title: Co-cultured, ex vivo 24h, Celecoxib, replicate 2

city: Suita

first: Takehiro

last: Hiraoka

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

description: Library name: Embryo 11

data_processing:
Paired-end sequencing was performed by NovaSeq 6000 (Illumina, USA) and the raw fastq files were analyzed by RaNA-seq (https://ranaseq.eu/) and Metascape (https://metascape.org/gp/index.html).
Assembly: GRCm38
Supplementary files format and content: tsv files include raw and TPM counts for each sample

source_name: Embryo

extract_protocol:
Solely cultured and co-cultured ex vivo embryos were collected at 24h. Embryos were immediately dissolved in SMART-Seq HT Kit 10X Lysis Buffer (Takara Bio, Japan) and processed for RNA sequencing library preparation. In total, 24 embryos from 3 donor mice were used and divided into four groups. Consequently, 6 embryos in each group were integrated and regarded as one biological replicate. For endometrial samples, 3 ex vivo ISs from a recipient mouse were cut with micro scissors in 500 μm size and combined as one biological replicate. RNA was extracted with TRIzol RNA Isolation Reagents (Thermo Fisher Scientific, USA).
RNA sequencing library was prepared using SMART-Seq mRNA HT LP (TAKARA Bio, Japan).

value: Embryo

value: Celecoxib


title: Co-cultured, ex vivo 24h, DMSO, replicate 3

status: Public on May 05 2025

type: SRA

description: Library name: Embryo 10

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment

value: DMSO


title: DM6

city: Houston

first: Michael

last: Jochum

state: TX

address: 1 Baylor Plaza

department: Obstetrics and Gynecology

country: USA

institute: Baylor College of Medicine

data_processing:
trimmed_PE.fastq.gz, adapter trimmed and paired-end combined sequence files for each sample.
Reads were pre-processed, and quality filtered using FastqQC (v0.11.9) and barcodes and adapters were trimmed using Trimmomatic (v0.33)25. Reads were aligned to the human transcriptome (GRCh38.p13) using STAR (v2.7.8)26. PCR duplicate reads were removed using Picard (v2.24.0)27. Unique reads were counted using HTseq (v0.11.1)28. Counts were used for differential expression analysis in R (v4.0.2) using DEseq2 (v3.12)29 relative to the healthy control placenta samples. GO Biological Processes functional enrichment analysis was done utilizing clusterProfiler (v4)30 to identify significantly enriched terms. The custom scripts used for bulk transcriptomics analyses are available at https://github.com/Aagaardlab/GDMA-Subtype-Transcriptomics.
Assembly: GRCh38.p13
Supplementary files format and content: count_matrix.tsv, a pre-processed htseq raw counts matrix used as input for DESeq2 analysis.

organism: Homo sapiens

source_name: Placenta

extract_protocol:
RNA was extracted from placental tissue as previously described.24 The Machery Nagel Nucleospin II kit was used to extract RNA from each sample and samples were stored at -80°C. Each sample was analyzed for quality control on the Agilent Bioanalyzer, with a minimum RNA Integrity Number (RIN) of 4.0 accepted for transcriptomic analysis. For each library, mRNA was purified from 10µg of total RNA using the DynaBeads mRNA Purification Kit (Invitrogen) and fragmented using the RNA Fragmentation Reagents (Ambion). Double-stranded cDNA was synthesized from fragmented mRNA using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and Random Hexamer primers (50ng/ul, Invitrogen). cDNA libraries were prepared according to the manufacturer’s protocol (TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina Hiseq 2000.
For each library, mRNA was purified from 10µg of total RNA using the DynaBeads mRNA Purification Kit (Invitrogen) and fragmented using the RNA Fragmentation Reagents (Ambion). Double-stranded cDNA was synthesized from fragmented mRNA using the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) and Random Hexamer primers (50ng/ul, Invitrogen). cDNA libraries were prepared according to the manufacturer’s protocol (TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina Hiseq 2000.

value: Placenta

tag: cell type

value: Heterogeneous

tag: disease state

value: diabetes

tag: diabetes subtype


title: Low light, 2 mM nitrate, rep 3

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

data_processing:
Raw reads were filtered for low quality reads using BBDuk (BBtools, Joint Genome Institute)
Reads were aligned to the Arabidopsis thaliana (TAIR10) reference genome using STAR aligner (v2.5.3a)(Dobin et al., 2013)
Gene-level counts were obtained using featureCounts (Liao et al. 2014)
Assembly: Arabidopsis thaliana (thale cress) TAIR10
Supplementary files format and content: tab delimited file contains raw counts for each sample

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Surface-sterilized Arabidopsis thaliana (Col-0) seeds were vernalized for 72 h at 4°C and plated on 0.5x Murashige and Skoog (MS) media with 1% sucrose. The seedlings were transferred to 3” pots containing a 1:1 mixture of coarse calcined clay (Turface MVP, PROFILE) and fine clay, 10 days after germination.

extract_protocol:
On the 30th day after transplanting, two leaf punches were taken from each individual plant and immediately flash-frozen for RNA-sequencing. Frozen samples were powdered in 2ml tubes with 8-12 beads of Matrix D (cat #116540434 MP biomedicals) with the FastPrep-24 cryo rotor using the following program (2x 5.5m/s2 x 60 sec).
Kapa Hyper Stranded mRNA library kit (Roche)

treatment_protocol: After transfer, the plants were treated with 30 mL ½ Hoagland’s solution with nitrate concentrations of 2 mM, 5 mM, 10 mM and 20 mM. The plants were grown under three light levels with photon flux densities of 100, 250 and 500 𝜇mol m-2 s-1 under 8/16 h day/night cycle and 23/21 °C day/night temperature regime.

value: Leaf

value: Low light

value: 2 mM nitrate


title: peanut-XN_SY01_P1_A24_180926C_SPRI-475_210107

type: genomic

city: Qingdao

first: jing

last: xu

address: 126 Wannianquan Road

country: China

institute: Shandong Peanut Research Institute

description:
XN_SY01_P1_A24_180926C_SPRI-475_210107
47K SNPs

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics process, and scanned using the Symbol® Cyclone™ M2000 Scanner.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console® (version 2.0). The raw data CEL files were typed using Axiom Analysis Suite 3.1.51, according to each site A set of indicators assigned to a specified type: PolyHighResolution, NoMinorHom,  MonoHighResolution, OTV,  CallRateBelowThreshold, Other.
Genotype Call (SNP call): AA, AB, BB, NC.

label: biotin

molecule: genomic DNA

organism: Arachis hypogaea

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Peanuts were grown according to standard conditions

extract_protocol: Young healthy leaves from each accession were collected, with extraction of total genomic DNA via a Plant Genomic DNA Kit (Tiangen Biotech (Beijing) Co., Ltd.). The extracted DNA quality and concentration were determined via 0.8% agarose gel electrophoresis using standard lambda DNA and a NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Wilmington, DE, USA)

tag: tag

value: leaf


title: WT_HFD_rep3

city: Shanghai

first: Zixuan

last: Wang

state: Shanghai

address: 1665 Kongjiang Road, Shanghai, China

institute: Xin Hua Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: WT_HFD_rep3

data_processing:
Read counts mapped to exons of RefSeq-annotated genes were quantified and normalized to FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Differential gene expression analyses were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: text file of raw counts for each sample

molecule: total RNA

source_name: Liver

extract_protocol:
RNA was harvested using Trizol reagent. 1 μg total RNA  was used for the construction of sequencing libraries.
Polyadenylated RNA was isolated from 1 μg of total RNA using two rounds of purification with Dynabeads™ Oligo(dT)25 magnetic beads (Thermo Fisher, Catalog #61005, USA). The enriched poly(A) RNA was subsequently fragmented into small pieces using  the NEBNext® Magnesium RNA Fragmentation Module (NEB, Catalog #E6150, USA) at 94°C for 5–7 minutes. Fragmented RNA was reverse-transcribed into first-strand cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, Catalog #1896649, USA). Second-strand cDNA synthesis was performed with E. coli DNA Polymerase I (NEB, Catalog #M0209, USA), RNase H (NEB, Catalog #M0297, USA), and dUTP Solution (Thermo Fisher, Catalog #R0133, USA) to incorporate deoxyuridine triphosphate (dUTP) into the second strand. An A-base was then added to the blunt ends of each strandpreparing them for ligation to the indexed adapters. Each adapter contains a T-base overhana for ligaling the adapter to the A-tailedfragmented DNA. Single- or dual-index adapters were ligated to the fragments, followed by size selection using AMPure XP beads. After treatment of the U-labeled second-strand DNAs with heat-labile UDG enzyme (NEB, Cat. #M0280, USA), the ligated products were amplified by PCR under the following conditions: initial denaturation at 95°C for 3 min; 8 cycles of denaturation at 98°C for 15 s, annealing at 60°C for 15 s, and extension at 72°C for 30 s; with a final extension at 72°C for 5 min. The average insert size of the final cDNA library was 300 ± 50 bp.

treatment_protocol: ATP7B-knockout mice were subjected to a high-fat diet for 24 weeks.

value: Liver

value: Wild type

value: High-fat diet for 24 weeks


title: KO_HFD_rep1

description: Library name: KO_HFD_rep1

value: ATP7B knockout


title: High light, 5 mM nitrate, rep 4

value: High light

value: 5 mM nitrate


title: NCS39


title: peanut-XN_SY01_P1_A24_180926A_SPRI_224_200507

description:
XN_SY01_P1_A24_180926A_SPRI_224_200507
47K SNPs


title: peanut-XN_SY01_P1_A22_180926C_SPRI-470_210107

description:
XN_SY01_P1_A22_180926C_SPRI-470_210107
47K SNPs


title: peanut-XN_SY01_P1_A23_180926C_SPRI-026_210107

description:
XN_SY01_P1_A23_180926C_SPRI-026_210107
47K SNPs


title: Mid light, 5 mM nitrate, rep 4

value: Mid light


title: DM8


title: peanut-XN_SY01_P1_A21_180926C_SPRI-025_210107

description:
XN_SY01_P1_A21_180926C_SPRI-025_210107
47K SNPs


title: Solely cultured, ex vivo 24h, Celecoxib, replicate 2

description: Library name: Embryo 7

value: Embryo


title: peanut-XN_SY01_P1_A21_180926A_SPRI_021_200507

description:
XN_SY01_P1_A21_180926A_SPRI_021_200507
47K SNPs


title: peanut-XN_SY01_P1_B01_180926A_SPRI_311_200507

description:
XN_SY01_P1_B01_180926A_SPRI_311_200507
47K SNPs


title: Low light, 5 mM nitrate, rep 4


title: Co-cultured, ex vivo 24h, DMSO, replicate 2

description: Library name: Embryo 9


title: High light, 10 mM nitrate, rep 3

value: 10 mM nitrate


title: Low light, 5 mM nitrate, rep 3


title: Solely cultured, ex vivo 24h, Celecoxib, replicate 3

description: Library name: Embryo 8

value: Celecoxib


title: RPM thyroid tumor RPM-H7691-thy

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Library name: RPM-H7691-thy

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4.
For RNASeq analysis, low quality reads were filtered out prior to alignment to mm10 using TopHat v2.1.0.
Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1. Normalization and gene expression results were done using EdgeR.
Assembly: mm10
Supplementary files format and content: For RNA-seq data, EdgeR count tables with Log2Fold gene expression changes and adjusted p values.

source_name: thyroid tumor

growth_protocol: Mouse cell lines were isolated and grown in DMEM supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), and 10 % fetal bovine serum. Cells were maintained at 37°C in a humidified atmosphere containing 5 % CO2 and 95 % air.

extract_protocol:
Total RNA was extracted using Trizol, and Zymogenetics Direct-Zol Miniprep kit.
Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Cells were grown in DMEM supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), and 10 % fetal bovine serum.

value: thyroid tumor

value: Rb/p53/Max mutant


title: DM1

value: Placenta

value: Heterogeneous

value: diabetes


title: High light, 10 mM nitrate, rep 4

value: Leaf


title: IS ex vivo 24h, Celecoxib, replicate 2

description: Library name: Endometrium 6

source_name: Endometrium

value: Endometrium


title: peanut-XN_SY01_P1_A22_180926A_SPRI_223_200507

description:
XN_SY01_P1_A22_180926A_SPRI_223_200507
47K SNPs

value: leaf


title: peanut-XN_SY01_P1_A19_180926A_SPRI_018_200507

description:
XN_SY01_P1_A19_180926A_SPRI_018_200507
47K SNPs


title: Solely cultured, ex vivo 24h, DMSO, replicate 3

description: Library name: Embryo 6

value: DMSO


title: IS ex vivo 24h, DMSO, replicate 3

description: Library name: Endometrium 5


title: peanut-XN_SY01_P1_A20_180926C_SPRI-466_210107

description:
XN_SY01_P1_A20_180926C_SPRI-466_210107
47K SNPs


title: RPM thyroid tumor RPM-H7698-thy

description: Library name: RPM-H7698-thy


title: Mid light, 10 mM nitrate, rep 4


title: peanut-XN_SY01_P1_A19_180926C_SPRI-024_210107

description:
XN_SY01_P1_A19_180926C_SPRI-024_210107
47K SNPs


title: IS ex vivo 24h, Celecoxib, replicate 3

description: Library name: Endometrium 7


title: IS ex vivo 24h, DMSO, replicate 2

description: Library name: Endometrium 4


title: peanut-XN_SY01_P1_A20_180926A_SPRI_222_200507

description:
XN_SY01_P1_A20_180926A_SPRI_222_200507
47K SNPs


title: RPM thyroid tumor RPM-H7634-thy

description: Library name: RPM-H7634-thy


title: Solely cultured, ex vivo 24h, DMSO, replicate 2

description: Library name: Embryo 5


title: peanut-XN_SY01_P1_A17_180926C_SPRI-023_210107

description:
XN_SY01_P1_A17_180926C_SPRI-023_210107
47K SNPs


title: RP thyroid tumor RP-K2032-thy

description: Library name: RP-K2032-thy

value: Rb/p53 mutant


title: Low light, 10 mM nitrate, rep 4

value: Low light


title: RP thyroid tumor RP-H9822-thy

description: Library name: RP-H9822-thy


title: kidney,vehicle,rep4

city: Taiyuan

first: Rui

last: Gao

address: Shanxi University of Medical Sciences, 98 University Street, Yuci District, Jinzhong City, Shanxi Province

institute: shanxi medical university

description: Library name: ICR_Vehicle_RNA-seq rep4

data_processing:
After raw data filtering, sequencing error rate assessment and GC content distribution evaluation, gene expression levels were determined by gene quantification.  The differential expression analysis was conducted using the DESeq2 R package (1.20.0), while enrichment analysis of differentially expressed genes was performed by the cluster Profiler R package (3.8.1).
Assembly: GRCm38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: kidney

extract_protocol:
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads
n. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: kidney

value: VEHICLE


title: Low light, 10 mM nitrate, rep 3


title: RP thyroid tumor RP-H9939-thy

description: Library name: RP-H9939-thy


title: peanut-XN_SY01_P1_A18_180926A_SPRI_221_200507

description:
XN_SY01_P1_A18_180926A_SPRI_221_200507
47K SNPs


title: Low light, 20 mM nitrate, rep 4

value: 20 mM nitrate


title: kidney,vehicle,rep2

description: Library name: ICR_Vehicle_RNA-seq rep2


title: RPM pituitary tumor PIT-RPM-H7636

description: Library name: RPM-H7636-PIT

source_name: pituitary tumor

value: pituitary tumor


title: Mid light, 20 mM nitrate, rep 4

value: Mid light


title: High light, 20 mM nitrate, rep 4

value: High light


title: RPM pituitary tumor PIT-RPM-H7436

description: Library name: RPM-H7436-PIT


title: peanut-XN_SY01_P1_A17_180926A_SPRI_011_200507

description:
XN_SY01_P1_A17_180926A_SPRI_011_200507
47K SNPs


title: Mid light, 20 mM nitrate, rep 3


title: peanut-XN_SY01_P1_A18_180926C_SPRI-463_210107

description:
XN_SY01_P1_A18_180926C_SPRI-463_210107
47K SNPs


title: kidney,vehicle,rep3

description: Library name: ICR_Vehicle_RNA-seq rep3


title: kidney,BPA,rep4

description: Library name: ICR_BPA_RNA-seq rep4

value: BPA


title: RP pituitary tumor PIT-RP-K2035

description: Library name: RP-K2035-PIT


title: RPM pituitary tumor PIT-RPM-H7634

description: Library name: RPM-H7634-PIT

value: Rb/p53/Max mutant


title: High light, 20 mM nitrate, rep 2


title: RP pituitary tumor PIT-RP-K2101

description: Library name: RP-K2101-PIT


title: kidney,vehicle,rep1

description: Library name: ICR_Vehicle_RNA-seq rep1


title: RPM pituitary tumor PIT-RP-H7533

description: Library name: RPM-H7533-PIT


title: Low light, 20 mM nitrate, rep 3


title: High light, 20 mM nitrate, rep 3


title: peanut-XN_SY01_P1_A15_180926C_SPRI-019_210107

description:
XN_SY01_P1_A15_180926C_SPRI-019_210107
47K SNPs


title: kidney,BPA,rep3

description: Library name: ICR_BPA_RNA-seq rep3


title: kidney,BPA,rep2

description: Library name: ICR_BPA_RNA-seq rep2


title: peanut-XN_SY01_P1_A15_180926A_SPRI_010_200507

description:
XN_SY01_P1_A15_180926A_SPRI_010_200507
47K SNPs


title: RP pituitary tumor PIT-RP-K2032

description: Library name: RP-K2032-PIT


title: High light, 20 mM nitrate, rep 1


title: RP pituitary tumor PIT-RP-H9939

description: Library name: RP-H9939-PIT


title: Mid light, 20 mM nitrate, rep 1


title: peanut-XN_SY01_P1_A14_180926C_SPRI-457_210107

description:
XN_SY01_P1_A14_180926C_SPRI-457_210107
47K SNPs


title: Co-cultured, ex vivo 24h, Celecoxib, replicate 1

value: Embryo

value: Celecoxib


title: peanut-XN_SY01_P1_A16_180926A_SPRI_220_200507

description:
XN_SY01_P1_A16_180926A_SPRI_220_200507
47K SNPs


title: Mid light, 20 mM nitrate, rep 2


title: kidney,BPA,rep1

description: Library name: ICR_BPA_RNA-seq rep1


title: peanut-XN_SY01_P1_A14_180926A_SPRI_219_200507

description:
XN_SY01_P1_A14_180926A_SPRI_219_200507
47K SNPs


title: Solely cultured, ex vivo 24h, Celecoxib, replicate 1


title: RP pituitary tumor PIT-RP-H9822

description: Library name: RP-H9822-PIT


title: peanut-XN_SY01_P1_A13_180926A_SPRI_009_200507

description:
XN_SY01_P1_A13_180926A_SPRI_009_200507
47K SNPs


title: peanut-XN_SY01_P1_A13_180926C_SPRI-017_210107

description:
XN_SY01_P1_A13_180926C_SPRI-017_210107
47K SNPs


title: Low light, 20 mM nitrate, rep 2


title: peanut-XN_SY01_P1_A12_180926C_SPRI-449_210107

description:
XN_SY01_P1_A12_180926C_SPRI-449_210107
47K SNPs


title: peanut-XN_SY01_P1_A12_180926A_SPRI_218_200507

description:
XN_SY01_P1_A12_180926A_SPRI_218_200507
47K SNPs


title: High light, 10 mM nitrate, rep 2

value: 10 mM nitrate


title: RPM pituitary tumor PIT-RPM-H7688

description: Library name: PIT-RPM-H7688


title: RPM pituitary tumor PIT-RPM-H7698

description: Library name: PIT-RPM-H7698


title: High light, 10 mM nitrate, rep 1

value: Leaf


title: Solely cultured, ex vivo 24h, DMSO, replicate 1


title: Co-cultured, ex vivo 24h, DMSO, replicate 1


title: peanut-XN_SY01_P1_A11_180926C_SPRI-015_210107

description:
XN_SY01_P1_A11_180926C_SPRI-015_210107
47K SNPs


title: RPM pituitary tumor PIT-RPM-H9468

description: Library name: PIT-RPM-H9468


title: IS ex vivo 24h, Celecoxib, replicate 1

value: Endometrium


title: Mid light, 10 mM nitrate, rep 3


title: RPM pituitary tumor PIT-RPM-H7093

description: Library name: PIT-RPM-H7093


title: RP pituitary tumor PIT-RP-K2102

description: Library name: PIT-RP-K2102


title: peanut-XN_SY01_P1_A11_180926A_SPRI_006_200507

description:
XN_SY01_P1_A11_180926A_SPRI_006_200507
47K SNPs

value: leaf


title: RP pituitary tumor PIT-RP-K2037

description: Library name: PIT-RP-K2037


title: I-IS ex vivo 24h, DMSO, replicate 1

value: DMSO


title: RP pituitary tumor PIT-RP-K2027

description: Library name: PIT-RP-K2027

value: Rb/p53 mutant


title: mouse ovarian granulosa cells, Cebp-P, 12 h post-hCG, rep3

city: Ithaca

first: Yi

last: Ren

address: 203 Morrison Hall

department: Animal Science

institute: Cornell University

data_processing:
Raw RNA-seq reads were aligned to the mouse (GRCm38/mm10) genome using HISAT2 (version 2.0.5) by default parameters. Raw read counts for each gene were generated using featureCounts (v1.5.0-p3) and Transcripts Per Million (TPM) values of each gene were generated using EdgeR (version 1.3.3).
Assembly: mm10
Supplementary files format and content: excel sheet file includes TPM values for each sample

source_name: Ovary

extract_protocol:
Total messenger RNA (mRNA) was extracted using RNeasy Micro Kit. Library preparation and transcriptome sequencing were conducted by Novogene Co., LTD
poly A enrichment

treatment_protocol: 21-23 days old female mice weighing 10~11 g were injected intraperitoneally with 5 IU pregnant mare serum gonadotropin (PMSG) followed 44-48 h later by the injection of 5 IU human chorionic gonadotropin (hCG). Ovarian granulosa cells were isolated from ovaries that collected at indicated time point post-hCG treatment.

value: Ovary

value: ovarian granulosa cells

value: Cebpa/bfl/fl;Pgr-Cre

value: 12 h post-hCG


title: Mid light, 10 mM nitrate, rep 1


title: IS ex vivo 24h, DMSO, replicate 1


title: Low light, 10 mM nitrate, rep 1

value: Low light


title: peanut-XN_SY01_P1_A10_180926C_SPRI-444_210107

description:
XN_SY01_P1_A10_180926C_SPRI-444_210107
47K SNPs


title: mouse ovarian granulosa cells, Cebp-P, 12 h post-hCG, rep1


title: peanut-XN_SY01_P1_A09_180926A_SPRI_005_200507

description:
XN_SY01_P1_A09_180926A_SPRI_005_200507
47K SNPs


title: Low light, 20 mM nitrate, rep 1

value: 20 mM nitrate


title: RP thyroid tumor H7533

description: Library name: H7533

value: thyroid tumor


title: peanut-XN_SY01_P1_A10_180926A_SPRI_217_200507

description:
XN_SY01_P1_A10_180926A_SPRI_217_200507
47K SNPs


title: peanut-XN_SY01_P1_A08_180926C_SPRI-443_210107

description:
XN_SY01_P1_A08_180926C_SPRI-443_210107
47K SNPs


title: mouse ovarian granulosa cells, Cebp-P, 12 h post-hCG, rep2


title: peanut-XN_SY01_P1_A09_180926C_SPRI-014_210107

description:
XN_SY01_P1_A09_180926C_SPRI-014_210107
47K SNPs


title: mouse ovarian granulosa cells, Cebp-C, 12 h post-hCG, rep3


title: Mid light, 10 mM nitrate, rep 2

value: Mid light


title: RP thyroid tumor H7436 T2

description: Library name: H7436 T2


title: Mid light, 5 mM nitrate, rep 2

value: 5 mM nitrate


title: High light, 5 mM nitrate, rep 1

value: High light


title: mouse ovarian granulosa cells, Cebp-C, 12 h post-hCG, rep2


title: Low light, 10 mM nitrate, rep 2


title: Mid light, 5 mM nitrate, rep 1


title: mouse ovarian granulosa cells, Cebp-C, 12 h post-hCG, rep1


title: RP thyroid tumor H7436 T1

description: Library name: H7436 T1


title: peanut-XN_SY01_P1_A07_180926C_SPRI-012_210107

description:
XN_SY01_P1_A07_180926C_SPRI-012_210107
47K SNPs


title: Low light, 5 mM nitrate, rep 2


title: RP pituitary tumor PIT-RP-H9960

description: Library name: PIT-RP-H9960

value: pituitary tumor


title: RP thyroid tumor G8917-thy

description: Library name: G8917-thy


title: High light, 5 mM nitrate, rep 2


title: peanut-XN_SY01_P1_A07_180926A_SPRI_004_200507

description:
XN_SY01_P1_A07_180926A_SPRI_004_200507
47K SNPs


title: mouse ovarian granulosa cells, WT, 12 h post-hCG, rep2

value: wild type


title: RP thyroid tumor G8874-thy

description: Library name: G8874-thy


title: RPM pituitary tumor PIT-RPM-H7691

description: Library name: RPM-H7691-PIT

value: Rb/p53/Max mutant


title: RP thyroid tumor G8471-thy

description: Library name: G8471-thy


title: Low light, 5 mM nitrate, rep 1

value: Leaf


title: High light, 2 mM nitrate, rep 1

value: 2 mM nitrate


title: High light, 2 mM nitrate, rep 2


title: Mid light, 2 mM nitrate, rep 2


title: RP thyroid tumor G8735-thy

description: Library name: G8735-thy


title: RP thyroid tumor G8918-thy

description: Library name: G8918-thy


title: peanut-XN_SY01_P1_A08_180926A_SPRI_216_200507

description:
XN_SY01_P1_A08_180926A_SPRI_216_200507
47K SNPs

value: leaf


title: peanut-XN_SY01_P1_A06_180926A_SPRI_215_200507

description:
XN_SY01_P1_A06_180926A_SPRI_215_200507
47K SNPs


title: mouse ovarian granulosa cells, Cebp-P, 8 h post-hCG, rep2

value: 8 h post-hCG


title: RPM_M3_MYC

description: Library name: RPM_M3_MYC

library_source: genomic

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment was to mm10 with Bowtie 2,  reads >700bp filtered out
Data were aligned using Bowtie2. Bigwig files were produced using bedtools genomecov, and WigToBigWig scripts.
Assembly: mm10
Supplementary files format and content: Bigwig files are provided for ChIP-Seq data
Supplementary files format and content: Bigwig files are provided for Cut&Run data
Library strategy: CUT&Run

source_name: cultured thyroid cells

growth_protocol: Mouse cell lines were isolated and grown in DMEM supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), and 10 % fetal bovine serum.

extract_protocol:
For ChIP-Seq formaldehyde cross-linking was used, followed by Micrococcal nuclease treatment, sonication, and Chromatin IP with specific or control antibodies. CUT&RUN was performed according to published methods using pA-MNase as secondary reagent. Yeast DNA was spiked into the samples after DNA extraction to normalize signal between samples. Cells were processed on an automated system at the Fred Hutch Cancer Center to carry out MNase cleavage, DNA extraction, and library construction.
for ChIP-Seq, libraries were prepared using the Kapa system, 25x25 paired-end sequencing was performed on an Illumina HiSeq 2500 instrument. For CUT&RUN, cells were processed on an automated system at the Fred Hutch Cancer Center using KAPA DNA polymerase method for library preparation.

value: cultured thyroid cells


title: Mid light, 2 mM nitrate, rep 1


title: peanut-XN_SY01_P1_A05_180926A_SPRI_003_200507

description:
XN_SY01_P1_A05_180926A_SPRI_003_200507
47K SNPs


title: peanut-XN_SY01_P1_A04_180926C_SPRI-431_210107

description:
XN_SY01_P1_A04_180926C_SPRI-431_210107
47K SNPs


title: peanut-XN_SY01_P1_A06_180926C_SPRI-434_210107

description:
XN_SY01_P1_A06_180926C_SPRI-434_210107
47K SNPs


title: RPM_M3_IgG

description: Library name: RPM_M3_IgG


title: Low light, 2 mM nitrate, rep 2


title: mouse ovarian granulosa cells, WT, 12 h post-hCG, rep3

value: Ovary

value: ovarian granulosa cells


title: mouse ovarian granulosa cells, Cebp-C, 8 h post-hCG, rep3


title: RPM_M2_MYC

description: Library name: RPM_M2_MYC


title: mouse ovarian granulosa cells, WT, 12 h post-hCG, rep1

value: 12 h post-hCG


title: peanut-XN_SY01_P1_A04_180926A_SPRI_214_200507

description:
XN_SY01_P1_A04_180926A_SPRI_214_200507
47K SNPs


title: mouse ovarian granulosa cells, Cebp-P, 8 h post-hCG, rep3

value: Cebpa/bfl/fl;Pgr-Cre


title: peanut-XN_SY01_P1_A05_180926C_SPRI-007_210107

description:
XN_SY01_P1_A05_180926C_SPRI-007_210107
47K SNPs


title: RPM_M2_IgG

description: Library name: RPM_M2_IgG


title: peanut-XN_SY01_P1_A03_180926B_SPRI-499_210107

description:
XN_SY01_P1_A03_180926B_SPRI-499_210107
47K SNPs


title: RPM_M1_MYC

description: Library name: RPM_M1_MYC


title: mouse ovarian granulosa cells, Cebp-C, 8 h post-hCG, rep1


title: peanut-XN_SY01_P1_A03_180926A_SPRI_002_200507

description:
XN_SY01_P1_A03_180926A_SPRI_002_200507
47K SNPs


title: mouse ovarian granulosa cells, Cebp-P, 8 h post-hCG, rep1


title: RPM_M1_IgG

description: Library name: RPM_M1_IgG


title: peanut-XN_SY01_P1_A02_180926C_SPRI-428_210107

description:
XN_SY01_P1_A02_180926C_SPRI-428_210107
47K SNPs


title: mouse ovarian granulosa cells, WT, 8 h post-hCG, rep2


title: peanut-XN_SY01_P1_A02_180926A_SPRI_213_200507

description:
XN_SY01_P1_A02_180926A_SPRI_213_200507
47K SNPs


title: RP_C3_MYC

description: Library name: RP_C3_MYC

value: Rb/p53 mutant


title: peanut-XN_SY01_P1_A01_180926B_SPRI-498_210107

description:
XN_SY01_P1_A01_180926B_SPRI-498_210107
47K SNPs


title: mouse ovarian granulosa cells, WT, 8 h post-hCG, rep1


title: peanut-XN_SY01_P1_A01_180926A_SPRI_001_200507

description:
XN_SY01_P1_A01_180926A_SPRI_001_200507
47K SNPs


title: RP_C3_IgG

description: Library name: RP_C3_IgG


title: RP_C3_MAX

description: Library name: RP_C3_MAX


title: Low light, 2 mM nitrate, rep 1

value: Low light


title: mouse ovarian granulosa cells, Cebp-C, 8 h post-hCG, rep2


title: IV-27681

description: DEGS.txt

data_processing:
DESeq2 Differential Expression
Assembly: GRCm38 - mm10
Supplementary files format and content: tab delimited counts file with DESEq2 output

extract_protocol:
Baylor College of Medicine Protocol
NEBNext Ultra II Directional RNA library prep kit

value: Placenta

tag: strain


title: mouse ovarian granulosa cells, WT, 8 h post-hCG, rep3


title: IV-27680

description: DEGS.txt


title: In Vitro SreA transcript, SAM, 1M7

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

description: RNA was 3' ligated to adapter, cDNA was generated by MaP RT with a template-switching oligo

data_processing:
fastqs were processed, aligned, and had mutations counted by shapemapper2 software
SHAPE reactivities were used to inform RNA secondary structure modeling in the RNAStructure software, generating minimum-free energy structure.
No SAM mutation rates were scaled to SAM mutation rates by median difference minimization (generalized reduced gradient package in Microsoft Excel), and scaled differences were used to calculate z-scores for each nucleotide.
Assembly: SreA fasta files used for alignment are included as processed data files.
Supplementary files format and content: profile.txt files tab-separated value outputs of shapemapper2, which include mutation rates and calculated normalized SHAPE reactivities
Supplementary files format and content: .shape files are tab-separated value SHAPE reactivities for use in RNAStructure software
Supplementary files format and content: .fa files are fasta files containg the SreA aptamer sequences used in analysis
Supplementary files format and content: mfe.ct files are RNA structure files used to represent the minimum free-energy secondary structures (output of RNAStructure)
Supplementary files format and content: zscores.csv are comma-separated values files containing mutation rates and scaled differences used for calculating z-scores between SAM and No SAM samples.
Library strategy: SHAPE-MaP

organism: Listeria monocytogenes

source_name: bacterial cells

growth_protocol: SreA aptamer RNA was transcribed in solution with T7 RNA polymerase

extract_protocol:
RNAs were buffer exchanged by centrifugation filter before library preparation
RNAs were ligated to a 3' end adapter including an RT primer binding site. cDNA was generated by MaP RT with Superscript II including a template-switching oligonucleotide. Final sequencing libraries were generated by PCR using primers complentary to 3' adapter and template-switching oligo sequences, with additional indexing barcodes included.

treatment_protocol: RNAs were folded for 20 minutes at 37C in folding buffer in the presence or absence of SAM, followed by treatment of 10 mM 1M7 SHAPE reagent or DMSO control for 2 minutes at 37C.

value: bacterial cells

value: 37C folding 20 min with 1mM SAM, 10mM 1M7 37C 2min


title: RP_C2_MYC

description: Library name: RP_C2_MYC


title: peanut-XN_SY01_P1_A16_180926C_SPRI-460_210107

description:
XN_SY01_P1_A16_180926C_SPRI-460_210107
47K SNPs


title: RP_C2_MAX

description: Library name: RP_C2_MAX


title: PBMC_t1_POMJ_patient14

type: RNA

city: Parma

first: Ilaria

last: Minato

address: Parco Area delle Scienze 23/a

country: Italy

institute: Università di Parma

description: Gene expression in PBMCs after 12 weeks of intervention with pomegranate juice

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60 °C for 30 minutes following the manufacturer’s instructions. Then, hybridization was performed for 17 h at 65 °C at 10 rpm in a rotating Agilent hybridization oven. Microarrays were subsequently washed according to the Agilent Gene Expression Hybridization protocol.

scan_protocol: Using the one-color scan setting, the slides were immediately scanned on an Agilent G2565AA Microarray Scanner System.

data_processing: Microarray images were processed using the Feature Extraction Software version 12.0 (Agilent Technologies Inc.) using default parameters (GE1_1200_Jun14 and Grid: 072363_D_F_20150612) to obtain the features for data analysis.

source_name: peripheral blood mononuclear cells, t1, pomegranate juice, patient 14

label_protocol: RNA (200 ng) was labeled with the fluorescent dye Cyanine3 (Cy3) after reverse transcription and amplification using a Low Input Quick Amp Labeling Kit and a One-Color RNA Spike-In Kit (Agilent). Cy3-labeled cRNA was purified using the RNeasy Mini Kit (Qiagen). cRNA yield (μg) and specific activity (pmol Cy3 per µg cRNA) were assessed using the Micro Array measurement tab of a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc.).

extract_protocol: RNA was extracted using column separation (Quick-RNA Whole Blood kit; Zymo Research Corporation, Irvine, CA, USA), followed by DNase treatment to avoid DNA contamination, according to the manufacturer’s instructions. The RNA yield and purity were evaluated with a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). RNA samples were then run on a 2100 Bioanalyzer system (Agilent Technologies Inc., Santa Clara, CA, USA) using an RNA 6000 Nano kit to assess its quality.

treatment_protocol: IBD patients received either pomegranate juice or placebo for a 12–week period, twice daily. PBMCs were purified from whole blood samples collected at enrolment (t0) and the end of the intervention (t1).

value: peripheral blood mononuclear cells (PBMCs)

tag: gender

value: female

tag: disease

value: Crohn's disease


title: PBMC_t1_POMJ_patient10

source_name: peripheral blood mononuclear cells, t1, pomegranate juice, patient 10


title: PBMC_t0_POMJ_patient09

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, pomegranate juice, patient 09

value: male

value: Ulcerative colitis


title: In Vitro SreA transcript, SAM, DMSO

value: 37C folding 20 min with 1mM SAM, DMSO 37C 2min


title: IV-27588

description: DEGS.txt


title: RP_C2_IgG

description: Library name: RP_C2_IgG


title: PBMC_t0_POMJ_patient10

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, pomegranate juice, patient 10


title: PBMC_t0_POMJ_patient14

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, pomegranate juice, patient 14


title: IV-27587

description: DEGS.txt

value: Wild Type


title: PBMC_t1_POMJ_patient09

source_name: peripheral blood mononuclear cells, t1, pomegranate juice, patient 09


title: In Vitro SreA transcript, No SAM, 1M7

value: 37C folding 20 min, 10mM 1M7 37C 2min


title: IV-27586

description: DEGS.txt


title: RP_C1_MAX

description: Library name: RP_C1_MAX

value: cultured thyroid cells


title: IV-27585

description: DEGS.txt


title: IV-27589

description: DEGS.txt


title: RP_C1_MYC

description: Library name: RP_C1_MYC


title: SW48 cells, Myricone C, Biol rep 3

city: Gangneung

first: Myungsuk

last: Kim

state: Gangwon

address: 679 Saimdang-ro

country: South Korea

institute: Korea Institute of Science & Technology

description:
Library name: Sample 12
Column name in MF_SW48_Processed.csv: SW48_MyrC_4

data_processing:
Raw sequencing data (fastq files) were assessed for quality using FastQC and trimmed to remove adapter sequences and low-quality reads.
Trimmed reads were aligned to the human reference genome (GRCh38) using STAR aligner with default parameters.
Gene expression levels were quantified using featureCounts18 with gene annotations from GENCODE v39.
Assembly: GRCh38
Supplementary files format and content: csv files include raw counts for each Sample

source_name: Large intestine, colon

growth_protocol: Cell lines were maintained using RPMI-1640 media (HyClone, Logan, Utah, USA), supplemented with 10% heat-inactivated fetal bovine serum (Gibco, USA) and 1% penicillin-streptomycin (HyClone, Logan, Utah, USA), and incubated at 37°C with 5% CO2 Experiments were performed using cells between passages 5 and 20.

extract_protocol:
Total RNA was extracted using the HybridR RNA isolation kit (GeneAll, Seoul, Republic of Korea). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies) to ensure RNA integrity number (RIN) values > 8.0. Three biological replicates were prepared for each condition.
Libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Cell lines were treated with either 10µM MyrC or vehicle control (0.1% DMSO)

value: Large intestine, colon

tag: cell line

value: colorectal adenocarcinoma

value: WT

value: Myricone C 10µM

tag: time


title: PBMC_t0_pbo_patient07

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, placebo, patient 07


title: SW48 cells, Myricone C, Biol rep 2

description:
Library name: Sample 11
Column name in MF_SW48_Processed.csv: SW48_MyrC_3


title: PBMC_t1_pbo_patient07

description: Gene expression in PBMCs after 12 weeks of intervention with placebo

source_name: peripheral blood mononuclear cells, t1, placebo, patient 07


title: PBMC_t1_pbo_patient06

source_name: peripheral blood mononuclear cells, t1, placebo, patient 06


title: In Vitro SreA transcript, No SAM, DMSO

value: 37C folding 20 min, DMSO 37C 2min


title: RP_C1_IgG

description: Library name: RP_C1_IgG

value: Rb/p53 mutant


title: PBMC_t1_POMJ_patient05

source_name: peripheral blood mononuclear cells, t1, pomegranate juice, patient 05


title: MondoA_H7536_vector_Dox_rep2

description: Library name: MondoA_H7536_vector_Dox_rep2

value: Rb/p53/Max/mutant + vector control

value: cells transduced with empty vector control


title: SW48 cells, Myricone C, Biol rep 1

description:
Library name: Sample 10
Column name in MF_SW48_Processed.csv: SW48_MyrC_2


title: IV-27584

description: DEGS.txt

source_name: Placenta

value: Placenta


title: MondoA_H7536_vector_Dox_rep1

description: Library name: MondoA_H7536_vector_Dox_rep1


title: WY-g-3,Colon tissue, DSS-induced, modeling for 9 days

city: Hangzhou

first: Yingying

state: Zhejiang

address: No. 260, Baichuan Street, Fuyang District, Hangzhou City

institute: Zhejiang Chinese Medical University

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Colon

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Colon

tag: group

value: LRWE

value: DSS-induced, modeling for 9 days


title: SW48 cells, Control, Biol rep 3

description:
Library name: Sample 9
Column name in MF_SW48_Processed.csv: SW48_CON_3

value: DMSO (vehicle control)


title: PBMC_t0_pbo_patient06

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, placebo, patient 06

value: peripheral blood mononuclear cells (PBMCs)

value: male

value: Crohn's disease


title: WY-g-2,Colon tissue, DSS-induced, modeling for 9 days


title: PBMC_t0_POMJ_patient05

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, pomegranate juice, patient 05

value: Ulcerative colitis


title: MondoA_H7536_Max_Dox_rep2

description: Library name: MondoA_H7536_Max_Dox_rep2

source_name: cultured thyroid cells

value: cultured thyroid cells

value: Rb/p53/Max/mutant + MAX addback

value: cells transduced with Max expressing vector


title: MondoA_H7536_Max_Dox_rep1

description: Library name: MondoA_H7536_Max_Dox_rep1


title: SW48 cells, Control, Biol rep 2

description:
Library name: Sample 8
Column name in MF_SW48_Processed.csv: SW48_CON_2

value: Large intestine, colon

value: colorectal adenocarcinoma

value: WT


title: Max_H7536_vector_Dox_rep2

description: Library name: Max_H7536_vector_Dox_rep2

value: Rb/p53/Max/mutant + vector control


title: SW48 cells, Control, Biol rep 1

description:
Library name: Sample 7
Column name in MF_SW48_Processed.csv: SW48_CON_1


title: MC-2, Colon tissue, DSS-induced, modeling for 9 days

value: MC


title: Max_H7536_vector_Dox_rep1

description: Library name: Max_H7536_vector_Dox_rep1

value: cells transduced with empty vector control


title: MC-3, Colon tissue, DSS-induced, modeling for 9 days

value: Colon


title: 23132/87 cells, Myricone C, Biol rep 2

description:
Library name: Sample 5
Column name in MF_23132_Processed.csv: 23132_MyrC_2

source_name: Stomach

value: Stomach

value: gastric adenocarcinoma

value: Myricone C 10µM


title: 23132/87 cells, Myricone C, Biol rep 3

description:
Library name: Sample 6
Column name in MF_23132_Processed.csv: 23132_MyrC_3


title: PBMC_t1_POMJ_patient04

source_name: peripheral blood mononuclear cells, t1, pomegranate juice, patient 04

value: peripheral blood mononuclear cells (PBMCs)


title: MC-1, Colon tissue, DSS-induced, modeling for 9 days

value: DSS-induced, modeling for 9 days


title: NC-3, Colon tissue

value: NC

value: control


title: PBMC_t1_POMJ_patient03

source_name: peripheral blood mononuclear cells, t1, pomegranate juice, patient 03

value: female

value: Ulcerative colitis


title: Max_H7536_Max_Dox_rep2

description: Library name: Max_H7536_Max_Dox_rep2

value: cultured thyroid cells

value: Rb/p53/Max/mutant + MAX addback

value: cells transduced with Max expressing vector


title: PBMC_t1_pbo_patient02

source_name: peripheral blood mononuclear cells, t1, placebo, patient 02

value: male


title: PBMC_t1_POMJ_patient01

source_name: peripheral blood mononuclear cells, t1, pomegranate juice, patient 01


title: NC-1, Colon tissue


title: IgG_H7536_vector_Dox_rep2

description: Library name: IgG_H7536_vector_Dox_rep2

value: Rb/p53/Max/mutant + vector control


title: Max_H7536_Max_Dox_rep1

description: Library name: Max_H7536_Max_Dox_rep1


title: 23132/87 cells, Myricone C, Biol rep 1

description:
Library name: Sample 4
Column name in MF_23132_Processed.csv: 23132_MyrC_1

value: WT


title: PBMC_t0_POMJ_patient03

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, pomegranate juice, patient 03


title: 23132/87 cells, Control, Biol rep 3

description:
Library name: Sample 3
Column name in MF_23132_Processed.csv: 23132_CON_3

value: DMSO (vehicle control)


title: IgG_H7536_vector_Dox_rep1

description: Library name: IgG_H7536_vector_Dox_rep1

value: cells transduced with empty vector control


title: 23132/87 cells, Control, Biol rep 2

description:
Library name: Sample 2
Column name in MF_23132_Processed.csv: 23132_CON_2

value: Stomach


title: PBMC_t0_POMJ_patient04

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, pomegranate juice, patient 04


title: PBMC_t0_POMJ_patient01

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, pomegranate juice, patient 01


title: IgG_H7536_Max_Dox_rep2

description: Library name: IgG_H7536_Max_Dox_rep2


title: PTH-C1_3_Tg 24h

city: Indianapolis

middle: A

last: Kalwat

state: IN

address: 1210 Waterway Blvd Suite 2000

department: Lilly Diabetes Center of Excellence

institute: Indiana Biosciences Research Institute

data_processing:
Quality control: The sequencing reads were first quality checked using FastQC (v.0.11.5) for quality control.
Read mapping: The sequence data were then mapped to either the mouse reference genome mm10, the human reference genome hg38, or the rat reference genome rn6 using the RNA-seq aligner STAR (v.2.710a) with the following parameter: “--outSAMmapqUnique 60”. To evaluate the quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bam-stats (from NGSUtilsJ v.0.4.17).
Feature counting: Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p –countReadPairs Q 10”.  Transcripts per million (TPM) were calculated using length values determined by using the “makeTxDbFromGFF” and “exonsBy” functions in the “GenomicFeatures” library and the “reduce” function in the “GenomicRanges” library in R to find the length of the union of non-overlapping exons for each gene.
Assembly: mm10, hg38, rn6
Supplementary files format and content: One processed data file is an excel file containing multiple sheets including read mapping statistics and raw reads, edgeR results per cell line, and TPMs.

organism: Rattus norvegicus

growth_protocol: MIN6 β-cells (RRID: CVCL_0431) were cultured in high glucose DMEM containing 10% fetal bovine serum (FBS), 50 µM β-mercaptoethanol, 4 mM L-glutamine, 1 mM pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin. The mouse intestinal L cell line GLUTag (RRID: CVCL_J406) was cultured in low glucose DMEM containing 10% FBS, 4 mM L-glutamine, 1 mM pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin. Human somatostatinoma QGP-1 (RRID: CVCL_3143) cells (Iguchi, Hayashi et al. 1990) were cultured in RPMI-1640 with 10% FBS, 1 mM pyruvate, 4 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin. The mouse ghrelinoma cell line MGN3 (RRID: CVCL_C4PL) (Iwakura, Li et al. 2010) was cultured in high glucose DMEM supplemented with 10% FBS and containing 4 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. Successful culture required pre-coating flasks with diluted Matrigel (1:20) for 1 h at 37°C prior to seeding. The rat thyroid cell line PCCL3 (RRID: CVCL_6712) (Morishita, Kabil et al. 2020) was cultured in Coons F-12 supplemented with 1 mIU/mL thyrotropin, 1 µg/mL insulin, 5 µg/mL apo-transferrin, 1 nM  hydrocortisone, 5% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin. The mouse pancreatic alpha cell line αTC1 clone 6 (αTC1-6) (RRID: CVCL_B036) was previously described (Hamaguchi and Leiter 1990). αTC1-6 cells were cultured in 15 mM glucose DMEM supplemented with 15 mM HEPES, 0.1 mM non-essential amino acids, 10% FBS, 0.03% BSA, 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
RNA extraction was done with the BioRad Aurum RNA miniprep kit with on-column DNAse digestion.
Total RNA samples were first evaluated for their quantity and quality using Agilent Bioanalyzer 2100. All samples had good quality with RIN (RNA Integrity Number) greater than 9. 100 nanograms of total RNA was used for library preparation with the KAPA mRNA Hyperprep Kit (KK8581) on Biomek following the manufacturer’s protocol. Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation, and multiple libraries were pooled in equal molarity. The pooled libraries were sequenced with 2×100bp paired-end configuration on an Illumina NovaSeq 6000 sequencer using the v1.5 reagent kit.

treatment_protocol: GLUTag, QGP-1, PCCL3, aTC1, MGN3, PTH-C1 and MIN6 cells were plated in 6-well dishes and exposed to DMSO 0.1% or thapsigargin 100 nM (GLUTag, QGP1, MGN3 and MIN6) or 500 nM (PCCL3 and αTC1-6) for 6 and 24 hours before harvesting for RNA purification, downstream gene expression analysis and RNA sequence transcriptome. For drug treatments, all cells were treated with DMSO (0.1%) for 24 h or thapsigargin (100 nM for MIN6, MGN3, QGP1, GLUTag, PTH-C1; 500 nM for αTC1-6 and PCCL3) for 6 and 24 hours and RNA was collected for each time point at the end of the time course.

value: parathyroid cell

tag: time point

value: thapsigargin, 500nM


title: IgG_H7536_Max_Dox_rep1

description: Library name: IgG_H7536_Max_Dox_rep1


title: MGN3_4_Tg 24h

value: ghrelin cell

value: thapsigargin, 100nM


city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

description: Library name: RNA_zebrafish_larvae_treated_PM2.5_rep_1

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome (GRCz11) using STAR version 2.6.1c.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Danio rerio

source_name: larvea

extract_protocol:
RNA was isolated using the peqGold total RNA kit (VWR Peqlab, Erlangen, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced onNovoSeq XPlus as indicated  (Illumina).

value: larvea

value: treatment with PM2.5


title: PTH-C1_3_Tg 6h


title: MGN3_4_Tg 6h


description: Library name: RNA_zebrafish_larvae_treated_PM2.5_rep_2


title: ESCC2（KYSE410 cells_50 ng/mL CCL22）

city: beijing

first: di

last: zhao

address: 52 Fucheng Road, Haidian District, Beijing

institute: beijng cancer hospital

description: whole gene exression

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

scan_protocol: Slides were scanned using Agilent Scanner G2505C.

data_processing: Data was extracted and normalized using Feature Extraction v10.7.1.1 software. Further Data analysis was performed using Agilent GeneSpring v13.1 software.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy  column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).

extract_protocol: Total RNA was extracted using mirVanaTM RNA Isolation Kit (ABI, AM1561).

treatment_protocol: KYSE410 cells were treated with or without 10 uM defactinib for 4 hours and 24 hours.

value: KYSE410 cells


title: PBMC_t0_pbo_patient02

description: Gene expression in PBMCs at baseline

source_name: peripheral blood mononuclear cells, t0, placebo, patient 02

value: peripheral blood mononuclear cells (PBMCs)

value: Ulcerative colitis


title: MGN3_4_ DMSO


title: RNA_zebrafish_larvae_control_rep_2

description: Library name: RNA_zebrafish_larvae_control_rep_2

value: control


title: MGN3_3_Tg 6h


title: DO-223_TIC

city: New York City

first: Ragavi

last: Vijayakumar

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: Sloan Kettering Institute

description:
Library name: Sample 12
Ribodepleted bulk RNA_seq

data_processing:
The fastq files were processed using salmon to generate the "quant" files
The "quant" files were used as input for Rstudio (deseq2 package)
Assembly: mm10
Supplementary files format and content: Salmon-outputs and sample description (samples_info.txt)

extract_protocol:
Frozen cells were lysed in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro or Mini Kit (Qiagen catalog # 217084/217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 20-35 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 71-500 ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 or S4 NovaSeq Reagent Kit (200 or 300 Cycles) (Illumina).  An average of 69 million paired reads was generated per sample. Ribosomal reads represented 0.1-1.7% of the total reads generated and the percent of mRNA bases averaged 91%.

value: TIC


title: B6.129_TIC

description:
Library name: Sample 10
Ribodepleted bulk RNA_seq


title: MGN3_3_ DMSO


title: PTH-C1_2_ DMSO


title: 23132/87 cells, Control, Biol rep 1

description:
Library name: Sample 1
Column name in MF_23132_Processed.csv: 23132_CON_1

value: gastric adenocarcinoma


title: MGN3_3_Tg 24h


title: RNA_zebrafish_larvae _control_rep_1

description: Library name: RNA_zebrafish_larvae _control_rep_1


title: DO-202_TIC

description:
Library name: Sample 11
Ribodepleted bulk RNA_seq


title: MGN3_2_Tg 6h


title: PTH-C1_2_Tg 24h


title: B6.129_B27-TIC

description:
Library name: Sample 7
Ribodepleted bulk RNA_seq


title: DO-223_B27-TIC

description:
Library name: Sample 9
Ribodepleted bulk RNA_seq


title: PTH-C1_2_Tg 6h


title: NC-2, Colon tissue

value: Colon

value: NC


title: KEC40

first: Saptarshi

last: Roy

state: Indiana

address: 1210 Waterway Blvd Ste 4100, 16 Tech Innovation Bldg 1

institute: CDMD Indiana University School of Medicine, India

description: Library name: KEC40

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the porcine reference genome susScr11 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p –countReadPairs -Q 10”.
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.40.2) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: UCSC susScr11
Supplementary files format and content: The excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts
Supplementary files format and content: csv filles include FPKM values of all samples

organism: Sus scrofa

source_name: Kidney endothelilal cells

growth_protocol: The porcine primary kidney and aorta endothelial cell lines were purchased at passage P-3 and P-2 respectively from Cell Biologics (Catalog Nos. P-6014 and P-6052, respectively). The cells were cultured in tissue culture flasks pre-coated with gelatin solution (Catalog No. Cell Biologics 6950) and maintained by using Cell Biologics complete endothelial cell medium kit (Catalog No. M1168). This medium includes 0.5 mL VEGF, 0.5 mL ECGS, 0.5 mL Heparin, 0.5 mL EGF, 0.5 mL Hydrocortisone, 5.0 mL Antibiotic-Antimycotic Solution, and 25.0 mL FBS in 500 mL of basal media. The cells were kept at 37°C in 5% CO2 and passaged using 0.05% Trypsin-EDTA (Catalog No. 25200-056, Gibco). At passage 5, cells were harvested from the flasks and cryopreserved in vials, with each vial containing 0.5 × 10^6 cells per mL.

extract_protocol:
Porcine kidney endothelial cells overexpressing ST8Sia6 and control-GFP cells were collected from four individual experiment after 24 hours transfection for total RNA extraction. Similarly, cells overexpressing ST8Sia6 and control-GFP were collected from co-culturing with four individuals PBMCs as previously described. Cells from different experimental conditions were collected keeping in ice, maintaining temperature at 4°C, washed with cold PBS, and stored as cell pellets at -80°C for total-RNA isolation. Total RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen, Cat No. 74136) following the manufacturer’s protocol. RNA purity and concentration were measured using the Thermo Scientific™ NanoDrop™ 2000/2000c Spectrophotometer.
Illumina totalRNA

treatment_protocol: he primary porcine endothelial kidney and aorta cell lines, the Lipofectamine LTX reagent (Catalog No. 15338100) was employed, and the transfection was performed according to the manufacturer's instructions. All downstream functional experiments were conducted 24 hours after transfection. he primary porcine endothelial kidney and aorta cell lines, the Lipofectamine LTX reagent (Catalog No. 15338100) was employed, and the transfection was performed according to the manufacturer's instructions. All downstream functional experiments were conducted 24 hours after transfection.

value: Kidney endothelilal cells

value: Endothelial Cell

value: negative (Kec plus all cells)


title: KEC27

description: Library name: KEC27

value: Cell-cell interaction


title: KEC39

description: Library name: KEC39

value: Wild type


title: KEC25

description: Library name: KEC25


title: MGN3_2_Tg 24h

value: ghrelin cell


title: DO-202_B27-TIC

description:
Library name: Sample 8
Ribodepleted bulk RNA_seq


title: KEC31

description: Library name: KEC31


title: PTH-C1_1_Tg 24h

value: parathyroid cell

value: thapsigargin, 500nM


title: DO-202_ImmatureTRM2

description:
Library name: Sample 4
Ribodepleted bulk RNA_seq

value: Immature TRM


title: KEC29

description: Library name: KEC29


title: PTH-C1_1_Tg 6h


title: ESCC1（KYSE410 cells_control）

description: whole gene exression

value: KYSE410 cells


title: MGN3_2_ DMSO


title: PTH-C1_3_ DMSO


title: PCCL3_3_Tg 6h

value: thyrocyte cell


title: WY-g-1,Colon tissue, DSS-induced, modeling for 9 days

value: LRWE

value: DSS-induced, modeling for 9 days


title: KEC21

description: Library name: KEC21


title: DO_223_ImmatureTRM2

description:
Library name: Sample 6
Ribodepleted bulk RNA_seq


title: PCCL3_3_ DMSO


title: DO-223_ImmatureTRM1

description:
Library name: Sample 5
Ribodepleted bulk RNA_seq


title: PCCL3_2_Tg 24h


title: PCCL3_3_Tg 24h


title: GLUTag_3_Tg 6h

source_name: GLUTag

value: GLUTag

value: L cell

value: thapsigargin, 100nM


title: GLUTag_3_Tg 24h


title: B6.129_ImmatureTRM1

description:
Library name: Sample 1
Ribodepleted bulk RNA_seq


title: GLUTag_2_Tg 24h


title: DO-202_ImmatureTRM1

description:
Library name: Sample 3
Ribodepleted bulk RNA_seq


title: GLUTag_3_ DMSO


title: KEC19

description: Library name: KEC19

value: St8i6a plasmid


title: B6.129_ImmatureTRM2

description:
Library name: Sample 2
Ribodepleted bulk RNA_seq


title: GLUTag_2_Tg 6h


title: KEC17

description: Library name: KEC17

value: Kidney endothelilal cells


title: KEC15

description: Library name: KEC15

value: Endothelial Cell


title: PCCL3_2_Tg 6h


title: PTH-C1_1_ DMSO


title: KEC23

description: Library name: KEC23


title: Embryonic_stem_cell_ATAC_seq_72CAG_rep3_1

city: Cambridge

last: Leventhal

state: MA

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

institute: Massachusetts Institute of Technology

description:
Library name: Embryonic_stem_cell_ATAC_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

data_processing:
We processed the ATAC-seq data using the ENCODE-DCC ATAC-seq pipeline v.1.7.1. Using this pipeline, we identified FASTQ read adaptors with the detect_adapter.py script in GGR_code (https://github.com/nboley/GGR_code). We trimmed read adaptors with the trim_adaptors function in cutadapt 1.9.1. Processed FASTQs, were aligned using Bowtie2 version 2.2.6, requiring SAMtools version 1.7 and SAMstats version 0.2.1. Picard tools version 1.126 MarkDuplicates was used to deduplicate the aligned reads. These tools were used with default parameters except for setting the parameters “atac.auto_adect_adapter” and “atac.enable_xcor” to “true”.
The ChIP-seq data was analyzed using the ENCODE-DCC ChIP-seq pipeline v1.3.6. In this pipeline, FASTQ data were cropped with Trimmomatic 0.39, aligned with Bowtie2 version 2.26 and deduplicated with Picard version 1.126 MarkDuplicates. Default parameters were used for all arguments except for setting “chip.pipeline_type” to “histone”.
From the aligned, deduplicated ATAC-seq data, MACS2 version 2.1.0 was used to identify peaks that had significant local enrichments at a p-value threshold of 0.01. For the aligned, deduplicated ChIP-seq data, peak calling was performed using SPP version 1.14, GEM 2.4.1 and PeakSeq version 1.25. IDR 2.0.4 was run to determine a high-quality set of consensus peaks from the results of the multiple peak callers. Upon identifying peaks, DiffBind version 2.10.0 was used to perform differential analysis between ChIP-seq or ATAC-seq peaks for the following comparisons: HTT knock-out vs. control, HTT HD knockdown vs HTT wild-type HD, 56/22 (adult onset) HD vs control, and 72/20 (expanded repeat length) HD vs control. We refer to the union of peaks found in 20/20 and 22/20 cells as “control” in these comparisons. DiffBind in R version 3.5.2 was used to identify differential peaks as those with an FDR-adjusted p-value less than 0.1
To determine similarities and differences across cortical neuron replicates and genotypes in the ATAC-seq or ChIP-seq data, Principal Component Analysis (PCA) was used as implemented in Scikit-Learn version 0.23.2. To preprocess the data, peaks were limited to those that were within 5kb from a protein-coding gene. The signal of the filtered peaks was standardized before performing PCA with 10 principal components. Replicates were removed from the analysis if they failed the ATAC-seq or ChIP-seq ENCODE benchmarks determined from FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with peaks quantified with MACS2

source_name: Human pluripotent stem cell line

extract_protocol:
For Atac-seq, We used 50,000 nuclei for the transposase reaction, following the method described previously. Subsequently, samples were purified with the DNA Clean & Concentrator–5 Kit (Zymo Research), and then PCR-amplified using Nextera indexing primers (Illumina). The number of PCR cycles were optimized by qPCR to avoid over amplification of the libraries. The final libraries were purified using 1x PCRClean DX beads (Aline Biosciences). The enrichment of accessible chromatin regions in the libraries were assessed by qPCR using primers mapped to open chromatin region and gene desert regions. For ChIP-seq data 1X106 cells were incubated in lysis buffer (50 mM Tris-HCL pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% Na- deoxycholate, and 5 mM CaCl2 supplemented with protease inhibitors and 10 mM sodium butyrate for K27ac ChIP) for 20 min on ice. The chromatin was digested to 1-5 nucleosomes using Micrococcal Nuclease (NEB # M0247S), at concentration determined by titration experiments, for 10 min at 37oC. To terminate the digestion, 20 mM EDTA was added to the samples. The antibody was added and incubated overnight at 4oC. On the next day, 25 µl of protein G Dynabeads (Thermo Scientific # 10004D,) was added and the samples rotated for 2 hr at 4oC. The beads were washed 6 times: 2 washes with RIPA buffer (10 mM Tris-HCl pH8, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), 2 washes with high salt buffer (10 mM Tris-HCl pH8, 1 mM EDTA, 360 mM NaCl, 1% Triton X- 100, 0.1% Na-deoxycholate, 0.1% SDS), 2X washes with LiCl buffer (10 mM Tris-HCl pH8, 1  mM EDTA, 250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% Na-deoxycholate) and 1 wash with TE (10 mM Tris-HCl pH8, 1 mM EDTA). The DNA was eluted by incubation of the beads in elution buffer (10 mM Tris-HCl pH8, 5 mM EDTA, 300 mM NaCl, 0.1% SDS, 50 µg Proteinase K) for 1 hr. at 62 and purified with 1X PCRClean DX beads (Aline Biosciences).
For Atac-seq, samples were purified with the DNA Clean & Concentrator–5 Kit (Zymo Research), and then PCR-amplified using Nextera indexing primers (Illumina). The number of PCR cycles were optimized by qPCR to avoid over amplification of the libraries. For ChIP-seq, The sequencing libraries were constructed using the NEBNext®Ultra™ II DNA Library Prep Kit for Illumina (NEB # E7645S), followed by analysis using Fragment Analyzer™ instrument (Advanced Analytical), and quantification by a qPCR-based method (KAPA Library Quantification Kit for Illumina Sequencing Platforms)

value: Human pluripotent stem cell line


title: KEC13

description: Library name: KEC13


title: PCCL3_1_Tg 24h


title: GLUTag_1_Tg 24h


title: GLUTag_1_Tg 6h


title: Embryonic_stem_cell_ATAC_seq_72CAG_rep2_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: PCCL3_2_ DMSO


title: KEC11

description: Library name: KEC11


title: PCCL3_1_Tg 6h


title: Embryonic_stem_cell_ATAC_seq_72CAG_rep1_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: GLUTag_1_ DMSO


title: PCCL3_1_ DMSO


title: KEC9

description: Library name: KEC9

value: GFP control


title: Embryonic_stem_cell_ATAC_seq_56CAG_rep2_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: KEC7

description: Library name: KEC7


title: aTC1-6_3_Tg 24h

value: alpha cell


title: GLUTag_2_ DMSO


title: KEC5

description: Library name: KEC5


title: Embryonic_stem_cell_ATAC_seq_56CAG_rep1_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: SC5314 hgt17ΔΔ, bio rep2, citrate

city: Athens

first: Amelia

middle: M

last: White

state: GA

address: 120 E Green Street

department: Microbiology

institute: University of Georgia

description: Library name: AW157_2

data_processing:
Original  data file from high-throughput sequencing platform (Illumina) is transformed to sequenced reads by CASAVA base recognition.
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Remove reads with adapter contamination. Removed reads when uncertain nucleotides constitute more than 10% of either read. Remove reads when low quality nucleotides constitute more than 50% of the read.
Assembly: HISAT2 was used to align reads to provided reference genome
Supplementary files format and content: comma deliminated files include FPKM values for each sample based on condition

organism: Candida albicans

source_name: Yeast

growth_protocol: C. albicans cells were grown in either YNB+1% citrate or YNB+1% acetate for 4h at 37C.

extract_protocol:
RNA extraction was done by disrupting cells with Zirconia beads (Ambion, Fisher Scientific, Waltham) and isolating RNA using 25:24:1 phenol:chloroform:isoamyl alcohol in combination with a Qiagen RNeasy Mini Kit
Sequencing libraries were generated by purifying messenger RNA from total RNA using poly-T oligo–attached magnetic beads. The first cDNA was synthesized using random hexamer primers, followed by sequencing of both ends of cDNA fragments using the Illumina platform

value: Yeast

value: YNB+1% citrate, 4h


title: Embryonic_stem_cell_ATAC_seq_22CAG_rep3_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: KEC3

description: Library name: KEC3


title: SC5314 hgt17ΔΔ, bio rep1, citrate

description: Library name: AW157_1


title: KEC1

description: Library name: KEC1


title: aTC1-6_2_Tg 6h

value: thapsigargin, 500nM


title: aTC1-6_3_ DMSO


title: aTC1-6_2_ DMSO


title: aTC1-6_2_Tg 24h


title: SC5314 WT, bio rep3, citrate, 060126

description: Library name: 06_01_24_MC22_3

value: WT


title: SC5314 WT, bio rep1, citrate, 060124

description: Library name: 06_01_24_MC22_1


title: Embryonic_stem_cell_ATAC_seq_22CAG_rep2_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: aTC1-6_1_Tg 24h


title: Embryonic_stem_cell_ATAC_seq_22CAG_rep1_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: SC5314 WT, bio rep2, citrate, 060125

description: Library name: 06_01_24_MC22_2


title: Embryonic_stem_cell_ATAC_seq_56CAG_rep3_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: aTC1-6_3_Tg 6h


title: Embryonic_stem_cell_ATAC_seq_20CAG_rep3_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: 20CAG control


title: aTC1-6_1_Tg 6h


title: aTC1-6_1_ DMSO


title: SC5314 adr1ΔΔ, bio rep2, citrate

description: Library name: AW10_2


title: Embryonic_stem_cell_ATAC_seq_20CAG_rep2_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: ctr_30_Tumor bearing mice，PBS

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Sequence reads were aligned to the reference human genome, GRCh38 using STAR (2.7.0d).
With the cufflinks program and corresponding sequence reads data we estimated the expression level for each gene for Homo sapiens.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
With the cufflinks program and corresponding sequence reads data we estimated the expression level for each gene for Mus musculus.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: subcutaneous tumor

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies), then the concentration, quality and integrity of RNA were determined by NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: subcutaneous tumor

value: murine melanoma cell

value: PBS, 150ul, every two days, oral gavage


title: SC5314 adr1ΔΔ, bio rep3, citrate

description: Library name: AW10_3


title: Embryonic_stem_cell_ATAC_seq_20CAG_rep1_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: 10_ShBNIP3

city: Philadelphia

first: Makarand

middle: V

last: Risbud

state: Pennsylvania

address: Walnut 1025, College Building, Suite 511

department: Orthopaedic Surgery

institute: Thomas Jefferson University

description: Total RNA from ShBNIP3; sst-rma normalization; DABG FDR<0.05%; FDR<0.05%; FC 2.0

hyb_protocol: Affymetrix Gene chips, Rat Clariom S, were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail.

scan_protocol: Array scanning was performed on an Affymetrix GeneChip Scanner 3000 7G using Command Console Software (Affymetrix)

data_processing: Raw data were processed and .CHP files were generated by sst-rma normalization from Affymetrix .CEL files, and quality control of the expeirment was performed in Transcriptome Analysis Console (TAC) v4.0.2 (Affymetrix). The experimental group was compared to the control group in the TAC, including all probe sets where at least 50% of the samples had a DABG (detected above background) p < 0.05. Inclusion cutoffs were defined at a 2.00-fold change and p-value < 0.05.

label_protocol: Single-stranded cDNA was generated, then fragmented and biotin-labeled using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: NP cells were isolated from 300 gram male Sprague Dawley rat from Charles River and housed for week at Thomas Jefferson University.

extract_protocol: NP and AF tissues were micro-dissected from caudal and lumbar intervertebral discs of 4 WT control and 4 N153S mice and immediately placed in RNAlater® Reagent (INVITROGEN). Tissues were homogenized with a After 4 days of viral transduction RNA was extracted from cell lysates using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Lentivral transduction to knowckdown mitophagy receptor BNIP3

value: Nucleus Pulposus


title: 09_ShBNIP3


title: Embryonic_stem_cell_ATAC_seq_HTT_KO_rep1_1

first: Matthew

description:
Library name: Embryonic_stem_cell_ATAC_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data

value: HTT KO


title: 08_ShBNIP3


title: SC5314 WT, bio rep1, citrate

description: Library name: MC22_1


title: SC5314 adr1ΔΔ, bio rep3, acetate

description: Library name: SC5314_A1_3

value: YNB+1% acetate, 4h


title: 07_ShBNIP3


title: Embryonic_stem_cell_ATAC_seq_HTT_KO_rep3_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: 04_ShCtrl

description: Total RNA from ShCtrl; sst-rma normalization; DABG FDR<0.05%; FDR<0.05%; FC 2.0

source_name: ShCtrl


title: SC5314 adr1ΔΔ, bio rep1, citrate

description: Library name: AW10_1


title: Cortical_neuron_ATAC_seq_72CAG_rep1_1

description:
Library name: Cortical_neuron_ATAC_seq_72CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: 03_ShCtrl


title: SC5314 WT, bio rep3, citrate

description: Library name: MC22_3


title: Embryonic_stem_cell_ATAC_seq_HTT_KO_rep2_1

description:
Library name: Embryonic_stem_cell_ATAC_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: SC5314 adr1ΔΔ, bio rep2, acetate

description: Library name: SC5314_A1_2


title: 06_ShBNIP3


title: ctr_4_Tumor bearing mice，PBS


title: SC5314 adr1ΔΔ, bio rep1, acetate

description: Library name: SC5314_A1_1


title: Plus3 on V8 media repeat 3

city: Zhengzhou

first: Youbao

last: Zhao

state: Henan

address: 218 Pingan Ave. Jinshui District

institute: Henan Agricultural University

description:
Library name: Sample 12
Column name in ReadsPerGene.tab: Plus3_V8_15ReadsPerGene.out.tab

data_processing:
For RNA-seq analysis, the quality of sequenced clean data was analyzed using FastQC software. Subsequently, sequences from approximately 2 GB of clean data for each sample were mapped to the genome sequence of C. deneoformans XL280α using STAR. Gene expression levels were measured in transcripts per million (TPM) by Stringtie to determine unigenes. All unigenes were subsequently aligned against the well-annotated genome of JEC21, which served as the parent strain to generate XL280α through a cross with B3501α. The differential expression of genes (DEGs) was assessed using DEseq2 of the R package and defined based on the fold change criterion (log2|fold-change | > 1.0, adjusted p value < 0.05).
Assembly: ASM9104v1
Supplementary files format and content: tab-delimited text files including reads count per gene for each sample

organism: Cryptococcus neoformans

source_name: Strain

growth_protocol: Seed cultures were diluted to OD600 equals to 3, and spotted onto V8 media, then cultured at room temperature in dark for 12 hours

extract_protocol:
Cryptococcus strains were cultured in liquid YPD with shaking at 220 rpm at 30 °C overnight, or on solid V8 medium at room temperature in the dark for 24 h. The cultures were collected, flash frozen in liquid nitrogen, and lyophilized for 24 h. Total RNA was isolated with the PureLink RNA Mini Kit (Invitrogen).
The transcriptome libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) according to the manufacturer’s instructions.

treatment_protocol: Cultred in dark for 12 hours

value: yeast cells

value: Plus5 expressing strain

value: Grown on V8

tag: batch

value: 12 hours


title: Cortex_hom2_bsseq

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
meRanTK were used to determine the methylation level for all the sequenced cytosine sites
Assembly: mm10
Supplementary files format and content: txt files for each sample were generated by meRanTK
Library strategy: RNA-BS-Seq

source_name: cortex

growth_protocol: cortex were isolated from the tails of WT, Het and Hom mice

extract_protocol:
In vitro transcribed Luciferase Control L4561 RNA was used as negative control in the amplicon-bsRNA-seq experiments. RNAs were transcribed using the MEGAscript® T7 Kit (Life Technologies) according to the manufacturer’s protocol. Total mRNA of mouse cortex was extracted by the Ribo-Zero rRNA depletion kit. Then 1 μg of the mRNA combined with 1 ng Control L4561 RNA  were used for bisulfite treatment by EZ Methylation Kit (Zymo) following the protocols provided by the manufacturer.
After bisulfite conversion, the purified RNA was used for library construction by NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

value: cortex

tag: age

value: HOM


title: 05_ShCtrl


title: Cortical_neuron_ATAC_seq_56CAG_rep2_1

description:
Library name: Cortical_neuron_ATAC_seq_56CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: SC5314 WT, bio rep3, acetate

description: Library name: SC5314_WT3

value: Yeast


title: ctr_3_Tumor bearing mice，PBS

city: Shanghai


title: Cortex_hom1_bsseq


title: Cortical_neuron_ATAC_seq_72CAG_rep2_1

description:
Library name: Cortical_neuron_ATAC_seq_72CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data


title: Y_13_Tumor bearing mice，YM201636

value: YM201636, 3 mg/kg, every two days, oral gavage


title: SC5314 WT, bio rep2, citrate

description: Library name: MC22_2

value: WT

value: YNB+1% citrate, 4h


title: SC5314 WT, bio rep2, acetate

description: Library name: SC5314_WT2


title: Cortical_neuron_ATAC_seq_72CAG_rep3_1

description:
Library name: Cortical_neuron_ATAC_seq_72CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Cortical_neuron_ATAC_seq_22CAG_rep2_1

description:
Library name: Cortical_neuron_ATAC_seq_22CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: Skin, Reba, 7day, rep3

city: Nanjing

first: Chenjie

last: Feng

state: Jiangsu

address: #24 TongJiaXiang, Gulou District

institute: Cna Pharmaceutical University

description:
Library name: Sample 6
Expression_with_annotation.xls

data_processing:
Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis. The reference genome and gene annotation files were downloaded from genome website.
The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Use HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: GRCm39
Supplementary files format and content: .bw files containing genome-wide coverage tracks for each sample
Supplementary files format and content: Expression_with_annotation.xls file contains a comprehensive gene expression matrix with raw read counts and FPKM values for each sample.

source_name: skin

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent)

treatment_protocol: mice were shaved dorsally in telogen at 7 weeks of age. Vehicle control (30% [v/v] dipropylene glycol, 70% distilled water) or 3% rebamipide was topically applied to the shaved skin every day for 7 days.

value: skin

value: 3% Reba


title: 02_ShCtrl

value: Nucleus Pulposus


title: Y_11_Tumor bearing mice，YM201636

value: subcutaneous tumor

value: murine melanoma cell


title: 01_ShCtrl


title: Plus3 on V8 media repeat 2

description:
Library name: Sample 11
Column name in ReadsPerGene.tab: Plus3_V8_14ReadsPerGene.out.tab

value: yeast cells

value: Plus4 expressing strain


title: Cortical_neuron_ATAC_seq_56CAG_rep3_1

description:
Library name: Cortical_neuron_ATAC_seq_56CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: rtf1D on V8 media repeat 3

description:
Library name: Sample 6
Column name in ReadsPerGene.tab: rtf1D_V8_09ReadsPerGene.out.tab

value: RTF1 deletion

value: Grown on V8


title: Cortical_neuron_ATAC_seq_20CAG_rep2_1

description:
Library name: Cortical_neuron_ATAC_seq_20CAG_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: 20CAG control


title: Skin, Reba, 7day, rep1

description:
Library name: Sample 4
Expression_with_annotation.xls


title: rtf1D on V8 media repeat 2

description:
Library name: Sample 5
Column name in ReadsPerGene.tab: rtf1D_V8_08ReadsPerGene.out.tab

value: 12 hours


title: Cortical_neuron_ATAC_seq_56CAG_rep1_1

description:
Library name: Cortical_neuron_ATAC_seq_56CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line


title: Cortex_wt2_bsseq

value: cortex


title: Y_12_Tumor bearing mice，YM201636

value: YM201636, 3 mg/kg, every two days, oral gavage


title: rtf1D on V8 media repeat 1

description:
Library name: Sample 4
Column name in ReadsPerGene.tab: rtf1D_V8_07ReadsPerGene.out.tab


title: Plus3 on V8 media repeat 1

description:
Library name: Sample 10
Column name in ReadsPerGene.tab: Plus3_V8_13ReadsPerGene.out.tab

value: Plus3 expressing strain


title: Cortex_het5_bsseq

value: HET


title: HMD on V8 media repeat 3

description:
Library name: Sample 9
Column name in ReadsPerGene.tab: HMD_V8_12ReadsPerGene.out.tab

value: HMD expressing strain


title: Cortical_neuron_ATAC_seq_22CAG_rep3_1

description:
Library name: Cortical_neuron_ATAC_seq_22CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data

value: 22CAG control


title: SC5314 WT, bio rep1, acetate

description: Library name: SC5314_WT1

value: Yeast

value: WT

value: YNB+1% acetate, 4h


title: XL280 on V8 media repeat 3

description:
Library name: Sample 3
Column name in ReadsPerGene.tab: XL280_V8_06ReadsPerGene.out.tab


title: Cortex_het4_bsseq


title: HMD on V8 media repeat 2

description:
Library name: Sample 8
Column name in ReadsPerGene.tab: HMD_V8_11ReadsPerGene.out.tab


title: XL280 on V8 media repeat 2

description:
Library name: Sample 2
Column name in ReadsPerGene.tab: XL280_V8_05ReadsPerGene.out.tab


title: Cortex_het3_bsseq


title: Cortical_neuron_ATAC_seq_HTT_KO_rep2_1

description:
Library name: Cortical_neuron_ATAC_seq_HTT_KO_rep2
binary alignment sequencing data and peaks called for epigenetic data

value: HTT KO


title: HMD on V8 media repeat 1

description:
Library name: Sample 7
Column name in ReadsPerGene.tab: HMD_V8_10ReadsPerGene.out.tab

value: yeast cells


title: Cortical_neuron_ATAC_seq_22CAG_rep1_1

description:
Library name: Cortical_neuron_ATAC_seq_22CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data


title: Skin, Reba, 7day, rep2

description:
Library name: Sample 5
Expression_with_annotation.xls

value: skin

value: 3% Reba


title: Cortical_neuron_ATAC_seq_20CAG_rep3_1

description:
Library name: Cortical_neuron_ATAC_seq_20CAG_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: SLC15a3_KO_BLM_2

first: Jun

last: Luo

state: State...

address: College of Pharmaceutical Sciences, Zhejiang University， Hangzhou, Zhejiang P. R. China 31005

institute: Zhejiang University

data_processing:
Illumina HiSeq X Ten platform
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
Raw data (raw reads) were processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
Differential expression analysis was performed using the DESeq (2012) R package.P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression.
FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung

growth_protocol: Mice were housed with free access to water and diet, and maintained on a 12h light/12h dark cycle at 23°C throughout the study.

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

treatment_protocol: WT and Slc15a3-/- mice (8 weeks old)  were intratracheally administered BLM (2 mg/kg) in 50 μl of normal saline on day 0. Mice administered with same volume of normal saline served as controls.  The mice were euthanized on day 21.

value: lung

value: BLM


title: Cortex_het1_bsseq


title: RNA-Seq of WT MCF-7 - Replicate 3

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

description: RNA-Seq of WT MCF-7 - Replicate 3

data_processing:
Quality controls was performed with FastQC
Read alignment on Gencode v32 annotation was performed with STAR
Gene expression quantification was performed with RSEM
Assembly: hg38
Supplementary files format and content: Raw read count table

growth_protocol: MCF-7 cell lines were cultured in high glucose Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum.

extract_protocol:
Total RNA was harvested from cultured cells using Qiagen RNeasy Plus Mini Kit according to manufacturer’s instructions.
Triplicates of each condition were sent to BU’s Microarray and Sequencing core for library preparation using Kapa RNA HyperPrep with RiboErase and run on two high output 75-paired end sequencing runs on Illumina NextSeq.

treatment_protocol: GPS2 KO MCF-7 cells were previously made in laboratory using CRISPR/Cas9-mediated genomic recombination using gRNAs against GPS2. Specifically, CRISPR-Cas9 genome editing was performed using two different sets of sgRNAs. In each case, sgRNAs targeted exons 2 and 6 of the human GPS2 sequence. The two sets of sgRNAs each targeting were cloned separately into the LentiCRISPRv2 lentiviral vector (Kindly shared by Dr. Feng Zhang, Addgene plasmid #52961). 3.5 mg of each viral plasmid was co-transfected along with packaging plasmids pCMV-VSV-G and ps.PAX2 (Addgene plasmids #8454 and #12260) into HEK293T cells using Lipofectamine 3000. Media was changed after 24 hours and viral supernatant collected at 60 h. The virus was filtered through a 0.46 μm low protein binding filter membrane and either used immediately or stored at -80°C for later use. Transduction of target cell lines was performed in a six-well plate with 1–1.5 ml of viral supernatant and 8μg/ml polybrene in DMEM with 10% FBS. Media was changed after 24 h and cells split into selection media (puromycin 2.5 μg/ml) at 48 h. The KO lines were maintained as heterogeneous pools without selection of individual clones.


title: SVF_9

city: Beijing

first: Yuandong

last: Tao

state: --- Select One ---

address: Beijing

institute: Chinese PLA General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Hisat2 v2.0.5
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Kidney

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher). 1.5 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using mRNA-seq Library Prep Kit following manufacture’s protocols.

value: Kidney

value: SVF


title: Skin, Vehicle, 7day, rep3

description:
Library name: Sample 3
Expression_with_annotation.xls

value: vehicle


title: SLC15a3_KO_BLM_1


title: RNA-Seq of WT MCF-7 - Replicate 2

description: RNA-Seq of WT MCF-7 - Replicate 2


title: Cortical_neuron_ATAC_seq_20CAG_rep1_1

description:
Library name: Cortical_neuron_ATAC_seq_20CAG_rep1
binary alignment sequencing data and peaks called for epigenetic data

value: Human pluripotent stem cell line

value: 20CAG control


title: Skin, Vehicle, 7day, rep2

description:
Library name: Sample 2
Expression_with_annotation.xls


title: SVF_8


title: Cortex_het2_bsseq

value: cortex

value: HET


title: Cortical_neuron_ATAC_seq_HTT_KO_rep3_1

description:
Library name: Cortical_neuron_ATAC_seq_HTT_KO_rep3
binary alignment sequencing data and peaks called for epigenetic data


title: Skin, Vehicle, 7day, rep1

description:
Library name: Sample 1
Expression_with_annotation.xls


title: Cortex_wt1_bsseq


title: SLC15a3_KO_BLM_4


title: G1, SMC4_-IAA, rep2

city: State College

first: Yi

last: Li

state: PA

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

description: Library name: SMC4_-IAA_rep2

data_processing:
Next generation sequencing was performed on NextSeq 2000, and 100 million of  50 bp paired-end reads were generated for each replicate. Hi-C data analysis was performed with HiC-pro (version 3.1.0), cooler(version 0.10.0), cooltools (version 0.7.0) and HiCExplorer (version 3.7.2).
Assembly: sacCer3
Supplementary files format and content: cool files

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were incubated in 200 mL SCD medium until OD660 reached 0.3.

extract_protocol:
Standard method was used to perform Hi-C and extract DNA.
Hi-C libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Yeast strains were cultured in synthetic media SCD to log phase, and then incubated in SCD + 5 μM alpha factor (Zymo, Y1001) for ~2.5 hrs to arrest the cells in G1 phase. For experiments involving auxin-induced degradation, cells were first treated with α-factor for 1.5 hrs, followed by the addition of IAA for another 1 hr.

value: MATa, tor1-1, fpr::NAT, bar1, HO::OsTIR1-URA3, SMC4-V5-AID-Hyg

value: G1 arrest by alpha factor, -IAA


title: SC5314 hgt17ΔΔ, bio rep3, citrate

description: Library name: AW157_3

value: Yeast

value: YNB+1% citrate, 4h


title: SVF_11

value: WT


title: SLC15a3_KO_BLM_3


title: WT_BLM_2


title: PBS_4

value: PBS


title: RNA-Seq of GPS2-KO MCF-7 - Replicate 2

description: RNA-Seq of GPS2-KO MCF-7 - Replicate 2

value: GPS2 KO


title: Cortical_neuron_ATAC_seq_HTT_KO_rep1_1

description:
Library name: Cortical_neuron_ATAC_seq_HTT_KO_rep1
binary alignment sequencing data and peaks called for epigenetic data

value: HTT KO


title: SVF_10


title: XL280 on V8 media repeat 1

description:
Library name: Sample 1
Column name in ReadsPerGene.tab: XL280_V8_04ReadsPerGene.out.tab

value: yeast cells

value: Grown on V8

value: 12 hours


title: G1, WT, rep2

description: Library name: WT_rep2

value: G1 arrest by alpha factor


title: RNA-Seq of GPS2-KO MCF-7 - Replicate 1

description: RNA-Seq of GPS2-KO MCF-7 - Replicate 1


title: PBS_5

value: Kidney


title: WT_BLM_4

value: lung

value: BLM


title: G1, SMC4_+IAA, rep1

description: Library name: SMC4_+IAA_rep1

value: G1 arrest by alpha factor, +IAA


title: WT_BLM_3


title: G1, WT, rep1

description: Library name: WT_rep1

value: MATa, tor1-1, fpr::NAT, bar1


title: G1, SMC4_+IAA, rep2

description: Library name: SMC4_+IAA_rep2

value: MATa, tor1-1, fpr::NAT, bar1, HO::OsTIR1-URA3, SMC4-V5-AID-Hyg


title: RNA-Seq of GPS2-KO MCF-7 - Replicate 3

description: RNA-Seq of GPS2-KO MCF-7 - Replicate 3


title: G1, SMC4_-IAA, rep1

description: Library name: SMC4_-IAA_rep1

value: G1 arrest by alpha factor, -IAA