title: CO134.FFPE

extract_protocol: RNA was extracted from FF tissue using RNA-Bee (Tel-Test inc., USA) and Trizol (ABP Biosciences, Rockville, USA) according to manufacturer’s protocol. Samples with a tumor percentage <30% were excluded. For FFPE tissue, three 10 µm-slides with flanking H&Es were prepared and tissue deparaffinisation was performed with Xylene. Subsequently, tumor tissue was macro-dissected to enrich for tumor tissue. RNA was extracted using the RNeasy FFPE kit (QIAGEN GmbH, Hilden, Germany) according to manufacturer’s instructions. RNA quantity and quality were measured using Tapestation (Agilent).

value: CRC tumor

value: FFPE


title: PBMC, Control, day 0, Individual 01

status: Public on May 22 2025

type: SRA

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description:
Before vitamin D bolus intake
d0_Ind01

library_source: transcriptomic

data_processing:
Trimming of files using Trimmomatic v0.39
Read alignment using STAR v2.7.10b using default parameters
Quantification using FastQC v0.12.1 and featureCounts v2.0.3 using default parameters for reverse strand
Filtering for protein coding genes and read counts normalization via EdgeR v4.0.14 (TMM-normalized CPM)
Assembly: GRCh38.p14, Aligned to Ensembl annotation version 112, final annotation (via Biomart) to Ensembl version 112.38
Supplementary files format and content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: no in vitro culture

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: Before and after intake of 1000 IU/kg of vitamin D3

tag: individual

value: Individual 01

tag: disease state

value: Healthy Individuals

tag: cell type

value: PBMC

tag: treatment

value: control

tag: time

value: day 0


title: Human kidney, normothermic perfusion, RBC, 0 hrs, HF20, donor 6

city: Leiden

first: Roan

middle: Hugo

last: van Scheppingen

address: Albinusdreef 2

country: Netherlands

institute: LUMC

description:
Library name: AF1
150bp_pe

data_processing:
Data was aligned to using hg38p14 using Rsubread (v2.18.0)
A count matrix was generated, genes were annotated using useMart(v2.60.1) and genes without gene name or starting with "MT" were excluded.
A DESeqDataSet was generated using DESeq2(v1.44.0).
Data was processed and analysed using R (v4.4.1). For full code and packages, see the Github repository
Assembly: HG38p14
Supplementary files format and content: norm_counts_all is a comma separated file containing the normalized counts for the gene names per sample
Supplementary files format and content: metadata is a comma separated file containing extra data per sample.

molecule: polyA RNA

source_name: Kidney

extract_protocol:
RNA was isolated using the QIAGEN mini RNA isolation kit according to manufacturer's protocol, subsequently mRNA was enriched for poly-A tails using oligo(dT)-magnetic beads.
After enrichment, mRNA was fragmented using fragmentation buffer, followed by reverse transcription using random N5 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was then end-repaired and 5' phosphorylated, with a protruding 'A' at the 3'end forming a blunt end, followed by ligation of a  bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation producs were PCR amplified using specific primers. The PCR products were denatrued to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and seuenced after passing the quality control. (BGI's DNB-seq protocol)

tag: tissue

value: Kidney

tag: Sex

value: Male

tag: donor type

value: DCD

tag: preservation

value: SCS

tag: dialysis filter


title: Ru corresponding to Rubus ulmifolius aqueous extract intake 2

type: RNA

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

description: Gene expression after 20 days of gavage (D20)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mus musculus Sure Print GE 4x44 v2 microarrays with oligonucleotide 45,220 probes (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides 4x44 were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: hepatic tissues

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Standard chow and water ad libitum (Diet A04C-10, Scientific Animal Food and Engineering, Augy, France)

extract_protocol: Total RNA was extracted from hepatic tissues using RNAspin columns (Macherey-Nagel). RNA quality was observed with Nanodrop and absorbance ratios A260/280 and A260/230 were found between 2.0 and 2.2. RNA quality was also examined by RNA ScreenTape Analysis (Agilent) and a minimal RNA integrity number (RIN) of 0.8 was required for all samples.

treatment_protocol: Mice were fed for 20 days with an aqueous extract of Artemisia campestris (Ar) or Rubus ulmifolius (Ru). The mice gavages consisted in a daily force-feeding of 500 µl of Ar or Ru solution (6mg/mL) besides the standard chow. The administrated dose was calculated to correspond to the concentration used as an infusion for moderate daily consumption. Controls underwent an equivalent force-feeding with water (Ctr).

value: liver

tag: gender

value: male

tag: age

value: 8 weeks of age at D0


title: CO129.FFPE

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

institute: Amsterdam UMC

hyb_protocol: Samples were hybridized for 16 hours at 65C

scan_protocol: Detection and scanning were performed by the nCounter SPRINT Profiler analysis system.

data_processing: Raw count data from nCounter

label: fluorescence microscope

source_name: tumor

label_protocol: Sample RNA is hybridized with target-specific capture and reporter probes. This creates a library of unique target-probe complexes. Each target is labelled with a specific barcode, which can be detected and counted using an automated fluorescence microscope.

tag: tissue type

tag: cms (ssp)


title: CO160.FFPE


title: PBMC, Control, day 0, Individual 02

description:
Before vitamin D bolus intake
d0_Ind02

value: Individual 02


title: BMAT-MSCS, AML-2 SR1, 18h

city: Ankara

first: Bihter

last: Muratoğlu

state: Ankara

address: Sihhiye

department: Stem Cell Sciences

country: Turkey

institute: Hacettepe University

description:
Library name: Sample_7
Column name in FPKM_All_Samples.csv: AML-SR1_FPKM

data_processing:
Base calling was performed using bcl2fastq (v2.20) to convert raw Illumina sequencing signals into FASTQ files. These files were used as input for downstream analysis.
Quality control of raw RNA-seq reads was performed using FastQC (v0.11.9) to identify adapter contamination, sequence quality scores, and GC content distribution.
Reads were trimmed using Trimmomatic (v0.39) to remove adapters, low-quality bases (Phred score <20), sequences with unidentified bases (N >5), and reads shorter than 32 bases.
RNA-seq reads were aligned to the human reference genome GRCh38 by using STAR (v2.7.10b) (default parameters).
Normalized FPKM values were calculated for library size and gene length normalization  using Cuffdiff (v2.2.1) with default parameters, including a false discovery rate (FDR) threshold of ≤ 0.01.
Assembly: GRCh38
Supplementary files format and content: Processed data files are provided in CSV format.
Supplementary files format and content: FPKM_All_Samples.csv:  contains normalized FPKM values for each sample, representing FPKM mapped reads.

source_name: Bone marrow adipose tissue

growth_protocol: Cells were cultured in low-glucose Dulbecco’s Modified Eagle Medium (LG-DMEM) (Biowest) supplemented with penicillin-streptomycin (100 U/ml and 100 μg/ml, respectively), 1% L-Glutamine (Biowest),  and 10% FBS (Gibco) in a humidified incubator at 5% CO2 and 37°C.

extract_protocol:
RNA was harvested using the RNeasy Miniprep Kit (Qiagen #74104), with optional on-column DNase treatment, following the manufacturer’s instructions.
RNA libraries for RNA-seq were generated from 1 μg total RNA using the Illumina Stranded Total RNA Library Prep with Ribo-Zero Plus Kit (Illumina #20040529), following the manufacturer’s instructions.

treatment_protocol: BMAT-MSCs were seeded into 6-well plates at 1 × 10^6 cells per well. After seeding, the medium was supplemented with 100 nM Dexamethasone (DEX) (Sigma-Aldrich, #50-02-2), and the plates were incubated for 1 hour. After synchronization, cells were treated with 1.5 μM SR1, 100 nM FICZ, and 100ng/ml TNFa for 18h.

value: Bone marrow adipose tissue

tag: cell line

value: primary cells

value: mesenchymal stem cells

value: AML-2 SR1


title: BMAT-MSCS, AML-2 FICZ, 18h

description:
Library name: Sample_6
Column name in FPKM_All_Samples.csv: AML-FICZ_FPKM

value: AML-2 FICZ


title: BMAT-MSCS, AML-3 SR1, 18h

description:
Library name: Sample_4
Column name in FPKM_All_Samples.csv: AML-SR1_FPKM

value: AML-3 SR1


title: Human kidney, normothermic perfusion, RBC, 24 hrs, HF20, donor 5

description:
Library name: AE3
150bp_pe

value: HMP


title: CO150.FFPE

value: CRC tumor

value: FFPE


title: Ar corresponding to Artemisia campestris aqueous extract intake 3


title: BMAT-MSCS, AML-2 Control, 18h

description:
Library name: Sample_5
Column name in FPKM_All_Samples.csv: AML-Control_FPKM

value: AML-2 Control


title: CO123.FFPE


title: BMAT-MSCS, AML-3 TNFa, 18h

description:
Library name: Sample_3
Column name in FPKM_All_Samples.csv: AML-TNFa_FPKM

value: AML-3 TNFa


title: Human kidney, normothermic perfusion, RBC, 6 hrs, HF20, donor 5

description:
Library name: AE2
150bp_pe

value: Kidney

value: Male

value: DCD


title: Human kidney, normothermic perfusion, RBC, 24 hrs, HF20, donor 6

description:
Library name: AF3
150bp_pe

value: SCS


title: BMAT-MSCS, AML-3 FICZ, 18h

description:
Library name: Sample_2
Column name in FPKM_All_Samples.csv: AML-FICZ_FPKM

value: AML-3 FICZ


title: Human kidney, normothermic perfusion, RBC, 48 hrs, HF20, donor 5

description:
Library name: AE4
150bp_pe


title: LM41.FF

value: FF


title: CO140.FFPE


title: Human kidney, normothermic perfusion, RBC, 0 hrs, HF20, donor 5

description:
Library name: AE1
150bp_pe


title: Human kidney, normothermic perfusion, RBC, 48 hrs, HF20, donor 4

description:
Library name: AD4
150bp_pe


title: Human kidney, normothermic perfusion, RBC, 24 hrs, HF20, donor 4

description:
Library name: AD3
150bp_pe


title: LM40.FF


title: Ar corresponding to Artemisia campestris aqueous extract intake 2

value: liver

value: male

value: 8 weeks of age at D0


title: BMAT-MSCS, AML-3 Control, 18h

description:
Library name: Sample_1
Column name in FPKM_All_Samples.csv: AML-Control_FPKM

value: Bone marrow adipose tissue

value: primary cells

value: mesenchymal stem cells

value: AML-3 Control


title: Ar corresponding to Artemisia campestris aqueous extract intake 1


title: Ru corresponding to Rubus ulmifolius aqueous extract intake 1


title: Human kidney, normothermic perfusion, RBC, 0 hrs, HF20, donor 4

description:
Library name: AD1
150bp_pe

value: HMP


title: LM39.FF

value: CRC tumor


title: Donor3, unstimulated, day 0, RNA-seq

city: Minneapolis

first: Pedram

last: Motallebnejad

state: MN

address: 421 Washington Ave SE

country: USA

institute: University of Minnesota

data_processing:
Fastq files were mapped to the human genome (hg38) using STAR, and raw counts were obtained with HT-seq.
Genes expressed in at least 3 samples with counts per million (CPM)>1 were retained for analysis (14790 genes).
Filtered genes underwent TMM normalization for PCA and clustering in R. EdgeR identified differentially expressed genes (DEGs) at day 7 vs unstimulated, with differential expression criterion of |log2(fold change)| > 1 and adjusted P value < 0.05.
Assembly: hg38
Supplementary files format and content: Comma-separated value (csv) file includes raw counts for all genes and each sample

source_name: Peripheral Blood

growth_protocol: K562 cells expressing mb-4-1BBL and mb-IL-21 (referred to as feeder cells, mb stands for membrane-bound) were cultured in RPMI 1640 Medium containing 10% fetal bovine serum. Feeder cells were irradiated at 10,000 rads, cryopreserved and thawed for co-culture with NK cells. Peripheral blood mononuclear cells (PBMCs) were extracted from leukocyte reduction system chambers using Ficoll-Paque Premium (Cytiva). NK cell enrichment was carried out with the EasySep Human NK Cell Enrichment Kit. NK cells were cultured overnight in B0 medium supplemented with 100 U/mL of IL-2 (R&D Systems) for recovery. B0 medium is a 2:1 (vol:vol) mixture of DMEM with 4.5 g/L glucose, L-glutamine, and sodium pyruvate (Gibco) and Ham’s F12 Medium (Corning) supplemented with 20 µM 2-mercaptoethanol (Gibco), 50 µM ethanolamine (Sigma), 10 µg/mL ascorbic acid (Sigma), 1.6 ng/mL sodium selenite (Sigma), 100 U/mL penicillin/streptomycin (Gibco), and 20% heat-inactivated human AB serum (Valley Biomedical).

extract_protocol:
Total RNA from collected samples was purified using the Qiagen™ RNeasy Mini Kit.
The Illumina TruSeq® Stranded mRNA Sample Prep Kit protocol was employed to isolate poly-A containing mRNA molecules and generate sequence libraries. Pooled libraries were sequenced using the Illumina HiSeq 2500 at the University of Minnesota Genomics Center.

treatment_protocol: Enriched NK cells from PBMCs were cultured in media containing IL-2 overnight. Subsequently, NK cells were co-cultured with irradiated feeder cells at 2×105 cells/mL and 4×105 cells/mL, respectively, in B0 media with IL-2 supplementation for 7 days (Figure 1A). Samples were collected right after enrichment (unstimulated) and 7 days after co-culture initiation (day 7) for RNA-seq and ATAC-seq.

value: Peripheral Blood

value: Primary cells

value: Natural Killer Cells

tag: genotype

value: WT

value: Unstimulated


title: Human kidney, normothermic perfusion, RBC, 48 hrs, HF20, donor 3

description:
Library name: AC4
150bp_pe

value: Kidney

value: Male

value: DCD

value: SCS


title: Donor2, cocultured, day 7, RNA-seq

value: Cocultured with feeder cells


title: Control corresponding to water intake 2

value: liver

value: male

value: 8 weeks of age at D0


title: LM38.FF

value: FF


title: LM37.FF


title: input fraction WT E. coli subject to heat stress (replicate 2)

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

description:
F-, λ-, rph-1
input fraction (total RNA) wild-type E. coli subject to heat stress (replicate 2)

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 16
Genome read mapping using Bowtie (1.2.2), parameters: -l 16 -n 1 -e 50 -m 1 --strata --best -y -S
Read counting using Bedtools coverage, version v2.26.0
Assembly: Escherichia coli str. K-12 substr. MG1655 Ensemble (GCA_000005845; assembly: ASM584v2)
Supplementary files format and content: tab-delimited text files include unique read counts per gene per kilobase and million mapped reads RPKM for each sample

organism: Escherichia coli

source_name: MG1655 E. coli cells

growth_protocol: Overnight cultures of cells were grown in Luria-Bertani (LB) medium and resuspended the following day in LB medium. Cells were grown to mid-exponential phase before stresses were applied, or RNA was extracted.

extract_protocol:
Total RNA was extracted using TriZol reagent. 5µg total RNA of each sample was saved as the input control fraction. The m6A fraction was collected by immunoprecipitating with anti-m6A antibodies as described in (Anders et al. 2018; DOI: 10.26508/lsa.201800113 ), then eluting using hot acid-phenol chloroform. The input control RNA was  Spiked-in with ERCC standard spike-in, and all RNA fractions were rRNA depleted using the siTools rRNA depletion kit, and the E. coli ribopool.
The generation of the cDNA libraries was performed as described in (Anders et al. 2018; DOI: 10.26508/lsa.201800113  ). The PCR amplification of the libraries was performed as described in (Zhou et al. 2015; doi.org/10.1038/nature15377). Expected m6A DNA libraries at 200-300bp were excised from the gel and eluted in DNA elution buffer, then precipitated and re-suspended in nuclease-free H2O.

treatment_protocol: For oxidative stress, cells were grown in LB to mid-exponential phase then paraquat 1mM was added to the medium and cells were grown for a further 1.5 h.  For heat stress, cells in mid-exponential phase were pelleted and re-suspended in LB pre-warmed to 47°c, then incubated at 47°c for 7 mins.

value: F-, lambda-, rph-1

tag: strain

value: incubated at 47degree C for 7 min


title: Control corresponding to water intake 1


title: Human kidney, normothermic perfusion, RBC, 24 hrs, HF20, donor 3

description:
Library name: AC3
150bp_pe


title: m6A fraction WT E. coli subject to heat stress (replicate2)

description:
F-, λ-, rph-1
m6A-immunoprecipitated fraction wild-type E. coli subject to heat stress (replicate 2)


title: LM29.FF

value: CRC tumor


title: LM28.FF


title: Human kidney, normothermic perfusion, RBC, 6 hrs, HF20, donor 3

description:
Library name: AC2
150bp_pe


title: m6A fraction WT E. coli subject to heat stress (replicate1)

description:
F-, λ-, rph-1
m6A-immunoprecipitated fraction wild-type E. coli subject to heat stress (replicate1)


title: CO172.FF


title: Donor1 unstimulated, day 0, RNA-seq

value: Peripheral Blood


title: input fraction WT E. coli subject to heat stress (replicate 1)

description:
F-, λ-, rph-1
input fraction (total RNA) wild-type E. coli subject to heat stress (replicate 1)


title: Wild type control clone 2, day 35, replicate 4

city: London

first: Mariya

last: Moosajee

address: 11-43 Bath Street

department: Institute of Ophthalmology

country: United Kingdom

institute: UCL

description: Library name: WT02_35_4

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimgalore
Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters.
Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates
Count files were created using featurecounts (v2.0.3) and modelled using DESeq2 (v1.40)
Assembly: GRCh38
Supplementary files format and content: raw count per gene per sample
Supplementary files format and content: transcripts per million (TPM) values of genes per sample

source_name: iPSC derived

growth_protocol: adapted protocol based upon Eintracht et al 2022

extract_protocol:
Total RNA was isolated using Rneasy plus kit from Qiagen
RNA-seq libraries were prepared with Illumina Stranded Total RNA Prep with Ribo-Zero Plus as per manufacturers instructions

value: iPSC derived

value: Retinal organoids


title: Human kidney, normothermic perfusion, RBC, 0 hrs, HF20, donor 3

description:
Library name: AC1
150bp_pe


title: Human kidney, normothermic perfusion, RBC, 48 hrs, HF20, donor 2

description:
Library name: AB4
150bp_pe


title: Human kidney, normothermic perfusion, RBC, 6 hrs, HF20, donor 4

description:
Library name: AD2
150bp_pe

value: HMP


title: m6A fraction WT E. coli subject to oxidative stress (replicate2)

description:
F-, λ-, rph-1
m6A-immunoprecipitated fraction wild-type E. coli subject to oxidative stress (replicate 2)

value: grown with 1mM Paraquat for 1.5 h


title: Human kidney, normothermic perfusion, RBC, 24 hrs, HF20, donor 2

description:
Library name: AB3
150bp_pe

value: Kidney


title: Control corresponding to water intake 3


title: input fraction WT E. coli subject to oxidative stress (replicate 2)

description:
F-, λ-, rph-1
input fraction (total RNA) wild-type E. coli subject to oxidative stress (replicate 2)


title: Wild type control clone 2, day 35, replicate 3

description: Library name: WT02_35_3

value: WT


title: input fraction WT E. coli subject to oxidative stress (replicate 1)

description:
F-, λ-, rph-1
input fraction (total RNA) wild-type E. coli subject to oxidative stress (replicate 1)


title: CO169.FF


title: Human kidney, normothermic perfusion, RBC, 6 hrs, HF20, donor 2

description:
Library name: AB2
150bp_pe

value: Male

value: DCD


title: m6A fraction WT E. coli subject to oxidative stress (replicate1)

description:
F-, λ-, rph-1
m6A-immunoprecipitated fraction wild-type E. coli subject to oxidative stress (replicate1)


title: Wild type control clone 2, day 35, replicate 2

description: Library name: WT02_35_2


title: CO170.FF


title: Human kidney, normothermic perfusion, RBC, 0 hrs, HF20, donor 2

description:
Library name: AB1
150bp_pe

value: SCS


title: Wild type control clone 2, day 35, replicate 1

description: Library name: WT02_35_1


title: Donor2, unstimulated, day 0, RNA-seq

value: Primary cells

value: Natural Killer Cells

value: Unstimulated


title: input fraction E. coli ΔymfD strain

description:
F-, Δ(araD-araB)567, ΔlacZ4787(::rrnB-3), λ-, ΔymfD725::kan, rph-1, Δ(rhaD-rhaB)568, hsdR514
input fraction (total RNA) E. coli ΔymfD strain

source_name: ΔymfD Keio strain: JW1124

value: F-, delta(araD-araB)567, deltalacZ4787(::rrnB-3), lambda-, deltaymfD725::kan, rph-1, delta(rhaD-rhaB)568, hsdR514

value: Keio strain:JW1124


title: Human kidney, normothermic perfusion, RBC, 48 hrs, HF20, donor 1

description:
Library name: AA4
150bp_pe


title: CO164.FF

value: FF


title: CO163.FF

value: CRC tumor


title: Wild type control clone 2, day 20, replicate 4

description: Library name: WT02_20_4


title: m6A fraction E. coli ΔymfD strain

description:
F-, Δ(araD-araB)567, ΔlacZ4787(::rrnB-3), λ-, ΔymfD725::kan, rph-1, Δ(rhaD-rhaB)568, hsdR514
m6A-immunoprecipitated fraction E. coli ΔymfD strain

source_name: ΔymfD Keio strain: JW1123

value: Keio strain:JW1123


title: CO162.FF


title: Wild type control clone 2, day 20, replicate 3

description: Library name: WT02_20_3

value: iPSC derived


title: input fraction E. coli ΔyjhP strain

description:
F-, Δ(araD-araB)567, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, ΔyjhP773::kan, hsdR514
input fraction (total RNA) E. coli ΔyjhP strain

source_name: ΔyjhP Keio strain: JW4268

value: F-, delta(araD-araB)567, deltalacZ4787(::rrnB-3), lambda-, rph-1, delta(rhaD-rhaB)568, deltayjhP773::kan, hsdR514

value: Keio strain:JW4268


title: CO160.FF


title: m6A  fraction E. coli ΔyjhP strain

description:
F-, Δ(araD-araB)567, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, ΔyjhP773::kan, hsdR514
m6A-immunoprecipitated fraction E. coli ΔyjhP strain


title: CO154.FF


title: Wild type control clone 2, day 20, replicate 2

description: Library name: WT02_20_2

value: Retinal organoids


title: CO150.FF


title: Seedlings, pifq, Light, Rep1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Column name in raw_counts_all_samples.txt: pifq-L-Rep1

data_processing:
Reads were quality-checked with FASTQC (Andrews, 2010) and mapped on TAIR10 genome assembly of A. thaliana genome using STAR (Dobin et al., 2013) with relevant options “--alignIntronMin 20 --alignIntronMax 5000 --alignMatesGapMax 10000”.
Reads were quality-checked with FASTQC (Andrews, 2010) and mapped on TAIR10 genome assembly of A. thaliana genome using STAR (Dobin et al., 2013) with relevant options “--alignIntronMin 20 --alignIntronMax 5000 --alignMatesGapMax 10000”.
Duplicated alignments were removed using samtools markdup -r (Li et al., 2009).
Read counts were retrieved using QoRTs (Hartley and Mullikin, 2015) using gene coordinates obtained from file Arabidopsis_thaliana.TAIR10.42.gtf.
Differential expression was analyzed with DESeq2 (Love et al., 2014) using default options.
Assembly: Arabidopsis_thaliana.TAIR10.42
Supplementary files format and content: Tab-delimited text file containing raw counts for all samples

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seedlings were sterilized with a solution of 75% sodium hypochlorite and 0.1% Tween-20 and stratified at 4°C during 2 days in darkness. Seedlings were seeded on a 350 µm pore nylon mesh (Distribuciones Quimebora S.L., Madrid, Spain) placed over solid Murashige and Skoog (MS) medium with 1% sucrose and 0.6% agar.

extract_protocol:
Total RNA was extracted with the Favorprep Plant Total RNA Purification Mini kit (Favorgen). Messenger (polyA+) RNAs were purified from total RNA using oligo(dT)
Stranded libraries were prepared using DNB-seq (BGI). A 100-bp paired read end sequencing was performed on DNBSEQ-G400 system (BGI).

treatment_protocol: For experiments in the dark, seeds were exposed to light for 2h to synchronize germination, wrapped in aluminium foil and after 62 hours transferred, on the top of the mesh, to plates containing ethanol (mock) or ABA (Sigma Aldrich) and kept in the dark for four additional days, unless otherwise stated. For experiments under low light, seeds were placed at under fluorescent white light (10 mol m-2 s-1) with a 16-h light/8-h dark period and transferred to mock or ABA containing plates after 72 hours and kept under low light for five days, unless otherwise stated. All the plant were grown at 22ºC. For the hormone inhibitors, 0.5 uM NPA (Duchefa Biochemie); 0.5 uM BZR (MedChemExpress) and 0.1 uM Paclo (Duchefa Biochemie) were used.

value: Seedlings

tag: ecotype

value: pifq mutant

tag: growth conditions

value: Light


title: Seedlings, pifq, Light, Rep2

description: Column name in raw_counts_all_samples.txt: pifq-L-Rep2


title: Seedlings, pifq, Light, ABA, Rep2

description: Column name in raw_counts_all_samples.txt: pifq-L+ABA-Rep2

value: ABA


title: Wild type control clone 2, day 0, replicate 4

description: Library name: WT02_00_4

tag: cell type

value: WT


title: Seedlings, pifq, Light, ABA, Rep3

description: Column name in raw_counts_all_samples.txt: pifq-L+ABA-Rep3

tag: treatment


title: input fraction E. coli ΔyafS strain

description:
F-, Δ(araD-araB)567, ΔyafS732::kan, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, hsdR514
input fraction (total RNA) E. coli ΔyafS strain

source_name: ΔyafS Keio strain: JW0203

value: F-, delta(araD-araB)567, deltayafS732::kan, deltalacZ4787(::rrnB-3), lambda-, rph-1, delta(rhaD-rhaB)568, hsdR514

value: Keio strain:JW0203


title: Wild type control clone 2, day 20, replicate 1

description: Library name: WT02_20_1


title: Seedlings, pifq, Light, Rep3

description: Column name in raw_counts_all_samples.txt: pifq-L-Rep3


title: CO123.FF


title: CO134.FF


title: Seedlings, pifq, Dark, Rep2

description: Column name in raw_counts_all_samples.txt: pifq-D-Rep2

value: Dark


title: Seedlings, pifq, Light, ABA, Rep1

description: Column name in raw_counts_all_samples.txt: pifq-L+ABA-Rep1


title: Wild type control clone 2, day 0, replicate 2

description: Library name: WT02_00_2


title: input fraction E. coli ΔyafE strain

description:
F-, Δ(araD-araB)567, ΔyafE729::kan, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, hsdR514
input fraction (total RNA) E. coli ΔyafE strain

source_name: ΔyafE Keio strain: JW0200

value: F-, delta(araD-araB)567, deltayafE729::kan, deltalacZ4787(::rrnB-3), lambda-, rph-1, delta(rhaD-rhaB)568, hsdR514

value: Keio strain:JW0200


title: m6A fraction WT E. coli (replicate2)

description:
F-, λ-, rph-1
m6A-immunoprecipitated fraction wild-type E. coli (replicate 2)

value: F-, lambda-, rph-1


title: PFC in snATACseq in monkey SM45, replicate 2

city: PITTSBURGH

first: William

middle: R.

last: Stauffer

state: PA

address: 3501 Fifth Ave

department: Neurobiology

institute: University of Pittsburgh

library_source: genomic single cell

data_processing:
We used standard Seurat v3 and ArchR pipline
Assembly: Macaca mulatta
Supplementary files format and content: RDS files for filtered and raw counting matrix and final processed clustering and processed feather files for snATACseq data.

molecule: genomic DNA

organism: Macaca mulatta

source_name: Prefrontal cortex

extract_protocol:
We isolated nuclei using a loose glass dounce homogenizer followed by a tight glass homogenizer in EZ PREP buffer (Millipore Sigma, Cat# NUC-101). Or using pipet tip to break the tissue followed by detergent treatment and wash.
We used either 10x genomics v3.1 or multiomics kit for standard library construction.

value: Prefrontal cortex

value: Wildtype


title: CO140.FF

value: CRC tumor

value: FF


title: m6A fraction E. coli ΔyafE strain

description:
F-, Δ(araD-araB)567, ΔyafE729::kan, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, hsdR514
m6A-immunoprecipitated fraction E. coli ΔyafE strain


title: Seedlings, pifq, Dark, Rep3

description: Column name in raw_counts_all_samples.txt: pifq-D-Rep3


title: Wild type control clone 1, day 35, replicate 4

description: Library name: WT01_35_4

value: iPSC derived


title: Seedlings, pifq, Dark, Rep1

description: Column name in raw_counts_all_samples.txt: pifq-D-Rep1


title: CO129.FF


title: CO153.FF


title: Seedlings, pifq, Dark, ABA, Rep3

description: Column name in raw_counts_all_samples.txt: pifq-D+ABA-Rep3


title: input fraction WT E. coli (replicate 1)

description:
F-, λ-, rph-1
input fraction (total RNA) wild-type E. coli (replicate 1)


title: Wild type control clone 1, day 35, replicate 2

description: Library name: WT01_35_2

value: Retinal organoids


title: Seedlings, pifq, Dark, ABA, Rep2

description: Column name in raw_counts_all_samples.txt: pifq-D+ABA-Rep2

value: Seedlings


title: m6A fraction WT E. coli (replicate1)

description:
F-, λ-, rph-1
m6A-immunoprecipitated fraction wild-type E. coli (replicate1)


title: input fraction WT E. coli (replicate 2)

description:
F-, λ-, rph-1
input fraction (total RNA) wild-type E. coli (replicate 2)


title: Wild type control clone 1, day 20, replicate 4

description: Library name: WT01_20_4


title: Wild type control clone 2, day 0, replicate 3

description: Library name: WT02_00_3


title: m6A fraction E. coli ΔyafS strain

description:
F-, Δ(araD-araB)567, ΔyafS732::kan, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, hsdR514
m6A-immunoprecipitated fraction E. coli ΔyafS strain


title: PFC in snRNAseq in monkey SM45, replicate 2

library_source: transcriptomic single cell


title: PFC in snRNAseq in monkey SM45, replicate 1


title: PFC in snATACseq in monkey SM45, replicate 1


title: Wild type control clone 2, day 0, replicate 1

description: Library name: WT02_00_1


title: Seedlings, WT, Light, Rep3

description: Column name in raw_counts_all_samples.txt: WT-L-Rep3

value: Wild Type


title: PFC snATACseq in monkey SM20


title: Seedlings, pifq, Dark, ABA, Rep1

description: Column name in raw_counts_all_samples.txt: pifq-D+ABA-Rep1

value: pifq mutant


title: Seedlings, WT, Light, Rep2

description: Column name in raw_counts_all_samples.txt: WT-L-Rep2

value: Light


title: Wild type control clone 1, day 20, replicate 2

description: Library name: WT01_20_2

value: WT


title: PFC snATACseq in monkey SM19, replicate 2


title: Wild type control clone 1, day 35, replicate 1

description: Library name: WT01_35_1


title: U0128

city: Philadelphia

first: Brian

middle: C.

last: Capell

address: 421 Curie Boulevard Biomedical Research Building 1020 Biomedical Research Building 1020

department: Dermatology

institute: University of Pennsylvania

description: Library name: U0128

data_processing:
Aligned using RNA STAR under default settings
Differential expression analysis was performed via DESeq2
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: DESeq2 output

source_name: murine epidermis

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA-seq NEBNext Poly(A) mRNA magnetic isolation module, followed by NEBNext Ultra Directional RNA library prep kit for Illumina

value: murine epidermis

value: Cre+; Utx fl/Y


title: U0127

description: Library name: U0127

value: Cre-; Utx fl/Y


title: Wild type control clone 1, day 20, replicate 3

description: Library name: WT01_20_3


title: Seedlings, WT, Light, Rep1

description: Column name in raw_counts_all_samples.txt: WT-L-Rep1


title: U140

description: Library name: U140


title: U30

description: Library name: U30


title: Wild type control clone 1, day 35, replicate 3

description: Library name: WT01_35_3


title: PFC snRNAseq in monkey SM20


title: PFC snATACseq in monkey SM19, replicate 1


title: Seedlings, WT, Light, ABA, Rep3

description: Column name in raw_counts_all_samples.txt: WT-L+ABA-Rep3

value: ABA


title: Wild type control clone 1, day 0, replicate 4

description: Library name: WT01_00_4


title: U143

description: Library name: U143


title: Seedlings, WT, Light, ABA, Rep2

description: Column name in raw_counts_all_samples.txt: WT-L+ABA-Rep2


title: PFC snRNAseq in monkey SM16


title: PFC snRNAseq in monkey SM19


title: U28

description: Library name: U28


title: Seedlings, WT, Light, ABA, Rep1

description: Column name in raw_counts_all_samples.txt: WT-L+ABA-Rep1


title: Wild type control clone 1, day 0, replicate 2

description: Library name: WT01_00_2


title: Wild type control clone 1, day 0, replicate 3

description: Library name: WT01_00_3


title: U0137

description: Library name: U0137

value: Cre+; Utx fl/fl


title: Wild type control clone 1, day 20, replicate 1

description: Library name: WT01_20_1


title: U601

description: Library name: U601


title: Seedlings, WT, Dark, Rep3

description: Column name in raw_counts_all_samples.txt: WT-D-Rep3

value: Dark


title: PX Clone 2, day 35, replicate 4

description: Library name: PX02_35_4

value: PX


title: Seedlings, WT, Dark, Rep2

description: Column name in raw_counts_all_samples.txt: WT-D-Rep2


title: N2 adult day 16, DMSO, rep 4

city: Eugene

first: Patrick

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

description: Library name: N2_16_DMSO_r4

data_processing:
Subread v2.0.2 was used to build a custom C. elegans reference genome package with default parameters.
Sequenced reads contained in single-end FASTQ files were mapped to the WBcel235 reference genome using Subread with parameter -t 0.
Uniquely mapped reads were assigned to genes using the Subread featureCounts package with parameters -t exon -g gene_id.
Assembly: WBcel235 (build 108)
Supplementary files format and content: Tab-delimited table of raw gene counts for every gene and sample.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans N2 strains were maintained at 20°C and 80% RH on 60 mm nematode growth medium (NGM) plates seeded with E. coli OP50-1.

extract_protocol:
Worms were picked into 0.2 mL tubes containing 45 µL lysis buffer, 4 µL RNA-secure, 5 µL proteinase K and flash frozen with liquid nitrogen.
Libraries were prepared using the KAPA mRNA HyperPrep kit (KK8580 from Kapa Biosystems) as per manufacture protocol except that the total volume was adjusted to 1/4 per reaction.

treatment_protocol: Sulforaphane (Santa Cruz Biotech, sc-207495D) was mixed with DMSO (dimethyl sulfoxide) to create a stock solution. Stock solutions (DMSO for the controls) were then diluted with water to create working solutions and distributed onto 35 mm NGM plates containing 51 µM FUdR and previously seeded with OP50-1. Plates were treated with compound solutions such that the final volume was assumed equal to the volume of agar and the final concentration of DMSO was 0.25%. Worms were synchronized and added to treatment plates beginning on day 1 of adulthood. Biological replicates were aged and collected in tandem, with approximately 50 worms total per age, intervention, and replicate.

value: whole worm

value: adult day 16

value: DMSO control


title: Wild type control clone 1, day 0, replicate 1

description: Library name: WT01_00_1

value: iPSC derived


title: PFC snRNAseq in monkey SM11

value: Prefrontal cortex

value: Wildtype


title: N2 adult day 12, DMSO, rep 4

description: Library name: N2_12_DMSO_r4

value: adult day 12


title: Seedlings, WT, Dark, Rep1

description: Column name in raw_counts_all_samples.txt: WT-D-Rep1

value: Seedlings

value: Wild Type


title: U603

description: Library name: U603

value: Cre-; Utx fl/fl


title: N2 adult day 8, DMSO, rep 4

description: Library name: N2_8_DMSO_r4

value: adult day 8

value: WT


title: U0138

description: Library name: U0138

value: murine epidermis


title: N2 adult day 4, DMSO, rep 4

description: Library name: N2_4_DMSO_r4

value: adult day 4


title: PX Clone 2, day 35, replicate 2

description: Library name: PX02_35_2

value: Retinal organoids


title: U0462

description: Library name: U0462

value: Cre+; Utx fl/Y


title: Seedlings, WT, Dark, ABA, Rep3

description: Column name in raw_counts_all_samples.txt: WT-D+ABA-Rep3

value: Dark

value: ABA


title: PX Clone 2, day 35, replicate 1

description: Library name: PX02_35_1

value: PX


title: U0223

description: Library name: U0223

value: Cre-; Utx +/Y


title: PX Clone 2, day 20, replicate 4

description: Library name: PX02_20_4

value: iPSC derived


title: N2 adult day 2, DMSO, rep 4

description: Library name: N2_2_DMSO_r4

value: whole worm

value: adult day 2

value: DMSO control


title: PX Clone 2, day 20, replicate 3

description: Library name: PX02_20_3


title: FA19, Gen 2, Rep 2

city: Decatur

first: Concerta

last: Holley

state: GA

address: 1670 Clairmont Rd, Research 5A181

institute: Emory University

description: Library name: Sample 4

data_processing:
Fastq files generated by the sequencing platform were aligned to the N. gonorrhoeae FA19 genome (Refseq Accesion: NZ_CP012026.1) using the Bowtie2 tool to generate BAM files.
Counts were calculated from the bam files using the htseq-count tool and differential expression between samples determined using the DEseq2 tool.
Transcript differential expression analyses were conducted between the transcriptomes of a wild type FA19 strain in the absence of Gentamicin compared to the presence of gentamicin
Assembly: N. gonorrhoeae FA19 genome (Refseq Accesion: NZ_CP012026.1)
Supplementary files format and content: Excel sheet including RPKM values for all samples

organism: Neisseria gonorrhoeae

source_name: whole cells

growth_protocol: Plate-grown FA19 was inoculated into pre-warmed GCB broth containing Kellogg's supplements I and II and 0.043% (w/v) sodium bicarbonate and grown in a 37°C water bath with shaking for two doublings to ensure cell viability and entry into log phase. Each condition was sequenced in duplicates.

extract_protocol:
RNA was harvested using the Rneasy Mini Plus Kit (Qiagen). Quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer
The Agilent SureSelect Strand Specific mRNA library kit as per the manufacturer’s instructions (Agilent, Santa Clara, CA).  Library construction began with ribosome reduction using the RiboMinus rRNA depletion kit for bacteria as described by the manufacturer (Invitrogen).  The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.  Cluster generation was performed according to the manufacturer’s recommendations for onboard clustering (Illumina).

treatment_protocol: The culture was split into two equal volumes and either 2 µg/mL Gentamicin or equivalent volume of sterile vehicle was added to the broth. The cultures were grown for an additional 4 hours then harvested and the pellets stored at −70°C.

value: whole cells

value: Gentamicin 2 ug/mL


title: Seedlings, WT, Dark, ABA, Rep2

description: Column name in raw_counts_all_samples.txt: WT-D+ABA-Rep2

value: Seedlings

value: Wild Type


title: U0458

description: Library name: U0458

value: Cre-; Utx fl/Y


title: N2 adult day 12, DMSO, rep 3

description: Library name: N2_12_DMSO_r3

value: adult day 12

value: WT


title: Seedlings, WT, Dark, ABA, Rep1

description: Column name in raw_counts_all_samples.txt: WT-D+ABA-Rep1


title: FA19, Gen 0, Rep 2

description: Library name: Sample 2

value: Gentamicin 0 ug/mL


title: FA19, Gen 2, Rep 1

description: Library name: Sample 3


title: U0113

description: Library name: U0113

value: murine epidermis


title: PX Clone 2, day 20, replicate 2

description: Library name: PX02_20_2

value: Retinal organoids


title: U0224

description: Library name: U0224

value: Cre+; Utx fl/Y


title: PX Clone 2, day 35, replicate 3

description: Library name: PX02_35_3

value: PX


title: U0112

description: Library name: U0112


title: U0468

description: Library name: U0468

value: Cre+; Utx fl/fl


title: PX Clone 2, day 0, replicate 4

description: Library name: PX02_00_4

value: iPSC derived


title: FA19, Gen 0, Rep 1

description: Library name: Sample 1


title: PX Clone 2, day 0, replicate 3

description: Library name: PX02_00_3


title: U0253

description: Library name: U0253


title: TOP1-AID_WAPL-dTAG_nn -aux -dtag, repl. 2

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description:
Library name: 298013
TOP1-AID_WAPL-dTAG_nn.merged-n.ref.hic

library_source: genomic

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.4
bowtie2 version 2.2.5 mapping against hg19 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan)

extract_protocol:
Cells were cross-linked in falcon tube. The DNA was fragmented, biotynilated at both ends, and ligated at newly blunted ends together. Biotinylated DNA was captured and prepared for paired-end Illumina sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells

tag: group

value: nn = -aux -dtag


title: N2 adult day 2, DMSO, rep 3

description: Library name: N2_2_DMSO_r3

tag: tissue

value: whole worm

value: adult day 2

value: DMSO control


title: N2 adult day 4, DMSO, rep 3

description: Library name: N2_4_DMSO_r3

value: adult day 4


title: U0252

description: Library name: U0252


title: N2 adult day 16, DMSO, rep 2

description: Library name: N2_16_DMSO_r2

value: adult day 16


title: N2 adult day 16, DMSO, rep 3

description: Library name: N2_16_DMSO_r3


title: PX Clone 2, day 0, replicate 2

description: Library name: PX02_00_2


title: TOP1-AID_WAPL-dTAG_nY -aux +dtag, repl. 2

description:
Library name: 297198
TOP1-AID_WAPL-dTAG_nY.merged-n.downS.122mio.hic

value: nY = -aux +dtag


title: N2 adult day 12, DMSO, rep 2

description: Library name: N2_12_DMSO_r2

value: adult day 12

value: WT


title: PX Clone 2, day 0, replicate 1

description: Library name: PX02_00_1


title: TOP1-AID_WAPL-dTAG_Yn +aux -dtag, repl. 2

description:
Library name: 297197
TOP1-AID_WAPL-dTAG_Yn.merged-n.downS.122mio.hic

value: Yn = +aux -dtag


title: N2 adult day 8, DMSO, rep 3

description: Library name: N2_8_DMSO_r3

value: adult day 8


title: N2 adult day 8, DMSO, rep 2

description: Library name: N2_8_DMSO_r2


title: PX Clone 2, day 20, replicate 1

description: Library name: PX02_20_1

value: Retinal organoids


title: U0114

description: Library name: U0114

value: murine epidermis


title: TOP1-AID_WAPL-dTAG_YY +aux +dtag, repl.2

description:
Library name: 298014
TOP1-AID_WAPL-dTAG_YY.merged-n.downS.122mio.hic

value: YY = +aux +dtag


title: U0460

description: Library name: U0460

value: Cre+; Utx +/fl


title: PX Clone 1, day 35, replicate 4

description: Library name: PX01_35_4

value: iPSC derived

value: PX


title: SMC1-4E, WAPL-dTAG CTCF-dTAG SMC1-AID YY +dtag +aux, repl. 2

description:
Library name: 316661
SMC1_4E_WAPL-dTAG_CTCF-dTAG_SMC1-AID_YY.merged.downS.hic

value: HeLa Kyoto

value: human cervical cancer cells

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL/GFP-P2A-HA-FKBP12F36V-CTCF; SMC1-4E

value: YY = +dtag +aux


title: PX Clone 1, day 35, replicate 3

description: Library name: PX01_35_3


title: N2 adult day 2, DMSO, rep 2

description: Library name: N2_2_DMSO_r2

value: whole worm

value: adult day 2

value: DMSO control


title: SMC1-4E, WAPL-dTAG CTCF-dTAG SMC1-AID nY -dtag +aux, repl. 2

description:
Library name: 316660
SMC1_4E_WAPL-dTAG_CTCF-dTAG_SMC1-AID_nY.merged.downS.hic

value: nY = -dtag +aux


title: U0256

description: Library name: U0256


title: N2 adult day 16, DMSO, rep 1

description: Library name: N2_16_DMSO_r1

value: adult day 16

value: WT


title: U0255

description: Library name: U0255


title: SMC1-wt, WAPL-dTAG CTCF-dTAG SMC1-AID YY +dtag +aux, repl. 2

description:
Library name: 316659
SMC1_wt_WAPL-dTAG_CTCF-dTAG_SMC1-AID_YY.merged.ref.hic

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL/GFP-P2A-HA-FKBP12F36V-CTCF; SMC1-WT


title: PX Clone 1, day 35, replicate 2

description: Library name: PX01_35_2

value: Retinal organoids


title: N2 adult day 8, DMSO, rep 1

description: Library name: N2_8_DMSO_r1

value: adult day 8


title: PX Clone 1, day 20, replicate 4

description: Library name: PX01_20_4


title: U0465

description: Library name: U0465

value: murine epidermis

value: Cre-; Utx fl/fl


title: U0254

description: Library name: U0254


title: U0115

description: Library name: U0115

value: Cre+; Utx fl/fl


title: PX Clone 1, day 35, replicate 1

description: Library name: PX01_35_1

value: iPSC derived

value: PX


title: SMC1-wt, WAPL-dTAG CTCF-dTAG SMC1-AID nY -dtag +aux, repl. 2

description:
Library name: 316658
SMC1_wt_WAPL-dTAG_CTCF-dTAG_SMC1-AID_nY.merged.downS.hic

value: HeLa Kyoto

value: human cervical cancer cells


title: SMC1-4E, WAPL-dTAG CTCF-dTAG SMC1-AID YY +dtag +aux, repl. 1

description:
Library name: 297207
SMC1_4E_WAPL-dTAG_CTCF-dTAG_SMC1-AID_YY.merged.downS.hic

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL/GFP-P2A-HA-FKBP12F36V-CTCF; SMC1-4E

value: YY = +dtag +aux


title: PX Clone 1, day 20, replicate 3

description: Library name: PX01_20_3


title: SMC1-4E, WAPL-dTAG CTCF-dTAG SMC1-AID nY -dtag +aux, repl. 1

description:
Library name: 298020
SMC1_4E_WAPL-dTAG_CTCF-dTAG_SMC1-AID_nY.merged.downS.hic


title: N2 adult day 4, DMSO, rep 1

description: Library name: N2_4_DMSO_r1

value: whole worm

value: adult day 4


title: PX Clone 1, day 20, replicate 2

description: Library name: PX01_20_2


title: PX Clone 1, day 20, replicate 1

description: Library name: PX01_20_1


title: N2 adult day 2, DMSO, rep 1

description: Library name: N2_2_DMSO_r1

value: adult day 2

value: DMSO control


title: U0110

description: Library name: U0110


title: SMC1-wt, WAPL-dTAG CTCF-dTAG SMC1-AID nY -dtag +aux, repl. 1

description:
Library name: 298019
SMC1_wt_WAPL-dTAG_CTCF-dTAG_SMC1-AID_nY.merged.downS.hic

value: nY = -dtag +aux


title: U0111

description: Library name: U0111


title: N2 adult day 12, DMSO, rep 1

description: Library name: N2_12_DMSO_r1

value: adult day 12

value: WT


title: SMC1-wt, WAPL-dTAG CTCF-dTAG SMC1-AID YY +dtag +aux, repl. 1

description:
Library name: 297205
SMC1_wt_WAPL-dTAG_CTCF-dTAG_SMC1-AID_YY.merged.ref.hic

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL/GFP-P2A-HA-FKBP12F36V-CTCF; SMC1-WT


title: N2 adult day 12, SFN, rep 4

description: Library name: N2_12_SFN_r4

value: sulforaphane


title: N2 adult day 4, DMSO, rep 2

description: Library name: N2_4_DMSO_r2


title: PX Clone 1, day 0, replicate 4

description: Library name: PX01_00_4

value: Retinal organoids


title: X1250 Input

description: Library name: X1250 Input

data_processing:
Sequence quality was verified using fastqc and bowtie2 was used to map reads to the genome of mouse (mm10) with default parameters. Bedtools were used to remove the reads that contained low quality bases (MAPQ < 10) and undetermined bases. Mapped reads of IP and input libraries were processed by macs2 callpeak function, which identifies ChIP-seq peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser.
Peaks were called using the threshold of FDR < 0.05, no shifting model building, extension-size of 200bp and the removal of duplicates. ChIP-seq peaks were annotated using the R package ChIPpeakAnno. Heatmaps and metaplots were generated using the computeMatrix and plotHeatmap functions using deepTools2.0. Peaks were visualized and figure images were exported using the GRCm39/mm39 mouse genome on the UCSC genome browser.
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: Peak files in Excel

extract_protocol:
Mouse epidermis single cell suspension
Crosslinked samples by addition of formaldehyde (Fisher chemical, F79) to 1% and incubating for 10min at RT at 1000rpm in thermomixer. Quenched crosslinking reaction by the addition of glycine (Fisher scientific, BP381) to 125mM and incubating at 1000rpm for 5min at RT. Centrifuge at 1200rpm for 5min at 4°C. Resuspend pellet with 1mL cold DPBS (Gibco, 14190-136) and centrifuge at 1200rpm for 5min at 4°C. Remove supernatant and store cell pellet at -80°C; (n = 3 for all groups, WT females, Utx-cKO females). Primary antibodies used: H3K27ac (Abcam, ab4729); : UTX (D3Q1I) Rabbit mAb (#33510, Cell signaling) Lot 4.

value: murine epidermis

value: Cre+; Utx fl/fl


title: X1247 Input

description: Library name: X1247 Input


title: X1258 Input

description: Library name: X1258 Input


title: 4E+dTag WAPL-depleted Replicate 2

description:
Library name: 281969__4E+
4E-Wko.2reps.merged.hic

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL; SMC1-4E


title: N2 adult day 8, SFN, rep 4

description: Library name: N2_8_SFN_r4

value: adult day 8


title: PX Clone 1, day 0, replicate 3

description: Library name: PX01_00_3

value: iPSC derived

value: PX


title: PX Clone 1, day 0, replicate 2

description: Library name: PX01_00_2


title: N2 adult day 16, SFN, rep 4

description: Library name: N2_16_SFN_r4

value: adult day 16


title: X1249 Input

description: Library name: X1249 Input

value: Cre-; Utx fl/fl


title: 4E-dTag Replicate 2

description:
Library name: 281968__4E-
4E-.2reps.merged.hic

value: HeLa Kyoto

value: human cervical cancer cells


title: N2 adult day 4, SFN, rep 4

description: Library name: N2_4_SFN_r4

value: whole worm

value: adult day 4


title: N2 adult day 2, SFN, rep 4

description: Library name: N2_2_SFN_r4

value: adult day 2


title: X1245 Input

description: Library name: X1245 Input


title: w.t.+dTag WAPL-depleted Replicate 2

description:
Library name: 281967__wt+
wt-Wko.2reps.merged.hic

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL; SMC1-WT


title: PX Clone 1, day 0, replicate 1

description: Library name: PX01_00_1


title: AN Clone 2, day 35, replicate 5

description: Library name: AN02_35_5

value: AN


title: X1244 Input

description: Library name: X1244 Input


title: N2 adult day 16, SFN, rep 3

description: Library name: N2_16_SFN_r3

value: WT

value: sulforaphane


title: 4E+dTag WAPL-depleted Replicate 1

description:
Library name: 281965__4E+
4E-Wko.2reps.merged.hic


title: AN Clone 2, day 35, replicate 4

description: Library name: AN02_35_4

value: Retinal organoids


title: N2 adult day 12, SFN, rep 3

description: Library name: N2_12_SFN_r3

value: adult day 12


title: X1258 H3K27ac

description: Library name: X1258 H3K27ac

value: murine epidermis

value: Cre+; Utx fl/fl


title: AN Clone 2, day 35, replicate 3

description: Library name: AN02_35_3

value: iPSC derived


title: N2 adult day 8, SFN, rep 3

description: Library name: N2_8_SFN_r3

value: adult day 8


title: X1250 H3K27ac

description: Library name: X1250 H3K27ac


title: w.t.+dTag WAPL-depleted Replicate 1

description:
Library name: 281963__wt+
wt-Wko.2reps.merged.hic


title: AN Clone 2, day 35, replicate 2

description: Library name: AN02_35_2


title: N2 adult day 4, SFN, rep 3

description: Library name: N2_4_SFN_r3


title: 4E-dTag-dTag Replicate 1

description:
Library name: 281964__4E-
4E-.2reps.merged.hic

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL; SMC1-4E


title: w.t.-dTag Replicate 1

description:
Library name: 281962__wt-
wt-.2reps.merged.hic


title: 278_CD_ascending_colon

city: Miami

first: Maria

middle: T

last: Abreu

state: Florida

address: 1475 NW 12th Ave floor 1

department: Gastroenterology

institute: University of Miami

data_processing:
All data processing was performed using CLC Genomics Workbench software (version 23.0). Imported reads were trimmed and quality checked before mapping to the human genome (hg38). Human gene expression tracks were normalized to RPKM.
Assembly: hg38
Supplementary files format and content: .csv file containing gene expression counts per sample in RPKM

source_name: ascending colon

extract_protocol:
AllPrep DNA/RNA Kit (QIAGEN)
Total RNA was prepped with the TECAN Universal Plus Total RNA-Seq with NuQuant, Human AnyDeplete using 5-60 ng via Qubit and 19 cycles of PCR.

value: ascending colon

tag: disease state

value: Crohn's disease


title: AN Clone 2, day 20, replicate 4

description: Library name: AN02_20_4


title: N2 adult day 2, SFN, rep 3

description: Library name: N2_2_SFN_r3


title: N2 adult day 16, SFN, rep 2

description: Library name: N2_16_SFN_r2

value: adult day 16


title: AN Clone 2, day 35, replicate 1

description: Library name: AN02_35_1


title: X1245 H3K27ac

description: Library name: X1245 H3K27ac

value: Cre-; Utx fl/fl


title: 278_CD_terminal_ileum

source_name: terminal ileum

value: terminal ileum


title: X1249 H3K27ac

description: Library name: X1249 H3K27ac


title: X1247 H3K27ac

description: Library name: X1247 H3K27ac


title: 294_Control_ascending_colon

value: non-IBD


title: X1258 UTX

description: Library name: X1258 UTX


title: AN Clone 2, day 20, replicate 3

description: Library name: AN02_20_3


title: w.t.-dTag Replicate 2

description:
Library name: 281966__wt-
wt-.2reps.merged.hic

value: HeLa Kyoto

value: human cervical cancer cells

value: HeLa Kyoto SMC1-AID-mKate2/SCC1-Halo-P2A-TIR1/Blast-P2A-HA-FKBP12F36V-WAPL; SMC1-WT


title: AN Clone 2, day 20, replicate 2

description: Library name: AN02_20_2

value: AN


title: X1250 UTX

description: Library name: X1250 UTX


title: AN Clone 2, day 20, replicate 1

description: Library name: AN02_20_1

value: Retinal organoids


title: N2 adult day 4, SFN, rep 2

description: Library name: N2_4_SFN_r2

value: whole worm

value: adult day 4

value: WT

value: sulforaphane


title: X1247 UTX

description: Library name: X1247 UTX

value: murine epidermis

value: Cre+; Utx fl/fl


title: 608_Control_ascending_colon

value: ascending colon


title: 294_Control_terminal_ileum


title: AN Clone 2, day 0, replicate 4

description: Library name: AN02_00_4

value: iPSC derived


title: N2 adult day 2, SFN, rep 2

description: Library name: N2_2_SFN_r2

value: adult day 2


title: 608_Control_terminal_ileum


title: AN Clone 2, day 0, replicate 3

description: Library name: AN02_00_3


title: N2 adult day 12, SFN, rep 2

description: Library name: N2_12_SFN_r2

value: adult day 12


title: N2 adult day 16, SFN, rep 1

description: Library name: N2_16_SFN_r1

value: adult day 16


title: X1249 UTX

description: Library name: X1249 UTX

value: Cre-; Utx fl/fl


title: 606_Control_ascending_colon

value: non-IBD


title: X1244 UTX

description: Library name: X1244 UTX


title: N2 adult day 8, SFN, rep 1

description: Library name: N2_8_SFN_r1

value: adult day 8


title: N2 adult day 12, SFN, rep 1

description: Library name: N2_12_SFN_r1


title: AN Clone 2, day 0, replicate 2

description: Library name: AN02_00_2


title: N2 adult day 8, SFN, rep 2

description: Library name: N2_8_SFN_r2


title: N2 adult day 4, SFN, rep 1

description: Library name: N2_4_SFN_r1


title: X1042 IgG

description: Library name: X1042 IgG

data_processing:
Paired-end reads were aligned to both the mm10 mouse genome and the Saccharomyces cerevisiae (SacCer3) genome using the bowtie2 tool (version 2.3.4.3).
After alignment, the outputs are converted to BAM format. This format is then filtered to eliminate unmapped reads and those with a mapping quality below 10, using samtools version 1.9. Following this, the BAM files are sorted and processed with samtools. The files are further filtered to retain only those reads that are mapped in a proper pair. They are then transformed into paired-end BED format using bedtools (version 2.27.1) with the -bedpe option. The resultant BED files are sorted by position, and the coordinates for both 5’ and 3’ read pairs are extracted. The data is then converted into bedGraph format, excluding regions without signals. Spike-in normalization is implemented using a normalization factor. This factor is derived by dividing the lowest number of unique reads aligned to the spike-in genome reference by the number of unique reads aligned to the spike-in genome reference in each sample, facilitating the calculation with the command genomecov -bg -scale. Lastly, RPKM normalized tracks in BigWig format were generated using the bamCoverage function using deepTools2.0. Peak files for CUT&RUN data can be found in table S7.
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: Peak files in Excel
Library strategy: CUT&Run

extract_protocol:
Mouse epidermis single cell suspension
Performed using CUT&RUN Assay Kit from Cell Signaling (Cat No. 86652) on single cell suspensions of epidermal keratinocytes harvested from Utx-cKO and WT females for IgG and H3K27me3 (Cell Signaling, #9733).


title: 606_Control_terminal_ileum

value: terminal ileum


title: X1033 IgG

description: Library name: X1033 IgG


title: AN Clone 2, day 0, replicate 1

description: Library name: AN02_00_1

value: AN


title: 599_Control_terminal_ileum


title: AN Clone 1, day 35, replicate 3

description: Library name: AN01_35_3

value: Retinal organoids


title: AN Clone 1, day 35, replicate 4

description: Library name: AN01_35_4


title: 599_Control_ascending_colon


title: 646_Control_ascending_colon


title: N2 adult day 2, SFN, rep 1

description: Library name: N2_2_SFN_r1

value: whole worm


title: AN Clone 1, day 35, replicate 2

description: Library name: AN01_35_2


title: X1061 IgG

description: Library name: X1061 IgG


title: I01543_TLR8_2.5_mg_kg

city: Foster City

first: Cameron

last: Soulette

address: 333 Lakeside Dr

institute: Gilead Sciences

description:
I01543_L2
50bp

data_processing:
Reads were demultiplexed and adapter sequences were clipped
Paired-end reads were aligned to Hg19 reference genome using STAR
RSEM 1.2.0 was used for gene count quantification
Assembly: hg19
Supplementary files format and content: rsem gene counts with gene annoation information

organism: Macaca fascicularis

source_name: Liver

extract_protocol:
Isolation of total cellular RNA was conducted by Expression Analysis (Durham, NC).
Total RNA samples were converted into cDNA libraries using the TruSeq Stranded Total RNA-RiboZero Gold Sample Prep Kit (Illumina, San Diego, CA).
Pair-end sequencing was conducted using Illumina HiSeq 2000 with read length of 50 nucleotides.

value: Liver

value: Female

value: TLR8 agonist

tag: treatment/dose


title: X1245 UTX

description: Library name: X1245 UTX

value: murine epidermis


title: AN Clone 1, day 20, replicate 4

description: Library name: AN01_20_4


title: I01542_TLR8_2.5_mg_kg

description:
I01542_L6.D708
50bp


title: X1041 IgG

description: Library name: X1041 IgG


title: X1026 IgG

description: Library name: X1026 IgG


title: I01541_TLR8_2.5_mg_kg

description:
I01541_L5.D705
50bp


title: 645_Control_terminal_ileum


title: 637_CD_ascending_colon

value: Crohn's disease


title: AN Clone 1, day 20, replicate 3

description: Library name: AN01_20_3


title: I01540_TLR8_0.5_mg_kg

description:
I01540_L3.D705
50bp


title: X1033 H3K27me3

description: Library name: X1033 H3K27me3

value: Cre+; Utx fl/fl


title: AN Clone 1, day 20, replicate 2

description: Library name: AN01_20_2

value: iPSC derived


title: I01539_TLR8_0.5_mg_kg

description:
I01539_L3.D702
50bp


title: AN Clone 1, day 0, replicate 4

description: Library name: AN01_00_4


title: I01538_TLR8_0.5_mg_kg

description:
I01538_L2.D711
50bp


title: 518_CD_terminal_ileum


title: 637_CD_terminal_ileum


title: X1027 IgG

description: Library name: X1027 IgG


title: X1042 H3K27me3

description: Library name: X1042 H3K27me3


title: 518_CD_ascending_colon_

value: ascending colon


title: AN Clone 1, day 0, replicate 1

description: Library name: AN01_00_1


title: AN Clone 1, day 0, replicate 2

description: Library name: AN01_00_2


title: X1061 H3K27me3

description: Library name: X1061 H3K27me3


title: 645_Control_ascending_colon


title: No Template Control

city: Saskatoon

first: Kundanika

last: Mukherjee

state: Saskatchewan

address: 107 Wiggins Rd,  2D40 Health Sciences Building

department: APP

country: Canada

institute: University of Saskatchewan

description: Library name: DSP-1002990011571-A-A01

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: GeoMx Mouse Whole Transcriptome Atlas
Supplementary files format and content: Digital Count Conversion file (DCC)
Library strategy: Spatial Transcriptomics

organism: synthetic construct

source_name: Jejunum

extract_protocol:
Fresh frozen jejunal tissues were sectioned in Tissue-Tek® O.C.T. Compound using a Leica microtome at 6 um thickness. The section containing slides were stained with UV- cleavable probes. Slides were loaded into GeoMx DSP instrument and scanned to capture fluorescent images used to select regions of interest (ROIs).
Other: GeoMx DSP SeqCode

treatment_protocol: Mesenteric lymph duct cannulated rats were randomly divided into three groups to receive three different treatments by intracerebroventricular infusion: 1) GLP-2R antagonist (GLP-2(11-33)) 2) MC4R antagonist (SHU9119) 3) saline as control.

value: Jejunum

value: Sprague Dawley

value: No Template Control


title: 520_Control_ascending_colon

value: non-IBD


title: I01536_TLR8_0.1_mg_kg

description:
I01536_L5.D708
50bp


title: X1041 H3K27me3

description: Library name: X1041 H3K27me3

value: Cre-; Utx fl/fl


title: 437_CD_ascending_colon


title: I01535_TLR8_0.1_mg_kg

description:
I01535_L4.D705
50bp


title: X1026 H3K27me3

description: Library name: X1026 H3K27me3


title: 663_Control_ascending_colon


title: 437_CD_terminal_ileum

value: terminal ileum


title: microglia, wild type, repeat2

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

country: China

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Clean reads after filtering were aligned to the reference genome with HISAT.
Bowtie2 were used to align the clean reads to the reference genes.
Differential expression analysis was performed using DESeq2.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes fpkm, tpm, read count, and normalized read count.

source_name: Cortex and Hippocampus

growth_protocol: Mice were maintained in a specific pathogen-free animal facility with a 12 h light/12 h dark cycle.

extract_protocol:
At 9-month-old, Mice were anesthetized and transcardially perfused with ice-cold HBSS. The brains were isolated with the meninges removed, followed by dissection of the cortex and hippocampus, which were then minced and digested by 1% papain. Microglia were isolated from the resulting cell suspension via immunopanning with the rat-anti-mouse CD45 antibody (BD, 553076) and the secondary goat-anti-rat antibody (Jackson ImmunoResearch, 112-005-003), and directly lysed on the panning plate by Trizol (Thermo, 15596018), and stored at -80℃ before RNA extraction.
Poly-A selected method was used to prepare the RNA-seq library. Sequencing was performed on the DNBSEQ platform with SE50 sequencing length

treatment_protocol: At 8-month-old, mice were treated with tamoxifen via gavage at 0.1mg/g for 5 consequtive days to induce Cre-mediated genomic recombination.

value: Cortex and Hippocampus

value: Microglia

value: wild type


title: I01534_control

description:
I01534_L3.D705
50bp

value: Liver

value: Control

value: Vehicle


title: Null, Replicate 3

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: Osr2Cre_Hnf4a_Null_JP1218
Osr2Cre_Hnf4a_Null_JP1218

data_processing:
Sequencing reads were aligned to UCSC mouse genome mm10 using STAR aligner. Only uniquely mapped reads were retained for downstream analysis.
Read count mapped to each gene was measured using featureCounts with options ‘-O --fracOverlap 0.8’.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: kidney

extract_protocol:
Total RNA from FACS isolated cells were prepared using Single Cell RNA Purification Kit (Norgen). From total RNA, mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) following manufacturer’s instructions. Fragmentation of RNA followed by reverse transcription and second strand cDNA synthesis was done using NEBNext RNA First Strand Synthesis Module (E7525L) and NEBNext RNA Second Strand Synthesis Module (E6111L) following manufacturer’s instructions.
The resulting double-stranded cDNA’s were further processed to DNA sequencing libraries using ThruPLEX DNA-seq 12S Kit (R400428, Clontech Laboratories). Libraries were size-selected by gel purification for an average size of 350bp.

value: kidney

value: Rosa26 Ai3/+; Hnf4a c/c; Osr2 cre/+

value: FACS-isolated nephron tubules targeted by Osr2Cre


title: X1027 H3K27me3

description: Library name: X1027 H3K27me3

value: murine epidermis

value: Cre+; Utx fl/fl


title: I01537_TLR8_0.1_mg_kg

description:
I01537_L5.D711
50bp

value: Female

value: TLR8 agonist


title: microglia, APP/PS1, repeat3


title: Het, Replicate 2

description:
Library name: Osr2Cre_Hnf4a_Het_JP1215
Osr2Cre_Hnf4a_Het_JP1215

value: Rosa26 Ai3/+; Hnf4a c/+; Osr2 cre/+


title: I01533_control

description:
I01533_L2.D702
50bp


title: 658_Control_ascending_colon

value: ascending colon

value: non-IBD


title: I01530_TLR8_2.5_mg_kg

description:
I01530_L4.D711
50bp

value: Male


title: microglia, APP/PS1, repeat1

value: Cortex and Hippocampus


title: 657_CD_terminal_ileum

value: terminal ileum

value: Crohn's disease


title: microglia, APP/PS1, repeat2

value: Microglia


title: Het, Replicate 3

description:
Library name: Osr2Cre_Hnf4a_Het_JP1216
Osr2Cre_Hnf4a_Het_JP1216


title: I01532_control

description:
I01532_L2.D711
50bp

value: Liver

value: Control


title: Null, Replicate 2

description:
Library name: Osr2Cre_Hnf4a_Null_JP1217
Osr2Cre_Hnf4a_Null_JP1217

value: kidney


title: 654_CD_ascending_colon


title: 657_CD_ascending_colon


title: Null, Replicate 1

description:
Library name: Osr2Cre_Hnf4a_Null_JP1196
Osr2Cre_Hnf4a_Null_JP1196

value: Rosa26 Ai3/+; Hnf4a c/c; Osr2 cre/+


title: microglia, wild type, repeat3

value: wild type


title: microglia, APP/PS1:Cx3cr1-CreER:Cx43-flox/flox, repeat3


title: 654_CD_terminal_ileum


title: I01529_TLR8_2.5_mg_kg

description:
I01529_L4.D708
50bp


title: I01528_TLR8_0.5_mg_kg

description:
I01528_L2.D708
50bp


title: microglia, APP/PS1:Cx3cr1-CreER:Cx43-flox/flox, repeat2


title: microglia, wild type, repeat1


title: SAM2_3

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

data_processing:
The resulting reads were analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.0 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse genome (GRCm39) with TopHat2 using Bowtie1 and Samtools, allowing 3 mismatches and 20 multihits. The Gencode vM29 gene annotation for GRCm39 was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, keeping only those genes where the normalized count value was higher than 10 in at least 30% of the samples. Finally, those genes that had an adjusted p-value below 0.05 FDR were selected. GSEAPreranked was used to perform gene set enrichment analysis for the selected gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file with DESeq2 normalized counts

source_name: MEFs

growth_protocol: MEFs were cultured in Dulbecco's modified Eagle's medium (DMEM) DMEM medium supplemented with 10 % of fetal bovine serum (FBS) and with 5 µg/mL of Ppenicillin/sStreptomycin (P/S).

extract_protocol:
Total RNA from MEFs was extracted using the RNeasy kit (QIAGEN, Cat No. #74134) following the manufacturer’s instructions.
Total RNA samples from empty vector and sgRNA2 MEFs were converted into sequencing libraries with the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760), as recommended by the manufacturer. Briefly, the polyA+ fraction was purified and randomly fragmented, converted to double-stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. The adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on a NextSeq500 (Illumina) instrument in a paired-end 43+43 base format by following the manufacturer's protocols.

treatment_protocol: Not applicable

value: MEFs


title: I01527_TLR8_0.5_mg_kg

description:
I01527_L1.D705
50bp


title: 653_CD_ascending_colon


title: 535_CD_ascending_colon


title: I01531_TLR8_2.5_mg_kg

description:
I01531_L5.D702
50bp


title: eTAM-seq_RNA_WT_replicate2

city: Chicago

first: Jingxuan

last: Jia

state: IL

address: 929E 57th St

institute: University of Chicago

data_processing:
Quality trimming using cutadapt, version 3.5, parameters -e 0.1 -n 1 -O 1 --cores 10 -q 6 -m 97 -g GACGCTCTTCCGATCT -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
5S rRNA read mapping using hisat-3n and removing aligned sequence,  version 3.5, parameters: --time --base-change A,G --no-spliced-alignment --no-softclip --norc --no-unal --rna-strandness "F"
16S rRNA read mapping using hisat-3n and removing aligned sequence, version 3.5, parameters: --time --base-change A,G --no-spliced-alignment --no-softclip --norc --no-unal --rna-strandness "F"
23S rRNA read mapping using hisat-3n and removing aligned sequence, version 3.5, parameters:  --time --base-change A,G --no-spliced-alignment --no-softclip --norc --no-unal --rna-strandness "F"
Genome read mapping with the data removed rRNA using hisat-3n,  version 3.5, parameters: --time --base-change A,G --no-spliced-alignment --bowtie2-dp 0 --no-unal --rna-strandness "F"
Removing reads with low A to G conversion rate using samtools, version 1.21, parameters: samtools view -hb -e "([Yf]+[Zf]>0) && ([Yf]/([Yf]+[Zf])>= 0.5)"
Conversion table generation with pileup2var to a txt file, version 1.1.0 , parameters -f 524 -a A -c 1 -s "F"
Assembly: rRNA-5S ribosomal RNA Gene ID: 948471
Assembly: Escherichia coli 16S ribosomal RNA, complete sequence GenBank: J01859.1
Assembly: Escherichia coli strain K-12 23S ribosomal RNA gene, complete sequence NR_103073.1
Assembly: Escherichia coli str. K-12 substr. MG1655 Ensemble (GCA_000005845; assembly: ASM584v2)
Supplementary files format and content: Txt file, a tab-separetd and 13-column plain file with reads number of certain base in the alignment site.

source_name: bacterial cells

extract_protocol:
Total RNA was extracted using TriZol reagent. 5µg total RNA of each sample was saved as the input control fraction. All RNA fractions were rRNA depleted using the siTools rRNA depletion kit, and the E. coli ribopool.
TadA8.20 was overexpressed and purified following a previously published protocol (PMID: 36593412). 50 ng of rRNA-depleted E. coli RNA was subjected to the eTAM-seq workflow. Briefly, RNA was deaminated with 200 pmol of TadA8.20 in 20 μL 1 × deamination buffer supplemented with 10% (v:v) SUPERase•In RNase Inhibitor at 53 °C for 1h. The treated RNA was purified using RNA Clean & Concentrator kits (Zymo), and the deamination reaction was repeated twice at 44 °C. TadA8.20-treated RNA was built into libraries using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, catalog no. E7760L), following the manufacturer’s protocol (section 4 for purified mRNA, skipping fragmentation). The input library was constructed using the same kit with 50 ng RNA as input. Libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, catalog no. KK4824) and sequenced on a NextSeq 2000 instrument (R1 25 cycles, R2 97 cycles, Illumina, catalog no. 20024906).

value: F-, Lamda-, rph-1


title: I01526_TLR8_0.5_mg_kg

description:
I01526_L1.D702
50bp


title: SAM2_2


title: 535_CD_terminal_ileum


title: I01525_TLR8_0.1_mg_kg

description:
I01525_L4.D702
50bp


title: SAM1_3


title: I01524_TLR8_0.1_mg_kg

description:
I01524_L4.D711
50bp


title: Het, Replicate 1

description:
Library name: Osr2Cre_Hnf4a_Het_JP1195
Osr2Cre_Hnf4a_Het_JP1195

value: FACS-isolated nephron tubules targeted by Osr2Cre


title: NeuN- cells from vehicle-treated brain, rep 3

city: La Jolla

first: Jerold

last: Chun

state: CA

address: 1090 N. Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
10x Genomics CellRanger software (v4.0.0) was used to demultiplex samples, align reads, quantify unique molecular identifiers (UMIs), and generate cell count matrices. Default parameters were used, with the exception of a pre-mRNA reference file (mm10), to capture intronic reads originating from pre-mRNA species present in the nuclei.
Assembly: mm10
Supplementary files format and content: [sample]_barcodes.tsv.gz, [sample]_features.tsv.gz, [sample]_matrix.mtx.gz are all output from running CellRanger on each sample as described above

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Mice injected with LPA or vehicle were perfused with Hanks’ Balanced Salt Solution (HBSS) and RNAse inhibitors (0.2%) (Takara). Whole brains (except for the olfactory bulbs and the cerebellum) were stored at -80° C and were removed from frozen storage and immediately submerged in 1 ml of nuclei isolation buffer (20 mM Tris, 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton-X 100, 0.2% RNase inhibitors, (Takara Bio recombinant RNAse Inhibitor). Extracted nuclei were washed twice in PBS + 0.25mM EGTA + 1% BSA + 0.2% RNase inhibitors (Takara Bio, Mountain View, CA). They were then suspended in PBS + EGTA (250µM) + 1% BSA + 0.2% RNase inhibitors + 1.25 µg/ml 4’,6-diamidino-2-phenylindole (DAPI) (Sigma, St. Louis, MO) + NeuN antibody (1:500, Abcam), to label neuronal populations. Stained nuclei were sorted on a FACSAria Fusion (BD Biosciences, Franklin Lakes, NJ) gating for NeuN- populations, and collecting non-neuronal nuclei.
Sorted nuclei were diluted to ~700-1,500 nuclei/ml, and a final concentration was determined using a fluorescent cell counter. The 10x Genomics Single Cell 3’ v3 kit was then used to prepare samples targeting 10,000 profiled cells.

value: Brain

value: NeuN- cells

value: Vehicle


title: I01523_TLR8_0.1_mg_kg

description:
I01523_L3.D708
50bp

value: TLR8 agonist


title: 530_CD_terminal_ileum


title: 530_CD_ascending_colon

value: ascending colon


title: SAM2_1


title: eTAM-seq_RNA_WT_replicate1


title: 526_CD_ascending_colon


title: SAM1_2


title: NeuN- cells from vehicle-treated brain, rep 2


title: I01522_control

description:
I01522_L1.D708
50bp

value: Male


title: Empty_3

value: Empty vector


title: SAM1_1


title: NeuN- cells from vehicle-treated brain, rep 1


title: 526_CD_terminal_ileum

value: terminal ileum

value: Crohn's disease


title: microglia, APP/PS1:Cx3cr1-CreER:Cx43-flox/flox, repeat1

value: Cortex and Hippocampus

value: Microglia


title: I01521_control

description:
I01521_L1.D705
50bp

value: Liver

value: Control


title: NeuN- cells from LPA-treated brain, rep 3

value: LPA


title: Empty_2

value: MEFs


title: 525_CD_ascending_colon


title: NeuN- cells from LPA-treated brain, rep 2


title: I01520_control

description:
I01520_L1.D702
50bp


title: Empty_1


title: 525_CD_terminal_ileum


title: NeuN- cells from LPA-treated brain, rep 1


title: XX_D4_scRNAseq_rep1_XistTitration

status: Public on May 21 2025

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

description: Library name: scRNAseq_rep1_XistTitration

data_processing:
Sequencing reads from the 10x cDNA library were mapped to the mouse mm10 genome with STARsolo (v.2.7.11a) with settings [soloType=CB_UMI_Simple, soloFeatures=GeneFull_Ex50pAS](Kaminow et al. 2021; Dobin et al. 2013). To map reads to either the reference B6 or the alternative Cast alleles, the “Diploid Genome” options of STARsolo were used together with experimentally determined single nucleotide variants from the TX1072 cell line(Barros de Andrade E Sousa et al. 2019).
To remove empty droplets and assign a quality metric to the mapping of allelic reads EmptyDrops(Lun et al. 2019) and WASP(van de Geijn et al. 2015) were used within STARsolo (v.2.7.11a)(Kaminow et al. 2021).
Outlier cells were filtered using default settings of scater (v1.26.1)(McCarthy et al. 2017).
MULTI-seq sample barcodes were extracted from the separately sequenced MULTIseq library and assigned to cells using deMULTIplex2 (v1.0.1)(Zhu et al. 2024).
To generate allele-specific count tables of X-chromosomal reads, reads were filtered for high-quality assignments by the presence of the vW:i:1 WASP filter read tag. Next, X-chromosomal reads were extracted and split into separate .bam files for each haplotype. The .bam files were sorted and indexed with samtools (v1.19.2)(Li et al. 2009).
Count tables were generated using featureCounts (v2.0.6)(Liao et al. 2014) to assign reads to genes and UMI-tools (v1.1.4) to quantify UMI-level counts with option [--per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell --umi-tag=CB --cell-tag=CB –extract-umi-method=tag](Smith et al. 2017). Non-allelic count tables were generated in the same manner, using the unfiltered .bam file as input.
Further downstream analyses were performed with Scanpy (v1.9.8) and Anndata (v0.10.5)(Wolf et al. 2018; Virshup et al. 2021). Cells with ≥3% mitochondrial reads were removed. Read counts were normalized to 10,000 reads per cell and log-transformed using the [sc.pp.normalize_total] and [sc.pp.log1p] functions.
To filter XO cells, cells with normalized Xist expression ≤0.5 and an X-chromosomal ratio (B6 chrX reads/total chrX reads) ≥0.85 or ≤0.15 were removed.
Assembly: mm10
Supplementary files format and content: XistTitration_sample_info.tsv
Supplementary files format and content: XistTitration_FilteredCounts_plusMetadata.txt
Supplementary files format and content: XistTitration_filtered_Counts_chrX.txt

growth_protocol: TX1072 SP427 B2 CasTuner mESCs were cultured on 0.1% gelatin-coated flasks in serum-containing medium supplemented with LIF (SL conditions) (DMEM (Sigma), 15% ESC-grade FBS (GIBCO), 0.1 mM b-mercaptoethanol, 1000 U/ml LIF (Millipore), 3 mM Gsk3 inhibitor CT-99021, 1 mM MEK inhibitor PD0325901 (Axon)). 500 nM dTAG-13 (Tocris) was added to the cell medium to repress the dCas9-HDAC4 system. The cells were cultured at a density of 4*10^4 cells/cm2 and passaged every second day. To titrate Xist expression, the cells were transduced with guides targeting either the Xist Promoter (sgXist-Promoter) or the Xist-regulating REs 61, 85, 93 and 96 (sgXist-Distal REs).

extract_protocol:
For sample multiplexing, MULTI-seq barcode-lipid complexes were used according to the published protocol with minor modifications(McGinnis et al. 2019). Sample barcodes were chosen from a list of compatible barcodes(Rosen et al. 2022). Lipid-modified anchor and co-anchor oligos were purchased from Sigma-Aldrich. Barcode- and library preparation oligos were purchased from Eurofins with NGSgrade quality. Per sample, 1*105 cells were transferred to a 96-well ultra-low attachment plate (Costar) and kept on ice during the procedure. After two washes with PBS, the cells were incubated 5-10 min with an Anchor:Barcode solution (45 µl PBS, 5 µl Anchor:Barcode). The mixture was incubated for another 5-10 min after adding 5 µl of Co-Anchor solution. Labeling was quenched by adding 1% BSA in PBS, samples washed once in the same solution and resuspended in 0.4% BSA in PBS. Afterwards, cells were counted, pooled equally, and filtered using a Flowmi cell strainer 40 µm (Sigma-Aldrich). 2.5*104 cells were used for scRNA-seq gene expression library preparation .
The 10x Genomics library preparation protocol was performed according to manufacturer’s instructions (CG000315 Rev E, 10X Genomics) with the additional steps required to generate the separate MULTI-seq libraries for the sample-to-cell barcode assignment(McGinnis et al. 2019). During cDNA amplification, 0.5 µL of 1.25 μM “MULTI-seq additive primer” was added. 50% of the purified gene expression cDNA was carried forward, and the cycle number in the index PCR was reduced by one accordingly, to increase library complexity(Bolondi et al. 2024). During the first step of cDNA cleanup the supernatant was kept, which contained the short MULTI-seq library. This MULTI-seq library was then cleaned up two times using SPRI beads (KAPA HyperPure Beads, Roche). Sequencing adapters containing indexes (“TruSeq_RPIX_”, and “Universal_I5_with_index”) were added by PCR, using 2.5 µL primer at 10 µM each, 10 ng of cDNA, 26.25 µL Kapa HiFi HotStart ReadyMix 2x, and water to 50 µL final volume, with a program of 95 °C 5 min, 11 cycles of 98 °C 15 sec, 60 °C 30 sec, 72 °C 30 sec; followed by 72 °C 1 min and 4 °C hold. The resulting sequencing library was then cleaned up another time with SPRI beads. 10X gene expression libraries and MULTI-seq libraries were sequenced asynchronous 90/28 bp paired-end on the NovaSeq 6000 platform.

treatment_protocol: 2 days prior to differentiation, variable levels of the CasTuner system were induced via variation in the dTAG-13 (Tocris) concentration in the medium (0, 1, 2, 4, 8 and 500 nM). Differentiation was induced at a density of 2.1*10^4 cells/cm2 on 10 µg/ml fibronectin (Merck or Corning) via 2i/LIF withdrawal (-2iL conditions) (DMEM, 10% FBS (GIBCO), 0.1 mM b-mercaptoethanol). Cells were harvested after 4 days.

value: Embryonic stem cells

value: CAST / C57BL/6


title: XX_D4_MULTIseq_rep2_XistTitration

description: Library name: MULTIseq_rep2_XistTitration


title: XX_D4_MULTIseq_rep1_XistTitration

description: Library name: MULTIseq_rep1_XistTitration


title: NH4Cl_1

city: Changzhou

first: sainan

last: zhang

state: Jiangsu

address: Gehuzhonglu

institute: Changzhou University

description:
Library name: sample4
NH-1_FPKM

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions. The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud(www.biocloud.net) online platform.
Assembly: The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results
Supplementary files format and content: In the Excel table, different columns contain the raw counts for each sample.
Supplementary files format and content: Different columns contain the FPKM values for each sample.

organism: Irpex lacteus

source_name: straw

extract_protocol:
The plant total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer. The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: straw

tag: agent


title: NH4Cl_2

description:
Library name: sample5
NH-2_FPKM


title: NaNO3_1

description:
Library name: sample7
NO-1_FPKM


title: CK_1

description:
Library name: sample1
CK-1_FPKM

value: distilled water


title: CK_3

description:
Library name: sample3
CK-3_FPKM


title: CK_2

description:
Library name: sample2
CK-2_FPKM


title: lampposcontrol

city: Mountain View

first: Gabriel

last: Meca-Laguna

address: 110 Pioneer Way, Suite J

institute: Lifespan Research Institute

description:
Library name: lampposcontrol
Illumina 2x150bp

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with a p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: Raw counts for all samples plus gene names in one .csv file.

source_name: Lung

extract_protocol:
Lungs were harveted to then generate a single-cell suspension. Enriched and depleted samples were cell sorted based on Lamp1 cell surface expression.
RNA was prepared from sorted single-cells

treatment_protocol: Control mice received sterile saline. Treated mice received Bleomycin sulfate. Delivered through oropharyngeal instillation.

value: Lung


title: NaNO3_3

description:
Library name: sample9
NO-3_FPKM


title: lampnegblm

description:
Library name: lampnegblm
Illumina 2x150bp

value: Bleomycin


title: lampnegcontrol

description:
Library name: lampnegcontrol
Illumina 2x150bp


title: NaNO3_2

description:
Library name: sample8
NO-2_FPKM


title: RNA_Piezo1KO_CA_rep3

city: Xiamen

first: Lanfen

last: Chen

state: Fujian

address: Xiang'an south rd, Xiang'an district

department: Life Science

institute: Xiamen University

description: Library name: KOCA-3

data_processing:
Basecalls were performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence and low quality bases using cutadapt(v.2.6)
Clean reads were mapped to mm10 refernece genome using STAR (v.2.7.5a) .
Read counts were obtained by mapping the aligned reads to the transcripts of known genes from UCSC by using GenomicAlignments (v.1.30.0).
Differential expression analysis was performed with methods based on the negative binomial distribution in DESeq2 (v.1.34.0), using default parameters. Benjamini and Hochberg correction were used for significance tests and multiple comparisons.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each gene in each sample.

source_name: Piezo1 KO BMDMs

growth_protocol: For BMDMs, the femur and tibia were collected from mice of each genotype, and bone marrow cells were flushed with complete DMEM containing 50 mg ml−1 streptomycin and 10% FBS. Erythrocytes were removed via treatment with red blood cell lysis buffer, and the cell suspensions were filtered through a 40-μm cell strainer for the removal of any cell clumps. The single-cell suspensions were then plated in complete DMEM with recombinant mouse M-CSF (carrier-free, 50 ng ml−1). For full differentiation of BMDMs, the cells were cultured for an additional 8 days with replacement of the medium every day. All cells were CD11b+F4/80+ when analyzed by flow cytometry.

extract_protocol:
Total RNA was isolated using RaPure Total RNA Micro Kit (Magen, R4012).
The cDNA libraries were constructed from 1 mg RNA sample using mRNA-seq Lib Prep Kit for illumina (ABclonal, RK20302) following the guidelines of the manufacturers.

treatment_protocol: BMDSs were treated with PBS or Candida albicans.

value: Bone marrow derived macrophages

value: Piezo1 KO

value: Candida albicans


title: RNA_Piezo1KO_CA_rep2

description: Library name: KOCA-2


title: allblm

description:
Library name: allblm
Illumina 2x150bp


title: allcontrol

description:
Library name: allcontrol
Illumina 2x150bp


title: RNA_Piezo1KO_DMSO_rep3

description: Library name: KO-3

value: PBS


title: RNA_Piezo1KO_CA_rep1

description: Library name: KOCA-1


title: RNA_Piezo1KO_DMSO_rep2

description: Library name: KO-2


title: RNA_WT_CA_rep3

description: Library name: WTCA-3

source_name: WT BMDMs

value: WT


title: RNA_Piezo1KO_DMSO_rep1

description: Library name: KO-1


title: RNA_WT_CA_rep1

description: Library name: WTCA-1


title: RNA_WT_CA_rep2

description: Library name: WTCA-2


title: RNA_WT_PBS_rep3

description: Library name: WT-3


title: XX_D4_scRNAseq_rep2_XistTitration

description: Library name: scRNAseq_rep2_XistTitration


title: NH4Cl_3

description:
Library name: sample6
NH-3_FPKM


title: lampposblm

description:
Library name: lampposblm
Illumina 2x150bp


title: RNA_WT_PBS_rep2

description: Library name: WT-2


title: M-cre-KO-CD8-2

city: China

first: Nannan

last: Xu

state: Shanghai

address: 280s chongqing road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using  fqtools
Trimmed seaence reads were mapped to GRCm39 using Hisat2
Read count extraction and normalization were performed using subread featureCounts
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes counts values for each Samples

growth_protocol: Naïve CD8+ T cells were sorted from spleen and lymph nodes of 8-week-old MondoAfl/fl and MondoAfl/flCD4cre mice.

extract_protocol:
Total RNA was isolated using Trizol reagent.
RNA libraries were prepared using Vazyme mRNA-Seq library Prep Kit following manufacturer's protocols

treatment_protocol: Naïve CD8+ T cells from MondoAfl/fl and MondoAfl/flCD4cre mice were activated with anti-CD3/CD28 for 24 hours.

value: KO


title: M-cre-WT-CD8-1


title: M-cre-WT-CD8-3


title: M-cre-WT-CD8-2


title: MOLM-13, Assay 2, day2, plate 4, rep 3

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Combined compounds for plate 4, replicate 3
Assay_2_day2_plate4_rep3

library_source: other

data_processing:
Demultiplex reads, trim with Cutadapt, extract UMI, align with STAR, sort and index, deduplicate with UMI-tools, concatenate counts, remove batch effects with ComBat, normalize CLR.
Assembly: NA
Supplementary files format and content: Processed data files are matrices of raw read counts for all the features (cell surface proteins) for each compound treatment and replicate
Library strategy: Surface-plex, a new high-throughput technology for amplification of antibody-oligo conjugates from plates.

molecule: other

growth_protocol: MOLM-13 cultured in compound and RPMI media (with 10% FBS and 1% P/S) at 37C and 5% atmospheric CO2

extract_protocol:
Oligos from antibody-oligo conjugates were directly amplified from cells bound with Total-Seq B antibodies.
Illumina sequencing libraries were constructed directly from the antibody-oligos with two rounds of PCR, adding TruSeq adapters.

value: acute myeloid leukemia


title: MOLM-13, Assay 2, day2, plate 3, rep 3

description:
Combined compounds for plate 3, replicate 3
Assay_2_day2_plate3_rep3


title: MOLM-13, Assay 2, day2, plate 1, rep 3

description:
Combined compounds for plate 1, replicate 3
Assay_2_day2_plate1_rep3


title: MOLM-13, Assay 2, day2, plate 1, rep 4

description:
Combined compounds for plate 1, replicate 4
Assay_2_day2_plate1_rep4


title: MOLM-13, Assay 2, day1, plate 4, rep 1

description:
Combined compounds for plate 4, replicate 1
Assay_2_day1_plate4_rep1


title: MOLM-13, Assay 2, day2, plate 2, rep 4

description:
Combined compounds for plate 2, replicate 4
Assay_2_day2_plate2_rep4


title: MOLM-13, Assay 2, day2, plate 2, rep 3

description:
Combined compounds for plate 2, replicate 3
Assay_2_day2_plate2_rep3


title: MOLM-13, Assay 2, day1, plate 4, rep 2

description:
Combined compounds for plate 4, replicate 2
Assay_2_day1_plate4_rep2


title: MOLM-13, Assay 2, day1, plate 2, rep 1

description:
Combined compounds for plate 2, replicate 1
Assay_2_day1_plate2_rep1


title: MOLM-13, Assay 2, day1, plate 2, rep 2

description:
Combined compounds for plate 2, replicate 2
Assay_2_day1_plate2_rep2


title: MOLM-13, Assay 2, day1, plate 1, rep 1

description:
Combined compounds for plate 1, replicate 1
Assay_2_day1_plate1_rep1


title: MOLM-13, Assay 2, day1, plate 3, rep 2

description:
Combined compounds for plate 3, replicate 2
Assay_2_day1_plate3_rep2


title: MOLM-13, Assay 2, day1, plate 3, rep 1

description:
Combined compounds for plate 3, replicate 1
Assay_2_day1_plate3_rep1