title: drug-resistant cell line T24_THP, biological rep1

city: Shenyang

first: Chuize

last: Kong

state: Liaoning

address: 155 Nanjing North Street, Heping District

department: Department of Urology

institute: The First Hospital of China Medical University

description: Gene expression data from drug-resistant bladder cancer cell T24_THP established by repeated exposure to pirarubicin treatment

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing:
Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.
The standard for differently expressed genes screening: 1) Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2 2) p-value (Condition pair) < 0.05

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix WT PLUS Reagent Kit(Cat#902280, Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: The human bladder cancer cell line T24 were bought from the Type Culture Collection of the Chinese Academy of Sciences (Shanghai, China) and cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) under environment where the temperature is 37°C and CO2 concentration in the air is 5%.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: In order to establish the multiple drug resistance (MDR) bladder cancer cell line, T24 was initially cultured in the medium containing 5ng/ml pirarubicin for 24 hours and then replaced with normal culture medium without drug. Once the cells returned to an optimal state, the exposure to pirarubicin as described above was repeated with a gradually increasing concentration gradient containing 5, 10, 20, 50, 100, 200, 500 to 1000 ng/ml. In order to maintain the resistance, we added drugs at regular interval (every 2-3 weeks depends on cell state and counts). Parent cell line T24 were also cultured during the process of resistance cell establishment so that we can measure and compare IC50 continuously to ensure the development of resistance. The whole process lasted for over 6 months and finally we obtained the MDR bladder cell line T24/THP after a series of drug resistance tests were carried out.

tag: cell line

value: bladder cancer cell

tag: phenotype

value: drug-resistant


title: H200

status: Public on Nov 01 2024

type: RNA

city: Washington

first: Nikki

last: Posnack

state: DC

address: 111 Michigan Avenue, NW

country: USA

institute: Children's National Research Institute

hyb_protocol: Overnight 16 hours at 45 degrees celcius

data_processing: Transcriptome Analysis Console (Applied Biosystems)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Right atrial tissue

label_protocol: GeneChip WT Plus Reagent kit

growth_protocol: Fresh cardiac tissue removed during surgery

extract_protocol: RNeasy fibrous tissue kit

tag: age group

value: Toddler/Pre School


title: IyerS_RNA028_17

type: SRA

city: Pittsburgh

first: Smita

last: Iyer

state: Pennsylvania

address: 3550 Terrace Street

department: Pathology

institute: University of Pittsburgh School of Medicine

description: FFPE Spatial Transcriptome sequencing

library_source: transcriptomic

data_processing:
Raw sequencing data was processed using Nanostring's GeoMx DSP Control Center Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode) Library strategy: Spatial Transcriptomics
Assembly: N/A, sequencing of synthetic tags and aligment to whitelist of RTS IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: dcc

organism: Macaca mulatta

source_name: Brain-Prefrontal Cortex

extract_protocol:
5um sections were cut from Paraformaldehyde-Fixed Paraffin-Embedded slides. Samples were incubated with either DNA-oligo barcoded RNA-ISH probes or antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring reagents according to manufacturer's specifications

treatment_protocol: rhesus macaques were infected intravenousely with SIVmac251

tag: tissue

value: Brain-Prefrontal Cortex

tag: treatment

value: IgG


title: drug-sensitive parental cell line T24, biological rep1

country: China

description: Gene expression data from drug-sensitive bladder cancer cell T24

tag: cell type

value: drug-sensitive parental


title: Caco-2 site 2 rep 1 conc3

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
cell lysate
h3.h3.2.c08
2.1.C08

data_processing:
Reads were aligned using STAR alignment on Qiagen's online analysis portal RAP version 1.0
match score 1, mismatch cost 2, discard short reads (<15), insertion and deletion cost 3, length and similarity fraction 0.8
Raw counts were logCPM normalized and filtered for low abundance (4) and variance (15).
Normalized counts were analyzed for differential expression using Limma.
Assembly: for human GRCh38.noalt.106, for rainbow trout USDA_OmykA_1.1.105
Supplementary files format and content: count files are provided as .txt files

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to extract of interest 24 hours after seeding at 35,000 cells per well

tag: site


title: B16-HSV1

city: 上海

first: 玮玮

last: 代

state: 上海

address: 徐汇区东安路131号

institute: 复旦大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

growth_protocol: B16 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 mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: B16 cells were treated with 0.1MOIHSV for 12h

value: melanoma cell lines

tag: genotype

value: WT

value: B16 cells were infected with HSV for 12 hr


title: IyerS_RNA028_15

description: FFPE Spatial Transcriptome sequencing


title: B16-HSV2


title: B16-PBS3

value: DMEM


title: Caco-2 site 2 rep 1 conc4

description:
cell lysate
h3.h3.2.d08
2.1.D08


title: Caco-2 site 2 rep 1 conc1

description:
cell lysate
h3.h3.2.a08
2.1.A08


title: B16-PBS2


title: B16-PBS1


title: drug-resistant cell line T24_THP, biological rep2


title: IyerS_RNA028_14

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA028_13

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA028_16

description: FFPE Spatial Transcriptome sequencing


title: H199


title: H197

value: Infant


title: H185


title: EXP1_REPLICATE_3_IRF1.KO.FoB.03

city: New York

first: Jessica

middle: N

last: Peel

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Trimming: TrimGalore v.0.4.4 with settings: phred33 scores, paired, nextera adapters
Alignment: STAR aligner v.2.5.2a with default setings
Counting: Htseq-count v0.6.1p1 with settings: unstranded and using GRCm39 annotations
edgeR for downstream analysis to find differentially expressed genes among pairs of sample groups
Assembly: mm10
Supplementary files format and content: JPEEL_2023_RNAseq_count_table.txt

molecule: polyA RNA

source_name: spleen

extract_protocol:
RNA was isolated using the Single Cell RNA Purification kit (Norgen)
RNA libraries were prepared for sequencing using standard Illumina protocols. All libraries were prepared at Genewiz.
Ultra-Low Input RNA-Seq

tag: strain

value: spleen

value: IRF1 KO Follicular B cells

value: IRF1 KO

value: non-infected


title: H190


title: HAEC_Normoxia_2

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

department: Medicine

institute: The University of Chicago

data_processing:
RNA-seq reads were pseudoaligned using kallisto 0.46.1
The Kallisto index was made with default parameters and the GENCODE (Release 39 (GRCh38.p13) and was run in quant mode with default parameters
Assembly: hg38
Supplementary files format and content: tsv

source_name: Aorta

growth_protocol: 1% O2 hypoxia chamber for Sustained Hypoxia,

extract_protocol:
Total
Oligo-dT mRNA directional

treatment_protocol: Normoxia vs Sustained Hypoxia

value: Aorta

value: Primary HAEC

value: Endotheial cells

value: Room Air


title: drug-resistant cell line T24_THP, biological rep3

value: bladder cancer cell

value: drug-resistant


title: drug-sensitive parental cell line T24, biological rep2


title: H175

value: Toddler/Pre School


title: H182


title: HAEC_Normoxia_1


title: drug-sensitive parental cell line T24, biological rep3

value: drug-sensitive parental


title: Caco-2 site 2 rep 1 conc2

description:
cell lysate
h3.h3.2.b08
2.1.B08


title: EXP1_REPLICATE_3_IRF1.KO.Trans.2.03

value: IRF1 KO Transitional 2 cells


title: HAEC_ 1% Sustained Hypoxia_4

value: WT

value: Hypoxia


title: EXP1_REPLICATE_3_IRF1.KO.MZB.03

value: IRF1 KO Marginal Zone B cells


title: EXP1_REPLICATE_3_IRF1.KO.Trans.1.03

value: IRF1 KO Transitional 1 cells


title: H172

value: Adolescent/Young Adult


title: EXP1_REPLICATE_2_IRF1.KO.MZB.02

value: spleen


title: IyerS_RNA028_10

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex

value: IgG


title: H166

value: School Age


title: H164


title: HAEC_ 1% Sustained Hypoxia_3

value: Aorta

value: Primary HAEC


title: EXP1_REPLICATE_2_IRF1.KO.Trans.1.02

value: IRF1 KO

value: non-infected


title: EXP1_REPLICATE_2_IRF1.KO.Trans.2.02


title: IyerS_RNA028_8

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_2_IRF1.KO.FoB.02

value: IRF1 KO Follicular B cells


title: HAEC_ 1% Sustained Hypoxia_2

value: Endotheial cells


title: IyerS_RNA028_12

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA028_9

description: FFPE Spatial Transcriptome sequencing


title: H163

value: Infant


title: PDAC PDX, Sample 8, replicate 12

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 conversion software 2.20.0
Individual lane files were combined into one FASTQ file for each sample
Salmon (v1.5.2 with options gcBias and seqBias) was used to derive read count, gene-length and total read count normalized counts (TPM)
Assembly: GENCODE Release 38 (GrCh38.p13)
Supplementary files format and content: comma-separated file containing normalized TPM for all samples

source_name: PDAC PDX

growth_protocol: Primary PDAC tumors from de-identified patients were confirmed by H&E staining before being implanted subcutaneously into 6 to 8-week-old female NSG mice.

extract_protocol:
Total RNA was extracted from cassettes using the AllPrep DNA/RNA FFPE Kit (Qiagen, 80234). RNA was quantified using the Qubit RNA HS Assay Kit (Invitrogen, Q32852) and quality assessed with the 4150 TapeStation System (Agilent) and RNA ScreenTape Analysis Kit (Agilent, 5067-5576).
For samples below dv200 30%, a 1.1X or a 1.1X and successive 1.0X bead cleanups was completed using RNAClean XP Beads (Beckman Coulter, A63987) cDNA libraries were prepped with the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche, KR1151) if total RNA was >25ng and >24% dv200. If dv200 was below 50%, the low input KAPA Prep protocol was used. 17 cycles were used for the final PCR cycle. The remaining samples were prepped using AmpliSeq for Illumina Transcriptome Human Gene Expression Panel (Illumina, 20019170, 20019102).16 cycles were used to amplify target regions in the cDNA

value: PDAC PDX


title: HAEC_ 1% Sustained Hypoxia_1

value: WT


title: IyerS_RNA028_7

description: FFPE Spatial Transcriptome sequencing


title: H162

value: Toddler/Pre School


title: PDAC PDX, Sample 8, replicate 11


title: IyerS_RNA028_11

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_1_IRF1.KO.MZB.01

value: IRF1 KO Marginal Zone B cells


title: IyerS_RNA028_5

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 8, replicate 10


title: H157


title: EXP1_REPLICATE_1_IRF1.KO.FoB.01


title: H155


title: EXP1_REPLICATE_1_IRF1.KO.Trans.2.01

value: IRF1 KO Transitional 2 cells


title: H148


title: PDAC PDX, Sample 1, replicate 9


title: PDAC PDX, Sample 1, replicate 8


title: EXP1_REPLICATE_1_IRF1.KO.Trans.1.01

value: IRF1 KO Transitional 1 cells


title: IyerS_RNA028_3

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA028_1

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_3_WT.MZB.03

value: C57BL/6 mouse

value: spleen

value: WT Marginal Zone B cells


title: PDAC PDX, Sample 2, replicate 7


title: PDAC PDX, Sample 2, replicate 8


title: IyerS_RNA027_24

description: FFPE Spatial Transcriptome sequencing

source_name: Brain-Hippocampus

value: Brain-Hippocampus

value: IgG


title: EXP1_REPLICATE_3_WT.FoB.03

value: WT Follicular B cells


title: EXP1_REPLICATE_3_WT.Trans.2.03

value: WT Transitional 2 cells


title: IyerS_RNA028_4

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: H146


title: PDAC PDX, Sample 6, replicate 14


title: H145


title: H161


title: EXP1_REPLICATE_3_WT.Trans.1.03

value: WT Transitional 1 cells

value: non-infected


title: H137

value: Adolescent/Young Adult


title: H139


title: PDAC PDX, Sample 6, replicate 13

value: PDAC PDX


title: PDAC PDX, Sample 1, replicate 7


title: IyerS_RNA028_2

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_2_WT.MZB.02

value: WT


title: H125

value: Infant


title: IyerS_RNA027_22

description: FFPE Spatial Transcriptome sequencing


title: H129

value: Toddler/Pre School


title: PDAC PDX, Sample 6, replicate 12


title: IyerS_RNA027_25

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_2_WT.FoB.02


title: IyerS_RNA027_21

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 6, replicate 11


title: H123


title: IyerS_RNA027_23

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_2_WT.Trans.2.02


title: PDAC PDX, Sample 6, replicate 8


title: IyerS_RNA027_19

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 6, replicate 10


title: H119

value: School Age


title: H115


title: PDAC PDX, Sample 6, replicate 7


title: IyerS_RNA027_18

description: FFPE Spatial Transcriptome sequencing


title: H106


title: IyerS_RNA027_17

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_1_WT.FoB.01


title: PDAC PDX, Sample 8, replicate 9


title: EXP1_REPLICATE_1_WT.Trans.2.01


title: IyerS_RNA027_16

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 8, replicate 8


title: EXP1_REPLICATE_1_WT.Trans.1.01


title: IyerS_RNA027_20

description: FFPE Spatial Transcriptome sequencing


title: H103


title: H102


title: IyerS_RNA027_15

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_2_WT.Trans.1.02


title: IyerS_RNA027_14

description: FFPE Spatial Transcriptome sequencing


title: EXP1_REPLICATE_1_WT.MZB.01


title: PDAC PDX, Sample 8, replicate 6


title: H101


title: PDAC PDX, Sample 8, replicate 7


title: cMyc-GFP+ LZ GC-B cells, KO4

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO4

data_processing:
The RSEM package (version 1.3.0) and STAR (2.5.2a) were used to align reads to the mouse Ensembl GRCm38 transcriptome.
Raw counts were normalised and differential expression analysis was performed with the DESeq2 package (version 1.18.1) within the R programming (version 3.4.3)
Assembly: Mouse Ensembl GRCm38
Supplementary files format and content: VSD normalised expression values, where rows represent mouse Ensembl genes and columns represent individual samples.

source_name: Spleen

extract_protocol:
Spleens were crushed and filtered with a 70µM mesh strainer. Harvested splenic B-cells were enriched by CD43, Ter119 and CD4 negative selection using MACS LS Columns (Miltenyi Biotec). Single-cell suspensions were stained with antibodies and sorted by flow cytometry. RNA was extracted from the sorted samples by TRIzol coupled to RNAeasy Mini Kit (#74104, QIAGEN, for cMyc+ GC-B cells).
Libraries were prepared with TruSeq Standard mRNA Sample Prep Kit (Illumina) following the manufacturer's protocols.

treatment_protocol: B cells from 8-15 week old HEL-specific BCR expressing B cells from male and female mice were adoptively transferred into congenic mice and immunized with 2x10^8 HEL3x-SRBC. Splenic GC-B cells from these mice were sorted by flow cytometry after five days. B cells from females and males from miR-155-sufficient and -deficient, respectively, were mainly used for adoptive transfer.

value: Spleen

value: Primary

value: GC-B cells

value: miR-155 KO

value: 5 days after HEL3x-SRBC immunization


title: cMyc-GFP+ LZ GC-B cells, KO5

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO5


title: IyerS_RNA027_13

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus

value: IgG


title: H096


title: IyerS_RNA027_12

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 8, replicate 5


title: H083


title: cMyc-GFP+ LZ GC-B cells, KO3

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO3


title: cMyc-GFP+ LZ GC-B cells, KO2

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO2


title: PDAC PDX, Sample 8, replicate 4


title: H097


title: cMyc-GFP+ LZ GC-B cells, KO1

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO1


title: H081


title: PDAC PDX, Sample 10, replicate 12


title: cMyc-GFP+ LZ GC-B cells, WT5

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT5


title: IyerS_RNA027_9

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 10, replicate 11


title: IyerS_RNA027_10

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 10, replicate 10


title: cMyc-GFP+ LZ GC-B cells, WT4

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT4


title: IyerS_RNA027_8

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 10, replicate 9


title: cMyc-GFP+ LZ GC-B cells, WT3

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT3


title: H079


title: IyerS_RNA027_7

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 10, replicate 8


title: cMyc-GFP+ LZ GC-B cells, WT2

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT2


title: IyerS_RNA027_11

description: FFPE Spatial Transcriptome sequencing


title: H073


title: PDAC PDX, Sample 10, replicate 7


title: HAEC_Normoxia_3

value: Aorta

value: Primary HAEC

value: Endotheial cells

value: Room Air


title: PDAC PDX, Sample 4, replicate 9


title: IyerS_RNA027_5

description: FFPE Spatial Transcriptome sequencing


title: cMyc-GFP+ LZ GC-B cells, WT1

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT1


title: IyerS_RNA027_6

description: FFPE Spatial Transcriptome sequencing


title: RNA-seq_Dif-FGSC_Rep3

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
For RNA pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using Hisat2 (version 4.8.2) (Pertea et al., 2016) with default parameters
Gene expression FPKM was calculated by Cufflinks (version 2.2.1) (Trapnell et al., 2012) using the RefSeq database from the UCSC genome browser. Sequencing depth was normalized.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: Differentiated female germ stem cells

growth_protocol: FGSCs were cultured on mitotically inactivated SIM mouse embryo-derived thioguanine-and ouabain-resistant (STO; ATCC) feeders in minimum essential medium alpha (MEMα; Invitrogen), which was supplemented with 10% fetal bovine serum (FBS; Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (mLif; Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF; PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF; BD Biosciences), 10 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF; R&D Systems), 1 mM nonessential amino acids (NEAA; Invitrogen Life Sciences), 2 mM L-glutamine (Amresco), 1 mM sodium pyruvate (Amresco) and 0.1 mM-mercaptoethanol (Sigma-Aldrich).

extract_protocol:
Total RNA were extracted from 2-6 million cells using Trizol Reagent (Invitrogen). The RNA quality was assessed using Agilent Bioanalyzer 2100
RNA-Seq libraries were prepared using the KAPA Stranded mRNA-Seq kit following the manufacturer’s instructions

treatment_protocol: Induction of FGSC differentiation, STO feeder cells were removed from FGSCs cultured by differential adherence. FGSCs were then harvested and seeded on freshly mitotically inactivated granulosa cells (GCs) in differentiation medium containing MEMα supplemented with 10% FBS, 10 ng/mL bFGF, 10 ng/mL bone morphogenic protein (BMP4; PeproTech), 0.1 μmol/L retinoic acid (RA; Sigma-Aldrich), 1 mM nonessential amino acids (NEAA; Invitrogen Life Sciences), 2 mM L-glutamine (Sigma-Aldrich), 1 mM sodium pyruvate (Amresco) and 0.1 mM -mercaptoethanol (Sigma-Aldrich).

value: Differentiated female germ stem cells

tag: passages


title: H078


title: RNA-seq_Dif-FGSC_Rep2


title: PDAC PDX, Sample 4, replicate 8

value: PDAC PDX


title: H055


title: PDAC PDX, Sample 4, replicate 7


title: IyerS_RNA027_3

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA027_2

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA028_6

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: H052


title: H051

value: Adolescent/Young Adult


title: H067

value: Infant


title: H050

value: Toddler/Pre School


title: RNA-seq_FGSC_Rep3

source_name: Female germ stem cells

value: Female germ stem cells


title: PDAC PDX, Sample 4, replicate 6


title: H048


title: IyerS_RNA027_1

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 4, replicate 5


title: H057


title: IyerS_RNA027_4

description: FFPE Spatial Transcriptome sequencing


title: No Template Control 2

description: FFPE Spatial Transcriptome sequencing


title: H044


title: RNA-seq_FGSC_Rep2


title: RNA-seq_FGSC_Rep1


title: IyerS_RNA026_24

description: FFPE Spatial Transcriptome sequencing


title: Dif-FGSC-Rep2

library_source: genomic

data_processing:
For Hi-C pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16). Then HiCPro (version 2.7) (Servant et al., 2015) was used to map, process and iteratively corrected normalization. Briefly, reads were independently aligned to the mouse reference genome (mm9) with the bowtie2 algorithm (Langmead and Salzberg, 2012). We discarded the uncut DNA reads, re-ligation reads, continuous reads and PCR artifacts. Unique mapped reads (MAPQ>10) were used to build the contact matrix.
Compartment analysis are used R package (HiTC) (Servant et al., 2012) pca.hic function to generate the PC1 eigenvectors using 400kb normalized matrices with following options: (normPerExpected=TRUE, npc=1)
TAD calling is done using Direction Index  method as previously described (Dixon et al., 2012)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files

molecule: genomic DNA

source_name: Differentiated Female germline stem cell

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014)
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Induction of FGSC differentiation, STO feeder cells were removed from FGSCs cultured by differential adherence. FGSCs were then harvested and seeded on freshly mitotically inactivated granulosa cells (GCs) in differentiation medium containing MEMα supplemented with 10% FBS, 10 ng/mL bFGF, 10 ng/mL bone morphogenic protein (BMP4; PeproTech), 0.1 μmol/L retinoic acid (RA; Sigma-Aldrich), 1 mM nonessential amino acids (NEAA; Invitrogen Life Sciences), 2 mM L-glutamine (Sigma-Aldrich), 1 mM sodium pyruvate (Amresco) and 0.1 mM -mercaptoethanol (Sigma-Aldrich).

tag: restriction enzyme

value: HindIII


title: RNA-seq_Dif-FGSC_Rep1


title: PDAC PDX, Sample 13, replicate 1


title: IyerS_RNA026_23

description: FFPE Spatial Transcriptome sequencing


title: H046


title: PDAC PDX, Sample 10, replicate 5


title: PDAC PDX, Sample 10, replicate 4


title: IyerS_RNA026_22

description: FFPE Spatial Transcriptome sequencing


title: Dif-FGSC-Rep1


title: FGSC-Rep2

source_name: Female germline stem cell


title: H042

value: School Age


title: PDAC PDX, Sample 6, replicate 6


title: IyerS_RNA026_21

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 6, replicate 5


title: H037


title: H040


title: PDAC PDX, Sample 4, replicate 4


title: RAW 264.7 cells, Media control (c_MEDIA3)

city: Singapore

first: Brenda

last: Tien

address: 60 Nanyang Drive

country: Singapore

institute: NTU

description: Mouse mRNA

data_processing:
Raw reads were quality and adapter trimmed using bbduk
Using the rsem-calculate-expression wrapper script from RSEM, the mRNA reads were mapped using bowtie2 v 2.4.1 to the GRCm39 reference genome and feature counts were obtained sequentially using with the rsem-calculate-expression wrapper
Differential expression was determined using DESeq2
Genome_build: Mus musculus GRCm39
Supplementary_files_format_and_content: counts.txt (Text file containing raw counts of sequencing reads for each sample)
Supplementary_files_format_and_content: normalizedTMM_counts.txt (Normalized abundance (using trimmed means of M values))
Supplementary_files_format_and_content: conditions.csv (Sample metadata csv file used in DGE analysis in DESeq2)

source_name: RAW 264.7 macrophages media control

growth_protocol: RAW264.7 macrophages were grown overnight in DMEM with 10% FBS supplementation at 37ᵒC with 5% CO2.

extract_protocol:
Cells were washed once with PBS and resuspended in 1 mL  Trizol. RNA was extracted using zymo direct-zol rna miniprep kit and purified using RNA Clean & concentrator (Zymo Research) as per manufacturer's protocol.
The total RNA was converted to double stranded cDNA and made into libraries using the TruSeq Stranded mRNA Sample Preparation as per manufacturer's instruction but without the oligo dT purification. The sequencing was done using the HiSeq Rapid SBS Kit V2 200 cycles.

treatment_protocol: Macrophages were either treated with LPS control or with E. faecalis at various MOI indicated in the presence or absence of LPS stimulation and incubated for 6 hours at 37ᵒC with 5% CO2.

value: macrophage

value: WT

tag: infection

value: CTRL

tag: moi

value: no LPS


title: FGSC-Rep1


title: IyerS_RNA026_20

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: IyerS_RNA026_19

description: FFPE Spatial Transcriptome sequencing


title: H039

value: Neonate


title: RAW 264.7 cells, Media control (c_MEDIA2)

description: Mouse mRNA


title: PDAC PDX, Sample 6, replicate 4


title: H026


title: RAW 264.7 cells, Media control (c_MEDIA1)

description: Mouse mRNA


title: IyerS_RNA026_17

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 12, replicate 3


title: IyerS_RNA026_18

description: FFPE Spatial Transcriptome sequencing


title: RAW 264.7 cells, Media + LPS control (c_LPS2)

description: Mouse mRNA

source_name: RAW 264.7 macrophages media with LPS control

value: LPS


title: RAW 264.7 cells, Media + LPS control (c_LPS3)

description: Mouse mRNA


title: PDAC PDX, Sample 12, replicate 2


title: H012


title: RAW 264.7 cells, Media + LPS control (c_LPS1)

description: Mouse mRNA


title: H032


title: IyerS_RNA026_15

description: FFPE Spatial Transcriptome sequencing


title: H007


title: IyerS_RNA026_16

description: FFPE Spatial Transcriptome sequencing


title: RAW 264.7 cells, MOI 1 +LPS (c_1XLPS3)

description: Mouse mRNA, OG1RF total RNA

source_name: RAW 264.7 macrophages infected with E. faecalis

value: Enterococcus faecalis OG1RF


title: PDAC PDX, Sample 2, replicate 5


title: IyerS_RNA026_13

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 7, replicate 6


title: PDAC PDX, Sample 7, replicate 5


title: H010


title: PDAC PDX, Sample 12, replicate 1


title: RAW 264.7 cells, MOI 1 +LPS (c_1XLPS2)

description: Mouse mRNA, OG1RF total RNA


title: IyerS_RNA026_12

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA026_11

description: FFPE Spatial Transcriptome sequencing


title: RAW 264.7 cells, MOI 1 +LPS (c_1XLPS1)

description: Mouse mRNA, OG1RF total RNA


title: HR_28_V3

city: Haifa

first: Shai

middle: S

last: Shen-Orr

address: 1st Efron Street

department: Immunology

country: Israel

institute: Rappaport Institute of Medical Research, Faculty of Medicine and Faculty of Biology, Technion

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre- mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Fragmented and labeled sscDNA were diluted in hybridization buffer at a concentration of 23 ng/ul for a 2.3 ug total and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Human Clariom S was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis

data_processing: Preprocessing was perfomed in R using the oligo package. Raw CEL files were summarized and normalized using RMA and quantile normalization (oligo::rma), using the probe definition and annotation packages pd.clariom.s.human and clariomshumantranscriptcluster.db

source_name: Whole blood

label_protocol: The quality of total RNA was first assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT Plus Kit (Affymetrix, Santa Clara, CA). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix, starting from 5.5 ug of ssDNA. Each eukaryotic GeneChip® probe array contains probe sets for several B. subtilis genes that are absent in the samples analyzed (lys, phe, thr, and dap). This Poly-A RNA Control Kit contains in vitro synthesized, polyadenylated transcripts for these B. subtilis genes that are pre-mixed at staggered concentrations to allow GeneChip® probe array users to assess the overall success of the assay. Poly-A RNA Controls final concentration in each target are lys 1:100,000, phe 1:50,000, thr 1:25,000 and dap 1:6,667

extract_protocol: Total RNA was extracted from Paxgene-cryopreserved whole blood using PreAnalytiX standard protocol. Quality was verified using Agilent Bioanalyzer TapeStation

tag: disease

value: Crohn's disease

value: Infliximab

tag: patient

tag: response status

value: Responder

tag: visit

tag: crp


title: PDAC PDX, Sample 11, replicate 2

value: PDAC PDX


title: PDAC PDX, Sample 1, replicate 6


title: RAW 264.7 cells, MOI 1 (c_1X3)

description: Mouse mRNA, OG1RF total RNA

tag: cell line


title: HR_28_V1

value: Baseline


title: IyerS_RNA026_10

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: IyerS_RNA026_14

description: FFPE Spatial Transcriptome sequencing


title: HR_28_V2


title: PDAC PDX, Sample 1, replicate 5


title: HR_27_V3

value: Non-responder


title: PDAC PDX, Sample 10, replicate 3


title: RAW 264.7 cells, MOI 1 (c_1X1)

description: Mouse mRNA, OG1RF total RNA


title: HR_27_V2


title: IyerS_RNA026_9

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 1, replicate 4


title: IyerS_RNA026_7

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 10, replicate 2


title: IyerS_RNA026_5

description: FFPE Spatial Transcriptome sequencing


title: RAW 264.7 cells, MOI 10 + LPS (c_10XLPS2)

description: Mouse mRNA, OG1RF total RNA


title: IyerS_RNA026_6

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 10, replicate 1


title: HR_27_V1


title: HR_26_V3


title: RAW 264.7 cells, MOI 10 + LPS (c_10XLPS1)

description: Mouse mRNA, OG1RF total RNA


title: HR_26_V2


title: RAW 264.7 cells, MOI 10 (c_10X3)

description: Mouse mRNA, OG1RF total RNA


title: IyerS_RNA026_8

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 8, replicate 3


title: IyerS_RNA026_4

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 8, replicate 2


title: RAW 264.7 cells, MOI 1 (c_1X2)

description: Mouse mRNA, OG1RF total RNA


title: HR_24_V3


title: HR_24_V2


title: HR_26_V1


title: RAW 264.7 cells, MOI 10 (c_10X2)

description: Mouse mRNA, OG1RF total RNA


title: PDAC PDX, Sample 8, replicate 1


title: HR_24_V1


title: IyerS_RNA026_2

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA026_1

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 7, replicate 2


title: RAW 264.7 cells, MOI 100 + LPS (c_100XLPS2)

description: Mouse mRNA, OG1RF total RNA


title: HR_23_V3


title: RAW 264.7 cells, MOI 10 (c_10X1)

description: Mouse mRNA, OG1RF total RNA


title: IyerS_RNA025_24

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus


title: IyerS_RNA025_23

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 7, replicate 1


title: RAW 264.7 cells, MOI 100 + LPS (c_100XLPS1)

description: Mouse mRNA, OG1RF total RNA


title: RAW 264.7 cells, MOI 100 + LPS (c_100XLPS3)

description: Mouse mRNA, OG1RF total RNA


title: PDAC PDX, Sample 6, replicate 3


title: IyerS_RNA026_3

description: FFPE Spatial Transcriptome sequencing


title: RAW 264.7 cells, MOI 100 (c_100X3)

description: Mouse mRNA, OG1RF total RNA


title: IyerS_RNA025_22

description: FFPE Spatial Transcriptome sequencing


title: RAW 264.7 cells, MOI 100 (c_100X2)

description: Mouse mRNA, OG1RF total RNA


title: PDAC PDX, Sample 6, replicate 2


title: PDAC PDX, Sample 6, replicate 1


title: RAW 264.7 cells, MOI 100 (c_100X1)

description: Mouse mRNA, OG1RF total RNA


title: IyerS_RNA025_21

description: FFPE Spatial Transcriptome sequencing


title: HR_22_V3


title: HR_22_V2


title: HR_23_V1


title: IyerS_RNA025_20

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 5, replicate 3


title: DN thymocytes Toxf/fCd4Cre rep3

city: Nanjing

first: qifeng

last: he

state: JIANGSU

address: zhongshan Road

department: general surgery

institute: nanjing university

data_processing:
to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows:
1) removing reads containing adapters;
2) removing reads containing more than 10% of unknown nucleotides (N);
3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
Genome_build: Ensembl_release100
Supplementary_files_format_and_content: tab-delimited text files include fpkm,count values and symbol of genes for each Sample

source_name: Thymus

extract_protocol:
Thymi were obtained and prepared for FACS sorting, and the pellets of sorted DN2 thymocytes were frozen on dry ice. RNA was extracted using Trizol reagent. The NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age


title: RAW 264.7 cells, MOI 10 + LPS (c_10XLPS3)

description: Mouse mRNA, OG1RF total RNA


title: HR_21_V3


title: HR_22_V1


title: HR_23_V2


title: IyerS_RNA025_19

description: FFPE Spatial Transcriptome sequencing

tag: tissue


title: DN thymocytes Toxf/fCd4Cre rep1

tag: treatment


title: DN thymocytes Toxf/fCd4Cre rep2


title: PDAC PDX, Sample 5, replicate 1


title: PDAC PDX, Sample 5, replicate 2


title: IyerS_RNA025_17

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 4, replicate 3


title: IyerS_RNA025_18

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA025_16

description: FFPE Spatial Transcriptome sequencing


title: HR_21_V2


title: HR_20_V3


title: IyerS_RNA025_15

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 4, replicate 1


title: HR_21_V1


title: DN thymocytes Toxf/f (Cd4 control) rep1

value: Toxf/f


title: HR_20_V1


title: PDAC PDX, Sample 3, replicate 3


title: IyerS_RNA025_13

description: FFPE Spatial Transcriptome sequencing


title: Donor4

city: Boston

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

library_source: transcriptomic single cell

data_processing:
The generated gene expression libraries were sequenced to an average of 30,000 reads per cell, and the surface protein libraries to an averahe of 15,000 reads per cell, using the Illumina Novaseq platform at DFCI.   ScRNA-seq reads were processed with Cell Ranger, which quantified transcript counts per putative cell. Quantification was performed using the STAR aligner against the GRCh38 transcriptome.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Raw and filtered count matrices in h5 format, output from the CellRanger pipeline. Seurat object of filtered mast cells used in the manuscript, in rds format.

source_name: Ethmoid Sinus

extract_protocol:
Flow-sorted mast cells were resuspended in 0.4% BSA in PBS at a concentration of 1,000 cells per μl, and loaded onto a single lane (Chromium chip, 10X Genomics) for encapsulation in lipid droplets, using the Single Cell 3′kit V3.1 (10X Genomics).
cDNA synthesis, gene expression and protein library generation were performed according to the 10X Genomics protocol (CG000317_ChromiumNextGEMSingleCell3-v3.1_CellSurfaceProtein_RevE).

value: Ethmoid Sinus

tag: cell type

value: Mast cell


title: Donor3


title: HR_37_V3


title: DN thymocytes Toxf/f (Cd4 control) rep3


title: Donor2


title: PDAC PDX, Sample 3, replicate 1


title: IyerS_RNA025_12

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA025_11

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 4, replicate 2


title: PDAC PDX, Sample 2, replicate 2


title: Donor1


title: IyerS_RNA025_10

description: FFPE Spatial Transcriptome sequencing


title: HR_37_V1


title: DN thymocytes Toxf/f (Cd4 control) rep2


title: HR_37_V2


title: IyerS_RNA025_9

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA025_14

description: FFPE Spatial Transcriptome sequencing


title: HR_20_V2


title: HR_36_V2


title: PDAC PDX, Sample 3, replicate 6


title: PDAC PDX, Sample 1, replicate 3


title: PDAC PDX, Sample 1, replicate 2


title: HR_36_V3


title: PDAC PDX, Sample 3, replicate 5


title: PDAC PDX, Sample 3, replicate 2


title: PDAC PDX, Sample 3, replicate 4


title: HR_35_V3


title: PDAC PDX, Sample 1, replicate 1


title: IyerS_RNA025_7

description: FFPE Spatial Transcriptome sequencing


title: MIA-034

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Raw reads were processed using SpaceRanger version 2.0.0.
Assembly: GRCh38
Supplementary files format and content: HDF5 file containing per-molecule information for all molecules and H&E staining image.
Library strategy: Spatial transcriptomics

source_name: Minimally invasive adenocarcinoma of the lung

extract_protocol:
FFPE slides were mounted onto Visium slides using CytAssist
Libraries were constructed using the 10x Visium from FFPE supplied reagents


title: MIA-039

value: Minimally invasive adenocarcinoma of the lung


title: PDAC PDX, Sample 13, replicate 3


title: IyerS_RNA025_5

description: FFPE Spatial Transcriptome sequencing


title: CTS2 circRNA (biol rep2)

city: Guangzhou

first: Haoyu

last: Xie

state: Guangdong

address: 183 Zhongshan avenue west

institute: The Third Affiliated Hospital of Southern Medical University

data_processing:
FastQC software was used to evaluate the quality of Raw reads.The sequencing data was filtered: (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%.
The reads were first mapped to the latest UCSC transcript set using Bowtie2 (v2.1.0) and STAR.
DCC software was used to identify the cirRNA and to calculate the circRNA expression following the protocol from Cheng J, et al., Bioinformatics, 2002. TMM normalization was used to filter out underexpressed circrnas (CPM > 0.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads count for all Sample.

source_name: cartilage

growth_protocol: Human primary chondrocytes were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from cells using TRIzol (Takara). Total RNA was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).1.1 ug of total RNA was used for the construction of sequencing libraries.
Total RNA were digested with RNase R to remove linear RNA, followed by Ribomoval rRNA Depletion Kit (Human/Mouse/Rat) (Geneseed,Guangzhou). The designed DNA probe was hybridized to the RNA sample, thereby removing rRNA from the total RNA. Then, the RNA was fragmented and the first strand cDNA was synthesized using Rna-Seq Library Prep Kit for Illumina (Geneseed,Guangzhou). The second strand cDNA was labeled with dUTP in a strand-specific method. At the same time, the end repair is completed in this step. Then, the circRNA-Seq library was obtained by adding A-tail, connecting adaptor, purification of ligation product, fragment size sorting, and library amplification.

value: cartilage

value: Primary cell

value: chondrocyte

value: WT

value: cyclic tensile strain loading (20%)


title: PDAC PDX, Sample 10, replicate 6


title: IyerS_RNA025_6

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: HR_35_V2

value: Crohn's disease

value: Infliximab


title: HR_36_V1


title: HR_35_V1

value: Responder


title: IyerS_RNA025_4

description: FFPE Spatial Transcriptome sequencing


title: CTS1 circRNA (biol rep1)


title: IyerS_RNA025_8

description: FFPE Spatial Transcriptome sequencing


title: PDAC PDX, Sample 9, replicate 5

value: PDAC PDX


title: PDAC PDX, Sample 9, replicate 4


title: NC2 circRNA (biol rep2)


title: PDAC PDX, Sample 7, replicate 3


title: PDAC PDX, Sample 2, replicate 6


title: IyerS_RNA025_2

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA025_3

description: FFPE Spatial Transcriptome sequencing


title: HR_33_V3


title: IyerS_RNA025_1

description: FFPE Spatial Transcriptome sequencing


title: NC1 circRNA (biol rep1)


title: HR_33_V2


title: PDAC PDX, Sample 2, replicate 4


title: HR_32_V3


title: 4CL_GFP_RFP_2

city: Houston

first: Florencia

last: Levin

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Total RNA
22017R-05-18

data_processing:
Mapping using STAR
Annotating using featureCounts
Normalized counts using EdgeR
Assembly: GRCh38
Supplementary files format and content: XLSX files with DEseq2 analysis for UCLA4 MER51-GFP+ and MER51-GFP+/LTR5_Hs+ and normalized counts (RPKM)

source_name: Naïve ES cells

extract_protocol:
miRNeasy mini kit (Qiagen)
Polyadenylated RNAs were enriched and librares were constructed using the SMART-Seq V4 ultra + Nextera XT.

value: Naïve ES cells

value: hESC

value: 4CL medium


title: PDAC PDX, Sample 7, replicate 4


title: HR_33_V1

value: Baseline


title: 4CL_GFP_2

description:
Total RNA
22017R-05-17


title: IyerS_RNA024_23

description: FFPE Spatial Transcriptome sequencing

source_name: Brain-Prefrontal Cortex

value: Brain-Prefrontal Cortex


title: HR_32_V2

value: Non-responder


title: PDAC PDX, Sample 9, replicate 3

source_name: PDAC PDX


title: IyerS_RNA024_22

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA024_21

description: FFPE Spatial Transcriptome sequencing


title: 4CL_GFP_1

description:
Total RNA
22017R-05-15


title: PDAC PDX, Sample 9, replicate 2


title: MEKi_2

description:
Total RNA
22017R-05-13

source_name: Differentiated ES cells

value: Differentiated ES cells


title: HR_32_V1


title: IyerS_RNA024_20

description: FFPE Spatial Transcriptome sequencing


title: 4CL_GFP_RFP_1

description:
Total RNA
22017R-05-16


title: PDAC PDX, Sample 9, replicate 1


title: IyerS_RNA024_18

description: FFPE Spatial Transcriptome sequencing


title: HR_31_V2


title: AEb9-2_207_CTR

city: Medford

first: rebecca

last: batorsky

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

data_processing:
10x Data analysis and clustering: 10x scRNA-seq data was aligned with 10x Genomics Cell Ranger (v3.0) against the GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Placenta

extract_protocol:
Placental chorionic villi were separated from fetal membranes and decidua, washed in DPBS wash, and mechanically homogenized. Placental tissue was then serially digested in Collagenase Digestion Buffer, Trypsin Digestion Buffer, and Collagenase Digestion Buffer 2. Undigested tissue was removed by passage through sterile gauze and 100uM filter. The cell suspension was centrifuged at 257g for 8 min at 4°C, washed, spun again, and resuspended in media.  The cells were then suspended in 4mL of 20% Percoll and 5mL of 35% Percoll was underlayed through a #1 glass Pasteur pipette. After centrifugation for 30 minutes at 4°C without brake at 1000g, cells were isolated from the interphase layer, washed in media, and spun at 257g for 8 minutes at 4°C. Cell pellets were immunopurified by negative selection by incubation with anti-EGFR (to remove syncytiotrophoblasts) and anti-CD10 (to remove fibroblasts) conjugated to magnetic Dynabeads, prepared as previously described, for 20 minutes at 4°C. Tubes were placed on a DynaMagTM magnet for 5 minutes to magnetically bind cytotrophoblasts
Cryopreserved HBCs were thawed at 37°C and diluted with RPMI 1640 including 10% FBS and 1% Pen/Strep. The cell suspension was centrifuged at 300g for 5 min at room temperature, with the brake off. The supernatant was aspirated and the cell pellet was resuspended in media.  Dead cells were removed using OptiPrepTM Density Gradient Medium (Sigma) and cell count and viability of cells were calculated using LunaFX7 automated counter.
10x Genomics platform with a loading target of approximately 10,000 viable cells/sample.  Libraries were sequenced on an Illumina NextSeq 2000 P3 flowcell machine with a sequencing target of 25,000 reads per cell.

treatment_protocol: In this study, 24 pregnant individuals with full-term, singleton pregnancies delivering at Massachusetts General Hospital (March 2021 - June 2023) were included. Participants were classified as SARS-CoV-2 positive (N=10) if they had symptomatic COVID-19 infection during pregnancy confirmed by positive SARS-CoV-2 nasopharyngeal PCR test, or were asymptomatic but tested positive on routine SARS-CoV-2 screening at delivery.  Participants were classified as SARS-CoV-2 negative (N=14) if they did not have a positive SARS-CoV-2 nasopharyngeal PCR or COVID-19 symptoms during pregnancy and had a negative SARS-CoV-2 nasopharyngeal PCR at delivery upon universal COVID-19 screening on Labor and Delivery.

value: CD11b+ cells

value: Placenta

value: full term pregnancy

tag: Sex

value: M

value: control


title: MEKi_1

description:
Total RNA
22017R-05-11


title: HR_31_V1


title: IyerS_RNA024_17

description: FFPE Spatial Transcriptome sequencing

data_processing:
Raw sequencing data was processed using Nanostring's GeoMx DSP Control Center Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode) Library strategy: Spatial Transcriptomics
Assembly: N/A, sequencing of synthetic tags and aligment to whitelist of RTS IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary files format and content: dcc

extract_protocol:
5um sections were cut from Paraformaldehyde-Fixed Paraffin-Embedded slides. Samples were incubated with either DNA-oligo barcoded RNA-ISH probes or antibodies which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Spatial transcriptome sequencing libraries were prepared with Nanostring reagents according to manufacturer's specifications

value: IgG


title: PDAC PDX, Sample 11, replicate 3


title: AEb8-2_135_CTR


title: HR_30_V3

value: Crohn's disease


title: Naïve_1

description:
Total RNA
22017R-05-07

value: PXGL medium


title: HR_31_V3

value: Infliximab

value: Responder


title: primed_GFP_RFP_2

description:
Total RNA
22017R-05-04

source_name: Primed ES cells

value: Primed ES cells

value: mTeSR1 medium


title: HR_30_V2


title: primed_GFP_2

description:
Total RNA
22017R-05-03

value: hESC


title: AEb14-4_012_REC_M

value: COVID Recovered


title: IyerS_RNA024_15

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: IyerS_RNA024_19

description: FFPE Spatial Transcriptome sequencing


title: AEb14-2_157_CTR_M


title: HR_30_V1

value: Non-responder

value: Baseline


title: IyerS_RNA024_14

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA024_13

description: FFPE Spatial Transcriptome sequencing


title: Naïve_2

description:
Total RNA
22017R-05-10

value: Naïve ES cells


title: primed_GFP_RFP_1

description:
Total RNA
22017R-05-02


title: IyerS_RNA024_12

description: FFPE Spatial Transcriptome sequencing


title: primed_GFP_1

description:
Total RNA
22017R-05-01


title: AEb13_9-110

value: CD11b+ cells

value: Placenta


title: AEb7_145_CTR

value: full term pregnancy

value: M


title: HR_48_V3


title: HR_29_V1


title: IyerS_RNA024_16

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: GIP-Venus negative, sample 2

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

institute: University of Cambridge

data_processing:
Sequenced reads were trimmed for adapter sequences using cutadapt, mapped to the primary human genome (GRCh38) using STAR, and raw counts generated with featureCounts.
Differential gene expression modelling and normalised counts per million were generated using DESeq2.
Assembly: hs38 genome, downloaded from the UCSC genome browser and manually included the sequence for Venus.
Supplementary files format and content: Count matrix, exported by featureCounts, are in tab-separated delimited (tsv) text format.

source_name: duodenum organoid

growth_protocol: To promote K-cell differentiation, EGF was removed from culture medium 2-3 days after seeding, and subsequently grown in IF medium for 10-14 days. To promote increased EEC differentiation, cultures were supplemented with 10 μmol/l Notch inhibitor DAPT and 100 nmol/l MEK inhibitor PD0325901 overnight. Domes were further cultured in IF until optimal K-cell differentiation was achieved (3-7 days later).

extract_protocol:
Differentiated organoids were dissociated to single cell, and sorted into two populations (Venus-positive and -negative) using an Influx Cell Sorter (BD Biosciences) at the Cambridge Institute of Medical Research (CIMR) Flow Cytometry Core Facility. DAPI and DRAQ5 staining, side scatter, forward scatter and pulse width gates were used to remove debris and cell clusters.
RNA extraction and isolation were performed using RNAeasy Micro Plus kit (Qiagen). RNA concentration and quality (RIN 7-9) were assessed using RNA6000 Pico Kit and Bioanalyser 2000 (Agilent). The library was constructed with using the SMARTer Stranded Total RNA-Seq v2 Pico Input Mammalian kit (Takara Bio).

value: duodenum organoid

value: non-K-cells

tag: genotype

value: GIP-Venus negative


title: IyerS_RNA024_11

city: Pittsburgh

first: Smita

last: Iyer

address: 3550 Terrace Street

institute: University of Pittsburgh School of Medicine

description: FFPE Spatial Transcriptome sequencing


title: GIP-Venus negative, sample 3


title: AEb13_OB54


title: IyerS_RNA024_10

description: FFPE Spatial Transcriptome sequencing


title: GIP-Venus negative, sample 1


title: AEb13_170


title: IyerS_RNA024_9

description: FFPE Spatial Transcriptome sequencing


title: AEb13_285

value: control


title: AEb13_318


title: GIP-Venus positive, sample 4

value: K-cells

value: GIP-Venus positive


title: HR_48_V1

value: Crohn's disease

value: Infliximab

value: Responder


title: HR_29_V3


title: AEb12


title: HR_48_V2


title: HR_47_V3


title: IyerS_RNA024_8

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: HR_29_V2


title: GIP-Venus positive, sample 3


title: AEb11-2_171

value: F


title: IyerS_RNA024_7

description: FFPE Spatial Transcriptome sequencing


title: HR_47_V2


title: 08 MAC infection 7day

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

data_processing:
illumina Local Run Manager v2.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSC hg19 using STAR v2.7.3a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: blood

value: macrophage

value: Cocultured with Mycobacterium Avium for 7days


title: IyerS_RNA024_6

description: FFPE Spatial Transcriptome sequencing


title: HR_47_V1

value: Baseline


title: GIP-Venus positive, sample 2


title: GIP-Venus positive, sample 1


title: IyerS_RNA024_5

description: FFPE Spatial Transcriptome sequencing


title: 07 MAC infection 3day

value: Cocultured with Mycobacterium Avium for 3days


title: HR_46_V3


title: 06 Control3

value: Control


title: IyerS_RNA024_4

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: HR_46_V2


title: 05 anti-CD74(agonist)

value: Cocultured with anti-CD74 agonistic antibody


title: siMG-OKS

city: Kobe

first: Tomohiro

last: Miyamoto

state: Hyogo-ken

address: Kusunokicho Chuo-ku 7-5-2

institute: Kobe University

data_processing:
HISAT2 version 2.1.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using HISAT2
Trimmed sequence reads  were mapped to GRCh38 using HISAT2
Read count extraction and normalization were performed using HISAT2
Assembly: hg38
Supplementary files format and content: excel file includes read count, TPM value and FPKM value for each sample

source_name: MG-OKS

growth_protocol: MG-OKS cells were mainteined in DMEM supplemented with 10% fetal bovine serum (FBS), and maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells using the RNeasy mini kit (Qiagen) according to the manufacturer’s protocol.  14 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA LT sample Prep kit following manufacturer's protocols.

treatment_protocol: MG-OKS were seeded in a 6-well plate 24 h before transfection to achieve 70–80% confluency on the day of transfection. Before transfection, 7.2 μL of Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) and 1.2 μL of Silencer™ Pre-Designed siRNA SPRR1A or scramble siRNA (Invitrogen) was diluted in 240 μL of Opti-MEM™ I Reduced Serum Medium (Gibco). The complexes were then incubated at 25℃ for 5 min. After incubation, the complexes were added dropwise to each well. After 24 h of incubation at 37 °C in a CO2 incubator, the medium was replaced with a fresh complete culture medium.

value: MG-OKS

value: mesenchymal cells

value: SPRR1A knock down


title: scMG-OKS

value: scramble siRNA transfected


title: 04 anti-CD74(blocking)

value: Cocultured with anti-CD74 blocking antibody


title: IyerS_RNA024_2

description: FFPE Spatial Transcriptome sequencing


title: CD4+ T lymphocytes , PKP2 mutated, donor2

city: Toulouse

first: Victorine

last: Douin-Echinard

address: 4bis Avenue Hubert Curien

country: France

institute: RESTORE UMR-1301 INSERM

description:
HTO
Patients_barcodes.tsv.gz
Patients_features.tsv.gz
Patients_matrix.mtx.gz

data_processing:
CellRanger v4.0.0 count function was used to obtain single set of barcodes.tsv, features.tsv, matrix.mtx for the pooled donors 1-5 for the Controles and Patients groups
Assembly: CGRCh38-3.0.0
Supplementary files format and content: CellRanger output files for the 5 Controles donors: Controles_barcodes.tsv.gz, Controles_features.tsv.gz, Controles_matrix.mtx.gz
Supplementary files format and content: CellRanger output files for the 5 Patients donors: Patients_barcodes.tsv.gz,Patients_features.tsv.gz, Patients_matrix.mtx.gz

source_name: PBMC (frozen)

growth_protocol: Frozen PBMC

extract_protocol:
blood
10x Genomics 3’ scRNA-seq

treatment_protocol: 3h resting at 37°C 5% CO2 in X-vivo 15 medium supplemented with 2% heat inactivated AB human serum prior to cell sorting

value: PBMC (frozen)

value: CD4+ T lymphocytes

value: PKP2 mutated


title: IyerS_RNA024_3

description: FFPE Spatial Transcriptome sequencing

value: Brain-Prefrontal Cortex


title: IyerS_RNA024_1

description: FFPE Spatial Transcriptome sequencing


title: HR_44_V2

value: Crohn's disease

value: Infliximab

value: Responder


title: HR_42_V3


title: CD4+ T lymphocytes , PKP2 mutated, donor1

description:
RNA
Patients_barcodes.tsv.gz
Patients_features.tsv.gz
Patients_matrix.mtx.gz


title: HR_44_V3


title: 02 AGP

value: blood

value: macrophage

value: Cocultured with AGP


title: HR_44_V1

value: Baseline


title: CD4+ T lymphocytes , wild type, donor2

description:
HTO
Controles_barcodes.tsv.gz
Controles_features.tsv.gz
Controles_matrix.mtx.gz

value: PKP2 WT


title: HR_42_V2


title: 01 Control1

value: Control


title: IyerS_RNA023_24

description: FFPE Spatial Transcriptome sequencing

source_name: Brain-Hippocampus

value: Brain-Hippocampus

value: IgG


title: Large tumor sample, scRNAseq

city: Paris

first: Jules

last: Russick

address: 1 avenue Claude Vellefaux

institute: Commissariat à l'Energie Atomique

description: 10X Genomics

data_processing:
Data filtering and normalization: For the subsequent analysis, only cells exhibiting less than 5% of mitochondrial gene content and a gene count ranging from 200 to 3000 were retained. Additionally, ribosomal genes were excluded from the analysis. Normalization was performed using the “LogNormalize method” (natural-log transformation using log1p) through Seurat’s “NormalizeData” function. The relative expression of each gene was centered using the Seurat “ScaleData” method and linear dimensional reduction was conducted with the Seurat “RunPCA” function.
Assembly: mm10
Supplementary files format and content: Comma-separated matrix files

source_name: Tumoral part of a large tumor

extract_protocol:
The lungs of euthanized mice were flushed with 10mL of PBS (Gibco, 14190-094) to remove blood. Non-tumoral parts of the lung were then separated from the tumoral parts (with IVIS verification) and harvested in RPMI 1640 medium (Gibco) in gentleMacs C tubes (Miltenyi). Single-cell suspensions were obtained after enzymatic disruption using the Tumor Dissociation Kit (Miltenyi, 130-096-730) in the gentleMACS Octo Dissociator (program “mouse tumor dissociation kit - 37°C”) at 37°C and filtered through a 70 µm cell strainer (Falcon, 352350). Cells were washed in PBS + 5% FCS + 0.5mM EDTA (Invitrogen, AM9262), and the number of cells obtained was determined by manual counting on Kova slides (Kova, 87144). Cells from single-cell suspensions were stained as mentioned in Flow cytometry section and resuspended at 7.106 cells/mL. The sorting was performed using a fluorescence activated cell sorting (FACS) Aria III cell sorter (BD Biosciences), using 100µm noodle. Sorted NK cells were defined as Live/Dead-, CD45+, CD3-, NK1.1+ and CD11b and CD27 markers were added to sort NK cell subsets. After sorting, purity was analyzed by flow cytometry using Diva software (BD Biosciences).
After cell sorting, NK cells from each sample were subjected to Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, Pleasanton, California, USA), following the Chromium Single Cell 3 Reagent Kits v3.1 protocol targeting 10,000 cells per condition. Briefly, Single-cell Gel Bead-In-Emulsions (GEMs) were generated in oil droplets with barcoded beads using a Chromium Controller instrument (10X Genomics). cDNA was generated from each droplet, purified using DynaBeads MyOne Silane Beads, and amplified by PCR (11 cycles) using reagents from the kit. Fragments size estimation of the amplified cDNA was assessed using SPRIselect Reagent Kit and fragmented with High SensitivityTM HS DNA kit on 2100 Bioanalyzer (Agilent), and quantified using QubitTM dsDNA High Sensitivity HS assay (ThermoFisher Scientific). Libraries were then sequenced with HighOutput flowcell using an Illumina Nextseq500.

value: Tumoral part of a large tumor

value: In vivo Orthotopic injection of LLC cells

value: Albino B6(C)/Rj-Tyrc/c mice

value: 6-8 weeks old


title: CD4+ T lymphocytes , wild type, donor1

description:
RNA
Controles_barcodes.tsv.gz
Controles_features.tsv.gz
Controles_matrix.mtx.gz

value: PBMC (frozen)

value: CD4+ T lymphocytes


title: HR_46_V1

source_name: Whole blood

value: Crohn's disease


title: MG-OKS

value: MG-OKS

value: mesenchymal cells

value: WT


title: IyerS_RNA023_21

description: FFPE Spatial Transcriptome sequencing


title: 03 Control2

value: blood

value: macrophage

value: Control cocultured with control IgG


title: IyerS_RNA023_22

description: FFPE Spatial Transcriptome sequencing


title: NA3

first: Qinghai

last: Ye

state: Shanghai

address: 180 Fenglin Road, Shanghai 200032, China

institute: Zhongshan Hospital, Fudan University

description: 10X Genomics

data_processing:
Single-cell RNA-sequencing (scRNA-seq) data processing reads were processed using the Cell Ranger 3.0.1 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version mm10, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Aorta

extract_protocol:
Fresh tissues were kept in RPMI 1640 containing 10% FBS on ice. Tissues were transported in sterile culture dish with 10 ml 1x Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to remove the residual tissue storage solution, then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no.25200-072) and 10 ug/mL DNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues. Tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min. We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40-um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher).
10× library preparation and sequencing Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in emulsion (GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: Aorta

value: human aorta


title: NA2

description: 10X Genomics


title: Non-tumoral sample, scRNAseq

description: 10X Genomics

source_name: Non-tumoral part of the lung

value: Non-tumoral part of the lung


title: IyerS_RNA023_20

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus

value: IgG


title: HR_40_V3

value: Infliximab

value: Responder


title: HR_42_V1

value: Baseline


title: ventricle, 24 month,  scRNA, sample 2

city: Chapel Hill

first: Yiran

last: Song

state: NC

address: 111 Mason Farm Road

institute: The University of North Carolina

data_processing:
Single-cell RNA-seq: Raw sequencing reads were processed with Cell Ranger v7.2.0 pipeline. For each sample, the raw FASTQ files were aligned to the mouse reference genome (refdata-gex-mm10-2020-A) using the cellranger count pipeline with default parameters. This step generated gene expression matrices for each sample individually.
Assembly: mm10
Supplementary files format and content: scRNA: tab-separated values file, matrix file and feature name

source_name: heart ventricle

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
Male mouse hearts at 3 months of age, 12 months of age, and 24 months of age were collected for non-cardiomyocyte isolation. In accordance with UNC-Chapel Hill LARC guidelines, all animals were euthanized using CO2 and cervical dislocation. Hearts were perfused with Langendorff apparatus as described with minor modifications. Briefly, male mice of three ages groups were anesthetized with isoflurane (1%-2%), the heart was removed, retrograde perfusion was performed through an aortic cannulation, and continuous flow of 16-24 drops/min in a Langendorff apparatus. Both ventricles were digested with 1 mg/ml collagenase IaI for 10-15min, and the ventricle were further mechanically dissociated by pipetting. Then, the cell suspension was collected and filtered through a 100µm cell strainer. CMs were removed by centrifuging at 50g (200 rpm) for 3min, and nonCMs were enriched by centrifuge at 450g (2,000 rpm) for 5 min. The pelleted nonCMs were treated with 1ml red blood cell lysis buffer (Gibco) at room temperature (RT) and washed twice with wash buffer (4% FBS/PBS). Single live cells were FACS-sorted by 7-Amino Actinomycin D (7-AAD, R&D Systems), and Pacific Blue-conjugated Annexin V and SYTOX (Thermo) staining. Following sorting, cell concentration and viability of each sample were counted using automated cell counter (LUNA system, Logos biosytems) plus Acridine orange (AO)/ propidium iodide (PI) dual nuclear staining. Cell concentration was adjusted to 1x106 cells/ml for subsequent scRNA-seq via 10x Gemonics platform. Cells (50,000 per sample) for scATAC-seq were subjected to lysis for 3min and counted again with cell counter to determine the viability (lower than 5%) and concentration again.
Single-cell transcriptome library preparation and sequencing: Single live cells were loaded to 10x Genomics Chromium chip per factory recommendations. Reverse transcription and library preparation were conducted using Chromium Single Cell 3′ Library and Gel Bead Kit v.2 and Chromium i7 Multiplex kit. Sequencing was performed on Illumina NextSeq 500 with a high output kit.

value: heart ventricle

tag: time

value: 24 months

value: wild type


title: NA1

description: 10X Genomics


title: HR_40_V2

value: Crohn's disease


title: IyerS_RNA023_19

description: FFPE Spatial Transcriptome sequencing


title: HR_40_V1


title: IyerS_RNA023_23

description: FFPE Spatial Transcriptome sequencing


title: ATAD3

description: 10X Genomics


title: IyerS_RNA023_18

description: FFPE Spatial Transcriptome sequencing


title: ventricle, 24 month,  scRNA, sample 1


title: Small tumor sample, scRNAseq

description: 10X Genomics

source_name: Tumoral part of a small tumor

value: Tumoral part of a small tumor

value: In vivo Orthotopic injection of LLC cells

value: Albino B6(C)/Rj-Tyrc/c mice

value: 6-8 weeks old


title: ventricle, 12 month,  scRNA, sample 2

value: 12 months


title: IyerS_RNA023_17

description: FFPE Spatial Transcriptome sequencing


title: HR_39_V3


title: ATAD1

description: 10X Genomics

value: Aorta


title: IyerS_RNA023_16

description: FFPE Spatial Transcriptome sequencing


title: ventricle, 12 month,  scRNA, sample 1


title: antibody hashtag CD4 T and B cells for patient 748, 934, 954

first: Kevin

last: Louis

institute: Inserm U976, Paris Cité University

data_processing:
The Cell Ranger (v.6.0 multi; 10× Genomics) pipeline was used to demultiplex the samples and create FASTQ files. From these FASTQ files, counts matrices were generated by mapping to the human genome GRCh38-2020-A. QC metrics from the Cell Ranger web_summary files were checked to ensure that the sequencing output was suitable for downstream analyses.
Assembly: GRCh38-2020-A
Supplementary files format and content: tab-separated values files and matrix files

extract_protocol:
RNA was extracted from fluorescence-activated cell sorting (FACS) sorted CD4 T cells and CD19 B cells, cellw were labeled with TotalSeq-A Cell Hashing hashtag-oligos Ab (BioLegend), then resuspended in PBS+0.04% bovine serum albumin. Ready-to sequence Illumina libraries were generated using the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry; 10× Genomics; Pleasanton, CA). Sequencing single-indexed libraries (5 nM) were pooled.
Ready-to sequence Illumina libraries were generated using the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry; 10× Genomics; Pleasanton, CA). Sequencing single-indexed libraries (5 nM) were pooled. The resulting pooled library was loaded on a NovaSeq S2-100 (Illumina). The following parameters of sequencing were used: Read 1: 28 cycles; i7 Index 8 cycles; Read 2: 91 cycles, as specified by the 10× Genomics guidelines.

value: blood

value: CD4 T cells

value: B cells


title: HR_39_V1


title: antibody hashtag CD4 T and B cells for patient 60, 870, 1017


title: HR_39_V2


title: IyerS_RNA023_15

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus

value: IgG


title: ventricle, 3 month, scRNA, sample 1

value: 3 months


title: IyerS_RNA023_14

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA023_13

description: FFPE Spatial Transcriptome sequencing


title: ventricle, 3 month,  scRNA, sample 2


title: antibody hashtag CD4 T and B cells for patient 17, 602, 703


title: antibody hashtag CD4 T and B cells for patient 488, 505, 845


title: aDCP1

city: Qingdao

first: yunfeng

last: Yang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: REY15A
Supplementary files format and content: bigWig

organism: Saccharolobus islandicus

source_name: cell

growth_protocol: Strains  were cultured in MTSV medium

extract_protocol:
The cells were then resuspended in TBS-TT buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween-20, 0.1% Triton X-100, pH 7.5) and fragmented by sonication until the DNA fragments were of 200-500 bp. After centrifugation (10,000 g for 15 minutes), a 100 µl aliquot of the DNA-containing supernatant was kept apart to be uses as an input control and the remaining sample was divided into two aliquots. One aliquot was incubated with anti-aDCP1 antibody-coated protein A beads (Cytiva). After incubation at 60 °C for 10 hrs, the samples were collected and the captured DNA was purified by using the DNA Cycle-Pure Kit (Omega) according to the manufacturer's instruction. The input samples were treated as above without the addition of antiserum and beads. The purified DNA was used for ChIP-Seq library preparation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: the cells were collected 3 hours after synchronization, cross-linked by adding 1% formaldehyde for 15 minutes, and quenched with a final concentration of 125 mM glycine.

value: cell

tag: strain


title: ARNT_ff macrophages with L. major promastigote parasite infected parasites 2

city: Little Rock

first: Stephanie

last: Byrum

state: AR

address: 4301 W Markham St, slot 510

department: Dept of Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
read quality was assessed using FastQC (version 0.11.7) and multiQC (version 1.6)
Adaptors, polyA tails, and low-quality bases (Q < 20), and the first 12bp were trimmed using BBTools BBDuk (version 38.52) (minimum read length: 20 base pairs). Parameters: ref=polyA.fa.gz, truseq_rna.fa.gz ktrim=r k=13 useshortkmers=t mink=5 forcetrimleft=12 qtrim=lr trimq=20 minavgquality=20 minlength=20
Trimmed reads were aligned to the mouse reference genome (GRCm38 / mm10) using STAR (version 2.6.1a) allowing up to 2 mismatches depending on the alignment length. Reads mapping to more than 20 locations were discarded. Parameters: --sjdbGTFfile Mus_musculus.GRCm38.84.gtf --outFilterType BySJout --sjdbOverhang 74 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.03
Gene level expression counts based on known gene annotation were quantified using HTSeq (htseq-counts) (version 0.9.1) in intersection-nonempty mode. Parameters: --mode intersection-nonempty --stranded yes  --type exon <gff_file> Mus_musculus.GRCm38.84.gtf
A counts-per-million (CPM) filter was applied to remove low abundant genes. Criteria for Retention: Genes with unique Entrez IDs and a minimum of 2 CPM in 4 or more samples.
The filtered counts were TMM normalized and observation-level and sample-specific quality weights calculated using edgeR's (version 3.28.1) calcNormFactors() and limma's (version 3.42.2) voomWithQualityWeights() functions (R version 3.6.3), respectively.
Assembly: GRCm38 / mm10
Supplementary files format and content: tab-delimited text file of gene level counts for each sample

source_name: Ears

growth_protocol: Leishmania major (WHO/MHOM/IL/80/Friedlin) was used. Parasites were maintained in vitro in Schneider's Drosophilia medium supplemented with 20% heat-inactivated FBS, 2mM L-glutamine, 100U/mL penicillin, and 100 mg/ml streptomycin. Metacyclic stationary phase promastigotes were isolated from 4-5 days cultures by Ficoll density gradient seperation. Parasites were used to infect bone marrow-derived macrophages (BMDM) from 2 starins of mice on a C57BL/6 background. Specifically, BMDM were generate from mice that have intact ARNT/HIF-alpha signaling in myeloid cells (LysM Cre ARNT f/+) or mice with deleted ARNT/HIF-alpha signaling in myeloid cells (LysM Cre ARNT f/f). BMDM were generated from mouse bone marrow using L929 supernatants at 25% as a source of MCSF for 7 days. At day 7, BMDM were replated at 1x10^6 cells per well, then incubated overnight in complete DMEM media prior to infection with parasites.

extract_protocol:
The total RNA was isolated from the cell lysate of macrophages under the 3 different conditions by using RNeasy plus mini kit according to the manufacturer's instruction.
cDNA libraries were prepared from total RNA using Lexogen's QuantSeq 3‘ (FWD) mRNA-Seq Library Prep Kit for Illumina following the manufacturer’s protocol. Library fragment sizes were validated using a Fragment Analyzer and quantified by a Qubit fluorometer. Equal amounts of each library were pooled for sequencing on the NextSeq 500 platform using a high output flow cell to generate approximately 25 million 75bp SE reads per sample.

treatment_protocol: For conditions where macrophages get infected with parasites in vitro, 1x10^6 bone marrow-derived macrophages were infected or not with L. major promastigote parasites (MOI 5:1) in 500 uL DMEM in triplicate. Macrophages were incubated with parasites for 2 hours in culture at 37 degrees. Macrophages were washer 2x to remove extracellular parasites. Next, macrophages were cultured for 8 hours of 3 conditions including: 1) media alone (no infection), 2) L. major infection, or 3) L. major infection plus 100ng/mL LPS plus 10ng/mL of IFNg.

value: Ears

value: C57BL/6 LysM Cre ARNT f/f

value: L. major promastigote parasite infected


title: HR_38_V2

first: Shai

last: Shen-Orr

address: 1st Efron Street

institute: Rappaport Institute of Medical Research, Faculty of Medicine and Faculty of Biology, Technion

data_processing: Preprocessing was perfomed in R using the oligo package. Raw CEL files were summarized and normalized using RMA and quantile normalization (oligo::rma), using the probe definition and annotation packages pd.clariom.s.human and clariomshumantranscriptcluster.db

extract_protocol: Total RNA was extracted from Paxgene-cryopreserved whole blood using PreAnalytiX standard protocol. Quality was verified using Agilent Bioanalyzer TapeStation

value: Crohn's disease

value: Infliximab

value: Non-responder


title: ARNT_ff macrophages with L. major promastigote parasite infected parasites 3


title: ATAD2

city: Shanghai

description: 10X Genomics

value: human aorta


title: Input (aDCP1 control)

value: Input

value: DNA-containing supernatant was kept apart to be uses as an input control


title: ARNT_ff macrophages with L. major promastigote parasite infected parasites 1


title: IyerS_RNA023_12

description: FFPE Spatial Transcriptome sequencing


title: IyerS_RNA023_11

description: FFPE Spatial Transcriptome sequencing


title: HR_38_V1

city: Haifa

value: Baseline


title: Oxiplasma Meridianum M1 early stationary phase, after 5 days

city: Bangor

first: Rafael María

last: Bargiela Bargiela

state: Gwynedd

address: Deniol Road

department: Center for Environmental Biotechnology

institute: Bangor University

data_processing:
SeqPrep and Sickle were employed for removing low-quality and adapter contamination from raw sequencing data.
Clean data of each sample were aligned with the reference genome using Bowtie2. Then perform statistics on sequencing saturation and sequencing coverage.
Assembly: CP133772
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
Supplementary files format and content: Tab-delimited text file including TPM (transcripts per million) values for each sample

organism: archaeon

extract_protocol: none provided


title: ARNT_ff macrophages with L. major promastigote parasite infected parasites and LPS/IFNg treatment 3

value: LPS IFNg treated


title: Oxiplasma Meridianum M1 mid-log phase, after 3 days


title: gene expression CD4 T and B cells for patient 60, 870, 1017

value: blood

value: CD4 T cells


title: HR_38_V3


title: IyerS_RNA023_10

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus


title: S143

city: Davis

first: Barbara

last: Blanco-Ulate

state: California

address: One Shields Ave

department: Plant Sciences

institute: University of California Davis

description: Rh19-32 D

data_processing:
Quality and adapter trimming were done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of Rhizopus stolonifer and each of the fruit hosts with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the Bowtie2 alignments using the script sam2counts.py v.0.91
Assembly: Rhizopus stolonifer BLUCD01v1, Solanum licopersicum build SL4.0 with ITAG 4.0 annotations, Vitis vinifera PN40024, Fragaria x ananassa Camarosa v1.0.a1, Prunus salicina Zhongli No. 6 v1.0
Supplementary files format and content: Processed data file contains read counts per sample, with each sample being listed on one column from column B-AZ, and transcript IDs being listed on column A
Supplementary files format and content: -

organism: Prunus domestica

source_name: Plum

extract_protocol:
RNA was extracted from 1 g of ground tissue as described in Blanco-Ulate et al. (2013). Culture media-grown samples and resulting libraries were obtained from Petrasch et al. (2019) (GEO accession GSE122555).
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

value: Plum

tag: agent

value: Rhizopus stolonifer

tag: time point

value: (hours_post_inoculation)  48


title: gene expression CD4 T and B cells for patient 17, 602, 703

value: B cells


title: ARNT_ff macrophages with L. major promastigote parasite infected parasites and LPS/IFNg treatment 2

value: Ears

value: C57BL/6 LysM Cre ARNT f/f


title: S142


title: IyerS_RNA023_9

state: Pennsylvania

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: ARNT_ff macrophages with L. major promastigote parasite infected parasites and LPS/IFNg treatment 1


title: S141

description: Rh19-29 C


title: IyerS_RNA023_8

description: FFPE Spatial Transcriptome sequencing


title: Dox_Exos, replicate 1, scRNAseq

city: Chaoyang District

first: Youkun

last: Bi

state: Beijing

address: NO.15, Datun Road

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
Cellranger  (10X Genomics)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The adherent LO2 cells were digested with 0.25% trypsin for 4 minutes and digestion was terminated by adding high-glucose DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS) (GIBCO). The dissociated cells were centrifuged at 1,000 rpm and 4 °C for 5 min, then resuspended in 15 mL red blood cell lysis buffer (BD Biosciences) at 37 °C for 5 min. Subsequently, these cells underwent another round of centrifugation at 1,000 rpm and 4 °C for 5 min, followed by two washes with cold PBS and resuspended in cold PBS containing 10% PBS. The cell suspension was filtered through a 40 μm strainer (BD Falcon), subjected to two PBS washes, centrifuged at 1,000 rpm and 4 °C for 5 min, and resuspended in cold PBS supplemented with 10% FBS.
The library was performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10ÍGenomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retro-transcripted to cDNA, which contains an Ilumina R1 primer sequence. Unique Molecular Identifier (UMI) and the 10ÍBarcode. The pooled barcode cDNA was then cleaned up with Silane DynaBead, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequence P5 and P7 sequences and a sample index were added.

value: hESC-Exos


title: ARNT_ff macrophages in media 3


title: IyerS_RNA023_7

description: FFPE Spatial Transcriptome sequencing


title: gene expression CD4 T and B cells for patient 748, 934, 954


title: S140

description: Rh19-28 B

value: (hours_post_inoculation)  24


title: ARNT_ff macrophages in media 1


title: Dox_pbs, replicate 1, scRNAseq

value: pbs


title: (PPRE)-eGEP-THP-1,M2 differentiation+DMSO,24H,rep3

city: Beijing

first: Hui

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

description:
M2_DMSO3
M2 differentiation+DMSO
Control

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

growth_protocol: The THP-1 cell line was maintained in RPMI 1640 complete medium with 10% (vol/vol) FBS and 1% (vol/vol) penicillin/streptomycin. Cells were maintained in an atmosphere of 37°C, 5% carbon dioxide (CO2), and 95% humidity.

extract_protocol:
Total RNA was extracted from cultured cells with TRIzol reagent. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, 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 was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: PPRE-eGEP-THP-1 cells were seeded in 6-well plates at 150,0000 cells/well with culture medium containing phorbol 12-myristate 13-acetate (25 ng/mL). After adhesion for 48 h, the cells were allowed to rest in fresh media for 24 h to acquire M0 macrophages. To induce the polarization of M1 or M2 macrophages, M0 macrophages were treated with lipopolysaccharide (LPS; 100 ng/mL) and recombinant human interferon gamma (IFN-γ; 20 ng/mL) or interleukin-4 (IL-4; 20 ng/mL) and IL-13(20 ng/mL), respectively, for 24H. Simultaneously add MCHP (100 μM) during the polarization of M1 or M2 macrophages.

value: monocyte

tag: condition

value: M2 polarization of macrophages

value: DMSO


title: IyerS_RNA023_6

description: FFPE Spatial Transcriptome sequencing


title: S139

description: Rh19-27 B


title: ARNT_ff macrophages in media 2


title: S138

description: Rh19-26 B


title: ARNT_fplus macrophages with L. major promastigote parasite infected parasites 3

value: C57BL/6 LysM Cre ARNT f/+

value: L. major promastigote parasite infected


title: (PPRE)-eGEP-THP-1,M2 differentiation+DMSO,24H,rep2

description:
M2_DMSO2
M2 differentiation+DMSO
Control


title: (PPRE)-eGEP-THP-1,M2 differentiation+DMSO,24H,rep1

description:
M2_DMSO1
M2 differentiation+DMSO
Control


title: IyerS_RNA023_4

description: FFPE Spatial Transcriptome sequencing


title: S137

description: Rh19-24 B

value: (hours_post_inoculation)  12


title: IyerS_RNA023_3

description: FFPE Spatial Transcriptome sequencing

value: Brain-Hippocampus


title: gene expression CD4 T and B cells for patient 488, 505, 845

value: blood

value: CD4 T cells


title: S136

description: Rh19-23 B

value: Plum

value: Rhizopus stolonifer


title: (PPRE)-eGEP-THP-1,M2 differentiation+MCHP,24H,rep3

description:
M2_MCHP3
M2 differentiation+MCHP

value: MCHP


title: ARNT_fplus macrophages with L. major promastigote parasite infected parasites 2

value: Ears


title: IyerS_RNA023_2

description: FFPE Spatial Transcriptome sequencing

value: IgG


title: ARNT_fplus macrophages with L. major promastigote parasite infected parasites 1


title: (PPRE)-eGEP-THP-1,M2 differentiation+MCHP,24H,rep2

description:
M2_MCHP2
M2 differentiation+MCHP


title: S135

description: Rh19-21 B


title: ARNT_fplus macrophages with L. major promastigote parasite infected parasites and LPS/IFNg treatment 2

value: LPS IFNg treated


title: (PPRE)-eGEP-THP-1,M2 differentiation+MCHP,24H,rep1

description:
M2_MCHP1
M2 differentiation+MCHP


title: IyerS_RNA023_5

description: FFPE Spatial Transcriptome sequencing


title: S133

description: Rh19-18 B

value: (hours_post_inoculation)  6


title: IyerS_RNA023_1

description: FFPE Spatial Transcriptome sequencing