title: TU, VPA, 5 uM, 4

description:
Library name: Cell_232
mRNA from single larvae


title: RW, VPA, 0 uM, 3

status: Public on Aug 10 2025

type: SRA

city: Sagamihara

first: Hiromi

last: Hirata

state: Kanagawa

address: 5-10-1, Fuchinobe, Chuo-ku

country: Japan

institute: Aoyama Gakuin University

description:
Library name: Cell_247
mRNA from single larvae

library_source: transcriptomic

data_processing:
The PCA was performed in R software using NormalizedDarta, ScaleData, FindVariable Fretures, and RunPCA functions in Seurat (version 5.1.0) (Hao et al., 2024) with default parameters except for “do.scale = F” for ScaleData.
Assembly: Danio_rerio.GRCz11.cdna.al.fa
Supplementary files format and content: csv-delimited text file includes rawcnt values for each sample

molecule: total RNA

organism: Danio rerio

source_name: whole-mount

growth_protocol: Zebrafish (Danio rerio) were reared and maintained in 1.7 L tanks in a recirculating Meito System (Meito System) under a 14 h light and 10 h dark photoperiod according to the standard protocol.

extract_protocol:
RNA extraction from zebrafish larvae and RNA purification were described previously (Ujibe et al. 2021). The RNA concentration was determined using the Quantus Fluorometer with QuantiFluor RNA System Kit (Promega) according to the manufacturer’s manual. RNA was diluted to a final concentration of 2 ng/µl and used to prepare library for RNA-Seq.
Library preparation was conducted according to the Lasy-Seq ver 1.1 5 method (Kashima et al., 2021). In brief, reverse transcription was done using SuperScript IV reverse transcriptase (Thermo Fisher Scientific) and indexed reverse transcription primers. Following program was used for reverse transcription: 65 °C 10 min; 80 °C 15 min; 4 °C forever. Products of reverse transcription were pooled and then purified using an equal volume of AMpure XPKAPA Pure beads (Beckman CoulterRoche) according to the manufacturer’s manual. Second strand synthesis was conducted with RNase H (Enzymatics) and DNA polymerase I (Enzymatics) at 16 °C for 2 h. Synthetic double-strand DNA (dsDNA) were treated with RNase T1 (Thermo Fisher Scientific) at 37 °C for 5 min. Fragmentation was conducted using 5x WGS Fragmentation Mix (Enzymatics) at 32 °C for 5.5 min followed by heat inactivation at 65 °C for 30 min. Ligation was conducted using 5x Ligation Mix (Enzymatics) at 20 °C for 15 min. One cycle PCR was performed using a P7 primer containing a 5′ biotin modification ([BioON]CAAGCAGAAGACGGCATACGAGAT) to allow for selective purification of properly ligated molecules containing the original 3’-ends of the cDNAs. Biotin-labeled DNA was captured using Dynabeads M-280 Streptavidin (Thermo Fisher Scientific) in binding buffer (1M NaCl, 10 mM Tris-HCl pH 7.6), which were washed with TE-TW (10 mM Tris pH 7.6, 1 mM EDTA, 0.01% Tween20), twice. Subsequent amplification was performed with KAPA HiFi HotStart ReadyMix (Roche), and the optimal PCR cycle number was determined by EvaGreen (Biotium) -based qPCR using the following program: initial denaturation at 95 °C for 5 minutes; followed by cycles of 98 °C for 20 seconds, 60 °C for 15 seconds, and 72 °C for 40 seconds; a final extension at 72 °C for 3 minutes; and a hold at 4 °C indefinitely. The library was purified using an equal volume of KAPA Pure beads (Roche), and subjected to electrophoresis in Bioanalyzer 2,100 (Agilent Technologies) with the Agilent High Sensitivity DNA kit (Agilent Technologies). Library concentration was determined using Quantus Fluorometer (Promega) with the QuantiFluor ONE dsDNA System kit (Promega). Sequencing of 150-bp paired-end reads was conducted using NovaSeq X Plus (Illumina). Raw RNA-Seq reads were aligned to the Danio rerio genome assembly GRCz11 (Ensembl release 111), and gene-level quantification was conducted as previously described (Kashima et al. 2021).

treatment_protocol: To evaluate inter-strain variability in chemical susceptibility during zebrafish embryogenesis, we conducted malformation and embryo-fetal lethality (MEFL) testing, which is based on the established protocol of the OECD test guideline 236 (TG236), with minor procedural modifications tailored to our experimental needs (Figure 1). This assay enables the systematic assessment of developmental toxicity by tracking visible morphological outcomes and survival over early developmental stages. Fertilized eggs were obtained from adult zebrafish representing five distinct strains (AB, TU, RW, WIK, and PET), and were collected during 1–3 hours post-fertilization (hpf) to ensure early and synchronized developmental timing. Prior to chemical treatment, embryos were microscopically examined at 4–6 hpf to screen for and exclude those exhibiting any spontaneous developmental defects, such as irregular cleavage, abnormal yolk shape, or delayed development. This quality control step was essential to eliminate confounding variables and to ensure that subsequent observations would reflect chemical-specific effects rather than intrinsic developmental failure. Embryos that passed this screening were then allocated into experimental groups and exposed to test compounds from 5–6 hpf through 5 days post-fertilization (dpf) in a static exposure setup without medium replacement. At 5 dpf, embryos were individually inspected under a stereomicroscope, and their phenotypes were categorized into normal, malformed, or dead, enabling a quantitative comparison of teratogenic and lethal responses among strains.

tag: tissue

value: whole-mount

tag: strain

value: RW

tag: treatment

value: valproic acid


title: TU, VPA, 1uM, 7

description:
Library name: Cell_227
mRNA from single larvae

value: TU


title: MYO10 KO CLONE 99 BIO REP 3

city: Atlanta

first: Raaven

last: Goffe

state: GA

address: 100 Woodruff Circle

country: USA

institute: Emory University School of Medicine

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_339

data_processing:
Read quality and contamination were assessed using FastQC v0.12.0 and Fastq-Screen v0.15.3 and reports generated with MultiQC v1.24.1
Reads were trimmed using fastp v0.23.4 and were then aligned to the human reference genome hg38 using STAR aligner v2.7.11b
HTSeq-Count v2.0.5 was used to generate raw count tables.
Assembly: Human reference genome hg38
Supplementary files format and content: Open XML Spreadsheet file includes raw counts for all samples

organism: Homo sapiens

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen, Cat. No. 74104) followed by RNA quality and quantity assessments using Nanodrop (Thermo Fisher Scientific, USA) and Bioanalyzer (Agilent Technologies, USA).
Library preparation and sequencing were performed using the NEBNext® Ultra™ II DNA Library Prep kit for Illumina (New England Biolabs, Cat. No. E7465) and Novaseq X-Plus (Illumina Inc., USA).

tag: cell line

tag: cell type

value: lung carcinoma cells

tag: genotype

value: MYO10 KO

value: CRISPR-Cas9 edited


title: TU, VPA, 1uM, 6

description:
Library name: Cell_226
mRNA from single larvae


title: TU, VPA, 1uM, 5

description:
Library name: Cell_225
mRNA from single larvae


title: MYO10 KO CLONE 99 BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_337


title: MYO10 KO CLONE 99 BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_338


title: TU, VPA, 1uM, 3

description:
Library name: Cell_223
mRNA from single larvae


title: H1299 PARENTALS BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_352

value: MYO10 JAG1 WT


title: TU, VPA, 1uM, 2

description:
Library name: Cell_222
mRNA from single larvae


title: MYO10 KO CLONE 99 BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_340


title: MYO10 KO CLONE 98 BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_328


title: TU, VPA, 1uM, 1

description:
Library name: Cell_221
mRNA from single larvae


title: JAG1 KO CLONE 72 BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_329

value: JAG1 KO


title: MYO10 KO CLONE 98 BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_327


title: TU, VPA, 0 uM, 7

description:
Library name: Cell_219
mRNA from single larvae


title: JAG1 KO CLONE 72 BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_317


title: MYO10 KO CLONE 84 BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_316

value: MYO10 KD


title: MYO10 KO CLONE 98 BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_325


title: MYO10 KO CLONE 84 BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_314


title: MYO10 KO CLONE 98 BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_326


title: TU, VPA, 0 uM, 6

description:
Library name: Cell_218
mRNA from single larvae


title: TU, VPA, 1uM, 4

description:
Library name: Cell_224
mRNA from single larvae


title: JAG1 KO CLONE 35 BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_341


title: TU, VPA, 0 uM, 4

description:
Library name: Cell_216
mRNA from single larvae


title: TU, VPA, 0 uM, 3

description:
Library name: Cell_215
mRNA from single larvae


title: TU, VPA, 0 uM, 2

description:
Library name: Cell_214
mRNA from single larvae


title: TU, VPA, 0 uM, 5

description:
Library name: Cell_217
mRNA from single larvae


title: TU, VPA, 0 uM, 8

description:
Library name: Cell_220
mRNA from single larvae


title: JAG1 KO CLONE 72 BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_305


title: E. faecium mutant strain G482V, replicate 2

city: PITTSBURGH

first: Daria

last: Van Tyne

state: PA

address: 200 Lothrop St

department: Department of Medicine

institute: University of Pittsburgh

description:
Library name: G482V_2
Column name in featureCounts_all_output.xlsx is the same as library name

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)
Sequencing reads were processed using Trim galore v0.6.10. Reads passed quality control if the Phred score was >33 and the sequence length was >142 bp
Trimmed reads were then mapped to the annotated WT genome using STAR v2.7.11b
Reads mapping to coding sequences were counted using featureCounts v2.0.6 against the annotated WT sequence
Read counts extraction and normalization to library size was done using the DESeq2 package in Rstudio. Only genes with read counts of >10 were included in the analysis
Assembly: WT strain were sequenced and used as reference for read alignment
Supplementary files format and content: excel file includes counts for all samples

organism: Enterococcus faecium

source_name: Bacterial cell

growth_protocol: Overnight cultures were re-inoculated into 5 mL of fresh BHI and grown until mid-log phase. Then, 2x v/v of RNAprotect was added to each culture

extract_protocol:
RNA was extracted with the Rneasy Mini Kit (Qiagen) and DNAse treated
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI)

treatment_protocol: Pellet was treated with 10 µL of 2500 U/mL mutanolysin and 50 µL 50 mg/mL lysozyme at 37°C for 30 minutes prior to RNA extraction

value: Bacterial cell


title: MYO10 KO CLONE 84 BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_313


title: TU, VPA, 0 uM, 1

description:
Library name: Cell_213
mRNA from single larvae


title: AB, VPA, 20 uM, 8

description:
Library name: Cell_212
mRNA from single larvae

value: AB


title: MYO10 WT CLONE 75 BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_303


title: AB, VPA, 20 uM, 7

description:
Library name: Cell_211
mRNA from single larvae


title: MYO10 WT CLONE 75 BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_301


title: AB, VPA, 20 uM, 6

description:
Library name: Cell_210
mRNA from single larvae


title: MYO10 WT CLONE 75 BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_302


title: AB, VPA, 20 uM, 5

description:
Library name: Cell_209
mRNA from single larvae


title: AB, VPA, 20 uM, 4

description:
Library name: Cell_208
mRNA from single larvae


title: MYO10 WT CLONE 38 BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_292


title: MYO10 KO CLONE 84 BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_315


title: MYO10 WT CLONE 38 BIO REP 3

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_291


title: AB, VPA, 20 uM, 3

description:
Library name: Cell_207
mRNA from single larvae


title: MYO10 WT CLONE 75 BIO REP 4

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_304


title: AB, VPA, 20 uM, 2

description:
Library name: Cell_206
mRNA from single larvae


title: MYO10 WT CLONE 38 BIO REP 2

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_290


title: MYO10 WT CLONE 38 BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_289


title: AB, VPA, 5 uM, 8

description:
Library name: Cell_204
mRNA from single larvae


title: JAG1 KO CLONE 72 BIO REP 1

description: Library name: X22MY2JLT3_s1_1_IDT8_UDI_293


title: HCT215-1, untreated

city: Ariake

first: Ryoji

last: Yao

state: Tokyo

institute: Cancer Institute, JFCR

library_source: transcriptomic single cell

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Raw data produced from the 10x Genomic platform were processed by Cell Ranger (v6.1.2).
Assembly: GRCH38
Supplementary files format and content: A cell x gene data matrix in AnnData format

source_name: colorectal cancer

extract_protocol:
Organoids were colected and single cells were prepared in TrypLE.
10x Genomics Chromium was used for single cell capture and cDNA preparations according to the Single Cell 3' v3 Protocol recommended by the manufacturer.

value: colorectal cancer

tag: patient id

value: organoid

value: untreated


title: AB, VPA, 5 uM, 7

description:
Library name: Cell_203
mRNA from single larvae


title: HCT191-1, untreated


title: HCT202-1, untreated


title: HCT128-1, untreated


title: HCT24-8, trametinib treated

value: trametinib


title: AB, VPA, 5 uM, 5

description:
Library name: Cell_201
mRNA from single larvae


title: AB, VPA, 20 uM, 1

description:
Library name: Cell_205
mRNA from single larvae


title: AB, VPA, 5 uM, 4

description:
Library name: Cell_200
mRNA from single larvae


title: AB, VPA, 5 uM, 3

description:
Library name: Cell_199
mRNA from single larvae


title: HCT24-8, untreated


title: AB, VPA, 5 uM, 2

description:
Library name: Cell_198
mRNA from single larvae


title: AB, VPA, 1 uM, 8

description:
Library name: Cell_196
mRNA from single larvae


title: Subcutaneous adipose tissue, Cow 10, Control

city: Lubbock

first: Clarissa

last: Strieder-Barboza

state: Texas

address: ESB II, 1006 Canton Ave.

department: Veterinary Sciences

institute: Texas Tech University

description:
Library name: 19SAT
10X Genomics

data_processing:
Demultiplexing, barcode processing, counting and alignment were performed using the CellRanger pipeline (v.6.0.1)
Assembly: Bos taurus (ARS-UCD2.0)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Bos taurus

source_name: subcutaneous adipose tissue

extract_protocol:
Approximately 500 mg of each adipose tissue sample was washed in cold, sterile, RNase-free 1X PBS (CAT# AM9625, Invitrogen) diluted in nuclease-free water (CAT# AM9932, Invitrogen), then minced using a scalpel in a petri dish on ice in 0.5 mL lysis Buffer comprised of nuclease-free water with 3 mmol/L MgCl2 (CAT# AM9530G, Invitrogen), 10 mmol/L Tris Buffer, pH 8 (CAT# AM9855G, Invitrogen), 25 mmol/L KCl (CAT# AM9640G, Invitrogen), 250 mmol/L sucrose (CAT# S0389-500G, Sigma-Aldrich), 0.1% Triton X-100 (CAT# T8787, Sigma-Aldrich), and 100 µmol/L DTT (CAT# 646563, Sigma-Aldrich). After mincing, samples were transferred and homogenized in a pre-cooled 15 mL glass dounce homogenizer (CAT# 357544, Duran Wheaton Kimble) by performing 10 strokes with Pestel A and 15 strokes with Pestel B on ice. Samples were then strained through a 40 µm filter (CAT# 22363547, ThermoFisher Scientific), pre-wet with ± 200 µL of Nuclei Isolation Medium (NIM; composed of Lysis Buffer without Triton and DTT) into a 50 mL conical tube. The strained homogenates were then transferred into pre-cooled, sterile, RNase-free microcentrifuge tubes and centrifuged at 500 x g for 5 min at 4 ºC. The resulting supernatant was discarded, leaving ± 50 µL in the tube. The pellet was then resuspended in 500 µL of nuclei resuspension buffer containing 1% BSA (CAT# 9048-46-8, ThermoFisher Scientific), and 0.2 U/µL RNase inhibitor (CAT# 11836170001, Roche) in DPBS (CAT# 14190-144, Gibco). The samples were then centrifuged at 300 x g for 5 min at 4 ºC, after which the supernatant was removed, leaving ± 50 µL in the tube. The sample was gently resuspended in the remaining volume and 5 µL was removed for counting nuclei using Trypan Blue (CAT# 15250-061, Gibco), while the remaining sample was utilized for sequencing.
Nuclei libraries, targeting 6,000 - 10,000 nuclei, were prepared using the 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits (10X Genomics). Library quality was assessed via DS 5000 HS assay kit using Tape Station 4200 (Agilent Technologies, Santa Clara, CA, United States) and quantified using Qubit dsDNA HS assay kit on Qubit Fluorometer version 2.0 (Life Technologies Inc., Carlsbad, CA, United States). Nuclei libraries were sequenced via 150bp paired-end sequencing using an Illumina NovaSeq 6000 (Illumina). FASTQ files were generated using the Bcl2fastq2 Conversion Software (Illumina), and the CellRanger Pipeline (10X Genomics) was utilized for alignment and generating count matrices.

treatment_protocol: Dairy cows with and without subclinical ketosis

value: subcutaneous adipose tissue

value: control


title: Subcutaneous adipose tissue, Cow 9, Subclinical ketosis

description:
Library name: 17SAT
10X Genomics

value: subclinical ketosis


title: Visceral adipose tissue, Cow 10, Control

description:
Library name: 20VAT
10X Genomics

source_name: visceral adipose tissue

value: visceral adipose tissue


title: AB, VPA, 1 uM, 5

description:
Library name: Cell_193
mRNA from single larvae

value: whole-mount

value: valproic acid


title: AB, VPA, 1 uM, 6

description:
Library name: Cell_194
mRNA from single larvae


title: AB, VPA, 5 uM, 1

description:
Library name: Cell_197
mRNA from single larvae


title: Visceral adipose tissue, Cow 8, Control

description:
Library name: 16VAT
10X Genomics


title: Visceral adipose tissue, Cow 9, Subclinical ketosis

description:
Library name: 18VAT
10X Genomics


title: Subcutaneous adipose tissue, Cow 8, Control

description:
Library name: 15SAT
10X Genomics


title: AB, VPA, 1 uM, 3

description:
Library name: Cell_191
mRNA from single larvae


title: Visceral adipose tissue, Cow 7, Subclinical ketosis

description:
Library name: 14VAT
10X Genomics


title: AB, VPA, 1 uM, 4

description:
Library name: Cell_192
mRNA from single larvae


title: AB, VPA, 5 uM, 6

description:
Library name: Cell_202
mRNA from single larvae


title: Subcutaneous adipose tissue, Cow 7, Subclinical ketosis

description:
Library name: 13SAT
10X Genomics


title: AB, VPA, 1 uM, 1

description:
Library name: Cell_189
mRNA from single larvae


title: AB, VPA, 0 uM, 8

description:
Library name: Cell_188
mRNA from single larvae


title: Visceral adipose tissue, Cow 6, Control

description:
Library name: 12VAT
10X Genomics


title: Subcutaneous adipose tissue, Cow 6, Control

description:
Library name: 11SAT
10X Genomics


title: AB, VPA, 0 uM, 7

description:
Library name: Cell_187
mRNA from single larvae


title: Subcutaneous adipose tissue, Cow 5, Subclinical ketosis

description:
Library name: 9SAT
10X Genomics


title: Visceral adipose tissue, Cow 4, Control

description:
Library name: 8VAT
10X Genomics


title: Subcutaneous adipose tissue, Cow 4, Control

description:
Library name: 7SAT
10X Genomics


title: AB, VPA, 0 uM, 4

description:
Library name: Cell_184
mRNA from single larvae


title: Visceral adipose tissue, Cow 5, Subclinical ketosis

description:
Library name: 10VAT
10X Genomics


title: AB, VPA, 0 uM, 6

description:
Library name: Cell_186
mRNA from single larvae


title: AB, VPA, 1 uM, 7

description:
Library name: Cell_195
mRNA from single larvae


title: AB, VPA, 0 uM, 3

description:
Library name: Cell_183
mRNA from single larvae


title: Visceral adipose tissue, Cow 3, Control

description:
Library name: 6VAT
10X Genomics


title: AB, VPA, 0 uM, 5

description:
Library name: Cell_185
mRNA from single larvae


title: TU, warfarin, 300 uM, 6

description:
Library name: Cell_180
mRNA from single larvae

value: TU

value: warfarin


title: AB, VPA, 0 uM, 1

description:
Library name: Cell_181
mRNA from single larvae


title: AB, VPA, 0 uM, 2

description:
Library name: Cell_182
mRNA from single larvae


title: TU, warfarin, 300 uM, 5

description:
Library name: Cell_179
mRNA from single larvae


title: AB, VPA, 1 uM, 2

description:
Library name: Cell_190
mRNA from single larvae


title: TU, warfarin, 300 uM, 4

description:
Library name: Cell_178
mRNA from single larvae


title: Visceral adipose tissue, Cow 2, Subclinical ketosis

description:
Library name: 4VAT
10X Genomics


title: TU, warfarin, 300 uM, 2

description:
Library name: Cell_176
mRNA from single larvae


title: Subcutaneous adipose tissue, Cow 1, Subclinical ketosis

description:
Library name: 1SAT
10X Genomics


title: TU, warfarin, 300 uM, 3

description:
Library name: Cell_177
mRNA from single larvae


title: TU, warfarin, 300 uM, 1

description:
Library name: Cell_175
mRNA from single larvae


title: TU, warfarin, 150 uM, 7

description:
Library name: Cell_174
mRNA from single larvae


title: TU, warfarin, 150 uM, 6

description:
Library name: Cell_173
mRNA from single larvae


title: TU, warfarin, 150 uM, 3

description:
Library name: Cell_170
mRNA from single larvae


title: Visceral adipose tissue, Cow 1, Subclinical ketosis

description:
Library name: 2VAT
10X Genomics


title: TU, warfarin, 150 uM, 5

description:
Library name: Cell_172
mRNA from single larvae


title: TU, warfarin, 150 uM, 4

description:
Library name: Cell_171
mRNA from single larvae


title: TU, warfarin, 150 uM, 2

description:
Library name: Cell_169
mRNA from single larvae


title: Subcutaneous adipose tissue, Cow 3, Control

description:
Library name: 5SAT
10X Genomics


title: TU, warfarin, 150 uM, 1

description:
Library name: Cell_168
mRNA from single larvae


title: TU, warfarin, 0 uM, 7

description:
Library name: Cell_167
mRNA from single larvae


title: TU, warfarin, 0 uM, 6

description:
Library name: Cell_166
mRNA from single larvae


title: PDAC, Patient: 96_1287495-U-M

city: Magdeburg

first: Ulf

last: Kahlert

address: Leipziger Str. 44

department: Molekulare und Experimentelle Chirurgie

country: Germany

institute: Universitaetsklinikum Magdeburg

description: Library name: 96_1287495-U-M

library_source: other

data_processing:
The raw reads were converted from BCL to FASTQ format using bcl2fastq (v2.20.0.4.422), and were then filtered using FastQ Screen to remove potential contamination by microorganisms or artefacts resulting from technical issues. The processed reads were then mapped, annotated (using miRBase version 22.0) and quantified using mirPRo.
Assembly: miRBase version 22.0
Supplementary files format and content: Excel file includes raw miRNA counts for each Sample

molecule: other

source_name: plasma

extract_protocol:
Total RNA was extracted from plasma samples using exoRNeasy Serum/Plasma Midi kit (Qiagen).
Small RNA libraries were prepared using the SMARTer smRNA-Seq Kit for Illumina (Takara Bio), following the manufacturer’s protocol. The libraries were sequenced on an Illumina NextSeq500 platform, generating single-end reads of 76 bp.

value: plasma


title: PDAC, Patient: 98_107799-F-B

description: Library name: 98_107799-F-B


title: PDAC, Patient: 97A_849688-P-B

description: Library name: 97A_849688-P-B


title: TU, warfarin, 0 uM, 4

description:
Library name: Cell_164
mRNA from single larvae


title: PDAC, Patient: 95_801159-K-L

description: Library name: 95_801159-K-L


title: TU, warfarin, 0 uM, 5

description:
Library name: Cell_165
mRNA from single larvae


title: SU-DHL-5_cells_Anti-FCRL2_24h_rep2

type: RNA

city: Ibaraki

first: Satoshi

last: Nagata

state: Osaka

institute: Epitope Science Co. Ltd.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in genome studio (V2010.2).

label: biotin

source_name: SU-DHL-5 cells_treated with anti-FCRL2 MAbs_24h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HS-Sultan, RPMI8226 or SU-DHL-5 cell lines (10^6 cells/ 5 ml in a T25 flask) were cultured in 10% FBS IMDM medium in a CO2 incubator (5% CO2). After 16 hr, the cells were added with 100 µl of PBS containing both of anti-FCRL2 B24 and B62 MAbs (final 10 µg/ml of each MAb). After subsequent 24 hr-culture, cell pellets were harvested, flash frozen, and stored at -80C until RNA extraction.

extract_protocol: RNA was extracted with TRI reagent (MRC Inc.) according to the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

value: Diffuse large B-cell lymphoma (DLBCL) cell line

tag: treated with

value: anti-FCRL2 Mabs for 24hr


title: SU-DHL-5_cells_Anti-FCRL2_24h_rep1


title: RPMI8226_cells_Anti-FCRL2_24h_rep2

source_name: RPMI8226 cells_treated with anti-FCRL2 MAbs_24h

value: myeloma (MM) cell line


title: TU, warfarin, 0 uM, 3

description:
Library name: Cell_163
mRNA from single larvae


title: RPMI8226_cells_Anti-FCRL2_24h_rep1


title: PDAC, Patient: 99_1205421-L-S

description: Library name: 99_1205421-L-S


title: RPMI8226_cells_untreated_24h_rep2

source_name: RPMI8226 cells_untreated_24h

value: none for 24hrs (untreated control)


title: TU, warfarin, 0 uM, 2

description:
Library name: Cell_162
mRNA from single larvae


title: TU, warfarin, 0 uM, 1

description:
Library name: Cell_161
mRNA from single larvae


title: PDAC, Patient: 93_1179253-B-B

description: Library name: 93_1179253-B-B


title: AB, warfarin, 300 uM, 7

description:
Library name: Cell_160
mRNA from single larvae

value: AB


title: SU-DHL-5_cells_untreated_24h_rep1

source_name: SU-DHL-5 cells_untreated_24h


title: RPMI8226_cells_untreated_24h_rep1


title: SU-DHL-5_cells_untreated_24h_rep2


title: AB, hydroxyurea, 33 mM, 7

description:
Library name: Cell_159
mRNA from single larvae

value: hydroxyurea


title: PDAC, Patient: 92_836883-H-M

description: Library name: 92_836883-H-M


title: AB, hydroxyurea, 33 mM, 5

description:
Library name: Cell_157
mRNA from single larvae


title: PDAC, Patient: 94_601381-U-I

description: Library name: 94_601381-U-I


title: AB, hydroxyurea, 33 mM, 4

description:
Library name: Cell_156
mRNA from single larvae


title: AB, hydroxyurea, 33 mM, 3

description:
Library name: Cell_155
mRNA from single larvae


title: HS-Sultan_cells_Anti-FCRL2_24h_rep1

source_name: HS-Sultan cells_treated with anti-FCRL2 MAbs_24h

value: HS-Sultan

value: Burkitt's lymphoma cell line


title: HS-Sultan_cells_Anti-FCRL2_24h_rep2


title: AB, hydroxyurea, 33 mM, 1

description:
Library name: Cell_153
mRNA from single larvae


title: AB, hydroxyurea, 33 mM, 2

description:
Library name: Cell_154
mRNA from single larvae


title: PDAC, Patient: 90_1191376-M-G

description: Library name: 90_1191376-M-G


title: AB, hydroxyurea, 6.6 mM, 4

description:
Library name: Cell_149
mRNA from single larvae


title: PDAC, Patient: 88_582169-C-P

description: Library name: 88_582169-C-P


title: L540_cells_PW30_24h_rep2

description: HL cell line

data_processing: The data were normalized using quantile normalization in genome studio

source_name: CD30+ L540 cells, treated with anti-CD30 PW30 mouse/human chimeric MAb, 24h, rep2

growth_protocol: L540 cell line (10^6 cells/ 5 ml in a T25 flask) was cultured in 10% FBS IMDM medium in a CO2 incubator (5% CO2). After 16 hr, the cells were added with 100 µl of PBS containing CD153(CD30L)-Fc fusion protein and/or indicated anti-CD30 MAb (final 10 µg/ml of each protein). After subsequent 24 hr-culture, cell pellets were harvested, flash frozen, and stored at -80 ºC until RNA extraction.

value: Hodgkin's lymphoma


title: PDAC, Patient: 91_852082-W-H

description: Library name: 91_852082-W-H


title: AB, hydroxyurea, 6.6 mM, 3

description:
Library name: Cell_148
mRNA from single larvae


title: AB, hydroxyurea, 33 mM, 6

description:
Library name: Cell_158
mRNA from single larvae


title: PDAC, Patient: 87_1169830-L-B

description: Library name: 87_1169830-L-B


title: PDAC, Patient: 89_799595-Q-L

description: Library name: 89_799595-Q-L


title: PDAC, Patient: 8A_1124865-B-C

description: Library name: 8A_1124865-B-C


title: AB, hydroxyurea, 1.3 mM, 7

description:
Library name: Cell_145
mRNA from single larvae


title: AB, hydroxyurea, 6.6 mM, 7

description:
Library name: Cell_152
mRNA from single larvae


title: AB, hydroxyurea, 6.6 mM, 6

description:
Library name: Cell_151
mRNA from single larvae


title: AB, hydroxyurea, 1.3 mM, 5

description:
Library name: Cell_143
mRNA from single larvae


title: L540_cells_T408_24h_rep2

description: HL cell line

source_name: CD30+ L540 cells, treated with anti-CD30 T408 MAb, 24h, rep2

value: treated with anti-CD30 T408 MAb


title: L540_cells_T427_24h_rep2

description: HL cell line

source_name: CD30+ L540 cells, treated with anti-CD30 T427 MAb, 24h, rep2

value: treated with anti-CD30 T427 MAb


title: IPMN, Patient: 85_820826-W-M

description: Library name: 85_820826-W-M


title: L540_cells_T408_24h_rep1

description: HL cell line

source_name: CD30+ L540 cells, treated with anti-CD30 T408 MAb, 24h, rep1


title: AB, hydroxyurea, 6.6 mM, 2

description:
Library name: Cell_147
mRNA from single larvae


title: AB, hydroxyurea, 6.6 mM, 1

description:
Library name: Cell_146
mRNA from single larvae


title: L540_cells_T104_24h_rep2

description: HL cell line

source_name: CD30+ L540 cells, treated with anti-CD30 T104 MAb, 24h, rep2

value: treated with anti-CD30 T104 MAb


title: IPMN, Patient: 83_1117384-W-D

description: Library name: 83_1117384-W-D


title: IPMN, Patient: 86_1170597-H-S

description: Library name: 86_1170597-H-S


title: L540_cells_T427_24h_rep1

description: HL cell line

source_name: CD30+ L540 cells, treated with anti-CD30 T427 MAb, 24h, rep1


title: IPMN, Patient: 82_370751-R-H

description: Library name: 82_370751-R-H


title: AB, hydroxyurea, 1.3 mM, 6

description:
Library name: Cell_144
mRNA from single larvae

source_name: whole-mount

value: whole-mount


title: AB, hydroxyurea, 0 mM, 6

description:
Library name: Cell_137
mRNA from single larvae


title: AB, hydroxyurea, 1.3 mM, 2

description:
Library name: Cell_140
mRNA from single larvae


title: AB, hydroxyurea, 1.3 mM, 1

description:
Library name: Cell_139
mRNA from single larvae


title: AB, hydroxyurea, 1.3 mM, 4

description:
Library name: Cell_142
mRNA from single larvae


title: L540_cells_T104_24h_rep1

description: HL cell line

source_name: CD30+ L540 cells, treated with anti-CD30 T104 MAb, 24h, rep1


title: AB, hydroxyurea, 1.3 mM, 3

description:
Library name: Cell_141
mRNA from single larvae


title: AB, hydroxyurea, 0 mM, 4

description:
Library name: Cell_135
mRNA from single larvae


title: HS-Sultan_cells_untreated_24h_rep2

source_name: HS-Sultan cells_untreated_24h


title: L540_cells_CD153_24h_rep2

description: HL cell line

source_name: CD30+ L540 cells, treated with CD30L(CD153)-Fc, 24h, rep2

value: treated with CD30L(CD153)-Fc


title: AB, hydroxyurea, 0 mM, 7

description:
Library name: Cell_138
mRNA from single larvae


title: AB, hydroxyurea, 0 mM, 2

description:
Library name: Cell_133
mRNA from single larvae


title: AB, hydroxyurea, 0 mM, 1

description:
Library name: Cell_132
mRNA from single larvae


title: PET, hydroxyurea, 33 mM, 5

description:
Library name: Cell_131
mRNA from single larvae

value: PET


title: AB, hydroxyurea, 6.6 mM, 5

description:
Library name: Cell_150
mRNA from single larvae


title: AB, hydroxyurea, 0 mM, 5

description:
Library name: Cell_136
mRNA from single larvae


title: IPMN, Patient: 81_1069680-K-M

description: Library name: 81_1069680-K-M


title: PET, hydroxyurea, 33 mM, 2

description:
Library name: Cell_128
mRNA from single larvae


title: AB, hydroxyurea, 0 mM, 3

description:
Library name: Cell_134
mRNA from single larvae


title: PET, hydroxyurea, 33 mM, 3

description:
Library name: Cell_129
mRNA from single larvae


title: IPMN, Patient: 77_775574-W-J

description: Library name: 77_775574-W-J


title: L540_cells_CD153_24h_rep1

description: HL cell line

source_name: CD30+ L540 cells, treated with CD30L(CD153)-Fc, 24h, rep1


title: IPMN, Patient: 79_819237-H-R

description: Library name: 79_819237-H-R

source_name: plasma


title: PET, hydroxyurea, 6.6 mM, 7

description:
Library name: Cell_126
mRNA from single larvae


title: chronic pancreatitis, Patient: 76_582454-F-R

description: Library name: 76_582454-F-R


title: IPMN, Patient: 78_874173-R-M

description: Library name: 78_874173-R-M


title: PET, hydroxyurea, 6.6 mM, 6

description:
Library name: Cell_125
mRNA from single larvae


title: L540_cells_untreated_24h_rep2

description: HL cell line

source_name: CD30+ L540 cells, untreated, 24h, rep2

value: untreated


title: PET, hydroxyurea, 33 mM, 1

description:
Library name: Cell_127
mRNA from single larvae


title: PET, hydroxyurea, 6.6 mM, 4

description:
Library name: Cell_123
mRNA from single larvae


title: Karpas299_cells_CD153_P_T104_P_8h_rep2

description:
ALCL cell line
Sample8

data_processing: The data were normalized using quantile normalization in Genome studio

source_name: CD30+ Karpas299 cells, treated with CD30L(CD153)-Fc plus anti-CD30 T104 MAb, 8h, rep2

growth_protocol: Karpas 299 cell line (10^6 cells/ 5 ml in a T25 flask) was cultured in 10% FBS IMDM medium in a CO2 incubator (5% CO2). After 16 hr, the cells were added with 100 µl of PBS containing CD153(CD30L)-Fc fusion protein and/or anti-CD30 agonostic T104 MAb (final 10 µg/ml of each protein). After subsequent 8 hr-culture, cell pellets were harvested, flash frozen, and stored at -80 ºC until RNA extraction.

value: Karpas 299

value: Anaplastic Large Cell Lymphoma


title: Karpas299_cells_CD153_N_T104_P_8h_rep2

description:
ALCL cell line
Sample6

source_name: CD30+ Karpas299 cells, treated with anti-CD30 T104 MAb, 8h, rep2


title: Karpas299_cells_CD153_N_T104_P_8h_rep1

description:
ALCL cell line
Sample5

source_name: CD30+ Karpas299 cells, treated with anti-CD30 T104 MAb, 8h, rep1


title: IPMN, Patient: 80_1065347-S-H

description: Library name: 80_1065347-S-H

value: plasma


title: Karpas299_cells_CD153_P_T104_P_8h_rep1

description:
ALCL cell line
Sample7

source_name: CD30+ Karpas299 cells, treated with CD30L(CD153)-Fc plus anti-CD30 T104 MAb, 8h, rep1


title: chronic pancreatitis, Patient: 72_414328-B-H

description: Library name: 72_414328-B-H


title: PET, hydroxyurea, 6.6 mM, 1

description:
Library name: Cell_120
mRNA from single larvae


title: PET, hydroxyurea, 6.6 mM, 5

description:
Library name: Cell_124
mRNA from single larvae


title: L540_cells_untreated_24h_rep1

description: HL cell line

source_name: CD30+ L540 cells, untreated, 24h, rep1


title: PET, hydroxyurea, 1.3 mM, 7

description:
Library name: Cell_119
mRNA from single larvae


title: PET, hydroxyurea, 33 mM, 4

description:
Library name: Cell_130
mRNA from single larvae


title: Karpas299_cells_CD153_P_T104_N_8h_rep2

description:
ALCL cell line
Sample4

source_name: CD30+ Karpas299 cells, treated with CD30L(CD153)-Fc, 8h, rep2


title: PET, hydroxyurea, 6.6 mM, 3

description:
Library name: Cell_122
mRNA from single larvae


title: chronic pancreatitis, Patient: 73_420668-M-E

description: Library name: 73_420668-M-E


title: PET, hydroxyurea, 1.3 mM, 6

description:
Library name: Cell_118
mRNA from single larvae


title: chronic pancreatitis, Patient: 70_326163-W-K

description: Library name: 70_326163-W-K


title: Karpas299_cells_CD153_N_T104_N_8h_rep1

description:
ALCL cell line
Sample1

source_name: CD30+ Karpas299 cells, untreated, rep1


title: PET, hydroxyurea, 1.3 mM, 2

description:
Library name: Cell_114
mRNA from single larvae


title: PDAC, Patient: 6B_125779-S-S

description: Library name: 6B_125779-S-S


title: Karpas299_cells_CD153_N_T104_N_8h_rep2

description:
ALCL cell line
Sample2

source_name: CD30+ Karpas299 cells, untreated, rep2


title: PET, hydroxyurea, 1.3 mM, 5

description:
Library name: Cell_117
mRNA from single larvae


title: chronic pancreatitis, Patient: 71_409727-R-F

description: Library name: 71_409727-R-F


title: PET, hydroxyurea, 1.3 mM, 4

description:
Library name: Cell_116
mRNA from single larvae


title: chronic pancreatitis, Patient: 74_423374-B-C

description: Library name: 74_423374-B-C


title: Karpas299_cells_CD153_P_T104_N_8h_rep1

description:
ALCL cell line
Sample3

source_name: CD30+ Karpas299 cells, treated with CD30L(CD153)-Fc, 8h, rep1


title: PET, hydroxyurea, 0 mM, 7

description:
Library name: Cell_112
mRNA from single larvae


title: PET, hydroxyurea, 1.3 mM, 1

description:
Library name: Cell_113
mRNA from single larvae


title: PDAC, Patient: 66_717118-M-W

description: Library name: 66_717118-M-W


title: PET, hydroxyurea, 0 mM, 6

description:
Library name: Cell_111
mRNA from single larvae


title: PET, hydroxyurea, 0 mM, 4

description:
Library name: Cell_109
mRNA from single larvae


title: chronic pancreatitis, Patient: 68_352519-D-K

description: Library name: 68_352519-D-K


title: PET, hydroxyurea, 6.6 mM, 2

description:
Library name: Cell_121
mRNA from single larvae


title: Ramos_cells_IgM_P_CD40_N_FCRL1_P_8h_rep2

description:
B cell line
Sample12

source_name: Ramos cells, treated with anti-IgM pAb anti-FCRL1 (clone E3) mAb, 8h, rep2

growth_protocol: Ramos cell line (10^6 cells/ 5 ml in a T25 flask) was cultured in 10% FBS IMDM medium in a CO2 incubator (5% CO2). After 16 hr, the cells were added with 100 µl of PBS containing goat anti-human IgM (Fab)2 polyclonal antibody (Jackson, final 10 ug/ml) and/or anti-CD40 agonostic G28-5 mAb (final 1 ug/ml) or anti-FCRL1 E3 mAb (final 10 µg/ml). After subsequent 8 hr-culture, cell pellets were harvested, flash frozen, and stored at -80 ºC until RNA extraction.

value: Ramos, B cell line

value: EBV negative


title: PET, hydroxyurea, 0 mM, 3

description:
Library name: Cell_108
mRNA from single larvae

source_name: whole-mount


title: chronic pancreatitis, Patient: 69_358213-B-J

description: Library name: 69_358213-B-J


title: Ramos_cells_IgM_P_CD40_N_FCRL1_P_8h_rep1

description:
B cell line
Sample11

source_name: Ramos cells, treated with anti-IgM pAb anti-FCRL1 (clone E3) mAb, 8h, rep1


title: Ramos_cells_IgM_P_CD40_P_FCRL1_N_8h_rep2

description:
B cell line
Sample10

source_name: Ramos cells, treated with anti-IgM pAb plus anti-CD40 (clone G28-5) mAb, 8h, rep2


title: PET, hydroxyurea, 0 mM, 2

description:
Library name: Cell_107
mRNA from single larvae


title: Ramos_cells_IgM_P_CD40_P_FCRL1_N_8h_rep1

description:
B cell line
Sample9

source_name: Ramos cells, treated with anti-IgM pAb plus anti-CD40 (clone G28-5) mAb, 8h, rep1


title: AB, warfarin, 300 uM, 6

description:
Library name: Cell_105
mRNA from single larvae

value: AB

value: warfarin


title: PET, hydroxyurea, 1.3 mM, 3

description:
Library name: Cell_115
mRNA from single larvae

value: hydroxyurea


title: PET, hydroxyurea, 0 mM, 5

description:
Library name: Cell_110
mRNA from single larvae


title: PDAC, Patient: 62_1083287-P-G

description: Library name: 62_1083287-P-G


title: AB, warfarin, 300 uM, 5

description:
Library name: Cell_104
mRNA from single larvae


title: AB, warfarin, 300 uM, 4

description:
Library name: Cell_103
mRNA from single larvae


title: AB, warfarin, 300 uM, 3

description:
Library name: Cell_102
mRNA from single larvae


title: Ramos_cells_IgM_P_CD40_N_FCRL1_N_8h_rep1

description:
B cell line
Sample7

source_name: Ramos cells, treated with anti-IgM pAb, 8h, rep1


title: AB, warfarin, 300 uM, 2

description:
Library name: Cell_101
mRNA from single larvae


title: Ramos_cells_IgM_P_CD40_N_FCRL1_N_8h_rep2

description:
B cell line
Sample8

source_name: Ramos cells, treated with anti-IgM pAb, 8h, rep2


title: PDAC, Patient: 61_601722-S-H

description: Library name: 61_601722-S-H

source_name: plasma


title: AB, warfarin, 150 uM, 7

description:
Library name: Cell_99
mRNA from single larvae


title: AB, warfarin, 300 uM, 1

description:
Library name: Cell_100
mRNA from single larvae


title: PDAC, Patient: 65_1053529-W-M

description: Library name: 65_1053529-W-M


title: PDAC, Patient: 60_1082539-W-H

description: Library name: 60_1082539-W-H


title: AB, warfarin, 150 uM, 4

description:
Library name: Cell_96
mRNA from single larvae


title: AB, warfarin, 150 uM, 6

description:
Library name: Cell_98
mRNA from single larvae


title: PDAC, Patient: 59_794594-W-J

description: Library name: 59_794594-W-J


title: PET, hydroxyurea, 0 mM, 1

description:
Library name: Cell_106
mRNA from single larvae


title: Sample77

city: Ultimo

first: Alen

last: Faiz

state: NSW x

address: Thomas St,

country: Australia

institute: University of Technology Sydney

data_processing:
Trimmed fastQ files where aligned to build b37 of the human reference genome using HISAT (version 0.1.5) and gene level quantification was performed by HTSeq (version 0.6.1p1) using Ensembl version 75 as gene annotation database.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including CPM normalised counts for each sample

source_name: Bronchial biopsy

extract_protocol:
Bronchial biopsies were taken from segmental divisions of the main bronchi and immediately frozen in Tissue-Tek (VWR, Radnor, PA) at -80°C. After thawing at room temperature, biopsies were cut from the blocks when they were semi-solid. Samples were lysed in 600 μl RLT-plus using a IKA Ultra Turrax T10 Homogenizer. Total genomic DNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit, according to the manufacturer’s instructions (Qiagen, Venlo, the Netherlands). DNA samples were dissolved in 30 μl elution buffer. Concentrations of DNA were measured in 1 μl of fluid using a Nanodrop-1000 and in 2 μl of fluid run on a Labchip GX (Perkin Elmer, Waltham, MA).
RNA samples from airway wall biopsies were processed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). The cDNA fragment libraries were loaded unto an Illumina HiSeq2500 sequencer for paired-end sequencing (2×100 bp).

value: Bronchial biopsy

value: tissue

tag: smoking status

value: smoker

tag: Sex

value: male


title: PDAC, Patient: 56_738667-H-I

description: Library name: 56_738667-H-I


title: AB, warfarin, 150 uM, 3

description:
Library name: Cell_95
mRNA from single larvae


title: Sample76

value: female


title: AB, warfarin, 150 uM, 1

description:
Library name: Cell_93
mRNA from single larvae

value: whole-mount


title: Ramos_cells_IgM_N_CD40_N_FCRL1_P_8h_rep2

description:
B cell line
Sample6

source_name: Ramos cells, treated with anti-FCRL1 (clone E3) mAb, 8h, rep2


title: Ramos_cells_IgM_N_CD40_P_FCRL1_N_8h_rep1

description:
B cell line
Sample3

source_name: Ramos cells, treated with anti-CD40 (clone G28-5) mAb, 8h, rep1


title: Ramos_cells_IgM_N_CD40_N_FCRL1_P_8h_rep1

description:
B cell line
Sample5

source_name: Ramos cells, treated with anti-FCRL1 (clone E3) mAb, 8h, rep1


title: AB, warfarin, 150 uM, 2

description:
Library name: Cell_94
mRNA from single larvae


title: PDAC, Patient: 55_381805-H-H

description: Library name: 55_381805-H-H


title: Ramos_cells_IgM_N_CD40_P_FCRL1_N_8h_rep2

description:
B cell line
Sample4

source_name: Ramos cells, treated with anti-CD40 (clone G28-5) mAb, 8h, rep2


title: L540_cells_PW30_24h_rep1

description: HL cell line

source_name: CD30+ L540 cells, treated with anti-CD30 PW30 mouse/human chimeric MAb, 24h, rep1

value: Hodgkin's lymphoma


title: Ramos_cells_IgM_N_CD40_N_FCRL1_N_8h_rep2

description:
B cell line
Sample2

source_name: Ramos cells, untreated, rep2


title: Ramos_cells_IgM_N_CD40_N_FCRL1_N_8h_rep1

description:
B cell line
Sample1

source_name: Ramos cells, untreated, rep1


title: AB, warfarin, 0 uM, 6

description:
Library name: Cell_91
mRNA from single larvae


title: Sample75


title: PDAC, Patient: 54_269480-D-I

description: Library name: 54_269480-D-I


title: Sample74

value: nonsmoker


title: PDAC, Patient: 53_428465-P-M

description: Library name: 53_428465-P-M


title: AB, warfarin, 0 uM, 5

description:
Library name: Cell_90
mRNA from single larvae


title: Sample73


title: AB, warfarin, 0 uM, 4

description:
Library name: Cell_89
mRNA from single larvae


title: PDAC, Patient: 52_1059743-D-U

description: Library name: 52_1059743-D-U


title: AB, warfarin, 0 uM, 2

description:
Library name: Cell_87
mRNA from single larvae


title: AB, warfarin, 0 uM, 7

description:
Library name: Cell_92
mRNA from single larvae


title: AB, warfarin, 150 uM, 5

description:
Library name: Cell_97
mRNA from single larvae


title: AB, warfarin, 0 uM, 1

description:
Library name: Cell_86
mRNA from single larvae


title: RW, warfarin, 300 uM, 5

description:
Library name: Cell_85
mRNA from single larvae

value: RW


title: Sample72


title: RW, warfarin, 300 uM, 4

description:
Library name: Cell_84
mRNA from single larvae


title: PDAC, Patient: 51_599428-F-C

description: Library name: 51_599428-F-C


title: Sample70


title: HS-Sultan_cells_untreated_24h_rep1

source_name: HS-Sultan cells_untreated_24h

value: HS-Sultan

value: Burkitt's lymphoma cell line

value: none for 24hrs (untreated control)


title: Sample69


title: PDAC, Patient: 49_452396-W-H

description: Library name: 49_452396-W-H

value: plasma


title: RW, warfarin, 300 uM, 1

description:
Library name: Cell_81
mRNA from single larvae


title: PDAC, Patient: 50_675444-G-W

description: Library name: 50_675444-G-W


title: RW, warfarin, 300 uM, 2

description:
Library name: Cell_82
mRNA from single larvae


title: RW, warfarin, 150 uM, 5

description:
Library name: Cell_80
mRNA from single larvae


title: RW, warfarin, 300 uM, 3

description:
Library name: Cell_83
mRNA from single larvae


title: Sample68


title: RW, warfarin, 150 uM, 2

description:
Library name: Cell_77
mRNA from single larvae


title: AB, warfarin, 0 uM, 3

description:
Library name: Cell_88
mRNA from single larvae


title: PDAC, Patient: 48_631346-M-R

description: Library name: 48_631346-M-R


title: PDAC, Patient: 47_1234814-N-M

description: Library name: 47_1234814-N-M


title: RW, warfarin, 150 uM, 3

description:
Library name: Cell_78
mRNA from single larvae


title: RW, warfarin, 150 uM, 4

description:
Library name: Cell_79
mRNA from single larvae


title: RW, warfarin, 150 uM, 1

description:
Library name: Cell_76
mRNA from single larvae


title: Sample66


title: Sample67


title: RW, warfarin, 0 uM, 4

description:
Library name: Cell_74
mRNA from single larvae


title: PDAC, Patient: 45_1128045-E-C

description: Library name: 45_1128045-E-C


title: RW, warfarin, 0 uM, 3

description:
Library name: Cell_73
mRNA from single larvae


title: RW, warfarin, 0 uM, 5

description:
Library name: Cell_75
mRNA from single larvae


title: RW, warfarin, 0 uM, 2

description:
Library name: Cell_72
mRNA from single larvae


title: Sample71


title: RW, warfarin, 0 uM, 1

description:
Library name: Cell_71
mRNA from single larvae


title: PDAC, Patient: 43_477816-J-M

description: Library name: 43_477816-J-M


title: Sample64


title: PET, warfarin, 300 uM, 7

description:
Library name: Cell_70
mRNA from single larvae

value: PET


title: Sample63


title: PET, warfarin, 300 uM, 6

description:
Library name: Cell_69
mRNA from single larvae


title: PET, warfarin, 300 uM, 5

description:
Library name: Cell_68
mRNA from single larvae


title: PDAC, Patient: 41_713180-W-A

description: Library name: 41_713180-W-A


title: PDAC, Patient: 42_646707-G-R

description: Library name: 42_646707-G-R


title: PET, warfarin, 300 uM, 4

description:
Library name: Cell_67
mRNA from single larvae


title: PET, warfarin, 300 uM, 3

description:
Library name: Cell_66
mRNA from single larvae


title: Sample62


title: Sample61


title: PET, warfarin, 300 uM, 2

description:
Library name: Cell_65
mRNA from single larvae


title: PDAC, Patient: 40A_1215747-H-H

description: Library name: 40A_1215747-H-H


title: RNA-seq of  CM-specific Asna1 KO mice  E14.5  heart replicate 4

city: San Diego

first: Zengming

last: Zhang

address: 9500 Gilman Drive, La Jolla

institute: UCSD

description:
Library name: Asna1_CKO_rep4
conditional KO

data_processing:
Raw RNA-seq reads were assessed for quality using FastQC.
Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.7).
Clean reads were aligned to the mouse reference genome (mm10, Mus musculus) using HISAT2 (v2.2.1) with default parameters.
Gene expression quantification was performed using StringTie (v2.2.1).
Gene counts were obtained with featureCounts and used for differential expression analysis with DESeq2. Differentially expressed genes (DEGs) were identified using the criteria: |Fold change| ≥ 1.2 and q < 0.05.
Assembly: mm10 (Mus musculus)
Supplementary files format and content: Gene-level expression matrix in CSV format. File name: ASNA1_merged_TPM.csv. Rows represent gene IDs, columns represent individual samples. Values are TPM (Transcripts Per Million) calculated using StringTie against the mm10 Mus musculus genome assembly.

organism: Mus musculus

source_name: E14.5 heart ventricular

growth_protocol: All mice were housed in a pathogen-free facility under standard laboratory conditions with a 12-hour light/dark cycle. Mice were maintained on a standard rodent chow diet with water provided ad libitum. Timed matings were set up, and noon on the day of vaginal plug detection was considered embryonic day 0.5 (E0.5). Pregnant dams were euthanized at E14.5 to collect embryonic heart tissues.

extract_protocol:
Total RNA was extracted from cultured primary cortical neurons using the Quick-RNA Miniprep Kit (Zymo Research; Cat# R1054) following the manufacturer's instructions. RNA concentration and purity were assessed using a Nanodrop spectrophotometer. For downstream applications, equal amounts of RNA were used for either RNA-seq library preparation or reverse transcription into cDNA using the High-Capacity cDNA Reverse Transcription Kit (Invitrogen™). Gene expression validation was performed by quantitative PCR (qPCR) using the Applied Biosystems 7300 Real-Time PCR System, and analyzed with the ΔΔCt method.
RNA-seq libraries were constructed following ribosomal RNA (rRNA) depletion protocols to enrich for non-rRNA transcripts. Total RNA was subjected to rRNA depletion using a commercial RNA depletion kit according to the manufacturer’s instructions. Libraries were then generated from the rRNA-depleted RNA and sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

treatment_protocol: No chemical or pharmacological treatments were applied in this study. All embryos were harvested under baseline physiological conditions without experimental perturbation.

value: E14.5 heart ventricular

value: CM-specific Asna1 KO

tag: batch


title: PET, warfarin, 300 uM, 1

description:
Library name: Cell_64
mRNA from single larvae

source_name: whole-mount

value: warfarin


title: Sample65

value: Bronchial biopsy


title: RNA-seq of  CM-specific Asna1 KO mice  E14.5  heart replicate 3

description:
Library name: Asna1_CKO_rep3
conditional KO


title: Sample60

value: tissue


title: PDAC, Patient: 64_785889-A-M

description: Library name: 64_785889-A-M


title: PDAC, Patient: 38_677989-W-G

description: Library name: 38_677989-W-G


title: PDAC, Patient: 37_267605-T-A

description: Library name: 37_267605-T-A


title: RNA-seq of  CM-specific Asna1 KO mice  E14.5  heart replicate 2

description:
Library name: Asna1_CKO_rep2
conditional KO


title: Sample59


title: PET, warfarin, 150 uM, 7

description:
Library name: Cell_63
mRNA from single larvae


title: PET, warfarin, 150 uM, 6

description:
Library name: Cell_62
mRNA from single larvae


title: Sample58


title: PET, warfarin, 150 uM, 5

description:
Library name: Cell_61
mRNA from single larvae


title: PDAC, Patient: 36_696332-P-A

description: Library name: 36_696332-P-A


title: RNA-seq of  CM-specific Asna1 KO mice  E14.5  heart replicate 1

description:
Library name: Asna1_CKO_rep1
conditional KO


title: Sample57


title: PDAC, Patient: 46_118887-G-S

description: Library name: 46_118887-G-S


title: PDAC, Patient: 35_262879-K-H

description: Library name: 35_262879-K-H


title: RNA-seq of  Control mice  E14.5  heart replicate 3

description:
Library name: Asna1_WT_rep3
control

value: Control


title: PDAC, Patient: 34_676718-L-K

description: Library name: 34_676718-L-K


title: RNA-seq of  Control mice  E14.5  heart replicate 4

description:
Library name: Asna1_WT_rep4
control


title: Sample56


title: PET, warfarin, 150 uM, 4

description:
Library name: Cell_60
mRNA from single larvae


title: PET, warfarin, 150 uM, 3

description:
Library name: Cell_59
mRNA from single larvae


title: PDAC, Patient: 30_683599-B-G

description: Library name: 30_683599-B-G


title: PET, warfarin, 150 uM, 2

description:
Library name: Cell_58
mRNA from single larvae


title: Sample55

value: male


title: RNA-seq of  Control mice  E14.5  heart replicate 2

description:
Library name: Asna1_WT_rep2
control


title: RNA-seq of  Control mice  E14.5  heart replicate 1

description:
Library name: Asna1_WT_rep1
control


title: Sample54

value: female


title: PDAC, Patient: 28_545998-T-M

description: Library name: 28_545998-T-M


title: TV Ibu (+)

city: Seoul

first: Jeong-Hwan

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Veterinary Medicine

country: South Korea

institute: Konkuk University

description: Library name: Sample 7

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0 (KIM et al, 2015)
Assembly: mm10
Supplementary files format and content: The Excel file contains Read Count, FPKM and TPM data for each sample.

source_name: Peripheral Blood Mononuclear Cell

extract_protocol:
Total RNA from mouse PBMCs was purified using RNeasy mini kit according to the manufacturer’s instructions (74104, Qiagen, USA).
A library was independently prepared with 1μg of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (20020595, Illumina, Inc., San Diego, CA, USA).

value: Peripheral Blood Mononuclear Cell

tag: group

value: TV

value: Ibu (+)


title: PET, warfarin, 150 uM, 1

description:
Library name: Cell_57
mRNA from single larvae

value: whole-mount


title: Sample52

value: nonsmoker


title: PDAC, Patient: 29_1273953-K-G

description: Library name: 29_1273953-K-G


title: RP Ibu (+)

description: Library name: Sample 5

value: RP


title: PET, warfarin, 0 uM, 6

description:
Library name: Cell_56
mRNA from single larvae


title: PDAC, Patient: 26_463977-F-M

description: Library name: 26_463977-F-M


title: TV Ibu (-)

description: Library name: Sample 6

value: Ibu (-)


title: PET, warfarin, 0 uM, 5

description:
Library name: Cell_55
mRNA from single larvae


title: PDAC, Patient: 27_778240-R-W

description: Library name: 27_778240-R-W

value: plasma


title: PDAC, Patient: 25_182326-P-W

description: Library name: 25_182326-P-W


title: PET, warfarin, 0 uM, 4

description:
Library name: Cell_54
mRNA from single larvae

value: PET


title: PET, warfarin, 0 uM, 3

description:
Library name: Cell_53
mRNA from single larvae


title: RP Ibu (-)

description: Library name: Sample 4


title: PDAC, Patient: 24_590781-S-P

description: Library name: 24_590781-S-P


title: Sample49


title: PET, warfarin, 0 uM, 2

description:
Library name: Cell_52
mRNA from single larvae


title: FV Ibu (+)

description: Library name: Sample 3

value: FV


title: PDAC, Patient: 14A_494302-K-R

description: Library name: 14A_494302-K-R


title: FV Ibu (-)

description: Library name: Sample 2


title: Sample48

value: smoker


title: Sample53


title: PET, warfarin, 0 uM, 1

description:
Library name: Cell_51
mRNA from single larvae

value: warfarin


title: PDAC, Patient: 13A_531564-K-D

description: Library name: 13A_531564-K-D


title: Non

description: Library name: Sample 1

value: Non


title: Sample47

value: Bronchial biopsy

value: tissue


title: Sample51

value: male


title: TU, hydroxyurea, 33 mM, 7

description:
Library name: Cell_50
mRNA from single larvae

value: TU

value: hydroxyurea


title: TU, hydroxyurea, 33 mM, 6

description:
Library name: Cell_49
mRNA from single larvae


title: IPMN, Patient: 114_1199351-S-R

description: Library name: 114_1199351-S-R


title: Sample45


title: Sample50

value: female


title: TU, hydroxyurea, 33 mM, 5

description:
Library name: Cell_48
mRNA from single larvae


title: chronic pancreatitis, Patient: 113_728178-L-T

description: Library name: 113_728178-L-T


title: TU, hydroxyurea, 33 mM, 4

description:
Library name: Cell_47
mRNA from single larvae


title: chronic pancreatitis, Patient: 112_487317-K-G

description: Library name: 112_487317-K-G


title: Sample43


title: PNS_P14_3

city: Rehovot

first: Alon

last: Chen

address: Herzl 234

country: Israel

institute: The Weizmann Institute of Sciencee

description: Library name: PNS_P14_3

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the mouse genome using STAR  v2.7.3a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count
Normalization was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: Excel files includes the normalized counts

molecule: polyA RNA

source_name: Mouse prefrontal cortex

extract_protocol:
RNAeasy micro kit (Qiagen) according to manufacturer’s protocol
Inhouse poly A based RNA seq

value: Mouse prefrontal cortex

value: ICR

tag: gender

tag: condition

value: Prenatally stress


title: PNS_P14_2

description: Library name: PNS_P14_2


title: Sample42

value: nonsmoker


title: PDAC, Patient: 111_1120124-J-E

description: Library name: 111_1120124-J-E


title: TU, hydroxyurea, 33 mM, 3

description:
Library name: Cell_46
mRNA from single larvae

value: whole-mount


title: Ctrl_P14_4

description: Library name: Ctrl_P14_4

value: control (unstressed)


title: Sample46


title: TU, hydroxyurea, 33 mM, 2

description:
Library name: Cell_45
mRNA from single larvae


title: PNS_P14_1

description: Library name: PNS_P14_1


title: Sample41


title: PDAC, Patient: 110_1243999-L-R

description: Library name: 110_1243999-L-R

value: plasma


title: Ctrl_P14_3

description: Library name: Ctrl_P14_3


title: PDAC, Patient: 12A_503378-K-E

description: Library name: 12A_503378-K-E


title: PNS_P14_4

description: Library name: PNS_P14_4


title: Sample40


title: TU, hydroxyurea, 33 mM, 1

description:
Library name: Cell_44
mRNA from single larvae


title: Ctrl_P14_2

description: Library name: Ctrl_P14_2


title: Sample39


title: TU, hydroxyurea, 6.6 mM, 6

description:
Library name: Cell_42
mRNA from single larvae


title: PDAC, Patient: 10A_178621-V-S

description: Library name: 10A_178621-V-S


title: TU, hydroxyurea, 6.6 mM, 7

description:
Library name: Cell_43
mRNA from single larvae


title: PDAC, Patient: 109_1262197-M-B

description: Library name: 109_1262197-M-B


title: Sample44


title: Ctrl_P14_1

description: Library name: Ctrl_P14_1


title: PNS_P1_4

description: Library name: PNS_P1_4


title: TU, hydroxyurea, 6.6 mM, 5

description:
Library name: Cell_41
mRNA from single larvae


title: PDAC, Patient: 108_1293913-R-C

description: Library name: 108_1293913-R-C


title: PDAC, Patient: 107_821683-S-A

description: Library name: 107_821683-S-A


title: Sample38


title: Sample37


title: PNS_P1_3

description: Library name: PNS_P1_3


title: Sample36


title: Sample35


title: TU, hydroxyurea, 6.6 mM, 3

description:
Library name: Cell_39
mRNA from single larvae


title: PDAC, Patient: 105_687567-E-W

description: Library name: 105_687567-E-W


title: PDAC, Patient: 106_484897-B-H

description: Library name: 106_484897-B-H


title: PNS_P1_1

description: Library name: PNS_P1_1


title: PNS_P1_2

description: Library name: PNS_P1_2


title: PDAC, Patient: 104A_839990-W-B

description: Library name: 104A_839990-W-B


title: TU, hydroxyurea, 6.6 mM, 2

description:
Library name: Cell_38
mRNA from single larvae


title: Ctrl_P1_4

description: Library name: Ctrl_P1_4


title: Sample34


title: TU, hydroxyurea, 6.6 mM, 1

description:
Library name: Cell_37
mRNA from single larvae


title: Sample33


title: PDAC, Patient: 101A_527418-J-G

description: Library name: 101A_527418-J-G


title: Ctrl_P1_2

description: Library name: Ctrl_P1_2


title: TU, hydroxyurea, 1.3 mM, 6

description:
Library name: Cell_36
mRNA from single larvae


title: Sample32


title: TU, hydroxyurea, 1.3 mM, 5

description:
Library name: Cell_35
mRNA from single larvae


title: PDAC, Patient: 100_631843-G-S

description: Library name: 100_631843-G-S


title: TU, hydroxyurea, 6.6 mM, 4

description:
Library name: Cell_40
mRNA from single larvae


title: TU, hydroxyurea, 1.3 mM, 3

description:
Library name: Cell_33
mRNA from single larvae


title: Sample31


title: Ctrl_P1_1

description: Library name: Ctrl_P1_1


title: Sample29


title: TU, hydroxyurea, 1.3 mM, 2

description:
Library name: Cell_32
mRNA from single larvae


title: Sample30


title: Skin, Y7, rep1

city: Chengdu City

first: Ting

last: Zheng

address: No.211, Huimin Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

data_processing:
Raw sequencing reads from DNBSEQ-T7 were filtered and demultiplexed using PISA (v0.2; https:// github.com/shiquan/PISA). Reads were aligned to the Macaca_fascicularis_ 5.0 genome using STAR (v2.7.4a) and sorted by sambamba (v0.7.0). Reads were aligned to the exons of mRNA as normal. Then, a cell versus gene UMI count matrix was generated with PISA.
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: Dorsal skin

extract_protocol:
The skin samples were fully dissected into small pieces in 4 mL tube and then transferred into 50 mL centrifuge tube with 15 mL mix digestion medium containing 1 mg/mL collagenase type I, II, IV, and V, 1 mg/mL elastase, and 2 U/mL DNase I in Dulbecco’s Modified Eagle Medium (DMED). The skin samples were digested at 37°C for 120–180 min and simultaneously gently shaken once every 10 min. The digestion reaction was interrupted by DMEM including 10% fetal bovine serum (FBS). Then, the tissue suspension was filtered with 70 μm and 40 μm cell strainer and transfected into a 15 ML centrifuge tube to obtain cell sediment by centrifugation at 350 × g for 5 min at 4°C until there was no undissociated tissue debris. The cell sediment was added to 2 mL Red Blood Cells Lysis Solution at room temperature for 5 min to remove red blood cells. The cell sediment was added to 2 mL TrypLE at 37°C for 45 min to dissolve cell clot. The dissociated cells were washed twice and resuspended in cold DMED supplemented with 10% FBS. Finally, cells staining with 0.4% Trypan Blue Solution was used to estimate cell activity rate and concentration by Countess Cell Counting Chamber Slides.
Approximately 20,000 cells were captured in droplet emulsions, and the mRNA of single-cell Libraries were constructed according to the DNBelab C Series Single-Cell Library Prep Set (MGI, Shenzhen, China). Briefly, single-cell suspensions were subjected to a series of progress, including droplet encapsulation, emulsion breakage, mRNA captured bead collection, reverse transcription, and cDNA amplification and purification, to generate barcoded libraries. Indexed sequencing libraries were established based on the instruction’s protocol.

value: Dorsal skin

value: Skin cells

tag: age

value: 7 years old


title: Skin, Y7, rep3


title: C32

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

institute: Adelaide University

description: Library name: C32

data_processing:
FASTQ files from cellular fractionation experiments were analysed at various stages for quality and content using FastQC v0.11.9
UMIs were extracted to the read header and adapter sequences removed simultaneously using UMI-tools v1.0.1, setting --extract-method=regex
Reads shorter than 18 nt were removed using Cutadapt version 2.8, setting --minimum-length 18
The resulting reads were mapped against the human reference genome (build hg38) using the BWA v0.7.17 alignment algorithmwith default parameters
Subsequently, PCR duplicate reads were collapsed using the UMI-tools ‘dedup’ method (using --method=percentile for practicable memory usage)
Alignments were visualized and interrogated using the Integrative Genomics Viewer v2.8.0
Annotation obtained from miRBase (www.mirbase.org) was used to obtain miR level read counts using custom scrips (https://bitbucket.org/sacgf/saunders_umi_2020/src/master/).
Assembly: hg38
Supplementary files format and content: Comma-separated file miR_counts.csv contains counts of reads aligning to each miR in each sample.

growth_protocol: All cell lines were cultured in DMEM (Dulbecco’s Modified Eagle Medium-Gibco) supplemented with 10% fetal calf serum (FCS; Cytiva, #SH30071.03) and incubated at 37°C in a humidified atmosphere containing 5% CO2, with mycoplasma testing performed regularly.

extract_protocol:
For each cell line RNA was extracted according to Trizol Reagent (Ambion, #15596018) manufacturer instructions. The quantity and of the RNA samples were checked using nanodrop Qubit HS RNA (Invitrogen, #Q32852) and Bioanalyser small RNA assay (Agilent, #5067-1548).
Libraries were generated using 1 ug of the total RNA via QIAseq miRNA kit (Qiagen, # 331502) with 14 cycles of amplification. Amplified barcoded libraries were then size selected using auto gel-purification Pippin prep 3% agarose (SAGE science) which targets ranges from 100-250bp. Libraries (size between 180-190bp) were then confirmed by Qubit HS DNA and Bioanalyzer HS DNA assay for size and concentration. The libraries were then pooled together in equimolar amounts and sequenced using an Illumina MiSeq Reagent Kit v3 kit in accordance with the manufacturer’s guidelines

treatment_protocol: Sequenicng was performed on untreated cells

value: melanoma

value: WT


title: TU, hydroxyurea, 1.3 mM, 4

description:
Library name: Cell_34
mRNA from single larvae


title: HEK_293T

description: Library name: HEK_293T

value: embryonic kidney


title: Sample27

value: Bronchial biopsy

value: tissue


title: Skin, Y7, rep2


title: PDAC, Patient: 102_794409-T-W

description: Library name: 102_794409-T-W


title: HeLa

description: Library name: HeLa

source_name: HeLa

value: HeLa

value: cervical cancer


title: Sample28

value: female


title: TU, hydroxyurea, 1.3 mM, 1

description:
Library name: Cell_31
mRNA from single larvae

value: TU

value: hydroxyurea


title: MDA_MB_231

description: Library name: MDA_MB_231

value: Breast cancer


title: Skin, Y3, rep3

value: 3 years old


title: Skin, Y3, rep2


title: Sample26

value: smoker

value: male


title: Ctrl_P1_3

description: Library name: Ctrl_P1_3

value: Mouse prefrontal cortex

value: ICR

value: control (unstressed)


title: Skin, Y3, rep1

value: Dorsal skin

value: Skin cells


title: TU, hydroxyurea, 0 mM, 4

description:
Library name: Cell_28
mRNA from single larvae

value: whole-mount


title: TU, hydroxyurea, 0 mM, 6

description:
Library name: Cell_30
mRNA from single larvae


title: D6 rep3 control

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description: F12 medium with 10% fetal calf serum, and 1% penicillin-streptomycin, at 37°C and 5% carbon dioxide

library_source: genomic

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences ≥25 nucleotides (nt) in length were considered for further analysis.
Reads were mapped against human genome using bowtie2 v2.1.0  with custom parameters (-X2000 --dovetail --no-mixed --no-discordant --end-to-end --very-sensitive).
Duplicated reads were removed with markDuplicates from picard-tools v1.94 and blacklisted regions were excluded using bedTools intersectBed v2.17.
Nucleosome-free fragments (fragments smaller than 120 base pairs) were selected using awk command.
Accessible peaks were called using MACS2 v2.1.0 with following parameters: --nomodel --extsize=100 -p 0.01.
Reproducible peaks are selected using the irreproducible discovery rate (IDR) method. A union peak file is created by merging the reproducible peaks list for all the conditions of the experiment using bedTools merge with default parameters.
A count matrix is generated using this union peak file and all BAM files, with featureCounts v1.4.6-p3  from Subreads package.
Count matrix was analyzed using R version 4.0.2 and the Bioconductor package DESeq2 version 1.28.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential accessibility between D0, D2 and D6, with or without prestimulation by flagellin. For each pairwise comparison, raw P-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure  and peaks with an adjusted P-value lower than 0.05 were considered differentially accessibles.
Assembly: hg38 from ensembl release 94
Supplementary files format and content: Bigwig files were generated using Deeptools v2.4.2 bamCoverage (--binSize 10 --normalizeTo1x 2913022398 --extendReads 250)
Supplementary files format and content: Reproducible peaks

molecule: genomic DNA

growth_protocol: Human BEC (BEAS-2B; American Type Culture Collection) were maintained at 37°C and 5% CO2 in F12 medium (Invitrogen) supplemented with 10% fetal calf serum, 1% penicillin-streptomycin, and 10 mM HEPES and stimulated in F12 without antibiotics.

extract_protocol:
Cells were lysed by adding 20 µL/well of ATAC suspension buffer (RSB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40 (Sigma Aldrich), 0. 1% Tween-20 (Sigma Aldrich) and 0.01% Digitonin (Promega), and incubated for 3 min on ice, then washed with 0.1 mL of cold ATAC-RSB containing 0.1% Tween-20 without NP-40 and digitonin. The extracted nuclei were centrifuged at 500 g for 10 min at 4°C.
DNA libraries for ATAC-Seq were prepared at Institute Cochin’s GENOM’IC facility, from transposed DNA using the Nextera® DNA kit from Illumina, following the final amplification by PCR step instructions. Reaction tubes contained 15µL Nextera PCR Master Mix, 5µL Illumina PCR Primer Cocktail, 5µL Index Primer i7, 5µL Index Primer i5, 10µL H2Oand 10µL of Transposed DNA. A PCR was performed with the following parameters : 3’ @72°C, 30’’ @98°C, and eight cycles of 10’’ @98°C, 30’’ @60°C, 2’ @72°C. PCR products were purified using AMPureXP™ beads from Agencourt at a 1X ratio. Final libraries quality was assessed on a DNA High Sensitivity™ chip on the Bioanalyzer 2100 from Agilent, and concentration was measured using the Qubit dsDNA HS Assay™ kit from Thermo Fisher Scientific (average yield was 12.1 ng/µL). Molarity from each library was calculated with the following formula: Qubit measure * 1000000 / ((average peak size in bp * 607.4)+157.9).  Each library was diluted to reach molarity of 10nM, and a final pool was set at 2nM prior to sequencing.  Sequencing of the ATAC-Seq libraries was performed on a NextSeq™ 500 from Illumina (GENOM’IC). Sequencer parameters were set as following : read 1 = 76 cycles, index 1 = 8 cycles, index 2 = 8 cycles, read 2 = 76 cycles (using a NextSeq 500 High Output 150 cycles reagent kit from Illumina). Internal PhiX control was added in the library pool to reach 1% of the total reads. The sequenced pool was diluted to a 2pM concentration and loaded in the sequencer.

treatment_protocol: On day 0, BEC were stimulated or not with ultrapure flagellin (InvivoGen) from Pseudomonas aeruginosa (5 μg/mL) for 48 hours. On day 2, cells were washed twice and incubated with medium, for resting period of 4 days, until day 6. BEC were lysed at D0 just before pre-stimulation by flagellin, D2 at the time of washing, and at D6 after the resting period to extract DNA.

tag: time

value: Bronchial epithelial cells


title: TU, hydroxyurea, 0 mM, 5

description:
Library name: Cell_29
mRNA from single larvae


title: D6 rep 3 with flagellin

value: Flagellin


title: Sample25

value: Bronchial biopsy

value: tissue


title: D6 rep 2 with flagellin


title: TU, hydroxyurea, 0 mM, 3

description:
Library name: Cell_27
mRNA from single larvae


title: TU, hydroxyurea, 0 mM, 2

description:
Library name: Cell_26
mRNA from single larvae


title: Sample23

value: nonsmoker

value: female


title: Sample21


title: D6 rep 1 with flagellin


title: Sample20


title: Skin, D180, rep3

value: 180 days old


title: Skin, D180, rep1


title: Sample22


title: D6 rep1 control


title: RW, hydroxyurea, 33 mM, 6

description:
Library name: Cell_23
mRNA from single larvae

value: RW

value: hydroxyurea


title: D6 rep 2 control


title: Skin, D90, rep3

value: 90 days old


title: D2 rep 3 control


title: RW, hydroxyurea, 33 mM, 7

description:
Library name: Cell_24
mRNA from single larvae


title: Skin, D90, rep2


title: Sample19

value: smoker

value: male


title: D2 rep 3 with flagellin


title: Skin, D3, rep3

value: 3 days old


title: D2 rep 2 control


title: RW, hydroxyurea, 33 mM, 5

description:
Library name: Cell_22
mRNA from single larvae


title: TU, hydroxyurea, 0 mM, 1

description:
Library name: Cell_25
mRNA from single larvae

value: TU


title: Sample24


title: Sample18


title: RW, hydroxyurea, 33 mM, 4

description:
Library name: Cell_21
mRNA from single larvae


title: Skin, D3, rep2

value: Dorsal skin


title: Sample17


title: D2 rep 2 with flagellin


title: Sample16


title: RW, hydroxyurea, 33 mM, 3

description:
Library name: Cell_20
mRNA from single larvae


title: RW, hydroxyurea, 33 mM, 2

description:
Library name: Cell_19
mRNA from single larvae


title: Sample15


title: Skin, D90, rep1

value: Skin cells


title: D0 rep 3  control


title: RW, hydroxyurea, 33 mM, 1

description:
Library name: Cell_18
mRNA from single larvae

value: whole-mount


title: Skin, D3, rep1


title: Sample14


title: Skin, E105, rep2

value: 105 days of gestation


title: D2 rep 1 with flagellin

value: Bronchial epithelial cells

value: Flagellin


title: Sample13

value: Bronchial biopsy

value: tissue


title: Skin, E105, rep1


title: RW, hydroxyurea, 6.6 mM, 6

description:
Library name: Cell_16
mRNA from single larvae


title: D0 rep 1 control


title: Sample12

value: nonsmoker


title: RW, hydroxyurea, 6.6 mM, 5

description:
Library name: Cell_15
mRNA from single larvae


title: Skin, E86, rep3

value: 86 days of gestation


title: D2 rep 1 control


title: Skin, E86, rep2


title: Sample11

value: female


title: RW, hydroxyurea, 6.6 mM, 4

description:
Library name: Cell_14
mRNA from single larvae

value: RW

value: hydroxyurea


title: Sample10

value: smoker


title: RW, hydroxyurea, 6.6 mM, 3

description:
Library name: Cell_13
mRNA from single larvae


title: Sample9


title: Skin, E105, rep3


title: Tet2/3 DKO CD4 BR1

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
bcl2fastq ver 2.20.0
Adapter trimming and quality filtering of the sequencing libraries was done using fastp (0.21.0) with the default parameters.
MiXCR (v4.7.0) was used to assess TCR repertoire from TCR-seq data using the  takara-mouse-rna-tcr-smarter preset (mixcr analyze takara-mouse-rna-tcr-smarter).
Assembly: mm10
Supplementary files format and content: MiXCR produced clone count information.
Library strategy: TCR-seq

source_name: spleen

extract_protocol:
Live CD4+CD25- TCRb+, aGalCerCd1d tetramer- cells were sorted with purity of 98% or higher. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
In order to analyze TCR repertoire, we used the SMARTer mouse TCR a/b profiling kit (Takara, cat no 634403) following the manufacturer’s instructions. We used 20 ng of total RNA  in order to synthesize cDNA for each library. The kit employs a 5'-RACE-based approach to capture complete V(D)J variable regions of TCR transcripts. The libraries were sequenced using a Miseq sequencer (Illumina) at the UNC High Throughput Sequencing Facility.  The alignment and assembly of the RNAseq reads and the exporting of the clonotypes were conducted using MiXCR.

value: spleen

value: CD4 T cells

value: Tet2/3 DKO


title: Skin, E76, rep3

value: Dorsal skin

value: 76 days of gestation


title: RW, hydroxyurea, 6.6 mM, 7

description:
Library name: Cell_17
mRNA from single larvae

data_processing:
The PCA was performed in R software using NormalizedDarta, ScaleData, FindVariable Fretures, and RunPCA functions in Seurat (version 5.1.0) (Hao et al., 2024) with default parameters except for “do.scale = F” for ScaleData.
Assembly: Danio_rerio.GRCz11.cdna.al.fa
Supplementary files format and content: csv-delimited text file includes rawcnt values for each sample

value: whole-mount


title: RW, hydroxyurea, 6.6 mM, 1

description:
Library name: Cell_11
mRNA from single larvae


title: D0 rep 2 control

description: F12 medium with 10% fetal calf serum, and 1% penicillin-streptomycin, at 37°C and 5% carbon dioxide


title: Sample8

value: male


title: Tet2/3 DKO CD4 peripheral T cells

description:
cd4 cells from spleen DKO
spl b56-6

data_processing:
Library strategy: TCR-seq
bcl2fastq ver 2.20.0
Adapter trimming and quality filtering of the sequencing libraries was done using fastp (0.21.0) with the default parameters.
MiXCR (v4.7.0) was used to assess TCR repertoire from TCR-seq data using the  takara-mouse-rna-tcr-smarter preset (mixcr analyze takara-mouse-rna-tcr-smarter)
Genome_build: mm10
Supplementary_files_format_and_content: MiXCR produced clone count information.

source_name: Spleen

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions at University of North Carolina (UNC) Genetic Medicine building, in a facility managed by the Division of Comparative Medicine at UNC Chapel Hill. The experimental procedures were approved by the UNC Institutional Animal Care and Use Committee.

extract_protocol:
RNA was isolated using RNA was isolated using the micro RNeasy plus kit (Qiagen) or the Rneasy plus mini kit (Qiagen) depending on the available starting material.
In order to analyze TCR repertoire, we used the SMARTer mouse TCR a/b profiling kit (Takara, cat no 634403) following the manufacturer’s instructions. We used 20 ng of total RNA  in order to synthesize cDNA for each library. The kit employs a 5'-RACE-based approach to capture complete V(D)J variable regions of TCR transcripts. The libraries were sequenced using a Miseq sequencer (Illumina) at the UNC High Throughput Sequencing Facility.  The alignment and assembly of the RNAseq reads and the exporting of the clonotypes were conducted using MiXCR.

treatment_protocol: Mice were euthanized by CO2 asphyxiation and thymi were isolated and dissociated to acquire single-cell suspensions. Total thymocytes were depleted of CD24hi cells by staining with biotinylated mouse anti-CD24 (clone:M1/69) purchased from Biolegend. Unwanted cells were depleted by binding to mouse streptavidin magnetic beads (anti-mouse Rapidspheres, cat no 19860, Stemcell Technologies) according to the manufacturer’s instructions. Enriched cells were stained with viability dye (eBioscience) to distinguish live cells from. Cells were stained with aGalactosyl-Ceramide loaded tetramer (conjugated with PE, obtained from NIH tetramer core), TCRb (clone:H57-597) conjugated with PERCP/Cy5.5 (Biolegend), anti-mouse CD4 AF488 (clone:RM4-5), CD8 (clone:53-6.7) conjugated with Brilliant Violet 650 or APC.  Live, CD24 low enriched cells CD4+, TCRb+, aGalCerCd1d tetramer-, CD8- cells were sorted in a purity higher than 98% and were used for RNA isolation. Splenocytes were lysed with ACK buffer (Life Technologies) to remove erythrocytes and were depleted for B cells using biotinylated anti-mouse CD19 (clone: 6D5), any remaining blood cells using biotinylated anti-mouse TER119/ Erythroid cells (clone: TER119). Cells were stained with CD4AF488 (clone: RM4-5), TCR PERCPCy5.5 (clone: H57-597), CD25 APC (clone: PC61), aGalactocyl-Ceramide (aGal-Cer) loaded Tetramer PE. Live CD4+, CD25-, TCR+, tetramer- cells were sorted and used in downstream applications. Expanded cells in congenic recipients were sorted after staining with CD45.1BV421 (clone: A20) and CD45.2PE (clone: 104).   In all cases, dead cells were excluded using a fixable viability dye eFluor780 (eBioscience).   The cells were sorted using an Aria Sorter (Becton Dickinson).

tag: tag

tag: cells


title: Skin, E76, rep2

tag: tissue

value: Skin cells


title: Tet2/3 DKO CD4 SP BR3

description:
cd4 cells from thymus of dko
thy b56-6

source_name: Thymus


title: Skin, E76, rep1


title: WT BR2

value: WT


title: RW, hydroxyurea, 1.3 mM, 6

description:
Library name: Cell_10
mRNA from single larvae

tag: strain

tag: treatment


title: RW, hydroxyurea, 6.6 mM, 2

description:
Library name: Cell_12
mRNA from single larvae


title: RW, hydroxyurea, 1.3 mM, 5

description:
Library name: Cell_9
mRNA from single larvae


title: Tet2/3 DKO CD4 SP BR2

description:
cd4 cells from thymus of dko
thy b56-1


title: Sample5

source_name: Bronchial biopsy

value: Bronchial biopsy

tag: cell line

tag: cell type


title: Skin, E66, rep2

value: 66 days of gestation


title: WT BR1

tag: genotype


title: Sample6

value: tissue

value: nonsmoker


title: RW, hydroxyurea, 1.3 mM, 4

description:
Library name: Cell_8
mRNA from single larvae


title: Sample4


title: Skin, E86, rep1

value: 86 days of gestation


title: Skin, E66, rep1


title: Tet2/3 DKO CD4 BR2


title: RW, hydroxyurea, 1.3 mM, 3

description:
Library name: Cell_7
mRNA from single larvae

value: RW


title: Tet2/3 DKO CD4 2nd transfer BR5

description:
expanded cells 1st transfer
j3-5

value: ex CD4,TCRb+, cd45.2+ cells


title: Skin, E56, rep3

value: 56 days of gestation


title: RW, hydroxyurea, 1.3 mM, 2

description:
Library name: Cell_6
mRNA from single larvae

value: hydroxyurea


title: Sample7

value: smoker


title: Skin, E56, rep2


title: RW, hydroxyurea, 1.3 mM, 1

description:
Library name: Cell_5
mRNA from single larvae


title: Skin, E66, rep3


title: wt4_thy CD4 SP

description:
cd4 cells from wt thymus
wt4_thy

value: wild type


title: wt5_thy CD4 SP

description:
cd4 cells from wt thymus
wt5_thy


title: Skin, E56, rep1

value: Dorsal skin


title: wt3_CD4 SP

description:
cd4 cells from wt thymus
wt3_thy


title: RW, hydroxyurea, 0 mM, 3

description:
Library name: Cell_3
mRNA from single larvae


title: RNA-seq of Pectobacterium carotovorum PCC27 hexA mutant at early stationary phase (replicate 3)

first: EUNHYE

last: GOO

address: 1, Gwanak-ro, Gwanak-gu

department: Agricultural Biotechnology

institute: Seoul National University

description:
Library name: PCC27_hexA_earlystat_rep3
hexA mutant strain harvested at early stationary phase; total RNA was extracted and rRNA-depleted prior to sequencing.

data_processing:
Adapter sequences and low-quality bases were trimmed using Trimmomatic v0.39.
Quality of trimmed reads was assessed using FastQC v0.11.9.
Trimmed reads were aligned to the P. carotovorum PCC27 reference genome (GCF_045277235.1) using HISAT2 v2.2.1.
Read counts per gene were calculated using HTSeq-count v0.12.4.
Differential expression analysis was performed using DESeq2 in R v4.2.1.
Assembly: GCF_045277235.1 (ASM4527723v1)
Supplementary files format and content: Processed data files include raw gene count tables in plain text format (.count) generated by HTSeq-count. Each file contains gene IDs and corresponding raw read counts.

organism: Pectobacterium carotovorum

source_name: bacterial cells

growth_protocol: Cells were grown in LB medium at 28°C with shaking at 220 rpm. Samples were collected at mid-log phase or early stationary phase, depending on the experimental condition.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, followed by DNase I treatment to remove genomic DNA contamination.
Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit (Bacteria, Illumina). Strand-specific RNA-seq libraries were constructed using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: bacterial cells

value: hexA mutant

value: early stationary phase


title: RW, hydroxyurea, 0 mM, 4

description:
Library name: Cell_4
mRNA from single larvae

extract_protocol:
RNA extraction from zebrafish larvae and RNA purification were described previously (Ujibe et al. 2021). The RNA concentration was determined using the Quantus Fluorometer with QuantiFluor RNA System Kit (Promega) according to the manufacturer’s manual. RNA was diluted to a final concentration of 2 ng/µl and used to prepare library for RNA-Seq.
Library preparation was conducted according to the Lasy-Seq ver 1.1 5 method (Kashima et al., 2021). In brief, reverse transcription was done using SuperScript IV reverse transcriptase (Thermo Fisher Scientific) and indexed reverse transcription primers. Following program was used for reverse transcription: 65 °C 10 min; 80 °C 15 min; 4 °C forever. Products of reverse transcription were pooled and then purified using an equal volume of AMpure XPKAPA Pure beads (Beckman CoulterRoche) according to the manufacturer’s manual. Second strand synthesis was conducted with RNase H (Enzymatics) and DNA polymerase I (Enzymatics) at 16 °C for 2 h. Synthetic double-strand DNA (dsDNA) were treated with RNase T1 (Thermo Fisher Scientific) at 37 °C for 5 min. Fragmentation was conducted using 5x WGS Fragmentation Mix (Enzymatics) at 32 °C for 5.5 min followed by heat inactivation at 65 °C for 30 min. Ligation was conducted using 5x Ligation Mix (Enzymatics) at 20 °C for 15 min. One cycle PCR was performed using a P7 primer containing a 5′ biotin modification ([BioON]CAAGCAGAAGACGGCATACGAGAT) to allow for selective purification of properly ligated molecules containing the original 3’-ends of the cDNAs. Biotin-labeled DNA was captured using Dynabeads M-280 Streptavidin (Thermo Fisher Scientific) in binding buffer (1M NaCl, 10 mM Tris-HCl pH 7.6), which were washed with TE-TW (10 mM Tris pH 7.6, 1 mM EDTA, 0.01% Tween20), twice. Subsequent amplification was performed with KAPA HiFi HotStart ReadyMix (Roche), and the optimal PCR cycle number was determined by EvaGreen (Biotium) -based qPCR using the following program: initial denaturation at 95 °C for 5 minutes; followed by cycles of 98 °C for 20 seconds, 60 °C for 15 seconds, and 72 °C for 40 seconds; a final extension at 72 °C for 3 minutes; and a hold at 4 °C indefinitely. The library was purified using an equal volume of KAPA Pure beads (Roche), and subjected to electrophoresis in Bioanalyzer 2,100 (Agilent Technologies) with the Agilent High Sensitivity DNA kit (Agilent Technologies). Library concentration was determined using Quantus Fluorometer (Promega) with the QuantiFluor ONE dsDNA System kit (Promega). Sequencing of 150-bp paired-end reads was conducted using NovaSeq X Plus (Illumina). Raw RNA-Seq reads were aligned to the Danio rerio genome assembly GRCz11 (Ensembl release 111), and gene-level quantification was conducted as previously described (Kashima et al. 2021).

value: whole-mount


title: D3: ureter ligation last for 14 days

city: Qingdao

first: wei

last: jiao

state: Shandong

address: No. 16 Jiangsu Road, Qingdao 266000, Shandong Province, China

department: urology

institute: The Affiliated Hospital of Qingdao University

description:
Library name: Sample 18
Column name in gene_expression_anno.txt:D3_FPKM

data_processing:
The raw data (raw reads) in fastq format underwent initial processing using the fastp software (version 0.19.7). In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing ploy-N (N represents reads for which base information cannot be determined), and low-quality reads from the raw data. The Q20, Q30, and GC-content of the clean data were calculated. All subsequent analyses were conducted based on the high-quality clean data. The clean data were mapped to the reference genome using Hisat2 (v2.0.4). The quantification of gene expression levels was performed as follows: the gene expression levels were estimated using the fragments per kilobase of transcript per million mapped fragments (FPKM) method.
Assembly: not provided
Supplementary files format and content: FPKM, count values for each sample

organism: Rattus norvegicus

source_name: renal parenchyma

extract_protocol:
kidney tissues were thawed at 4 ◦C and homogenized using a grinding pestle. A 100 μL aliquot of the homogenized sample was transferred into a 2 mL centrifuge tube containing 400 μL of methanol, followed by vortexing for 1 min. The sample was then centrifuged at 10,000 g for 10 min at 4 ◦C. The supernatant was transferred into a new 2 mL centrifuge tube and concentrated until dry. The residue was reconstituted in 150 μL of 2‑chloro-L-phenylalanine (4 ppm) solution prepared in 80 % methanol water (stored at 4 ◦C), filtered through a 0.22 μm membrane, and transferred to a vial for LC-MS analysis.
The total RNA was extracted from kidney tissues using RNAiso Plus (TaKaRa, Dalian, China). The RNA quality and integrity were evaluated and high-quality mRNA from samples were used to construct libraries. The mRNA in the sample was enriched using magnetic beads with oligo (dT) and fragmented into short segments. The synthesis of the first strand cDNA utilized a random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-), followed by the subsequent performance of second strand cDNA synthesis using DNA Polymerase I and RNase H. After 3′ -end repair, ligation of a poly(A)-tail to the sequencing linker, and selection of the fragment sizes, the double-stranded cDNA was purified and PCR amplified. Then, the PCR products were purified using the AMPureXP system (Beckman Coulter, Beverly, MA, USA) for sequencing.

value: renal parenchyma

value: unilateral ureteral obstruction (UUO) animal model

value: ureter ligation last for 14 day

value: Day  5


title: RW, hydroxyurea, 0 mM, 2

first: Hiromi

last: Hirata

institute: Aoyama Gakuin University

description:
Library name: Cell_2
mRNA from single larvae


title: Sample3

value: Bronchial biopsy

value: tissue

value: nonsmoker

value: female


title: D2: ureter ligation last for 14 days

description:
Library name: Sample 17
Column name in gene_expression_anno.txt:D2_FPKM


title: wt2_CD4 SP

description:
cd4 cells from wt thymus
wt2_thy


title: RNA-seq of Pectobacterium carotovorum PCC27 hexA mutant at early stationary phase (replicate 1)

description:
Library name: PCC27_hexA_earlystat_rep1
hexA mutant strain harvested at early stationary phase; total RNA was extracted and rRNA-depleted prior to sequencing.


title: wt1_ CD4 SP thy

description:
cd4 cells from wt thymus
wt1_thy


title: Tet2/3 DKO CD4 SP BR1

description:
cd4 cells from thymus of dko
thy b39-1


title: RW, hydroxyurea, 0 mM, 1

description:
Library name: Cell_1
mRNA from single larvae

value: RW


title: C5: ureter ligation last for 7 days

description:
Library name: Sample 15
Column name in gene_expression_anno.txt:C5_FPKM

value: ureter ligation last for 7 day


title: Sample2

value: male


title: RNA-seq of Pectobacterium carotovorum PCC27 hexA mutant at mid-log phase (replicate 3)

description:
Library name: PCC27_hexA_midlog_rep3
hexA mutant strain harvested at mid-log phase; total RNA was extracted and rRNA-depleted prior to sequencing.

value: mid-log phase


title: Tet2/3 DKO CD4 2nd transfer BR3

description:
2ndary transfer
splj22_3

value: ex CD4,TCRb+, cd45.2+ cells


title: D1: ureter ligation last for 14 days

description:
Library name: Sample 16
Column name in gene_expression_anno.txt:D1_FPKM


title: RNA-seq of Pectobacterium carotovorum PCC27 hexA mutant at early stationary phase (replicate 2)

description:
Library name: PCC27_hexA_earlystat_rep2
hexA mutant strain harvested at early stationary phase; total RNA was extracted and rRNA-depleted prior to sequencing.

value: bacterial cells


title: Sample1

value: smoker


title: C4: ureter ligation last for 7 days

description:
Library name: Sample 14
Column name in gene_expression_anno.txt:C4_FPKM


title: Tet2/3 DKO CD4 2nd transfer BR4

description:
2ndary transfer
splj22_4


title: Tet2/3 DKO CD4 2nd transfer BR2

description:
2ndary transfer
splj22_2


title: RNA-seq of Pectobacterium carotovorum PCC27 hexA mutant at mid-log phase (replicate 2)

description:
Library name: PCC27_hexA_midlog_rep2
hexA mutant strain harvested at mid-log phase; total RNA was extracted and rRNA-depleted prior to sequencing.

value: hexA mutant


title: RNA-seq of Pectobacterium carotovorum PCC27 hexA mutant at mid-log phase (replicate 1)

description:
Library name: PCC27_hexA_midlog_rep1
hexA mutant strain harvested at mid-log phase; total RNA was extracted and rRNA-depleted prior to sequencing.


title: C3: ureter ligation last for 7 days

description:
Library name: Sample 13
Column name in gene_expression_anno.txt:C3_FPKM


title: Skin, D180, rep2

value: Dorsal skin

value: Skin cells

value: 180 days old


title: RNA-seq of Pectobacterium carotovorum PCC27 WT at early stationary phase (replicate 3)

description:
Library name: PCC27_WT_earlystat_rep3
WT strain PCC27 harvested at early stationary phase; total RNA was extracted and rRNA-depleted prior to sequencing.

value: wild type

value: early stationary phase


title: Tet2/3 DKO CD4 2nd transfer BR1

description:
2ndary transfer
splj22_1


title: C2: ureter ligation last for 7 days

description:
Library name: Sample 12
Column name in gene_expression_anno.txt:C2_FPKM

value: renal parenchyma

value: unilateral ureteral obstruction (UUO) animal model

value: Day  5


title: RNA-seq of Pectobacterium carotovorum PCC27 WT at early stationary phase (replicate 2)

description:
Library name: PCC27_WT_earlystat_rep2
WT strain PCC27 harvested at early stationary phase; total RNA was extracted and rRNA-depleted prior to sequencing.


title: C1: ureter ligation last for 7 days

description:
Library name: Sample 11
Column name in gene_expression_anno.txt:C1_FPKM


title: Tet2/3 DKO CD4 1st transfer BR6

description:
1st transfer
splj15_2


title: 13_D6-1F

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Human (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using R with Version 23 of Entrezgene CDF brain array.

label: Biotin

source_name: BEAS-2B cell line, 6 day with flagellin

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

extract_protocol: RNA was isolated using a NucleoSpin RNA/Protein kit (Macherey Nagel, Duren, Germany).

treatment_protocol: On day 0, BEC were stimulated or not with ultrapure flagellin (InvivoGen) from Pseudomonas aeruginosa (5 μg/mL) for 48 hours. On day 2, cells were washed twice and incubated with medium, for resting period of 4 days, until day 6. BEC were lysed at D0 just before pre-stimulation by flagellin, D2 at the time of washing, and at D6 after the resting period to extract RNA .

tag: cells type

value: Bronchial epithelial cells

tag: stimulation

value: Flagellin


title: Tet2/3 DKO CD4 1st transfer BR5

description:
1st transfer
splj13_1


title: RNA-seq of Pectobacterium carotovorum PCC27 WT at early stationary phase (replicate 1)

description:
Library name: PCC27_WT_earlystat_rep1
WT strain PCC27 harvested at early stationary phase; total RNA was extracted and rRNA-depleted prior to sequencing.


title: 14_D6-2F


title: B4: ureter ligation last for 3 days

description:
Library name: Sample 9
Column name in gene_expression_anno.txt:B4_FPKM

value: ureter ligation last for 3 day


title: B5: ureter ligation last for 3 days

description:
Library name: Sample 10
Column name in gene_expression_anno.txt:B5_FPKM


title: RNA-seq of Pectobacterium carotovorum PCC27 WT at mid-log phase (replicate 2)

description:
Library name: PCC27_WT_midlog_rep2
WT strain PCC27 harvested at mid-log phase; total RNA was extracted and rRNA-depleted prior to sequencing.


title: Tet2/3 DKO CD4 2nd transfer BR6

description:
2ndary transfer
splj3_6