title: C10V_Rep2

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

data_processing:
Adapter and quality trimming done with trim_galore.
Alignment done with STAR v2.7.10a using reference GRCh38.v40 downloaded from GENCODE
Gene-level quantification was done using featureCounts for Rsubread v2.16.1 and R v4.1.2
Linear Models and differential expression performed on log2 transformed "voom" counts from limma v3.50.3 and edgeR v3.36.0 biofonductor.org R packages
Assembly: GRCh38.v40
Supplementary files format and content: .tsv file of raw counts from Rsubreads featureCounts

source_name: iPSC

growth_protocol: iPSC lines were cultured as embryoid bodies (EBs) with dual SMAD inhibition in DMEM/F12 containing 20% KOSR, 100 µm BME, 1X glutamax, 1X non-essential amino acids (NEAA), 2 µM A-83 (Cayman Chemical, #9001799) and 2 µM dDorsomorphin (Cayman Chemical, #11967). After 5 days, the medium was changed to neural induction medium (NIM): DMEM/F12 containing 1X N2 (Thermo Fisher Scientific, #17502-048), 1X glutamax, 1X NEAA, and 300 nM of the Sonic Hedgehog Agonist (SAG) (Cayman Chemi-cal, #11914), and grown for an additional 2 days as EBs. Next, they were plated on 0.04 mg/mL Mmatrigel for 14 days in NIM to form rosettes. They were fed every other day for the first 7 days and every day for the next 7 days. Following rosette formation, neuro-spheres were picked and grown in suspension in NIM for 6 days. Neurospheres were dissociated using a gentleMACS dissociator (Miltenyi Biotec), and these neural progenitor cells (NPCs) were then plated in NIM on dishes coated in 0.1% pPoly(ethyleneimine) (pEI) (Millipore Sigma, P3143) and 20 µg/mL laminin (Corning, #354232). For neuronal differen-tiation, NPCs were cultured in neuronal differentiation medium (NDM); Brainphys neu-ronal media (Stem Cell Technologies, #05792), with 1X SM-1, 1X N2, 20 ng/mL BDNF (Peprotech, #450-02), and 20 ng/mL GDNF (Peprotech, #450-010). At the initial medium change with NDM, 200 nM Compound E was added (Calbiochem #56579). One mM Bu-cladesine (cAMP) (Millipore Sigma, #D0260) was added at every medium change for the first two weeks of neuronal differentiation. GABAergic neurons were cultured for up to 6 weeks with half media changes twice a week;, 1 µg/mL laminin was added at every other medium change for 2 weeks in culture.

extract_protocol:
total RNA was extracted from cells using Trizol (Life Technologies, #15596018) followed by purification with the RNAeasy mRNA Isolation Kit (Qiagen, #74104) according to the manufacturer’s instructions.
BGI Group (BGI) prepared libraries using the TruSeq (polyA) stranded kit and sequenced using the HiSeq 4000 platform (Illumina)

treatment_protocol: The rs1006737 risk allele in three BP iPSC were targeted for correction via CRISPR-Cas9- mediated editing and repair at WiCell (Madison, WI, USA). Clonal lines were established and CRISPR correction was confirmed via Sanger sequencing

value: iPSC

value: GABAergic interneurons

value: AA

value: Control


title: C9G_Rep2

status: Public on Jul 23 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: genotype

tag: disease state


title: C10V_Rep1


title: MT519_81_2_D10CNCC_RNA_rep3

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
RNA-seq data were quanitfied using kallisto. Differential gene expression was determined using DESeq2 in R.
Assembly: hg19 (homo sapiens)
Supplementary files format and content: kallisto quantified abundance files for RNA-seq data
Supplementary files format and content: bigwig files for ChIP-seq & ATAC-seq
Supplementary files format and content: peak files for ChIP-seq and ATAC-seq

molecule: polyA RNA

growth_protocol: Human iPSCs were plated on Geltrex LDEV-Free hESC-qualified Reduced Growth Factoer Basement Membrane Matrix and maintained in feeder-free, serum-free mTeSR1 medium in small clusters

extract_protocol: Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).

treatment_protocol:
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® Ultra II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1μg of total RNA input was used for each library. Libraries were sequenced on Illumina NextSeq2000, producing 138 single-end reads
iPSCs were cultured with CNCC specification media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 5 μg/ml bovine insulin, 20 ng/ml EGF, and 20 ng/ml hFGF for 6 days. At day ~7 when early migratory CNCCs first appeared, the cells were transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, serum replacement grade, 20 ng/ml EGF, and 20 ng/ml hFGF for 7 days. After 14 full days of CNCC specification, the cells were maintained in an “early CNCC” state for up to 21 days for subsequent experiments, or immediately transitioned to CNCC late maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium, 1X penicillin-streptomycin solution, 1x Glutamax supplement, 0.5x B-27 supplement with Vitamin A, 0.5x N-2 supplement, 1 mg/ml bovine serum albumin, 20 ng/ml EGF, 20 ng/ml hFGF, 3uM ChIRON 99021, and 50ng/mL BMP2.

tag: cell line

value: day 10 cranial neural crest cell

tag: treatment

value: cranial neural crest cell specification


title: HRI_pre_cDCs

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
Illumina reads were aligned to the Macaca mulatta genome (Mmul_10 build 102) using the STAR aligner (version 2.7.10a) and counted using HTSeq (2.0.2).
Assembly: Mmu_10 build 102
Supplementary files format and content: raw gene count file

organism: Macaca mulatta

source_name: lymph node

extract_protocol:
Total RNA was isolated from cell lysates using the RNAzol RT protocol as per the manufacturer’s instructions
RNA Illumina-ready libraries were generated using NEBNext Ultra II RNA Prep reagents (New England BioLabs). Using oligo dT beads (Invitrogen), poly-adenylated RNA was purified and subsequently fragmented, followed by double-stranded cDNA synthesis, end repair, and adapter ligation. The ligated DNA was then barcoded and amplified by a limited cycle PCR and the libraries were sequenced using a paired-end 150-base protocol on either a HiSeq 4000 or a NovaSeq 6000 (Illumina).

value: lymph node

value: cDCs

value: DEL bNAb Tx

tag: animal id

value: HRI

tag: timepoint

value: pre


title: DGL9_wk8_CD4MEM

data_processing:
Illumina reads were aligned to the Macaca mulatta genome (Mmul_10, build NCBI:GCA_003339765.3) using the STAR aligner (version 2.7.10a) and counted using HTSeq (2.0.2).
Assembly: Mmu_10
Supplementary files format and content: raw gene count file

extract_protocol:
Total RNA was isolated from cell lysates using the RNAzol RT protocol as per the manufacturer’s instructions
RNA Illumina-ready libraries were generated using NEBNext Ultra II RNA Prep reagents (New England BioLabs). Using oligo dT beads (Invitrogen), poly-adenylated RNA was purified and subsequently fragmented, followed by double-stranded cDNA synthesis, end repair, and adapter ligation. The ligated DNA was then barcoded and amplified by a limited cycle PCR and the libraries were sequenced using a paired-end 150-base protocol on NovaSeq 6000 (Illumina).

value: CD4+ mem.

value: WT bNAb Tx


title: MT518_SV20_D10CNCC_RNA_rep3

source_name: SV20 (CTRL1)

value: SV20 (CTRL1)


title: HRI_D14_pDCs

value: pDCs


title: C9G_Rep1


title: DGL9_wk8_CD4

value: total CD4+


title: HRI_D14_NKcells

value: NK cells


title: DGL9_wk8_CD8CM

value: CD8+ central mem.


title: C8WW_Rep2

value: iPSC

value: GABAergic interneurons


title: MT501_64_4_D10CNCC_RNA_rep2


title: DGL9_pre_nonTfh

value: non-Tfh


title: HRI_pre_NKcells


title: C8WW_Rep1

value: AA

value: Control


title: MT499_81_2_D10CNCC_RNA_rep2

value: day 10 cranial neural crest cell

value: cranial neural crest cell specification


title: DGL9_pre_nonfCD8

value: lymph node


title: MT500_64_9_D10CNCC_RNA_rep2


title: HRI_D14_cDCs

value: cDCs

value: DEL bNAb Tx

value: HRI


title: HRI_D14_monocytes

value: monocytes


title: C5G_Rep1


title: HRI_D14_Bcells

value: B cells


title: DGL9_pre_GCTfh

value: GCTfh

value: WT bNAb Tx

value: pre


title: BP19D_Corrected_Rep2

value: GG

value: BP-Corrected


title: MT465_64_4_D10CNCC_RNA_rep1_R1


title: BP19D_Corrected_Rep1

value: iPSC

value: GABAergic interneurons


title: HR8_wk8_pDCs

value: pDCs

value: Untreated


title: MT464_64_9_D10CNCC_RNA_rep1_R1

value: day 10 cranial neural crest cell


title: DGL9_pre_CD8NA

value: CD8+ naive


title: DGL9_pre_CD8EM

value: lymph node

value: CD8+ effector mem.


title: HR8_wk8_NKcells

value: NK cells


title: BP19D_Rep2

value: AA

value: BP


title: BP19D_Rep1


title: MT463_81_2_D10CNCC_RNA_rep1_R1

value: cranial neural crest cell specification


title: MT462_SV20_D10CNCC_RNA_rep1_R1

value: SV20 (CTRL1)


title: BP18A_Corrected_Rep2


title: DGL9_pre_CD4NA

value: CD4+ naive

value: WT bNAb Tx


title: HR8_D14_pDCs


title: HR8_wk8_Bcells

value: B cells


title: DGL9_pre_CD8

value: total CD8+

value: pre


title: DGL9_pre_CD8CM

value: CD8+ central mem.


title: BP18A_Corrected_Rep1

value: iPSC

value: GABAergic interneurons

value: GG

value: BP-Corrected


title: MT498_SV20_D10CNCC_RNA_rep2

value: day 10 cranial neural crest cell


title: MT602_64_4_iPSC_RNA_rep3

value: induced pluripotent stem cell


title: DGL9_pre_fCD8

value: lymph node


title: HR8_wk8_cDCs

value: cDCs

value: Untreated


title: BP18A_Rep2

value: AA

value: BP


title: DGL9_pre_CD4MEM

value: CD4+ mem.


title: MT601_64_9_iPSC_RNA_rep3


title: HR8_D14_NKcells

value: NK cells


title: HR8_wk8_monocytes

value: monocytes


title: BP18A_Rep1


title: DGL9_D14_nonTfh

value: non-Tfh

value: WT bNAb Tx


title: BP17A_Corrected_Rep2


title: DGL9_pre_CD4

value: total CD4+

value: pre


title: MT599_SV20_iPSC_RNA_rep3

value: SV20 (CTRL1)


title: MT525_64_4_iPSC_RNA_rep2


title: HR8_D14_cDCs


title: HR8_D14_monocytes


title: DGL9_D14_nonfCD8


title: BP17A_Corrected_Rep1

value: iPSC

value: GABAergic interneurons

value: GG


title: HR8_D14_Bcells

value: B cells


title: BP17A_Rep2


title: MT523_81_2_iPSC_RNA_rep2

value: induced pluripotent stem cell


title: DGL9_D14_fCD8

value: lymph node


title: HR6_wk8_NKcells


title: DGL9_D14_GCTfh

value: GCTfh


title: BP17A_Rep1

value: AA


title: HR6_wk8_pDCs

value: pDCs


title: BP11E_Rep2

value: BP


title: MT522_SV20_iPSC_RNA_rep2


title: MT600_81_2_iPSC_RNA_rep3


title: BP11E_Rep1


title: DGL9_D14_CD8NA

value: CD8+ naive


title: HR6_wk8_cDCs

value: cDCs


title: HR6_wk8_monocytes

value: monocytes


title: MT476_64_9_iPSC_RNA_rep1


title: DGL9_D14_CD8CM

value: CD8+ central mem.

value: WT bNAb Tx


title: HR6_wk8_Bcells


title: MT524_64_9_iPSC_RNA_rep2


title: GIMEN_D30_3

city: Boston

first: Lien

middle: Dieu

last: Nguyen

state: MA

address: 60 Fenwood Road, Hale Building for Transformative Medicine, Lab: 9006.009

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Fastq files were uploaded to the web application https://maayanlab.cloud/biojupies for alignment and generation of raw counts.
Assembly: Human reference genome
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: GIMEN

growth_protocol: Naive SK-N-AS cells were maintained in DMEM, 1X I-Glutamax, 10% FBS, and 1% P/S. Naïve GIMEN cells were maintained in RPMI, 1X I-Glutamax, 10% FBS, and 1% P/S

extract_protocol:
Total RNA from cells was extracted using the Norgen Total RNA Purification Kit (Norgen Biotek) following the manufacturer's protocol. DNAse1 was applied during RNA extraction to remove genomic DNA. RNA was eluted in nuclease-free water, and the concentration was measured using Nanodrop (Thermo Fisher Scientific).
After quality control by Agilent 2100 Bioanalyzer, the total RNA was used as input for library preparation by Novogene Co., Ltd, followed by high-throughput sequencing on Illumina HiSeq X with PE150 mode to produce approximately 20 M reads per sample.

treatment_protocol: Treatment with PP121+bufalin for up to 30 days as desribed above for each samples

value: GIMEN

value: MES neuroblastoma cell lines

value: Naïve cells treated with 2.5 uM PP121 +10 nM bufalin in RPMI, 1% FBS, 1%P/S, 1X i-Glutamax for 30 days


title: MT475_81_2_iPSC_RNA_rep1


title: GIMEN_D30_2


title: DGL9_D14_CD8

value: total CD8+


title: DGL9_D14_CD4NA

value: CD4+ naive


title: MT477_64_4_iPSC_RNA_rep1


title: DGL9_D14_CD8EM

value: CD8+ effector mem.


title: 231 EV, small RNAs

city: Wuhan

first: Yan

last: Wei

address: Bayi road 229

country: China

institute: wuhan university

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller soft-ware, v1.8).
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5’,3‘-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature miRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor miRNA sequences with bowtie software.
The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2. The abundance of miRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads(CPM).
The miRNAs differentially expressed are screened based on the count value with R package edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts and CPM values for each Sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3‘-aminoacyl (charged)deacylation to 3‘-OH for 3’-adaptor ligation, 3‘-cP (2’,3‘-cyclic phosphate) removal to 3’-OH for 3‘-adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5‘-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription.
1) 3’-adapter ligation; 2) 5‘-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 134∼160bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range).
The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq 500 system per the manufacturer?s instructions.

treatment_protocol: The medium from 90% confluent cells grown in EV-free was collected and pre-cleared by centrifugation at 500 × g for 15 min and then at 10,000 × g for 20 min.EVs were pelleted by ultracentrifugation at 110,000 × g for 70 min, and resuspended in PBS.

value: epithelial cell

value: WT

tag: fraction

value: EV


title: 10A EV, small RNAs


title: HR6_pre_monocytes

value: lymph node

value: pre


title: DGL9_D14_CD4MEM

value: CD4+ mem.


title: DEC_rep4

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

data_processing:
RNAseq reads were aligned to the mouse reference genome (mm10) using the TopHat (v.1.3.1).
RNAseq expression was quantified as reads per kilo base of total exon length per million mapped (RPKM) reads using Partek Genomics Suite v.6.12.0713. Minimally expressed genes (<0.1 RPKM) were excluded. Gene Expression measurement was log2 transformed with 0.01 offset for differential gene expression analysis using ANOVA with FDR<0.05 and fold change >1.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: CMM

growth_protocol: CMM (GFP+) cells IV engrafted in C57BL/6 mice

extract_protocol:
Harvest spleen 1 day post last treatment and make single cell suspension, enrich c-Kit+ leukemia cells using STEMCELL EasySep™ PE Positive Selection Kit, extract RNA using Promega Maxwell RSC simplyRNA kit.
RNA libraries for RNA-seq were prepared illumina RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: start treatment when %GFP+ leukemia cells reached ~1% in blood, treat mice IV with PBS/CpG-scrODN/CpG-STAT3dODN every other day for 3 times

value: CMM

value: AML


title: DGL9_D14_CD4

value: total CD4+


title: HR6_pre_cDCs

value: cDCs


title: DGH1_wk8_nonfCD8

value: DEL bNAb Tx


title: GIMEN_Naive_1

value: GIMEN

value: Maintain in RPMI, 10% FBS, 1% PS, 1X i-Glutamax


title: GIMEN_Naive_3

value: MES neuroblastoma cell lines


title: GIMEN_Naive_2


title: HR6_pre_pDCs

value: pDCs

value: WT bNAb Tx


title: HR6_pre_NKcells

value: NK cells


title: HR6_pre_Bcells

value: B cells


title: DEC_rep2


title: DGH1_wk8_nonTfh

value: non-Tfh


title: MT474_SV20_iPSC_RNA_rep1

value: SV20 (CTRL1)

value: induced pluripotent stem cell


title: DEC_rep3


title: DGH1_wk8_GCTfh

value: lymph node

value: GCTfh


title: SKNAS_S2D30_3

source_name: SK-N-AS

value: SK-N-AS

value: S1D4 cells treated with 5 uM PP121 + 100 nM bufalin in Neurobasal, 1X B27, 0.25X i-Glutamax for 30 days


title: HH7_wk8_pDCs

value: Untreated


title: GIMEN_D30_1

value: Naïve cells treated with 2.5 uM PP121 +10 nM bufalin in RPMI, 1% FBS, 1%P/S, 1X i-Glutamax for 30 days


title: SKNAS_S2D30_2


title: SCR_rep4

value: CMM

value: AML

value: CpG-scrODN


title: DGM4_pre_GCTfh

value: UnTx

value: pre


title: HH7_wk8_monocytes

value: monocytes


title: SKNAS_S2D30_1

value: MES neuroblastoma cell lines


title: DGH1_wk8_CD8EM

value: CD8+ effector mem.

value: DEL bNAb Tx


title: SKNAS_S2D30_4


title: SCR_rep3


title: SKNAS_S2D4_4

value: S1D4 cells treated with 5 uM PP121 + 100 nM bufalin in Neurobasal, 1X B27, 0.25X i-Glutamax for 4 days


title: HH7_wk8_NKcells

value: NK cells


title: HH7_wk8_Bcells

value: lymph node

value: B cells


title: HH7_wk8_cDCs

value: cDCs


title: SKNAS_S2D4_3

value: SK-N-AS


title: DGH1_wk8_CD8CM

value: CD8+ central mem.


title: DGH1_wk8_fCD8


title: SCR_rep1


title: DEC_rep1


title: SCR_rep2


title: PBS_rep4

value: PBS


title: SKNAS_S2D4_1


title: DGH1_wk8_CD4NA

value: CD4+ naive


title: DGH1_wk8_CD8

value: total CD8+


title: SKNAS_S2D4_2


title: HH7_pre_pDCs

value: pDCs

value: Untreated


title: SKNAS_S1D4_4

value: Naïve cells treated with 5 uM PP121 in DMEM, 1% FBS, 1%P/S, 1X i-Glutamax for 4 days


title: PBS_rep3

value: CMM

value: AML


title: HH7_pre_cDCs

value: pre


title: PBS_rep2


title: HH7_pre_NKcells


title: HH7_pre_monocytes

value: monocytes


title: SKNAS_S1D4_3

value: MES neuroblastoma cell lines


title: DGH1_wk8_CD4

value: total CD4+

value: DEL bNAb Tx


title: DGH1_wk8_CD4MEM

value: lymph node

value: CD4+ mem.


title: DGH1_pre_nonTfh

value: non-Tfh


title: PBS_rep1


title: HH7_pre_Bcells

value: B cells


title: SKNAS_S1D4_2

value: SK-N-AS


title: DGH1_pre_nonfCD8


title: HEL_wk8_pDCs

value: WT bNAb Tx

value: HEL


title: doxycycline_rep3

data_processing:
RNAseq reads were aligned to the mouse reference genome (mm10) using the STAR (v2.7.9) software.
RNAseq expression was quantified as reads per kilo base of total exon length per million mapped (RPKM) reads using Partek Genomics Suite v7.18.0723. Minimally expressed genes (<0.1 RPKM) were excluded. Gene Expression measurement was log2 transformed with 0.01 offset for differential gene expression analysis using ANOVA with FDR<0.05 and fold change >1.5.
Read count extraction and normalization were performed using Partek GS
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: CMM-tetON-shStat3(GFP+mCh+)cells IV engrafted in NSG mice

extract_protocol:
Harvest spleen 1 day post last treatment and make single cell suspension, sort GFP+mCh+ leukemia cells using FACSAria III, extract RNA using Promega Maxwell RSC simplyRNA kit.
RNA libraries for RNA-seq were prepared illumina RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: start treatment when %GFP+mCh+ leukemia cells reached ~1% in blood, treat mice IV with PBS/CpG1668 /CpG+Dox /Dox daily for 6 time

value: doxycycline


title: doxycycline_rep2


title: HEL_wk8_NKcells

value: NK cells


title: DGH1_pre_GCTfh

value: GCTfh


title: SKNAS_S1D4_1

value: Naïve cells treated with 5 uM PP121 in DMEM, 1% FBS, 1%P/S, 1X i-Glutamax for 4 days


title: DGH1_pre_fCD8


title: doxycycline_rep1

value: CMM

value: AML


title: HEL_wk8_monocytes

value: monocytes


title: SKNAS_Naive_4

value: MES neuroblastoma cell lines

value: Maintain in DMEM, 10% FBS, 1% PS, 1X i-Glutamax


title: Combination_rep3


title: HEL_wk8_cDCs

value: cDCs


title: DGH1_pre_CD8NA

value: lymph node

value: CD8+ naive

value: DEL bNAb Tx

value: pre


title: DGH1_pre_CD8EM

value: CD8+ effector mem.


title: Combination_rep2


title: DGH1_pre_CD8CM

value: CD8+ central mem.


title: SKNAS_Naive_1

value: SK-N-AS


title: SKNAS_Naive_3


title: DGH1_pre_CD8

value: total CD8+


title: CpG1668_rep3


title: NGN2, HD3, rep 2

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
Illumina base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.6.0c
Reads counted on GENCODE release 27 gene models using htseq-count 0.9.1
Assembly: hg38
Supplementary files format and content: Two-column tab-delimited text file with gene identifier and raw read count columns

extract_protocol:
Total RNA was extracted using the Qiagen isolation kit
rRNA-depleted RNA was fragmented and processed into strand-specific cDNA libraries using TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: HEL_wk8_Bcells

value: B cells

value: WT bNAb Tx

value: HEL


title: HEL_pre_NKcells

value: NK cells


title: NGN2, HD3, rep 1


title: HEL_pre_pDCs

value: pDCs


title: DGH1_pre_CD4NA

value: CD4+ naive


title: CpG1668_rep2

value: CMM

value: AML


title: HEL_pre_monocytes

value: monocytes


title: NGN2, HD2, rep 1


title: CpG1668_rep1


title: DGH1_pre_CD4MEM

value: lymph node

value: CD4+ mem.


title: HEL_pre_Bcells


title: SKNAS_Naive_2

value: MES neuroblastoma cell lines

value: Maintain in DMEM, 10% FBS, 1% PS, 1X i-Glutamax


title: DGH1_D14_nonTfh

value: non-Tfh

value: DEL bNAb Tx


title: DGIV_wk8_pDCs

value: DGIV


title: DGH1_D14_nonfCD8


title: PBS rep3

value: PBS


title: DGIV_wk8_NKcells


title: NGN2, HD2, rep 2


title: Combination_rep1


title: DGIV_wk8_monocytes


title: NGN2, C3, rep 2

value: WT/WT


title: PBS rep1


title: NGN2, HD1, rep 1


title: DGH1_pre_CD4

value: total CD4+

value: pre


title: DGH1_D14_GCTfh

value: GCTfh


title: DGH1_D14_fCD8


title: DGIV_wk8_Bcells

value: B cells

value: WT bNAb Tx


title: NGN2, C3, rep 1


title: DGIV_pre_pDCs

value: pDCs


title: D4_DnmtWT_TET1-epiedit_4Cseq_target_sgRNAs

city: Paris

first: Julien

last: Richard Albert

address: 15 Rue Hélène Brion

country: France

institute: Institut Jacques Monod, CNRS, Université de Paris

description: TET1-dCas9 targetted cell line with target sgRNAs

library_source: genomic

data_processing:
CUT&Run data: PCR duplicate removal using BBmap clumpify (Bushnell et al., 2014)(v38.18) and parameters: reorder dedupe=t k=19 passes=6 subs=(0.01 x readlength). Trimmomatic (Bolger et al., 2014) (v0.39) and parameters: CROP:36 ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:24
Read pairs that survived trimming were aligned to the mouse reference genome (build mm10) using Bowtie2 (Langmead et al., 2019)(v2.4.5) for CUT&Run using parameters: --local –very-sensitive –no-mixed –dovetail –no-discordant –phred33 -I 10 -X 700
Processed bigwig files were generated using deeptools (Ramírez et al., 2016) bamCoverage (v3.5.1) and parameters: --binSize 1 –smoothLength 0 –minMappingQuality 10 –normalizeUsing CPM –outFileFormat bigwig –blackListFileName ENCFF547MET.bed –ignoreForNormalization chrX chrM chrY
HiChIP data: the HiC-Pro pipeline (v3.1.0) (Servant et al. 2015) was used to digest the mm10 genome (^GATC G^ANTC), align reads and generate contact map matrices. Single-end alignment bam files were used for peak calling using macs2 (v2.2.7.1) (Zhang et al. 2008) and generating bigwigs using bamCompare (as described above). Loops were called using hichipper (v0.7.7) (Lareau and Aryee 2018b) and parameters “-mu -pp 1000” and differential loops were calculated using diffloop (Lareau and Aryee 2018a) and quickAssoc normalization. bigInteract tracks of differential looping were colour coded based on statistical significance (FDR<0.05).
4C-seq: data were processed using the c4ctus pipeline (Miranda et al. 2022) and default parameters.
Assembly: mm10
Supplementary files format and content: Bigwig format. CUT&Run: CPM-normalized counts. HiChIP: CPM-normalized counts and bigBedInteract loop files (considering 1kb padding around achors). 4C: for each locus, tracks were normalised to the total number of aligned reads +/- 2 TADs (as defined by Bonev et al. 2017).

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)

extract_protocol:
RNA extraction from cell pellets was performed using the KingFisher Duo Prime Magnetic Particle Processor and the MagMAX mirVana Total RNA kit, according to the manufacturer's instructions. To measure H3K27me3 enrichment after epigenome editing, we used the original CUT&RUN l protocol with minor modifications. Briefly, 2.5-5 x 105 cells per sample were pelleted and washed twice with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine containing protease inhibitor). The cells were then incubated for the binding with Concavalin A magnetic beads (Polysciences) by rotating for 10 min at RT. The antibody incubation was carried out overnight on a rotor at 4ºC in 100 µL antibody solution (wash buffer with 0.1% digitonin and 2 mM EDTA) containing 1 µL of αH3K27me3 Ab (Cell Signaling C36B11). Samples were then washed in dig-wash buffer (wash buffer with 0.1% digitonin), and incubated with pAG-Mnase on a rotor for 10 min followed by two more washes. The Mnase reaction was then activated by adding 2 mM CaCl2. After incubating at 0°C for 30 min the reaction was stopped with 1x final concentration of STOP solution (2x: 340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% digitonin, 1:200 Rnase A). Chromatin was released by incubating samples at 37°C for 10 min. After centrifuging at full speed for 5 min, the supernatant was collected after incubation on magnet stand. Purified DNA was obtained by phenol/chloroform extraction and precipitated with 100% ethanol by centrifugation. The DNA pellet was washed in 70% ethanol, spun down and air-dried before being resuspended in 35 µl of 5 mM Tris-HCl pH 8.5. The pAG-Mnase plasmid was obtained from Addgene (# 123461), and the protein was purified by the Curiecoretech Recombinant Protein Platform.
Total RNA was sent to Novogene Co. for polyA-RNA library constructions and sequencing on an Illumina NovaSeq X (paired-end, 150 nucleotide-long reads).
Sequencing libraries were constructed from purified CUT&RUN DNA fragments using the xGen low-input DNA library preparation kit from IDT (Cat. #10009859) following the supplier's instructions. Library quality was assessed using 4200 TapeStation system (Agilent) and sequenced on an Illumina NovaSeq X (paired-end, 150 nucleotide-long reads) by Novogene Co.

treatment_protocol: Day 0, 4 or 7 post-FGF2/Activin A treatment

value: mouse embryonic stem cells

value: DnmtWT

value: Day 4 post-FGF2/Activin A treatment


title: D4_DnmtWT_TET1-epiedit_4Cseq_scrambled_sgRNAs

description: TET1-dCas9 targetted cell line with scrambled sgRNAs

value: N2B27 medium supplemented with 12 ng/mL FGF2 (R&D) and 20 ng/mL Activin A (R&D)


title: NGN2, C2, rep 2


title: DGH1_D14_CD8NA

value: lymph node

value: CD8+ naive


title: NSC_IgG_CUT&Tag_rep2

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
For RNA-seq, libraries were sequenced using the Illumina Novoseq 6000 platform. Adaptor and low-quality trimming were performed with trim galore (v0.6.5, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to Mus musculus reference genome mm10 using STAR (v2.7.3a) with default parameters. Counts were extracted from mapped reads with featureCounts using the –largestOverlap parameter. DESeq2 (v1.40.2) was used to identify differentially expressed genes (FDR < 0.05, fold change > 2) from raw counts using the standard package documentation
For WGBS, paired-end sequencing on a DNBseq platform was performed at BGI Genomics. Raw read filtering was performed by BGI Genomics using SOAPnuke with the parameters -n 0.001 -l 20 -q 0.4 –adaMR 0.25 –ada_trim –polyX 50 to remove adaptors and filter out low-quality reads. Clean reads were mapped to mm10 using Bismark (v0.22.3) with default parameters. Read deduplication was performed using deduplicate_bismark and cytosine methylation levels were extracted with bismark_methylation_extractor. BAM files were balanced to the sample with the lowest number of reads with SAMtools (v1.9)
For CUT&Tag, libraries were sequenced on an Illumina NextSeq 500 platform at the Einstein Epigenomics Shared Facility. Adaptor and low-quality trimming were performed with trim galore. Clean reads were mapped to mm10 using bowtie293 using options -local -sensitive -very-sensitive-local --no-unal -no-mixed -no-discordant -phred33 -I 10 -X 700. Duplicate reads were removed with Picard tools (v2.26.10, https://broadinstitute.github.io/picard/).
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: normalized gene counts
Supplementary files format and content: bedgraph
Library strategy: CUT&Tag

source_name: Neural stem cells

growth_protocol: ESCs preplated and cultured on gelatin in serum/LIF for 24 hours before harvest for high-throughput sequencing. NSCs were generated following the protocol of Okabe et al. (1996) as modified by Lee et al. (2000), passaged once, and then harvested for high-throughput sequencing.

extract_protocol:
For RNA-seq, RNA was extracted from ESCs and NSCs using Qiagen RNeasy Mini kit. For WGBS, DNA was extracted from ESCs and NSCs using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI Genomics (https://en.genomics.cn/). CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix.

treatment_protocol: For CUT&Tag, ESC and NSCs were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex.

value: Neural stem cells

tag: Sex

value: Male

tag: strain

tag: antibody

value: Anti-IgG antibody (CST, 3900)

value: Tet wildtype & triple knockout


title: NGN2, HD1, rep 2


title: DGIV_pre_cDCs

value: cDCs

value: DGIV


title: NGN2, C2, rep 1

value: WT/WT


title: NSC_IgG_CUT&Tag_rep1


title: DGIL_wk8_pDCs

value: DEL bNAb Tx

value: DGIL


title: NGN2, C1, rep 2


title: DGH1_D14_CD8EM

value: CD8+ effector mem.


title: DGH1_D14_CD8CM

value: CD8+ central mem.


title: NGN2, C1, rep 1


title: DGH1_D14_CD8

value: total CD8+


title: Tet_TKO_NSC_H3K27ac_CUT&Tag_rep2

value: Anti-H3K27ac antibody (Abcam, ab4729)

value: Tet triple knockout


title: DGIL_wk8_NKcells

value: NK cells


title: DGIL_wk8_monocytes

value: lymph node

value: monocytes


title: DGH1_D14_CD4NA

value: CD4+ naive


title: DGIL_wk8_cDCs


title: WildType_TYMV_treated_rosette_leaves_Replicate3

city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

data_processing:
Quality filtering and adapter trimming of the raw FASTQ files was performed using Trim Galore with default settings.
Following this, the trimmed reads were alignment to a genome index created from the TAIR10 genome fasta file and all transcripts within the GTF of Ensembl build TAIR10 annotation set (release version 56) using STAR (Dobin et al., 2013).
The resulting transcriptome bam files were subsequently employed for quantifying read counts per gene using Salmon ( Patro, Rob, et al., 2017)  in the alignment-based mode.
Differential gene expression analysis was then conducted using DESeq2 (Love et al., 2014) for genes with a minimum of five aligned reads.
Assembly: TAIR10 genome , Ensemble General Feature Format version 56
Supplementary files format and content: Tab-separated values containing raw counts for genes as rows and columns as samples
Supplementary files format and content: Tab-separated values containing Transcripts Per Million (TPM) for genes as rows and columns as samples

organism: Arabidopsis thaliana

source_name: Rosetteleaves

growth_protocol: Plants were grown for 21-days in 12h light/12h dark (120 mmol.m-2) water-saturated peat-based substrate (Klasmann Substrat 2, Klasmann-Deilmann GmbH, Gerste, DE) containing both fertilizer (Wuxal). A solution containing Bacillus thuringiensis was applied as a preventative control against fungus gnat (Gnatrol, Valent BioSciences, Libertyville, Il, USA). Illumination was supplied by a multi-channel LED light is a custom co-development together with the company RHENAC GreenTec AG (Germany) which was optimized for highest uniformity (spatial light quality distribution; intensity and spectrum), with the following LED channels: 400nm, white_4500K, 660nm and 730nm

extract_protocol:
Total RNA was extracted with a high-performance RNA bead isolation kit (Molecular Biology Service, VBC Core Facilities, Vienna), using a KingFisher Duo Prime System (Thermo Fisher Scientific).
To 80ng of total RNA, 1 μl of barcoded RT primer (GACGTGTGCTCTTCCGATCT<7 bp barcode>NNNNNNNNTTTTTTTTTTTTTTTTTTTTN, 0.2μM) was added, heated to 72°C, 3 min and immediately moved to a -20°C. RNA-primer was then added to the Reverse Transcriptase (RT) mix consisting of SmartScribe RT (1 μl), 25 mM dNTP mix (0.7 μl), 20 mM DTT (1 μl), 100 mM MnCl2 (0.3 μl), and 5x SmartScribe buffer added to the RNA-primer mix. The RT reaction was conducted at 42°C for 1 hour, followed by 70°C for 15 minutes. Samples with different barcodes were pooled and purified using SPRI beads with addition of SPRI buffer (20% PEG, 2.5M NaCl, adjusted to pH 5.5-6.0) to dilute the beads. Next, Tn5 was used to cut the cDNA: the DNA-RNA substrate was mixed with Tn5 activation buffer (20 mM Tris, 10 mM MgCl2, 20% dimethylformamide, pH 7.6) and loaded Tn5 enzyme (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG + [phos]CTGTCTCTTATACACATCT). The reaction was incubated at 55°C for 8 minutes, followed by deactivation and removal of Tn5 with 0.2% SDS at room temperature. PCR amplification was performed using KAPA HotStart ReadyMix (with primers: AATGATACGGCGACCACCGAGATCTACAC<8 bp barcode>TCGTCGGCAGCGTCAGATGTG and CAAGCAGAAGACGGCATACGAGAT<8 bp barcode>GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT). The amplification protocol included an initial denaturation at 95°C for 90 seconds, followed by 12 cycles of denaturation, annealing, and extension, with a final extension at 72°C for 5 minutes. The PCR products were purified using a 0.8x SPRI cleanup protocol and eluted in Elution Buffer.
Poly A RNA seq. Poly A mRNAs Enriched with Oligo DT strategy. cDNA generated was tagmented with Tn5

treatment_protocol: Col-0 or atg2-2 (n=10 per genotype~treatment) plants were rub-inoculated with TCV or TYMV-containing sap (50 mM phosphate buffer pH 7.4, 0.2% sodium sulfite) using carborundum and q-tips. Excess inoculum was rinsed off and plants were shifted to 16h light/8h dark (110 mmol.m-2) growth conditions for the reminder of the experiment. Systemic leaves were collected at the indicated 12 days post inoculation

value: Rosetteleaves

value: Wild Type (WT), Col-0

value: Turnip yellow mosaic virus


title: Tet_TKO_NSC_H3K27ac_CUT&Tag_rep1

value: Neural stem cells

value: Male


title: DGIL_wk8_Bcells

value: B cells


title: DGH1_D14_CD4

value: total CD4+

value: DEL bNAb Tx


title: Tet_WT_NSC_H3K27ac_CUT&Tag_rep2

value: Tet wildtype


title: DGIL_pre_pDCs

value: pDCs

value: DGIL

value: pre


title: Tet_WT_NSC_H3K27ac_CUT&Tag_rep1

value: Anti-H3K27ac antibody (Abcam, ab4729)


title: DGG6_wk8_nonTfh

value: non-Tfh

value: UnTx


title: Tet_TKO_NSC_H3K4me1_CUT&Tag_rep2

value: Anti-H3K4me1 antibody (Abcam, ab8895)

value: Tet triple knockout


title: DGH1_D14_CD4MEM

value: lymph node

value: CD4+ mem.


title: WildType_TYMV_treated_rosette_leaves_Replicate1

value: Rosetteleaves

value: Wild Type (WT), Col-0

value: Turnip yellow mosaic virus


title: Tet_TKO_NSC_H3K4me1_CUT&Tag_rep1

value: Neural stem cells

value: Male


title: WildType_TCV_treated_rosette_leaves_Replicate3

value: Turnip crinkle virus


title: PBS rep2

value: CMM

value: AML

value: PBS


title: DGIL_pre_NKcells

value: NK cells

value: DEL bNAb Tx

value: DGIL

value: pre


title: Tet_WT_NSC_H3K4me1_CUT&Tag_rep2

value: Anti-H3K4me1 antibody (Abcam, ab8895)

value: Tet wildtype


title: WildType_TCV_treated_rosette_leaves_Replicate1


title: Tet_WT_NSC_H3K4me1_CUT&Tag_rep1


title: WildType_TYMV_treated_rosette_leaves_Replicate2


title: WildType_MOCK_treated_rosette_leaves_Replicate1

value: Mock


title: ESC_IgG_CUT&Tag_rep1

source_name: Embryonic stem cells

value: Embryonic stem cells

value: Anti-IgG antibody (CST, 3900)

value: Tet wildtype & triple knockout


title: ESC_IgG_CUT&Tag_rep2


title: DGIL_D14_monocytes

value: lymph node

value: monocytes


title: DGIL_D14_NKcells


title: DGG6_wk8_GCTfh

value: GCTfh

value: UnTx


title: DGG6_wk8_fCD8


title: atg2-2_TYMV_treated_rosette_leaves_Replicate3

value: Rosetteleaves

value: Turnip yellow mosaic virus


title: DGG6_wk8_CD8EM

value: CD8+ effector mem.


title: DGG6_wk8_CD8CM

value: CD8+ central mem.


title: DGG6_wk8_CD8

value: total CD8+


title: DGIL_D14_cDCs

value: cDCs

value: DEL bNAb Tx

value: DGIL


title: atg2-2_TYMV_treated_rosette_leaves_Replicate2


title: Tet_TKO_ESC_H3K27ac_CUT&Tag_rep1

value: Male

value: Anti-H3K27ac antibody (Abcam, ab4729)

value: Tet triple knockout


title: Tet_TKO_ESC_H3K27ac_CUT&Tag_rep2

value: Embryonic stem cells


title: WildType_TCV_treated_rosette_leaves_Replicate2

value: Wild Type (WT), Col-0

value: Turnip crinkle virus


title: DGG6_wk8_nonfCD8

value: lymph node


title: atg2-2_TYMV_treated_rosette_leaves_Replicate1


title: DGGC_wk8_pDCs

value: pDCs

value: DGGC


title: DGG6_wk8_CD4NA

value: CD4+ naive

value: UnTx


title: Tet_WT_ESC_H3K27ac_CUT&Tag_rep2

value: Tet wildtype


title: atg2-2_TCV_treated_rosette_leaves_Replicate2

value: Rosetteleaves


title: DGIL_pre_monocytes

value: monocytes

value: pre


title: Tet_WT_ESC_H3K27ac_CUT&Tag_rep1


title: DGG6_wk8_CD4MEM

value: CD4+ mem.


title: DGIL_pre_Bcells

value: B cells

value: DEL bNAb Tx

value: DGIL


title: DGGC_wk8_NKcells

value: NK cells


title: atg2-2_TCV_treated_rosette_leaves_Replicate1


title: WildType_MOCK_treated_rosette_leaves_Replicate2

value: Mock


title: DGGC_wk8_monocytes


title: DGG6_pre_nonTfh

value: non-Tfh


title: DGIL_D14_Bcells


title: Tet_TKO_ESC_H3K4me1_CUT&Tag_rep1

value: Embryonic stem cells

value: Male

value: Anti-H3K4me1 antibody (Abcam, ab8895)

value: Tet triple knockout


title: DGGC_wk8_cDCs

value: lymph node

value: cDCs

value: DGGC


title: atg2-2_TCV_treated_rosette_leaves_Replicate3

value: Rosetteleaves

value: Turnip crinkle virus


title: DGG6_pre_nonfCD8

value: UnTx

value: pre


title: DGG6_wk8_CD4

value: total CD4+


title: atg2-2_MOCK_treated_rosette_leaves_Replicate1


title: DGGC_wk8_Bcells

value: B cells

value: DEL bNAb Tx


title: atg2-2_MOCK_treated_rosette_leaves_Replicate2


title: Tet_WT_ESC_H3K4me1_CUT&Tag_rep2

value: Tet wildtype


title: DGGC_pre_pDCs

value: pDCs


title: DGG6_pre_GCTfh

value: GCTfh


title: Mock_nrpe1-11_rep3

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
PCR duplicates were removed using unique molecular identifier (UMI) information, and adapters were trimmed using fastp (v0.23.2).
Clean reads were mapped to the reference genome (TAIR10) using HISAT2 (v2.2.1) with default parameters.
The expression level of each gene was normalized to Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using StringTie (v2.1.7) with strand-specific parameter (--rf).
Assembly: Arabidopsis TAIR10

source_name: 2-week-old seedlings

growth_protocol: All plants were grown under long photoperiod conditions (16 h light, 22 °C/8 h dark, 18 °C). Two-week-old seedlings were collected for mRNA-seq.

extract_protocol:
Total RNAs were purified from 2-week-old Arabidopsis seedlings using the RNeasy Plant Mini Kit (QIAGEN, 74904). Poly(A)+ RNAs were isolated using the Dynabeads mRNA Purification Kit (Invitrogen, 61006) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using the NEXTflex RNA-Seq Kit (Bioo Scientific, 5129-01) according to the manufacturer’s instructions.

treatment_protocol: Mock

value: 2-week-old seedlings

tag: ecotype

value: Mock


title: DGGC_pre_NKcells

value: NK cells


title: DGG6_pre_fCD8


title: DGG6_pre_CD8NA

value: CD8+ naive


title: Tet_WT_ESC_H3K4me1_CUT&Tag_rep1

value: Embryonic stem cells

value: Male

value: Anti-H3K4me1 antibody (Abcam, ab8895)


title: ME_rep17_lib2

first: Sarah

last: Pfau

address: 220 Longwood Avenue

institute: Harvard Medical School

library_source: transcriptomic single cell

data_processing:
bc-bio nextgen indrops3 (default settings); See https://bcbio-nextgen.readthedocs.io/en/latest/contents/single_cell.html
Assembly: mm10
Supplementary files format and content: compressed csv, abundance measurements with cell labels

source_name: brain

extract_protocol:
microdissection, papain dissociation, ovomucoid gradient separation of single cells, inDrops single cell encapsulation
inDrops v3

tag: region

value: ME

value: brain

value: male

value: WT


title: Mock_nrpe1-11_rep2


title: DGGC_pre_monocytes

value: lymph node

value: monocytes

value: DGGC

value: pre


title: ME_rep16_lib1


title: ME_rep15_lib2


title: Tet_TKO_ESC_H3K4me1_CUT&Tag_rep2

value: Tet triple knockout


title: Mock_nrpe1-11_rep1


title: DGG6_pre_CD8EM

value: CD8+ effector mem.

value: UnTx


title: Mock_nrpd1-3_rep3

value: 2-week-old seedlings

value: Mock


title: DGGC_pre_Bcells

value: B cells

value: DEL bNAb Tx


title: DGG6_pre_CD8CM

value: CD8+ central mem.


title: DGGC_D14_pDCs

value: pDCs


title: ME_rep14_lib1

value: ME


title: ME_rep13_lib2

value: brain


title: DGG6_pre_CD8

value: total CD8+


title: DGGC_D14_NKcells

value: NK cells


title: Mock_nrpd1-3_rep2


title: DGG6_pre_CD4NA

value: lymph node

value: CD4+ naive


title: ME_rep13_lib1

value: male

value: WT


title: DGGC_D14_monocytes

value: monocytes

value: DGGC


title: Mock_nrpd1-3_rep1


title: Mock_Col-0_rep3

value: wildtype


title: Mock_Col-0_rep2

value: 2-week-old seedlings


title: DGG6_pre_CD4

value: total CD4+

value: UnTx

value: pre


title: DGGC_D14_Bcells

value: B cells

value: DEL bNAb Tx


title: Mock_Col-0_rep1

value: Mock


title: ME_rep12_lib1

value: ME

value: brain


title: DGG6_D14_nonTfh

value: non-Tfh


title: ME_rep11_lib2


title: DGFJ_wk8_pDCs

value: lymph node

value: pDCs

value: DGFJ


title: ME_rep11_lib1

value: male

value: WT


title: DGG6_D14_nonfCD8


title: Mutant 3

city: HOUSTON

first: Emily

last: Busse

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Genome alignment, normalization, differential expression, hierarchical clustering, and GO analysis were then performed using RNA-Seq analysis pipeline in Partek Genomics Suite (Partek).
Assembly: mm39
Supplementary files format and content: Excel sheet with raw gene counts for each sample

source_name: Whole bone

extract_protocol:
Total RNA from pulverized bone was extracted using TRIzol (Thermo Fisher Scientific).
RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations.

value: Whole bone


title: DGFJ_wk8_NKcells

value: NK cells


title: DGG6_D14_GCTfh

value: GCTfh


title: ME_rep10_lib2


title: Mutant 2


title: DGG6_pre_CD4MEM

value: CD4+ mem.


title: ME_rep10_lib1


title: DGG6_D14_fCD8

value: UnTx


title: DGFJ_wk8_monocytes

value: monocytes


title: ME_rep9_lib2


title: Control 2


title: DGGC_D14_cDCs

value: cDCs

value: DGGC


title: DGFJ_wk8_cDCs

value: DEL bNAb Tx


title: ME_rep12_lib2

value: ME


title: DGG6_D14_CD8NA

value: CD8+ naive


title: DGG6_D14_CD8EM

value: CD8+ effector mem.


title: DGFJ_wk8_Bcells

value: lymph node

value: B cells


title: DGFJ_pre_pDCs

value: pDCs

value: DGFJ

value: pre


title: Mutant 1

value: Whole bone


title: ME_rep9_lib1

value: brain

value: male

value: WT


title: DGG6_D14_CD8CM

value: CD8+ central mem.

value: UnTx


title: DGFJ_pre_NKcells

value: NK cells


title: Control 3


title: ME_rep8_lib2


title: DGG6_D14_CD8

value: total CD8+


title: ME_rep8_lib1


title: DGFJ_pre_monocytes

value: monocytes

value: DEL bNAb Tx


title: JP_rep3

city: Zagreb

first: Tomislav

last: Domazet-Loso

state: Grad Zagreb

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Institut Rudjer Bošković

data_processing:
Sequence quality and read coverage were checked using FastQC V0.11.7.
RNA sequences were mapped onto the reference genome using BBMap V38.75.
SAMtools package V1.11. was used to generate, sort and index BAM files.
Subsequent RNAseq data processing was performed in R V4.0.4.
Mapped reads were quantified per each V. vinifera open reading frame using R samtools package V2.10.0.
Raw counts for open reading frames were retrieved using the GenomicAlignments R package V1.30.0.
Assembly: Vitis vinifera NCBI 12X GCA_000003745.2
Supplementary files format and content: The processed data file contains a matrix of raw count values for each replicate and each mapped gene.

organism: Vitis vinifera

source_name: somatic embryos

growth_protocol:
Early induction (EI) samples were grown on auxin and in constant dark.
Preglobular (PG) samples were grown on auxin and in constant dark.
Globular 1 (G1) samples were grown on auxin and in constant dark.
Globular 2 (G2) samples were grown on auxin and in constant dark.
Heart (H) samples were grown on hormone-free medium and in constant dark.
Torpedo 1 (T1) samples were grown on hormone-free medium and in constant dark.
Torpedo 2 (T2) samples were grown on hormone-free medium and in constant dark.
Cotiledonary 1 (C1) samples were grown on hormone-free medium and in constant dark.
Cotiledonary 2 (C2) samples were grown on hormone-free medium and in long day.
Seedling (S) samples were grown on gibberelin and in long day.
Seedling with epicotyl (EP) samples were grown on gibberelin and in long day.
Juvenile plant (JP) samples were grown on gibberelin and in long day.

extract_protocol:
Total RNA was isolated from somatic embryos using Rneasy Plant Mini kit (Qiagen) with slight modification of the manufacturer's protocol.
Samples consisted of 50 to 70 individual embryos, depending on the developmental stage.
Samples were incubated for 5 min at room temperature and stored at -20 °C before sequencing.
The library was constructed according to the standard RNAseq library protocol at the EMBL Genomics Core Facility (Heidelberg, Germany).

value: somatic embryos

tag: development stage

value: SE juvenile plant (JP) developmental stage

value: grown with gibberelin in long day


title: DGG6_D14_CD4NA

value: lymph node

value: CD4+ naive


title: ME_rep7_lib2

value: ME


title: JP_rep2


title: DGFJ_pre_cDCs

value: cDCs

value: DGFJ

value: pre


title: JP_rep1


title: ME_rep7_lib1

value: brain

value: male


title: DGG6_D14_CD4MEM

value: CD4+ mem.


title: Control 1

value: Whole bone


title: ME_rep6_lib2

value: WT


title: DGFJ_D14_pDCs

value: pDCs


title: EP_rep5

value: SE seeedling with epicotyl (EP) developmental stage


title: DGG4_wk8_nonTfh

value: non-Tfh

value: WT bNAb Tx


title: DGG6_D14_CD4

value: total CD4+

value: UnTx


title: DGFJ_pre_Bcells

value: lymph node

value: B cells

value: DEL bNAb Tx


title: EP_rep4

value: somatic embryos

value: grown with gibberelin in long day


title: DGFJ_D14_NKcells

value: NK cells

value: DGFJ


title: DGG4_wk8_nonfCD8


title: ME_rep5_lib2

value: ME

value: brain

value: male


title: EP_rep3


title: DGFJ_D14_monocytes

value: monocytes


title: DGG4_wk8_GCTfh

value: GCTfh


title: ME_rep5_lib1

value: WT


title: ME_rep6_lib1


title: DGFJ_D14_cDCs

value: cDCs


title: EP_rep1

value: SE seeedling with epicotyl (EP) developmental stage


title: S_rep3

value: SE seedling (S) developmental stage


title: ME_rep4_lib2


title: DGG4_wk8_fCD8

value: WT bNAb Tx


title: DGG4_wk8_CD8NA

value: lymph node

value: CD8+ naive


title: ME_rep4_lib1


title: DGFJ_D14_Bcells

value: B cells

value: DEL bNAb Tx


title: DGFD_wk8_pDCs

value: pDCs

value: DGFD


title: S_rep2

value: somatic embryos

value: grown with gibberelin in long day


title: DGG4_wk8_CD8EM

value: CD8+ effector mem.


title: ME_rep3_lib2

value: ME

value: brain

value: male


title: DGFD_wk8_NKcells

value: NK cells


title: S_rep1


title: ME_rep3_lib1

value: WT


title: EP_rep2

value: SE seeedling with epicotyl (EP) developmental stage


title: DGFD_wk8_monocytes

value: monocytes


title: ME_rep2_lib2


title: DGG4_wk8_CD8

value: total CD8+

value: WT bNAb Tx


title: DGFD_wk8_cDCs

value: lymph node

value: cDCs


title: DGG4_wk8_CD4NA

value: CD4+ naive


title: C2_rep4

value: SE cotiledonary 2 (C2) developmental stage

value: grown on hormone-free medium in long day


title: C2_rep2

value: somatic embryos


title: DGFD_pre_NKcells

value: DEL bNAb Tx

value: DGFD

value: pre


title: ME_rep1_lib2

value: ME

value: brain


title: ME_rep2_lib1

value: male


title: DGFD_pre_pDCs

value: pDCs


title: ME_rep1_lib1

value: WT


title: C2_rep1


title: DGFD_pre_monocytes

value: monocytes


title: cortex_rep11_lib2

value: cortex


title: DGFD_pre_cDCs


title: C1_rep3

value: SE cotiledonary 1 (C1) developmental stage

value: grown on hormone-free medium in constant dark


title: DGG4_pre_nonfCD8

value: lymph node

value: WT bNAb Tx


title: cortex_rep11_lib1


title: DGG4_pre_nonTfh

value: non-Tfh


title: DGG4_wk8_CD8CM

value: CD8+ central mem.


title: DGFD_pre_Bcells

value: B cells


title: C2_rep5

value: somatic embryos

value: SE cotiledonary 2 (C2) developmental stage

value: grown on hormone-free medium in long day


title: DGG4_pre_GCTfh

value: GCTfh

value: pre


title: C1_rep2


title: C2_rep3


title: DGG4_wk8_CD4MEM

value: CD4+ mem.


title: cortex_rep10_lib1

value: brain

value: male


title: cortex_rep10_lib2

value: WT


title: DGFD_D14_NKcells

value: NK cells

value: DEL bNAb Tx

value: DGFD


title: DGG4_pre_fCD8

value: lymph node


title: DGG4_wk8_CD4

value: total CD4+

value: WT bNAb Tx


title: DGFD_D14_pDCs

value: pDCs


title: cortex_rep9_lib2

value: cortex


title: T2_rep2

value: somatic embryos

value: SE torpedo 2 (T2) developmental stage

value: grown on hormone-free medium in constant dark


title: DGFD_D14_monocytes

value: monocytes


title: DGG4_pre_CD8NA

value: CD8+ naive

value: pre


title: DGG4_pre_CD8EM

value: CD8+ effector mem.


title: DGG4_pre_CD8CM

value: CD8+ central mem.


title: cortex_rep8_lib2

value: brain

value: male

value: WT


title: T1_rep3

value: SE torpedo 1 (T1) developmental stage


title: DGFD_D14_Bcells

value: lymph node

value: B cells

value: DEL bNAb Tx

value: DGFD


title: DGG4_pre_CD8

value: total CD8+

value: WT bNAb Tx


title: DGEM_wk8_pDCs

value: pDCs

value: Untreated

value: DGEM


title: DGG4_pre_CD4NA

value: CD4+ naive


title: T1_rep2

value: somatic embryos

value: grown on hormone-free medium in constant dark


title: cortex_rep7_lib2

value: cortex


title: C1_rep1

value: SE cotiledonary 1 (C1) developmental stage


title: T2_rep3

value: SE torpedo 2 (T2) developmental stage


title: DGEM_wk8_NKcells

value: NK cells


title: T1_rep1

value: SE torpedo 1 (T1) developmental stage


title: cortex_rep7_lib1

value: brain

value: male

value: WT


title: DGEM_wk8_monocytes

value: lymph node

value: monocytes


title: DGG4_pre_CD4MEM

value: CD4+ mem.

value: WT bNAb Tx

value: pre


title: DGEM_wk8_cDCs

value: cDCs

value: Untreated

value: DGEM


title: cortex_rep9_lib1


title: H_rep2

value: somatic embryos

value: SE heart (H) developmental stage

value: grown on hormone-free medium in constant dark


title: DGG4_pre_CD4

value: total CD4+


title: T2_rep1

value: SE torpedo 2 (T2) developmental stage


title: DGG4_D14_nonTfh

value: non-Tfh


title: DGEM_wk8_Bcells

value: B cells


title: cortex_rep6_lib1

value: cortex

value: brain

value: male


title: H_rep1


title: DGFD_D14_cDCs

value: lymph node

value: DEL bNAb Tx

value: DGFD


title: DGG4_D14_nonfCD8

value: WT bNAb Tx


title: cortex_rep5_lib2

value: WT


title: G2_rep3

value: SE globular 2 (G2) developmental stage

value: grown with auxin in constant dark


title: cortex_rep8_lib1


title: DGEM_pre_pDCs

value: pDCs

value: Untreated

value: DGEM

value: pre


title: cortex_rep5_lib1


title: DGEM_pre_NKcells

value: NK cells


title: G2_rep2

value: somatic embryos


title: DGG4_D14_GCTfh

value: GCTfh


title: cortex_rep4_lib2

value: cortex


title: DGG4_D14_fCD8


title: cortex_rep6_lib2

value: brain


title: DGEM_pre_monocytes

value: monocytes


title: DGG4_D14_CD8NA

value: lymph node

value: CD8+ naive


title: G2_rep1


title: H_rep3

value: SE heart (H) developmental stage

value: grown on hormone-free medium in constant dark


title: cortex_rep4_lib1

value: male

value: WT


title: DGEM_pre_cDCs

value: cDCs


title: G1_rep3

value: SE globular 1 (G1) developmental stage

value: grown with auxin in constant dark


title: cortex_rep3_lib2


title: DGEM_pre_Bcells

value: B cells

value: Untreated

value: DGEM


title: G1_rep2

value: somatic embryos


title: DGG4_D14_CD8CM

value: CD8+ central mem.

value: WT bNAb Tx


title: DGG4_D14_CD8EM

value: CD8+ effector mem.


title: G1_rep1


title: cortex_rep3_lib1

value: cortex

value: brain


title: cortex_rep2_lib2


title: DGDL_wk8_NKcells

value: lymph node

value: NK cells

value: DGDL


title: DGDL_wk8_pDCs

value: pDCs


title: PG_rep3

value: SE preglobular (PG) developmental stage


title: DGG4_D14_CD8

value: total CD8+


title: cortex_rep2_lib1

value: male

value: WT


title: DGG4_D14_CD4NA

value: CD4+ naive


title: cortex_rep1_lib2


title: DGDL_wk8_cDCs

value: cDCs


title: DGDL_wk8_monocytes

value: monocytes


title: DGG4_D14_CD4MEM

value: CD4+ mem.


title: PG_rep1

value: somatic embryos

value: grown with auxin in constant dark


title: DGG4_D14_CD4

value: total CD4+

value: WT bNAb Tx


title: cortex_rep1_lib1

value: cortex

value: brain


title: DGDL_wk8_Bcells

value: lymph node

value: B cells


title: Emcn-/-_320

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole maaløes vej 5

department: BRIC & The Finsen Laboratory

country: Denmark

institute: University of Copenhagen & Rigshospitalet/National University hospital

data_processing:
adapter removal and trimming using cutadapt
mapping against the transcriptome using salmon
generating counts table using tximport in R
Assembly: GENCODE M25
Supplementary files format and content: csv file containing raw gene counts for each of the analysed samples

source_name: Bone marrow

extract_protocol:
Femura, illia and tibiae were isolated from the hind legs and the bones were crushed in a mortar. The bone marrow was re-suspended in PBS/3%FCS and filtered through a 70μm cell strainer (Falcon) to obtain single-cell suspensions.  For cell sorting, bone marrow cells were depleted of lineage positive cells using a Lineage Cell Depletion kit (Miltenyi Biotec, cat-nr.130-090-858) according to manufacturer’s instructions, then stained with antibodies of interest (PE/Cy5 anti-mouse Gr-1, PE/Cy-5 anti-mouse CD11b, PE/Cy5 anti-mouse/human B220, PE/Cy5 anti-mouse CD3e, PE/Cy5 anti-mouse Ter119, Pacific Blue anti-mouse Sca-1, APC-efluor780 anti-mouse c-kit, Alexa Fluor700 anti-mouse CD16/CD32, BV650 anti-mouse CD150, PE/Cy7 CD48) and incubated for 30 min at 4°C. After washing with PBS/3%FCS at 300g for 5 min, 4°C, cells were re-suspended in PBS/3%FCS containing 1:1000 7-Aminoactinomycin D (7-AAD, Lifetechnologies, cat-nr. A1310) for discrimination of dead cells. HSPC populations were sorted on FACS Aria III (BD Biosciences).   RNA was isolated from sorted cells using the RNeasy Plus micro kit (Qiagen).
RNA libraries were constructed using the SMARTer stranded total RNA-Seq Kit V2 Pico Input (TaKaRa) according to manufacturer’s instructions. Final library library concentrations were measured using Qubit 2.0 Fluorometer in combination with Qubit dsDNA HS Assay Kit (Invitrogen). Size distribution and fragment length were assessed using Agilent Bioanalyzer HS-DNA Chips. Molarity of individual libraries was calculated considering the concentration and average fragment size. Pair-end sequencing of 2.0 pM pooled libraries were performed using an Illumina NextSeq 500 System in combination with NextSeq 500/550 Mid Output v2 kit (150 cycles). PhiX Control (Illumina) was added at 1% to the pool as an internal control before sequencing.

value: Bone marrow

value: C57BL/6N-EMCN em1(IMPC)Wtsi /WtsiH

value: LT-HSC

value: Emcn KO

value: F


title: DGA7_wk8_nonfCD8

value: UnTx


title: EI_rep3

value: SE early induction (EI) developmental stage


title: DGA7_wk8_nonTfh

value: non-Tfh


title: DGDL_D14_pDCs

value: pDCs

value: DGDL


title: Emcn-/-_314


title: EI_rep1

value: somatic embryos

value: grown with auxin in constant dark


title: DGDL_D14_monocytes

value: monocytes

value: WT bNAb Tx


title: Emcn+/+_312

value: Emcn WT


title: DGA7_wk8_GCTfh

value: lymph node

value: GCTfh


title: DGDL_D14_NKcells

value: NK cells


title: DGA7_wk8_fCD8


title: PG_rep2

value: SE preglobular (PG) developmental stage


title: DGDL_D14_cDCs

value: cDCs


title: Emcn+/+_310

value: Bone marrow

value: C57BL/6N-EMCN em1(IMPC)Wtsi /WtsiH

value: LT-HSC


title: DGA7_wk8_CD8NA

value: CD8+ naive

value: UnTx


title: DGDL_D14_Bcells

value: B cells


title: Emcn-/-_306

value: Emcn KO

value: F


title: Emcn+/+_290


title: DGA7_wk8_CD8CM

value: CD8+ central mem.


title: DGCK_pre_pDCs

value: pDCs

value: DGCK

value: pre


title: EI_rep2

value: somatic embryos

value: SE early induction (EI) developmental stage

value: grown with auxin in constant dark


title: Emcn+/+_284

value: Emcn WT


title: DGCK_pre_NKcells

value: lymph node

value: NK cells

value: WT bNAb Tx


title: DGA7_wk8_CD8

value: total CD8+


title: GMP_4

extract_protocol:
Femura, illia and tibiae were isolated from the hind legs and the bones were crushed in a mortar. The bone marrow was re-suspended in PBS/3%FCS and filtered through a 70μm cell strainer (Falcon) to obtain single-cell suspensions.  For cell sorting, bone marrow cells were depleted of lineage positive cells using a Lineage Cell Depletion kit (Miltenyi Biotec, cat-nr.130-090-858) according to manufacturer’s instructions, then stained with antibodies of interest (PE anti-mouse EMCN, PE/Cy5 anti-mouse Gr-1, PE/Cy-5 anti-mouse CD11b, PE/Cy5 anti-mouse/human B220, PE/Cy5 anti-mouse CD3e, PE/Cy5 anti-mouse Ter119, Pacific Blue anti-mouse Sca-1, APC-efluor780 anti-mouse c-kit, Alexa Fluor700 anti-mouse CD16/CD32, BV650 anti-mouse CD150, PE/Cy7 CD48) and incubated for 30 min at 4°C. After washing with PBS/3%FCS at 300g for 5 min, 4°C, cells were re-suspended in PBS/3%FCS containing 1:1000 7-Aminoactinomycin D (7-AAD, Lifetechnologies, cat-nr. A1310) for discrimination of dead cells. HSPC populations were sorted on FACS Aria III (BD Biosciences).   RNA was isolated from sorted cells using the RNeasy Plus micro kit (Qiagen).
RNA libraries were constructed using the SMARTer stranded total RNA-Seq Kit V2 Pico Input (TaKaRa) according to manufacturer’s instructions. Final library library concentrations were measured using Qubit 2.0 Fluorometer in combination with Qubit dsDNA HS Assay Kit (Invitrogen). Size distribution and fragment length were assessed using Agilent Bioanalyzer HS-DNA Chips. Molarity of individual libraries was calculated considering the concentration and average fragment size. Pair-end sequencing of 2.0 pM pooled libraries were performed using an Illumina NextSeq 500 System in combination with NextSeq 500/550 Mid Output v2 kit (150 cycles). PhiX Control (Illumina) was added at 1% to the pool as an internal control before sequencing.

value: Bone marrow

value: GMP

tag: mouse id


title: DGCK_pre_monocytes

value: monocytes


title: HCT116_DMSO2_2: DMSO treated HCT116, replicate 2

type: RNA

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

institute: Centre Léon Bérard

description: Gene expression data from HCT116, treated with DMSO

hyb_protocol: following fragmentation, 15µg cRNA were hybridized for 16h at 45°C on Human Genome U133 Plus 2.0 array. Genechips were washed and stained in the Affymetrix Fluidics Station 450

data_processing: Gene expression analysis was performed using Array Studio software (Omicsoft Corporation). Raw microarray data (CEL files) were processed using quantile normalization and robust multiarray average algorithm.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

extract_protocol: the Nucleospin RNA kit (Macherey-Nagel) was used for total RNA extraction

treatment_protocol: Cells were plated and treated with DMSO or EI-52 at 8 µM for the indicated times.

value: DMSO


title: LTHSC_EMCNminus_4

value: EMCN- LT-HSC

value: F


title: DGA7_wk8_CD4NA

value: CD4+ naive

value: UnTx


title: HCT116_DMSO3_3: DMSO treated HCT116, replicate 3


title: HCT116_CER3_6: EI-52 (CER) treated HCT116, replicate 3

description: Gene expression data from HCT116, treated with EI-52

value: EI-52 (CER)


title: HCT116_DMSO1_1: DMSO treated HCT116, replicate 1


title: Tet_WT_NSC_WGBS

data_processing:
For RNA-seq, libraries were sequenced using the Illumina Novoseq 6000 platform. Adaptor and low-quality trimming were performed with trim galore (v0.6.5, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Clean reads were mapped to Mus musculus reference genome mm10 using STAR (v2.7.3a) with default parameters. Counts were extracted from mapped reads with featureCounts using the –largestOverlap parameter. DESeq2 (v1.40.2) was used to identify differentially expressed genes (FDR < 0.05, fold change > 2) from raw counts using the standard package documentation
For WGBS, paired-end sequencing on a DNBseq platform was performed at BGI Genomics. Raw read filtering was performed by BGI Genomics using SOAPnuke with the parameters -n 0.001 -l 20 -q 0.4 –adaMR 0.25 –ada_trim –polyX 50 to remove adaptors and filter out low-quality reads. Clean reads were mapped to mm10 using Bismark (v0.22.3) with default parameters. Read deduplication was performed using deduplicate_bismark and cytosine methylation levels were extracted with bismark_methylation_extractor. BAM files were balanced to the sample with the lowest number of reads with SAMtools (v1.9)
For CUT&Tag, libraries were sequenced on an Illumina NextSeq 500 platform at the Einstein Epigenomics Shared Facility. Adaptor and low-quality trimming were performed with trim galore. Clean reads were mapped to mm10 using bowtie293 using options -local -sensitive -very-sensitive-local --no-unal -no-mixed -no-discordant -phred33 -I 10 -X 700. Duplicate reads were removed with Picard tools (v2.26.10, https://broadinstitute.github.io/picard/).
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap. Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: normalized gene counts
Supplementary files format and content: bedgraph

value: Neural stem cells

value: Male

value: Tet wildtype


title: DGA7_wk8_CD4MEM

value: CD4+ mem.


title: LTHSC_EMCNplus_4

value: EMCN+ LT-HSC


title: DGA7_wk8_CD4

value: lymph node

value: total CD4+


title: GMP_3


title: DGCK_pre_Bcells

data_processing:
Illumina reads were aligned to the Macaca mulatta genome (Mmul_10 build 102) using the STAR aligner (version 2.7.10a) and counted using HTSeq (2.0.2).
Assembly: Mmu_10 build 102
Supplementary files format and content: raw gene count file

extract_protocol:
Total RNA was isolated from cell lysates using the RNAzol RT protocol as per the manufacturer’s instructions
RNA Illumina-ready libraries were generated using NEBNext Ultra II RNA Prep reagents (New England BioLabs). Using oligo dT beads (Invitrogen), poly-adenylated RNA was purified and subsequently fragmented, followed by double-stranded cDNA synthesis, end repair, and adapter ligation. The ligated DNA was then barcoded and amplified by a limited cycle PCR and the libraries were sequenced using a paired-end 150-base protocol on either a HiSeq 4000 or a NovaSeq 6000 (Illumina).

value: B cells

value: WT bNAb Tx

value: DGCK

value: pre


title: DGCK_D14_pDCs

value: pDCs


title: Tet_TKO_NSC_WGBS

value: Tet triple knockout


title: HCT116_CER2_5: EI-52 (CER) treated HCT116, replicate 2


title: DGA7_pre_nonTfh

data_processing:
Illumina reads were aligned to the Macaca mulatta genome (Mmul_10, build NCBI:GCA_003339765.3) using the STAR aligner (version 2.7.10a) and counted using HTSeq (2.0.2).
Assembly: Mmu_10
Supplementary files format and content: raw gene count file

extract_protocol:
Total RNA was isolated from cell lysates using the RNAzol RT protocol as per the manufacturer’s instructions
RNA Illumina-ready libraries were generated using NEBNext Ultra II RNA Prep reagents (New England BioLabs). Using oligo dT beads (Invitrogen), poly-adenylated RNA was purified and subsequently fragmented, followed by double-stranded cDNA synthesis, end repair, and adapter ligation. The ligated DNA was then barcoded and amplified by a limited cycle PCR and the libraries were sequenced using a paired-end 150-base protocol on NovaSeq 6000 (Illumina).

value: non-Tfh


title: Tet_TKO_ESC_WGBS

value: Embryonic stem cells


title: DGCK_D14_NKcells

value: NK cells


title: LTHSC_EMCNplus_3

value: Bone marrow

value: F


title: DGCK_D14_monocytes

value: monocytes


title: HCT116_CER1_4: EI-52 (CER) treated HCT116, replicate 1

value: EI-52 (CER)


title: DGA7_pre_nonfCD8

value: UnTx


title: Tet_WT_ESC_WGBS

value: Male

value: Tet wildtype


title: DGA7_wk8_CD8EM

value: lymph node

value: CD8+ effector mem.


title: GMP_2

value: GMP


title: DGCK_D14_Bcells

value: B cells

value: WT bNAb Tx

value: DGCK


title: kidney SCF-3

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: kidney

extract_protocol:
Kidney were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: kidney

tag: age

value: 10 weeks

value: STZ+control-FMT


title: DGA7_pre_GCTfh

tag: tissue

value: GCTfh

value: pre


title: DGBG_wk8_NKcells

tag: cell type

value: NK cells

value: DEL bNAb Tx

value: DGBG


title: DGA7_pre_fCD8

value: UnTx


title: kidney SCF-2


title: DGA7_pre_CD8NA

value: CD8+ naive


title: DGBG_wk8_monocytes

value: lymph node

value: monocytes


title: GMP_1

value: Bone marrow

value: GMP

value: F


title: LTHSC_EMCNplus_2

value: EMCN+ LT-HSC


title: LTHSC_EMCNminus_2

value: EMCN- LT-HSC


title: kidney SAF-3

value: ICR

value: kidney


title: LTHSC_EMCNminus_1


title: DGA7_pre_CD8CM

value: CD8+ central mem.


title: DGA7_pre_CD8EM

value: CD8+ effector mem.


title: DGBG_wk8_cDCs

value: cDCs


title: DGBG_wk8_Bcells

value: B cells


title: LTHSC_EMCNplus_1


title: kidney SAF-2

value: 10 weeks


title: DGA7_pre_CD4NA

value: CD4+ naive

value: pre


title: kidney SA10-3


title: DGBG_pre_NKcells

value: NK cells

value: DEL bNAb Tx

value: DGBG


title: DGA7_pre_CD4MEM

value: lymph node

value: CD4+ mem.

value: UnTx


title: Meninges_1 (VDJ)

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the meninges of 10 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices and VDJ output generated using the Cellranger count and vdj pipelines 3.0.2
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.
Supplementary files format and content: Compressed folders containing the outs directory from cellranger vdj

source_name: Meninges

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq
5' RNAseq + VDJ

value: Meninges

tag: gender

value: male

value: 2 months

tag: genotype


title: DGA7_pre_CD4

value: total CD4+


title: kidney SA10-2

value: ICR

value: kidney


title: DGBG_pre_monocytes

value: monocytes


title: Blood (VDJ)


title: DGBG_pre_Bcells

value: B cells


title: kidney SCF-1

value: 10 weeks

value: STZ+control-FMT


title: kidney SA10-1


title: Diaphragm (VDJ)


title: kidney STZ-3

value: STZ


title: S3, TCR

description:
RNA was isolated from the spinal cords of 18 mice.
tVDJ

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices and VDJ output generated using the Cellranger multi pipeline 3.0.2
Assembly: mm10
Supplementary files format and content: *.tar archives contain the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes, or VDJ output.
Library strategy: scVDJ

source_name: spinal cord

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

treatment_protocol: Before being assigned to surgery, the body weight of mice was assessed and mice lighter than 19 grams were removed. Mice were anesthetized with a ketamine (100 mg kg-1)–xylazine (10 mg kg-1) mixture. The hair on the back was shaved and cleaned with betadine and alcohol. A 15-mm midline skin incision was performed over the T6-T13 vertebra, and the connective and muscle tissues were bluntly dissected to expose the lamina. A laminectomy was performed using rongeurs at T9 to expose the dorsal spinal cord. The vertebral column was stabilized with angled clamps attached to the T7 and T12 and a calibrated contusion injury of the spinal cord was induced at T9 by an Infinite Horizon Impactor (IH-0400 Impactor Precision Systems and Instrumentation) at a force of 80K dynes. After the injury, the muscles and skin were sutured separately and mice were allowed to recover from anesthesia on heating pads. After recovering from anesthesia, mice were injected intra-subcutaneously with buprenorphine (0.05 mg kg-1) daily for the first three days. Water containing sulfamethoxazole and trimethoprime oral suspension (200 mg/ 40 mg L-1) was supplied. Soft food and nutra-gel diet (S5769-TRAY, Bio-Serv) were supplied daily. Bladders of all mice were manually voided twice a day during the experiments.

value: spinal cord

value: female

value: 2-3 months

value: spinal cord injury


title: DGBG_D14_NKcells

source_name: lymph node

value: lymph node

value: NK cells

value: DEL bNAb Tx

value: DGBG


title: DGA7_D14_GCTfh

value: GCTfh

value: UnTx


title: kidney STZ-2

value: ICR


title: DGBG_pre_pDCs

value: pDCs

value: pre


title: kidney SAF-1

value: kidney


title: S3, transcriptome

description:
RNA was isolated from the spinal cords of 18 mice.
total mRNA
5' RNAseq

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices and VDJ output generated using the Cellranger multi pipeline 3.0.2
Assembly: mm10
Supplementary files format and content: *.tar archives contain the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes, or VDJ output.


title: DGBG_D14_Bcells

value: B cells


title: kidney STZ-1

value: 10 weeks


title: DGA7_D14_fCD8


title: S2, TCR

description:
RNA was isolated from the spinal cords of 12 mice.
tVDJ


title: DGA7_D14_CD8NA

value: CD8+ naive


title: DGAM_wk8_pDCs

value: Untreated

value: DGAM


title: DGA7_D14_CD8EM

value: CD8+ effector mem.


title: DGAM_wk8_Bcells


title: S2, transcriptome

description:
RNA was isolated from the spinal cords of 12 mice.
total mRNA
5' RNAseq

value: spinal cord

value: female

value: 2-3 months

value: spinal cord injury


title: DGA7_D14_CD8CM

value: lymph node

value: CD8+ central mem.


title: Meninges_2 (VDJ)

value: Meninges

value: male

value: 2 months


title: Meninges_2

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 3.0.2. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

growth_protocol: Not applicable

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

treatment_protocol: Not applicable


title: kidney Kcon-1

value: ICR

value: control


title: C6/36 cells, Triptolide

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome AaloF1 with STAR aligner (version 2.7.3a ), using EnsGenembl 50 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Assembly: AaloF1
Supplementary files format and content: TPM gene expression in csv file for RNA-seq data.

organism: Aedes albopictus

source_name: C6/36 cells

growth_protocol: Aedes albopictusC6/36cells were obtained from ATCC[CRL-1660] and were cultured in Leibovitz’s L-15 medium supplemented with 10% fetal bovine serum (FBS), 0.02% L-glutamine, 100 U/ml of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of amphotericin B (Fungizone).

extract_protocol:
RNA was extracted from cells using TRIzol (Invitrogen) and isopropanol precipitation according to the manufacturer’s instructions. After precipitation, the RNA pellet was washed twice with ice-cold freshly prepared 75% ethanol and subsequently air-dried and resuspended in water. RNA was quantified using Qubit RNA broad range kit.
Full length cDNA generation was conducted on a Formulatrix Mantis liquid handling robot using Takara SMART-Seq v4 Ultra Low Input RNA kit. Then, sequencing libraries were created using the Illumina Nextera XT DNA Library Prep Kiton a SPT Labtech Mosquito liquid handling robot. Using these low-volume liquid handling robots, we were able to miniaturize reactions to 1/8. The resulting libraries were quantified, pooled and sequenced on an Illumina NextSeq 500 System using standard operating procedures.

treatment_protocol: Aedes albopictus C6/36 cells were sub-cultured in a 24-well plate at a relatively low passage and set overnight to reach 70% confluency the day of treatment. Triptolide, Flavopiridol or DRB were added into the well, with final concentration of 5 uM, 0.5 uM and 30uM, respectively, in 0.1% DMSO. Cells were directly collected in Trizol for RNA extraction at 6 h post treatment.

value: Triptolide

tag: protocol

value: Clontech/Nextera Non-stranded RNA-Seq


title: DGA7_D14_CD8

first: Slim

last: Fourati

institute: Northwestern University

value: total CD8+

tag: treatment

value: UnTx


title: DGA7_D14_nonTfh

value: non-Tfh

tag: animal id


title: DGBG_D14_pDCs

value: pDCs

value: DEL bNAb Tx

value: DGBG

tag: timepoint


title: Meninges_1


title: C6/36 cells, Flavopiridol

value: Flavopiridol


title: DGA7_D14_CD4NA

value: CD4+ naive


title: kidney A10-3_KA-3

value: kidney

value: 10 weeks

value: AOS 10mg/kg


title: DGA7_D14_CD4MEM

value: lymph node

value: CD4+ mem.


title: kidney A10-2_KA-2

value: ICR


title: C6/36 cells, DRB

value: DRB


title: Blood

source_name: Blood

value: 2 months

value: male

value: Blood


title: Diaphragm

source_name: Diaphragm

value: Diaphragm


title: C6/36 cells, DMSO

value: DMSO

value: Clontech/Nextera Non-stranded RNA-Seq


title: kidney A10-1_KA-1


title: kidney Kcon-2

value: control


title: DGA7_D14_CD4

value: total CD4+

value: UnTx


title: kidney Kcon-3


title: Bulk ATACseq HSPC-enriched BM cells, vehicle, rep3

status: Public on Jul 22 2024

city: Munich

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

institute: LMU Hospital

data_processing:
Libraries were sequenced 2x60 reads base pairs paired-end on an Illumina NextSeq 2000 to a depth of 300,000-600,000 reads/sample.
BulkATAC-seqdata wasaligned to the mouse genomeand read filtering, peak calling and IDR based peak filtering was performed by implementing the ENCODE ATAC-seq pipeline.The bigwig coverage track was generated using Deeptools (v3.1.3).
Assembly: mm10
Supplementary files format and content: bw files are provided for each indvidual sample

extract_protocol:
After appropiate treatment conditions, cells were harvested, and ATAC-Seq kit libraries were prepared using the ATAC-Seq Kit from Active Motif (Cat#53150), following the manufacturer’s instructions.
ATAC-Seq Kit from Active Motif (Cat#53150)

treatment_protocol: Bone marrow (from femur) cells were flushed out, homogenized and filtered through 40 μm cell strainers to obtain single cell suspensions.  Cells were then cultured for 24h at 37ºC and 5% CO2 at a density of 2,5·10^5/mL in StemSpan™ SFEM medium supplemented with Priomicin (1:500), thrombopoietin (TPO) (100 ng/ml), and stem cell factor (SCF) (20 ng/ml) to maintain the stemness of the progenitors and prevent extensive differentiation. Then, cells were exposed to either Isotype or recombinant IL-1b at a concentration of 10 ng/ml overnight at 37ºC.

value: Bone marrow

tag: cell line

value: HSPC enriched fraction

value: WT

value: vehicle


title: Bulk ATACseq HSPC-enriched BM cells, rIL1b, rep2


title: Bulk ATACseq HSPC-enriched BM cells, rIL1b, rep3


title: Bulk ATACseq HSPC-enriched BM cells, vehicle, rep4


title: Bulk ATACseq HSPC-enriched BM cells, rIL1b, rep4


title: Bulk ATACseq HSPC-enriched BM cells, vehicle, rep2


title: Bulk ATACseq HSPC-enriched BM cells, rIL1b, rep1


title: Heart, Stroke, ScRNAseq, rep2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Cell suspensions were prepared by mechanically cutting the hearts into small pieces with a scalpel and incubating with an enzymatic digestion mix (see protocol) for 30 min, under magnetic stirring at 250rpm, 37ºC. The cell suspension was passed through a 40 mm cell strainer to remove cardiomyocytes, small fragment of undigested tissue. Cells were spun at 300g for 5 min and pre-warmed red cell lysis buffer was added for 1 min to remove blood cells. After washing, cell pellets were resuspended in 200 mL Dead Cell Removal MicroBeads and incubated 10 min at room temperature in the dark. The mix of cells and beads was diluted in binding buffer and pass through the magnatic columns to remove dead cells. After centrifugation, cells were resuspended in and stained with  3 mM DAPI. Single live nucleated cells were sorted on a BD AriaII with 130mm nozzle to minimize pressure over cells and sorted in 0.04%BSA, centrifuged for 8min at 400g, resuspended and diluted to 1000cells/ul for scRNaseq (10x Genomics). Cells were then further processed according to manufacturer’s (10X) instructions. The scRNA-seq libraries were prepared using the 10x Chromium Single Cell 3′ Solution. Quality control of all cDNA samples was performed with a Bioanalyzer 2100 (Agilent Technologies) and libraries were quantified with the Qubit dsDNA HS kit. Gene expression libraries were sequenced on an Illumina NextSeq 1000 using 20,000 reads per cell.
Libraries were performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, dual index, 10x Genomics).

value: Heart

value: Cardiac interstitial cells

tag: disease state

value: Stroke


title: Heart, Control, ScRNAseq, rep2

description: 10x Genomics

tag: strain

value: Control


title: Heart, Stroke, ScRNAseq, rep1

description: 10x Genomics


title: Heart, Control, ScRNAseq, rep1

description: 10x Genomics


title: Bone marrow, Control, scRNA-seq, rep2

description: 10x Genomics

extract_protocol:
Bone marrow cells suspensions were stained with a cocktail of antibodies against markers of the lymphoid lineage (CD3, CD4, CD8a, CD19 and Ter119) and mature neutrophils (Ly6G, see antibodies list). Immediately prior to cell sorting, PI  were also added to label dead cells. Cells were sorted according to the surface markers (FACS Aria II Fusion cell sorter, BD Biosciences, Inc.) and the negative fraction of BM myeloid cells (depleted of lymphoid lineage cells and neutrophils) was collected. After sorting, cells were centrifuged and cautiously resuspended to a final concentration of 1200-1400 cells/ul. Cells were then further processed according to manufacturer’s (10X) instructions. The scRNA-seq libraries were prepared using the 10x Chromium Single Cell 3′ Solution. Quality control of all cDNA samples was performed with a Bioanalyzer 2100 (Agilent Technologies) and libraries were quantified with the Qubit dsDNA HS kit. Gene expression libraries were sequenced on an Illumina NextSeq 2000 using 20,000 reads per cell.
Libraries were performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, dual index, 10x Genomics).

value: Lymphoid lineage (CD3, CD4, CD8a, CD19, Ter119) negative  and neutrophil (Ly6G) negative


title: Bone marrow, Stroke, scRNA-seq, rep1

description: 10x Genomics


title: Bone marrow, Control, scRNA-seq, rep1

description: 10x Genomics


title: Bone marrow, Stroke, scRNA-seq, rep2

description: 10x Genomics


title: Recipient bone marrow, Stroke donor, ScRNAseq, rep2, GEX

description:
10x Genomics
Sample 4 - GEX
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz

source_name: Blood and heart

extract_protocol:
Mononuclear cell suspensions from the heart and the blood were incubated with anti-CD16/CD32 antibody to block nonspecific binding and stained for CD45+CD11b+ myeloid cells. Two unique cell hashtags antibodies were also used to label cells from blood and heart independently. All surface antibodies and hashtag antibodies were incubated for 30 min at 4ºC. Immediately prior to cell sorting, PI was added to all samples to label dead cells. Cells were sorted according to their surface markers (SH800S Cell Sorter, Sony Biotechnology). Sorted and organ-specific labeled cells from the heart and blood from the same animal were pooled together in the same collecting tube. After sorting, all cells were centrifuged and cautiously resuspended to a final concentration of 500 cells/ul. Cells were then transferred to the Next GEM chip according to manufacturer’s instructions. ScRNA-seq and cell hashing (cell surface protein) libraries were prepared using the 10x Chromium Single Cell 3′ Solution combined with feature barcoding technology for Cell surfacte protein, as per established protocols.
Quality control of all cDNA samples was performed with a Bioanalyzer 2100 (Agilent Technologies) and libraries were quantified with the Qubit dsDNA HS kit. Gene expression libraries were sequenced on an Illumina NextSeq 2000 using 20,000 reads per cell. Cell-surface protein expression libraries (cell hashtags) were sequenced on an Illumina NextSeq 2000 aiming for 5,000 reads per cell.
Libraries were performed according to the manufacter’s instructions ( single cell 3' v3.1 with feature barcoding technology for Cell surface protein, dual index, 10x Genomics).

value: Blood and heart

value: Myeloid cells (CD45+, CD11b+)

value: Mx1Cre:c-Mybfl/fl recipient mice

tag: library type

value: GEX


title: Recipient bone marrow, Control donor, ScRNAseq, rep2, GEX

description:
10x Genomics
Sample 3 - GEX
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz


title: Recipient bone marrow, Stroke donor, ScRNAseq, rep1, GEX

description:
10x Genomics
Sample 2 - GEX
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz


title: Recipient bone marrow, Control donor, ScRNAseq, rep1, GEX

description:
10x Genomics
Sample 1 - GEX
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz


title: Recipient bone marrow, Control donor, ScRNAseq, rep1, CSP

description:
10x Genomics
Sample 1 - CSP
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz

library_source: other

molecule: protein

value: HTO (antibody-based cell-hashtag)


title: Recipient bone marrow, Stroke donor, ScRNAseq, rep2, CSP

description:
10x Genomics
Sample 4 - CSP
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz


title: tissue Treg,Repl_3,ChIPInput

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

description:
FACS sort: live CD4+CD206-CD64-CD25+Foxp3-hCD2+
GreyList_Input.bed

data_processing:
demultiplexed with bclconvert Illumina Dragon (v-3.8.4 NextSeq 2000)
Fastq files were trimmed and mapped using snakePipes (v2.5.1) DNA-mapping workflow with the parameters: aligner: Bowtie2, fragmentLength:200, insertSizeMax:1000.
Peaks were called using the ChIP-Seq/ATAC-Seq workflow applying MACS2 --qvalue 0.001
bigwig: Binsize:25.
Assembly: GRCm38_gencode_release23 (ftp://ftp.ebi.ac.uk/pub/ databases/gencode/Gencode_mouse/release_M23/GRCm38.primary_assembly.genome.fa.gz)
Supplementary files format and content: MACS2_peaks.xls (except for input): peak size and reads score

source_name: spleens and lymphnodes

growth_protocol: For tisTreg and IL-2 Treg cultures used for ChIP-seq experiments, Foxp3tm1(CD2/CD52)Shori animals were used which express a GPI-anchored human CD2-CD52 fusion protein in all Foxp3 positive cells. Staining for anti-human CD2 can be used as a surrogate marker for Foxp3 expression. Treg cells were isolated from spleen and LNs of these animals by sorting for live CD4+CD206-CD64-CD25+Foxp3-hCD2+ cells.

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and the reaction was quenched with glycine at a final concentration of 0.125 M, Chromatin was sheared using the Covaris S220 focused-ultrasonicator to an average size of 250–350 bp. Input control was collected.A total of 2.5 µg of antibody against H3K27ac (Abcam, ab4729) was added to sonicated chromatin of 2 × 106 cells and incubated overnight at 4 °C. Protein A sepharose beads (GE healthcare) were added to the ChIP reactions and incubated for 2 h at 4 °C. Beads were washed and chromatin was eluted. After reversal crosslink, RNase A and proteinase K treatment, DNA was extracted with the Monarch PCR & DNA Cleanup kit (NEB)
the Monarch PCR & DNA Cleanup kit (NEB) with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: Then, 50.000 cells were stimulated with CD3/CD28 microbeads at a 4 to 1 bead to cell ratio and treated with the respective cytokine cocktails for 6 days at 37°C. After 3 days, cytokine medium was replenished. IL-2 Treg cultures were treated with 2000U/ml human IL-2 (Proleukin S®, Novartis). Tissue Treg cultures were treated with 2000U/ml human IL-2 (Proleukin S®, Novartis), 5ng/ml murine IL-4 (Peprotech), 50ng/ml IL-33 (Peprotech) and 10 µg/ml anti-mouse IFNγ blocking antibodies (BioXCell). After 6 days, cells were resorted to exclude dead cells and ensure high purity for ChIP Seq assays. Naïve Treg cells were additionally sorted on CD62L+ and directly subjected to the ChIP Seq assay.

value: spleens and lymphnodes

value: tissue Treg

tag: chip antibody

value: none (input)


title: tissue Treg,Repl_2,ChIPInput

value: 2000U/ml human IL-2 (Proleukin S®, Novartis), 5ng/ml murine IL-4 (Peprotech), 50ng/ml IL-33 (Peprotech) and 10 µg/ml anti-mouse IFNγ blocking antibodies (BioXCell)


title: Recipient bone marrow, Stroke donor, ScRNAseq, rep1, CSP

description:
10x Genomics
Sample 2 - CSP
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz


title: tissue Treg,Repl_3,H3K27ac,ChIP

description: FACS sort: live CD4+CD206-CD64-CD25+Foxp3-hCD2+


title: Recipient bone marrow, Control donor, ScRNAseq, rep2, CSP

description:
10x Genomics
Sample 3  - CSP
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz


title: tissue Treg,Repl_1,H3K27ac,ChIP


title: tissue Treg,Repl_1,ChIPInput


title: naive Treg,Repl_2,ChIPInput

description:
FACS sort: live CD4+CD206-CD64-CD25+Foxp3-hCD2+CD62L
GreyList_Input.bed

value: naive Treg cells


title: tissue Treg,Repl_2,H3K27ac,ChIP


title: naive Treg,Repl_2,H3K27ac,ChIP

description: FACS sort: live CD4+CD206-CD64-CD25+Foxp3-hCD2+CD62L


title: naive Treg,Repl_3,ChIPInput


title: IL2 Treg,Repl_2,ChIPInput

value: 2000U/ml human IL-2 (Proleukin S®, Novartis)


title: Bulk ATACseq HSPC-enriched BM cells, vehicle, rep1

value: Bone marrow

value: HSPC enriched fraction

value: WT

value: vehicle


title: naive Treg,Repl_3,H3K27ac,ChIP


title: naive Treg,Repl_1,H3K27ac,ChIP


title: IL2 Treg,Repl_1,H3K27ac,ChIP


title: IL2 Treg,Repl_2,H3K27ac,ChIP


title: IL2 Treg,Repl_1,ChIPInput


title: tissue Treg, Repl_2,ATAC

extract_protocol:
For each ATAC reaction 5 × 104 cells were were sorted into a tube and spun down at 500 × g for 5 min at 4 °C, before the supernatant was discarded completely. Cells were washed with PBS and lysed by resuspension in a lysis buffer with 0.1% NP-40 and 0.01% Digitonin for 3 min on ice. Lysis was stopped by adding ATAC-Resuspension Buffer (10mM TrisHCl, 10mM NaCl, 0.1% Tween-20) and centrifugation at 500g for 10 min at 4°C. Tagmentation was performed in 1x Tagmentation Buffer (Illumina) with 0.01% Digitonin using Tagment DNA TDE1 Enzyme (Illumina) at 37°C for 30 min while shaking at 1000 rpm. DNA was purified using Monarch PCR & DNA clean-up columns (NEB).
libraries were prepared by PCR (11 cycles) using Phusion polymerase (NEB) and IDT for llumina UD Indexes (Illumina) with 1.18 M Betaine


title: naive Treg, Repl_3,ATAC


title: naive Treg, Repl_2,ATAC


title: naive Treg, Repl_1,ATAC


title: tissue Treg, Repl_3,ATAC


title: tissue Treg, Repl_1,ATAC


title: IL-2 Treg, Repl_1, ATAC


title: Sham_PCT_AB_14_05

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version Version 0.11.9) then quality trimmed using Trimgalore (version 0.6.7)
Trimmed reads were mapped to mouse genome using STAR aligner (version 2.7.9a) with default settings.
Mapped reads were counted using RsubRead (version 2.8.1)
Raw counts were normalized using DESeq2 (version 1.36.0)
Assembly: ENSMBL Mus_musculus.GRCm39, release 104
Supplementary files format and content: txt matrix with log2 normalized values per sample.

source_name: lung

extract_protocol:
Lung lobes were prepared and transferred to an enzyme mix to dissociate cells. CD45-positive cells were bound to CD45 antibody-coupled beads and then discarded. CD45-negative cells were bound to CD31 antibody-coupled magnetic beads for positive cell sorting. After washing, RNA was isolated from cells. PolyA+RNA was purified  from 100 ng total RNA using Poly(A) mRNA Magnetic Isolation module Kit (NEB E7490L, New England Biolabs).
The RNA Sequencing library was prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs).
Directional RNA Library Prep, single reads run 72 Nu with an average of 26.9 M reads per sample

treatment_protocol: Mice were anesthetized, the cecum mobilized after median laparotomy and the cecum ligated and punctured. The abdomen was closed and antibodies injected invtravenously. Mice were awakened and sacrificed after 18h.

value: lung

value: endothelial cells


title: naive Treg,Repl_1,ChIPInput


title: Sham_PCT_AB_13_04


title: Sham_IgG_ctrl_28_19


title: Sham_IgG_ctrl_27_18


title: Sham_IgG_ctrl_29_20


title: Sham_IgG_ctrl_19_10


title: CLP_PCT_AB_20_11


title: Sham_IgG_ctrl_18_09


title: CLP_PCT_AB_12_03


title: CLP_PCT_AB_21_12


title: CLP_PCT_AB_11_02


title: CLP_PCT_AB_10_01


title: CLP_IgG_ctrl_26_17


title: Sham_PCT_AB_22_13


title: CLP_IgG_ctrl_17_08


title: Recipient bone marrow, Control donor, ScRNAseq, rep2

description:
10x Genomics
BMtransplant_barcodes.tsv
BMtransplant_genes.tsv
BMtransplant_matrix.mtx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Three mouse single-cell RNA experiments were performed in this study: one on a pool of myeloid cells isolated from the heart, lung, liver, spleen and blood; and the other two on bone marrow myeloid cells, either from stroke and control mice, or from naïve recipients after BM transplantation. For the first experiment, mononuclear cell suspensions from peripheral organs were incubated with anti-CD16/CD32 antibody to block nonspecific binding and stained for CD45+CD11b+ myeloid cells (see antibodies list). Five unique cell hashtags antibodies were also used to label cells from each organ. All surface antibodies and hashtag antibodies were incubated for 30 min at 4ºC. Immediately prior to cell sorting, PI was added to all samples to label dead cells. Cells were sorted according to their surface markers (SH800S Cell Sorter, Sony Biotechnology). Sorted and organ-specific labeled cells from the heart, lung, liver, spleen and blood from the same animal were pooled together in the same collecting tube (cell ratio of 1:4:4:4:4, respectively). After sorting, all cells were centrifuged and cautiously resuspended to a final concentration of 1000 cells/l. Cells were then transferred to the Next GEM chip according to manufacturer’s instructions. ScRNA-seq and cell hashing libraries were prepared using the 10x Chromium Single Cell 3′ Solution combined with cell hashing, as per established protocols.10    For the second and third experiments, bone marrow cells suspensions were stained with a cocktail of antibodies against markers of the lymphoid lineage (CD3, CD4, CD8a, CD19 and Ter119) and mature neutrophils (Ly6G, see antibodies list). Immediately prior to cell sorting, PI or 7-AAD were also added to label dead cells. Cells were sorted according to the surface markers (SH800S Cell Sorter, Sony Biotechnology, or FACS Aria II Fusion cell sorter, BD Biosciences, Inc.) and the negative fraction of BM myeloid cells (depleted of lymphoid lineage cells and neutrophils) was collected. After sorting, cells were centrifuged and cautiously resuspended to a final concentration of 1000-1200 cells/l. Cells were then further processed according to manufacturer’s (10X) instructions. The scRNA-seq libraries were prepared using the 10x Chromium Single Cell 3′ Solution.   In all three experiments, quality control of all cDNA samples was performed with a Bioanalyzer 2100 (Agilent Technologies) and libraries were quantified with the Qubit dsDNA HS kit. Gene expression libraries were sequenced on an Illumina NextSeq 1000 using 20,000 reads per cell. Cell-surface protein expression libraries were sequenced on an Illumina NextSeq 1000 aiming for 5,000 reads per cell.
Libraries were performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol and single cell 3' v3.1 with feature barcoding technology for Cell surface protein, 10x Genomics).

value: Lymphoid lineage (CD3, CD4, CD8a, CD19, Ter119) negative  and neutrophil (Ly6G) negative

value: Control


title: Recipient bone marrow, Stroke donor, ScRNAseq, rep1

value: Stroke


title: Bone marrow, Stroke, ScRNAseq, rep4

description:
10x Genomics
BM_barcodes.tsv
BM_genes.tsv
BM_matrix.mtx


title: Recipient bone marrow, Stroke donor, ScRNAseq, rep2


title: CLP_IgG_ctrl_25_16


title: Bone marrow, Control, ScRNAseq, rep4


title: Sham_PCT_AB_23_14


title: Bone marrow, Control, ScRNAseq, rep3


title: Sham_PCT_AB_24_15


title: CLP_IgG_ctrl_15_06


title: Recipient bone marrow, Control donor, ScRNAseq, rep1


title: Bone marrow, Stroke, ScRNAseq, rep3


title: Bone marrow, Stroke, ScRNAseq, rep2


title: Bone marrow, Stroke, ScRNAseq, rep1


title: Bone marrow, Control, ScRNAseq, rep1