title: DNase-seq_ALP, rep2

description:
Library name: DNase-seq_ALP_2
DNase-seq_ALP_2
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677392

value: Bone Marrow

value: All Lymphoid Progenitor


title: DNase-seq_ILCP, rep3

status: Public on Oct 30 2025

type: SRA

city: Nantes

first: Christelle

last: Harly

address: 8 quai Moncousu

country: France

institute: CNRS

description:
Library name: DNase-seq_ILCP_3
DNase-seq_ILCP_3
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677399

library_source: genomic

data_processing:
Basecalling was done by RTA 1.18.66.3, Illumina instrument run time analysis software
Duplicates reads were eliminated from raw FASTQ files using Clumpify (BBMap 39.00) and adapter sequences and low-quality reads were removed using Trimmomatic (0.39)
Remaining reads were mapped to mouse genome (mm39) using Bowtie2 (2.5.1), and reads with MAPQ score<10 were filtered out using Samtools (2.23.5)
Peak calling was done with MACS2 (2.2.7.1)
Satistical analysis of differentially open regions was done with DiffBind (3.4.11)
Peaks were annotated using HOMER (4.11) with Ensembl GTF (mm39 release 108)
Assembly: mm39
Supplementary files format and content: Tab-delimited annotated peak table generated by HOMER with chromatin profile clustering

molecule: genomic DNA

organism: Mus musculus

source_name: Bone Marrow

growth_protocol: Samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
For DNase I digestion, 300 cells from each cell type were collected by FACS sorting. 0.3 unit of DNase I (Roche, 04716728001) was added to each cell type and incubated at 37 °C for 5 minutes. Reaction were stop by adding 80 μl of stop buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.15% SDS, 10 mM EDTA) containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 55 °C for overnight and DNA purified by phenol–chloroform extraction, followed by precipitation with ethanol in the presence of 20 μg glycogen.
The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10"; 67°C, 30"; 72°C, 30" for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10"; 68°C, 30"; 72°C, 30" for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq3000.

tag: strain background

tag: genotype/variation

tag: tissue

tag: cell type

value: Innate Lymphoid Cell Progenitor

tag: treatment

value: ex vivo

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ GFP+ Thy1+ IL-7Ra+

tag: batch


title: B10007_Btheta_M3807_colon_4

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

address: 415 Main Street, 415M-7175 - Xavier lab

department: Immunology Program

country: USA

institute: Broad Institute

description: Library name: 20220907_ENS_BT_3807_BT_B10007_Btheta_M3807_colon_4

library_source: transcriptomic single cell

data_processing:
Demultiplex and basecall to fastq with bcl2fastq
FASTQ reads were aligned to the mm10 mouse transcriptome
Alignment with STAR
Counting of transcripts with RSEM
Assembly: mm10
Supplementary files format and content: ens_raw_geo_upload.h5ad: Anndata object of  gene counts of genes quantified by RSEM before processing
Supplementary files format and content: ens_atlas_geo_upload.h5ad: Anndata object of  ENS atlas based on Smart-seq2

molecule: polyA RNA

source_name: Colon

extract_protocol:
RNA lysate clean-up was performed using RNAClean XP beads (A63987, Beckman Coulter, CA, USA) followed by reverse transcription with Maxima H minus Reverse Transcriptase (EP0743, Thermo Fisher Scientific, MA, USA) and whole-transcription amplification (WTA) with KAPA HotStart HIFI 2 × ReadyMix (07958927001, Roche, Switzerland) for 21 cycles. WTA products were purified with Ampure XP beads (A63881, Beckman Coulter, CA, USA), quantified with Qubit dsDNA HS Assay Kit (Q32854, Thermo Fisher, MA, USA) and assessed with D5000 screentape on a 2200 Agilent TapeStation system (5067-5588, 5067-5589, Agilent, CA, USA). Diluted WTA products underwent tagmentation and indexing using the Nextera XT DNA Library Preparation Kit (FC-131-1096, Illumina, CA, USA), followed by size selection with Ampure XP beads. Size and concentration were then assessed with D1000 screentape (5067-5582, 5067-5583, Agilent, CA, USA) on 2200 Agilent TapeStation system.
Libraries from four 96-well plates were pooled together and sequenced with the Illumina NextSeq 500/550 75-cycle high output kit (20024906, Illumina, CA, USA) on a NextSeq 500/550 system.

value: Colon

value: enteric neuron

tag: Sex

value: M

tag: mouse id

value: BT

tag: batch label

tag: plate label


title: DNase-seq_ALP, rep1

description:
Library name: DNase-seq_ALP_1
DNase-seq_ALP_1
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677391

value: Lin- Kit+ 2B4+ a4b7- Flt3high IL-7Ra+


title: B29_OVAc_M102_DJ_1

description: Library name: 20220825_ENS_SPF_102_OVAc_B29_OVAc_M102_DJ_1

value: OVAc


title: B30_OVAc_M103_DJ_3

description: Library name: 20220824_ENS_SPF_IL4C_103_OVAc_B30_OVAc_M103_DJ_3


title: B30_OVAc_F66_ileum_1

description: Library name: 20220824_ENS_SPF_IL4C_66_OVAc_B30_OVAc_F66_ileum_1

source_name: Ileum

value: Ileum

value: F


title: B30_OVAc_F67_ileum_1

description: Library name: 20220824_ENS_SPF_IL4C_67_OVAc_B30_OVAc_F67_ileum_1


title: B30_OVAc_F109_DJ_1

description: Library name: 20220824_ENS_SPF_IL4C_109_OVAc_B30_OVAc_F109_DJ_1


title: sRNA-seq_dcr1_rep4

city: Cold Spring Harbor

first: Teri

last: Cheng

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
Reads were processed and filtered using fastp v.0.23.4. Duplicated reads and reads smaller than 20nt or larger than 70nt were discarded. Reads were mapped using Bowtie2 v2.4.2 and normalized using Deeptools v3.5.0.
Assembly: ASM294v2
Supplementary files format and content: Normalized bigwig file after in silico size selection of sRNA ranging from 20-70nt.

molecule: total RNA

organism: Schizosaccharomyces pombe

growth_protocol: All cultures were grown at 30°C in standard media with supplement (YES) and harvested in mid-log phase.

extract_protocol:
Total RNA was purified from mid-log phase cells using Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions, including the use of ZR BashingBead Lysis Tubes to lyse open the cells in TRI Reagent. DNA was removed using DNase I (Zymo Research) and purified using RNA Clean & Concentrator (Zymo Research).
Libraries were prepared using NextFlex Small RNA-seq v3 Kits (PerkinElmer).

tag: cell line

value: yeast cells

tag: genotype


title: sRNA-seq_WT_rep3

value: WT


title: sRNA-seq_rnh12_rep2

value: rnh1 rnh201


title: sRNA-seq_dcr1rnh12_rep1

value: dcr1 rnh1 rnh201


title: Mouse2_inferior

city: BOSTON

first: Jeong-Mi

last: Lee

state: MASSACHUSETTS

address: 221 Longwood Avenue, EBRC 3rd Floor

institute: Brigham and Women's Hospital

description: Library name: AdaptiveTCR_2l

data_processing:
The TCRseq data were processed using Adaptive Biotechnology's immunoSEQ pipeline. Raw FASTQ files were not made available to customers. The TCR arrangement files included here represent the complete dataset.
Assembly: mm10
Supplementary files format and content: TCR arrangement  files
Library strategy: TCR-Seq

source_name: Spleen

extract_protocol:
Splenic Tfr cells were sorted into PBS with 2% FBS and 0.025M HEPES and genomic DNA per sample was extracted in 50 uL TE buffer.
Sequencing libraries are generated following the instruction for Survey resolution of the immunoSEQ kit for mouse TCRB assay (Adaptive Biotechnologies).

value: Spleen

value: Mouse CD4 T  cell


title: sRNA-seq_dcr1_rep2


title: sRNA-seq_dcr1_rep3


title: B25_SPF_M122_DJ_4

description: Library name: 20220823_ENS_OVA_SPF_122_SPF_B25_SPF_M122_DJ_4

value: SPF


title: B25_OVAc_M103_DJ_2

description: Library name: 20220823_ENS_OVA_SPF_103_OVAc_B25_OVAc_M103_DJ_2


title: B25_SPF_M122_DJ_3

description: Library name: 20220823_ENS_OVA_SPF_122_SPF_B25_SPF_M122_DJ_3


title: B24_SPF_M122_DJ_1

description: Library name: 20220821_ENS_OVA_122_SPF_B24_SPF_M122_DJ_1


title: B29_OVAc_F109_ileum_1

description: Library name: 20220825_ENS_SPF_109_OVAc_B29_OVAc_F109_ileum_1


title: sRNA-seq_rnh12_rep1


title: sRNA-seq_WT_rep1


title: sRNA-seq_dcr1_rep1


title: B24_SPF_F124_DJ_3

description: Library name: 20220821_ENS_OVA_124_SPF_B24_SPF_F124_DJ_3


title: dcr1rnh12_input_rep2

data_processing:
Demultiplexed reads were first trimmed with cutadapt v3.4 before mapping to the genome using Bowtie2 2.4.2. Reads were converted to sorted bam files using Samtools, which were then used to generate normalized tracks using deepTools v3.5.0.
Assembly: ASM294v2
Supplementary files format and content: Normalized bigwig file for each sample.

extract_protocol:
ChIP was performed as described (Kim et al., 2014 Cell Reports) with slight modifications. Briefly, 40 mL of mid-log phase cells in YES were crosslinked with 1% formaldehyde for 20 minutes and quenched with 360 mM glycine and 2.4 mM Tris for 5 minutes. Whole cell extracts were then prepared with FastPrep-24 and the chromatin was sheared with BioRuptor using 15 cycles of 30s ON/30s OFF. 2 μg of antibodies were pre-conjugated to 15 μL of Pierce Protein A/G Magnetic Beads (Thermo Scientific) for ~3 hours at 4 °C before being added to the sheared chromatin and were incubated overnight at 4 °C. The beads were washed and de-crosslinked with proteinase K and overnight incubation at 65°C. ChIP DNA Clean & Concentrator (Zymo Research) was used to clean up the DNA.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB).

value: input


title: dcr1_input_rep2


title: Opa1KO_Treg_rep2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
Reads were trimmed for adaptors and low-quality reads by Trimmomatic (v0.36) and aligned to mouse genome mm10 by BWA (v0.7.16).
Duplicated reads were then marked with Picard (v2.9.4) and only non-duplicated proper paired reads were kept by Samtools (v1.9, parameter: -q 1 -F 1804).
After adjustment of the Tn5 shift (reads were offset by +4 bp for the sense strand and -5 bp for the antisense strand), reads were separated into nucleosome-free reads.
Next, peaks were called on nucleosome-free reads by MACS2 (v2.1.1, parameter: -extsize 200- nomodel). To assure reproducibility, we finalized nucleosome-free regions for each sample and retained a peak only if called with a higher cutoff (MACS2 -q 0.05). Consensus peaks were generated by keeping peaks present in at least 50% of replicates and discarding the remaining non-reproducible peaks. Reproducible peaks were further merged among samples if they overlapped by 100 bp and nucleosome-free reads were counted by bedtools (v2.25.0).
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples.

growth_protocol: Mixed BM chimera mice were generated at a 1:1 ratio with BM from CD45.1+ and Foxp3Cre (called WT) or Foxp3CreOpa1fl/fl (called Opa1 KO) mice.

extract_protocol:
5x104 total Treg cells were sorted from the indicated mice and lysed in 50 uL ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice for 10 min, followed by centrifugation at 500g for 10 min at 4 ºC to pellet nuclei. After careful removal of supernatant, nuclei were resuspended in 50 uL transposase reaction mix (Illumina) and incubated at 37 ºC for 30 min. Following tagmentation, DNA was purified using MinElute kit (Qiagen).
Purified DNA was then indexed using Nextera barcoding and amplified for 5 cycles using NEBNext HiFi kit (NEB). A 5 uL aliquot from the previous PCR reaction was used for real-time PCR (KAPA SYBR Fast; Kapa Biosystems) to determine the optimal remaining cycles. The final PCR products were cleaned using AMPure XP beads (Beckman Coulter).

treatment_protocol: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells from mixed BM chimera.

value: Primary mouse Treg cells

value: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells sorted from Foxp3CreOpa1fl/fl mixed BM chimera

value: Opa1 KO


title: B24_SPF_F124_DJ_2

description: Library name: 20220821_ENS_OVA_124_SPF_B24_SPF_F124_DJ_2

value: enteric neuron


title: rnh12_input_rep2


title: sRNA-seq_dcr1rnh12_rep2


title: B24_SPF_F124_DJ_1

description: Library name: 20220821_ENS_OVA_124_SPF_B24_SPF_F124_DJ_1


title: B25_SPF_M122_DJ_2

description: Library name: 20220823_ENS_OVA_SPF_122_SPF_B25_SPF_M122_DJ_2

value: M


title: dcr1rnh12_H2AX_rep2


title: sRNA-seq_WT_rep2


title: Opa1KO_Treg_rep1


title: WT control_Treg_rep4

value: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells sorted from WT mixed BM chimera


title: WT_H2AX_rep2


title: B28_OVAc_F65_DJ_3

description: Library name: 20220820_ENS_OVA_65_OVAc_B28_OVAc_F65_DJ_3

value: OVAc


title: WT control_Treg_rep3


title: dcr1rnh12_H2A_rep2


title: WT control_Treg_rep2


title: dcr1_H2A_rep2


title: B28_OVAc_F65_DJ_2

description: Library name: 20220820_ENS_OVA_65_OVAc_B28_OVAc_F65_DJ_2


title: B28_OVAc_F65_DJ_1

description: Library name: 20220820_ENS_OVA_65_OVAc_B28_OVAc_F65_DJ_1


title: dcr1rnh12_input_rep1


title: Opa1KO_Treg_rep3


title: dcr1_input_rep1


title: WT_input_rep2


title: B26_OVAc_M103_ileum_1

description: Library name: 20220819_ENS_OVA_103_OVAc_B26_OVAc_M103_ileum_1

value: Ileum


title: B26_OVAc_M102_ileum_3

description: Library name: 20220819_ENS_OVA_102_OVAc_B26_OVAc_M102_ileum_3


title: FlcnKO_Treg_rep4

data_processing:
Reads were trimmed for adaptors and low-quality reads by Trimmomatic (v0.36) and aligned to mouse genome mm10 by BWA (v0.7.16).
Duplicated reads were then marked with Picard (v2.9.4) and only non-duplicated proper paired reads were kept by Samtools (v1.9, parameter: -q 1 -F 1804).
After adjustment of the Tn5 shift (reads were offset by +4 bp for the sense strand and –5 bp for the antisense strand), reads were separated into nucleosome-free reads.
Next, peaks were called on nucleosome-free reads by MACS2 (v2.1.1, parameter: –extsize 200– nomodel). To assure reproducibility, we finalized nucleosome-free regions for each sample and retained a peak only if called with a higher cutoff (MACS2 –q 0.05). Consensus peaks were generated by keeping peaks present in at least 50% of replicates and discarding the remaining non-reproducible peaks. Reproducible peaks were further merged among samples if they overlapped by 100 bp and nucleosome-free reads were counted by bedtools (v2.25.0).
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples.

growth_protocol: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera and Foxp3CreFlcnfl/fl mixed BM chimera mice (n = 4 biological replicates per group).

treatment_protocol: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells from mixed BM chimera.

value: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells

value: Flcn KO

value: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells sorted from Foxp3CreFlcnfl/fl mixed BM chimera


title: rnh12_input_rep1

value: yeast cells

value: rnh1 rnh201


title: WT_input_rep1

value: WT


title: dcr1rnh12_H2AX_rep1

value: dcr1 rnh1 rnh201


title: B28_OVAc_F65_DJ_4

description: Library name: 20220820_ENS_OVA_65_OVAc_B28_OVAc_F65_DJ_4

value: F


title: dcr1_H2AX_rep2


title: rnh12_H2AX_rep2


title: FlcnKO_Treg_rep3

value: Spleen


title: B26_OVAc_M102_ileum_2

description: Library name: 20220819_ENS_OVA_102_OVAc_B26_OVAc_M102_ileum_2


title: rnh12_H2AX_rep1


title: WT_H2AX_rep1


title: FlcnKO_Treg_rep2

value: Primary mouse Treg cells


title: WT_H2A_rep2


title: rnh12_H2A_rep2


title: dcr1rnh12_H2A_rep1


title: FlcnKO_Treg_rep1


title: dcr1_H2A_rep1


title: WT_Treg_rep4


title: WT control_Treg_rep1


title: B27_Btheta_Colon_M3807_1

description: Library name: 20220816_ENS_OVA_3807_BT_B27_Btheta_Colon_M3807_1

value: Colon

value: BT


title: WT_H2A_rep1


title: RNA-seq_dcr1 rnh1 rnh201, rep 2

data_processing:
The reads were trimmed using cutadapt and quantified using Salmon, using transcriptome annotation data from PomBase.
Assembly: ASM294v2
Supplementary files format and content: Raw quantification output from Salmon for each sample.

growth_protocol: All cultures were grown at 30°C in standard media with supplement (YES) and harvested at mid-log phase.

extract_protocol:
Total RNA was purified from mid-log phase cells using Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions, including the use of ZR BashingBead Lysis Tubes to lyse open the cells in TRI Reagent. DNA was removed using DNase I (Zymo Research) and purified using RNA Clean & Concentrator (Zymo Research).
Ribosomal RNAs were depleted using RiboMinus Transcriptome Isolation Kit, Yeast (Invitrogen), and libraries were made using NEBNext Ultra II Directional RNA Library Prep Kit (NEB).


title: B27_ASF_Colon_M3805_1

description: Library name: 20220816_ENS_OVA_3805_ASF_B27_ASF_Colon_M3805_1

value: enteric neuron

value: ASF


title: WT_Treg_rep3

value: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells sorted from WT mixed BM chimera


title: RNA-seq_dcr1 rnh1 rnh201, rep 1


title: WT_Treg_rep2


title: RNA-seq_dcr1, rep2


title: B31_OVAs_Msense3_ileum_1

description: Library name: 20220815_ENS_OVA_OVASense3_OVAs_B31_OVAs_Msense3_ileum_1

value: M

value: OVAs


title: RNA-seq_dcr1, rep1


title: RNA-seq_rnh1 rnh201, rep 2


title: dcr1_H2AX_rep1


title: B31_OVAs_Msense1_ileum_1

description: Library name: 20220815_ENS_OVA_OVASense1_OVAs_B31_OVAs_Msense1_ileum_1

value: Ileum


title: RNA-seq_rnh1 rnh201, rep 1


title: B26_OVAc_M102_ileum_1

description: Library name: 20220819_ENS_OVA_102_OVAc_B26_OVAc_M102_ileum_1

value: OVAc


title: WT_Treg_rep1

value: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells


title: dcr1-K38A, rep 2

data_processing:
Reads were processed and filtered using fastp v.0.23.4
Processed reads were mapped with Bowtie2 v.2.4.2, and clipped to the 5’ position using Bedtools v.2.29.2 to map the position of Pol II at nucleotide resolution.
The resulting BedGraph file was normalized by the total amount of reads and converted to normalized BigWig using DeepTools v.3.5.0.
Assembly: ASM294v2
Supplementary files format and content: Normalized bigwig file
Library strategy: PRO-seq

extract_protocol:
Cell permeabilization, run-on, and RNA extraction were performed following Mahat et al. 2016 Nature Protocols. Total RNA was extracted using hot phenol approach as described. The RNA was base hydrolyzed and excess unincorporated biotin-NTPs were removed before undergoing on-bead library prep.
On-bead library prep was performed following the instructions on Judd et al. 2020, Biorxiv (https://www.biorxiv.org/content/10.1101/2020.05.18.102277v1.abstract)

value: yeast cells


title: RNA-seq_WT, rep 1


title: rnh12_H2A_rep1

value: rnh1 rnh201


title: B10006_GF_Col_M3631_3

description: Library name: 20220615_ENS_GF_3631_GF_B10006_GF_Col_M3631_3

value: GF


title: dcr1-K38A, rep 1


title: B27_OVAc_M103_ileum_2

description: Library name: 20220816_ENS_OVA_103_OVAc_B27_OVAc_M103_ileum_2


title: dcr1-K38R, rep 2


title: Bruceine A  treatment 5

city: Taipa

first: Huating

last: Hu

address: Avenida WaiLong

country: China

institute: Macau University of Science and Technology

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

organism: Rattus norvegicus

source_name: Kidney

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

treatment_protocol: The anti-Thy1 nephritis model group and the healthy control group were given intraperitoneal injection of normal saline, BA treatment group was given intraperitoneal injection of Bruceine A, and the Olmesartan group was given oral administration of Olmesartan

value: Kidney

value: Bruceine A


title: Bruceine A  treatment 4


title: dcr1-K38R, rep 1


title: B10006_GF_Col_M3631_2

description: Library name: 20220615_ENS_GF_3631_GF_B10006_GF_Col_M3631_2


title: dcr1 rpb1-T481K, rep 2


title: dcr1 rpb1-T481K, rep 1


title: rpb1-T481K, rep 2


title: B10006_GF_Col_M3631_1

description: Library name: 20220615_ENS_GF_3631_GF_B10006_GF_Col_M3631_1


title: Bruceine A  treatment 2


title: B22_SPF_M1_ileum_4

description: Library name: 20220414_ENS_SPF_122_SPF_B22_SPF_M1_ileum_4

value: SPF


title: dcr1 rnh1 rnh201 med20-1, rep 3


title: RNA-seq_WT, rep 2

value: WT


title: Bruceine A  treatment 1


title: rpb1-T481K, rep 1


title: Bruceine A  treatment 6


title: dcr1 rnh1 rnh201 med20-1, rep 2


title: dcr1 rnh1 rnh201 med20-1, rep 1


title: Olmesartan treatment 6

value: Olmesartan


title: dcr1 med20-1, rep 3

value: dcr1 med20-1


title: B10006_GF_Col_M3631_4

description: Library name: 20220615_ENS_GF_3631_GF_B10006_GF_Col_M3631_4

value: Colon

value: enteric neuron


title: B22_SPF_M1_ileum_3

description: Library name: 20220414_ENS_SPF_122_SPF_B22_SPF_M1_ileum_3


title: B22_SPF_M1_ileum_2

description: Library name: 20220414_ENS_SPF_122_SPF_B22_SPF_M1_ileum_2


title: Olmesartan treatment 5


title: Olmesartan treatment 4


title: dcr1 med20-1, rep 1


title: B23_SPF_F1_ileum_2

description: Library name: 20220414_ENS_SPF_OVA_124_SPF_B23_SPF_F1_ileum_2

value: F


title: med20-1, rep 3


title: med20-1, rep 1


title: med20-1, rep 2


title: B22_SPF_M1_ileum_1

description: Library name: 20220414_ENS_SPF_122_SPF_B22_SPF_M1_ileum_1

value: M


title: Olmesartan treatment 3


title: Bruceine A  treatment 3


title: dcr1 rnh1 rnh201, rep 3


title: B23_SPF_F1_ileum_1

description: Library name: 20220414_ENS_SPF_OVA_124_SPF_B23_SPF_F1_ileum_1


title: dcr1 rnh1 rnh201, rep 2


title: dcr1 rnh1 rnh201, rep 1


title: Olmesartan treatment 2


title: B23_OVAs_M3_ileum_2

description: Library name: 20220414_ENS_SPF_OVA_OVASense3_OVAs_B23_OVAs_M3_ileum_2

value: OVAs


title: rnh1 rnh201, rep 2


title: B23_OVAs_M3_ileum_1

description: Library name: 20220414_ENS_SPF_OVA_OVASense3_OVAs_B23_OVAs_M3_ileum_1

value: Ileum


title: rnh1 rnh201, rep 1


title: dcr1 med20-1, rep 2


title: rnh1 rnh201, rep 3


title: healthy control 6

value: normal saline


title: B10005_SPF_Col_F13_2

description: Library name: 20220411_ENS_GF_SPF_13_SPF_B10005_SPF_Col_F13_2


title: B10005_SPF_Col_F13_1

description: Library name: 20220411_ENS_GF_SPF_13_SPF_B10005_SPF_Col_F13_1


title: dcr1, rep3


title: healthy control 4


title: Olmesartan treatment 1


title: dcr1, rep1


title: WT, rep 7


title: dcr1, rep2


title: healthy control 3


title: B10005_GF_Col_M3613_1

description: Library name: 20220411_ENS_GF_SPF_3613_GF_B10005_GF_Col_M3613_1


title: WT, rep 6


title: WT, rep 5


title: dcr1, rep4


title: healthy control 5


title: B21_OVAs_M2_ileum_1

description: Library name: 20220406_ENS_OVA_OVASense2_OVAs_B21_OVAs_M2_ileum_1


title: WT, rep 3


title: WT, rep 4


title: B21_OVAs_M1_ileum_1

description: Library name: 20220406_ENS_OVA_OVASense1_OVAs_B21_OVAs_M1_ileum_1


title: healthy control 1


title: WT, rep 2


title: dcr1, rep5


title: WT, rep 1


title: B21_OVAc_F68_ileum_1

description: Library name: 20220406_ENS_OVA_68_OVAc_B21_OVAc_F68_ileum_1

value: OVAc


title: anti-Thy1 nephritis model 6


title: anti-Thy1 nephritis model 5


title: dcr1rnh12_rep2

data_processing:
Demultiplexed reads were first trimmed with cutadapt v3.4 before mapping to the genome using Bowtie2 2.4.2. Reads were remapped into the first nucleotide using bedtools v.2.29.2, before converted to sorted bam files using Samtools, which were then used to generate normalized tracks using deepTools v3.5.0.
Assembly: ASM294v2
Supplementary files format and content: Normalized bigwig file, merging multiple replicates
Library strategy: GLOE-seq

extract_protocol:
high molecular weight DNA was extracted as described Sriramachandran et al, 2020 Mol Cell.
GLOE-seq libraries were prepared as described (Sriramachandran et al, 2020 Mol Cell) except Zymolyase 100T was used instead of 20T for a more efficient spheroplasting.

value: yeast cells

value: dcr1 rnh1 rnh201


title: dcr1_rep2


title: rnh12_rep2

value: rnh1 rnh201


title: B21_OVAc_F66_ileum_1

description: Library name: 20220406_ENS_OVA_66_OVAc_B21_OVAc_F66_ileum_1


title: anti-Thy1 nephritis model 4

value: Kidney


title: WT_rep2


title: dcr1rnh12_rep1


title: B10005_GF_Col_F3616_1

description: Library name: 20220411_ENS_GF_SPF_3616_GF_B10005_GF_Col_F3616_1

value: GF


title: B20_OVAc_F65_ileum_5

description: Library name: 20220402_ENS_OVA_65_OVAc_B20_OVAc_F65_ileum_5


title: healthy control 2


title: dcr1_rep1


title: anti-Thy1 nephritis model 2


title: WT_rep1


title: B20_OVAc_F65_ileum_4

description: Library name: 20220402_ENS_OVA_65_OVAc_B20_OVAc_F65_ileum_4


title: B20_OVAc_F65_ileum_3

description: Library name: 20220402_ENS_OVA_65_OVAc_B20_OVAc_F65_ileum_3


title: rnh12_rep1


title: anti-Thy1 nephritis model 3


title: sample_28

type: genomic

city: Guangzhou

first: Wei

last: Tang

state: Guangdong

address: Zhongshan 2nd Street, No. 58

department: Center of Gastrointestinal Surgery

institute: First Affiliated Hospital of Sun Yat-sen University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Standard Illumina Protocol.

data_processing:
ChAMP package in R was used for quality control, probe filtering, BMIQ normalization, batch effect correction (SVA, ComBat), and CpG annotation (EPICanno.ilm10b4.hg19). After preprocessing, the methylation dataset contained 726,710 probes and 30 samples.
*processed value definition: Average β value

label: Cy3 and Cy5

organism: Homo sapiens

source_name: primary tumor

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted from FFPE tissue using Tissue Kit (Qiagen) according to standard instructions.

value: primary tumor

value: R

tag: subject status

value: patients with advanced gastric cancer


title: sample_30

value: NR


title: anti-Thy1 nephritis model 1


title: sample_29


title: B20_OVAc_F65_ileum_2

description: Library name: 20220402_ENS_OVA_65_OVAc_B20_OVAc_F65_ileum_2


title: sample_27


title: sample_25


title: B19_OVAc_M64_ileum_3

description: Library name: 20220401_ENS_OVA_64_OVAc_B19_OVAc_M64_ileum_3


title: sample_24


title: D6 KDR+ rep1

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description:
ETV2-overexpressed fibroblast
Ad.rEC.D6.Sorted.KDR_minus.1

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to human genome by Tophat2 (v2.1.1)
Gene expression value was estimated by Cufflinks (v2.2.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene expression values for each sample

source_name: HDF

growth_protocol: Human fibroblast cells were converted into endothelial-like cells with ETV2 overexpression.

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HDF

value: Fibroblast

tag: time

value: Day 6

tag: sort

value: KDR+

tag: induction


title: D6 KDR+ rep2

description:
ETV2-overexpressed fibroblast
Ad.rEC.D6.Sorted.KDR_minus.2


title: sample_26


title: D6 KDR- rep2

description:
ETV2-overexpressed fibroblast
Ad.rEC.D6.Sorted.KDR_plus.2

value: KDR-


title: sample_21


title: sample_23


title: B19_OVAc_M64_ileum_2

description: Library name: 20220401_ENS_OVA_64_OVAc_B19_OVAc_M64_ileum_2

value: Ileum

value: enteric neuron

value: M


title: B19_OVAc_M64_ileum_1

description: Library name: 20220401_ENS_OVA_64_OVAc_B19_OVAc_M64_ileum_1

value: OVAc


title: D6 KDR- rep1

description:
ETV2-overexpressed fibroblast
Ad.rEC.D6.Sorted.KDR_plus.1


title: sample_19


title: D6 rep2

description:
ETV2-overexpressed fibroblast
Ad.rEC.D6.Presorted.2


title: sample_20


title: sample_22


title: sample_18


title: B19_OVAc_F65_ileum_1

description: Library name: 20220401_ENS_OVA_65_OVAc_B19_OVAc_F65_ileum_1

value: F


title: sample_17


title: sample_14


title: B18_OVA_F65_1

description: Library name: 20220108_ENS_OVA_65_OVAc_B18_OVA_F65_1


title: sample_16


title: sample_13


title: D6 rep1

description:
ETV2-overexpressed fibroblast
Ad.rEC.D6.Presorted.1


title: sample_15


title: D4 rep2

description:
ETV2-overexpressed fibroblast
Ad.rEC.D4.2

value: Day 4


title: B18_OVA_F65_2

description: Library name: 20220108_ENS_OVA_65_OVAc_B18_OVA_F65_2


title: D4 rep1

description:
ETV2-overexpressed fibroblast
Ad.rEC.D4.1


title: sample_12


title: B17_OVA_M4_1

description: Library name: 20211218_ENS_OVA_63_OVAc_B17_OVA_M4_1


title: sample_11


title: D1.5 rep2

description:
ETV2-overexpressed fibroblast
Ad.rEC.D1.5.2

value: Day 1.5


title: sample_10


title: sample_8


title: sample_9


title: B17_OVA_M3_3

description: Library name: 20211218_ENS_OVA_62_OVAc_B17_OVA_M3_3


title: D1.5 rep1

description:
ETV2-overexpressed fibroblast
Ad.rEC.D1.5.1


title: sample_7


title: B17_OVA_M3_2

description: Library name: 20211218_ENS_OVA_62_OVAc_B17_OVA_M3_2


title: D0 rep2

description:
ETV2-overexpressed fibroblast
Ad.rEC.D0.2

value: Day 0


title: B17_OVA_M3_1

description: Library name: 20211218_ENS_OVA_62_OVAc_B17_OVA_M3_1


title: sample_5

value: primary tumor


title: B18_OVA_F66_1

description: Library name: 20220108_ENS_OVA_66_OVAc_B18_OVA_F66_1


title: sample_6

value: R


title: sample_4

value: patients with advanced gastric cancer


title: sample_2


title: sample_1


title: B10004_Btheta_M3807_colon_1

description: Library name: 20211123_ENS_Pool3_3807_BT_B10004_Btheta_M3807_colon_1

value: Colon

value: BT


title: B16_HPneg_F1_ileum_3

description: Library name: 20211123_ENS_Pool3_1_HP_neg_B16_HPneg_F1_ileum_3


title: D0 rep1

description:
ETV2-overexpressed fibroblast
Ad.rEC.D0.1

value: HDF

value: Fibroblast


title: sample_3

value: NR


title: BRI-1986_HumanLN_GEX_HTO_Library

description: Library name: BRI-1986

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10/hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
(BRI-2314, BRI-2316, BRI-2322, BRI-2324) Live CD4+CD19-CXCR5+ cells were sorted from spleens of the NP-OVA immunized mice based on GFP and TdTomato expression into Tfr (GFP-TdTomato+) and ExTfr (GFP-TdTomato+). Cells were stained with TotalSeq-C Hashtags (Biolegend) and pooled in a single sample before loading.
(BRI-2146, BRI-2148) Live CD4+CD19-CXCR5+GITR+ Tfr cells were sorted from the inguinal lymph nodes of the NP-OVA immunized mice. Cells were stained with TotalSeq-C Hashtags (Biolegend) and pooled in a single sample before loading.
(BRI-1986) Live CD4+CD19-CXCR5+ cells were isolated by FACS-sort from cryopreserved human peripheral blood mononuclear cells (n=3) and iliac lymph node mononuclear cells  (n=3) obtained from six different donors.
Cells were resuspended in 0.4% BSA in PBS at a concentration of 2,000 cells per μl, then loaded onto a single lane (Chromium chip K, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′kit V2, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. 5’ mRNA library was sequenced to an average of 50,000 reads per cell, V(D)J library and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, all using Illumina Novaseq.

value: Lymph node

value: Human CD4 T cell


title: RNA-seq of meningioma control dura 1

city: Shanghai

first: Guanghui

state: Shanghai

address: NO.1279 Sanmen Road

department: Plastic and Reconstructive Surgery

institute: The Affiliated Shanghai Fourth People's Hospital of Tongji University

description:
Library name: Lib_Ctrl_001
Bulk RNA-seq of normal dura mater

data_processing:
Raw reads were quality-checked (FastQC/MultiQC), aligned to GRCh38 using STAR v2.7.11b, and quantified via featureCounts v2.0.7 to generate FPKM values.
Assembly: GRCh38 (hg38) primary assembly with GENCODE v35 annotations.
Supplementary files format and content: Tab-delimited FPKM matrix (SYMBOL Gene names × Sample IDs) containing all protein-coding genes.

source_name: Dura mater

extract_protocol:
RNA was extracted from 4-5μm FFPE sections using SHBIO RNA purification kit (#72302-50), followed by quality control (Agilent Bioanalyzer), RNAClean XP cleanup, and DNase treatment (QIAGEN #79254).
200ng total RNA was used for strand-specific library prep with SMARTer Stranded Total RNA-seq Kit v2 (Takara #634412), including poly-A selection and dual-indexing, with final libraries (300-400bp) validated on Agilent Bioanalyzer.

value: Dura mater

value: normal cells


title: RNA-seq of primary WHO G3 meningioma 3

description:
Library name: Lib_Primary_G3_003
Bulk RNA-seq of tumor (anaplastic subtype)

source_name: Meningioma

value: Meningioma

value: tumor cells


title: B15_ASF_M2_ileum_1

description: Library name: 20211123_ENS_Pool2_3806_ASF_B15_ASF_M2_ileum_1

value: Ileum

value: enteric neuron

value: M

value: ASF


title: B15_ASF_M2_ileum_2

description: Library name: 20211123_ENS_Pool2_3806_ASF_B15_ASF_M2_ileum_2


title: RNA-seq of primary WHO G3 meningioma 2

description:
Library name: Lib_Primary_G3_002
Bulk RNA-seq of tumor (papillary subtype)


title: B14_GF_M2_ileum_5

description: Library name: 20211123_ENS_Pool1_3613_GF_B14_GF_M2_ileum_5

value: GF


title: RNA-seq of primary WHO G3 meningioma 1

description:
Library name: Lib_Primary_G3_001
Bulk RNA-seq of tumor (rhabdoid subtype)


title: CUT&RUN_ALP_NFIL3-HA, rep2

description:
Library name: 26_ALP_HA
ALP_NFIL3-HA_2

data_processing:
Base calling was performed directly by sequencing facility using phred-33 standard quality scores
Duplicates reads were eliminated from raw FASTQ files using Clumpify (BBMap 39.00) and adapter sequences and low-quality reads were removed using Trimmomatic (0.39)
Remaining reads were mapped to mouse genome (mm39) using Bowtie2 (2.5.1), and reads with MAPQ score<10 were filtered out using Samtools (2.23.5)
Peak calling was done with HOMER (4.11) on merged samples while using NFIL3-neg samples as control input
Peaks were annotated using HOMER (4.11) with Ensembl GTF (mm39 release 108)
Assembly: mm39
Supplementary files format and content: Tab-delimited annotated peak table generated by HOMER
Library strategy: CUT&RUN

extract_protocol:
Genomic DNA fragments were extracted using CUTANA ChIC/CUT&RUN Kit Version 3 (EpiCypher) with anti-HA antibody after nuclei extraction
Librairies were prepared using MGIEasy Universal DNA Library Prep Set

treatment_protocol: Treated cells were transduced and cultured on irradiated OP9 stromal layers in α-MEM media supplemented with 5% fetal bovine serum, glutamine, penicillin and streptomycin. All cultures were supplemented with mouse stem cell factor, mouse Flt3-ligand and mouse IL-7 at 30 ng.ml−1. For transduction, retroviral supernatant and polybrene (4 ng.ml−1, Sigma-Aldrich) were added to the cells, and centrifuged for 2 hours at 32°C, 2000rpm

tag: strain background

value: Bone Marrow

value: All Lymphoid Progenitor

value: NFIL3-HA-Thy1.1-transduced + 2 days culture

value: Thy1.1+ Mac1-


title: B14_GF_F1_ileum_4

description: Library name: 20211123_ENS_Pool1_3816_GF_B14_GF_F1_ileum_4

value: F


title: RNA-seq of recurrent WHO G2 meningioma 1

description:
Library name: Lib_Recur_G2_001
Bulk RNA-seq of recurrent tumor (chordoid subtype)


title: RNA-seq of recurrent WHO G2 meningioma 2

description:
Library name: Lib_Recur_G2_002
Bulk RNA-seq of recurrent tumor (atypical with bizarre nuclei)


title: RNA-seq of primary WHO G2 meningioma 3

description:
Library name: Lib_Primary_G2_003
Bulk RNA-seq of tumor (atypical subtype)


title: RNA-seq of primary WHO G2 meningioma 1

description:
Library name: Lib_Primary_G2_001
Bulk RNA-seq of tumor (atypical subtype)


title: SEA102

city: Seattle

first: Jesse

last: Bengtsson

state: WA

address: 720 Broadway

institute: Pacific Northwest Research Institute

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

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 12.1.1.1)

data_processing: Agilent Feature Extraction Software (version 12.1.1.1) was used for background subtraction and normalization.

source_name: Whole Blood Extracted Genomic DNA from SEA102

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C, 65°C for 20 minutes. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from either peripheral blood or LCLs with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

value: Female

value: whole blood

source_name: Genomic DNA extracted from Male LCL GM12156

value: Male

tag: reference

value: Reference Sample


title: CUT&RUN_ALP_NFIL3-HA, rep1

description:
Library name: 25_ALP_HA
ALP_NFIL3-HA_1

tag: genotype/variation

tag: tissue


title: RNA-seq of recurrent WHO G1 meningioma 2

description:
Library name: Lib_Recur_G1_002
Bulk RNA-seq of recurrent tumor (meningothelial subtype)

tag: cell type


title: B14_Btheta_M2_ileum_2

description: Library name: 20211123_ENS_Pool1_3808_BT_B14_Btheta_M2_ileum_2

tag: treatment

value: BT


title: SEA103

source_name: Whole Blood Extracted Genomic DNA from SEA103

source_name: Genomic DNA extracted from Male LCL GM10851


title: RNA-seq of primary WHO G2 meningioma 2

description:
Library name: Lib_Primary_G2_002
Bulk RNA-seq of tumor (mixed meningothelial-fibrous)

value: Meningioma


title: B14_Btheta_M2_ileum_1

description: Library name: 20211123_ENS_Pool1_3808_BT_B14_Btheta_M2_ileum_1

tag: batch


title: CUT&RUN_ALP_NFIL3-neg, rep2

description:
Library name: 24_ALP_NF
ALP_NFIL3-neg_2

value: NFIL3-Thy1.1-transduced + 2 days culture

tag: sorting profile


title: RNA-seq of recurrent WHO G1 meningioma 1

description:
Library name: Lib_Recur_G1_001
Bulk RNA-seq of recurrent tumor (meningothelial-angiomatous)

value: tumor cells


title: CUT&RUN_ALP_NFIL3-neg, rep1

description:
Library name: 23_ALP_NF
ALP_NFIL3-neg_1


title: RNA-seq of primary WHO G1 meningioma 2

description:
Library name: Lib_Primary_G1_002
Bulk RNA-seq of tumor (meningothelial subtype)


title: B13_HPneg_M1_ileum_4

description: Library name: 20211030_ENS_Pool3_3_HP_neg_B13_HPneg_M1_ileum_4

value: Ileum

value: enteric neuron

tag: Sex

tag: mouse id


title: RNA-seq of primary WHO G1 meningioma 1

description:
Library name: Lib_Primary_G1_001
Bulk RNA-seq of tumor (meningothelial subtype)


title: RNA-seq of primary WHO G1 meningioma 3

description:
Library name: Lib_Primary_G1_003
Bulk RNA-seq of tumor (fibrous subtype)


title: RL-P0-1

first: jingyu

last: Ma

address: No. 7 Jinsui Rd

institute: SUN YAT-SEN UNIVERSITY

description: Library name: RL-P0-1

data_processing:
lumina Bcl2FastQ software used for basecalling
Sequenced reads were trimmed for adaptor seguence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11 .2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: hg38
Supplementary files format and content: excel file includes normalized counts for all sample

source_name: ROR1+ cells

extract_protocol:
Total RNA was extracted from ROR1+ cells using TRIzol reagent (15596-018; Thermo Fisher, USA). The analysis was performed with 3 biological replicates. The RNA was quantified via the K5500 system (Beijing Kaiao, China), and RNA integrity was assessed via the Agilent 2200 TapeStation (Agilent Technologies, USA).
The sequencing libraries were generated via the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (#7775, NEB, USA) following the manufacturer's instructions.

value: ROR1+ cells


title: RL-P0-3

description: Library name: RL-P0-3


title: TOX_KO, batch4, rep2

description:
Library name: TOX_KO2
TOX_KO_2_4

data_processing:
Base calling was performed directly by sequencing facility using phred-33 standard quality scores
Adapter sequences and low-quality reads were removed using SOAPnuke directly after FASTQ generation by the sequencing facility
Estimation of levels of gene expression from FASTQ files was performed using RSEM (1.3.2) by alignment to the mouse genome (mm39) using STAR (2.7.10b) with Ensembl GTF (release 108)
Gene expression changes and statistics were realized using Limma-Voom (edgeR 3.36.0), with quantile normalization
Assembly: mm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes counts after quantile normalization and batch effect removal, average expressions by conditions, and results of statistical analysis by Limma-Voom (logFC, pval, padj)

extract_protocol:
RNA was extracted by RNeasy Plus Micro Kits (Qiagen)
Messenger RNA-Seq libraries were prepared using a SMART-SeqII combined with transposase-based library construction, libraries were circularized, and sequencing was executed by DNA Nanoballs (DNBTM™) technology

treatment_protocol: Cells were transduced and cultured on irradiated OP9 stromal layers in α-MEM media supplemented with 5% fetal bovine serum, glutamine, penicillin and streptomycin. All cultures were supplemented with mouse stem cell factor, mouse Flt3-ligand and mouse IL-7 at 30 ng.ml−1. For transduction, retroviral supernatant and polybrene (4 ng.ml−1, Sigma-Aldrich) were added to the cells, and centrifuged for 2 hours at 32°C, 2000rpm

value: Tcf7YFP+ Nfil3-KO

value: TOX-GFP-transduced + 4 days culture

value: Mac1- GFP+


title: RL-P0-2

description: Library name: RL-P0-2


title: B13_GF_M1_ileum_3

description: Library name: 20211030_ENS_Pool3_3608_GF_B13_GF_M1_ileum_3

data_processing:
Demultiplex and basecall to fastq with bcl2fastq
FASTQ reads were aligned to the mm10 mouse transcriptome
Alignment with STAR
Counting of transcripts with RSEM
Assembly: mm10
Supplementary files format and content: ens_raw_geo_upload.h5ad: Anndata object of  gene counts of genes quantified by RSEM before processing
Supplementary files format and content: ens_atlas_geo_upload.h5ad: Anndata object of  ENS atlas based on Smart-seq2

extract_protocol:
RNA lysate clean-up was performed using RNAClean XP beads (A63987, Beckman Coulter, CA, USA) followed by reverse transcription with Maxima H minus Reverse Transcriptase (EP0743, Thermo Fisher Scientific, MA, USA) and whole-transcription amplification (WTA) with KAPA HotStart HIFI 2 × ReadyMix (07958927001, Roche, Switzerland) for 21 cycles. WTA products were purified with Ampure XP beads (A63881, Beckman Coulter, CA, USA), quantified with Qubit dsDNA HS Assay Kit (Q32854, Thermo Fisher, MA, USA) and assessed with D5000 screentape on a 2200 Agilent TapeStation system (5067-5588, 5067-5589, Agilent, CA, USA). Diluted WTA products underwent tagmentation and indexing using the Nextera XT DNA Library Preparation Kit (FC-131-1096, Illumina, CA, USA), followed by size selection with Ampure XP beads. Size and concentration were then assessed with D1000 screentape (5067-5582, 5067-5583, Agilent, CA, USA) on 2200 Agilent TapeStation system.
Libraries from four 96-well plates were pooled together and sequenced with the Illumina NextSeq 500/550 75-cycle high output kit (20024906, Illumina, CA, USA) on a NextSeq 500/550 system.

value: M

value: GF

tag: batch label

tag: plate label


title: SKOV3-gMETTL5_5-C

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
Data were quantified as transcripts per million reads mapped (TPM) using kallisto
Assembly: GRCh38
Supplementary files format and content: Excel file includes TPM values for each sample

extract_protocol:
RNAs were extracted from cells in triplicate using a Direct-zol RNA Miniprep Plus kit per manufactuer's instructions
Poly-A RNA libraries for RNA-seq were prepared by Novogene company

treatment_protocol: Cas9-expressing cells were transduced with either non-targeting control gRNA or gRNAs targeting METTL5(human)/Mettl5(mouse). After selection, cell lines with verified Mettl5 knockout were used for RNAseq

tag: cell line

value: Ovarian cancer cell line

tag: replicate

value: C

value: METTL5 sgRNA5


title: TOX_KO, batch4, rep1

description:
Library name: TOX_KO1
TOX_KO_1_4

value: Bone Marrow

value: All Lymphoid Progenitor


title: SEA101

source_name: Whole Blood Extracted Genomic DNA from SEA101

value: Female

value: whole blood

value: Male

value: Reference Sample


title: SKOV3-gMETTL5_5-B

value: B


title: B13_ASF_M1_ileum_4

description: Library name: 20211030_ENS_Pool3_3805_ASF_B13_ASF_M1_ileum_4

value: Ileum

value: enteric neuron

value: ASF


title: TOX_KO, batch4, rep3

description:
Library name: TOX_KO3
TOX_KO_3_4

value: Tcf7YFP+ Nfil3-KO

value: TOX-GFP-transduced + 4 days culture


title: SKOV3-gMETTL5_5-A

value: A


title: TOX_WT, batch4, rep3

description:
Library name: TOX_WT3
TOX_WT_3_4

value: Mac1- GFP+


title: SKOV3-gMETTL5_3-C

value: Ovarian cancer cell line

value: METTL5 sgRNA3


title: TOX_WT, batch4, rep1

description:
Library name: TOX_WT1
TOX_WT_1_4


title: B12_HPneg_M1_ileum_3

description: Library name: 20211030_ENS_Pool2_3_HP_neg_B12_HPneg_M1_ileum_3

value: M


title: B12_HPneg_M1_ileum_2

description: Library name: 20211030_ENS_Pool2_3_HP_neg_B12_HPneg_M1_ileum_2


title: SKOV3-gMETTL5_3-A


title: SKOV3-gMETTL5_3-B


title: GFP_KO, batch4, rep3

description:
Library name: GFP_KO3
GFP_KO_3_4

value: Bone Marrow

value: GFP-transduced + 4 days culture


title: B13_BT_M1_ileum_4

description: Library name: 20211030_ENS_Pool3_3807_BT_B13_BT_M1_ileum_4

value: BT


title: SKOV3-gNC-C

value: C

value: Control sgRNA


title: B12_GF_M2_ileum_4

description: Library name: 20211030_ENS_Pool2_3613_GF_B12_GF_M2_ileum_4

value: GF


title: B12_HPneg_M1_ileum_1

description: Library name: 20211030_ENS_Pool2_3_HP_neg_B12_HPneg_M1_ileum_1


title: GFP_KO, batch4, rep2

description:
Library name: GFP_KO2
GFP_KO_2_4

value: All Lymphoid Progenitor


title: ACTCA_03

city: Helsinki

first: Christopher

middle: B.

last: Jackson

state: - Select -

address: Hartmanninkatu 8

department: Department of Biochemistry and Developmental Biology

country: Finland

institute: University of Helsinki, Faculty of Medicine

library_source: other

data_processing:
quality control (PHRED >20)
trimmed sequence reads where mapped to gRNA table
Read count extraction
MAGeCK-MLE
Assembly: n/a
Supplementary files format and content: tab-delimited text file including count table
Library strategy: PCR amplicon sequencing

molecule: other

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), glutamine, pyruvate, uridine and antibiotics in 5% CO2 at 37°C.

extract_protocol:
Nucleospin blood XL
Column-purified PCR samples were sequenced using PCR-free library preparation

treatment_protocol: treatment encompassed low-dose treatment of indicated drugs or ETOH as control over 15-days.

value: human embryonic kidney

value: ACTCAP


title: GFP_KO, batch4, rep1

description:
Library name: GFP_KO1
GFP_KO_1_4


title: ACTCA_01


title: ACTCA_02


title: B11_GF_M2_ileum_3

description: Library name: 20211030_ENS_Pool1_3613_GF_B11_GF_M2_ileum_3

value: Ileum

value: enteric neuron


title: SKOV3-gNC-A


title: GFP_WT, batch4, rep3

description:
Library name: GFP_WT3
GFP_WT_3_4


title: SKOV3-gNC-B

value: B


title: CAP_01

value: CAP


title: CAP_03


title: GFP_WT, batch4, rep2

description:
Library name: GFP_WT2
GFP_WT_2_4

value: Mac1- GFP+


title: Twist KO neoplasm

city: Vienna

first: Patricio

last: Ferrer Murguia

state: Vienna

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

description: Library name: Nv_twistKO_neoplasm

data_processing:
Sequencing reads were mapped to the Nematostella vectensis genome (Zimmermann et al. 2023) using standard parameters of Cellranger v7.1.0 (Zheng et al. 2017). Filtered matrices were then used to proceed with analysis using Seurat v5 (Butler et al. 2018; Stuart et al. 2019). Cells with low read or feature counts were excluded, and downstream analyses were performed using custom R scripts (available upon request).
Assembly: Nvec200 (https://simrbase.stowers.org/starletseaanemone)
Supplementary files format and content: Seurat object

organism: Nematostella vectensis

source_name: neoplasm

extract_protocol:
Single-cell RNA-seq libraries were prepared from dissociated Nematostella vectensis tentacle and neoplasm tissues using the 10x Genomics Chromium Single Cell 3′ v2 platform. Libraries were sequenced as paired-end reads (2 × 150 bp) on an Illumina NovaSeq 6000 instrument and processed with Cell Ranger v5.1.0.
Libraries for sequencing were prepared using the 10x Genomics Chromium Single Cell 3′ v2 pipeline for scRNA-seq according to the manufacturer’s instructions.

tag: developmental stage

value: Adult

value: neoplasm

tag: genotype

value: Twist-/-


title: CAP_02


title: B11_GF_M2_ileum_2

description: Library name: 20211030_ENS_Pool1_3613_GF_B11_GF_M2_ileum_2

value: M


title: ACT_02

value: ACT


title: TOX_WT, batch4, rep2

description:
Library name: TOX_WT2
TOX_WT_2_4

source_name: Bone Marrow

value: Bone Marrow

value: TOX-GFP-transduced + 4 days culture


title: B10_SPF_M1_ileum_1

description: Library name: 20211020_ENS_GF_77318_SPF_B10_SPF_M1_ileum_1

value: SPF


title: BRI-2148_FExDTR_TCR_Library

description: Library name: BRI-2148

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10/hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-seq

value: Lymph node

value: Mouse CD4 T cell


title: B11_HPpos_F2_ileum_7

description: Library name: 20211030_ENS_Pool1_17102_HP_pos_B11_HPpos_F2_ileum_7

value: F


title: GFP_WT, batch4, rep1

description:
Library name: GFP_WT1
GFP_WT_1_4

value: All Lymphoid Progenitor

value: GFP-transduced + 4 days culture


title: ACT_01

value: human embryonic kidney


title: B10_GF_M2_ileum_1

description: Library name: 20211020_ENS_GF_3613_GF_B10_GF_M2_ileum_1

value: Ileum

value: enteric neuron

value: GF


title: AIM-Cmax

city: Beijing

first: Wu

last: Hao

address: No.5 Yiheyuan Road Haidian District, Beijing

department: School of Life Science

institute: Pecking University

description: RNA-seq data of newly developed REWRITE-Cmax RNA cytocine base editor.

data_processing:
The raw reads (.fastq) were first processed using Trim Glore (v0.6.7) to remove adapter sequences with default parameters.
Then the trimmed data were used to remove rRNA data by Bowtie2 (v2.5.0) with key parameters –no-unal -I 1 -X 1000.
Targeted amplicon sequencing data was analyzed using the published toolkit CRlSPResso2 (v2.0.45).
The cleaned reads data were then aligned to the indexed human GRCh38 reference genome by STAR (v2.7.1a) with key parameters --outSAMstrandField intronMotif  --outFilterIntronMotifs RemoveNoncanonical.
Sanger sequencing data was analyzed using the Snapgene.
The aligned BAMs were added RG tag of sample information, sorted, indexed, stated by Samtools (v1.15.1) with default parameters. Then the processed BAMs were removed duplications by the Picard Markduplicates tool (v2.23.9) with key parameters ASO=coordinate REMOVE_DUPLICATES=true.
Then remove duplicate BAMs were used to filter reads containing clips by Samtools with default parameters. Finally, all the cleaned BAMs were downsampled to an equivalent level for subsequent analysis to ensure a fair comparison of transcriptome-wide off-targets. The uniquely mapped reads in final BAMs were used to calculate gene expression level by Cuffdiff (v2.2.1) with default parameters. Finally, we filtered the differential expression genes using cutoff |Log2FoldChange| > 1 and P-value < 0.05, based on the Cuffdiff quantification results.
genome build: The aligned hg38 genome was built with BWA using default parameters.
Supplementary files format and content: _gene_exp.diff

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured and maintained at 37 °C in DMEM medium plus additional 10% FBS.

extract_protocol:
The total RNAs were extracted using TRIzol solubilization. Following cell lysis, add chloroform to produce phase separation. Then precipitated RNA with isopropyl alcohol.
We performed reverse-transcription of 20ng total RNA as RNA-DNA hybrids, followed by tagmentation using Tn5. After fragmentation, the libraries were constructed by single-strand extension and PCR amplifications.
The construction of RNA-seq libraries followed by the TRACE-seq protocol.

treatment_protocol: Plasmid transfections into HEK293T cells were conducted with lipofectamine LTX  as the manufacturer’s instructions.

value: HEK293T cells


title: B10_BT_M1_ileum_3

description: Library name: 20211020_ENS_GF_3807_BT_B10_BT_M1_ileum_3

source_name: Ileum

value: BT


title: NT_02

value: ETOH


title: AIM-Amax_NT

description: RNA-seq data of newly developed REWRITE-Amax RNA adenine base editor with non-targeting gRNA.


title: NT_03


title: B10_ASF_M1_ileum_3

description: Library name: 20211020_ENS_GF_3805_ASF_B10_ASF_M1_ileum_3

value: M

value: ASF


title: BRI-2322_D24_GEX_HTO_Library

description: Library name: BRI-2322

source_name: Spleen

value: Spleen


title: NT_01


title: AIM-Amax

description: RNA-seq data of newly developed REWRITE-Amax RNA adenine base editor with targeting gRNA.


title: B11_ASF_M2_ileum_1

description: Library name: 20211030_ENS_Pool1_3806_ASF_B11_ASF_M2_ileum_1


title: ACT_03

value: ACT


title: B9_OVA_B6_M1_ileum_2

description: Library name: 20210824_ENS_OVA_HP_522213_OVAc_B9_OVA_B6_M1_ileum_2

value: OVAc


title: BRI-2316_D10_TCR_Library

description: Library name: BRI-2316


title: ABE8e

description: RNA-seq data of ABE-8e base editing on RNA.


title: Twist KO tentacle

description: Library name: Nv_twistKO_tentacle

source_name: tentacle

value: Adult

value: tentacle

value: twist-/-


title: BRI-2314_D10_GEX_HTO_Library

description: Library name: BRI-2314

value: Mouse CD4 T cell


title: p1_pLNA-181c

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: HEST

country: Switzerland

institute: ETH Zürich

description:
B_20
igNeuron_pLNA-181c_DEA.csv

data_processing:
Reads were mapped to GRCh38.p13 and counted with Salmon.
Differential expression analysis was performed using edgeR.
For further infos please see the methods section of the publication.
Assembly: Ensembl107
Supplementary files format and content: tab-delimited text file including logcpm values for each sample
Supplementary files format and content: tab-delimited text files including a differential expression analysis of miRNA-inhibitor treated neurons against the control samples.

source_name: Brain

growth_protocol: Differentiation of human neurons with an optimized Ngn2-overexpression protocol ("igNeurons") for 21 days.

extract_protocol:
RNA was extracted using the miRVana kit (Thermo).
RNA libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina followed by SMARTer amplification (Takara). One sample B_8, had to be excluded due to moderate degradation in the SMARTer amplification.

treatment_protocol: Treatment with in vivo ready (short) pLNA miRNA inhibitors (Qiagen) from day 9 on.

value: Brain

tag: agent

value: igNeurons

tag: differentiation

value: Differentiation p1


title: AIM-A&Cmax

description: RNA-seq data of newly developed REWRITE-A&Cmax RNA dual-functional base editor.

value: human embryonic kidney


title: p4_pLNA-181c

description:
B_19
igNeuron_pLNA-181c_DEA.csv

value: Differentiation p4


title: B9_HPpos_F2_ileum_6

description: Library name: 20210824_ENS_OVA_HP_17102_HP_pos_B9_HPpos_F2_ileum_6

value: Ileum

value: enteric neuron

value: F


title: B9_OVA_B6_M1_ileum_1

description: Library name: 20210824_ENS_OVA_HP_522213_OVAc_B9_OVA_B6_M1_ileum_1

value: M


title: AIM-A&C

data_processing:
The raw reads (.fastq) were first processed using Trim Glore (v0.6.7) to remove adapter sequences with default parameters.
Then the trimmed data were used to remove rRNA data by Bowtie2 (v2.5.0) with key parameters –no-unal -I 1 -X 1000.
Targeted amplicon sequencing data was analyzed using the published toolkit CRlSPResso2 (v2.0.45).
The cleaned reads data were then aligned to the indexed human GRCh38 reference genome by STAR (v2.7.1a) with key parameters --outSAMstrandField intronMotif  --outFilterIntronMotifs RemoveNoncanonical.
Sanger sequencing data was analyzed using the Snapgene.
The aligned BAMs were added RG tag of sample information, sorted, indexed, stated by Samtools (v1.15.1) with default parameters. Then the processed BAMs were removed duplications by the Picard Markduplicates tool (v2.23.9) with key parameters ASO=coordinate REMOVE_DUPLICATES=true.
Then remove duplicate BAMs were used to filter reads containing clips by Samtools with default parameters. Finally, all the cleaned BAMs were downsampled to an equivalent level for subsequent analysis to ensure a fair comparison of transcriptome-wide off-targets. The uniquely mapped reads in final BAMs were used to calculate gene expression level by Cuffdiff (v2.2.1) with default parameters. Finally, we filtered the differential expression genes using cutoff |Log2FoldChange| > 1 and P-value < 0.05, based on the Cuffdiff quantification results.
Assembly: The aligned hg38 genome was built with BWA using default parameters.
Supplementary files format and content: TXT format: mutation information.
Library strategy: TRACE-seeq

value: human embryonic kidney 293 cells

value: HEK293T cells

tag: sample type

value: newly developed REWRITE-A&C (TadA CG82T mutatnt) RNA dual-functional base editor.


title: p1_Empty

value: Empty


title: AIM-A_NT

value: newly developed REWRITE-A RNA adenine base editor with non-targeting gRNA.


title: BRI-2146_FExDTR_GEX_HTO_Library

description: Library name: BRI-2146

value: Lymph node


title: BRI-2324_D24_TCR_Library

description: Library name: BRI-2324

value: Spleen


title: AIM-A

value: newly developed REWRITE-A RNA adenine base editor with targeting gRNA.


title: WT, scRNA-seq

city: Hefei

first: Jiarui

last: Li

state: Anhui

address: Huangshan road #443

institute: University Of Science And Technology Of China

description: 10 × Genomics

data_processing:
The raw gene expression data were converted to Seurat data using the Seurat (v4.0) R toolkit.
Low quality cells with unique feature counts < 200 or > 4500 and > 20% mitochondrial counts were removed by quality control.
CD45+ cells from the WT (5216 cells) or CD94-KO (5014 cells) populations were retained for subsequent analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous tumor

extract_protocol:
To obtain CD45+ tumor‑infiltrating lymphocytes (TILs) from WT B6 or CD94-KO mice, the TILs were incubated with an anti-CD45 mAb for 30 min at 4°C. Subsequently, 7AAD was added to the CD45+ cell suspension, which was subsequently sorted using a FACSAria Fusion (BD Biosciences, San Diego, USA). The purity of the sorted cell populations was >  90%. Purified CD45+ live cells were labelled with 0.4% Trypan blue to determine their viability (> 90% before processing for scRNA-seq).
Single-cell barcode scRNA-seq libraries were generated using the Chromium Single Cell 3’ Library (v2 chemistry; Nugen) according to the manufacturer’s standard protocol. The libraries were sequenced on a NovaSeq 6000 (Illumina). Gene-barcode matrices were generated by counting UMIs and filtering non-cell-associated barcodes.

value: subcutaneous tumor

value: CD45+  tumor-infiltrating lymphocytes

tag: strain

value: WT (C57BL/6J)

tag: age

value: 6-8 weeks old


title: B9_HPpos_F2_ileum_5

description: Library name: 20210824_ENS_OVA_HP_17102_HP_pos_B9_HPpos_F2_ileum_5

tag: tissue

tag: cell type


title: CD94-KO, scRNA-seq

description: 10 × Genomics


title: B8_HPpos_M3_ileum_4

description: Library name: 20210728_ENS_HP_17105_HP_pos_B8_HPpos_M3_ileum_4

tag: batch

tag: treatment


title: REPAIRv2_NT

value: REPAIRv2 RNA base editing approach with non-targeting gRNA.


title: ID8-sgMettl5 5_4-C

value: Ovarian cancer cell line

value: C

value: Mettl5 sgRNA5_4


title: p4_pLNA-Ctrl

value: Brain

value: pLNA-Ctrl

value: igNeurons

value: Differentiation p4


title: p2_pLNA-1229

description:
B_16
igNeuron_pLNA-1229_DEA.csv

value: Differentiation p2


title: B8_HPpos_M3_ileum_3

description: Library name: 20210728_ENS_HP_17105_HP_pos_B8_HPpos_M3_ileum_3

value: Ileum

value: enteric neuron

tag: Sex

value: M


title: B8_HPpos_M2_ileum_2

description: Library name: 20210728_ENS_HP_17104_HP_pos_B8_HPpos_M2_ileum_2

tag: mouse id


title: ID8-sgMettl5 5_4-B

value: B


title: p3_pLNA-181c

description:
B_15
igNeuron_pLNA-181c_DEA.csv

value: Differentiation p3


title: ID8-sgMettl5 5_4-A

value: A


title: B8_HPpos_F2_ileum_4

description: Library name: 20210728_ENS_HP_17102_HP_pos_B8_HPpos_F2_ileum_4

value: F

tag: batch label


title: REPAIRv1_NT

value: human embryonic kidney 293 cells

value: HEK293T cells

value: REPAIRv1 RNA base editing approach with non-targeting gRNA.


title: ID8-sgMettl5 5_3-C

value: Ovarian cancer cell line

value: C

value: Mettl5 sgRNA5_3


title: REPAIRv2

value: REPAIRv2 RNA base editing approach with targeting gRNA.


title: REPAIRv1

value: REPAIRv1 RNA base editing approach with targeting gRNA.


title: ID8-sgMettl5 5_3-B


title: B7_GF_M1_ileum_2

description: Library name: 20210531_ENS_pool3_3608_GF_B7_GF_M1_ileum_2

value: GF

tag: plate label


title: p2_pLNA-3943

description:
B_12
igNeuron_pLNA-3943_DEA.csv

value: Brain

value: igNeurons

value: Differentiation p2


title: p4_pLNA-3943

description:
B_14
igNeuron_pLNA-3943_DEA.csv

value: Differentiation p4


title: LELvector

tag: cell line

value: negtive control samples which only express blank vectors with both nuclear exporting signals (NES) and nuclear localization signals (NLS).


title: ID8-sgMettl5 5_3-A

tag: replicate


title: p3_pLNA-1229

description:
B_11
igNeuron_pLNA-1229_DEA.csv

value: Differentiation p3


title: ID8-sgNC-C

value: Control sgRNA


title: B7_BT_M1_ileum_2

description: Library name: 20210531_ENS_pool3_3807_BT_B7_BT_M1_ileum_2

value: Ileum

value: enteric neuron

value: M

value: BT


title: p2_pLNA-Ctrl

value: pLNA-Ctrl


title: B7_BT_M1_ileum_1

description: Library name: 20210531_ENS_pool3_3807_BT_B7_BT_M1_ileum_1


title: ID8-sgNC-B

value: Ovarian cancer cell line

value: B


title: Vaginal_HSVpos_Shedpos_1

type: RNA

first: Rachael

middle: M

last: Zemek

state: Washington

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Centre

hyb_protocol: Probe hybridization of 377 genes in the Xenium Human Multi-Tissue and Cancer panel (10x Genomics, 2023) was performed overnight at 50oC. Ligation and amplification were performed as instructed in CG000582 Rev E, followed by nuclei staining and removal of background fluorescence.

scan_protocol: Imaging and decoding of fluorescent probe optical signatures were performed onboard the 10x Genomics Xenium platform (software version 1.7.6.0 and analysis version xenium-1.7.1.0).

data_processing:
The 10x Genomics Xenium on-board data processing (software version 1.7.6.0 and analysis version xenium-1.7.1.0) decoded transcript counts and morphology images, and performed secondary analysis to localize transcript signals to cells and create a feature-cell matrix and segmetation. Next, we used Proseg v1.1.8 cell segmentation algorithm. Samples were then processed with Xenium Ranger v 3.0.1.
Raw data: Xenium OA output. Processed data: (after Proseg and XeniumRanger) cell_feature_matrix (barcodes.tsv, features.tsv, matrix.mtx), cell_boundaries.csv, cells.csv, and transcripts.csv

label: Xenium Fluorescent Probes

source_name: Vaginal tract, HSV seropositive, Shed positive

label_protocol: Tissue sections were fixed in paraformaldehyde and permeabilized following the protocol CG000581 Rev C.

extract_protocol: 10um thick fresh-frozen sections were placed within the capture area of two Xenium slides, according to the 10x Genomics tissue preparation protocol (CG000579, Rev C).

treatment_protocol: Fresh frozen VT biopsies in OCT

tag: patient id

tag: gender

value: Female

value: Vaginal tract biopsy

tag: hsv-2 status

value: seropositive

tag: active hsv-2 shedding

value: positive

tag: leuteul phase

value: no

tag: folicular phase

value: yes

tag: nugent result

value: normal

tag: nugent score

tag: region

value: 1 of 1

tag: sample number (manuscript)


title: B7_ASF_M1_ileum_2

first: Jacques

address: 415 Main Street, 415M-7175 - Xavier lab

institute: Broad Institute

description: Library name: 20210531_ENS_pool3_3805_ASF_B7_ASF_M1_ileum_2

tag: tissue

tag: cell type

tag: batch

tag: treatment

value: ASF


title: ID8-sgNC-A

value: A

value: Control sgRNA


title: p2_Empty

value: Brain

tag: agent

value: Empty

value: igNeurons

tag: differentiation

value: Differentiation p2


title: Vaginal_HSVpos_Shedpos_3

value: intermediate


title: B7_ASF_M1_ileum_1

description: Library name: 20210531_ENS_pool3_3805_ASF_B7_ASF_M1_ileum_1

value: Ileum

value: enteric neuron

tag: Sex

value: M

tag: mouse id

tag: batch label

tag: plate label


title: OPA1KO_Treg_scRNAseq_rep2

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

growth_protocol: DTR chimera mice (generated at a 9:1 ratio with BM from Foxp3DTR and Foxp3Cre (called WT) or Foxp3CreOpa1fl/fl (called Opa1 KO) mice) were treated with DT, and, 7 days later, CD4+Foxp3-YFP+ Treg cells sorted for input to scRNA-seq.

extract_protocol:
Treg cells were  loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library and Gel Bead Kit (10x Genomics).

treatment_protocol: WT DTR chimera and Foxp3CreOpa1fl/fl DTR chimera mice were treated with DT.

value: Spleen

tag: cell line

value: Primary mouse Treg cells

value: CD4+Foxp3-YFP+ Treg cells

tag: genotype

value: Opa1 KO

value: DT-treated Foxp3CreOpa1flox/flox DTR chimera mice


title: p4_pLNA-1229

description:
B_6
igNeuron_pLNA-1229_DEA.csv

value: Differentiation p4


title: p3_Empty

value: Differentiation p3


title: Vaginal_HSVpos_Shedneg_1

source_name: Vaginal tract, HSV seropositive, Shed negative

tag: patient id

tag: gender

value: Female

value: Vaginal tract biopsy

tag: hsv-2 status

value: seropositive

tag: active hsv-2 shedding

value: negative

tag: leuteul phase

value: no

tag: folicular phase

value: normal

value: 1 of 1


title: OPA1KO_Treg_scRNAseq_rep1

tag: tissue

tag: cell type


title: B6_HPneg_F1_ileum_2

description: Library name: 20210531_ENS_pool2_17101_HP_neg_B6_HPneg_F1_ileum_2

value: Ileum

value: F

tag: batch

tag: treatment


title: B7_GF_M1_ileum_1

description: Library name: 20210531_ENS_pool3_3608_GF_B7_GF_M1_ileum_1

value: enteric neuron

value: M

value: GF


title: B6_HPpos_M3_ileum_2

description: Library name: 20210531_ENS_pool2_17105_HP_pos_B6_HPpos_M3_ileum_2


title: WT control_Treg_scRNAseq_rep1

value: Spleen

value: Primary mouse Treg cells

value: CD4+Foxp3-YFP+ Treg cells

value: WT

value: DT-treated WT DTR chimera mice


title: Vaginal_HSVpos_Shed_unknown

source_name: Vaginal tract, HSV seropositive, Shed unknown

value: Female

value: unknown

tag: nugent result

tag: nugent score

tag: region

tag: sample number (manuscript)


title: Vaginal_HSVneg_1_region2

source_name: Vaginal tract, HSV seronegative

value: Vaginal tract biopsy

value: seronegative

value: yes

value: bacterial vaginosis

value: 2 of 2


title: p2_pLNA-181c

description:
B_5
igNeuron_pLNA-181c_DEA.csv

value: Brain

tag: agent

value: igNeurons

tag: differentiation

value: Differentiation p2


title: WT control_Treg_scRNAseq_rep2

tag: cell line

tag: genotype


title: B6_HPpos_M2_ileum_1

description: Library name: 20210531_ENS_pool2_17104_HP_pos_B6_HPpos_M2_ileum_1

value: Ileum

value: enteric neuron

tag: Sex

value: M

tag: mouse id

tag: batch label

tag: plate label


title: Vaginal_HSVpos_Shedneg_2

tag: patient id

tag: gender

tag: hsv-2 status

value: seropositive

tag: active hsv-2 shedding

value: negative

tag: leuteul phase

value: no

tag: folicular phase

value: normal

value: 1 of 1


title: p1_pLNA-Ctrl

tag: tissue

value: pLNA-Ctrl

tag: cell type

value: Differentiation p1


title: Vaginal_HSVpos_Shedpos_2_region2

value: Female

value: Vaginal tract biopsy

value: positive

tag: nugent result

tag: nugent score

tag: region

tag: sample number (manuscript)


title: B6_HPpos_F2_ileum_3

description: Library name: 20210531_ENS_pool2_17102_HP_pos_B6_HPpos_F2_ileum_3

value: F

tag: batch

tag: treatment


title: Vaginal_HSVpos_Shedpos_2_region1

value: bacterial vaginosis

value: 1 of 2


title: Vaginal_HSVneg_1_region1

value: seronegative

value: yes


title: p1_pLNA-3943

description:
B_2
igNeuron_pLNA-3943_DEA.csv

value: Brain

tag: agent

value: igNeurons

tag: differentiation


title: B5_HPneg_F1_ileum_1

description: Library name: 20210531_ENS_pool1_17101_HP_neg_B5_HPneg_F1_ileum_1

value: Ileum

value: enteric neuron

tag: Sex

tag: mouse id

tag: batch label

tag: plate label


title: B5_HPpos_M3_ileum_1

description: Library name: 20210531_ENS_pool1_17105_HP_pos_B5_HPpos_M3_ileum_1

value: M


title: p4_Empty

value: Empty

value: Differentiation p4


title: p3_pLNA-3943

description:
B_4
igNeuron_pLNA-3943_DEA.csv

value: Differentiation p3


title: Vaginal_HSVneg_4

tag: patient id

tag: gender

tag: hsv-2 status

tag: active hsv-2 shedding

value: no

value: normal

value: 1 of 1


title: SC3_Day9

data_processing:
Reads were mapped to GRCh38.p10 using STAR.
Counts were obtained with featureCounts.
Differential expression analysis was performed using edgeR.
The analysis can be additionally accessed at: https://ethz-ins.org/igNeuronsTimeCourse
For further infos please see the methods section of the publication.
Assembly: Ensembl91
Supplementary files format and content: tab-delimited text file including logcpm values for each sample
Supplementary files format and content: tab-delimited text file including a differential expression analysis over all samples.

growth_protocol: Time course of human neuronal differentiation with an optimized Ngn2-overexpression protocol ("igNeurons").

extract_protocol:
RNA was extracted using the miRVana kit (Thermo) and subsequently DNase treated (Thermo - Turbo DNase).
RNA libraries for the ribosomal depletion sequencing were prepared using Illumina TruSeq RNA stranded and Ribosomal Depletion Ribozero gold kits.

tag: tissue

tag: time point

tag: cell type

value: Differentiation SC3


title: B5_HPpos_F2_ileum_2

description: Library name: 20210531_ENS_pool1_17102_HP_pos_B5_HPpos_F2_ileum_2

value: F


title: SC3_Day40


title: B5_HPpos_F2_ileum_1

description: Library name: 20210531_ENS_pool1_17102_HP_pos_B5_HPpos_F2_ileum_1


title: WT_Treg_scRNAseq_rep1

growth_protocol: DTR chimera mice (generated at a 9:1 ratio with BM from Foxp3DTR and Foxp3Cre (called WT) or Foxp3CreFlcnfl/fl (called Flcn KO) mice) were treated with DT, and, 7 days later, CD4+Foxp3-YFP+ Treg cells sorted for input to scRNA-seq.

extract_protocol:
For all scRNA-seq experiments, samples were centrifuged (950g for 5 min) and then pellets were resuspended in 1x PBS plus 0.04% BSA (Amresco) at a concentration of 1x106 cells per mL. Single-cell suspensions were loaded onto a Chromium Controller (10x Genomics) to generate 10,000 single-cell gel beads in emulsion per sample, and each sample was loaded into a separate channel.
Libraries were prepared using the Chromium Next GEM Single Cell 3’ v3.1 (dual index) and Gel Bead kit (10x Genomics).

treatment_protocol: WT DTR chimera and Foxp3CreFlcnfl/fl DTR chimera mice were treated with DT.

value: Spleen

tag: cell line

value: Primary mouse Treg cells

value: CD4+Foxp3-YFP+ Treg cells

tag: genotype

value: WT

value: DT-treated WT DTR chimera mice


title: Vaginal_HSVneg_5

value: Female

value: Vaginal tract biopsy

value: seronegative

tag: leuteul phase

tag: folicular phase

value: yes

tag: nugent result

tag: nugent score

tag: region

tag: sample number (manuscript)


title: p3_pLNA-Ctrl

value: Brain

tag: agent

value: pLNA-Ctrl

value: igNeurons

tag: differentiation


title: Vaginal_HSVneg_6

tag: patient id

value: no


title: B4_HPpos_F33_ileum_1

description: Library name: 20210402_SS2_ENS_HP_33_HP_pos_B4_HPpos_F33_ileum_1

value: Ileum

value: enteric neuron

tag: Sex

tag: batch

tag: mouse id

tag: treatment

tag: batch label

tag: plate label


title: FlcnKO_Treg_scRNAseq_rep2

tag: tissue

tag: cell line

tag: cell type

value: Flcn KO

value: DT-treated Foxp3CreFlcnfl/fl DTR chimera mice


title: SC3_Day33

tag: time point

value: Differentiation SC3


title: WT_Inflammation_VDJ_rep2

data_processing:
*library strategy: scTCR-seq
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina Novaseq run.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotations for scTCR-seq

growth_protocol: DTR chimera mice (generated at a 9:1 ratio with BM from Foxp3DTR and Foxp3Cre mice) were treated with DT (called inflammation) or PBS (called steady-state), and, 7 days later, CD4+Foxp3-YFP+ Treg cells and CD45+ (non-Treg) cells were sorted and then mixed 1:1 for input to scRNA-seq and scTCR-seq.

extract_protocol:
For all scRNA-seq experiments, samples were centrifuged (950g for 5 min) and then pellets were resuspended in 1x PBS plus 0.04% BSA (Amresco) at a concentration of 1x106 cells per mL. Single-cell suspensions were loaded onto a Chromium Controller (10x Genomics) to generate 10,000 single-cell gel beads in emulsion per sample, and each sample was loaded into a separate channel.
The cDNA was amplified (11 cycles) and either used for TCR enrichment/library preparation with the Chromium Single Cell V(D)J TCR kit or for preparation of a gene expression library. For scRNA-seq, libraries were prepared using the Chromium Next GEM 5’ v2 (dual index) and Gel Bead kit (10x Genomics).

treatment_protocol: DTR chimera mice were treated with PBS (steady-state) or DT (inflammation).

value: Spleen

value: Primary mouse immune cells

value: CD4+Foxp3-YFP+ Treg cells and CD45+ (non-Treg) cells (1:1 mix)

tag: genotype

value: Wild type

value: DT-treated DTR chimera mice (TCR)


title: SC3_Day27


title: Vaginal_HSVneg_2

tag: gender

value: Female

value: Vaginal tract biopsy

tag: hsv-2 status

tag: active hsv-2 shedding

tag: leuteul phase

tag: folicular phase

tag: nugent result

value: bacterial vaginosis

tag: nugent score

value: 1 of 1


title: FlcnKO_Treg_scRNAseq_rep1

value: Primary mouse Treg cells

value: CD4+Foxp3-YFP+ Treg cells


title: B4_HPneg_F49_ileum_2

description: Library name: 20210402_SS2_ENS_HP_49_HP_neg_B4_HPneg_F49_ileum_2

tag: Sex

value: F

tag: batch


title: Vaginal_HSVneg_3

tag: patient id

value: seronegative

value: negative

value: yes

value: no

tag: region

tag: sample number (manuscript)


title: FBC_B4_Sample4_20240315

description: Library name: FBC_B4_Sample4_20240315

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq pipeline made available by CellRanger v7.2.0 software (10x Genomics)
FASTQ reads were aligned to the mm10 mouse transcriptome, to extract cell barcodes and UMI barcodes using the cellranger count function. A digital gene expression (DGE) matrix for each sample was processed further
Assembly: mm10
Supplementary files format and content: ens_PerturbSeq_atlas.h5ad : Anndata object of ENS profiled of 10x in in vivo Perturbseq screen

source_name: Intestine

extract_protocol:
Submucosal and myenteric plexus layers were isolated from AAV-PHP.S Perturb-seq transduced mice. 8,000 single nuclei were sorted based on tdtomato+.
Single nucleus RNA-sequencing and CRISPR-sgRNA detection were performed using Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for CRISPR Screening (10x Genomics, PN-1000263, PN-1000190, PN-1000451). Gene expression, labeled as GEX, and CRISPR feature barcode libraries, labeled as FBC, were constructed. CRISPR perturbation analysis declared the target gene of each gRNA from Read2 using CRISPR protospacer sequence and constant sequence TTCCAGCATAGCTCTTAAAC(BC). Cells containing non-targeting guides  were used as controls.

tag: tissue

value: Intestine

value: enteric neurons

tag: strain

value: male


title: FBC_B4_Sample5_20240315

description: Library name: FBC_B4_Sample5_20240315

tag: cell type

value: female


title: SC3_Day21

value: Brain

tag: time point

value: igNeurons

tag: differentiation

value: Differentiation SC3


title: WT_SteadyState_VDJ_rep2

value: Spleen

tag: cell line

value: Primary mouse immune cells

value: CD4+Foxp3-YFP+ Treg cells and CD45+ (non-Treg) cells (1:1 mix)

tag: genotype

value: Wild type

tag: treatment

value: PBS-treated DTR chimera mice (TCR)


title: B3_GF_F1_ileum_3

description: Library name: 20210402_SS2_ENS_GF_BT_3816_GF_B3_GF_F1_ileum_3

value: Ileum

value: enteric neuron

value: F

tag: mouse id

value: GF

tag: batch label

tag: plate label


title: WT_Inflammation_VDJ_rep1

value: DT-treated DTR chimera mice (TCR)


title: WT_SteadyState_VDJ_rep1


title: WT_Treg_scRNAseq_rep3

value: Primary mouse Treg cells

value: CD4+Foxp3-YFP+ Treg cells

value: WT

value: DT-treated WT DTR chimera mice


title: WT_Treg_scRNAseq_rep2


title: SC3_Day0

value: Brain


title: FBC_B3_Sample2_20240210

description: Library name: FBC_B3_Sample2_20240210

value: Intestine

value: enteric neurons

value: female


title: FBC_B3_Sample3_20240210

description: Library name: FBC_B3_Sample3_20240210

value: male


title: WT_Inflammation_GEX_rep2

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina Novaseq run.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotations for scTCR-seq

value: Spleen

value: Primary mouse immune cells

value: CD4+Foxp3-YFP+ Treg cells and CD45+ (non-Treg) cells (1:1 mix)

value: DT-treated DTR chimera mice (gene expression)


title: B4_HPneg_F49_ileum_1

description: Library name: 20210402_SS2_ENS_HP_49_HP_neg_B4_HPneg_F49_ileum_1

value: Ileum

value: enteric neuron


title: FBC_B3_Sample1_20240210

description: Library name: FBC_B3_Sample1_20240210


title: SC2_Day9

value: igNeurons

value: Differentiation SC2


title: SC2_Day40


title: FBC_B2_NMU_20231216

description: Library name: FBC_B2_NMU_20231216

value: pooled male and female


title: WT_SteadyState_GEX_rep2

value: Wild type

value: PBS-treated DTR chimera mice (gene expression)


title: WT_SteadyState_GEX_rep1


title: SC3_Day15

value: Differentiation SC3


title: FBC_B1_20230626

description: Library name: FBC_B1_20230626


title: SC2_Day27

value: Brain


title: SC2_Day21


title: B3_BT_F1_ileum_1

description: Library name: 20210402_SS2_ENS_GF_BT_3811_BT_B3_BT_F1_ileum_1

value: F

value: BT


title: B2_ASF_F1_ileum_1

description: Library name: 20210402_SS2_ENS_ASF_SPF_3602_ASF_B2_ASF_F1_ileum_1

value: ASF


title: B2_SPF_F1_ileum_1

description: Library name: 20210402_SS2_ENS_ASF_SPF_77319_SPF_B2_SPF_F1_ileum_1

value: SPF


title: B4_Sample4_20240315

description: Library name: B4_Sample4_20240315

value: Intestine

value: enteric neurons

value: male


title: B4_Sample5_20240315

description: Library name: B4_Sample5_20240315

value: female


title: WT_Inflammation_GEX_rep1

value: Spleen

value: Primary mouse immune cells

value: CD4+Foxp3-YFP+ Treg cells and CD45+ (non-Treg) cells (1:1 mix)

value: DT-treated DTR chimera mice (gene expression)


title: SC2_Day15

value: igNeurons

value: Differentiation SC2


title: B2_ASF_F1_ileum_2

description: Library name: 20210402_SS2_ENS_ASF_SPF_3602_ASF_B2_ASF_F1_ileum_2

value: Ileum

value: enteric neuron


title: SC2_Day33

value: Brain


title: B3_Sample3_20240210

description: Library name: B3_Sample3_20240210


title: B2_SPF_F1_ileum_2

description: Library name: 20210402_SS2_ENS_ASF_SPF_77319_SPF_B2_SPF_F1_ileum_2

value: F


title: SC2_Day0


title: B3_GF_F1_ileum_2

description: Library name: 20210402_SS2_ENS_GF_BT_3816_GF_B3_GF_F1_ileum_2

value: GF


title: B3_Sample2_20240210

description: Library name: B3_Sample2_20240210


title: B10003_SPF_F77319_colon_1

description: Library name: 20210210_SS2_ENS_77319_SPF_B10003_SPF_F77319_colon_1

source_name: Colon

value: Colon


title: KO ILC2-3

first: Dongdi

last: Wang

address: 227 South Chongqing Road, Shanghai, China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were aligned to the mouse reference genome (version mm10) by using Hisat2 RNASeq alignment software.
Quantitated relative mRNA expression levels (FPKM) were calculated based on exon regions using Cufflinks and the mm10 reference genome annotations.
Assembly: mm10
Supplementary files format and content: comma-separated values files include readcounts  for each Sample and every gene
Supplementary files format and content: comma-separated values files include FPKM values  for each Sample and every gene

source_name: lung

extract_protocol:
Total RNA from sorted lung ILC2s of R5/+ (WT) and R5/+ Rptorf/f (KO) mice in steady state was extracted by Trizol reagent.  RNA quality was examined with an Agilent Bioanalyzer 2100 (Agilent). The concentration of RNA was from 7ng/ul to 14ng/ul. The SMART-Seq HT Kit (Takara Bio USA, Inc) was used to generate high-quality, full-length cDNA.
Libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocol.

value: lung


title: B1_GF_F1_ileum_1

last: Deguine

description: Library name: 20210326_SS2_ENS_GF_3816_GF_B1_GF_F1_ileum_1


title: SC1_Day9

value: Differentiation SC1


title: KO ILC2-2


title: B10002_ASF_F3602_colon_1

description: Library name: 20210202_SS2_ENS_3602_ASF_B10002_ASF_F3602_colon_1

value: ASF


title: B3_BT_F1_ileum_2

description: Library name: 20210402_SS2_ENS_GF_BT_3811_BT_B3_BT_F1_ileum_2

value: BT


title: B3_Sample1_20240210

description: Library name: B3_Sample1_20240210

value: Intestine

value: enteric neurons

value: female


title: KO ILC2-1


title: SC1_Day40


title: SC1_Day27


title: SC1_Day33


title: WT ILC2-3


title: B2_NMU_20231216

description: Library name: B2_NMU_20231216

value: pooled male and female


title: B10001_Btheta_M3608_colon_1

description: Library name: 20200603_SS2_ENS_3608_BT_B10001_Btheta_M3608_colon_1

value: M


title: IL-10 neg splenic B cells, control mouse 4, D3 aBCR IL-5 IFNg IL-2

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

institute: Université Rennes

data_processing:
Sequence reads were trimmed for low quality reads, adaptor sequence, contaminant DNA or PCR duplicates using Trimmomatic program.
Trimmed reads were mapped to reference genome GrCM38/mm10 with HISAT2, splice-aware aligner.
Transcript was assembled by StringTie with aligned reads.
Read count extraction and normalization were performed using -e option of StringTie.
DEG analysis was conducted using DESeq2 tool. Samples were grouped using Hierarchical Clustering Analysis or Multidimensional Scaling Analysis. Gene-set enrichment analysis was performed based on gene ontoloy on significant DEG lists.
Assembly: GrCM38/mm10
Supplementary files format and content: tab-delimited text file including read counts, FPKM and TPM values of all the samples

source_name: CD25+ IL10- splenic B cells

growth_protocol: B cells were harvested from mice spleen using "B Cell Isolation Kit, mouse" (Miltenyi #130-090-892) and cultured at 500.000 cells/mL in RPMI supplemented with 10% Fetal Bovine Serum (FBS) and sodium pyruvate, non-essential amino acids, HEPES, beta-mercaptoéthanol and anitbiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Sorted cells were frozen direclty in lysis buffer. RNA extraction was performed using "NucleoSpin RNA Plus XS" kit from Macherey-Nagel.
RNA library for RNA-seq were prepared using Watchmaker mRNA Library Prep Kit.

treatment_protocol: Splenic B cells were stimulated with anti-BCR (8 µg/mL, Invitrogen #16-5092-85), IL-5 (50 U/mL, Stemcell #78049.1), IFNg (1 ng/mL, Miltenyi #130-105-790) and IL-2 (50 U/mL, Miltenyi #130-120-662) for 3 days. IL-10pos CD25pos B cells and IL-10neg CD25pos B cells were sorted by FACS at D3.

value: Female

tag: age

value: 25 weeks

value: CD25+ IL10- splenic B cells

value: Il2rb fl/fl, CD19 +/+

value: in vitro stimulation:anti-BCR + IL-5 + IFNg + IL-2

tag: time

value: Day 3


title: SC1_Day21

value: Brain

value: igNeurons


title: WT ILC2-2

value: lung


title: IL-10 pos splenic B cells, control mouse 4, D3 aBCR IL-5 IFNg IL-2

source_name: CD25+ IL10+ splenic B cells

tag: Sex

value: CD25+ IL10+ splenic B cells


title: WT ILC2-1


title: B1_20230626

description: Library name: B1_20230626

tag: batch


title: scRNA-seq_Il7rLTpos_NFIL3-KO

city: Nantes

first: Christelle

last: Harly

address: 8 quai Moncousu

institute: CNRS

description:
Library name: SCAF461
Il7rLTpos_NFIL3-KO
RDS_ILC_WT-KO_Integrated_Pseudotime.rds
Table_LEAP_Network.txt
Table_LEAP_Nfil3_Targets.txt

data_processing:
Raw FASTQ files were processed using CellRanger (7.0.1) with default parameters
Quality check and data processing was performed using Seurat package (4.3.0) and R (4.1.3)
Read counts were Log Normalized, scaled scaled while cell cycle difference scores and mitochondrial percentages were regressed, and integrated using Cluster Similarity Spectrum (simspec 0.0.0.9000)
Pseudotime reconstruction analysis was performed using Slingshot (2.2.1) and added to Seurat-Object metadata. Gene regulatory network inferrence was done using LEAP algorithm
Assembly: mm39
Supplementary files format and content: R-Seurat object save containing integrated cells and pseudotime trajectories for WT analysis
Supplementary files format and content: R-Seurat object save containing integrated cells and pseudotime trajectories for WT+KO analysis
Supplementary files format and content: Tab-delimited results from LEAP algorithm of inferred gene regulatory network of factors known to be involved in ILC development (filtered as lag>0, cor>0,1675)
Supplementary files format and content: Tab-delimited results from LEAP algorithm of Nfil3 predicted targets (filtered as lag>0, cor>0,1675)

extract_protocol:
Samples were isolated by cell sorting from bone marrow single cell suspensions
Libraries were prepared using Chromium Single Cell 3′ kits, according to the manufacturer’s instructions (version 2 chemistry; 10x Genomics). a4b7hi and Il7rLTpos samples were prepared in a separated batch from ALP and Tcf7pos ILpro

tag: strain background

tag: genotype/variation

value: Il7r-iCre R26-stop-YFP Tcf7GFP/+ Nfil3-KO

value: Bone Marrow

value: Il7rLTpos NFIL3-KO intermediates

value: ex vivo

tag: sorting profile

value: Lin- Thy1.2- Kit+ 2B4+ Flt3high YFP+


title: IL-10 neg splenic B cells, control mouse 3, D3 aBCR IL-5 IFNg IL-2

tag: strain


title: Papain ILC2-3

extract_protocol:
Total RNA from sortedlung ILC2s mRNA profiles of PBS treated mice and Papain treated mice was extracted by Trizol reagent.  RNA quality was examined with an Agilent Bioanalyzer 2100 (Agilent). The concentration of RNA was from 7ng/ul to 14ng/ul. The SMART-Seq HT Kit (Takara Bio USA, Inc) was used to generate high-quality, full-length cDNA.
Libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocol.

tag: tissue

tag: cell type

value: Papain


title: SC1_Day15

tag: time point

tag: differentiation

value: Differentiation SC1


title: SC1_Day0


title: scRNA-seq_Tcf7pos_ILCpro

description:
Library name: 3_ABSC_EILP_WT
Tcf7pos_ILCpro
RDS_ILC_WT_Integrated_Pseudotime.rds
RDS_ILC_WT-KO_Integrated_Pseudotime.rds
Table_LEAP_Network.txt
Table_LEAP_Nfil3_Targets.txt

value: Tcf7pos ILC progenitors

value: Lin- Kit+ 2B4+ a4b7high GFPhigh


title: IL-10 pos splenic B cells, control mouse 3, D3 aBCR IL-5 IFNg IL-2

value: Female

value: 25 weeks

tag: genotype


title: scRNA-seq_a4b7hi

description:
Library name: 2_ABSC_TULIP
a4b7hi
RDS_ILC_WT_Integrated_Pseudotime.rds
RDS_ILC_WT-KO_Integrated_Pseudotime.rds
Table_LEAP_Network.txt
Table_LEAP_Nfil3_Targets.txt

value: a4b7hi ILC intermediates

tag: treatment

value: Lin- Thy1.2- Kit+ 2B4+ Flt3high a4b7high GFP-


title: AIM-C

value: human embryonic kidney 293 cells

tag: cell line

value: HEK293T cells

tag: sample type

value: newly developed REWRITE-C (TadA PG82T mutatnt) RNA cytocine base editor.


title: PBS ILC2-3

value: lung

value: PBS


title: Papain ILC2-1


title: MCF10A, 25 µM etoposide

city: Boulder

first: Brianna

last: Fernandez

state: CO

address: 3415 Colorado Avenue

department: Biochemistry

institute: University of Colorado Boulder

description:
Library name: Sample 4
10x Genomics

data_processing:
scRNA-seq data were processed and analyzed using the Seurat (v5.1.0) package in R (v4.4.1). Raw sequencing reads were pre-processed using CellRanger (v7.1.0) and aligned to the Human (GRCh38) 2020-A reference genome. Gene-cell count matrices were generated, and low-quality cells were filtered out based on the number of detected genes, unique molecular identifiers (UMIs), and mitochondrial gene percentage. Cells with fewer than 3,500 genes were excluded to remove low-quality cells. Cells with greater than 15% mitochondrial gene expression were also removed. Data were log-normalized using Seurat’s NormalizeData() function with a scale factor of 10,000.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: matrix files for counts, features, and barcodes

extract_protocol:
Single-cell suspensions were prepared following the 10x Genomics “Cell Preparation for Single Cell Protocols” guide with a viability of >95%. Single-cell encapsulation, barcoding, cDNA amplification, library preparation, and sequencing were performed by the University of Colorado Anschutz Genomics Shared Resource facility. Cells were encapsulated into droplets using the Chromium Controller, where reverse transcription occurred within individual gel beads-in-emulsion (GEMs).
Single-cell RNA sequencing (scRNA-seq) libraries were generated using the 10x Genomics Chromium platform with the 3' mRNA capture kit. Single-cell suspensions were prepared following the 10x Genomics “Cell Preparation for Single Cell Protocols” guide with a viability of >95%. Single-cell encapsulation, barcoding, cDNA amplification, library preparation, and sequencing were performed by the University of Colorado Anschutz Genomics Shared Resource facility. Cells were encapsulated into droplets using the Chromium Controller, where reverse transcription occurred within individual gel beads-in-emulsion (GEMs). Following barcoding and cDNA amplification, sequencing libraries were constructed according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeqX to a depth of 81,810 reads per cell for untreated, 74,214 reads per cell for 2.5µM, 81,254 reads per cell for 10µM, and 76,973 reads per cell for 25µM.

treatment_protocol: MCF10A cells were split 1:10 (from a confluent plate) into a plastic 10cm culture plate before being treated with 2.5, 10, or 25μM etoposide the following day for 24 h. Cells were then washed twice with PBS before being returned to full-growth media. Full-growth media was refreshed every 3d during the drug recovery period.

value: normal human breast epithelial cell

value: 25 µM etoposide


title: IL-10 neg splenic B cells, control mouse 2, D3 aBCR IL-5 IFNg IL-2

value: CD25+ IL10- splenic B cells

value: Il2rb fl/fl, CD19 +/+

value: in vitro stimulation:anti-BCR + IL-5 + IFNg + IL-2

value: Day 3


title: scRNA-seq_ALP

description:
Library name: 1_ABSC_CLP
ALP
RDS_ILC_WT_Integrated_Pseudotime.rds
RDS_ILC_WT-KO_Integrated_Pseudotime.rds
Table_LEAP_Network.txt
Table_LEAP_Nfil3_Targets.txt

value: Bone Marrow

value: All Lymphoid Progenitors

value: ex vivo

value: Lin- Kit+ 2B4+ Flt3high a4b7high IL-7Ra+


title: scRNA-seq_Il7rLTpos_TOX-KO

description:
Library name: SCAF460
Il7rLTpos_TOX-KO
RDS_ILC_WT-KO_Integrated_Pseudotime.rds
Table_LEAP_Network.txt
Table_LEAP_Nfil3_Targets.txt

value: Il7r-iCre R26-stop-YFP Tcf7GFP/+ Tox-KO

value: Il7rLTpos TOX-KO intermediates

value: Lin- Thy1.2- Kit+ 2B4+ Flt3high YFP+


title: PBS ILC2-2


title: MCF10A, 10 µM etoposide

description:
Library name: Sample 3
10x Genomics

value: 10 µM etoposide


title: scRNA-seq_Il7rLTpos_WT

description:
Library name: SCAF459
Il7rLTpos_WT
RDS_ILC_WT_Integrated_Pseudotime.rds
RDS_ILC_WT-KO_Integrated_Pseudotime.rds
Table_LEAP_Network.txt
Table_LEAP_Nfil3_Targets.txt

value: Il7r-iCre R26-stop-YFP Tcf7GFP/+

value: Il7rLTpos WT ILC intermediates


title: IL-10 pos splenic B cells, control mouse 2, D3 aBCR IL-5 IFNg IL-2

value: Female

value: 25 weeks

value: CD25+ IL10+ splenic B cells


title: IL-10 neg splenic B cells, control mouse 1, D3 aBCR IL-5 IFNg IL-2

value: CD25+ IL10- splenic B cells


title: MCF10A, 2.5 µM etoposide

description:
Library name: Sample 2
10x Genomics

value: normal human breast epithelial cell

value: 2.5 µM etoposide


title: PBS ILC2-1

value: lung

value: PBS