title: mesLN, GF, WT, d02, m11

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

institute: University of Chicago

data_processing:
We used the RNA-seq pipeline in the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/).
Reads were aligned to the mouse mm10 transcriptomes with RapMap.
Transcripts were counted with fasttagcount in umis (https://github.com/vals/umis).
Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (https://github.com/ewels/MultiQC).
Assembly: mm10
Supplementary files format and content: raw_count.csv

source_name: Mesenteric lymph nodes

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies).
For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293). Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

value: Mesenteric lymph nodes

value: Primary tissue cells

value: Whole tissue cells

value: WT

value: non-treatment


title: mesLN, Gavaged, WT, d02, m18

status: Public on Apr 29 2025

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Human Fecal contents


title: Term_Female_White_s104716

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_White_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Female_White_Trisect_vs_Term_full_DESeq2_results.txt

data_processing:
Adapter sequences in raw reads were trimmed out using Trimmomatic (v.0.32)
STAR (v.2.5.2b) was used to align trimed sequencing reads to the hg38 human reference genome.
HTSeq (v.0.6.1) was used to quantify gene-level abundance corresponding to the hg38 human reference transcriptome file.
DESeq2 (v.1.18.1) was used to perform differential expression analysis to compare transcriptomic changes in (1) Preterm versus Term and (2) Mid-Trimester versus Term in sex- and race-specific samples.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include mapped read values per gene for each sample that passed QC (Placenta_htseq_gene.txt) and gene level-based differential expression results in 8 files for the  (1) Preterm versus Term and (2) Mid-Trimester versus Term stratified by sex and race.

organism: Homo sapiens

source_name: placenta

extract_protocol:
Total RNA was extracted from frozen placenta using TRIzol® Reagent (Invitrogen), followed by Qiagen RNeasy® Mini Columns following manufacturer’s instructions.
Multiplexed libraries were created using Agilent SureSelect strand-specific RNA library preparation kit following manufacturer’s instructions. Illumina unique dual indexes (UDI) were used.

value: placenta

tag: status

value: Term

tag: Sex

value: Female

tag: race

value: White

value: ACTAAGAT

value: AACCGCGG


title: mesLN, GF, WT, d02, m13


title: Rice_GLORI_rep1

city: Guangzhou

first: Yingyuan

last: Xie

state: GuangDong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

data_processing:
Raw reads were preprocessed using cutadapt (v4.1), seqkit (v0.8.1) rmdup module and fastp (v0.21.0) for adaptor trimming, deduplication and quality control as well as UMI trimming, respectively.
Then, the clean data were processed using the RNA-m5C pipeline developed by Huang T et al., 2022, with some modifications described.
All A sites with signal greater than 0.9 (representing the ratio of reads with no more than 3 non-converted A to all reads) and coverage greater than 20 after discarding non-converted reads were retained for methylation rate calculation
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text file, quantification of m6A in all As with coverage >= 15.

molecule: polyA RNA

organism: Oryza sativa

source_name: root

extract_protocol:
After extracting total RNA from the samples using TRIzol (Thermo Fisher Scientifific, 15596026), mRNA was isolated via a Dynabeads mRNA Purifification Kit (Thermo Fisher Scientifific, 61006) with genomic DNA removal using TuRBO DNase kit (Thermo Fisher, AM2238).
GLORI experiments were conducted following instructions provided in Cong Liu et al., 202214, with an adjusted incubation temperature in deamination step of 25 ℃.

value: root


title: Term_Female_AA_s104713

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_AA_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Female_AA_Trisect_vs_Term_full_DESeq2_results.txt

value: AA

value: CCGCGGTT

value: AGCGCTAG


title: Mid-Trimester_Female_AA_s104436

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_AA_Trisect_vs_Term_full_DESeq2_results.txt

value: Mid-Trimester

value: CCATTCGA

value: GTTGTCCG


title: mesLN, GF, WT, d02, m12

value: Mesenteric lymph nodes

value: Primary tissue cells

value: Whole tissue cells


title: Term_Male_White_s104717

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_White_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Male_White_Trisect_vs_Term_full_DESeq2_results.txt

value: Male

value: TACCGAGG

value: CCTGAACT


title: mesLN, Gavaged, WT, d02, m17

value: WT

value: Human Fecal contents


title: Mid-Trimester_Male_AA_s104437

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_AA_Trisect_vs_Term_full_DESeq2_results.txt

value: placenta

value: GTCTACAC

value: GCCAAGGT


title: Term_Female_White_s104434

value: Term

value: Female

value: White

value: ACCTTGGC

value: GGCCTCAT


title: mesLN, GF, IL10KOm d01, d10

value: IL10 knockout

value: non-treatment


title: Preterm_Female_AA_s104435

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_AA_Preterm_vs_Term_full_DESeq2_results.txt

value: Preterm

value: AA

value: GAATGAGA

value: GAGGCATT


title: mesLN, Gavaged, WT, d02, m15

value: Mesenteric lymph nodes

value: Primary tissue cells

value: Whole tissue cells


title: Term_Female_White_s104432

value: placenta

value: AATGCCTC

value: TCGATCCA


title: mesLN, GF, IL10KOm d01, d08


title: mesLN, Gavaged, WT, d02, m16

value: WT

value: Human Fecal contents


title: Term_Male_White_s104433

value: Term

value: Male

value: White

value: CGGACAAC

value: TCCGGATT


title: mesLN, GF, IL10KOm d01, d07

value: IL10 knockout

value: non-treatment


title: mesLN, GF, IL10KOm d01, d09


title: Mid-Trimester_Female_AA_s104430

value: Mid-Trimester

value: Female

value: AA

value: AATCCGGA

value: CTACAGTT


title: mesLN, GF, IL10KOm d01, d06

value: Mesenteric lymph nodes

value: Primary tissue cells

value: Whole tissue cells


title: Mid-Trimester_Male_White_s104431

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_White_Trisect_vs_Term_full_DESeq2_results.txt

value: placenta

value: ATGAGGCC

value: GTTAATTG


title: mesLN, Gavaged, IL10KO, d01, m05

value: Human Fecal contents


title: Preterm_Male_White_s104429

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_White_Preterm_vs_Term_full_DESeq2_results.txt

value: Preterm

value: Male

value: White

value: TGGATCGA

value: GTGCGATA


title: mesLN, Gavaged, IL10KO, d01, m04

value: IL10 knockout


title: Preterm_Male_AA_s104428

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_AA_Preterm_vs_Term_full_DESeq2_results.txt

value: TCGATATC

value: ACACGAGT


title: mesLN, Gavaged, IL10KO, d01, m03


title: mesLN, Gavaged, WT, d02, m14

value: WT


title: Preterm_Female_White_s104426

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_White_Preterm_vs_Term_full_DESeq2_results.txt

value: Female

value: ACAGGCGC

value: CTCTGCCT


title: mesLN, Gavaged, IL10KO, d01, m01

value: Mesenteric lymph nodes

value: Primary tissue cells

value: Whole tissue cells


title: LU, GF, WT, d02, m13

source_name: Lung

value: Lung

value: non-treatment


title: Term_Male_AA_s104427

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Male_AA_Preterm_vs_Term_full_DESeq2_results.txt
Placenta_stratification_by_Male_AA_Trisect_vs_Term_full_DESeq2_results.txt

value: placenta

value: Term

value: AA

value: CTCACCAA

value: CTAGGCAA


title: Term_Male_AA_s104424

value: Male

value: TTGCCTAG

value: ACCACTTA


title: Preterm_Male_AA_s104418

value: Preterm

value: GGCTTAAG

value: TCGTGACC


title: LU, GF, WT, d02, m12

value: WT


title: LU, Gavaged, WT, d02, m17

value: Human Fecal contents


title: Term_Female_AA_s104425

value: Female

value: ACTCGTGT

value: ATTGGAAC


title: Preterm_Female_AA_s104423

value: AGGCAGAG

value: AGAATGCC


title: LU, GF, WT, d02, m11

value: Lung

value: Primary tissue cells

value: Whole tissue cells

value: non-treatment


title: Mid-Trimester_Female_White_s104421

description:
Placenta_htseq_gene.txt
Placenta_stratification_by_Female_White_Trisect_vs_Term_full_DESeq2_results.txt

value: placenta

value: Mid-Trimester

value: White

value: TAAGTGGT

value: CTTAAGCC


title: LU, Gavaged, WT, d02, m18


title: LU, Gavaged, WT, d02, m14


title: LU, Gavaged, WT, d02, m15


title: LU, Gavaged, WT, d02, m16


title: Term_Male_White_s104419

value: Term

value: Male

value: GCAGAATT

value: ACCGGCCA


title: Term_Female_AA_s104420

value: Female

value: AA

value: GGCATTCT

value: CTAGCTTG


title: Term_Female_White_s104422

value: GTTCCAAT

value: AATTCTGC


title: Preterm_Male_White_s104160

value: Preterm

value: TAAGGTCA

value: TGTCGTAG


title: LU, GF, IL10KO, d01, m10

value: Lung

value: Primary tissue cells

value: Whole tissue cells

value: IL10 knockout

value: non-treatment


title: Mid-Trimester_Male_AA_s104159

value: placenta

value: Mid-Trimester

value: Male

value: TGGTGGCA

value: TCCTGTAA


title: LU, GF, IL10KO, d01, m08


title: Mid-Trimester_Male_AA_s104417

value: AA

value: CAAGCTAG

value: ACATAGCG


title: mesLN, Gavaged, IL10KO, d01, m02

value: Mesenteric lymph nodes

value: Human Fecal contents


title: Term_Male_AA_s104158

value: Term

value: GCAATGCA

value: GGAACGTT


title: LU, GF, IL10KO, d01, m07

value: Lung

value: Primary tissue cells


title: LU, GF, IL10KO, d01, m06

value: Whole tissue cells

value: IL10 knockout


title: Mid-Trimester_Male_White_s104156

value: placenta

value: White

value: TTACAGGA

value: TGACAAGC


title: LU, Gavaged, IL10KO, d01, m05


title: Mid-Trimester_Female_White_s104155

value: Mid-Trimester

value: Female

value: AACGTTCC

value: GGAGTACT


title: LU, Gavaged, IL10KO, d01, m04


title: Preterm_Female_White_s104157

value: Preterm

value: CTACGACA

value: GAGTCCAA


title: Mid-Trimester_Female_AA_s104153

value: AA

value: GCTTGTCA

value: GAACATAC


title: LU, Gavaged, IL10KO, d01, m01

value: Lung

value: Primary tissue cells

value: Human Fecal contents


title: Mid-Trimester_Male_White_s104152

value: placenta

value: Male

value: TACTCATA

value: CCTGTGGC


title: Preterm_Female_AA_s104150

value: TGCGAGAC

value: CATTGTTG


title: LU, Gavaged, IL10KO, d01, m03

value: Whole tissue cells

value: IL10 knockout


title: LU, GF, IL10KO, d01, m09

value: non-treatment


title: KI, GF, WT, d02, m13

source_name: Kindey

value: Kindey

value: WT


title: Term_Female_White_s104149

value: Term

value: Female

value: White

value: GCCACAGG

value: CATGCCAT


title: LU, Gavaged, IL10KO, d01, m02

value: Lung

value: Primary tissue cells

value: Human Fecal contents


title: KI, Gavaged, WT, d02, m18


title: Preterm_Male_AA_s104151

value: placenta

value: Preterm

value: Male

value: AA

value: AGGTTATA

value: CAGTTCCG


title: Preterm_Male_White_s104146

value: ATGGCATG

value: AAGGTACC


title: Term_Female_AA_s104154

value: TTGGACTC

value: GGAAGCAG


title: Preterm_Female_White_s104145

value: Female

value: TCGTAGTG

value: AGACTTGG


title: KI, Gavaged, WT, d02, m15

value: Kindey

value: Whole tissue cells

value: WT


title: Term_Male_AA_s104148

value: Term

value: CGGAACTG

value: CACTACGA


title: KI, Gavaged, WT, d02, m16

value: Primary tissue cells

value: Human Fecal contents


title: KI, GF, WT, d02, m12

value: non-treatment


title: KI, GF, WT, d02, m11


title: KI, Gavaged, WT, d02, m14


title: Mid-Trimester_Female_AA_s104143

value: placenta

value: Mid-Trimester

value: AA

value: GGTACCTT

value: AAGACGTC


title: Mid-Trimester_Female_White_s104144

value: Female

value: White

value: CCGTGAAG

value: CAGTGGAT


title: Term_Male_White_s104142

value: Male

value: CCAAGTCT

value: AAGGATGA


title: KI, GF, IL10KO, d01, m10

value: Kindey

value: Whole tissue cells

value: IL10 knockout


title: KI, GF, IL10KO, d01, m09

value: Primary tissue cells


title: Preterm_Male_AA_s104141

value: Preterm

value: ATCCACTG

value: AGGTGCGT


title: Preterm_Female_AA_s104140

value: placenta

value: AA

value: ACGCACCT

value: GGTGAAGG


title: Mid-Trimester_Female_AA_s104147

value: Mid-Trimester

value: Female

value: CAACAATG

value: CTTCACGG


title: KI, Gavaged, WT, d02, m17

value: WT

value: Human Fecal contents


title: KI, GF, IL10KO, d01, m08

value: Kindey

value: non-treatment


title: Preterm_Female_White_s104139

value: White

value: TCATCCTT

value: AGCGAGCT


title: KI, GF, IL10KO, d01, m07

value: Primary tissue cells

value: Whole tissue cells

value: IL10 knockout


title: KI, GF, IL10KO, d01, m06


title: Mid-Trimester_Male_AA_s104138

value: placenta

value: Male

value: AA

value: GACGTCTT

value: GGTTCACC


title: Preterm_Male_White_s104135

value: Preterm

value: GGTGAACC

value: GCGTTGGA


title: KI, Gavaged, IL10KO, d01, m01

value: Human Fecal contents


title: Mid-Trimester_Male_AA_s104132

value: Mid-Trimester

value: TCCAACGC

value: TTGGACTT


title: Term_Female_White_s104137

value: Term

value: Female

value: White

value: CCTTCACC

value: GACGCTCC


title: KI, Gavaged, IL10KO, d01, m04

value: Kindey

value: Primary tissue cells

value: Whole tissue cells

value: IL10 knockout


title: ILE, GF, WT, d02, m13

source_name: Ileum

value: Ileum

value: WT

value: non-treatment


title: Term_Male_White_s104136

value: placenta

value: Male

value: AGCTCGCT

value: GCAGAATC


title: KI, Gavaged, IL10KO, d01, m02

value: Human Fecal contents


title: Mid-Trimester_Male_White_s104131

value: Mid-Trimester

value: GCACGGAC

value: GTCTCGCA


title: Mid-Trimester_Female_White_s104134

value: Female

value: White

value: GGAGCGTC

value: GTCCGTGC


title: KI, Gavaged, IL10KO, d01, m03

value: Kindey

value: Primary tissue cells

value: Whole tissue cells


title: ILE, GF, WT, d02, m12

value: Ileum

value: WT


title: ILE, Gavaged, WT, d02, m18


title: Term_Female_AA_s104133

value: placenta

value: Term

value: AA

value: GATTCTGC

value: GACGAGAG


title: Preterm_Female_AA_s104130

value: Preterm

value: CTCTCGTC

value: TATAACCT


title: Term_Male_AA_s104129

value: Male

value: AAGTCCAA

value: TATGAGTA


title: ILE, GF, WT, d02, m11

value: non-treatment


title: RASF, biol rep 6, hUCMSC-exos6 group [miRNA-seq]

city: Taiyuan

first: Liangyu

last: Mi

state: Shanxi

address: 99 Longcheng Street

institute: Third Hospital of Shanxi Medical University

data_processing:
The basic reads were converted into sequence data (also called raw data/reads) by base calling. Low quality reads were filtered, and the reads with 5' primer contaminants and poly (A) were removed. The reads without 3'adapter and insert tag, the reads shorter than 15 nt or longer than 41 nt from the raw data were filtered, and the clean reads were obtained.
For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and So on. These RNAs were aligned and then subjected to the Bowtie search against Rfam v.10.1 (http://www.sanger.ac.uk/software/Rfam).
For primary analysis, the length distribution of the clean sequences in the reference genome was determined.   Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and So on. These RNAs were aligned and then subjected to the Bowtie search against Rfam v.10.1 (http://www.sanger.ac.uk/software/Rfam).The known miRNAs were identified by aligning against miRBasev22 database(http://www.mirbase.org/),and the known miRNA expression patterns in different samples were analyzed.
After that, unannotated reads were analyzed by mirdeep2 to predict novel miRNAs.Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence and miRNA mature sequence were also identified.Differentially expressed miRNAs were calculated and filtered with the threshold of p value < 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: synovium

growth_protocol: hUCMSCs were maintained in Serum-free Media in humidified atmosphere with 5% CO2 at 37°C. hUCMSC-Exos was obtained from hUCMSC supernatant by ultra-high speed centrifugation. RASFs were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer's protocol. Quantitation of total RNA was carried out using the Nanodrop 2000 (Thermo Fisher Scientific Inc., USA). RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technology, USA). 1 ug total RNA of each sample was used for the small RNA library construction using TruSeq Small RNA Sample Prep Kits (Cat. No. RS-200-0012, Illumina, USA.) following the manufacturer's recommendations.
Briefly, total RNA were ligated to adapters at each end. Then the adapter-ligated RNA were reverse transcribed to cDNA and performed PCR amplification. The PCR products ranging from 140-160 bp were isolated and purified as small RNA libraries. Library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. The libraries were finally sequenced using the Illumina HiSeq X Ten platform. 150 bp paired-end reads were generated.

treatment_protocol: The hUCMSC-Exo group RASFs were treated with 150 μg/ml hUCMSC-Exos for 48 hours.

value: synovium

value: primary cell

value: synovioblast

value: hUCMSC-Exos intervention group


title: KI, Gavaged, IL10KO, d01, m05

value: Kindey

value: Primary tissue cells

value: Whole tissue cells

value: IL10 knockout

value: Human Fecal contents


title: ILE, Gavaged, WT, d02, m16

value: Ileum

value: WT


title: ILE, Gavaged, WT, d02, m17


title: RASF, biol rep 5, hUCMSC-exos5 group [miRNA-seq]


title: ILE, Gavaged, WT, d02, m15


title: ILE, GF, IL10KO, d01, m10


title: RASF, biol rep 4, hUCMSC-exos4 group [miRNA-seq]


title: RASF, biol rep 2, hUCMSC-exos2 group [miRNA-seq]


title: RASF, biol rep 3, hUCMSC-exos3 group [miRNA-seq]


title: ILE, Gavaged, WT, d02, m14


title: RASF, biol rep 1, hUCMSC-exos1 group [miRNA-seq]


title: ILE, GF, IL10KO, d01, m08


title: RASF, biol rep 4, NC4 group [miRNA-seq]

value: blank control group


title: ILE, GF, IL10KO, d01, m07


title: RASF, biol rep 6, NC6 group [miRNA-seq]


title: RASF, biol rep 3, NC3 group [miRNA-seq]


title: ILE, Gavaged, IL10KO, d01, m03


title: ILE, Gavaged, IL10KO, d01, m05


title: ILE, GF, IL10KO, d01, m06


title: RASF, biol rep 5, NC5 group [miRNA-seq]


title: RASF, biol rep 2, NC2 group [miRNA-seq]


title: RASF, biol rep 1, NC1 group [miRNA-seq]


title: ILE, Gavaged, IL10KO, d01, m04


title: hUCMSC-EXOs, biol rep 1,exo3 [miRNA-seq]

source_name: Umbilical cord

value: Umbilical cord

value: Mesenchymal stem cells


title: ILE, Gavaged, IL10KO, d01, m01


title: hUCMSC-EXOs, biol rep 1,exo1 [miRNA-seq]


title: ILE, Gavaged, IL10KO, d01, m02


title: hUCMSC-EXOs, biol rep 1,exo2 [miRNA-seq]


title: DUO, GF, WT, d02, m13

source_name: Duodenum

value: Duodenum


title: DUO, GF, WT, d02, m12


title: RASF, biol rep 6, hUCMSC-exos6 group

data_processing:
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
The raw reads for each sample were generated. Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
Then the clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the human genome (GRCh38) using HISAT2.
FPKM of each gene was calculated using Cufflinks 4, and the read counts of each gene were obtained by HTSeq- count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.


title: RASF, biol rep 5, hUCMSC-exos5 group


title: ILE, GF, IL10KO, d01, m09


title: DUO, GF, WT, d02, m11


title: RASF, biol rep 3, hUCMSC-exos3 group


title: DUO, Gavaged, WT, d02, m17


title: DUO, Gavaged, WT, d02, m16


title: RASF, biol rep 4, hUCMSC-exos4 group


title: RASF, biol rep 2, hUCMSC-exos2 group


title: RASF, biol rep 6, NC6 group


title: RASF, biol rep 5, NC5 group


title: DUO, Gavaged, WT, d02, m14


title: DUO, GF, IL10KO, d01, d10


title: DUO, GF, IL10KO, d01, d09


title: RASF, biol rep 4, NC4 group


title: RASF, biol rep 3, NC3 group


title: DUO, GF, IL10KO, d01, d07


title: DUO, Gavaged, IL10KO, d01, m05


title: RASF, biol rep 2, NC2 group


title: DUO, GF, IL10KO, d01, d06


title: DUO, Gavaged, IL10KO, d01, m03


title: DUO, Gavaged, IL10KO, d01, m04


title: DUO, Gavaged, IL10KO, d01, m01


title: DUO, Gavaged, WT, d02, m18


title: RASF, biol rep 1, hUCMSC-exos1 group


title: DUO, Gavaged, WT, d02, m15


title: Exp2_3D_GBA010197_1

city: Medford

first: Nicholas

middle: James

last: Fiore

state: MA

address: 200 College Ave

department: Biomedical Engineering

institute: Tufts University

data_processing:
Illumina pipeline CASAVA v1.8.2 was used for base calling.
Raw sequencing data was uploaded to the Tufts University Galaxy Server for quality and adapter trimming with Trim Galore, read alignment with RNA STAR (reference human genome build 38), and read quantification with FeatureCounts using default settings.
Normalized read count tables, obtained by dividing the read counts by their size factors, were generated and extracted with the DESeq2 R package.
Genome_build: reference human genome build 38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: dopaminergic neurons

growth_protocol: On day 0, a single cell suspension of hiPSCs (maintained with mTeSR1) was seeded in 50:50 (v/v) mTeSR1:floor plate specification medium (neurobasal medium (ThermoFisher 21103049) with 1X floor plate specification supplement (ThermoFisher A3146801)) supplemented with 10 μM Y-27632 (STEMCELL Technologies 72302) at a density of 2 x 10^5 cells/cm2 on 6-well plates coated with Matrigel. The next day, cells were washed with Dulbecco’s phosphate buffered saline (DPBS, ThermoFisher) and fresh specification medium was added. Medium was carefully changed every 48 hours. On day 11, floor plate progenitors (FPPs) were split 1:2 using Accutase (Innovative Cell Technologies AT104, San Diego, CA, USA) onto new Matrigel-coated 6-well plates with FPP expansion medium (ThermoFisher A3165801) + 10 μm Y-27642. FPPs were expanded (replacing FPP expansion medium every 48 hours) until cryopreservation on day 22 with Synth-a-Freeze reagent (ThermoFisher A1254201) to establish batches of cells for experimental consistency. For each individual experiment, FPPs were thawed and plated at a density of 6.25 x 10^5 cells/cm2 in Matrigel coated 6-well plates supplemented with 10 μM Y-27642. On day 28, FPPs were differentiated to DA neurons starting with a 72 hour treatment of maturation medium (DMEM/F12 (ThermoFisher 10565018) with 1X maturation supplement (ThermoFisher A3147401)) containing 1 μM PD0325901 (MilliporeSigma PZ0162, Burlington, MA, USA) and 5 μM SU5402 (MilliporeSigma SML0443). PD0325901 and SU5402 were employed to inhibit progenitor cell proliferation and promote neurogenesis.

extract_protocol:
Total RNA was isolated from independent cultures using the RNeasy mini kit (Qiagen 74106, Hilden, Germany) utilizing the on-column DNA-digestion procedure according to manufacturer’s instructions. To improve extraction efficiency, the 2D cultures and 3D constructs were gently sonicated in the kit’s lysis buffer prior to extraction (ThermoFisher model no. FB120, 20% power, 1 second on followed by 1 second off for 10 pulses total). Sample purity and concentration was measured with a Nanodrop (ThermoFisher) spectrophotometer and 1 μg RNA per sample with a 260/280 nm reading greater than 2 were sent to Novogene for additional quality control tests, library preparation, and sequencing. First, RNA degradation and contamination were assessed on 1% agarose gels and RNA purity was checked using a NanoPhotometer spectrophotometer (Implen, Munich, Germany). RNA integrity and quantitation were assessed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).
Library preparation was achieved using the NEBNext Ultra RNA library prep kit for Illumina systems following manufacturer’s recommendations (New England Biolabs, Ipswich, MA, USA) 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. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand complementary DNA (cDNA) was synthesized using random hexamer primer and M-MuLV reverse transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Brea, CA, USA). Then 3 μL USER Enzyme (New England Biolabs) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 minutes followed by 5 minutes 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, Beckman Coulter) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on an Illumina Novaseq sequencer according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated at a read depth of 20 million reads.

treatment_protocol: On day 31, cells were pre-differentiated DA neurons were seeded into 2D and 3D culture condition

value: hiPSC-derived dopaminergic neurons

value: GBA N370S

tag: parkinson's disease (pd) status

value: Healthy

tag: culture condition

value: Three dimensional (3D)

tag: experiment number


title: Exp2_2D_WT050598_2

value: Wild Type

value: Two dimensional (2D)


title: Exp2_3D_WT050598_1


title: Exp2_3D_GBA010198_1

value: PD


title: Exp2_3D_WT050598_2


title: Exp2_3D_GBA010198_2


title: Exp2_3D_GBA010197_2


title: CO, GF, WT, d02, m13

source_name: Colon

value: Colon

value: Primary tissue cells

value: non-treatment


title: CO, GF, WT, d02, m12

value: Whole tissue cells


title: CO, GF, WT, d02, m11


title: DUO, GF, IL10KO, d01, d08

value: IL10 knockout


title: CO, Gavaged, WT, d02, m18

value: WT

value: Human Fecal contents


title: Exp2_2D_WT050598_1


title: RASF, biol rep 1, NC1 group

value: synovium

value: primary cell

value: synovioblast

value: blank control group


title: Exp2_2D_GBA010198_1

value: hiPSC-derived dopaminergic neurons

value: GBA N370S


title: CO, Gavaged, WT, d02, m16


title: Exp2_2D_GBA010198_2


title: Exp2_2D_GBA010197_2

value: Healthy


title: CO, Gavaged, WT, d02, m17


title: CO, Gavaged, WT, d02, m15


title: CO, Gavaged, WT, d02, m14


title: DUO, Gavaged, IL10KO, d01, m02

value: Duodenum


title: CO, GF, IL10KO, d01, m10


title: CO, GF, IL10KO, d01, m09


title: Exp1_3D_GBA010198_2

value: Three dimensional (3D)


title: CO, GF, IL10KO, d01, m08


title: Exp1_3D_GBA010198_1

value: PD


title: Exp1_3D_GBA010197_2


title: CO, GF, IL10KO, d01, m07

value: Colon


title: Exp1_2D_WT050598_1

value: Wild Type

value: Two dimensional (2D)


title: CO, GF, IL10KO, d01, m06

value: Primary tissue cells

value: Whole tissue cells

value: non-treatment


title: Exp1_3D_GBA010197_1


title: CO, Gavaged, IL10KO, d01, m05

value: IL10 knockout

value: Human Fecal contents


title: Exp1_2D_GBA010197_2


title: CO, Gavaged, IL10KO, d01, m02


title: Tumor from patient 118

type: genomic

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

institute: NYU Langone Health

hyb_protocol: DNA bisulfite conversion, amplification, fragmentation, and hybridization to human Infinum MethylationEPIC BeadChip (Illumina) according to standard Illumina protocol

scan_protocol: Raw IDATs generated from iScan were analyzed

data_processing:
R package Random Forest using brain tumor classifier version 11 using previously described criteria. Minfi R package.
processed value definition: Beta value (normalized)

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Pituitary neuroendocrine tumor

label_protocol: Standard Illumina protocol

extract_protocol: Formalin-fixed paraffin-embedded (FFPE) tissue scrolls were subjected to DNA extraction using the automated Maxwell nucleic acid purification platform (Promega, Madison, WI, USA)

value: Pituitary neuroendocrine tumor

tag: clinical class

value: GH

tag: gender

value: Female

tag: pathologic immunophenotying

value: Sparsely granulated mammosomatotroph tumor


title: Tumor from patient 116

value: Male

value: Gonadotroph tumor


title: Exp2_2D_GBA010197_1

value: hiPSC-derived dopaminergic neurons

value: GBA N370S

value: Healthy


title: Exp1_3D_WT050598_2

value: Three dimensional (3D)


title: Tumor from patient 117


title: CO, Gavaged, IL10KO, d01, m01

value: Colon


title: Exp1_3D_WT050598_1

value: Wild Type


title: Tumor from patient 114


title: Tumor from patient 113


title: DLD1-TetOff-flag-Cdx2 (ChIP)

city: Yoshida-gun

first: Koji

last: Aoki

state: Fukui

address: 23-3 Matsuokashimoaizuki, Eiheiji-cho

department: Faculty of Medical Sciences

country: Japan

institute: University of Fukui

description:
Library name: DLD1-TetOff-flag-Cdx2, ChIP
DLD1 (CCL-221) expressing pTetOff (TAKARA) and not expressing flag-tagged Cdx2 in the presence of DOX

library_source: genomic

data_processing:
The preparation of ChIP-seq libraries and sequenced on a Hiseq 2500 machine (Illumina), as paired-end, 101 base paires reads.
Basecalls were performed using bcl2fastq v1.8.3 for Hiseq 2500 output.
Sequencing adapters were removed using CutAdapt v1.1. Low quality reads were trimmed with Trimmomatic version 0.32. Low complexity reads trimmed with In-house scripts.
Trimmed reads were aligned to the GRCh37 genome assembly using Bowti v1.1.1  with the following options: -n 2 --best --strata -m 1 --sam -q.
Peaks were called uing MACS2 v2.0.10 with default settings.
Assembly: GRCh37
Supplementary files format and content: peaks.xls and narrowPeak files are generated using MACS2 software.

growth_protocol: The cells were cultured in DMEM supplemented with 5% FBS. Doxycycline, a tetracycline analog, was added to the culture medium at a final concentration of 0.5 µg/mL. 4-5 x 106 DLD1-TetOff cells were seeded onto ten 150-mm dishes, and the expression of flag-tagged Cdx1 or Cdx2 was induced by withdrawing DOX from the culture medium.

extract_protocol:
Twenty hours after induction, the cells were fixed by adding 540 µL of formaldehyde (a final concentration, 1%; 064-03843; FUJIFILM) to 20 mL of the culture medium and incubated for 5 min at 25 °C. Glycine (10x, 2mL; 077-00735; FUJIFILM) was added to the ten dishes, which were gently rotated for 5 min at 25 °C. The cells were washed twice with 10 mL of ice-cold phosphate-based saline (PBS) and scraped with 1 mL of ice-cold PBS. Cells from the ten dishes were pooled into a 15-mL centrifuge tube and centrifuged at 3,500 rpm (2,380 g; AX-320, TOMY) for 3 min at 4 °C, after which the supernatant was then discarded.  According to the manufacturer’s instructions of the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Agarose Beads; 9004; Cell Singnaling Tech.), nuclei were prepared and treated with 0.5 µL of micrococcal nuclease solution per sample at 37 °C for 50 min (MNase; Worthington Bio. Corp.). The MNase digestion reaction was terminated by adding 10 µl of 0.5 M ethylenediaminetetraacetic acid (EDTA). The length of the digested DNA (approximately 150 bp) was confirmed via agarose gel electrophoresis. The samples were centrifuged at 13,000 rpm (15,300 g; MX-307, TOMY) for 1 min at 4 °C, and the supernatant was discarded. The cell pellet was re-suspended in 100 µL of a ChIP dilution buffer (150 mM NaCl, 20 mM Trsi-HCl, 1% Triton X-100, and 2 mM EDTA), incubated for 10 min on ice, transferred to TPX tubes, and sonicated to disrupt the nuclear membrane at 4 °C using a Biorupter II (Sonicbio). The samples were then centrifuged at 10,000 rpm (9,100 g; MX-307, TOMY) for 10 min at 4 °C, and the supernatant was transferred to a new tube. A 19-fold volume of the ChIP dilution buffer was added to the digested chromatin, and the mixture was incubated with anti-flag M2-antibody-conjugated agarose beads (A2220; Sigma Aldrich) for 12 h at 4 °C with rotation. The beads were washed six times with ChIP dilution buffer and treated with an RNase (final concentration, 20 µg/mL; Worthington Bio. Corp.) for 1.5 h at 4 °C. To elute the flag-Cdx complex, the beads were incubated with 200 µL of the ChIP dilution buffer containing the 3 x FLAG peptide (F4799; Sigma Aldrich) at 37 °C for 1 h. The samples were centrifuged at 15,000 rpm (20,400 g; MX-307, TOMY) for 1 min at 4 °C, and 180 µL of the supernatant was transferred to a new tube. A 2 x elution buffer of 2% sodium dodecyl sulfate (SDS) and 0.2 M NaHCO3 was added to the samples, and the mixtures were incubated at 65 °C overnight. The DNA was purified by the standard phenol-chloroform extraction method.
ChIP-seq libraries were prepared using the Illumina TruSeq ChIP Sample Prep Kit following manufacturer's protocols.

treatment_protocol: The expression of flag-Cdx1 and flag-Cdx2 was induced by the withdrawal of DOX.

value: Human colon cancer


title: Tumor from patient 112


title: 22RV1_NMYC_T12_Rep01

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

data_processing:
Sequenced files were demultiplexed from illumina
Read counts were calculated using the package from Li, et al. Genome Biology 15:554 (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Prostate

growth_protocol: 7x10^8 cells were infected at an MOI of 0.3 with a viral library (lentiCRISPRv2_B) containing 65,000 sgRNAs to yield a library coverage of 300x.  Infected cells were selected for with puromycin.  T0 replicates of 2.5x10^7 cells were collected and duplicate culture were plated at 2x10^7 per replicate.

extract_protocol:
genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194)
libraries were constructed following the previously described method in Shalem O et al Science 2014
amplicon sequencing

treatment_protocol: Cells were cultured and passaged every 72 hours for a period of 12 generations.  2x10^7 cells were collected from each replicate following each passage.  2x10^7 cells were maintained in culture for replicate for the subsequent generation to maintain 300x library coverage

value: Prostate

tag: condition

value: T12 Timepoint Replicate 1

value: NMYC overexpressed


title: Exp1_2D_GBA010198_1

value: PD

value: Two dimensional (2D)


title: DLD1-TetOff-flag-Cdx1 (ChIP)

description:
Library name: DLD1-TetOff-flag-Cdx1, ChIP
DLD1 (CCL-221) expressing pTetOff (TAKARA) and not expressing flag-tagged Cdx1 in the presence of DOX


title: 8 CDX1 induction 24hr/7 CDX1 non-induction 24hr

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: A TetOff clone was cultured in a dish prior to the induction of Cdx1.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: 7 CDX1 non-induction 24hr

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: The cells were cultured in DMEM supplemented with 5% FBS. Doxycycline, a tetracycline analog, was added to the culture medium at a final concentration of 0.5 µg/mL.

extract_protocol: RNA was isolated from DLD1-TetOff cells expressing wild-type Cdx1 or Cdx2 for 12 and 24 hours, using the TRI Reagent (Sigma-Aldrich). The cells were treated with DNase, and the total RNA was purified using the RNeasy Midi kit (QUIAGEN).

value: DLD1 (CCL-221) expressing pTetOff (TAKARA) and flag-tagged Cdx1 in the absence of DOX

source_name: 8 CDX1 induction 24hr

value: DLD1 (CCL-221) expressing pTetOff (TAKARA) and not expressing flag-tagged Cdx1 in the presence of DOX


title: 22RV1_NMYC_T12_Rep02

value: T12 Timepoint Replicate 2


title: Tumor from patient 111

value: Pituitary neuroendocrine tumor

value: Male


title: 22RV1_NMYC_T6_Rep02

value: T6 Timepoint Replicate 2


title: 22RV1_NMYC_T0

value: T0 Timepoint Replicate 1


title: CO, Gavaged, IL10KO, d01, m03

value: Primary tissue cells

value: Whole tissue cells

value: IL10 knockout

value: Human Fecal contents


title: Exp1_2D_GBA010197_1

value: hiPSC-derived dopaminergic neurons

value: GBA N370S

value: Healthy


title: 22RV1_T12_Rep02

value: Prostate

value: Parental


title: 22RV1_T12_Rep01

value: T12 Timepoint Replicate 1


title: Tumor from patient 115

value: Densely granulated mammosomatotroph tumor


title: 22RV1_T6_Rep02


title: 22RV1_NMYC_T6_Rep01

value: T6 Timepoint Replicate 1

value: NMYC overexpressed


title: Tumor from patient 106

value: Pituitary neuroendocrine tumor

value: Gonadotroph tumor


title: Tumor from patient 104

value: Female

value: Densely granulated corticotroph tumor


title: 22RV1_T0

value: T0 Timepoint Replicate 1


title: Tumor from patient 107

value: PRL


title: Tumor from patient 103

value: Male


title: 22RV1_T6_Rep01


title: Tumor from patient 102


title: CDX2 induction 24hr/CDX2 non-induction 24h

description: A TetOff clone was cultured in a dish prior to the induction of Cdx2.

source_name: CDX2 non-induction 24h

value: DLD1 (CCL-221) expressing pTetOff (TAKARA) and flag-tagged Cdx2 in the absence of DOX

source_name: CDX2 induction 24h

value: DLD1 (CCL-221) expressing pTetOff (TAKARA) and not expressing flag-tagged Cdx2 in the presence of DOX


title: A2a_sal_WD1_8

city: Portland

first: Alex

middle: B

last: Kawa

state: OR

address: 3181 SW Sam Jackson Park Rd, L470

department: BEHN

institute: OHSU

data_processing:
Fastq files were assembled from the base call files using bcl2fastq (Illumina)
The fastq files were trimmed with Trimmomatic using the built-in filters for Illumina adapters
sequence files were aligned with the STAR aligner. The reference genome was Rattus norvegicus Rnor_6.0, downloaded with annotations from Ensembl
the SAM files were converted to BAM format using SAMtools
Assembly: Rnor 6.0
Supplementary files format and content: excel file with read-counts per gene

organism: Rattus norvegicus

source_name: A2a medium spiny neuron

extract_protocol:
TRAP was carried out on all 48 brains from the rats that completed the cocaine or saline self-administration procedure, as previously described (Heiman et al., 2014) with modifications (Sanz et al., 2009). Briefly, homogenization buffer (HB) was used as described (Sanz et al., 2009), with heparin omitted. Lysed tissue in HB were centrifuged at 10,000 g for 10 min at 4°C to remove insoluble debris, and the supernatant was used for all subsequent steps. Input samples, equivalent to 12.5% of the initial HB volume, were saved from the supernatant prior to the immunoprecipitation, and RNA was extracted at the same time as TRAP samples. 6.25 μg of two GFP antibodies (bioreactor supernatant, clones 19C8 and 19F7 from the Memorial Sloan-Kettering Institute Monoclonal Antibody Facility) was added to each sample for 4 h at 4C under gentle end-over-end rotation. Samples were transferred to tubes containing 25 μl of Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific; 88803; lot VF298063) and incubated overnight at 4◦C with end-over-end rotation. The following day, beads were washed in high-salt buffer as described (Sanz et al., 2009), and RNA was isolated from the beads and input samples using TRIzol (Thermo Fisher Scientific, 15596018) and the Direct-zol RNA Microprep Kit (Zymo Research, R2062). RNA concentration was determined using the Quant-iT RiboGreen RNA Assay (Thermo Fisher Scientific, R11490) using a CLARIOstar Plus plate reader (BMG Labtech). TRAP IP controls with either no antibody or using wild-type tissue resulted in no measurable RNA based on the RiboGreen assay and only trace amounts of RNA detected using qRT-PCR.
RNA-seq libraries were profiled on a 4200 Tapestation (Agilent)

treatment_protocol: Rats self-administered cocaine or saline for 10 sessions and were euthanized 1 or 40 days after the last session

value: A2a medium spiny neuron

value: saline early WD


title: Tumor from patient 109


title: A2a_sal_WD1_7


title: Tumor from patient 101


title: A2a_sal_WD1_6


title: Tumor from patient 100


title: Tumor from patient 110


title: 6 CDX1 induction 12hr/5 CDX1 non-induction 12hr

source_name: 5 CDX1 non-induction 12hr

value: DLD1 (CCL-221) expressing pTetOff (TAKARA) and flag-tagged Cdx1 in the absence of DOX

source_name: 6 CDX1 induction 12hr

value: DLD1 (CCL-221) expressing pTetOff (TAKARA) and not expressing flag-tagged Cdx1 in the presence of DOX


title: A2a_sal_WD1_5


title: Tumor from patient 98

value: GH


title: Tumor from patient 99


title: Tumor from patient 97


title: Tumor from patient 105

value: Immature PIT1-lineage tumor


title: A2a_sal_WD1_4


title: A2a_sal_WD1_3


title: A2a_sal_WD1_2


title: Tumor from patient 96


title: A2a_sal_WD1_1


title: Tumor from patient 94

value: Densely granulated lactotroph tumor


title: D1_sal_WD1_7

source_name: D1 medium spiny neuron

value: D1 medium spiny neuron


title: Tumor from patient 95

value: Pituitary neuroendocrine tumor


title: D1_sal_WD1_8


title: Tumor from patient 93

value: Gonadotroph tumor


title: Tumor from patient 92


title: D1_sal_WD1_6


title: Tumor from patient 91

value: Female


title: Tumor from patient 90


title: D1_sal_WD1_4


title: Tumor from patient 89

value: Densely granulated corticotroph tumor


title: D1_sal_WD1_3


title: Tumor from patient 88


title: D1_sal_WD1_2


title: Tumor from patient 87

value: Sparsely granulated lactotroph tumor


title: Tumor from patient 86


title: A2a_coc_WD1_8

value: cocaine early WD


title: A2a_coc_WD1_7


title: Tumor from patient 85

value: Male


title: A2a_coc_WD1_5


title: A2a_coc_WD1_3


title: A2a_coc_WD1_4


title: A2a_coc_WD1_6


title: Tumor from patient 83


title: Tumor from patient 82


title: Tumor from patient 84


title: Tumor from patient 81


title: A2a_coc_WD1_2


title: A2a_coc_WD1_1


title: Tumor from patient 79


title: D1_sal_WD1_5


title: Tumor from patient 78


title: Tumor from patient 80


title: D1_coc_WD1_8


title: D1_coc_WD1_7


title: D1_coc_WD1_6


title: D1_sal_WD1_1


title: Tumor from patient 76


title: Tumor from patient 74

value: Densely granulated mammosomatotroph tumor


title: D1_coc_WD1_5


title: D1_coc_WD1_4


title: D1_coc_WD1_3


title: Tumor from patient 73

value: Sparsely granulated somatotroph tumor


title: Tumor from patient 71


title: A2a_coc_WD40_8

value: A2a medium spiny neuron

value: cocaine late WD


title: Tumor from patient 69


title: D1_coc_WD1_2


title: Tumor from patient 70

value: PRL


title: A2a_coc_WD40_5


title: Tumor from patient 68


title: A2a_coc_WD40_6


title: Tumor from patient 66


title: A2a_coc_WD40_4


title: Tumor from patient 77


title: A2a_coc_WD40_3


title: A2a_coc_WD40_7


title: A2a_coc_WD40_2


title: Tumor from patient 67


title: Tumor from patient 64


title: Tumor from patient 63

value: Null cell tumor


title: D1_coc_WD1_1


title: Tumor from patient 62


title: D1_coc_WD40_8


title: Tumor from patient 61


title: Tumor from patient 75


title: D1_coc_WD40_7


title: D1_coc_WD40_6


title: A2a_coc_WD40_1


title: Tumor from patient 72


title: Tumor from patient 60


title: D1_coc_WD40_5


title: Tumor from patient 59

value: Sparsely granulated multiple lineage tumor


title: D1_coc_WD40_4


title: Tumor from patient 57


title: D1_coc_WD40_3


title: D1_coc_WD40_2


title: Tumor from patient 56


title: D1_coc_WD40_1


title: Tumor from patient 55

value: ACTH


title: Tumor from patient 54


title: Arabidopsis_GLORI_rep2

data_processing:
Raw reads were preprocessed using cutadapt (v4.1), seqkit (v0.8.1) rmdup module and fastp (v0.21.0) for adaptor trimming, deduplication and quality control as well as UMI trimming, respectively.
Then, the clean data were processed using the RNA-m5C pipeline developed by Huang T et al., 2022, with some modifications described.
All A sites with signal greater than 0.9 (representing the ratio of reads with no more than 3 non-converted A to all reads) and coverage greater than 15 after discarding non-converted reads were retained for methylation rate calculation
Assembly: mm10, TAIR10, Creinhardtii_281_v5.0
Supplementary files format and content: tab-delimited text file, quantification of m6A in all As with coverage >= 15.
Supplementary files format and content: tab-delimited text file, methylation rate of all As in DRACN motifs predicted by SingleMod

organism: Arabidopsis thaliana

source_name: seedlings

value: seedlings


title: Tumor from patient 53

value: GH


title: Tumor from patient 52

value: Pituitary neuroendocrine tumor


title: Arabidopsis_GLORI_rep1


title: Tumor from patient 51

value: Gonadotroph tumor


title: m74

city: ILLKIRCH

first: Wojciech

last: Krezel

address: 1 rue L.Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using TopHat v.2.0.14 and Bowtie 2 v.2.1.0
Quantification : Gene Expression was quantified using HTSeq v.0.6.1 (intersection-nonempty mode) and Ensembl release 90 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: Mouse Accumbens Shell Nucleus (Nac)

extract_protocol:
NAc samples were punched from 300µm frozen brain sections and RNA was extracted using micro RNeasy kit according to manufacturer instructions
RNA-Seq libraries were generated from 200ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Mouse Accumbens Shell Nucleus (Nac)

tag: strain

value: CBA/C57BL6J/129svEmx mixed background

tag: age

value: 8 weeks old


title: Tumor from patient 50

tag: tissue

value: Female

value: Densely granulated corticotroph tumor


title: m57


title: m83


title: Tumor from patient 48


title: Tumor from patient 47

value: Male


title: m61


title: m44


title: m89


title: Tumor from patient 49


title: Tumor from patient 46


title: m101


title: m73


title: Tumor from patient 58


title: Tumor from patient 44

value: Sparsely granulated lactotroph


title: m47


title: m49


title: Eurasian Tree Sparrow, Male 7

city: Bloomington

first: Kimberly

middle: A

last: Rosvall

state: IN

address: Dept of Biology, Indiana Univ., 1001 E. 3rd St, Jordan Hall

institute: Indiana University

data_processing:
Sequence reads were trimmed for adapters and low quality bases using Trimmomatic v0.36 (Bolger et al. 2014) and fastp v0.20.1 (Chen et al. 2019).
Transcriptomes from species-specific reads were assembled using Trinity v2.13.2 (Grabherr et al. 2011)
Assembled transcripts were aligned to the zebra finch proteome using tblastn v2.2.9 (Gertz et al. 2006)
Transcript abundance was quantified using Bowtie2 v2.4.4 (Langmead and Salzberg 2012)
Reads were sorted and indexed using Samtools v1.10 (Li et al. 2009)
Orthologous reads were assigned to zebra finch proteins using featureCounts from the Subread package v2.02z (Liao et al. 2014)
Assembly: GCF_003957565.2_bTaeGut1.4.pri_protein.faa (Rhie et al. 2021)
Supplementary files format and content: tab-delimited text file of raw gene count values for each Sample

organism: Passer montanus

source_name: Ventromedial telencephalon

extract_protocol:
RNA was isolated from brain tissue using a phenol chloroform extraction
TruSeq Stranded mRNA HT sample preparation kit (Illumina)

treatment_protocol: Nesting strategies included obligate cavity nesting, facultative cavity nesting, and open cup nesting. Adult females and males were sampled during territorial establishment and nest-building phases, before egg laying, in the Midwestern United States

tag: family

value: Passeridae

value: Ventromedial telencephalon

value: Obligate cavity nester


title: Tumor from patient 43

value: Sparsely granulated somatotroph


title: m115


title: Prothonotary Warbler, Male 9

organism: Protonotaria citrea

value: Parulidae


title: Eurasian Tree Sparrow, Male 6


title: Prothonotary Warbler, Male 8


title: Tumor from patient 42

value: Null cell tumor


title: Tumor from patient 41


title: Eurasian Tree Sparrow, Male 4


title: Prothonotary Warbler, Male 7


title: Eurasian Tree Sparrow, Male 3


title: Tumor from patient 40


title: Prothonotary Warbler, Male 5


title: Prothonotary Warbler, Male 2


title: CO, Gavaged, IL10KO, d01, m04

value: Colon

tag: cell line

value: Primary tissue cells

tag: cell type

value: Whole tissue cells

value: IL10 knockout

value: Human Fecal contents


title: Prothonotary Warbler, Female 9

tag: treatment


title: Tumor from patient 45

value: Pituitary neuroendocrine tumor

value: GH

value: Densely granulated lactotroph tumor


title: Prothonotary Warbler, Female 8


title: Eurasian Tree Sparrow, Male 2


title: Prothonotary Warbler, Female 7


title: Tumor from patient 39

value: Female

value: Gonadotroph tumor


title: Prothonotary Warbler, Female 6


title: Eurasian Tree Sparrow, Male 1


title: Eurasian Tree Sparrow, Female 6


title: Prothonotary Warbler, Female 5


title: Tumor from patient 38

value: Densely granulated mammosomatotroph tumor


title: Tumor from patient 37

value: PRL

value: Densely granulated corticotroph tumor


title: Prothonotary Warbler, Female 2

value: Ventromedial telencephalon

value: Obligate cavity nester


title: Eurasian Tree Sparrow, Female 5

value: Passeridae


title: House Sparrow, Male 11

organism: Passer domesticus

value: Facultative cavity nester


title: House Sparrow, Male 10


title: Tumor from patient 36

value: Male


title: House Sparrow, Male 7


title: Prothonotary Warbler, Male 3

value: Parulidae


title: Eurasian Tree Sparrow, Female 4


title: House Sparrow, Male 6


title: Eurasian Tree Sparrow, Female 3


title: House Sparrow, Male 4


title: Tumor from patient 34


title: House Sparrow, Female 7


title: Eurasian Tree Sparrow, Female 2


title: Tumor from patient 108

value: Sparsely granulated somatotroph tumor


title: House Sparrow, Female 5


title: House Sparrow, Male 3


title: House Sparrow, Female 4


title: Tumor from patient 33


title: House Sparrow, Female 3


title: Tumor from patient 32


title: House Sparrow, Female 2


title: Eurasian Tree Sparrow, Female 1


title: Tumor from patient 31


title: Carolina Wren, Male 8

organism: Thryothorus ludovicianus

value: Troglodytidae


title: Eastern Bluebird, Male 14

organism: Sialia sialis

value: Turdidae


title: House Sparrow, Female 1


title: Eastern Bluebird, Male 13


title: Carolina Wren, Male 7


title: Tumor from patient 30

value: Pituitary neuroendocrine tumor


title: Tumor from patient 35


title: Eastern Bluebird, Male 12


title: Carolina Wren, Male 6


title: Eastern Bluebird, Male 10


title: Eastern Bluebird, Male 11


title: Carolina Wren, Male 5


title: Eastern Bluebird, Male 9


title: Eastern Bluebird, Female 16


title: Tumor from patient 28


title: Carolina Wren, Male 4


title: Eastern Bluebird, Female 15


title: Carolina Wren, Male 3


title: Eastern Bluebird, Female 14


title: Tumor from patient 27


title: Eastern Bluebird, Female 11


title: Tumor from patient 25


title: Tumor from patient 26


title: Eastern Bluebird, Female 12


title: Eastern Bluebird, Female 9


title: All, 5d DSS, Distal Colon, biol. rep. 10

city: Wien

first: Cornelia

last: Vesely

state: Österreich

address: Schwarzspanierstr 17

department: Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description: Library name: 24E

data_processing:
Quality Control: cutadapt: --nextseq-trim=30 --minimum-length=10
Adapter Trimming: cutadapt: -a  -A  --minimum-length=10
Mapping: Hisat2 (Standard configuration)
Editing Call: Jacusa2 (Standard configuration)
Assembly: GRCm39 from Ensemble, Mapper: Hisat2 (standard configuration)
Supplementary files format and content: Columns: Library Name, Sequence of Primers used to add barcodes, Number of raw or processed read, Cell Type, Tissue Type, Condition, counts of nucleotides at editing site and calculated editing ratio (%)

source_name: Intestine

extract_protocol:
The large intestine was removed from freshly sacrificed animals, cut open longitudinally and fecal contents were removed by vigorous shaking in PBS. Colon cells were incubated at 37°C for 20min in 4mL solution 1 (3% FCS, 20mM HEPES, 5mM EDTA, and 1mM DTT in RPMI (Gibco)) at 180rpm in a 6-well plate. Tissues were rinsed with 1xPBS, transferred to a fresh 6-well plate 700 containing 4mL of digest1 solution (0.8mg/ml Dispase, 20mM HEPES, 2mM EDTA in RPMI) and again incubated at 37°C at 180rpm for 5min. Next, tissues were agitated vigorously in digest1 solution before transferring them into digest2 solution (0.1mg/ml Liberase TL, 0.5mg/ml DNAseI, 20 mM HEPES in RPMI). After another incubation for 20min, tissue and solution were transferred into a gentleMACS™ M tube and dissociated in an octo-gentleMACS dissociator (Myltenyi Biotech, Germany). Suspensions were then filtered through a 100μM cell strainer, washed with 1xPBS containing 2% FCS to remove remaining enzymes. immune cells, B cells (CD45+, CD19+), T cells (CD45+, CD19-, CD3+), neutrophils (CD45+,CD3-, CD19-, Ly-6G+, CD11b+) and a myeloid cell-enriched fraction (CD45+, CD3-, CD19-, Ly-6G-, CD11b+) were sorted directly into RNA lysis buffer. Endothelial cells and a fibroblast/SMC-enriched fraction, cells were stained with anti-CD31, anti-EpCAM and anti-CD45 antibodies and sorted into RNA lysis buffer (endothelial cells: CD45-, EpCam-, CD31+, fibroblast/SMC fraction: CD45-, EpCam-, CD31-). RNA was extracted using the NucleoSpin 96 RNA Core Kit (Macherey-Nagel). CarrierRNA (Macherey-Nagel) was added to samples with cell counts <104 cells. cDNA was synthesized using the LunaScript RT Mastermix (NEB).
cDNA was subjected to a 2-step PCR: In a first round, Flna editing site primers (amplification of the region around the editing site) and Q5 High-Fidelity DNA Polymerase (NEB) were used to perform 25 cycles. 2μl of this PCR served as a template for PCR2: Using the ampSeq barcoding primers for 15 cycles, thereby adding Illumina-compatible adapters with dual-indices. PCR products were gel-eluted using the Monarch DNA Gel Extraction Kit (NEB) followed by quantification by Qubit Fluorometry (Thermo Fisher Scientific). A maximum of 96 samples were pooled into one multiplex for sequencing on an Illumina Nova-Seq instrument.

treatment_protocol: DSS-colitis was induced in 8-10-week-old mice by adding 2-2.5% DSS in the drinking water for 2,5 or 10 days

value: Intestine

value: Endothelial Cells

tag: genotype

value: WT

value: Ctrl


title: All, 5d DSS, Distal Colon, biol. rep. 9

description: Library name: 23E


title: Carolina Wren, Female 7


title: Tumor from patient 24


title: All, 5d DSS, Distal Colon, biol. rep. 8

description: Library name: 22E


title: Carolina Wren, Female 6


title: All, 5d DSS, Distal Colon, biol. rep. 7

description: Library name: 21E

value: 2d DSS


title: Tumor from patient 23

value: Densely granulated lactotroph tumor


title: All, 5d DSS, Distal Colon, biol. rep. 6

description: Library name: 20E


title: Tumor from patient 29

value: Female

value: Gonadotroph tumor


title: Carolina Wren, Female 3

value: Ventromedial telencephalon


title: Tumor from patient 22


title: All, 5d DSS, Distal Colon, biol. rep. 5

description: Library name: 19E


title: All, 5d DSS, Distal Colon, biol. rep. 4

description: Library name: 18E

value: 5d DSS


title: Tumor from patient 21


title: All, 5d DSS, Distal Colon, biol. rep. 2

description: Library name: 16E


title: Carolina Wren, Female 1

value: Facultative cavity nester


title: Tumor from patient 20


title: All, 10d DSS, Distal Colon, biol. rep. 7

description: Library name: 14E

value: 10d DSS


title: American Robin, Male 11

organism: Turdus migratorius

value: Open cup nester


title: All, 10d DSS, Distal Colon, biol. rep. 6

description: Library name: 13E


title: All, 10d DSS, Distal Colon, biol. rep. 5

description: Library name: 12E


title: All, 2d DSS, Distal Colon, biol. rep. 12

description: Library name: 11E


title: American Robin, Male 9


title: Tumor from patient 18

value: Male

value: Densely granulated corticotroph tumor


title: Carolina Wren, Female 8

value: Troglodytidae


title: All, 2d DSS, Distal Colon, biol. rep. 11

description: Library name: 10E


title: Tumor from patient 17

value: Pituitary neuroendocrine tumor

value: Null cell tumor


title: American Robin, Male 7

value: Turdidae


title: All, 5d DSS, Distal Colon, biol. rep. 1

description: Library name: 8E

value: Intestine

value: Endothelial Cells

value: WT


title: American Robin, Male 8


title: Tumor from patient 16

value: TSH

value: Densely granulated somatotroph tumor


title: All, 2d DSS, Distal Colon, biol. rep. 10

description: Library name: 9E

value: 2d DSS


title: All, 10d DSS, Distal Colon, biol. rep. 4

description: Library name: 7E


title: All, 10d DSS, Distal Colon, biol. rep. 3

description: Library name: 6E


title: Carolina Wren, Female 2

value: Ventromedial telencephalon


title: All, 10d DSS, Distal Colon, biol. rep. 2

description: Library name: 5E

value: 5d DSS


title: All, 5d DSS, Distal Colon, biol. rep. 3

description: Library name: 17E


title: All, 10d DSS, Distal Colon, biol. rep. 1

description: Library name: 4E


title: Tumor from patient 65

value: Female

value: Gonadotroph tumor


title: American Robin, Male 2

value: Open cup nester


title: All, 10d DSS, Distal Colon, biol. rep. 8

description: Library name: 15E

value: 10d DSS


title: Tumor from patient 19

value: Densely granulated corticotroph tumor


title: Tumor from patient 14

value: ACTH

value: Densely granulated lactotroph tumor


title: All, 2d DSS, Distal Colon, biol. rep. 9

description: Library name: 3E


title: All, 2d DSS, Distal Colon, biol. rep. 8

description: Library name: 2E


title: All, 2d DSS, Distal Colon, biol. rep. 6

description: Library name: 39D

source_name: Distal Colon

value: Distal Colon

value: All


title: All, 2d DSS, Distal Colon, biol. rep. 5

description: Library name: 38D


title: American Robin, Female 8

value: Turdidae


title: American Robin, Female 5


title: Tumor from patient 13

value: Pituitary neuroendocrine tumor

value: PRL

value: Male


title: All, 2d DSS, Distal Colon, biol. rep. 4

description: Library name: 37D

value: WT


title: Tumor from patient 12


title: All, 2d DSS, Distal Colon, biol. rep. 7

description: Library name: 1E

value: Intestine

value: Endothelial Cells


title: American Robin, Female 4

value: Ventromedial telencephalon


title: Tumor from patient 11


title: American Robin, Female 3


title: Tumor from patient 10

value: Female


title: American Robin, Male 3


title: Tumor from patient 15

value: GH

value: Densely granulated somatotroph tumor


title: All, 2d DSS, Distal Colon, biol. rep. 1

description: Library name: 34D

value: 5d DSS


title: American Robin, Female 2

value: Open cup nester


title: All, Ctrl, Distal Colon, biol. rep. 8

description: Library name: 33D


title: Tumor from patient 9

value: Gonadotroph tumor


title: All, Ctrl, Distal Colon, biol. rep. 6

description: Library name: 31D


title: All, Ctrl, Distal Colon, biol. rep. 7

description: Library name: 32D


title: American Robin, Female 1


title: All, Ctrl, Distal Colon, biol. rep. 5

description: Library name: 30D


title: Tumor from patient 8

value: Densely granulated lactotroph tumor


title: All, Ctrl, Distal Colon, biol. rep. 4

description: Library name: 29D

value: Distal Colon

value: 10d DSS


title: Barn Swallow, Male 6

organism: Hirundo rustica

value: Hirundinidae


title: Tumor from patient 7

value: Pituitary neuroendocrine tumor


title: All, Ctrl, Distal Colon, biol. rep. 3

description: Library name: 28D

value: All


title: All, Ctrl, Distal Colon, biol. rep. 2

description: Library name: 26D


title: Tumor from patient 6

value: PRL


title: Endothelial Cells, Ctrl, Intestine, biol. rep. 6

description: Library name: 24D

value: WT


title: All, 2d DSS, Distal Colon, biol. rep. 3

description: Library name: 36D


title: Barn Swallow, Male 4


title: All, Ctrl, Distal Colon, biol. rep. 1

description: Library name: 25D


title: All, 2d DSS, Distal Colon, biol. rep. 2

description: Library name: 35D


title: Endothelial Cells, Ctrl, Intestine, biol. rep. 5

description: Library name: 23D


title: Tumor from patient 5

value: TSH

value: Male


title: Endothelial Cells, Ctrl, Intestine, biol. rep. 4

description: Library name: 22D


title: Barn Swallow, Male 3

value: Ventromedial telencephalon


title: Endothelial Cells, 2d DSS, Intestine, biol. rep. 6

description: Library name: 21D


title: Endothelial Cells, 2d DSS, Intestine, biol. rep. 4

description: Library name: 19D

value: 2d DSS


title: Endothelial Cells, 2d DSS, Intestine, biol. rep. 5

description: Library name: 20D


title: Barn Swallow, Male 2


title: Tumor from patient 3

value: GH


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 8

description: Library name: 18D


title: Tumor from patient 2

value: Sparsely granulated somatotroph tumor


title: Barn Swallow, Male 1


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 6

description: Library name: 16D


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 7

description: Library name: 17D


title: Endothelial Cells, 10d DSS, Intestine, biol. rep. 6

description: Library name: 15D


title: Barn Swallow, Female 7


title: Barn Swallow, Female 8


title: Barn Swallow, Male 5


title: Endothelial Cells, 10d DSS, Intestine, biol. rep. 5

description: Library name: 14D


title: Yellow Warbler, Male 8

organism: Setophaga petechia

value: Parulidae


title: Barn Swallow, Female 4

value: Open cup nester


title: Endothelial Cells, Ctrl, Intestine, biol. rep. 2

description: Library name: 11D


title: Yellow Warbler, Male 6


title: Endothelial Cells, Ctrl, Intestine, biol. rep. 1

description: Library name: 10D


title: Barn Swallow, Female 3


title: Tumor from patient 4


title: Endothelial Cells, 2d DSS, Intestine, biol. rep. 3

description: Library name: 9D


title: Barn Swallow, Female 2


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 5

description: Library name: 6D

value: Ctrl


title: Barn Swallow, Female 1


title: Yellow Warbler, Male 3


title: Endothelial Cells, 10d DSS, Intestine, biol. rep. 3

description: Library name: 3D


title: E10.5_PGC_Female_TRIM28KO_ATAC_4

city: Los Angeles

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

data_processing:
Adapter trimming performed with TrimGalore v0.6.10. Alignment was performed with STAR 2.7.9a. PCR duplicates were removed using Picard Tools MarkDuplicates v2.25.0.
Bigwig files of merged replicates. Generated using DeepTools v3.5.1.
Assembly: GRCm39 (ENSEMBL) v109
Supplementary files format and content: BigWig

source_name: PGC

extract_protocol:
PGCs from dissected embryonic gonads (E12.5, E13.5, E14.5) and dissected embryo trunks (E10.5, E11.5) were dissociated in 0.05% Trypsin in 5% CO2/37C for 5 minutes. Digestions was quenched using 10% FBS in DMEM High Glucose media and cells were pelleted at 1200 rpm x 5 minutes. Resulting pellet was resuspended in 10% FBS, High Glucose DMEM + DNAse and treated for 5 minutes at 5%CO2/37C and pelleted by centrifugation at 1,200 RPM for 5 minutes. PGCs were then suspended in DPBS + 1% BSA and GFP+, 7AAD- cells were collected in DPBS + 1% BSA. .
Libraries were prepared according to the protocols published in Corces et al., Nature Methods 2017 (DOI: https://doi.org/10.1038/nmeth.4396) Briefly: Samples were spun down at 750 r.c.f at 4C for 10 minutes, resuspended in buffer RSB and spun again at 750 r.c.f at 4C for 10 minutes. After last centrifugation, buffer RSB was removed and Tn5 Enzyme mix added. Samples were treated at 37C for 30 minutes, shaking at 1000 rpm. Reaction was immediately quenched on ice with ice-cold PBS. DNA was purified using NEB Monarch DNA Purification kit according to the manufacturer's instructions. Purified DNA was used as a template and Nexteera indexing adapters added to the reaction with NEB Next High fidelity PCR mix. Samples were run for 5 cycles, split and run for an additional 4 and 8 cycles. Resulting libraries were purified using Agencourt XP beads and quantified using the Quibit HS DNA quantification kit according to manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 (E14.5) or Illumina NovaSeq X Plus (E10.5).

value: PGC

tag: embryonic day

tag: Sex

value: Female


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 3

description: Library name: 4D

value: Distal Colon


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 4

description: Library name: 5D


title: Tumor from patient 1

value: Null cell tumor


title: Endothelial Cells, 10d DSS, Intestine, biol. rep. 4

description: Library name: 13D


title: E10.5_PGC_Female_TRIM28KO_ATAC_3


title: Yellow Warbler, Male 2


title: B-Cell, 10d DSS, Blood, biol. rep. 3

description: Library name: 163

source_name: Blood

value: Blood

value: B-Cell

value: 10d DSS


title: Endothelial Cells, 10d DSS, Intestine, biol. rep. 1

description: Library name: 1D

value: All

value: WT


title: Yellow Warbler, Female 9


title: Endothelial Cells, Ctrl, Intestine, biol. rep. 3

description: Library name: 12D


title: E10.5_PGC_Female_TRIM28KO_ATAC_2


title: Endothelial Cells, 10d DSS, Intestine, biol. rep. 2

description: Library name: 2D


title: B-Cell, 10d DSS, Blood, biol. rep. 2

description: Library name: 162


title: B-Cell, Ctrl, Blood, biol. rep. 2

description: Library name: 160


title: E10.5_PGC_Female_TRIM28KO_ATAC_1


title: Endothelial Cells, 2d DSS, Intestine, biol. rep. 2

description: Library name: 8D


title: Endothelial Cells, 2d DSS, Intestine, biol. rep. 1

description: Library name: 7D


title: Yellow Warbler, Female 7


title: B-Cell, 10d DSS, Blood, biol. rep. 1

description: Library name: 161


title: Yellow Warbler, Male 5


title: Yellow Warbler, Male 4


title: Macrophage, 10d DSS, Blood, biol. rep. 4

description: Library name: 158

value: Macrophage


title: B-Cell, Ctrl, Blood, biol. rep. 1

description: Library name: 159


title: E10.5_PGC_Female_Control_ATAC_4

value: Control


title: Yellow Warbler, Female 6

value: Ventromedial telencephalon


title: Macrophage, 10d DSS, Blood, biol. rep. 3

description: Library name: 157


title: Yellow Warbler, Female 4


title: E10.5_PGC_Female_Control_ATAC_3


title: Macrophage, 10d DSS, Blood, biol. rep. 1

description: Library name: 155


title: E10.5_PGC_Female_Control_ATAC_2


title: Macrophage, Ctrl, Blood, biol. rep. 1

description: Library name: 153


title: Yellow Warbler, Female 3


title: Neutrophil, 10d DSS, Blood, biol. rep. 4

description: Library name: 152

value: Neutrophil


title: House Wren, Male 9

organism: Troglodytes aedon

value: Troglodytidae

value: Obligate cavity nester


title: Neutrophil, 10d DSS, Blood, biol. rep. 3

description: Library name: 151


title: House Wren, Male 7


title: E10.5_PGC_Male_TRIM28KO_ATAC_6

value: Male


title: Macrophage, Ctrl, Blood, biol. rep. 2

description: Library name: 154

value: Ctrl


title: Neutrophil, 10d DSS, Blood, biol. rep. 2

description: Library name: 150


title: E10.5_PGC_Female_Control_ATAC_1

value: PGC


title: Neutrophil, Ctrl, Blood, biol. rep. 2

description: Library name: 148


title: Neutrophil, Ctrl, Blood, biol. rep. 1

description: Library name: 147


title: House Wren, Male 6


title: House Wren, Male 5


title: E10.5_PGC_Male_TRIM28KO_ATAC_5


title: E10.5_PGC_Male_TRIM28KO_ATAC_4


title: E10.5_PGC_Male_TRIM28KO_ATAC_3


title: Yellow Warbler, Female 8

value: Parulidae

value: Open cup nester


title: T-Cell, 10d DSS, Blood, biol. rep. 3

description: Library name: 145

value: T-Cell


title: T-Cell, 10d DSS, Blood, biol. rep. 2

description: Library name: 144

value: Blood


title: House Wren, Male 3


title: T-Cell, 10d DSS, Blood, biol. rep. 4

description: Library name: 146


title: Macrophage, 10d DSS, Blood, biol. rep. 2

description: Library name: 156


title: T-Cell, 10d DSS, Blood, biol. rep. 1

description: Library name: 143


title: E10.5_PGC_Male_TRIM28KO_ATAC_2


title: T-Cell, Ctrl, Blood, biol. rep. 2

description: Library name: 142


title: T-Cell, Ctrl, Blood, biol. rep. 1

description: Library name: 141


title: House Wren, Male 1


title: E10.5_PGC_Male_Control_ATAC_4


title: House Wren, Female 7


title: B-Cell, 10d DSS, Bone Marrow, biol. rep. 4

description: Library name: 140

source_name: Bone Marrow

value: Bone Marrow

value: B-Cell


title: E10.5_PGC_Male_Control_ATAC_3


title: Neutrophil, 10d DSS, Blood, biol. rep. 1

description: Library name: 149

value: 10d DSS


title: B-Cell, 10d DSS, Bone Marrow, biol. rep. 3

description: Library name: 139

value: WT


title: House Wren, Female 5


title: B-Cell, 10d DSS, Bone Marrow, biol. rep. 1

description: Library name: 137


title: B-Cell, Ctrl, Bone Marrow, biol. rep. 2

description: Library name: 136


title: E10.5_PGC_Male_Control_ATAC_2


title: Macrophage, 10d DSS, Bone Marrow, biol. rep. 4

description: Library name: 134

value: Macrophage


title: House Wren, Female 4


title: B-Cell, Ctrl, Bone Marrow, biol. rep. 1

description: Library name: 135


title: E10.5_PGC_Male_Control_ATAC_1

value: Control


title: Macrophage, 10d DSS, Bone Marrow, biol. rep. 3

description: Library name: 133


title: House Wren, Female 3

value: Ventromedial telencephalon


title: House Wren, Female 2


title: Macrophage, 10d DSS, Bone Marrow, biol. rep. 2

description: Library name: 132


title: Chlamydomonas_GLORI_rep1

data_processing:
Raw reads were preprocessed using cutadapt (v4.1), seqkit (v0.8.1) rmdup module and fastp (v0.21.0) for adaptor trimming, deduplication and quality control as well as UMI trimming, respectively.
Then, the clean data were processed using the RNA-m5C pipeline developed by Huang T et al., 2022, with some modifications described.
All A sites with signal greater than 0.9 (representing the ratio of reads with no more than 3 non-converted A to all reads) and coverage greater than 20 after discarding non-converted reads were retained for methylation rate calculation
Assembly: Creinhardtii_281_v5.0
Supplementary files format and content: tab-delimited text file, quantification of m6A in all As with coverage >= 15.

organism: Chlamydomonas reinhardtii

source_name: cells

value: cells


title: Macrophage, Ctrl, Bone Marrow, biol. rep. 2

description: Library name: 130


title: Macrophage, 10d DSS, Bone Marrow, biol. rep. 1

description: Library name: 131


title: Neutrophil, 10d DSS, Bone Marrow, biol. rep. 3

description: Library name: 127

value: Neutrophil


title: Macrophage, Ctrl, Bone Marrow, biol. rep. 1

description: Library name: 129


title: Neutrophil, 10d DSS, Bone Marrow, biol. rep. 2

description: Library name: 126


title: Neutrophil, 10d DSS, Bone Marrow, biol. rep. 4

description: Library name: 128


title: Met_DMSO_0_0uM_TC00003602_H12

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

institute: US EPA

description:
Library name: TC00003602_H12
TC00003602_H12

data_processing:
Read alignment: Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Probe counts: Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: aime_prepilot_count_data.csv.gz: A table of probe counts in CSV format, with rows corresponding to TempO-seq probe IDs (see httr_aime_prepilot-probe_manifest.csv file for probe ID mapping information) and columns corresponding to sample IDs.
Supplementary files format and content: httr_aime_prepilot-probe_manifest.csv: For each probe ID listed in the table of probe counts (aime_prepilot_count_data.csv.gz), a corresponding mapping of probe sequence, Entrez ID, and gene symbol are listed.

growth_protocol: Experiments were peformed in VM7Luc4E2 cells, a sub-clone of MCF-7 breast adenocarcinoma cells that stably expresses and estrogen receptor trans-activation reporter construct. Prior to experimentation, VM7Luc4E2 cultures were maintained in growth medium (Minimum Essential Medium alpha (MEMa) supplemented with 10% fetal bovine serum (FBS) and 1X Gibco Anti-Anti antibiotics). Four days prior to seeding in assay plates, cultures were switched to estrogen-stripping medium (Dulbecco’s Modified Eagle Medium (DMEM) (low glucose, with pyruvate, no phenol red) supplemented with 5% charcoal/dextran-treated FBS and 4 mM L-Glutamine). Estrogen stripping was performed by refreshing the estrogen-stripping media daily for four days. For chemical testing experiments, VM7Luc4E2 cells were passaged, resuspended in assay medium (DMEM (low glucose, with pyruvate, no phenol red) supplemented with 1% charcoal/dextran-treated FBS, 4 mM L-Glutamine and 10 mM HEPES), and plated in 384-well plates in a volume of 30 µL per well and an initial seeding density of 7,500 cells / well. Cells were allowed a 24 hour recovery period prior to treatment with AIME conditioned medium.  Cells were lysed for TempO-Seq analysis 24 hours after treatment with AIME conditioned medium.

extract_protocol:
At 24 hours after treatment with condition media, assay plates were removed from the incubator, assay wells were washed twice with 1X phosphate-buffered saline and the final PBS wash was aspirated from each well leaving a residual volume of 10 µL.  Cells were subsequently lysed by adding 10 µL of 2X BioSpyder Enhanced Lysis buffer.  Assay plates were then sealed, agitated for 30 seconds on the stage of a MultiFlo FX washer / dispenser and then placed in a hybridization oven at 37°C for 10 minutes. Plates were then immediately transferred to a -80°C freezer for storage. Plates were subsequently shipped frozen to BioSpyder Technologies (Carlsbad, CA) for analysis with the human whole transcriptome TempO-Seq assay.  The TempO-Seq assay was conducted directly on cell lysates with no RNA extraction step.
Plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. Cell lysates were then analyzed by BioSpyder using the unattenuated TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). The TempO-seq libraries were sequenced to a target read depth of 3.0x106 mapped reads per sample.

treatment_protocol: The experiments were carried out using the alginate immobilization of metabolic enzymes (AIME) technology. DMSO solubilized chemicals (120 nL) were dispensed into 384-well microplates. Locations of treatments were randomized by well coordinate on the 384-well plate. After chemical dispensing, 60 µL of assay medium charged with phase 1 and phase 2 metabolic co-factors (NADPH (1:11.4), uridine S’-diphosphoglucuronic acid trisodium salt (UDPGA; 0.5 mM), glutathione (GSH; 1 mM), and adenosine 3-phosphate 5-phosphosulfate lithium salt hydrate (PAPS; 2 µM)) was dispensed into each well and plates were shaken at 500 RPM for 7 minutes on an orbital shaker. AIME peg lids with hydrogels containing either hepatic rat S9 (AIME+ condition) or deionized water (AIME- condition) were inserted into the plates and incubated for 2 hours to create conditioned media. Then, 30 µL of conditioned media was transferred to assay plates containing VM7Luc4E2 cells and 30 µL of assay medium.  The final concentration of DMSO in all treatment wells was 0.1%. Assy plates were then incubated for 24 hours in a cell culture incubator (37°C and 5% CO2).

value: 0.5% DMSO vehicle control

tag: media

value: VM7Luc4E2 Assay Medium

tag: chemical name

value: DMSO

tag: chemical sample_id

tag: chemical concentration

value: 0 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: sample qc_issue

value: OK


title: B-Cell, 10d DSS, Bone Marrow, biol. rep. 2

description: Library name: 138

tag: tissue


title: Neutrophil, 10d DSS, Bone Marrow, biol. rep. 1

description: Library name: 125


title: Met_DMSO_0_0uM_TC00003602_H10

description:
Library name: TC00003602_H10
TC00003602_H10


title: Neutrophil, Ctrl, Bone Marrow, biol. rep. 2

description: Library name: 124

value: Ctrl


title: Neutrophil, Ctrl, Bone Marrow, biol. rep. 1

description: Library name: 123


title: T-Cell, 10d DSS, Bone Marrow, biol. rep. 4

description: Library name: 122

value: T-Cell


title: Met_transstilbene_139939_4_3.73uM_TC00003602_H09

description:
Library name: TC00003602_H09
TC00003602_H09

value: 24h exposure of 3.73 uM of trans-Stilbene

value: trans-Stilbene


title: T-Cell, 10d DSS, Bone Marrow, biol. rep. 3

description: Library name: 121

value: Bone Marrow


title: Mouse skin single-cell RNA-seq - SED9, sedentary

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Belanger

institute: Montreal Heart Institute

description: Library name: SED9

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to Cellranger’s mm10-2020-A reference using the count function of cellranger-7.0.1 for each sample (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-reference-release-notes). To remove the ambient RNA contamination, we used the SoupX tool. For downstream analyses, we used Seurat v4. We removed low-quality cells using the following thresholds: >200 and <5000 detected genes, mitochondrial reads <20, 500 and <40,000 sequence reads, RNA complexity >0.8. To normalize and regress out mitochondrial read percentage, we used SCTransform. We integrated the data using Harmony on 30 principal components. To annotate cell types, we obtained the skin canonical markers from two different databases: Tabula muris and immunesinglecell skin atlas. We plotted the expression levels of key marker genes obtained from both databases onto the UMAP representation of our dataset to assign cel-type to each cluster. We identified doublets using scDblFinder. We removed cells for which the scDblFinder score was >0.5. We sub-clustered each main cell-type and removed subclusters showing doublet enrichment.
Assembly: Mouse mm10
Supplementary files format and content: Processed data consists of SCT-normalized single-cell expression matrices after filtering out keratinocyte cells. Files are provided in .rds format.

source_name: skin

extract_protocol:
Upon sacrifice, a piece of skin from the leg was harvested and immediately processed as detailed below. Two pieces of 1cm2 of skin were harvested per mouse and were dissociated using the Whole Skin Dissociation Kit (Miltenyi Biotec, Germany) with some variations regarding the manufacturer’ instructions. Skin tissue was incubated at 37oC in a water bath for 1h30 in the enzyme mix. Mechanical dissociation was then processed using the ThermoMixer (Eppendorf) for 1-hour at 37oC and 400 rpm. Following completion of the dissociation, the homogenate was filtered through a 70-µm cell strainer into a 50-mL centrifuge tube. The cell suspension was then centrifuged at 600g for 10 min at 4oC. Once complete, the supernatant was removed and the pellet was incubated in 500 µL of Red Blood Cell Lysis Buffer for 1min30 (Roche). Cells were again centrifuged at 600g for 10 min at 4oC and then resuspended in 500 µL of PBS + 0.04% BSA. Cell count and viability were estimated using the Countess II FL cell counter (Thermo Fisher). Endothelial cells were then enriched using the CD31 MicroBeads mouse Kit (Miltenyi Biotec, Germany), following the manufacturer’ instructions. Briefly, cells were incubated for 30-min with 10µL of beads. After a wash step, cells were loaded onto an MS column on the OctoMACS Separator.
Library was performed according to the manufacter's instruction (single cell 3' v2 protocol, 10X Genomics

value: skin

value: sedentary


title: Mouse skin single-cell RNA-seq - SED5, sedentary

description: Library name: SED5


title: Met_daidzein_D7802_7_53.5uM_TC00003602_H11

description:
Library name: TC00003602_H11
TC00003602_H11

value: 24h exposure of 53.5 uM of Daidzein

value: Daidzein


title: Mouse skin single-cell RNA-seq - SED6, sedentary

description: Library name: SED6


title: Chlamydomonas_GLORI_rep2


title: Mouse skin single-cell RNA-seq - SED2, sedentary

description: Library name: SED2


title: T-Cell, 10d DSS, Bone Marrow, biol. rep. 2

description: Library name: 120

value: WT

value: 10d DSS


title: Met_bestradiol_E2758_1_0.0001uM_TC00003602_G12

description:
Library name: TC00003602_G12
TC00003602_G12

value: 24h exposure of 1e-04 uM of 17beta-Estradiol


title: House Wren, Female 1

tag: family

value: Troglodytidae

value: Ventromedial telencephalon

value: Obligate cavity nester


title: T-Cell, 10d DSS, Bone Marrow, biol. rep. 1

description: Library name: 119


title: T-Cell, Ctrl, Bone Marrow, biol. rep. 2

description: Library name: 118


title: Met_DMSO_0_0uM_TC00003602_G11

description:
Library name: TC00003602_G11
TC00003602_G11

tag: cell line

value: 0.5% DMSO vehicle control

value: VM7Luc4E2 Assay Medium

value: DMSO

value: 0 uM


title: Mouse skin single-cell RNA-seq - SED3, sedentary

description: Library name: SED3


title: SMC, 10d DSS, Intestine, biol. rep. 4

description: Library name: 116

value: Intestine

tag: cell type

value: SMC


title: Mouse skin single-cell RNA-seq - SED10, sedentary

description: Library name: SED10

tag: treatment


title: T-Cell, Ctrl, Bone Marrow, biol. rep. 1

description: Library name: 117

value: Bone Marrow

value: T-Cell

tag: genotype

value: Ctrl


title: SMC, 10d DSS, Intestine, biol. rep. 2

description: Library name: 114


title: Met_transstilbene_139939_2_0.093uM_TC00003602_G09

description:
Library name: TC00003602_G09
TC00003602_G09

value: 24h exposure of 0.093 uM of trans-Stilbene

value: trans-Stilbene

value: OK


title: SMC, 10d DSS, Intestine, biol. rep. 3

description: Library name: 115

value: WT

value: 10d DSS


title: Mouse skin single-cell RNA-seq - AP9, exercise

description: Library name: AP9

value: skin

value: exercise


title: Met_ethyl4hydroxybenzoate_111988_8_100uM_TC00003602_G10

description:
Library name: TC00003602_G10
TC00003602_G10

value: 24h exposure of 100 uM of Ethylparaben

value: Ethylparaben


title: Met_ethyl4hydroxybenzoate_111988_1_0.001uM_TC00003602_F12

description:
Library name: TC00003602_F12
TC00003602_F12

value: 24h exposure of 0.001 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium


title: SMC, Ctrl, Intestine, biol. rep. 2

description: Library name: 112


title: Mouse skin single-cell RNA-seq - AP6, exercise

description: Library name: AP6


title: SMC, Ctrl, Intestine, biol. rep. 1

description: Library name: 111


title: Mouse skin single-cell RNA-seq - AP5, exercise

description: Library name: AP5


title: Met_daidzein_D7802_8_100uM_TC00003602_F11

description:
Library name: TC00003602_F11
TC00003602_F11

value: 24h exposure of 100 uM of Daidzein

value: Daidzein


title: Mouse skin single-cell RNA-seq - AP3, exercise

description: Library name: AP3


title: B-Cell, 10d DSS, Intestine, biol. rep. 3

description: Library name: 109

value: Intestine

value: B-Cell


title: Mouse skin single-cell RNA-seq - AP2, exercise

description: Library name: AP2


title: Met_daidzein_D7802_6_26.1uM_TC00003602_F10

description:
Library name: TC00003602_F10
TC00003602_F10

value: 24h exposure of 26.1 uM of Daidzein


title: Met_daidzein_D7802_2_0.093uM_TC00003602_F09

description:
Library name: TC00003602_F09
TC00003602_F09

value: 24h exposure of 0.093 uM of Daidzein


title: B-Cell, 10d DSS, Intestine, biol. rep. 4

description: Library name: 110


title: Macrophage, 10d DSS, Intestine, biol. rep. 3

description: Library name: 104

value: Macrophage


title: Macrophage, 10d DSS, Intestine, biol. rep. 4

description: Library name: 105


title: Met_bestradiol_E2758_1_0.0001uM_TC00003602_E12

description:
Library name: TC00003602_E12
TC00003602_E12

value: 24h exposure of 1e-04 uM of 17beta-Estradiol


title: Macrophage, 10d DSS, Intestine, biol. rep. 2

description: Library name: 103


title: Mouse skin single-cell RNA-seq - AP10, exercise

description: Library name: AP10


title: B-Cell, 10d DSS, Intestine, biol. rep. 2

description: Library name: 108


title: Macrophage, 10d DSS, Intestine, biol. rep. 1

description: Library name: 102


title: Met_transstilbene_139939_3_0.865uM_TC00003602_E11

description:
Library name: TC00003602_E11
TC00003602_E11

value: 24h exposure of 0.865 uM of trans-Stilbene

value: trans-Stilbene

value: OK


title: SMC, 10d DSS, Intestine, biol. rep. 1

description: Library name: 113

value: SMC

value: WT

value: 10d DSS


title: Neutrophil, 10d DSS, Intestine, biol. rep. 3

description: Library name: 99

value: Neutrophil


title: Neutrophil, 10d DSS, Intestine, biol. rep. 4

description: Library name: 100


title: Met_transstilbene_139939_6_26.1uM_TC00003602_E10

description:
Library name: TC00003602_E10
TC00003602_E10

value: 24h exposure of 26.1 uM of trans-Stilbene


title: Neutrophil, 10d DSS, Intestine, biol. rep. 2

description: Library name: 98


title: Met_daidzein_D7802_3_0.865uM_TC00003602_E09

description:
Library name: TC00003602_E09
TC00003602_E09

value: 24h exposure of 0.865 uM of Daidzein

value: VM7Luc4E2 Assay Medium


title: Mfap2-/- reverse-4, CCl4 treatment for 8 weeks, CCl4 cessation for 4 weeks, bulk RNA-seq

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

description:
Library name: KO-R-4
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx

data_processing:
The HISAT software was used to align clean reads to the mouse genome.
Read counts and FPKM values for each identified gene were calculated using Cufflinks software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: liver

growth_protocol: Mfap2+/+ and Mfap2-/- mice

extract_protocol:
Total RNA was extracted from the mouse frozen liver tissues using the RNA simple Total RNA k.
cDNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs, Hitchin, UK) or the Illumina VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme, Nanjing, China).

treatment_protocol: Intraperitoneal injection of CCl4 for 8 weels or CCl4 cessation for 4 weeks

value: liver

value: KO

value: Intraperitoneal injection of CCl4 for 8 weeks, CCl4 cessation for 4 weeks


title: Neutrophil, 10d DSS, Intestine, biol. rep. 1

description: Library name: 97

value: Intestine


title: Mfap2-/- reverse-3, CCl4 treatment for 8 weeks, CCl4 cessation for 4 weeks, bulk RNA-seq

description:
Library name: KO-R-3
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx


title: Mfap2-/- reverse-1, CCl4 treatment for 8 weeks, CCl4 cessation for 4 weeks, bulk RNA-seq

description:
Library name: KO-R-1
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx


title: Mfap2-/- reverse-2, CCl4 treatment for 8 weeks, CCl4 cessation for 4 weeks, bulk RNA-seq

description:
Library name: KO-R-2
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx


title: Neutrophil, Ctrl, Intestine

description: Library name: 96

value: Ctrl


title: Met_transstilbene_139939_8_100uM_TC00003602_D12

description:
Library name: TC00003602_D12
TC00003602_D12

value: 24h exposure of 100 uM of trans-Stilbene


title: B-Cell, 10d DSS, Intestine, biol. rep. 1

description: Library name: 107

value: B-Cell


title: T-Cell, 10d DSS, Intestine, biol. rep. 4

description: Library name: 95

value: T-Cell


title: B-Cell, Ctrl, Intestine

description: Library name: 106


title: Mfap2+/+ reverse-4, CCl4 treatment for 8 weeks, CCl4 cessation for 4 weeks, bulk RNA-seq

description:
Library name: WT-R-4
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx


title: T-Cell, 10d DSS, Intestine, biol. rep. 2

description: Library name: 93


title: T-Cell, 10d DSS, Intestine, biol. rep. 3

description: Library name: 94


title: Met_ethyl4hydroxybenzoate_111988_2_0.093uM_TC00003602_D11

description:
Library name: TC00003602_D11
TC00003602_D11

value: 24h exposure of 0.093 uM of Ethylparaben

value: Ethylparaben


title: EC, 10d DSS, Intestine, biol. rep. 4

description: Library name: 90

value: EC


title: Mfap2+/+ reverse-3, CCl4 treatment for 8 weeks, CCl4 cessation for 4 weeks, bulk RNA-seq

description:
Library name: WT-R-3
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx

value: WT


title: Met_ethyl4hydroxybenzoate_111988_7_53.5uM_TC00003602_D10

description:
Library name: TC00003602_D10
TC00003602_D10

value: 24h exposure of 53.5 uM of Ethylparaben

value: OK


title: Mfap2+/+ reverse-2, CCl4 treatment for 8 weeks,CCl4 cessation for 4 weeks, bulk RNA-seq

description:
Library name: WT-R-2
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx


title: T-Cell, 10d DSS, Intestine, biol. rep. 1

description: Library name: 92

value: 10d DSS


title: Spatial Transcriptomics Sample 4-4

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

description: Library name: S8_R2

data_processing:
Libraries were sequenced using an Illumina NextSeq2000 at a reading depth of 100 million paired-end reads per sample using the following read metrics: Read1: 28bp; Index1: 10bp; Index2: 10bp; Read 2: 90bp. Raw FASTQ files were processed with Space Ranger 1.3.0 and aligned to mm10-2020-A reference genome (refdata-gex-mm10-2020-A).
Computational analysis was performed in R using a combination of Seurat Version 5.1.048 and custom scripts.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: RDS files that can be read into R as a Seurat Object via readRDS()
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Mice were anesthetized, the animal was decapitated, and brain extracted. The brain was subsequently flash frozen in OCT via isopentane and liquid nitrogen bath.
Processing of slices and library preparation were performed for Visium as recommended by the manufacturer (10x Genomics).

treatment_protocol: Mice underwent a CHIMERA TBI or sham TBI.

value: Brain

value: FoxTRAP x Ai14

value: TBI


title: Mfap2+/+ reverse-1, CCl4 treatment for 8 weeks, CCl4 cessation for 4 weeks, bulk RNA-seq

description:
Library name: WT-R-1
Mfap2_bulk_RNA-seq_processed data-reverse.xlsx

value: liver