Diagenode C05030001). Indexes were attached using the D-Plex Single Indexes for Illumina - Set A (Diagenode C05030010) according to the manufacturer’s protocol.

value: Brain


title: 163


title: B6xPWK_MPac_atac_rep1


title: 162


title: Chronic infection without CNS pathology (CP-)-EVs-3

description:
Yiyao8_EV_combined
EVs14


title: Chronic infection without CNS pathology (CP-)-EVs-2

description:
Yiyao8_EV_combined
EVs13


title: 161


title: B6xPWK_MLep_atac_rep2

value: leptotene spermatocyte


title: lesionalskinRNA-DAR9-pretreatment


title: 158

value: Human pancreas


title: B6xPWK_MLep_atac_rep1


title: B6xPWK_MDip_rna_rep2

value: diplotene spermatocyte


title: 157


title: Acue-EVs-5

description:
Yiyao8_EV_combined
EVs11


title: Chronic infection without CNS pathology (CP-)-EVs-1

description:
Yiyao8_EV_combined
EVs12


title: Acue-EVs-4

description:
Yiyao8_EV_combined
EVs10


title: 167


title: 153


title: 154


title: B6xPWK_MDip_rna_rep1


title: 151


title: 164


title: Acue-EVs-3

description:
Yiyao8_EV_combined
EVs9


title: B6xPWK_MPac_rna_rep2


title: Acue-EVs-2

description:
Yiyao8_EV_combined
EVs8


title: 147


title: 146


title: B6xPWK_MPac_rna_rep1


title: 159


title: Acue-EVs-1

description:
Yiyao8_EV_combined
EVs7


title: 143


title: 156


title: Uninfected-EVs-6

description:
Yiyao8_EV_combined
EVs6


title: B6xPWK_MZyg_rna_rep2

value: zygotene spermatocyte


title: 140


title: 139


title: B6xPWK_MZyg_rna_rep1


title: 138


title: Uninfected-EVs-5

description:
Yiyao8_EV_combined
EVs5


title: B6xPWK_MLep_rna_rep2


title: Uninfected-EVs-4

description:
Yiyao8_EV_combined
EVs4


title: 136


title: 137


title: B6xPWK_MLep_rna_rep1


title: 149


title: 148


title: 134


title: Uninfected-EVs-3

description:
Yiyao8_EV_combined
EVs3


title: B6xPWK_SGA_rna_rep2

value: SGA


title: 133


title: 132


title: 145


title: 131


title: 130


title: Uninfected-EVs-2

description:
Yiyao8_EV_combined
EVs2


title: B6xPWK_SGA_rna_rep1


title: Uninfected-EVs-1

description:
Yiyao8_EV_combined
EVs1


title: 127


title: B6xPWK_FDip_rna_rep2

source_name: ovary

value: ovary

value: diplotene oocyte


title: 126


title: 123


title: 124


title: Chronic infection with CNS pathology (CP+)-BH-4

description:
Yiyao8_BH_combined
BH22


title: B6xPWK_FDip_rna_rep1


title: 122


title: B6xPWK_FPac_rna_rep2

value: pachytene oocyte


title: B6xPWK_FPac_rna_rep1


title: 97


title: B6xPWK_FZyg_rna_rep2

value: zygotene oocyte


title: Chronic infection with CNS pathology (CP+)-BH-1

description:
Yiyao8_BH_combined
BH19


title: 98


title: 99


title: Chronic infection without CNS pathology (CP-)-BH-7

description:
Yiyao8_BH_combined
BH18


title: 121


title: 95


title: 96


title: B6xPWK_FZyg_rna_rep1


title: Chronic infection without CNS pathology (CP-)-BH-6

description:
Yiyao8_BH_combined
BH17


title: 94


title: 92


title: 93


title: B6xPWK_FLep_rna_rep2

value: leptotene oocyte


title: Chronic infection without CNS pathology (CP-)-BH-5

description:
Yiyao8_BH_combined
BH16


title: 91


title: Chronic infection without CNS pathology (CP-)-BH-4

description:
Yiyao8_BH_combined
BH15


title: 90


title: Chronic infection with CNS pathology (CP+)-BH-3

description:
Yiyao8_BH_combined
BH21


title: B6xPWK_FLep_rna_rep1


title: 9


title: Chronic infection without CNS pathology (CP-)-BH-3

description:
Yiyao8_BH_combined
BH14


title: Chronic infection with CNS pathology (CP+)-BH-2

description:
Yiyao8_BH_combined
BH20


title: B6xPWK_FPGC_rna_rep2

value: PGC


title: 120


title: 89


title: B6xPWK_FPGC_rna_rep1


title: 86


title: Chronic infection without CNS pathology (CP-)-BH-2

description:
Yiyao8_BH_combined
BH13


title: 85


title: Chronic infection without CNS pathology (CP-)-BH-1

description:
Yiyao8_BH_combined
BH12


title: 84


title: 88


title: 83


title: 82


title: 81


title: 87


title: 80


title: Acue-BH-3

description:
Yiyao8_BH_combined
BH9

value: Acue


title: 79


title: 8


title: Acue-BH-4

description:
Yiyao8_BH_combined
BH10


title: huIFNAR mouse liver, Human Peg-IFNα2 treatment, 16h, rep 1

data_processing:
Raw reads were trimmed using trim_galore (quality limit: 25)
Trimmed reads were mapped to mm10 using HISAT2 (parameters: default)
Read count extraction and normalization were performed using featureCounts(v2.0.1)(parameters: default)
Assembly: mm10
Supplementary files format and content: E5vE2-1-counts-formal: tab-delimited text files include raw counts for each sample (blood)
Supplementary files format and content: E5vE2-2-counts-formal: tab-delimited text files include raw counts for each sample (liver)
Supplementary files format and content: E5vE2-3-counts-formal: tab-delimited text files include raw counts for each sample (spleen)
Supplementary files format and content: E5vE2-4-counts-formal: tab-delimited text files include raw counts for each sample (lung)
Supplementary files format and content: E5vE2-5-counts-formal: tab-delimited text files include raw counts for each sample (kidney)
Supplementary files format and content: E5vE2-6-counts-formal: tab-delimited text files include raw counts for each sample (heart)
Supplementary files format and content: E5vE2-7-counts-formal: tab-delimited text files include raw counts for each sample (muscle)
Supplementary files format and content: E5vE2-8-counts-formal: tab-delimited text files include raw counts for each sample (intestine)
Supplementary files format and content: E5vE2-9-counts-formal: tab-delimited text files include raw counts for each sample (brain)

source_name: Liver

extract_protocol:
Total RNA was extracted from tissues using RNeasy with DNase treatment (Qiagen).
RNA libraries for RNA-Seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina(NR604-01) following manufacturer's protocols.

value: Liver

value: Human Peg-IFNα2


title: Acue-BH-2

description:
Yiyao8_BH_combined
BH8


title: 77


title: 76


title: 74


title: Acue-BH-1

description:
Yiyao8_BH_combined
BH7


title: 73


title: Uninfected-BH-6

description:
Yiyao8_BH_combined
BH6

value: Uninfected


title: 71


title: Uninfected-BH-5

description:
Yiyao8_BH_combined
BH5


title: 70


title: 7


title: Uninfected-BH-4

description:
Yiyao8_BH_combined
BH4


title: Acue-BH-5

description:
Yiyao8_BH_combined
BH11


title: 66


title: Uninfected-BH-2

description:
Yiyao8_BH_combined
BH2


title: 65


title: Uninfected-BH-3

description:
Yiyao8_BH_combined
BH3


title: 63


title: 62


title: 60


title: Uninfected-BH-1

description:
Yiyao8_BH_combined
BH1


title: 6


title: Rnase R treated-Chronic infection with CNS pathology (CP+)-BH-4

description:
circRNA_CiRISeq_Yiyao9_R1R2_mmul_circRNA_041121_final
circRNA_circExp-raw_counts

data_processing:
The raw reads were first trimmed from contaminating adapter sequences using cutadapt software. The trimmed and size-selected (>15 nt) reads were then aligned using Bowtie2 (default settings) to the manually curated M. mulatta mRNA reference containing a single (main) transcript per each gene (designated with a gene symbol, e.g., GAPDH). All reads which did not align to the above mRNA were mapped to the combined M. mulatta cDNA and ncRNA references from Ensembl (designated with transcript ID, e.g., ENSMMUT00000047080.3). The numbers of reads mapped to each transcript were extracted using eXpress software based on a previous publication (Roberts and Pachter, 2013).
circRNA identification by Sequential Alignment (CiRISeqA):  All reads aligned to the M. mulatta combined cDNA and ncRNA references from Ensembl were discarded. The remaining reads were additionally filtered from non-circular RNA sequences by removing all reads mapped to "non-modified" M. mulatta CircAtlas v.2 references (downloaded from: http://circatlas.biols.ac.cn/) using the same Bowtie settings. Next, the remaining reads were aligned to "duplicated" CircAtlas v.2 reference transcripts that correspond to sequences mapped to the junction regions of circRNAs. The numbers of reads mapped to each duplicated RNA reference were extracted using eXpress software based on a previous publication (Roberts and Pachter, 2013). See also Supplementary Figure 2.
circRNA identification by circExplorer2:  The genome and gene annotations for M. mulatta were obtained from UCSC (BCM Mmul_8.0.1/rheMac8). First, raw files were aligned to the genome using STAR (chimSegmentMin 10), and the chimeric junction files were used to count circRNAs using circExplorer2. circRNAs identified by both our custom pipeline (above) and circExplorer2 were included in the following analysis.
Assembly: M. mulatta
Supplementary files format and content: Excel files contains all mapped reads

extract_protocol:
BH RNA was extracted by adding Trizol (Thermo Fisher15596018) and homogenizing tissues with Lysing Matrix D (MP Biomedicals116913100) in a benchtop homogenizer (FastPrep-24, MP Biomedicals) at 4.0 m/s for 20 seconds. After homogenization, the supernatant was collected, and RNA was isolated by miRNeasy Mini Kit solutions (Qiagen217004) and Zymo-Spin IIICG Columns (Zymo Research C1006-50-G) following the manufacturer's instructions.
1 µg of BH RNAs was incubated with 1 U/µg RNase R (Lucigen RNR07250) at 37°C for 30 min. RNase R-treated RNAs were then re-isolated by RNA Clean & Concentrator™-5 (Zymo Research R1014) according to the manufacturer’s protocol. 100 ng of total BH RNA with and without RNase R treatment was then used to construct cDNA libraries by Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina 20072063). A Ribo-Zero Plus kit was used to deplete ribosomal RNA in these samples, and library construction was then done per manufacturer’s protocol. Indexes were attached using IDT for Illumina RNA UD Indexes according to the manufacturer’s protocol. The yield and size distribution of the total RNA libraries were assessed using the Fragment Bioanalyzer™ system with DNA 1000 chip (Agilent 5067-1505). Multiplexed libraries were equally pooled to 1nM and sequenced with the NovaSeq 6000 system (Illumina) and NovaSeq 6000 S2 Reagent Kit v1.5 (300 cycles) (Illumina 20028314).


title: 57


title: Rnase R treated-Chronic infection with CNS pathology (CP+)-BH-2


title: 58


title: 56


title: 72


title: 55


title: Rnase R treated-Chronic infection with CNS pathology (CP+)-BH-1


title: Rnase R treated-Chronic infection without CNS pathology (CP-)-BH-6


title: 52


title: Rnase R treated-Chronic infection without CNS pathology (CP-)-BH-7


title: 51


title: 53


title: 54


title: 5


title: 50


title: 67


title: 48


title: 47


title: 69


title: Rnase R treated-Chronic infection without CNS pathology (CP-)-BH-3


title: 44


title: 46


title: 42


title: Rnase R treated-Chronic infection without CNS pathology (CP-)-BH-2


title: 41


title: Rnase R treated-Chronic infection without CNS pathology (CP-)-BH-1


title: Rnase R treated-Acue-BH-5

value: Rnase R treated-Acue-BH-5


title: 40


title: 4


title: 37


title: R431

city: Los Angeles

first: Suhas

middle: G

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

description: scRNA seq

data_processing:
Bulk RNA-seq  The reads were mapped with STAR 2.5.3a to the Macaca mulatta genome (Mmul 8.0.1) or to the human genome (GRCh38). The counts for each gene were obtained by using the options --quantMode GeneCounts. Differential expression analyses were carried out using DESeq2. The normalized counts were obtained from the DESeq2 analysis. Principal Component Analysis (PCA) was performed with the plotPCA function in DESeq2 after regularized log transformation. Heatmaps were plotted on the log2 value of the normalized counts. Inference of GO terms, Wiki pathways, and KEGG pathways were generated using Enrichr 63.
Single-cell (sc)RNA-seq: Data processing including quality control, read alignment (to the reference genome Mmul 8.0.1), and gene quantification was conducted using the 10X Cell Ranger software (version 2.1.1). The samples were then merged into a single expression matrix using the cellranger aggr pipeline. The R package Seurat (v3.1.2) was used to cluster the cells in the merged matrix. Cells with less than 500 transcripts or 100 genes, or more than 5% of mitochondrial expression were first filtered out as low-quality cells. The Seurat function NormalizeData was used to normalize the raw counts. Variable genes were identified using the FindVariableGenes function. The ScaleData function was used to scale and center expression values in the dataset, the number of unique molecular identifiers (UMI) was regressed against each gene. Principal component analysis (PCA), and uniform manifold approximation and projection (UMAP) were used to reduce the dimensions of the data, and the first two dimensions were used in the plots. The FindClusters function was used to cluster the cells. Marker genes were found using the FindAllMarkers function for each cluster, which employs the Wilcoxon Rank Sum Test to determine the significance and the Benjamini-Hochberg Procedure to correct for multiple comparisons. Cell types were annotated based on the marker genes and their match to canonical markers. The module scores were calculated using the AddModuleScore function. Sub-clustering on the amnion cells was performed. The same functions described above were used to obtain the sub-clusters. We obtained eight high-quality scRNA-seq profiles from CAD samples. Analysis of cellular trajectory by RNA velocity was performed using the Python package scVelo 64. In one Ctrl sample we did not detect any amnion cells and therefore we excluded this sample from the analysis. Thus, final analyses were conducted on 7 samples (ctrl n=1; LPS n=3; and Adalimumab+LPS n=3). In order to illustrate the variations of cell types in amnion after intrauterine infection we used hdWGCNA package 28 to perform co-expression network analysis on genes expressed in at least 5% of the cells. MetacellsByGroups function was used to construct metacells in each treatment group.  The resulting metacells expression matrix was normalized by calling NormalizeMetacells function and then used for network analysis. In order to ensure scale-free topology of the co-expression network TestSoftPowers function was used to perform parameter sweep. The sweep identified 10 as the optimum soft power threshold to use when constructing the co-expression network by calling ConstructNetwork function with otherwise default parameters. WGCNA dendrogram was visualized with PlotDendrogram function whereas ModuleFeaturePlot was used to map harmonized module eigengenes, computed with ModuleEigengene function, onto the dimensionality reduction plot. The modules identified by hdWGCNA analysis were functionally characterized by performing enrichment tests with enrichR package. For each of the modules, a set of 100 most connected genes (ModuleConnectivity function) was tested for enrichment. Top 10 GO Biological Process terms for each module with adjusted p-value <0.05 were shown along with the enrichment score.
Assembly: Macaca mulatta genome (Mmul 8.0.1)
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Bulk RNA-seq_Raw counts_Rhesus_Amnion_Presicce.txt
Supplementary files format and content: Bulk RNA-seq_Raw counts_Human_Amnion_Presicce.txt

organism: Macaca mulatta

source_name: chorioamniondecidua

extract_protocol:
For scRNA seq experiements of chorioamniondecidua samples were collected right after delivery, digested, and cell suspension was sorted for live cells. For both human and rhesus bulk RNA seq experiments, amnion was physically separated from chorion and decidua, snap-frozen, and RNA was harvested using Trizol reagent.
Bulk RNAseq:  Fifteen amnion samples were used (ctrl n=3; LPS n=6; and Adal+LPS n=6). The integrity of purified total RNA from amnion was assessed using the RNA High-Sensitivity Assay on the TapeStation 2200 (Agilent Technologies). 200-300 ng of starting material were used as input material for the NEBNext rRNA Depletion kit (cat# E6350). RNA libraries were then prepared using the NEBNext Ultra II RNA kit (cat# E7765). Two hundred ng of each final library was subject to capture hybridization using Illumina TruSeq Exome, (cat #20020490) using Illumina Exome Panel (cat #20020183) according to the manufacturer’s instructions. Quality control for the final libraries was performed using the DNA D1000 Assay (TapeStation 2200 - Agilent Technologies) and quantified using a Qubit dsDNA BR Assay (Life Technologies). Diluted libraries were pooled and sequenced 50 single-end on a HiSeq3000 (Illumina).
Single-cell (sc)RNA-seq: For scRNA-seq analysis, eight unseparated chorioamnion-decidua (CAD) samples were used (Ctrl n=2; LPS n=3; and Adal+LPS n=3. Note that 6/8 tissues were also used for bulk RNA-seq analysis (Supplementary Table I). Live-sorted CAD cells were microfluidically partitioned with single cell capture, barcoding, and library construction (10X genomics chromium platform, Pleasanton, California).  Single-cell RNA-seq libraries were prepared using the 10X Single Cell 3′ v2 Reagent Kits. Specifically, single cell suspensions were loaded on a Chromium Controller instrument to generate single-cell Gel Bead-In- EMulsions (GEMs). GEM-RT were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA), following which, GEMs were harvested and the cDNAs were amplified and cleaned up with SPRIselect Reagent Kit. Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA). Sequencing libraries were loaded on a NovaSeq2 (Illumina, San Diego, CA) with a custom sequencing setting (26bp for Read 1 and 91bp for Read 2).

treatment_protocol: intra-amniontic injection of LPS or saline. Intra-amniotic + subcutaneous injection Adalimumab

value: chorioamniondecidua

value: chorioamniondecidua cells

value: IA+SC Adal + IA LPS


title: R438

description: scRNA seq


title: R439

description: scRNA seq


title: Rnase R treated-Chronic infection without CNS pathology (CP-)-BH-5

value: Brain


title: 34

value: Human pancreas


title: 35


title: 33


title: R442

description: scRNA seq

value: IA LPS


title: R437

description: scRNA seq


title: 32


title: 31


title: Rnase R treated-Acue-BH-2

value: Rnase R treated-Acue-BH-2


title: Rnase R treated-Acue-BH-1

value: Rnase R treated-Acue-BH-1


title: Rnase R treated-Acue-BH-3

value: Rnase R treated-Acue-BH-3


title: 30


title: 3


title: Rnase R treated-Uninfected-BH-5

value: Rnase R treated-Uninfected-BH-5


title: 36


title: 25


title: R430

description: scRNA seq

value: IA saline


title: R423

description: scRNA seq


title: R429

description: scRNA seq


title: 38


title: 2


title: Rnase R treated-Uninfected-BH-4

value: Rnase R treated-Uninfected-BH-4


title: 19


title: Rnase R treated-Acue-BH-4

value: Rnase R treated-Acue-BH-4


title: 18


title: AM443T

description:
bulk RNAseq
AM443 Ad+LPS

source_name: amnion

value: amnion

value: amnion cells


title: Rnase R treated-Uninfected-BH-3

value: Rnase R treated-Uninfected-BH-3


title: 16


title: 17


title: 14


title: Rnase R treated-Uninfected-BH-2

value: Rnase R treated-Uninfected-BH-2


title: AM439T

description:
bulk RNAseq
AM439 Ad+LPS


title: AM438T

description:
bulk RNAseq
AM438 Ad+LPS


title: Rnase R treated-Uninfected-BH-1

value: Rnase R treated-Uninfected-BH-1


title: 13


title: AM431T

description:
bulk RNAseq
AM431 Ad+LPS


title: Rnase R untreated-Chronic infection with CNS pathology (CP+)-BH-4

description: mRNA_Yiyao9_TMM_normalized_cpm_cdna_ncrna_121