title: Ileum week 3 sample 3

status: Public on Nov 30 2025

type: SRA

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

country: USA

institute: Harvard T.H. Chan School of Public Health

description:
3wk I-3
Mouse whole thickness ileum at indicated time point

library_source: transcriptomic

data_processing:
Reads were aligned to NCBI build mm10 of the mouse genome (Mus musculus) using STAR aligner (version 2.6.1d)
Transcripts were quantified through a quasi-alignment approach using Salmon (version 0.14.2). Transcript-level counts were aggregated at the gene level and imported into R using tximport.
Differential expression analyses and normalization (variance stabilization transformation) were performed with DESeq2 (version 1.30.1). Additional transcript-level information was sourced from Ensembl release 94.
Assembly: mm10
Supplementary files format and content: comma-separated values of raw counts
Supplementary files format and content: comma-separated values of normalized counts

molecule: total RNA

organism: Mus musculus

source_name: Ileum

growth_protocol: C57/Bl6 mice (Jackson labs) mice were collected across postnatal ages to the extent possible (usually 2-3 time points per litter), to limit potential variation in microbial exposures. Mice were housed in standard germ-free conditions and kept with the dam until 21 days postnatal and then transitioned to standard rodent chow. We used both male and female mice for all experiments.

extract_protocol:
Intestinal tissue was placed into Trizol LS (ThermoFisher) and homogenized with a bead homogenizer. RNA was isolated using the Direct-zol kit (Zymo Research) according to the manufacturer’s instructions.
The library was prepared by the Dana Farber Next Generation Sequencing Core Facility using a KAPA library quantification kit (Roche). Sequencing was done on an Illumina NovaSeq 6000 with total RNA.

treatment_protocol: Mice were euthanized at day 0, day 2, day 4, day 6, day 8, 2 weeks, 3 weeks, and 4 weeks.

tag: tissue

value: Ileum

tag: cell type

value: Whole tissue

tag: genotype


title: Ileum week 3 sample 2

description:
3wk I-2
Mouse whole thickness ileum at indicated time point


title: Ileum week 3 sample 1

description:
3wk I-1
Mouse whole thickness ileum at indicated time point


title: Ileum week 2 sample 3

description:
2wk I-3
Mouse whole thickness ileum at indicated time point


title: Ileum week 2 sample 2

description:
2wk I-2
Mouse whole thickness ileum at indicated time point


title: Ileum week 2 sample 1

description:
2wk I-1
Mouse whole thickness ileum at indicated time point


title: Ileum day 8 sample 3

description:
8d I-3
Mouse whole thickness ileum at indicated time point


title: Ileum day 8 sample 2

description:
8d I-2
Mouse whole thickness ileum at indicated time point


title: Ileum day 8 sample 1

description:
8d I-1
Mouse whole thickness ileum at indicated time point


title: Ileum day 6 sample 3

description:
6d I-3
Mouse whole thickness ileum at indicated time point


title: Ileum day 6 sample 2

description:
6d I-2
Mouse whole thickness ileum at indicated time point


title: Ileum day 6 sample 1

description:
6d I-1
Mouse whole thickness ileum at indicated time point


title: Ileum day 4 sample 3

description:
4d I-3
Mouse whole thickness ileum at indicated time point


title: Ileum day 4 sample 2

description:
4d I-2
Mouse whole thickness ileum at indicated time point


title: Ileum day 4 sample 1

description:
4d I-1
Mouse whole thickness ileum at indicated time point


title: Ileum day 2 sample 3

description:
2d I-3
Mouse whole thickness ileum at indicated time point


title: Ileum day 2 sample 1

description:
2d I-1
Mouse whole thickness ileum at indicated time point


title: Ileum day 0 sample 3

description:
0d I-3
Mouse whole thickness ileum at indicated time point


title: Ileum day 2 sample 2

description:
2d I-2
Mouse whole thickness ileum at indicated time point


title: Ileum day 0 sample 2

description:
0d I-2
Mouse whole thickness ileum at indicated time point


title: Ileum day 0 sample 1

description:
0d I-1
Mouse whole thickness ileum at indicated time point


title: Duodenum week 4 sample 1

description:
4wk D-1
Mouse whole thickness duodenum at indicated time point

source_name: Duodenum

value: Duodenum


title: Duodenum week 4 sample 3

description:
4wk D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum week 4 sample 2

description:
4wk D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum week 3 sample 2

description:
3wk D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum week 2 sample 2

description:
2wk D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum week 3 sample 3

description:
3wk D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum week 2 sample 1

description:
2wk D-1
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 8 sample 3

description:
8d D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum week 3 sample 1

description:
3wk D-1
Mouse whole thickness duodenum at indicated time point


title: Duodenum week 2 sample 3

description:
2wk D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 8 sample 2

description:
8d D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 8 sample 1

description:
8d D-1
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 6 sample 3

description:
6d D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 6 sample 1

description:
6d D-1
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 4 sample 3

description:
4d D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 4 sample 2

description:
4d D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 4 sample 1

description:
4d D-1
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 6 sample 2

description:
6d D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 2 sample 3

description:
2d D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 2 sample 2

description:
2d D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 0 sample 3

description:
0d D-3
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 0 sample 2

description:
0d D-2
Mouse whole thickness duodenum at indicated time point


title: Duodenum day 0 sample 1

description:
0d D-1
Mouse whole thickness duodenum at indicated time point


title: Case 30

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Thirty samples from St. Jude Children’s Research Hospital (SJCRH, pediatric), Ospedale Pediatrico Bambino Gesù (pediatric), and Aga Khan University Hospital (AKUH, pediatric and adult) were analyzed using Illumina Methylation BeadChip (EPIC) arrays according to the manufacturer’s instructions. Data were generated from formalin-fixed paraffin-embedded (FFPE) tissue samples. DNA of 29 patients was extracted and hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays.

scan_protocol: Illumina protocol

data_processing:
All methylation data were analyzed in R (http://www.r-project.org, version 3.5.3), using a number of packages from Bioconductor and other repositories. Specifically, array data were preprocessed using the minfi package (v.1.28.4) (13). Background correction with dye-bias normalization was performed for all samples using noob (normal-exponential out-of-band) with “single” dye method (14). Filtering was performed to remove probes located on sex chromosomes, probes containing nucleotide polymorphisms (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, or probes mapping to multiple sites on hg19 (allowing for one mismatch), and cross-reactive probes.
Average beta values that were normalized by functional normalization from minfi R package

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Soft tissue myoepithelial tumors

label_protocol: Standard Illumina protocol

value: Soft tissue myoepithelial tumors


title: Duodenum day 2 sample 1

description:
2d D-1
Mouse whole thickness duodenum at indicated time point


title: Case 29

extract_protocol: Data were generated from formalin-fixed paraffin-embedded (FFPE) tissue samples. DNA of 29 patients was extracted and hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays


title: Case 27


title: Case 26


title: Case 28


title: Case 25


title: Case 22


title: Case 20


title: Case 24


title: Case 21


title: Case 23


title: Case 17


title: Case 18


title: Case 16


title: Case 15


title: Case 14


title: Case 13


title: Case 12


title: Case 11


title: Case 10


title: Case 5


title: Case 6


title: Case 4


title: Ileum week 4 sample 1

description:
4wk I-1
Mouse whole thickness ileum at indicated time point


title: Case 7


title: Case 8


title: Case 19


title: Ileum week 4 sample 3

description:
4wk I-3
Mouse whole thickness ileum at indicated time point


title: Case 9


title: Ileum week 4 sample 2

description:
4wk I-2
Mouse whole thickness ileum at indicated time point


title: Case 3


title: Case 2


title: ASC VPR ZNF865 2

city: Salt Lake City

first: Jason

last: Gertz

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description: Library name: 19746X8

data_processing:
Sequencing reads were aligned to the hg38 build of the human genome using HISAT2.
SAMtools was used to convert SAM files to BAM files.
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads mapped to known genes were assigned with featureCounts.
Within each cell line, read counts were normalized and analyzed for differential expression via the DESeq2 package in R.
Assembly: hg38
Supplementary files format and content: rna_seq_asc_hek293_normalized_counts.txt
Supplementary files format and content: rna_seq_patient_data_normalized_counts.txt

molecule: polyA RNA

source_name: ASC

growth_protocol: Primary human nucleus pulposus cells (hNPCs) were cultured in complete growth medium containing DMEM-HG (ThermoFisher Scientific) supplemented with 10% FBS (ThermoFisher Scientific), 50 g/mL gentamicin (Corning), 25 mM HEPES (ThermoFisher Scientific), and 2 ng/mL of recombinant human fibroblast growth factor-basic (rhFGF, Peprotech, Cranbury, NJ, 100-18C).

extract_protocol:
RNA was harvested using Quick-RNA-Kit (Zymo Research, Irvine, CA).
Isolated total RNA (100-1000ng) was prepared using an Illumina TruSeq stranded mRNA Library prep Kit with PolyA Selection.

treatment_protocol: hNPCs (p1-p2) were plated at a density of 20,000 cells/cm2, allowed to attach overnight, and transduced with EF-1a-dCas9-VPR-eGFP (Addgene, #241307) lentivirus, (1:2 dilution) in growth medium containing 4 g/mL polybrene, the following day. 72-hours following transduction, hNPCs were subjected to fluorescence activated cells sorting (FACS) to select for GFP+ expressing cells.

tag: cell line

value: ASC

value: Adipose stromal

tag: treatment

value: CRISPRa ZNF865

tag: replicate


title: HEK VPR ZNF865 2

description: Library name: 19746X12

source_name: HEK 293

value: HEK 293

value: Human embryonic kidney


title: HEK VPR ZNF865 1

description: Library name: 19746X11


title: HEK VPR NTC 1

description: Library name: 19746X9

value: Non-targeting gRNA


title: ASC VPR ZNF865 1

description: Library name: 19746X7


title: ASC VPR NTC 2

description: Library name: 19746X6


title: ASC VPR NTC 1

description: Library name: 19746X5


title: 21D_1

city: Changsha

first: Qun

last: Tang

address: Yuelu District

country: China

institute: Hunan University of Chinese Medicine

description:
Library name: Sample5
W3_1

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/) to map reads to the reference genome of homo sapiens Ensembl_v112. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: homo_sapiens Ensembl_v112
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: dental pulp tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 400±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ X Plus (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: dental pulp tissue


title: 7D_2

description:
Library name: Sample4
W1_2


title: Case 1


title: 21D_2

description:
Library name: Sample6
W3_2


title: magzc1

city: Xi'an

first: Shuqin

last: Xu

address: Zhuque street

institute: xianjiaotong univeisity

description:
Library name: sample1
MCA group biological replicate 1

data_processing:
Raw read counts were normalized as FPKM (fragments per kilobase per million) values. FPKM matrices were log₂-transformed for downstream analysis.
Differentially expressed genes between MCA and suture groups were identified using the limma R package (p < 0.05,
Assembly: Rattus norvegicus reference genome (Ensembl release 104).
Supplementary files format and content: The processed data file is a tab-delimited text matrix containing FPKM expression values for all genes across six samples (three MCA and three Suture groups).

organism: Rattus norvegicus

source_name: Colon anastomosis site

growth_protocol: Male Sprague-Dawley rats (200–230 g) were housed under standard laboratory conditions (12 h light/dark cycle, 22 ± 2°C, 50–60% humidity) with free access to food and water.

extract_protocol:
Total RNA was isolated from frozen anastomotic tissue using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA integrity and concentration were assessed using NanoDrop One (Thermo Fisher Scientific).
RNA samples were previously sequenced by Annoroad Gene Technology Co., Ltd. (Beijing, China). Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit (New England Biolabs, USA) and sequenced on the DNBSEQ-T7 (MGI Tech Co., Ltd.) platform. The data uploaded here represent normalized FPKM expression matrices derived from that sequencing.

treatment_protocol: Rats were randomly divided into two groups: magnetic compression anastomosis (MCA) and conventional suture (control). Colonic end-to-end anastomosis was performed as described in the manuscript. Two weeks after surgery, anastomotic tissues were collected for RNA extraction.

value: Colon anastomosis site

value: Magnetic compression anastomosis


title: 0D_1

description:
Library name: Sample1
D0_1


title: fxzc1

description:
Library name: sample4
Suture group biological replicate 1

value: Conventional suture anastomosis


title: magzc3

description:
Library name: sample3
MCA group biological replicate 3


title: magzc2

description:
Library name: sample2
MCA group biological replicate 2


title: fxzc2

description:
Library name: sample5
Suture group biological replicate 2


title: 0D_2

description:
Library name: Sample2
D0_2


title: 7D_1

description:
Library name: Sample3
W1_1


title: MGG65_Mouse3_BloodVessel PDX

city: Rehovot

first: Rony

last: Chanoch

state: Israel

address: Weizmann Institute of Science, 234 Herzl Street

country: Israel

institute: Weizmann Instititue

description: Library name: MGG65_Mouse3_BloodVessel

library_source: transcriptomic single cell

data_processing:
Paired-end reads from were mapped to GRCh38 human transcriptome using Bowtie. Expression values were calculated by RSEM in paired-end mode using parameters, from which TPM values for each gene were extracted.
Assembly: GRCh38
Supplementary files format and content: tab-separated log tpm matrix

source_name: Brain

growth_protocol: Mice were euthanized upon reaching pre-determined clinical endpoints such as such as significant body weight loss, seizures, and a persistent hunched posture with diminished activity. The collected mice brains were imaged with a fluorescent stereomicroscope with 0.63 objective magnification (Olympus MVX10, Leica M205), which covers both the entire brain and cell morphology at single-cell resolution. Under the microscope, the brains were observed from the ipsilateral hemisphere for tumor-peripheral invasion to the contralateral hemisphere for distal invasion. For distal invasion, collected brains were physically separated into the hemisphere with the primary tumor (injection side) and the other contained invading tumor cells excluding the midline border region. For local blood vessel-associated invasion, tube-structured GFP+ cell clusters were dissected under a stereomicroscope without introducing any primary bulk tumor mass.

extract_protocol:
Tissue from each location were mechanically and enzymatically dissociated using a papain-based neural tissue dissociation kit (Miltenyi Biotec) supplemented with 0.1% Type I collagenase (Thermo Fisher Scientific)/PBS. The dissociated cells were first stained with calcein Blue AM (BD Biosciences) and Zombie NIR (BioLegend) for 25 min at 4C, and with anti-mouse CD16/32 (BD Biosciences) for 5 min. After washing cells with ice-cold 1% BSA/PBS, the cells were then stained with PerCP anti-mouse CD45 (clone 30-F11, BD Biosciences) for 30 min at 4C. Sorting was performed with Becton Dickinson Influx cytometer (Becton Dickinson). Side scatter (SSC) width versus forward scatter (FSC) area and Trigger Pulse Width versus FSC criteria were used to discriminate doublets and gate-only singleton cells. Viable single cells were identified as calcein blue AM positive and Zombine NIR negative to low cells. We sorted viable CD45 negative/GFP positive cells from blood-vessel associated invasion samples into 96-well plates containing 10uL of TCL buffer (QIAGEN) with 1% beta-mercaptoethanol (Sigma Aldrich). Plates were frozen immediately after sorting and stored at -80 degree prior to whole transcriptome amplification, library preparation, and sequencing.
Smart Seq 2

value: Brain

value: Glioblastoma

value: malignant


title: MGG65_Mouse3_Primary PDX

description: Library name: MGG65_Mouse3_Primary


title: PBS liver, A100, D20 rep3

city: Lisboa

first: Alice

last: Borges

address: Av. Rovisco Pais

country: Portugal

institute: IBB

description: Library name: sample 18

data_processing:
3D: Raw reads were filtered by removing reads containing (1) adapters, (2) N > 10% (N represents base that could not be determined) and (3) low quality (when Qscore - Quality value - of over 50% bases of the read is <= 5). Paired-end clean reads were mapped to hg38 reference genome using HISAT2 software. Counts were obtained using Featurecounts. 2D: Sample read quality, reads mapping and counting were performed by a standard protocol from BlueBee Genomics Platform. For each sample individually, the pipeline includes reads trimming using BBDuk, alignment against genomic sequence using STAR aligner, gene read counting using HTSeq and quality control using RSeQC.
Assembly: grch38
Supplementary files format and content: comma-delimiyed file includes  raw gene counts for every gene and every sample

growth_protocol: Human induced pluripotent stem cells (iPS-DF6-9-9T.B, WiCell Bank, Wisconsin, USA) were maintained in mTeSR™1 medium (STEMCELL Technologies™) supplemented 1:200 (v/v) with penicillin/streptomycin (Gibco™, Thermo Fisher Scientific) on Matrigel-coated (Corning®) six-well culture plates in humidified incubators at 37ºC and 5% CO2. Culture medium was changed daily. Cell passaging was performed every three to four days when reaching a confluency ~70% using 0.5 mM EDTA (Invitrogen™, Thermo Fisher Scientific)

extract_protocol:
organoids: Total RNA from cells of dissociated liver organoids was extracted using High Pure RNA Isolation Kit following the provided instructions. 2d culture: For sample collection at selected time points, culture medium was removed, and cells were washed with PBS. Then cells were incubated with Accutase® solution (Sigma-Aldrich®, #A6964) in the case of hiPSCs or 0.25% (v/v) trypsin-EDTA (Gibco™, #R001100) in PBS for differentiated cells, both at 37ºC for 7 min. Culture medium was added to inactivate enzymatic digestion and cells were homogenized and centrifuged at 200 xg for 3 min. The cell pellet was washed with PBS and centrifuged again at 200 xg for 3 min. After removing the PBS, cell pellet was stored at -80ºC until further analysis. Total RNA was extracted using the High Pure RNA Isolation Kit (Roche, #11828665001) following the provided instructions.
3d organoid: Illumina NovaSeq 6000 system with a paired end 150 bp strategy; 2D cells: Libraries were prepared using Lexogen QuantSeq 3′mRNA-Seq Library Prep. Kit FWD for Illumina using standard protocols.Sequencing was performed using Illumina HiSeq (50 cycle’s protocol) or NextSeq (75 cycle’s protocol) platforms

treatment_protocol: 3D differentiation: For liver organoid generation cells were seeded in a vertical-wheel bioreactor PBS Mini 0.1L (PBS Biotech,USA), 27 rpm, at a density of 250 000 cells/mL in 60 mL of mTeSR™1 supplemented with 10μM ROCKi Y-27632 (STEMCELL Technologies™). 24h after inoculation, full medium volume was replaced, and aggregates were maintained in mTeSR™1 without ROCKi at 25 rpm. For definitive endoderm differentiation, RPMI 1640 medium (Gibco™) supplemented with 1% (v/v) B-27™ minus insulin (Gibco™) and 1:200 (v/v) penicillin/streptomycin (Gibco™) was used as differentiation medium. On day 0 of differentiation, differentiation medium was supplemented with 10ng/mL or 100 ng/mL of Activin A (PeproTech) and 6 μM of CHIR99021 (CHIR, Stemgent™) and agitation speed set to 30 rpm. After 24h, total media was replaced, and agitation speed changed to 33 rpm. For hepatic induction (day 3 of differentiation) cells were cultured in differentiation medium additionally supplemented with 10 ng/mL of FGF2 (PeproTech) and 20 ng/mL of BMP4 (PeproTech). From day 6 to day 20, cells were refreshed every three days with hepatocyte culture medium (HCM) BulletKit™ (Lonza) without the addition of human epidermal growth factor (hEGF). Medium was supplemented with 10 ng/mL oncostatin M (OSM, R&D Systems™), 0.1 μM dexamethasone (Dex, Sigma-Aldrich) and 20ng/mL of hepatic growth factor (HGF, Sigma-Aldrich).  2D differentiation: For hiPSC differentiation into definitive endoderm, Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco™, #21875034) was used as basal medium. RPMI was supplemented with 1% (v/v) B-27™ minus insulin (Gibco™, #A1895601) and supplemented 1:200 (v/v) with penicillin/ streptomycin (Gibco™, #15140122). At day 0 (D0) of differentiation, basal medium was supplemented with 100 ng/mL of Activin A (PeproTech, #120-14P), 1 mM of sodium butyrate (NaB, Sigma-Aldrich®, #B5887) and 50 ng/mL of Wnt3a (R&D Systems™, #5036-WN) or 2 µM of CHIR99021 (CHIR, Stemgent™, #04-0004). At day 1 and 2, basal medium was again supplemented with 100 ng/mL of Activin A. Cells continued to be cultured in RPMI 1640 medium supplemented with 1% (v/v) B-27™ minus insulin and 1:200 (v/v) with penicillin/ streptomycin, from D3 to D5 of differentiation. At D3, for hepatic induction, medium was additionally supplemented with 10 ng/mL of FGF2 (PeproTech, #100-18B) and 20 ng/mL of BMP4 (PeproTech, #120-05ET). From D6 to D20, cells were refreshed every three days with hepatocyte culture medium (HCM) BulletKit™ (Lonza, #CC-3198) without the addition of human epidermal growth factor (hEGF). Medium was supplemented with 10 ng/mL of oncostatin M (OSM, R&D Systems™, #295-OM), 0.1 µM of dexametasone (Dex, Sigma-Aldrich®, #D4902) and 20 ng/mL of hepatic growth factor (HGF, Sigma-Aldrich®, #H1404). Working volume throughout differentiation was 1 mL per well."

tag: source

value: foreskin fibroblasts

value: iPSC-derived liver organoids

tag: mode of_growth

value: 3D - dynamic

value: 100ug activin A

tag: time

value: 20 days


title: PBS liver, A10, D20 rep2

description: Library name: sample 14

value: 10ug activin A


title: fxzc3

description:
Library name: sample6
Suture group biological replicate 3


title: MGG123_Mouse4_BloodVessel PDX

description: Library name: MGG123_Mouse4_BloodVessel


title: MGG65_Mouse2_Primary PDX

description: Library name: MGG65_Mouse2_Primary


title: MGG65_Mouse2_BloodVessel PDX

description: Library name: MGG65_Mouse2_BloodVessel


title: PBS liver, A10, D20 rep1

description: Library name: sample 13


title: HEK VPR NTC 2

description: Library name: 19746X10


title: PBS liver, A100, D20 rep2

description: Library name: sample 17


title: MGG123_Mouse4_Primary PDX

description: Library name: MGG123_Mouse4_Primary


title: PBS liver, A100, D3 rep3

description: Library name: sample 12

value: 3 days


title: PBS liver, A100, D20 rep1

description: Library name: sample 16


title: PBS liver, A100, D3 rep1

description: Library name: sample 10


title: MGG123_Mouse3_Primary PDX

description: Library name: MGG123_Mouse3_Primary


title: PBS liver, A100, D3 rep2

description: Library name: sample 11


title: MGG123_Mouse2_BloodVessel PDX

description: Library name: MGG123_Mouse2_BloodVessel


title: MGG123_Mouse2_Primary PDX

description: Library name: MGG123_Mouse2_Primary


title: PBS liver, A10, D3 rep2

description: Library name: sample 8


title: Pool2_Mouse2_Primary_PDX

description: 10X genomics (3' SC)

data_processing:
Utilized CellRanger for initial alignment, filtering, and quantification of single-cell RNA-seq data.
Utilized SpaceRanger for initial alignment, filtering, and quantification of ST RNA-seq data.
Assembly: scRNA-seq aligned to GRCh38;  PDX samples were aligned to a concatenated human/mouse genome: GRCh38-and-mm10-2020-A
Supplementary files format and content: tab-separated tpm and metadata files.

extract_protocol:
Mice were euthanized upon reaching pre-determined clinical endpoints such as such as significant body weight loss, seizures, and a persistent hunched posture with diminished activity. The collected mice brains were imaged with a fluorescent stereomicroscope with 0.63 objective magnification (Olympus MVX10, Leica M205), which covers both the entire brain and cell morphology at single-cell resolution. Under the microscope, the brains were observed from the ipsilateral hemisphere for tumor-peripheral invasion to the contralateral hemisphere for distal invasion. For distal invasion, collected brains were physically separated into the hemisphere with the primary tumor (injection side) and the other contained invading tumor cells excluding the midline border region. For local blood vessel-associated invasion, tube-structured GFP+ cell clusters were dissected under a stereomicroscope without introducing any primary bulk tumor mass. Then, each location were mechanically and enzymatically dissociated using a papain-based neural tissue dissociation kit (Miltenyi Biotec) supplemented with 0.1% Type I collagenase (Thermo Fisher Scientific)/PBS. The dissociated cells were first stained with calcein Blue AM (BD Biosciences) and Zombie NIR (BioLegend) for 25 min at 4C, and with anti-mouse CD16/32 (BD Biosciences) for 5 min. After washing cells with ice-cold 1% BSA/PBS, the cells were then stained with PerCP anti-mouse CD45 (clone 30-F11, BD Biosciences) for 30 min at 4C. Sorting was performed with Becton Dickinson Influx cytometer (Becton Dickinson). Side scatter (SSC) width versus forward scatter (FSC) area and Trigger Pulse Width versus FSC criteria were used to discriminate doublets and gate-only singleton cells. Viable single cells were identified as calcein blue AM positive and Zombine NIR negative to low cells. We sorted viable CD45 negative/GFP positive cells from blood-vessel associated invasion samples into 96-well plates containing 10uL of TCL buffer (QIAGEN) with 1% beta-mercaptoethanol (Sigma Aldrich). Plates were frozen immediately after sorting and stored at -80 degree prior to whole transcriptome amplification, library preparation, and sequencing. For multiplexed samples, CD45 negative/GFP positive cells were sorted into 15mL tumors for subsequent 10X scRNA-seq processing.
The spheroid models in vitro were processed as a pool using TotalSeq-B/Hashtag anti-bodies (BioLegend), described previously19. Each of the dissociated cells was first stained with HumanTruStain FcX (BioLegend) in Cell Staining Buffer (BioLegend) for 10 min at 4C, and then stained with barcoded TotalSeq-B anti-bodies targeting human CD298 and b2 microglobulin in a separated tube for 30 min at 4C. We generated a single cell suspension of the pool in 0.04% PBS-BSA and loaded approximately 9,900 single cells to the Chromium Controller with a targeted recovery of 6,000 cells. Single cells, reagents and single gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized droplets and subjected to reverse transcription. Droplets were broken and the barcoded cDNAs were purified with DynaBeads and amplified by 12 cycles of PCR (98C for 3 min; [98C for 15 s, 63C for 20 s, 72C for 1 min] x 12; 72C for 1 min). Gene expression cDNA and TotalSeq antibody derived barcode cDNA were size-selected and separated with SPRIselect Reagent (Beckman Coulter), and then fragmented, end-repaired, ligated with index adaptors. Quality control of the resulting libraries was performed with the Bio-analyzer High Sensitivity DNA Analysis (Agilent). The constructed gene expression library and barcode library were combined at 4:1 ratio and sequenced with paired-end, 28 and 55-base reads, using a NextSeq 2000 sequencer (Illumina).


title: PBS liver, A100, D0 rep1

description: Library name: sample 4

value: induced pluripotent stem cells

value: 0 days


title: Pool2_Mouse2_Invasion_PDX

description: 10X genomics (3' SC)


title: PBS liver, A10, D0 rep3

description: Library name: sample 3


title: PBS liver, A100, D0 rep2

description: Library name: sample 5


title: PBS liver, A10, D0 rep1

description: Library name: sample 1


title: Pool1_Mouse2_Primary_PDX

description: 10X genomics (3' SC)


title: Pool1_Mouse2_Invasion_PDX

description: 10X genomics (3' SC)


title: PBS liver, A10, D0 rep2

description: Library name: sample 2


title: Pool2_Mouse1_Invasion_PDX

description: 10X genomics (3' SC)


title: W_WT_rep1

city: St. Louis

first: Charles

last: Kaufman

state: Missouri

address: 4565 McDonnell Science Building

institute: Washington University School of Medicine

description: Library name: sample.wm115_wt5_1

data_processing:
Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 4.0.3-8 software.
Assembly: Ensembl release 101 primary assembly (GRCh38).
Supplementary files format and content: Processed data files are provided as TPM matrices in tab-delimited text format.

source_name: Skin

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's protocol. RNA concentration and quality were assessed using a NanoDrop spectrophotometer and RNA integrity was determined using an Agilent Bioanalyzer or 4200 Tapestation. Samples with a RIN score >8.0 were used for library preparation.
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was fragmented in reverse transcriptase buffer by heating to 94°C for 8 minutes. cDNA was synthesized using SuperScript III reverse transcriptase (Life Technologies) and random hexamers. A second strand synthesis reaction was performed to create double-stranded cDNA. Fragments were blunt-ended, an A base was added to the 3’ ends, and Illumina sequencing adapters were ligated. The ligated fragments were amplified with primers containing unique dual index tags for 12-15 PCR cycles.

value: Skin

value: Melanoma Cells

value: WT


title: Pool1_Mouse1_Primary_PDX

description: 10X genomics (3' SC)


title: MGG123_Mouse1_BloodVessel PDX

description: Library name: MGG123_Mouse1_BloodVessel


title: pD_ICF2_LCL

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

description: methylation profiling using bisulfite converted

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing: Genome-wide methylation analysis was performed by the Illumina Infinium methylation Epic array on bisulfite converted DNA extracted from the three tissues of the patient. Data were analyzed using R version 4.1.0. Beta values (Bvalues) were derived from “idat” files by the “champ.load” module of the “ChAMP” R package (v.2.22.0), with quality control options set as default and array type as “EPIC.” To adjust the Bvalues of type 2 probes, we applied BMIQ normalization with the default options for array type as “EPIC.”

label: Cy5 and Cy3

source_name: Lymphoblastoid

label_protocol: Standard llumina Protocol

growth_protocol: LCLs were cultured in RMPI supplemented with 15% bovine serum, glutamine and antibiotics

extract_protocol: Genomic DNA from LCLs and whole blood was extracted using Cells and Tissue Isolation kit (#53100, Norgen Biotek Corp.)

tag: patient id

value: pD

tag: gender

value: M

tag: condition

value: Lymphoblastoid


title: pV_ICF2_LCL

value: pV


title: Ctrl_LCL

value: Ctrl

value: Control


title: human PBMC  CF

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

description: 10X Genomics

data_processing:
Cell Ranger workflow using the DropletUtils was used to generate FASTQ files
Assembly: hg19, Sscorfa11.1
Supplementary files format and content: barcodes.tsv.gz features.tsv.gz matrix.mtx.gz

source_name: Peripheral Blood

extract_protocol:
MNC were isolated from pig lung and bone-marrow as well as human or pig blood and stored in liquid nitrogen. For each genotype and species constellation, cryopreserved samples were thawn and equal numbers of cells from n=4 donors were pooled. Bone marrow specimens were FACS-sorted for live CD45-positive cells after thawing.
10 000 cells for each sample (targeted cell recovery) were processed using Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1 (1000128, 10x Genomics) and the Chromium Chip B Single Cell Kit (10x Genomics; PN- 1000073) to generate Gel Bead-In-EMulsions (GEMs) and single cell sequencing libraries. Libraries were sequenced using The NextSeq2000 (Ilumina, San Diego USA, P2 flowcell with a depth of  > 16 000 pair reads per cell.

value: Peripheral Blood

value: PBMC

value: CF

value: pre-school children


title: W_WT_rep4

description: Library name: sample.wm115_wt5_4


title: MGG65_Mouse1_Primary PDX

description: Library name: MGG65_Mouse1_Primary

value: Brain

value: Glioblastoma

value: malignant


title: W_4.1_rep1

description: Library name: sample.wm115_c3_1


title: Pool2_Mouse1_Primary_PDX

description: 10X genomics (3' SC)


title: W_4.1_rep2

description: Library name: sample.wm115_c3_2


title: human PBMC WT

description: 10X Genomics


title: Human PSC Day9 foregut endoderm plus RA plus CHIR BMP rep2

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

description: Library name: Human_PSC_Day9_FG_plus_RA_plus_CHIR_BMP_rep2

data_processing:
Quality of reads was asessed with factqc
Quality trimmed reads in fastq format were mapped and quantified using STAR 2.7.9
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Raw counts and TPM(Transcripts per million) per gene across samples were reported

source_name: ESC-differentiated foregut endoderm

extract_protocol:
RNA was extracted using the Macherey-Nagel Nucleospin RNA extraction kit according to manufacturer's insructions.
Library prep was performed using Illumina’s TruSeq stranded mRNA library preparation kit according to manufacturer's instructions.

treatment_protocol: 2uM all-trans Retionic Acid (Sigma R2625) treatment for 24 hours (day5>6) of differentiation.  Treatment with 2uM CHIR99021 (TOCRIS #4423) and 50ng/mL BMP4 (R&D systems #314-BP)  for 72 hours (days6-9) done to mimic respiratory fate inducing signals.

value: ESC-differentiated foregut endoderm

value: Human H1 ESCs

value: wt Human H1 ESCs

value: Day9 FG endo +RA + CHIR+BMP4


title: Human PSC Day9 foregut endoderm plus RA plus CHIR BMP rep1

description: Library name: Human_PSC_Day9_FG_plus_RA_plus_CHIR_BMP_rep1


title: W_WT_rep3

description: Library name: sample.wm115_wt5_3

value: Skin

value: Melanoma Cells

value: WT


title: Human PSC Day9 foregut endoderm plus RA rep2

description: Library name: Human_PSC_Day9_FG_plus_RA_rep2

value: Day9 FG endo + RA


title: RZ_ICF2_LCL

value: RZ

value: F

value: Lymphoblastoid


title: W_4.2_rep1

description: Library name: sample.wm115_c4_1


title: W_WT_rep2

description: Library name: sample.wm115_wt5_2


title: W_4.1_rep3

description: Library name: sample.wm115_c3_3


title: ISO-seq of Monopterus albus

city: Wuhan

first: Yuan

last: Zhao

address: Donghu Road 7th

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description:
Library name: ISO-seq_ALL
Full-length transcriptome sequencing using PacBio Iso-Seq

data_processing:
We employed multiple programs from PacBio SMRT Analysis, following the guidelines outlined in the SMRT Tools Reference Guide. Consensus sequences were generated from raw subread data using CCS and full-length reads were constructed using lima by primer removal and demultiplexing. Full-Length Non-Chimeric transcripts were identified using Isoseq3 refine by removing polyA and concatemers from full-length reads. Full-Length Non-Chimeric reads were then clustered and polished using the cluster and polish subcommands of Isoseq3, respectively. Specialized long-read aligners minimap2 were selected to map the polished transcripts to the M. albus genome (M_albus_1.0).
Assembly: NCBI, M_albus_1.0
Supplementary files format and content: transcritome assembly includes gtf and fa

organism: Monopterus albus

source_name: gonad

extract_protocol:
The mixed RNA sample was reverse transcribed using the SMARTer PCR cDNA Synthesis Kit.
The resulting cDNA underwent amplification, and fragments ranging from 0.5 to 10 kb were selected for subsequent library preparation. Finally, SMRTbell libraries were constructed using the Pacific Biosciences DNA Template Prep Kit 2.0 and sequenced on the PacBio Sequel platform.

value: gonad


title: Human PSC Day9 foregut endoderm plus RA plus CHIR BMP rep3

description: Library name: Human_PSC_Day9_FG_plus_RA_plus_CHIR_BMP_rep3


title: W_4.2_rep2

description: Library name: sample.wm115_c4_2


title: Human PSC Day9 foregut endoderm plus RA rep1

description: Library name: Human_PSC_Day9_FG_plus_RA_rep1


title: Human PSC Day9 foregut endoderm plus RA rep3

description: Library name: Human_PSC_Day9_FG_plus_RA_rep3


title: W_4.2_rep3

description: Library name: sample.wm115_c4_3


title: RNA-seq of Monopterus albus: male8

description: Library name: T_IV3

data_processing:
Data quality of RNA-seq data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to remove adapters and low-quality bases in raw reads. Filtered reads were aligned to the M. albus genome (M_albus_1.0) using the STAR aligner with the two-pass mapping mode. The uniquely mapped reads were kept for further analysis. Gene expression matrices were generated using the featureCounts program. Differential gene expression analysis was performed by DESeq2, genes with fold change > 2 and adjusted p-value < 0.01 were defined as differentially expressed genes (DEGs).
Assembly: NCBI, M_albus_1.0
Supplementary files format and content: tab-delimited text file includes FPKM gene expression for each sample

source_name: Testis

extract_protocol:
RNA was extracted by trizol method
Messenger RNA was isolated utilizing poly-T oligo-attached magnetic beads. Fragmentation was conducted with divalent cations at elevated temperatures in First Strand Synthesis Reaction Buffer (5X). The synthesis of first-strand cDNA was carried out using random hexamer primers and M-MuLV Reverse Transcriptase. Second-strand cDNA synthesis employed DNA Polymerase I and RNase H. After adenylation at the 3’ ends, hairpin loop adaptors were ligated. cDNA fragments between 370-420 bp were purified using the AMPure XP system (Beckman Coulter, Beverly, USA).

value: Testis


title: RZ_ICF2_blood

source_name: Blood

value: Blood


title: Human PSC Day6 foregut endoderm plus RA rep1

description: Library name: Human_PSC_Day6_FG_plus_RA_rep1

value: Day6 FG endo + RA


title: RNA-seq of Monopterus albus: male6

description: Library name: T_IV1


title: RNA-seq of Monopterus albus: male7

description: Library name: T_IV2


title: Human PSC Day6 foregut endoderm plus RA rep2

description: Library name: Human_PSC_Day6_FG_plus_RA_rep2


title: RNA-seq of Monopterus albus: male5

description: Library name: T_III2


title: Human PSC Day9 foregut endoderm plus CHIR BMP rep2

description: Library name: Human_PSC_Day9_FG_plus_CHIR_BMP_rep2

value: Day9 FG endo CHIR+BMP4


title: Human PSC Day9 foregut endoderm plus CHIR BMP rep3

description: Library name: Human_PSC_Day9_FG_plus_CHIR_BMP_rep3


title: W_1.1_rep2

description: Library name: sample.wm115_c10_2


title: Human PSC Day9 foregut endoderm rep3

description: Library name: Human_PSC_Day9_FG_rep3

value: Day9 FG endo


title: RNA-seq of Monopterus albus: male4

description: Library name: T_III1


title: Human PSC Day9 foregut endoderm rep2

description: Library name: Human_PSC_Day9_FG_rep2

value: ESC-differentiated foregut endoderm


title: W_1.1_rep1

description: Library name: sample.wm115_c10_1


title: Pool1_Mouse1_Invasion_PDX

description: 10X genomics (3' SC)

value: Brain

value: Glioblastoma


title: W_1.1_rep3

description: Library name: sample.wm115_c10_3


title: Human PSC Day9 foregut endoderm rep1

description: Library name: Human_PSC_Day9_FG_rep1

value: Human H1 ESCs

value: wt Human H1 ESCs


title: RNA-seq of Monopterus albus: male3

description: Library name: T_I3


title: Human PSC Day6 foregut endoderm plus RA rep3

description: Library name: Human_PSC_Day6_FG_plus_RA_rep3


title: W_1.1_rep4

description: Library name: sample.wm115_c10_4

value: Skin

value: Melanoma Cells


title: Human PSC Day6 foregut endoderm rep3

description: Library name: Human_PSC_Day6_FG_rep3

value: Day6 FG endo


title: Human PSC Day6 foregut endoderm rep2

description: Library name: Human_PSC_Day6_FG_rep2


title: PBS liver, A10, D3 rep3

description: Library name: sample 9

value: foreskin fibroblasts

value: iPSC-derived liver organoids

value: 3D - dynamic

value: 10ug activin A

value: 3 days


title: PBS liver, A10, D3 rep1

description: Library name: sample 7


title: PBS liver, A10, D20 rep3

description: Library name: sample 15

value: 20 days


title: Human PSC Day6 foregut endoderm rep1

description: Library name: Human_PSC_Day6_FG_rep1


title: W_1.1_rep5

description: Library name: sample.wm115_c10_5


title: RNA-seq of Monopterus albus: male2

description: Library name: T_I2

value: Testis


title: RNA-seq of Monopterus albus: male1

description: Library name: T_I1


title: Human PSC Day9 foregut endoderm plus CHIR BMP rep1

description: Library name: Human_PSC_Day9_FG_plus_CHIR_BMP_rep1

value: Day9 FG endo CHIR+BMP4


title: MGG123_Mouse1_Primary PDX

description: Library name: MGG123_Mouse1_Primary

value: malignant


title: Day6 Foregut  Endoderm ATAC-eq rep2

description: Library name: Human_PSC_Day6_FG_ATACseq_rep2

library_source: genomic

data_processing:
Quality of reads was asessed with factqc
Raw reads in fastq format were mapped using bowtie2
Deduplications with samtools
Peaks calling with macs2 (narrow and broad peaks)
Assembly: Homo sapiens hg19
Supplementary files format and content: Bigwig files created by bedtools (.bw)
Supplementary files format and content: Peak files created by macs2 (narrowPeaks)

source_name: foregut endoderm (day6)

extract_protocol:
For ATAC-seq, 50,000 cells from replicate biological wells were collected from independent differentiations to the desired stage, and lysed in 50mL of ATAC-lysis buffer (10mM Tris-HCl, pH 7.4. 10mM NaCl, 3mM MgCl2, 0.1% NP-40) to obtain a crude nuclei prep. All centrifugation steps were performed at 4°C at 2000 rpm. The nuclei pellet was then resuspended in the 50ul of the transposition reaction mix (25ul Tagment DNA buffer, 2.5ul TD Tn5 Transposase enzyme, 22.5ul nuclease-free water) (Illumina; 20034197). The transposition reaction was incubated at 37°C for 30 min on a thermomixer with constant gentle shaking at 1000 rpm. Immediately after transposition, DNA was purified using a Qiagen MinElute PCR Purification (Qiagen; 28004 kit) and eluted in 10mL Elution Buffer. The eluted DNA was then amplified in a reaction with 25mL NEBNext High-Fidelity 2x PCR Mastermix (NEB; M0541L) and custom 25um Nextera PCR Primers (Ad1_noMx universal primer, 0.5um Ad2.x indexing primer). PCR was performed as follows: 1 cycle of 72°C for 5min, 98°C for 30s, 5 cycles of 98°C for 10s, 63°C for 30s, 72°C for 1min. 5ul of the amplified DNA was then used to perform qPCR to determine the optimal number of additional cycles to prevent amplification saturation of DNA libraries. In all cases, either 4 or 5 additional cycles of PCR was performed at: 98°C for 10s, 63°C for 30s and 72°C for 1 min. Double size selection of amplified libraries (0.5x – left sided, 1.8x – right sided) was performed using AMPure XP beads and the DNdA was eluted in a final volume of 20ul in 0.1x TE buffer. Purified libraries were sequenced on an Illumina NextSeq 500 instrument with a 2 × 75bp read length.
Library construction performed using Nextera XT DNA Library Preparation Kit (FC-131-1024) according to manufacturer's instructions

treatment_protocol: Differentiation of definitive endoderm and foregut endoderm from human H1 ESCs: For differentiation, hESCs were plated as single cells in a Matrigel-coated 24-well dish using accutase (Stem Cell Technologies), at a density of 200,000 cells per well in mTesR1 with ROCK inhibitor Y-27632 (10 μM; Stemgent). On the following day, hESCs were differentiated to DE as follows: cells were treated with Activin A (100 ng/mL; Cell Guidance Systems) for three days (72hours) in RPMI 1640 media (Invitrogen) containing increasing concentrations of defined fetal bovine serum (dFBS; Invitrogen):  0% (day1), 0.2% (day2), and 2.0% (day3 onwards). In addition, BMP4 (50 ng/mL; R&D Systems) was added for 24 hours on the first day of DE induction. For foregut endoderm differentiation, cells were cultured in RPMI 1640 media with 2.0% dFBS and Noggin (200 ng/mL R&D Systems) for 72 hours (days4-6).  Retinoic acid (RA; 2 μM; Sigma Aldrich) was added for 24 hours from day5-6 to promote posterior foregut fate.

value: foregut endoderm (day6)

value: human H1 ESC

value: wild type H1 ESCs

value: Activin A 72 hours (day1-3) (BMP4 day1); Noggin 72 hours (day4-6)


title: Day6 Foregut  Endoderm plus RA ATAC-seq rep2

description: Library name: Human_PSC_Day6_FG_plus_RA_ATACseq_rep2

source_name: foregut endoderm  exposed to RA (day6)

value: foregut endoderm  exposed to RA (day6)

value: Activin A 72 hours (day1-3) (BMP4 day1); Noggin 72 hours (day4-6); Retionic Acid (day5-6)


title: Day6 Foregut  Endoderm plus RA ATAC-seq rep1

description: Library name: Human_PSC_Day6_FG_plus_RA_ATACseq_rep1


title: Day6 Foregut  Endoderm ATAC-seq rep1

description: Library name: Human_PSC_Day6_FG_ATACseq_rep1


title: RNA-seq of Monopterus albus: intersex7

description: Library name: OT_III3

source_name: Intersex Gonad

value: Intersex Gonad


title: W_1.2_rep2

description: Library name: sample.wm115_c11_2

value: Skin

value: Melanoma Cells


title: Day3 Definitive Endoderm ATAC-seq rep2

description: Library name: Human_PSC_Day3_DE_ATACseq_rep2

source_name: definitive endoderm (day3)

value: definitive endoderm (day3)

value: Activin A 72 hours (day1-3) (BMP4 day1)


title: W_1.2_rep3

description: Library name: sample.wm115_c11_3


title: RNA-seq of Monopterus albus: intersex5

description: Library name: OT_III1


title: Day3 Definitive Endoderm ATAC-seq rep1

description: Library name: Human_PSC_Day3_DE_ATACseq_rep1


title: P56-FUP1, F, LTR

city: Birtinya

first: Nathan

last: Wellington

state: QLD

address: 12 Innovation Pkwy,

department: Thompson Institute

country: Australia

institute: University of the Sunshine Coast

description:
Library name: P56-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

data_processing:
CLC Genomics Workbench 25.0 (Qiagen)
Assembly: The data underwent quality control, trimming, alignment, annotation, and and mapped to GRCh38.p14 for differential expression analysis using CLC Genomics Workbench 25.0 (Qiagen)
Supplementary files format and content: Trimmed paired sequences .csv format

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
RNA was extracted via the RNeasy mini kit (Qiagen) as per manufacturer’s instructions for cells
The Illumina DRAGEN BCL Convert pipeline (07.021.645.4.0.3) was used to produce sequence data

tag: Sex

value: Female

tag: age

value: Peripheral Blood Mononuclear Cells

value: 1 Week Post Treatment (FUP1)

tag: disease

value: Post Traumatic Stress Disorder

value: Ketamine

tag: response -_pcl-5

value: Long Term Responder  (>4 weeks post treatment)


title: P56-BAS, F, LTR

description:
Library name: P56-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Baseline


title: RNA-seq of Monopterus albus: intersex6

description: Library name: OT_III2


title: P56-FUP2, F, LTR

description:
Library name: P56-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 4 Weeks Post Treatment (FUP2)


title: PBS liver, A100, D0 rep3

description: Library name: sample 6

value: foreskin fibroblasts

value: induced pluripotent stem cells

value: 3D - dynamic

value: 100ug activin A

value: 0 days


title: W_1.3_rep2

description: Library name: sample.wm115_c14_2

value: Skin


title: RNA-seq of Monopterus albus: intersex4

description: Library name: OT_II2

value: Intersex Gonad


title: RNA-seq of Monopterus albus: intersex3

description: Library name: OT_II1


title: P53-FUP1, F, LTR

description:
Library name: P53-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: W_1.2_rep1

description: Library name: sample.wm115_c11_1

value: Melanoma Cells


title: W_1.3_rep3

description: Library name: sample.wm115_c14_3


title: RNA-seq of Monopterus albus: intersex2

description: Library name: OT_I2


title: P52-FUP2, M, LTR

description:
Library name: P52-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Male


title: MGG123_Mouse3_BloodVessel PDX

description: Library name: MGG123_Mouse3_BloodVessel

value: Brain

value: Glioblastoma

value: malignant


title: P52-FUP1, M, LTR

description:
Library name: P52-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Peripheral Blood Mononuclear Cells

value: 1 Week Post Treatment (FUP1)

value: Post Traumatic Stress Disorder


title: P53-BAS, F, LTR

description:
Library name: P53-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Female

value: Baseline

value: Ketamine

value: Long Term Responder  (>4 weeks post treatment)


title: P52-BAS, M, LTR

description:
Library name: P52-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: RNA-seq of Monopterus albus: female7

description: Library name: O_V3

source_name: Ovary

value: Ovary


title: A_WT_rep1

description: Library name: sample.a375_wt_1

value: WT


title: RNA-seq of Monopterus albus: intersex1

description: Library name: OT_I1


title: A_WT_rep2

description: Library name: sample.a375_wt_2


title: KOXII5,IgG

city: wuhan

first: xue

last: lilan

state: 请选择...

address: shizishan

institute: huazhong agriculture university

data_processing:
Raw sequencing data were initially filtered using fastp (version 0.23.1) to remove low-quality reads and trim adaptor-contaminated sequences
Clean reads were mapped to the T. gondii reference genome (TGME49) using Bowtie2 (version 2.2.6) with default parameters
RSeQC (version 2.6) was used for read distribution analysis, and insert lengths were calculated using Picard’s Collect Insert Size Metrics tool (version 2.8.2).
DeepTools (version 2.4.1) was used to visualize read distribution upstream and downstream of transcription start sites (TSS).
MACS2 (version 2.2.7.1) was used for peak calling, and bedtools (version 2.30.0) for peak annotation and distribution analysis
Assembly: T. gondii reference genome (TGME49)
Supplementary files format and content: bw
Library strategy: CUT&Tag

organism: Toxoplasma gondii

source_name: ME49 deltaXII-5

growth_protocol: ME49 and ME49ΔXII-5  were cultured in human foreskin fibroblasts (HFF), in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma-Aldrich, USA), supplemented with 2% heat-inactivated fetal bovine serum (FBS) (Gibco, USA), 1% penicillin-streptomycin, and 5 mM L-glutamine.

extract_protocol:
Intracellular parasites were released by needle passage and purified through filtration with 3 μm pore-size membranes. Approximately 5 x 10⁶ tachyzoites were collected and processed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China), following the manufacturer’s instructions.
The resulting DNA was amplified for library construction using the TD202 TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China). The libraries were enriched, quantified, and sequenced on a NovaSeq 6000 sequencer (Illumina) using the PE150 model.

tag: strain

value: ME49 deltaXII-5

tag: chip antibody

value: rabbit anti IgG


title: P53-FUP2, F, LTR

description:
Library name: P53-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

tag: cell type

value: 4 Weeks Post Treatment (FUP2)


title: P51-FUP1, M, NR

description:
Library name: P51-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Non Responder


title: KOXII5,HDAC3,biol rep 3

value: rabbit anti-TgHDAC3(generated by immunizing rabbit with the synthetic peptide sequence 'CPYRIRRKDYANDFE' conjugated to KLH)


title: RNA-seq of Monopterus albus: female6

description: Library name: O_V2

tag: tissue


title: KOXII5,HDAC3,biol rep 2


title: RNA-seq of Monopterus albus: female5

description: Library name: O_V1


title: P50-FUP2, F, LTR

description:
Library name: P50-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: P51-BAS, M, NR

description:
Library name: P51-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Male


title: W_1.3_rep1

description: Library name: sample.wm115_c14_1

value: Skin

tag: cell line

value: Melanoma Cells

tag: genotype


title: A_WT_rep4

description: Library name: sample.a375_wt_4


title: RNA-seq of Monopterus albus: female4

description: Library name: O_IV3


title: A_1.1_rep2

description: Library name: sample.a375_3b3_2


title: A_1.1_rep1

description: Library name: sample.a375_3b3_1


title: P50-BAS, F, LTR

description:
Library name: P50-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Peripheral Blood Mononuclear Cells

tag: treatment


title: P49-FUP2, F, NR

description:
Library name: P49-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: RNA-seq of Monopterus albus: female3

description: Library name: O_IV2


title: A_1.1_rep3

description: Library name: sample.a375_3b3_3


title: ME49,IgG


title: P51-FUP2, M, NR

description:
Library name: P51-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: ME49,HDAC3,biol rep 3


title: P50-FUP1, F, LTR

description:
Library name: P50-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 1 Week Post Treatment (FUP1)


title: A_WT_rep3

description: Library name: sample.a375_wt_3


title: RNA-seq of Monopterus albus: female1

description: Library name: O_I1


title: ME49,HDAC3,biol rep 2


title: P49-BAS, F, NR

description:
Library name: P49-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Post Traumatic Stress Disorder


title: KOXII5,HDAC3,biol rep 1


title: ME49,HDAC3,biol rep 1


title: P46-FUP2, M, NR

description:
Library name: P46-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: ATAC-seq of Monopterus albus: female6

description:
Library name: VO_rep2
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing

data_processing:
Adapter sequences of ATAC-seq reads were trimmed by trim_galore. Trimmed reads were aligned to the M. albus genome by Bowtie2. Duplicate reads were filtered out by Picard MarkDuplicates (http://broadinstitute.github.io/picard/) and reads mapped to mitochondria were also removed. Filtered reads were shifted + 4 bp for positive strand and − 5 bp for negative strand, and shifted reads were applied to MACS2 for peak calling. Normalized tracks were generated by bamCoverage in deepTools with the parameters: --binSize 10 --normalizeUsing RPKM –extendReads. To identify DARs between different stages, ATAC peaks were processed with DiffBind. DARs were identified with a cutoff of FDR < 0.01.
Assembly: NCBI, M_albus_1.0
Supplementary files format and content: narrowPeak file includes peak for each sample

extract_protocol:
Isolation of intact nuclei using a hypotonic lysis buffer.Cells are gently lysed to release nuclei, which are then pelleted and washed. These purified nuclei are used directly in the tagmentation reaction.
Transposition of permeabilized nuclei using the Tn5 transposase, which simultaneously fragments DNA and adds adapter sequences.Isolated nuclei are incubated with the Tn5 transposase ("tagmentation"). The resulting DNA fragments are then purified and amplified by PCR with indexed primers to create the sequencing library.


title: A_1.2_rep2

description: Library name: sample.a375_2g1_2


title: P49-FUP1, F, NR

description:
Library name: P49-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Female


title: P46-FUP1, M, NR

description:
Library name: P46-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: A_4.1_rep1

description: Library name: sample.a375_1e3_1


title: ATAC-seq of Monopterus albus: female5

description:
Library name: VO_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P46-BAS, M, NR

description:
Library name: P46-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Baseline


title: RNA-seq of Monopterus albus: female2

description: Library name: O_IV1


title: ATAC-seq of Monopterus albus: female4

description:
Library name: PVO_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: A_1.2_rep1

description: Library name: sample.a375_2g1_1


title: P40-FUP2, F, STR

description:
Library name: P40-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Ketamine

value: Short Term Responder


title: A_1.2_rep3

description: Library name: sample.a375_2g1_3


title: P40-BAS, F, STR

description:
Library name: P40-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: ATAC-seq of Monopterus albus: male14

description:
Library name: MS_rep9
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing

value: Testis


title: A_4.1_rep3

description: Library name: sample.a375_1e3_3


title: A_4.1_rep4

description: Library name: sample.a375_1e3_4


title: ATAC-seq of Monopterus albus: female7

description:
Library name: VO_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing

value: Ovary


title: ATAC-seq of Monopterus albus: male12

description:
Library name: MS_rep7
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: A_4.2_rep1

description: Library name: sample.a375_1e12_1


title: P39-BAS, F, NR

description:
Library name: P39-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: A_1.2_rep4

description: Library name: sample.a375_2g1_4


title: ATAC-seq of Monopterus albus: male13

description:
Library name: MS_rep8
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: A_4.2_rep2

description: Library name: sample.a375_1e12_2


title: Ubi_OsVAL2_FLAG_1,rep1

city: Shanghai

first: Han

last: Lu

address: No.220 Handan Road Shanghai

institute: Fudan university

description: Library name: Ubi_OsVAL2_FLAG_1

data_processing:
The raw reads were trimmed with Trimmomatic v.0.39 with parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20 LEADING:20 TRAILING:20 MINLEN:50.
Clean reads were then aligned to the TAIR10 transcriptome using Hisat2 v2.2.1.
Expression levels were extracted for each gene using TPMCalculator v0.0.3 and featureCounts v2.0.6.
Assembly: Oryza_sativa.IRGSP-1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Oryza sativa

source_name: leaf

extract_protocol:
Around  5-6 leaves were pooled as one replicate. Total RNAs were extracted with the RNAprep Pure Plant Plus Kit Kit (TIANGEN) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TransNGS Fast RNA-Seq Library Prep Kit for Illumina  following the manufacturer’s instructions.

value: leaf

value: We collected rice leaves at the pre-heading stage.Besides this, there were no additional treatments.


title: Ubi_OsVAL2_FLAG_3,rep3

description: Library name: Ubi_OsVAL2_FLAG_3


title: A_4.1_rep2

description: Library name: sample.a375_1e3_2


title: A_4.2_rep3

description: Library name: sample.a375_1e12_3


title: P37-FUP1, F, LTR

description:
Library name: P37-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Long Term Responder  (>4 weeks post treatment)


title: P37-FUP2, F, LTR

description:
Library name: P37-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 4 Weeks Post Treatment (FUP2)


title: ATAC-seq of Monopterus albus: male9

description:
Library name: MS_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: ATAC-seq of Monopterus albus: male10

description:
Library name: MS_rep5
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P37-BAS, F, LTR

description:
Library name: P37-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: CR_osval2_2,rep2

description: Library name: CR_osval2_2


title: Ubi_OsVAL2_FLAG_2,rep2

description: Library name: Ubi_OsVAL2_FLAG_2


title: ATAC-seq of Monopterus albus: female3

description:
Library name: MO_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: CR_osval2_1,rep1

description: Library name: CR_osval2_1


title: ATAC-seq of Monopterus albus: male8

description:
Library name: MS_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P39-FUP2, F, NR

description:
Library name: P39-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Non Responder


title: P36-FUP2, F, NR

description:
Library name: P36-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: P36-FUP1, F, NR

description:
Library name: P36-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: RA_R

city: Taichung

first: Chih-Hsin

address: 91 Xueshi

country: Taiwan

institute: China Medical University

data_processing:
Bcl2fastq (v2.20.0.422) was used to processed the original image data for base calling and preliminary quality analysis.Trimmomatic (v0.30) was used to process the raw data (Pass Filter Data )to obtain the clean data for subsequent data analysis.
The clean reads were aligned to the Rfam database (similarity <90%) using blastn. The best query-reference match was used as alignment result.
The microRNA differential analysis was performed using the Bioconductor package DESeq2 (V1.26.0).The results from DESeq2 analysis was further analyzed to determine genes with significant differential expression according to the criteria of fold change greater than 2 and pvalue less than 0.05.
GOSeq (v1.34.1) provides information on how the differentially expressed genes are related to certain biological functions.Threshold for filtering here is: over_represented_pvalue <= 0.05.
Assembly: miRbase (V22)
Supplementary files format and content: excel file include raw reads for each sample

source_name: synovium

growth_protocol: Synovial fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA extraction was delegated to AZENTA Life Sciences. 2ug of total RNA was used for the construction of sequencing library.
1μg total RNA or 10ng small RNA was used for library preparation. 3 ́SR Adaptor for Illumina was ligated to the small RNA using 3 ́Ligation Enzyme. To prevent adaptor-dimer, the excess of 3 ́SR Adaptor were hybrid with SR RT Primer for Illumina. 5 ́SR Adaptor for Illumina was ligated to the small RNA using 5 ́Ligation Enzyme and first strand cDNA was synthesized using ProtoScript II Reverse Transcriptase. Each sample was then amplified by PCR using P5 and P7 primers, the PCR product were purified by DNA clean beads. The purified products of 140- 160bp were recovered and cleaned up using PAGE, validated using an Agilent 2100 Bioanalyzer. Then libraries with different indexes were multiplexed. The qualified libraries were sequenced pair end PE150 on the illumina Novaseq System.

treatment_protocol: Synovial fibroblasts treated with RANKL (50ng/ml) in serum free DMEM for 24h

value: synovium

value: primary cell

value: synovial fibroblast

value: RANKL


title: Ubi_OsDOF3_FLAG_2,rep2

description: Library name: Ubi_OsDOF3_FLAG_2


title: Ubi_OsDOF3_FLAG_3,rep3

description: Library name: Ubi_OsDOF3_FLAG_3


title: ATAC-seq of Monopterus albus: male11

description:
Library name: MS_rep6
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P36-BAS, F, NR

description:
Library name: P36-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Peripheral Blood Mononuclear Cells


title: RA_Ctrl


title: Ubi_OsDOF3_FLAG_1,rep1

description: Library name: Ubi_OsDOF3_FLAG_1


title: OA_R


title: ATAC-seq of Monopterus albus: female1

description:
Library name: MO_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: ATAC-seq of Monopterus albus: female2

description:
Library name: MO_rep2
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P35-FUP2, M, LTR

description:
Library name: P35-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Male

value: Post Traumatic Stress Disorder


title: ATAC-seq of Monopterus albus: male7

description:
Library name: LS_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: CR_osval2_3,rep3

description: Library name: CR_osval2_3


title: TP309_3,rep3

description: Library name: TP309_3


title: OA_Ctrl


title: P35-FUP1, M, LTR

description:
Library name: P35-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 1 Week Post Treatment (FUP1)


title: ATAC-seq of Monopterus albus: male6

description:
Library name: LS_rep2
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P35-BAS, M, LTR

description:
Library name: P35-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Baseline

value: Ketamine


title: TP309_2,rep2

description: Library name: TP309_2


title: ATAC-seq of Monopterus albus: male5

description:
Library name: LS_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing

value: Testis


title: ATAC-seq of Monopterus albus: intersex9

description:
Library name: ISM_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing

value: Intersex Gonad


title: P31-FUP2, F, LTR

description:
Library name: P31-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Female


title: osmail1-1 21SDs 3

city: MILANO

first: Vittoria

middle: Francesca

last: Brambilla

state: MI

address: via Celoria 2

department: Department of Agricultural and Environmental Sciences

institute: Università degli Studi di Milano

data_processing:
Quality check (FastQC)
Trimming (Trimmomatic 0.39)
Mapping to ref genome (STAR)
Reads counting (HTseq)
Differential expression analysis (DESeq2)
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: Reads count in .txt format

source_name: young panicle

growth_protocol: Plants were subjected to 6 weeks of long days followed by 15/21 short days

extract_protocol:
Qiagen RNAeasy kit
non-stranded cDNA

value: young panicle

value: 21 short days


title: TP309_1,rep1

description: Library name: TP309_1

value: leaf

value: We collected rice leaves at the pre-heading stage.Besides this, there were no additional treatments.


title: P31-BAS, F, LTR

description:
Library name: P31-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Long Term Responder  (>4 weeks post treatment)


title: osmail1-1 21SDs 2


title: osmail1-1 21SDs 1


title: P30-BAS, M, LTR

description:
Library name: P30-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: osmail1-1 15SDs 3

source_name: inflorescence meristem

value: inflorescence meristem

value: 15 short days


title: P29-FUP2, M, NR

description:
Library name: P29-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 4 Weeks Post Treatment (FUP2)

value: Non Responder


title: ATAC-seq of Monopterus albus: intersex6

description:
Library name: ISL_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: ATAC-seq of Monopterus albus: intersex5

description:
Library name: ISL_rep2
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: osmail1-1 15SDs 2


title: ATAC-seq of Monopterus albus: intersex4

description:
Library name: ISL_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: ATAC-seq of Monopterus albus: intersex7

description:
Library name: ISM_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: osmail1-1 15SDs 1


title: P29-FUP1, M, NR

description:
Library name: P29-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Male

value: Peripheral Blood Mononuclear Cells


title: wt 21SDs 3

value: wild type


title: ATAC-seq of Monopterus albus: intersex3

description:
Library name: ISE_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P28-FUP1, M, STR

description:
Library name: P28-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 1 Week Post Treatment (FUP1)

value: Post Traumatic Stress Disorder

value: Short Term Responder


title: ATAC-seq of Monopterus albus: intersex2

description:
Library name: ISE_rep2
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing

value: Intersex Gonad


title: P29-BAS, M, NR

description:
Library name: P29-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Baseline

value: Ketamine


title: P27-FUP2, F, STR

description:
Library name: P27-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Female


title: wt 21SDs 2

value: young panicle

value: 21 short days


title: ATAC-seq of Monopterus albus: male4

description:
Library name: ES_rep5
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing

value: Testis


title: P31-FUP1, F, LTR

description:
Library name: P31-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Long Term Responder  (>4 weeks post treatment)


title: P28-BAS, M, STR

description:
Library name: P28-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: wt 15SDs 3

value: inflorescence meristem

value: 15 short days


title: wt 21SDs 1


title: ATAC-seq of Monopterus albus: intersex1

description:
Library name: ISE_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: ATAC-seq of Monopterus albus: intersex8

description:
Library name: ISM_rep2
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: wt 15SDs 2


title: P21-FUP2, F, NR

description:
Library name: P21-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 4 Weeks Post Treatment (FUP2)

value: Non Responder


title: wt 15SDs 1


title: P27-FUP1, F, STR

description:
Library name: P27-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Peripheral Blood Mononuclear Cells


title: ATAC-seq of Monopterus albus: male3

description:
Library name: ES_rep4
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P21-FUP1, F, NR

description:
Library name: P21-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: C7

city: Nanjing

first: Yixin

last: Zhong

state: Jiangsu

address: Zhongda Hospital, Southeast University, Nanjing, China.

department: Center of Interventional Radiology and Vascular Surgery

institute: Zhongda Hospital, Southeast University

description:
Library name: Sample 8
Perivascular saline (0.9%, 5 min) filter paper induction.

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mRatBN7.2
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Abdominal aorta

extract_protocol:
mirVana™ miRNA Isolation Kit (Ambion-1561)
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: Abdominal aorta

value: WT

value: Saline

tag: batch


title: ATAC-seq of Monopterus albus: male2

description:
Library name: ES_rep3
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: P21-BAS, F, NR

description:
Library name: P21-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Post Traumatic Stress Disorder


title: ATAC-seq of Monopterus albus: male1

description:
Library name: ES_rep1
ATAC-seq was performed using transposase (Tn5) to tagment accessible chromatin regions, followed by PCR amplification and sequencing


title: C4

description:
Library name: Sample 7
Perivascular saline (0.9%, 5 min) filter paper induction.


title: P19-FUP1, M, STR

description:
Library name: P19-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Male

value: 1 Week Post Treatment (FUP1)

value: Short Term Responder


title: Testis,IGF2BP3,eCLIP,rep1

city: Guangzhou

first: Zhenyi

last: Huang

state: GuangDong

address: ShaTaiNan Street 1023-1063,Baiyun

department: Development

institute: Southern Medical University

description: IP

data_processing:
eCLIP pipeline developed by Gene Yeo's lab was used to identify the peaks. The full protocol is available here: https://github.com/YeoLab/eclip
Reads were trimmed and adapters were removed using Cutadapt: Quality cutoff 6, Minimum length 18.
Reads were mapped to rRNA using Bowtie2. Mapped reads were removed.
Reads were mapped to mm10 genome using STAR.. --alignEndsType EndToEnd
PCR duplicates were removed using a custom script (https://github.com/YeoLab/eCLIP/blob/master/bin/barcodecollapsepe.py).
Peaks were called for each treatment using clipper, which is available at: https://github.com/YeoLab/clipper.
Assembly: mm10
Supplementary files format and content: The processed data file contains the peaks identified by eCLIP-Seq pipeline and the gene annotations
Library strategy: eCLIP-seq

growth_protocol: 8-week-old male mice were housed in a light and temperature-controlled room (light: 12 h dark and 12 h light cycles; temperature: 24 ± 0.5 °C) with ad libitum access to food and water.

extract_protocol:
Testes were homogenized in ice-cold lysis buffer.Total RNAs were fragmented by RNase A to achieve the Input sample (2% of the lysate) was retained, and the protein-RNA complexes were immunoprecipitated with the IGF2BP3 antibody to obtain the IP samples, followed by thoroughly washing.
Library amplification was conducted using Q5 PCR master mix.Library visualization by TBE-Urea gel and post amplification libraries were size selected at 275-450bp in length.

treatment_protocol: Two testes from adult C57BL/6J mice were gently triturated using a loose glass pestle to ensure mild mechanical digestion. The testis suspension was crosslinked three times with 400 mJ/cm2 UV at 254 nm on ice.

value: Germ cells and somatic cells

value: 8 weeks old

value: wild type

tag: eclip antibody

value: IGF2BP3(Abcam, #ab177942)


title: C3

description:
Library name: Sample 6
Perivascular saline (0.9%, 5 min) filter paper induction.


title: Testis,IGF2BP3,eCLIP,rep2

description: IP

value: Testis


title: Testis,input,rep2

description: input


title: P19-BAS, M, STR

description:
Library name: P19-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

tag: time

value: Baseline

value: Ketamine


title: C2

description:
Library name: Sample 5
Perivascular saline (0.9%, 5 min) filter paper induction.


title: P18-FUP1, M, LTR

description:
Library name: P18-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Long Term Responder  (>4 weeks post treatment)


title: A9

description:
Library name: Sample 4
Perivascular FeCl₃ (10%, 5 min) filter paper induction.

value: Iron chloride


title: P15-FUP2, F, LTR

description:
Library name: P15-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Female

value: Peripheral Blood Mononuclear Cells

value: 4 Weeks Post Treatment (FUP2)


title: replace feeders with integrin α5β1 inhibitor ATN161 in culturing ESCs,rep3

city: 沈阳市

first: Zonghua

last: Ma

state: 辽宁省

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

institute: Northeastern University

description: Library name: ATNm3

data_processing:
The reads were mapped to Ensembl mouse (mm10/GRCm38) reference genomes by HISAT2 software (version 2.1.0). Binary Alignment Map (BAM) files were generated by SAMtools (version 1.4). Fragments per kilobase of exon model per million mapped fragments (FPKM) values of genes were calculated by StringTie (version 1.3.3b). DESeq2 (version 1.2.10) was used for differential gene expression analysis.
Assembly: Ensembl mouse (mm10/GRCm38) reference genomes

source_name: Embryonic stem cells

extract_protocol:
Total cellular RNA was isolated using Trizol reagent
Library construction was carried out using the Illumina TruSeq mRNA Library Construction Kit.

value: Embryonic stem cells


title: A7

description:
Library name: Sample 3
Perivascular FeCl₃ (10%, 5 min) filter paper induction.

value: Abdominal aorta

value: WT


title: Testis,input,rep1

description: input


title: P18-BAS, M, LTR

description:
Library name: P18-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Male

value: Post Traumatic Stress Disorder


title: P15-FUP1, F, LTR

description:
Library name: P15-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: 1 Week Post Treatment (FUP1)


title: replace feeders with integrin α5β1 inhibitor ATN161 in culturing ESCs,rep2

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: ATNm2


title: A5

description:
Library name: Sample 2
Perivascular FeCl₃ (10%, 5 min) filter paper induction.


title: A1

description:
Library name: Sample 1
Perivascular FeCl₃ (10%, 5 min) filter paper induction.


title: ES cells cultured on control feeders but removal of feeders, rep3

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DeCFm3


title: Single nuclei, Acute Day 3 post injection of iECM,  biol rep 3 and 4

city: La Jolla

first: Karen

last: Christman

state: California

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

description:
Library name: iECM2
Nuclei
iECM2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger Cell Ranger software v7.1.0 (10X v3.1 HT kit), or Space Ranger v1.3.1
Further processing was done with Seurat v4.1(cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using FindVariableFeatures from Seurat R package version 4.1
Assembly: Rnor-6.0-premrna
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Cardiac

extract_protocol:
Nuclei from cardiac tissue was isolated as mentioned previously. In brief, flash frozen LV free wall samples were resuspended in nuclei lysis buffer (Millipore Sigma, Nuclei EZ prep, NUC101), 0.2 U/L RNase inhibitor (Enzymatic Y9240L) and finely chopped with scissors. Samples were homogenized with a 2 mL dounce grinder (KIMBLE) with the lysates filtered through a 100 µm, 50 µm, 20 µm strainers (CellTrics filters), respectively. The samples were centrifuged at 1000g for 5 min at 4C to pellet nuclei. The nuclear pellet was resuspended in a sucrose gradient buffer  and centrifuged at 1000g at 4ºC for 10 minutes. The pellet was then washed with a nuclei storage buffer containing 10 μg ml−1 4′,6-diamidino-2-phenylindole DAPI and centrifuged at 500 g and 4ºC for 5 minutes, with the pellet resuspending in 200 mL of 2% BSA in 1x PBS. Nuclei were then counted on a hemocytometer and volume adjusted to 1000 nuclei/µL for loading. snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics (Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 7.1.0 or Space Ranger v1.3.1 from 10X Genomics.
snRNA-seq was performed with a microfluidic droplet-based technique provided by 10X Genomics (Chromium Next GEM Single Cell 3’ HT v3.1). Quality control for cDNA and libraries were performed on Aligent TapeStation, and library concentrations were determined via Qubit HS DNA kit. Paired-end sequencing was run on a NovaSeq6000 or NovaSeq X Plus instrument. Demultiplexing of sequenced samples were mapped to a rat reference genome (Rnor6.0, including introns). Redundant unique molecular identifiers (UMIs) were eliminated via the Cell Ranger 7.1.0 pipeline or Space ranger v1.3.1 from 10X Genomics.

value: Cardiac

value: intracoronary infusion of iECM


title: P13-FUP2, F, LTR

description:
Library name: P13-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: Single nuclei, Acute Day 3 post injection of iECM,  biol rep 1 and 2

description:
Library name: iECM1
Nuclei
iECM1


title: P13-FUP1, F, LTR

description:
Library name: P13-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: ES cells cultured on control feeders but removal of feeders, rep1

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DeCFm1


title: p53-defective feeders, rep3

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DF3

source_name: Embryonic fibroblasts

value: Embryonic fibroblasts


title: ES cells cultured on control feeders but removal of feeders, rep2

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DeCFm2


title: Single nuclei,Acute Day 3 post injection of saline,  biol rep 3 and 4

description:
Library name: Sal2
Nuclei
Sal2

value: intracoronary infusion of saline


title: P11-FUP2, F, NR

description:
Library name: P11-FUP2
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Non Responder


title: Control feeders, rep3

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: CF3


title: Single nuclei, Acute Day 3 post injection of saline,  biol rep 1 and 2

description:
Library name: Sal1
Nuclei
Sal1


title: Visium, Acute Day 7 post injection of iECM,  biol rep 2

description:
Library name: 7_2_4
7_2_4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger Cell Ranger software v7.1.0 (10X v3.1 HT kit), or Space Ranger v1.3.1
Further processing was done with Seurat v4.1(cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using FindVariableFeatures from Seurat R package version 4.1
Assembly: Rnor-6.0-premrna
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics


title: p53-defective feeders, rep2

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DF2


title: replace feeders with integrin α5β1 inhibitor ATN161 in culturing ESCs,rep1

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: ATNm1


title: Control feeders, rep1

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: CF1


title: Control feeders, rep2

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: CF2


title: Visium, Acute Day 7 post injection of iECM,  biol rep 1

description:
Library name: 7_2_3
7_2_3


title: Visium, Acute Day 7 post injection of saline,  biol rep 2

description:
Library name: 7_2_2
7_2_2


title: scw2

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: Library name: scw2

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, v.20 101 214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: The seven-day-old whole seedlings (ca 50 seedlings) grown on vertical plates (23oC, 16/8 light/dark) were used as a source of RNA, always as three replicates for each mutant line and WT.

extract_protocol:
RNeasy Plant MiniKit (Qiagen)
performed by Eurofins Genomics

treatment_protocol: No treatment was applied for exo70B1, exo70B2 and double mutant exo70B1xBexo70B2, and their corresponding control WT; one set was treated with chitosan (0.001%) by spraying for 24 h.

value: whole seedlings

value: chitosan


title: swt2

description: Library name: swt2


title: swt3

description: Library name: swt3


title: Visium, Acute Day 7 post injection of saline,  biol rep 1

description:
Library name: 7_2_1
7_2_1


title: scw3

description: Library name: scw3


title: P15-BAS, F, LTR

description:
Library name: P15-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Baseline

value: Ketamine

value: Long Term Responder  (>4 weeks post treatment)


title: ES cells cultured on p53-defective feeders, rep3

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DFm3

source_name: Embryonic stem cells and embryonic fibroblasts


title: swt1

description: Library name: swt1


title: P13-BAS, F, LTR

description:
Library name: P13-BAS
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench

value: Female

value: Peripheral Blood Mononuclear Cells


title: scw1

description: Library name: scw1


title: Visium, Acute Day 3 post injection of iECM,  biol rep 2

description:
Library name: 5_2
5_2


title: sbb2

description: Library name: sbb2


title: ES cells cultured on control feeders, rep3

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: CFm3

value: Embryonic stem cells and embryonic fibroblasts


title: Visium, Acute Day 3 post injection of iECM,  biol rep 1

description:
Library name: iECM7
iECM7


title: P11-FUP1, F, NR

description:
Library name: P11-FUP1
Gene Expression Data QC'd, trimmed and paired through CLC Genome Workbench


title: ES cells cultured on p53-defective feeders, rep1

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DFm1


title: p53-defective feeders, rep1

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DF1


title: sbb1

description: Library name: sbb1


title: sbb3

description: Library name: sbb3


title: sb23

description: Library name: sb23


title: Visium, Acute Day 3 post injection of saline,  biol rep 1

description:
Library name: iECM6
iECM6


title: ES cells cultured on control feeders, rep1

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: CFm1


title: Visium, Acute Day 1 post injection of iECM,  biol rep 2

description:
Library name: 8_4
8_4


title: ES cells cultured on control feeders, rep2

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: CFm2


title: sb22

description: Library name: sb22


title: 5-AZA+DSS 3

city: London

first: Samuel

last: Asfaha

address: 1151 Richmond St

country: Canada

institute: Univeristy of Western Ontario

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: Preprocessing of IDAT files was done using the R package SeSaMe and included calculation of detection p values (probes with a detection p value of <0.05 were retained), background subtraction, strain interference, and dye bias correction.

source_name: Colon

extract_protocol: DNA was extracted from isolated colonic epithelial cells using the Invitrogen DNA isolation kit according to manufacturer's instructions.

treatment_protocol: C57Bl6/J mice were treated with one dose 5 mg/kg 5-AZA-2'-deoxycytidine or vehicle (saline) 2 days prior to 2.5% DSS treatment for 5 days. 5 and 10 days post the end of DSS mice recevied additional doses of 5mg/kg 5-AZA or vehicle. 14 days post the end of DSS, colonic epithelial cells were isolated for analysis.

value: Colon

value: Colonic epithelial cells


title: Visium, Acute Day 1 post injection of iECM,  biol rep 1

description:
Library name: 8_3
8_3


title: 5-AZA+DSS 2


title: sb21

description: Library name: sb21


title: Single nuclei, Acute Day 7 post injection of iECM,  biol rep 3 and 4

description:
Library name: D7i2
Nuclei
D7i2


title: ES cells cultured on p53-defective feeders, rep2

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: DFm2


title: Visium, Acute Day 1 post injection of saline,  biol rep 2

description:
Library name: 8_2
8_2


title: sb11

description: Library name: sb11


title: Single nuclei, Acute Day 7 post injection of iECM,  biol rep 1 and 2

description:
Library name: D7i1
Nuclei
D7i1


title: 5-AZA+DSS 1


title: sb12

description: Library name: sb12


title: 5-AZA 2

value: Male


title: 5-AZA 3


title: sb13

description: Library name: sb13


title: 5-AZA 1


title: Visium, Acute Day 1 post injection of saline,  biol rep 1

description:
Library name: 8_1
8_1


title: W_4

description: Library name: W_4

source_name: leaf tissue

growth_protocol: A. thaliana plants were grown for 5-6 weeks  in jiffy pellets, 21 oC, 10/14 light/dark

treatment_protocol: Rosettes were sprayed and left for 24 h with elicitor chitosan (0.001% with 0.005% Silwett), or with mock (0.005% Silwett).

value: leaf tissue

value: whole leaf tissues and cells

value: WT

value: mock


title: W_3

description: Library name: W_3


title: DSS 3

value: Saline+2.5% DSS


title: Single nuclei,Acute Day 7 post injection of saline,  biol rep 3 and 4

description:
Library name: D7S2
Nuclei
D7S2

value: Cardiac

value: intracoronary infusion of saline


title: W_1

description: Library name: W_1


title: DSS 2


title: Single nuclei, Acute Day 7 post injection of saline,  biol rep 1 and 2

description:
Library name: D7S1
Nuclei
D7S1


title: DSS 1


title: CW_19a

description: Library name: CW_19a

value: chitosan


title: CW_20

description: Library name: CW_20


title: Single nuclei, Acute Day 1 post injection of iECM,  biol rep 1 and 2

description:
Library name: 1Fi1
Nuclei
1Fi1

value: intracoronary infusion of iECM


title: Visium, Acute Day 3 post injection of saline,  biol rep 2

description:
Library name: 5_1
5_1


title: CW_18a

description: Library name: CW_18a


title: Single nuclei, Acute Day 1 post injection of saline,  biol rep 1 and 2

description:
Library name: 1FS1
Nuclei
1FS1