title: Cd4CreFlcnfl/fl iTreg rep1

source_name: Flcnfl/fl iTreg

value: Cd4CreFlcnfl/fl iTreg cells were generated in vitro by culturing Cd4CreFlcnfl/fl naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).


title: Cnep1r1ΔIEC mouse

status: Public on Oct 30 2025

type: RNA

city: Beijing

first: Cunzhen

last: Li

address: No 15 Datun Road, Chaoyang District

country: China

institute: Chinese Academy of Sciences

hyb_protocol: The fragmented and labeled samples were loaded onto the corresponding chip model and placed in the GeneChip Hybridization Oven 645. Hybridization was then performed at 45 degree.

scan_protocol: GeneChips were scanned using theGeneChip 3000 7G.

data_processing: Affymetrix CEL files were read and RAN normalized using the R package affy(version 1.46.1).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Cnep1r1ΔIEC mice

label_protocol: Total RNA (with PolyA control added) was used to synthesize the first and second strands of cDNA. Through in vitro transcription, cRNA was synthesized, followed by purification and quantification of the cRNA. The cRNA was then diluted to 625 ng/μl for subsequent experiments. Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: The mice we used were C57BL/6 background and maintained under specific pathogen-free conditions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: After removing fat and connective tissues, a 5-cm-long section of distal ileum was opened longitudinally and rinsed with cold PBS. Villi were carefully scraped away and the tissue was washed vigorously in 20 mL cold PBS in a 50 mL tube for 1 min and repeated for at least four times to remove intestinal contents completely. The tissues were cut into small pieces (5 mm) and incubated in 10 ml collagenase solution (DMEM/F12 medium, containing 0.1% type I collagenase (Worthington; LS004197), 100 units/ml penicillin, 0.1 mg/ml streptomycin and 10 mM HEPES) at 37°C for 20 min. Digestion was stopped by dilution with 20 mL cold PBS when around 70% of the crypts had been released.

tag: tissue

value: small intetstine crypts


title: PD-1–CXCR3+_rep4

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦C while rotating at 60 rpm.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.4.1.46.

source_name: Treg states sorted from DT-treated DTR chimera mice

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: DTR chimera mice were generated at a 9:1 ratio with BM from Foxp3DTR and Foxp3Cre mice.

extract_protocol: Total RNA extraction was performed using Qiagen RNeasy micro kit (74004, Qiagen) according to manufacturer’s instructions.

treatment_protocol: DTR chimera mice were treated with DT and, 7 d later, CD4+Foxp3-YFP+ Treg cells were sorted into four states based upon expression of PD-1 and CXCR3.

tag: strain background

tag: cell type

value: CD4+Foxp3-YFP+PD-1–CXCR3+ Treg cells from DT-treated DTR chimera mice.


title: WT Treg_rep2

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.4.1.46

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.

treatment_protocol: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera and Foxp3CreOpa1fl/fl mixed BM chimera mice (n = 4 biological replicates per group).


title: Cd4CreFlcnfl/flTfebfl/fl iTreg rep2

source_name: Flcnfl/flTfebfl/fl iTreg

growth_protocol: iTreg cells were generated in vitro by culturing naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1) (n = 2 biological replicates per group).

treatment_protocol: iTreg cells were harvested and enriched for live cells using LymphoSep (MP Biomedicals).

value: Cd4CreFlcnfl/flTfebfl/fl iTreg cells were generated in vitro by culturing Cd4CreFlcnfl/flTfebfl/fl naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).


title: Cd4CreFlcnfl/fl iTreg rep2


title: WT  mouse

source_name: Wild type mice IEC


title: PD-1–CXCR3+_rep3


title: PD-1+CXCR3–_rep3

value: CD4+Foxp3-YFP+PD-1+CXCR3– Treg cells from DT-treated DTR chimera mice.


title: PD-1–CXCR3–_rep4

value: CD4+Foxp3-YFP+PD-1–CXCR3– Treg cells from DT-treated DTR chimera mice.


title: PD-1+CXCR3–_rep4


title: Cd4CreTfebfl/fl iTreg rep2

source_name: Tfebfl/fl iTreg

value: Cd4CreTfebfl/fl iTreg cells were generated in vitro by culturing Cd4CreTfebfl/fl naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).


title: PD-1+CXCR3+_rep4

value: CD4+Foxp3-YFP+PD-1+CXCR3+ Treg cells from DT-treated DTR chimera mice.


title: PD-1–CXCR3+_rep2


title: WT iTreg rep1

source_name: WT iTreg

value: WT iTreg cells were generated in vitro by culturing WT naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1).


title: PD-1–CXCR3–_rep3


title: PD-1+CXCR3+_rep2


title: PD-1+CXCR3+_rep3


title: T1013_IFNb_plus_RV16

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description:
Library name: lib106339
combined_counts_IFN.csv

library_source: transcriptomic

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. Resulting bcl files were deconvoluted and converted to fastq format using Casava from Illumina. Fastq files were aligned to the Ensembl version of the human genome (GRCh38, Ensembl 91) by using STAR (version 2.4.2a). HTSeq-count (version 0.4.1) was used to generate gene counts with mode as “intersection (nonempty)” and minimum alignment quality set to 20 and otherwise set to default parameters. Quality metrics were compiled from PICARD (version 1.134), FASTQC (version 0.11.3), Samtools (version 1.2), and HTSeq-count (version 0.4.1). For quality control, samples that had human aligned counts greater than 1 million mapped reads and a median coefficient of variation coverage less than 0.7 were kept. Genes were filtered to include those that had a trimmed mean of M value normalization count of at least 0.3 in at least 10% of samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights by using voomWithQualityWeights from the limma R package (version 4.2.1).
Assembly: Human GRCh38
Supplementary files format and content: csv file voom normalized counts

organism: Homo sapiens

source_name: Organotypic airway epithelial cell culture

extract_protocol:
Bronchial epithelial cells (BECs) from children with asthma (n=37) and healthy children (n=3)  ages 6-18 years of age were obtained from subjects while under general anesthesia for an elective surgery using 4-mm Harrell unsheathed bronchoscope cytology brushes (CONMED®) inserted through an endotracheal tube as we have previously described (8, 42). Cells were then seeded onto T-25 cell culture flasks (Corning®) precoated with type I collagen and proliferated under submerged culture conditions using PneumaCult™EX-Plus medium (Stemcell™) (8). BECs (passage 2 or 3) were proliferated on transwells under submerged culture conditions using PneumaCult™EX-Plus medium (Stemcell™) for 4-7 days then differentiated to an organotypic pseudostratified ciliated state (Supplemental Figure 1) for 21 days at ALI using PneumaCult™ALI medium (Stemcell™) as previously described (8, 43–45). We have previously demonstrated stability of gene expression in primary BEC ALI cultures between passages 1 and 3 (46).RNA was collected from BEC cultures pre-infection and at 2d, 4d, 7d, and 10d post RV infection. To collect RNA from BEC cultures, media was first removed from the basolateral chamber of transwells. 800 µL of lysis buffer (Invitrogen®, Product No. AM1912) was added to the apical surface of cultures. A pipet tip was then used to gently scratch each apical well in a crosshatch pattern to loosen BECs from the transwell membrane. RNA was extracted using the RNAqueous™ kit for total RNA isolation (Thermo Fisher Scientific). BEC cultures from SE (n=6) and NSE (n=6) donors were treated with IFN-β or CXCL10 starting 2 days prior to RV infection and continued for 2 days following RV infection. Recombinant human recombinant human IFN-β (1 ng/mL; AbcamⓇ) or CXCL10 (2 ng/mL; R&D SystemsⓇ) was added to BEC ALI medium starting 2 days prior to RV infection and refreshed with each medium change (every other day). Two days following initiation of treatment with IFN-β or CXCL10 BEC cultures were infected with human RV-A16 at an MOI of 0.5 as described above. RNA was collected from BEC cultures pre-infection and 2d following RV infection.
Total RNA was used to construct libraries by using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, San Jose, Calif), with reverse transcription followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed by using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina, San Diego, Calif) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, Mass). Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 53-base reads with a target depth of 5 million reads per sample

tag: studygroup

value: Asthma

tag: donorid

tag: exacerbation status

value: Severe Exacerbation

tag: treatment

value: IFNb + RV16

tag: infection

tag: timepoint

tag: age

tag: Sex

value: female

tag: ethnicity

value: White

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

value: Yes

tag: viral load

tag: median cv_coverage

tag: total reads

tag: pct aligned

tag: batch


title: T1014_RV16

description:
Library name: lib106333
combined_counts_IFN.csv

tag: studygroup

tag: donorid

tag: cell type

value: Organotypic airway epithelial cell culture

tag: exacerbation status

value: No Severe Exacerbation

tag: treatment

value: None + RV16

value: male


title: T1013_RV16

description:
Library name: lib106337
combined_counts_IFN.csv

tag: infection

tag: timepoint

tag: age

tag: Sex

tag: ethnicity


title: T1013_CXCL10_plus_RV16

description:
Library name: lib106338
combined_counts_IFN.csv

value: CXCL10 + RV16

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio


title: T1014_CTL

description:
Library name: lib106332
combined_counts_IFN.csv

value: None + None

tag: fef25-75 (%_predicted)

tag: viral load

tag: median cv_coverage

tag: total reads

tag: pct aligned


title: PD-1–CXCR3–_rep2

tag: strain background

tag: cell type


title: PD-1–CXCR3+_rep1

value: CD4+Foxp3-YFP+PD-1–CXCR3+ Treg cells from DT-treated DTR chimera mice.


title: PD-1+CXCR3–_rep1

value: CD4+Foxp3-YFP+PD-1+CXCR3– Treg cells from DT-treated DTR chimera mice.


title: PD-1+CXCR3+_rep1


title: T1010_IFNb_plus_RV16

description:
Library name: lib106331
combined_counts_IFN.csv

tag: studygroup

tag: donorid

tag: exacerbation status

tag: treatment

tag: infection

value: No

tag: batch


title: T1010_CXCL10_plus_RV16

description:
Library name: lib106330
combined_counts_IFN.csv

tag: timepoint

tag: age

tag: Sex

tag: ethnicity

tag: allergic sensitization

tag: eos absolute_(mm2)


title: T1010_RV16

description:
Library name: lib106329
combined_counts_IFN.csv

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: viral load

tag: median cv_coverage


title: T1010_CTL

description:
Library name: lib106328
combined_counts_IFN.csv

tag: studygroup

tag: donorid

tag: cell type

tag: total reads

tag: pct aligned


title: T1012_CXCL10_plus_RV16

description:
Library name: lib106326
combined_counts_IFN.csv

tag: exacerbation status

tag: treatment

tag: infection

tag: timepoint

tag: batch


title: T1012_IFNb_plus_RV16

description:
Library name: lib106327
combined_counts_IFN.csv

tag: age

tag: Sex

tag: ethnicity

tag: allergic sensitization

tag: eos absolute_(mm2)


title: T1014_IFNb_plus_RV16

description:
Library name: lib106335
combined_counts_IFN.csv

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: viral load


title: T1012_RV16

description:
Library name: lib106325
combined_counts_IFN.csv

tag: studygroup

tag: donorid

tag: cell type

tag: median cv_coverage

tag: total reads


title: T1013_CTL

description:
Library name: lib106336
combined_counts_IFN.csv

tag: exacerbation status

tag: treatment

tag: infection

tag: timepoint

tag: pct aligned


title: T1014_CXCL10_plus_RV16

description:
Library name: lib106334
combined_counts_IFN.csv

tag: age

tag: Sex

tag: ethnicity

tag: allergic sensitization

tag: batch


title: T1007_RV16

description:
Library name: lib106321
combined_counts_IFN.csv

value: American Indian/Native Alaskan

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)


title: T1007_CXCL10_plus_RV16

description:
Library name: lib106322
combined_counts_IFN.csv

tag: studygroup

tag: donorid

tag: cell type

tag: viral load

tag: median cv_coverage


title: T1007_CTL

description:
Library name: lib106320
combined_counts_IFN.csv

tag: exacerbation status

tag: treatment

tag: infection

tag: timepoint

tag: total reads


title: PD-1+CXCR3–_rep2

tag: strain background


title: T170_IFNb_plus_RV16

description:
Library name: lib106319
combined_counts_IFN.csv

tag: age

tag: Sex

tag: ethnicity

tag: allergic sensitization

tag: pct aligned

tag: batch


title: T170_CXCL10_plus_RV16

description:
Library name: lib106318
combined_counts_IFN.csv

tag: studygroup

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)


title: T170_RV16

description:
Library name: lib106317
combined_counts_IFN.csv

tag: donorid

tag: cell type

tag: exacerbation status

tag: treatment

tag: viral load

tag: median cv_coverage


title: T1004_RV16

description:
Library name: lib106313
combined_counts_IFN.csv

tag: infection

tag: timepoint

tag: age

tag: Sex

tag: total reads


title: T1004_CXCL10_plus_RV16

description:
Library name: lib106314
combined_counts_IFN.csv

tag: studygroup

tag: ethnicity

tag: allergic sensitization

tag: pct aligned

tag: batch


title: T170_CTL

description:
Library name: lib106316
combined_counts_IFN.csv

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)


title: PD-1–CXCR3–_rep1

tag: strain background

tag: cell type

value: CD4+Foxp3-YFP+PD-1–CXCR3– Treg cells from DT-treated DTR chimera mice.


title: T1004_IFNb_plus_RV16

description:
Library name: lib106315
combined_counts_IFN.csv

value: Asthma

tag: donorid

tag: exacerbation status

tag: treatment

tag: infection

tag: viral load

tag: median cv_coverage


title: T1003_IFNb_plus_RV16

description:
Library name: lib106311
combined_counts_IFN.csv

tag: studygroup

tag: timepoint

tag: age

tag: Sex

tag: ethnicity

tag: total reads


title: T1012_CTL

description:
Library name: lib106324
combined_counts_IFN.csv

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: pct aligned

tag: batch


title: T1003_CTL

description:
Library name: lib106308
combined_counts_IFN.csv

tag: donorid

tag: cell type

tag: exacerbation status

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)


title: T1003_CXCL10_plus_RV16

description:
Library name: lib106310
combined_counts_IFN.csv

tag: studygroup

tag: treatment

tag: infection

tag: viral load

tag: median cv_coverage


title: T1003_RV16

description:
Library name: lib106309
combined_counts_IFN.csv

tag: timepoint

tag: age

tag: Sex

tag: ethnicity

tag: total reads


title: T1007_IFNb_plus_RV16

description:
Library name: lib106323
combined_counts_IFN.csv

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: pct aligned


title: T197_IFNb_plus_RV16

description:
Library name: lib106307
combined_counts_IFN.csv

tag: donorid

tag: cell type

tag: exacerbation status

value: Hispanic

tag: fev1/fvc ratio

tag: batch


title: T197_CXCL10_plus_RV16

description:
Library name: lib106306
combined_counts_IFN.csv

tag: studygroup

tag: treatment

tag: infection

tag: fef25-75 (%_predicted)

tag: viral load


title: T187_IFNB_plus_RV16

description:
Library name: lib106303
combined_counts_IFN.csv

value: Severe Exacerbation

value: IFNb + RV16

tag: timepoint

tag: age

tag: Sex

tag: ethnicity

tag: median cv_coverage


title: T187_CTL

description:
Library name: lib106300
combined_counts_IFN.csv

value: White

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: total reads


title: T197_RV16

description:
Library name: lib106305
combined_counts_IFN.csv

tag: donorid

tag: cell type

tag: exacerbation status

tag: fev1/fvc ratio

tag: pct aligned


title: T197_CTL

description:
Library name: lib106304
combined_counts_IFN.csv

tag: studygroup

tag: treatment

tag: infection

tag: fef25-75 (%_predicted)

tag: batch


title: T187_RV16

description:
Library name: lib106301
combined_counts_IFN.csv

tag: timepoint

tag: age

tag: Sex

tag: ethnicity

value: Yes

tag: viral load


title: T199_IFNB_plus_RV16

description:
Library name: lib106299
combined_counts_IFN.csv

value: Organotypic airway epithelial cell culture

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: median cv_coverage


title: T199_RV16

description:
Library name: lib106297
combined_counts_IFN.csv

tag: donorid

tag: cell type

tag: exacerbation status

tag: fev1/fvc ratio

tag: total reads


title: T194_CXCL10_plus_RV16

description:
Library name: lib106294
combined_counts_IFN.csv

tag: studygroup

tag: treatment

tag: infection

tag: fef25-75 (%_predicted)

tag: pct aligned


title: T194_RV16

description:
Library name: lib106293
combined_counts_IFN.csv

tag: timepoint

tag: age

tag: Sex

tag: ethnicity

tag: batch


title: T194_IFNb_plus_RV16

description:
Library name: lib106295
combined_counts_IFN.csv

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: viral load


title: T199_CTL

description:
Library name: lib106296
combined_counts_IFN.csv

tag: donorid

tag: cell type

tag: exacerbation status

tag: fev1/fvc ratio

tag: median cv_coverage


title: T194_CTL

description:
Library name: lib106292
combined_counts_IFN.csv

tag: studygroup

tag: treatment

tag: infection

tag: fef25-75 (%_predicted)

tag: total reads


title: T199_CXCL10_plus_RV16

description:
Library name: lib106298
combined_counts_IFN.csv

tag: timepoint

tag: age

tag: Sex

tag: ethnicity

tag: pct aligned


title: 3_T1007_RV16

description:
Library name: 3_T1007_RV16
10X Chromium Flex RNA protocol

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-sequencing (scRNA-seq) 10x dataset preprocessing including cell demultiplexing and alignment were performed using Cell Ranger Single-Cell Software Suite (version 7.0.0, 10x Genomics Inc). We used the human reference genome (GRCh38, Ensembl 91) for alignment and generated raw and filtered cell by gene count matrix files.
Assembly: Human GRCh38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per cell barcode per gene ID for all barcodes

molecule: polyA RNA

source_name: Bronchial epithelial cells

extract_protocol:
Bronchial epithelial cells (BECs) from children were obtained while under general anesthesia for an elective surgery using 4-mm Harrell unsheathed bronchoscope cytology brushes inserted through an endotracheal tube. BECs (passage 2 or 3) were proliferated on transwells under submerged culture conditions using PneumaCult™EX-Plus medium (Stemcell™) for 4-7 days then differentiated to an organotypic pseudostratified ciliated state for 21 days at ALI. BEC cultures were infected on the apical surface with human rhinovirus A16 (RV-A16, Source: ATCC®) at a multiplicity of infection (MOI) of 0.5. Viral suspension was removed from the apical surface after 2 hours of incubation with no subsequent rinsing. RNA was collected from BECs pre-infection and 2 days post-infection for scRNA-seq data. The 10X Genomics Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit was used to fix the BECs. Samples were stored at -80°C until further post-storage processing and sequencing.
Fixed samples were processed according to manufacturer’s instructions, using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics).  Briefly, fixed samples were thawed and hybridized overnight to one of four human probe sets (10x Genomics), with or without additional spiked-in custom rhinovirus probes. Pooled samples were washed and loaded onto the Chromium X (10x Genomics) for partitioning into GEMs.  Gene expression libraries were generated according to the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples user guide.  Sequencing was carried out on a NextSeq 2000 sequencer, using NextSeq 2000 P4 XLEAP-SBS flowcells (Illumina) with a target depth of 10,000 reads/cell.

tag: tissue

value: Bronchial epithelial cells

value: Airway epithelial

tag: donor group

value: NSE

tag: condition


title: 1_T1007_Uninfected

description:
Library name: 1_T1007_Uninfected
10X Chromium Flex RNA protocol

tag: cell type

value: Uninfected


title: 1_T176_Uninfected

description:
Library name: 1_T176_Uninfected
10X Chromium Flex RNA protocol

value: SE


title: 3_T170_RV16

description:
Library name: 3_T170_RV16
10X Chromium Flex RNA protocol


title: 1_T383_Uninfected

description:
Library name: 1_T383_Uninfected
10X Chromium Flex RNA protocol

value: Healthy


title: 3_T176_RV16

description:
Library name: 3_T176_RV16
10X Chromium Flex RNA protocol


title: 3_T383_RV16

description:
Library name: 3_T383_RV16
10X Chromium Flex RNA protocol


title: T1004_CTL

description:
Library name: lib106312
combined_counts_IFN.csv

tag: donorid

tag: exacerbation status

value: No Severe Exacerbation

value: None + None

value: female

tag: allergic sensitization

tag: eos absolute_(mm2)

tag: feno (ppb)

tag: fev1 (%_predicted)

tag: viral load

tag: batch


title: 1_T170_Uninfected

description:
Library name: 1_T170_Uninfected
10X Chromium Flex RNA protocol


title: T187_CXCL10_plus_RV16

description:
Library name: lib106302
combined_counts_IFN.csv

tag: studygroup

tag: treatment

value: CXCL10 + RV16

tag: infection

tag: timepoint

value: male

tag: fev1/fvc ratio

tag: fef25-75 (%_predicted)

tag: median cv_coverage

tag: total reads


title: 1_T1004_Uninfected

description:
Library name: 1_T1004_Uninfected
10X Chromium Flex RNA protocol

tag: tissue

tag: cell type

tag: donor group

tag: condition


title: 3_T187_RV16

description:
Library name: 3_T187_RV16
10X Chromium Flex RNA protocol


title: 1_T187_Uninfected

description:
Library name: 1_T187_Uninfected
10X Chromium Flex RNA protocol


title: 3_T3030_RV16

description:
Library name: 3_T3030_RV16
10X Chromium Flex RNA protocol


title: 3_T197_RV16

description:
Library name: 3_T197_RV16
10X Chromium Flex RNA protocol


title: 3_T1004_RV16

description:
Library name: 3_T1004_RV16
10X Chromium Flex RNA protocol


title: 1_T197_Uninfected

description:
Library name: 1_T197_Uninfected
10X Chromium Flex RNA protocol


title: 1_T186_Uninfected

description:
Library name: 1_T186_Uninfected
10X Chromium Flex RNA protocol


title: 1_T3030_Uninfected

description:
Library name: 1_T3030_Uninfected
10X Chromium Flex RNA protocol


title: 1_T199_Uninfected

description:
Library name: 1_T199_Uninfected
10X Chromium Flex RNA protocol


title: 3_T199_RV16

description:
Library name: 3_T199_RV16
10X Chromium Flex RNA protocol


title: 3_T3027_RV16

description:
Library name: 3_T3027_RV16
10X Chromium Flex RNA protocol


title: 1_T3027_Uninfected

description:
Library name: 1_T3027_Uninfected
10X Chromium Flex RNA protocol


title: 1_T179_Uninfected

description:
Library name: 1_T179_Uninfected
10X Chromium Flex RNA protocol


title: 1_T194_Uninfected

description:
Library name: 1_T194_Uninfected
10X Chromium Flex RNA protocol


title: 3_T194_RV16

description:
Library name: 3_T194_RV16
10X Chromium Flex RNA protocol


title: 1_T1003_Uninfected

description:
Library name: 1_T1003_Uninfected
10X Chromium Flex RNA protocol


title: 3_T179_RV16

description:
Library name: 3_T179_RV16
10X Chromium Flex RNA protocol


title: 3_T1003_RV16

description:
Library name: 3_T1003_RV16
10X Chromium Flex RNA protocol


title: HEK293T, P300 ChIP, 2M cells, 0.5ug antibody

city: La Jolla

first: Alon

last: Goren

state: CA

address: 9375 Gilman Dr

department: Department of Medicine

institute: University of California San Diego

description: Library name: HEK293T_P300_2M_0-5ug

library_source: genomic

data_processing:
Reads were trimmed with Trimmomatic, aligned to human reference genome hg38 using Bowtie2, and duplicated reads were removed with Samtools markdup.
HOMER was used to make tag directories, create bigWig files, find peaks, annotate peaks, and identify motifs.
Assembly: hg38
Supplementary files format and content: bigWig files containing quantified signal

molecule: genomic DNA

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 110mg/L sodium pyruvate, 2 mM L-glutamine, and 1% Antibiotic-Antimycotic, and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were either single (FA) or double (DSG+FA) crosslinked. Chromatin was sonicated with lysis buffer to obatin fragments of 200-500bp. Sheared chromatin was incubated with antibody and Protein A beads overnight at 4C. ChIP samples were washed and input samples were cleaned up with Speedbeads before library prep.
Libraries of ChIP and input samples were prepared with the NEBNext Ultra II Library Prep Kit for Illumina and cleaned with Speedbeads. Indexing adapters were from NEXTflex DNA Barcodes. Libraries were PCR amplified with Solexa 1GA and 1GB primers and size selected with a final Speedbeads cleanup. Library size was estimated with agarose gel, concentrations measured with Qubit HS DNA assay kit.

tag: cell line

value: kidney epithelial cell

tag: genotype

value: wild-type

tag: chip antibody


title: HEK293T, input control for P300 antibody titration experiment

description: Library name: HEK293T_input_forP300AbTitr


title: HEK293T, P300 ChIP, 200K cells, 0.5ug antibody

description: Library name: HEK293T_P300_200K_0-5ug


title: HEK293T, P300 ChIP, 2M cells, 5ug antibody

description: Library name: HEK293T_P300_2M_5ug


title: HEK293T, P300 ChIP, 200K cells, 2.5ug antibody

description: Library name: HEK293T_P300_200K_2-5ug


title: HEK293T, P300 ChIP, 2M cells, 0.05ug antibody

description: Library name: HEK293T_P300_2M_0-05ug


title: HEK293T, P300 ChIP, 200K cells, 0.05ug antibody

description: Library name: HEK293T_P300_200K_0-05ug


title: HEK293T, P300 ChIP, 20K cells, 5ug antibody

description: Library name: HEK293T_P300_20K_5ug


title: HEK293T, P300 ChIP, 200K cells, 5ug antibody

description: Library name: HEK293T_P300_200K_5ug


title: HEK293T, P300 ChIP, 2M cells, 2.5ug antibody

description: Library name: HEK293T_P300_2M_2-5ug


title: 3_T186_RV16

description:
Library name: 3_T186_RV16
10X Chromium Flex RNA protocol


title: HEK293T, P300 ChIP, 20K cells, 2.5ug antibody

description: Library name: HEK293T_P300_20K_2-5ug


title: HEK293T-FKBP12F36V, dTAG treated, input control

description: Library name: HEK293T_FKBP_dTAG_input

value: 500nM dTAG-13


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 5ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_HA_5ul_2

value: CST HA-tag (C29F4)


title: HEK293T, P300 ChIP, 20K cells, 0.05ug antibody

description: Library name: HEK293T_P300_20K_0-05ug


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 2.5ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_HA_2-5ul_2


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 5ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_HA_5ul_1


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 2.5ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_HA_2-5ul_1


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 1ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_HA_1ul_1


title: HEK293T, P300 ChIP, 20K cells, 0.5ug antibody

description: Library name: HEK293T_P300_20K_0-5ug


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 1ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_HA_1ul_2


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 0.5ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_HA_0-5ul_1


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 5ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_BRD4_5ul_2


title: HEK293T-FKBP12F36V, dTAG treated, HA-tag ChIP, 0.5ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_HA_0-5ul_2


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 5ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_BRD4_5ul_1


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 1ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_BRD4_1ul_1


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 2.5ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_BRD4_2-5ul_2


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 0.5ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_BRD4_0-5ul_2


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 1ul antibody, rep2

description: Library name: HEK293T_FKBP_dTAG_BRD4_1ul_2


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 2.5ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_BRD4_2-5ul_1


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 5ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_HA_5ul_1

value: DMSO

value: HA-tag (CST, C29F4)


title: HEK293T-FKBP12F36V, DMSO treated, input control

description: Library name: HEK293T_FKBP_DMSO_input


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 1ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_HA_1ul_2


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 2.5ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_HA_2-5ul_2


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 2.5ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_HA_2-5ul_1


title: HEK293T-FKBP12F36V, dTAG treated, BRD4 ChIP, 0.5ul antibody, rep1

description: Library name: HEK293T_FKBP_dTAG_BRD4_0-5ul_1


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 0.5ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_HA_0-5ul_1


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 5ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_BRD4_5ul_1


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 1ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_HA_1ul_1


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 0.5ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_HA_0-5ul_2


title: HEK293T-FKBP12F36V, DMSO treated, HA-tag ChIP, 5ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_HA_5ul_2


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 5ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_BRD4_5ul_2


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 2.5ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_BRD4_2-5ul_2


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 1ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_BRD4_1ul_1


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 0.5ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_BRD4_0-5ul_2


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 1ul antibody, rep2

description: Library name: HEK293T_FKBP_DMSO_BRD4_1ul_2


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 2.5ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_BRD4_2-5ul_1


title: HEK293T-FKBP12F36V, DMSO treated, BRD4 ChIP, 0.5ul antibody, rep1

description: Library name: HEK293T_FKBP_DMSO_BRD4_0-5ul_1


title: 48hr SAHA Treated ATAC-seq Bio rep 3

city: Los Alamos

first: Eric

middle: M

last: Small

state: New Mexico

address: Bikini Atoll Rd.

department: Earth and Environmental Sciences Division

institute: Los Alamos National Laboratory

description: Library name: 2501_047

data_processing:
ATAC-seq libraries were sequenced as described above and analysis was performed as previously described (Roth et al., 2023; Venu et al., 2024). Twelve ATAC-seq libraries were sequenced to a median depth of 57 million read pairs per library. Briefly, raw reads were trimmed and filtered to remove Nextra adaptors and reads with repetitive sequences using Fastp (Chen et al., 2018) . Bases with low quality scores (q < 15) were removed. Processed reads were aligned to the telomere-to-telomere (T2T) human reference genome, version 2 (Nurk et al., 2022) via BWA (Li and Durbin, 2009). Duplicate sequenced pairs and mitochondrial reads were marked and removed from analysis via Samblaster (Faust and Hall, 2014). Samples were further filtered using samtools with the following flags:  -F 4 -F 256 -F 512 -F 1024 -F 2048 -q 30.  Samples were then passed to MACS2 in BAMPE mode. Loci displaying significant enrichment of paired-end reads were identified as peaks using MACS2 (Gaspar, 2018; Zhang et al., 2008). Replicate correlation was assessed using deepTools (Ramirez et al., 2016) -plotCorrelation function on SPMR normalized MACS2 output big wig files. Open chromatin regions (OCRs) were defined by MACS2-called peaks followed the BEDtools (Quinlan and Hall, 2010) merge function. OCR differential accessibility analysis was performed using the DESeq2 (Love et al., 2014) matrix design (~time + treatment).
MACS2 output treat pileup bedgraph files are converted to bigwig format using bedGraphToBigwig function from UCSC
Processed .narrowPeak files, treat pileup bigwig files, DESeq2 result files are provided. Single DESeq2 file present differential peak analysis across all samples at a given time point.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: .narrowPeak files: Peaks called uisng MACS2 as mentioned in the data processing tab
Supplementary files format and content: .bw files: contain signal track visualizable in any genome browser
Supplementary files format and content: DESeq2 result table includes timepoint specific DESeq output. This file is used to identify regions with significant difference in accessibility.

source_name: lung carcinomatous tissue

growth_protocol: A549 cells, isolated from the lung tissue of a 58-year-old Caucasian male with lung cancer, were obtained from ATCC (Cat. #CCL-185). Cells were maintained in Complete Medium consisting of Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 4 mM L-Glutamine (ATCC, Cat. #30-2002) and 10% (v/v) Fetal Bovine Serum (FBS, ATCC, Cat. #30-2020). Cells were incubated at 37°C with 5% CO2 and 95% relative humidity. Multiple vials were cryopreserved at passage #2 in liquid nitrogen vapor until needed for cell culture experiments. For cryopreservation, cells were resuspended to a density of 106 cells per mL in ice-cold Freezing Medium consisting of DMEM,  20% (v/v) FBS, and 5% (v/v) dimethylsulfoxide (DMSO, ATCC, Cat. # 4-X).

extract_protocol:
During cell harvest (at 24 and 48 hrs post-treatment), drug-treated and mock-treated culture flasks for each biological replicate were processed in parallel. Cells were washed once in 1X PBS, detached using 1X TrypLE Express Enzyme for 20 min, then resuspended in Complete Medium to create a uniform single-cell suspension. Cell suspensions were held at room temperature and counted using the Scepter 3.0 Handheld Cell Counter and 60 µm Counter Sensors, then immediately divided as needed for downstream processing. Approximately 2x105 cells were cryopreserved in triplicate 1 mL aliquots using ice-cold Freezing Medium 24 and 48 hrs after treatment as previously described (Roth et al., 2023).
Aliquots were subsequently thawed into Complete Medium, counted to achieve ~80,000 cells per sample, and processed for ATAC-seq analysis using the Active Motif ATAC-seq Kit manual (Cat. #53150) as previously described (Roth et al., 2023). Briefly, cells were lysed and tagmented DNA was prepared and purified; DNA libraries were prepared via PCR using primers provided in the kit. Libraries were purified and additional size-selected using AmpureXP beads (Beckman, Cat. #A63880) per the manufacturer's protocol to retain fragments between 150 bp and 600 bp. Libraries were quantified using a high-sensitivity Qubit dsDNA Quantification Assay Kit (Thermo Scientific, Cat. #Q32851) and a KAPA Library Quantification Kit (Roche, Cat. #KR0405). Libraries were sequenced via the Illumina NextSeq 2000 sequencer (LANL Genome Center) in paired-end mode (PE151) using P3 chemistry.

treatment_protocol: For cell culture experiments, A549 cells were propagated for at least two additional passages prior to seeding for HDACi drug treatments. Cells were washed once in 1X PBS (Gibco, Cat. # 10010049), detached using 1X TrypLE Express Enzyme (Thermo Scientific, Cat. # 12604021), resuspended into Complete Medium, and counted using the Scepter 3.0 Handheld Cell Counter and 60 µm Counter Sensors (Millipore, Cat. #PHCC360KIT). Cells were seeded for HDACi drug treatments at passage #7-8 into replicate tissue culture flasks (surface area = 175 cm2) in three biological replicates using 5x106 cells per flask. Seeded flasks were incubated for 72 hrs at 37°C, yielding a confluent monolayer (~10x106 cells per flask) at the time of drug treatment. Cell-seeding medium was removed after 72 hrs from replicate tissue culture flasks and replaced with Complete Medium containing 10 µM of the HDACi drug suberoylanilide hydroxamic acid (SAHA) or containing an equivalent volume of the drug vehicle only, DMSO (Pierce, Cat. #85190). Mock-treated (control) and drug-treated culture flasks were incubated in parallel for 24 or 48 hrs at 37°C.

value: lung carcinomatous tissue

value: Treated with 10 µM SAHA


title: 48hr Control ATAC-seq Bio rep 3

description: Library name: 2501_043

value: Untreated


title: 48hr SAHA Treated ATAC-seq Bio rep 2

description: Library name: 2501_041


title: 48hr SAHA Treated ATAC-seq Bio rep 1

description: Library name: 2501_040


title: 48hr Control ATAC-seq Bio rep 1

description: Library name: 2501_036


title: 48hr Control ATAC-seq Bio rep 2

description: Library name: 2501_037


title: 24hr SAHA Treated ATAC-seq Bio rep 1

description: Library name: 2501_034


title: 24hr Control ATAC-seq Bio rep 2

description: Library name: 2501_031


title: 24hr SAHA Treated ATAC-seq Bio rep 3

description: Library name: 2501_046


title: 24hr SAHA Treated ATAC-seq Bio rep 2

description: Library name: 2501_035


title: 24hr Control ATAC-seq Bio rep 1

description: Library name: 2501_030


title: 24hr Control ATAC-seq Bio rep 3

description: Library name: 2501_042


title: rnh1/2 dRNH-FLAG input rep 2

city: Cold Spring Harbor

first: Teri

last: Cheng

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Library name: C290

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.

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:
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: rnh1 rnh201

value: input


title: tri dRNH-FLAG input rep 2

description: Library name: C298

value: dcr1 rnh1 rnh201


title: dcr dRNH-FLAG input rep 1

description: Library name: C293


title: tri dRNH-FLAG input rep 1

description: Library name: C297


title: tri NLS-FLAG input rep 1

description: Library name: C295


title: dcr NLS-FLAG input rep 2

description: Library name: C292


title: tri NLS-FLAG input rep 2

description: Library name: C296


title: rnh1/2 dRNH-FLAG input rep 1

description: Library name: C289


title: rnh1/2 NLS-FLAG input rep 1

description: Library name: C287


title: WT dRNH-FLAG input rep 2

description: Library name: C286

value: WT


title: dcr dRNH-FLAG input rep 2

description: Library name: C294


title: rnh1/2 NLS-FLAG input rep 2

description: Library name: C288


title: WT dRNH-FLAG input rep 1

description: Library name: C285


title: WT NLS-FLAG input rep 1

description: Library name: C283


title: WT NLS-FLAG input rep 2

description: Library name: C284


title: dcr NLS-FLAG input rep 1

description: Library name: C291


title: tri NLS-FLAG chip rep 2

description: Library name: C280

value: NLS-FLAG


title: tri dRNH-FLAG chip rep 1

description: Library name: C281

value: dRNH-FLAG


title: tri NLS-FLAG chip rep 1

description: Library name: C279


title: dcr dRNH-FLAG chip rep 2

description: Library name: C278


title: dcr NLS-FLAG chip rep 2

description: Library name: C276


title: dcr NLS-FLAG chip rep 1

description: Library name: C275


title: rnh1/2 dRNH-FLAG chip rep2

description: Library name: C274


title: dcr dRNH-FLAG chip rep 1

description: Library name: C277


title: rnh1/2 NLS-FLAG chip rep2

description: Library name: C272


title: rnh1/2 dRNH-FLAG chip rep1

description: Library name: C273


title: WT dRNH-FLAG chip rep1

description: Library name: C269


title: rnh1/2 NLS-FLAG chip rep1

description: Library name: C271


title: WT dRNH-FLAG chip rep2

description: Library name: C270


title: WT NLS-FLAG chip rep2

description: Library name: C268


title: Ubp16_ser2_15min_rep2

city: Barcelona

first: Montserrat

last: Vega

state: Barcelona

address: C/ Dr. Aiguader 88, lab 383

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra

description: Library name: Sample 41

data_processing:
BBDuk was used for quality and adapter trimming of reads
aligned using Bowtie2
low-quality alignments were filtered with SAMtools
BigWig file generation were performed using deepTools
Assembly: Schizosaccharomyces pombe ASM294v2
Supplementary files format and content: BigWig files

source_name: S.pombe ubp16 cells

growth_protocol: WT, ubp8 and ubp16 strains were grown in YE5S media at 30ºC at OD600 of 0.5

extract_protocol:
ChIP of PolII, Ser2 and GFP
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, following manufacturer’s  instructions

treatment_protocol: untreated samples and 1 mM H2O2 treatment during  5 and 15 minutes

value: S.pombe ubp16 cells

value: 15 min 1 mM  H2O2


title: WT NLS-FLAG chip rep1

description: Library name: C267


title: ubp16_ser2_INPUT

description: Library name: Sample 44

value: untreated


title: tri dRNH-FLAG chip rep 2

description: Library name: C282


title: Ubp16_ser2_15min_rep1

description: Library name: Sample 39


title: ubp8_ser2_INPUT

description: Library name: Sample 43

source_name: S.pombe ubp8 cells

value: S.pombe ubp8 cells


title: Ubp8_ser2_15min_rep2

description: Library name: Sample 37


title: Ubp16_ser2_untreated_rep2

description: Library name: Sample 40


title: WT_ser2_INPUT

description: Library name: Sample 42

source_name: S.pombe wt cells

value: S.pombe wt cells


title: Ubp8_ser2_untreated_rep1

description: Library name: Sample 34


title: WT_ser2_untreated_rep2

description: Library name: Sample 32


title: Ubp16_ser2_untreated_rep1

description: Library name: Sample 38


title: Ubp8_ser2_untreated_rep2

description: Library name: Sample 36


title: WT_ser2_15min_rep1

description: Library name: Sample 31


title: WT_ser2_untreated_rep1

description: Library name: Sample 30


title: Ubp16_GFP_INPUT

description: Library name: Sample 29

value: WT (Ubp16-GFP)


title: Ubp8_ser2_15min_rep1

description: Library name: Sample 35


title: Ubp8_GFP_INPUT

description: Library name: Sample 28

value: WT (Ubp8-GFP)


title: Ubp16_GFP_15min_rep2

description: Library name: Sample 27


title: WT_ser2_15min_rep2

description: Library name: Sample 33


title: Ubp16_GFP_5min_rep2

description: Library name: Sample 26

value: 5 min 1 mM H2O2


title: Ubp16_GFP_5min_rep1

description: Library name: Sample 23


title: Ubp8_GFP_15min_rep2

description: Library name: Sample 21


title: Ubp8_GFP_untreated_rep2

description: Library name: Sample 19


title: Ubp16_GFP_untreated_rep2

description: Library name: Sample 25


title: Ubp8_GFP_5min_rep2

description: Library name: Sample 20


title: Ubp16_GFP_15min_rep1

description: Library name: Sample 24


title: Ubp16_GFP_untreated_rep1

description: Library name: Sample 22


title: Ubp8_GFP_15min_rep1

description: Library name: Sample 18


title: Ubp8_GFP_5min_rep1

description: Library name: Sample 17


title: Ubp8_GFP_untreated_rep1

description: Library name: Sample 16


title: ubp16_pol2_15min_rep2

description: Library name: Sample 14

value: ubp16 (Rpb1-HA)


title: ubp16_pol2_15min_rep1

description: Library name: Sample 12


title: ubp16_pol2_untreated_rep2

description: Library name: Sample 13


title: ubp16_pol2_untreated_rep1

description: Library name: Sample 11


title: ubp8_pol2_INPUT

description: Library name: Sample 10

value: ubp8 (Rpb1-HA)


title: ubp16_pol2_INPUT

description: Library name: Sample 15


title: ubp8_pol2_untreated_rep1

description: Library name: Sample 6


title: WT_pol2_15min_rep2

description: Library name: Sample 4

value: WT (Rpb1-HA)


title: WT_pol2_untreated_rep1

description: Library name: Sample 1


title: ubp8_pol2_15min_rep1

description: Library name: Sample 7


title: WT_pol2_INPUT

description: Library name: Sample 5


title: MNase, ubo16_5min_rep2

data_processing:
Alignment using Bowtie2
BAM files, and quality aligment (supllementary, improper paired, non-primary alignments and reads with less than 20 of mapping quality) using SAMtools
Picard MarkDuplicated function employed to remove duplicated reads from BAM files
DANPOS2 was used to remove clonal reads, adjust read length, perfom quantile normalization and calculate differences in nucleosome occupancy
Assembly: Schizosaccharomyces pombe ASM294v2
Supplementary files format and content: Big Wig files

extract_protocol:
Micrococcal nuclease digestion
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, following manufacturer’s  instructions


title: MNase, ubp16_15min_rep2

value: 15 min 1 mM H2O2


title: MNase, ubp16_untreated_rep1


title: ubp8_pol2_untreated_rep2

description: Library name: Sample 8


title: ubp8_pol2_15min_rep2

description: Library name: Sample 9


title: WT_pol2_15min_rep1

description: Library name: Sample 2


title: MNase, ubp16_untreated_rep2


title: MNase, ubp8_15min_rep1


title: MNase, ubp8_5min_rep1


title: MNase, ubo8_5min_rep2


title: MNase, ubp8_untreated_rep2


title: MNase, ubp8_untreated_rep1


title: MNase, ubp8_15min_rep2


title: MNase, 972_15min_rep2


title: MNase, 972_15min_rep1


title: MNase, 972_5min_rep2


title: MNase, 972_untreated_rep2


title: WT_pol2_untreated_rep2

description: Library name: Sample 3


title: MNase, 972_untreated_rep1


title: ubp16_treated_rep2

data_processing:
Quality controls for FASTQ files using FastQC
Trim of low quality read bases from FASTQ files as well as removal of adapters and other contaminants using Trimmomatic
Alignment against the Schizosaccharomyces pombe all chromosomes  20230315 genone reference using STAR
Confirmation that no coverage biases are present in the aligned data according to genomic reference file using QualiMap2
Read count overlapping Schizosaccharomyces pombe  all chromosomes  20230315 genomic features using htseq-count
Test for differentially expressed features between conditions using DESeq2
Assembly: Schizosaccharomyces pombe all chromosomes  20230315
Supplementary files format and content: tab-separated .txt table of Raw counts for all the samples

growth_protocol: WT, ubp8 and ubp16 mutant strains were grown in YE5S media at 30ºC at OD600 of 0.5

extract_protocol:
Hot phenol extraction
TrueSeq Stranded mRNA sample Prep kit following manufacterer's instructions

treatment_protocol: untreated and 1 mM H2O2 treatment during 30 minutes

value: 30 min 1 mM H2O2


title: ubp16_untreated_rep1


title: ubp16_untreated_rep2


title: ubp8_untreated_rep1


title: WT_untreated_rep2


title: ubp8_treated_rep1


title: ubp8_treated_rep2


title: WT_treated_rep2


title: RIP-seq_rnh12_input_rep1

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 18-25nt.

extract_protocol:
Immunoprecipitation was performed similar to ChIP 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 and treated with RQ1 DNase.
Libraries were prepared using NextFlex Small RNA-seq v4 Kits (Revvity).

value: yeast cells

value: rnh1 rnh201 ago1-flag

value: input


title: ubp16_treated_rep1


title: WT_treated_rep1


title: RIP-seq_WT_input_rep1


title: RIP-seq_dcr1_input_rep1

value: dcr1 ago1-flag


title: MNase, ubp16_15min_rep1

value: S.pombe ubp16 cells


title: ubp8_untreated_rep2


title: RIP-seq_dcr1_input_rep2


title: RIP-seq_dcr1rnh12_ago1_flag_rep2

value: dcr1 rnh1 rnh201 ago1-flag

value: anti-FLAG


title: RIP-seq_WT_input_rep2


title: RIP-seq_dcr1rnh12_ago1_flag_rep1


title: MNase, ubp16_5min_rep1


title: RIP-seq_rnh12_ago1_flag_rep2


title: MNase, 972_5min_rep1


title: RIP-seq_dcr1_ago1_flag_rep2


title: RIP-seq_rnh12_ago1_flag_rep1


title: RIP-seq_WT_ago1_flag_rep2


title: RIP-seq_dcr1_ago1_flag_rep1


title: RIP-seq_WT_ago1_flag_rep1


title: WT_untreated_rep1

value: untreated


title: RIP-seq_rnh12_input_rep2


title: RIP-seq_dcr1rnh12_input_rep2


title: RIP-seq_dcr1rnh12_input_rep1


title: dcr1rnh12_input_rep1

value: dcr1 rnh1 rnh201 Ago1-FLAG


title: dcr1rnh12_input_rep2


title: rnh12_input_rep2

value: rnh1 rnh201 Ago1-FLAG


title: dcr1rnh12_flag_rep1


title: WT_input_rep1

value: WT (Ago1-FLAG)


title: rnh12_flag_rep2


title: dcr1rnh12_flag_rep2


title: rnh12_flag_rep1


title: dcr1_flag_rep2

value: dcr1 Ago1-FLAG


title: sample_69

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

description: Library name: sample_69

data_processing:
Raw reads were assessed using FastQC v0.11.7. Trimmomatic v0.36 was used for quality trimming
Assembly: hg38
Supplementary files format and content: Text tab-delimited file includes methylation beta value of 20 CpG probes for each sample

source_name: primary tumor

extract_protocol:
Genomic DNA from FFPE sample was bisulfite-converted using the EZ DNA Methylation-Gold Kit according to the manufacturer’s instructions.
Bisulfite-specific PCR (BSP) primers were designed using MethPrimer software. PCR amplification was performed with KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (Kapa Biosystems) for 35 cycles. BSP products from multiple genes were pooled equally, 5′-phosphorylated, 3′-dA-tailed, and ligated to barcoded adapters using T4 DNA ligase (New England Biolabs). Barcoded libraries from all samples were combined and sequenced on the Illumina platform

value: primary tumor

tag: response to_ici

value: R

tag: disease state

value: Advanced Gastric Cancer


title: sample_68

description: Library name: sample_68

value: NR


title: sample_66

description: Library name: sample_66


title: sample_67

description: Library name: sample_67


title: sample_61

description: Library name: sample_61


title: sample_62

description: Library name: sample_62


title: sample_65

description: Library name: sample_65


title: sample_63

description: Library name: sample_63


title: sample_64

description: Library name: sample_64


title: sample_59

description: Library name: sample_59


title: sample_56

description: Library name: sample_56


title: sample_58

description: Library name: sample_58


title: sample_57

description: Library name: sample_57


title: rnh12_input_rep1


title: WT_input_rep2


title: dcr1_input_rep1


title: dcr1_input_rep2


title: WT_flag_rep2


title: dcr1_flag_rep1


title: sample_54

description: Library name: sample_54


title: WT_flag_rep1


title: sample_53

description: Library name: sample_53


title: sample_52

description: Library name: sample_52


title: sample_50

description: Library name: sample_50


title: sample_49

description: Library name: sample_49


title: sample_47

description: Library name: sample_47


title: sample_48

description: Library name: sample_48


title: sample_60

description: Library name: sample_60


title: sample_42

description: Library name: sample_42


title: sample_44

description: Library name: sample_44


title: sample_43

description: Library name: sample_43


title: sample_41

description: Library name: sample_41


title: sample_40

description: Library name: sample_40


title: sample_39

description: Library name: sample_39


title: sample_37

description: Library name: sample_37


title: sample_34

description: Library name: sample_34


title: sample_35

description: Library name: sample_35


title: sample_36

description: Library name: sample_36


title: sample_55

description: Library name: sample_55


title: sample_32

description: Library name: sample_32


title: sample_30

description: Library name: sample_30


title: sample_51

description: Library name: sample_51


title: sample_31

description: Library name: sample_31


title: sample_46

description: Library name: sample_46


title: sample_28

description: Library name: sample_28


title: sample_27

description: Library name: sample_27


title: sample_33

description: Library name: sample_33


title: sample_26

description: Library name: sample_26


title: sample_25

description: Library name: sample_25


title: sample_45

description: Library name: sample_45


title: sample_24

description: Library name: sample_24


title: sample_21

description: Library name: sample_21


title: sample_29

description: Library name: sample_29


title: sample_22

description: Library name: sample_22


title: sample_17

description: Library name: sample_17


title: sample_16

description: Library name: sample_16


title: sample_19

description: Library name: sample_19


title: sample_18

description: Library name: sample_18


title: sample_15

description: Library name: sample_15


title: sample_14

description: Library name: sample_14


title: sample_38

description: Library name: sample_38


title: sample_12

description: Library name: sample_12


title: sample_11

description: Library name: sample_11


title: sample_10

description: Library name: sample_10


title: sample_09

description: Library name: sample_09


title: sample_05

description: Library name: sample_05


title: sample_07

description: Library name: sample_07


title: sample_23

description: Library name: sample_23


title: sample_03

description: Library name: sample_03


title: sample_08

description: Library name: sample_08


title: sample_02

description: Library name: sample_02


title: sample_04

description: Library name: sample_04


title: sample_06

description: Library name: sample_06


title: C-3 H-Treg

city: Cincinnati

first: Alexander

last: Miethke

state: OH

address: 3333 Burnet Ave, MLC 2010

institute: Cincinnati Childrens Hospital Medical Ce

data_processing:
To analysis differential gene expression, sequence reads were aligned to the genome by using standard Illumina sequence analysis pipeline, which was analyzed by The Laboratory for Statistical Genomics and Systems Biology at the University of Cincinnati.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human peripheral blood mononuclear cells

growth_protocol: CD25+CD127-/lowCD4+CD3+CD56-CD45+eflour506-cells FACS sorted from peripheral blood of healthy donors. FACs sorted Tregs were cultured with  α-CD3, α-CD28 (Beads 1:1ratio), hIL-2(100U), with either H2O(Vehicle) or with TCDCA (100 μM), 48hrs.

extract_protocol:
Post culture cells were snap frozen prior to RNA isolation, further cells were lysed with lysis/binding buffer. Total RNA was extracted according to the protocol and was eluted with 60 µl Elution Buffer. RNA concentration was measured by Nanodrop and its integrity was determined by Bioanalyzer. NEBNext Poly(A) mRNA magnetic isolation module was used for polyA RNA purification with a total of 50 ng to 1 µg of good quality total RNA as input. ployA RNA isolation was done using SMARTer Apollo NGS library prep system.
Libraries for RNA-seq was prepared by using NEBNext Ultra II Directional RNA Library Prep kit as per manusfacturers protocol.
To study differential gene expression, individually indexed and compatible libraries were proportionally pooled (~25 million reads per sample in general) for clustering in cBot system (Illumina, San Diego, CA). Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell v3 using Illumina TruSeq SR Cluster kit v3 and sequenced to 51 bp using TruSeq SBS kit v3 on Illumina HiSeq system

value: anti-CD3, anti-CD28 beads 1:1ratio, hIL-2(100U), H2O

tag: time


title: TCDCA-1 H-Treg

value: Human peripheral blood mononuclear cells

tag: treatment

value: anti-CD3, anti-CD28 beads 1:1ratio, hIL-2(100U), TCDCA (100 microM)


title: C-2 H-Treg


title: SPF_stroma_8

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

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

department: Immunology Program

institute: Broad Institute

description:
Library name: SPF_stroma_8
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq pipeline made available by CellRanger v3.1.0 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: whole_tissue_sc_epi_geo_upload.h5ad: Anndata object of processed meta-analyzed data of epithelial compartment
Supplementary files format and content: whole_tissue_sc_immune_geo_upload.h5ad: Anndata object of processed meta-analyzed data of immune compartment
Supplementary files format and content: whole_tissue_sc_stroma_geo_upload.h5ad: Anndata object of processed meta-analyzed data of stroma compartment
Supplementary files format and content: whole_tissue_sc_raw_geo_upload.h5ad: Anndata object of raw meta-analyzed data before dimensionality reduction and clustering

source_name: large intestine

extract_protocol:
To obtain all cell types from the intestine for single-cell RNA-seq, we collected intestine segments from GF and SPF male and female C57BL6/J mouse pairs in ice-cold 2% FBS/PBS. After removing fat tissue, segments were cut open longitudinally and washed with ice-cold PBS. Epithelial cells were stripped with a stripping buffer (5 mM EDTA, 1 mM DTT, 2.5 mM HEPES, and 5% FBS in HBSS) for 30 min at 37°C with stirring. Tissues were collected and rinsed with ice-cold 2% FBS/PBS, followed by enzymatic digestion with 5 mL digestion buffer (0.2 mg/mL collagenase IV, 0.2 mg/mL dispase II, 0.1 mg/mL DNase I in DMEM/F12) at 40 °C for 10 min. Digested tissues were allowed to rest for 5 min, and the supernatants were collected into ice-cold complete media (CO2 independent media,18045088, Thermo Fisher Scientific; with 2% FBS) with 10 mM EDTA and kept on ice. This process was repeated for approximately 45 min with gentle vortex until no tissue chunks remained. Cells were pooled together and filtered through a 70 μm cell strainer, centrifuged at 500g at 4°C for 10 min. Cell pellets were resuspended in complete media (CO2 independent media with 2% FBS) with 10 mM EDTA. 150uL of the cell suspension was immediately loaded on a 10x controller as "bulk", while the remaining 850uL were sorted to enrich for stromal cells by excluding cells positive for Epcam, Ter119 and CD45 using a MoFlo Astrios sorter. The sorted negative cells were then loaded on a 10x controller as "stroma".
Single cell suspensions were processed using the Chromium Single Cell 3’ Gene Expression kit (v2, 10x Genomics) per manufacturer’s instructions.

value: large intestine

tag: strain

tag: Sex

value: female

value: specific pathogen free


title: TCDCA-2 H-Treg


title: TCDCA-3 H-Treg


title: sample_20

description: Library name: sample_20


title: C-1 H-Treg


title: SPF_bulk_6

description:
Library name: SPF_bulk_6
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: SPF_bulk_7

description:
Library name: SPF_bulk_7
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: SPF_stroma_5

description:
Library name: SPF_stroma_5
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: SPF_bulk_8

description:
Library name: SPF_bulk_8
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: sample_13

description: Library name: sample_13


title: GF_stroma_3

description:
Library name: GF_stroma_3
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad

value: germ free


title: GF_stroma_4

description:
Library name: GF_stroma_4
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: SPF_bulk_5

description:
Library name: SPF_bulk_5
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: GF_stroma_2

description:
Library name: GF_stroma_2
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: GF_stroma_1

description:
Library name: GF_stroma_1
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: GF_bulk_4

description:
Library name: GF_bulk_4
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: sample_01

description: Library name: sample_01


title: GF_bulk_2

description:
Library name: GF_bulk_2
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: GF_bulk_3

description:
Library name: GF_bulk_3
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: GF_bulk_1

description:
Library name: GF_bulk_1
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: Il7rLTneg_a4b7hi, batch3, rep3

city: Nantes

first: Christelle

last: Harly

address: 8 quai Moncousu

country: France

institute: CNRS

description:
Library name: YFP_3
Il7rLTneg_a4b7hi_3_3

data_processing:
Basecalling was done by RTA 1.18.66.3, Illumina instrument run time analysis software, and barcode demultiplexing by Bcl2fastq 2.17 allowing 1 mismatch
Adapter sequences and low-quality reads were removed from raw FASTQ files using Trimmomatic (0.39)
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)

source_name: Bone Marrow

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

extract_protocol:
RNA was extracted by RNeasy Plus Micro Kits (Qiagen)
Messenger RNA-Seq libraries were prepared using a SMARTer Ultra Low Input RNA Kit version 3 (Clontech) and Nextera XT DNA Library Preparation Kit (Illumina)

tag: strain background

tag: genotype/variation

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

value: Bone Marrow

value: ex vivo

tag: sorting profile

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

tag: batch


title: SPF_stroma_7

description:
Library name: SPF_stroma_7
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad

tag: tissue


title: Il7rLTneg_a4b7hi, batch3, rep2

description:
Library name: YFP_2
Il7rLTneg_a4b7hi_2_3

tag: cell type


title: Il7rLTpos_a4b7hi, batch3, rep2

description:
Library name: TULIP_2
Il7rLTpos_a4b7hi_2_3

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


title: Il7rLTpos_a4b7hi, batch3, rep1

description:
Library name: TULIP_1
Il7rLTpos_a4b7hi_1_3


title: SPF_stroma_6

description:
Library name: SPF_stroma_6
whole_tissue_sc_raw_geo_upload.h5ad
whole_tissue_sc_epi_geo_upload.h5ad
whole_tissue_sc_immune_geo_upload.h5ad
whole_tissue_sc_stroma_geo_upload.h5ad


title: Il7rLTneg_a4b7hi, batch3, rep1

description:
Library name: YFP_1
Il7rLTneg_a4b7hi_1_3


title: Il7rLTpos_a4b7hi, batch3, rep3

description:
Library name: TULIP_3
Il7rLTpos_a4b7hi_3_3


title: Il7rLTpos_a4b7lo, batch3, rep1

description:
Library name: ALP_1
Il7rLTpos_a4b7lo_1_3

value: Lin- Thy1.2- Kit+ 2B4+ Flt3high YFP+ GFP- a4b7low


title: Il7rLTpos_Tcf7pos, batch3, rep3

description:
Library name: EILP_3
Il7rLTpos_Tcf7pos_3_3

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


title: ILCP, batch2, rep2

description: Library name: ILCp_2

data_processing:
Basecalling was done by RTA 1.18.66.3, Illumina instrument run time analysis software, and barcode demultiplexing by Bcl2fastq 2.17 allowing 1 mismatch
Adapter sequences and low-quality reads were removed from raw FASTQ files using Trimmomatic (0.39)
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 and batch correction using ComBat-Seq (sva 3.35)
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)

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

value: Innate Lymphoid Cell Progenitor

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+


title: ILCP, batch2, rep1

description: Library name: ILCp_1


title: Il7rLTpos_a4b7lo, batch3, rep2

description:
Library name: ALP_2
Il7rLTpos_a4b7lo_2_3


title: Il7rLTpos_Tcf7pos, batch3, rep1

description:
Library name: EILP_1
Il7rLTpos_Tcf7pos_1_3


title: Il7rLTpos_a4b7lo, batch3, rep3

description:
Library name: ALP_3
Il7rLTpos_a4b7lo_3_3


title: ILCP, batch2, rep3

description: Library name: ILCp_3


title: cEILP, batch2,  rep3

description: Library name: PLZFposEILP_3

value: Tcf7GFP Zbtb16GFP

value: commited Early Innate Lymphoid Progenitor

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1- Zbtb16high Flt3low


title: cEILP, batch2, rep1

description: Library name: PLZFposEILP_1


title: ALP, batch2, rep4

description: Library name: CLP_4

value: All Lymphoid Progenitor

value: Lin- Kit+ 2B4+ a4b7low Flt3high IL-7Ra+


title: sEILP, batch2, rep3

description: Library name: PLZFnegEILP_3

value: specified Early Innate Lymphoid Progenitor

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1- Zbtb16low Flt3high


title: cEILP, batch2, rep2

description: Library name: PLZFposEILP_2


title: sEILP, batch2, rep1

description: Library name: PLZFnegEILP_1


title: sEILP, batch2, rep2

description: Library name: PLZFnegEILP_2


title: ALP, batch2, rep3

description: Library name: CLP_3


title: ALP, batch2, rep2

description: Library name: CLP_2


title: ALP, batch2, rep1

description: Library name: CLP_1


title: NFIL, batch1, rep2

description: Library name: NFIL_2_1

value: NFIL3-GFP-transduced + 4 days culture

value: Mac1- B6+ GFP+


title: GFP, batch1, rep3

description: Library name: GFP_3_1

value: Bone Marrow

value: GFP-transduced + 4 days culture


title: cEILP, batch1, rep2

description: Library name: cEILP_2_1

value: ex vivo


title: Il7rLTpos_Tcf7pos, batch3, rep2

description:
Library name: EILP_2
Il7rLTpos_Tcf7pos_2_3

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


title: cEILP, batch1, rep3

description: Library name: cEILP_3_1


title: sEILP, batch1, rep2

description: Library name: sEILP_2_1


title: sEILP, batch1, rep1

description: Library name: sEILP_1_1


title: GFP, batch1, rep1

description: Library name: GFP_1_1


title: GFP, batch1, rep2

description: Library name: GFP_2_1


title: NFIL, batch1, rep3

description: Library name: NFIL_3_1


title: ALP, batch1, rep3

description: Library name: ALP_3_1


title: ALP, batch1, rep1

description: Library name: ALP_1_1


title: NFIL, batch1, rep1

description: Library name: NFIL_1_1


title: cEILP, batch1, rep1

description: Library name: cEILP_1_1


title: Flcn KO Treg rep4

data_processing:
Raw sequencing data were first preprocessed by Trimmomatic (v0.36) to trim adapters and low-quality reads (PE, -phred33, ILLUMINACLIP=2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:18 MINLEN:25). Preprocessed RNA-seq reads were aligned to the mouse reference genome (mm9) and transcript annotations (GENCODE release M1, gencode.vM1.annotation.gtf) using STAR (v2.5.3a). Expression levels of all transcripts were quantified by RSEM (v1.3.1). DE genes were determined by DESeq2 (v1.24.0).
Assembly: mm9
Supplementary files format and content: FLCN_KO_vs_WT_08032017.xlsx includes normalizaed count, log2FCs, p values and adjusted p values

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

growth_protocol: Mixed BM chimera mice were generated at a 1:1 ratio with BM from CD45.1+ and Foxp3Cre (called WT) or Foxp3CreFlcnfl/fl (called Flcn KO) mice.

extract_protocol:
RNA extraction was performed using Qiagen RNeasy micro kit (74004, Qiagen) according to manufacturer’s instructions.
The cDNA libraries were constructed using the NuGEN cDNA synthesis low RNA input method.

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

value: Spleen

value: Primary mouse Treg cells

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

value: Flcn KO


title: Flcn KO Treg rep3


title: Flcn KO Treg rep5


title: Flcn KO Treg rep1


title: Flcn KO Treg rep2


title: WT Treg rep5

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

value: WT


title: HeLaS3, P300 ChIP, 5ug antibody, rep1

description: Library name: HeLaS3_P300_5ug_1

value: cervical adenocarcinoma epithelial cells

value: wild-type


title: WT Treg rep4


title: WT Treg rep1


title: HeLaS3, P300 ChIP, 5ug antibody, rep2

description: Library name: HeLaS3_P300_5ug_2


title: WT Treg rep3


title: WT Treg rep2


title: HeLaS3, input control for P300 antibody titration experiment

description: Library name: HeLaS3_input_forP300AbTitr


title: HeLaS3, P300 ChIP, 2.5ug antibody, rep2

description: Library name: HeLaS3_P300_2-5ug_2


title: HeLaS3, P300 ChIP, 2.5ug antibody, rep1

description: Library name: HeLaS3_P300_2-5ug_1


title: HeLaS3, P300 ChIP, 1ug antibody, rep2

description: Library name: HeLaS3_P300_1ug_2


title: HeLaS3, P300 ChIP, 1ug antibody, rep1

description: Library name: HeLaS3_P300_1ug_1


title: ALP, batch1, rep2

description: Library name: ALP_2_1

value: All Lymphoid Progenitor


title: HeLaS3, P300 ChIP, 0.5ug antibody, rep2

description: Library name: HeLaS3_P300_0-5ug_2


title: HeLaS3, H3K9ac ChIP, 1ug antibody, rep2

description: Library name: HeLaS3_H3K9ac_1ug_2

value: H3K9ac (CST, C5B11)


title: HeLaS3, input control for H3K9ac antibody titration experiment

description: Library name: HeLaS3_input_forH3K9acAbTitr


title: HeLaS3, P300 ChIP, 0.5ug antibody, rep1

description: Library name: HeLaS3_P300_0-5ug_1


title: HeLaS3, H3K9ac ChIP, 1ug antibody, rep1

description: Library name: HeLaS3_H3K9ac_1ug_1


title: HeLaS3, H3K9ac ChIP, 0.4ug antibody, rep1

description: Library name: HeLaS3_H3K9ac_0-4ug_1


title: HeLaS3, H3K9ac ChIP, 0.2ug antibody, rep2

description: Library name: HeLaS3_H3K9ac_0-2ug_2


title: HeLaS3, H3K9ac ChIP, 0.4ug antibody, rep2

description: Library name: HeLaS3_H3K9ac_0-4ug_2


title: HeLaS3, H3K9ac ChIP, 0.04ug antibody, rep1

description: Library name: HeLaS3_H3K9ac_0-04ug_1


title: HeLaS3, lysis buffer LB3, input control

description: Library name: HeLaS3_LB3_input


title: HeLaS3, H3K9ac ChIP, 0.2ug antibody, rep1

description: Library name: HeLaS3_H3K9ac_0-2ug_1


title: HeLaS3, H3K9ac ChIP, 0.04ug antibody, rep2

description: Library name: HeLaS3_H3K9ac_0-04ug_2


title: HeLaS3, lysis buffer LB3, manual workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_LB3_manual_H3K27me3_2


title: HeLaS3, lysis buffer LB3, manual workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_LB3_manual_H3K27me3_1


title: HeLaS3, lysis buffer LB3, manual workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_LB3_manual_H3K27ac_1

value: H3K27ac (CST, D5E4)


title: HeLaS3, lysis buffer LB3, Bravo workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_LB3_Bravo_H3K27me3_2


title: HeLaS3, lysis buffer LB3, Bravo workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_LB3_Bravo_H3K27me3_1


title: HeLaS3, lysis buffer LB3, manual workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_LB3_manual_H3K27ac_2


title: HeLaS3, lysis buffer EBB, input control

description: Library name: HeLaS3_EBB_input


title: HeLaS3, lysis buffer EBB, manual workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_EBB_manual_H3K27me3_2


title: HeLaS3, lysis buffer LB3, Bravo workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_LB3_Bravo_H3K27ac_1


title: HeLaS3, lysis buffer LB3, Bravo workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_LB3_Bravo_H3K27ac_2


title: HeLaS3, lysis buffer EBB, manual workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_EBB_manual_H3K27ac_2


title: HeLaS3, lysis buffer EBB, manual workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_EBB_manual_H3K27ac_1


title: HeLaS3, lysis buffer EBB, manual workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_EBB_manual_H3K27me3_1


title: HeLaS3, lysis buffer EBB, Bravo workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_EBB_Bravo_H3K27me3_1


title: HeLaS3, lysis buffer EBB, Bravo workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_EBB_Bravo_H3K27me3_2


title: HeLaS3, lysis buffer EBB, Bravo workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_EBB_Bravo_H3K27ac_2


title: HeLaS3, crosslinked with FA only, manual workflow, input control

description: Library name: HeLaS3_FA_manual_input


title: HeLaS3, crosslinked with FA only, manual workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_FA_manual_H3K27me3_1


title: HeLaS3, lysis buffer EBB, Bravo workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_EBB_Bravo_H3K27ac_1


title: HeLaS3, crosslinked with FA only, manual workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_FA_manual_H3K27me3_2


title: HeLaS3, crosslinked with FA only, Bravo workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_FA_Bravo_H3K27me3_2


title: HeLaS3, crosslinked with FA only, manual workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_FA_manual_H3K27ac_2


title: HeLaS3, crosslinked with FA only, manual workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_FA_manual_H3K27ac_1


title: HeLaS3, crosslinked with FA only, Bravo workflow, input control

description: Library name: HeLaS3_FA_Bravo_input


title: HeLaS3, crosslinked with FA only, Bravo workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_FA_Bravo_H3K27ac_2


title: HeLaS3, crosslinked with FA only, Bravo workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_FA_Bravo_H3K27ac_1


title: HeLaS3, crosslinked with DSG and FA, manual workflow, input control

description: Library name: HeLaS3_DSG_manual_input


title: HeLaS3, crosslinked with DSG and FA, manual workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_DSG_manual_H3K27ac_1


title: HeLaS3, crosslinked with FA only, Bravo workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_FA_Bravo_H3K27me3_1


title: HeLaS3, crosslinked with DSG and FA, manual workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_DSG_manual_H3K27me3_2


title: HeLaS3, crosslinked with DSG and FA, manual workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_DSG_manual_H3K27ac_2


title: HeLaS3, crosslinked with DSG and FA, Bravo workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_DSG_Bravo_H3K27me3_1


title: HeLaS3, crosslinked with DSG and FA, Bravo workflow, input control

description: Library name: HeLaS3_DSG_Bravo_input


title: HeLaS3, crosslinked with DSG and FA, Bravo workflow, H3K27me3 ChIP, rep2

description: Library name: HeLaS3_DSG_Bravo_H3K27me3_2


title: HeLaS3, crosslinked with DSG and FA, Bravo workflow, H3K27ac ChIP, rep2

description: Library name: HeLaS3_DSG_Bravo_H3K27ac_2


title: HeLaS3, crosslinked with DSG and FA, Bravo workflow, H3K27ac ChIP, rep1

description: Library name: HeLaS3_DSG_Bravo_H3K27ac_1


title: AU565 Sph with Primed+Treated TZM_2

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
RNA-seq libraries were prepared using Illumina’s TruSeq protocol and were sequenced on an Illumina NextSeq 500. Reads were aligned to the hg38 genome using Rsubread v1.5.3. Gene counts were quantified by Entrez Gene IDs using featureCounts and Rsubread’s built-in annotation. Gene symbols were provided by NCBI gene annotation. Genes with count-per-million above 0.5 in at least 3 samples were kept in the analysis. Differential expression analysis was performed using limma-voom
Assembly: hg38
Supplementary files format and content: CSV files containing read counts values for each Sample

growth_protocol: AU565 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol extraction method
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol:
AU565 Sph with primed TZM: Treatment of Trastuzumab (20ug/ml), 24 hour treatment time (monolayer). liquid overlay + 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction
AU565 Sph with primed+treated TZM: Treatment of Trastuzumab (20ug/ml), 24 hour treatment time (monolayer),  liquid overlay + 5% matrigel following trastuzumab treatment, 96 hours incubation + Trastuzumab treatment (50ug/ml) 24 hour treatment time prior to rna extraction
AU565 Sph with treated TZM:  liquid overlay + 5% matrigel, 96 hours incubation + Trastuzumab treatment (50ug/ml) 24 hour treatment time prior to rna extraction
AU565 Sph: liquid overlay +5% matrigel, 96hours incubation
AU565 2D with TZM: Treatment of Trastuzumab (20ug/ml), 24 hour treatment time (monolayer) prior to rna extraction
AU565 2D with TZM: Treatment of Trastuzumab (20ug/ml), 24 hour treatment time (monolayer), + 96hour incubation prior to rna extraction
AU565_2D: (control) incubation prior to rna extraction

value: epithelium

value: Trastuzumab 20ug/ml, 24hr + 96hr aggregate + 50ug/ml Trastuzumab, 24hrs


title: AU565 Sph with Primed+Treated TZM_1


title: AU565 Sph with Treated TZM_3

value: Aggregate(96hr) + 50ug/ml Trastuzumab, 24hrs


title: AU565 Sph with Treated TZM_2


title: AU565 Sph with Treated TZM_1


title: AU565 2D with primed TZM_3

value: Trastuzumab 20ug/ml, 24hr + 96hr incubation


title: AU565 2D with primed TZM_2


title: AU565 Sph with Primed+Treated TZM_3


title: AU565 Sph_3

value: Aggregate(control, 96hr)


title: AU565 Sph_2


title: AU565 2D with primed TZM_1


title: AU565 Sph with TZM_3

value: Trastuzumab 20ug/ml, 24hr + 96hr aggregate


title: HeLaS3, crosslinked with DSG and FA, manual workflow, H3K27me3 ChIP, rep1

description: Library name: HeLaS3_DSG_manual_H3K27me3_1


title: AU565 Sph with TZM_1


title: AU565 Sph with TZM_2


title: AU565 2D_1

value: control


title: AU565 Sph_1


title: AU565 2D with TZM_3

value: Trastuzumab 20ug/ml, 24hrs


title: AU565 2D_3


title: AU565 2D_2


title: AU565 2D with TZM_1


title: SC3_Day40

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: HEST

country: Switzerland

institute: ETH Zürich

description:
smallRNA sequencing
SC3_40

data_processing:
SmallRNA detection was conducted using Oasis on hg38.
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: GRCh38, miRBase (v21), piRNAbank (v2), Ensembl84
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.

source_name: Brain

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).
RNA libraries for the smallRNA sequencing were prepared using the Illumina TruSeq Small RNA kit.

value: Brain

tag: time point

value: igNeurons

tag: differentiation

value: Differentiation SC3


title: AU565 2D with TZM_2

tag: cell line

value: WT


title: SC3_Day33

description:
smallRNA sequencing
SC3_33


title: SC3_Day9

description:
smallRNA sequencing
SC3_9


title: SC3_Day21

description:
smallRNA sequencing
SC3_21


title: SC3_Day27

description:
smallRNA sequencing
SC3_27


title: SC3_Day15

description:
smallRNA sequencing
SC3_15


title: SC3_Day0

description:
smallRNA sequencing
SC3_0


title: SC2_Day9

description:
smallRNA sequencing
SC2_9

value: Differentiation SC2


title: SC2_Day27

description:
smallRNA sequencing
SC2_27


title: SC2_Day40

description:
smallRNA sequencing
SC2_40


title: SC2_Day21

description:
smallRNA sequencing
SC2_21


title: SC2_Day33

description:
smallRNA sequencing
SC2_33


title: SC2_Day15

description:
smallRNA sequencing
SC2_15


title: SC2_Day0

description:
smallRNA sequencing
SC2_0


title: SC1_Day33

description:
smallRNA sequencing
SC1_33

value: Differentiation SC1


title: SC1_Day9

description:
smallRNA sequencing
SC1_9


title: SC1_Day27

description:
smallRNA sequencing
SC1_27


title: SC1_Day15

description:
smallRNA sequencing
SC1_15


title: SC1_Day0

description:
smallRNA sequencing
SC1_0


title: SC1_Day21

description:
smallRNA sequencing
SC1_21


title: SC1_Day40

description:
smallRNA sequencing
SC1_40


title: B10010_SPF_F0214_Colon_1

description: Library name: 20240215_ENS_SPF_F0214_SPF_B10010_SPF_F0214_Colon_1

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

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

value: F

tag: mouse id

value: SPF

tag: batch label

tag: plate label


title: B37_OVAs_MOVASense5_DJ_2

description: Library name: 20230406_ENS_OVAs_DJ_OVASense5_OVAs_B37_OVAs_MOVASense5_DJ_2

value: M

value: OVAs


title: B36_OVAc_M116_DJ_1

description: Library name: 20230406_ENS_OVAc_DJ_116_OVAc_B36_OVAc_M116_DJ_1

value: OVAc


title: B10011_SPF_M0214_Colon_3

description: Library name: 20240216_ENS_SPF_M0214_SPF_B10011_SPF_M0214_Colon_3


title: B10010_SPF_F0215_Colon_4

description: Library name: 20240215_ENS_SPF_F0215_SPF_B10010_SPF_F0215_Colon_4


title: B37_OVAs_MOVASense6_DJ_1

description: Library name: 20230406_ENS_OVAs_DJ_OVASense6_OVAs_B37_OVAs_MOVASense6_DJ_1


title: B37_OVAs_MOVASense5_DJ_1

description: Library name: 20230406_ENS_OVAs_DJ_OVASense5_OVAs_B37_OVAs_MOVASense5_DJ_1


title: B10010_SPF_F0214_Colon_2

description: Library name: 20240215_ENS_SPF_F0214_SPF_B10010_SPF_F0214_Colon_2


title: B36_OVAc_M115_DJ_2

description: Library name: 20230406_ENS_OVAc_DJ_115_OVAc_B36_OVAc_M115_DJ_2


title: B10011_SPF_M0214_Colon_2

description: Library name: 20240216_ENS_SPF_M0214_SPF_B10011_SPF_M0214_Colon_2


title: B10011_SPF_F0215_Colon_5

description: Library name: 20240216_ENS_SPF_F0215_SPF_B10011_SPF_F0215_Colon_5


title: B10010_SPF_F0215_Colon_3

description: Library name: 20240215_ENS_SPF_F0215_SPF_B10010_SPF_F0215_Colon_3


title: B10011_SPF_M0214_Colon_1

description: Library name: 20240216_ENS_SPF_M0214_SPF_B10011_SPF_M0214_Colon_1


title: B35_OVAs_MOVASense3_DJ_2

description: Library name: 20221218_ENS_OVAs_OVASense3_OVAs_B35_OVAs_MOVASense3_DJ_2


title: B37_OVAc_M116_DJ_2

description: Library name: 20230406_ENS_OVAs_DJ_116_OVAc_B37_OVAc_M116_DJ_2


title: B35_OVAs_MOVASense4_DJ_2

description: Library name: 20221218_ENS_OVAs_OVASense4_OVAs_B35_OVAs_MOVASense4_DJ_2


title: B35_OVAs_MOVASense4_DJ_1

description: Library name: 20221218_ENS_OVAs_OVASense4_OVAs_B35_OVAs_MOVASense4_DJ_1


title: B36_OVAc_M115_DJ_3

description: Library name: 20230406_ENS_OVAc_DJ_115_OVAc_B36_OVAc_M115_DJ_3


title: B35_OVAs_MOVASense3_DJ_1

description: Library name: 20221218_ENS_OVAs_OVASense3_OVAs_B35_OVAs_MOVASense3_DJ_1


title: B34_OVAs_MOVASense2_Ileum_1

description: Library name: 20221217_ENS_OVA_GF_OVASense2_OVAs_B34_OVAs_MOVASense2_Ileum_1

source_name: Ileum

value: Ileum


title: B34_OVAs_MOVASense2_DJ_1

description: Library name: 20221217_ENS_OVA_GF_OVASense2_OVAs_B34_OVAs_MOVASense2_DJ_1


title: B34_OVAc_F109_DJ_2

description: Library name: 20221217_ENS_OVA_GF_109_OVAc_B34_OVAc_F109_DJ_2


title: B33_OVAc_M103_DJ_2

description: Library name: 20221216_ENS_OVAc_103_OVAc_B33_OVAc_M103_DJ_2


title: B33_OVAc_F109_DJ_1

description: Library name: 20221216_ENS_OVAc_109_OVAc_B33_OVAc_F109_DJ_1


title: B33_OVAc_M103_DJ_3

description: Library name: 20221216_ENS_OVAc_103_OVAc_B33_OVAc_M103_DJ_3


title: B34_GF_F3616_Colon_1

description: Library name: 20221217_ENS_OVA_GF_3616_GF_B34_GF_F3616_Colon_1

value: GF


title: B33_OVAc_M103_DJ_1

description: Library name: 20221216_ENS_OVAc_103_OVAc_B33_OVAc_M103_DJ_1


title: B32_SPF_PBS_F126_DJ_2

description: Library name: 20221215_ENS_SPF_126_SPF_B32_SPF_PBS_F126_DJ_2


title: B32_SPF_PBS_F126_DJ_1

description: Library name: 20221215_ENS_SPF_126_SPF_B32_SPF_PBS_F126_DJ_1


title: B36_OVAc_M115_DJ_1

description: Library name: 20230406_ENS_OVAc_DJ_115_OVAc_B36_OVAc_M115_DJ_1


title: B32_SPF_PBS_F125_DJ_2

description: Library name: 20221215_ENS_SPF_125_SPF_B32_SPF_PBS_F125_DJ_2


title: DNase-seq_ALP, rep3

description:
Library name: DNase-seq_ALP_3
DNase-seq_ALP_3
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677393

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

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.

value: Bone Marrow

value: All Lymphoid Progenitor

value: ex vivo

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


title: B10009_ASF_M3806_colon_1

description: Library name: 20220913_ENS_BT_ASF_3806_ASF_B10009_ASF_M3806_colon_1

value: ASF


title: DNase-seq_ILCP, rep1

description:
Library name: DNase-seq_ILCP_1
DNase-seq_ILCP_1
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677397

value: Innate Lymphoid Cell Progenitor

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


title: DNase-seq_EILP, rep2

description:
Library name: DNase-seq_EILP_2
DNase-seq_EILP_2
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677395

value: Early Innate Lymphoid Progenitor

value: Lin- Kit+ 2B4+ a4b7+ GFP+ Thy1-


title: B10007_Btheta_M3807_colon_3

description: Library name: 20220907_ENS_BT_3807_BT_B10007_Btheta_M3807_colon_3

value: Colon

value: enteric neuron

value: BT


title: B10009_ASF_M3806_colon_2

description: Library name: 20220913_ENS_BT_ASF_3806_ASF_B10009_ASF_M3806_colon_2

value: M


title: B32_SPF_PBS_F125_DJ_1

description: Library name: 20221215_ENS_SPF_125_SPF_B32_SPF_PBS_F125_DJ_1

value: F

value: SPF


title: B10008_ASF_M3805_colon_4

description: Library name: 20220908_ENS_ASF_3805_ASF_B10008_ASF_M3805_colon_4


title: B10009_Btheta_F3811_colon_1

description: Library name: 20220913_ENS_BT_ASF_3811_BT_B10009_Btheta_F3811_colon_1


title: DNase-seq_ILCP, rep2

description:
Library name: DNase-seq_ILCP_2
DNase-seq_ILCP_2
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677398


title: B10009_Btheta_F3811_colon_2

description: Library name: 20220913_ENS_BT_ASF_3811_BT_B10009_Btheta_F3811_colon_2


title: B10008_ASF_M3805_colon_3

description: Library name: 20220908_ENS_ASF_3805_ASF_B10008_ASF_M3805_colon_3


title: DNase-seq_EILP, rep1

description:
Library name: DNase-seq_EILP_1
DNase-seq_EILP_1
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677394


title: B10008_ASF_M3805_colon_2

description: Library name: 20220908_ENS_ASF_3805_ASF_B10008_ASF_M3805_colon_2


title: DNase-seq_EILP, rep3

description:
Library name: DNase-seq_EILP_3
DNase-seq_EILP_3
The BAM files are based on FASTQ files that are already available in GSE128483.
Corresponds to GSM3677396


title: Mouse3_superior

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_3u

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

tag: genotype


title: Mouse2_superior

description: Library name: AdaptiveTCR_2u


title: B10007_Btheta_M3807_colon_2

description: Library name: 20220907_ENS_BT_3807_BT_B10007_Btheta_M3807_colon_2


title: B10007_Btheta_M3807_colon_1

description: Library name: 20220907_ENS_BT_3807_BT_B10007_Btheta_M3807_colon_1


title: B29_OVAc_M103_DJ_1

description: Library name: 20220825_ENS_SPF_103_OVAc_B29_OVAc_M103_DJ_1

value: OVAc


title: Mouse1_inferior

description: Library name: AdaptiveTCR_1l


title: B29_OVAc_M102_DJ_2

description: Library name: 20220825_ENS_SPF_102_OVAc_B29_OVAc_M102_DJ_2


title: Mouse3_inferior

description: Library name: AdaptiveTCR_3l


title: B10008_ASF_M3805_colon_1

description: Library name: 20220908_ENS_ASF_3805_ASF_B10008_ASF_M3805_colon_1


title: Mouse1_superior

description: Library name: AdaptiveTCR_1u