title: Control_8

value: Uterine Post Mortem Biopsy

value: Holstein-Freisan

value: Female

value: Control


title: Control_6

status: Public on Aug 01 2022

type: SRA

city: Dunsany

first: Paul

last: Cormican

address: Grange

department: Bioscience

country: Ireland

institute: Teagasc

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to genome using STAR (v2.6.1b)
Read counts per gene for each sample were estimated using featurCounts from the subread package (v.1.6.3).
Supplementary files format and content: Bos_taurus_UMD_3.1.1
Supplementary files format and content: Individual matrix tables with raw gene counts for every gene in a sample

molecule: polyA RNA

organism: Bos taurus

source_name: Uterine Post Mortem Biopsy

extract_protocol:
Uterine samples were taken, flash frozen before subsequent RNA extraction in TRIzol reagent. Total RNA concentration was quantified using the Nanodrop ND-1000 UV-Vis Spectophotometer. Quality of RNA was ascertained with the use of 2100 Agilent Bioanalyzer .
RNA libraries were prepared for sequencing using Illumina® TruSeq® Stranded mRNA Library preparation Kits

tag: tissue

tag: breed

tag: Sex

tag: treatment


title: 16345_AML

city: New York

first: Richard

last: Koche

state: New York

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences using Trim_galore with cutadapt
Reads were aligned to mouse genome assembly hg38 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with un-normalized read counts over all genes.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells (PBMCs)

extract_protocol:
RNA was isolated by TRIzol extraction
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

tag: cell type

tag: disease state

value: blast phase disease (acute myeloid leukemia; AML)


title: Control_5


title: IMR32_DMSO_D4_rep1

type: RNA

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to8x60K whole human genome oligonucleotide microarray (Agilent G4851B, grid ID 039494), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays (SureScan Microarray Scanner), and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background-subtracted and spatially detrended processed signal intensities.

source_name: human neuroblastoma cell line IMR32, 0.1%DMSO, day4, replicate1

label_protocol: Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Human NB cell line IMR32 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). The total RNAs were extracted 4 days after the treatment.

treatment_protocol: NB cells were treated with 0.1% DMSO, EPZ-6438 1 μM, 5-aza-dC 1 μM, EPZ-6438 1 μM and  5-aza-dC 1 μM on a 6 cm dish.

tag: cell line

value: neuroblastoma cell line

value: 0.1%DMSO, day4


title: Control_7


title: HepaRG-Differentiated-2

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

country: France

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C 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°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20110325). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies).

source_name: HepaRG differentiated state - Replicate 2

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 150 ng total RNA, amplification yield was 9.7 ± 0.6 µg cRNA and specific activity was 20.3 ± 1.3 pmol Cy3 per µg cRNA.

growth_protocol: HepaRG cells were cultured as previously described [PMID: 25098666]. Briefly, cells were grown in William's E medium supplemented with 10% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin, 5 mg/mL insulin, and 50 mmol/L hydrocortisone hemisuccinate. Differentiation of HepaRG from progenitors to mature well-differentiated hepatocytes was achieved in 4 weeks by culturing the cells in the supplemented medium in presence of 2% dimethyl sulfoxide (DMSO) for the last 2 weeks. All experiments referred to as progenitor HepaRG were carried out using cells isolated 3 days after plating, while experiments referred to as differentiated HepaRG were carried out using hepatocytes selectively isolated by mild trypsinization from DMSO-treated cultures 4 weeks after the initial plating.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: All cell cultures were conducted at 37°C in a 5% CO2 atmosphere and then submitetd to RNA extration and gene expression profiling. Independent culture experiments were carried out in triplicate: HepaRG progenitors (n=3), HepaRG differentiated (n=3).

value: Differentiated


title: HepaRG-Differentiated-3

source_name: HepaRG differentiated state - Replicate 3


title: HepaRG-Progenitor-2

source_name: HepaRG progenitor state - Replicate 2

value: Progenitor


title: Hpmut_6h_3

city: Erlangen

first: Bodo

last: Linz

address: Staudtstrasse 5

country: Germany

institute: Friedrich Alexander University Erlangen

data_processing:
Preparation of the Illumina sequencing library included depletion of ribosomal RNA from each sample.
Quality filtering was performed using cutadapt v. 1.9.1
High quality reads were mapped against the human reference genome using STAR aligner v. 2.5.2b
Differential gene expression between four replicates each of infected cells and uninfected controls was evaluated using the DESeq2 package v.1.32.0  in R.
Read counts per gene were obtained using featureCounts v. 1.5.1 and the Ensembl gtf annotation file
Assembly: Ensembl GRCh37, release 87
Supplementary files format and content: Table with normalized read counts for every gene and every sample

source_name: H. pylori-infected MKN-28 cells

growth_protocol: Human MKN-28 cells, originally isolated from gastric adenocarcinoma, were cultured at 37 °C in RPMI-1640 medium, containing 4 mM glutamine and 10% FCS.

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Differentiated monolayers were infected with H. pylori from the apical side at a multiplicity of infection (MOI) of 100. After 2 or 6 hours of infection, the MKN-28 cells were harvested.

value: H. pylori htrA deletion mutant

tag: time point

value: 6 h


title: Hpmut_6h_4


title: TUT7 Mut 2 8hrs into S Phase

city: Chapel Hill

first: William

last: Marzluff

state: NC

address: 1 Medical Drive

department: Biology

institute: UNC Chapel Hill

description: TUT7 Mut 2 8hrs into S Phase

data_processing:
Identify H2A and H2B genes in Read 2, discard others
Identify Linker sequence in Read 1, discard others, including Read 2 for paired seq (all files)
Read bases 5' of linker sequence for non-templated nt additions in read 1 only
Assembly: HG19
Supplementary files format and content: _tails.txt (CSV comma delimited) Read 1 after processing
Supplementary files format and content: _tails.xls (CSV comma delimited) Read 1 after processing, opened in excel
Library strategy: EnD-Seq

source_name: Colon Carcinoma

extract_protocol:
Trizol RNA extraction followed by Ethanol Precipitation
EnD-Seq (doi: 10.1261/rna.048785.114)
Paired End RNA Sequencing

treatment_protocol: Double Thymidine Block and Hydroxyurea Treatment: doi 10.1098/rstb.2018.0170

value: Colon Carcinoma

tag: genotype

value: TUT7 KO

value: Double Thymidine Block


title: TUT7 Mut 2 7hrs into S Phase

description: TUT7 Mut 2 7hrs into S Phase


title: Wild Type 5hrs into S Phase

description: Wild Type 5hrs into S Phase

value: WT


title: HepaRG-Progenitor-3

source_name: HepaRG progenitor state - Replicate 3


title: TUT7 Mut 1 6hrs into S Phase

description: TUT7 Mut 1 6hrs into S Phase


title: TUT7 Mut 1 7hrs into S Phase

description: TUT7 Mut 1 7hrs into S Phase


title: Low_Fertility_10

value: Low Fertility


title: 3hExo Mut 2 10hrs into S Phase

description: 3hExo Mut 2 10hrs into S Phase

value: 3'hExo KO


title: 3hExo Mut 1 10hrs into S Phase

description: 3hExo Mut 1 10hrs into S Phase


title: Wild Type 0min into S Phase

description: Wild Type 0min into S Phase


title: Wild Type 6hrs into S Phase

description: Wild Type 6hrs into S Phase


title: Hpmut_6h_2


title: TUT7 Mut 2 40min into S Phase

description: TUT7 Mut 2 40min into S Phase

value: Double Thymidine Block, Hydroxyurea


title: HepaRG-Progenitor-1

source_name: HepaRG progenitor state - Replicate 1


title: Hpmut_6h_1


title: Low_Fertility_7

value: Uterine Post Mortem Biopsy

value: Holstein-Freisan


title: TUT7 Mut 2 0min into S Phase

description: TUT7 Mut 2 0min into S Phase


title: TUT7 Mut 2 20min into S Phase

description: TUT7 Mut 2 20min into S Phase


title: Hpwt_6h_4

value: H. pylori wild-type


title: SK-N-BE_EPZ-6438_D3_rep2

source_name: human neuroblastoma cell line SK-N-BE, EPZ-6438 1 µM, day3, replicate2

growth_protocol: Human NB cell line SK-N-BE, SK-N-SH, NGP, IMR32 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). The total RNAs were extracted 3 days (SK-N-BE, SK-N-SH, NGP) or 4 days (IMR32) after the treatment.

treatment_protocol: NB cells were treated with 0.1% DMSO or EPZ-6438 1 μM on a 6 cm dish.

value: SK-N-BE

value: EPZ-6438 1 µM, day3


title: Low_Fertility_9

value: Female


title: TUT7 Mut 1 40min into S Phase

description: TUT7 Mut 1 40min into S Phase


title: High_Fertility_5

value: High Fertility


title: 3hExo Mut 1 0min into S Phase

description: 3hExo Mut 1 0min into S Phase


title: Hpwt_6h_2


title: Wild Type 20min into S Phase

description: Wild Type 20min into S Phase


title: High_Fertility_3


title: TUT7 Mut 1 0min into S Phase

description: TUT7 Mut 1 0min into S Phase


title: Low_Fertility_8


title: 3hExo Mut 1 40min into S Phase

description: 3hExo Mut 1 40min into S Phase


title: Hpwt_6h_3


title: TUT7 Mut 1 20min into S Phase

description: TUT7 Mut 1 20min into S Phase


title: Hpwt_6h_1


title: Low_Fertility_6


title: High_Fertility_2


title: Hpmut_2h_4

value: 2 h


title: 3hExo Mut 1 20min into S Phase

description: 3hExo Mut 1 20min into S Phase


title: High_Fertility_4


title: Wild Type 40min into S Phase

description: Wild Type 40min into S Phase


title: High_Fertility_1


title: Hpmut_2h_2

value: H. pylori htrA deletion mutant


title: Hpmut_2h_1


title: Control_4

value: Control


title: HepaRG-Differentiated-1

source_name: HepaRG differentiated state - Replicate 1

value: Differentiated


title: Control_3


title: Control_2


title: Hpwt_2h_4


title: Hpmut_2h_3


title: Hpwt_2h_2


title: wa_ola 306

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing:
The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.
RMA expression value derived from Expression Console software

label: biotin

organism: Mus musculus

source_name: white adipose tissue

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

growth_protocol: Diabetes-prone NZO/Hl, 129p2/OlaHsD  and C3HeB/FeJ  mice were housed at three to six mice per cage (Macrolon type III) at a constant temperature of 22°C and a 12-h light-dark cycle (lights on at 6 a.m.).

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: After weaning at the age of 21 days, all experimental animals received a high-fat diet (HFD) containing 45 kcal% fat,  20 kcal% protein and 35 kcal% carbohydrates with 4.73 kcal/gm energy (D12451 Research Diets Inc., New Jersey, USA). At the age of 6 weeks, mice were sacrificed by cervical dislocation and the pancreatic islets were isolated by ductal collagenase perfusion of the pancreas, as previously described (PMID: 21099271 ). Subsequently, the islets were allowed to regenerate overnight at 37°C with 5% CO2 in CMRL (Connaught Medical Research Laboratories) medium containing 15% fetal calf serum, 0.05 mM β-mercaptoethanol , 1 % penicillin/streptomycin, 10 mM glucose and 39.2 mM NaHCO3.

tag: strain

tag: gender

value: male

tag: age

value: 6 weeks

value: white adipose tissue


title: Hpwt_2h_1


title: Hpwt_2h_3


title: wa_ola 307


title: wa_ola 304


title: wa_ola 298


title: Low_Fertility_5

value: Low Fertility


title: Low_Fertility_4


title: MKN-28 cells 4

source_name: MKN-28 cells

value: uninfected

value: 0 h


title: wa_NZO 577

value: NZO/Hl (NZO; German Diabetes Centre Dusseldorf (HERBERG and COLEMAN 1977))


title: MKN-28 cells 3


title: wa_ola 285


title: wa_C3H112

value: C3H (000658, Jackson Lab)


title: wa_NZO 658


title: wa_C3H114


title: wa_C3H110


title: wa_NZO 545


title: wa_C3H111


title: wa_NZO 543


title: wa_NZO 542


title: wa_C3H109


title: rosette leaves, smax1 smxl2, dehydrated 4 h, rep4

city: Changchun

first: Weiqiang

last: Li

address: No. 4888 Shengbei Street

department: Center for Sustainable Resource Science

country: China

institute: Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences

description: Gene expression data from dehydrated smax1 smxl2

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented at 60°C for 30 minutes following the manufacturer's instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray slides were washed and dried immediately by a brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX12.6.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: smax1 smxl2, dehydrated 4 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2  µg RNA using the Low Input Quick Amp Labeling 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-1000 Spectrophotometer.

growth_protocol: Two-week-old WT and smax1 smxl2 mutant plants were transferred from GM plates to soil and grown for 10 additional day (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The aerial of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 4h.

value: smax1 smxl2

value: rosette leaves

value: 24 day-old

tag: stress

value: dehydrated

tag: time

value: 4 h


title: MKN-28 cells 1


title: Proliferation_Fetal_CPC_Sample4

city: Lausanne

first: Mohamed

last: Nemir

state: Vaud

address: Bugnon 27

department: Cœur et Vaisseau

country: Switzerland

institute: Lausanne University Hospital

data_processing:
Reads were pseudoaligned with kallisto software (version 0.44.0) to estimate the transcript level expression per sample
Gene level estimation was performed with sleuth R package (version 0.33.0) and transctipt expression was aggregated to gene level, followed by differential expression. For the transctipt to gene mapping gencode version 29 annotation was used.
Assembly: hg38
Supplementary files format and content: matrix table with TPM expression values for all genes and samples

source_name: Human Fetal CPCs

growth_protocol: Adult CPCs were expanded in expansion medium (3:1 DMEM 1g/l glucose/Medium 199 [Invitrogen] supplemented with 10% horse serum [Serotec, Kidlington, United Kingdom], 5% fetal bovine serum [Serotec], 100 U/ml penicillin [Invitrogen], and 100 μg/ml streptomycin [Invitrogen]). For inducing differentiation, cells were switched to MEM alpha (Invitrogen) containing 2% horse serum, 1 μmol/l dexamethasone (Sigma-Aldrich, St. Louis, Missouri), 50 μg/ml ascorbic acid (Sigma-Aldrich), 10 mmol/l β-glycerophosphate (Sigma-Aldrich), 100 U/ml penicillin (Invitrogen), and 100 μg/ml streptomycin (Invitrogen) (differentiation medium). Fetal CPCs  were expanded in culture in proliferation medium, a 3:1 mixture of DMEM 1 g/L glucose and Medium 199 (Invitrogen) supplemented with 10% Horse serum (Serotec), 5% fetal bovine serum (Serotec), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen). After three passages, cells were switched to a serum-free differentiation medium. Differentiation medium contained MEM alpha (Invitrogen) supplemented with 1 μM dexamethasone (Sigma-Aldrich), 50 μg/mL ascorbic acid (Sigma-Aldrich), 10 mM β-glycerophosphate (Sigma-Aldrich), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen)

extract_protocol:
Cells were lysed in Qiazol and RNA was purified using miRNeasy RNA prufication kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fetal CPCs


title: Low_Fertility_3

value: Uterine Post Mortem Biopsy

value: Holstein-Freisan

value: Female


title: rosette leaves, WT, dehydrated 4 h, rep1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4 h

value: WT


title: rosette leaves, smax1 smxl2, dehydrated 4 h, rep2


title: rosette leaves, WT, dehydrated 4 h, rep4

description: Gene expression data from dehydrated WT


title: rosette leaves, smax1 smxl2, dehydrated 4 h, rep3


title: rosette leaves, WT, dehydrated 4 h, rep2

description: Gene expression data from dehydrated WT


title: Low_Fertility_2

source_name: Uterine Post Mortem Biopsy


title: rosette leaves, WT, dehydrated 4 h, rep3

description: Gene expression data from dehydrated WT


title: rosette leaves, smax1 smxl2, dehydrated 4 h, rep1


title: MKN-28 cells 2


title: Proliferation_Fetal_CPC_Sample2


title: Proliferation_Fetal_CPC_Sample3


title: Low_Fertility_1


title: rosette leaves, smax1 smxl2, dehydrated 2 h, rep4

description: Gene expression data from dehydrated WT

source_name: smax1 smxl2, dehydrated 2 h

value: 2 h


title: bes1.D_BRZ250_NA_3

city: Ames

first: Yanhai

last: Yin

state: Iowa

address: 1111 WOI Street

department: GDCB

institute: Iowa State University

data_processing:
Adapters trimmed using bbduk
Reads mapped using STAR
Counts obtained using htseq-counts
TMM normalization performed using edgeR
Differential expression performed using QuantSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: processed file TMM values for each gene in each sample

source_name: bes1.D_BRZ250_whole seedling

growth_protocol: Sterilized seeds were grown on ½ Linsmaier and Skoog (LS, LSP03-1LT, Caisson Laboratories) plus 1% sucrose plates at 22°C under long-day (16 h light/8 h dark) conditions with a photon fluence rate of ~120-150 mmol m-2s-1.

extract_protocol:
Total RNA was extracted from 7-d-old seedlings growing on control ½ LS media or plus 250 nM BRZ media using Zymo DirecZol Kit (Zymo Research), and genomic DNA contamination was removed using RNase-free DNase in column during RNA extraction according to the manufacturer’s protocols.
Library was constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit from Illumina.

treatment_protocol: For BRZ response assays in the light, sterilized seeds were grown on ½ LS medium with 1% sucrose containing DMSO (control, BRZ0) or BRZ 250 nM plates under continuous light for 7 days at 22°C.

tag: ecotype

tag: genotype/variation

value: 250nM brassicanazole

tag: developmental stage

value: whole seedling


title: bes1.D_BRZ250_NA_1

tag: tissue


title: Diff (day7)_FetalCPC_Sample4


title: bes1.D_BRZ0_NA_4

source_name: bes1.D_BRZ0_whole seedling

value: none (untreated)


title: bes1.D_BRZ0_NA_3


title: bes1.D_BRZ250_NA_5


title: Diff (day7)_FetalCPC_Sample3


title: bes1.D_BRZ0_NA_2


title: bes1.D_BRZ0_NA_1


title: Diff (day7)_FetalCPC_LentivirusMutated(exon2CARMN7mutated)_Sample4


title: Diff (day7)_FetalCPC_Sample1


title: rosette leaves, smax1 smxl2, dehydrated 2 h, rep3

description: Gene expression data from dehydrated WT


title: rosette leaves, WT, dehydrated 2 h, rep4

source_name: WT, dehydrated 2 h


title: rosette leaves, smax1 smxl2, dehydrated 2 h, rep1

description: Gene expression data from dehydrated WT


title: rosette leaves, smax1 smxl2, dehydrated 2 h, rep2

description: Gene expression data from dehydrated WT


title: baf1_BRZ250_NA_4

source_name: baf1_BRZ250_whole seedling


title: rosette leaves, WT, dehydrated 2 h, rep3


title: Diff (day7)_FetalCPC_LentivirusMutated(exon2CARMN7mutated)_Sample3


title: rosette leaves, smax1 smxl2, well-watered (0 h), rep4

description: Gene expression data from well-watered smax1 smxl2

source_name: smax1 smxl2, well-watered

value: well-watered

value: control


title: baf1_BRZ250_NA_3


title: Diff (day7)_FetalCPC_LentivirusMutated(exon2CARMN7mutated)_Sample1


title: rosette leaves, WT, dehydrated 2 h, rep1


title: Young2-bulk

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

description: bulk RNA-seq of bone marrow monocytes

data_processing:
 For RNA-seq raw data processing, trimming was performed using cutadapt.
Alignment was performed using STAR (version 2.5.3) and raw read counts were generated using HTSeq.
Differential analysis was performed using DESeq2 R package.
Assembly: mm10

source_name: Bone marrow derived cells

extract_protocol:
Total RNA from FACS-isolated monocytes was obtained using PureLink RNA Minikit (Invitrogen). RNA quality was determined by measuring A260/A280 and A260/A230 ratios via nanodrop. RNA integrity was determined by running an Agilent Bioanalyzer gel to measure the ratio of ribosomal peaks. Samples used for library preparation had RIN values greater than 8
mRNA was purified from ~200 ng of total RNA with oligo-dT beads and sheared by incubation at 94oC in the presence of Mg2+ with the KAPA mRNA HyperPrep kit (Roche). Following first-strand synthesis with random primers, second strand synthesis and A-tailing were performed with dUTP to generate strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs were ligated to library insert fragments. Library amplification of fragments carrying the appropriate adapter sequences at both ends was undertaken. Strands marked with dUTP were not amplified. Indexed libraries were quantified by qRT-PCR using a commercially available kit (Roche, KAPA Biosystems) and insert size distribution was determined with the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/µl and a size distribution of 150-300 bp were used for sequencing.

value: Bone marrow

tag: disease

value: Atherosclerosis

value: 3 months

value: Wild type


title: baf1_BRZ250_NA_2


title: Young1-bulk

description: bulk RNA-seq of bone marrow monocytes


title: Diff (day7)_FetalCPC_Lentivirus(exon2CARMN7)_Sample4


title: rosette leaves, smax1 smxl2, well-watered (0 h), rep3

value: smax1 smxl2

value: rosette leaves

value: 24 day-old


title: Aged2-bulk

description: bulk RNA-seq of bone marrow monocytes

value: 18 months


title: rosette leaves, smax1 smxl2, well-watered (0 h), rep1


title: rosette leaves, WT, well-watered (0 h), rep4

description: Gene expression data from well-watered WT

source_name: WT, well-watered


title: rosette leaves, WT, dehydrated 2 h, rep2

value: dehydrated


title: rosette leaves, WT, well-watered (0 h), rep2


title: rosette leaves, smax1 smxl2, well-watered (0 h), rep2


title: baf1_BRZ250_NA_1


title: Aged1-bulk

description: bulk RNA-seq of bone marrow monocytes


title: Diff (day7)_FetalCPC_Lentivirus(exon2CARMN7)_Sample3

value: Fetal CPCs


title: Mo_CO3

first: Simone

last: Caielli

state: NY

address: 413 E 69th Street

department: Department of Pediatrics

institute: Weill Cornell Medicine

data_processing:
Sequencing reads were aligned with STAR_2.4.0f1  against the mm10 mouse genome
SAMTOOLS v0.1.19 was used for sorting and indexing reads
Gene counts were generated using htseq-count
Assembly: mm10
Supplementary files format and content: csv file with raw gene counts for every gene and every sample

source_name: Lung

growth_protocol: Six week old mice maintained under standard conditions with free access to food and water.

extract_protocol:
RNA was extracted using Promega Maxwell 16 MDx instrument (Maxwell 16 LEV simplyRNA Tissue Kit).
Specimens were prepared for RNA sequencing using TruSeq RNA Library Preparation Kit v2 or riboZero.
RNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies). cDNA was synthesized from total RNA using Superscript III (Invitrogen).

treatment_protocol: 2 high fat diets: A. FO (Fish oil-enriched Harlan Teklad; TD. 07500); B. CO (Coconut oil-enriched Harlan Teklad; TD. 08081)

value: Whole lung (flushed with PBS)

value: 14 weeks

tag: group


title: Mo_CO2


title: baf1_BRZ0_NA_4

source_name: baf1_BRZ0_whole seedling

tag: treatment


title: baf1_BRZ0_NA_3


title: baf1_BRZ0_NA_2


title: Diff (day7)_FetalCPC_Lentivirus(exon2CARMN7)_Sample1

tag: cell type


title: Mo_CO1


title: Mo_FO3


title: rosette leaves, WT, well-watered (0 h), rep3

value: WT


title: Mo_FO5


title: Mo_FO2


title: Diff (day1)_FetalCPC_Sample4


title: Mo_CO5


title: baf1_BRZ0_NA_1

value: whole seedling


title: Mo_FO4


title: rosette leaves, WT, well-watered (0 h), rep1


title: Diff (day1)_FetalCPC_Sample3


title: WT_BRZ250_NA_3

source_name: WT_BRZ250_whole seedling

value: 250nM brassicanazole


title: Mo_CO4


title: Mo_FO1


title: Diff (day1)_FetalCPC_Sample1


title: YTHDC1-RIPSeq_IP rep2

city: Nanjing City

first: Haifeng

last: Sun

state: JiangSu province

address: Tianyuan East Road 818

institute: Nanjing Medical University

data_processing:
Reads were quality controlled using fastqc and aligned to GRCm38 using HISAT2 with default parameters;
All bigWig files were obtained by using bamCoverage in deepTools;
For RNA-Seq, read counts were quantified using featureCounts;
Differential expression testing was performed with R package DESeq2;
Alternative Splicing (AS) analysis was performed by using rMATS;
For m6A-Seq, m6A peaks was called by using exomePeak8 with default parameters;
Peaks annotation was performed using ChIPseeker9 and m6A motif was called by findMotifsGenome in Homer;
Metagene plot of m6A was performed by using Guitar;
Genome_build: mm10
Supplementary_files_format_and_content: bw files

source_name: left ventricular tissue

extract_protocol:
Total RNA from left ventricular tissue was extracted to establish RNAseq libraries. RNA samples were pre-treated with RiboMinus Eukaryote Kit to remove abundant ribosomal RNAs.
RNA was fragmented and ligated with a unique Illumina adapter. All individually indexed samples were subsequently pooled together and multiplexed for sequencing.
RNA-Seq;MeDIP-Seq;RIP-Seq


title: WT_BRZ250_NA_2


title: YTHDC1-RIPSeq_IP rep1


title: YTHDC1-RIPSeq_Input rep2


title: Diff (day1)_FetalCPC_LentivirusMutated(exon2CARMN7mutated)_Sample3


title: WT_BRZ250_NA_1


title: YTHDC1-RIPSeq_Input rep1


title: RNASeq_8W_WT rep2

description: RNA-Seq


title: RNASeq_8W_WT rep1

description: RNA-Seq


title: Diff (day1)_FetalCPC_LentivirusMutated(exon2CARMN7mutated)_Sample1


title: RNASeq_8W_KO rep2

description: RNA-Seq

value: Ythdc1 KO


title: Diff (day1)_FetalCPC_Lentivirus(exon2CARMN7)_Sample4


title: WT_BRZ0_NA_5

source_name: WT_BRZ0_whole seedling

value: none (untreated)


title: RNASeq_8W_KO rep1

description: RNA-Seq


title: WT_BRZ0_NA_4


title: Diff (day1)_FetalCPC_Lentivirus(exon2CARMN7)_Sample3


title: RNASeq_2W_WT rep3

description: RNA-Seq


title: RNASeq_2W_WT rep2

description: RNA-Seq


title: RNASeq_2W_WT rep1

description: RNA-Seq


title: WT_BRZ0_NA_2


title: Diff (day1)_FetalCPC_Lentivirus(exon2CARMN7)_Sample1


title: RNASeq_2W_KO rep3

description: RNA-Seq


title: WT_BRZ0_NA_1


title: RNASeq_2W_KO rep2

description: RNA-Seq


title: RNASeq_2W_KO rep1

description: RNA-Seq


title: HDAC6-KD-11-12-days-male

city: Beijing

first: Jing-Dong

middle: Jackie

last: Han

address: 5 Yiheyuan Rd, Haidian District

institute: Peking University

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were mapped by using STAR (v2.5.2a) with 2% max mismatch.
Cuffdiff (v2.2.1) 37 with default parameters was used to generate RPKM.
Genome_build: dmel r6.21
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values and q-values for each samples derived from cuffdiff (v2.2.1) with default parameters.

organism: Drosophila melanogaster

source_name: RNA Drosophila head AD12 HDAC6 KD

growth_protocol: Drosophila stocks were raised on cornmeal-molasses fly food (unless otherwise noted) at 25 °C on a 12 h:12 h light–dark cycle.

extract_protocol:
Total RNA was extracted according to TRIzol standard procedures.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: head

value: adult day 12

tag: Sex

value: male

value: HDAC6 KD


title: repl 5 MCF7 LTED ESR1 MUT plus e2 and elacestrant

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

country: United Kingdom

institute: Institute of Cancer Research

data_processing:
tophat-2.1.0.Linux_x86_64/tophat aligment with UCSC/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf
htseq-count -f bam  -r name  -s reverse -t exon -i gene_id
Genome_build: hg19
Supplementary_files_format_and_content: htseq raw counts

source_name: breast cancer cell line

growth_protocol: Human breast cancer cell lines were cultured in phenol red-free RPMI1640 medium supplemented with 10% fetal bovine serum and 1nM E2. All cell lines were banked in multiple aliquots to reduce the risk of phenotypic drift and identity confirmed using STR. Long-term E deprived (LTED) cells modelling resistance to an AI were derived from all parental cell lines as previously described in  PMID: 29192207.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen)
Libraries were created after Ribo-zero rRNA Removal Kit (Illumina) using NEBNext Ultra Directional RNA (NEB) or Truseq Stranded Total RNA (Illumina) Library Prep Kit and sequenced using the HiSeq2500 (paired-end 100 bp v4 chemistry)

treatment_protocol: 10% DCC + 0.1nM E2 or 10% DCC + 0.1nM E2 + 1μM elacestrant or 10% DCC + 0.1nM E2 + 100nM fulvestrant

tag: long term estrogen deprivation (lted)

value: LTED

tag: esr1 mutation status

value: mutated ESR1 Y537C

tag: source

value: LTED derived from ATCC MCF7

tag: estradiol (e2)

value: E2 added

tag: selective er modulator treatment

value: elacestrant


title: m6A_IP rep2

description: MeDIP-Seq

tag: strain


title: repl 4 MCF7 LTED ESR1 MUT plus e2 and elacestrant


title: m6A_IP rep1

description: MeDIP-Seq


title: m6A_Input rep2

description: MeDIP-Seq


title: repl 3 MCF7 LTED ESR1 MUT plus e2 and elacestrant


title: WT-11-12-days-male

source_name: RNA Drosophila head AD12 control

tag: age

tag: genotype


title: m6A_Input rep1

description: MeDIP-Seq


title: repl 2 MCF7 LTED ESR1 MUT plus e2 and elacestrant


title: 2b-2

city: Jena

first: Amelia

middle: E

last: Barber

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Fungal Informatics

institute: Leibniz-HKI

data_processing:
data processing was performed by StarSEQ GmbH (Mainz, Germany)
Assembly: Reads were aligned to the NCBI reference genome for S. iranensis (Assembly GCA_000938975.1)
Supplementary files format and content: Microsoft-excel-CSV files include TPM values for each sample

organism: Streptomyces iranensis

source_name: strain HM35

growth_protocol: S. iranensis wildtype was maintained in TSB at 28°C for 48 h

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA MiniPrep Plus Purification Kit (Zymo Research Europe, Freiburg, Germany) after cell disruption by bead beating for 4 min in a Speed Mill homogenizer (Analytik Jena, Germany).
NEBNext Ultra II directional, dual index RNA library preparation

treatment_protocol: S. iranensis ΔbldA was maintained in TSB at 28°C for 48 h

value: strain HM35

value: delta_bldA (knockout)

value: 48 h cultivation in TSB medium


title: 2b-1


title: repl 1 MCF7 LTED ESR1 MUT plus e2 and elacestrant


title: 2a-1


title: 2a-2


title: 1b-1

value: wildtype


title: repl 5 MCF7 LTED ESR1 MUT plus e2 and fulvestrant

value: fulvestrant


title: 1b-2


title: 1a-2


title: HDAC6-KD-1-2-days-male

source_name: RNA Drosophila head AD2 HDAC6 KD

value: adult day 2


title: 1a-1


title: repl 4 MCF7 LTED ESR1 MUT plus e2 and fulvestrant


title: repl 2 MCF7 LTED ESR1 MUT plus e2 and fulvestrant


title: YR_P3

city: Guangzhou

first: Liu

last: Hailun

address: Tianhe District

description: P.litchii treatment

data_processing:
Illumina Casava1.8 software used for basecalling.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
GO analysis was performed by the GO Annotation of TAIR.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Assembly: 'Feizixiao'. Feizixiao Genome sequencing and assembly can be found in the NCBI database under accession number PRJNA747875.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

organism: Litchi chinensis

source_name: leaves

growth_protocol: Lichi trees were planted in National Litchi Germplasm Nursery located in Institute of Fruit Tree Research Guangdong Academy of Agricultural Sciences.

extract_protocol:
Total RNA was extracted from the treated leaves by Plant RNA Kit (Promega, LS1040).
The libraries constructed using Ultra RNA sample preparation kit (Illumina) reached high quality before RNA-sequencing. RNA sequencing was performed by the Allwegene Technologies Corporation (Beijing, China) using an Illumina NovaSeq platform.

treatment_protocol: Litchi leaves were inoculated with P.litchii (1 × 104 spores·mL−1) or mock (sterile water).

value: leaves

value: Peronophythora litchii

value: Inoculation with P.litchii ( 1x104 spores*mL-1)

tag: time


title: NSC rep 1

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to human genome using HISAT2
Reads counts for each gene, including miRNA genes
Assembly: Human genome GRCH38/hg38
Supplementary files format and content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

source_name: Neural stem cells

growth_protocol: H9s were maintained in E8 medium for routine culture. Then H9s were differentiated into ECs, NSCs and VSMCs in 2D, 3D PEG hydrogel and alginate hydrogel cell culture system according to their differentiation protocol. mRNAs were sequenced.

extract_protocol:
Cells were harvested after differentiation and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
The Small RNA Sample Pre Kit was used to construct the library. Since the small RNA has a phosphate group at the 5 'end and a hydroxyl group at the 3' end, the T4 RNA ligase 1 and T4 RNA Ligase 2 (truncated) was ligated to the 5 'end and the 3' end of the small RNA, respectively.

treatment_protocol: no treatment

value: hESC-derived neural stem cells


title: EC rep 2

source_name: Vascular endothelial cells

value: hESC-derived vascular endothelial cells


title: Control_1

city: Dunsany

first: Paul

last: Cormican

address: Grange

institute: Teagasc

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to genome using STAR (v2.6.1b)
Read counts per gene for each sample were estimated using featurCounts from the subread package (v.1.6.3).
Supplementary files format and content: Bos_taurus_UMD_3.1.1
Supplementary files format and content: Individual matrix tables with raw gene counts for every gene in a sample

source_name: Uterine Post Mortem Biopsy

extract_protocol:
Uterine samples were taken, flash frozen before subsequent RNA extraction in TRIzol reagent. Total RNA concentration was quantified using the Nanodrop ND-1000 UV-Vis Spectophotometer. Quality of RNA was ascertained with the use of 2100 Agilent Bioanalyzer .
RNA libraries were prepared for sequencing using Illumina® TruSeq® Stranded mRNA Library preparation Kits

value: Uterine Post Mortem Biopsy

tag: breed

value: Holstein-Freisan

value: Female

value: Control


title: repl 1 MCF7 LTED ESR1 MUT plus e2 and fulvestrant

value: LTED

value: mutated ESR1 Y537C

value: LTED derived from ATCC MCF7

value: E2 added


title: YR_P2

institute: Guangdong Academy of Agricultural Sciences

description: P.litchii treatment


title: WT-ctl-1-2-days-male

source_name: RNA Drosophila head AD2 control

value: head

value: male

value: WT


title: Treated-6

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Transfected with miR-6126

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: HepG2-NTCP cells were cultured in DMEM (Life Technologies, Carlsbad, CA, USA) supplemented with 10% FBS, 100 U/mL penicillin, 100 µg⁄mL streptomycin and 100 U/mL nonessential amino acids (Life Technologies).

extract_protocol: Total RNA was extracted from cultured cells using the miRNeasy Mini kit (Qiagen, Venlo, The Netherlands).

treatment_protocol: miRNA mimics (Thermo Fisher Scientific) were transfected using Lipofectamine RNAiMAX® Reagent (Thermo Fisher Scientific) and Opti-MEM® (Thermo Fisher Scientific) according to the manufacturer’s protocol. miRNA mimics were used at a final concentration 50 nM.

tag: cell line

tag: genotype/variation

value: Transfected with miR-6126


title: Treated-4


title: Treated-5


title: NSC rep 3


title: YR_P1

description: P.litchii treatment

tag: tissue

value: leaves


title: NSC rep 2


title: repl 5 MCF7 LTED ESR1 MUT plus e2

description: repl 5 MCF7 LTED ESR1 MUT plus e2


title: H9 rep 3

source_name: Human embryo stem cell (H9)


title: YR_M3

description: Mock treatment

value: mock

value: Sterile water (Mock-inoculation)


title: repl 3 MCF7 LTED ESR1 MUT plus e2 and fulvestrant

value: fulvestrant


title: Treated-3


title: EC rep 3

value: hESC-derived vascular endothelial cells


title: YR_M2

description: Mock treatment


title: H9 rep 2


title: repl 4 MCF7 LTED ESR1 MUT plus e2

description: repl 4 MCF7 LTED ESR1 MUT plus e2


title: H9 rep 1


title: YR_M1

description: Mock treatment


title: repl 3 MCF7 LTED ESR1 MUT plus e2

description: repl 3 MCF7 LTED ESR1 MUT plus e2


title: Treated-1


title: repl 2 MCF7 LTED ESR1 MUT plus e2

description: repl 2 MCF7 LTED ESR1 MUT plus e2


title: Control-6

source_name: Transfected with negative control

value: Transfected with negative control


title: EC rep 1


title: P-16-PRE

city: Shanghai

first: Qi

last: Wang

address: 160 Pujian Road

institute: Shanghai Jiao Tong University

data_processing:
Raw reads of fastq format were firstly processed using Trimmomatic and the low-quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2.
The read counts of each gene were obtained by HTSeq-count.
FPKM of each gene was calculated using Cufflinks.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: prostate cancer sample

extract_protocol:
RNA sequencing was performed on 11 paired pre- and post-neoadjuvant chemohormonal therapy tumor samples. Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

treatment_protocol: Docetaxel-based neoadjuvant chemohormonal therapy

tag: individual

value: patient ID P_16

value: control

value: pre-chemohormonal therapy

value: prostate cancer sample


title: Treated-2


title: GW_P3

description: P.litchii treatment

value: Peronophythora litchii

value: Guiwei

tag: treatment

value: Inoculation with P.litchii ( 1x104 spores*mL-1)


title: repl 1 MCF7 LTED ESR1 MUT plus e2

description: repl 1 MCF7 LTED ESR1 MUT plus e2

value: LTED

value: mutated ESR1 Y537C

value: LTED derived from ATCC MCF7

value: E2 added


title: Control-5


title: repl 5 MCF7 LTED ESR1 WT plus e2 and elacestrant

value: wildtype

value: elacestrant


title: GW_P2

description: P.litchii treatment

value: leaves


title: P-14-PRE

value: patient ID P_14


title: GW_P1

description: P.litchii treatment


title: P-9-PRE

value: patient ID P_9


title: repl 4 MCF7 LTED ESR1 WT plus e2 and elacestrant


title: P-12-PRE

value: patient ID P_12


title: Control-4

value: Transfected with negative control


title: P-8-PRE

value: patient ID P_8

value: control


title: GW_M2

description: Mock treatment

value: mock

value: Sterile water (Mock-inoculation)


title: Retained placenta cow - rep4

city: Karaj

first: Mehdi

last: Moradi

state: Alborz

address: Daneshkadeh st.

department: Animal Science

country: Iran

institute: University of Tehran

data_processing:
Illumina Casava1.7 software used for basecalling.
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left for further analyzes. Then, the sequences were mapped to ARS-UCD1.2 whole bovine genome using HISAT2.
Read counts obtained using featureCounts and finally raw read counts were used for DEG analysis using edgeR.
Genome_build: HISAT2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Retained placenta cow

extract_protocol:
Placentome were collected after parturtion. Small cuboid samples were taken from the fetomaternal conjunction sites of placentome. The samples from each cow pooled and snap frozen in liquid nitrogen. RNAs harvested from the samples were used for RNA-sequencing using Illumina HiSeq 2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta


title: Control-2


title: repl 3 MCF7 LTED ESR1 WT plus e2 and elacestrant


title: Control-3


title: GW_M1

description: Mock treatment

value: Guiwei


title: repl 1 MCF7 LTED ESR1 WT plus e2 and elacestrant

value: LTED


title: P-6-PRE

value: patient ID P_6

value: pre-chemohormonal therapy

value: prostate cancer sample


title: Retained placenta cow - rep3


title: P-5-PRE

value: patient ID P_5


title: Control-1


title: Retained placenta cow - rep2


title: repl 5 MCF7 LTED ESR1 WT plus e2 and fulvestrant

value: wildtype

value: LTED derived from ATCC MCF7

value: E2 added

value: fulvestrant


title: P-4-PRE

value: patient ID P_4


title: Biliary tract cancer, tumor 4, scRNAseq

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger version 3.1.0 (10x Genomics) was used to align the raw sequencing data and to generate count matrices.
Assembly: Genome Build: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Intrahepatic cholangiocarcinoma

extract_protocol:
Tumor samples were digested in RPMI containing Collagenase I & II and DNAse I, minced, and digested for one hour using the GentleMACS system. Isolation of live cells was performed using MACS LS columns (Miltenyi Biotec).
Library was performed according to the manufacter’s instructions (single cell 10x 5’ version 1 protocol, 10x Genomics). Briefly, cell suspensions were combined with master mix and loaded into the chip with gel beads to generate the gel bead-in-emulsion (GEM), which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Reverse transcription was performed on the poly-A RNA within each GEM. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified by PCR. To prepare libraries from cDNA, SPRIselect beads were used to isolate the correct size fragments. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added during library construction.

value: Intrahepatic cholangiocarcinoma

tag: cell type

value: Live cells


title: Retained placenta cow - rep1


title: GW_M3

description: Mock treatment

value: leaves


title: Biliary tract cancer, tumor 2, scRNAseq

description: 10x Genomics


title: repl 3 MCF7 LTED ESR1 WT plus e2 and fulvestrant


title: Healthy cow - rep3

source_name: Healthy cow


title: repl 2 MCF7 LTED ESR1 WT plus e2 and fulvestrant


title: Biliary tract cancer, tumor 1, scRNAseq

description: 10x Genomics

source_name: Extrahepatic cholangiocarcinoma

value: Extrahepatic cholangiocarcinoma


title: P-2-PRE

value: patient ID P_2

value: control


title: repl 2 MCF7 LTED ESR1 WT plus e2 and elacestrant

source_name: breast cancer cell line

value: elacestrant


title: P-1-PRE

value: patient ID P_1


title: Healthy cow - rep1

value: placenta


title: Healthy cow - rep2


title: T cells, mRNA-derived cDNA

description:
3' mRNA library
poly A RNA

data_processing:
CellRanger version 3.1.0 (10x Genomics) was used to align the raw sequencing data and to generate count matrices (gene expression and ADT barcode counts). The ADT library sequences were aligned to a customized reference genome provided by BD containing the oligonucleotide sequences corresponding to each antibody.
Pre-processing of aligned sequencing data and identification of single nucleotide polymorphisms was performed using the Genome Analysis Toolkit (McKenna et al., 2010). We used demuxlet (Kang et al., 2018) (https://github.com/statgen/demuxlet) for sample deconvolution of multiplexed PBMC samples.
Further processing was done with Scanpy v1.4.6 (concatenation of samples, filtering for high quality cells, normalization, batch correction, clustering, annotation, and differential gene expression analysis). The .h5ad files are demultiplexed, concatenated, filtered, and annotated, but otherwise represent raw data prior to all processing steps.
Assembly: Genome Build: GRCh38 3.0.0
Supplementary files format and content: Scanpy output files: .h5ad
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Blood

extract_protocol:
Blood samples from patients with biliary tract cancer (BTC) and healthy donors were processed using ficoll; after centrifugation, the peripheral blood mononuclear cell (PBMC) layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered human serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine. Samples were then incubated for DNAse I before washing and counting. 1 x10>6 cells from 16 unique samples were combined and stained with one pooled cocktail containing 99 AbSeq antibody-oligonucleotide conjugates (BD Biosciences).
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3, according to manufacturer instructions. For preparation of ADT libraries, we followed the standard protocol available from Olvera JG et al., 2018 (available at: https://medschool.ucsd.edu/som/medicine/research/labs/chang-lab/immunology/Documents/Olvera%20et%20al.pdf), following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution, Biolegend). Briefly, cell suspensions were combined with master mix and loaded into the chip with gel beads to generate the gel bead-in-emulsion (GEM), which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Reverse transcription was performed on the poly-A RNA within each GEM. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified by PCR. To prepare libraries from cDNA, SPRIselect beads were used to isolate the correct size fragments. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added during library construction.

value: Blood

value: PBMC

tag: library type

value: mRNA

tag: antibodies/tags


title: T cells, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library
Antibody-derived oligonucleotide (ADT)

library_source: other

molecule: other

value: ADT

value: Details on 99 antibody panel from BD Biosciences are available from lead author


title: Input_rep2

city: Nanjing

first: huang

middle: ran

last: ran

address: weigang 1

institute: Nanjing Agricultural College

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequences using trim_galore
BWA (Burrows-Wheeler Aligner) with default parameters was used to align all cleaned reads to the MSU v7.0 reference genom
MACS  was used to call IP-G4 (referred to as G4s pulled down by anti-BG4 antibody) peaks from reads with an alignment length greater than 50.
Assembly: MSU v7.0
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Oryza sativa

source_name: seedling

growth_protocol: temperature of 28–30 °C and a 14 h/10 h light/dark cycle

extract_protocol:
collected and cut into small slices of 1–1.5 cm in size, followed by cross-linking with a 1% final concentration of formaldehyde for 10 min under vacuum.
The BG4-DNA-IPed DNA or input DNA was recovered for library preparation. All libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S), and sequenced using the Illumina platform, followed by data analyses.

value: seedling

value: WT

tag: antibody

value: none (input)


title: Biliary tract cancer, tumor 3, scRNAseq

description: 10x Genomics

value: Intrahepatic cholangiocarcinoma


title: repl 5 MCF7 LTED ESR1 WT plus e2

description: repl 5 MCF7 LTED ESR1 WT plus e2

tag: long term estrogen deprivation (lted)

value: LTED

tag: esr1 mutation status

value: wildtype

tag: source

value: LTED derived from ATCC MCF7

value: E2 added


title: P-16-POST

value: patient ID P_16

value: Docetaxel-based neoadjuvant chemohormonal therapy

value: post-chemohormonal therapy

value: prostate cancer sample


title: Input_rep1


title: repl 4 MCF7 LTED ESR1 WT plus e2

description: repl 4 MCF7 LTED ESR1 WT plus e2

tag: estradiol (e2)

tag: selective er modulator treatment


title: Myeloid cells, ADT-derived cDNA

value: Blood


title: P-3-PRE

value: patient ID P_3

value: control

value: pre-chemohormonal therapy


title: Myeloid cells, mRNA-derived cDNA

description:
3' mRNA library
poly A RNA

value: PBMC

value: mRNA


title: repl 4 MCF7 LTED ESR1 WT plus e2 and fulvestrant

value: fulvestrant


title: P-12-POST

value: patient ID P_12


title: Na+PEG_rep2

value: seedling

tag: genotype

value: WT


title: P-14-POST

value: patient ID P_14

tag: time


title: repl 3 MCF7 LTED ESR1 WT plus e2

description: repl 3 MCF7 LTED ESR1 WT plus e2

value: LTED

value: wildtype

value: LTED derived from ATCC MCF7


title: Immune cells, ADT-derived cDNA

value: ADT

value: Details on 99 antibody panel from BD Biosciences are available from lead author


title: repl 2 MCF7 LTED ESR1 WT plus e2

description: repl 2 MCF7 LTED ESR1 WT plus e2

value: E2 added


title: P-9-POST

value: patient ID P_9

value: Docetaxel-based neoadjuvant chemohormonal therapy

value: post-chemohormonal therapy

value: prostate cancer sample


title: P-8-POST

value: patient ID P_8


title: Na+PEG_rep1


title: P-6-POST

value: patient ID P_6


title: repl 1 MCF7 LTED ESR1 WT plus e2

description: repl 1 MCF7 LTED ESR1 WT plus e2


title: Immune cells, mRNA-derived cDNA

description:
3' mRNA library
poly A RNA

value: Blood

value: PBMC

value: mRNA


title: repl 1 MCF7 LTED ESR1 WT plus e2 and fulvestrant

value: fulvestrant


title: repl 5 MCF7 plus e2 and elacestrant

description: repl 5 MCF7 plus e2 and elacestrant

value: not LTED

value: ATCC

value: elacestrant


title: K+PEG_rep1

value: seedling

value: WT


title: P-4-POST

value: patient ID P_4


title: RNA HSPC, 7th day, rep1

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: 500 S State St

department: DCMB

institute: University of Michigan

description:
3423-MV-2_barcodes.tsv.gz
3423-MV-2_features.tsv.gz
3423-MV-2_matrix.mtx.gz
3423-MV-2_feature_linkage.bedpe

data_processing:
Raw sequencing data were mapped and preprocessed to gene expressions and peaks using CellRanger ARC 2.0.0.
Secondary analyses by CellRanger ARC produced feature linkages between peaks and genes.
Unspliced and spliced mRNA expressions were quantified using Velocyto (v0.17.17) (La Manno et al. 2018) with the GTF (GRCh38) provided in CellRanger.
Assembly: GRCh38
Supplementary files format and content: Combined RNA and ATAC count data from CellRanger in zipped Matrix Market format
Supplementary files format and content: CellRanger linkage file in text format
Supplementary files format and content: ATAC peak annotation file in text format
Supplementary files format and content: Unspliced and spliced counts from Velocyto in loom format

growth_protocol: Cells were either immediately prepared for single-cell processing or maintained at 37ºC with 5% CO2 in Stemspan II medium supplemented with 100 ng/ml stem cell factor, 100 ng/ml thrombopoietin, 100 ng/ml Flt3 ligand (all from Stemcell Technologies), and 100 ng/ml insulin-like growth factor binding protein 2 (R&D Systems) for seven days.

extract_protocol:
Cells were washed in PBS supplemented with 0.04% BSA and sorted using fluorescence actived cell sorting. Nuclei were isolated following the 10X Genomics Nuclei Isolation Signle Cell multiome ATAC + Gene expression Sequencing demonstrrated Low Cell Input protocol.
Single Cell Multiome ATAC and Gene Expression libraries were prepared according to the 10X Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide for standard Illumina paired-end sequencing.

value: Primary Cells

value: Mobilized CD34+ Hematopoietic Stem and Progenitor Cells


title: repl 3 MCF7 plus e2 and elacestrant

description: repl 3 MCF7 plus e2 and elacestrant

value: wildtype

value: E2 added


title: RNA HSPC, 0th day, rep1

description:
3423-MV-1_barcodes.tsv.gz
3423-MV-1_features.tsv.gz
3423-MV-1_matrix.mtx.gz
3423-MV-1_feature_linkage.bedpe


title: elongating 6 day rep 2 (JA47)

city: Blacksburg

first: Song

last: Li

state: VA

institute: Virginia Tech

data_processing:
raw reads were mapped using STAR, number of mapped reads were counted using featureCounts and differentially expressed genes were identified using DESeq2
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: ReadCounts_022017.xlsx

source_name: elongating 6 day

growth_protocol: Rice plants were grown in pots in a greenhouse until the 4.2-leaf stage.

extract_protocol:
Total RNAs were extracted from frozen tissues using a miRNeasy Mini kit (Qiagen, Hilden, Germany). Genomic DNA was eliminated by on-column digestion.
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
paired-end

treatment_protocol: Plants were completely submerged for 0, 1, 3, and 6 days. Immediately after de-submergence at each time point, the 5th (elongating) leaves and lower (non-elongating) leaves were separated, frozen in liquid nitrogen, and stored at -80C until use.

value: elongating leaves

value: submergence

value: 6 day


title: elongating 6 day rep 3 (JA48)


title: P-2-POST

value: patient ID P_2

value: Docetaxel-based neoadjuvant chemohormonal therapy

value: post-chemohormonal therapy

value: prostate cancer sample


title: repl 2 MCF7 plus e2 and elacestrant

description: repl 2 MCF7 plus e2 and elacestrant

value: not LTED


title: elongating 6 day rep 1 (JA46)


title: P-1-POST

value: patient ID P_1


title: repl 1 MCF7 plus e2 and elacestrant

description: repl 1 MCF7 plus e2 and elacestrant

value: ATCC

value: elacestrant


title: K+PEG_rep2

value: seedling

value: WT


title: non-elongating 6 day rep 2 (JA44)

source_name: non-elongating 6 day

value: non-elongating leaves


title: non-elongating 6 day rep 1 (JA43)


title: elongating 6 day rep 3 (JA42)


title: EIF2AK2_2nd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cell

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion) and was further purified with two phenol-chloroform treatments.The purified RNA was then treated with RQ1 DNase (RNase free) (Promega, Madison, WI, USA) and its quality and quantity were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: Plasmids transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

tag: transfection

value: EIF2AK2 overexpression

value: HeLa


title: HeLa control plasmid Ctrl_2nd

value: control plasmid

tag: cell line


title: repl 4 MCF7 plus e2 and elacestrant

description: repl 4 MCF7 plus e2 and elacestrant

value: wildtype

value: E2 added


title: repl 3 MCF7 plus e2 and fulvestrant

description: repl 3 MCF7 plus e2 and fulvestrant

value: fulvestrant


title: repl 2 MCF7 plus e2 and fulvestrant

description: repl 2 MCF7 plus e2 and fulvestrant


title: elongating 6 day rep 2 (JA41)

value: elongating leaves

value: submergence

value: 6 day


title: P-5-POST

value: patient ID P_5

value: Docetaxel-based neoadjuvant chemohormonal therapy

value: post-chemohormonal therapy

value: prostate cancer sample


title: HepG2 Cell, vehicle_3

city: Kobe

first: Wataru

last: Ogawa

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe University Graduate School of Medicine

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HepG2 cells were maintained under a mixture of 95% air and 5% CO2 at 37℃ in six-well plates containing high-glucose (25 mmol/l) DMEM supplemented with 10% heat-inactivated FBS.

extract_protocol:
Total RNA was extracted from the cells with the use of an RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were incubated in 12-well plates and stimulated with 0.25 or 3 mmol/l metformin or imeglimin, with 1 mmol/l 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), or with vehicle for 12 h.

value: Human hepatoma cell line

value: wild type

value: vehicle


title: EIF2AK2_1st


title: P-3-POST

value: patient ID P_3


title: HepG2 Cell, vehicle_2


title: repl 1 MCF7 plus e2 and fulvestrant

description: repl 1 MCF7 plus e2 and fulvestrant

value: not LTED

value: ATCC


title: repl 5 MCF7 plus e2 and fulvestrant

description: repl 5 MCF7 plus e2 and fulvestrant


title: non-elongating 6 day rep 3 (JA45)

value: non-elongating leaves


title: HepG2 Cell, vehicle_1


title: repl 5 MCF7 plus e2

description: repl 5 MCF7 plus e2

value: wildtype


title: Sp_blastula_Input2_ChIPseq

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

country: Italy

institute: Stazione Zoologica Anton Dohrn

description:
spur5_bra_chip_24hpf.bed
peaks_empirical_24hM_spur5_c05_s05.tsv

data_processing:
Raw reads were trimmed from adapter sequences TACACTCTTTCCCTACACGACGCTCTTCCGATCT, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, TACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA, GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, AGATGTGTATAAGAGACAG, AGATGTGTATAAGAGACAG, TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTGACGCTGCCGACGA, GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG and bad quality bases using Trimmomatic (v0.38).
Trimmed reads were quasi-mapped using Salmon (v0.11.3) to the Strongylocentrotus purpuratus genome v5.0 associated transcriptome.
The generated count files were used as input to DESeq2 (v1.28.1).
Genes with adjusted p-value of 0.05 filtered using independent hypothesis weighting (IHW) are considered as differentially expressed.
For ChIP-seq reads were aligned to S. purpuratus genome (v5.0) using BWA (v0.7.17) aligner using the BWA-MEM algorithm.
ChIP-seq peaks were called using Peakzilla
Assembly: S. purpuratus genome (v5.0)
Supplementary files format and content: tab separated values

organism: Strongylocentrotus purpuratus

source_name: whole embryo

growth_protocol: Adult Strongylocentrotus individuals were kept in circulating seawater aquaria at Stazione Zoologica Anton Dohrn in Naples. Spawning was induced by vigorous shaking of gravid animals. Embryos were raised at 15°C in filtered Mediterranean Sea water (FSW) diluted 9:1 with deionized water.

extract_protocol:
Embryos at 24hpf (blastula stage) were treated with 1% formaldehyde for 12 min. Embryos were homogenized using Dounce homogenizer. Chromatin was fragmented to an average size of 100-200bp using a Covaris S1 ultrasonicator.
Illumina ChIP-seq DNA Sample Prep Kit instructions (Catalog number IP-102-1001) were used to prepare the library. The quantity and quality (size distribution) of the libraries was assessed using an Bioanalyzer (Agilent).
Libraries were multiplexed and sequenced on Illumina HiSeq 2500 to generate 50bp SE reads.

value: Embryo cells

tag: developmental stage

value: blastula


title: non-elongating 6 day rep 3 (JA39)

tag: tissue


title: Sp_blastula_Input1_ChIPseq

description:
spur5_bra_chip_24hpf.bed
peaks_empirical_24ha_spur5_c05_s05.tsv


title: repl 4 MCF7 plus e2 and fulvestrant

description: repl 4 MCF7 plus e2 and fulvestrant

value: E2 added

value: fulvestrant


title: HeLa control plasmid Ctrl_1st

value: control plasmid

value: HeLa


title: non-elongating 6 day rep 2 (JA38)

value: submergence

value: 6 day


title: Sp_blastula_AB2_ChIPseq


title: HepG2 Cell, AICAR 1 mM_3

value: AICAR 1 mM


title: HepG2 Cell, AICAR 1 mM_2

value: Human hepatoma cell line


title: non-elongating 6 day rep 1 (JA37)


title: repl 3 MCF7 plus e2

description: repl 3 MCF7 plus e2


title: Sp_blastula_AB1_ChIPseq


title: repl 2 MCF7 plus e2

description: repl 2 MCF7 plus e2


title: repl 1 MCF7 plus e2

description: repl 1 MCF7 plus e2


title: Sp_blastula_bra_3_RNAseq

extract_protocol: 3  biological replicates of translational morpholino and control were generated. Libraries were multiplexed and sequenced on Illumina HiSeq 2500 to generate 100bp PE reads.

treatment_protocol: Translation blocking Sp-Bra morpholino CGCTCATTGCAGGCATAGTGGCG. 2-4 pl of 200 µM of the morpholino were injected into zygotes.

tag: morpholino

value: translation  morpholino


title: elongating 3 day rep 3 (JA36)

source_name: elongating 3 day

value: elongating leaves

tag: treatment

value: 3 day


title: HepG2 Cell, Imeglimin 3 mM_3

tag: cell type

value: wild type

value: Imeglimin 3 mM


title: elongating 3 day rep 2 (JA35)


title: HepG2 Cell, Imeglimin 3 mM_2


title: HepG2 Cell, AICAR 1 mM_1


title: elongating 3 day rep 1 (JA34)


title: repl 4 MCF7 plus e2

description: repl 4 MCF7 plus e2

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen)
Libraries were created after Ribo-zero rRNA Removal Kit (Illumina) using NEBNext Ultra Directional RNA (NEB) or Truseq Stranded Total RNA (Illumina) Library Prep Kit and sequenced using the HiSeq2500 (paired-end 100 bp v4 chemistry)

value: not LTED

value: ATCC


title: elongating 6 day rep 1 (JA40)


title: PARN mutant patient1 iPSCs_PAPD5 inhibitor (BCH001)_2

city: Boston

first: Suneet

last: Agarwal

state: MA

address: Karp 07214, 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
basecalling and demultiplex with Illumina bcl2fastq
Reads mapping to genome using HISAT2
Produces normalized read count FPKM and differential expression analysis using Cuffdiff (of the Cufflink package v2.1.1)
Normalized read count is then further analyzed and visualized with Qlucore Omics Explorer (v3.7)
Genome_build: hg38

source_name: PARN mutant patient1 iPSCs

extract_protocol:
Total RNA was extracted using TRIzol (Ambion) according to manufacturer’s protocol.
RNA-Seq library prepared using Illumina TruSeq stranded total RNA with RiboZero Gold or RiboZero Plus, per the manufacturer instruction

value: Fibroblast derived iPSCs

value: PAPD5 inhibitor (BCH001)


title: HepG2 Cell, Imeglimin 3 mM_1


title: Sp_blastula_bra_1_RNAseq

value: Embryo cells

value: blastula


title: PARN mutant patient1 iPSCs_PAPD5 inhibitor (RG7834)

value: PAPD5 inhibitor (RG7834)


title: HepG2 Cell, Imeglimin0.25 mM_3

value: Imeglimin 0.25 mM


title: non-elongating 3 day rep 2 (JA32)

source_name: non-elongating 3 day

value: non-elongating leaves

value: submergence


title: Sp_blastula_wt_2_RNAseq

value: wild type control


title: Sp_blastula_wt_3_RNAseq


title: HepG2 Cell, Imeglimin0.25 mM_2

value: Human hepatoma cell line


title: PARN mutant patient1 iPSCs_CRISPR-Cas9 mediated PAPD5 knockout

value: CRISPR-Cas9 mediated PAPD5 knockout


title: PARN mutant patient1 iPSCs_PAPD5 inhibitor (BCH001)_1


title: HepG2 Cell, Imeglimin0.25 mM_1


title: PARN mutant patient3 iPSCs_PAPD5 inhibitor (BCH001)

source_name: PARN mutant patient3 iPSCs


title: non-elongating 3 day rep 3 (JA33)


title: Sp_blastula_bra_2_RNAseq

value: translation  morpholino


title: Sp_blastula_wt_1_RNAseq


title: PARN mutant patient3 iPSCs_CRISPR-Cas9 mediated PAPD5 knockout


title: HepG2 Cell, Metformin 3 mM_3

value: Metformin 3 mM


title: elongating 3 day rep 3 (JA30)

value: elongating leaves

value: 3 day


title: non-elongating 3 day rep 1 (JA31)


title: HepG2 Cell, Metformin 3 mM_2

value: wild type


title: elongating 3 day rep 2 (JA29)


title: PARN mutant patient3 iPSCs_PAPD5 inhibitor (RG7834)


title: elongating 3 day rep 1 (JA28)


title: Sample 3 Isotype CUT&RUN

city: New York

first: Bjorn

middle: FC

last: Kafsack

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

data_processing:
Reads in sequenced libraries were checked for quality with FASTQC v0.11.9, adapter and quality-trimmed with trimmomatic v0.39
Properly paired reads were aligned against P.falciparum 3D7 genome v51 with bwa v.0.7.17 and sorted by name using samtools v1.13
Differential genome-wide enrichment between relative to matched isotype controls  was calculated using macs2 v2.2.7.1 to generate poisson-based FDR and fold-enrichment tracks and significant peaks
Peak annotation and visualization were carried out in R using GenomicRanges v1.44.0, Gviz v1.36.1, and ChIPpeakAnno v3.26.2 packages from Bioconductor using P.falciparum 3D7 genome annotation v51 from PlasmoDB
Assembly: Plasmodium falciparum 3D7 v51 from PlasmoDB
Supplementary files format and content: bedgraph
Library strategy: Cut&Run

organism: Plasmodium falciparum

source_name: early Schizonts

growth_protocol: synchronous early schizonts

extract_protocol:
1e7 parasites were used per sample for cut & run
Libraries were prepared according to Illumina's instructions accompanying the KAPA library preparation kit (KK8230) and sequenced at PE75 on a NextSeq500 machine

value: early Schizonts

tag: strain

value: NF54 pfpeg4-tdTomato

tag: chip antibody

value: Rabbit IgG isotype control Invitrogen  02-6102


title: HepG2 Cell, Metformin 0.25 mM_3

value: Metformin 0.25 mM


title: non-elongating 3 day rep 3 (JA27)


title: PARN mutant patient2 iPSCs_CRISPR-Cas9 mediated PAPD5 knockout

source_name: PARN mutant patient2 iPSCs

value: Fibroblast derived iPSCs


title: PARN mutant patient2 iPSCs_PAPD5 inhibitor (BCH001)

value: PAPD5 inhibitor (BCH001)


title: HepG2 Cell, Metformin 0.25 mM_2


title: HepG2 Cell, Metformin 3 mM_1


title: PARN mutant patient2 iPSCs_PAPD5 inhibitor (RG7834)

value: PAPD5 inhibitor (RG7834)


title: non-elongating 3 day rep 1 (JA25)

value: non-elongating leaves


title: Sample 2 Isotype CUT&RUN


title: non-elongating 3 day rep 2 (JA26)

value: submergence


title: PARN mutant patient3 iPSCs_Untreated

value: Untreated


title: elongating 1 day rep 3 (JA24)

source_name: elongating 1 day

value: 1 day


title: PARN mutant patient1 iPSCs_Untreated


title: RPE, Cys247X, Rep2

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

data_processing:
Image analysis and base calling is performed using the Illumina Real Time Analysis (3.4.4) software with default parameters.
Pass-filtered reads were mapped using STAR 2.7.3a
Count table of the gene features was obtained using FeatureCounts
Stattistics and Differential expression analysis done with EdgeR
Pathways analysis representation done with the package GOPlot
Assembly: Ensembl genome assembly GRCh38 (release 98)
Supplementary files format and content: Tab-delimited text files of the raw counts

source_name: Retinal pigmented epithelium

extract_protocol:
Total RNAs were extracted using the NucleoSpin RNA XS kit according to the manufacturer’s protocol. RNA yields and quality were determined using a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer.
For RPE cells, RNA-seq libraries were constructed from 1 µg of total RNAs using the TruSeq Stranded mRNA Sample Prep (Illumina) and paired-end sequencing of 75 bases length was performed on a HiSeq 4000 system (Illumina). For retinal organoids, RNA-seq libraries were constructed from 1 µg of total RNAs using the NEB Next Ultra II Directional RNA (New England Biolabs) and paired-end sequencing of 100 bases length was performed on a Novaseq system (Illumina).

value: Retinal pigmented epithelium

value: iPSCs

value: Symptomatic


title: HepG2 Cell, Metformin 0.25 mM_1

value: Human hepatoma cell line


title: non-elongating 1 day rep 3 (JA21)

source_name: non-elongating 1 day


title: RPE, Cys247X, Rep1


title: PARN mutant patient2 iPSCs_DMSO

value: DMSO


title: RPE, Cys247X.AS, Rep3

value: Asymptomatic


title: elongating 1 day rep 1 (JA22)

value: elongating leaves


title: RPE, Cys247X, Rep3


title: elongating 1 day rep 2 (JA23)


title: Dendrobium officinale protocorm

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

description:
miRNA_novel_miRdeep2.xls
miRNA.expr.xls
Dcp

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then detected miRNA using miRDeep2 v2_0_0_8; mapper.pl with parameters -d -c -i -j -l 18 -m,miRDeep2.pl with default parameter
miRNA expression were calcuated using quantifier.pl from miRDeep2 v2_0_0_8 with parameters, then differential analysis using R package Ballgown
Genome_build: GCF_001605985.1
Supplementary_files_format_and_content: miRNA_novel_miRdeep2.xls (miRdeep2 analysis output), miRNA.expr.xls (abundance measurements)

organism: Dendrobium officinale

source_name: Dendrobium officinale protocorm

growth_protocol: The original plants of Dendrobium species were collected from Chishui City, Guizhou Province, China. The capsules were washed thoroughly under running tap for 30 minutes. Then treated with 75% ethanol for 30 seconds, and washed three times with sterile water. After this, the capsules were dipped in 0.1% mercuric chloride for 10 minutes and washed six times with sterile water. Finally, the sterilized capsules were excised longitudinally with a sterile surgical blade and around 1g of seeds was inoculated on improved 1/2 Murashige and Skoog (MS) medium, which was supplemented with potato juice (potato 30g/L, the juice was boiled for 20 min), 3% (w/v) sucrose, 0.2 mg/L NAA and 0.6% (w/v) agar, pH 5.8. After germinating to protocorms, the protocorms were transferred to proliferation media: 1/2 MS+ potato 30 g/L+ 3% (w/v) sucrose+ 0.3% (w/v) powder milk+ 1.5 mg/L 6-BA + 0.5 mg/L NAA and 0.6% (w/v) agar, pH 5.8. The protocorms were kept in a greenhouse. The temperature is 23 ± 1℃, the light/dark cycle is 12/12 h and relative humidity is 60-70%. Protocorms were collected after culturing for 30 days

extract_protocol:
Total small RNA was extracted by QIAGEN miRNeasy Mini Kit (QIAGEN, USA) according to the manufacturer’s instructions. RNA concentration and purity were measured on a NanoDrop ND-2000 UV-Vis Spectrophotometer (Thermo Fisher Scientific, USA). RNA integrity was confirmed by denaturing agarose gel electrophoresis
Small RNA sequencing libraries were prepared using TruSeq Small RNA Sample Prep Kit (Illumina, USA). Briefly, the RNA fragments were firstly ligated to 5'- and 3’-adapters using T4 RNA Ligase, and reverse-transcribed with miScriptII RT-Kit (Qiagen, Germany). The resultant cDNA fragments were electrophoresed on a 4% agarose gel. Bands between 140 and 160 bp were excised and extracted by MinElute Gel Extraction Kit (Qiagen, Germany)

value: protocorm

value: culturing for 30 days


title: PARN mutant patient1 iPSCs_DMSO


title: RPE, Cys247X.AS, Rep2


title: non-elongating 1 day rep 1 (JA19)


title: PARN mutant patient2 iPSCs_Untreated


title: non-elongating 1 day rep 2 (JA20)


title: K562_TSA_StrePD_rep2

city: Baltimore

first: Joseph

last: Tran

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

description: Streptavidin pulldown DNA

data_processing:
DNA was aligned using bowtie v2.3.2
DNA reads were counted into 10kb or 100kb windows using bedtools v2.26.0 coverage, and calculated as a log2(StrepD/input). The data was covnerted to a z-score and these z-score values were averaged for the indicated samples.
Hidden Markov Model (HMM) was called using depmixS4 v1.4-0 in RStudio v0.98.953 (R v3.5.1). Note we used a three state model
HMM calls were intersected between replicates to generate a consensus bed file for downstream analysis.
Assembly: hg19 and mm10
Supplementary files format and content: bedgraph files of the cTSA-seq or H3K9me3 ChIP-seq data at either 20kb or 100kb resolution.

growth_protocol: K562 cells were grown in T25/T75 flasks with IMDM + 15% FBS. Mice were housed @12h/12h light/dark cycle and fed ad libitum. Mice were anesthsized, perfused with saline, and then paraformaldehyde. The brain was removed and post-fixed for 16-24h at 4 C. Brains were saturated in a 30% sucrose solution and embedded in O.C.T. freezing media for cryosectioning.

extract_protocol:
Cultured cells were permeabilized with PBS +0.25% Triton X-100 and stained for Lamin B1, and then a secondary HRP antibody. THe TSA reaction was performed according the kit [Biotin-XX-Tyramide Superboost kit (Invitrogen, #2005939)]. The cells were digested with Proteinase K in RIPA buffer overnight. DNA was extracted using phenol/chloroform/isoamy alcohol. Pure DNA was sonicated with a Misonix sonicator and biotinylation of DNA was monitored by dot blot onto positively charged nylon membranes. Streptavidin pulldown was done in a manner similar Chen, et al., 2018 and we used the modified protocol for washes. For tissue sections, cells/nuclei were isolated by brief sonication and collagenase type 2 digestion. The TSA reaction was done as described for cultured cells. Chromatin fragmentationn was done using a combination of sonication and MNase digestion in RIPA buffer and Streptavidin pulldown was done for 1 hour at room temperature.
Rubicon Genomics (Takara) ThruPlex 48 kit.

treatment_protocol: Cells were fixed with 4% PFA for 10 minutes at room temperature and neutralized with glycine.

value: Cultured cells


title: K562_TSA_StrePD_rep1

description: Streptavidin pulldown DNA


title: PARN mutant patient3 iPSCs_DMSO

value: Fibroblast derived iPSCs


title: Rat WT testis

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

data_processing:
CellRanger v6 used for demultiplexing + read mapping + barcode assignment + UMI counting
Seurat v4.2.1 used for quality control + normalization + dimensionality reduction + clustering
Assembly: Rnor_6.0
Supplementary files format and content: Filtered count matrices from Cell Ranger

organism: Rattus norvegicus

source_name: Testis

extract_protocol:
Chromium Single Cell 3’ Reagents kits v3.1 user guide RevD
Single Cell 3’ v3.1 chemistry
10x scRNA-seq

value: Testicular cells

tag: host

value: goGermline


title: K562_TSA_input_rep2

description: input DNA


title: RPE, Control, Rep3

value: Control


title: Sample 1 Isotype CUT&RUN

value: early Schizonts

value: NF54 pfpeg4-tdTomato

value: Rabbit IgG isotype control Invitrogen  02-6102


title: rTTF_3

data_processing:
bcl2fastq v2.19 software used for demultiplexing + basecalling
fastp v0.20 used for trimming adapter sequences and low quality reads
STAR v2.7a used for read mapping
Rsubread v2.2.4 used for quantifying gene expression
edgeR v3.30.3 used for differential gene expression analysis
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab delimited raw counts

source_name: Adult tail tissue

extract_protocol:
RNA was isolated using Qiagen RNeasy kit (Cat. #74104, Qiagen) and treated with RNase-Free DNase (Cat. #79254, Qiagen).
TruSeq Stranded mRNA protocol (Illumina, Inc, California, USA)

tag: strain/genotype

value: Sprague Dawley

value: Tail Tip Fibroblasts


title: elongating 1 day rep 2 (JA17)

value: submergence

value: 1 day


title: elongating 1 day rep 3 (JA18)


title: RPE, Control, Rep2

value: Retinal pigmented epithelium

value: iPSCs


title: rTTF_2

value: Brown Norway


title: K562_TSA_input_rep1

description: input DNA


title: RPE, Control, Rep1


title: rESC

source_name: Embryonic stem cell

value: Dark Agouti

value: Embryonic stem cell


title: Organoids, Cys247X.Iso, D130, Rep2

source_name: patient derived Retinal organoids

value: patient derived Retinal organoids

value: Isogenic


title: rTTF_1


title: non-elongating 1 day rep 2 (JA14)

value: non-elongating leaves


title: Organoids, Cys247X.Iso, D130, Rep3


title: Organoids, Cys247X.Iso, D130, Rep1


title: non-elongating 1 day rep 3 (JA15)


title: RPE, Cys247X.AS, Rep1

value: Asymptomatic


title: Organoids, Cys247X, D130, Rep4

value: Symptomatic


title: non-elongating 1 day rep 1 (JA13)


title: Diff (day1)_FetalCPC_LentivirusMutated(exon2CARMN7mutated)_Sample4

city: Lausanne

first: Mohamed

last: Nemir

state: Vaud

address: Bugnon 27

institute: Lausanne University Hospital

data_processing:
Reads were pseudoaligned with kallisto software (version 0.44.0) to estimate the transcript level expression per sample
Gene level estimation was performed with sleuth R package (version 0.33.0) and transctipt expression was aggregated to gene level, followed by differential expression. For the transctipt to gene mapping gencode version 29 annotation was used.
Assembly: hg38
Supplementary files format and content: matrix table with TPM expression values for all genes and samples

source_name: Human Fetal CPCs

growth_protocol: Adult CPCs were expanded in expansion medium (3:1 DMEM 1g/l glucose/Medium 199 [Invitrogen] supplemented with 10% horse serum [Serotec, Kidlington, United Kingdom], 5% fetal bovine serum [Serotec], 100 U/ml penicillin [Invitrogen], and 100 μg/ml streptomycin [Invitrogen]). For inducing differentiation, cells were switched to MEM alpha (Invitrogen) containing 2% horse serum, 1 μmol/l dexamethasone (Sigma-Aldrich, St. Louis, Missouri), 50 μg/ml ascorbic acid (Sigma-Aldrich), 10 mmol/l β-glycerophosphate (Sigma-Aldrich), 100 U/ml penicillin (Invitrogen), and 100 μg/ml streptomycin (Invitrogen) (differentiation medium). Fetal CPCs  were expanded in culture in proliferation medium, a 3:1 mixture of DMEM 1 g/L glucose and Medium 199 (Invitrogen) supplemented with 10% Horse serum (Serotec), 5% fetal bovine serum (Serotec), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen). After three passages, cells were switched to a serum-free differentiation medium. Differentiation medium contained MEM alpha (Invitrogen) supplemented with 1 μM dexamethasone (Sigma-Aldrich), 50 μg/mL ascorbic acid (Sigma-Aldrich), 10 mM β-glycerophosphate (Sigma-Aldrich), 100 U/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen)

extract_protocol:
Cells were lysed in Qiazol and RNA was purified using miRNeasy RNA prufication kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fetal CPCs


title: Notch3 normoxia

city: Columbus

first: Brenda

middle: J.

last: Lilly

state: OH

address: 700 CHILDREN'S DRIVE

institute: NATIONWIDE CHILDREN'S HOSPITAL

data_processing:
 The Illumina bcl files were demultiplexed and converted into fastq files using the Cell Ranger “mkfastq” command. The fastq files were aligned against mouse genome version mm10 genome version index from 10x Genomics (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) using the “count” function of the Cell Ranger version 5.0 (10x Genomics) implemented at the Franklin high-performance computing facility at The Abigail Wexner Research Institute at Nationwide Children’s Hospital.
 Subsequent processing, quality control, principal component analysis, dimensionality reduction, batch correction, and integration were performed using the Seurat (v4.0) [19, 20] package in the R Shiny app Natian [21].
Cell types were identified using cluster-specific markers and compared to previously annotated cell types identified in LungMAP datasets (www.lungmap.net), Mouse Cell Atlas (http://bis.zju.edu.cn/MCA/), and Lung Aging Atlas – Schiller and Theis labs @ Helmholtz Zentrum München (http://146.107.176.18:3838/MLAA_backup/using the R shiny app Ryabhatta) [21]
Assembly: mouse  mm10
Supplementary files format and content: Compressed 10x CellRanger counts output `outs` folder (matrix.mtx, feature.tsv, barcodes.tsv)

source_name: lung

extract_protocol:
Lungs isolated from 12-week-old mice were washed in cold PBS then digested in 2mg/ml Collagenase Type II (Worthington Biochemical, LS004174) for 45 minutes at 37°C, pipette mixing every 10 minutes to dissociate the cells. 100µm and 70µm cell strainers (BD Falcon) were used to filter cells before a 5-minute wash in red blood cell lysis buffer (Qiagen). Cells were resuspended in 250µl culture media (10% Fetal Bovine Serum, DMEM High Glucose with Glutamine, Penicillin Streptomycin) and cell viability (>85%) was measured using the Automated Cell Counter (Thermo Fisher, AMQAF1000).
Chromium Single Cell 3’ Reagent Kit v2 controller (10x Genomics)

value: lung

value: disease/genotype

value: normoxia


title: Notch3 hypoxia

value: nypoxia


title: elongating 0 day rep 2 (JA11)

source_name: elongating 0 day

value: elongating leaves

value: control

value: 0 day


title: Wild-type (wt) hypoxia

value: wild-type

value: hypoxia


title: Organoids, Cys247X, D130, Rep3

value: iPSCs


title: elongating 0 day rep 3 (JA12)


title: Wild-type (wt) normoxia


title: elongating 0 day rep 1 (JA10)


title: Organoids, Cys247X, D130, Rep2


title: elongating 1 day rep 1 (JA16)

value: submergence

value: 1 day


title: miR-145 Lung

data_processing:
Illumina.bcl files were demultiplexed and converted into Fastq files using the  cellranger  `mkfastq`  pipeline.  The  Fastq  files  were aligned  against  mouse  genome  version  mm10  genome version  index  from  10X  genomics  (https://cf.10xge nomics.com/supp/cell- exp/refda ta- gex- mm10- 2020- A.tar.gz)  using  `count`  function  of  the  cell  ranger  ver-sion  5.0  (10x  Genomics)  using  the  High  Performance Computing  Facility  at  The  Abigail  Wexner  Research Institute at Nationwide Children's Hospital.
Subsequent processing, quality control, principal component analysis,  dimensionality  reduction,  batch- correction,  and integration  were  performed  using  the  Seurat  (v  3.2) package  in  R  (Stuart  &  Satija,  2019).
Assembly: Mouse mm10
Supplementary files format and content: Compressed 10x CellRanger counts output `outs` folder (matrix.mtx, feature.tsv, barcodes.tsv)

extract_protocol:
Lungs from postnatal day 12 mice were collected and washed in cold PBS. Tissue was cut into pieces and digested in 2mg/ml Collagenase Type II (Worthington Biochemical, LS004174) for 45 minutes at 37°C, pipette mixing was carried out to dissociate cells every 10 minutes. Cells were filtered through 100µm and 70µm cell strainers (BD Falcon) and treated with red blood cell lysis buffer (Qiagen) for 5 minutes. Cells were resuspended in 250µl culture media (10% Fetal Bovine Serum, DMEM High Glucose with Glutamine, Penicillin Streptomycin). Cell viability (>85%) was measured using the Automated Cell Counter (Thermo Fisher, AMQAF1000).
Chromium Single Cell 3’ Reagent Kit v2 controller (10x Genomics)

value: miR-145 Transgenic


title: Control Lung


title: non-elongating 0 day rep 3 (JA9)

source_name: non-elongating 0 day

value: non-elongating leaves


title: non-elongating 0 day rep 2 (JA8)


title: Organoids, Cys247X, D130, Rep1

value: patient derived Retinal organoids


title: Organoids, Cys247X.AS, D130, Rep3

value: Asymptomatic


title: KO3exp

data_processing:
Analysis was performed employing a combination of programs including STAR, HTseq, Cufflink and wrapped scripts by Novagene.
Differential expression between the two groups were determined through edgeR (package 3.16.5).
Assembly: Mouse mm10
Supplementary files format and content: Gene normalized expression per sample csv file

source_name: Aorta

extract_protocol:
RNAeasy Mini spin columns (Qiagen)
Novagene

value: Aorta


title: Organoids, Cys247X.AS, D130, Rep2


title: elongating 0 day rep 3 (JA6)

extract_protocol:
Total RNAs were extracted from frozen tissues using a miRNeasy Mini kit (Qiagen, Hilden, Germany). Genomic DNA was eliminated by on-column digestion.
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
paired-end


title: KO2exp


title: KO1exp