title: Ectoderm Half-life 1h Repeat 1

description:
hPSCs differnetiated to ectoderm and treated with actinomycin D
half_life_ectoderm_0_1_8.count.tsv.gz
half_life_ectoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_ectoderm_1h.rp1


title: Ectoderm Half-life 0h Repeat 2

status: Public on Jul 30 2025

type: SRA

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

description:
hPSCs differnetiated to ectoderm and treated with actinomycin D
half_life_ectoderm_0_1_8.count.tsv.gz
half_life_ectoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_ectoderm_0h.rp2

library_source: transcriptomic

data_processing:
RSEM and STAR was used to align reads to the custon long-read transcripts assembled from the long-read RNA-seq data
Assembly: hg38
Supplementary files format and content: TSV files containing transcript counts or TPMs are provided. Each TSV is assmebled against the cell type-specific GTF, or against the combined_assembly of all transcripts in all four cell types. Where a transcript matches a known GENCODE transcript it will have an ENST, ENSG and SYMBOL accession. Where a transcript has any matching exon nucleotide, it will be annotated with the matching ENSG and SYMBOL. Where a transcript has no match to GENCODE it will not have ant accession number. Each table contains 0, 1 and 8 hour treated cells with Actinomycin D

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: H1 human pluripotent stem cell lines were maintained on a Matrigel treatment plate, cultured in mTeSR1 (STEMCELL TECHNOLOGIES, 85850) medium and digested with Accutase (Sigma, A6964) every 5-7 days. In vitro germ layers were generated by changing the medium and adding inhibitors or cytokines when human PSC reached 60-70% confluency as previously reported1. For endoderm differentiation, cells were cultured in RPMI supplemented with 2X GlutaMax (Thermo Fisher, 35050061), 0.2x MEM Non-Essential Amino Acids Solution (Thermo Fisher,11140050), 55 µM b-mercaptoethanol (BBI, A600194), 0.5% FBS (BIOWEST, S1580), 50nM/ml WNT3A (MedChemExpress, HY-P70453A), and 100ng/ml Activin A (PEPROTECH, 120-14E-100). For mesoderm differentiation, at the first 24 hour, Activin A was introduced to the culture medium. The cells were cultured in DMEM/F12 supplemented with 2X GlutaMax, 0.2X MEM Non-Essential Amino Acids Solution, 55µM b-mercaptoethanol, 0.5% FBS, 100ng/ml VEGF (PEPROTECH,100-20-50), 100ng/ml BMP4 (PEPROTECH, 120-05ET), 10 ng/ml bFGF (PEPROTECH, 100-18B-100), and 100ng/ml Activin A. Then Activin A was removed from the culture. For ectoderm differentiation from the PSC, the cells were cultured in DMEM/F12 supplemented with 0.2X MEM Non-Essential Amino Acids Solution, and 55 µM b-mercaptoethanol 15% KOSR (Life Technologies) 2µM A83-01(Tocris, 2939), 2µM PNU-74654(Tocris, 113906), and 2uM Dorsomorphin (Tocris, 3093). Media was changed daily and the cells were collected after 5 days

extract_protocol:
RNA was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocol. Samples for short-read RNA-Seq was prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530). Short-read RNA sequencing was performed on Illumina Novaseq 6000 platform.
Samples for short-read RNA-Seq was prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530).

treatment_protocol: Human PSC and differentiated three germ cells were cultured in 6-well plates. Then Actinomycin B was added to inhibit the synthesis of new RNA. RNA was extracted at 0, 1, and 8 hours after the addition of Actinomycin B. Short-read sequencing was then done for RNA extracted at the time points after transcription stoppage. For each time point, short-read transcript quantification was first done using RSEM and STAR as highlighted above. Relative stability was then computed using the average expression of each transcript as the specified time, relative to the expression at time 0 hour after actinomycin treatment. For transcript x with the average TPM expressions x0 at time 0hr and xT at time T hour, relative stability is given as;    Relative stability=(log2(xT+0.01))/(log2(x0+0.01))

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: Ectoderm


title: Treg, LAYN_flox, Foxp3CreERT2;Laynfl/fl, K02

city: San Francisco

first: Victoire

last: Gouirand

state: CALIFORNIA

address: 513 Parnassus av

department: Dermatology

country: USA

institute: UCSF

data_processing:
Read alignment done with kallisto (v. 0.46.2) using Ensembl reference genome GRCm39 (110)
Assembly: GRCm39
Supplementary files format and content: Abundance tsv files for individual samples

molecule: polyA RNA

organism: Mus musculus

source_name: Skin

extract_protocol:
Treg cells were isolated respectively by gating on live CD45+CD3+CD4+CD8-CD25hiCD62LhiGFP+  cells. Cells were sorted into lysis buffer from the kit and frozen on dry ice before being processed using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) according to the manufacture’s protocol.
100pg of amplified cDNA obtained was used to generate a library using Nextera XT DNA prep-aration kit (Illumina).

value: Skin

value: Treg

tag: genotype

tag: treatment

value: Imiquimod


title: WAT_RD_2WK_M_8

city: Barcelona

first: Vicent

last: Ribas

state: Choose a State or Province

address: Rosselló 149, 5th floor, Centre Esther Koplowitz

department: Pathogenesis and prevention of diabetes

country: Spain

institute: IDIBAPS

data_processing:
Reads quality control performed using Fast!C software
Raw reads were then mapped to the reference genome (Mus_musculus_GRCm38) using the pseudo-aligner Kallisto.
Transcript counts were imported to R statistical software using the Tximport package, where data was filtered and normalized with EdgeR, and differentially expressed genes were obtained through the Deseq2 package.
Assembly: Mus_musculus_GRCm38
Supplementary files format and content: Raw counts in a tab-delimited text spreadheet, genes in rows and samples in columns.

source_name: White adipose tissue (visceral)

growth_protocol: Animals were fed from 8 weeks of age, either with regular chow or High-fat diet.

extract_protocol:
Tissues were homogenized in trizol, and purified by Rneasy columns. RNA was initially quantified with Nanodrop, and
Messenger RNA strand-specific RNA libraries were created from 200 ng of total RNA using the Illumina® Stranded mRNA Prep Ligation

treatment_protocol: Animals were fed at libitum with diets for 2 weeks or 12 weeks

value: White adipose tissue (visceral)

tag: diet

value: RD

tag: time on_diet

tag: Sex

value: M

tag: group number


title: WRC21, leaf, control, Day 5, rep 1

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

description: Library name: C33

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

organism: Oryza sativa

source_name: leaf

growth_protocol: Rice seeds were surface sterilized with 375 ppm of pefurazoate at 15°C for 24 h. Then the seeds were soaked in water to germinate in a dark place at 30°C for two days. The calcined clay (Profile Greens Grade, PROFILE Products LLC, http://www.profileevs.com) was used as the soil. The soil was washed with water before use, then dried, filled in the pots (24.5 cm upper outer diameter, 20 cm lower outer diameter, 30 cm height; SP2530P, Tecs Inc., http://www.tecs.ne.jp) up to a depth of 25cm, and irrigated with modified Kimura B (Yoshida et al., 1976) culture solution (273.2 µM K2SO4, 546.9 µM MgSO4.7H2O, 182.0 µM NaH2PO4.2H2O, 182.3 µM CaCl2.2H2O, 182.4 µM CaSO4.2H2O, 1.2 mM KNO3, 411.2 µM NH4Cl, and 4 mg L-1 FeC6H5O7.nH2O [pH 5.5]). The germinated seeds were individually planted in separate pots, and they were cultivated in a growth chamber (Nippon Medical & Chemical Instruments Co., http://www.nihonika.co.jp) under a 14 h light/ 10 h dark photoperiod, with 50% relative humidity (R.H.) at daytime and 60% R.H. at nighttime. The temperature in the growth chamber was maintained at 25°C at nighttime and varied from 25°C to 30°C at daytime.  We used iPOTs (Numajiri et al. 2021), which is a pot that incorporates auto-irrigation system to mimic soil condition similar to the drought stress in the field. The water level in the supply pot, connected in parallel with the pots through a hose, was maintained at a height of 10 cm to ensure that the upper layers of the pots were moistened during the irrigation period.

extract_protocol:
The fully expanded latest leaves and second latest leaves were collected and frozen in liquid nitrogen. Samples were ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.

treatment_protocol: Plants at 14 days after sowing were subjected to severe drought treatment for 9 days, and then watered for 6 days. In the severe drought treatment, the height of the pots was elevated above the hose to promote faster drainage. In the control treatment, irrigation was maintained.

value: leaf

tag: cultivar

value: control

tag: days after_treatment

tag: replicate


title: WRC48, leaf, control, Day 5, rep 1

description: Library name: C32


title: WAT_RD_12WK_M_4


title: Ectoderm Half-life 0h Repeat 1

description:
hPSCs differnetiated to ectoderm and treated with actinomycin D
half_life_ectoderm_0_1_8.count.tsv.gz
half_life_ectoderm_0_1_8.tpm.tsv.gz
half_life_combined_assembly_0_1_8.count.tsv.gz
half_life_combined_assembly_0_1_8.tpm.tsv.gz
Hs_halflife_ectoderm_0h.rp1


title: WRC15, leaf, control, Day 5, rep 1

description: Library name: C37


title: Treg, LAYN_flox, Foxp3CreERT2;Laynfl/fl, K01


title: WRC42, leaf, control, Day 5, rep 1

description: Library name: C31


title: D10_CD36_PHF8_3

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

description: CUT&RUN

library_source: genomic

data_processing:
Bowtie2 alignment to Hg38 genome
Picard dupliate removal
bamCoverage RPKM normalization
Assembly: Hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: CD34 HSPC

growth_protocol: Human CD34 HSPCs were provided by the Yale Cooperative Center of Excellence in Hematology, and subjected to erythroid culture using semi synchronous CD36+ selection culture system, as previously described (Gautier). Early basophilic erythroblasts (Day 7) or orthochromatic erythroblasts (Day 10) were collected for CUT&Tag (approximately 100,000 cells per replicate)

extract_protocol:
CUT&RUN assays were performed using the Epicypher CUTANA CUT&RUN protocol v1.6.
Libraries were generated using the NEBNext Ultra II DNA Library Prep kit (NEB). PHF8, size selection was optimized for small fragments (end prep for 20C for 30 minutes followed by 50C for 60 minutes, ligation AMPure XP cleanup at 1.75X, annealing temperature of 65C for library amplification, and library AMPure XP cleanup using 1st round negative selection at 0.8X followed by a 2nd round positive selection at 1.2X). Libraries were sequenced with illumina HiSeq, paired end 150 bp length reads.

value: CD34 HSPC

value: Erythroblast

value: wt


title: WAT_RD_12WK_M_3


title: Thymocytes, CLP, Day1-biol rep 4

city: Shanghai

first: Zimei

last: Cheng

state: None Selected

address: 399 Wanyuan Rd, Minhang

institute: Children's Hospital, Fudan University

data_processing:
After sequencing, the data were analyzed using the BMKCloud platform (www.biocloud.net) for bioinformatics analysis. Raw sequencing data were filtered to obtain clean data, which were then aligned to the reference genome to generate mapped data. Subsequent analyses included quality assessment, structural analysis, differential expression analysis, functional annotation, and enrichment analysis of the mapped data.
Assembly: Mus_musculus.GRCm38 (release 95)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

source_name: Thymus

extract_protocol:
For thymocytes extraction, thymus tissues were homogenized. The homogenized tissue was passed through a 40 µm cell strainer to obtain a single-cell suspension, which was then filtered to separate thymocytes from remaining stromal cells. The resulting thymocyte suspension was used for further downstream analyses.
The mRNA was enriched using magnetic beads with Oligo (dT) and subsequently fragmented using Fragmentation Buffer. First and second strands of cDNA were synthesized from the fragmented mRNA, and the cDNA was then purified. The double-stranded cDNA underwent end repair, A-tailing, and adapter ligation, followed by size selection with AMPure XP beads. Finally, PCR amplification was performed to generate the cDNA library.

value: Thymus

value: thymocytes

value: WT

value: CLP


title: WRC35, leaf, control, Day 5, rep 1

description: Library name: C30


title: WAT_RD_12WK_M_2


title: D10_CD36_PHF8_2

description: CUT&RUN


title: D10_CD36_PHF8_1

description: CUT&RUN


title: WAT_HFD_12WK_M_4

value: HFD


title: Thymocytes, CLP, Day1-biol rep 2


title: D7_CD36_PHF8_3

description: CUT&RUN

value: Day7_Early basophilic


title: WAT_HFD_12WK_M_3


title: Thymocytes, Sham-biol rep 4

value: sham


title: Thymocytes, CLP, Day1-biol rep 1


title: WRC22, leaf, control, Day 5, rep 1

description: Library name: C28


title: WAT_RD_2WK_F_4

value: F


title: D7_CD36_PHF8_2

description: CUT&RUN


title: WAT_HFD_12WK_M_2


title: Thymocytes, Sham-biol rep 3


title: WRC37, leaf, control, Day 5, rep 1

description: Library name: C26


title: D7_CD36_PHF8_1

description: CUT&RUN


title: WRC09, leaf, control, Day 5, rep 1

description: Library name: C24


title: Thymocytes, Sham-biol rep 2


title: WAT_RD_2WK_F_2


title: WRC27, leaf, control, Day 5, rep 1

description: Library name: C25


title: D10_CD36_H4K20me3_2

description: CUT&RUN


title: WAT_RD_2WK_F_1


title: Thymocytes, CLP, Day1-biol rep 3


title: D10_CD36_H4K20me3_3

description: CUT&RUN


title: Thymocytes, Sham-biol rep 1


title: WRC47, leaf, control, Day 5, rep 1

description: Library name: C29


title: WAT_HFD_2WK_F_5


title: WRC50, leaf, control, Day 5, rep 1

description: Library name: C23


title: WRC46, leaf, control, Day 5, rep 1

description: Library name: C22


title: C3TAG_1820_met

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

description:
14_LM7
gene_list C3TAg.txt
gene_list C3TAg.txt

data_processing:
fastq files were uploaded to PartekFlow. Unaligned reads were filtered and aligned using STAR 2.7.8a alignment rool.
Gene and transcript counts were then normalized by Median Ratio and a batch removal was performed.
Gene specific analysis was performed in order to compare changes in gene expression between primary tumors and metastases using DESeq2
Assembly: mm39
Supplementary files format and content: tab delimited text files for each group of samples

source_name: Lung metastasis

growth_protocol: autochthonous tumors and matching metastases were harvested from animals when they reached humane endpoints

extract_protocol:
total RNA was isolated from tissues following the Trizol manufacturers recommended protocol
the libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: Lung metastasis


title: WRC18, leaf, control, Day 5, rep 1

description: Library name: C27


title: D7_CD36_H4K20me3_3

description: CUT&RUN


title: WAT_HFD_2WK_F_2

value: White adipose tissue (visceral)


title: D10_CD36_H4K20me3_1

description: CUT&RUN


title: WAT_RD_12WK_F_8

value: RD


title: C3TAG_1696_met

description:
13_LM6
gene_list C3TAg.txt
gene_list C3TAg.txt


title: D7_CD36_H4K20me3_2

description: CUT&RUN


title: D7_CD36_H4K20me3_1

description: CUT&RUN


title: WAT_HFD_2WK_F_1


title: WRC01, leaf, control, Day 5, rep 1

description: Library name: C19


title: IR64, leaf, control, Day 5, rep 1

description: Library name: C20


title: C3TAG_1503_met

description:
11_LM4
gene_list C3TAg.txt
gene_list C3TAg.txt


title: Huh7_ZL_03

city: stockholm

first: mengzhen

last: Li

address: Drottning Kristinas Väg 36A

country: Sweden

institute: KTH Royal Institute of Technology

data_processing:
The fastq files were first explored by FastQC (Babraham Institute, Cambridge, UK) for quality control. Gene expression count data was quantified using the standard protocol of kallisto (Bray et al. 2016). The reference cDNA for alignment and quantification was GRCh38.p13 (v108) for Homo sapiens, which was retrieved from the Ensembl website. After filtering only protein-coding genes and genes with an average count greater than 5, the kallisto data was used for the downstream analysis.
Assembly: GRCh38.p13 (v108)
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

source_name: liver

extract_protocol:
NA samples for RNA sequencing were extracted with RNeasy Plus Mini Kit (74134, QIAGEN).
Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit is used for the construction of NGS libraries from the samples with acceptable quality parameters.

value: liver

value: hepatocellular carcinoma cell line

value: Polyporus umbellatus  extracts


title: WAT_RD_12WK_F_7


title: C3TAG_1693_met

description:
12_LM5
gene_list C3TAg.txt
gene_list C3TAg.txt


title: WAT_RD_12WK_F_5


title: Huh7_ZL_02


title: WRC13, leaf, control, Day 5, rep 1

description: Library name: C18

value: leaf

value: control


title: C3TAG_1456_met

description:
10_LM3
gene_list C3TAg.txt
gene_list C3TAg.txt


title: WRC16, leaf, control, Day 5, rep 1

description: Library name: C17


title: C3TAG_123_met

description:
9_LM2
gene_list C3TAg.txt
gene_list C3TAg.txt


title: Huh7_ZL_01


title: WAT_HFD_12WK_F_7


title: Huh7_Control_03

value: Control


title: C3TAG_NT07217_met

description:
8_LM1
gene_list C3TAg.txt
gene_list C3TAg.txt


title: WRC06, leaf, control, Day 5, rep 1

description: Library name: C15


title: C3TAG_1820_primary

description:
7_PT7
gene_list C3TAg.txt
gene_list C3TAg.txt

source_name: Mammary tumor

value: Mammary tumor


title: WAT_HFD_12WK_F_3


title: WAT_HFD_12WK_F_6


title: C3TAG_1696_primary

description:
6_PT6
gene_list C3TAg.txt
gene_list C3TAg.txt


title: LV_RD_2WK_M_8

source_name: Liver

value: Liver

value: M


title: WRC05, leaf, control, Day 5, rep 1

description: Library name: C14


title: Huh7_Control_01

value: WT


title: WRC33, leaf, control, Day 5, rep 1

description: Library name: C13


title: Huh7_CH_03

value: Bupleurum chinense extracts


title: LV_RD_2WK_M_7


title: C3TAG_1693_primary

description:
5_PT5
gene_list C3TAg.txt
gene_list C3TAg.txt


title: KP, leaf, control, Day 5, rep 1

description: Library name: C12

value: KP


title: C3TAG_1503_primary

description:
4_PT4
gene_list C3TAg.txt
gene_list C3TAg.txt


title: LV_RD_2WK_M_6


title: Dro1-NIL, leaf, control, Day 5, rep 1

description: Library name: C16


title: Huh7_CH_02


title: C3TAG_123_primary

description:
2_PT2
gene_list C3TAg.txt
gene_list C3TAg.txt


title: LV_HFD_2WK_M_14

value: HFD


title: Huh7_BTW_03

value: Pulsatilla chinensis extracts


title: Huh7_Control_02


title: WRC34, leaf, control, Day 5, rep 1

description: Library name: C10


title: WRC32, leaf, control, Day 5, rep 1

description: Library name: C21


title: WRC51, leaf, control, Day 5, rep 1

description: Library name: C9


title: C3TAG_NT07217_primary

description:
1_PT1
gene_list C3TAg.txt
gene_list C3TAg.txt


title: LV_HFD_2WK_M_13


title: LV_HFD_2WK_M_12


title: MCF7 H3wt replicate1

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Library name: MCF7_H3wt_rep1_S27_R1_001.fastq.gz
cDNA library derived from steady-state poly-adenylated mRNA extracted from cells treated continuously with DMSO

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using star aligner.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

growth_protocol: MCF-7 human epithelia cells from breast adenocarsinoma cells from American Type Cell Culture (ATCC) were maintained in MEM supplemented with 5% calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin. MCF-7 cells were maintained in phenol red-free MEM supplimented with 5% charcoal-dextrantreated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin for at least 3 days prior to experimentation.

extract_protocol:
MCF-7 cells were seeded at at density of 0.5x10^6 cells per well in a 6-well plate and treated as described above. Total RNA was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol.
RNA-seq libraries were generated as previously described with the following modifications [24]. Total RNA from MCF-7 cells treated as indicated was isolated using the Qiagen RNeasy Plus Mini kit (Qiagen, 74136) according to the manufacturer's protocol. Total RNA was then enriched for mRNA using Dynabeads Oligo(dT)25 (Invitrogen, 61002). Further fragmentation, first-strand cDNA synthesis, and subsequent procedures have been done as described [25].The libraries were subjected to quality control analyses, such as optimizing the number of PCR cycles required to amplify each set of libraries, quantifying the final library yield by Qubit fluorometer (Invitrogen, Q32851), and checking the size distribution of the final library by DNA ScreenTape system (Agilent Technologies, G2964AA, 5067–5584, and 5067–5603). The libraries were barcoded with indices as described for the Illumina TruSeq RNA Prep kit, multiplexed, and sequenced using Illumina NextSeq (2000) by 100 bp single-end sequencing.

treatment_protocol: MCF-7 cells  maintained in phenol red-free MEM supplimented with 5% charcoal-dextran treated calf serum, 2mM GlutaMax, 100u/mL penicillin-streptomycin, and 25ug/mL gentamicin were seeded at a density of 0.5 x 10^6 cells per well in a 6-well dish one day prior to experimentation. At least biological replicates were used for each experimental condition. For E2 continuous treatment, 100 nM E2 was applied to the cells for the indicated times prior to collection. For E2 washout treatments, cells were treated with 100 nM of E2 for 40 mins., washed onced in stripped medium, then inclubated in stripped medium for the remainder of the experiment.

value: Epithelia cells from breast adenocarsinoma cells

value: Cells ectipically express wild-type H3


title: Huh7_BTW_02


title: Her2_11371_met

description:
CR051-24
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt

value: Lung metastasis


title: LV_RD_12WK_M_4

value: RD


title: Huh7_BTW_01

value: liver

value: hepatocellular carcinoma cell line


title: WRC31, leaf, control, Day 5, rep 1

description: Library name: C7

value: leaf


title: C3TAG_1456_primary

description:
3_PT3
gene_list C3TAg.txt
gene_list C3TAg.txt


title: A549_ZL_03

source_name: lung

value: lung

value: lung carcinoma cell

value: Polyporus umbellatus  extracts


title: Huh7_CH_01


title: LV_RD_12WK_M_3

value: Liver


title: Her2_10658_met

description:
CR051-22
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: WRC44, leaf, control, Day 5, rep 1

description: Library name: C5

value: control


title: A549_ZL_02

value: WT


title: Her2_10658_primary

description:
CR051-21
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt

value: Mammary tumor


title: LV_RD_12WK_M_2

value: M


title: A549_ZL_01


title: WRC57, leaf, control, Day 5, rep 1

description: Library name: C4


title: LV_HFD_12WK_M_4

value: HFD


title: WRC03, leaf, control, Day 5, rep 1

description: Library name: C11


title: Her2_11445_met

description:
CR051-20
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: Her2_11371_primary

description:
CR051-23
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: A549_Control_03

value: Control


title: WRC23, leaf, control, Day 5, rep 1

description: Library name: C8


title: LV_HFD_12WK_M_3


title: A549_Control_02


title: Her2_11445_primary

description:
CR051-19
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: WRC55, leaf, control, Day 5, rep 1

description: Library name: C3


title: WRC36, leaf, control, Day 5, rep 1

description: Library name: C6


title: LV_HFD_12WK_M_2


title: Her2_11740_met

description:
CR051-18
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: A549_Control_01


title: WRC25, leaf, control, Day 5, rep 1

description: Library name: C2


title: LV_RD_2WK_F_4

value: F


title: LV_RD_2WK_F_2


title: Her2_11740_primary

description:
CR051-17
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: IR64, second latest leaf, rehydration after severe drought, Day 0 (2h), rep 3

description:
Library name: IR9BD3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BD3L2

source_name: second latest leaf

value: second latest leaf

value: rehydration after severe drought


title: A549_CH_03

value: Bupleurum chinense extracts


title: A549_CH_02


title: LV_RD_2WK_F_1

value: RD


title: IR64, latest leaf, rehydration after severe drought, Day 0 (2h), rep 3

description:
Library name: IR9BD3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BD3L1

source_name: latest leaf

value: latest leaf


title: Her2_12432_primary

description:
CR051-15
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: LV_HFD_2WK_F_5


title: IR64, second latest leaf, rehydration after severe drought, Day 0 (2h), rep 2

description:
Library name: IR9BD2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BD2L2


title: IR64, latest leaf, rehydration after severe drought, Day 0 (2h), rep 2

description:
Library name: IR9BD2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BD2L1


title: A549_BTW_03

value: Pulsatilla chinensis extracts


title: LV_HFD_2WK_F_2


title: A549_BTW_02

value: lung


title: LV_HFD_2WK_F_1


title: Her2_NT072121_primary

description:
CR051-13
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: Her2_NT072121_met

description:
CR051-14
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt

value: Lung metastasis


title: Myc_771_met

description:
CR051-12
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt

value: MMTV-Myc


title: A549_BTW_01

value: lung carcinoma cell


title: WRC100, leaf, control, Day 5, rep 1

description: Library name: C1

value: leaf

value: control


title: Myc_771_primary

description:
CR051-11
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt

value: Mammary tumor


title: Her2_12432_met

description:
CR051-16
gene_list_MMTV_Her2.txt
gene_list_MMTV_Her2.txt


title: K-3_3

city: Nagatsuta-cho, Midori-ku

first: Shoen

last: Kume

state: Kanagawa-pref.

department: Life Science and Technology

institute: Tokyo institute of technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.  At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and 3 utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.  The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre-defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG, Reactome, DO and DisGeNET data sets were used for GSEA independently.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: count normalized by DESeq2, count and FPKM in excel file

source_name: human iPS cells Ff-I01s01

extract_protocol:
RNA was extracted using the RNeasy micro Kit (Qiagen) according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: human iPS cells Ff-I01s01

value: iPSC-derived Pancreatic Progenitor cells

value: WT

value: From D6 to D8 under S3 with 2 µM K-3


title: IR64, second latest leaf, rehydration after severe drought, Day 0 (2h), rep 1

description:
Library name: IR9BD1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BD1L2

value: second latest leaf


title: LV_RD_12WK_F_7

value: Liver

value: F


title: IR64, second latest leaf, control (rehydration), Day 0 (2h), rep 3

description:
Library name: IR9BC3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BC3L2

value: control (rehydration)


title: Myc_628_met

description:
CR051-10
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt


title: IR64, latest leaf, rehydration after severe drought, Day 0 (2h), rep 1

description:
Library name: IR9BD1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BD1L1

value: latest leaf

value: rehydration after severe drought


title: Myc_628_primary

description:
CR051-9
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt


title: IR64, latest leaf, control (rehydration), Day 0 (2h), rep 3

description:
Library name: IR9BC3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BC3L1


title: LV_HFD_12WK_F_7

value: HFD


title: K-3_1


title: A549_CH_01

value: lung

value: Bupleurum chinense extracts


title: LV_RD_12WK_F_5

value: RD


title: K-3_2


title: IR64, second latest leaf, control (rehydration), Day 0 (2h), rep 2

description:
Library name: IR9BC2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BC2L2


title: Control_3

value: From D6 to D8 under S3 without K-3


title: IR64, latest leaf, control (rehydration), Day 0 (2h), rep 2

description:
Library name: IR9BC2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BC2L1


title: Control_2


title: LV_HFD_12WK_F_6


title: LV_HFD_12WK_F_3


title: Myc_397_met

description:
CR051-6
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt

value: Lung metastasis

value: MMTV-Myc


title: LV_RD_12WK_F_8


title: IR64, second latest leaf, control (rehydration), Day 0 (2h), rep 1

description:
Library name: IR9BC1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BC1L2


title: Myc_397_primary

description:
CR051-5
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt

value: Mammary tumor


title: Midbrain organoid Line 15 SARS-CoV-2 infection 28dpi biol rep 4

city: Esch-sur-Alzette

first: Javier

last: Jarazo

address: 6A, avenue des Hauts-Fourneaux

country: Luxembourg

institute: OrganoTherapeutics

description: Library name: LCSB_16_EKRN240002121-1A

data_processing:
RNA-seq
The raw RNA sequencing data was pre-processed using the software package Rsubread of R
Gene-level differential expression analysis was conducted in R using the software package DESeq2
Filtering out genes with low expression counts (sum of counts < 10 across all samples)
Assembly: Hg38
Supplementary files format and content: Thefile feature_counts_covid19_midbrain_2024.txt has the counts of all in samples (each column corresponds to one library name)

source_name: Midbrain organoid

growth_protocol: Midbrain organoids generated in successive batches were cultured in N2B27 differentiation media for 30-33 days

extract_protocol:
Five organoids were pooled per line per batch, and RNA was extracted using the QIAshredder (Qiagen, 79654) and the RNeasy Mini kit (Qiagen, 74104) after 28 dpi following manufacturer’s protocol
A total of 750 ng of RNA was used for library preparation using TruSeq stranded mRNA library preparation kit (Illumina, 20020594) as per the protocol provided. The libraries were quantified using Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32851) and the size distribution was determined using Agilent 2100 Bioanalyzer (RRID:SCR_019389)

treatment_protocol: Either SARS-CoV-2 infection or mock treatment was done to the organoids. The organoids were kept for 28 days post infection until RNA was extracted

value: Midbrain organoid

value: hiPSC

value: Wild type

value: SARS-CoV-2 infection


title: Midbrain organoid Line 15 SARS-CoV-2 infection 28dpi biol rep 3

description: Library name: LCSB_15_EKRN240002120-1A


title: IR64, second latest leaf, severe drought, Day 9, rep 3

description:
Library name: IR9AD3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AD3L2

value: second latest leaf

value: severe drought


title: Treatment, MAH042822-006

city: Chicago

first: Gail

middle: B

last: Mahady

state: IL

address: 833 S Wood St

department: Pharmacy Practice

institute: University of Illinois

data_processing:
[Gene expression quantification] Raw reads were aligned to human reference genome hg38 using STAR (Dobin et al., 2013). ENSEMBL genes were quantified using FeatureCounts (Liao, Smyth, & Shi, 2014). Differential expression statistics were computed using edgeR (McCarthy, Chen, & Smyth, 2012; Robinson, McCarthy, & Smyth, 2010) on raw expression counts with the exactTest function. P-values were adjusted for multiple testing using the false discovery rate (FDR) correction of Benjamini and Hochberg (Benjamini & Hochberg, 1995).
Assembly: hg38
Supplementary files format and content: Table of raw counts per gene – tabular text file

source_name: ATCC

growth_protocol: MCF-7 cells were cultured and maintained in MEM (10010CV) + 10% FBS + 1% penicillin/streptomycin

extract_protocol:
RNA was isolated and analyzed for integrity using Agilent 4200 TapeStation and RNA Screen Tape
RNA-seq libraries were prepared using a Universal Plus mRNASeq kit, and library fragment size distribution was confirmed by electrophoresis using a 2200 TapeStation system with D1000 ScreenTape.
Sequencing was carried out on NovaSeq 6000, SP flowcell, 2x50 nt reads. General quality-control metrics were obtained using FastQC and raw reads were aligned to human reference genome hg38 using STAR and BWA MEM. ENSEMBL genes were quantified using FeatureCounts, and differential expression statistics were computed using edgeR. Specific gene expression was measured and verified using qPCR.

treatment_protocol: treated with a combination of vitamin A and D (1.5 mcg/ml) for 4 hours

value: combination of vitamins A and D


title: Myc_NT100219_primary

description:
CR051-3
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt


title: Myc_162_met

description:
CR051-8
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt


title: IR64, latest leaf, severe drought, Day 9, rep 3

description:
Library name: IR9AD3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AD3L1

value: latest leaf


title: Treatment, MAH042822-005


title: Treatment, MAH042822-004


title: IR64, second latest leaf, severe drought, Day 9, rep 2

description:
Library name: IR9AD2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AD2L2


title: Myc_162_primary

description:
CR051-7
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt


title: Myc_NT112619_primary

description:
CR051-1
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt


title: Myc_NT112619_met

description:
CR051-2
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt


title: Midbrain organoid Line 15 SARS-CoV-2 infection 28dpi biol rep 1

description: Library name: LCSB_13_EKRN240002118-1A


title: Control, MAH042822-003

value: Control


title: Midbrain organoid Line 11 SARS-CoV-2 infection 28dpi biol rep 3

description: Library name: LCSB_11_EKRN240002116-1A


title: Control, MAH042822-002


title: IR64, latest leaf, severe drought, Day 9, rep 2

description:
Library name: IR9AD2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AD2L1


title: IR64, latest leaf, control (rehydration), Day 0 (2h), rep 1

description:
Library name: IR9BC1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9BC1L1

value: control (rehydration)


title: Control_1

value: human iPS cells Ff-I01s01

value: iPSC-derived Pancreatic Progenitor cells

value: WT


title: SEA/Gn_E_Met

description:
CR055_36
gene_list_BALB.txt
gene_list_BALB.txt

value: Lung Metastasis

value: BALB/NJ x MMTV-PyMT


title: Midbrain organoid Line 15 SARS-CoV-2 infection 28dpi biol rep 2

description: Library name: LCSB_14_EKRN240002119-1A


title: Control, MAH042822-001


title: IR64, second latest leaf, severe drought, Day 9, rep 1

description:
Library name: IR9AD1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AD1L2


title: SEA/Gn_C_primary

description:
CR055_35
gene_list_BALB.txt
gene_list_BALB.txt


title: Midbrain organoid Line 11 SARS-CoV-2 infection 28dpi biol rep 2

description: Library name: LCSB_10_EKRN240002115-1A


title: Myc_NT100219_met

description:
CR051-4
gene_list_MMTV_Myc.txt
gene_list_MMTV_Myc.txt

value: Lung metastasis

value: MMTV-Myc


title: Midbrain organoid Line 11 SARS-CoV-2 infection 28dpi biol rep 1

description: Library name: LCSB_9_EKRN240002114-1A

value: Midbrain organoid


title: IR64, second latest leaf, control (severe drought), Day 9, rep 3

description:
Library name: IR9AC3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AC3L2

value: control (severe drought)


title: IR64, latest leaf, severe drought, Day 9, rep 1

description:
Library name: IR9AD1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AD1L1


title: AKRJ_11024_primary

description:
CR055_33
gene_list_BALB.txt
gene_list_BALB.txt

value: Mammary tumor


title: AKRJ_11158_Met

description:
CR055_34
gene_list_BALB.txt
gene_list_BALB.txt


title: IR64, latest leaf, control (severe drought), Day 9, rep 3

description:
Library name: IR9AC3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AC3L1


title: Midbrain organoid Line 11 SARS-CoV-2 infection 28dpi biol rep 4

description: Library name: LCSB_12_EKRN240002117-1A

value: hiPSC

value: Wild type

value: SARS-CoV-2 infection


title: Midbrain organoid Line 15 Mock infection 28dpi biol rep 4

description: Library name: LCSB_8_EKRN240002113-1A

value: Mock infection


title: Midbrain organoid Line 15 Mock infection 28dpi biol rep 3

description: Library name: LCSB_7_EKRN240002112-1A


title: Midbrain organoid Line 15 Mock infection 28dpi biol rep 2

description: Library name: LCSB_6_EKRN240002111-1A


title: IR64, second latest leaf, control (severe drought), Day 9, rep 2

description:
Library name: IR9AC2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AC2L2

value: second latest leaf


title: BALB_10889_Met

description:
CR055_31
gene_list_BALB.txt
gene_list_BALB.txt


title: IR64, latest leaf, control (severe drought), Day 9, rep 2

description:
Library name: IR9AC2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AC2L1

value: latest leaf


title: BALB_10844_Met

description:
CR055_#30_new_41822
gene_list_BALB.txt
gene_list_BALB.txt


title: P2146737

city: Guangzhou

first: Rufu

last: Chen

address: No. 106, Zhongshan 2nd Road, Guangzhou

institute: Guangdong Provincial People's Hospital

description: Library name: Sample 2

data_processing:
Disembarkation data quality control
Matching genome
Modification site recognition
Differential site recognition
Functional enrichment analysis
Assembly: HG19
Supplementary files format and content: The table contains the circRNA information identified by each sample

source_name: PDAC tissue

extract_protocol:
total RNA was extracted from tissue samples and RNA samples were detected in three main ways: (1) Nanodrop performs preliminary concentration and purity detection of RNA (2) Qubit accurately quantified RNA concentration (3) Agilent 2100 accurately detects RNA integrity (RIN value)
ncRNA-seq

value: PDAC tissue

tag: phenotype

value: PNI


title: P2119706

description: Library name: Sample 5

value: non-PNI


title: P2141182

description: Library name: Sample 6


title: P2143318

description: Library name: Sample 1


title: P2101119

description: Library name: Sample 4


title: Midbrain organoid Line 15 Mock infection 28dpi biol rep 1

description: Library name: LCSB_5_EKRN240002110-1A


title: IR64, second latest leaf, control (severe drought), Day 9, rep 1

description:
Library name: IR9AC1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AC1L2


title: IR64, latest leaf, control (severe drought), Day 9, rep 1

description:
Library name: IR9AC1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR9AC1L1


title: SEA/Gn_11545_Met

description:
CR055_29
gene_list_BALB.txt
gene_list_BALB.txt


title: Midbrain organoid Line 11 Mock infection 28dpi biol rep 3

description: Library name: LCSB_3_EKRN240002108-1A


title: SEA/Gn_E_primary

description:
CR055_28
gene_list_BALB.txt
gene_list_BALB.txt


title: IR64, second latest leaf, severe drought, Day 6, rep 3

description:
Library name: IR6D3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6D3L2

value: severe drought


title: P2156092

description: Library name: Sample 3


title: Midbrain organoid Line 11 Mock infection 28dpi biol rep 4

description: Library name: LCSB_4_EKRN240002109-1A


title: 2029430EM_HHT

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description: Library name: Sample 19

library_source: transcriptomic single cell

data_processing:
The raw sequencing data from all of the datasets were processed with 10x Genomics’ Cell Ranger v6.1.2 using GRCh38-2020-A as the GEX reference. Upon checking the average read depths across the blood and skin datasets, the gene expression data was rerun using cellranger aggr to account for significant differences among datasets.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output

extract_protocol:
Whole blood samples were collected in separate blood collection tubes for sera, DNA extraction, and peripheral blood mononuclear cell (PBMC) isolation. Ficoll-Paque PLUS purified PBMCs isolated as described previously were cryopreserved in 90% human AB negative sera (GeminiBio) and 10% DMSO for bulk BCR and TCR sequencing. Three mm skin punch biopsies were obtained from the leading edge of the EM lesion and from uninvolved skin at least 2 cm away from the EM lesion. Biopsies were placed into MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) for transport to the laboratory where they were immediately processed into single-cell suspensions using the Whole Skin Dissociation Kit (Miltenyi Biotec, 130-101-540) according to the manufacturer’s recommendation, as previously described. Sequencing of single cell suspensions was performed using the 10x Genomics Chromium 5’ Kit for library construction (both gene expression and immune profiling) and the Illumina MiSeq platform.
we followed the 10x protocol described in https://cdn.10xgenomics.com/image/upload/v1722286172/support-documents/CG000331_Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_RevF.pdf

value: Skin


title: BALB_11115_Met

description:
CR055_32
gene_list_BALB.txt
gene_list_BALB.txt

value: Lung Metastasis

value: BALB/NJ x MMTV-PyMT


title: Midbrain organoid Line 11 Mock infection 28dpi biol rep 2

description: Library name: LCSB_2_EKRN240002107-1A


title: SEA/Gn_B_Met

description:
CR055_27
gene_list_BALB.txt
gene_list_BALB.txt


title: IR64, latest leaf, severe drought, Day 6, rep 3

description:
Library name: IR6D3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6D3L1


title: 2029430B_HHT

description: Library name: Sample 18

source_name: Blood

value: Blood

value: PBMC


title: AKRJ_11158_primary

description:
CR055_26
gene_list_BALB.txt
gene_list_BALB.txt


title: Midbrain organoid Line 11 Mock infection 28dpi biol rep 1

description: Library name: LCSB_1_EKRN240002106-1A

value: Midbrain organoid


title: IR64, second latest leaf, severe drought, Day 6, rep 2

description:
Library name: IR6D2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6D2L2


title: AKRJ_10787_Met

description:
CR055_25_new
gene_list_BALB.txt
gene_list_BALB.txt


title: PMA-induced THP-1 macrophages, LDL treated, 100 μg/mL LDL, biol rep 3

city: Moscow

first: Diana

last: Kiseleva

address: 2, Abricosovskiy Pereulok

country: Russia

institute: Petrovsky National Research Center of Surgery

description:
Library name: Sample 12
Column name in normalized_counts_THP_EAHY.xlsx:  THPLDL3

data_processing:
Quality control of sequencing was performed using the FastQC, QoRTs and MultiQC software packages.
Reads were mapped to the genome using the STAR program, using the GRCh38 genome assembly and GENCODE.R42 annotations as a reference.
After mapping, data on the number of mapped reads to individual genes were obtained using the HTSeq-count program.
Differential expression analysis between the study groups was performed using the R software package: DESeq2.
Assembly: GRCh38
Supplementary files format and content: xlsx file includes counts normalized by sequencing depth (DESeq2) for each Sample

growth_protocol: THP-1 cells were grown in RPMI-1640 and supplemented with 10% FBS, Penicillin–Streptomycin, and 3.6 μL 2-Mercaptoethanol in a 5% CO2 humidified atmosphere at 37 °C. EA.hy926 cells were grown in DMEM under the same conditions, except for supplementation with 2-Mercaptoethanol.

extract_protocol:
RNA was isolated from cell culture lysate samples using the SKYEasy Fast Tissue/Cell Kit (SKYGen, Russia).
The resulting RNA samples were immediately used to prepare libraries using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, China).

treatment_protocol: On the third day, the control dishes were washed three times with PBS solution and then incubated for 24 h with RPMI-1640 (without FBS and 2-Mercaptoethanol, with Penicillin–Streptomycin) or DMEM (without FBS, with Penicillin–Streptomycin) depending on cell line type. The test dishes were incubated under the same conditions except for the medium containing 100 μg/mL of previously isolated LDL. Culturing medium without FBS and 2-Mercaptoethanol was used to eliminate additional factors that might provoke lipid droplet accumulation by cells.

value: monocytes

value: LDL


title: 2029410SC_HHT

description: Library name: Sample 17

source_name: Skin


title: 2029410EM_HHT

description: Library name: Sample 16


title: PMA-induced THP-1 macrophages, LDL treated, 100 μg/mL LDL, biol rep 2

description:
Library name: Sample 11
Column name in normalized_counts_THP_EAHY.xlsx:  THPLDL2


title: 2029430SC_HHT

description: Library name: Sample 20


title: BALB_10889_primary

description:
CR055_23
gene_list_SEAGn.txt
gene_list_SEAGn.txt

value: Mammary tumor

value: SEA/GNJ x MMTV-PyMT


title: PMA-induced THP-1 macrophages, LDL treated, 100 μg/mL LDL, biol rep 1

description:
Library name: Sample 10
Column name in normalized_counts_THP_EAHY.xlsx:  THPLDL1


title: BALB_11115_primary

description:
CR055_24
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: 2029400SC_HHT

description: Library name: Sample 14


title: IR64, second latest leaf, severe drought, Day 6, rep 1

description:
Library name: IR6D1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6D1L2


title: PMA-induced THP-1 macrophages, Control, without LDL, biol rep 3

description:
Library name: Sample 9
Column name in normalized_counts_THP_EAHY.xlsx:  THP3

value: control


title: BALB_10844_primary

description:
CR055_22
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: IR64, second latest leaf, control (severe drought), Day 6, rep 3

description:
Library name: IR6C3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6C3L2

value: second latest leaf

value: control (severe drought)


title: 2029400EM_HHT

description: Library name: Sample 13


title: PMA-induced THP-1 macrophages, Control, without LDL, biol rep 2

description:
Library name: Sample 8
Column name in normalized_counts_THP_EAHY.xlsx:  THP2


title: SEA/Gn_11545_primary

description:
CR055_21
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: 2029400B_HHT

description: Library name: Sample 12


title: PMA-induced THP-1 macrophages, Control, without LDL, biol rep 1

description:
Library name: Sample 7
Column name in normalized_counts_THP_EAHY.xlsx:  THP1


title: EA.hy926 cells, LDL treated, 100 μg/mL LDL, biol rep 3

description:
Library name: Sample 6
Column name in normalized_counts_THP_EAHY.xlsx:  EAHYLDL3

value: endothelial cells


title: IR64, latest leaf, severe drought, Day 6, rep 2

description:
Library name: IR6D2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6D2L1

value: latest leaf


title: SEA/Gn_B_primary

description:
CR055_19
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: 2029390EM_HHT

description: Library name: Sample 11


title: IR64, latest leaf, control (severe drought), Day 6, rep 3

description:
Library name: IR6C3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6C3L1


title: IR64, latest leaf, severe drought, Day 6, rep 1

description:
Library name: IR6D1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6D1L1


title: 2029390B_HHT

description: Library name: Sample 10


title: AKRJ_11034_Met

description:
CR055_18_new
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: IR64, second latest leaf, control (severe drought), Day 6, rep 1

description:
Library name: IR6C1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6C1L2


title: U19L202398_0SC_5P_HHT

description: Library name: Sample 9


title: EA.hy926 cells, LDL treated, 100 μg/mL LDL, biol rep 2

description:
Library name: Sample 5
Column name in normalized_counts_THP_EAHY.xlsx:  EAHYLDL2


title: 2029410B_HHT

description: Library name: Sample 15


title: EA.hy926 cells, LDL treated, 100 μg/mL LDL, biol rep 1

description:
Library name: Sample 4
Column name in normalized_counts_THP_EAHY.xlsx:  EAHYLDL1


title: EA.hy926 cells, Control, without LDL, biol rep 3

description:
Library name: Sample 3
Column name in normalized_counts_THP_EAHY.xlsx:  EAHY3


title: IR64, second latest leaf, rehydration after severe drought, Day 6, rep 3

description:
Library name: IR15D3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15D3L2

value: rehydration after severe drought


title: U19L202398_0EM_5P_HHT

description: Library name: Sample 8


title: U19L202398_0B_5P_HHT

description: Library name: Sample 7


title: AKRJ_10787_primary

description:
CR055_17
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: BALB_10900_Met

description:
CR055_16
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: SEA/Gn_D_Met

description:
CR055_#20_new_41822
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: IR64, latest leaf, control (severe drought), Day 6, rep 1

description:
Library name: IR6C1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6C1L1


title: IR64, latest leaf, rehydration after severe drought, Day 6, rep 3

description:
Library name: IR15D3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15D3L1


title: 202937_0EM_5P_HHT

description: Library name: Sample 6


title: IR64, latest leaf, control (severe drought), Day 6, rep 2

description:
Library name: IR6C2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6C2L1


title: EA.hy926 cells, Control, without LDL, biol rep 1

description:
Library name: Sample 1
Column name in normalized_counts_THP_EAHY.xlsx:  EAHY1


title: IR64, second latest leaf, rehydration after severe drought, Day 6, rep 2

description:
Library name: IR15D2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15D2L2


title: BALB_10863_Met

description:
CR055_15
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: 202937_0SC_5P_HHT

description: Library name: Sample 5


title: SEA/Gn_H_Met

description:
CR055_13
gene_list_SEAGn.txt
gene_list_SEAGn.txt


title: IR64, latest leaf, rehydration after severe drought, Day 6, rep 2

description:
Library name: IR15D2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15D2L1


title: V_Set_Sample_17_574

city: Morgantown

first: Florin

middle: V

last: Chirila

state: WV

address: 895 Vandalia Rd

department: Diagnostic

institute: Spot Dx

description: Library name: Validation Set Sample 17

data_processing:
The data processing pipeline for this RNA-seq involved several standard bioinformatics steps to ensure high-quality expression analysis.
Sequencing Platform: Illumina (2×75 bp paired-end reads; ~20 million reads per sample).
Alignment Reference: Reads were aligned to the Homo sapiens reference genome GRCh38.
Quantification: StringTie was used for gene expression estimation, likely generating FPKM values
Assembly: The RNA-seq data were aligned to the Homo sapiens reference genome (GRCh38).
Supplementary files format and content: Tab-delimited text file, "gene.fpkm.txt", includes quantified expression values per gene or transcript (e.g., FPKM).

source_name: skin

growth_protocol: For the NGS RNA-Seq, skin fibroblasts were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 2% penicillin-streptomycin (PS) in a 5% CO2 water-jacketed incubator.

extract_protocol:
The RNA was extracted using the Norgen Total RNA Purification Kit, adhering to the manufacturer’s protocol.
The sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit, following the manufacturer’s standard protocol.

treatment_protocol: Cell synchronization involves culturing the fibroblasts to 100% confluence and then serum-starving them overnight.  Fresh skin fibroblast pellets were flash-frozen immediately after harvest.

value: skin

value: fibroblast

value: PD, CEREBROVAS (NC)

value: Synchronized

tag: batch

value: Validsation Set


title: 202937_0B_5P_HHT

description: Library name: Sample 4

value: Blood

value: PBMC


title: V_Set_Sample_18_39

description: Library name: Validation Set Sample 18

value: Healthy Control (HC)


title: SEA/Gn_D_primary

description:
CR055_12
gene_list_AKR.txt
gene_list_AKR.txt

value: AKR/J x MMTV-PyMT


title: 202936_0EM_5P_HHT

description: Library name: Sample 3

value: Skin


title: V_Set_Sample_16_586

description: Library name: Validation Set Sample 16

value: Non-AD dementia (non-ADD) FTLD-MLD/MNI, CEREBROV(NC), PERIVAS LYMPH CUFF


title: 202936_0SC_5P_HHT

description: Library name: Sample 2


title: IR64, latest leaf, rehydration after severe drought, Day 6, rep 1

description:
Library name: IR15D1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15D1L1


title: AKRJ_11034_primary

description:
CR055_10
gene_list_AKR.txt
gene_list_AKR.txt

value: Mammary tumor


title: AKRJ_11163_Met

description:
CR055_11_new
gene_list_AKR.txt
gene_list_AKR.txt

value: Lung Metastasis


title: EA.hy926 cells, Control, without LDL, biol rep 2

description:
Library name: Sample 2
Column name in normalized_counts_THP_EAHY.xlsx:  EAHY2

value: control


title: IR64, second latest leaf, control (rehydration), Day 6, rep 3

description:
Library name: IR15C3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15C3L2

value: second latest leaf

value: control (rehydration)


title: 202936_0B_5P_HHT

description: Library name: Sample 1


title: V_Set_Sample_15_50

description: Library name: Validation Set Sample 15


title: IR64, second latest leaf, control (severe drought), Day 6, rep 2

description:
Library name: IR6C2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR6C2L2

value: control (severe drought)


title: V_Set_Sample_14_44

description: Library name: Validation Set Sample 14

value: skin


title: AKRJ_10784_Met

description:
CR055_9
gene_list_AKR.txt
gene_list_AKR.txt


title: IR64, latest leaf, control (rehydration), Day 6, rep 3

description:
Library name: IR15C3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15C3L1

value: latest leaf


title: BALB_10737_Met

description:
CR055_14
gene_list_SEAGn.txt
gene_list_SEAGn.txt

value: SEA/GNJ x MMTV-PyMT


title: IR64, second latest leaf, control (rehydration), Day 6, rep 2

description:
Library name: IR15C2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15C2L2


title: V_Set_Sample_13_54

description: Library name: Validation Set Sample 13

value: fibroblast

value: Synchronized


title: BALB_10900_primary

description:
CR055_8
gene_list_AKR.txt
gene_list_AKR.txt


title: V_Set_Sample_12_598

description: Library name: Validation Set Sample 12

value: Alzheimer's disease (AD)

value: Validsation Set


title: BALB_10863_primary

description:
CR055_7
gene_list_AKR.txt
gene_list_AKR.txt


title: IR64, latest leaf, control (rehydration), Day 6, rep 2

description:
Library name: IR15C2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15C2L1


title: 2029430EM_TCR

description: Library name: Sample 19

data_processing:
The raw sequencing data from all of the datasets were processed with 10x Genomics’ Cell Ranger v6.1.2 using  vdj_GRCh38_alts_ensembl-5.0.0 as the VDJ reference. Upon checking the average read depths across the blood and skin datasets, the gene expression data was rerun using cellranger aggr to account for significant differences among datasets
Assembly: vdj_GRCh38_alts_ensembl-5.0.0
Supplementary files format and content: CellRanger output
Library strategy: TCR-Seq


title: 2029430SC_TCR

description: Library name: Sample 20


title: 2029410SC_TCR

description: Library name: Sample 17


title: V_Set_Sample_11_52

description: Library name: Validation Set Sample 11

value: Healthy Control (HC)


title: BALB_10737_primary

description:
CR055_6
gene_list_AKR.txt
gene_list_AKR.txt

value: AKR/J x MMTV-PyMT


title: IR64, second latest leaf, rehydration after severe drought, Day 6, rep 1

description:
Library name: IR15D1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15D1L2

value: rehydration after severe drought


title: V_Set_Sample_10_656

description: Library name: Validation Set Sample 10


title: 2029410EM_TCR

description: Library name: Sample 16

value: Skin


title: SEA/Gn_H_primary

description:
CR055_5
gene_list_AKR.txt
gene_list_AKR.txt

value: Mammary tumor


title: IR64, second latest leaf, control (rehydration), Day 6, rep 1

description:
Library name: IR15C1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15C1L2


title: IR64, latest leaf, control (rehydration), Day 6, rep 1

description:
Library name: IR15C1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR15C1L1


title: V_Set_Sample_9_564

description: Library name: Validation Set Sample 9

value: Non-AD dementia (non-ADD) (CBD, CEREBROVAS DIS NC)


title: 2029410B_TCR

description: Library name: Sample 15

value: Blood

value: PBMC


title: AKRJ_11163_primary

description:
CR055_3_new
gene_list_AKR.txt
gene_list_AKR.txt


title: 2029430B_TCR

description: Library name: Sample 18


title: T_Set_Sample_8_599

description: Library name: Training Set Sample 8

value: Training Set


title: IR64, second latest leaf, rehydration after severe drought, Day 3, rep 3

description:
Library name: IR12D3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12D3L2

value: second latest leaf


title: T_Set_Sample_7_579

description: Library name: Training Set Sample 7

value: skin

value: Mixed Alzheimer's disease (AD) VASC, FTLD-MND/MNI-TDP43


title: 2029400SC_TCR

description: Library name: Sample 14


title: AKRJ_11024_Met

description:
CR055_2
gene_list_AKR.txt
gene_list_AKR.txt

value: Lung Metastasis


title: SEA/Gn_C_Met

description:
CR055_4
gene_list_AKR.txt
gene_list_AKR.txt


title: 2029400EM_TCR

description: Library name: Sample 13


title: IR64, latest leaf, rehydration after severe drought, Day 3, rep 2

description:
Library name: IR12D2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12D2L1

value: latest leaf


title: T_Set_Sample_6_596

description: Library name: Training Set Sample 6

value: fibroblast

value: Synchronized


title: AKRJ_10784_primary

description:
CR055_1_new
gene_list_AKR.txt
gene_list_AKR.txt


title: IR64, second latest leaf, rehydration after severe drought, Day 3, rep 2

description:
Library name: IR12D2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12D2L2


title: B100-LKO Female-6

city: Lexington

first: Robert

middle: N

last: Helsley

state: KY

address: 741 S. Limestone St.

department: Intern

institute: University of Kentucky

description:
LKOFvsWTF_deg.txt
S24

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Novogenes methods
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Assembly: mm39
Supplementary files format and content: xls files include RPKM and total counts for each Sample

extract_protocol:
Total RNA was isolated from livers using the Qiagen Rneasy Mini kit. Novogene isolated mRNA from the total RNA provided by the investigators using poly-T oligo-attached magnetic beads.
mRNA libraries were constructed by Novogene using random hexamers and dUTP. The library was complete after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, following Novogenes methods.

value: Liver

value: Female

value: WD-fed for 16-weeks; Necropsied in the fed state


title: 2029400B_TCR

description: Library name: Sample 12


title: T_Set_Sample_5_539

description: Library name: Training Set Sample 5

value: Alzheimer's disease (AD)


title: 2029390EM_TCR

description: Library name: Sample 11

value: Skin


title: IR64, second latest leaf, rehydration after severe drought, Day 3, rep 1

description:
Library name: IR12D1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12D1L2

value: rehydration after severe drought


title: IR64, latest leaf, rehydration after severe drought, Day 3, rep 1

description:
Library name: IR12D1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12D1L1


title: B100-LKO Female-5

description:
LKOFvsWTF_deg.txt
S23


title: T_Set_Sample_4_586

description: Library name: Training Set Sample 4

value: Non-AD dementia (non-ADD) FTLD-MLD/MNI, CEREBROV(NC), PERIVAS LYMPH CUFF


title: B100-LKO Female-4

description:
LKOFvsWTF_deg.txt
S22


title: IR64, second latest leaf, control (rehydration), Day 3, rep 3

description:
Library name: IR12C3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12C3L2

value: control (rehydration)


title: U19L202398_0SC_TCR

description: Library name: Sample 9


title: IR64, latest leaf, rehydration after severe drought, Day 3, rep 3

description:
Library name: IR12D3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12D3L1


title: T_Set_Sample_2_538

description: Library name: Training Set Sample 2


title: 2029390B_TCR

description: Library name: Sample 10

value: Blood

value: PBMC


title: B100-LKO Female-3

description:
LKOFvsWTF_deg.txt
S21


title: IR64, latest leaf, control (rehydration), Day 3, rep 3

description:
Library name: IR12C3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12C3L1


title: T_Set_Sample_1_702

description: Library name: Training Set Sample 1

value: Training Set


title: B100-LKO Female-2

description:
LKOFvsWTF_deg.txt
S20


title: U19L202398_0EM_TCR

description: Library name: Sample 8


title: IR64, second latest leaf, control (rehydration), Day 3, rep 2

description:
Library name: IR12C2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12C2L2

value: second latest leaf


title: B100-LKO Female-1

description:
LKOFvsWTF_deg.txt
S19


title: U19L202398_0B_TCR

description: Library name: Sample 7


title: IR64, latest leaf, control (rehydration), Day 3, rep 2

description:
Library name: IR12C2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12C2L1


title: 202937_0EM_TCR

description: Library name: Sample 6


title: p4503.c01w1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description:
Library name: p4503.c01w1
CTCL patient p4503, treatment cycle 1, week 1

data_processing:
Raw RNA-seq reads were aligned to the GRCh37 reference human genome using TopHat (v2.0.3). For paired-end data, only the first read was aligned. Mapped reads were then assembled to transcripts using Cufflinks. Assemblies were merged across all sequenced samples using Cuffmerge and FPKM values were used for downstream analyses
Assembly: GRCh37
Supplementary files format and content: FPKM values for genes across sample

source_name: PBMC

extract_protocol:
Peripheral blood samples (PBMC) were collected into CPT tubes (BD) at baseline and before each romidepsin intravenous infusion. RNA purification was carried out using TRI Reagent® (Molecular Research Center), as recommended, and controlled for quality using the Bioanalyzer (Agilent)
RNA-Seq was carried out on tru-seq and script libraries

tag: subject status

value: CTCL patient

tag: treatment cycle

tag: cycle week

value: romidepsin

tag: subject id


title: B100-Control Female-6

description:
LKOFvsWTF_deg.txt
S18

tag: tissue


title: IR64, second latest leaf, control (rehydration), Day 3, rep 1

description:
Library name: IR12C1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12C1L2


title: p4502.c01w1

description:
Library name: p4502.c01w1
CTCL patient p4502, treatment cycle 1, week 1


title: p4510.rec

description:
Library name: p4510.rec
CTCL patient p4510, treatment cycle recurrence, week na

value: recurrence


title: 202937_0SC_TCR

description: Library name: Sample 5

tag: cell type


title: T_Set_Sample_3_545

description: Library name: Training Set Sample 3

value: skin

tag: cell line

value: fibroblast

tag: genotype

value: Non-AD dementia (non-ADD) (Frontotemporal lobar degeneration with TDP-43 inclusions)


title: B100-Control Female-5

description:
LKOFvsWTF_deg.txt
S17

value: Liver

value: Female

tag: treatment


title: B100-Control Female-4

description:
LKOFvsWTF_deg.txt
S16

value: WD-fed for 16-weeks; Necropsied in the fed state


title: 202936_0EM_TCR

description: Library name: Sample 3

value: Skin


title: IR64, second latest leaf, severe drought, Day 0, rep 3

description:
Library name: IR0D3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0D3L2

value: severe drought


title: IR64, latest leaf, severe drought, Day 0, rep 3

description:
Library name: IR0D3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0D3L1

value: latest leaf


title: p4510.c08w1

description:
Library name: p4510.c08w1
CTCL patient p4510, treatment cycle 8, week 1


title: B100-Control Female-3

description:
LKOFvsWTF_deg.txt
S15


title: p4509.c01w1

description:
Library name: p4509.c01w1
CTCL patient p4509, treatment cycle 1, week 1


title: 202936_0SC_TCR

description: Library name: Sample 2


title: B100-Control Female-2

description:
LKOFvsWTF_deg.txt
S14


title: IR64, second latest leaf, severe drought, Day 0, rep 2

description:
Library name: IR0D2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0D2L2


title: p4510.c04w3

description:
Library name: p4510.c04w3
CTCL patient p4510, treatment cycle 4, week 3


title: B100-Control Female-1

description:
LKOFvsWTF_deg.txt
S13


title: 202936_0B_TCR

description: Library name: Sample 1


title: p4510.c04w1

description:
Library name: p4510.c04w1
CTCL patient p4510, treatment cycle 4, week 1


title: IR64, second latest leaf, severe drought, Day 0, rep 1

description:
Library name: IR0D1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0D1L2


title: CXCL9_18h Rep2

city: Irvine

first: Jiachun

state: CA

address: Samueli School of Engineering University of California, Irvine

institute: University of California Irvine

data_processing:
Data processing, including demultiplexing, trimming, and mapping to the reference genome (hg38), was performed using the pipe4C pipeline
Assembly: hg19
Supplementary files format and content: wiggle
Library strategy: 4C-seq

growth_protocol: 10 million THP-1 cells were seeded in 10 cm dishes and treated with 20 nM phorbol 12-myristate 13-acetate for 48 hours, followed by stimulation with 100 ng/ml ultrapure lipopolysaccharide.

extract_protocol:
Cells were fixed with 2% paraformaldehyde for 10 minutes at room temperature, quenched with 10 ml of cold 0.13 M glycine, and lysed using cell lysis buffer comprising 1M Tris-HCl, NP-40, Triton X-100, 5M NaCl, 0.5M EDTA, and 100X proteinase inhibitor. The mixture was shaken on ice for 15 minutes, then scraped and shaken for another 5 minutes on ice. The nuclei were collected by centrifugation at 500g for 5 minutes at 4oC, resuspended in 1.2X restriction enzyme buffer, and treated with 0.3% SDS and 2.5% Triton X-100, with incubation at 37oC for 1 hour. Then clean up DNA by DNA precipitation.
Chromatin was fragmented by subjecting isolated nuclei to primary restriction enzyme digestion overnight with shaking at 750rpm, using the 4-bp cutter restriction enzyme to achieve optimal contact-mapping resolution, followed by in situ ligation in a reaction mix containing ligase buffer and ligase, incubated overnight at 16oC. Post-ligation, cross-links were reversed by overnight incubation with Proteinase K at 65oC. DNA was purified using SPRI beads and subjected to a second 4-bp cutter restriction enzyme digestion. The digested DNA was then ligated again, and the resulting 3C templates were purified using SPRI beads, and quantified using the Qubit dsDNA BR Assay Kit. Next, two rounds of PCR amplification were conducted: an inverse PCR to amplify captured regions, followed by an indexing PCR to generate sequencing-ready libraries.

tag: time

value: Macrophage


title: B100-LKO Male-6

description:
LKOMvsWTM_deg.txt
S12

tag: Sex

value: Male


title: IR64, latest leaf, control (rehydration), Day 3, rep 1

description:
Library name: IR12C1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR12C1L1

data_processing:
The sequence reads were mapped onto the reference genome of the rice cultivar Nipponbare (IRGSP-1.0) using STAR aligner with options ‘--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4’ (Dobin et al., 2013). The read count matrix was obtained using featureCounts (v2.0.0) with option ‘-p’ (Liao et al., 2014).
Assembly: IRGSP-1.0
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

value: control (rehydration)


title: AD3_TBEV-3_biolRepl_3

city: Brno

first: Katerina

last: Amruz Cerna

state: Czech Republic

address: Kamenice 3

department: Department of Histology and Embryology

country: Czech Republic

institute: Faculty of Medicine, Masaryk University

description: Library name: AD3_TBEV-3

data_processing:
Data analysis was performed in R statistical environment v4.4.2. The quality of raw reads was verified using FastQC v0.11.9, and the potential contamination was screened by FastQ_Screen v0.11.1.
The low-quality reads, and adaptor sequences were removed using TrimmomaticSE v0.36 with parameters “HEADCROP:10 ILLUMINACLIP: Lexogen_quantseq.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
Ribosomal and mitochondrial reads were removed using sortmerna v2.1b. BAM files with alignment were created with STAR v2.7.0f  [reference Homo sapiens genome version GRCh38].
The count tables were generated using the script htseq-count v0.11.4 with annotation version GRCh38.87 and parameter “-m union”.
ENSEMBL-IDs were used as identifiers of transcripts. The counted data were subsequently analyzed using R-package DESeq2 v1.46.0. Differentially expressed genes (DEGs) were identified by the command ‘DESEQ’ with default parameters.
ENSEMBL-IDs were converted into Gene symbol using org.Hs.eg.db v3.20.0 database. DEGs (p.adjust<0.1, |log2FC|>0.5, baseMean>100) were used in further analyses.
Assembly: GRCh38.87
Supplementary files format and content: Xlsx files with DEGs including comparison of infected COs in comparison to ther corresponding non-infected controls.

source_name: cerebral organoids

growth_protocol:
In this study, we used previously established and well-characterized human iPSC lines, including both wild-type (WT) and familial AD patient-derived lines (PSEN1/2 mutant).
All iPSCs were cultured in mTeSR medium (85850, StemCell Technologies) on Matrigel-coated plates (734-1440, Corning) and routinely passaged using TrypLE (12605036, Thermo Fisher Scientific) or 50mM EDTA (AM9260G, Thermo Fisher Scientific).
These lines were subsequently differentiated into inducible 2D neurons and 3D COs.
To generate COs, both WT and PSEN1/2 mutant iPSC lines were differentiated using a modified version of the Lancaster et al. (2013) protocol, as previously optimized by our group.
Organoids were used for viral infection studies at days 53 and 93 of development (with embryoid body seeding designated as day 0).

extract_protocol:
RNA was isolated with RNABlue (TopBio, R013)  combined with column extraction with Dnase I pretreatment (Direct-zol RNA Microprep kit (ZymoResearch)). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared with QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen) in combination with UMI Second Strand Synthesis Module for QuantSeq FWD and Lexogen i5 6 nt Unique Dual Indexing Add-on Kit (Lexogen).

treatment_protocol:
Two viruses (HSV-1 and TBEV) were used to infect mature neurons and COs.
COs were infected on day 53 (D53, early timepoint) of differentiation. HSV-1 (MOI 0.0001) or mCherry-TBEV (MOI 0.1), diluted in the viral infection medium, was applied for 24 hours.
After infection, organoids were transferred to fresh CO differentiation medium (COII) and cultured for up to 7 days post-infection (dpi). Control organoids underwent the same procedure but were not exposed to the virus.

value: cerebral organoids

value: MUNIi007-A (fAD3)

value: iPSC cell lines

value: PSEN2 I144N

value: TBEV


title: B100-LKO Male-5

description:
LKOMvsWTM_deg.txt
S11


title: CXCL9_6h Rep2


title: 202937_0B_TCR

description: Library name: Sample 4

value: Blood

value: PBMC


title: p4510.c09w1

description:
Library name: p4510.c09w1
CTCL patient p4510, treatment cycle 9, week 1

value: CTCL patient

value: romidepsin


title: CXCL9_0h Rep2

value: Control


title: B100-LKO Male-4

description:
LKOMvsWTM_deg.txt
S10

value: Liver

value: WD-fed for 16-weeks; Necropsied in the fed state


title: CXCL9_1h Rep2


title: AD3_HSV-3_biolRepl_3

description: Library name: AD3_HSV-3


title: IR64, second latest leaf, control (severe drought), Day 0, rep 3

city: Tsukuba

first: Taiji

institute: National Agriculture and Food Research Organization

description:
Library name: IR0C3L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0C3L2

extract_protocol:
The fully expanded latest leaves and second latest leaves were collected and frozen in liquid nitrogen. Samples were ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.

value: second latest leaf

value: control (severe drought)


title: IR64, latest leaf, severe drought, Day 0, rep 1

description:
Library name: IR0D1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0D1L1

value: latest leaf

value: severe drought


title: IR64, latest leaf, control (severe drought), Day 0, rep 3

description:
Library name: IR0C3L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0C3L1


title: B100-LKO Male-3

description:
LKOMvsWTM_deg.txt
S9

value: Male


title: WT3_TBEV-4_biolRepl_3

description: Library name: WT3_TBEV-4

value: cerebral organoids

value: MUNIi010-A (fWT3)

value: WT


title: WT3_HSV-4_biolRepl_3

description: Library name: WT3_HSV-4

value: iPSC cell lines


title: IL15_6h Rep2

value: Macrophage


title: IR64, latest leaf, severe drought, Day 0, rep 2

description:
Library name: IR0D2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0D2L1


title: B100-LKO Male-1

description:
LKOMvsWTM_deg.txt
S7


title: IR64, second latest leaf, control (severe drought), Day 0, rep 2

description:
Library name: IR0C2L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0C2L2


title: AD3_CTRL-3_biolRepl_3

description: Library name: AD3_CTRL-3

value: MUNIi007-A (fAD3)

value: PSEN2 I144N

value: non-treated


title: IL15_18h Rep2


title: WT3_CTRL-4_biolRepl_4

description: Library name: WT3_CTRL-4


title: IR64, latest leaf, control (severe drought), Day 0, rep 2

description:
Library name: IR0C2L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0C2L1


title: IL15_1h Rep2


title: IR64, second latest leaf, control (severe drought), Day 0, rep 1

description:
Library name: IR0C1L2
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0C1L2


title: IL15_0h Rep2


title: B100-Control Male-6

description:
LKOMvsWTM_deg.txt
S6


title: AD2_TBEV-2_biolRepl_2

description: Library name: AD2_TBEV-2

value: MUNIi006-A (fAD2)

value: PSEN1 A246E

value: TBEV


title: B100-Control Male-4

description:
LKOMvsWTM_deg.txt
S4

value: Liver

value: WD-fed for 16-weeks; Necropsied in the fed state


title: IR64, latest leaf, control (severe drought), Day 0, rep 1

description:
Library name: IR0C1L1
Column name in rawCounts_IR64_rehydration_All_samples.txt: IR0C1L1

value: control (severe drought)


title: AD2_HSV-2_biolRepl_2

description: Library name: AD2_HSV-2


title: B100-Control Male-3

description:
LKOMvsWTM_deg.txt
S3


title: CXCL10_18h Rep2


title: IR64, leaf, severe drought, Day 12, rep 3

description:
Library name: IRLS12D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS12D3

source_name: leaf

extract_protocol:
The leaf samples were frozen in liquid nitrogen immediately after sampling, ground to a fine powder with a multi-beads shocker and used for RNA extraction. Total RNA was extracted using guanidine isothiocyanate based buffer and magnetic beads as described previously (Yoshino et al., 2020).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760L) according to the manufacture’s protocol.

treatment_protocol: In the moderate drought treatment, water supply from the supply pot was stopped on the 14 days after sowing, allowing water to drain from the inside of the pots through the hose. In the severe drought treatment, the height of the pots was elevated above the hose to promote faster drainage. In the control treatment, irrigation was maintained.

value: leaf


title: CXCL10_6h Rep2


title: AD2_CTRL-2_biolRepl_2

description: Library name: AD2_CTRL-2


title: B100-Control Male-2

description:
LKOMvsWTM_deg.txt
S2


title: B100-LKO Male-2

description:
LKOMvsWTM_deg.txt
S8


title: CXCL10_1h Rep2


title: CXCL10_0h Rep2

value: Control


title: B100-Control Male-1

description:
LKOMvsWTM_deg.txt
S1

value: Male


title: IR64, leaf, severe drought, Day 12, rep 1

description:
Library name: IRLS12D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS12D1

value: severe drought


title: WT2_HSV-3_biolRepl_2

description: Library name: WT2_HSV-3

value: cerebral organoids

value: MUNIi009-A (fWT2)


title: Refed Male LKO-4

value: CPT1a LKO

value: HFD-fed for 12-weeks; Refed at necropsy


title: Refed Male LKO-3


title: IR64, leaf, severe drought, Day 11, rep 3

description:
Library name: IRLS11D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS11D3


title: WT2_CTRL-3_biolRepl_3

description: Library name: WT2_CTRL-3

value: iPSC cell lines

value: WT


title: IL6_18h Rep1

value: Macrophage


title: Refed Male LKO-2


title: AD1_TBEV-1_biolRepl_1

description: Library name: AD1_TBEV-1

value: MUNIi005-A (fAD1)

value: PSEN1 A243E


title: IL6_6h Rep1


title: IL6_1h Rep1


title: AD1_HSV-1_biolRepl_1

description: Library name: AD1_HSV-1


title: IR64, leaf, severe drought, Day 10, rep 3

description:
Library name: IRLS10D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS10D3


title: IL6_0h Rep1


title: Refed Male Control-4


title: IR64, leaf, severe drought, Day 12, rep 2

description:
Library name: IRLS12D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS12D2


title: WT2_TBEV-3_biolRepl2

description: Library name: WT2_TBEV-3

value: TBEV


title: IR64, leaf, severe drought, Day 10, rep 2

description:
Library name: IRLS10D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS10D2


title: Refed Male LKO-1

value: Liver


title: AD1_CTRL-1_biolRepl_1

description: Library name: AD1_CTRL-1

value: non-treated


title: Refed Male Control-3


title: WT1_HSV-2_biolRepl_1

description: Library name: WT1_HSV-2

value: MUNIi008-A (fWT1)


title: CXCL9_18h Rep1


title: CXCL9_6h Rep1


title: IR64, leaf, severe drought, Day 11, rep 2

description:
Library name: IRLS11D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS11D2

value: leaf


title: CXCL9_1h Rep1


title: IR64, leaf, severe drought, Day 9, rep 3

description:
Library name: IRLS9D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS9D3


title: WT1_TBEV-1_biolRepl_1

description: Library name: WT1_TBEV-1


title: WT1_CTRL-2_biolRepl_2

description: Library name: WT1_CTRL-2


title: Refed Male Control-1

value: Control


title: IR64, leaf, severe drought, Day 11, rep 1

description:
Library name: IRLS11D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS11D1


title: IR64, leaf, severe drought, Day 9, rep 2

description:
Library name: IRLS9D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS9D2


title: WT1_CTRL-1_biolRepl_1

description: Library name: WT1_CTRL-1


title: Fasted Male LKO-4

value: Male

value: HFD-fed for 12-weeks; Fasted at necropsy


title: CXCL9_0h Rep1


title: IR64, leaf, severe drought, Day 9, rep 1

description:
Library name: IRLS9D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS9D1

value: severe drought


title: CXCL10_18h Rep1


title: Fasted Male LKO-3


title: 1205Lu, IgG (CutRun)

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Library name: S08_1205Lu-IgG

data_processing:
RNAseq: Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1). Processed raw reads were then aligned to human genome GRCh38 using STAR (v2.7.7a). Gene expression was evaluated as read count at gene level with RSEM (v1.3.0) and Gencode gene model v30. Gene express data were then normalized and differential expression between experimental groups were evaluated using DEseq2.
Cut&Run:  Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1) (34). Processed raw reads were then aligned to human genome GRCh38 using BOWTIE2 (v2.4.1). Peak Calling was performed to identify regions of open chromatin using MACS2 (v 2.1.1.20160309). Only peaks significantly enriched over background with q <0.01 were considered confident and subjected to downstream analysis. Peaks were annotated by ChIPseeker (v1.32.1) with gene model TxDb.Hsapiens.UCSC.hg38.knownGene (v 3.15.0). Consensus peak identifiers were obtained by GenomicRanges (v1.48.0). Peaks were then normalized and differential enrichment between experimental groups evaluated using DEseq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: text file, raw reads count data
Library strategy: CUT&Run

extract_protocol:
RNAseq: RNA extracted from A375 and 1205Lu cells was quantified with a Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA). Cut&Run: Cut&Run was performed with A375 and 1205Lu cells using CUTANA ChIC/CUT&RUN Kit version 4.0 (EpiCypher, Cat. # SKU: 14–1048). Briefly, 500,000 cells were collected and re-suspended in Wash Buffer and mixed with 10 μl activated ConA beads. 0.5 μg FRA1 antibody (Abcam, Cat. # ab252421) or 1 μl IgG antibody were added and incubated overnight at 4°C. Beads were washed twice in 200 μl Cell Permeabilization Buffer (CPB) prior to the addition of 2.5 μl CUTANA pAG-MNase in 50 μl of CPB per reaction. Beads were again washed twice in 200 μl CPB and suspended in 50 μl CPB. For chromatin digestion, 1 μl of 100 mM CaCl2 was added to activate the MNase. 33 μl of Stop Master Mix was added to terminate the MNase activity after 2h incubation at 4°C. To isolate DNA from the supernatant, 119 μl SPRlselect were added and incubated for 5 minutes at room temperature. SPRIselect beads were washed twice with 85% Ethanol and air-dried. To elute DNA, 17 μl of 0.1X TE Buffer were added.
RNAseq: The samples were then processed for RNA sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA). Briefly, 100 ng of RNA were used to generate cDNA and a strand-specific library following the manufacturer’s protocol. Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA). The final libraries were normalized, denatured, and sequenced on the Illumina NovaSeq 6000 sequencer with the S1–200 reagent kit to generate approximately 60 million 100-base read pairs per sample (Illumina, Inc., San Diego, CA). Cut&Run:  Eluted DNA was quantified with the Qubit fluorometer, and 0.6 to 5 nanograms of enriched DNA was used for library preparation using the Kapa HyperPrep Kit (Roche, Cat. # 07962347001) following EpiCypher’s parameters for indexing PCR and library amplification as described in the CUT&RUN Library Prep Manual. The final libraries were Qubit quantitated and screened on the Agilent TapeStation D1000 ScreenTape (Agilent Technologies) to assess the fragment size distribution. Following final quantification using the Kapa Library Quantification Kit (Roche, Cat. # 07960140001), the libraries were sequenced on the NextSeq 500 using a Mid-output 150-cycle Kit in 2×50 configuration to generate 6–8 million read-pairs per sample (Illumina).

value: human melanoma cell


title: IR64, leaf, severe drought, Day 10, rep 1

last: Kawakatsu

address: 3-1-3 Kan-nondai

description:
Library name: IRLS10D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS10D1


title: CXCL10_6h Rep1


title: 1205Lu, FRA1 (CutRun), #3

description: Library name: S07_1205Lu-FRA1-3


title: Fasted Male LKO-2

value: CPT1a LKO


title: IR64, leaf, severe drought, Day 8, rep 2

description:
Library name: IRLS8D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS8D2


title: CXCL10_1h Rep1


title: 1205Lu, FRA1 (CutRun), #2

description: Library name: S06_1205Lu-FRA1-2


title: Refed Male Control-2

value: HFD-fed for 12-weeks; Refed at necropsy


title: CXCL10_0h Rep1


title: IR64, leaf, severe drought, Day 8, rep 1

description:
Library name: IRLS8D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS8D1


title: 1205Lu, FRA1 (CutRun), #1

description: Library name: S05_1205Lu-FRA1-1


title: Fasted Male Control-4


title: IR64, leaf, severe drought, Day 7, rep 3

description:
Library name: IRLS7D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS7D3


title: IL15_18h Rep1


title: A375, IgG (CutRun)

description: Library name: S04_A375-IgG


title: IR64, leaf, severe drought, Day 7, rep 2

description:
Library name: IRLS7D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS7D2


title: A375, FRA1 (CutRun), #3

description: Library name: S03_A375-FRA1-3


title: Fasted Male Control-2


title: IL15_6h Rep1


title: IL15_1h Rep1


title: Fasted Male Control-1


title: A375, FRA1 (CutRun), #2

description: Library name: S02_A375-FRA1-2


title: IR64, leaf, severe drought, Day 7, rep 1

description:
Library name: IRLS7D1
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS7D1


title: IR64, leaf, severe drought, Day 8, rep 3

description:
Library name: IRLS8D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS8D3


title: IL15_0h Rep1


title: Duodenum tissue，GR3

city: Nanjing

first: Xiaohan

last: Jiang

state: Jiangsu

address: No. 300 guangzhou road, nanjing city, China

institute: Department of digestive endoscopy

description: All.DEG.Expression

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp  software.
Reference genome and gene model annotation files were downloaded  from genome website directly. Index of the reference genome was built using  Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference  genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to  each gene. And then FPKM of each gene was calculated based on the length  of the gene and reads count mapped to this gene.
(For DESeq2 with biological replicates) Differential expression analysis of  two conditions/groups (two biological replicates per condition) was performed  using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: Csv files with FPKM data.

source_name: duodenum tissue

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels. RNA concentration and purity was measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （ 5X）. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.

value: duodenum tissue

value: Celiac disease delayed-type hypersensitivity (DTH) mouse model pre-administrated gliadin-rapamycin composite nanoparticles with enhanced gluten stimulation


title: IR64, leaf, severe drought, Day 6, rep 2

description:
Library name: IRLS6D2
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS6D2


title: pilot_PGP1,DDX4-tdTomato/REC8-mGreenLantern,Unsorted,meiosis_day15

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

institute: Harvard University

data_processing:
NextFlow methylseq pipeline (https://nf-co.re/methylseq/), version 2.6.0 with default settings
Assembly: hg38 plus lambda phage and pUC19 spike-in controls
Supplementary files format and content: Methylation coverage (bismark output)

growth_protocol: Plasmids for constitutive expression of BCL2 and doxycycline-inducible expression of HOXB5, BOLL, and MEIOC were integrated into F2 D4TDZG, F3 D4TT2G, and PGP1 D4TR8G reporter hiPSCs. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632. For 6-well plates, 1.5 mL of medium was used per well. After one day, the media was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days, and GSK3484862 was withdrawn starting on day 7. Cells were harvested at each day from day 0 (hiPSC) to day 15.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Micro kit from hiPSCs and cells from the meiosis induction at various time points. For some of the samples, DDX4+ and DDX4- cells were sorted prior to extraction (see sample information). Libraries were prepared from 200 ng DNA using the NEB Enzymatic Methyl-Seq kit (NEB #E7120) following the manufacturer’s instructions. Briefly, control DNA (methylated pUC19 and unmethylated λ phage) was spiked into each sample. Next, samples were sheared to ~300 bp using a Covaris S2 sonicator. Enzymatic methyl conversion was performed, and libraries were amplified using unique dual index primers. For the pilot experiment, 2 x 150 bp paired end sequencing was performed on an Illumina MiSeq. For the follow-up experiment, 2 x 150 bp paired end sequencing was performed on an Illumina NovaSeq.
Methyl-seq (NEB enzymatic kit)

treatment_protocol: Samples in the pilot experiment were fixed cells, and samples in the follow-up experiment were unfixed cells.

value: Unsorted


title: Duodenum tissue，GR2

description: All.DEG.Expression


title: Duodenum tissue，GR1

description: All.DEG.Expression


title: pilot_ATCC-BXS0116,DDX4-tdTomato/TFAP2C-mGreenLantern,Unsorted,meiosis_day15


title: IR64, leaf, severe drought, Day 5, rep 3

description:
Library name: IRLS5D3
Column name in rawCounts_IR64_timeseries_All_samples.txt: IRLS5D3