title: wild type adult hermaphrodite, sample group 3 rep 3

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

data_processing:
Deep sequencing data were analyzed using the miTRATA web interface (https://wasabi.ddpsc.org/~apps/ta/) after preprocessing the data using miTRATA’s accompanying Python3-based preprocess.seq pipeline, installed on the NIH High Performance Computing Cluster in a dedicated miniconda environment. The matureC. elegansmiRNAs from miRBase Release 22.1 were used for miTRATA mapping. A custom C++ script reformatted the miTRATA output by consolidating read numbers for all reads meeting the following criteria into a tabular format: a tail:head ratio >0.12 and a tail length≤3nt. These reformatted tailing data were further analyzed in RStudio. (One non-unique miRNA pair was of sufficient abundance to be included in tailing analysis—mir-44/45-3p;mir-45-3pwas therefore culled from tabular data to avoid plotting this data twice). To calculate reads per million, reads were normalized by the number of genome-mapping reads in the library (Supplementary Table S3). The number of genome-mapping reads was determined using Bowtie to align to the C. elegans genome (WS215) with the arguments -v 3 -f -B 1 -a –best –strata. Alignments were then filtered based on the length of the reads and the number of mismatches as follows: for sequence lengths 16–17, 18–19, 20–24or >24: zero, one, twoor three mismatches were allowed, respectively. Reads passing this threshold were considered ‘genome-mapping reads’. A custom bash/R pipeline was used to calculate trimming relative to canonical miRNA length from the miTRATA output files.
Assembly: WBcel_235
Assembly: WS215
Supplementary files format and content: xlsx file containing sample metadata, normalized reads and percent tailing for microRNAs above minimum abundance threshhold

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: N2 (wild type) and SX1137 (pash-1(mj100) I) worms were maintained at 15°C. For RNA samples, L1s were synchronized by alkaline hypochlorite lysis of gravid adults followed by hatching in M9 with 1 mM cholesterol at 15°C for 48–72 h. L1s were plated on NGM seeded with either OP50 or RNAi bacteria and maintained at 15°C until early day one of gravid adulthood (until just a few embryos were laid on the plate, ∼76 h after plating). (This time point was chosen because it achieved the best synchrony of SX1137, which tends to develop slightly asynchronously, even at permissive temperature). This time point was harvested for N2 samples, SX1137 samples in the RNAi screen, and served as 0h in time courses involving SX1137. Additional SX1137 plates were shifted to 25°C, and samples were collected at the indicated time points after upshift for time courses on OP50 or RNAi. pup-1(tm1021), pup-2(tm4344) and pup-1/-2(om129) mutations were maintained over a balancer chromosome at 15–20°C; RNA was isolated from homozygous F2 (M-Z-) 1-day adult hermaphrodites raised at 22°C.

extract_protocol:
Total RNA was isolated by Trizol extraction. Spike-ins were added at a final concentration of 0.1pg/μl (OP50 samples) or 1pg/μl (RNAi samples) in 100ng/μl total RNA.
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

treatment_protocol: RNAi plates were supplemented with 1μg/ml IPTG and 1μg/ml Carbenicillin (and poured no more than two weeks prior to use and stored at 4°C). The RNAi bacteria (HT115 expressing an RNAi vector) were prepared from single clones derived from the Ahringer library (Source Bioscience), the Vidal library (Source Bioscience), or custom RNAi vectors (Supplementary Table S1). All previously-reported RNAi phenotypes were observed. Furthermore, a robust RNAi response in each sample was confirmed by the presence of abundant siRNAs mapping to the targeted locus.

tag: sample

tag: time point

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage

value: adult

value: wild type

tag: Sex

value: hermaphrodite

value: whole animal


title: wild type adult hermaphrodite, sample group 3 rep 2

status: Public on Jun 01 2024

type: SRA

country: USA

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: genotype

tag: tissue


title: hTERT-RPE1, siNeg, ATAC-seq, rep 2

city: Chicago

first: Sakshi

last: Khurana

state: IL

address: SQBRC Room 7-400, 303 E Superior St.

department: Biochemistry and Molecular Genetics

institute: Northwestern University

library_source: genomic

data_processing:
Data was processed using the nf-core/atacseq pipeline (https://nf-co.re/atacseq/2.1.2)
Base calls were performed using bcl2fastq2.20 for HiSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with TrimGalore and then reads were aligned to GRCh38 with BWA
Bigwig files were produced using bedtools
Assembly: GRCh38
Supplementary files format and content: bigWig for each sample

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Transposition was conducted with Tagment DNA Enzyme and Buffer Kit from Illumina and purified using Qiagen MinElute Reaction Cleanup Kit
Transposed DNA was PCR amplified and library prepped using Nextera adaptors from Illumina

treatment_protocol: 20nM siRNA treatment overnight, cells collected 48 hours after siRNA treatment

tag: cell line

tag: cell type

value: epithelial

value: WT

tag: treatment

value: siNeg


title: Heart, control, WT6

city: London

first: Alison

last: Thomas

address: Charterhouse Square, William Harvey Heart Centre, 1st Floor

department: Clinical Pharmacology and Precision Medicine

country: United Kingdom

institute: QMUL

data_processing:
PartekFlow was used for data processing.
Contaminants filtered and quality controlled using Bowtie2
Sequences aligned to the mouse reference genome (Mm10) using STAR (v3.7.1)
Genes were annotated and counted using PartekFlow Quantify to annotation model (Partek E/M) and Ensembl 102.
DeSeq2 used for differential expression within PartekFlow.
Assembly: Mm10
Supplementary files format and content: tab delimited text file containing gene counts for each sample.

organism: Mus musculus

source_name: Heart

extract_protocol:
RNA was extracted using Rneasy Fibrous Tissue mini kit (Qiagen).
Library preparation for RNA-seq was carried out using NEB Next UltraTM II RNA library prep kit (New England Biolabs) following manufacturer's protocols.

treatment_protocol: 1mg tamoxifen/25g body weight was injected intraperitoneally in mice for 3 consecutive days. Two days after the last injection, hearts were removed and stored in RNAlater.

value: Heart

value: Control


title: wild type adult hermaphrodite, sample group 3 rep 1


title: GLV, model, rep1

city: Beijing

first: Shutao

last: Pan

address: Liangxiang University Town, Fangshan District, Beijing, 102488, China

country: China

institute: Beijing University of Chinese Medicine

data_processing:
High-quality clean reads were filtered by SOAPnuke (v1.5.2 ; https://github.com/BGI-flexlab/SOAPnuke) with a low-quality base ratio (≤5) of >20%, and an unknown base ("N" base) ratio of > 5%.
The reads were mapped to ribosome RNA (rRNA) database by Bowtie2 (v2.2.5; http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and then the rRNA mapped reads were removed.
Reads were mapped onto the Rattus norvegicus reference genome using HISAT2 (version 2.2.4), and >80% alignment was achieved.
The gene expression levels were normalized as fragments per kilobase of transcript per million (FPKM).
Assembly: Rnor_6.0
Supplementary files format and content: Excel file include FPKM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Gastric lymphatic vessel (GLV)

growth_protocol: Male Sprague-Dawley rats (180-220 g) were purchased from SPF (Beijing) Biotechnology Co., Ltd. (Beijing, China, Animal Production License No. SCXK2019-0010) and underwent an adaption period of 3d under standard conditions of temperature (22 ± 2 °C) and humidity (40-70%) with 12 h light and dark cycles and free access to standard rodent pellet chow and water

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and purified by chloroform/isoamyl alcohol extraction and 75% ethanol precipitation. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.
RNA quality was detected by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The qualified RNA samples are denatured at suitable temperature, and the mRNA is enriched by oligo (dT) -attached magnetic beads. The target mRNA fragments were reverse transcribed into cDNA, and the complementary cDNA chain was synthesized. The cDNA fragments were purified with the QiaQuick PCR extraction kit and eluted with EB buffer. The purified cDNA was end-repaired and the poly(A) were added. Suitable fragments were selected, purified, and subsequently PCR-amplified to establish cDNA library template. The prepared DNA library was sequenced on the Illumina HiSeq2500 platform.

treatment_protocol: The rats were randomly assigned into a normal control group (CON), a model group (MOD), a BXD treated group (BXD), and an anti-ulcer positive control drug (omeprazole) group (OME) with 6 rats in each group (n = 6). All rats were fasted for 12h before the experiment. On the day of the experiment, the rats in the CON group were left without intervention, and the other 3 groups were subjected to a classical water-immersion stress modeling process (Rajagopal et al., 2018). Briefly, the rats were placed individually in an opaque 13×13 cm cubic pool of 40 cm height filled with water up to 15 cm for 4h. The water temperature was maintained at 22 ± 2 °C. Afterwards, all rats were removed from the pool, wiped by dry towel, and put into their original cages. Any rats that may have appeared to drown would have been removed from the experiment, but no such outcomes occurred. 30 min afterward, the rats in the BXD and OME groups were administered BXD or omeprazole respectively at a dose of 10ml/kg body weight by gavage, and rats in the CON and MOD groups were administered the same dose of distilled water. All the gavage solutions were kept in a 37 °C water bath before use.

value: Gastric lymphatic vessel (GLV)

value: SIGU modeling+saline gavage


title: soil sample under control in 2018, block B2

type: RNA

first: Yifan

last: Su

address: Haidian District

department: School of Environment

institute: Tsinghua University

hyb_protocol: As previously described (Guo et al. Nature Communication, 2020), Labeled DNA was resuspended into DNase-free water, and then mixed completely with hybridization solution. After denaturation and incubation, the DNA solution was centrifuged to collect liquid at the bottom of the tube. The solution was hybridized at 67 °C for 24 h at 20 rpm in a hybridization oven.

scan_protocol: The resulting GeoChip arrays were scanned as Multi-TIFF images with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Inc., Madison, WI, USA).

data_processing: Raw signals extracted from scanned images were submitted to the Microarray Data Manager on our website (http://ieg.ou.edu/microarray/) for cleaning and normalizing. To remove unrepresentative data, we assigned probes detected in less than three out of twelve samples for warmed litterbag, control litterbag, warmed bulk soil, and control bulk soil samples to undetectable. We then logarithmically transformed the remaining data and scaled the sum of signal intensity for each sample with the maximum sum value.

organism: soil metagenome

source_name: bulk soil, control

label_protocol: As previously described (He et al. 2010; Shi et al. 2019; Guo et al., Nature Communication, 2020), purified DNA from each sample was labeled with fluorescent dye Cy-3 dUTP.

growth_protocol: Stored at -80 °C

extract_protocol: Microbial DNA was extracted for each sample by freeze-grinding and SDS-based cell lysis (Zhou, Bruns, and Tiedje 1996), and purified with the PowerSoil DNA Isolation Kit (MoBio Laboratories, Carlsbad, CA, USA). The quality of extracted DNA was assessed by the absorbance ratios of O.D. 260/230 nm and O.D. 260/280 nm with an ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA). The DNA concentration was quantified using a FLUOstar Optima fluorescence plant reader (BMG Labtech, Jena, Germany).

tag: sample type

value: bulk soil


title: hTERT-RPE1, Input, rep 1

data_processing:
Data was processed using the nf-core/chipseq pipeline (https://nf-co.re/chipseq/2.0.0)
Base calls were performed using bcl2fastq2.20 for HiSeq output
Demultiplexed fastq files were trimmed according to trailing quality scores with TrimGalore and then reads were aligned to GRCh38 with BWA
Bigwig files were produced using bedtools and peak calling was done using Macs2
Assembly: GRCh38
Supplementary files format and content: bigWig for each sample

extract_protocol:
Cells were fixed with 1% formaldehyde and sonicated using the E220 Covaris ultrasonicator. Protein-DNA complexes were then immunoprecipitated with respective antibodies overnight.
ChIP DNA was extracted using Qiagen PCR Purification Kit and library prepped using NEBNext DNA Ultra II Library Preperation Kit

tag: chip-antibody


title: soil sample under control in 2018, block B1


title: soil sample under control in 2018, block B4


title: hTERT-RPE1, siNeg, ATAC-seq, rep 1


title: soil sample under control in 2017, block B2


title: soil sample under control in 2017, block B1


title: soil sample under control in 2018, block B3


title: soil sample under control in 2016, block B2


title: hTERT-RPE1, siCENP-F, ATAC-seq, rep 2

value: CENP-F KD

value: siCENPF


title: Heart, control, WT5


title: soil sample under control in 2017, block B4


title: pup-2(tm4344) III adult hermaphrodite, sample group 3 rep 3

value: pup-2(tm4344) III


title: Heart, control, WT4


title: pup-2(tm4344) III adult hermaphrodite, sample group 3 rep 2


title: NL4 iPSCs, 5 passages, E8.2

city: macau

first: Chengcheng

last: SONG

address: universtiy of macau

department: fhs

country: Macau

institute: university of macau

data_processing:
Quality control of RNA-seq raw data was performed using Trimmomatic version 0.36
RNA-seq clean data alignment was conducted using STAR version 020201 with the reference genome hg38.
All genes expression were quantified using FeatureCounts version 1.5.3
Assembly: hg38

growth_protocol: H1/H9 ESCs and NL1/NL4 hiPSCs were maintained in E8 medium supplemented with  antibiotics  with 5% CO2 at 37C. E8 medium contained DMEM/F12, sodium selenite, ascorbic acid trisodium, transferrin, insulin, FGF2 and TGFβ.

extract_protocol:
Cells was harvested in RNAiso Plus reagent (Takara). The poly(A) mRNA isolation was performed using Oligo(dT) beads according to manufacturer’s instructions
1 μg total RNA was used for following library preparation. The RNA Library were sequenced for paired end reads on Illumina NextSeq 500 (Illumina).

treatment_protocol: H1/H9 ESCs and NL1/NL4 hiPSCs were cultured in E8 medium. Cells dissociated by EDTA-DPBS. Cell passages were conducted with E8 medium with Y-27632 at the the ratio of 1:6 when 80-90% cell fluence.

value: Human induced plurpotency stem cells

value: E8 for 5 passages in NL4 iPSCs


title: soil sample under control in 2017, block B3


title: NL4 iPSCs, 5 passages, E8.1


title: pup-2(tm4344) III adult hermaphrodite, sample group 3 rep 1

value: adult


title: Heart, control, WT2


title: NL1 iPSCs, 5 passages, E8.2

value: E8 for 5 passages in NL1 iPSCs


title: Heart, control, WT1


title: soil sample under control in 2016, block B1


title: soil sample under control in 2016, block B4


title: NL1 iPSCs, 5 passages, E8.1


title: cid-1(tm1021)/qC1 [dpy-19(e1259); glp-1(q339); qIs26] III  adult hermaphrodite, sample group 3 rep 3

value: hermaphrodite


title: cid-1(tm1021)/qC1 [dpy-19(e1259); glp-1(q339); qIs26] III  adult hermaphrodite, sample group 3 rep 2

value: whole animal


title: RNAseq_PDAC_SB1557_CB6644_r3

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

description:
TOC_PDAC_SB1557_CB6644.tsv
DGE_PDAC_SB1557_CB6644.tsv

data_processing:
STAR alignment to the mm39 reference sequence
gene-level reads (Ensembl version 111) were counted using GenomicAlignments R package (version 1.38.2)
Differential gene expression analysis using edgeR (version 4.0.16)
Assembly: mm39
Supplementary files format and content: .tsv file containing the results of differential gene expression analysis for each cell line upon CB-6644 treatment.

growth_protocol: 8661, 9091, 9172, 24033 and SB1557 cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.

extract_protocol:
total RNA was extracted using miRNeasy kit (Qiagen)
NEBNext rRNA Depletion v2 followed by NEBNext Ultra II RNA Library Prep kit

treatment_protocol: Cells were treated with 1 µM CB-6644 or DMSO for 24 h.

value: pancreatic ductal adenocarcinoma

value: Ptf1a-Cre +, LSL-Kras G12D mut/wt, TgfBr2 ko/ko


title: H9 ESCs, 5 passages, E8.2

value: Human embryonic stem cells

value: WT

value: E8 for 5 passages in H9 ESCs


title: RNAseq_PDAC_SB1557_CB6644_r2


title: cid-1(tm1021)/qC1 [dpy-19(e1259); glp-1(q339); qIs26] III  adult hermaphrodite, sample group 3 rep 1


title: H9 ESCs, 5 passages, E8.1


title: RNAseq_PDAC_SB1557_CB6644_r1


title: cid-1/-2(om129)/qC1 [dpy-19(e1259); glp-1(q339); qIs26] III  adult hermaphrodite, sample group 3 rep 3


title: RNAseq_PDAC_SB1557_DMSO_r3

value: DMSO 24 h


title: H1 ESCs, 5 passages, E8.3

value: E8 for 5passages in H1 ESCs


title: H1 ESCs, 5 passages, E8.2


title: cid-1/-2(om129)/qC1 [dpy-19(e1259); glp-1(q339); qIs26] III  adult hermaphrodite, sample group 3 rep 2


title: H1 ESCs,5 passages, E8.1

value: E8 for 5 passages in H1 ESCs


title: cid-1/-2(om129)/qC1 [dpy-19(e1259); glp-1(q339); qIs26] III  adult hermaphrodite, sample group 3 rep 1


title: RNAseq_PDAC_SB1557_DMSO_r1


title: litter sample under control in 2018, block B2

organism: decomposition metagenome

source_name: litterbag contain cellulose paper, control

value: litterbag


title: litter sample under control in 2017, block B2


title: NL4 iPSCs，5 passages ,E8+2DG3.2

description: 19_Batch_2_NL4_E8+2-DG_3mM_FRAS202204696-1r

data_processing:
Quality control of RNA-seq raw data was performed using Trimmomatic version 0.36
RNA-seq clean data alignment was conducted using STAR version 020201 with the reference genome hg38.
All genes expression were quantified using FeatureCounts version 1.5.3
Differential expression genes (DEGs) were identified with the criteria of p adjusted value < 0.05 and the absolute value of log2(Fold Change) > 1 after profile normalized using DESeq2 version 1.26.0
DEGs analysis were performed the GO and KEGG enrichment analysis through the R package ClusterProfiler 4.0

treatment_protocol: 2DG treated with 1/3mM in E8 medium for 5 passages in H1/H9 ESCs and NL1/NL4 hiPSCs. Cells dissociated by EDTA-DPBS. Cell passages were conducted with E8 medium with Y-27632 at the the ratio of 1:6 when 80-90% cell fluence. 2DG treatment was added only cell cluture ,and no 2DG was added during seeding cells.

value: E8 with 2DG 3 mM for 5 passages in NL4 iPSCs


title: litter sample under control in 2016, block B1


title: soil sample under control in 2016, block B3

value: bulk soil


title: litter sample under control in 2016, block B2


title: litter sample under control in 2017, block B1


title: RNAseq_PDAC_24033_CB6644_r3

description:
TOC_PDAC_24033_CB6644.tsv
DGE_PDAC_24033_CB6644.tsv

value: Pdx1-Cre +, LSL-Kras G12D mut/wt, Cdkn2a ko/ko


title: RNAseq_PDAC_24033_CB6644_r2


title: NL4 iPSCs，5 passages ,E8+2DG3.1

description: 18_Batch_1_NL4_E8+2-DG_3mM_FRAS202204695-1r

value: Human induced plurpotency stem cells


title: RNAseq_PDAC_SB1557_DMSO_r2


title: NL4 iPSCs，5 passages ,E8+2DG1.2

description: 17_Batch_2_NL4_E8+2-DG_1mM_FRAS202204694-1r

value: E8 with 2DG 1 mM for 5 passages in NL4 iPSCs


title: RNAseq_PDAC_24033_CB6644_r1


title: NL4 iPSCs，5 passages ,E8+2DG1.1

description: 16_Batch_1_NL4_E8+2-DG_1mM_FRAS202204693-1r


title: NL4 iPSCs，5 passages ,E8.2

value: E8 for 5 passages in NL4 iPSCs


title: RNAseq_PDAC_24033_DMSO_r3


title: litter sample under control in 2018, block B4


title: litter sample under control in 2017, block B4


title: RNAseq_PDAC_24033_DMSO_r2


title: NL4 iPSCs，5 passages ,E8.1


title: RNAseq_PDAC_24033_DMSO_r1


title: litter sample under control in 2016, block B4


title: NL1 iPSCs，5 passages ,E8+2DG1.2

description: 23_Batch_2_NL1_E8+2-DG_1mM_FRAS202204700-1r

value: E8 with 2DG 1 mM for 5 passages in NL1 iPSCs


title: litter sample under control in 2018, block B3


title: litter sample under control in 2018, block B1


title: RNAseq_PDAC_9172_CB6644_r3

description:
TOC_PDAC_9172_CB6644.tsv
DGE_PDAC_9172_CB6644.tsv

value: Ptf1a-Cre +, LSL-Kras G12D mut/wt, LSL-Trp53 R172H mut/wt


title: NL1 iPSCs，5 passages ,E8+2DG1.1

description: 22_Batch_1_NL1_E8+2-DG_1mM_FRAS202204699-1r


title: litter sample under control in 2017, block B3


title: HT03

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo
Gene expression interrogating 31099 transcripts

hyb_protocol: The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26].  Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through Partek GS ANOVA statistic and ToppCluster.

label: biotin

source_name: The pup was cared for in >90% oxygen chamber (HOX) and treated with taurine 100 mg/kg daily i.p.  from postnatal day 1 to day 10 (P1-P10), rat3

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo (Madison, WI) and were acclimated to our animal facility for 7 days. The use of animals was approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee and conformed to the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol: Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA).  RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. According to the study design, two or four pregnant rats were used for each experiment. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10), and then all of them were caged in room air between P11 and P21.  Oxygen concentrations were continuously monitored with an oxygen sensor (Reming Bioinstruments Co., Redfield, NY). Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity. Taurine 100 mg/kg/d was given i.p. between P1 and P10. One dose of tunicamycin 0.3 mg/kg was given at P3 i.p. TUDCA 100 mg/kg was given i.p. between P1 and P10.

value: Lung

value: Sprague-Dawley

tag: age

value: 10 days old


title: HT06

source_name: The pup was cared for in >90% oxygen chamber (HOX) and treated with taurine 100 mg/kg daily i.p.  from postnatal day 1 to day 10 (P1-P10), rat6


title: HT04

source_name: The pup was cared for in >90% oxygen chamber (HOX) and treated with taurine 100 mg/kg daily i.p.  from postnatal day 1 to day 10 (P1-P10), rat4


title: HT05

source_name: The pup was cared for in >90% oxygen chamber (HOX) and treated with taurine 100 mg/kg daily i.p.  from postnatal day 1 to day 10 (P1-P10), rat5


title: NL1 iPSCs，5 passages ,E8.2

value: WT

value: E8 for 5 passages in NL1 iPSCs


title: soil sample under warming in 2018, block B3

source_name: bulk soil, +3°C warming


title: RNAseq_PDAC_9172_CB6644_r2

value: pancreatic ductal adenocarcinoma


title: RNAseq_PDAC_9172_CB6644_r1


title: NL1 iPSCs，5 passages ,E8.1


title: H06

source_name: The pup was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat6


title: soil sample under warming in 2018, block B4


title: soil sample under warming in 2018, block B1


title: RNAseq_PDAC_9172_DMSO_r3

value: DMSO 24 h


title: litter sample under control in 2016, block B3


title: H9 ESCs，5 passages ,E8+2DG1.2

description: 13_Batch_2_H9_E8+2-DG_1mM_FRAS202204690-1r

value: Human embryonic stem cells

value: E8 with 2DG 1 mM for 5 passages in H9 ESCs


title: HT02

source_name: The pup was cared for in >90% oxygen chamber (HOX) and treated with taurine 100 mg/kg daily i.p.  from postnatal day 1 to day 10 (P1-P10), rat2


title: H04

source_name: The pup was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat4


title: RNAseq_PDAC_9172_DMSO_r1


title: H9 ESCs，5 passages ,E8.2

value: E8 for 5 passages in H9 ESCs


title: RNAseq_PDAC_9172_DMSO_r2


title: H05

source_name: The pup was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat5


title: H03

source_name: The pup was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat3


title: soil sample under warming in 2017, block B1

value: bulk soil


title: H9 ESCs，5 passages ,E8+2DG1.1

description: 12_Batch_1_H9_E8+2-DG_1mM_FRAS202204689-1r


title: HT01

source_name: The pup was cared for in >90% oxygen chamber (HOX) and treated with taurine 100 mg/kg daily i.p. from postnatal day 1 to day 10 (P1-P10), rat1


title: H01

source_name: The pup was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat1


title: H1 ESCs，5 passages ,E8+2DG3.2

description: 8_Batch_2_H1_E8+2-DG_3mM_FRAS202204685-1r

value: E8 with 2DG 3 mM for 5 passages in H1 ESCs


title: Mon_SplC_R3

city: 昆明市

first: Lin

last: dongdong

state: 云南

address: 云南省昆明市五华区茭菱路

institute: Peking Union Medical College

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Deduplicated Reads were mapped to the reference genome of macaca mulatta and mus Musculus from Mmul_8.0.1 and GRCm38 respectively using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with an FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
For lncRNA analysis, new lncRNAs were predicted. briefly, The mapped reads were spliced to obtain new transcripts by Stringtie(version 1.3.2). Then，new transcripts were fileted by four principle:1) Filter out the transcripts less than 200bp in length; 2) Filter out the transcripts containing less than 2 exons; 3) Include the transcripts containing at least 3 reads; 4) Remove known transcripts from the genome annotation file. Then, CPC2(version beta)、CPAT(version 1.2.4)、CNCI(version 2) and Pfam(version 27.0)were used to predict the coding potential of the selected transcripts. The transcripts predicted to be non-coding in all four softwares or database were referred to them as novel lncRNA.
The expression of novel lncRNA and genome annotated known lncRNA were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. LncRNA differentially expressed between groups were identified using the edgeR package (version 3.12.1). P-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of lncRNA expression differences.
Assembly: Mmul_8.0; GRCm38

molecule: polyA RNA

organism: Macaca mulatta

source_name: spleen

extract_protocol:
Total RNAs were extracted from （monkey and mouse’ organs including heart, liver, spleen, lung, kidney, brain) using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies，Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: spleen

value: CHIKV control

tag: time


title: Mon_SplT_R3

address: 云南省昆明市五华区茭菱路

value: CHIKV infection


title: soil sample under warming in 2017, block B4


title: Mon_SplT_R2

address: 云南省昆明市五华区茭菱路


title: soil sample under warming in 2017, block B3


title: RNAseq_PDAC_9091_CB6644_r2

description:
TOC_PDAC_9091_CB6644.tsv
DGE_PDAC_9091_CB6644.tsv

value: Ptf1a-Cre +, LSL-Kras G12D mut/wt, mesenchymal


title: H1 ESCs，5 passages ,E8+2DG3.3

description: 9_Batch_3_H1_E8+2-DG_3mM_FRAS202204686-1r


title: H1 ESCs，5 passages ,E8+2DG3.1

description: 7_Batch_1_H1_E8+2-DG_3mM_FRAS202204684-1r


title: Mon_SplT_R1

address: 云南省昆明市五华区茭菱路


title: H02

source_name: The pup was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat2


title: RNAseq_PDAC_9091_CB6644_r3


title: RNAseq_PDAC_9091_CB6644_r1


title: H9 ESCs，5 passages ,E8.1


title: RNAseq_PDAC_9091_DMSO_r1


title: soil sample under warming in 2016, block B3


title: soil sample under warming in 2018, block B2


title: litter sample under warming in 2018, block B3

source_name: litterbag contain cellulose paper, +3°C warming

value: litterbag


title: H1 ESCs，5 passages ,E8+2DG1.2

description: 5_Batch_2_H1_E8+2-DG_1mM_FRAS202204682-1r

value: E8 with 2DG 1 mM for 5 passages in H1 ESCs


title: RNAseq_PDAC_9091_DMSO_r3


title: soil sample under warming in 2017, block B2


title: soil sample under warming in 2016, block B4


title: Mon_SplC_R2

address: 云南省昆明市五华区茭菱路


title: RNAseq_PDAC_8661_CB6644_r3

description:
TOC_PDAC_8661_CB6644.tsv
DGE_PDAC_8661_CB6644.tsv

value: Ptf1a-Cre +, LSL-Kras G12D mut/wt, klassisch


title: Mon_SplC_R1

address: 云南省昆明市五华区茭菱路


title: Mon_LunT_R2

address: 云南省昆明市五华区茭菱路

source_name: lung

value: lung


title: H1 ESCs，5 passages ,E8+2DG1.3

description: 6_Batch_3_H1_E8+2-DG_1mM_FRAS202204683-1r

value: WT


title: RNAseq_PDAC_9091_DMSO_r2


title: Mon_LunT_R3

address: 云南省昆明市五华区茭菱路


title: RNAseq_PDAC_8661_CB6644_r2


title: RNAseq_PDAC_8661_CB6644_r1


title: RNAseq_PDAC_8661_DMSO_r3


title: Mon_LunC_R3

address: 云南省昆明市五华区茭菱路


title: soil sample under warming in 2016, block B2


title: Mon_LunC_R2

address: 云南省昆明市五华区茭菱路


title: H1 ESCs，5 passages ,E8+2DG1.1

description: 4_Batch_1_H1_E8+2-DG_1mM_FRAS202204681-1r


title: Mon_LunT_R1

address: 云南省昆明市五华区茭菱路


title: H1 ESCs，5 passages ,E8.3

value: E8 for 5 passages in H1 ESCs


title: H1 ESCs，5 passages ,E8.1


title: litter sample under warming in 2017, block B3


title: soil sample under warming in 2016, block B1


title: RNAseq_PDAC_8661_DMSO_r1

value: pancreatic ductal adenocarcinoma


title: Mon_LivT_R3

address: 云南省昆明市五华区茭菱路

source_name: liver

value: liver


title: RNAseq_PDAC_8661_DMSO_r2

value: DMSO 24 h


title: Mon_LivT_R2

address: 云南省昆明市五华区茭菱路


title: litter sample under warming in 2018, block B1


title: litter sample under warming in 2016, block B3


title: Mon_LunC_R1

address: 云南省昆明市五华区茭菱路


title: iPSC-derived neurons, Control treated 1

city: Cleveland

first: Feixiong

last: Cheng

state: Ohio

address: 9500 Euclid Ave

department: Genomic Medicine

institute: Cleveland Clinic

description: pair-end 75bp

data_processing:
We used SQuIRE software for analyzing transposable element expression and gene expresison at the same time. Then we used fixed/mixed effects modelling to adjust for possible factors mentioned above on TMM-normalized count matrix table under the edgeR and voom package79. P values were adjusted for multiple testing using Benjamini-Hochberg method, with TEs considered differentially expressed at |log2FC| ≥ 0.5 and q < 0.10.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each group

source_name: Cell line

growth_protocol: The virus was titrated in iPSCs by antibiotics selection. For CRISPRi experiments, iPSCs were first differentiated into 2-week excitatory neurons. The neurons were then treated with lentivirus expressing sgRNAs (multiplicity of infection ~3) and subjected to puromycin selection (0.5 ug/mL) for 4 days. Cells were collected for mRNA extraction 7 days post-transfection.

extract_protocol:
DNase treated samples were sent to the genomics core of Lerner Research Institute, Cleveland Clinic for RNA-seq. Pair-end 75 bp RNA-seq libraries were constructed following Illumina’s protocols. RNA-seq analysis were conducted with two biologically independent replicates.
Pair-end 75 bp RNA-seq libraries were constructed following Illumina’s protocols.

treatment_protocol: i3N-WTC11 neurons were differentiated with a two-step protocol as previously described105. dCas9-KRAB driven by CAG promoters was knocked-in to a safe harbor locus in the intronic region of CLYBL to enable robust transgene expression through differentiation106. sgRNAs targeting locus TEs and promoters of target genes were designed by CHOP-CHOP107 with high efficiency. The mismatch number of MM1 and MM2 were set to 0 and MM3 was lower than 5 mismatches. Two independent sgRNAs were used for each locus TE. sgRNA oligoes were inserted into lentiGuide-puro vector (Addgene 52963) and the plasmids were co-transfected with lentivirus packaging plasmids including pMD2.G (Addgene, 12259) and psPAX (Addgene, 12260) into 293T cells by PolyJet (SignaGen Laboratories SL100688). Virus-containing media was collected for 48 h, filtered through 0.45 μm filters (Millipore SLHV033RS), and concentrated with Amicon Ultra centrifugal filters (Millipore UFC801024).

value: Cell line

value: iPSC-derived neurons

value: i3N-WTC11 neurons

value: Control


title: iPSC-derived neurons, Control treated 2

description: pair-end 75bp


title: ChIPseq_A375_RUVBL1_Auxin

data_processing:
Illumina NextSeq500/2000
Base calling was performed using bcl2fastq (version 3.7.4)
KPC-AID-RUVBL1: Alignment against mouse (mm10) and human (hg19, spike-in) genome with Bowtie2 (version 2.3.4.1), A375-MYC-AID: Alignment against human (hg19) and mouse (mm10, spike-in) genome with Bowtie2 (version 2.3.4.1)
Normalization according to spike-in
Conversion to bedgraphs with bedtools genomecov (version 2.26.0)
Peak calling with MACS2 (version 2.2.7.1) and p-value cutoffs 0.01 (MYC) and 0.001 (RUVBL1)
Assembly: mm10/hg19
Supplementary files format and content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Supplementary files format and content: narrowPeak files contain MYC and RUVBL1 peak locations

growth_protocol: KPC-AID-Ruvbl1 cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin. A375-MYC-AID cells were grown in RPMI-1640 supllemented with 10 % FCS and 1 % Penicillin/Streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Formaldehyde was quenching with glycine, cells were lysed and chromatin was sonicated.
NEBNext Ultra II DNA Library Prep Kit for Illumina, libraries were amplified for 13 cycles and concentration and size distribution were evaluated using an Agilent Fragment Analyzer.

treatment_protocol: KPC-AID-Ruvbl1 cells were treated with 1 µM 5-Ph-IAA for 15 h. A375-MYC-AID cells were treated with 1 µM 5-Ph-IAA for 3 h

value: KPC

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, AID-Ruvbl1

value: 1 µM 5-Ph-IAA 3 h


title: H1 ESCs，5 passages ,E8.2

value: Human embryonic stem cells


title: litter sample under warming in 2017, block B1

value: litterbag


title: iPSC-derived neurons,CRISPRi treated1

description: pair-end 75bp

value: CRISPRi


title: iPSC-derived neurons,CRISPRi treated2

description: pair-end 75bp


title: ChIPseq_A375_RUVBL1_Control


title: Mon_LivT_R1

address: 云南省昆明市五华区茭菱路

value: CHIKV infection


title: litter sample under warming in 2018, block B4


title: Mon_LivC_R2

address: 云南省昆明市五华区茭菱路

value: CHIKV control


title: Mon_LivC_R3

address: 云南省昆明市五华区茭菱路


title: Exosome,NOR8

first: Qihui

last: Feng

address: Xizhimen South street

institute: Peking University People's Hospiotal

data_processing:
Original image data obtained from Illumina Hiseq2500 platform is converted into Raw data (raw reads) rhtough base calling perfomred by fastp (0.23.1, fastp --in1 sample_L2_1.fq.gz --in2  sample_L2_2.fq.gz --out1 sample_L2_1.fq.gz --out2         sample_L2_2.fq.gz -g -q 5 -u 50 -n 1 -l 15 --min_trim_length 10 --overlap_diff_limit 1 --overlap_diff_percent_limit 10 -j sample_L2.json -h sample__L2.html)
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. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Use Bowtie tools soft (v1.0.0, -v 0), The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats.
The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase.
Assembly: GRCh38
Supplementary files format and content: excel files include raw counts and TPM values for each sample

source_name: follicular fluid exosome

growth_protocol: During oocyte retrieval, the follicular fluid from the dominant follicle was collected and then centrifuged at 500 ×g for 10 min to remove blood and debris. The supernatant was then collected and cryopreserved at −80°C for further analysis

extract_protocol:
Exosomal miRNAs were extracted using the miRNeasy Serum/Plasma Advanced Kit (#217204, Qiagen, Frederick, MD, USA) according to the manufacturer’s protocol.
For small RNA libraries, an input of 1 ng to 500 ng of RNA per sample was used for RNA sample preparations. Sequencing libraries were generated using the QIAseq miRNA Library Kit (Qiagen) following the manufacturer’s recommendations, and index codes were added to assign sequences to each sample. Library quality was evaluated using the Agilent Bioanalyzer 2100 and qPCR. The index-coded samples were clustered using the acBot Cluster Generation System with the TruSeq PE Cluster Kitv3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform, and paired-end reads were generated.

treatment_protocol: Exosomes were isolated from the follicular fluid using the ultracentrifugation method. After thawing at 37 °C, follicular fluid samples were centrifugated at 3,000 ×g for 15 min to remove cell debris. The resulting supernatant was diluted by a seven-fold volume of phosphate-buffered saline (PBS) and then centrifuged at 13,000 ×g for 30 min. Subsequently, the supernatant was filtered through a 0.22 μm filter to eliminate large particles. The supernatant was ultracentrifuged using a P50A72-986 rotor (CP100NX; Hitachi, Brea, CA, USA) at 100,000 ×g, 4 °C for 2 h to pellet the exosomes. The pellet was resuspended in PBS and centrifuged again at 100,000 ×g, 4 °C for 2 h. After washing with PBS, the pellet containing exosomes was resuspended in 100 µL of PBS.

value: follicular fluid exosome

tag: condition

value: normal ovarian reserve (NOR)


title: litter sample under warming in 2017, block B4


title: ChIPseq_A375_MYC_Auxin

value: pancreatic ductal adenocarcinoma


title: Exosome,NOR9


title: ChIPseq_A375_Input_merged

value: Input


title: Exosome,NOR7


title: Mon_LivC_R1

address: 云南省昆明市五华区茭菱路

value: liver


title: litter sample under warming in 2017, block B2


title: SLAMseq_AID_Ruvbl1_Ctrl_15h_R3

data_processing:
GRAND SLAM (version 2.0.5g, Jürges et al., 2018, Bioinformatics)
Trimming of 5' 10 nt UMI, and 3' Adapter
STAR alignment to the mm10 reference sequence
Differential gene expression analysis using DESeq2 (version 1.36.0)
Assembly: mm10
Supplementary files format and content: .tsv/.csv file containing the results of differential gene expression analysis

growth_protocol: KPC-AID-Ruvbl1 and KPC-MYC-ER cells were grown in DMEM suplemented with 10 % FCS and 1% Penicillin/Streptomycin.

extract_protocol:
total RNA was extracted using miRNeasy kit (Qiagen)
QuantSeq 3' mRNA-Seq Library Prep Kit (FWD)
OTHER: SLAMseq

treatment_protocol: KPC-AID-Ruvbl1 cells were treated with 1 µM 5-Ph-IAA for 3 or 15 h respectively followed by 2 h of labelling with 800 µM 4sU. KPC-MYC-ER cells were treated with 1 µM CB-6644 for 20 h followed by 4 h treatment with 4-OHT and 2 h of labelling with 400 µM 4sU.

value: Ctrl


title: litter sample under warming in 2016, block B1


title: captured mRNA-derived cDNA, foliar sample, rep 3, second experiment

city: Beaucouzé

first: Martial

last: Briand

address: 42, rue Georges Morel

country: France

institute: INRAE

data_processing:
Sequence reads were trimmed for adapter and low-quality sequence directly within Illumina NextSeq 550 software
Genomic sequence of strain CFBP 7767 was annotated using Eugene-PP and InterproScan results for structural and functional annotations, respectively.
Salmon was used to assign reads to predicted CFBP7767 mRNA.
Assembly: GCF_002759375.1 : Pacbio assembly of genomic sequence of CFBP 7767  (ASM275937v2: NZ_CP021012.1, NZ_CP021013.1, and NZ_CP021014.1) was used  for alignment (Briand, M., Ruh, M., Darrasse, A., Jacques, M.-A., and Chen, N. W. (2021). Complete and Circularized Genome Sequences of 17 Xanthomonas Strains Responsible for Common Bacterial Blight of Bean. Microbiol Resour Announc 10, e00371-21).
Supplementary files format and content: tab-delimited text files (.sf) include count and TPM values for each sample

organism: Xanthomonas citri pv. fuscans

source_name: leaf

growth_protocol: Bacterial suspension (106 cfu/ml) were spray-inoculated on bean at pre-flowering stage. Seeds of five plants were harvested and bulked to form a sample. Seeds were sampled 24, 35 and 42 days after pollination (DAP).

extract_protocol:
RNA was extracted using Trizol at 65°C. Depending on RNA quality, 100 to 200 ng of total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SureSelectXT RNA Direct technology (Agilent) according to supplier instructions. Probes (120 nt) for bacterial mRNA capture were designed from  annotated CFBP 7767 genomic sequence.

treatment_protocol:
Bacteria were extracted by soaking seeds overnight in PBS containing 20% blocking agent (RNAlater, ThermoFisher scientific).
Macerates were centrifuged 15 min at 15,000 g and total RNAs were extracted from the pellet.

value: leaf

value: Day 3

value: bacteria

value: 7767-R pBBR1MCS-2::gfp6

value: spray inoculation of bean with 10^6 cfu/ml


title: Exosome,NOR6


title: Mon_KidT_R3

address: 云南省昆明市五华区茭菱路

source_name: kidney

value: kidney


title: captured mRNA-derived cDNA, foliar sample, rep 2, second experiment


title: litter sample under warming in 2016, block B4


title: SLAMseq_AID_Ruvbl1_Ctrl_15h_R2

value: KPC

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, AID-Ruvbl1


title: captured mRNA-derived cDNA, foliar sample, rep 1, second experiment


title: Exosome,DOR7

value: diminished ovarian reserve (DOR)


title: SLAMseq_AID_Ruvbl1_Ctrl_15h_R1


title: captured mRNA-derived cDNA, 42-DAP seeds, rep 3, second experiment

source_name: developing seed

value: developing seed

value: Day 42


title: Mon_KidT_R1

address: 云南省昆明市五华区茭菱路

value: CHIKV infection


title: SLAMseq_AID_Ruvbl1_Ctrl_15h_4sU_minus


title: Exosome,DOR6

value: follicular fluid exosome


title: ChIPseq_A375_MYC_Control

value: pancreatic ductal adenocarcinoma

value: Control


title: Mon_KidC_R3

address: 云南省昆明市五华区茭菱路

value: CHIKV control


title: captured mRNA-derived cDNA, 42-DAP seeds, rep 1, second experiment


title: Exosome,DOR5


title: Mon_KidC_R2

address: 云南省昆明市五华区茭菱路


title: SLAMseq_AID_Ruvbl1_Auxin_15h_R2

value: 1 uM 5-Ph-IAA 15 h


title: SLAMseq_AID_Ruvbl1_Auxin_15h_R1


title: Exosome,DOR4


title: captured mRNA-derived cDNA, 35-DAP seeds, rep 3, second experiment

value: Day 35


title: litter sample under warming in 2016, block B2

value: litterbag


title: Mon_KidC_R1

address: 云南省昆明市五华区茭菱路


title: SLAMseq_AID_Ruvbl1_Auxin_15h_4sU_minus


title: litter sample under warming in 2018, block B2


title: Exosome,DOR3


title: Exosome,NOR5

value: normal ovarian reserve (NOR)


title: captured mRNA-derived cDNA, 35-DAP seeds, rep 1, second experiment

value: bacteria

value: 7767-R pBBR1MCS-2::gfp6


title: Mon_HeaT_R3

address: 云南省昆明市五华区茭菱路

source_name: heart

value: heart


title: Mon_HeaT_R2

address: 云南省昆明市五华区茭菱路


title: Mon_KidT_R2

address: 云南省昆明市五华区茭菱路

value: kidney


title: captured mRNA-derived cDNA, 42-DAP seeds, rep 3, first experiment

value: spray inoculation of bean with 10^6 cfu/ml


title: captured mRNA-derived cDNA, 24-DAP seeds, rep 2, second experiment

value: Day 24


title: Mon_HeaT_R1

address: 云南省昆明市五华区茭菱路


title: Mon_HeaC_R2

address: 云南省昆明市五华区茭菱路


title: SLAMseq_AID_Ruvbl1_Auxin_3h_R2

value: KPC

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, AID-Ruvbl1

value: 1 uM 5-Ph-IAA 3 h


title: Exosome,DOR2

value: follicular fluid exosome

value: diminished ovarian reserve (DOR)


title: Exosome,DOR1


title: captured mRNA-derived cDNA, 24-DAP seeds, rep 1, second experiment

value: developing seed


title: Exosome,NOR2


title: Mon_HeaC_R1

address: 云南省昆明市五华区茭菱路

value: CHIKV control


title: SLAMseq_AID_Ruvbl1_Auxin_3h_4sU_minus

value: pancreatic ductal adenocarcinoma


title: Exosome,NOR4


title: SLAMseq_AID_Ruvbl1_Auxin_3h_R1


title: K84

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: Nugen UniversalPlus

data_processing:
The raw sequencing reads were first trimmed with cutadapt to remove adaptor sequences, short sequences, and low quality bases (-m17, -q10, 17).
Trimmed reads were mapped to the 13-lined ground squirrel mitochondrial genome with hisat2 and remaining reads were mapped to transcript annotations on the HiC_Itri_2 genome (19) using Salmon (20) with -numBootstraps 50.
These Salmon assignments were imported into R, summarized by gene using tximport, and filtered to retain only genes with rlog-normalized counts of at least seven in at least 4/5 individuals from at least one group.
The counts were then transformed using rlog from the DESeq2 package and processed with limma’s removeBatchEffect to generate count tables corrected for library type.
Assembly: HiC_Itri_2 (https://www.ncbi.nlm.nih.gov/assembly/GCA_004006685.1; DOI: 10.3389/fphys.2020.624677)
Supplementary files format and content: csv file with batch-corrected rlog (log2) count matrix from DESeq2

organism: Ictidomys tridecemlineatus

source_name: Kidney

extract_protocol:
RNA extracted by homogenization with polytron in trizol, cleaned up with Direct-zol RNA MiniPrep Kit (Zymo Research)
Libraries were prepared using either the TruSeq Stranded mRNA Library Prep Kit (Illumina) or the Universal Plus mRNA Sequencing Kit (Nugen) as indicated in the sample metadata.

treatment_protocol: Animals implanted with temperature devices, kidney and adrenal gland tissue collected based on time and body temperature, flash frozen in LN2 immediately after dissection and kept continuously below -70C until RNA extraction.

value: Kidney

tag: hibernation state

value: SpD

value: F

tag: animal number


title: Mon_HeaC_R3

address: 云南省昆明市五华区茭菱路


title: captured mRNA-derived cDNA, 42-DAP seeds, rep 1, first experiment

value: Day 42

value: bacteria


title: Exosome,NOR3

value: normal ovarian reserve (NOR)


title: captured mRNA-derived cDNA, 42-DAP seeds, rep 2, first experiment

value: 7767-R pBBR1MCS-2::gfp6


title: Mon_BraT_R3

address: 云南省昆明市五华区茭菱路

source_name: brain

value: brain

value: CHIKV infection


title: K167

description: Nugen UniversalPlus

value: Ent

value: M


title: captured mRNA-derived cDNA, 35-DAP seeds, rep 2, first experiment

value: Day 35

value: spray inoculation of bean with 10^6 cfu/ml


title: captured mRNA-derived cDNA, 35-DAP seeds, rep 3, first experiment


title: K171

description: Nugen UniversalPlus

value: IBA


title: Mon_BraT_R2

address: 云南省昆明市五华区茭菱路


title: E54

city: Edmonton

first: Shima

last: Shahbaz

state: Alberta

address: 7-096 Katz Group Center for Pharmacy and Health Research

country: Canada

institute: University of Alberta

description: Healthy Controls

data_processing:
Kallisto v 0.46.0
Sequence reads were not trimmed
Sequence reads were mapped to GRCh38 using Kallisto pseudo‐alignment (parameters- 100 permutations, bias correction, default parameters)
Read count extraction and normalization were performed using Kallisto
Assembly: GRCh38
Supplementary files format and content: There are 35 folders named E20-E54. Each folder contains 2fq files and one MD5.txt file. The count data file is located in a tab-delimited file "PMN_Project_consolidate.counts.txt"

source_name: Neutrophils

extract_protocol:
RNA was isolated fromneutrophils using the RNeasy Mini Kit (Qiagen). The quantity and quality of RNA were evaluated using a NanoDrop ND-1000 spectrophotometer
100 ng of total RNA was used to make RNAseq libraries using the TruSeq RNA Library Prep Kit v2 (Illumina). Oligo dTs conjugated to paramagnetic beads were used to pull down polyadenylated mRNAs through sequential EtOH washes that eliminated non‐polyadenylated transcripts, and the recovered mRNA was fragmented chemically to be used for the first- and second-strand cDNA synthesis. cDNAs were blunted, A‐tailed and 12 cycles of PCR were used to incorporate Illumina adapters containing multiplexing barcodes.Sequencing was performed on a HiSeq 2500 instrument using a paired-end 150-cycle protocol with demultiplexing carried out in the instrument.

value: Neutrophils

value: WT


title: K165

description: Nugen UniversalPlus

value: EAr


title: SLAMseq_AID_Ruvbl1_Auxin_3h_R3

value: KPC

value: pancreatic ductal adenocarcinoma

value: Kras G12D/+; Tp53 R172H/+; Ptf1a-Cre, AID-Ruvbl1

value: 1 uM 5-Ph-IAA 3 h


title: Mon_BraT_R1

address: 云南省昆明市五华区茭菱路


title: K158

description: Nugen UniversalPlus

value: Kidney


title: E53

description: Healthy Controls


title: captured mRNA-derived cDNA, 24-DAP seeds, rep 1, first experiment

value: developing seed

value: Day 24

value: bacteria


title: E52

description: Healthy Controls


title: captured mRNA-derived cDNA, 35-DAP seeds, rep 1, first experiment

value: 7767-R pBBR1MCS-2::gfp6


title: Mon_BraC_R2

address: 云南省昆明市五华区茭菱路

value: brain

value: CHIKV control


title: K157

description: Nugen UniversalPlus

value: M


title: Mon_BraC_R3

address: 云南省昆明市五华区茭菱路


title: Exosome,NOR1

value: follicular fluid exosome

value: normal ovarian reserve (NOR)


title: Palnc-3_raw

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library qualty assessement
illumina sequencing
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: prostate gland

growth_protocol: cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: prostate gland

value: prostate cancer

value: the control group of DMSO


title: E51

description: Healthy Controls

value: Neutrophils

value: WT


title: captured mRNA-derived cDNA, 24-DAP seeds, rep 3, second experiment

value: spray inoculation of bean with 10^6 cfu/ml


title: K155

description: Nugen UniversalPlus

value: Ent

value: F


title: Mon_BraC_R1

address: 云南省昆明市五华区茭菱路


title: E49

description: COVID-19 patients addmitted in Ward


title: E50

description: Healthy Controls


title: E48

description: COVID-19 patients addmitted in Ward


title: Palnc-1_raw


title: K154

description: Nugen UniversalPlus

value: Kidney

value: EAr


title: K141

description: Nugen UniversalPlus

value: SA


title: E47

description: COVID-19 patients addmitted in Ward


title: K140

description: Nugen UniversalPlus


title: cDNA_xrn1+cRat1

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
RA xrn1+cRat1
cDNA labelling for xrn1+cRat1 strain, Replicates 1-2

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Deviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.

organism: Saccharomyces cerevisiae

source_name: xrn1 + cytoplasmic Rat1 mutant

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC for at least 15 hours to reach early exponential phase at 0.4-0.5 OD600. Then, cells were spun-down and collected. Each sample was done in triplicate.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: genotype/variation

value: xrn1 + cytoplasmic Rat1 mutant


title: cDNA_wt+cRat1

description:
RA WT+cRat1
cDNA labelling for wt+cRat1 strain, Replicates 1-2

source_name: wild type + cytoplasmic Rat1

value: wild type + cytoplasmic Rat1


title: Pal-3_raw

value: the treat group of Palbociclib


title: GRO_xrn1+cRat1

description:
TR xrn1+cRat1
GRO labelling for xrn1+cRat1 strain, Replicates 1-3


title: cDNA_wt

description:
RA WT
cDNA labelling for wt strain. Replicates 1-2

source_name: wild type

value: wild type


title: K139

description: Nugen UniversalPlus


title: Pal-2_raw


title: E45

description: COVID-19 patients addmitted in Ward


title: E46

description: COVID-19 patients addmitted in Ward


title: K156

description: Nugen UniversalPlus


title: K138

description: Nugen UniversalPlus

value: M


title: Pal-1_raw


title: K137

description: Nugen UniversalPlus


title: Dupalnc-3_raw

description: gene_count paldu145.xls


title: E44

description: COVID-19 patients addmitted in Ward


title: cDNA_xrn1

description:
RA xrn1
cDNA labelling for xrn1 strain, Replicates 1-2

source_name: xrn1 mutant

value: xrn1 mutant


title: K130

description: Nugen UniversalPlus

value: SpD


title: KO_VSV

city: Shanghai

first: Shulei

last: Yin

state: Shanghai

address: No.800 Xiangyin Road, Yangpu District

department: Department of Immunology

institute: Naval Medical University

data_processing:
High-quality reads were aligned to the mouse reference genome (GRCm38.p6) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).
Assembly: mm10
Supplementary files format and content: FPKM values for each sample

source_name: Bone marrow-derived macrophages

growth_protocol: BMDMs were maintatined in DMEM supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (QIAGEN)
cDNA library construction and sequencing were performed by Beijing Genomics Institute using MGISEQ-2000RS platform.

treatment_protocol: BMDMs were infected with VSV for 8 hours

value: Bone marrow-derived macrophages

value: VSV infection for 8 hours


title: Palnc-2_raw

value: prostate gland

value: prostate cancer

value: the control group of DMSO


title: E43

description: COVID-19 patients addmitted in ICU

value: Neutrophils

value: WT


title: GRO_wt+cRat1

description:
TR WT+cRat1
GRO labelling for wt+cRat1 strain, Replicates 1-3


title: K116

description: Nugen UniversalPlus

value: Kidney

value: LAr


title: GRO_xrn1

description:
TR xrn1
GRO labelling for xrn1 strain, Replicates 1-3


title: E42

description: COVID-19 patients addmitted in ICU


title: E41

description: COVID-19 patients addmitted in ICU


title: Dupalnc-1_raw

description: gene_count paldu145.xls


title: WT_VSV


title: GRO_wt

description:
TR WT
GRO labelling for wt strain. Replicates 1-3


title: CLP_K3

first: Xiangyi

last: Shen

address: D303 Zhengyutong Medical Building, Tsinghua University

department: The Institute for Immunology, School of Medicine

data_processing:
Raw reads were filtered with SOAPnuke v1.5.2 (-l 15 -q 0.5 -n 0.1).
Clean reads were mapped to the mm10 reference genome by HISAT2 v2.0.4 (-p 8 --phred64 --sensitive -I 1 -X 10000) to generate BAM files.
For gene expression analysis, we mapped clean reads to reference using Bowtie2 v2.2.5 (-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) and calculated gene expression level with  RSEM v1.2.12.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files indicating the gene FPKM of each sample are provided.

source_name: Common lymphoid progenitor

extract_protocol:
Total RNA was extracted from fluorescent-activated cell sorting-purified cells by TRIzol.
BGI-Tech (Shenzhen, China) constructed the mRNA library and performed sequencing. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. The mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. A single 'A' base was added to the cDNA fragments, followed by subsequent ligation of adapter. The products were then purified and enriched with PCR amplification to generate single strand DNA circles (ssDNA circles). DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end read of 50 bp were read through on the BGISEQ-500 platform for the following data analysis study.

value: Bone marrow

value: Common lymphoid progenitor


title: E40

description: COVID-19 patients addmitted in ICU


title: CLP_K2


title: K113

description: Nugen UniversalPlus


title: CLP_K1


title: DUpal-2_raw

description: gene_count paldu145.xls


title: E39

description: COVID-19 patients addmitted in ICU


title: K109

description: Nugen UniversalPlus

value: F


title: K112

description: Nugen UniversalPlus


title: E36

description: Healthy Controls


title: CLP_C1


title: NULG350851

city: Seongnam-si

first: Dong Min

last: Shin

address: 700, Daewangpangyo-ro, Bundang-gu

country: South Korea

institute: Theragen Bio

data_processing:
Sequecne Reads were trimmed for adaptor sequence / low-quality sequence using cutadapt (version : 2.8, parameter : quality-cutoff (20), minimum-length (50))
Trimmed Sequence reads were mapped to reference genome
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options  with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Gene expression estimation was performed by RSEM v.1.3.1 considering the direction of the reads which are corresponding to the library protocol using option --strandedness. To improve the accuracy of the measurement, “--estimate-rspd” option was applied. All other options were set to default values. To normalize sequencing depth among samples, FPKM and TPM values were calculated.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes TPM for each sample

source_name: Ovarian cancer

extract_protocol:
RNA was harvested using Rnaesay mini plus kit (Qiazen).
The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA).

value: Ovarian cancer


title: NULG351151


title: E35

description: Healthy Controls


title: Dupalnc-2_raw

description: gene_count paldu145.xls


title: DUpal-1_raw

description: gene_count paldu145.xls

value: the treat group of Palbociclib


title: E38

description: COVID-19 patients addmitted in ICU


title: CD115-CDP_K2

source_name: CD115- common dendritic cell progenitor

value: CD115- common dendritic cell progenitor


title: K111

description: Nugen UniversalPlus


title: NULG349086


title: NULG351300


title: CLP_C2

value: wild type


title: E37

description: Healthy Controls


title: CLP_C3


title: CD115-CDP_K3


title: K104

description: Nugen UniversalPlus

value: IBA


title: K9

description: Illumina TruSeq stranded

value: SpD

value: M


title: E32

description: Healthy Controls


title: K6

description: Illumina TruSeq stranded


title: E31

description: COVID-19 patients addmitted in Ward


title: NULG255167


title: E30

description: COVID-19 patients addmitted in Ward


title: CD115-CDP_C2


title: DUpal-3_raw

description: gene_count paldu145.xls

value: prostate gland


title: E34

description: Healthy Controls


title: NULG349572


title: K4

description: Illumina TruSeq stranded


title: K115

description: Nugen UniversalPlus


title: K8

description: Illumina TruSeq stranded

value: Ent


title: CD115-CDP_K1


title: K7

description: Illumina TruSeq stranded


title: NULG332916


title: CD115-CDP_C3


title: E33

description: Healthy Controls


title: NULG250205


title: NULG253530


title: K5

description: Illumina TruSeq stranded


title: CD115-CDP_C1


title: K3

description: Illumina TruSeq stranded


title: NULG201926


title: E27

description: COVID-19 patients addmitted in Ward


title: MPP_K1

source_name: Multipoptent progenitor

value: multipoptent progenitor


title: K1

description: Illumina TruSeq stranded


title: MPP_K3


title: NULG180632


title: E28

description: COVID-19 patients addmitted in Ward

value: Neutrophils


title: MPP_C3


title: K2

description: Illumina TruSeq stranded


title: MPP_K2


title: E26

description: COVID-19 patients addmitted in Ward

value: WT


title: NULG180155


title: NULG249908


title: E25

description: COVID-19 patients addmitted in ICU


title: MPP_C2


title: E24

description: COVID-19 patients addmitted in ICU


title: KO_cDC2_3

description:
cDC_FPKM.txt
cDC_TPM.txt

data_processing:
Raw data was filtered with SOAPnuke (v1.5.2) to remove adapter-containing, low-quality, or > 5 % unknown base-containing reads to generate clean reads in FASTQ format.
Mapping to reference genome was done by HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was used for clean reads alignment to the reference coding gene set.
RSEM (v1.2.12) was used to quantify expression level of genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files indicating the gene FPKM and TPM of each sample are provided. The first column of each file represents NCBI gene ID.

source_name: Type 2 conventional dendritic cell

extract_protocol:
Total RNA of 3 -10 x 10^5 cells was extracted with the TRIzol reagent.
BGI-Tech (Shenzhen, China) constructed the mRNA library and performed sequencing. Briefly, total RNA was treated with DNase I and RNase H to remove DNA and rRNA. Purified mRNA was fragmented and subjected to first-strand and second-strand synthesis. A-Tailing Mix and RNA Index Adaptors were added to beads-purified reaction product for end repair. PCR was used to amplify cDNA fragments with adaptors, and Ampure XP Beads were used to purify product. Library was QC-checked with Agilent 2100, heat-denatured, and circularized by the splint oligo sequence to generate single strand circle DNA. This final library was rolling circle-amplified with phi29 DNA polymerase (Thermo) to produce DNA nanoballs, and more than 300 copies were generated for one molecule. DNA nanoballs were loaded into the patterned nanoarray, and the BGISEQ-500 platform (BGI-Shenzhen, China) was used to generate single end 50 bases reads.

value: Spleen


title: NULG071608


title: E22

description: COVID-19 patients addmitted in ICU


title: NULG179973


title: adipocyte_siGLS_TNFa_rep3

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw sequencing files were processed using CASAVA software with default settings, generating Fastq files for further downstream mapping and analysis
Fastq files were aligned to hg38 Human genome using STAR aligner tool
We next quantified reads for each gene transcript to generate a raw counts table
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes counts for each Samples

extract_protocol:
total RNA was extracted from in vitro differentiated human white adipocytes with column based method, as specified in the method section of the manuscript
100ng of total RNA were used to generate a library, cDNA libraries across samples were normalized and combined, the pool was therefore sequenced on Illumina Nextseq 2000 P2, 100 cycles sequencing run

value: siGLS and TNFa treatment


title: adipocyte_siC_TNFa_rep2

source_name: in vitro differentiated human white adipocytes

value: siC and TNFa treatment


title: adipocyte_siC_TNFa_rep3

value: in vitro differentiated human white adipocytes


title: MPP_C1

value: Bone marrow


title: KO_cDC2_2

description:
cDC_FPKM.txt
cDC_TPM.txt


title: adipocyte_siGLS_TNFa_rep2


title: E29

description: COVID-19 patients addmitted in Ward


title: KO_cDC2_1

description:
cDC_FPKM.txt
cDC_TPM.txt


title: E21

description: COVID-19 patients addmitted in ICU


title: adipocyte_siGLS_TNFa_rep1


title: NULG068084

value: Ovarian cancer


title: NULG067508


title: WT_cDC2_3

description:
cDC_FPKM.txt
cDC_TPM.txt

value: Wild type


title: OctA-2

city: New York

first: Ting-Hsiang

last: Huang

state: New York

institute: Memorial Sloan Ketteting Cancer Center

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and then aligned to human assembly hg38 with STAR v2.4 using default parameters.
Data quality and transcript coverage were assessed using the Picard tool CollectRNASeqMetrics.
Read count tables were generated with HTSeq v0.9.1. Normalization and expression dynamics were evaluated with DESeq2 using the default parameters and outliers were assessed by sample grouping in principal component analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Noramalized Raw counts and DESeq2 with padj

growth_protocol: A375 cells were maintained in DMEM with 10% FBS.

extract_protocol:
RNA was extracted by Zymo quick-RNA miniprep kit.
RNA library preparation using the NEBNext Ultra RNA Prep Kit for Illumina.

treatment_protocol: A375 cells were treated with 1mM octanoate or vehicle (isopropanol) in 100mm plates for 48-hrs.

value: melanoma

value: octanoate


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous) and Capecitabine (150mg/kg/d oral); 28 d; biol rep 2

city: Boston

first: Rinath

last: Jeselsohn

state: MA

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The VIPER pipeline was used for alignment, quality control, and downstream analysis.
Alignment to the hg19 human genome was done using STAR v2.7.0f followed by transcript assembly using cufflinks v2.2.1.
Quality control steps were done using STAR v2.7.0f and RseQC v2.6.4.
Assembly: hg19
Supplementary files format and content: comma-delimited text file containing raw counts (via STAR) for each sample
Supplementary files format and content: comma-delimited text file containing FPKM values (via Cufflinks) for each sample

source_name: PDX1526 model

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy kit with DNase digestion. RNA concentrations were measured by NanoDrop, and the quality of RNA was determined by a Bioanalyzer. RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina). Samples were sequenced on an Illumina Nextseq500.
RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: When tumors reached 150-200 mm3, mice were randomized into 4 arms (N=5-8): control (drug vehicle), fulvestrant 5mg/mouse/week subcutaneous, capecitabine 150mg/kg/daily oral and fulvestrant 5mg/mouse + capecitabine 150 mg/kg. Capecitabine was administered in a cycle consisting of 14 days on, 7 days off and again 7 days on. Fulvestrant vehicle was 10% ethanol and castor oil, while capecitabine vehicle was 10% Dimethylsulfoxide (DMSO), 40% polyethylene glycol, 2.5% Tween-80, and 47.5% normal saline.

value: PDX1526 model

value: Y537S mutant ER

value: Fulvestrant (5mg/mouse/week subcutaneous) and Capecitabine (150mg/kg/daily oral)

value: 28 days


title: E23

description: COVID-19 patients addmitted in ICU


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous) and Capecitabine (150mg/kg/d oral); 28 d; biol rep 3


title: WT_cDC2_2

institute: Tsinghua University

description:
cDC_FPKM.txt
cDC_TPM.txt


title: NULG018894


title: Veh-2

value: isopropanol


title: NULG016425


title: NULG178868


title: Veh-1


title: NUHU918240


title: PDX1526; Y537S mutant ER; Capecitabine (150mg/kg/d oral); 28 d; biol rep 2

value: Capecitabine (150mg/kg/daily oral)


title: E20

description: COVID-19 patients addmitted in ICU

value: Neutrophils


title: OctA-1

value: WT


title: WT_cDC2_1

description:
cDC_FPKM.txt
cDC_TPM.txt

value: Spleen


title: NUHU913449


title: PDX1526; Y537S mutant ER; Capecitabine (150mg/kg/d oral); 28 d; biol rep 1


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous) and Capecitabine (150mg/kg/d oral); 28 d; biol rep 1


title: PDX1526; Y537S mutant ER; Capecitabine (150mg/kg/d oral); 28 d; biol rep 3


title: KO_cDC1_2

description:
cDC_FPKM.txt
cDC_TPM.txt

source_name: Type 1 conventional dendritic cell


title: NULG071501


title: NUHU913148


title: KO_pDC_3

description:
pDC_FPKM.txt
pDC_TPM.txt

source_name: Plasmacytoid dendritic cell


title: KO_cDC1_1

description:
cDC_FPKM.txt
cDC_TPM.txt


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous); 28 d; biol rep 3


title: adipocyte_siC_TNFa_rep1


title: OctA-2_H3K27ac

data_processing:
Sequencing reads were trimmed and filtered for quality and adapter content using version 0.4.5 of TrimGalore, with a quality setting of 15, and running version 1.15 of cutadapt and version 0.11.5 of FastQC. Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 and were deduplicated using MarkDuplicates in version 2.16.0 of Picard Tools.
To ascertain regions of chromatin accessibility and ChIP-seq target enrichment, MACS2 was used with a p-value setting of 0.001 and scored against a publicly available input sample for cell line A375 (GSM3212794).
The BEDTools suite was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions an then merging all peaks within 500 bp for ChIP-seq or taking 500 bp windows around peak summits for ATAC and counting reads with version 1.6.1 of featureCounts.
DESeq2 was used to normalize read density (median ratio method) and to calculate differential enrichment for all pairwise contrasts.
Peak-gene associations were created by assigning all intragenic peaks to that gene, and otherwise using linear genomic distance to transcription start site.
Peak intersections were calculated using bedtools v2.29.1 and intersectBed with 1 bp overlap.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file includes DESeq2 with padj.

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 10-mins and quenched by glycine for 2-mins. After cell lysis, genomic DNA was sonicated by Branson digital 450 cell sonifier.
The DNA library was prepared using NEBNext Utra II DNA Library Prep with Sample Purification Beads (NEB #E7103S) according to the manufacture’s instruction.

tag: chip antibody

value: H3K27ac (abcam #ab4729)

value: octanoate for 48-hrs


title: NUHU858276


title: Veh_H3K27ac

value: vehicle


title: NULG015718


title: WT_cDC1_2

description:
cDC_FPKM.txt
cDC_TPM.txt


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous); 28 d; biol rep 2


title: NUHF355686


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous); 28 d; biol rep 4


title: Veh-2_H3K27ac


title: OctA_H3K27ac


title: WT_cDC1_1

description:
cDC_FPKM.txt
cDC_TPM.txt


title: KO_pDC_1

description:
pDC_FPKM.txt
pDC_TPM.txt


title: KO_pDC_2

description:
pDC_FPKM.txt
pDC_TPM.txt


title: OctA1_A375

extract_protocol:
Harvested cells from each condition were lysed in 50 µl ATAC lysis buffer (Tris 10 mM pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and incubated with Illumina Tn5 transposase at 37⁰C for 30 mins.
Samples were purified using Agencourt AMPure XP beads following which barcoding and library generation were performed using the NEBNext Q5 Hot Start HiFi PCR Master Mix with PCR amplification for 12 cycles. The size selected libraries were run on a HiSeq2500 to get an average of 40-50 million paired end reads per sample.

value: octanoate for 48hrs


title: OctA2_A375


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous); 28 d; biol rep 1


title: PDX1526; Y537S mutant ER; Vehicle (DMSO); 28 d; biol rep 3

value: Vehicle (DMSO)


title: WT_pDC_3

description:
pDC_FPKM.txt
pDC_TPM.txt

value: Wild type


title: WT_pDC_2

description:
pDC_FPKM.txt
pDC_TPM.txt


title: PDX1526; Y537S mutant ER; Vehicle (DMSO); 28 d; biol rep 2


title: NUHF355525

value: Ovarian cancer


title: NUHF354997


title: Veh1_A375

value: melanoma


title: WT_pDC_1

description:
pDC_FPKM.txt
pDC_TPM.txt


title: PDX1526; Y537S mutant ER; Vehicle (DMSO); 28 d; biol rep 1

value: PDX1526 model


title: MES28 cells, KU70MU-2

city: Chapel Hill

first: Daqi

last: Li

address: 450 West Dr

institute: Univerity of North Carolina at Chapel Hill

data_processing:
RNA sequencing was performed using BGISEQ-500 platforms. FASTQ sequencing reads were trimmed using Trim Galore (RRID:SCR_011847), and transcript quantification was performed using Salmon with the quasi-mapping mode
Assembly: hg38
Supplementary files format and content: MES28_MCT1_core_table_gene.txt includes FPKM values for 4 of total 12 Samples
Supplementary files format and content: MES28_KU70_core_table_gene.txt includes FPKM values for 4 of total 12 Samples
Supplementary files format and content: MES28_KU70_WT_MU_core_table_gene.txt includes FPKM values for 4 of total 12 Samples

source_name: glioblastoma

extract_protocol:
Total RNA was extracted with Trizol reagent (Takara) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: glioblastoma

value: glioma stem cells


title: shLibrary_plasmid

first: Elmar

last: Wolf

institute: Christian-Albrechts-University Kiel

description: PCR amplified gDNA

data_processing:
Fastq files were generated on Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
Bowtie1 (version 1.2.2) alignment (option -v 0) to the shRNA oligonucleotide reference
Counting of alignment per shRNA (bash script)
Differential enrichment (DESeq2)
Assembly: NA, fastq files were aligned to a custom reference containing the shRNA oligonucleotide sequences
Supplementary files format and content: .csv file containing raw read counts per shRNA sequence

organism: synthetic construct

growth_protocol: KPC cells were grown in DMEM supplemented with 10 % FCS and 1% Penicillin/Streptomycin. 100,000 KPC cells were orthotopically transplanted into the pancreata of C57BL/6J mice in 50 µl PBS/Matrigel (1:1)

extract_protocol:
Cells/Tumors were lysed in lysis buffer (10 mM TRIS/HCl, pH 8, 100 mM NaCl, 10 mM EDTA, 0.5 % SDS, 400 µg/ml proteinase K) at 56 °C overnight. gDNA was isolated by phenol/chloroform/isoamylalcohol extraction and isopropanol precipitation.
PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.
OTHER: PCR amplification of mirE sequences from gDNA followed by PCR amplification with barcoded index primers.

treatment_protocol: Cells were treated with 1 µg/ml doxycycline. Control cells were treated with ethanol. Mice were treated with doxycycline by feeding them with chow containing 625 mg/kg doxycycline (ssniff) ad libitum. Control mice received control chow.


title: NUHF046195


title: MS2-Contr_R2

city: Strasbourg

first: Isabelle

last: Caldelari

address: rue René Descartes

institute: CNRS

description: MS2 affinity purified RNA

data_processing:
Basecalling pipeline: 1. HiSeq Control Software 2.2.38; 2. RTA 1.18.61.0; 3. CASAVA-1.8.2
Adapter sequences and poor quality reads removed with Trimmomatic
Reads alignement on the HG001 genome (GenBank assembly accession: GCA_001900185.1) using BOWTIE2 (very sensitive end-to-end protocol with maximum 4 mismatches allowed).
Reads per feature counted with HTseq. The protocol chosen is interception non-empty, with reverse strand interpretation.
Differential analysis with DEseq2 (n=2)
Genome_build: GCA_001900185.1
Supplementary_files_format_and_content: Tables obtained by DEseq2 reporting the Fold Changes, p-values and p-adj-values

organism: Staphylococcus aureus

source_name: Bacterial cells

growth_protocol: Bacteria were grown in Brain Heart Infusion (BHI) medium for 5 hours, then 0.5% glucose-6-phosphate was added for another hour of incubation at 37°C. Erythromycin at 10 ug/ml final concentration was added to the medium for plasmid selection.

extract_protocol:
Bacterial cells were resuspended in lysis Buffer (20 mM Tris-HCl pH 8, 150 mM KCl, 1 mM MgCl2, 1 mM DTT) and broken using the FastPrep apparatus. Crude extract were loaded on a MS2-MBP coated column and purified by affinity chromatography. Eluted RNA were extracted with phenol/chloroform :isoamylalcohol prior to RNAseq analysis.
DNase I (0.1 U/ml) treatment was performed 1h at 37°C. The reactions mixtures were then purified by phenol/chloroform/isoamylalcohol and subsequent ethanol precipitation. RNA pellets were re-suspended in sterile milliQ water. RNA quality and quantity assessments were performed on Agilent Nano Chip on the Bioanalyzer 2100. RNAs were treated to deplete abundant rRNAs, and the cDNA libraries were performed using the ScriptSeq complete kit (bacteria) from Illumina. The libraries were sequenced using Illumina MiSeq with a V3 Reagent kit (Illumina), which preserves the information about the orientation of the transcripts and produces reads of 150 nts, which map on the complementary strand. Each RNA-seq was performed at least in duplicates.

value: HG001 delta-rsaG

tag: plasmid

value: pCN51-P3 MS2


title: MES28 cells, KU70MU-1


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous) and Capecitabine (150mg/kg/d oral); 10 d; biol rep 2

value: Y537S mutant ER

value: Fulvestrant (5mg/mouse/week subcutaneous) and Capecitabine (150mg/kg/daily oral)

value: 10 days


title: NUHF043772


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous) and Capecitabine (150mg/kg/d oral); 10 d; biol rep 1


title: Veh2_A375


title: MS2-Contr_R1

description: MS2 affinity purified RNA


title: MES28 cells, KU70WT-2


title: MES28 cells, KU70WT-1


title: MES28 cells, shKU70-1


title: ATAC_H_E115-WT_rep1

city: Bern

first: Marco

last: Osterwalder

address: Murtenstrasse 24

department: DBMR

country: Switzerland

institute: Universiy of Bern

description: Tn5-tagmentation of open chromatin regions

data_processing:
ATAC-seq datasets were subjected to adaptor trimming (trim_galore_v0.6.6) by Cutadapt with default parameters ‘-j 1 -e 0.1 -q 20 -O 1’ for single-end. Bowtie2 (version 2.4.2) was used for read mapping with parameters ‘-q --no-unal -p 8 -X2000’. Reads were aligned to the GRCm38/mm10 reference genome using pre-built Bowtie2 indexes from the Illumina’s iGenomes collection (http://bowtie-bio.sourceforge.net/bowtie2/). Duplicates and low-quality reads (MAPQ = 255) were removed using SAMtools (v1.12), with pipeline parameters ‘markdup -r’ and ‘-bh -q10’, respectively. Peak calling was performed using MACSv2 (v2.1.0) with p-value < 0.01 and parameters ‘-t -n -f BAM -g mm --nolambda --nomodel --shif 50 --extsize 100’.
Assembly: GRCm38/mm10

source_name: Embryonic Heart

growth_protocol: Pairs of embryonic hearts of wildtype embryos at E11.5 (49-51 somite-stage) were microdissected in cold PBS and subjected to tissue dissociation.

extract_protocol:
Tissues were dissociated in Lysis buffer using a Dounce tissue grinder and approx. 50000 cells were pelleted and resuspendend in 50uL transposition reaction mix.
Samples were incubated in transposition reaction mix (25 μL Nextera 2x TD buffer and 2.5 μL TDE1; Illumina) for 30 minutes at 37C with shaking. Following amplification, ATAC-libraries were purified, quantified and quality assessed using a Agilent Bioanalyzer. Libraries were pooled and sequences on an Illumina HiSeq 4000 (single end 50bp).

value: FVB

tag: embryonic day

value: WT

value: mouse embryonic heart


title: MES28 cells, shKU70-2


title: ATAC_H_E115-WT_rep2

tag: strain


title: NUGI847569


title: PDX1526; Y537S mutant ER; Capecitabine (150mg/kg/d oral); 10 d; biol rep 3

tag: genotype

value: Capecitabine (150mg/kg/daily oral)


title: PDX1526; Y537S mutant ER; Capecitabine (150mg/kg/d oral); 10 d; biol rep 2

tag: tissue


title: NUGI846843


title: MES28 cells, shKU70Control-2

tag: cell line

value: shKU70 Control


title: NUHE833211


title: MS2-RsaG_R2

description: MS2 affinity purified RNA

value: pCN51-P3 MS2-RsaG


title: NUGI846588


title: CHiC_MD_E115-WT

data_processing:
Sequencing was performed to have comparable depth among tissue samples and reads were mapped to the reference genome GRCm38/mm10, filtered and de-duplicated using HiCUP pipeline v0.8.1. The pipeline was set up with Bowtie2 v2.4.5 for short read mapping. Juicer command line tools v1.9.9 was used for the generation of binned contact maps from valid and unique read pairs with MAPQ ≥ 30. Normalization and diagonal filtering was performed using the Cooler v0.8.11 matrix balancing tool with options “--mad-max 5 --min-nnz 10 --min-count 0 --ignore-diags 2 --tol 1e-05 --max-iters 200 --cis-only”. For binning and normalization, only the genomic region chr3:65196079-68696078 (mm10) that represents the targeted interval was considered and read pairs mapping to this interval were retained and shifted by the offset of 65,196,078 bp using custom chrom.sizes files. Balanced maps were exported at 5kb resolution with corrected coordinates (transformed back to original values). Subtraction maps were directly generated from Cooler balanced HiCmaps using hicCompareMatrices tool (HiCExplorer v3.7.2) with option “--operation diff”. Hi-C maps were visualized from .cool files using pyGenomeTracks.
Normalized inter-domain insulation scores(Crane et al. 2015)and TAD boundaries were determined using FAN-C(Kruse et al., 2020)(v.0.9.26-b2-beta) with ‘fanc insulation -w 15000 25000 35000 50000 75000 100000 130000’ and‘fanc boundaries --min-score 0.21’, respectively, from input .cool matrices. Tissue-differential insulation scores and boundary values were calculated using ‘fanc compare -c difference’and‘fanc boundaries --min-score 0.21’.
For virtual Capture-C, to better visualize individual interactions of target regions, a 5kb viewpoint centered on the coordinates of each genomic element of interest was used. Capture-C-like profiles were generated as described (Paliou et al., 2019) from filtered unique read pairs (hicup.bam files) which also served as input for CHi-C maps. Read-pairs were mapped based on MAPQ ≥ 30 and relative position of the two reads inside and outside the viewpoint, respectively. After quantitation of reads outside of the viewpoint (per restriction fragment), read counts were distributed into 3kb bins with proportional distribution of read counts in case of overlap with more than one bin. Each binned profile was smoothened by averaging over a running window of 5 bins and scaled by 10^3 / sum of all its counts on chr3 (Paliou et al., 2019). Peak profiles were generated using custom Java code based on htsjdk v2.12.0 (https://samtools.github.io/htsjdk/). The viewpoint and neighboring +/-5kb regions were excluded from computation of the scaling factor. The following genomic interval was used as Virtual Capture-C viewpoint: chr3:66,978,288-66,983,288 (centering Shox2 TSS). BigwigCompare tool (deepTools v3.5.1) was further used to generate relative subtraction Capture-C-like profiles.
Assembly: GRCm38/mm10
Supplementary files format and content: hic output files containing binned contact maps from unique read pairs (MAPQ ≥ 30) were generated by Juicer command line tools v1.9.9 (Durand 2016).
Supplementary files format and content: cool files containing balanced contact matrices generated with the hicConvertFormat tool (HiCExplorer v3.7.2) from native .hic out-puts.

source_name: Embryonic Mandible

growth_protocol: Embryonic forelimbs, mandibular processes, and hearts of wildtype embryos at E11.5 (48-52 somite-stage) were microdissected in cold PBS and subjected to tissue dissociation.

extract_protocol:
Tissues were homogenized using a Dounce tissue grinder and fixed with 2% formaldehyde (37%) for 10 min. The reaction was quenched using 1.25M Glycine and pellets were snap-frozen for storage at -80°C. For nuclei isolation pellets were resuspended in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 0.1mM EGTA, Protease Inhibitor). After on wash with PBS samples were digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was sheared and after adaptor ligation and amplification of sheared DNA fragments, libraries were hybridized to custom-designed SureSelect beads (SureSelectXT Custom 0.5-2.9Mb library) and indexed following Agilent’s instructions. Multiplexed libraries were sequenced using a Illumina HiSeq 4000 (50bp paired-end).
3C-library, hybridization to custom-designed SureSelect beads (Agilent)

value: Embryonic Mandible


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous); 10 d; biol rep 1

tag: cell type


title: NUHE830126

value: Ovarian cancer


title: CHiC_FL_E115-WT

source_name: Embryonic Forelimb

value: Embryonic Forelimb


title: PDX1526; Y537S mutant ER; Vehicle (DMSO); 10 d; biol rep 2

value: PDX1526 model

tag: treatment

value: Vehicle (DMSO)


title: MES28 cells, shMCT1-1

value: glioblastoma

value: glioma stem cells


title: PDX1526; Y537S mutant ER; Fulvestrant (5mg/mouse/wk subcutaneous); 10 d; biol rep 2


title: MES28 cells, shKU70Control-1


title: NUFS270379


title: PDX1526; Y537S mutant ER; Capecitabine (150mg/kg/d oral); 10 d; biol rep 1


title: MES28 cells, shMCT1Control-2

value: shMCT1 Control


title: PDX1526; Y537S mutant ER; Vehicle (DMSO); 10 d; biol rep 1

value: Y537S mutant ER


title: HC2825, HC, replicate 2, scRNAseq

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
RNA samples of mononuclear/polymorphnuclear cells are harvested by Tri-zol (Invritrogen, Inc. Faraday Avenue, Carlsbad, CA). (500 μl Tri-zol/600 μl cell lyses buffer for each 1 × 105 cell)
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3’ Gel Bead and Library Kit (now sold as P/N 120262, 1000009, 120267, 10x Genomics). GEM-RT was performed in a Veriti 96-Well Thermal Cycler 2020/7/29 Version1 (Applied Biosystems; Model#: 9902)at 53 °C for 45 min, 85 °C for 5 min, and held at 4 °C.

value: WBC

value: peripheral blood

tag: disease state

value: healthy control


title: MCF7 cells; Y537S mutant ER; Fulvestrant (10nM) and 5FU (1000 nM); biol rep 2

source_name: Breast

extract_protocol:
Then, cells were harvested (as duplicates) for downstream RNA analysis. Total RNA was extracted using the QIAGEN RNeasy kit with DNase digestion. RNA concentrations were measured by NanoDrop, and the quality of RNA was determined by a Bioanalyzer. RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina). Samples were sequenced on an Illumina Nextseq500.
RNA-seq libraries were made using the TruSeq RNA Sample Preparation Kit (Illumina).

value: Breast

value: Breast cancer cell line

value: Fulvestrant (10nM) and 5FU (1000 nM)

value: 12 hours


title: HC2790, HC, replicate 1, scRNAseq


title: NUHF046557


title: MCF7 cells; Y537S mutant ER; Fulvestrant (10nM) and 5FU (1000 nM); biol rep 1


title: NUFS244754


title: NUFS269559


title: FC687, FC, replicate 2, scRNAseq

description: Re-analysis of GSM6042982

value: febrile control


title: FC665, FC, replicate 1, scRNAseq

description: Re-analysis of GSM6042981


title: B5_20OHD3

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

data_processing:
Raw FASTQ files were aligned to reference genome using STAR version 2.7.1a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using Cufflinks version 2.2.1 using parameters --library-type fr-firststrand -G -L
All 10 samples were merged using Cuffmerge (from above Cufflinks) using parameters -g -s
Differential expression was calculated using Cuffdiff (from above Cufflinks) using parameters --library-type fr-firststrand -L
Assembly: Gencode GRCh38 p7 Release25
Supplementary files format and content: tab-delimited text file containing FPKM values for each gene in each sample

source_name: WM164 melanoma line

growth_protocol: The cells were cultured using DMEM media supplemented with 10% serum (fetal bovine serum while growing cells and charcoal-treated serum during incubation with vitamin D compounds), 1% antibiotics and 5 µg/mL insulin (Sigma-Aldrich, St. Louis, MO, USA). Cells were cultured in 75 cm2plastic filtered flasks (TPP–Techno Plastic Products AG, Trasadingen, Switzerland) in an incubator at 37 °C with 5% CO2.

extract_protocol: RNA was isolated using Absolutly RNA Miniprep Kit  (Stratagen) . Approximately 120 ng/ul of each sample was sent for RNAseq analysis. BGI@CHOP genomics company sequenced the samples on Illumina HiSeq TM, analyzed, and sent us the results.

treatment_protocol: VDR-KO or scramble WM164 cells were plated onto 100 mm2Petri dishes and treated with 1,25(OH)2D3, 25(OH)D3, 20(OH)D3, 1,20(OH)2D3 or ethanol (control) in triplicates.  Cells were incubated in 10% charcoal-treated serum for 24 h. Cells were further harvested and RNA isolated using Absolutly RNA Miniprep Kit  (Stratagen)

value: WM164 melanoma line

value: VDR wild type (scrambled infection)


title: B4_1_20OH2D3


title: NUFS269957

value: Ovarian cancer


title: MCF7 cells; Y537S mutant ER; 5FU (1000 nM); biol rep 2


title: MES28 cells, shMCT1Control-1


title: B2_1_25OH2D3


title: MCF7 cells; Y537S mutant ER; Fulvestrant (10nM); biol rep 2

value: Fulvestrant (10nM)


title: NUFS208211


title: B3_25OHD3


title: MCF7 cells; Y537S mutant ER; 5FU (1000 nM); biol rep 1


title: KD1408-1, KD-CAL, replicate 2, scRNAseq

value: Kawasaki disease and coronary artery lesions


title: KD1409, KD-CAL, replicate 3, scRNAseq


title: MCF7 cells; Y537S mutant ER; Fulvestrant (10nM); biol rep 1


title: B1_EtOH_control

value: ethanol 0.1percent


title: NUFS176073


title: KD1053, KD, replicate 1, scRNAseq

description: Re-analysis of GSM6042979

value: Kawasaki disease


title: A5_20OHD3

value: VDR knockout


title: NUFS175676