title: KO uninfected PRO513A8

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Cellrnager was used to process the fastq files to produce the PRO513Ax.tar files below.
The Seurat package was used to produce the SeuratObect.rds file below from the Cellranger count and metadata files.  Quality control included restricting to cells with percent.mt < 10 and nCount_RNA > 5000 and restricting to genes with min.cells=10.  The resulting 8 individual Seurat objects were integrated using IntegrateData()

source_name: Tunica muscularis

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
For isolation of EGCs, the longitudinal smooth muscle layer and associated myenteric plexus were peeled off the wall of the smal intestineand subjected to enzymatic digestion to prepare a single-cell suspension. Single-cell suspensions were subjected to fluorescence activated cell sorting and live cells were isolated based on DAPI exclusion. Cells were quantified using the Eve Automatic Cell Counter and trypan blue. Approximately 10 000 cells were loaded into a 10x Chromium Chip G (10x 3’ v3.1) and partitioned into GEMs using the 10x Chromium Controller. cDNA was generated using the manufacturers protocol -and quantified using the Agilent TapeStation (D5000 ScreenTape).
Libraries were prepared according to the manufacturers guidelines and QC’d using the Agilent TapeStation and the High Sensitivity dsDNA Qubit.

treatment_protocol: All mice were injected with tamoxifen on two consecutive days 10 days prior single cell isolation and some mice were infected with H. poly 7 days prior single cell isolation.

tag: disease state

value: naive

tag: Stage

value: adult


title: WT uninfected PRO513A7

status: Public on Aug 21 2021

type: SRA

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus


title: KO infected PRO513A6

value: infected


title: Single blastomere WGA product (B1) from the embryo E03 in the pedigree Cross01 [E03_B1_Cross01]

type: genomic

city: Leuven

first: Joris

middle: R.

last: Vermeesch

address: Herestraat 49 box 606

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

description: Single blastomere WGA DNA from embryo was genotyped using BovineHD BeadChip arrays (Illumina).

hyb_protocol: According to the manufacturer's protocol of Infinium HD Assay for BovineHD BeadChip arrays.

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA) according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA)

data_processing:
Samples were genotyped using the BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA. The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. The discrete genotypes were determined using a threshold of 0,75. We subsequently analysed these data with haplarithmisis adapted for bovine (Zamani Esteki et al. 2015, AJHG).
[value definition] Genotypes: AA,AB,BB or NC (No Call); BAF: B-allele frequency; logR: log2ratio

molecule: genomic DNA

organism: Bos taurus

source_name: blastomere

label_protocol: 200 ng of gDNA and 600 ng of whole-genome amplified DNA was used as input for processing the samples according to the manufacturer's protocol of BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA).

growth_protocol: Embryos were in vitro produced according to previously described methods (Catteeuw et al., 2017). Cleavage-kinetics of the first division were monitored from 21 h post fertilization onwards by cultivation of embryos in a time-lapse monitoring system.

extract_protocol: Extraction of gDNA from sperm, blood and ovarian tissue was performed using the Qiagen DNeasy Blood and Tissue kit according to the manufacturer's protocol (sperm: user-developed protocol for purification of total DNA from animal sperm using the DNeasy® Blood & Tissue Kit; protocol 2). Single blastomere and whole-embryo DNA was whole-genome amplified using the REPLI-g SC kit (Qiagen) according to the manufacturer's instructions with full or half reaction volumes and a 3 h incubation reaction.

treatment_protocol: Single blastomeres or cells derived from bovine embryos identified to have undergone a multipolar zygotic division by time-lapse imaging were dissociated immediately following  the first division (E01_Cross01 to E25_Cross12) or at the blastocyst stage (E26_Cross13 to E30_Cross17) and whole-genome amplified. Briefly, the zona pellucida was removed by pronase treatment and single blastomeres were dissociated mehcanically and picked individually. For dissociation at the blastocyst stage, pronase treatment and a subsequent combination of trypisinsation and mechanical dissociation was used to pick single cells.

tag: tissue

value: Embryonic

tag: molecule subtype

value: Whole-genome amplified DNA


title: E1.R3

city: Nanjing

first: Shouyin

last: Li

state: Jiangsu

address: Nanjing, China

country: China

institute: Nanjing Forestry University

data_processing:
Raw reads were filtered by removing reads containing adapters and ambiguous ‘N’ nucleotides >10 %, and low quality reads (defined as reads with >20 % of the bases with quality scores < 10) in SeqPrep software (https://github.com/jstjohn/SeqPrep) before transcriptome assembly.
These clean reads of all samples were pooled, and then de novo assembled without a reference genome in TRINITY program with default parameters
The non-redundant sequences were obtained through removing redundancy in CD-HIT software (http://weizhongli-lab.org/cd-hit/), and the longest transcript of each gene was defined as a ‘unigene’. To annotate the obtained unigenes, six public databases including NR (NCBI non-redundant proteins, e-value ≤ 1.0 × 10-5), Swiss-Prot (e-value ≤ 1.0 × 10-5), Pfam (Protein families, e-value ≤ 1.0 ×10-5), COG (Cluster of orthologous group, e-value ≤ 1.0 ×10-5), GO (Gene ontology, e-value ≤ 1.0 ×10-5), KEGG (Kyoto Encyclopedia of Genes and Genomes, e-value ≤ 1.0 ×10-10), were searched.
Supplementary_files_format_and_content: Tap-delimited text files include TPM values for each Sample

organism: Pagiophloeus tsushimanus

source_name: The whole body

extract_protocol:
All RNA-seq samples were processed for total RNA extraction using TRIzol Reagent (TaKaRa, Japan) according to the manufacturer’s protocol. RNA quantity was checked using a Nanodrop 2000 (Termo Thermo Scientific, Waltham, MA, United States).The complementary DNA (cDNA) libraries were generated with NEBNext UltraTM RNA Library Prep Kits for Illumina (NEB, Beverly, MA, United States) following the manufacturer’s protocol. The high quality of the libraries was confirmed using a high sensitivity DNA chip on Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, United States).
RNA libraries were prepared for sequencing using standard illumina protocols

tag: treatment

value: Larvae feeding on the diet treated with D_camphor_41mg_g

tag: cell type

value: Body cell


title: E1.R1


title: E1.R2


title: D1.R3

value: Larvae feeding on the diet treated with D_camphor_17mg_g


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-3_Tim01

type: RNA

city: MILL VALLEY

first: Brian

middle: A

last: Hodge

state: CA

address: 338 EDGEWOOD AVE, A

country: USA

institute: Buck Institute

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the third of four replicates.

hyb_protocol: Samples were hybridized to the 12-plex Gene Expression array platform according to the manufacturers' protocol. NimbleGen's Sample Tracking Controls (05223512001), Hybridization Kit reagents (05583683001) and Wash Buffers (05584507001) were used. Each 12-plex array was sealed with a H12 mixer, provided with the Gene Expression array. 4µg of each Cy3 labeled sample was loaded onto an array on the 12-plex chip, using a Gilson M100 pipette. Hybridization was completed overnight on a NimbleGen Hybridization System 4 unit, at 42℃ for 16hrs.

scan_protocol: After the 12-plex chip was washed and dried, the chip was scanned on a GenePix 4200A scanner at 300PMT, 100POW. Arrays were then quantitated using NimbleGen's NimbleScan2 software.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003); The *Cycle data provides the processed data that has been analyzed with the JTK_CYCLE algorithm.

organism: Drosophila melanogaster

source_name: 35 female Tim01 mutant flies reared on AL-diet for seven days

label_protocol: For each experimental sample, approximately 150ng of total RNA was amplified with Sigma's TransPlex Complete Whole Transcriptome Amplification Kit (WTA2). Qiagen's QIAquick PCR Purification Kit (28104) was used to purify the amplified samples. Following purification, the samples were further processed on the QIAcube according to the manufacturers' protocol: QIAquick PCR Purification-Standard. For each biological sample the NimbleGen (Roche) One-Color DNA Labeling kit (05223555011) was used to label dscDNA with Cy3 according to the manufacturers' protocol.

extract_protocol: Total RNA was extracted from whole fly lystates of approximately 35 flies (4 biological replicates per diet and time-point) with Qiagen's Rneasy Lipid Tissue Mini Kit (74804). Samples were then lysed in Qiagen's Qiazol lysis buffer with Qiagen's TissueLyser (pulverized for approximately nine minutes). Qiagen's QIAcube robot was used to futher proccess the samples utilizing a modified version of Qiagen's QIAcube protocol: RNeasy Lipid Tissue Mini-Animal Tissues-Aqueous Phase.

treatment_protocol: Four-day old mated female flies (Canton-S and Tim01) were sorted on either Ad libitum (5.0% yeast-extract) or Dietary Restriction (0.5% yeast-extract) and reared in a 12:12hr light-dark cycle for seven days. On the seventh day flies were collected every four hours for 20 hours (6 timepoints) starting at ZT 0 (lights on).

tag: strain

tag: time of collection

value: ZT 0 (8:00am, lights on)

tag: diet

value: Ad libitum (5% yeast-extract)


title: D.Melanogaster_female_whole-fly-lysate_AL-diet_ZT0_Replicate-1_Tim01

description:
processed data file: Tim01_AL_JTK_CYCLE.txt
This sample is from mated Tim01 mutant females reared on AL (5% yeast-extract) diet for seven days and collected at ZT 0. RNA was extracted and pooled from whole-fly lysates from approximately 35 flies. This sample is the first of four replicates.


title: D1.R2


title: Pool of EAE mice 5 and 6 [EAE285302]

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
demultiplexing with bcl2fastq v2.17
adapter trimming with cutadapt v1.18; reads < 60bp after trimming are discarded
mapping to GRCm38 using STAR v2.6.1c
feature assignment to GRCm38 (GENCODE v23) using subread v1.6.1
differential expression analysis using DESeq2 v1.24.0
Genome_build: GRCm38 (GENCODE v23)
Supplementary_files_format_and_content: tab-separated text file containing rlog-normalized counts

source_name: oligodendrocytes

growth_protocol: Cells were directly isolated from the brain and not cultured.

extract_protocol:
Oligodendrocytes were isolated using magnetic beads with O4 antibodies. RNA was then extracted using the ReliaPrep RNA Miniprep System (Promega) according to the manufacturer's instructions.
Libraries of cDNA fragments were generated using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Mice were immunized with MOG 35-55 peptide or treated with ovalbumin.

value: MOG 35-55 immunization

value: oligodendrocytes


title: OVA mouse 1 [OVA304]

value: ovalbumin treatment


title: Pool of OVA mice 2 and 3 [OVA305306]


title: OVA mouse 4 [OVA300]


title: WT-DNAme rep2

city: Xiamen

first: liu

last: kai

state: Fujian

address: Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

library_source: genomic

data_processing:
Image analysis and base calling were performed with Illumina CASAVA pipeline
Adapter trimming was performed using trimmomatic version 0.36
Bismark software (version 0.16.3) was used to perform alignments of bisulfite-treated reads to a reference genome
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools version 3.2.1
Supplementary_files_format_and_content: peak text files in .gz

source_name: Spleen

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA mini kit (Qiagen).
A total amount of 1.5 μg genomic DNA spiked with moderate lambda DNA were handled by MspI, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to DNA as per manufacturer’s instructions. Then these DNA fragments were treated with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research).

treatment_protocol: On day 5 post-infection with LCMV Armstrong, transferred P14 cells were sorted from the spleen of donor mice.

value: spleen

tag: genotype

value: wild type

tag: Sex

value: male

value: day 5 post-infection

tag: age

value: 12 weeks


title: D1.R1


title: Pool of EAE mice 1 and 2 [EAE284303]


title: WT infected PRO513A5

value: adult


title: WT infected PRO513A4

value: infected


title: Single blastomere WGA product (B4) from the embryo E02 in the pedigree Cross01 [E02_B4_Cross01]

value: Embryonic


title: KO infected PRO513A1


title: KO uninfected PRO513A3

value: naive


title: C1.R2

value: Larvae feeding on the diet treated with EO_30mg_g


title: Single blastomere WGA product (B3) from the embryo E02 in the pedigree Cross01 [E02_B3_Cross01]

value: Whole-genome amplified DNA


title: Single blastomere WGA product (B2) from the embryo E02 in the pedigree Cross01 [E02_B2_Cross01]


title: WT Rep 1

city: South Bend

first: Qingfei

last: Wang

state: IN

address: 1234 N Notre Dame Ave, Harper Hall A121

department: Harper Cancer Research Institute

institute: University of Notre Dame

data_processing:
Library strategy: Drop-seq
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/).
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene…

source_name: naïve brain myeloid cells

extract_protocol:
Mice were perfused with PBS and brains extracted. Brains digested with papain-based neural tissue dissocation kit (Miltenyi). Mononuclear cells enriched by 70%/37%/30% percoll gradient centrifugation. Mononuclear cells enriched by MACS-based Cd11b enrichment (Miltenyi).
RNA libraries were prepared for sequencing using standard Illumina protocols for Nextera XT DNA sample prep kit

tag: mouse strain

tag: sequencer

value: HiSeq 2500

tag: 1 brain or pooled

value: 1 brain

tag: genotype/variation


title: WT uninfected PRO513A2


title: Single blastomere WGA product (B1) from the embryo E02 in the pedigree Cross01 [E02_B1_Cross01]


title: ATACseq  Brg1flox/flox rep4

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Mars-seq: Reads were trimmed using Cutadapt
Mars-seq: Reads were aligned to the genome using STAR
Mars-seq: Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
ATAC-seq: Reads were aligned to the genome using Bowtie2
ATAC-seq: Normalized read coverage files were computed by deepTools
ATAC-seq: Peaks were called using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with Deseq2 output, bigWig read coverage

growth_protocol: Splenic B cells were isolated using magnetic separation (CD43/Ly-48 Microbeads, Miltenyi Biotec) and cultivated in a density of 1 million/mL in RPMI-1640 medium including 25mM HEPES, supplemented with 10% fetal calf serum, L-glutamine, pyruvate, non-essential amino acids, β-mercapto-ethanol

extract_protocol:
50,000 cells were centrifuged (500g, 3 minutes), then washed using 50 μL of cold PBS, and centrifuged again (500g for 3 min). Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Next, the pellet was re-suspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 minutes at 37 °C and immediately transfered to ice. The sample was then purified using Qiagen MinElute kit.  Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification the libraries were purified using a Qiagen MinElute Kit.    50,000 cells were centrifuged (500g, 3 minutes), then washed using 50 μL of cold PBS, and centrifuged again (500g for 3 min). Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Next, the pellet was re-suspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 minutes at 37 °C and immediately transfered to ice. The sample was then purified using Qiagen MinElute kit.  Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification the libraries were purified using a Qiagen MinElute Kit.
As in Buenrstro et al. 2013

treatment_protocol: B cells taken into culture were immediately treated with with 10 µg/mL LPS and 20 ng/mL IL-4 for 72 hours, up until lysates were generated for RNA extraction and library preparation

value: B cells

value: Brg1fl/fl CD23Cre +/-


title: Single blastomere WGA product (B3) from the embryo E01 in the pedigree Cross01 [E01_B3_Cross01]


title: Met Rep 1

source_name: brain metastasis-associated myeloid cells

value: metastases


title: Pool of EAE mice 3 and 4 [EAE299283]

value: MOG 35-55 immunization

value: oligodendrocytes


title: Single blastomere WGA product (B2) from the embryo E01 in the pedigree Cross01 [E01_B2_Cross01]


title: S06_Z3_Y124

city: Boston

first: Amanda

middle: J.

last: Guise

state: MA

address: 3 Blackfan Circle

department: F.M. Kirby Center for Neurobiology

institute: Boston Children's Hospital & Harvard Medical School

description:
gene_exp.diff
genes_fpkm.tracking
genes.read_group_tracking

data_processing:
Fastq files were evaluated with FastQC for sequence quality (Mean Phred Score > 37)
Reads were mapped to the mouse genome (v. GRCm38.p5, (GRCm38), version M14 (Ensembl 89)) using Bowtie (v. 2.2.4) (Langmead et al., 2009) and Tophat (v. 2.1.1) (Kim et al., 2013) with the following options enabled: library type --fr-unstranded --coverage-search --no-mixed --no-discordant with the Gencode reference GTF supplied (-G option).
Following the first Tophat search, read insert size information was extracted using Picard for inclusion in a second refined Tophat search specifying --mate-inner-dist and --mate-std-dev.
Resulting .bam files were assembled using Cufflinks (v. 2.2.1) (Trapnell et al., 2010), followed by additional analysis using Cuffmerge, Cuffcompare, and Cuffdiff (Trapnell et al., 2013) specifying two sample groups (CNTL or ZIKV) for determination of differentially expressed genes and transcripts. For Cuffdiff analysis, FPKMs and fragment counts were scaled to the median of the geometric means of fragment counts across all libraries. Cuffdiff dispersion models were constructed using the “pooled” dispersion method, in which a single global model for all experimental conditions is generated from averaged models built from individual conditions and replicates
Genome_build: v. GRCm38.p5, (GRCm38), version M14 (Ensembl 89)
Supplementary_files_format_and_content: FPKMs, log2(fold_change)

source_name: E14.5 mouse brain

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit (Invitrogen) combined with TRIZOL purification and treated with Turbo DNA-free Kit (Invitrogen).Whole E14.5 brains were collected for RNA-seq analysis. Three embryos from different litters in which ZIKV copies were > 1010 copies/ug RNA were selected from the ZIKV-injected group, and 3 littermates with mock injection were selected as controls. RNA was extracted as described above. RNA integrity number (RIN) measured by Bioanalyzer (Agilent) for all samples was above 9.0.
Libraries were constructed using TruSeq RNA Kit (Illumina).

treatment_protocol: Timed-pregnant adult CD1 mice (Charles River Laboratories) were maintained under a 12-hour light/dark schedule to acclimate for >48 hours. Plug dates were considered to be E0.5. Pregnant CD-1 mice at specific embryonic dates were anesthetized continuously with isoflurane and laparotomy was performed for ZIKV injections. According to methods previously reported (Bonnin et al., 2011; Li and Tsutsui, 2000), 105 flow-infectious units (FIU; similar to plaque forming unit (PFU)) of ZIKV suspended in 1μl PBS were injected through the uterine wall into the labyrinth region in 50% of placentas for each pregnant mouse. The remaining 50% of placentas were injected with vehicle (PBS) only. To improve manipulation, 0.1% Fast Blue B Salt Dye (Sigma-Aldrich; D9805) was used to visually monitor diffusion of solution into fetal villi in the placenta.

tag: developmental stage

value: Brain

tag: litter number

tag: infection

value: ZIKV


title: C1.R3

value: Body cell


title: B1.R2

value: Larvae feeding on the diet treated with EO_10mg_g


title: C1.R1


title: ATACseq  Brg1flox/flox rep2


title: B1.R1


title: B1.R3


title: Paternal grandparental gDNA for pedigree of Cross12  (E24/E25) [Paternal grandparent_Bull_B]

description: Genomic DNA extracted from bull blood was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: blood

tag: tissue

value: sperm


title: Maternal grandparental gDNA for pedigree of Cross12  (E24/E25) [Maternal grandparent_Bull _B]

description: Genomic DNA extracted from cow blood was genotyped using BovineHD BeadChip arrays (Illumina).

value: Blood


title: S04_Z2_Y107


title: S03_C2_Y104

value: control


title: Bull gDNA  for pedigrees of Cross13 to Cross17 (E26-E31) [Bull_C]

description: Genomic DNA extracted from bull sperm was genotyped using BovineHD BeadChip arrays (Illumina).

source_name: semen

value: Sperm


title: ATACseq  Brg1 flox/plus rep4

value: Brg1fl/+ CD23Cre +/-


title: ATACseq  Brg1flox/flox rep1


title: A1.R3

value: Untreated


title: ATACseq  Brg1 flox/plus rep3


title: A1.R2


title: S02_Z1_Y094


title: Bull gDNA  for pedigrees of Cross09 to Cross12 (E21-E25) [Bull_B]


title: A1.R1


title: S01_C1_Y091


title: S05_C3_Y128


title: ATACseq Brg1flox/flox rep3


title: Bull gDNA  for pedigrees of Cross01 to Cross08 (E01-E20) [Bull_A]


title: Single blastomere WGA product (B1) from the embryo E01 in the pedigree Cross01 [E01_B1_Cross01]

value: Embryonic

tag: molecule subtype

value: Whole-genome amplified DNA


title: 22_month_injury_820_rep_4

status: Public on Aug 20 2021

city: Washington DC

first: Susan

middle: M

last: Knoblach

state: District of Columbia

address: 111 Michigan Ave NW

department: Research Ctr for Genetic Medicine

institute: CNH

hyb_protocol: One hundred ng of mRNA was applied to the NanoString nCounter Mouse Immunology panel (NanoString Technologies, Seattle, WA), following the manufacturer’s protocol.

scan_protocol: Scanned with NanoString SPRINT profiler following manufacturer's protocol.

data_processing: The raw digital transcript counts (RCC files) and corresponding reporter library files (RLF) were imported into NanoString nSolver v 4.0 software for analysis of quality control parameters, determination of the raw counts for each transcript. and data normalization using standard default software settings.  Raw counts were multiplied by scaling factors proportional to the sum of counts for spiked-in positive control probes to account for individual assay efficiency variation, and to the geometric average of the housekeeping gene probes to account for variability in the mRNA content.  Background signal was calculated as a median value of the negative hybridization control probes.  Normalized counts were log-transformed for downstream statistical analysis.

label: biotin

source_name: cortex, 22 months, mild injury

label_protocol: Followed manufacturer's protocol

extract_protocol: For NanoString, total RNA was extracted with an RNeasy isolation kit with on column DNase treatment (Qiagen, Valencia, CA).

treatment_protocol: Controlled cortical impact (CCI): The CCI device consists of a microprocessor-controlled pneumatic impactor with a 3.5 mm diameter tip.  Briefly, mice were anesthetized with isoflurane evaporated in a gas mixture containing 70% N2O and 30% O2, and placed on a heated pad to maintain core body temperature at 37°C.  The head was mounted in a stereotaxic frame, a 10-mm midline incision was made over the skull and the skin and fascia were reflected.  A 5-mm craniotomy was made on the central aspect of the left parietal bone.  The impounder tip of the injury device was then extended to its full stroke distance (44 mm), positioned to the surface of the exposed dura, and reset to impact the cortical surface.  Mild-level CCI was induced using an impactor velocity of 6 m/s, deformation depth of 1 mm, and a dwell time of 50 ms [8, 42].  After injury, the incision was closed with interrupted 6-0 silk sutures, anesthesia was terminated, and the animal was placed into a heated cage to maintain normal core temperature for 45 minutes post-injury.  Sham animals underwent the same procedure as CCI mice except for the impact.  At euthanasia 24 hours later, ice were anesthetized (100 mg/kg sodium pentobarbital, I.P.) and transcardially perfused with ice-cold 0.9% saline (100 ml).  Ipsilateral cortical and hippocampal tissue were rapidly dissected and snap-frozen on liquid nitrogen for RNA or protein extraction.

value: Male

value: cortex (brain)

value: 22 months

tag: subject id

tag: treatment

value: mild injury


title: 22_month_sham_injury_control_744_rep_2

source_name: cortex, 22 months, sham inury control

tag: strain

value: sham injury control


title: 22_month_injury_828_rep_6


title: 22_month_sham_injury_control_832_rep_6


title: 22_month_sham_injury_control_823_rep_3


title: 22_month_injury_827_rep_5


title: ATACseq  Brg1 flox/plus rep2

tag: cell type

value: B cells


title: 22_month_injury_732_rep_3


title: 22_month_sham_injury_control_741_rep_1


title: 3_month_injured_825_rep_4

source_name: cortex, 3 months, mild injury

value: 3 months


title: 3_month_injured_826_rep_5


title: 22_month_injury_728_rep_1


title: 3_month_sham_injury_control_821_rep_3

source_name: cortex, 3 months, sham inury control


title: 22_month_sham_injury_control_824_rep_4


title: 22_month_injury_730_rep_2


title: 3_month_sham injury control_735_rep_1


title: 3_month_injured_729_rep_3


title: 10day_cultured_mouse_myoblasts_rep1

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

description:
Tn5-transposed chromatin
results_d0_vs_d4_d10_mouse_ATACseq.xlsx

data_processing:
Mapping. Reads were then mapped to the human (hg38) or mouse (mm10) genome using Bowtie2 (parameters -I 38 -X 2000 --local --dovetail --no-mixed --no-discordant) and filtered to remove mitochondrial reads and PCR duplicates. Peaks were identified using MACS2.1.1 (parameters --nomodel --nolambda --keep-dup all --call-summits -q 0.05 -B).
Differential analysis. Analysis of differential accessibility was performed by generating a list of peaks representative of all samples using the peak summits identified by MACS2. Each summit was extended 50bp in both directions and the resulting lists of peaks were combined, sorted and merged to obtain a dataset of unique and non-overlapping loci. For each differential analysis, the respective list was then used to extrapolate the sequencing depth coverage from each sample bedGraph file using Bedtools map. Coverage files were then analyzed using DEseq2 to identify loci with differential chromatin accessibility. Loci in human and murine activated satellite cells vs cultured cells were selected based on q-value<0.01 (False Discovery Rate) and absolute log2FoldChange>3.
Analysis of the chromatin accessibility landscape in murine freshly-isolated satelite cells employed additional datasets from GSE89977 (GSM2394780 ATAC-seq Satellite cells).
Genome_build: hg38
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files represent the output of the comparisons freshly-isolated satellite cells (d0) vs cultured cells (d12 for human and d4-d10 for mouse) analysis using DESeq2. Each row represent one of the loci (100bp window around the summit) idenfied in the ATAC-seq samples (human or mouse), and includes genomic coordinates, log2FC and adjusted p-value (among the other).

source_name: whole hindlimb

growth_protocol: Human and murine satellite cells were isolated from the muscle mononuclear fraction obtained following tissue enzymatic digestion. More specifically, dissected muscles or sample biopsies were minced into fragments of 1-3mm size using a razor blade, transferred into a conical tube and incubated with a Collagenase II digestion solution (2mg/ml Collagenase II in DMEM high glucose and 1% penicillin/streptomycin) for 75 minutes (60 minutes for human tissue) at 37°C in a shaker set at 200rpm. Human biopsies (between 50-100mg) were incubated with 3ml of digestion solution in a 15ml tube; for murine tissues, 15ml of digestion solution were used to digest the muscles dissected from one hindlimb (using a 50ml tube). After digestion, tubes were then centrifuged at 1000g for 7 minutes at 4°C and, after aspirating the top 50% of the digestion solution, the remaining was washed with 2 volumes of Rinsing Solution (10% Horse Serum (Hyclone), 1% Penicillin/Streptomycin and 0.1?M HEPES in Ham's/F-10 media - Hyclone) and then centrifuged at 1000g for 7 minutes at 4°C, repeating this procedure twice. After the second wash, the pellet was further shredded with the help of a glass pipette (resuspending 5-7 times) and centrifuged at 1000g for 7 minutes at 4°C. The resulting supernatant was carefully aspirated (leaving approximately 3-4mm of volume above to not disturb the pellet), resuspended in a Dispase-Collagenase II digestion solution (0.1 mg/ml collagenase II and 0.5 mg/ml dispase in rinsing solution), vortexed for 20 seconds and incubated 30 minutes (20 minutes for human tissue) at 37°C in a shaker set at 200rpm. Following the second digestion, tubes were vortexed for 20 seconds and then further homogenized using a syringe equipped with a 16 gauge (G) followed by 18 G needle. The homogenate was then filtered through a 40µm filter and then centrifuged at 1000g for 7 minutes at 4°C. Before centrifuge, the tube used for the digestion was washed twice using 3ml of rinsing solution and each wash was applied to the 40µm filter, thus combining it to the original homogenate volume. After carefully aspirating the supernatant, the resulting pellet represented the mononuclear muscle fraction. In general, due to the small size of the biopsy, human samples were devoid of red cells. If necessary, cell pellets were incubated with ACK lysis buffer (Thermoscientific) following the manufacturers' instructions. Human samples were resuspended in 1ml of MACS buffer supplemented with 10µl of human Fc-Block (Miltenyi Biotec), incubated 5 minutes on ice and then supplemented with 10µl of PE-conjugated anti-CD82 (clone ASL-24 - Biolegend) and 10µl of APC-conjugated anti-CD56 (clone 5.1H11 - Biolegend) followed by a 30-minute incubation on ice. Cells were washed with 10ml of sterile PBS, centrifuged for 7 minutes at 4°C and resuspended in 1ml of MACS buffer (Miltenyi Biotec) supplemented with Propidium Iodide (PI). Human satellite cells were identified as CD56+CD82+. Sorted human cells were collected in human myoblast culture media (described below). Murine samples were obtained from 8-12 week old Pax7-ZsGreen reporter mice. In this case, cell pellets were resuspended in MACS buffer supplemented with PI (4ml for each hindlimb-derived fraction) and then processed for FACS. Murine satellite cells were identified as ZsGreen+. Sorted murine cells were collected in murine myoblast culture media (described below). All cell sorting experiments were performed using a FACS AriaII instrument (BD Biosciences).

extract_protocol:
Chromatin accessibility studies were performed following the protocol described by Buenrostro and colleagues (Buenrostro et al., 2015). Except for freshly isolated human cells, which isolation yield ranged between 5,000 and 10,000 cells, all other samples consisted of 50,000 cells (freshly sorted mouse cells, cultured mouse and human cells). Briefly, cells were washed with 200 µl of cold PBS then resuspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun at 500 g for 10 minutes at 4°C and resuspended in 50 µl of the transposition reaction mix. Transposition occurred at 37°C for 30 minutes.
Transposed DNA was purified using a Qiagen MinElute Kit and eluted in 10µl Elution Buffer. Primer extension followed by PCR amplification using Illumina-compatible adapter-barcodes and final library preparation were performed at the University of Minnesota Genomic Center.

treatment_protocol: Sorted human and murine satellite cells were plated onto 0.1% gelatin coated plates maintained in a humidified incubator at 37°C, 5% CO2, 5% O2. 500-1000 human satellite cells were plated in a 24-well plate following each isolation. Human cells were cultured using human myoblast culture media: Ham's/F-10 media (Hyclone) supplemented with 20% FBS (Sigma Aldrich), 1% penicillin/streptomycin (Thermoscientific), 500nM dexamethasone (Cayman Chemical), 2ng/ml basic fibroblast growth factor (Peprotech), 143µM ?-mercaptoethanol (Sigma Aldrich). Murine satellite cells were cultured using murine myoblast culture media: DMEM/F12 medium (Thermoscientific) supplemented with 20% FBS, 5ng/ml basic fibroblast growth factor, 1% penicillin/streptomycin, and 0.25% chick embryonic extract (US Biological). All cells were sub-cultured when density reached 40-50%.

value: skeletal muscle

value: in vitro cultured muscle cells

tag: days in culture

tag: clinical state

value: healthy muscle


title: ATACseq  Brg1 flox/plus rep1

tag: genotype


title: 3_month_sham_injury_control_822_rep_4

tag: Sex

tag: age


title: 4day_cultured_mouse_myoblasts_rep2


title: 4day_cultured_mouse_myoblasts_rep1


title: 3_month_sham_injury_control_829_rep_5


title: fresh_mouse_sat_cell_rep3

value: freshly-isolated satellite cells


title: 3_month_sham injury control_739_rep_2


title: 10day_cultured_mouse_myoblasts_rep2


title: 3_month_sham_injury_control_830_rep_6


title: 22_month_sham_injury_control_831_rep_5


title: 3_month_injured_727_rep_2


title: 3_month_injured_725_rep_1


title: TykNu ITF/AZA Combined [MeDIP-seq]

city: Washington

first: James

last: McDonald

state: DC

address: 800 22nd St, NW, Suite 8960

institute: The George Washington University

description:
MnM.sigDMR.TykNu.treat4.AZA.ITF.bed
mCRF.TykNu.treat4.AZA.ITF.sorted_methylCRF.bed

data_processing:
Check data with FastQC.
Reads were trimmed and adapters were removed using cutadapt using the -q 20 flags. The adapter sequences were -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
The reads were aligned to hg38 using bwa mem (0.7.12) on default settings. Importantly, though the samples underwent paired-end sequencing for convenience, MRE-seq is analyzed based on single end data. As a result, only the read one (R1) MRE-seq samples were aligned to the genome and used in subsequent analysis. MeDIP-seq is analyzed based on paired-end samples so both read one (R1) and read two (R2) samples were aligned for the MeDIP-seq data.
MeDIP and MRE data quality was further assessed using methylQA (0.2.1).
Reference files for hg19 are publicly available. We made the necessary hg38 reference files for the methylMnM analysis using custom scripts provided by the Wang lab.
Rscripts (R version 3.4.2) were used to further process the files and output DMRs (methylMnM) as well as predict methylation levels (methylCRF). Example code and parameters can be found in Xing et al. (Methods Mol Biol. 2018;1708:209-246. doi: 10.1007/978-1-4939-7481-8_12). The Xing et al. paper is the best resource for example code and lists URLs for additional resources in section 2.3 of the paper. If you do not have access to the Xing et al. paper, however, additional resources for methylMnM can be found here: https://epigenome.wustl.edu/MnM/. Additional resources for methylCRF can be found here: http://methylcrf.wustl.edu/.
Genome_build: hg38 GCA_000001405.15
Supplementary_files_format_and_content: Bed files indicating DMRs that are statistically significant relative to the mock sample.
Supplementary_files_format_and_content: Bed files containing the 5mC values for each CpG output by methylCRF.

organism: Homo sapiens

source_name: cell line

growth_protocol: The A2780, Hey, and TykNu cell lines were cultured in RPMI 1640 (Corning, 10-104-CV) with 10% Fetal Bovine Serum (X&Y Cell Culture, FBS-500-HI), and 1% penicillin and streptomycin solution (Gibco, 15070063). The Kuramochi cell line was cultured in RPMI 1640 media (Corning, 10-104-CV) with 10% fetal bovine serum (X&Y Cell Culture, FBS-500-HI), 1% penicillin and streptomycin solution (Gibco, 15070063) and 1% non-essential amino acids (Gibco, 11140050). Cell lines were periodically tested for mycoplasma via the Lonza MycoAlert kit.

extract_protocol:
DNA was extracted with phenol/chloroform.
MRE-seq library preparation was done by Ting Wang's lab at Washington University in St. Louis as described in Xing et al. (Methods Mol Biol. 2018;1708:209-246. doi: 10.1007/978-1-4939-7481-8_12). Briefly, 500 ng of genomic DNA was digested with each of the following methylation sensitive restriction enzymes: HpaII, SsiI, Hin6I, and HpyCH4IV. Digestion was done for 3 hrs with 2.5 U of enzyme. An additional 2.5 U of enzyme was added and digestion continued an additional 3 hours. The digestions were combined 100-500 bp fragments were isolated using gel electrophoresis. This DNA was end-repeaired and dA tails were added by Klenow 3'-5' exo minus prior to adapter ligation. The adapter ligated DNA was amplified, size selected for 100-400 bp insert size and sequenced.
MeDIP-seq library preparation was done by Ting Wang's lab at Washington University in St. Louis as described in Xing et al. (Methods Mol Biol. 2018;1708:209-246. doi: 10.1007/978-1-4939-7481-8_12). Briefly, 500-1000 ng of genomic DNA was fragmented in a Bioruptor Pico for 10-15 min using 30 sec on/off cycles. Fragmented DNA was end repaired with a mixture of T4 DNA polymerase, Klenow, and T4 Polynucleotide Kinase. dA-tailing was done with Klenow 3'-5' exo minus. Adapters were ligated to A-tailed fragments and the library was amplified prior to sequencing.

treatment_protocol: Cells were cultured in T75 dishes (Greiner, 658170) and treated with 500 nM 5-azacytidine (Sigma-Aldrich) or PBS. Media and AZA were replaced each day for five days (Fig. 1B). The cells were then split and allowed to reattach. ITF-2357 was added at a concentration of 100 nM and treatment was continued for two days. The sequential treatment of these cells by these drugs was optimized by Topper et al. (2017).

tag: cell line

value: TykNu

value: ITF/AZA Combined


title: TykNu Mock [MeDIP-seq]

description: mCRF.TykNu.treat1.mock.sorted_methylCRF.bed

value: Mock


title: TykNu ITF [MeDIP-seq]

description:
MnM.sigDMR.TykNu.treat2.ITF.bed
mCRF.TykNu.treat2.ITF.sorted_methylCRF.bed

value: ITF


title: Kuramochi AZA [MeDIP-seq]

description:
MnM.sigDMR.Kuramochi.treat3.AZA.bed
mCRF.Kuramochi.treat3.AZA.sorted_methylCRF.bed

value: Kuramochi

value: AZA


title: A2780 ITF/AZA Combined [MeDIP-seq]

description:
MnM.sigDMR.A2780.treat4.AZA.ITF.bed
mCRF.A2780.treat4.AZA.ITF.sorted_methylCRF.bed


title: Kuramochi ITF [MeDIP-seq]

description:
MnM.sigDMR.Kuramochi.treat2.ITF.bed
mCRF.Kuramochi.treat2.ITF.sorted_methylCRF.bed


title: A2780 AZA [MeDIP-seq]

description:
MnM.sigDMR.A2780.treat3.AZA.bed
mCRF.A2780.treat3.AZA.sorted_methylCRF.bed


title: Hey ITF/AZA Combined [MeDIP-seq]

description:
MnM.sigDMR.Hey.treat4.AZA.ITF.bed
mCRF.Hey.treat4.AZA.ITF.sorted_methylCRF.bed

value: Hey


title: Kuramochi Mock [MeDIP-seq]

description: mCRF.Kuramochi.treat1.mock.sorted_methylCRF.bed


title: Hey ITF [MeDIP-seq]

description:
MnM.sigDMR.Hey.treat2.ITF.bed
mCRF.Hey.treat2.ITF.sorted_methylCRF.bed


title: TykNu ITF/AZA Combined [MRE-seq]


title: TykNu ITF [MRE-seq]


title: Hey AZA [MeDIP-seq]

description:
MnM.sigDMR.Hey.treat3.AZA.bed
mCRF.Hey.treat3.AZA.sorted_methylCRF.bed


title: A2780 Mock [MeDIP-seq]

description: mCRF.A2780.treat1.mock.sorted_methylCRF.bed


title: A2780 ITF [MeDIP-seq]

description:
MnM.sigDMR.A2780.treat2.ITF.bed
mCRF.A2780.treat2.ITF.sorted_methylCRF.bed


title: TykNu AZA [MRE-seq]

description:
MnM.sigDMR.TykNu.treat3.AZA.bed
mCRF.TykNu.treat3.AZA.sorted_methylCRF.bed


title: Kuramochi AZA [MRE-seq]


title: Kuramochi Mock [MRE-seq]


title: Kuramochi ITF/AZA Combined [MRE-seq]

description:
MnM.sigDMR.Kuramochi.treat4.AZA.ITF.bed
mCRF.Kuramochi.treat4.AZA.ITF.sorted_methylCRF.bed


title: Kuramochi ITF [MRE-seq]


title: Hey ITF/AZA Combined [MRE-seq]


title: Hey ITF [MRE-seq]


title: Hey AZA [MRE-seq]


title: Hey Mock [MRE-seq]

description: mCRF.Hey.treat1.mock.sorted_methylCRF.bed


title: TykNu AZA [MeDIP-seq]


title: Kuramochi ITF/AZA Combined [MeDIP-seq]


title: A2780 AZA [MRE-seq]


title: A2780 ITF/AZA Combined [MRE-seq]


title: Hey Mock [MeDIP-seq]


title: A2780 ITF [MRE-seq]


title: S42145

city: Montréal

first: Bertrand

last: Routy

state: Quebec

address: 900 R. Saint-Denis

department: Axe Cancer

country: Canada

institute: CRCHUM

data_processing:
Trimming and filtering, BBMAP v38.87 last release 09oct2020
min length = 40, trim right quality = 20
kmer trim right, trim the leftmost 11 bases
tpo : recommandation to trim adapters based on pair overlap detection
tpe : trim both reads to the same length
Genome_build: GRCh38 Ensembl release 101
Supplementary_files_format_and_content: Kallisto v0.46.1 estimated counts

source_name: lung tumor

extract_protocol:
RNA was extracted from the same specimens using the Maxwell-16 LEV RNA FFPE Purification kit (Promega) according to the manufacturer’s protocol.
rRNA-depleted RNA was used for the library preparation with the NEBNext Ultra II Directional RNA library prep kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

value: lung tumor

tag: disease state

value: Advanced


title: S37138

value: detectable


title: S43155


title: S44109


title: S39013


title: S35136


title: S40023


title: S36137


title: TykNu Mock [MRE-seq]


title: S31041

value: Limited


title: S41584


title: S32043


title: S34133


title: S29123


title: S28118


title: S38139


title: S26104


title: S33594


title: S27105


title: S24101


title: S25103


title: S23065


title: S21056


title: S22064


title: S19055


title: A2780 Mock [MRE-seq]


title: S18054


title: S17049


title: S30038


title: S16048


title: S13044


title: S09578


title: S14027


title: S04022


title: S02006


title: S11129


title: S08097


title: S10026


title: S07053


title: S15046


title: S03017


title: S20056


title: S06037


title: S05035


title: S01008


title: siATF4_SRF_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to HG19 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in quasR and CPM (counts per million) was computed for each sample
Genome_build: hg19
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

growth_protocol: HLE cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions.
RNA-sequencing libraries were prepared from total RNA using poly(A) enrichment with the TruSeq stranded mRNA Sample prep from Illumina using 200 ng input RNA. QC was performed with a fragment analyzer using DNF-473-33-SS NGS Fragment 1-6000bp kit. The RNA-sequence libraries were sequenced on a NextSeq 500 using 75 cycles kit High Output (Illumina).

treatment_protocol: HLE cells were transfected with siCtrl or siYAP/TAZ or siATF4 and  treated with DMSO or 5μM Sorafenib

value: HLE

value: Hepatocellular carcinoma cancer cell line


title: siY_T_DMSO_2


title: siY_T_SRF_1


title: siCtr_SRF_1


title: siCtr_DMSO_2


title: siATF4_DMSO_2


title: siCtr_SRF_2


title: siATF4_SRF_1


title: siATF4_DMSO_1


title: siY_T_DMSO_1


title: S12617


title: siY_T_SRF_2


title: 2D_D20_3

city: Bozen/Bolzano

first: Christian

middle: X.

last: Weichenberger

state: BZ

address: Galvanistraße/via Galvani 31

department: Institute for Biomedicine

country: Italy

institute: EURAC Research

data_processing:
The preprocessing of the reads have been performed with the DriverMap scoring software (HGVv2_1a). This program demultiplexes and scores DriverMap sequencing data from the Illumina NextSeq platform.
Transcripts were quantified from raw reads with salmon (v 1.4.0) on the human transcriptome GRCh38 (Ensembl 100). Quantifications were summarized to gene level with tximeta (1.6.3).
Differential expression analysis was performed with DESeq2 package (v 1.28.1) using the Wald test for significance testing and independent filtering. Genes were considered differentially expressed with adjusted p value <0.05 and | log2FoldChange | >1.
Genome_build: GRCh38 (Ensembl 100)
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each Sample and quantified gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iPSC

growth_protocol: Human iPSCs were cultured under feeder-free conditions on Matrigel matrix (Corning) in StemMACS iPS-Brew XF (Miltenyi Biotech) with 1% penicillin-streptomycin (Thermo Fisher Scientific). Cells were maintained in a saturated humidified atmosphere at 37°C and 5% CO2, and medium was changed every day.

extract_protocol:
Cells were recovered from the beads at days 10, 20 and 35 of differentiation, and total RNA was isolated using the Direct-zol RNA Miniprep Kit (#R2052, Zymo research).
The targeted RNA-seq libraries were produced using the DriverMapT Human Genome-Wide Expression Profiling Kit, V2 (Cellecta, Inc.), that measures all 19,000 human protein-coding genes. All samples were sequenced in 38 paired-end reads on the Illumina NextSeq500 platform.

treatment_protocol: For the encapsulation, 106 hiPSCs were gently mixed with 1 ml 1% w/v Alg solution with Fn. Alg beads were formed by slowly dripping the prepared Alg-cell suspension in 0.1 M CaCl2 with a 19-gauge needle, beads were then incubated for 20 min in the CaCl2 solution and washed 3 times with 1X PBS pH 7.4 (Thermo Fisher Scientific). The differentiation with both the 2D and 3D methods was based on the floor-plate-based neural induction protocol established by Kriks et al., with minor modifications (Kriks et. 2011; Zanon et. al 2017).

tag: time point

value: control

tag: culture condition


title: 2D_D10_3


title: 2D_D35_2


title: 2D_D35_3


title: 2D_D10_2


title: 2D_D10_1


title: 2D_D35_1


title: 3D_D10_2


title: CTRL_T0_1

value: CTRL


title: 3D_D35_2


title: 3D_D20_2


title: 2D_D20_1


title: 3D_D20_1


title: 3D_D10_1


title: CTRL_T0_3


title: 3D_D10_3


title: CTRL_T0_2


title: 3D_D35_3


title: 3D_D20_3


title: UTHBC0096

city: Houston

first: Consuelo

last: Walss-Bass

state: Texas

address: 1941 East Road Rm. 3110

department: Louis A. Faillace Department of Psychiatry and Behavioral Sciences

institute: University of Texas Health Science Center at Houston

data_processing:
Reads were mapped to the GRCh38 genome with TopHat v2.1.0 4 and Cufflinks v2.2.1 using default parameters. The annotation file was downloaded from NCBI (GCF_000001405.39_GRCh38.p13.gtf).
Gene and transcripts raw counts were obtained using htseq-count
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: Raw counts matrices obtained from htseq-count used in determining the scientific conclusions from the manuscript Mendez et al 2021 are provided. This contains only the fully processed samples that were referenced in the paper. Columns include the Official Gene Symbol for each gene (geneName), gene transcript type (protein coding, long non-coding RNA, etc), and raw unnormalized counts for each sample.

source_name: Postmortem Brain Brodmann Area 9

extract_protocol:
RNA was extracted from 50mg of BA9 tissue using RNeasy Plus Mini kits (Qiagen, Hilden, Germany) and RNA integrity number (RIN) was measured for RNA quality (Agilent Bioanalyzer 2100 system, Agilent Technologies, Santa Clara, CA).
1 μg RNA per sample was used for mRNA library construction using NEBNext® Ultra™ RNA Library Prep Kit (Illumina Inc, San Diego, CA). Paired-end sequencing reads (150bp) were generated on an Illumina HiSeq2000 platform (Novogene Bioinformatics Institute, Chula Vista, CA).

tag: mendez et al 2021 molecular psychiatry subject label

value: Male

tag: age (years)

tag: race/ethnicity

value: White

tag: postmortem interval (hours)

tag: rna integrity number

tag: cerebellar ph


title: UTHBC0099


title: UTHBC0094

value: Black


title: UTHBC0093

value: Female


title: UTHBC0097


title: UTHBC0098

value: Hispanic


title: 2D_D20_2


title: UTHBC0089


title: UTHBC0087


title: UTHBC0088


title: 3D_D35_1


title: UTHBC0084


title: UTHBC0077


title: UTHBC0080


title: UTHBC0081


title: UTHBC0075


title: UTHBC0079


title: UTHBC0076


title: UTHBC0070


title: UTHBC0065

value: Asian


title: UTHBC0061


title: UTHBC0062


title: UTHBC0046


title: UTHBC0056


title: UTHBC0059


title: UTHBC0047


title: UTHBC0053


title: UTHBC0041


title: UTHBC0036


title: UTHBC0034


title: UTHBC0039


title: Gfi1aa_ChIP_input_rep2

city: Guangzhou

first: Mei

last: Wu

state: Guangdong

address: Waihuan Dong Road

department: School of Medicine

institute: South China University of Technology

data_processing:
ChIP-seq reads were mapped to GRCZ11 using BWA (v0.1.17)
Gfi1aa binding peaks were called using Macs2 (v2.2.6)
Genome_build: GRCz11
Supplementary_files_format_and_content: bw files were generated using the bamCoverage in deepTools (v3.5.1)
Supplementary_files_format_and_content: peak bed file

organism: Danio rerio

source_name: Whole embryos

extract_protocol:
Cross-linked embryos were lysed and sonicated with a Covaris M220 sonicator to a size range from 200 to 700 base pairs. Then sonicated chromatin was incubated together with Dynal Protein G magnetic beads and 5 mg of antibody. After washing and reversal of cross-linking, DNA was purified with phenol-chloroform-isoamyl alcohol.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

tag: tissue

value: Whole embryos

tag: developmental stage

value: 15 hpf

tag: chip antibody


title: Gfi1aa_ChIP_rep2

value: GFP (Abcam; ab6658)


title: UTHBC0032


title: UTHBC0030


title: Gfi1aa_ChIP_input_rep1


title: UTHBC0035


title: Gfi1aa_ChIP_rep1


title: UTHBC0044


title: UTHBC0028


title: UTHBC0027


title: siCtr_DMSO_1

tag: cell type

tag: treatment


title: APAP_1

city: Yanji

first: xiaolong

last: jiang

address: #977, Gongyuan Road

institute: Yanbian university

description: 300mg/kg APAP i.p. once.

data_processing:
Illumina Casava1.7 software used for basecalling.
Genome_build: mm10
Supplementary_files_format_and_content: merged_rpkm.txt: Tab-delimited text file includes RPKM values for each Sample.

source_name: liver

extract_protocol:
The purity and integrity of RNA were analyzed by agarose gel electrophoresis. Purity of RNA detected by Nanodrop (OD 260/280). Qubit 2.0 accurately quantifies RNA concentration. Agilent 2100 accurately detects RNA integrity.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: O. elatus chlorogenic-enriched fraction (OEB) was administrated orally daily for seven consecutive days, followed by a single intraperitoneal injection of an overdose of APAP after the final OEB administration.

value: liver

tag: strain

tag: pre-treatment

value: APAP


title: APAP_2

description: 300mg/kg APAP i.p. once.


title: APAP_3

description: 300mg/kg APAP i.p. once.


title: UTHBC0023

tag: Sex


title: wt1

city: Genève

first: Ozren

last: Stojanovic

address: 1, rue Michèl-Servet

department: Faculté de Médecine, Dept. PHYM

institute: University of Geneva

data_processing:
Sequencing: single read 100, TruSeq stranded, ribodepletion. The reads were mapped with the TopHat v.2 software to the UCSC mm10 reference; on new  junctions and known junctions annotations. Biological quality control and summarization were  done with PicardTools1.92
The table of counts with the number of reads mapping to each gene feature of UCSC mm10 reference was prepared with HTSeq v0.6p1 (htseq-count).
The differential expression analysis was performed with the statistical analysis R/Bioconductor package EdgeR v. 3.4.2, for the genes annotated in mm10. Briefly, the counts were normalized according to the library size and filtered. The genes having a count above 0.6 count per million reads (cpm), i.e. corresponding to 10 counts, in at least 3 samples were kept for the analysis. The differentially expressed genes tests were done with t-test, negative binomial distribution.
Fold change ob to wt. Ob to WT FC compared to cold-exposure experiment submitted in GSE74228, doi: 10.1016/j.cell.2015.11.004.

source_name: proximal jejunum

extract_protocol: 1 centimeter of proximal jejunum (at 1/3 length of small intestine) washed with PBS, RNA isolated by TRIzol

value: proximal jejunum

value: Whole tissue

tag: genotype


title: wt2


title: wt3


title: OEB_APAP_2

description: OEB 50mg/kg p.o. for 7days and 300 mg/kg APAP i.p. once.

value: OEB


title: OEB_APAP_1


title: ob3

value: ob/ob


title: UTHBC0020


title: Lame_crossbred_R2_1

city: Bareilly

first: Gyanendra

middle: Kumar

last: Gaur

state: UP

address: Izatnagar

department: LPM

country: India

institute: Indian Veterinary Research Institute

description: Gene expression in PBMCs

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Gene expression blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55μl of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Chicken (V2) Gene Expression Microarray, 4x44K (G2519F-026441) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 4 x 44K array slides. Dye channel is set to Green and Green PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PBMCs

label_protocol: One-colour microarray gene expression analysis was performed using the Bovine microarray slide (4X44K: Agilent - 023647). Total RNA (200 ng) was labelled with Low Input Quick Amp Labelling Kit as per manufacturer's instructions. RNA samples were proceeded (run as technical duplicates) for labelling. The quality check of the labelled cRNA was performed using NanoDrop and the yield and specific activity were estimated.

extract_protocol: RNA isolation from the PBMCs was performed using QIAGEN RNeasy® Mini Kit as per standard protocol. The purity and concentration of total RNA extracted was checked using NanoDrop spectrophotometer by using 1 µl of total RNA against nuclease-free water as blank to determine the absorbance ratio 260/280 nm. The quality check of the isolated RNA was performed in Agilent 2100 Bioanalyzer as per standard protocol using the Agilent RNA 6000 Nano Kit. The extracted RNA was found to be of good quality, having RNA integrity number (RIN) greater than 7.

tag: condition

value: Lame


title: d36-8

city: Mannheim

first: Mahak

last: Singhal

address: Ludolf-Krehl-Straße 13-17

institute: European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University

data_processing:
Sequencing strategy: 100bp Paired-End
RTA 1.18.64
The sequenced reads were aligned to the mouse reference genome mm10 using STAR (Dobin et al. 2013) allowing up to 10 mismatches.
DEseq2 was used to test for differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM_RNAseq_lungEC.txt includes RPKM values for each Sample as calculated by DEseq2.

source_name: lung endothelial cells

growth_protocol: C57BL/6N female mice were subcuataneously implanted with 1 mio Lewis Lung Carcinoma (LLC) cells. Lung endothelial cells were isolated from wild-type (d0), primary tumor-bearing (d15), post-tumor resection (d22), and metastasis-bearing (d36) mice.

extract_protocol:
Lung endothelial cells were isolated by FACS, and RNA was harvested using Arcturus PicoPure RNA Isolation Kit (Life Technologies).
Libraries were prepared with 10ng total RNA using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) according to manufacturer’s protocol

tag: stain

value: lung

value: endothelial cells

tag: time point


title: d36-9


title: Lame_crossbred_R1_2

description: Gene expression in PBMCs


title: Normal_Tharparkar_R2

description: Gene expression in PBMCs

value: Normal


title: Normal_Crossbred_R1

description: Gene expression in PBMCs


title: Lame_crossbred_R2_2

description: Gene expression in PBMCs


title: Normal_Crossbred_R2

description: Gene expression in PBMCs


title: Normal_Tharparkar_R1

description: Gene expression in PBMCs


title: Lame_crossbred_R1_1

description: Gene expression in PBMCs


title: d29-1


title: d22-4


title: ob2


title: d22-6


title: ob1


title: UTHBC0008

tag: mendez et al 2021 molecular psychiatry subject label

value: Male

tag: age (years)

value: White


title: OEB_APAP_3


title: UTHBC0016

tag: race/ethnicity

tag: postmortem interval (hours)


title: UTHBC0001

tag: rna integrity number

tag: cerebellar ph


title: lib4 [d36]

data_processing:
Sequencing strategy: 26+74 bp Paired-End
RTA 2.7.7
The sequenced reads were aligned to the mouse reference genome mm10 using Cell Ranger (v 2.1.1).
Low-quality cells containing less than 200 detected genes or more than 10% of transcripts from mitochondrial genes were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: AllDays_Gene_Cell_UMI_Matrix.csv includes UMI raw count matrix per cell as calculated by Cell Ranger.

extract_protocol:
Lung endothelial cells were isolated by FACS, and directly processed for single-cell library generation with 10x Genomics reagents.
Libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v2) (10x Genomics) according to manufacturer’s protocol.

tag: tissue


title: d15-5


title: lib3 [d36]


title: d15-6


title: d15-4


title: d22-1


title: lib2 [d36]


title: lib1 [d36]


title: d15-3


title: d0-4


title: d0-3


title: UTHBC0017


title: d0-2


title: d36-7


title: C4-2B IliA_10uM

city: guangzhou

first: zhang

middle: zhen

last: hua

state: guangdong

address: xiaoguwei

department: college of pharmacy

institute: Sun Yat-Sen University

data_processing:
First, we used Trim Galore to automate quality and adapter trimming as well as quality control for FastQ files.
Then, the FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie2-Cufflinks workflow.
the Cufflinks package was applied for transcript assembly, quantification of normalized gene and isoform expression in RPKM (Reads per kilobase per million mapped reads) or FPKM (fragments per kilobase of exon per million fragments mapped),
and testing for differential expression (Cuffdiff).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: C4-2B cells cultured in the presence of IliA (10 uM)

growth_protocol: C4-2B cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin . Cells were grown at 37℃ in 5% CO2 incubators.

extract_protocol:
RNA-seq libraries were from 1 μg total RNA which was extracted using the total RNA isolation kit (Tiangen, BJ, China) and reverse transcribed with reverse transcriptase M-MLV (Takara, DL, China), according to the manufacturer's instructions. Libraries were validated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Sequencing was performed on an MGISEQ2000 SE50 sequencer at BGI Tech (Wu Han, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C4-2B cells were treated with vehicle or the small molecule IliA (5 μM) and IliA (10 μM), for 48 h before RNA extraction

tag: cell line

value: C4-2B prostate cancer

tag: agent

value: Ilicicolinal A (Ili-A)


title: C4-2B IliA_5uM

source_name: C4-2B cells cultured in the presence of IliA (5 uM)


title: C4-2B  Vehicle

source_name: C4-2B cells cultured in medium with vehicle control.


title: d0-1

tag: cell type


title: lib4 [d22]


title: lib3 [d22]


title: MK-S3

city: Durham

first: Nupur

last: Aggarwal

state: North Carolina

address: Jones building, Research drive

department: Immunology

institute: Duke University Medical School

data_processing:
TrimGalore v0.4.0 for initial processing of fastq files
STAR v2.4.1d was used to align the reads ('--outFilterMultimapNmax 1' and '--alignSJoverhangMin 500' were the non-default parameters used)
HTSeq v0.6.1p1 to quantify gene expression ('-s reverse' was the non-default parameter used)
Genes were removed prior to normalization if they didn't have at least 10 reads in any one sample
Normalization and differential expression was carried out using the DESeq26 Bioconductor package with the R statistical programming environment
Genome_build: ENSEMBL release GRCm38v68 of the mouse genome and transcriptome
Supplementary_files_format_and_content: Tab separated text files (.tsv) that contain the raw HTSeq counts as well as the EdgeR normalized expression values

source_name: IgM[hi] CD23[lo]MZ B cells from Spp1-/- mice

growth_protocol: Obtained from mice

extract_protocol:
B cells were enriched from splenocytes using bead negative selection (antibodies used were CD3, CD4, CD8) and FACS-sorted to CD19+B220+CD93- and IgM/CD23 marker phenotypes as described above. RNA was extracted using Qiagen RNAeasykit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment in vivo and ex vivo

tag: strain

value: BALB/C

value: Spleen

value: IgM[hi] CD23[lo]MZ B cells


title: MK-S5

source_name: IgM[lo] CD23[hi]FB cells from Scid Spp1-/- mice

value: Scid Spp1-/-

value: IgM[lo] CD23[hi]FB cells


title: MK-S4

source_name: IgM[hi] CD23[lo]MZ B cells from Scid Spp1-/- mice


title: MK-S2

source_name: IgM[lo] CD23[hi]FB cells from naive mice

value: wild type


title: lib1 [d22]


title: MK-S1

source_name: IgM[hi] CD23[lo]MZ B cells from naive mice


title: lib4 [d15]


title: lib3 [d15]


title: d22-5


title: lib1 [d15]


title: lib2 [d15]


title: untranslated RNA. FP-2

city: Ann Arbor

first: Rachel

middle: Orion

last: Niederer

state: MI

address: 1150 W. Medical Center Dr

department: Biological Chemistry

institute: University of Michigan

description: The samples are RNA transcribed from a synthetic genome that was derived from sequencing yeast.

data_processing:
Illumina software was used for basecalling
reads were trimmed for adaptor with cutadapt and aligned to custom genomic file containing all the synthetic sequences with STAR. PCR duplicates were discared from the final file using 10N random barcode and fastuniq
sequences with less then 1 rpm in any input library and 2 raw reads in any other library was discarded from further analysis
Genome_build: "synthetic_genome.fa", custom genome based on synthetic sequences derived from yeast 5'UTRs
Supplementary_files_format_and_content: FPKM_counts.txt

molecule: other

organism: Saccharomyces cerevisiae

source_name: pool of RNA transcribed from a synthetic genome derived from sequencing yeast

growth_protocol: T7 RNA polymerase transcribed RNA

extract_protocol:
sucrose gradient; phenol/chloroform extraction; biotin pulldown
reverse transcription, ligation of 5'-linker, PCR amplification.

treatment_protocol: Capped, Incubated in translation extract generated from S. cerevisiae

tag: replicate

tag: fraction

value: untranslated RNA (untranslated fraction isolated from sucrose gradient)

tag: pulldown

value: phenol/chloroform extracted; biotin pulldown


title: untranslated RNA. FP-1


title: lib2 [d22]


title: 80S.replicate.2

value: 80S-bound RNA (80S fraction isolated from sucrose gradient)


title: 80S.replicate.3


title: SCNT-hPSC 17-EB-MPC_rep2

city: Seongnam-si

first: Dong Ryul

last: Lee

state: Gyeonggi-do

address: 335, Pangyo-ro

country: South Korea

institute: CHA University

description: gene expression data from SCNT-PSC derived MPCs via EB-platform differentiation method

hyb_protocol: Fragmented end-labeled cDNA was hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Transcriptome Analysis Console software. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Transcriptome Analysis Console software was used.

source_name: CHA-SCNT-hPSC 17-EB-MPC

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA ( cRNA) was generated from the double-stranded cDNA template though an IVT ( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Human PSC derived MPCs were cultured in DMEM/F12 media supplemented with 10% FBS, 1% NEAA, 1% P/S, and 0.1mM β-ME, and passaged using trypsin-EDTA when they reached 80-90% confluency.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: human SCNT-PSC derived mesenchymal progenitor cell

tag: treatment

value: EB-platform differentiation method


title: MK-S6

source_name: IgM[lo] CD23[lo] B cells from Scid Spp1-/- mice

tag: genotype

value: IgM[lo] CD23[lo] B cells


title: 80S.replicate.1


title: lib4 [d0]

tag: stain

value: lung

value: endothelial cells

tag: time point


title: RNA.input

value: Input RNA

value: phenol/chloroform extracted


title: lib3 [d0]


title: SCNT-hPSC 17-Direct-MPC_rep2

description: gene expression data from SCNT-PSC derived MPCs via direct differentiation method

source_name: CHA-SCNT-hPSC 17-Direct-MPC

value: direct differentiation method


title: lib2 [d0]


title: Roots2

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

data_processing:
Briefly, library quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Adapters were trimmed using Trimmomatic v0.32 (PMID: 24695404) with a minimum and maximum length of 18 nt and 34 nt
Mapped to the new genome wa done with Bowtie2
miRNA and phasiRNA predictions were done using both ShortStack (PMID: 27175019) and miR-PREFeR (PMID: 24930140) and filtering criteria recommended in Axtell and Meyers (PMID: 29343505)
Genome_build: Ae. tauschii acc. AL8/78 reference genome sequence v. 5 (an updated version of the assembly (Aet v4.0) under the BioProject PRJNA341983)
Supplementary_files_format_and_content: Count file containing sequence and abundance

organism: Aegilops tauschii

source_name: Roots

growth_protocol: Seeds of Ae. tauschii accessions were germinated in dark, grown, and corresponding materials were collected

extract_protocol:
RNA was extracted from roots, spikes, mature leaves, and seedlings of AL8/78 using TriReagent (Millpore-Sigma, St. Louis, USA) following manufacturer’s protocols
Libraries were generated using 20 ng of RNA after size selection on polyacrylamide gels, and using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, USA)

tag: cultivar

value: Roots


title: Roots


title: Spikes

source_name: Spikes

value: Spikes


title: lib1 [d0]


title: Mature Leaves2

source_name: Mature Leaves

value: Mature Leaves


title: SCNT-hPSC 17-Direct-MPC_rep1


title: SCNT-hPSC 18-EB-MPC_rep1

source_name: CHA-SCNT-hPSC 18-EB-MPC


title: SCNT-hPSC 18-Direct-MPC_rep2

source_name: CHA-SCNT-hPSC 18-Direct-MPC


title: AD5

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GrCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsies

extract_protocol:
Normal human skin sheets (>10x10cm2) from healthy individuals undergoing skin reduction surgery or punch-biopsies from lesional skin of AD patients were minced and treated with 500 U/ml collagenase IV (Worthington Biochemical) and 50 U/ml DNAse I (Sigma-Aldrich) in RPMI Medium 1640 (Gibco), and incubated at 37°C for 40 min. Then samples were sieved using a 70 µm cell strainers and, in case of NHS, subjected to gradient purification. Cells were stained with fluorescently labeled antibodies and FACS-sorted. Immediately after sorting, single-cell suspensions were subjected to scRNA-seq processing (10x Genomics, Pleasanton, Calif).
Single-cell libraries were generated using the Chromium Controller and Single Cell 3− Library & Gel Bead Kit versions 2 and 3 (10x Genomics) according to the manufacturer’s protocol.

tag: diagnosis

value: Atopic Dermatitis

tag: chemistry

value: Single Cell 3' v3


title: Mature Leaves


title: SCNT-hPSC 18-Direct-MPC_rep1


title: SCNT-hPSC 18-EB-MPC_rep2


title: SCNT-hPSC 17-EB-MPC_rep1


title: forelimb blastema mesenchyme, am580_rep6

city: Gainesville

first: Malcolm

last: Maden

state: Florida

department: Biology

institute: University of Florida

data_processing:
All reads were evaluated using fastQC [fastqc/0.11.7].
Low quality reads and reads with adapter sequences were trimmed using Trimmomatic [trimmomatic/0.36, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36], and the trimmed read were analyzed again using fastqc.
Reads were aligned to the axolotl genome using HISAT2 [hisat2/2.1.0, -q --dta].
SAM files were converted to BAM files using samtools [samtools/1.8, samtools view -S], sorted [samtools sort], and indexed [samtools index -c].
Novel genes were identified and a transcriptome assembled using StringTie [stringtie/1.3.4d] and gffread [gffread/0.9.8c]
Transcript counts were produced with featureCounts [subread/1.6.2, featureCounts -s 2 -p -t exon -g gene_id].
Differential expression analysis was conducted using edgeR [edgeR/3.26.8, glmQLFit, adjust.method = "BH", p.value = 0.05].
Genome_build: AmexG_v3.0.0
Supplementary_files_format_and_content: am580_featureCounts_raw_counts.txt (Matrix table containing raw gene counts, generated by featureCounts, for all detected genes in all 12 samples)
Supplementary_files_format_and_content: am580_edgeR_abundance.txt (Matrix table containing normalized abundance counts, generated by edgeR, for all detected genes in all 12 samples)
Supplementary_files_format_and_content: am580_transcriptome.fa (Transcriptome containing sequences of all detected genes. Prepared from StringTie gff using gffread.)
Supplementary_files_format_and_content: am580_stringtie_merged.gff (GFF constructed using StringTie)

organism: Ambystoma mexicanum

source_name: forelimb blastema mesenchyme

growth_protocol: Axolotls were maintained in 40% Holtfreter's solution.

extract_protocol:
Total RNA was extracted using a RNeasy Fibrous Tissue Mini Kit (QIAGEN 74704) according to the manufacturer’s protocol.
Illumina TruSeq stranded libraries were constructed via poly-A selection by HudsonAlpha Discovery in Huntsville, Alabama, USA.

treatment_protocol: Axolotl forelimbs were amputated mid-zeugopod and treated 24 hours later with systemic 25 nM Am580 or equal volume DMSO vehicle control for 5 days. The blastemas were collected 24 hours after treatment, the epidermis physically removed, and the mesenchyme tissue stored in RNALater.

value: albino

value: forelimb blastema mesenchyme


title: forelimb blastema mesenchyme, am580_rep5


title: MEF-Rev3-/-_p60

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

description:
Nascent DNA
MEF-Rev3-/-_p60_replication timing

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray or 4x 180K mouse microarray

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the START-R software (Hadjadj D, Denecker T, Guérin E, Kim SJ, Fauchereau F, Baldacci G, Maric C, Cadoret JC. Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite. NAR Genom Bioinform. 2020 Jun 19;2(2):lqaa045. doi: 10.1093/nargab/lqaa045. PMID: 33575597; PMCID: PMC7671386.).

source_name: nascent DNA from early S-phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipitated DNA, whole genome amplification (WGA) was conducted (Seq-plex, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Each cells grown in culture condition defined by ATCC

extract_protocol: cells were incubated with BrdU (50µM) for two hours, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipitated by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) . To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

value: MEF

tag: passage

tag: phase

value: early S-phase

source_name: nascent DNA from late S-phase

value: late S-phase


title: MEF-Rev3-/-_p7

description:
Nascent DNA
MEF-Rev3-/-_p7_ replication timing


title: forelimb blastema mesenchyme, am580_rep4

tag: tissue


title: forelimb blastema mesenchyme, dmso_rep5

value: Dimethyl sulfoxide


title: MEF-Rev3+/+_p60

description:
Nascent DNA
MEF-Rev3+/+_p6_replication timing

tag: cell line


title: forelimb blastema mesenchyme, dmso_rep6


title: AD4


title: forelimb blastema mesenchyme, dmso_rep4


title: forelimb blastema mesenchyme, am580_rep2


title: Seedlings leaves

source_name: Seedlings leaves

value: Seedlings leaves


title: dHD2_rec_tgfb_3

description: Response to canonical TGFb signaling, EMT

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in qusaR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

source_name: Breast cancer cells

growth_protocol: Tumor-derived trasgenic cell lines with different genotypes were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from all samples at the same time using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions. RNA quality control was performed using RNA ScreenTape on an Agilent 4200 TapeStation, and RNA concentration was measured using Quanti-iT RiboGreen RNA assay Kit (Life Technologies).
Library preparation was performed, starting from 200ng total RNA, using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA). Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical) revealing excellent quality of libraries (average concentration was 129±14 nmol/L and average library size was 350±11 base pairs). Samples were pooled to equal molarity. The pool was quantified by Fluorometry using the QuantiFluor ONE dsDNA System (Cat# E4871, Promega, Madison, WI, USA). Libraries were sequenced Single-reads 101 bases (in addition: 8 bases for index 1 and 8 bases for index 2) using the NovaSeq 6000 instrument (Illumina) and the S1 Flow-Cell loaded at 400pM and including 1% PhiX. Primary data analysis was performed with the Illumina RTA version V3.4.4. Two Novaseq S1 Flow-Cells runs were performed to compile enough reads (on average per sample: 34.8±3.2 millions pass-filter reads).

treatment_protocol: Established epithelial tumor cell line from above were plated at the same time for no, Wnt3a or TGF-beta tratments. A day after cell plating, we treated cells with no cytokine (only growth medium), TGF-beta (2 ng/ml, 4 days) or Wnt3a (100 ng/ml, 3 days). We changed cytokines every second day and for controls only with growth medium. Total RNA is isolated from all samples at the same time. For biological replicates we used two transgenic cell lines drived from two different mice with the same genotype.

value: MMTV-PyMT (FVB/N)

value: Tumor developed in a thoracic mammary gland

tag: transgene

value: Bcl9/Bcl9L_deltaHD2/-, MMTV-PyMT

value: TGFbeta


title: DC2.4 cells, Cat 2

city: Orlando

first: Justine

middle: T.

last: Tigno-Aranjuez

state: FL

address: 6900 Lake Nona Blvd., BSBS Bldg, Rm 370

department: BSBS, Immunity and Pathogenesis Division

institute: University of Central Florida

data_processing:
[Read mapping]  Bowtie2 version 2.1.0:  The reads were mapped to the latest UCSC transcript set.
[Gene expression level estimation]  RSEM v1.2.15:  TMM (trimmed mean of M-values) was used to normalize the gene expression.
[Identification of differentially expressed genes]  edgeR:  Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Excel (*.xlsx) files contain differentially expressed genes for each treatment condition and AllDetectedGenes_raw_counts

growth_protocol: maintained in RPMI containing 10% FBS, 1% antibiotic-antimycotic

extract_protocol:
Rneasy mini kit as directed by manufacturer (Qiagen)
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consists of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.
Illumina Hiseq3000 for sequencing, Illumina Bcl2fastq2 v 2.17 program for demultiplexing

treatment_protocol: serum-starved for 4hrs in RPMI containing 0.1%FBS prior to treatment with 250 PNU/ml of allergen for 4hrs

tag: cell type

value: mouse dendritic cells

value: Cat hair allergen extract, 250 PNU/ml for 4 hrs


title: MEF-Rev3+/+_p5

description:
Nascent DNA
MEF-Rev3+/+_p5 _replication timing


title: NHS2

source_name: Skin Sheet

value: Healthy Control

value: Single Cell 3' v2


title: DC2.4 cells, HDM 1

tag: strain

value: house dust mite allergen extract, 250 PNU/ml for 4 hrs


title: forelimb blastema mesenchyme, am580_rep1


title: forelimb blastema mesenchyme, am580_rep3


title: AD3

value: Atopic Dermatitis

value: Single Cell 3' v3


title: dHD2_fl_tgfb_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

institute: University of Basel

value: Bcl9/Bcl9L_deltaHD2/fl, MMTV-PyMT


title: AD2


title: DC2.4 cells, untreated 1


title: dHD2_fl_tgfb_1


title: dHD2_rec_tgfb_2


title: DC2.4 cells, Grass 2

value: Timothy grass allergen extract, 250 PNU/ml for 4 hrs


title: dHD1_rec_tgfb_2

value: Bcl9/Bcl9L_deltaHD1/-, MMTV-PyMT


title: DC2.4 cells, Grass 1


title: NHS3


title: DC2.4 cells, HDM 2


title: dHD2_rec_tgfb_1


title: DC2.4 cells, untreated 2


title: dHD1_rec_tgfb_1


title: NHS1


title: Patient 1 Prefrontal cortex sample 3

city: New York

first: Robert

last: Sebra

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Counts matrix generated through Cell Ranger v3.1.0
Raw base call files demultiplexed with Cell Ranger mfastq pipeline
Cell Range count pipeline used for alignment to GRCh38 human reference
Filter cell barcodes with low Unique Molecular Identifier, sample dependent filtering
Filter cell barcodes with high total feature count, sample dependent filtering
Filter cell barcodes with high percentage mitochondrial genes, sample dependent filteirng
Supplementary_files_format_and_content: tsv.gz files are generated by Cellranger. Each contain either detected cellular barcodes or features for expression matrices.
Supplementary_files_format_and_content: mtx.gz files are the expression matrices generated by Cellranger.

source_name: Brain tissue

extract_protocol:
Nuclei were isolated from fresh frozen autopsy tissue following the 10x Genomics (Pleasanton, CA) recommended protocol using 0.1% Nonident NP40 lysis buffer. Suspensions were filtered through a 40 um mesh to remove debris and concentrated to a density of 1x10^6 nuclei/mL in Dulbecco's PBS + 0.04% BSA (Sigma Aldrich).
Nuclei were processed according to Chromium 3’ Gene Expression V3 Kit (10X Genomics, Pleasanton, CA) using manufacturer’s guidelines. An estimated 15,000 nuclei were loaded onto each channel with a targeted cell recovery of 10,000 nuclei/sample. This was followed by sequencing on a S4 NovaSeq chip (Illumina Inc., San Diego, CA). Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) were used for quality check of cDNA. The output BAM file, a binary text file containing the sequence alignment data from sequencing, was processed through 10X Genomics Cell Ranger software v3.1.0. Sequencing generated scRNA-seq data with ~41,000 2x100bp reads per nucleus and 63,653 total cells sequenced

tag: patient id

tag: sample replicate number

tag: sample state

value: Nuclei


title: Patient 1 Olfactory bulb sample 3


title: Patient 1 Prefrontal cortex sample 2


title: Patient 1 Prefrontal cortex sample 1


title: S96_IL17_100_D6

city: Seoul

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

institute: Samsung Medical Center

description:
input_data_CPM_IL17
input_data_Count_IL17

data_processing:
Reads from files in the FASTQ format were mapped to the hg19 human reference genome using HISAT 2.2.0, with default parameters. Raw read counts mapped to genes were measured using the BAM format file in HTSeq version 0.12.3, to quantify transcript abundance. The coding genes were selected, and raw read counts were normalized to the trimmed mean of M-values. Differential expression analysis of RNA-seq experiments was conducted with edgeR (version 3.28.1). Unsupervised hierarchical clustering analysis with the Euclidean distance and complete linkage algorithm was used to create a heatmap with the associated dendrogram.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include raw read counts for samples

source_name: small intestinal organoid (enteroid)

growth_protocol: Human intestinal organoids was constructed as a previous described method. In brief, we obtained small intestinal mucosa specimens using endoscopic biopsy from the three patients without any mucosal lesions in small intestine, who underwent single-balloon enteroscopy (SBE) at the Samsung Medical Center, Seoul, Korea, after receiving informed consent. Control patients underwent SBE due to small bowel submucosal tumor (heterotopic pancreas and gastrointestinal stromal tumor) and unexplained abdominal pain. This study was approved by the institutional ethical committee of the Samsung Medical Center (IRB No. 2016-02-022).  The intestinal crypts were isolated from endoscopic biopsy specimens using 10 mM EDTA (Thermo Scientific, San Jose, CA, USA) and 1 mM DTT (Thermo Scientific) chelation. The isolated crypts were resuspended into Matrigel (Corning) and plated in 48-well culture plates (Corning). The 250 μl of maintenance medium (50 % Wnt3a-conditioned medium (ATCC#CRL-2647, Manassas, VA, USA) + 50 % 2× basal medium (Basal medium: advanced DMEM/F12 (Thermo Scientific) supplemented with antibiotic–antimycotic solution (Thermo Scientific), 10 mmol/L HEPES (Thermo Scientific), GlutaMAX (Thermo Scientific), 1× N2 (Thermo Scientific), 1× B27 (Thermo Scientific), and 1 mmol/L N-acetylcysteine (Sigma–Aldrich, St. Louis, MO, USA)), supplemented with 50 ng/ml recombinant human epidermal growth factor (Sigma–Aldrich), 100 ng/ml recombinant human noggin (R&D Systems, Minneapolis, MN, USA), 500 ng/ml recombinant human R-spondin 1 (PeproTech, Cranbury, NJ, USA), 10 mM nicotinamide (Sigma–Aldrich), 10 μM p160ROCK inhibitor (Y27632, Selleckchem, Houston, TX, USA), 10 μM p38 MAP kinase inhibitor (SB202190, Sigma–Aldrich), and 10 nM Prostaglandin E2 (PGE2, Cayman Chemical, Ann Arbor, MI, USA) were added. GSK3 inhibitor (CHIR99021, Stemgent, Cambridge, MA, USA) was added to the medium during the first 2 days.   After culturing the organoids for 7 days, the organoids in Matrigel were disrupted mechanically via pipetting, and chemically using TrypLE Express Enzyme (Thermo Scientific). The cell pellet was resuspended in Matrigel and plated in 48-well culture plates (Corning). The medium was changed every 2 days, and organoids were passaged at a ratio of 1:2 – 1:4 on 7 days after crypt plating. To recapitulate the structure and function of the intestinal epithelium, the intestinal organoids (enteroids) were cultured in a differentiation medium (maintenance medium without Wnt3A conditional medium, SB202190, nicotinamide, and PGE2). The differentiation medium was changed every 2 days.

extract_protocol:
After 7th day after embedding (5th days after treatment with IL-17), total RNA was extracted from enteroids using an RNeasy Mini Kit (QIAGEN, Hilden, Germany).
Total RNA was extracted from enteroids using RNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA sequencing was conducted using total RNA samples with >10 μg of RNA and an integrity number > 8. Reverse transcription reactions were performed with 2 μg of isolated total RNA, poly(dT) primers, and SuperScript™ II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA). cDNA libraries were prepared via complementary DNA amplification, end repair, 3'-end adenylation, adapter ligation, and amplification. The libraries were sequenced with HiSeq2500 using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).

treatment_protocol: To evaluate the IL-17-induced responses in the enteroids, the intestinal organoids were cultured in a maintenance medium for 2 days to obtain a stable number of organoids, before inducing organoid differentiation and treatment with concentrations of human recombinant IL-17A (R&D Systems). Then, the maintenance medium was replaced with a differentiation medium every 2 days. Different concentrations of human recombinant IL-17 were added to the culture medium every 24 hours.

value: small intestine (jejunum)

tag: disease

value: control (no small intestinal lesions)

tag: status

value: conventional organoid culture condition with differentiation medium & 100 ng/ml IL-17


title: dHD1_fl_tgfb_2

address: Mattenstrasse 28

value: MMTV-PyMT (FVB/N)

value: Tumor developed in a thoracic mammary gland

value: Bcl9/Bcl9L_deltaHD1/fl, MMTV-PyMT

tag: treatment


title: forelimb blastema mesenchyme, dmso_rep3

value: albino

value: forelimb blastema mesenchyme

value: Dimethyl sulfoxide


title: Patient 1 Olfactory bulb sample 2


title: breast cancer tissue_T5

city: Lanzhou

first: HongLei

last: Wang

state: Gansu

address: 1 Donggang West Road

department: Department of Galactophore

institute: The First Hospital of Lanzhou University

description: circRNA expression in breast cancer and adjacent non-tumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified . Differentially expressed circRNAs between two samples were identified through Fold Change filtering.

source_name: breast cancer tissue

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

treatment_protocol: Five cancer tissues and paired adjacent non-cancerous tissues from primary breast cancer patients were used for circRNA microarray. Tissues specimens were obtained during surgery and immediately flash frozen with liquid nitrogen and then frozen at -80℃ until further use.

value: breast tumor

tag: gender

value: female

tag: age


title: dHD1_fl_tgfb_1

tag: time point

value: TGFbeta


title: Patient 1 Olfactory bulb sample 1


title: S96_IL17_10_D6

value: conventional organoid culture condition with differentiation medium & 10 ng/ml IL-17


title: forelimb blastema mesenchyme, dmso_rep1


title: breast cancer tissue_T4


title: DC2.4 cells, Cat 1

value: mouse dendritic cells

value: Cat hair allergen extract, 250 PNU/ml for 4 hrs


title: S96_IL17_1_D6

value: conventional organoid culture condition with differentiation medium & 1 ng/ml IL-17


title: HeLa_siNT

description:
Nascent DNA
HeLa_siNT_replication timing

value: HeLa

value: control

value: early S-phase

value: late S-phase


title: HeLa_siRev3l

description:
Nascent DNA
HeLa_siRev3l_replication timing

value: siRNA against Rev3l


title: patient 1 kidney rep 2

data_processing:
The raw RNAseq data was aligned to the hg38 genome using the STAR(v2.7.3a) mapper.
Aligned data were annotated using GENCODE v35 gene annotations and counted using featureCounts(v1.6.3).
Genes with fewer than 50 counts across all samples were excluded from the analysis, and the counts were subsequently log2-transformed for differential gene expression analysis using DESeq2. A pairwise comparison between infected tissues (lung, nasopharynx) and uninfected tissues (olfactory bulb, prefrontal cortex, oropharynx, salivary gland, tongue, heart, liver, kidney) with an adjusted p-value < 0.05 for differentially expressed (DE) genes.
Gene Set Enrichment Analysis (clusterProfiler) was performed to probe for Gene Ontology (GO) categories that were significantly overrepresented and statistically different in infected versus non-infected tissues.
Genome_build: hg38
Supplementary_files_format_and_content: featureCount tsv file summarizes raw counts from featureCounts for each sample.
Supplementary_files_format_and_content: DESeq csv file contains DE genes found by DESeq2.
Supplementary_files_format_and_content: GSEA csv file contains GESA results for GO categories.

source_name: kidney autopsy tissue

extract_protocol:
Total RNA was extracted from the autopsy tissues by first flash freezing each tissue in liquid nitrogen and then using the CryoPREP Tissue Disruption System (Covaris) to pulverize the tissue into a fine powder. The powder was then immediately resuspended in cell lysis buffer and RNA was extracted using the ReliaPrep RNA Tissue Miniprep System (Promega, #Z6112) by following the manufacturer’s instructions. A DNase digestion was also performed during the RNA extraction workflow to remove any potential contamination from carryover genomic DNA (reagents included in the kit). The extracted RNA was then purified using 1.8X RNAClean XP beads (Beckman Coulter) to remove any molecular impurities.
Stranded total RNA libraries were generated according to the manufacturer's instructions, using the TruSeq Stranded Total RNA Gold kit for Illumina sequencing
RNAseq, 2x100 PE reads, Illumina NovaSeq 6000

tag: replicate type

value: technical replicate 2

tag: viral rna detected?

value: no


title: dHD2_rec_wnt3a_3

description: Response to canonical Wnt signaling

value: MMTV-PyMT (FVB/N)

value: Tumor developed in a thoracic mammary gland

value: Bcl9/Bcl9L_deltaHD2/-, MMTV-PyMT


title: dHD2_rec_wnt3a_2

description: Response to canonical Wnt signaling


title: patient 1 lung rep 2

source_name: lung autopsy tissue

value: yes


title: dHD2_fl_wnt3a_2

description: Response to canonical Wnt signaling

value: Bcl9/Bcl9L_deltaHD2/fl, MMTV-PyMT


title: patient 1 lung rep 1

value: technical replicate 1


title: dHD2_rec_wnt3a_1

description: Response to canonical Wnt signaling


title: S96_IL17_0_D6

value: small intestine (jejunum)

value: control (no small intestinal lesions)

value: conventional organoid culture condition with differentiation medium


title: N2_IL17_100_D6

value: small intestine (ileum)

value: conventional organoid culture condition with differentiation medium & 100 ng/ml IL-17


title: breast cancer tissue_T2

value: breast tumor

value: female


title: dHD2_fl_wnt3a_1

description: Response to canonical Wnt signaling


title: patient 1 liver rep 2

source_name: liver autopsy tissue


title: patient 1 liver rep1


title: N2_IL17_1_D6

value: conventional organoid culture condition with differentiation medium & 1 ng/ml IL-17


title: adjacent non-tumor tissue_N5

source_name: adjacent non-tumor tissue

value: breast tissue