title: soil-N-62

city: Yangling

first: jingjing

last: li

address: xi nong road 26

institute: Northwest A&F University

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 6 g N m–2 y–1 addition , replicate 2

hyb_protocol: Then, the labeled DNA was mixed with 42 μL of buffer and incubated at 95 °C for 3 min, then hybridized to the microarray,

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Inc., Madison, WI, USA) at 633 nm. The images were converted, digitalized, processed, and analyzed using the ImaGene 6.0 software.

data_processing: For quality control, based on the raw data, the signal-to-noise ratio (SNR) was adjusted and poor-quality spots with a SNR <2.0 were removed. Then, the signal intensity of each probe was log-transformed and divided by the average signal intensity in the sample to standardize the data, and probes that appeared in only one of four replicates of each treatment were removed as noise, to obtain normalized data. The normalize data were used to profile C-cycling functional gene structure and to calculate alpha diversity. Gene intensities normalized to total signal intensity were used to analyze the relative abundance of each gene category or family in each sample.

source_name: soil sample collected from artificial Pinus tabulaeformis forest with N addition

label_protocol: As previously described (Qingyun Yan et al 2013), DNA samples were labeled with the fluorescent dye Cy3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried in a SpeedVac (Thermo Savant, NY, USA).

extract_protocol: Microbial DNA was extracted from 0.5 g of soil using the MoBio PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA) according to the manufacturer’s protocol. DNA quality was assessed based on the 260/280 nm and 260/230 nm absorbance ratios. DNA was quantified with the PicoGreen method (Ahn et al. 1996) and stored at −20 °C until use.

treatment_protocol: Soil samples were taken on 22 July 2018. After removing surface litter and O horizon material, five soil cores (5 cm inner diameter) were randomly collected from the top 0–10 cm mineral soil layer and pooled (~1 kg). The samples were placed on ice in a low-temperature box and transported to the laboratory. The samples were sieved through a 2.0-mm mesh.Part of each sample (~10 g) was frozen and stored at –80 °C until DNA extraction.

tag: soil type

value: artificial Pinus tabulaeformis forest soil

tag: n addition level

value: N addition levels:6 g N m-2 y-1


title: soil-N-34

status: Public on Mar 01 2022

type: genomic

country: China

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 3 g N m–2 y–1 addition , replicate 4

molecule: genomic DNA

organism: uncultured soil microorganism

value: N addition levels:3 g N m-2 y-1


title: Biopsy_DBD_Non-EVLP_4

type: RNA

city: Toronto

first: Mingyao

last: Liu

state: ON

address: 101 College Street

department: Latner Thoracic Resaerch Laboratories

country: Canada

institute: University Health Network

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing:
Affymetrix CEL files were imported and processed using RMA in R version 3.5.0 with the affy package. We used an alternative CDF probset description file from Brainarray at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): clariomdhumanhsentrezgcdf_22.0.0.zip
clariomdhumanhsentrezgcdf_22.0.0.zip

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Biopsy, donor type: DBD

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: donor type

value: DBD

tag: evlp type

value: Non-EVLP


title: soil-N-32

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 3 g N m–2 y–1 addition , replicate 2


title: soil-N-93

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 9 g N m–2 y–1 addition , replicate 3

value: N addition levels:9 g N m-2 y-1


title: soil-N-02

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 0 g N m–2 y–1 addition , replicate 2

value: N addition levels:0 g N m-2 y-1


title: soil-N-92

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 9 g N m–2 y–1 addition , replicate 2


title: soil-N-33

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 3 g N m–2 y–1 addition , replicate 3


title: soil-N-61

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 6 g N m–2 y–1 addition , replicate 1


title: soil-N-04

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 0 g N m–2 y–1 addition , replicate 4


title: soil-N-94

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 9 g N m–2 y–1 addition , replicate 4


title: soil-N-03

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 0 g N m–2 y–1 addition , replicate 3


title: soil-N-31

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 3 g N m–2 y–1 addition , replicate 1


title: soil-N-64

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 6 g N m–2 y–1 addition , replicate 4

value: collected from:artificial Pinus tabulaeformis forest  N addition levels:6 g N m-2 y-1


title: TLCN106

type: SRA

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: Hepatocellular carcinoma

library_source: transcriptomic

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCh38) by STAR (v2.6.1a) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts.

source_name: Hepatocellular carcinoma

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Libraries were constructed using Illumina TruSeq Stranded mRNA kit according to the manufacturers

tag: etiology

value: HCV

tag: ctnnb1 status

value: wt

tag: efs days

tag: efs event

tag: os days

tag: os event


title: soil-N-63

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 6 g N m–2 y–1 addition , replicate 3


title: CT24WT2

city: Changsha

first: Xuedan

last: Lu

state: Hunan

address: No. 1 Nongda Road

institute: Hunan Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Filtered reads were aligned to the reference rice genome (Oryza sativa R498_IGDBv3_coreset_MSU) using HISAT(2.0.4).
Genome_build: Oryza sativa R498_IGDBv3_coreset_MSU
Supplementary_files_format_and_content: a text file include count number for each sample.

organism: Oryza sativa

source_name: chilling temperature from ZT20 to ZT24_seedlings

growth_protocol: Rice cultivar “93-11” (O. sativa ssp. indica) was used for this study. Seeds were soaked in water for 36 hrs and then incubated at 30 °C for 6 days. The germinated seeds were sown in a round pot (diameter 8cm) for RNA sampling (25 seedlings per pot). The seedlings were incubated in 12 h light/12 h dark cycles (12L:12D) at 28 °C (white light intensity: 248 μmol m–2 s–1; relative humidity: 70 ± 5%) for about 10 days until the three-leaf stage, in a growth chamber (R4630, Ningbo Dongnan Instrument Co., Ltd., China).

extract_protocol:
Total RNA was extracted from up-ground rice seedlings using Trizol (Invitrogen, Carlsbad, CA, USA) following manufacturer's guidelines. For each treatment, RNA extraction was performed in three biological repeats (5 plants per repeat). NanoPhotometer® (IMPLEN, CA, USA) and Qubit® RNA Assay Kit in a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) were used for purity and quantitative assessment of RNA samples, respectively. In addition, the integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according the manufacturer’s instructions and index codes were added to attribute sequences to each sample.

treatment_protocol: 10-day seedlings at three-leaf stage were treated with chilling temperature (13°C) for 4 hrs at different Zeitgeber Time (ZT) (ZT0-ZT36) before harvesting for RNA extraction on the 11th day. For transcriptome analyses, CT12 group seedlings experienced 4 hrs treatment of chilling temperature from ZT8-ZT12, while NT12 group seedlings were kept at 28°C before harvesting at ZT12 as controls. CT24 group seedlings were chilling-treated from ZT20 to ZT24 before being harvested, while NT24 group seedlings were harvested at the same time at normal growth temperature. The samples were immediately frozen in liquid nitrogen and stored in –80°C freezer until RNA extraction.

tag: cultivar

value: 93-11 (O. sativa ssp. indica)

tag: developmental stage

value: three-leaf stage

tag: tissue

value: above ground part of seedlings

tag: treatment

value: 4 hrs treatment of chilling temperature (13°C)  from ZT20 to ZT24 before harvesting


title: soil-N-91

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 9 g N m–2 y–1 addition , replicate 1


title: BP-1(BP adenovirus overexpression)

city: Harbin

first: Jiyuan

last: Zhu

address: Xiangfang District, No. 600 Changjiang Road

department: College of Animal Science and Technology

institute: Northeast Agricultural University

data_processing:
The raw data of RNA-SEQ includes splice sequences and sequenced low-quality sequences. In order to ensure the accuracy of information analysis, the sequenced raw data needs to be filtered to obtain clean data.(1) The reads linker was removed and the sequence length was less than 30 BP; (2) cut off the sequence of Q < 5 at the beginning and end of reads; (3) remove reads with Q < 15; (4) detect the quality of the sliding window with a width of 5bp for each sequence. If the average quality of a window is lower than 15, cut off the sequence after the window.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
High quality reads were mapped to reference genome of S. scrofa (11.1) using HISAT2 program .
Transcript abundances were quantified with StringTie software, and normalized with FPKM (Fragments per kilobase of transcript per million mapped reads) method across libraries.FPKM value was used to measure the gene expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Preadipocytes

growth_protocol: Subcutaneous fat tissues were obtained after the newborn Min pigs were slaugh-tered, washed with sterile phosphate-buffered saline (PBS), and potentially contami-nated muscle and connective tissue was carefully removed. After washing three times in PBS containing 1% penicillin–streptomycin (Invitrogen), fat tissues were cut into small pieces and digested with 0.1% type I collagenase (Invitrogen) for 40–50 min at 37℃, then mixed with equal volumes of culture medium supplemented with penicillin–streptomycin and 10% fetal bovine serum (FBS) (Sigma, St. Louis, MO, USA), and fil-tered through 400-mesh filters. The filtrates were centrifuged at 1000 rpm for 5 min. The cell precipitation was resuspended with Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12 (DMEM/F12) containing 10% FBS and 1% penicillin–streptomycin. The medium was changed every 2 days until cells were grown to a desired density.

extract_protocol:
subcutaneous adipose tissues were collected from newborn Min pigs to culture cells. RNA was extracted with TRIzol reagent (Invitrogen, CA, USA)A total of six Ribo-Zero RNA-sequencing libraries including overexpressing and control groups were constructed, each with three replicates.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The recombinant adenoviruses were constructed using the AdEasy system (Hanbio, Shang, China) . BP CDS were inserted into the shuttle plasmid containing an enhanced green fluorescent protein (EGFP) and cyto-megalovirus promoters using Kpn Ⅰ and Xho Ⅰ sites, and homologous recombina-tion was performed in E. coli BJ5183 with adenoviral backbone pAdEasy 1. The recom-binant adenovirus plasmid was packaged in HEK-293A cells after linearized with Pac Ⅰ. Preadipocytes were infected with adenovirus virions at multiplicity of infection (MOI) of 300. At 48 h post-infection, cells were collected for RNA-Seq with Illumina NovoSeq 6000 platform (Illumina, San Diego, CA, USA) by Geneseeq Technology (Nanjing, China) using pair-end sequencing strategy according to the manufacturer’s protocols. Cells treated with empty adenovirus were used as a control.

tag: cell type

value: Preadipocytes

tag: cell source

value: subcutaneous adipose tissue

value: BP groups(BP adenovirus overexpression)


title: TLCN107

description: Hepatocellular carcinoma

value: mut


title: Control-1(empty adenovirus overexpression)

value: control groups（empty adenovirus overexpression）


title: CT24WT3


title: pro-B KO3

city: DALLAS

last: Yan

state: TEXAS

address: 6000 Harry Hines Blvd

country: USA

institute: UT Southwestern Medical Center

data_processing:
Raw sequencing data was processed with Astrocyte RNASeq Analysis Workflows at UT Southwestern Bioinformatics Core Facility (https://astrocyte.biohpc.swmed.edu/workflow/12/version/324/docs) to generate Fragments Per Kilobase Million (FPKM) for each transcript.
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: *.fpkm.txt: Tab-delimited text files include FPKM of each transcript.

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104).
mRNAseq-Strand specific library were prepared for sequencing.

tag: strain

tag: genotype

value: Bone marrow

value: pro-B cells

value: Adult


title: soil-N-01

description: GeoChip data for soil sample collected at an artificial Pinus tabulaeformis forest with 0 g N m–2 y–1 addition , replicate 1

tag: soil type

value: artificial Pinus tabulaeformis forest soil

tag: n addition level


title: pro-B KO2


title: CT12WT1

source_name: chilling temperature from ZT8-ZT12_seedlings

value: 4 hrs treatment of chilling temperature (13°C)  from ZT8-ZT12 before harvesting


title: TLCN105

description: Hepatocellular carcinoma


title: pro-B KO1


title: TLCN101

description: Hepatocellular carcinoma


title: NT24WT2

source_name: normal temperature from ZT20-ZT24_seedlings

value: 4 hrs treatment of normal temperature (28°C)  from ZT20-ZT24 before harvesting


title: CT12WT2


title: CT24WT1


title: CT12WT3


title: TLCN092

description: Hepatocellular carcinoma

value: HBV


title: CC.KO.29

city: Baton Rouge

first: Jaycob

middle: D

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

organism: Rattus norvegicus

source_name: Gastrocnemius Muscle Tissue

growth_protocol: Rats were maintained on chow 5001 diet at room temperature before and during cold exposure

extract_protocol:
Gastrocs were collected, snap frozen in liquid nitrogen, and tissue homogenization was done using Trizol reagent. Total RNA was isolated using RNeasy Mini kit from Qiagen.
Quant-Seq  3' mRNA-Seq Library Prep Kit

treatment_protocol: 8 WT and 8 Ucp1 KO female rats at 7 month of age from CC group were exposed to cold for 14 days at 4C, while 8 WT and 7 Ucp1 KO female rats at 7 month old age were maintained at RT for 14 days.

value: Sprague Dawley

tag: group

value: Ucp1 KO gastroc

tag: temperature

value: 4C exposed for 14 days


title: CC.KO.30


title: TLCN059

description: Hepatocellular carcinoma

tag: etiology

tag: ctnnb1 status

value: wt


title: TLCN103

description: Hepatocellular carcinoma

value: HCV

tag: efs days

tag: efs event


title: TLCN052

description: Hepatocellular carcinoma

tag: os days

tag: os event


title: NT24WT3

tag: cultivar

value: 93-11 (O. sativa ssp. indica)

tag: developmental stage

value: three-leaf stage

value: above ground part of seedlings


title: NT12WT3

source_name: normal temperature from ZT8-ZT12_seedlings

tag: tissue

tag: treatment

value: 4 hrs treatment of normal temperature (28°C)  from ZT8-ZT12 before harvesting


title: pro-B WT1

tag: cell type


title: miR21_KD_4

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Single-End 100bp reads were mapped to RefSeq mm10 genome build using subread  (Yang et al, 2013). Read counts at the gene level were quantified using featureCounts  (Yang et al., 2014).
Gene counts with counts-per-million (cpm) larger than 0.5 in at least four samples were retained and normalized by TMM normalization  (Robinson and Oshlack, 2010).
Differential gene expression analysis was performed using the edgeR (Robinson et al., 2010)
Quasi-likelihood Negative Binomial Generalized log-linear model framework. Genes with FDR < 0.05 were determined as differentially expressed.
Biological process-related gene ontology terms (annotated in the GO.db package) that are enriched in 4T1.13-miR21KD tumours were identified using the fry() function in the limma package.
Genome_build: mm10

source_name: 4T1.13 tumours

growth_protocol: 1 * 10^5 cells were injected into the mammary fat pad of BALB/c mice. 4T1.13-VC and 4T1.13-miR-21-KD orthotopic tumours were recovered at day 14 as regression of 4T1.13-miR-21-KD tumours commenced.

extract_protocol: Total RNA was isolated using the Ambion miRVana total RNA isolation kit (Thermo Fisher Scientific). RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and 5g treated with DNase I (Ambion Turbo DNA-free kit, Thermo Fisher Scientific).

tag: strain

value: BALB/c

tag: days after tumour cell injection

value: 4T1.13 tumours


title: CC.KO.28


title: NT12WT2


title: pro-B WT2

tag: genotype

value: Bone marrow

value: pro-B cells


title: TLCN154

description: Hepatocellular carcinoma


title: pro-B WT3

value: Adult


title: TLCN090

description: Hepatocellular carcinoma

value: mut


title: TLCN046

description: Hepatocellular carcinoma


title: CC.KO.27


title: TLCN150

description: Hepatocellular carcinoma


title: CC.KO.31


title: NT12WT1


title: CC.KO.26


title: NT24WT1

value: 4 hrs treatment of normal temperature (28°C)  from ZT20-ZT24 before harvesting


title: TG2

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

description: Marmoset

data_processing:
Data of RNA-seq (fastq file format) were quality-checked.
The remaining reads were mapped to the marmoset genome (cj1700) using the Kallisto (ver0.46.2) and STAR (ver.2.5.3a), and the output file of STAR (BAM file format) were summarized using the featureCounts (1.5.2).
Downstream analysis was performed using R software and TCC package.
Genome_build: cj1700
Supplementary_files_format_and_content: Star_raw_count_for_GEO.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: APP_transgene.fa: FASTA file

organism: Callithrix jacchus

source_name: Frontal cortex

extract_protocol:
RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols and KAPA Hyper (KAPA Biosystems).

value: APP transgene

value: Frontal cortex

tag: age

tag: Sex

value: Female


title: TLCN050

description: Hepatocellular carcinoma

value: HBV


title: miR21_KD_3


title: miR21_KD_2


title: CC.KO.24

value: Sprague Dawley

tag: group

value: Ucp1 KO gastroc

tag: temperature

value: 4C exposed for 14 days


title: TLCN043

description: Hepatocellular carcinoma

tag: etiology

tag: ctnnb1 status


title: CC.WT.23

value: Control gastroc


title: miR21_KD_1


title: WT1

description: Marmoset

value: WT


title: TLCN042

description: Hepatocellular carcinoma

tag: efs days

tag: efs event


title: Vector_control_2

value: Vector control


title: TLCN037

description: Hepatocellular carcinoma

tag: os days

tag: os event


title: TLCN038

description: Hepatocellular carcinoma

value: wt


title: Vector_control_3

value: BALB/c

value: 4T1.13 tumours


title: CC.KO.25


title: WT2

description: Marmoset


title: CC.WT.20


title: Vector_control_4


title: CC.WT.22


title: CC.WT.21


title: Vector_control_1


title: TG1

description: Marmoset


title: TLCN019

description: Hepatocellular carcinoma


title: CC.WT.19


title: CC.WT.18


title: SCC2_N

city: Salamanca

first: Sofía

last: Muñoz Félix

address: Campus Miguel de Unamuno

department: Cancer Research Institute (CIC)

country: Spain

institute: Universidad de Salamanca

library_source: genomic

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters -a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20”.
BWA (version 0.5.9-r16) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the yeast sacCer3 genome downloaded from the UCSC (Karolchik et al., 2004).
Alignments were filtered to remove read pairs that were discordant, mapped to different chromosomes, ambiguously mapped, had an insert size outside the range 120-200 bp, and mismatch > 4 in any reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: Genome-wide wig files were generated by treating each pair of reads as a single fragment, and normalising to 10 million reads.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in complete synthetic medium lacking methionine, arrested 1.5 hour with alpha-factor and treated with methionine and indole-3-acetic acid (IAA) for 30 minutes.

extract_protocol:
Preparation of mono-nucleosomal DNA was performed as described (Lantermann et al. 2009) followed by high throughput sequencing on Illumina HiSeq 4000 platform. Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehide. Spheroblasts were obtained and the chromatin digested with 30u/ml of Mnase (ThermoFisher) at 37°C for 20 minutes. The samples were then treated with Proteinase K and RNase A to isolate the undigested, mono-nucleosomal DNA. The DNA was then size selected and purified in a 1.5% agarose gel.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's protocol.

treatment_protocol: Cells were cross-linked with 1% Formaldehide for 20 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

value: MATa pADH1-OsTir1-Myc9::ADE2 URA3::pMET3::SCC2-IAA17::KANMX6 SCC2N-HA3::HIS3

tag: molecule subtype

value: nucleosomal DNA


title: TLCN016

description: Hepatocellular carcinoma


title: SCC2_FL

value: MATa pADH1-OsTir1-Myc9::ADE2 URA3::pMET3::SCC2-IAA17::KANMX6 SCC2-HA3::HIS3


title: SCC2_C

value: MATa pADH1-OsTir1-Myc9::ADE2 URA3::pMET3::SCC2-IAA17::KANMX6 SCC2C-HA3::HIS3


title: Wild type control

city: Callaghan

first: Tessa

last: Lord

state: NSW

address: University Dr

institute: University of Newcastle

description: scRNAseq data from wild-type mouse testis cells (spermatogonia enriched). Three biological replicates were pooled to create a single control sample for scRNAseq.

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline (v2.1.0) and aligned to the mouse mm10 transcriptome.
A total of 2 transcriptomes (control and Zscan2-KO) were merged in R using Seurat
Low quality cell transcriptomes and doublets were assessed within each library and excluded using the following criteria: >200 genes and <40,000 UMI counts for Wild type and >200 genes and <40,000 UMI counts for Zscan2-KO. Filtering based on percent mitochondrial genes detected was conservatively set at <20% for all libraries based on visual inspection of overall distribution and the variability of mitochondrial gene content that occurs based on cell type and proliferation status.
The entire dataset was normalized, scaled (“vars.to.regress” included number of genes, number of UMIs, and percent mitochondrial transcripts), and dimensionally reduced using Seurat.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Gene-Cell Matrix filled with Raw Read/Expression Values

source_name: Testis cell population (spermatogonia enriched)

extract_protocol:
Single cell suspensions of control and Zscan2-KO testis cells were created from n=3 mice for each. The spermatogonia population was isolated using THY1+ MACS beads, and a small number of cells from the total testis cell suspension were 'spiked' back in with these spermatogonia,creating a testis cell population enriched for spermatogonia. An equal number of cells from each of the 3 biological replicates was combined in a single 'wild type' or 'Zscan2-KO' tube. Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v2 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).
scRNA-seq

tag: developmental stage

value: Post-natal Day 8

value: Wild-type


title: TLCN009

description: Hepatocellular carcinoma


title: CC.WT.16


title: TLCN008

description: Hepatocellular carcinoma


title: DEGRON


title: Zscan2 knockout

description: scRNAseq data from Zscan2-KO mouse testis cells (spermatogonia enriched). Three biological replicates were pooled to create a single knockout sample for scRNAseq.

value: Zscan2-/- (global KO)


title: CC.WT.17


title: WT

value: MATa pADH1-OsTir1-Myc9::ADE2


title: Input_R1

city: Charlottesville

first: Shun

last: Fujinuma

state: Virginia

address: Jordan Hall, RM 4061B, 1340 Jefferson Park Ave

institute: University of Virginia

data_processing:
Read QC, trimming and filtering were performed using fastp
Reads were aligned using Bowtie2 against mm10/GRCm38 as reference genome with default parameters
Read counting was performed using featureCounts
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: mouse primary hepatocytes

extract_protocol:
Primary hepatocytes isolated rapidly from 10-week-old C57BL/6 male mice that had been deprived of food for 24 h with or without refeeding for 2 h were fixed with 1% formaldehyde in PBS for 10 min. After neutralization with 1 M glycine, the cells were suspended in ChIP buffer (5  mM HEPES-KOH [pH 8.0], 200  mM KCl, 1  mM CaCl2, 1.5  mM MgCl2, 5% sucrose, 0.5% Nonidet P-40, aprotinin [10  μg/ml], leupeptin [10  μg/ml], 1  mM phenylmethylsulfonyl fluoride, protease inhibitor cocktail [cOmplete, Roche]), subjected to ultrasonic treatment with a Bioruptor (Diagenode), and digested with micrococcal nuclease (New England Biolabs) for 1 h at 37°C. After the addition of EDTA to a final concentration of 20  mM followed by an equal amount of RIPA buffer (50 mM Tris-HCl [pH 8.0], 0.5% sodium deoxycholate, 1% Nonidet P-40, 0.1% SDS, 150 mM NaCl), the digested samples were centrifuged at 15,000 × g for 15  min at 4°C and the resulting supernatants were incubated overnight with rotation at 4°C with Dynabeads M-280 Sheep Anti-Rabbit IgG (Invitrogen) that had been conjugated with antibodies to FOXK1. After washing of the beads twice both with ChIP buffer and with Tris-EDTA buffer, bound proteins were eluted and cross-links were reversed by incubation for 24 h at 65°C with 1% SDS in Tris-EDTA buffer. DNA was purified with the use of a Qiaquick PCR Purification Kit (Qiagen) and was subjected to library preparation.
ChIP-seq libraries were prepared with a SMARTer ThruPLEX DNA-seq Kit (Clontech) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: 10-week-old mice were fasted for 24 hours or refed for 2 hours after 24-hour fasting.

tag: protocol

value: ChIP-seq

tag: treatment

value: Refed for 2 hours after a 24-hour fasting

tag: antibody


title: RT.KO.14

tag: strain

value: Sprague Dawley

value: Ucp1 KO gastroc

value: Room Temperature


title: Input_F2

tag: genotype

value: WT

value: Fasted for 24 hours


title: TLCN004

description: Hepatocellular carcinoma

value: HBV

value: wt


title: TLCN005

description: Hepatocellular carcinoma


title: RT.KO.15


title: TLCN003

description: Hepatocellular carcinoma

value: mut


title: hippocampus, Q808-4

city: Changchun

first: Wei

last: Li

state: Jilin

address: No 155 Chuangju Street

institute: Jilin Provincial Academy of Traditional Chinese Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then theclean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene  were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package  functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or  foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical  cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment  and KEGG pathway enrichment analysis of DEGs were respectively performed using R  based on the hypergeometric distribution
If it was transcript-level quantification, FPKM and read counts value of each transcript  (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using  the DESeq(2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and  foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential  expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts  expression pattern. GO enrichment and KEGGpathway enrichment analysis of DEGs were  respectively performed using R based on the hypergeometric distribution
The reads were reassembled using StringTie. Then gene structure extension and novel  transcripts identification were performed by comparing the reference genome and the known  annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was  performed using ASprofile.  SNP and INDEL were called using samtools and bcftools, and the details were shown on  samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff annotates  and predicts the effects of variants on genes.
Genome_build: ronr 6.0
Supplementary_files_format_and_content: FPKM

source_name: hippocampus

extract_protocol:
Total RNA was extracted from hippocampal tissue sample (about 100 mg)  using TRIzol kit (Invitrogen, USA)  according to the manufacturer’s instructions. RNA purity was checked and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA). Samples with an absorbance (260/280) ratio between 1.8 and 2.2 were considered acceptable. Agilent 2100 Bioanalyzer (Agilent Technologies,  USA) was used to assess the RNA integrity.
The sequencing library was generated by using MGIEasy Universal Library Convert Kit (MGI, China), VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, China), and VAHTS® mRNA Capture Beads (Vazyme, China) according to the manufacturer’s protocols.
instrument model: BGI T7

value: Wistar

tag: tissue

value: hippocampus

tag: weight

value: wild type

value: PTZ + Q808

tag: disease model

value: PTZ-induced seizure model


title: ChIP_R1

value: anti-FOXK1 (abcam, ab18196)


title: hippocampus, Q808-5


title: RT.KO.13

tag: group

tag: temperature


title: Input_F1


title: TLCN002

description: Hepatocellular carcinoma

tag: etiology

tag: ctnnb1 status


title: Input_R2


title: hippocampus, Q808-3


title: RT.KO.12


title: hippocampus, Q808-2


title: LV+TE_C

city: london

first: Alessia

last: Cavazza

state: Greater London

address: 30 guilford street

department: GOS Institute of Child Health

country: United Kingdom

institute: University College London

data_processing:
Sequence tags were mapped to reference genome Hg19 using STAR aligner version 2.5.3
raw read counts from HTSeq43 were used to estimate transcript levels.
DESeq2 was used to normalize data using size factors or rlog transformation and to identify significant (adjusted p-value £ 0.05) differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: File includes normalized FPKM values for each Sample

molecule: polyA RNA

source_name: CD38- hematopoietic stem and progenitor cells

growth_protocol: peripheral blood CD38- cells were harvested from three healthy donors and immediatelyCD38- sorted. They were cultuyred for a total of three days prior harvesting of RNA.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen, Crawley, UK).
RNA-seq libraries were prepared from 50ng RNA using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs, Hitchin, UK) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina, Cambridge, UK).

treatment_protocol: Cells were either transduced or not (NTC) with a lentiviral vector, with the addition (LV+TE) or not (LV) of transduction enhancers

tag: cell type

value: Peripheral Blood

value: transduction enhancer +lentiviral transduction

tag: transduction enhancer

value: LentiBoost+Protamine Sulphate


title: ChIP_F2

value: ChIP-seq


title: LV+TE_B

value: CD38- hematopoietic stem and progenitor cells


title: RT.KO.11

value: Sprague Dawley

value: Ucp1 KO gastroc

value: Room Temperature


title: LV+TE_A


title: RT.KO.09


title: hippocampus, Q808-1


title: RT.KO.10


title: ChIP_R2

value: WT

value: Refed for 2 hours after a 24-hour fasting


title: hippocampus, PTZ-5

value: PTZ


title: ChIP_F1

value: Fasted for 24 hours


title: SI_minus_1

city: San Francisco

first: Richard

last: Locksley

state: CA

address: 513 Parnassus Ave

department: Medicine

institute: UCSF

data_processing:
de-multiplexing raw sequencing results, trimming adapter sequences, and aligning to the reference genome
Sequence alignment and splice junction estimation was performed using STAR software ( 2.7.2b)
genomic alignments were restricted to unique Ensembl IDs (all protein coding mRNAs, coding and noncoding RNAs)
STAR aggregated mappings on a per-gene basis were used as raw input for normalization by DESeq2
Differential expression analysis was performed in the R version 36.1 using DESeq2 version 1.26. Significance thresholds were FDR<0.05 and log fold change >1 or <-1
Genome_build: GRCm38.96
Supplementary_files_format_and_content: counts matrix post-alignment contained in: counts.STARMOUSE.txt

source_name: proximal small intestine

growth_protocol: N/A primary cells

extract_protocol:
EDTA/DTT epithelial extraction followed by sorting on MoFlo XDP cell sorter for DAPI-, singlets, EpCam+, IL-25+ (RFP+ cells) and IL-25- cells
Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers according to manufacturer’s protocol (Illumina). Library fragment size distributions were assessed using the Bioanalyzer 2100 and the DNA high-sensitivity chip (Agilent Technologies). Library sequence quality was assessed by sequencing single-end 50 bp reads using the Illumina MiSeq platform and pooled for high-throughput sequencing on the Illumina HiSeq 4000 by using equal numbers of uniquely mapped reads (Illumina)

treatment_protocol: N/A homeostasis, IL-25 reporter mice (Flare25)

value: proximal small intestine


title: hippocampus, PTZ-4

value: Wistar

value: hippocampus

value: wild type


title: TE_B

value: transduction enhancer


title: RT.WT.08

value: Control gastroc


title: SI_minus_2


title: RT.WT.07


title: TE_A

value: Peripheral Blood


title: RT.WT.05


title: hippocampus, PTZ-2

value: PTZ-induced seizure model


title: LV_B

value: lentiviral transduction


title: SI_plus_1


title: RT.WT.06


title: hippocampus, PTZ-1


title: LV_C

value: CD38- hematopoietic stem and progenitor cells


title: SI_plus_2


title: SI_plus_3


title: hippocampus, control-4

value: control


title: RT.WT.04

value: Sprague Dawley


title: TE_C

value: LentiBoost+Protamine Sulphate


title: hippocampus, control-3


title: LV_A


title: NTC_C

value: untreated


title: RT.WT.03

value: Room Temperature


title: GB_minus_1

source_name: gallbladder

value: gallbladder

value: epithelium

value: mice treated with HDM AF647 (1 day before collection)


title: NTC_B


title: RT.WT.02


title: hippocampus, PTZ-3

value: Wistar

value: PTZ


title: GB_minus_2


title: SI_minus_3

value: proximal small intestine


title: hippocampus, control-2

value: hippocampus

value: wild type


title: GB_minus_3


title: hippocampus, control-1


title: RT.WT.01

value: Control gastroc


title: NTC_A

value: Peripheral Blood


title: GB_plus_2


title: GB_plus_1


title: GB_plus_3


title: NT12175_2

city: Cambridge

first: Pedro

last: Beltrao

address: Wellcome Genome Campus

institute: EMBL-EBI

description: batch: Galardini_HL3G2BGX9

data_processing:
Raw single-ended Illumina reads were trimmed to remove the TruSeq3 adaptors using trimmomatic v0.36.
Trimmed reads were pseudo-aligned to the NC_000913.3 E. coli K-12 genome’s transcripts using kallisto v0.44.0 with the sequence based bias correction and using an average fragment length of 130bp (70bp standard deviation).
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Files starting with the “kallisto_” prefix contain the transcripts counts

organism: Escherichia coli

source_name: E. coli strain culture

growth_protocol: Samples were grown in LB media until an O.D. concentration of about 0.2

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) followed by Dnaze treatment
Samples were subject ro rRNA depletion prior to library preparation

tag: growth condition

value: LB media


title: NT12175_3

description: batch: Galardini_HL3G2BGX9


title: NT12174_3

description: batch: Galardini_HL3G2BGX9


title: NT12131_2

description: batch: Galardini_HL3G2BGX9


title: MI_8wk

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

description: Single cells derived from MI tissues, 8 weeks post-MI surgery

data_processing:
Data were analyzed using CellRanger software 3.0.2 and a pipeline that produces sparse numerical matrices for each sample, with gene-level counts of unique molecular identifiers (UMI) identified for all single cells passing default quality control metrics.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output filtered_feature_bc_matrix in .tar

source_name: Heart

extract_protocol:
Mice were euthanized and perfused with PBS supplemented with EDTA, and hearts were harvested. Infarcted tissue was dissected under a stereomicroscope, and digested with DMEM medium with collagenase-II (5 mg/ml, Invitrogen 17101-015) and DNase (1 mg/ml, Sigma D4527). Single cell suspension was prepared after filtering with a mesh strainer (100-mm pores).
Cells were treated and analyzed following a manufacturer’s V3 library protocol (10x Genomics) and single-cell RNA-seq.

treatment_protocol: MI was induced by ligation of left anterior descending (LAD) coronary artery in Cdh5-CreERT2;Rosa-LSL-tdTomato mice (6-8 weeks old). MI tissue or normal LV tissue were collected 0, 1, 2, 3, or 8 weeks after MI surgery.

value: MI tissue

value: 8 week post-MI surgery


title: DP_thym_KO2

city: Chicago

first: Eva

last: Morgun

state: IL

address: 320 N Superior St

department: Department of Microbiology and Immunology

institute: Northwestern University

data_processing:
Trimmomatic 0.33 was used to trim reads (TRAILING:30 MINLEN:20)
STAR 2.5.2 was used to align reads to mm10 genome
Reads were counted using htseq-count
DESeq2 was used to analyze data for differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Counts for individual samples for every gene. Matrix table with raw gene counts for every gene and every sample. Matrix table with normalized gene expression and associated differential expression analysis results.

source_name: Thymus

extract_protocol:
Single cell suspesion was purified from the thymus and sorted for CD4+/CD8+ DP thymocytes were sorted by FACS BD Aria with a purity more than 98%. RNA was extracted with RNAeasy® Mini Kit according to the protocol of the manufacture (Qiagen).
Libraries were generated using the Illumina TruSeq preparation kit

value: Mettl14fl/fl; CD4-Cre+


title: DP_thym_KO3


title: NT12173_3

description: batch: Galardini_HL3G2BGX9


title: NT12174_2

description: batch: Galardini_HL3G2BGX9


title: DP_thym_WT3

value: WT


title: NT12087_3

description: batch: Galardini_HL3G2BGX9


title: NT12173_2

description: batch: Galardini_HL3G2BGX9


title: Liver_HF+P_4w_no7

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

institute: Kanagawa Institute of Industrial Science and Technology

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: CEL files were quantified with the Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: Liver of mouse administrated 45% high-fat diet added 5% propagule powder

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA ( GeneChip 3'IVT Express Kit User Manual, P/N702646 Rev.8, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Sex

value: male

value: 45% HF diet added 5% propagules powder group (HF+P)

value: liver


title: DP_thym_WT1


title: Liver_HF+P_4w_no4


title: NT12131_3

description: batch: Galardini_HL3G2BGX9


title: Liver_HF+P_4w_no1


title: Tumor D28 rep 2 TCRMsln + anti-PDL1

city: Minneapolis

first: Ingunn

middle: M

last: Stromnes

state: MN

address: 2101 6th St S

department: Microbiology & Immunology

institute: University of Minnesota

hyb_protocol: Standard Affymetrix Protocols

scan_protocol: Standard Affymetrix Protocols

data_processing: Data was RMA normalized, using the Bioconductor package 'oligo'

source_name: Intratumoral TCRmsln T cells

label_protocol: Standard Affymetrix Protocols

extract_protocol: TRIZol extraction

value: KPC tumor

value: Intratumoral TCRmsln T cells

tag: timepoint

value: Day 28 post transfer


title: Liver_HF+P_4w_no2


title: Tumor D28 rep 1 TCRMsln + anti-PDL1


title: Mu KPCY_Usp25-1

city: London

first: Jessica

last: Nelson

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Adaptor removal and quality trimming done with Trimmomatic v 0.36
Read aligngment and gene counts was performed with RSEM v 1.2.31 and STAR v 2.5.2a
Differential expression analysis was carried out with DESeq2 package ( version 1.20.0 ) with R version 3.5.1
Genome_build:  mouse Ensembl GRCm38 - release 89
Supplementary_files_format_and_content: Tab-delimited text includes normalized counts per gene and per sample (generated by DESeq2).

source_name: pancreatic tumor organoid

growth_protocol: Murine pancreatic tumor organoids were grown in Matrix gel, in a 24-well plate as 25-50µL drops. Organoids were grown in media composed of Advanced DMEM/F12 supplemented with 1x GlutaMAX, 1x B27 supplement, 1.25 mM NAcetylcysteine, 10 nM Gastrin, 50 ng/mL EGF, 10% RSPO1-conditioned media, 10% NOGGIN-conditioned media, 100 ng/mL hFGF10, 100 mM Nicotinamide and 50 U ml−1 penicillin/ streptomycin. Organoids were passaged every 5-7 days

extract_protocol:
Total RNA was extracted the RNeasy Mini Kit (Qiagen) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Organoids were dissociated from the Matrix gel, passed through a 40 µM filter, resuspended in filtered lentiviral supernatant supplemented with Polybrene. Cells were spin-infected (700 xg, 90 min, 25°C) on low-adhesion 6-well plates, followed by a rotation incubation at 37°C for 4-5 hrs.  Post-incubation, organoids were centrifuged at 400 xg for 3 min at 4°C, and seeded in Matrigel at 50 µL per well in 24-well plate. Puromycin selection was started 3 days post transduction for 30 hours prior to analysis.

value: pancreatic tumor-derived organoid

tag: age

value: passage 8

value: Pdx1-Cre; LSL-KrasG12D; Trp53flox/flox; Rosa26-LSL-YFP

tag: transduction

value: shRNAs targeting Usp25


title: Tumor D8 rep 4 TCRMsln + anti-PDL1

value: Day 8 post transfer


title: DP_thym_KO1


title: NT12086_3

description: batch: Galardini_HL3G2BGX9


title: Liver_HF+P_4w_no3

tag: treatment


title: Tumor D8 rep 1 TCRMsln + anti-PDL1


title: NT12086_2

description: batch: Galardini_HL3G2BGX9

tag: strain


title: NT12087_2

description: batch: Galardini_HL3G2BGX9


title: Liver_HF+P_4w_no8


title: Liver_HF_4w_no3 [re-analysis]

source_name: Liver of mouse administrated 45% high-fat diet

value: 45% high-fat diet group (HF)


title: Liver_HF_4w_no4 [re-analysis]


title: Spleen D28 rep 3 TCRMsln + anti-PDL1

source_name: Splenic TCRmsln T cells

value: KPC spleen

value: Splenic TCRmsln T cells


title: Spleen D28 rep 5 TCRMsln + anti-PDL1


title: Mu KPCY_Usp25-4

tag: genotype


title: DP_thym_WT2


title: Liver_HF_4w_no5 [re-analysis]

tag: tissue


title: NT12132_3

description: batch: Galardini_HL3G2BGX9

value: LB media


title: Mu KPCY_Usp25-3


title: Mu KPCY_Usp25-2


title: NT12131_1

description: batch: Galardini_HL3G2BGX9


title: Tumor D8 rep 3 TCRMsln + anti-PDL1


title: Mu KPCY_YFP-3

value: control


title: Spleen D28 rep 4 TCRMsln + anti-PDL1


title: Tumor D8 rep 2 TCRMsln + anti-PDL1


title: Mu KPCY_YFP-2


title: NT12132_2

description: batch: Galardini_HL3G2BGX9


title: Spleen D28 rep 2 TCRMsln + anti-PDL1


title: Liver_HF_4w_no8 [re-analysis]


title: Mu KPCY_YFP-1


title: NT12137_2

description: batch: Galardini_HL3G2BGX9


title: NT12025_2

description: batch: Galardini_HL3G2BGX9


title: MI_3wk

description: Single cells derived from MI tissues, 3 weeks post-MI surgery

value: MI tissue

value: 3 week post-MI surgery


title: NT12292_2

description: batch: Galardini_HL3G2BGX9


title: MI_2wk

description: Single cells derived from MI tissues, 2 weeks post-MI surgery

value: 2 week post-MI surgery


title: Liver_HF_4w_no2 [re-analysis]

value: male

value: liver


title: MI_1wk

description: Single cells derived from MI tissues, 1 week post-MI surgery

value: 1 week post-MI surgery


title: Liver_HF_4w_no8


title: Spleen D8 rep 3 TCRMsln + anti-PDL1


title: Liver_HF_4w_no5


title: NT12286_2

description: batch: Galardini_HL3G2BGX9


title: Spleen D8 rep 4 TCRMsln + anti-PDL1


title: Spleen D28 rep 1 TCRMsln + anti-PDL1

value: Day 28 post transfer


title: Liver_HF_4w_no4


title: Liver_HF_4w_no1 [re-analysis]


title: Spleen D8 rep 1 TCRMsln + anti-PDL1


title: Spleen D8 rep 2 TCRMsln + anti-PDL1


title: Control

description: Single cells derived from normal LV tissue

value: Normal LV tissue

value: Without MI surgery


title: Liver_HF_4w_no3


title: NT12285_2

description: batch: Galardini_HL3G2BGX9


title: Liver_HF_4w_no1


title: Liver_LF_4w_no8

source_name: Liver of mouse administrated low-fat diet

value: low-fat diet group (LF)


title: Spleen D8 rep 1 TCRMsln


title: Liver_LF_4w_no5


title: Tumor_D28_rep3 TCRMsln

value: KPC tumor

value: Intratumoral TCRmsln T cells


title: Tumor_D28_rep2 TCRMsln


title: NT12133_3

description: batch: Galardini_HL3G2BGX9


title: siPRMT7+IFNγ rep3

city: Montreal

first: Stephane

last: Richard

state: Quebec

address: 3755 Côte-Ste-Catherine Road

department: Departments of Oncology and Medicine

institute: Lady Davis Institute - JGH, McGill University

description:
SiPRMT7_plus_IFN__Serie3
rlogNorm.differential.xlsx

data_processing:
Illumina HiSeq 4000.
Sequenced reads were trimmed with Trimmomatic v0.39.
STAR v2.7.1a was then used to align the reads to the mouse genome (mm10/GRCm38).
Gene expression was quantified across all samples with HOMER v4.11.1, and the normalization was carried out through the regularized logarithm (rlog) transformation of DESeq2 v1.26.0.
Differential expression was calculated through DESeq2 v1.26.0, and the gene expression was considered significantly different if the absolute value of the log-fold-change (LFC) was higher than 2, the base means larger than 10 and the false discovery rate (FDR) less than 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rlogNorm.differential.xlsx: rlog table with fold change and p value.

source_name: B16.F10 melanoma cell line

extract_protocol:
B16.F10 melanoma cells were collected at 72h after siRNA treatment and RNA samples were purified using GenElute™ Mammalian Total RNA Miniprep Kit (RTN70, Sigma Aldrich). Total RNA was assessed for quality using an Agilent Tapestation 4200, and RNA sequencing libraries were generated using TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, Hiseq4000, SR75 platform located at San Diego, CA; UCSD IGM Genomics Facility, La Jolla, CA). Samples were processed following manufacturer’s instructions and 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: B16.F10 melanoma cell lines were transfected with siLuc (control) and siPRMT7 for 72h. 24h before collecting the samples, cells were exposed to 100IU/mM interferon gamma (Mouse IFN-γ, Cat#130-105-785, MACS, Miltenyibiotec). At 72 h, samples were collected for RNA extraction.

tag: cell line

value: Melanoma cell line

tag: strain/background

value: PRMT7 KD

value: IFNgamma 100ng/ml for 24h


title: NT12133_2

description: batch: Galardini_HL3G2BGX9

value: LB media


title: siLuc+IFNγ rep3

description:
SiLuc_plus_IFN__Serie3
rlogNorm.differential.xlsx

value: PRMT7 WT


title: siPRMT7-IFNγ rep3

description:
SiPRMT7-IFN__Serie3
rlogNorm.differential.xlsx

value: Untreated


title: Liver_HF_4w_no2

value: 45% high-fat diet group (HF)


title: Liver_LF_4w_no4


title: Spleen D8 rep 3 TCRMsln

value: KPC spleen

value: Splenic TCRmsln T cells

value: Day 8 post transfer


title: siLuc-IFNγ rep3

description:
SiLuc-IFN__Serie3
rlogNorm.differential.xlsx


title: NT12223_2

description: batch: Galardini_HL3G2BGX9


title: Sperm_B10

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

data_processing:
Programs FastQC (0.11.5) and Trim Galore (0.4.5) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus ARS-UCD1.2) using bowtie2 under the Bismark software (0.19.0)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position,strand, coverage for methylated cytosine, coverage for unmethylated cytosine, CG type, three bases near the cytosine.

organism: Bos taurus

source_name: Sperm

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

tag: breed

value: Holstein

value: Sperm


title: NT12576_2

description: batch: Galardini_HL3G2BGX9

value: NILS 43


title: siPRMT7+IFNγ rep2

description:
SiPRMT7_plus_IFN__Serie2
rlogNorm.differential.xlsx


title: NT12573_2

description: batch: Galardini_HL3G2BGX9

value: NILS 40


title: Sperm_A10


title: siPRMT7-IFNγ rep2

description:
SiPRMT7-IFN__Serie2
rlogNorm.differential.xlsx


title: NT12132_1

description: batch: Galardini_HL3G2BGX9


title: Liver_LF_4w_no3

value: male

value: low-fat diet group (LF)

value: liver


title: NT12572_2

description: batch: Galardini_HL3G2BGX9

value: NILS 39


title: siLuc+IFNγ rep2

description:
SiLuc_plus_IFN__Serie2
rlogNorm.differential.xlsx

value: Melanoma cell line


title: Tumor_D8_rep2 TCRMsln

value: KPC tumor

value: Intratumoral TCRmsln T cells


title: Liver_LF_4w_no2


title: Liver_LF_4w_no1


title: Tumor_D8_rep1 TCRMsln


title: siLuc-IFNγ rep2

description:
SiLuc-IFN__Serie2
rlogNorm.differential.xlsx

value: PRMT7 WT


title: Tumor_D28_rep1 TCRMsln

value: Day 28 post transfer


title: Effector_D12_rep2

source_name: In vitro activated and TCRmsln transduced mouse effector CD8 T cells

value: P14 spleen

value: In vitro activated (aCD3+aCD28) P14 T cells transduced w/ TCRMsln

value: Day 12 post 1st stim, Day 5 post 2nd stim


title: Naïve_D0_rep2

source_name: Naïve mouse splenic CD8 T cells

value: Naïve CD8 T cells

value: Ex vivo


title: Tumor_D8_rep3 TCRMsln

value: Day 8 post transfer


title: Effector_D12_rep1


title: NT12393_2

description: batch: Galardini_HL3G2BGX9

value: LB media


title: siPRMT7+IFNγ rep1

description:
SiPRMT7_plus_IFN__Serie1
rlogNorm.differential.xlsx

value: PRMT7 KD

value: IFNgamma 100ng/ml for 24h


title: NT12442_2

description: batch: Galardini_HL3G2BGX9


title: siPRMT7-IFNγ rep1

description:
SiPRMT7-IFN__Serie1
rlogNorm.differential.xlsx

value: Untreated


title: BMDM_LPS_rep3

city: Greifswald

first: Janine

last: Golchert

address: Felix-Hausdorff-Str. 8

department: Department of Functional Genomics

country: Germany

institute: University Medicine Greifswald

hyb_protocol: 2.5 µg of fragmented and biotinylated cDNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: Quality of hybridizations was assessed using Expression Console software and microarray data were analyzed using Rosetta Resolver software including RMA normalization.

label: Biotin

source_name: BMDM

label_protocol: Biotinylated cDNA were prepared according to the GeneChip® Whole Transcript PLUS Reagent Kit manual starting from 200 ng total RNA.

growth_protocol: BMDMs were isolated from C57Bl/6 mice (n=3) and maintained in RPMI medium in the presence of macrophage colony stimulating factor (MCSF) (20ng/ml) for 7days.

extract_protocol: Extraction of total RNA was performed with TRIzol reagent. After purification of total RNA, quality control was performed using an Agilent 2100 Bioanalyzer.

treatment_protocol: BMDMs were co-incubated with freshly prepared acinar cells +/-50µg Nafamostat or treated with 1µg LPS.

value: bone marrow derived macrophages (BMDM)

value: C57/Bl6 J

value: wild type


title: NT12551_2

description: batch: Galardini_HL3G2BGX9

value: NILS 18


title: BMDM_Acini_rep1


title: BMDM_LPS_rep2


title: NT12571_2

description: batch: Galardini_HL3G2BGX9

value: NILS 38


title: siLuc+IFNγ rep1

description:
SiLuc_plus_IFN__Serie1
rlogNorm.differential.xlsx

value: Melanoma cell line

value: PRMT7 WT


title: Mes_YesFGF2_biological_rep3

city: Albany

first: Nicholas

last: Moskwa

state: New York

address: 1400 Washington Avenue

institute: University at Albany

description: Stromal portion of organoids grown for 7 days

hyb_protocol: Samples were hybridized to the Affymetrix Clariom D Assay, Mouse for 16-18 h at 45°C.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000

data_processing:
Data were processed using Transcriptome Analysis Console software and R/Rstuio. The data were analyzed with the robust multichip analysis (RMA) algorithm using default analysis settings and global scaling as a normalization method. Values are presented according to log2 RMA signal intensity. We defined the genes with a fold-change of more than 1.99 or less than 1.99 and a p-value of less than 0.05 as different expression genes
MTA-1_0.r3.pgf
MTA-1_0.r3.Psrs.mps

label_protocol: Samples were enzymatically fragmented and biotinylated by terminal deoxynucleotidyl transferase (TdT) (Clariom D Kit)

growth_protocol: Organoids were cultured for 7 days with a 4 day media change

extract_protocol: Total RNA was extracted using RNeasy Mini-Kit (Qiagen), then cDNA synthesis and amplification (Clariom D Kit)

treatment_protocol: Grown with or without FGF2 containing media

value: organoids

value: Stromal


title: Naïve_D0_rep1

value: P14 spleen


title: NT12177_2

description: batch: Galardini_HL3G2BGX9


title: siLuc-IFNγ rep1

description:
SiLuc-IFN__Serie1
rlogNorm.differential.xlsx


title: Spleen D8 rep 2 TCRMsln

value: KPC spleen

value: Splenic TCRmsln T cells


title: BMDM_LPS_rep1


title: BMDM_Control_rep3


title: BMDM_Control_rep2


title: Mes_NoFGF2_biological_rep3

value: control


title: NT12175_1

description: batch: Galardini_HL3G2BGX9

value: LB media


title: NANOS3 overexpression rep3

city: Poznan

first: Jadwiga

last: Jaruzelska

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

data_processing:
The pair-end sequence reads obtained from HiSeq4000 platform were trimmed and quality filtered using TRIMMOMATIC V0.36.3 with the following parameters: ILLUMINACLIP:TruSeq2:PE MINLEN:50, SLIDINGWINDOW:5:20
Sequence reads that passed quality filters were mapped to the human reference genome hg38 using Bowtie 2 v2.3.4.1 with default parameters
Mapped reads were counted using featureCounts v1.6.0.3 with default parameters
Differential Gene Expression analysis was performed with DESeq2 v2.11.40.1
Genome_build: hg38
Supplementary_files_format_and_content: Tabular text file with gene counts after NANOS3 overexpression

source_name: TCam-2 cells

growth_protocol: TCam-2 cells were grown in 37oC and 5% CO2 in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS (HyClone) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) according to manufacturer protocol
The cDNA libraries were prepared using Illumina Truseq RNA Sample Prep V2 with standard protocol

treatment_protocol: TCam-2 cells were transfected with pCMV6-Entry plasmid containing NANOS1 or NANOS3  ORF or empty plasmid, using NEON transfection/electroporation system (Thermo Fisher Scientific). Transfections were performed in Buffer R using 10µl NEON tips. Subsequently after transfection cells were cultured in antibiotic-free RPMI 1640 (Gibco) supplemented with 10% FBS (HyClone), at 37 oC and 5 % CO2, for 24 hours.

tag: genotype/variation

value: NANOS3 overexpression

value: TCam-2 cells


title: Mes_YesFGF2_biological_rep2


title: NT12174_1

description: batch: Galardini_HL3G2BGX9


title: Injured nerve input2

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Illumina Pipeline  Casava 1.8.2
Reads were mapped to the reference genome rn5 using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) to produce BAM files, and the files from the two biological replicates were combined for further analysis.
BAM files were filtered for mapped reads using BamTools (Barnett et al., 2011; Quinlan and Hall, 2010) and peaks were called using MACS2 (Feng et al., 2012; Liu, 2014; Zhang et al., 2008).
BedTools bamCoverage generated bedgraphs of ChIP-seq samples.
Genome_build: Rn5
Supplementary_files_format_and_content: bedgraph and peak bed files

source_name: sciatic nerve

growth_protocol: Male Sprague Dawley rats (Harlan Laboratory) were housed with a normal light/dark cycles and ad libitum access to rat chow and water.

extract_protocol:
Freshly dissected rat sciatic nerve was used for ChIP-seq using the MNase protocol described previously (Ma et al., 2018) with 4μg of JUN antibody (Santa Cruz SC-1694, RRID:AB_631263).
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.
Two biological replicates were performed, and samples with respective inputs were sequenced on a Illumina HiSeq 2500 instrument at the UW Biotechnology Center.

treatment_protocol: Sciatic nerves of adult Sprague-Dawley rats were cut following the surgery protocol described previously (Hung et al., 2015). The nerve tissue distal to the transection awas isolated at 8 d post-transection.

value: Sprague Dawley

tag: developmental stage

value: Male

tag: fraction

value: input

value: Injury


title: NT12130_2

description: batch: Galardini_HL3G2BGX9


title: NT12173_1

description: batch: Galardini_HL3G2BGX9


title: Mes_NoFGF2_biological_rep2

tag: cell type


title: NANOS3 overexpression rep1


title: NT12165_2

description: batch: Galardini_HL3G2BGX9


title: Injury Sciatic nerve JUN ChIP-seq 2

value: ChIP DNA

tag: antibody

value: JUN


title: BMDM_Control_rep1

value: bone marrow derived macrophages (BMDM)

value: C57/Bl6 J

value: wild type


title: Injured nerve input1


title: Mes_NoFGF2_biological_rep1

value: organoids

value: Stromal


title: NT12167_2

description: batch: Galardini_HL3G2BGX9

tag: growth condition


title: calu3_072h_ctrl_zn089

city: Santa Cruz

first: Jeremy

last: Sanford

address: 1156 High St

department: Molecular, Cell and Developmental Biology

institute: UC Santa Cruz

description: small RNA (100bp)

data_processing:
Reads were mapped against human/African Green Monkey repeat elements in their respective genomes for initial repeat-filtering using Bowtie 2
Repeat-filtered reads were then mapped against their respective STAR indexes (joint hg38-wuhCor1 or chlSab2-wuhCor1) using STAR v2.5.3a "--alignEndsType EndToEnd" option
Gene-level quantification and comparisons using DESeq2
Called peaks in sRNA-seq data mapped to wuhCor1 using Piranha v1.2.1
Quantified unique wuhCor1-mapped sRNA-seq coordinates using in-house python script
Predicted duplexes between host (human or African Green Monkey) transcripts and SARS-CoV-2 sRNAs using RNAhybrid v2.1.2
Genome_build: UCSC (hg18, chlSab2 and wuhCor1)
Supplementary_files_format_and_content: Gene-level counts [mRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to host quantified with DESeq2 (.csv), sRNA mapping to SARS-CoV-2 quantified with in-house script (.csv)], SARS-CoV-2 sRNA peaks [called with Piranha (.bed)], sRNA Interactions [predicted with RNAhybrid (.csv)]

source_name: lung cancer cells – Calu-3

growth_protocol: DMEM + 1% heat inactivated FBS, 100U/mL penicillin, 100 μg/mL streptomycin in 5% CO2 at 37°C

extract_protocol:
Trypsin-EDTA 0.25% (ThermoFIsher Scientific), then 250 μl Trizol
NEXTFLEX small RNA-Seq Kit v3 (Perkin Elmer Applied Genomics)

value: lung cancer

value: control (uninfected)

tag: hours post-treatment

tag: moi


title: calu3_072h_ctrl_zn090

description: small RNA (100bp)


title: NT12160_2

description: batch: Galardini_HL3G2BGX9

source_name: E. coli strain culture


title: NANOS3 overexpression rep2


title: Mes_YesFGF2_biological_rep1

tag: age


title: N4

city: Mexico City

first: Luis

middle: Alonso

last: Herrera Montalvo

state: Mexico City

address: Periferico Sur 4809, Arenal Tepepan, Tlalpan

department: Unidad de Investigacion Biomedica en Cancer

country: Mexico

institute: Instituto Nacional de Cancerología / Instituto Nacional de Medicina Genómica

data_processing:
Adapter trimming and low-quality reads were filtered out using trimmomatic v.0.39
Reads were mapped to the rat genome with STAR v.2.7.1a, and also to the rat transcriptome with salmon v.0.14.1, using assembly version Rnor6 with ensembl annotations version 6.0.95
Gene level counts from reads mapped to the genome were quantified using featureCounts in the rsubread
Differential expression analysis was performed with DEseq2  and edgeR, with a paired design ~ specimen + treatment
Genome_build: Rnor6
Supplementary_files_format_and_content: tab separated text file with raw counts for genes (ENSEMBL ids) quantified with salmon

source_name: Hippocampus, Brain

growth_protocol: Primary hippocampal neuronal cultures were obtained from Wistar rat brains obtained from 17-day-old embryos. Hippocampi were dissected, minced with a scalpel in Krebs solution and incubated with 0.25% trypsin at 37 °C for 10 min. The hippocampi were mechanically dissociated using a cell strainer and the cellular suspension was homogenized in neurobasal medium (Gibco 21103049) supplemented with 2% B27 (Gibco 17504044), 0.5 mM L-Glutamine (Gibco 25030-081) and 20 µg/mL penicillin/streptomycin (Gibco 15140-122). Every plate and coverslip were previously coated with 10 µg/mL poly-L-lysine for 24 h. Cytosine arabinoside (10 µM) was added to cultures 3 days after plating to inhibit the growth of non-neuronal cells. Hippocampal neurons were used for experiments after 12 days in vitro (DIV) and were maintained at 37 °C in a humidified 5% CO2/95% air atmosphere.

extract_protocol:
Total RNA was isolated using TRIzolTM reagent (Thermo Fisher Scientific) as specified by the manufacturer.
Libraries were constructed using 500 ng of RNA, using the Truseq Stranded mRNA library prep kit from Illumina according to the manufacturer’s instruction. The libraries were sequenced using an Illumina HiSeq2500 equipment (Illumina, Inc.) in Pair-end (2x125 bases)

treatment_protocol: PA (Sigma-Aldrich) was added. PA was prepared as a stock solution in ethanol and the working solution was prepared the same day of use in 10% bovine serum albumin (BSA)/phosphate buffered saline (PBS) and was incubated at 37 °C for at least 2 h before adding it to the cell cultures.

value: Neuron primary cell culture

value: 200 uM Palmitic Acid

tag: specimen


title: N5

tag: treatment


title: Ad-Nox4 infected mouse articular chondrocytes_rep 1

city: Suwon

first: Jimin

last: Jeon

address: 206, World cup-ro, Yeongtong-gu

department: Biomedical Sciences

country: South Korea

institute: Ajou University Graduate School of Medicine

description: Gene expression data from Ad-Nox4 infected mouse articular chondrocytes

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Cultured were maintained at 37 °C in an humidified atmosphere containing 5% CO2 as a monolayer in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 10% fetal bovine serum and antibiotics (penicillin G and streptomycin). 37 °C, 5% CO2

extract_protocol: Total RNA was extracted from mouse articular chondrocytes using a Purelink RNA mini kit (Ambion). The concentration, purity, and integrity of the extracted RNA were determined by spectrophotometry.

treatment_protocol: mouse articular chondrocytes were infected with Ad-Nox4. The cells were harvested for total RNA extraction at 36 h post treatment.

value: mouse articular chondrocytes

value: Ad-Nox4 infection


title: calu3_072h_cov2_zn087

description: small RNA (100bp)

value: Infected – SARS-CoV-2


title: NT12567_2

description: batch: Galardini_HL3G2BGX9

tag: strain

value: NILS 34

value: LB media


title: N1


title: calu3_072h_cov2_zn086

description: small RNA (100bp)


title: Ad-C infected mouse articular chondrocytes_rep 1

description: Gene expression data from Ad-C infected mouse articular chondrocytes

value: Ad-C infection


title: NT12564_2

description: batch: Galardini_HL3G2BGX9

value: NILS 31


title: Ad-C infected mouse articular chondrocytes_rep 2


title: calu3_072h_cov2_zn085

description: small RNA (100bp)


title: calu3_048h_ctrl_zn084

description: small RNA (100bp)


title: Ad-Nox4 infected mouse articular chondrocytes_rep 2


title: NT12137_1

description: batch: Galardini_HL3G2BGX9


title: Ad-Activin A infected mouse articular chondrocytes_rep 2

description: Gene expression data from Ad-Activin A infected mouse articular chondrocytes

treatment_protocol: mouse articular chondrocytes were infected with Ad-Activin A. The cells were harvested for total RNA extraction at 36 h post treatment.

value: Ad-Activin A infection


title: N5CT

value: Vehicle


title: Ad-Activin A infected mouse articular chondrocytes_rep 1


title: NT12136_2

description: batch: Galardini_HL3G2BGX9


title: calu3_048h_ctrl_zn083

description: small RNA (100bp)


title: calu3_072h_ctrl_zn088

description: small RNA (100bp)


title: N4CT


title: N1CT


title: NT12133_1

description: batch: Galardini_HL3G2BGX9


title: calu3_048h_ctrl_zn082

description: small RNA (100bp)


title: NT12552_2

description: batch: Galardini_HL3G2BGX9

value: NILS 19


title: calu3_048h_cov2_zn081

description: small RNA (100bp)


title: NT12130_1

description: batch: Galardini_HL3G2BGX9


title: NT12119_2

description: batch: Galardini_HL3G2BGX9


title: GIST55

city: Yushima, Bunkyo-ku

first: Yoshimi

last: Yasukawa

institute: national cancer center research institute, Japan

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: The data were analyzed using GenomeStudio Methylation Module Software (v1.9.0). Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

source_name: GIST fibroblast

label_protocol: Standard Illumina Protocol

growth_protocol: CAFs or GIST fibroblasts were maintained in MF medium.

extract_protocol: High-quality DNA was extracted by the phenol/chloroform method.

value: fibroblasts from non-tumoral region of GIST patient

tag: pathological type

value: GIST, H.pylori(-)

tag: tumor stage


title: GIST54

tag: tissue


title: GIST70


title: calu3_048h_cov2_zn080

description: small RNA (100bp)

tag: cell line


title: iPSC derived cerebral organoid - Mock M3_D30

city: Milwaukee

first: Sridhar

last: Rao

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
Reference Genome was generated by combining the raw sequences for hg19 and human herpesvirus strain 5 (Genbank ID : EF999921.1)
Trascript sequences were extracted from the combined gtf file
The index for reference transcript genome was created using "Salmon index"
Mapping -based mode using "Salmon quant" to quantify only transcript sequences against combined transcripts
Genome_build: HG19 + Human herpesvirus strain 5
Supplementary_files_format_and_content: ReadCounts_Day30.xlsx in spreadasheet format giving the details of estimated readcounts

source_name: Cerebral Organoid

growth_protocol: iPSCs were maintained as colonies prior to the start of differentiation, cerebral organoid differentiation was initiated by dissociation of colonies to single cells, plating of 9,000 cells in a round bottom 96 well where they spontaneously form embryoid bodies, from there they're patterned to a neuroepithelial fate through media changes and rocking on a rocker. At D30 the organoids are mature an infected with HCMV TB40eGFP @ MOI of 1 or left uninfected.

extract_protocol:
Infected organoids were sorted for GFP expression 14 days post infection, this resolved three populations GFP (+), GFP Inter, and GFP (-) plus the mock group, which was used to set gates. After sorting, the cells were spun down and RNA was isolated from each population. As mentioned above, three organoids were combined within infected groups from the same line and differentiation to ensure high enough cell numbers.
After RNA was isolated and quantified, the NEBNext Poly(A) mRNA Magnetic Isolation Module Kit was used to generate cDNA libraries which were then quantified using qPCR and the tapestation ultimately run on a Illumina HiSeq 2000

treatment_protocol: For infection at D30 of organoid differentiation, organoids were weighed and then the amount of virus was determined based on weight with MOI of 1 being used and viral strain TB40eGFP. Fresh media and virus were left on the organoids for 2 hours while rocking, after this 2 hour period the virus was removed and organoids washed with PBS. Fresh media was then added and the infection was monitered for 14 days prior to sorting.

value: iPSC derived cerebral organoid

tag: line

value: Uninfected


title: Injury Sciatic nerve JUN ChIP-seq 1

value: Sprague Dawley

tag: Sex

value: Male

value: ChIP DNA

value: JUN

value: Injury


title: calu3_048h_cov2_zn079

description: small RNA (100bp)

value: lung cancer

value: Infected – SARS-CoV-2


title: CAF68

source_name: CAF

value: cancer-associated fibroblasts from scirrhous gastric cancer


title: iPSC derived cerebral organoid - Mock D

description: MockD


title: calu3_024h_ctrl_zn078

description: small RNA (100bp)

value: control (uninfected)


title: CAF67


title: calu3_024h_ctrl_zn077

description: small RNA (100bp)


title: BMDM_Acini+Nafamostat_rep3

value: bone marrow derived macrophages (BMDM)

value: C57/Bl6 J

tag: genotype

value: wild type


title: BMDM_Acini+Nafamostat_rep2


title: BMDM_Acini+Nafamostat_rep1


title: BMDM_Acini_rep3


title: CAF66


title: iPSC derived cerebral organoid - Mock C

description: MockC


title: NT12153_2

city: Cambridge

first: Pedro

last: Beltrao

institute: EMBL-EBI

description: batch: Galardini_HL3G2BGX9

data_processing:
Raw single-ended Illumina reads were trimmed to remove the TruSeq3 adaptors using trimmomatic v0.36.
Trimmed reads were pseudo-aligned to the NC_000913.3 E. coli K-12 genome’s transcripts using kallisto v0.44.0 with the sequence based bias correction and using an average fragment length of 130bp (70bp standard deviation).
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Files starting with the “kallisto_” prefix contain the transcripts counts

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) followed by Dnaze treatment
Samples were subject ro rRNA depletion prior to library preparation

value: LB media


title: BMDM_Acini_rep2


source_name: Ad-C infected mouse articular chondrocytes

value: mouse articular chondrocytes

value: Ad-C infection


title: iPSC derived cerebral organoid - Mock A

description: MockA

value: iPSC derived cerebral organoid


title: CAF63


title: calu3_024h_ctrl_zn076

description: small RNA (100bp)


title: calu3_024h_cov2_zn075

description: small RNA (100bp)


title: NT12148_2

description: batch: Galardini_HL3G2BGX9


title: CAF50


title: NT12140_2

description: batch: Galardini_HL3G2BGX9


title: VCAP RNF43i-4 Wnt3a 6hrs

city: Boston

first: Fen

last: Ma

state: MA

address: 3 Blackfan Circle

department: Hem/Onc

institute: BIDMC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 with parameters -p 8 -x hg38 -1 $read1 -2 $read2 -S
Samtools were used to generate sorted bam files
Count reads were annotated to the human genome with htseq-count to generate the count matrix file
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: VCaP

growth_protocol: VCaP cells were cultured in DMEM with 10% FBS

extract_protocol:
Total RNA was isolated using the RNeasy Mini Plus Kit (Qiagen, Cat No./ID: 74134)
1000 ng of total RNAs from each sample were sent to HudsonAlpha (https://www.dls.com/biopharma/research-services/hudsonalpha-discovery) for transcriptome library construction, libraries were generated using the NEB Ultra Directional RNA Library Prep Kit according to manufacture's instructions.

treatment_protocol: VCaP cells were transfected with control SiRNA, SiAPC-2/3(two independent SiRNAs) or SiRNF43-3/4(two independent SiRNAs) plus Wnt3a(100ng/ml, 7hrs) for 72hrs and harvested for RNA purification. All samples in biological duplicates.

value: prostate cancer

value: TMPRSS2_ERG Fusion

value: RNF43 knockdown plus Wnt3a stimulation


title: VCAP RNF43i-4


title: NT12087_1

address: Wellcome Genome Campus

description: batch: Galardini_HL3G2BGX9


title: calu3_024h_cov2_zn074

description: small RNA (100bp)


title: CAF36


title: VCAP RNF43i-3 Wnt3a 7hrs

value: RNF43 knockdown


title: CAF30

value: cancer-associated fibroblasts from non-scirrhous gastric cancer


title: NT12089_4

description: batch: Galardini_HL3G2BGX9


title: VCAP APCi-4

value: APC knockdown


title: calu3_024h_cov2_zn073

description: small RNA (100bp)

value: lung cancer


title: NT12082_2

description: batch: Galardini_HL3G2BGX9


title: NT12086_1

description: batch: Galardini_HL3G2BGX9


title: CAF42


title: CAF45


title: VCAP RNF43i-3


title: calu3_012h_ctrl_zn070

description: small RNA (100bp)


title: NT12118_2

description: batch: Galardini_HL3G2BGX9


title: NT12068_2

description: batch: Galardini_HL3G2BGX9


title: calu3_012h_ctrl_zn072

description: small RNA (100bp)


title: calu3_012h_cov2_zn069

description: small RNA (100bp)

value: Infected – SARS-CoV-2


title: VCAP APCi-2


title: NT12055_2

description: batch: Galardini_HL3G2BGX9


title: calu3_012h_ctrl_zn071

description: small RNA (100bp)


title: CAF23


title: NT12084_2

description: batch: Galardini_HL3G2BGX9


title: VCAP non target control_1

value: non target control knockdown


title: DB_HBO18_P2_2_S23

city: San Francisco

first: Hanbing

last: Song

address: 513 Parnassus Ave, HSE

department: Department of Medicine

institute: UCSF

data_processing:
Demultiplexed pair-end FASTQ files were aligned to mm8 whole genome using dropseq_workflow pipeline on Terra
Genome_build: hg19
Supplementary_files_format_and_content: txt format matrix table with raw gene counts for every gene and every cell barcode

source_name: Spheroid Grown from Tumor (Early Passage)

extract_protocol:
Tumor and adjacent normal liver tissues were dissociated by mincing tissue in 1-2mm squares, followed by incubation in Liver Perfusion Medium (ThermoFisher Scientific) for 15 min at 37°C in a rotating oven. After being washed in PBS (ThermoFisher Scientific), tissues were incubated with Liver Digest Medium (ThermoFisher Scientific) supplemented with HEPES and collagenase type IV (Worthington Biochemical, Lakewood, NJ) (600 to 800 U/ml) for 30 min at 37°C with rotation. Further dissociation was achieved by pipetting 10 times through a 25 mL serological pipette. Single cells were then separated from clumps using a 70 µm strainer (Fisher Scientific, Hampton, NH). After lysis of red blood cells with ACK RBC Lysis Buffer (Fisher Scientific), single cells were counted using a LUNA™ Automated Cell Counter (Logos biosystems, South Korea) and processed for scRNA-seq analysis. Patient derived spheroids embedded in Matrigel were washed with PBS, then digested in TrypLE 1X (ThermoFisher Scientific) for 30 to 45 min at 37°C with rotation to obtain a single cell suspension. Cells were washed, then, filtered through a 70-µm strainer, counted using a LUNA™ Automated Cell Counter, and processed for scRNA-seq analysis.
Libraries were prepared for each pool, using 800-1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides. Library products were purified using SPRI beads, first at 0.6x and then at a 1x volumetric ratio. Libraries were then run on an HSD1000 tape (Agilent, Cat: 50675584) to determine the concentration between 100-1000 bp. For each library, 3 nM dilutions were prepared. These dilutions were pooled for sequencing on a NovaSeq S4 flow cell.

tag: sample type

value: Spheroid (Early Passage)

value: liver

tag: patient


title: CAF17


title: CAF19


title: CAF38


title: NT12044_2

description: batch: Galardini_HL3G2BGX9


title: calu3_012h_cov2_zn068

description: small RNA (100bp)

tag: cell type


title: calu3_000h_ctrl_zn066

description: small RNA (100bp)

value: control (uninfected)


title: VCAP non target control_2


title: NT12027_2

description: batch: Galardini_HL3G2BGX9

tag: growth condition


title: NT12110_2

description: batch: Galardini_HL3G2BGX9


title: calu3_000h_ctrl_zn065

description: small RNA (100bp)

tag: hours post-treatment


title: DB_HBO16_P10_2_S13

source_name: Spheroid Grown from Tumor (Late Passage)

value: Spheroid (Late Passage)


title: CAF5


title: NT12105_2

description: batch: Galardini_HL3G2BGX9

value: LB media


title: CAF2


title: calu3_000h_ctrl_zn064

description: small RNA (100bp)

tag: moi


title: DB_HBO16_P2_2_S21


title: DB_HBO18_P2_1_S22


title: NT12004_4

description: batch: Galardini_HL3G2BGX9


title: NT12095_4

description: batch: Galardini_HL3G2BGX9


title: NT12113_2

description: batch: Galardini_HL3G2BGX9


title: DB_HBO16_P2_1_S20


title: calu3_000h_cov2_zn063

description: small RNA (100bp)


title: CAF3


title: ECs-Mg [RNA-seq]

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

source_name: Ecs-YHC-Mg

growth_protocol: All cell lines were cultured under an atmosphere of 5% CO2 at 37°C. Human Coronary Artery Endothelial Cells (HCAEC) purchased from ScienCellTM (San Diego, California) were cultured in Endothelial Cell Medium (ScienCellTM). The medium package consists of 500 ml of basal medium, 25 ml of fetal bovine serum (ScienCellTM), 5 ml of endothelial cell growth supplement (ECGS, ScienCellTM) and 5 ml of penicillin/streptomycin solution (P/S, ScienCellTM).

extract_protocol:
Total RNA from each sample was extracted using Trizol reagent (Invitrogen, CA, USA) as the manufacturer’s instruction.
After agarose gel electrophoresis for quality control and NANODROP check for quantification, total RNA was used to prepare the sequencing library. The quality control of library were conducted by Agilent 2100 and quantified by qPCR.

treatment_protocol: HCAECs cultued on Magnesium-based alloy discs 24h, and static cultured HCAECs were used as control

tag: passages

tag: catalog

value: ScienCell #6020

value: Magnesium-based alloy discs 24h


title: ECs-control [RNA-seq]

source_name: Ecs-YHC-Control

value: Human Coronary Artery Endothelial Cells (HCAEC)

tag: treatment

value: static cultured


title: DB_HBO16_P10_1_S12


title: NT12001_5

description: batch: Galardini_HL3G2BGX9

tag: strain


title: FS1_TCam, rep 4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

description: SAMPLE 16

hyb_protocol: Purified Cy3-labeled antisense RNA was hybridized overnight to Agilent 60-mer oligonucleotide spotted microarray slides.Hybridization and subsequent washing and drying of the slides were performed following the Agilent hybridization protocol.

scan_protocol: The slides were scanned using a GenePix 4100A Scanner (Axon Instruments at a resolution of 2 µm/pixel.

data_processing: Image analysis was performed using GenePix Pro 5.1 software (Axon Instruments) followed by data evaluation using the R software and the Bioconductor limma package [57, 58]. The log of the mean spot signals was recorded for further analysis. Signals of replicate spots (same probes) within arrays were averaged. Intensity data were normalized using quantile normalization before calculating the average probe intensity of the array. Genes were ranked for differential expression using a moderated t-statistic.

source_name: FS1 cells

label_protocol: After assessing RNA quality by capillary electrophoresis on a 2100 Bioanalyzer (Agilent Technologies), purified total RNA was amplified and labeled with Cy3 using a dual-color LIRAK kit (Agilent Technologies) according to manufacturer’s instructions. Briefly, the RNA samples (500 ng/ reaction) were labeled with Cy3.

growth_protocol:
Cell lines and cell culture
The human Sertoli cell line FS1 [FS1] was provided by Dr. V. Schumacher (Boston Children’s Hospital, Department of Urology; Harvard Medical School, Department of Surgery, Boston, MA, USA). The Sertoli cells were obtained from the testes of a 19 years old patient with Frazier syndrome, characterized by insufficient action of WT1 causing reduction of the downstream SOX9 expression, and with focal GCNIS. FS1 has been immortalized with both the wildtype large T-antigen and the temperature sensitive large T-antigen. FS1 was cultured in medium I, comprising Dulbecco’s modified Eagle medium (Invitrogen), supplemented with 4.5 g/l D-glucose, 40 µM L-glutamine (Sigma), 1% sodium pyruvate (Gibco, by Life Technologies), 20% fetal calf serum (PAA Laboratories GmbH), 1% nonessential amino acids, and 1% penicillin/ streptomycin (Biochrom GmbH).
The human seminoma cell line TCam-2 [TCam2] was provided by Prof. Dr. H. Schorle (University Hospital Bonn, Department of Developmental Pathology, Institute of Pathology, Bonn, Germany). It was cultured in medium II, comprising Rosewell Park Memorial Institute 1640 medium (Gibco) supplemented with 2 mM L-glutamine, 10% fetal calf serum, and 1% penicillin/streptomycin). Each cell line was incubated in 75-cm2 flasks (1 x 106 cells/flask) at 37°C in a humidified incubator with 5% CO2, with medium changes every 2 or 3 days. Cells reaching 80% of confluency were used in subsequent experiments. The cell lines were authenticated by the providers and checked for mycoplasma, using a LookOut® Mycoplasma PCR Detection Kit (Sigma-Aldrich).
Cell co-culture model
For direct co-culture, a defined number of FS1 cells (passages 14-16) were cultured in a 6-well plate. After 24 hours, medium was replaced by a 1:1 mixture of medium I and II and a defined number of TCam-2 cells was added. For insert co-culture, FS1 (passages 14-16) (50,000 cells/well) and TCam-2 cells (50,000 cells/well) were co-cultured for 3 weeks in medium I (1.5 ml) and medium II (2 ml) using 6 well ThinCert™ cell culture inserts (Greiner Bio-One). The medium was changed on every third day.
For control, FS1 cells were cultured in direct and in indirect co-culture with equine bone marrow derived mesenchymal stromal cells, eBM-MSC (kindly provided by Prof. Dr. C. Staszyk, Department of Veterinary Anatomy, Histology and Embryology, Justus-Liebig-University, Giessen, Germany). For further controls, monocultures of FS1 and TCam-2 cells were used. All control groups were cultured under the same conditions as the experimental group. For each condition, four biological replicates were generated. The co-culture experiments were repeated at least 10 times.
References:
[FS1] Schumacher, V.; Gueler, B.; Looijenga, L.H.; Becker, J.U.; Amann, K.; Engers, R.; Dotsch, J.; Stoop, H.; Schulz, W.; Royer-Pokora, B. Characteristics of testicular dysgenesis syndrome and decreased expression of SRY and SOX9 in Frasier syndrome. Mol Reprod Dev, 2008, 75, 1484-1494. DOI: 10.1002/mrd.20889
[TCam2] Eckert, D.; Nettersheim, D.; Heukamp, L.C.; Kitazawa, S.; Biermann, K.; Schorle, H. TCam-2 but not JKT-cells resemble seminoma in cell culture. Cell Tissue Res, 2008, 331, 529-538. DOI: 10.1007/s00441-007-0527-y

extract_protocol: RNA was extracted from the cell cultures using the peqGOLD Total RNA Kit (Peqlab Biotechnologie GmbH) and purified with a RNeasy Mini Kit (Qiagen) according to the manufacture instructions.

tag: culture

value: co-culture

tag: cell line(s)


title: DB_HBO14_P11_2_S15

tag: tissue


title: NT12879_2

description: batch: Galardini_HL3G2BGX9


title: calu3_000h_cov2_zn061

description: small RNA (100bp)

tag: cell line


title: NT12001_4

description: batch: Galardini_HL3G2BGX9


title: NT12002_4

description: batch: Galardini_HL3G2BGX9


title: DB_HBO14_P3_1_redo


title: DB_HB012T_P10_2_S16_L001


title: calu3_012h_cov2_zn067

description: small RNA (100bp)


title: calu3_000h_cov2_zn062

description: small RNA (100bp)


title: DB_HBO14_P11_1_S14


title: DB_HBO14_P3_2_redo


title: M2 input

city: Nanning

first: Lequn

last: Li

state: Guangxi

address: Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, He Di Rd #71

institute: Guangxi Medical University

data_processing:
The raw data were filtered using the Solexa/Illumina ‘chastity’ filter, and clean reads were aligned to the UCSC human genome database (HG19; http://genome.ucsc.edu/) using HISAT2 software (v.2.1.0)
MeDIP enriched regions (peaks) with statistical significance were identified using MACS (v.2), with a q-value threshold of 10-4. Both mRNA and LncRNA associated MeDIP enriched regions (peaks) were annotated to the nearest gene using the newest UCSC RefSeq database.
Differentially methylated regions (DMRs) within promoters and between two groups with statistical significance were identified as diffReps (cut-off: log2FC = 1.0, p-value = 10-5).
Both mRNA and LncRNA associated those DMRs that were within promoters were annotated to the nearest gene using the UCSC RefSeq database and an integration of multiple databases. DMRs between groups were then further examined via GO enrichment and KEGG pathway analyses.
Genome_build: HG19
Supplementary_files_format_and_content: wig

source_name: U937-M1 macrophages

growth_protocol: U937 cells were plated in 24-well plates at a density 2 × 10e5 cells per well and cultured with fresh RPMI-1640 medium supplemented with 5% FBS at 37˚C in humidified air with 5% CO2.

extract_protocol:
The genomic DNA in each group was extracted using a phenol and chloroform method and sonicated with a Bioruptor sonicator (Diagenode) to generate 200–700 bp fragments.
The libraries were constructed following the Illumina genomic DNA protocol and adaptor-ligated DNA was immunoprecipitated using 5′-methylcytidine antibodies. The MeDIP products and supernatant DNA were then purified using MinElute columns (Qiagen, Valencia, CA, USA) and eluted in 16 μL of elution buffer (EB; Qiagen). The products were verified using qPCR, with 5 μL of DNA examined per sample using single-end Illumina PCR primers. The methylated DNAs were amplified in situ using a TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina), and the quality of the fragments between 300–800 bp was evaluated using an Agilent BioAnalyzer. Sequencing was performed using an Illumina HiSeq 4000 according to the manufacturer’s instructions.

treatment_protocol: To acquire the M2 phenotype, the cells were stimulated with phorbol 12-myristate 13-acetate (PMA, 100 ng/mL) for 24 h, followed by the addition of interleukin (IL)-4 (20 ng/mL) and IL-13 (20 ng/mL) for 12 h. The M1 phenotype was obtained by pretreating with PMA (100 ng/mL) for 24 h, followed by incubating with lipopolysaccharide (LPS; 100 ng/mL) and interferon (IFN)-gamma (20 ng/mL).

value: macrophage

tag: phenotype

value: M2 (M2 macrophages induced from M0 U937 cells)

tag: ip antibody


title: DB_HB012T_P10_1_S15_L001


title: M2-U937-3

source_name: U937-M2 macrophages

value: anti-5-methylcytosine antibody


title: M1 input

value: M1 (M1 macrophages produced from M2 macrophages)


title: NT12670_2

description: batch: Galardini_HL3G2BGX9


title: DB_HB012T_P3_2_S19_L001


title: NT12025_1

description: batch: Galardini_HL3G2BGX9


title: FS1, rep 4

description: SAMPLE 15

value: monoculture


title: FS1, rep 3

description: SAMPLE 14


title: FS1, rep 2

description: SAMPLE 13


title: FS1_TCam, rep 3

description: SAMPLE 12


title: FS1_TCam, rep 2

description: SAMPLE 10


title: BEM3

city: Birmingham

first: Kai-Michael

last: Toellner

state: West Midlands

address: 4th Floor IBR, Wolfson Drive

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

data_processing:
Reads were aligned against the GCRm38 genome assembly with Ensembl release 86 transcript annotations and expected gene-level counts were calculated using either STAR v2.7.3a or Partek Flow.
Count data were rounded to integers and normalized for differences in sample library size using the standard median ratio method in DESeq2 (Anders and Huber, 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized log2 counts in tab-delimited text format.  Gene ids are represented by Ensembl v86 identifiers.

source_name: IgG1+ Bmem

extract_protocol:
Single cell suspensions from lymph nodes were depleted of erythrocytes by ACK lysis buffer and stained with live/dead marker and respective antibodies in FACS buffer (1x PBS with EDTA and FCS). Cells were directly sorted into 500ul of Trizol. The total RNA was purified using the RNeasy Plus Micro kit (QIAGEN) according to the manufacturer’s instructions.
Un-stranded, non-rRNA, non-polyA+ selected libraries were prepared using the SMARTer Ultra Low Input RNA kit for Sequencing v3 (Clontech Laboratories).
The libraries were sequenced on the Illumina HiSeq 2000 platform (Illumina, Crick advanced sequencing) as 75 bp paired-end runs.

treatment_protocol: Mice received adoptive cell transfers of 1x10^5 NP+B220+ splenocytes from IgHNP QM k-/- Cg1cre mTmG splenocytes, 24 hours later were immunised with 20µg/µl NP-CGG in alum precipitate with heat-inactivated bordetella pertussis adjuvant on the plantar surface of hind feet. At day 8 post-immunisation GC and emigrating memory B cells were isolated from popliteal (draining) lymph nodes and naive B cells and circulating memory B cells were isolated from distal (pooled axillary and brachial) lymph nodes were collected. All mice were aged 8-12 weeks.

tag: Sex

value: male

tag: organ

value: drainLN


title: M1-U937-3


title: NT12015_4

description: batch: Galardini_HL3G2BGX9


title: BEM2


title: NT12879_1

description: batch: Galardini_HC3HYBGX9


title: M2-U937-1


title: FS1, rep 1

description: SAMPLE 11


title: NT12023_4

description: batch: Galardini_HL3G2BGX9


title: GC3

source_name: GCs


title: DB_HB012T_P3_1_S35_L002

tag: sample type

value: Spheroid (Early Passage)

tag: patient


title: DB_HBO4th_P10_1_2

value: liver


title: GC4


title: NT12671_2

description: batch: Galardini_HL3G2BGX9

tag: growth condition


title: GC2


title: NT12670_1

description: batch: Galardini_HC3HYBGX9


title: DB_HB018T_1_2

source_name: Hepatoblastoma Patient Paired Tumor Tissue Sample

value: Paired Tumor


title: DB_HBO4th_P2_1_redo


title: DB_HBO4th_P2_2_redo


title: M1-U937-1

tag: cell type


title: M1-U937-2


title: M2-U937-2


title: FS1_TCam, rep 1

description: SAMPLE 9


title: GC1


title: NT12576_1

description: batch: Galardini_HC3HYBGX9

source_name: E. coli strain culture

value: NILS 43


title: DB_HB016T_2


title: NT12671_1

description: batch: Galardini_HC3HYBGX9

value: LB media


title: NT12573_1

description: batch: Galardini_HC3HYBGX9

value: NILS 40


title: DB_HB016T_1


title: BCM3

value: distLN


title: NT12572_1

description: batch: Galardini_HC3HYBGX9

value: NILS 39


title: DB_HB014T_1_2_redo


title: DB_HB015H_1

source_name: Hepatoblastoma Patient Paired Normal Tissue Sample

value: Paired Normal


title: NAIVE4

source_name: naïve from host


title: DB_HB017H_1_2