title: A431-GOF-IP2

first: Yura

last: Song

address: 808, route de Lennik

institute: Université Libre de Bruxelles

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “HEADCROP:10 CROP:65 ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50”
Reads were mapped against the human reference genome (hg38) using Bowtie2 using options “-X 2000 -q -p 6 -t --fr --very-sensitive --no-discordant --no-unal --no-mixed”.
Mitochondrial reads, reads from unmapped and random contigs, reads without unique alignment, reads with a mapping quality less than 20 and reads which are not properly mapped were removed using samtools
Duplicate reads were removed by Picard MarkDuplicates.
Peak calling was performed by macs2 (version 2.2.5) using options “-f BAMPE -g hs -p 0.01 --nomodel”.
Blacklisted regions are filtered out by bedtools (version 2.27.1).
Genome_build: hg38
Supplementary_files_format_and_content: .bed / Coordinate of called peaks

extract_protocol:
Chromatin was double fixed using DSG and Formaldehyde. Chromatin Shearing was performed using the ChIP-IT Express kit (Active Motif) according to the manufacturer's recommendations. Chromatin Immunoprecipitation was performed using Dynabeads Protein G (Invitrogen). Purification was performed using the iPure kit v2 (Diagenode).
NEB Next Ultra II DNA library Prep Kit for Illumina (Biolabs)

treatment_protocol: NR2F2 GoF induced cells were exposed to 1µg/mL Doxycycline for 48h.

tag: treatment


title: A431-GOF-input2

status: Public on Sep 27 2021

type: SRA

city: Bruxelles

country: Belgium

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Skin squamous cell carcinoma

growth_protocol: Cells were grown in EMEM culture medium, with 10% FBS tetracycline-free.

tag: cell line

tag: cell type

value: Skin squamous cell carcinoma


title: M202 Tip Control

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

description:
STAR_raw_count_table.txt
E

library_source: transcriptomic

data_processing:
Filtered fastq files with trimmomatic 0.36 (adapter removal, min. length of reads 80bp)
Alignment with STAR 2.7.1a against the Nipponbare reference genome
Generated raw count matrix based on STAR geneCount output (4th column)
Genome_build: EnsemblePlants Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Oryza sativa

source_name: Leaf

growth_protocol: Seed germination, planting and stress treatment were performed as previously described (Glaubitz et al. 2014; http://dx.doi.org/10.1071/FP13132).

extract_protocol:
Homogenized plant material of five replicate samples per cultivar, segment and treatment was pooled to 100 mg resulting into 48 samples for the analysis. Total RNA was isolated using a TRIzol protocol based on the ‘single step’ method (Sprenger, Kurowsky, Horn, Erban, Seddig, Rudack, Fischer, Walther, Zuther, Köhl, Hincha & Kopka, 2016). Four μg of each RNA sample was further treated with DNase (RapidOut DNA-removal Kit, Thermo Scientific). Absence of genomic DNA contamination was confirmed by qRT-PCR using intron-specific primers (At5g65080). Finally, RNA quality and integrity were verified with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Library preperation with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) and library type RNA library including polyA enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experiments were performed in a controlled climate chamber with 12 h light regime with 70% relative humidity and a temperature setting of 26°C in the light and 22°C at night for control conditions or 28°C constant in the light and at night.

tag: cultivar

tag: tissue

value: Tip

tag: hnt-sensitivity

value: sensitive

tag: subspecies

value: japonica

value: Control


title: Ezh2 KO PGCLC d4 rep2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
trimmomatic  (0.33) was applied for trimming adapter and low quality reads
Trimmed reads were mapped to mm9 whole genome using tophat2 (2.0.11) with default settings
Gene annotations were obtained from iGenome NCBIM37. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: NCBIM37
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

organism: Mus musculus

source_name: Primordial germ cell like cells

growth_protocol: Ezh2f/f, Cre-ERT2 ES cells were cultured in serum-free media containing N2B27 supplemented with 1 μM 7u7jPD0325091 (Cambridge Bioscience, 1643-5) and 3 μM CHIR99021 (Cambridge Bioscience, SM13-10) and 1200 U/ml LIF (ESG1107, Sigma)

extract_protocol:
PGCLC aggregates were trypsinased and sorted into cold PBS. The cells were centrifuged at 2,000 rpm for 3 min following liquid nitrogen snap freezing. Total RNA was extracted using ZR-Duet DNA and RNA Mini Prep kit (Zymo). The genotype of embryos was determined by PCR. RNA quality was measured by 2100 bioanalyzer (Agilent technologies).
RNA and cDNA were prepared by NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® according to the manufacturer’s instructions.

treatment_protocol: EpiLC induction and PGCLC induction were performed as previously described (Hayashi and Saitou, 2013). In brief, 1 × 10e5 cells were seeded in one well of a fibronectin-coated 12-well plate in EpiLCs differentiation medium (N2B27 medium supplemented with 12 ng/ml bFGF (Thermo Fisher, 13256-029), 20 ng/ml Activin A (Peprotech, 120-14E-10) and 1 % KSR (Gibco, 10828). Cells were kept in the plate at 37 °C in a CO2 incubator for 2 days and the media was changed at day 1 of culture. After 2 days EpiLCs were trypsinized. The cell suspension was diluted with PGCLC differentiation medium (GK15 medium containing 500 ng/ml BMP2 (Qkine, Qk007), 100 ng/ml mSCF (R&D Systems, 455-MC-010), 1,000 U/ml LIF and 50 ng/ml EGF (R&D Systems, 2028-EG-010) to a final concentration of 2 × 10e4 cells per ml. 100 µl of the cell suspension was pipetted into a 96-well PrimeSurface® 3D Culture Spheroid plate (MoBiTec, MS-9096VZ) and cultured for 4 days. To induce the depletion of Ezh2, 1 µl of 1 mM 4-Hydroxytamoxifen (H7904, Sigma) dissolved in ethanol was added to 10 ml PGCLC differentiation medium. 1 µl of ethanol was added to 10 ml PGCLC differentiation medium as control. After 2 days of culture, 50 µl of fresh PGCLC differentiation medium (without ethanol or 4-Hydroxytamoxifen) was added to the cells.

tag: genetic background

value: Primordial germ cell like cells

tag: genotype

value: Ezh2-/-, CreERT2

tag: group

value: Ezh2 KO

tag: time

value: day 4


title: A431-GOF-input1


title: A431-GOF-IP1

value: Doxycycline


title: Ezh2 KO PGCLC d4 rep1


title: Urothelial cells

city: Shen Zhen

first: Kang

last: Wu

state: Guang Dong

address: 47 Youyi Road, Luohu District

department: Urology

country: China

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

description: Bladder

data_processing:
Illumina Casava1.7 software used for basecalling.
raw sequencing data were timmed for adaptor sequence, and masked for low complexity or low-quanlity sequence.
trimmed data were mapped to mm10 genome using Hisat2.
Fragments Per Kilobase of gene or Transcript model per Million mapped fragments(FPKM) were calculated for analysis differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with FPKM for every gene in P group samples
Supplementary_files_format_and_content: Matrix table with FPKM for every gene in Bladder and Tumour samples

source_name: bladder

growth_protocol: in vivo

extract_protocol:
The whole RNA of tissue was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by NanoDrop ND-1000.1-2 ug of total RNA was selected for each sample for sequencing library construction.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina NovaSeq 6000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

treatment_protocol: non treatment

tag: sample type

value: tumor-bearing mice


title: SKMES KO S276I 2

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (hg38/GRCh87) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations GRCh38.87 and normalized to 20 millions of aligned reads.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: .csv / Normalized gene expression

source_name: human lung SCC cell line (Sk-MES-1) with NR2F2 deletion

extract_protocol:
RNA extraction from cultured cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: NR2F2 KO


title: AKP mouse (female) KPF1

type: RNA

city: Sendai

first: Shin

last: Hamada

state: Miyagi

address: 1-1 Seiryo-machi, Aobaku

department: Division of Gastroenterology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: AKP mouse (female)

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Data was obtained using the Agilent Feature Extraction software (v10.1), using default for all parameters.  The data were analyzed using GeneSpring GX software (v11.5) (Agilent).

source_name: Whole liver tissue

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole livers using Sepazol-RNA I Suger G (Nacalai Tesque).

tag: gender

value: female

value: liver


title: Ctrl PGCLC d4 rep3

value: Ezh2f/f, CreERT2

value: Ctrl


title: AKP::Keap1 mouse (male) KPKM1

description: AKP::Keap1 mouse (male)

value: male


title: IR62266-42-6-2 Tip Control

description:
STAR_raw_count_table.txt
B

value: indica


title: AKP::Keap1 mouse (male) KPKM2

description: AKP::Keap1 mouse (male)


title: AKP mouse (male) KPM2

description: AKP mouse (male)


title: SKMES KO S276I 1


title: WT control 2

source_name: human lung SCC cell line (Sk-MES-1)

value: NR2F2 WT


title: Ctrl PGCLC d4 rep1


title: mouse 2 rep5-s5

status: Public on Sep 26 2021

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description:
LCM mouse #2 rep5-ILF top
SCRBseq

data_processing:
bcl2fastq/2.15.0.4. Plate demultiplexing was provided to obtain plate specific reads in two fastq files (read 1 (R1) and read 2 (R2))
Pooled data of scRNAseq were demultiplexed using plate specific barcode. Specific sequences for each cell were demultiplexed using well specific barcode (attached). Pooled samples analyzed with laser capture microdissection were demultiplexed once based once to separate the pooled samples.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Jejunum-LCM

growth_protocol: C57bl6 male mice were fed regular chow ad libitum

extract_protocol:
Isolation of telocytes was performed as previously decribed (Shoshkes-Carmel, M. et al. Nature 2018).
for scRNAseq, 3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014). For bulk analysis, mcSCRBseq protocol was used (Bagnoli et al, Nat Commun. 2018). For LCM bulk analysis SMARTseq v4 Ultra Low Input RNA Kit (Clontech, 634888) was used

treatment_protocol: Mice were sacrificed by cervical dislocation

tag: strain

tag: age

value: post natal three months

tag: barcode

value: TGACCA


title: mouse 2 rep5-s2

description:
LCM mouse #2 rep5-FAE bottom
SCRBseq

value: TCGGCA


title: mouse 2 rep5-s4

description:
LCM mouse #2 rep5-ILF bottom
SCRBseq

value: TTAGGC


title: IR57311 Tip Control

description:
STAR_raw_count_table.txt
C

value: Tip

value: tolerant

value: Control


title: mouse 2 rep4-s4

description:
LCM mouse #2 rep4-ILF bottom
SCRBseq

value: CTAGCT


title: mouse 2 rep5-s1

description:
LCM mouse #2 rep5-villus bottom
SCRBseq

value: TCCCGA


title: mouse 2 rep4-s3

description:
LCM mouse #2 rep4-FAE top
SCRBseq

value: TACAGC


title: mouse 2 rep4-s5

description:
LCM mouse #2 rep4-ILF top
SCRBseq

value: CTATAC


title: mouse 2 rep4-s2

description:
LCM mouse #2 rep4-FAE bottom
SCRBseq

value: CGGAAT


title: mouse 2 rep5-s3

description:
LCM mouse #2 rep5-FAE top
SCRBseq

value: ATCACG


title: Ctrl PGCLC d4 rep2

value: Primordial germ cell like cells

value: Ezh2f/f, CreERT2

value: Ctrl

value: day 4


title: mouse 2 rep3-s5

description:
LCM mouse #2 rep3-ILF top
SCRBseq

value: post natal three months

value: CATTTT


title: mouse 2 rep3-s3

description:
LCM mouse #2 rep3-FAE top
SCRBseq

value: CCAACA


title: mouse 2 rep3-s2

description:
LCM mouse #2 rep3-FAE bottom
SCRBseq

value: ATGAGC


title: CT9993-5-10-1M Tip Control

description:
STAR_raw_count_table.txt
A

value: Tip

value: sensitive

value: japonica


title: mouse 2 rep3-s1

description:
LCM mouse #2 rep3-villus bottom
SCRBseq

value: GTAGAG


title: mouse 2 rep3-s4

description:
LCM mouse #2 rep3-ILF bottom
SCRBseq

value: CACTCA


title: mouse 1 rep2-s4

description:
LCM mouse #1 rep2-ILF bottom
SCRBseq

value: GAGTGG


title: AKP mouse (male) KPM1

description: AKP mouse (male)

value: male

value: liver


title: mouse 1 rep2-s5

description:
LCM mouse #1 rep2-ILF top
SCRBseq

value: ATTCCT


title: WT control 1

value: NR2F2 WT


title: MPP replicate 1

city: Chicago

first: Yan

last: Liu

state: Illinois

address: Northwestern University, 303 East Superior Street, Lurie 5-107

country: USA

institute: Department of Medicine

description: Biological replicate 1 of 3 MPPs

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: WT MPP1

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Hematopoietic stem cells and multipotent progenitors were purified from both WT and Bmi1 KO mice using FACS.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cells

value: Multipotent progenitors

value: 2 to 3 month old mice

tag: genotype/variation

value: wild type

tag: strain background

source_name: Bmi1 KO MPP1

value: Bmi1 KO


title: HSC replicate 3

description: Biological replicate 3 of 3 HSCs

source_name: WT HSC3

value: Hematopoietic stem cells

source_name: Bmi1 KO HSC3


title: mouse 1 rep2-s3

description:
LCM mouse #1 rep2-FAE top
SCRBseq

value: post natal three months

value: GACGAC


title: HSC replicate 1

description: Biological replicate 1 of 3 HSCs

source_name: WT HSC1

source_name: Bmi1 KO HSC1


title: mouse 2 rep4-s1

description:
LCM mouse #2 rep4-villus bottom
SCRBseq

value: CACCGG


title: MPP replicate 3

description: Biological replicate 3 of 3 MPPs

source_name: WT MPP3

source_name: Bmi1 KO MPP3


title: mouse 1 rep2-s1

description:
LCM mouse #1 rep2-villus bottom
SCRBseq

value: AGTTCC


title: mouse 1 rep1-s2

description:
LCM mouse #1 rep1-FAE bottom
SCRBseq

value: GCCAAT


title: mouse 1 rep1-s3

description:
LCM mouse #1 rep1-FAE top
SCRBseq

value: CAGATC


title: mouse 1 rep1-s1

description:
LCM mouse #1 rep1-villus bottom
SCRBseq

value: ACAGTG


title: HSC replicate 2

description: Biological replicate 2 of 3 HSCs

source_name: WT HSC2

source_name: Bmi1 KO HSC2


title: MPP replicate 2

description: Biological replicate 2 of 3 MPPs

source_name: WT MPP2

source_name: Bmi1 KO MPP2


title: mouse 1 rep1-s4

description:
LCM mouse #1 rep1-ILF bottom
SCRBseq

value: GTGAAA


title: Middle_KO_Ctrl_Rep2

city: Tianjin

first: Mo

last: Gou

address: China, Tianjin, Nankai University

institute: Nankai University

data_processing:
Sequencing reads were trimmed to remove the low-quality reads and reads containing adapters. Sequencing reads were trimmed with default setting of Trimmomatic software (Bolger et al., 2014), to remove the adapters and low-quality reads.
Trimmed reads were aligned to mouse reference mm10 by using Bismark (v12.5) (Krueger and Andrews, 2011).
Genome_build: mm10
Supplementary_files_format_and_content: bed files

source_name: 6-month-old Tet2 knockout control group

extract_protocol:
Female mice from the different age groups were superovulated by injection of 5 IU pregnant mare’s serum gonadotrophin (PMSG, Millipore, 5 IU per mouse), followed 46–48 h later by 5IU hCG. Females were humanely sacrificed and oocytes enclosed in cumulus masses collected into potassium simplex optimized medium (KSOM) by releasing from oviduct ampullae 14 h after hCG injection. Cumulus cells were removed by pipetting after brief incubation in 0.03% hyaluronidase prepared in KSOM containing 14 mM HEPES and 4 mM sodium bicarbonate (HKSOM).
DNA methylation libraries of mice MII oocytes were constructed according to a previously reported method (Smallwood et al., 2014), with minor changes.
DNA methylation libraries were sequenced using Hiseq4000 platform.

treatment_protocol: 30 mg resveratrol (R5010, Sigma) was dissolved in 500 μl of DMSO (D2650, Sigma), then 1L 37 ° C sterile water was added and the solution is incubated in water bath at 37 ° C for 2-3 hours to help dissolve 17. The control group was treated with 500 μl DMSO per 1L of drinking water. Drinking water was freshly prepared and changed every 5 days. The bottles containing resveratrol were covered with aluminum foil to protect from light. Mice were treated with medication at the age of 2 months (the young group) and the treatment continued to mouse age at o 6 and 10 months old.

value: Tet2 knockout

tag: treatment

value: control group

tag: cell type

value: mouse MII oocytes


title: Old_KO_Ctrl_Rep1

source_name: 10-month-old Tet2 knockout control group


title: Middle_WT_Res_Rep3

source_name: 6-month-old WT resveratrol treated group

value: resveratrol treated group


title: Middle_KO_Res_Rep1

source_name: 6-month-old Tet2 knockout resveratrol treated group


title: Old_KO_Res_Rep3

source_name: 10-month-old Tet2 knockout resveratrol treated group


title: mouse 1 rep1-s5

description:
LCM mouse #1 rep1-ILF top
SCRBseq

source_name: Jejunum-LCM

value: AGTCAA


title: Middle_KO_Res_Rep2


title: Middle_KO_Res_Rep3


title: Old_KO_Res_Rep1


title: Middle_WT_Res_Rep1


title: Middle_WT_Ctrl_Rep3

source_name: 6-month-old WT control group


title: Old_KO_Ctrl_Rep2


title: Middle_WT_Res_Rep2


title: Old_WT_Res_Rep2

source_name: 10-month-old WT resveratrol treated group


title: Middle_WT_Ctrl_Rep2


title: mouse 1 rep2-s2

description:
LCM mouse #1 rep2-FAE bottom
SCRBseq

value: CCGTCC


title: Middle_WT_Ctrl_Rep1

value: wild type


title: Old_KO_Res_Rep2


title: Middle_C57_Ctrl_Rep11

description: processed data file: RNAseq-counts-2.csv

data_processing:
Reads were mapped to mm10 from UCSC genome (http://genome.ucsc.edu/) by Hisat2 (v2.1.0) with default parameters. Read counts of each gene annotated in Gencode vM17 were calculated by Featurecounts, with default parameters. Sum factor normalization was applied with deconvolution of size factors within different batch samples using SCnorm.
Raw counts were normalized by library size via Transcripts Per Kilobase of exonmodel per Million mapped reads (TPM). Dynamic changes of differentially expressed genes (DEGs) between different groups were analyzed using Deseq2. DEGs were defined only if p value was < 0.05, and a fold change (log2Foldchange) was >1. All pathway enrichment sets were collected from KEGG pathway database (https://david.ncifcrf.gov/home.jsp).
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: mouse MII oocytes

extract_protocol:
Female mice from the different age groups were superovulated by injection of 5 IU pregnant mare’s serum gonadotrophin (PMSG, Millipore, 5 IU per mouse), followed 46–48 h later by 5IU hCG. Females were humanely sacrificed and oocytes enclosed in cumulus masses collected into potassium simplex optimized medium (KSOM) by releasing from oviduct ampullae 14 h after hCG injection. Cumulus cells were removed by pipetting after brief incubation in 0.03% hyaluronidase prepared in KSOM containing 14 mM HEPES and 4 mM sodium bicarbonate (HKSOM).   Isolation of GCs was based on the previous method. Briefly, PMSG was injected into the abdominal cavity of mice 46 h prior to isolating GCs. The mice were humanely sacrificed and the ovaries dissected. Insulin syringes were used to puncture visible follicles on the surface of ovaries under a stereomicroscope to release GCs into culture medium, and avoided isolated GCs from small follicles. In addition, oocytes were filtered out by 40 μm Cell Strainer (Falcon). Then, the isolated GCs were washed in phosphate-buffered saline (PBS) and dispersed into single cell, then counted up to 50 cells for RNA-seq library construction.
RNA-seq libraries were prepared using Smart-seq2 methods as previously described. Briefly, the libraries were prepared by using TruePrep DNA Library Prep Kit V2 for Illumina® (TD503-02, Vazyme Biotech) according to the manual instruction.
Samples were barcoded during library preparation and multiplex sequenced, with a 150-bp paired-end sequencing strategy on a HiSeq4000 (Illumina).

value: middle age(6-month-old) control group


title: Middle_C57_Ctrl_Rep10


title: Middle_C57_Ctrl_Rep8


title: Middle_C57_Ctrl_Rep7


title: Middle_C57_Ctrl_Rep9


title: Middle_C57_Ctrl_Rep4


title: Middle_C57_Ctrl_Rep2


title: Middle_C57_Ctrl_Rep3


title: Middle_C57_Ctrl_Rep1


title: Old_C57_Ctrl_Rep6

value: old age(10-month-old)


title: Old_C57_Ctrl_Rep1


title: Old_C57_Res_Rep9


title: Old_C57_Ctrl_Rep5


title: Old_C57_Res_Rep4


title: Old_WT_Res_Rep1


title: Old_C57_Res_Rep5


title: Old_C57_Res_Rep6


title: Old_C57_Res_Rep8


title: Old_C57_Res_Rep7


title: Middle_C57_Ctrl_Rep5


title: Old_C57_Ctrl_Rep4


title: Old_C57_Ctrl_Rep2


title: Old_C57_Ctrl_Rep3


title: Old_C57_Res_Rep1


title: Old_C57_Res_Rep2


title: Old_C57_Res_Rep11


title: Middle_C57_Ctrl_Rep6


title: Old_C57_Res_Rep10


title: MKOR20

description: processed data file: RNAseq-counts-1.csv

value: middle age(6-month-old)


title: MKOR19


title: Old_C57_Res_Rep3


title: MKOR18


title: MKOR16


title: Middle_KO_Ctrl_Rep1


title: MKOR17


title: MKOR9


title: MKOR14


title: MKOR11


title: MKOR13


title: MKOR6


title: MKOR5


title: MKOR7


title: MKOR4


title: MKOR1


title: MKOR10


title: MKOR2


title: MKOR3


title: MKOR8


title: MKOR15


title: MKOC19


title: MKOC14


title: MKOC13


title: MKOC11


title: MKOC16


title: MKOC9


title: MKOC18


title: MKOC6


title: MKOC4


title: MKOC20


title: MKOC17


title: MKOC1


title: YWT18


title: YWT16


title: MKOC3


title: YWT14


title: YWT15


title: MKOR12


title: MKOC15


title: YWT10


title: MKOC2


title: MKOC10


title: YWT11


title: YWT8


title: MKOC12


title: YWT6


title: YWT5


title: YWT4


title: Middle_KO_Ctrl_Rep3


title: YWT1


title: MKOC5


title: YKO12


title: YKO15


title: MKOC7


title: YWT13


title: YKO11


title: YWT17


title: YKO9


title: YKO14


title: YWT9


title: YKO4


title: YKO10


title: YKO6


title: YWT12


title: MKOC8


title: YKO2


title: OWTR12


title: OWTR9


title: YWT7


title: YKO13


title: YKO8


title: YKO7


title: YKO3


title: OWTR4


title: OWTR3


title: OWTC20


title: OWTR1


title: OWTC18


title: OWTC19


title: OWTC13


title: OWTC14


title: OWTR8


title: YKO5


title: OWTC8


title: OWTC5


title: OWTC7


title: YWT2


title: OWTR14


title: OWTC11


title: OWTR6


title: OWTC9


title: OWTC3


title: OWTC2


title: OWTR13


title: OWTC17


title: OWTC12


title: OWTR11


title: YKO1


title: OKOR14


title: OWTR10


title: OWTR5


title: YWT3


title: OKOR10


title: OKOR9


title: OKOR8


title: OWTR7


title: OWTR2


title: OWTC4


title: OWTC10


title: OKOR13


title: OWTC15


title: OKOR4


title: OKOR3


title: OWTC16


title: LLR039_sgSmarcb1_iTreg

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: sgSmarcb1-transduced iTreg cells after 20hrs' aCD3/aCD28 (0.25/5 ug) restimulation

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: iTreg in vitro differentiation, plate-bound condition

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: sgNTC-transduced iTreg cells


title: OKOR2


title: OKOC15


title: OKOC14


title: OWTC6


title: OKOR15


title: OWTC1


title: LLR033_sgSmarcb1_iTreg

source_name: sgSmarcb1-transduced iTreg cells after 3hrs' aCD3 (0.25ug) restimulation

value: 3hrs' aCD3 (0.25ug) restimulation


title: OKOR7


title: OKOR6


title: LLR032_sgSmarcb1_iTreg


title: OKOR11


title: OKOR5


title: OKOR12


title: LLR042_sgSmarcb1_iTreg

value: 20hrs' aCD3/aCD28 (0.25/5 ug) restimulation


title: LLR037_sgNTC_iTreg

source_name: sgNTC-transduced iTreg cells after 20hrs' aCD3/aCD28 (0.25/5 ug) restimulation


title: LLR040_sgSmarcb1_iTreg


title: LLR022_sgNTC_iTreg

source_name: sgNTC-transduced iTreg cells after 3hrs' aCD3 (0.25ug) restimulation


title: OKOC13


title: LLR041_sgSmarcb1_iTreg


title: OKOC11


title: OKOR1


title: LLR036_sgNTC_iTreg


title: OKOC12


title: LLR035_sgNTC_iTreg


title: OKOC10


title: OKOC9


title: OKOC8


title: LLR038_sgNTC_iTreg


title: OKOC5


title: LLR021_sgNTC_iTreg


title: OKOC6


title: LLR034_sgSmarcb1_iTreg


title: LLR020_sgNTC_iTreg


title: LLR019_sgNTC_iTreg


title: LLR020_sgCcdc101_iTreg

source_name: sgCcdc101-transduced iTreg cells after 20hrs' aCD3/aCD28 (0.25/5 ug) restimulation

value: sgCcdc101-transduced iTreg cells


title: LLR031_sgSmarcb1_iTreg


title: LLR018_sgCcdc101_iTreg


title: LLR017_sgCcdc101_iTreg


title: LLR019_sgCcdc101_iTreg


title: LLR016_sgNTC_iTreg


title: OKOC3


title: OKOC7


title: OKOC1


title: LLR015_sgNTC_iTreg


title: MWTR14


title: MWTR12


title: MWTR11


title: OKOC4


title: MWTR10


title: LLR006_sgCcdc101_iTreg

source_name: sgCcdc101-transduced iTreg cells at steady state


title: Ln4-dist

city: Salt Lake City

first: Gabor

middle: T

last: Marth

state: UT

department: Human Genetics

institute: University of Utah

data_processing:
RNA-seq data were processed with Rsubread v1.16.1
We aligned the reads to GRCh37 and used only uniquely mapped reads and the Hamming distance to break ties. The maximum indels allowed per alignment was 5
We used the Rsubread built-in annotation file which includes the exon annotation information from NCBI Build 37.2 and Entrez gene identifier
Gene-level expression values were processed to transcript per million mapped reads (TPM).
Genome_build: GRCh37
Supplementary_files_format_and_content: Text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Ln4 distant normal lung tissue

extract_protocol:
RNA from all 28 autopsy tumors and adjacent/distal normal samples was extracted by using Qiagen RNeasy Micro/Mini Kit
RNA-seq was performed using rRNA depletion-based library preparation followed by paired-end Illumina HiSeq sequencing

tag: tissue

value: lung

value: normal


title: LLR013_sgNTC_iTreg


title: LLR005_sgCcdc101_iTreg

value: sgCcdc101-transduced iTreg cells at steady state


title: LLR002_sgNTC_iTreg

source_name: sgNTC-transduced iTreg cells at steady state


title: LLR014_sgNTC_iTreg


title: LLR003_sgNTC_iTreg

value: sgNTC-transduced iTreg cells at steady state


title: Ln3

source_name: breast cancer lung metastatic tumor

value: breast metastatic tumor

value: cancer


title: Ln4-adj

source_name: Ln4 adjacent normal lung tissue


title: LLR001_sgNTC_iTreg


title: MWTR8

value: resveratrol treated group

value: mouse MII oocytes


title: MWTR9


title: LLR004_sgCcdc101_iTreg


title: MWTR7


title: Ln4


title: Ln1-dist

source_name: Ln1 distant normal lung tissue


title: Ln2


title: MWTR13


title: OKOC2

value: Tet2 knockout

value: control group


title: Bn4

source_name: breast cancer brain metastatic tumor


title: MWTR5

value: wild type


title: MWTR4


title: MWTR3


title: MWTR6


title: Ln1-adj

source_name: Ln1 adjacent normal lung tissue


title: Bo2

source_name: breast cancer bone metastatic tumor


title: Pa1

source_name: breast cancer peri-pancreatic metastatic tumor

value: peri-pancreas


title: MWTR2

value: middle age(6-month-old)


title: Ln2-dist

source_name: Ln2 distant normal lung tissue


title: Ln5-adj

source_name: Ln5 adjacent normal lung tissue


title: MWTC16

source_name: mouse MII oocytes


title: MWTC15


title: MWTR1


title: MWTC18


title: MWTC14


title: Ln9


title: Ly2

source_name: breast cancer peritracheal lymph node metastatic tumor


title: Lv3

source_name: breast cancer liver metastatic tumor


title: Ln2-adj

source_name: Ln2 adjacent normal lung tissue


title: MWTC10


title: MWTC11


title: Lv2


title: MWTC9


title: Lv4


title: MWTC7


title: Kd1-dist

source_name: Kd1 distant normal kidney tissue

value: kidney


title: MWTC17


title: MWTC20


title: Bo3


title: MWTC12


title: Ln1


title: Ln6-adj

source_name: Ln6 adjacent normal lung tissue


title: Bn1


title: MWTC8


title: MWTC4


title: Lv1


title: MWTC3


title: Kd1-adj

source_name: Kd1 adjacent normal kidney tissue


title: Kd1

source_name: breast cancer kidney metastatic tumor


title: Bn3


title: MWTC2


title: GC_YWT3

source_name: mouse granulosa cells

value: mouse granulosa cells (GC)


title: Ln11

source_name: breast cancer lung metastatic tumor


title: Sk1

source_name: breast cancer skin metastatic tumor


title: MWTC13


title: Ln12-adj

source_name: Ln12 adjacent normal lung tissue


title: Bo1


title: MWTC6


title: MWTC5


title: GC_YKO3


title: GC_YWT1


title: Ly1


title: MWTC19


title: GC_YKO1


title: GC_OWTR3

value: old age(10-month-old)


title: GC_OWTR2


title: Ln7-adj

source_name: Ln7 adjacent normal lung tissue


title: Ln7


title: GC_OWTC3


title: GC_OWTR1


title: GC_OWTC2


title: GC_OKOR3


title: Bn2

source_name: breast cancer brain metastatic tumor


title: Endothelial cell overexpressed Ptbp1(wt) plasmid rep3

city: Atlanta

first: Qiang

last: Zhao

state: GA

address: 157 Decatur St SE

institute: Georgia State University

data_processing:
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, counts

source_name: Total RNA isolated from Ptbp1(wt) plasmid overexpressed endothelial cells

growth_protocol: EBM with 10% FBS

extract_protocol:
Endothelial cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Endothelial cells transfected with Ptbp1(wt), Ptbp1(T138A) or Ptbp1(T138E) plasmid

tag: cell line

value: HUVEC

value: Endothelial cell

value: Ptbp1(wt) overexpression


title: GC_YWT2


title: Endothelial cell overexpressed Ptbp1(wt) plasmid rep1


title: Ln8-adj

source_name: Ln8 adjacent normal lung tissue

value: lung

value: normal


title: Ln8

value: breast metastatic tumor


title: GC_OKOC1


title: GC_OKOR1


title: GC_YKO2


title: MWTC1


title: Ln6

value: cancer


title: Ln12-dist

source_name: Ln12 distant normal lung tissue


title: Ln10


title: Ln5


title: GC_OWTC1


title: GC_OKOR2

value: resveratrol treated group


title: Endothelial cell overexpressed Ptbp1(wt) plasmid rep2


title: Endothelial cell overexpressed Ptbp1(T138E) plasmid rep1

source_name: Total RNA isolated from Ptbp1(T138E) plasmid overexpressed endothelial cells

value: Ptbp1(T138E) overexpression


title: GC_OKOC3

value: Tet2 knockout


title: Endothelial cell overexpressed Ptbp1(T138E) plasmid rep3


title: Ln12


title: Endothelial cell overexpressed Ptbp1(T138A) plasmid rep3

source_name: Total RNA isolated from Ptbp1(T138A) plasmid overexpressed endothelial cells

value: Ptbp1(T138A) overexpression


title: Endothelial cell overexpressed Ptbp1(T138E) plasmid rep2


title: GC_OKOC2

value: control group


title: scRNA-seq_Ccdc101KO1

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample for scRNAseq

source_name: CD45+ immune cells from mice with Treg specific deletion of Ccdc101

growth_protocol: Young (~8 weeks old, before systemic inflammation) Foxp3Cre;Ccdc101fl/fl and control mice were inoculated with MC38 colon adenocarcinoma. CD45+YFP+ Treg cells, CD45+YFP-CD11b- non-Treg cells and CD45+CD11b+ myeloid cells were sorted and mixed at 1:2:1 ratio at day 19 after tumor challenge

extract_protocol:
CD45+YFP+ Treg cells, CD45+YFP-CD11b- non-Treg cells and CD45+CD11b+ myeloid cells were sorted and mixed at 1:2:1 ratio from MC38 tumor and loaded onto the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell gene expression v3.1 Library and Gel Bead Kit (10x Genomics)

value: CD45+YFP+ Treg cells, CD45+YFP-CD11b- non-Treg cells and CD45+CD11b+ myeloid cells (mixed at 1:2:1 ratio)


title: scRNA-seq_Ccdc101KO2


title: Endothelial cell overexpressed Ptbp1(T138A) plasmid rep1


title: scRNA-seq_wild-type1

source_name: CD45+ immune cells from wild-type mice


title: Ccdc101KO4

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm9 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM37_um.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples

source_name: sgCcdc101-transduced iTreg cells

growth_protocol: iTreg cells transduced with indicated sgRNAs were sorted and restimulated with 0.25/5 ug/ml aCD3/28 overnight

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

value: sgCcdc101-transduced iTreg cells


title: HuH-7-T4-NI-1

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

data_processing:
Demultiplexing was performed (bcl2fastq2 V2.2.18.12) and adapters were trimmed with Cutadapt (v1.15); only reads longer than 10 bp were kept.
TopHat (version 2.1.1) was used for alignment on the reference genome
Data were evaluated through principal component analysis and hierarchical clustering after transformation of the count data using RLOG function.
Normalization and differential analysis were carried out using the DESeq2 package, with a pre-filter step to remove genes with low counts (sum of all replicates counts<10, in all conditions compared)
Genome_build: Ensembl-98 human genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatocytes

growth_protocol: Listeria monocytogenes EGDe strain was grown in brain-heart infusion (BHI) at 37°C. Human Huh7 hepatocytes (CLS 300156)  were grown as recommanded by ATCC, on 6-well plates.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) and genomic DNA was removed using TURBO DNA-freeTM kit (Ambion), according to the manufacturer’s instructions. The integrity, purity and concentration of RNA samples was assessed on an RNA 6000 pico chip using the Agilent 2100 electrophoresis Bioanalyzer.  RNA was quality checked an then store at -80°C.
RNA-seq libraries of infected and non-infected cell RNA were assembled using 500-1300 ng total RNA using the TruSeq® mRNA Stranded Library Prep kit (Illumina) which includes polyA-selection. The RNA-seq libraries were monitored for quality on the Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit. Libraries were pooled in equimolar proportions

treatment_protocol: Cells were non-infected or infected with Listeria at multiplicity of infection of 1-5. After 1h infection, extracellular bacteria were killed by adding gentamicin and cells were incubated for 3 days with 25 μg/ml gentamicin containing media.

value: Human hepatocarcinoma cell line Huh7

value: control (non-infected)


title: Ccdc101KO1


title: HuH-7-T3-NI-2


title: NTC4

source_name: sgNTC-transduced iTreg cells

value: sgNTC-transduced iTreg cells


title: NTC3


title: Endothelial cell overexpressed Ptbp1(T138A) plasmid rep2

value: HUVEC


title: HuH-7-T4-EGde-1

value: infected with Listeria monocytogenes EGDe


title: HuH-7-T2-NI-2


title: HuH-7-T2-EGde-1


title: scRNA-seq_wild-type2


title: NTC1


title: Nr4a1pos_Male4_Rep2

city: Novato

first: Lisa

last: Ellerby

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

data_processing:
Sequenced reads were trimmed for adaptor sequence and bases with quality score lower than 20 using Trim Galore! 0.6.4 with parameters trim_galore --fastqc --length 25 --cores 4 --paired --retain_unpaired
The external and internal rRNA contamination were filtered through SortMeRNA 2.1b with parameters sortmerna --ref $sortmernaREF --reads $merge --aligned $aligned --other $filtered -m 5120 --fastx --paired_out --log -a 30 -v
The filtered raw reads were mapped to the Genome Reference Consortium Mouse Build 38 striosome release 6(GRCm38.p6) assembly by GENCODE using STAR 2.7.2b with parameters STAR --runThreadN 15 --genomeDir Mus_musculus.GRCh38.p6.genome/ --sjdbGTFfile gencode.vM22.annotation.gtf --readFilesIn $read1 $read2 --outSAMtype BAM SortedByCoordinate
The raw counts of reads mapped to known genes were summarized by featureCounts, using GENECODE release M22 annotation with parameters featureCounts -a gencode.vM22.annotation.gtf -o final_counts.txt -g 'gene_name' -T 4 $dirlist
Then R Bioconductor package DESeq2 were used to normalize raw read counts logarithmically and perform differential expression analysis.
Genome_build: mm10(GRCm38.p6)
Supplementary_files_format_and_content: Comma-separated values files include TPM values for each sample.

source_name: Striatum

extract_protocol:
PND3 cells from Nr4a1-EGFP heterozygous mice were obtained from a time set  homozygote Nr4a1-EGFP and WT breedings using FACS cell sorter. The collected cells were subject to  RNA extraction. RNA was isolated using PicoPure RNA Isolation kit, which included a DNase treatment  step.
RNA libraries were prepared for sequencing using the standard protocol from Takara Clontech Laboratories SMARTer Stranded Total RNA-Seq Pico Kit (Cat#635005 Clontech) using 10ng total RNA. RNAseq libraries were analyzed on an  Agilent High Sensitivity D1000 TapeStation, and quantification of the libraries were performed using the  KAPA Library Quantification Kit.

value: Striatum

value: day 3

value: Male

tag: nr4a1-gfp status

value: Nr4a1-GFP positive


title: Nr4a1neg_Male4_Rep2

value: Nr4a1-GFP negative


title: Ccdc101KO3


title: Ccdc101KO2


title: Nr4a1neg_Male3_Rep2


title: HNSCC28 MDSC

city: Nijmegen

first: Glenn

middle: van

last: Wigcheren

address: Geert Grooteplein Zuid 28

department: Tumor Immunology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Single cell suspension

data_processing:
Sequence reads were processed using the seq2science pipeline (https://github.com/vanheeringen-lab/seq2science).
Reads were trimmed and mapped to the human reference genome GRCh38.
Gene counts were obtained with HTSeq.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.counts.tsv: Tab-delimited text files include raw counts.

source_name: HNSCC patient 28 isolated MDSC

extract_protocol:
M-MDSCs were isolated from HNSCC patient PBMCs based on CD14+ and HLA-DR- FACS sorting.
Dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
30ng of RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems).

value: MDSC

tag: donor

value: Patient 28

tag: diagnosis

value: HNSCC


title: HuH-7-T3-EGde-2


title: Nr4a1neg_Male3_Rep1


title: Nr4a1pos_Male4_Rep1


title: Nr4a1neg_Male4_Rep1


title: HNSCC27 MDSCiv

description: Single cell suspension

source_name: HNSCC patient 27 in vitro generated MDSC

extract_protocol:
Days in X-Vivo-15 + 2% human AB male serum.
Dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
30ng of RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems).

treatment_protocol: M-MDSC were generated in vitro according to generation protocol using recombinant human GM-CSF and IL-6 (see reference).

value: in vitro generated MDSC

value: Patient 27


title: HNSCC28 Mono

description: Single cell suspension

source_name: HNSCC patient 28 isolated Monocyte

extract_protocol:
Monocytes were isolated from HNSCC patient PBMCs based on CD14+ and HLA-DR+ FACS sorting.
Dry pellets using liquid nitrogen and storage at -80°C. Total RNA was extracted from cell pellets using RNeasy Plus Micro Kit (Qiagen) according to manufacturer’s instructions.
30ng of RNA per sample was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems).

value: Monocyte


title: NTC2


title: Nr4a1pos_Male3_Rep1


title: Nr4a1neg_Male2_Rep2


title: Nr4a1pos_Male3_Rep2


title: Nr4a1pos_Male2_Rep2


title: HNSCC27 MDSC

description: Single cell suspension

source_name: HNSCC patient 27 isolated MDSC


title: Nr4a1neg_Male2_Rep1


title: HNSCC25 MDSCiv

description: Single cell suspension

source_name: HNSCC patient 25 in vitro generated MDSC

value: Patient 25


title: HNSCC26 MDSCiv

description: Single cell suspension

source_name: HNSCC patient 26 in vitro generated MDSC

value: Patient 26


title: Nr4a1pos_Male2_Rep1


title: HNSCC26 Mono

description: Single cell suspension

source_name: HNSCC patient 26 isolated Monocyte


title: Nr4a1neg_Male1_Rep2


title: HNSCC25 MDSC

description: Single cell suspension

source_name: HNSCC patient 25 isolated MDSC


title: HNSCC25 Mono

description: Single cell suspension

source_name: HNSCC patient 25 isolated Monocyte


title: Nr4a1neg_Male1_Rep1


title: Transitional stem cell memory T cells CCR4 from healthy donor HD3

city: New York

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ polyA trimming
STAR alignment (version 2.7.3a): outFilterMismatchNmax 1, alignEndsType EndToEnd
Gene counts performed using quant3p
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix counts. Each column corresponds to gene counts for each generated BAM.

source_name: peripheral blood

extract_protocol:
Cells were FACSorted in Lysis Binding Buffer and mRNA was extracted through Dynabeads polyT
RNA was sample-barcodad by a RT reaction. After, cDNA was purified with SPRIselect and amplified using the T7 promotor as template. RNA molecules were fragmented and purified again. Afterwards, a ssRNA adaptor was ligated to the 3’-end of the RNA fragments and, finally, cDNA was amplified.


title: Nr4a1pos_Male1_Rep1


title: T cell helper 17 from healthy donor HD3

value: T cell helper 17


title: Nr4a1neg_Female2_Rep2

value: Female


title: HNSCC27 Mono

description: Single cell suspension

source_name: HNSCC patient 27 isolated Monocyte


title: Transitional stem cell memory T cells CXCR3 from healthy donor HD3

description: HD3_TSCM_CXCR3_S26.trim.star_hg19.sorted


title: T cell helper 2 from healthy donor HD3

value: T cell helper 2


title: HNSCC26 MDSC

description: Single cell suspension

source_name: HNSCC patient 26 isolated MDSC


title: T cell helper 1_17 from healthy donor HD3

value: T cell helper 1_17


title: Nr4a1neg_Female1_Rep1

value: Striatum


title: Nr4a1neg_Female1_Rep2

value: day 3


title: T cell helper 1 from healthy donor HD3

value: T cell helper 1


title: Nr4a1neg_Female2_Rep1


title: Nr4a1pos_Female2_Rep1

value: Nr4a1-GFP positive


title: T cells CCR6 from healthy donor HD3

value: T cells CCR6


title: Transitional stem cell memory T cells CXCR3 from healthy donor HD2

description: HD2_TSCM_CXCR3_S23.trim.star_hg19.sorted


title: Nr4a1pos_Female1_Rep1


title: T cells central memory from healthy donor HD3

value: T cells central memory


title: Transitional stem cell memory T cells CCR4 from healthy donor HD2


title: Nr4a1pos_Male1_Rep2

value: Male


title: Nr4a1pos_Female2_Rep2


title: T cell helper 2 from healthy donor HD2


title: Nr4a1pos_Female1_Rep2


title: T cells naïve from healthy donor HD3

value: T cells naive


title: γ-H2AX-IP-rep3

city: Hangzhou

first: Xiaochun

last: Yu

state: Zhejiang

address: 18 Shilongshan Street

institute: Westlake University

description: γ-H2AX-IP RNA from spermatocytes

data_processing:
Library strategy: RNA-ChIP
The STAR reference genome of mouse 45S rRNA is built with parameters: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir mmu_45S --genomeFastaFiles mmu_rRNA_45S.fa --sjdbGTFfile mmu_rRNA_45S.gtf --sjdbOverhang 150
RNA-seq reads were aligned to the pre-built mouse 45S ribosomal RNA using STAR version 2.7.6a with the following parameters: STAR --runMode alignReads --genomeLoad NoSharedMemory --runThreadN 8 --readFilesCommand gunzip -c --genomeDir [dir_of_mmu_rRNA_45S] --readFilesIn [read1.fq.gz] [read2.fq.gz] --twopassMode Basic --outFileNamePrefix [outdir_bam] --sjdbOverhang 150 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 50000000000 --outFilterMultimapNmax 50 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0
The aligned BAM files were processed using featureCounts v2.0.2 with 10nt-binned gtf annotation file to get binned read statistics. The parameter is shown below: featureCounts -T 8 -p -t exon -g gene_id -a [binned_gtf.gtf] -o [featureCounts.binned.txt] [Aligned.sortedByCoord.out.bam]
Genome_build: The mouse 45S rRNA sequence is extracted from NCBI (GenBank:X82564.1), and the GTF annotation is generated from submitted mouse ribosomal RNA sequences (GenBank: M20154.1, AH002077.2 and X00525.1). GTF file is then processed for a 10nt-binned read statistics.
Supplementary_files_format_and_content: TXT, FASTA and GTF

source_name: spermatocytes from testis of 3-week old wildtype mice

growth_protocol: Mouse spermatocytes were isolated from testis of 3-week old wildtype mice.

extract_protocol:
Lysates were clarified from sonicated nuclei and RNA-DNA-protein complexes were isolated with antibody. DNA was digested and RNA was extrated.
Library preparation and sequencing were finished by LC-Bio Technology CO., Ltd., Hangzhou, China. The protocol is as follows: 1) RNA fragment and reverse transcription; 2) End repair, add A and adaptor ligation; 3) PCR; 4)Single strand separation and cyclization; 5) DNA nanoball synthesis; 7) Sequencing.

treatment_protocol: IgG or γH2AX immunoprecipitated RNA in mouse spermatocytes.

value: testis

value: spermatocytes

value: 3-week old

tag: genotype

value: wildtype

value: RNA-ChIP by γ-H2AX

tag: ip antibody

value: Rabbit γH2AX antibody, NOVUS BIOLOGICALS, #NB100-384, #G


title: T cell helper 17 from healthy donor HD2

value: T cell helper 17


title: γ-H2AX-IP-rep1

description: γ-H2AX-IP RNA from spermatocytes


title: γ-H2AX-IP-rep2

description: γ-H2AX-IP RNA from spermatocytes


title: IgG-IP RNA-rep2

description: IgG-IP RNA from spermatocytes

value: RNA-ChIP by IgG

value: Rabbit IgG, Cell Signaling TECHNOLOGY, #2729S, #10


title: T cells CXCR3 CCR4 from healthy donor HD3

value: T cells CXCR3 CCR4


title: T cell helper 1_17 from healthy donor HD2

value: T cell helper 1_17


title: 10X_Circulation_Normal_1

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

description: Circulating hemocytes of w1118 120h AEL

data_processing:
Three 10X Chromium scRNA-seq datasets were aligned to the Drosophila reference genome (BDGP 6.22) and quantified using CellRanger (v3.1.0).
Outlier cells having UMI counts higher than two standard deviations from the mean count, mitochondrial contents higher than 10%, or gene counts less than 200 were removed using Seurat
Resulting 2128 cells were CPM normalized, log-transformed, and scaled
Cells were annotated using label transfer analysis based on lymph gland and circulating cells used in our previous study.
Genome_build: BDGP 6.22
Supplementary_files_format_and_content: Processed data files of each sample consisted of expression matrix, barcodes and genes which are Cellranger filtered output.  Merged files have also been provided.

organism: Drosophila melanogaster

source_name: circulating hemocytes

extract_protocol:
100 larvae were dissected for one single cell RNA seq library. Larvae were vortexed 1 min prior to dissection. 20 larvae were sacrificed in 10 ml of ice-cold Schneider's medium (Gibco, 21720024). Collected hemolymph was passed through a 40 mm cell strainer (Corning, 352340) and centrifuged at 7000 rpm at 4 °C for 5 min. After removal of the supernatant, 1X filtered PBS was added.
After the cell preparation, scRNA-seq library generation was followed in 10X Genomics manufacturer’s protocol (10X Chromium 3’ v2 kit).
Single Cell 3' Reagent Kit v2 (10x genomics)

tag: developmental stage

value: larvae

value: circulating hemocytes

tag: sequencing replicates


title: 10X_Circulation_Normal_3

description: Circulating hemocytes of w1118 120h AEL

tag: strain


title: 10X_Circulation_Normal_2

description: Circulating hemocytes of w1118 120h AEL


title: T cell helper 1 from healthy donor HD2

value: T cell helper 1


title: IgG-IP RNA-rep1

description: IgG-IP RNA from spermatocytes

tag: age


title: Infertile2

first: Jingtao

last: Guo

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Testicular cells

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane.
10X Genomics single cell RNA sequencing

value: Testicle

tag: disease

value: idiopathic male infertility


title: Infertile1_rep2


title: T cells CXCR3 CCR4 from healthy donor HD2

description: HD2_CXCR3_CCR4_S25.trim.star_hg19.sorted


title: Infertile1_rep1


title: Muscle_den_rep2, input

city: Shenzhen

first: Yuantong

address: 1017 Dongmen Bei Road

department: Spine Surgery

institute: The Second Clinical Medical College, Jinan University

description: input

data_processing:
Library strategy: MeRIP-seq
MeRIP-seq reads were aligned to human genome mm10 by using the STAR (version 2.4.2a) with reference annotation GENCODE version 25.
For transcriptomebased peak caller MeTPeak, the m6A peak region summit was defined as the site with the highest fragment pileup ratio between the IP and Input.
The top 5,000 peaks were chosen for motif analysis with MEME. Peaks falling in mRNA were assigned to 5 nonoverlapped regions with R, 5’UTR, CDS, and 3’UTR.Peaks were annotated by the function of annotatePeak of ChIPseeker.
GO Analysis: Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the gene in the experiment.
Pathway analysis was used to find out the significant pathway of the genes according to KEGG database.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using MeTPeak
Supplementary_files_format_and_content: peak text files

source_name: GAS muscle

growth_protocol: 10-week-old male mice were housed under specific pathogen-free conditions at 24 ± 2°C with a 12:12 h light-dark cycle and ad libitum access to food and water.

extract_protocol:
Muscles were removed, quick-frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. m6A-RNA complexes were isolated with m6A antibody.
The amount of 2 μl of 14 μl eluted RNA was reverse transcribed with High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Once successfully immunoprecipitated methylated RNA was confirmed, further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol.

treatment_protocol: Mouse GAS muscle suffered from denervation for 14 days

value: GAS muscle

value: 14 days after denervation


title: T cells central memory from healthy donor HD2

value: T cells central memory


title: vGlut2_rep1

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

description: single-nuclei RNA

data_processing:
Sample demultiplexing, read alignment and counting of barcodes and unique molecular identifiers (UMIs) were performed using Cell Ranger v3.1.0 (10x Genomics).
SoupX was used to correct raw counts for contamination by ambient RNA from the nuclei suspension (e.g. mitochondrial RNA) [Young & Behjati, 2020]
Data were processed using Seurat (v3.2) in R. Barcodes with fewer than 1000 UMIs, fewer than 450 detected genes or more than 5% mitochondrial genes were filtered out, and UMI normalization, highly variable gene selection and scaling were performed.
Barcodes with fewer than 1000 UMIs, fewer than 450 detected genes or more than 5% mitochondrial genes were filtered out. UMI normalization, highly variable gene selection and scaling were performed for each sample, followed by UMAP and SNN graph construction and clustering using the Louvain algorithm.
Potential multiplets were removed using DoubletFinder (McGinnis et al, 2019) and each sample was processed with SCTransform in Seurat to control for sequencing depth and reduce technical noise. Samples were integrated using the SCT workflow with 3000 features and 40 PCs. Processing steps were repeated as described above (40 PCs, res. 0.8). Clusters were identified based on canonical markers expressed by specific cell types and clusters expressing markers of multiple cell types were removed, retaining 34,144 genes, 21,494 cells.
A cluster expressing vGluT2 was identified (520 cells) and isolated for subclustering, then further filtered to remove Gad2+ inhibitory neurons and vGluT2+ Mog+ oligodendrocyte subclusters, retaining 480 cells. SCTransform was then applied using 3000 variable genes. PCA, UMAP generation, SNN graph construction, and Louvain clustering were repeated as described above, using 50 PCs and a range of clustering resolutions from 0.3-1.3. A resolution of 0.5 was used to identify cluster marker genes and generate plots for publication.
Genome_build: mm10-3.0.0_premrna
Supplementary_files_format_and_content: Sparse matrices of RNA counts for all genes after SoupX adjustment and filtration to remove multiplets and empty droplets
Supplementary_files_format_and_content: Sparse matrix of SoupX-adjusted RNA counts for filtered vGluT2 neurons in all samples

source_name: Deep cerebellar nuclei

extract_protocol:
Brains were extracted and dissected in pre-chilled cutting solution (250 mM Sucrose, 26 mM NaHCO3, 10 mM [D+] Glucose, 4 mM MgCl2, 3 mM Myo-inositol, 2.5 mM KCl, 2 mM Sodium pyruvate, 1.25 mM NaH2PO42H2O, 0.5 mM Ascorbic acid, 0.1 mM CaCl2, and 1 mM Kynurenic acid) and were sectioned using a vibratome (Leica VT-1200). The DCN was identified and micro-dissected from the cerebellar vibratome slices (Bregma -5.68 mm to -6.84 mm).
Homogenisatio: Tissue was Dounce homogenized with 2 ml homogenization buffer (0.25 M Sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine, pH 7.8), followed by addition of NP-40 (final concentration 0.3%) to lyse the cells. The suspension was filtered through a 40 µm filter (H13680-0040, Scienceware) to remove debris and multiplets.
Nuclei - iodixanol: The 2 ml filtrate was mixed with 2ml 50% iodixanol (15ml Optiprep, 3ml Dilution buffer [150 mM KCl, 30 mM MgCl2 and 120 mM Tricine-KOH, pH 7.8]) and layered on top of 3.5ml each of 40% and 30% iodixanol solutions in a pre-chilled centrifugation tube (#344059, Beckman Coulter Optima). Samples were centrifuged  at 10,000xg for 20 min at 4°C and nuclei were extracted from the 30-40% interface. Nuclei were mixed with 1X PBS, pelleted and resuspended.
Nuclei - sucrose cushion: The 2 ml filtrate was mixed with 4.6 ml of 1.8 M Sucrose cushion buffer (1.8 M sucrose, 10mM Tris-HCl, 1.5 mM MgCl2, pH 6.9). The 6.6 ml solution was then layered on top of 3 ml 1.8 M Sucrose cushion buffer in a pre-chilled centrifugation tube (#344059, Beckman Coulter Optima) and centrifuged at 30,000 x g for 45 min at 4°C. The supernatant was removed, and the pellet was resuspended in 90 µl of pre-chilled resuspension buffer (10 mM Tris-HCl, 0.25 M Sucrose, 25 mM KCl, 1.5 mM MgCl2, and 1.5 mM CaCl2, pH 6.9).
Isolated nuclei were diluted in nuclease-free water to a concentration of ~1000 nuclei/ml. Samples were captured for cDNA library generation using a microfluidics platform (10x Genomics) and prepared for sequencing using Chromium Single Cell 3’ Reagents Kits v3 (10x Genomics).

tag: Sex

value: Male

value: 2 months

tag: transgenic line parent 1

value: vGluT2-Cre (Tg(Slc17a6-icre)1Oki)

tag: transgenic line parent 2

tag: extraction method

value: Sucrose cushion


title: Ucn3_rep2

description: single-nuclei RNA

value: 3 months

value: Ucn3-Cre (Tg[Ucn3-cre]KF31Gsat/Mmucd)


title: vGlut2_rep2

description: single-nuclei RNA

value: Female

value: 2.5 months


title: Ucn3_rep1

description: single-nuclei RNA

value: Iodixanol gradient


title: Muscle_con_rep2, input

description: input

tag: treatment

value: untreated


title: Muscle_den_rep1, input

description: input

tag: tissue


title: Muscle_den_rep2

description: methylated RNA


title: T cells CCR6 from healthy donor HD2

tag: cell type

value: T cells CCR6


title: Muscle_con_rep1, input

description: input


title: Muscle_den_rep1

description: methylated RNA


title: Transitional stem cell memory T cells CXCR3 from healthy donor HD1

description: HD1_TSCM_CXCR3_S27.trim.star_hg19.sorted


title: Muscle_con_rep1

description: methylated RNA


title: Muscle_con_rep2

description: methylated RNA


title: 22Rv1_sgG3BP1-3

first: Deli

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Human cell line reads (FASTQ files) were mapped to the human reference genome sequence (hg19) using STAR v2.4.0j (Dobin et al., 2013)
BAM files were subsequently converted into mapped-read format (MRF) using RSEQtools (Habegger et al., 2011).
The read count of each gene was calculated via HTSeq (Anders et al. 2014) using GENCODE as reference gene annotation set.  Quantification of gene expression was performed via RSEQtools, and expression levels (RPKM) were estimated.
Differentially expression analyses were performed using DESeq2 (ref) based on the gene read count data.  Multiple-hypothesis testing was considered by using Benjamini-Hochberg (BH; FDR) correction.
Genome_build: hg19
Supplementary_files_format_and_content: First column represents GENCODE gene name, and second represents the raw read count for each gene.

growth_protocol: Control and G3BP1 knockout 22RV1 cells were grown in complete media for 48 hours and harvested for RNA in biological triplicate. Control and SPOP knockdown cells were grown in complete media for 48 hours and harvested for RNA in biological triplicate.

extract_protocol: RNA seq library preps for human cell lines were generated using Poly-A kit.  The murine organoids were sequenced to 150bp , paired end.

treatment_protocol: siSPOP or siCont were transiently transfected into 22RV1 cells.Cells were maintained in complete media for 48 hours and harvested for RNA in biological triplicate.

value: prostate cancer cell line

tag: cell line

tag: genotype/variation

value: G3BP1 knockout


title: 5439-CJ-6

city: Nashville

first: Lance

last: Riley

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Sequenced reads were mapped and gene counts were quantified using Illumina DRAGEN RNA pipeline v. 3.6.3
Gene count data was compiled using tximport
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.01 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with DEseq2 counts for every gene and every sample.

source_name: CDH11-/-_total bone marrow cells

growth_protocol: Bone marrow cells were isolated from the femur and tibia of experimental mice. Cells were plated for macrophage differentiation in non-adherent p100 dishes in 10 mL RPMI 1640 media + L-glutamine + 20% L929 conditioned media + 10% FBS + 1% P/S. On day 3, 5 more mL of media were added. On day 7, macrophages were ready for analysis.

extract_protocol:
Trizol reagent was added to cells plated on a p100 dish, mechanically agitated, then collected. RNA was extracted with a Zymo Direct-Zol Miniprep kit using the standard protocol.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits according to standard protocols.

treatment_protocol: Bone marrow was isolated from adult male mice. Macrophages were untreated prior to RNA extraction.

tag: strain background

value: Mixed; 129S1/Sv x C57BL/6

value: Bone marrow

value: Macrophage


title: 5439-CJ-5


title: T cell helper 2 from healthy donor HD1

value: T cell helper 2


title: 22Rv1_sgG3BP1-2


title: T cell helper 17 from healthy donor HD1

value: T cell helper 17


title: T cells naïve from healthy donor HD2

value: T cells naive


title: 22Rv1_sgG3BP1-1


title: Transitional stem cell memory T cells CCR4 from healthy donor HD1


title: T cells naïve from healthy donor HD1


title: 5439-CJ-3

source_name: WT_total bone marrow cells


title: 22Rv1_siSPOP-1

value: SPOP knockdown


title: 22Rv1_siSPOP-2


title: 5439-CJ-4


title: 22Rv1_Ctrl-3

value: Control


title: T cell helper 1_17 from healthy donor HD1

value: T cell helper 1_17


title: T cell helper 1 from healthy donor HD1

value: T cell helper 1


title: Wt for heart specific Jmjd2a KO, male

city: Dalals

first: zhi-ping

last: liu

state: TX

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

description: Gene expression profiling of mouse heart

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: heart

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: heart

value: adult


title: T cells CXCR3 CCR4 from healthy donor HD1

value: T cells CXCR3 CCR4


title: 22Rv1_Ctrl-2


title: T cells central memory from healthy donor HD1

value: T cells central memory


title: 5439-CJ-2


title: MLE-12_KO_VSV

city: Beijing

first: Shuo

address: 5 Dong Dan San Tiao

department: Department of Immunology

institute: Chinese Academy of Medical Sciences

data_processing:
Illumina Casava1.8 software was used for basecalling.
Reads containing adapter, ploy-N and low quality reads from raw data were removed to obtain clean data (clean reads).
For RNA seq, clean reads were aligned to the reference genome using Hisat2 v2.0.5, Cufflinks v2.2.1 was used to assemble transcripts, estimate the abundance of transcripts, and detect differential expression among samples. For transcriptome analysis, clean reads were aligned to the reference genome using Hisat2 v2.0.5, featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10

source_name: MLE-12 cells

growth_protocol: MLE-12 cells was maintained in DMEM/F12 50/50 medium (Corning) supplemented with 10% fetal bovine serum (Gibco).

extract_protocol:
Total RNA were extracted using trizol reagent.
Libraries were generated using NEBNext® UltraTM   RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s   recommendations

treatment_protocol: MLE-12 cells were infected with GFP-VSV (MOI = 1) or VSV (MOI = 1) for 12 h.

value: MLE-12 cells

tag: genotype

value: VSV infection for 12 h


title: 22Rv1_Ctrl-1

value: prostate cancer cell line


title: Heart specific Jmjd2a KO, male


title: Heart specific Jmjd2a KO, female


title: 5439-CJ-1

value: Mixed; 129S1/Sv x C57BL/6


title: Endothelial cell WT rep3

data_processing:
The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and counts

source_name: Total RNA isolated from WT endothelial cells

extract_protocol:
Endothelial cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild-type (WT)

value: Endothelial cell


title: 22Rv1_siSPOP-3


title: MLE-12_KO_ctrl

value: Non-infection


title: Y10 rep3

city: Guanghzou

first: Juan

last: Peng

address: No 164, Xingang west road,Haizhu district

department: Marine sciences

institute: Sun Yat-sen University

data_processing:
After quality control, the paired-end clean reads were aligned to reference genome using hisat2(V2.0.6)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Genome_build: ChrZofV5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Chromochloris zofingiensis

source_name: algal cells

growth_protocol: The seeds  were inoculated into CZ-M1 medium containing 30 g/L glucose and cultured in darkness. Batch cultures were provided with agitation of 150 rpm on orbital shaker at 25 ℃.

extract_protocol:
RNA was extracted from 100 mL of algal culture obtained from the control (without LEV treatment) and treatment (10 mg/L LEV treatment) under heterotrophic condition at mid-phase (15 days). RNA quality and quantity were determined by a NanoDrop 2000 sepectrophotometer (Thermo Scientific) and an Agilent 2100 RNA 6000 Nano kit, respectively.
cDNA libraries were constructed form 1 μg total RNA via a NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’ instructions. Afterwards, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)

treatment_protocol: exposing the microalgal cultures 10% (Vinoculum/Vmedia) to  10 mg/L LEV concentrations for 15 days.

tag: time point

value: at 15 days

tag: groups

value: treatment


title: Wt for heart specific Jmjd2a KO, female


title: T cells CCR6 from healthy donor HD1

value: T cells CCR6


title: MLE-12_WT_VSV

value: Wild-type


title: General Jmj2a KO


title: Endothelial cell WT rep1


title: Wt for general Jmjd2a KO


title: CTC2 scRNA-seq

city: Dunedin

first: Jiří

middle: C

last: Moravec

address: 133 Union Street East

department: Computer Science department

country: New Zealand

institute: University of Otago

data_processing:
Mapping, demultiplexing and the expression analysis was done using Cellranger v5.
Genome_build: GRCh38v15
Supplementary_files_format_and_content: Gene-feature expression count matrix in binary h5 format

source_name: human derived mouse explant CTC2

growth_protocol: MDA-MB-231-LM2 (GFP+) cells were injected into the R4 mammary fat pad of Nu/J mice ( 250, 000 cells per mouse, n = 3 ), and tumor growth was monitored for 8 weeks. Mice were euthanized when tumor size approached the endpoint (2 cm).

extract_protocol:
Tumors were resected and dissociated into single cells. To extract circulating tumor cells (CTC), up to 1 ml of blood was drawn immediately post euthanasia using cardiac puncture. Red blood cells were removed using RBC lysis bu_x001B_er. All cells (tumor derived and circulating tumor cells) were stained with DAPI and sorted for DAPI and GFP using a BD FACSAria cell sorter.
Libraries were generated using the 10x Chromium single cell gene expression system.

value: Circulating Tumor Cells


title: MLE-12_GFP_ap_2

last: Liu

value: GFP-VSV infection for 12 h


title: Endothelial cell WT rep2


title: Y10 rep2


title: T3 scRNA-seq

source_name: human derived mouse explant T3

value: Tumor


title: Endothelial cell Stk11-KO rep1

source_name: Total RNA isolated from Stk11-/- endothelial cells

value: Stk11-/- knock out


title: CTC1 scRNA-seq

source_name: human derived mouse explant CTC1


title: Endothelial cell Stk11-KO rep2


title: MLE-12_GFP_ap_1


title: MLE-12_WT_ctrl


title: Y0 rep3

value: control


title: T2 scRNA-seq

source_name: human derived mouse explant T2


title: Y0 rep2


title: Y0 rep1


title: Endothelial cell Stk11-KO rep3


title: T1 scRNA-seq

source_name: human derived mouse explant T1


title: NC_IAV

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And 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 samples was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Excel table with readcount of each gene in each sample

source_name: A549 cells

growth_protocol: A549 cells was maintained in F-12K medium (Gibco) containing 10% fetal bovine serum (Gibco).

extract_protocol:
Total RNA were extracted using trizol reagent, mRNA was purified from total RNA using polyT oligo-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, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.The clustering of the index-coded samples was performed using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina  Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: A549 cells were transfected with negative ctrl siRNA or lnc-CXCL2-4-1 siRNA (100 nM) for 24h followed by IAV infection (MOI = 1) for 12 h.

value: wild-type

value: IAV infection for 12 h


title: si_lnc_IAV

value: lnc-CXCL2-4-1 silenced


title: MLE-12_Ctrl_2

value: MLE-12 cells


title: MLE-12_Ctrl_1


title: Y10 rep1


title: Hep-G2-T5-Inf-C2

status: Public on Sep 25 2021

data_processing:
Demultiplexing was performed (bcl2fastq2 V2.2.18.12) and adapters were trimmed with Cutadapt (v1.15); only reads longer than 10 bp were kept.
TopHat (version 2.1.1) was used for alignment on the reference genome
Data were evaluated through principal component analysis and hierarchical clustering after transformation of the count data using RLOG function.
Normalization and differential analysis were carried out using the DESeq2 package, with a pre-filter step to remove genes with low counts (sum of all replicates counts<10, in all conditions compared)
Genome_build: Ensembl-98 human genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human hepatocarcinoma cell line HepG2

growth_protocol: Listeria monocytogenes EGDe strain was grown in brain-heart infusion (BHI) at 37°C. Human HepG2 hepatocytes (ATCC HB-8065) were grown as recommanded by ATCC, on collagen-coated 6-well plates.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) and genomic DNA was removed using TURBO DNA-freeTM kit (Ambion), according to the manufacturer’s instructions. The integrity, purity and concentration of RNA samples was assessed on an RNA 6000 pico chip using the Agilent 2100 electrophoresis Bioanalyzer.  RNA was quality checked an then store at -80°C.
RNA-seq libraries of infected and non-infected cell RNA were assembled using 500-1300 ng total RNA using the TruSeq® mRNA Stranded Library Prep kit (Illumina) which includes polyA-selection. The RNA-seq libraries were monitored for quality on the Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit. Libraries were pooled in equimolar proportions

treatment_protocol: Cells were uninfected or infected with Listeria at multiplicity of infection of 1-5. After 1h infection, extracellular bacteria were killed by adding gentamicin and cells were incubated for 3 days with 25 μg/ml gentamicin containing media.

value: infected

tag: time


title: Hep-G2-T1-NI-C1

value: control (non-infected)


title: Hep-G2-T5-NI-C2


title: Hep-G2-T6-Inf-C1


title: K562 ++ untreated ATAC-seq [WT_ut_1_S1]

city: Norman

first: Carol

last: Webb

state: Oklahoma

address: Stephenson Parkway

department: Department of Medicine

institute: OUHSC

data_processing:
Created Bowtie index using the GrCh37 assembly of the human genome
Estimated peaks with MACS2 using parameters -q 0.05 --nolambda --slocal 1000 --llocal 10000 -m 5 50 --shift 0 --extsize 200 --fe-cutoff 1.0.
Differential expression analysis performed using DESeq2
Genome_build: GrCh37
Supplementary_files_format_and_content: Differential expression analysis

source_name: K562 ++ untreated

extract_protocol:
MiniElute kit
ATAC libraries were prepared for sequencing using standard Illumina protocols

tag: sledai

value: ++ untreated

tag: replicate

value: replicate 1


title: Hep-G2-T1-Inf-C1


title: Hep-G2-T6-NI-C1


title: K562 ++ hemin ATAC-seq [WT_h_2_S20]

source_name: K562 ++ hemin

value: ++ hemin

value: replicate 2


title: K562 ++ untreated ATAC-seq [WT_ut_2_S2]


title: K562 ++ hemin ATAC-seq [WT_h_1_S19]


title: K562 ++ hemin ATAC-seq [P_h_1_S35]


title: K562 -- hemin ATAC-seq [BH_h_2_S28]

source_name: K562 -- hemin

value: -- hemin


title: K562 ++ hemin ATAC-seq [P_h_2_S36]


title: K562 -- untreated ATAC-seq [BH_ut_2_S10]

source_name: K562 -- untreated

value: -- untreated


title: K562 ++ untreated ATAC-seq [P_ut_2_S18]


title: K562 ++ untreated ATAC-seq [P_ut_1_S17]


title: K562 -- untreated ATAC-seq [BH_ut_1_S9]


title: K562 ++ untreated ATAC-seq [AR_ut_2_S4]


title: K562 -- hemin ATAC-seq [BH_h_1_S27]


title: K562 ++ hemin ATAC-seq [AR_h_2_S22]


title: K562 -- hemin ATAC-seq [AL_h_2_S24]


title: K562 -- untreated ATAC-seq [AL_ut_2_S14]


title: K562 ++ hemin ATAC-seq [AR_h_1_S21]


title: K562 -- hemin ATAC-seq [AL_h_1_S23]


title: X12c: Hemin + ARID3a shRNA

data_processing:
Created Bowtie index using the GrCh38 assembly of the human genome
Estimated abundances with RSEM using default parameters
Differential expression analysis performed using DESeq2
Genome_build: GrCh38

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

value: replicate 3


title: K562 -- untreated ATAC-seq [AL_ut_1_S13]


title: X12b: Hemin + ARID3a shRNA


title: X12a: Hemin + ARID3a shRNA


title: X11c: Hemin + scrambled shRNA


title: X11a: Hemin + scrambled shRNA


title: X9b: Untreated


title: X11b: Hemin + scrambled shRNA


title: X10b: Hemin


title: X9a: Untreated


title: X9c: Untreated


title: X8c: Hemin + ARID3a shRNA


title: K562 ++ untreated ATAC-seq [AR_ut_1_S3]


title: X10a: Hemin


title: X8b: Hemin + ARID3a shRNA


title: X8a: Hemin + ARID3a shRNA


title: X7b: Hemin + scrambled shRNA


title: X7a: Hemin + scrambled shRNA


title: X6c: Hemin


title: X6b: Hemin


title: X5c: Untreated


title: X5a: Untreated


title: X4b: Hemin + ARID3a shRNA

value: D


title: X4c: Hemin + ARID3a shRNA


title: X3c: Hemin + scrambled shRNA

value: C


title: X3b: Hemin + scrambled shRNA


title: X3a: Hemin + scrambled shRNA


title: X10c: Hemin


title: X2b: Hemin

value: B


title: X7c: Hemin + scrambled shRNA


title: X2a: Hemin


title: X1b: Untreated

value: A


title: X1c: Untreated


title: X1a: Untreated


title: X6a: Hemin


title: ko_input_3

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

data_processing:
RNA-Seq: Four biological replicates and two technical replicates were sequenced for each RNA sample, yielding 28 to 62 million paired-end reads of 101 bp. Reads were trimmed for low quality bases from the 5’ end (minimum quality = 20) using cutadapt v2.4. Raw RNA-Seq reads were aligned using HISAT2 v2.1.0 and reads quantified with featureCounts v1.6.4.
ChIP-Seq: Two to three biological replicates from WT and Lsd1-KO cells were sequenced for each ChIP-Seq sample (H3K4me1, n=2; H3K4me2, n=2; H3K4me3, n=3), yielding a total of 15 to 25 million single-end reads of 51 bp. Each histone mark was sequenced in an independent run, along with two biological replicates of input DNA from WT and Lsd1-KO samples. Raw ChIP-Seq reads were trimmed for low quality bases as above, using cutadapt v2.1 and aligned using bowtie2 v2.3.4.3. Redundant reads were removed and peak-calling was performed using SICER v1.1. Differential binding analysis comparing Lsd1-KO to WT was performed using DiffBind v2.10.0 with the DESeq2 analysis model using p-value < 0.01 to define statistical significance.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: BAM files from technical replicates were merged before the bamCoverage tool (deepTools v3.2.0) was used to generate coverage bigwigs using the following non-default parameters: --ignoreDuplicates --minMappingQuality 20 --normalizeUsing CPM --extendReads 300
Supplementary_files_format_and_content: peaks: BED files generated using SICER v1.1 with the following parameters: window size = 200 bp, gap size = 600 bp, fragment size = 150 bp, effective genomic fraction = 0.87, FDR < 0.01.
Supplementary_files_format_and_content: expression estimate: Read counts were estimated using the Gencode M18 annotation for mouse using featureCounts with the following non-default parameters: -s0 -p

source_name: thymocytes

extract_protocol:
For RNA sequencing, TCRb-low CD69-CD44- and TCRb-low CD69+CD44- DP thymocytes from control Lsd1fl/fl and CD2-iCre;Lsd1fl/fl mice were sorted using a FACSAria (BD Bioscience). Four biological replicates for each group. Total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Cat#: 12204-01, Applied Biosystems by Thermo Fisher Scientific). The libraries were sequenced using HiSeq Rapid run with 2 x 100bp sequencing. For ChIP-Seq, whole thymi were dissected, processed and thymocytes were fixed with 1% formaldehyde. Fixation was quenched with 0.125M glycine. Thymocytes were lysed using a lysis buffer containing: 5 mM PIPES (pH8), 85 mM KCl, 10ul/mL Ipegal and protease inhibitor. Lysates were then homogenized, and the nuclei lysed using a nuclear lysis buffer containing: 10mM Tris HCl (pH8), 10 mM EDTA (pH8), 1% SDS (v/v), 10 ul/ml protease inhibitor. Isolated chromatin was sonicated to 200-500 bp fragments (Diagenode Bioruptor). Sonicated DNA was then incubated with Protein A beads (Invitrogen Dynabeads) conjugated to H3K4Me3 (Milipore, MC315), H3K4Me2 (Milipore, AW30), or H3K4Me1 (abcam, ab8895) antibodies.  Immunoprecipitated DNA fragments were isolated using a Takara DNA isolation kit.
RNA-Seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Cat#: RS-122-2101, Illumina) with PolyA purification. Each sample use 1ug total RNA-Seq input. For ChIP-Seq, DNA libraries were prepared using a DNA SMART CHIP Seq Kit (Takara)
RNA-Seq: 2 x 101 bp paired-end sequencing, ChIP-Seq: 1x51 bp single-end sequencing.

tag: mouse strain

value: CD2-iCre;Lsd1 fl/fl

tag: strain


title: ko_me3_2


title: wt_me3_1

value: WT

value: Lsd1 fl/fl


title: wt_me3_2


title: ko_me3_1


title: wt_input_3


title: X5b: Untreated


title: ko_input_1_2


title: wt_input_1_2


title: wt_input_1_1


title: ko_input_1_1


title: wt_me2_2


title: X4a: Hemin + ARID3a shRNA


title: X2c: Hemin


title: wt_me2_1


title: ko_me2_1


title: wt_me1_2


title: wt_me1_1


title: ko_me1_2


title: ko_me1_1


title: ko_me2_2


title: wt_me3_3


title: ko_me3_3


title: cd69_plus_ko_4

tag: cell surface markers

value: TCRb-low CD69+CD44-


title: ko_input_2


title: wt_input_2


title: cd69_plus_ko_3


title: cd69_plus_ko_2


title: cd69_plus_wt_4


title: cd69_plus_ko_1


title: cd69_plus_wt_3


title: cd69_plus_wt_2


title: cd69_minus_ko_4

value: TCRb-low CD69-CD44-


title: cd69_minus_ko_3


title: cd69_minus_wt_1


title: cd69_minus_ko_2


title: cd69_minus_ko_1


title: cd69_minus_wt_4


title: RNA_Pik3cdE1020_OT1_d6_IL15_72h_rep3_s36_JC36

first: Han-Yu

last: Shih

address: 10 Center Drive Rm 5S261

institute: National Eye Institute

data_processing:
FastATAC-seq reads from two biological replicates for each sample were mapped to the  mouse genome (mm9 assembly) using Bowtie 0.12.8.
Redundant reads were  removed using fastquniq (Xu et al., 2012). Only one mapped read  to each unique regions of the genome that was less than 175 base pairs was kept and used  in peak calling. Regions of open chromatin were identified by MACS (version  1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Only regions called in  both replicates were used in downstream analysis.
Reads from FastQ files were mapped to the mouse genome mm9 using TopHat 2.0, assembled with Cufflinks and gene-level counts compiled with htseq-count (Anders et al., 2013).
Counts were then normalized, differentially expressed genes (DEG) called, and TPM values calculated using edgeR (Anders et al., 2013). To minimize normalization artifacts, transcripts failing to reach an empirically defined count threshold were purged using HTSFilter (Rau et al., 2013).DEG classification indicates >2 fold pairwise change and Benjamini-Hochberg (BH) adjusted p value < 0.05 (Figure 4A). An offset value was added to all TPM (TPM+1) and those failing to reach a value >2 TPM in any genotype/condition were excluded, as were micro-RNAs, sno-RNAs and sca-RNAs.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq and RNA-seq

source_name: CD8+ T cells

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction with GlycoBlue as co-precipitant (7-15μg per sample; Life Technologies) and poly(A)+ mRNA enriched by oligo-dT-based magnetic separation.
Single-end read libraries were prepared using the NEBNext Ultra RNA Library Prep Kit and sequenced with a HiSeq 2500 instrument (Illumina, San Diego, CA).
Cells from spleen were obtained by mechanical disruption. Isolated cells were further sorted as based on their surface markers.
All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10  ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
OT-1 (2.5x106) splenocytes were stimulated with OVA257-264 or T4 peptide for 3 days in complete media (Kapnick et al., 2017). On day 3, cells were washed, counted and 10 IU/ml of recombinant IL-2 or 10ng/ml IL-15 (NIH AIDS reagent program) was added to cultures (2x105 cells/ml) (O'Sullivan et al., 2014). Cells were washed, counted and fresh cytokines added every 24 hours. For IL-2 blocking, anti-mouse IL-2 (20µg/ml) or Ig control (20µg/ml) was added to the cultures. For assays including inhibitors: Idelalisib p110 inhibitor (CAL-101): 2nM, z-VAD-FKM caspase inhibitor: (100µM), AKTi: 50-200nM, Necrostatin-1: 0.3mM or DMSO vehicle control was added to cultures. Target and flow-based cytotoxicity assays were previously described (Kapnick et al., 2017). B cells were stimulated with LPS as previously described (Zhao et al., 2012).

value: Spleen

tag: surface marker

value: CD62L+CD44lo CD8+

tag: culture condition

value: ex vivo


title: cd69_minus_wt_3


title: RNA_Pik3cdE1020_OT1_d6_IL2_72h_rep3_s35_JC35


title: RNA_Pik3cdE1020_OT1_d5_IL2_48h_rep3_s33_JC33


title: RNA_Pik3cdE1020_OT1_d5_IL15_48h_rep3_s34_JC34


title: RNA_Pik3cdE1020_OT1_d3_rep3_s32_JC32


title: RNA_WT_OT1_d5_IL15_48h_rep3_s28_JC28

value: wildtype


title: RNA_WT_OT1_d6_IL2_72h_rep3_s29_JC29


title: RNA_Pik3cdE1020_OT1_naive_rep3_s31_JC31


title: RNA_WT_OT1_d6_IL15_72h_rep3_s30_JC30


title: RNA_WT_OT1_d3_rep3_s26_JC26


title: RNA_WT_OT1_d5_IL2_48h_rep3_s27_JC27


title: RNA_WT_OT1_naive_rep3_s25_JC25


title: RNA_Pik3cdE1020_OT1_d6_IL15_72h_rep2_s24_JC24


title: RNA_Pik3cdE1020_OT1_d6_IL2_72h_rep2_s23_JC23


title: RNA_Pik3cdE1020_OT1_d5_IL15_48h_rep2_s22_JC22


title: RNA_Pik3cdE1020_OT1_d5_IL2_48h_rep2_s21_JC21


title: cd69_plus_wt_1


title: cd69_minus_wt_2


title: RNA_Pik3cdE1020_OT1_naive_rep2_s19_JC19


title: RNA_WT_OT1_d6_IL15_72h_rep2_s18_JC18


title: RNA_WT_OT1_d5_IL15_48h_rep2_s16_JC16


title: RNA_WT_OT1_d6_IL2_72h_rep2_s17_JC17


title: RNA_Pik3cdE1020_OT1_d3_rep2_s20_JC20


title: RNA_WT_OT1_d3_rep2_s14_JC14


title: RNA_WT_OT1_naive_rep2_s13_JC13


title: RNA_Pik3cdE1020_OT1_d6_IL2_72h_rep1_s11_JC11


title: RNA_WT_OT1_d6_IL15_72h_rep1_s06_JC6


title: RNA_Pik3cdE1020_OT1_naive_rep1_s07_JC7


title: RNA_Pik3cdE1020_OT1_d5_IL2_48h_rep1_s09_JC9


title: RNA_Pik3cdE1020_OT1_d5_IL15_48h_rep1_s10_JC10


title: RNA_Pik3cdE1020_OT1_d3_rep1_s08_JC8


title: RNA_Pik3cdE1020_OT1_d6_IL15_72h_rep1_s12_JC12


title: RNA_WT_OT1_d6_IL2_72h_rep1_s05_JC5


title: RNA_WT_OT1_d5_IL15_48h_rep1_s04_JC4


title: RNA_WT_OT1_d5_IL2_48h_rep1_s03_JC3


title: RNA_WT_OT1_d3_rep1_s2_JC02


title: ATAC_Pik3cdE1020_OT1_d5_IL15_rep2_r1_s608

extract_protocol:
FastATAC-Seq was performed according to a published protocol(Corces et al., 2016). Ten thousand cells, isolated as above, were pelleted and washed with 50μl PBS. After pelleting the nuclei by centrifuging at 500 x g for 10 min at 4oC, the pellets were re-suspended in 50μl transposase mixture including 25μl of 2xTD buffer (Tagment DNA buffer, 15027866, Illumina), 2.5μl of TDE1 (Tagment DNA enzyme, 15027865, Illumina), 0.5μl of 1% digitonin (G9441, Promega), 22μl of nuclease-free water. The reaction was incubated at 37oC with shaking at 300 rpm for 30 min. The fragmentalized DNAs were then purified using a QIAGEN MinElute kit (28006) in 10ul elution buffer. Transposed fragments were amplified with 10 or 11 cycles of PCR based on the amplification curve using primers described previously (Buenrostro et al., 2013).
The purified libraries were further sequenced for 50 cycles (paired-end reads) on a HiSeq 2500.
Cells from spleen were obtained by mechanical disruption. Isolated cells were further sorted as based on their surface markers.
All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10  ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
OT-1 (2.5x106) splenocytes were stimulated with OVA257-264 or T4 peptide for 3 days in complete media (Kapnick et al., 2017). On day 3, cells were washed, counted and 10 IU/ml of recombinant IL-2 or 10ng/ml IL-15 (NIH AIDS reagent program) was added to cultures (2x105 cells/ml) (O'Sullivan et al., 2014). Cells were washed, counted and fresh cytokines added every 24 hours. For IL-2 blocking, anti-mouse IL-2 (20µg/ml) or Ig control (20µg/ml) was added to the cultures. For assays including inhibitors: Idelalisib p110 inhibitor (CAL-101): 2nM, z-VAD-FKM caspase inhibitor: (100µM), AKTi: 50-200nM, Necrostatin-1: 0.3mM or DMSO vehicle control was added to cultures. Target and flow-based cytotoxicity assays were previously described (Kapnick et al., 2017). B cells were stimulated with LPS as previously described (Zhao et al., 2012).


title: RNA_WT_OT1_naive_rep1_s01_JC1


title: ATAC_Pik3cdE1020_OT1_d5_IL2_rep2_r1_s607


title: ATAC_Pik3cdE1020_OT1_d3_rep2_r1_s606


title: ATAC_WT_OT1_d3_rep2_r1_s602


title: ATAC_WT_OT1_d5_IL2_rep2_r1_s603


title: ATAC_Pik3cdE1020_OT1_naive_rep2_r1_s605


title: ATAC_WT_OT1_naive_rep2_r1_s601


title: ATAC_Pik3cdE1020_OT1_d5_IL15_rep1_r1_s600


title: ATAC_WT_OT1_d5_IL15_rep2_r1_s604


title: RNA_WT_OT1_d5_IL2_48h_rep2_s15_JC15


title: ATAC_Pik3cdE1020_OT1_naive_rep1_r1_s597


title: ATAC_Pik3cdE1020_OT1_d3_rep1_r1_s598


title: ATAC_WT_OT1_d5_IL15_rep1_r1_s596


title: ATAC_WT_OT1_d3_rep1_r1_s594


title: Dia c3 rep1a

city: Mainz

first: Nir

last: Yogev

address: Langenbeck Str.1

institute: University Medical Center of the Johannes Gutenberg University of Mainz

description:
Dia c3 R1a
yogev_normcounts_2.tsv

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0j)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (Marini et al., 2016)
Differential expression analysis was performed with DESeq2 (version 1.20.0), setting the False Discovery Rate to 0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts from DESeq2 for each sample

source_name: Diaphragm C3 macrophages

extract_protocol:
Mice were anesthetized and peripheral blood was flushed by cardiac perfusion using saline solution. Dura mater was removed, digested, and dural macrophages were sorted using BD FACS Aria II flow cytometer. RNA was harvested from bulk sorted dural macrophages using Qiagen RNeasy Plus Micro Kit (Cat# 74034). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using standard NEBNext® Ultra™ II RNA library prep kit protocols. All samples were sequenced with reads of 75 nucleotides, using a single-end library preparation (unstranded sequencing kit).

value: Diaphragm

tag: age

value: 17 weeks

value: wild type

tag: condition

value: steady state


title: Dia c2 rep3a

description:
Dia c2 R3a
yogev_normcounts_2.tsv

source_name: Diaphragm C2 macrophages

tag: tissue


title: Dia c2 rep1a

description:
Dia c2 R1a
yogev_normcounts_2.tsv


title: ATAC_Pik3cdE1020_OT1_d5_IL2_rep1_r1_s599


title: Dia c3 rep3a

description:
Dia c3 R3a
yogev_normcounts_2.tsv


title: ATAC_WT_OT1_naive_rep1_r1_s593


title: Dia c3 rep1

description:
Dia c3 R1
yogev_normcounts_2.tsv


title: Dia c1 rep3a

description:
Dia c1 R3a
yogev_normcounts_2.tsv

source_name: Diaphragm C1 macrophages


title: Dia c1 rep1a

description:
Dia c1 R1a
yogev_normcounts_2.tsv


title: Dia c2 rep1

description:
Dia c2 R1
yogev_normcounts_2.tsv


title: Dia c2 rep2a

description:
Dia c2 R2a
yogev_normcounts_2.tsv


title: ATAC_WT_OT1_d5_IL2_rep1_r1_s595