title: stress-WT rep1 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_stress.csv, 5hmc_wt_stress-wt_control.csv
CNTNAP-39 5hmC-Chipseq

source_name: stress-WT rep1 5hmC-Chipseq

tag: cntnap2 genotype

value: Wild type

value: Stressed

tag: strain


title: 14_S2

status: Public on Dec 20 2021

type: SRA

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

library_source: transcriptomic

data_processing:
Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three  Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to mouse and human genomes using STAR aligner, version (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Tab delimeted text file containing unnormalized (raw) read counts per feature.

molecule: total RNA

organism: Mus musculus

source_name: Mouse cortex, no transplantation

growth_protocol: iPSC-astrocyte progenitors: The primary cells were reprogrammed with Cytotune 2.0 iPS Sendai Reprogramming Kit for Oct4, Sox2, Klf4, and c-myc. The emerged colonies were individually subcloned. For differentiation, iPSCs were cultured in feeder-free conditions with Matrigel-coating and Essential 8 culture medium. Astroglial differentiation was carried out as described (Stem Cell Reports. 2017;9:1885-1897) by maintaining neural progenitor spheres in astrocyte differentiation medium in suspension for 6–7 months before dissociation. Transplantation: hiPSC-astrocyte progenitors (100,000 cells/µl in PBS) dissociated from sphere cultures were transplanted into newborn Rag1 knockout mouse (B6.12957-Rag1tm1Mom/J, The Jackson Laboratory) forebrain using the published protocol  (Kim, et al., 2014). Cell transplantation was performed by injecting 300,000 cells into the brain at 5 locations: (0.8, 1.0, -1.5); (-0.8, 1.0, -1.5); (0.8, 2.0, -1.5); (-0.8, 2.0, -1.5); (0.0, -1.0, -1.5). The mice were killed when they were 11 months old and frontal cortex was separated.

extract_protocol:
Total RNA was extracted using Trizol and cleaned using RNeasy Mini Kit. The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.

treatment_protocol: No treatment was applied.

tag: sample number

tag: mouse strand

tag: tissue

value: cortex

tag: group status

value: non-transplanted

tag: mouse gender

value: female

tag: sample type

value: Mouse cortex, no transplantation


title: day 8 Isotype control mouse 1 Draining lymph node

type: RNA

city: Redwood City

first: Kyle

last: Halliwill

state: California

address: 1500 Seaport Blvd

country: USA

institute: Abbvie Inc

description: group 1 1 DLN

hyb_protocol: Samples processed as per NanoStringTM protocols.

scan_protocol: NanoStringTM nCounter.

data_processing: Normalization method NanoStringTM nSolver 4.0 advanced analysis, normalised to standards on NanoStringTM panel per their protocol.

source_name: draining lymph node

label_protocol: Labeled as to group, mouse number and tissue.

growth_protocol: The adherent colorectal carcinoma cell line CT26 (cat. # CRL-2638, ATCC, Manassas, VA) and mammary gland adenocarcinoma cell line JC (cat. # CRL-2116, ATCC, Manassas, VA) were expanded and maintained in RPMI-1640 (Roswell Park Memorial Institute medium cat. # SH30021.02 GE Healthcare Life Sciences) supplemented with 10% FBS (cat. # F442-500 Sigma-Aldrich).

extract_protocol: Total RNA processed from formalin fixed paraffin embedded (FFPE) blocks as per NanoStringTM protocols.

treatment_protocol: FFPE blocks prepared.

value: draining lymph nodes

tag: treatment

value: Isotype control

tag: time point

value: day 8


title: genomic DNA from RNA029VAT

type: genomic

city: Hong Kong

first: Nana

last: Jin

address: CUHK, Sha tin, NT

country: Hong Kong

institute: CUHK

description: genomic DNA from RNA029VAT

hyb_protocol: Bisulfite conversion of DNA was conducted using the EZ DNA methylation kit (Zymo Research)

scan_protocol: DNA methylation was quantified using the Illumina Infinium MethylationEPIC (EPIC) BeadChip (Illumina, CA) run on an Illumina iScan System (Illumina) using the manufacturer’s standard protocol.

data_processing: First, to reduce bias in probe-binding efficiency due to differences in individual genetic makeup, probes that overlapped with SNPs in the last three bases of the target sequence were removed. Second, the Greedycut algorithm was used for iterative removal of probes that produced unreliable measurements. Third, probes that did not target CpG sites or were located on sex chromosomes were removed. The remaining probes were subjected to background correction using the ENmix method and normalization using the beta-mixture quantile normalization method.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from RNA029VAT

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA samples were prepared using proteinase K digestion and phenol extraction.

tag: gender

value: M

value: VAT

tag: disease

value: DM


title: control-WT rep2 5hmC-distribution

city: Lincoln

first: Qi

last: Zhang

state: NE

address: 354C Hardin NW

department: Statistics

institute: University of Nebraska Lincoln

description:
processed data file: 5hmc_het_stress-wt_control.csv, 5hmc_wt_stress-wt_control.csv, 5hmc_het_control-wt_control.csv
CNTNAP-46 5hmC-Chipseq

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
5hmC reads were aligned to the mm9 genome assembly by Bowtie 0.12.7 allowing no more than two mixmatches, an only keeping uniquely mapped reads.
R package MOSAiCS was used to call peaks from each sample, adjusting for mappability, GC contents and ambiguity score.
Reshape the peaks as 1kb windows around its summit (found by R package segvis), merge the peaks from all three replicates in the same group, and define one such merged peak as a peak for this group if it overlapped with peaks from at least two subjects in thisgroup
For each comparison of two groups, merge the peaks of the two groups as the candidate regions for DhMR identification. Extend the mapped reads to its average length (estimated by SPP for each sample), and count the number of extended reads from each sample in each such candidate region.
genome build: mm9
processed data files format and content:  comma-delimited text of raw 5hmc read counts in the candidate regions for DhMR analysis for each contrast.

source_name: control-WT rep2 5hmC-Chipseq

extract_protocol:
Mice were sacrificed (2 hours after lights on) and whole brains were extracted and immediately flash frozen in 2-methylbutane and dry ice. Striatum tissue was excised by micropunch (1.53 to -0.95 mm posterior to bregma) and approximately 30 milligrams of tissue was homogenized with glass beads (Sigma) and DNA/RNA were extracted using AllPrep DNA/RNA mini kit (Qiagen).
5hmC-enriched libraries were generated using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina sequencing, according to the manufacturer’s protocol. Briefly, the 5hmC-enriched DNA fragments were purified after the adapter ligation step using AMPure XP beads (Agencourt A63880). Approximately 100 ng of total RNA was used for sequence library construction following instructions of NuGen mRNA sample prep kit (cat# 0348). In brief, total RNA was copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products were gel purified and enriched with PCR to create the final cDNA libraries.

treatment_protocol: Pregnant dams (carrying WT and Cntnap2 het embryos) were exposed to 7 days of variable stress starting at embryonic day 12.5; Offspring were ear-tagged at (postnatal day) (P) 12 and left undisturbed until weaning day (P18), at which time the mice were group housed with same sex littermates.

tag: prenatal condition

value: Non-stressed

value: brain

tag: brain region

value: striatum


title: genomic DNA from RNA042SAT

description: genomic DNA from RNA042SAT

source_name: genomic DNA from RNA042SAT

value: SAT


title: 28-24-T2_chip

city: East Lansing

first: Dae Kwan

last: Ko

state: MI

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

data_processing:
RNAseq analysis: RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Library (Illumina, San Diego, CA, USA) and sequenced in single-end mode on the Illumina HiSeq 4000 platform (50-nt) at Research Technology Support Facility Genomics Core at Michigan State University (RTSF-MSU). The quality of raw reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 2.2.4) and TopHat (version 2.0.14) with a 10 bp minimum intron length and 15,000 bp maximum intron length. Fragments per kilobase exon model per million mapped reads (FPKM) were calculated using TAIR10 gene model annotation with Cufflinks (version 1.3.0).
ChIP-seq analysis: The quality of raw ChIP-seq reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 1.1.2) with parameters “-n 2 -m 3 -k 1 --threads 7 --best --chunkmbs 256 -q”. Duplicated reads were removed using Samtools (version 1.8). Peak calling was performed using MACS2 (version 2.1.2) in individual samples with input samples pooled for DMSO-only and Tm treated samples and with a relaxed threshold of P-value (--pvalue=1e-2), as recommended by the IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr). Peaks across replicates with an IDR < 0.05 were retained for further analysis.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text file: for RNA-seq: The normalized read values (FPKM) for gene expression in all samples. Sample name consists of genotype, treatment, time-point and biological replicate with hyphen. 28, bzip28. 60, bzip60.
Supplementary_files_format_and_content: for ChIP-seq, UPR-specific binding peak coordinates, annotated genes and scores

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Surface-sterilized seeds were plated on half-strength Linsmaier Skoog (LS) medium (Caisson Labs, Ontario, Canada) supplemented with 1% sucrose (Sigma-Aldrich, St. Louis, MO, USA), and 1.2% Agar (Acumedia, Lansing, MI, USA). Appropriate antibiotics was also added for screening of transgenic lines. After stratification in the dark at 4 °C for 2 days, plates were transferred to a controlled growth chamber with 80 μmol m−2 s−1 under 16 h light:8 h dark with temperature 22 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed in two biological replicates using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) according to manufacturer’s protocol.

treatment_protocol: 5-day-old seedlings were transferred to half-strength LS liquid buffer containing either 0.5 g/mL Tm (Sigma-Aldrich, St. Louis, MO, USA) or DMSO alone as mock, and treated for 6 hours. After the incubation, the seedlings were transferred to 100x100 square petri dishes with grid (Fisher Scientific, Hampton, NH, USA) containing half-strength LS medium (Caisson Labs, Ontario, Canada) supplemented with 1% sucrose (Sigma-Aldrich, St. Louis, MO, USA), 1.2% Agar (Acumedia, Lansing, MI, USA).

value: whole seedlings

tag: genotype

tag: ecotype background

value: 500 ng/mL Tunicamycin treatment

tag: time (hours)

tag: chip antibody

value: GFP (Millipore, ab290)


title: 28-24-T1_input


title: stress-HT rep1 5hmC-distribution

description:
processed data file: 5hmc_het_stress-wt_control.csv, 5hmc_het_stress-het_control.csv, 5hmc_het_stress-wt_stress.csv
CNTNAP-38 5hmC-Chipseq

source_name: stress-HT rep1 5hmC-Chipseq

tag: cntnap2 genotype

value: Heterozygous

value: Stressed

tag: strain


title: genomic DNA from RNA047SAT

description: genomic DNA from RNA047SAT

source_name: genomic DNA from RNA047SAT


title: genomic DNA from RNA048SAT

description: genomic DNA from RNA048SAT

source_name: genomic DNA from RNA048SAT

value: F


title: WT Lung

city: Cambridge

first: Sangeeta

middle: N

last: Bhatia

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

data_processing:
Illumina NovaSeq6000 sequencer on an Illumina NovaSeq SP flow cell
Raw gene expression matrices were generated for each sample by the Cell Ranger (v.3.0.2) Pipeline coupled with mouse reference version GRCm38
The output filtered gene expression matrices were analyzed by Python software (v.3.9.0) with the scanpy package (v.1.7.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw counts; 10x-Genomics-formatted hdf5 file.
Supplementary_files_format_and_content: Filtered matrix table with raw counts; 10x-Genomics-formatted hdf5 file.

source_name: Lung

extract_protocol:
Eml4-Alk mice (10–12 weeks post tumor induction) and age-matched C57BL/6 healthy controls (Jackson Labs; 18–22 weeks) were euthanized by isoflurane overdose, and lungs were excised and separated into lobes. For tumor-bearing lungs, tumors were separated from healthy tissue using a dissecting microscope. Tissue was minced, treated with digestion buffer (Hank’s Balanced Salt Solution + 2% heat-inactivated FBS, supplemented with DNase and collagenase), and incubated at 37C for 30 minutes with rotation. Samples were filtered using a 70 μm filter and diluted with RPMI-1640 + 2% heat-inactivated FBS. Cell suspension was centrifuged at 1800 rpm for 5 minutes and the pellet was resuspended in ACK lysis buffer for 2 minutes, followed by quenching with buffer (PBS + 2% heat-inactivated FBS). Cell suspension was centrifuged and supernatant was discarded. CD45 cell depletion and viability enrichment was performed according to manufacturer’s instructions (StemCell Technologies). Single cells were processed using the 10X Genomics Single Cell 3’ platform using the Chromium Single Cell 3’ Library & Gel Bead Kit V2 kit (10X Genomics), per manufacturer’s protocol.
10X Genomics Single Cell 3' platform; Chromium Single Cell 3' Library & Gel Bead Kit V2

value: lung

tag: age

value: wild type


title: HFD-O304 islet rep7 - RNA-seq

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet

data_processing:
Fastq quality control (FastQC)
RNA-seq : Alignment with STAR (options: --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 --outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantMode GeneCounts)
RNA-seq : Read counts (obtained with STAR)
Genome_build: GRCm38, Ensembl genome version 96
Supplementary_files_format_and_content: Raw read counts

source_name: Pancreatic islets

extract_protocol:
Mice were killed by cervical dislocation and the pancreata were perfused with 2.5 ml cold collagenase (without Mg2+/Ca2+, GIBCO #14180). The pancreata were then dissected out and incubated at 37 °C for 10–15 min. Collagenase activity was stopped by adding 25 ml of Hanks’ solution (with Mg2+/Ca2+, GIBCO #14060) and vigorous shaking released the islets from the rest of the pancreatic tissue. Islets were rinsed in icecold Hanks’ three times and then picked manually under a stereo microscope.
Isolated islets from 5 mice were pooled and 150 islets were used for extraction of total RNA islets using RNeasy Micro Kit (Qiagen, #74004). RNA-seq libraries were prepared with the Illumina TruSeq RNA Library Kit according to the manufacturer’s instructions.

value: CBA

tag: tissue

value: Pancreatic islets

tag: diet


title: genomic DNA from RNA037SAT

description: genomic DNA from RNA037SAT

source_name: genomic DNA from RNA037SAT


title: 28-24-D2_input

value: mock treatment


title: 210509Bha_D21-4598

description: Model of Eml4-Alk NSCLC; 11-12 wks post tumor induction. Administered QZ1 activatable probe, sorted QZ1- cells.

data_processing:
Libraries were sequenced using an Illumina NextSeq500 on an Illumina NextSeq flow cell.
Feature counting was performed on BAM files using the Rsubread package.
Differential expression analysis on QZ1+ vs QZ1- cells was performed using the DESeq2 package in R. GSEA was performed using GenePattern, and results were visualized using the clusterProfiler R package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts, csv format. Rows provide Gene IDs. Columns provide sample names

extract_protocol:
Single cell lung suspensions from Eml4-Alk mice administered QZ1 were stained with the following antibodies (clone, fluorophore, dilution): CD44 (IM7, BV605, 1:200), CD105 (MJ7/18, BV786, 1:200), Ly6-A/E (D7, PE, 1:200), CD11b (M1/70, APC-Cy7, 1:200), CD45 (30-F11, AF488, 1:400), and EpCAM (G8.8, PE-Cy7, 1:200). Cells were stained for 20 minutes, and DAPI (1:10,000) was added immediately prior to sort. FACS sorting was performed on a FACSAria II (BD). Flow cytometry data was analyzed by the FlowJo software (Treestar). The sort strategy is shown in Fig. S15 of Soleimany et al., bioRxiv 2021. At least 100,000 cells from each of the QZ1+ and QZ1- compartments were collected into RPMI-1640 + 2% heat-inactivated FBS and pelleted via centrifugation at 1800 rpm for 5 minutes. Cell pellets were lysed in Trizol (ThermoFisher), and RNA was extracted using RNEasy Mini Kits (Qiagen).
Libraries were prepared using the Clontech SMARTer Stranded Total RNAseq Kit (Clontech) and precleaned.

treatment_protocol: The peptide QZ1 (Table S2 of Soleimany et al., bioRxiv 2021) was reconstituted to 1 mg/mL in water, then reacted with mPEG-Maleimide, MW 2000 g/mol (Laysan Bio), for PEG coupling via maleimide-thiol chemistry. After completion of the reaction, the final compound was purified using HPLC. All reactions were monitored using HPLC connected with mass spectrometry. Characterization of the final compound, QZ1-(PEG2K), using HPLC and MALDI-MS indicated that products were obtained with more than 90% purity and at the expected molecular weight. Eml4-Alk mice (11–12 weeks post tumor induction; 18-22 weeks in age; Jackson Labs) were anesthetized using isoflurane inhalation (Zoetis). QZ1-(PEG2K) (4.5 nmoles in 0.9% NaCl) was administered intravenously via tail vein injection. Two hours after probe injection, mice were subsequently euthanized by isoflurane overdose followed by cervical dislocation. Lungs were dissected and explanted.

value: 18-22 wks; 11-12 wks post tumor induction

value: Eml4-Alk translocation

tag: condition

value: QZ-

value: Intravenous administration of QZ1 protease-activatable imaging probe.


title: genomic DNA from RNA041SAT

description: genomic DNA from RNA041SAT

source_name: genomic DNA from RNA041SAT

value: DM


title: 28-24-D1_chip


title: 28-24-D2_chip


title: HFD-O304 islet rep6 - RNA-seq


title: Fungal mycelium_DMSO_D2_6

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

data_processing:
BaseCalls were converted and demultiplexed using Illumina bcl2fastq software to generate raw fastq files.
Raw pair-ended generated reads were first trimmed in paired-end mode to remove Illumina adapters and low-quality reads (Quality Phred score cutoff: 20) using Trim Galore version 0.4.0 (Krueger F, https://github.com/FelixKrueger/TrimGalore) and Cutadapt version 1.8.3 (Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12. doi:https://doi.org/10.14806/ej.17.1.200)
Trimmed reads were then aligned to the A. flavus NRRL3357 reference genome (JCVI-afl1-v2.0) with STAR software version 2.5.1b (Dobin et al. 2013) using the 2-pass mode and "--alignIntronMin   10  --alignIntronMax   25000 --outFilterMismatchNmax  18" parameters.
FeatureCounts (Liao et al. 2014) was applied in paired-end mode to perform read summarization at the gene level, generating a raw count matrix. Parameters "-s 2 -O -M -p -t exon" were used.
Count data matrix was filtered to select genes with count per million reads (cpm) >=1 in at least 5 samples among 18 AND genes with at least 1 read in at least 5 samples per condition in at least one condition). Then standard statistical analysis was conducted under R software and edgeR package () to generate "normalized" abundance measurements (log2CPM).
Genome_build: JCVI-afl1-v2.0
Supplementary_files_format_and_content: Matrix table (tab separated) with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table (tab separated) with log2CPM values for every gene and every sample

organism: Aspergillus flavus

source_name: Fungal mycelium

growth_protocol: To prepare the A. flavus inoculum, conidia from a 7-day culture at 27°C were collected and suspended in Tween-80 (0.05%). The concentration of conidia in the suspension was determined using a hemocytometer.

extract_protocol:
After incubation, mycelia were separated from the medium and grounded in liquid nitrogen with mortar and pestle. Total RNA was then extracted from 100 mg of mycelium using a Qiagen RNeasy PlusMinikit (Qiagen, Hilden, Germany) with an additional QIAshredder homogenizer column as recommended by the manufacturer.
Two µg of total RNA were used to build sequencing libraries using Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). Briefly, mRNAs were purified using poly-T magnetic beads, then chemically fragmented (around 300 bp) under 94°C. First and second strand cDNA synthesis were consecutively done according manufacturer’s protocol. After that, cDNA fragments were adenylated on 3’ ends, and Illumina indexed adapters were ligated on both ends. Specific tagged cDNA fragments were then enriched in a 10-cycles PCR.

treatment_protocol: MEA media were supplemented or not (Control) with a solution of DMSO to obtain a final concentration of 35.2 (D1) or 281.6 mM (D2), then were covered with sterile cellophane layers. Plates were then centrally inoculated with 1000 conidia and incubated for 4 days at 27°C in the dark.

tag: medium

value: MEA

value: DMSO

tag: dose


title: 12_S1

tag: sample number

tag: mouse strand

value: cortex

tag: group status

value: non-transplanted

tag: mouse gender

value: female

tag: sample type

value: Mouse cortex, no transplantation


title: genomic DNA from RNA039SAT

description: genomic DNA from RNA039SAT

source_name: genomic DNA from RNA039SAT

tag: gender

value: F

value: SAT

tag: disease

value: NoDM


title: HFD-O304 islet rep5 - RNA-seq

value: CBA


title: genomic DNA from RNA031SAT

description: genomic DNA from RNA031SAT

source_name: genomic DNA from RNA031SAT


title: 28-24-D1_input

value: whole seedlings

tag: genotype

tag: ecotype background

tag: treatment

tag: time (hours)


title: genomic DNA from RNA029SAT

description: genomic DNA from RNA029SAT

source_name: genomic DNA from RNA029SAT

value: M


title: genomic DNA from RNA035SAT

description: genomic DNA from RNA035SAT

source_name: genomic DNA from RNA035SAT


title: Fungal mycelium_DMSO_D2_5

tag: strain


title: genomic DNA from RNA034SAT

description: genomic DNA from RNA034SAT

source_name: genomic DNA from RNA034SAT

tag: tissue


title: 210509Bha_D21-4596

value: lung

tag: age

value: 18-22 wks; 11-12 wks post tumor induction


title: 210509Bha_D21-4595

description: Model of Eml4-Alk NSCLC; 11-12 wks post tumor induction. Administered QZ1 activatable probe, sorted QZ1+ cells.

value: Eml4-Alk translocation

tag: condition

value: QZ+


title: HFD-O304 islet rep4 - RNA-seq

value: Pancreatic islets

tag: diet


title: 28-12-T2_input

value: 500 ng/mL Tunicamycin treatment

tag: chip antibody


title: HFD-O304 islet rep3 - RNA-seq


title: 210509Bha_D21-4594

value: QZ-

value: Intravenous administration of QZ1 protease-activatable imaging probe.


title: HFD-O304 islet rep1 - RNA-seq

value: HFD


title: Fungal mycelium_DMSO_D2_4

tag: medium

value: MEA

value: DMSO

tag: dose


title: HFD islet rep7 - RNA-seq


title: 210509Bha_D21-4593


title: 210509Bha_D21-4592


title: 28-12-T2_chip

value: GFP (Millipore, ab290)


title: 28-12-T1_input


title: 28-12-D2_input

value: mock treatment


title: Fungal mycelium_DMSO_D2_3


title: Fungal mycelium_DMSO_D2_1


title: Fungal mycelium_DMSO_D2_2


title: 210509Bha_D21-4591


title: genomic DNA from RNA022SAT

description: genomic DNA from RNA022SAT

source_name: genomic DNA from RNA022SAT

value: SAT

value: NoDM


title: genomic DNA from RNA016SAT

description: genomic DNA from RNA016SAT

source_name: genomic DNA from RNA016SAT

value: DM


title: HFD islet rep6 - RNA-seq

value: CBA


title: HFD islet rep5 - RNA-seq


title: HFD-O304 islet rep2 - RNA-seq


title: HFD islet rep4 - RNA-seq


title: 28-12-D1_input

value: whole seedlings


title: 28-12-D2_chip


title: Fungal mycelium_DMSO_D1_6


title: 28-12-D1_chip


title: 28-0-T2_input


title: Lane2-mixed sample [AdiposeVSG.L2]

city: Ithaca

first: Paul

middle: D.

last: Soloway

state: NY

address: T4 018 Veterinary Research Tower

department: Biomedical Sciences

institute: Cornell University

data_processing:
snATAC by the Ren lab was used for alignment, correcting barcode errors, and removing PCR duplicates. Default parameters were used.
Sinto was used to generate fragment files from the BAM files
ArchR was for all downstream analysis
Genome_build: mm10
Supplementary_files_format_and_content: fragment files contain fragments for each cell which is suitable for use in ArchR
Supplementary_files_format_and_content: PeakMatrix is a summarized experiment of the processed ArchR object containing the peak matrix and metadata for all cells

source_name: Adipose

extract_protocol:
Whole adipose depots were finely minced on dry ice. Then 80mg of adipose tissue was transferred to a pre-chilled Dounce homogenizer (Wheaton #357546) with 30 mL of HB (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10mM Tris pH7.4, protease inhibitors (Pierce #88666), 0.016 mM PMSF). Samples were processed in groups of two (one SHAM and one VSG) to ensure any variation due to library preparation is equally applied to both SHAM and VSG. All steps were performed on ice or at 4°C. The tissue was first homogenized with 10-15 strokes using a loose pestle then an additional 10 strokes with the tight pestle. The homogenized tissue was then filtered through a 70 µm cell strainer (BD Biosciences #352350) and centrifuged for 5 mins at 500g in a centrifuge with a swinging bucket rotor. The supernatant was removed, the cell pellet washed with ATAC-RSB (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, H2O), then centrifuged for 10 minutes at 750g. After removing the supernatant, nuclei were resuspended in 1 mL of OMNI-ATAC buffer (10 mM Tris pH7.4, 5 mM MgCl2, 10% DMF, 33% 1x PBS(no Ca++ or Mg++), 0.1% Tween-20, 0.01% Digitonin (ThermoFisher #BN2006)), counted on a hemacytometer, and the concentration was adjusted to 100,000 nuclei/mL.
The snATAC library preparation protocol was based on Preissl et al. and Spektor et al. with some modifications (62,63). For tagmentation with Tn5 transposase, 8 µL of the nuclei suspension was added to each well of a 96 well plate. Then, 1 µL of ME-C barcoded transposome loaded Tn5 and 1 µL of ME-D barcoded transposome loaded Tn5 were added to each well. Tagmentation was carried out at 50°C for 30mins. 10 µL of 40 µM EDTA was added to each well, gently vortexed, and incubated for 15 minutes at 37°C to inactivate Tn5 transposase. 20µL of sorting buffer (2% BSA, 2mM EDTA in PBS (no Ca++ or Mg++)) was added to each well, and all wells were combined. For the freeze-thaw test, nuclei were centrifuged for 5 mins at 500g and resuspended in 500 µL of freeze buffer (10% DMSO, 90% sort buffer) and slowly frozen and stored at -80°C.
Nuclei were stained with Draq7(1:100; Abcam #ab109202), filtered through a 30 µm filcon cell strainer (BD Biosciences #340597), and 25 nuclei were sorted into each well of a 96 well plate containing 16.5 µL of sort EB (10mM Tris pH 8, 2% BSA, H2O) per well using a BD FACSAria Fusion. For PCR amplification, 2 µL of 0.2% SDS was added to each well and incubated for 7 minutes at 55°C. Next, 2.5 µL of 10% Triton X-100, 2 µL of 25 µM Primer i5, 2 µL of 25 µM Primer i7, and 25 µL of 2X PCR mix with Q5 DNA polymerase (NEB #M0491S) (Q5 5X buffer, dNTP, Q5 enzyme, GC enhancer, H2O) was added to each well. All PCR reactions were run in the same thermocycler with the following program: 72°C 5 minutes, 98°C 30 seconds, 15 cycles of (98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute), and 72°C 5 minutes. After PCR, all wells were pooled, then 24 mL buffer PB (5:1, Qiagen #19066) and 1.2mL NaOAc were added sequentially. Samples were each run through a separate MinElute column (Qiagen #28004) using a QIAvac apparatus (Qiagen #19413), then washed twice with 750 mL Buffer PE (Qiagen #19065). The sample was then eluted in 40 uL of Buffer EB (10 mM Tris pH 8) and centrifuged at max speed on a tabletop centrifuge for 2 minutes. The following size selection steps were performed at room temperature. First, large fragments were removed with 0.5X vol AMPure XP (Beckman Coulter #A63880) purification, and then size selected 3 times with 1.5X vol AMPure XP consecutively to remove PCR primers according to the manufacturer’s protocol.

treatment_protocol: At 2 months of age, C57/BL/6J mice were placed on a 60% energy from fat high-fat diet (HFD) for eight weeks then underwent VSG, or sham surgery. Mice were maintained on HFD throughout the study, euthanized at 2.5 months after surgery, and the inguinal (ING) and epididymal (EPI) adipose depots were dissected without removing lymph nodes, frozen, and stored.

value: mixed adipose depot


title: HFD islet rep2 - RNA-seq


title: Fungal mycelium_DMSO_D1_4


title: Lane3-mixed sample [AdiposeVSG.L3]

value: Epididymal adipose depot


title: 28-0-T1_input

source_name: Whole seedlings


title: Fungal mycelium_DMSO_D1_2


title: Fungal mycelium_DMSO_D1_3


title: Fungal mycelium_DMSO_D1_1


title: Fungal mycelium_DMSO_D1_5


title: HFD islet rep1 - RNA-seq


title: scRNAseq_Islets_NMMA_Rep2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: 18 hours NMMA treatement

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Islets

extract_protocol: 10x Genomics

treatment_protocol: Pancreatic islets were harvested from mice, exposed to cytokines ex vivo, dissociated, and loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles).

tag: agent

value: 18 hours NMMA treatement

value: Pancreas


title: scRNAseq_Islets_IL1B_IFNg_Rep2

description: 18 hours IL-1B and IFNg treatement

value: 18 hours IL-1B and IFNg treatement


title: 28-0-T2_chip

value: 500 ng/mL Tunicamycin treatment


title: scRNAseq_Islets_IL1B_IFNg_NMMA_Rep2

description: 18 hours IL-1B, IFNg, and NMMA treatement


title: 210509Bha_D21-4597

value: lung

value: 18-22 wks; 11-12 wks post tumor induction

value: Eml4-Alk translocation

value: QZ+

value: Intravenous administration of QZ1 protease-activatable imaging probe.


title: RD islet rep7 - RNA-seq

value: Pancreatic islets

value: RD


title: RD islet rep6 - RNA-seq


title: HF islet rep3 - RNA-seq

value: HFD


title: scRNAseq_Islets_Untreated_Rep2

description: Untreated

value: Untreated


title: RD islet rep5 - RNA-seq

value: CBA


title: 28-0-T1_chip

value: whole seedlings

value: GFP (Millipore, ab290)


title: 28-0-D2_input

value: mock treatment


title: Lane1-mixed sample [AdiposeVSG.L1]

value: Inguinal adipose depot


title: scRNAseq_Islets_NMMA_Rep1

description: 18 hours NMMA treatement

value: 18 hours NMMA treatement

value: Pancreas


title: RD islet rep3 - RNA-seq


title: scRNAseq_Islets_IL1B_IFNg_NMMA_Rep1

value: 18 hours IL-1B, IFNg, and NMMA treatement


title: Fungal mycelium_CTRL_4

value: MEA

value: Control


title: 28-0-D1_input


title: Fungal mycelium_CTRL_2


title: 28-0-D2_chip


title: scRNAseq_Islets_Untreated_Rep1

description: Untreated


title: RD islet rep1 - RNA-seq


title: Fungal mycelium_CTRL_3


title: scRNAseq_Islets_IL1B_IFNg_Rep1

description: 18 hours IL-1B and IFNg treatement

value: 18 hours IL-1B and IFNg treatement


title: 28-0-D1_chip


title: RD islet rep2 - RNA-seq


title: RD islet rep4 - RNA-seq


title: Fungal mycelium_CTRL_5


title: Col-TM-24h_3

extract_protocol:
Plants germinated and were subjected to the ER stress recovery assay as described above. Whole seedlings were harvested at 0 h, 12 h and 24 h of recovery in three biological replicates (n = 12 per each replicate), and immediately frozen in the liquid nitrogen. The frozen samples were ground to a fine powder in liquid nitrogen using a Retch MM400 Mixer Mill with zirconium oxide balls. Total RNA was extracted using the NucleoSpin RNA Plant kit (MACHEREY-NAGEL, Düren, Germany) according to the manufacturer’s instruction.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Library (Illumina, San Diego, CA, USA)

value: WT

value: 500 ng/mL Tunicamycin treatment


title: Fungal mycelium_CTRL_1


title: Col-TM-24h_2


title: Col-TM-24h_1


title: HFD-O304 islet rep2 - H3K27Me3

data_processing:
Fastq quality control (FastQC)
RNA-seq : Read counts (obtained with STAR)
ChIP-seq : Alignment with Bowtie2 (options: --threads 4 --very-sensitive)
ChIP-seq : Bam files merged per condition
ChIP-seq : Peak calling with MACS2 (options: callpeak --gsize 1.87e9 --broad --broad-cutoff 0.1 -f BAMPE -q 0.1 --nolambda --nomodel --shift 200 --extsize 200)
Genome_build: GRCm38, Ensembl genome version 96
Supplementary_files_format_and_content: Peak files

extract_protocol:
Mice were killed by cervical dislocation and the pancreata were perfused with 2.5 ml cold collagenase (without Mg2+/Ca2+, GIBCO #14180). The pancreata were then dissected out and incubated at 37 °C for 10–15 min. Collagenase activity was stopped by adding 25 ml of Hanks’ solution (with Mg2+/Ca2+, GIBCO #14060) and vigorous shaking released the islets from the rest of the pancreatic tissue. Islets were rinsed in icecold Hanks’ three times and then picked manually under a stereo microscope.
For ChIP-seq experiments ~ 600 islets were processed. Islets were fixed 15 min in 1 ml fixing solution (1% formaldehyde, 50 mM HEPES–KOH, 100 mM NaCl, 1 mM ethylenediaminetetraacetic acid (EDTA), 0.5 mM EGTA) at RT with gentle mixing. Crosslinking was stopped by adding 1/20 volume of 2.5 M glycine for 5 min at RT. Islets were then washed 2 × 5 min at 4 °C with cold 1 × PBS containing protease inhibitor cocktail (Roche, #4693132001), snap frozen and stored at − 80 °C until awaiting further processing. Pooled islets were lysed 5–10 min in 130 μl of lysis buffer at 4 °C and sonicated on a Covaris E220 device (PIP: 105, Duty factor: 2, Cycles/burst: 200, Duration: 9 min). ChIP was performed with rabbit anti-H3K27Ac (Abcam, ab4729) and rabbit anti-H3K27Me3 (Upstate #07-449) antibodies. ChIP-seq libraries were prepared with the Rubicon Thruplex DNA-Seq kit following manufacturer’s instructions library preparations and sequencing were performed.

value: Pancreatic islets


title: HFD-O304 islet rep1 - H3K27Me3


title: Foxn1TMhomo_rep1

city: Worcester

first: René

last: Maehr

address: 368 Plantation St

department: Program in Molecular Medicine/Diabetes Center of Excellence

institute: UMass Medical School

data_processing:
Base calling was performed using cellranger mkfastq version 3.0.1.
Count matrices were generated from fastq files using cellranger count version 3.0.1.
Counting used cellranger reference version mm10-1.2.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are gzipped tar archives containing 10x v3 format count matrices: a gzipped matrix market file of raw UMI counts with one feature per row and one cell per column. Feature names and barcodes are in separate tab-separated text files.

molecule: polyA RNA

source_name: pharyngeal endoderm

growth_protocol: Embryonic pharyngeal endoderm was isolated from timed mouse embryos.

extract_protocol:
From embryonic day 12.5 Pax9VENUS heterozygous/Foxn1 knockout reporter mice, embryonic pharynx was mechanically isolated and dissociated into a single cell solution using trypsin. Cells were stained with 7AAD cell viability dye and PE/Cy7-conjugated anti-mouse CD326 (Epcam) antibody. 7AAD negative, Epcam-positive, and VENUS-positive single cells were sorted using a BD FACS S-Aria IIu Cell Sorter.
Libraries were prepared according to the 10X Genomics Chromium Single Cell 3' v3 kit. Final libraries were sequenced on an Illumina NextSeq 500 using high-output 75-cycle kits.

value: pharyngeal endoderm

value: Pax9VENUS Foxn1TM-/-

tag: source tissue

value: embryo

tag: developmental day


title: Foxn1TMhomo_rep2


title: Foxn1TMhet_rep2

value: Pax9VENUS Foxn1TM+/-


title: HFD islet rep2 - H3K27Me3

value: CBA

value: HFD


title: Papille patient 6_2 implanted [S150]

city: Bruxelles

first: Anne

last: des Rieux

address: Drève de la Ferme, 92

country: Belgium

institute: UCLouvain

data_processing:
cleaning: trimmomatic v0.38 was used to remove low quality reads and trim the adapter from the sequences.
alignment: Hisat2 v 2.1.0
counting: featureCounts v2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Papille patient

growth_protocol: Apical papillae were collected on wisdom tooth and either snap frozen or implanted in a rat spinal cord hemisection model. After 24h, apical papilla were retrieved and treated for RNAseq.

extract_protocol:
Tissue was lyzed and RNA isolated with DNAse treatment.
Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).

treatment_protocol: 3 replicates with 2 patients

tag: subject status/id

value: Papille patient 6

value: Apical papillae

tag: group


title: HFD islet rep1 - H3K27Me3


title: genomic DNA from RNA008SAT

description: genomic DNA from RNA008SAT

source_name: genomic DNA from RNA008SAT

tag: gender

value: F

value: SAT

tag: disease

value: DM


title: Papille patient 6_1 implanted [S149]

value: implanted in a rat spinal cord hemisection model.


title: Papille patient 5_1 implanted  [S148]

value: Papille patient 5


title: Papille patient 6_2 [S153]

value: snap frozen


title: Foxn1TMhet_rep1

tag: genotype


title: RD islet rep2 - H3K27Me3

source_name: Pancreatic islets

value: RD


title: Papille patient 6_1 [S152]


title: Col-TM-12h_1

value: whole seedlings

value: WT

tag: ecotype background

tag: treatment

value: 500 ng/mL Tunicamycin treatment

tag: time (hours)


title: Col-TM-12h_2

tag: tissue


title: scRNA-seq_E12_5_rscRNA-seq_Ep2

data_processing:
Base calling was performed using cellranger mkfastq version 2.1.0.
Count matrices were generated from fastq files using cellranger count version 2.1.0.
Counting used cellranger reference version mm10-1.2.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are gzipped tar archives containing 10x v2 format count matrices: a matrix market format matrix of raw UMI counts with one gene per row and one cell per column. Gene names and barcodes are in separate tab-separated text files.

extract_protocol:
From Pax9VENUS heterozygous reporter mice, embryonic pharynx was mechanically isolated and dissociated into a single cell solution using trypsin. Cells were stained with 7AAD cell viability dye and PE/Cy7-conjugated anti-mouse CD326 (Epcam) antibody. 7AAD negative, Epcam-positive, and VENUS-positive single cells were sorted using a BD FACS S-Aria IIu Cell Sorter.
Libraries were prepared according to the 10X Genomics Chromium Single Cell 3' v2 kit. Final libraries were sequenced on an Illumina NextSeq 500 using high-output 75-cycle kits.

value: pharyngeal endoderm


title: RD islet rep1 - H3K27Me3

tag: strain

value: Pancreatic islets


title: Col-TM-0h_3


title: scRNA-seq_E12_5_rscRNA-seq_Ep1

value: embryo


title: Papille patient 5_1 [S151]


title: Col-TM-12h_3


title: scRNA-seq_E11_5_rscRNA-seq_Ep3


title: genomic DNA from RNA033SAT

description: genomic DNA from RNA033SAT

source_name: genomic DNA from RNA033SAT

value: M


title: Col-TM-0h_2


title: HFD-O304 islet rep1 - input

value: CBA

tag: diet


title: FDC4M

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: All_exp_FPKM.txt

source_name: Ovary

extract_protocol:
RNAstormTM FFPE kit (CELLDATA) was used to isolate total RNA from formalin-fixed paraffin-embedded surgically resected samples.
SMARTer Stranded Total RNA-Seq Kit—Pico Input Mammalian Library preparation kit (Clontech) was used for the preparation of strand-specific RNA-seq library.

tag: disease state

value: gastric adenocarcinoma

tag: pathological types

value: adenocarcinoma with low differentiation

value: ovarian metastasis of gastric adenocarcinoma

tag: individual


title: HFD islet rep1 - input

value: HFD


title: RD islet rep1 - input


title: scRNA-seq_E11_5_rscRNA-seq_Ep2b


title: HFD-O304 islet rep2 - H3K27Ac


title: Col-DMSO-24h_3

value: mock treatment

tag: chip antibody


title: Col-DMSO-24h_2


title: scRNA-seq_E11_5_rscRNA-seq_Ep2

tag: source tissue


title: FDC4N

source_name: Stomach

value: normal gastric mucosa


title: FDC3M


title: scRNA-seq_E10_5_rscRNA-seq_Ep6

tag: developmental day


title: scRNA-seq_E10_5_rscRNA-seq_Ep7


title: HFD-O304 islet rep1 - H3K27Ac


title: Col-DMSO-12h_3


title: scRNA-seq_E10_5_rscRNA-seq_Ep5


title: Col-DMSO-24h_1


title: HFD islet rep2 - H3K27Ac


title: 28-12-T1_chip

value: GFP (Millipore, ab290)


title: FDC4P


title: Col-DMSO-12h_2


title: HFD islet rep1 - H3K27Ac


title: scRNA-seq_E9_5_rscRNA-seq_Ep2


title: FDC3P


title: FDC3N


title: RD islet rep2 - H3K27Ac


title: Col-TM-0h_1


title: genomic DNA from RNA004SAT

description: genomic DNA from RNA004SAT

source_name: genomic DNA from RNA004SAT

value: F

value: SAT

value: NoDM


title: genomic DNA from RNA003SAT

description: genomic DNA from RNA003SAT

source_name: genomic DNA from RNA003SAT


title: genomic DNA from RNA005SAT

description: genomic DNA from RNA005SAT

source_name: genomic DNA from RNA005SAT


title: Col-DMSO-12h_1

value: whole seedlings

value: WT


title: FDC2M


title: scRNA-seq_E9_5_rscRNA-seq_Ep1

value: pharyngeal endoderm


title: E12.5_rep2

data_processing:
Base calling was performed using cellranger-atac version 1.0.0 except for E11.5_rep2 which used version 1.1.0
Processed files were generated from fastq files using cellranger-atac 1.0.0 except for E11.5_rep2 which used version 1.1.0
Counting used cellranger-atac reference version mm10-1.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are gzipped tar archives containing 10x fragment files, indices, and comma-separated cell metadata.

extract_protocol:
From Pax9VENUS heterozygous reporter mice, embryonic pharynx was mechanically isolated and dissociated into a single cell solution using trypsin. Cells were stained with 7AAD cell viability dye and PE/Cy7-conjugated anti-mouse CD326 (Epcam) antibody. 7AAD negative, Epcam-positive, and VENUS-positive single cells were sorted using a BD FACS S-Aria IIu Cell Sorter.
Libraries were prepared according to the 10X Genomics Chromium Single Cell ATAC kit. Final libraries were sequenced on an Illumina NextSeq 500 using high-output 75-cycle kits.

tag: molecule subtype

value: Transposase-accessible DNA


title: E12.5_rep1

value: embryo


title: FDC2N


title: FDC2P


title: FDC1N


title: Col-DMSO-0h_1


title: FDC1M


title: E11.5_rep1


title: bzip60-TM-24h_3

value: bzip60-2 knockout

value: 500 ng/mL Tunicamycin treatment


title: 4_kdm2bcKONPC_KDM2B

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

description: NPC culture medium

data_processing:
For the ChIP-Seq data analysis, all sequencing reads were mapped to NCBI build 37 (mm9) of the mouse genome using Bowtie2.
All mapped reads with high quality were filtered by “samtools view -q 40”. The potential PCR duplicated reads were removed by “samtools rmdup”.
The mapped sequencing reads were normalized as Counts Per Million Reads (CPM) using bamCoverage  --normalizeUsing CPM --extendReads 200.
Genome_build: mm9
Supplementary_files_format_and_content: bw

source_name: Neural progenitor cells

growth_protocol: The neural tissues were isolated from the subventricular zone of E16 brains and dissociated with 0.05% trypsin-EDTA (Life Technologies) at 37 °C for 15 min. The reaction was stopped by trypsin inhibitor (10 mg/ml, Worthington Biochemical Corporation). The dissociated cells were washed with cold PBS for 3 times and plated onto the non-coated petri dishes in the proliferation medium [Neurobasal medium (Life Technologies) supplemented with 1× B27 supplement (Gibco), 1x GlutaMAX (Life Technologies), 20 ng/ml murine epithelial growth factor (Peprotech), 20 ng/ml basic fibroblast growth factor (Peprotech), and 100U/ml penicillin/streptomycin (Life Technologies).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
ChIP DNA library was constructed for Novaseq6000 sequencing using NEBNext UltraII DNA library Prep Kit for Illumina (New England BioLabs, Inc) according to the manufacturer’s instructions. Adapter-ligated DNA was amplified by PCR for 12-14 cycles and followed by size selection using agarose gel electrophoresis. The DNA was purified using QIAquick gel extraction kit (Qiagen) and quantified both with an Agilent Bioanalyzer and Invitrogen Qubit. The DNA was diluted to a working concentration of 20nM prior to sequencing. Sequencing on a Novaseq6000 instrument was carried out by the Genomics Core Facility at Michigan State University.

tag: modification

tag: chip-antibody

value: KDM2B (Dr. Robert Klose, Oxford University)


title: FDC1P

value: gastric adenocarcinoma

value: adenocarcinoma with low differentiation


title: SZ20

data_processing:
Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to human genome hg38 using STAR aligner (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file containing unnormalized (raw) read counts per feature.

source_name: hiPSC-derived brain astrocytes

growth_protocol: The primary cells were reprogrammed with Cytotune 2.0 iPS Sendai Reprogramming Kit for Oct4, Sox2, Klf4, and c-myc. The emerged colonies were individually subcloned. For differentiation, iPSCs were cultured in feeder-free conditions with Matrigel-coating and Essential 8 culture medium. Astroglial differentiation was carried out as described (Stem Cell Reports. 2017;9:1885-1897) by maintaining neural progenitor spheres in astrocyte differentiation medium in suspension for 5–7 months before dissociation and plating the cells on Matrigel-coated dishes for maturation 7 days prior to experiments.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit. The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.

treatment_protocol: Matured astrocytes were not treated

tag: sample number

tag: cell type

value: hiPSC-derived brain astrocytes

tag: hipsc source

value: skin fibroblasts

tag: group status

value: Healthy control

value: Healthy, unrelated control person

tag: age

tag: patient gender

value: female

tag: patient disease status

value: healthy


title: MSC-OD-Donor6-Day28-rep2 [thBS_MSC_44]

city: Reykjavik

first: Ólafur

last: Sigurjónsson

address: Menntavegur 1

department: Department of Engineering

country: Iceland

institute: University of Reykjavik

description: total RNA

data_processing:
The RNA transcript expression was quantified with Kallisto version 0.46.1 using default parameters and the Ensembl Homo_sapiens GRCh38 reference transcriptome and generated FASTQ files as input.
We used DESeq2 version 1.26.0 to determine statistically significant differentially expressed genes (DEGs) across experimental conditions (p < 0.05 and Benjamini–Hochberg correction α = 0.1 adjusted p < 0.1). We also used DESeq2 to generate the TPM values table. All scripts to reproduce the analysis are available in https://github.com/adelomana/osteo
Genome_build: Ensembl Homo_sapiens GRCh38 reference transcriptome
Supplementary_files_format_and_content: TPM table with samples as columns and genes as rows.

source_name: Human bone marrow-derived mesenchymal stromal cells

growth_protocol: Cells were maintained in basal growth medium (BGM). BGM was prepared by adding 5000 IU/mL of heparin (LEO Pharma A/Sm, Ballerup, Denmark), 1% penicillin/streptomycin (Gibco, Grand Island, NE, USA), and 10% pathogen inactivated platelet lysate (PIPL) supernatant (Platome, Reykjavik, Iceland) into DMEM/F12 + Glutamax growth medium (Gibco, Grand Island, NE, USA). The PIPL was centrifuged at 5000 rpm (4975× g) for 10 min before the resulting supernatant was added to the medium.

extract_protocol:
Upon the day of assessment, the medium was discarded using a pipette and 1 mL of RNAzol® RT (Molecular Research Center, Inc., Cincinnati, OH, USA) was added to the wells in question in order to lyse the cells. Repeated pipetting was used to dislodge and lyse the cells completely before moving the resulting lysate to a 2-mL Eppendorf tube. In order to precipitate DNA, protein and polysaccharides 0.4 mL of water was added to the lysate, the mixture shaken for 15 sec and then stored at room temperature (RT) for 15 min. Samples were then centrifuged for 15 min at 12,000 g. Approximately 75% of the resulting supernatant was moved to a new Eppendorf tube. In order to precipitate the total RNA, 1 mL of isopropanol was added to the supernatant collected in the previous step. Samples were then incubated at RT for 10 min before being centrifuged for 10 min at 12,000 g. This collected a small RNA pellet at the bottom of the Eppendorf tube. The supernatant was discarded, and the resulting pellet washed twice by adding 0.5 mL 75% ethanol and centrifuging for two minutes at 5000 g. The pellet was then dissolved in 25 µL of RNase-free water to gain 20 ng/µL concentration for RNA sequencing.
cDNA libraries derived from Poly-A mRNA were generated using Illumina’s TruSeq RNA v2 Sample Prep Kit. Briefly, Poly-A mRNA was isolated from total RNA samples (0.2–1 μg input) using hybridizaton to Poly-T beads. Poly-A mRNA was fragmented at 94 °C in the presence of divalent cations, followed by first-strand cDNA synthesis using random hexamers and SuperScript IV reverse transcriptase (Invitrogen, Waltham, MA, USA). Following second-strand cDNA synthesis, end repair, the addition of a single A nucleotide, unique dual indexed adaptor ligation (IDT for Illumina), AMPure bead purification, and PCR amplification, the resulting cDNA sequencing libraries were measured on the LabChip GX, diluted to 3 nM, and stored at −20 °C.

tag: donor

tag: day

tag: replicate


title: MSC-OD-Donor6-Day28-rep3 [thBS_MSC_45]

description: total RNA

value: Human bone marrow-derived mesenchymal stromal cells


title: SZ19

tag: individual

value: male


title: bzip60-TM-24h_2

tag: tissue

value: whole seedlings

tag: genotype

tag: ecotype background

tag: treatment

tag: time (hours)

tag: chip antibody


title: Col-DMSO-0h_3

value: WT

value: mock treatment


title: bzip60-TM-12h_3


title: 6_kdm2bcKONPC_RING1B

description: NPC culture medium

tag: modification

tag: strain

tag: chip-antibody

value: RING1B (Cell signaling, 5694S)


title: RD islet rep1 - H3K27Ac

value: CBA

value: Pancreatic islets

tag: diet

value: RD


title: Col-DMSO-0h_2


title: 1_wtNPC_input

description: NPC culture medium

value: wild-type


title: 3_wtNSC_KDM2B

description: NPC culture medium

value: KDM2B (Dr. Robert Klose, Oxford University)


title: 2_kdm2bcKONPC_input

description: NPC culture medium


title: SZ18

tag: sample number

tag: cell type

value: hiPSC-derived brain astrocytes

tag: hipsc source

tag: group status

value: Pair 6, unaffected twin

value: Monozygotic twin without schizophrenia diagnosis

tag: age


title: SZ17

value: skin fibroblasts

value: Pair 6, affected twin

value: Monozygotic twin with schizophrenia diagnosis and medication

tag: patient gender

tag: patient disease status

value: schizophrenia


title: MSC-OD-Donor6-Day28-rep1 [thBS_MSC_43]

description: total RNA

tag: donor

value: Human bone marrow-derived mesenchymal stromal cells

tag: day

tag: replicate


title: E11.5_rep2

tag: tissue

value: pharyngeal endoderm

tag: genotype

value: embryo

tag: developmental day

tag: molecule subtype

value: Transposase-accessible DNA


title: bzip60-TM-24h_1

value: whole seedlings

value: bzip60-2 knockout

tag: ecotype background

tag: treatment

value: 500 ng/mL Tunicamycin treatment

tag: time (hours)

tag: chip antibody


title: 5_wtNPC_RING1B

description: NPC culture medium

tag: modification

tag: strain

tag: chip-antibody

value: RING1B (Cell signaling, 5694S)


title: MSC-OD-Donor17-Day28-rep3 [thBS_MSC_39]

description: total RNA

tag: cell type


title: SZ16

tag: sample number

tag: hipsc source

tag: group status

value: Healthy control

tag: individual

value: Healthy, unrelated control person

tag: age

tag: patient gender

value: female

value: healthy


title: G21d

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

description: spatial transcriptomics (10x Visium)

data_processing:
Data Formatting - spaceranger mkfastq, --run=. --samplesheet=spaceRanger.csv --output-dir ./spaceRanger --nopreflight --jobmode=slurm --localcores=24 --localmem=120 --qc
Read Quantification - spaceranger count, --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=${REF} --project=${PROJECT} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX} --slide=${SLIDE} --area=${AREA} --image=${IMAGE}
Genome_build: GRCm38.p6 + Gencode-M22 Annotation, 10X provided refdata-gex-mm10-2020-A
Supplementary_files_format_and_content: Compressed output directories from spaceRanger count

source_name: heart

extract_protocol:
For cryosection histology, hearts were oriented directly into a cryomold with Optimal Cutting Temperature media. The cryomold was subsequently placed into a prechilled bath of isopentane, with care taken not to introduce bubbles or alter the orientation of the heart. After OCT was completely frozen, hearts were transferred on dry ice and stored at -80°C until they were sectioned. One hour prior to sectioning, slides and hearts were equilibrated in the prechilled in the cryostat at -17°C. Cryosections of 12 µm were cut and placed carefully onto the specified capture area (containing the barcoded probes) on the Visium Spatial Gene Expression Slide from 10X Genomics (Pleasanton, CA, USA). Upon placing all sections appropriately on the slide, the slide was stored at -80°C for up to a week. For cryosection H&E, tissue sections were fixed in methanol and H\&E stained following the Visium Methanol Fixation and H&E Staining guide. Briefly, the slides were incubated on thermocycler for 1 minute at -37°C prior to a 30 minute incubation at -20°C in prechilled methanol. Slides were uniformly covered with 500 µL isopropanol and incubated at room temperature for 1 minute. Slides were air dried for up to 10 minutes before a 7 minute incubation at room temp with 1 mL hematoxylin. Slides were washed by dipping the slide (15x) in two beakers of water. Slides were incubated with 1mL Bluing Buffer at room temperature for 2 minutes before dipping the slide (5x) in water.  Slides were incubated with 1 mL Eosin for 1 minute at room temperature before dipping the slide into water (15x). Slides were incubated on tThermocycler for 5 minutes at 37°C before imaging on the VS120 Slide Scanner (Olympus, Center Valley, PA, USA). Images were saved as .tif (2000x2000 pixels) for each capture area for downstream analysis.
Tissue was permeabilized for 18 minutes and poly-adenylated mRNAs were released and captured by primers on the slide. Reverse transcription was performed to produce full-length cDNA using the Visium Spatial Gene Expression Kit, as per manufacture's recommendation. cDNA was assessed by KAPA qPCR to determine optimal cycle numbers for cDNA amplification. Post-amplification, cDNA was purified using SPRISelect beads (ThermoFisher) and quality was assessed with the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 25% of total cDNA yield was used to generate Illumina compatible sequencing libraries with Visium Library Construction Kit. Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the NovaSeq 6000 sequencer (Illumina, San Diego, CA) following the sequencing requirements in the Visium Spatial Gene Expression manual of 28x10x10x90.

treatment_protocol: Apical resection at P2

value: Postnatal day (P) 24

value: P2 apical resection + 21 days


title: MSC-OD-Donor17-Day28-rep2 [thBS_MSC_38]

description: total RNA

tag: donor

tag: day

tag: replicate


title: bzip60-TM-12h_1

data_processing:
RNAseq analysis: RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Library (Illumina, San Diego, CA, USA) and sequenced in single-end mode on the Illumina HiSeq 4000 platform (50-nt) at Research Technology Support Facility Genomics Core at Michigan State University (RTSF-MSU). The quality of raw reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 2.2.4) and TopHat (version 2.0.14) with a 10 bp minimum intron length and 15,000 bp maximum intron length. Fragments per kilobase exon model per million mapped reads (FPKM) were calculated using TAIR10 gene model annotation with Cufflinks (version 1.3.0).
ChIP-seq analysis: The quality of raw ChIP-seq reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 1.1.2) with parameters “-n 2 -m 3 -k 1 --threads 7 --best --chunkmbs 256 -q”. Duplicated reads were removed using Samtools (version 1.8). Peak calling was performed using MACS2 (version 2.1.2) in individual samples with input samples pooled for DMSO-only and Tm treated samples and with a relaxed threshold of P-value (--pvalue=1e-2), as recommended by the IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr). Peaks across replicates with an IDR < 0.05 were retained for further analysis.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text file: for RNA-seq: The normalized read values (FPKM) for gene expression in all samples. Sample name consists of genotype, treatment, time-point and biological replicate with hyphen. 28, bzip28. 60, bzip60.
Supplementary_files_format_and_content: for ChIP-seq, UPR-specific binding peak coordinates, annotated genes and scores

tag: tissue

tag: genotype

tag: ecotype background


title: SZ15

value: hiPSC-derived brain astrocytes

value: skin fibroblasts

tag: patient disease status


title: E14d

description: spatial transcriptomics (10x Visium)

value: Postnatal day (P) 17

tag: treatment

value: P2 apical resection + 14 days


title: bzip60-TM-12h_2

tag: time (hours)

tag: chip antibody


title: MSC-OD-Donor17-Day28-rep1 [thBS_MSC_37]

description: total RNA

tag: cell type

value: Human bone marrow-derived mesenchymal stromal cells


title: Fungal mycelium_CTRL_6

source_name: Fungal mycelium

tag: medium

value: MEA

value: Control

tag: strain


title: A3d

description: spatial transcriptomics (10x Visium)

value: Postnatal day (P) 5

value: P2 apical resection +3 days


title: C7d

description: spatial transcriptomics (10x Visium)

value: Postnatal day (P) 10

value: P2 apical resection + 7 days


title: MSC-OD-Donor17-Day16-rep3 [thBS_MSC_33]

description: total RNA


title: SZ13

tag: sample number

tag: hipsc source

tag: group status

value: Healthy control

value: male


title: MSC-OD-Donor17-Day16-rep1 [thBS_MSC_31]

description: total RNA


title: SZ14

tag: individual

value: Healthy, unrelated control person

tag: age

tag: patient gender

value: female


title: bzip60-DMSO-24h_3

source_name: Whole seedlings

value: whole seedlings

value: bzip60-2 knockout

value: mock treatment


title: bzip60-TM-0h_1

value: 500 ng/mL Tunicamycin treatment


title: 2D

city: JINAN

first: zenjun

last: li

address: 440 Jiyan Road, Huaiyin District

institute: Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.   The clean reads were mapped to reference genome using hisat 2.
The read counts of each gene were obtained by htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: Reads count

source_name: macrophages

extract_protocol:
Total RNA was extracted from purified and untreated RAW264.7 cells from 3D and 2D culture systems using TRIzol  reagent.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

tag: culture method

value: 2D culture

tag: cell line


title: SZ11

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

institute: University of Helsinki

value: hiPSC-derived brain astrocytes

value: skin fibroblasts

value: Pair 5, unaffected twin

value: Monozygotic twin without schizophrenia diagnosis

value: healthy


title: 3D

value: 3D culture


title: SZ12

value: Pair 5, affected twin

value: Monozygotic twin with schizophrenia diagnosis and medication

value: schizophrenia


title: MSC-OD-Donor17-Day16-rep2 [thBS_MSC_32]

description: total RNA

tag: donor

value: Human bone marrow-derived mesenchymal stromal cells

tag: day

tag: replicate


title: SZ10

value: Pair 4, unaffected twin

tag: patient disease status


title: bzip60-TM-0h_3

tag: tissue

tag: genotype

tag: ecotype background

tag: treatment

tag: time (hours)


title: singlecell_day5_hto (mixed-sample; non-demultiplexed)

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Each gel bead in emulsion (GEM) was identified and all gene specific reads were mapped via cellranger count (ver. 6.0.0) using the mouse reference genome (mm10) or antibody specific tags (HTOs and ADTs).
Gene level quantification was completed using cellranger count software (ver. 6.0.0) using a custom GTF (derived from GENCODE, version M23, Ensembl 98). HTO/ADT counts were generated by cellranger count using the specific antibody-oligo tags sequences used in this experiment. WT and IcosKO (strain) and kidney/spleen/siiel (tissues of origin) were classified using ADT and HTO counts respectivley via GMM-Demux software (ver. 0.2.1.3).
Raw counts data was imported into R (ver 4.0.3) for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc. primarily using the Seurat R package (ver. 4.0.1).
Genome_build: mm10 (ver. 3.0.0 provided by 10X Genomics)
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized read count values for each sample

extract_protocol:
Cells were extracted 5 days or 32 days post LCMV infection, from spleen, kidney, and small intestine. FACS analysis for completed for CD8+ cells. Antibody derived tags were used to identify WT vs IcosKO cells and hashtag oligos were used to track tissue of origin.
For 10X Genomics scRNA-seq, we generated three libraries that measure: (1) mRNA transcript expression (RNA), (2) tissue-specific hashtag oligos (HTO), and (3) protein marker levels using antibody derived tags (ADT). Cells were harvested and stained as described above. The sample was split into three libraries (RNA, HTO, and ADT). Reverse transcription PCR and library preparation were carried out under the Chromium Single Cell 3’ v3 protocol (10X Genomics) per manufacturer’s recommendations. The libraries were sequenced on the NovaSeq 6000 with 2x150 bp paired-end reads (Illumina).

treatment_protocol: CD8+ P14 cells were negatively enriched from WT (CD45.1/2) and Icos-/- (CD45.1/1) P14 mice with distinct congenic marker (CD45 allele). The cell populations were mixed at a ratio of 1:1 and a total of 2.5 x 10^4 P14 cells were co-adoptively transferred into B6 recipient CD45.2/2 mice, which were infected the next day with LCMV Armstrong strain by intraperitoneal injection.

tag: strain

value: IcosKO; WT;  mixed WT and IcosKO

value: spleen, kidney, or small intestine intraepithelial lymphocytes

tag: expression

value: FACS sorted retaining CD8alpha-iv- (SI-IEL and Kidney) markers or CD8alpha+TCR-Valpha2+CD45.1+ (spleen) markers

value: LCMV Armstrong strain infection


title: SZ9

city: Helsinki

tag: sample number

tag: cell type

tag: hipsc source

tag: group status

value: Pair 4, affected twin

value: female


title: MSC-OD-Donor16-Day16-rep3 [thBS_MSC_30]

description: total RNA


title: singlecell_day5_gex (mixed-sample; non-demultiplexed)


title: bzip60-DMSO-24h_2

value: whole seedlings

value: bzip60-2 knockout

value: mock treatment

tag: chip antibody


title: bzip60-DMSO-24h_1


title: bzip60-DMSO-12h_3


title: MSC-OD-Donor16-Day16-rep2 [thBS_MSC_29]

description: total RNA


title: MSC-OD-Donor16-Day16-rep1 [thBS_MSC_28]

description: total RNA


title: bzip60-TM-0h_2

value: 500 ng/mL Tunicamycin treatment


title: SZ8

value: hiPSC-derived brain astrocytes

value: skin fibroblasts

value: Pair 3, unaffected twin

tag: individual

value: Monozygotic twin without schizophrenia diagnosis

tag: age

tag: patient gender

value: male

value: healthy


title: singlecell_day5_adt (mixed-sample; non-demultiplexed)


title: MSC-OD-Donor6-Day9-rep3 [thBS_MSC_27]

description: total RNA

tag: donor

value: Human bone marrow-derived mesenchymal stromal cells

tag: day

tag: replicate


title: singlecell_day32_hto (mixed-sample; non-demultiplexed)

value: IcosKO; WT;  mixed WT and IcosKO

tag: tissue


title: MSC-OD-Donor6-Day9-rep2 [thBS_MSC_26]

description: total RNA


title: singlecell_day32_gex (mixed-sample; non-demultiplexed)

value: spleen, kidney, or small intestine intraepithelial lymphocytes


title: SZ7

value: Pair 3, affected twin

value: Monozygotic twin with schizophrenia diagnosis and medication

tag: patient disease status

value: schizophrenia


title: bzip60-DMSO-12h_1

tag: genotype

tag: ecotype background

tag: treatment


title: Heart.Visium.E15.5.rep2

city: La Jolla

first: Ju

last: Chen

address: 9500 Gilman Drive 0613

institute: University of California San Diego

data_processing:
Spatial transcriptomic reads were processed using spaceranger (version: 1.2.0)
Genome_build: mm10
Supplementary_files_format_and_content: features and barcodes in TSV and matrix in MTX generated by 10x Genomics software

source_name: Mouse heart

extract_protocol:
Embryonic mouse hearts were dissected and saturated in 5%, 10%, 15%, 20% sucrose in PBS, embedded in OCT, and cut to 6 μm sections. Sections were directly placed on capture areas of Visium Spatial Gene Expression Slide (10X Genomics) inside the cryostat chamber. Each of the four capture areas was placed with one Prdm16cKO section and one littermate control section, from one of the 2 pairs of E13.5 or the 2 pairs of E15.5 mouse hearts. After fixation, H&E staining and image capture, sections were incubated with permeabilization enzyme. Optimal tissue permeabilization time was pre-determined to be 8 min for both E13.5 and E15.5 heart sections using Visium Spatial Tissue Optimization Kit (10X Genomics). After permeabilization, mRNA was released from overlying cells and captured by primers on the gene expression spot (~5,000 per capture area).
Reverse transcriptase mix was then added to the permeabilized tissue sections and produced spatially barcoded cDNA. Following second strand synthesis and denaturation, the barcoded cDNA was released from capture area and amplified to generate sufficient mass for library construction. After end repair, A-tailing, adaptor ligation and sample index PCR, the library comprised constructs containing the sample index, UMI sequences, spatial barcode sequences, and Illumina standard sequencing primers P5 and P7 at each end.

tag: genetic  manipulation

value: Mock + Prdm16 condition knockout

tag: strain

value: heart


title: bzip60-DMSO-12h_2

value: whole seedlings

value: bzip60-2 knockout

tag: time (hours)


title: SZ1

tag: sample number

tag: cell type

tag: hipsc source

value: Pair 1, unaffected twin

value: female


title: SZ2

value: hiPSC-derived brain astrocytes

value: skin fibroblasts

tag: group status

value: Pair 1, affected twin

tag: individual


title: MSC-OD-Donor6-Day9-rep1 [thBS_MSC_25]

description: total RNA


title: Heart.Visium.E15.5.rep1


title: MSC-OD-Donor16-Day9-rep3 [thBS_MSC_24]

description: total RNA


title: bzip60-DMSO-0h_2

value: mock treatment

tag: chip antibody


title: SS_4

city: Bern

first: Emanuele

last: Pignatti

address: Freiburgstrasse 15

country: Switzerland

institute: University of bern

data_processing:
Cutadapt was used to remove adaptors and polyA and polyT tails;
Fastqc was used for quality check; Kallisto was used for alignment and quantification
Kallisto was used for alignment and quantification
The expression of each transcript ti was then estimated in units of transcripts per million (TPM)
Differential expression analysis was performed with EdgeR available through the R/Bioconductor package
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files were generated using Excel. Transcripts were selected based on average expression (above 30), false discovery rate lower than 0.1 and fold change higher than 1.5 or lower than 0.66.

source_name: NCI-H295R cells deprived of sterum and ITC

growth_protocol: NCI-H295R cells were grown in normal gorwth media composed of DMEM-F12+L-glut+HEPES 15mM (cat 11330032 from Thermo Fisher), supplemented with 1:1000 ITS supplement (GIBCO), 5% NU-I serum (BD biosciences) and 1:1000 Pen/Strep (Gibco)

extract_protocol:
Total RNA was isolated using Direct-zol RNA extraction kit from Zymo Research
Library preparation was performed from 200ng total RNA using the TruSeq Stranded mRNA Library Kit (Illumina, 20020594) and the TruSeq RNA UD Indexes (Illumina, 20020590). 15 cycles of PCR were performed. Libraries were quality-checked on a Fragment Analyzer (Advanced Analytical) using the Standard Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, DNF-474) revealing excellent quality of libraries (average concentration: 145±43 nmol/L, average library size: 339±8 base pairs). Samples were pooled to equal molarity. The pool was quantified by Fluorometry using the QuantiFluor ONE dsDNA System (Promega, E4871). Libraries were sequenced Single-reads 76 bases using a NextSeq 500 High Output Kit 75-cycles (Illumina, 20024906) loaded at 1.8pM and including 1% PhiX.

treatment_protocol: Serum starvation media includes all components of normal growth media described above, with the exeption of  NU-I serum and ITS supplement

tag: cell line

value: serum deprived


title: SS_2


title: bzip60-DMSO-0h_1

first: Dae Kwan

last: Ko

address: 612 Wilson Rd.  Plant Biology RM 122

institute: Michigan State University


title: SS_1


title: MSC-OD-Donor16-Day9-rep1 [thBS_MSC_22]

description: total RNA

tag: donor

value: Human bone marrow-derived mesenchymal stromal cells

tag: day


title: MSC-OD-Donor16-Day9-rep2 [thBS_MSC_23]

description: total RNA

tag: replicate


title: SS_3


title: MSC-OD-Donor17-Day9-rep2 [thBS_MSC_20]

description: total RNA


title: Ctrl_4

source_name: NCI-H295R cells in normal growth media

value: untreated


title: bzip60-DMSO-0h_3

tag: tissue


title: Ctrl_3


title: Heart.Visium.E13.5.rep2


title: bzip28-TM-24h_3

tag: genotype

value: bzip28-2 knockout

value: 500 ng/mL Tunicamycin treatment


title: Heart.Visium.E13.5.rep1


title: Heart.scRNA.Prdm16cKO2

data_processing:
Single cell transcriptomic reads were processed using cellranger (version: 4.0.0)
Further analysis was performed using Seurat (version: 3.2.0) on high quality cells with less than twenty percent of mitochondrial contaminations and larger than 2500 measured genes.
To sufficiently separate cell populations, high resolution graph-based clustering was carried out on 30 principal components followed by UMAP dimension reduction, generating 53 subclusters.
Genome_build: mm10
Supplementary_files_format_and_content: features and barcodes in TSV and matrix in MTX generated by 10x Genomics software

extract_protocol:
Tissue samples were digested with 0.25% trypsin and gently dispersed into single-cell suspension with pipetting. Cells were filtered with a 40 μm cell strainer and subjected to fluorescence-activated cell sorting (FACS) to select for live cardiomyocytes which had positive tdTomato fluorescence and negative DAPI staining. Sorted live cardiomyocytes were then captured with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics) following manufacturer’s instructions.
Single cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) using Chromium Next GEM Chip G in the chromium controller. Immediately following GEM generation, the Gel Bead was dissolved, primers were released, and co-partitioned cell was lysed, and its mRNA were reverse transcribed into barcoded cDNA. After further cleanup and amplification, the cDNA was enzymatically fragmented and amplified via PCR to generate sufficient mass for library construction. After end repair, A-tailing, adaptor ligation and sample index PCR, the library comprised constructs containing the sample index, UMI sequences, barcode sequences, and Illumina standard sequencing primers P5 and P7 at both ends.

value: Prdm16 condition knockout


title: MSC-OD-Donor17-Day9-rep3 [thBS_MSC_21]

description: total RNA


title: Heart.scRNA.WT1

value: Mock


title: MSC-OD-Donor17-Day9-rep1 [thBS_MSC_19]

description: total RNA


title: singlecell_day32_adt (mixed-sample; non-demultiplexed)

value: IcosKO; WT;  mixed WT and IcosKO

value: spleen, kidney, or small intestine intraepithelial lymphocytes

tag: expression

value: FACS sorted retaining CD8alpha-iv- (SI-IEL and Kidney) markers or CD8alpha+TCR-Valpha2+CD45.1+ (spleen) markers

value: LCMV Armstrong strain infection


title: Heart.scRNA.WT2

value: heart


title: bzip28-TM-12h_3

value: whole seedlings

tag: ecotype background

tag: treatment


title: bzip28-TM-24h_1


title: bzip28-TM-24h_2


title: Ctrl_2


title: Treg control rep 3

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

country: Japan

institute: Kyushu University

description:
Treg_ctrl-3
counts.txt

data_processing:
The reads were mapped to the reference genome using HISAT2 (v. 2.1.0).
The table of raw counts for each gene was generated by the software featureCounts (v. 1.6.3).
Genome_build: GRCh37
Supplementary_files_format_and_content: counts.txt: Tab-delimited matrix table of raw counts.

source_name: Treg cells

growth_protocol: Tfr cells and Treg cells are sorted from human PBMSs obtained from healthy donors.

extract_protocol:
The total RNA of each cell was extracted using RNeasy Micro Kit (Qiagen).
mRNA was purified and then cDNA library was made by NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEW ENGLAND BioLabs) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 & 2) (NEW ENGLAND BioLabs).

treatment_protocol: Freshly sorted Tfr and Treg cells were cultured in the presence of 50 U/ml IL-2, 1 ug/ml OKT3, and 2.5 ug/ml MR2-1 or mouse IgG1 for 3 days.

value: Treg

tag: stimulation

value: isotype IgG


title: MSC-OD-Donor16-Day6-rep2 [thBS_MSC_14]

description: total RNA


title: MSC-OD-Donor16-Day6-rep3 [thBS_MSC_15]

description: total RNA


title: bzip28-TM-12h_2

city: East Lansing

extract_protocol:
Plants germinated and were subjected to the ER stress recovery assay as described above. Whole seedlings were harvested at 0 h, 12 h and 24 h of recovery in three biological replicates (n = 12 per each replicate), and immediately frozen in the liquid nitrogen. The frozen samples were ground to a fine powder in liquid nitrogen using a Retch MM400 Mixer Mill with zirconium oxide balls. Total RNA was extracted using the NucleoSpin RNA Plant kit (MACHEREY-NAGEL, Düren, Germany) according to the manufacturer’s instruction.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Library (Illumina, San Diego, CA, USA)

tag: time (hours)


title: bzip28-TM-12h_1


title: Heart.scRNA.Prdm16cKO1

tag: genetic  manipulation

tag: strain


title: Left-over carotid artery Littermate Ctrl Repeat 3

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential expression analysis
(For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
(For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression.
Genome_build: Mouse Reference genome (mm9) and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample as well asa the fpkm values for every gene and every sample

source_name: Left-over carotid artery

growth_protocol: Mouse were fed with standard chow

extract_protocol:
Post sacrifice, the right and left carotid arteries were removed. The lumen of the carotid arteries were rapidly flushed using 29G insulin syringe containing 150uL Qiazol. The Qiazol flushings and the left-over artery samples were flash frozen in liquid Nitrogen. The RNAs were extracted using Qiagen's miREasy RNA extraction kit following standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Left-over carotid artery

tag: age

value: Littermate Control


title: Ctrl_1


title: Tfr control rep 3

description:
Tfr_ctrl-3
counts.txt

source_name: Tfr cells

tag: cell type

value: Tfr


title: Left-over carotid artery Littermate Ctrl Repeat 4


title: bzip28-TM-0h_2


title: Treg control rep 2

description:
Treg_ctrl-2
counts.txt


title: Left-over carotid artery Littermate Ctrl Repeat 2


title: bzip28-DMSO-24h_3

value: mock treatment


title: bzip28-DMSO-24h_2


title: bzip28-TM-0h_1


title: MSC-OD-Donor17-Day6-rep3 [thBS_MSC_12]

description: total RNA

value: Human bone marrow-derived mesenchymal stromal cells


title: Left-over carotid artery Global Poldip2-/- Repeat 4

value: Poldip2 knockout


title: MSC-OD-Donor16-Day6-rep1 [thBS_MSC_13]

description: total RNA


title: MSC-OD-Donor17-Day6-rep2 [thBS_MSC_11]

description: total RNA


title: bzip28-TM-0h_3

value: bzip28-2 knockout

value: 500 ng/mL Tunicamycin treatment


title: Treg control rep 1

description:
Treg_ctrl-1
counts.txt


title: Left-over carotid artery Littermate Ctrl Repeat 1


title: Left-over carotid artery Global Poldip2-/- Repeat 2


title: Treg Ab rep 3

description:
Treg_Ab-3
counts.txt


title: Tfr control rep 2

description:
Tfr_ctrl-2
counts.txt


title: MSC-OD-Donor17-Day6-rep1 [thBS_MSC_10]

description: total RNA


title: Left-over carotid artery Global Poldip2-/- Repeat 3


title: bzip28-DMSO-24h_1


title: MSC-OD-Donor6-Day3-rep3 [thBS_MSC_9]

description: total RNA


title: MSC-OD-Donor17-Day3-rep3 [thBS_MSC_6]

description: total RNA


title: MSC-OD-Donor6-Day3-rep1 [thBS_MSC_7]

description: total RNA


title: MSC-OD-Donor6-Day3-rep2 [thBS_MSC_8]

description: total RNA


title: Tfr control rep 1

description:
Tfr_ctrl-1
counts.txt


title: bzip28-DMSO-12h_3


title: Treg Ab rep 2

description:
Treg_Ab-2
counts.txt


title: bzip28-DMSO-12h_2


title: bzip28-DMSO-12h_1


title: Treg Ab rep 1

description:
Treg_Ab-1
counts.txt


title: MSC-OD-Donor17-Day3-rep2 [thBS_MSC_5]

description: total RNA


title: Endothelial enriched Littermate Ctrl Repeat 2

source_name: Carotid artery endothelium

value: Carotid artery endothelium


title: MSC-OD-Donor17-Day3-rep1 [thBS_MSC_4]

description: total RNA


title: Endothelial enriched Littermate Ctrl Repeat 1


title: Endothelial enriched Global Poldip2-/- Repeat 2


title: bzip28-DMSO-0h_2


title: Tfr Ab rep 3

description:
Tfr_Ab-3
counts.txt


title: Tfr Ab rep 2

description:
Tfr_Ab-2
counts.txt


title: MSC-OD-Donor16-Day3-rep3 [thBS_MSC_3]

description: total RNA


title: Endothelial enriched Global Poldip2-/- Repeat 1


title: bzip28-DMSO-0h_3


title: bzip28-DMSO-0h_1


title: Left-over carotid artery Global Poldip2-/- Repeat 1


title: Tfr Ab rep 1

description:
Tfr_Ab-1
counts.txt


title: MSC-OD-Donor16-Day3-rep1 [thBS_MSC_1]

description: total RNA


title: 40 day post-fertilization zebrafish ovaries cells, sorted germ cells

status: Public on Dec 19 2021

city: Davis

first: Yulong

last: Liu

state: CA

address: 3105 Life Science

department: Molecular and Cellular Biology

institute: University of California, Davis

data_processing:
A General Transfer Format (GTF) gene annotation file(release 96) for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger (v3.0.2; 10x Genomic) to retain the following attributes: protein_coding, lincRNA, and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file.
GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger (v3.0.2; 10x Genomic). “expect-cells” was setted to 10000 based on estimated cell recovery.
Genome_build: GRCz11
Supplementary_files_format_and_content: Filtered or raw matrix files generated from Cell Ranger in one zip file.

organism: Danio rerio

growth_protocol: Zebrafish husbandry was performed as previously described (Westerfield, 2000).

extract_protocol:
Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al., (2019). 40 pairs of 40 dpf ovaries were dissected from Tg(piwil1:egfp)uc02 transgenic fish (Leu et al., 2010) and stored in a LoBind tube (Cat.No. 0030108302; Eppendorf) containing 2 mL of L15 medium(Cat.No. L5520; Sigma-Aldrich). The tissue was minced with small scissors into <1 mm pieces. 200 µL of 20 mg/mL of type 2 collagenase in L15  (Cat.No. NC9870009; Worthington) were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL of 7 mg/mL trypsin (Cat.No. LS003708; Worthington) in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 µL of 20 mg/mL trypsin Inhibitor (Cat.No. 100612; MP Biomedicals) in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using  a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 µm nylon filter (Cat.No. 431752; Corning) and then through a 40 µm nylon filter (Cat.No. 431750; Corning) to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA (Cat.No. A8806; Sigma-Aldrich) in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine (Cat. No. P1304MP; Thermo Fisher) and Hoechst 33342 (Cat.No. H3570; Thermo Fisher) staining on a Fuchs-Rosenthal hemocytometer (Cat.No. DHC-F01; Incyto). Following cell dissociation of Tg(piwil1:egfp) transgenic ovaries, GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter (Beckman Coulter) with a 70 µm nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells.
Single-cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly, barcoded 3’ single-cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single-Cell 3’ Library and Gel Bead kit V3 (10X Genomics) for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10,000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100 (Agilent).  The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems) prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer (Illumina) with paired-end 100 bp reads.

value: Germ cells

value: AB wildtype


title: sncRNA organ atlas, Homo sapiens, pancreas_2 (2)

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

country: Germany

institute: Saarland University

data_processing:
We performed the primary data analysis using a stand-alone version of our web-based tool miRMaster, version 1.1. We carried out all analyses using the standard parameter settings as in the online version, allowing one mismatch in the quantification of ncRNAs. The following ncRNA databases are included in our analysis: miRBase version 22.1, Ensembl ncRNA version 100, RNACentral version 15 and GtRNAdb version 18.1.
Adapters at the 3′ end were trimmed, while allowing an error of maximum one base and requiring a minimum overlap with the read of 10 bases. Reads were quality trimmed when the average quality dropped below 20 in a window of four consecutive bases to ensure a high quality of reads used for the downstream processing. All reads shorter than 17 bases after trimming were discarded from all further analyses.
MiRNAs were quantified with up to one mismatch and a variability of two bases allowed at the 5′ end and five bases at the 3′ end.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: sncRNA_counts_human.txt: tab-delimited text file containing the RPMM normalized counts of all quantified sncRNAs in the human samples.
Supplementary_files_format_and_content: sncRNA_counts_mouse.txt: tab-delimited text file containing the RPMM normalized counts of all quantified sncRNAs in the mouse samples.

source_name: pancreas_2 (2)

growth_protocol: The bodies were stored at 4°C upon arrival at the anatomical institute and tissue samples were collected between 8 and 48 hours post-mortem. To increase the resolution for selected organs, e.g. brain or intestine, further dissection of these organs was performed to include several subareas. After collection, samples were immediately stored in RNALater (Sigma-Aldrich) or frozen at -80 °C to prevent further degradation. Mice tissues were prepared as described for GSE132042.

extract_protocol:
Total RNA including smallRNAs was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. In brief, tissues were lysed and homogenized in 700 µl QIAzol Lysis Reagent using 5 mm stainless steel beads and the TissueLyser LT (Qiagen) for 5 min at 50 Hz. After 5 min incubation, samples were mixed with 140 µl chloroform and phase separation was performed at 12000 x g and 4 °C for 15 min. The RNA in the aqueous phase was precipitated by adding 1.5 Volume of 100 % ethanol and purified using the RNeasy columns provided with the kit, either manually or semi-automated using the Qiacube instrument with the respective protocols provided for the miRNeasy Mini kit.
We performed library preparation for sequencing on the BGISEQ-500RS following the instructions of the MGIEasy Small RNA Library Prep Kit (MGI Technologies). To limit the bias the manual library preparation performed previously was replaced by a semi-automated workflow on the MGI-SP100. In general, 100 ng total RNA was used as input material for the library preparation. The library construction includes of 3’ adapter ligation, 3’ adapter digestion, 5’ adapter ligation followed by reverse transcription (RT) of RNA into cDNA using RT primers which contained specific barcodes. Next, cDNA was amplified by PCR in 22 cycles. The PCR products were separated using 6 % TBE gels and bands of the size around 110 bp were cut from the gel.  After purification, the DNA yield was measured with the Qubit® 1xdsDNA HS Assay Kit (Invitrogen). A total of 16 different barcoded samples were pooled together in equal amounts and circularized to generate a single-stranded DNA library. The BGISEQ-500RS uses DNA nanoballs (DNBs) for sequencing, which were generated by rolling circle amplification (RCA). DNBs were then loaded into the patterned nanoarray using the BGIDL-50 DNB loader. Finally, single-end sequencing was performed on the BGISEQ-500RS using the High-throughput Sequencing Set (SE50) (Small RNA) according to the manufacturer’s instructions. The mouse samples have been processed with an advanced pipeline using the higher-throughput SP-960 sample prep system and MGISEQ-400 sequencing system. In the latter case we made further use of the CoolMPS sequencing chemistry.

value: Not applicable

tag: age (years)

tag: developmental stage

value: adult

tag: Sex

value: male

value: pancreas


title: sncRNA organ atlas, Homo sapiens, esophagus_4

value: esophagus


title: sncRNA organ atlas, Homo sapiens, bowel-colon_5

value: female

value: bowel-colon


title: sncRNA organ atlas, Homo sapiens, tongue_5

value: tongue


title: sncRNA organ atlas, Homo sapiens, bone_5

value: bone


title: sncRNA organ atlas, Homo sapiens, spleen_5

value: spleen


title: sncRNA organ atlas, Homo sapiens, submandibular gland_4

source_name: submandibular gland_4

value: submandibular gland


title: sncRNA organ atlas, Homo sapiens, salivary gland_5

source_name: salivary gland_5

value: salivary gland


title: sncRNA organ atlas, Homo sapiens, kidney_2

value: kidney


title: sncRNA organ atlas, Homo sapiens, brain-pituitary gland_2

source_name: brain-pituitary gland_2

value: brain-pituitary gland


title: sncRNA organ atlas, Homo sapiens, bowel-small intestine_4 (2)

source_name: bowel-small intestine_4 (2)

value: bowel-small intestine


title: sncRNA organ atlas, Homo sapiens, heart-muscle_5

value: heart-muscle


title: sncRNA organ atlas, Homo sapiens, kidney_5


title: sncRNA organ atlas, Homo sapiens, pancreas_5


title: sncRNA organ atlas, Homo sapiens, diaphragm_4

value: diaphragm


title: 40 day post-fertilization zebrafish ovaries cells (zx2)

extract_protocol:
Somatic ovary cells were dissociated using a modification of Elkouby and Mullins (2016). 40 pairs of 40 dpf ovaries were dissected from Tg(piwil1:egfp) transgenic fish (Leu et al., 2010) were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. After the tissue had settled to the bottom of the tube, the media was replaced with 5mL of digestive enzyme mixture (3 mg/mL collagenase I (Cat.No. C0130; Sigma-Aldrich), 3 mg/mL collagenase II (Cat.No. C6885; Sigma-Aldrich), and 1.6 mg/mL hyaluronidase (Cat.No. H4272; Sigma-Aldrich) in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed (~30 min.). Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE (Cat.No. A1217701; Thermo Fisher) in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above.
Single-cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly, barcoded 3’ single-cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single-Cell 3’ Library and Gel Bead kit V3 (10X Genomics) for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10,000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro-capillary gel electrophoresis on a Bioanalyzer 2100 (Agilent).  The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems) prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer (Illumina) with paired-end 100 bp reads.

value: Ovary cells

value: AB wildtype


title: sncRNA organ atlas, Homo sapiens, testis_2

value: Not applicable

value: adult

value: male

value: testis


title: sncRNA organ atlas, Homo sapiens, brain-white matter_2 (2)

source_name: brain-white matter_2 (2)

value: brain-white matter


title: 40 day post-fertilization zebrafish ovaries cells (zx4)


title: sncRNA organ atlas, Homo sapiens, bladder_5

value: female

value: bladder


title: sncRNA organ atlas, Homo sapiens, brain-frontal lobe_2

source_name: brain-frontal lobe_2

value: brain-frontal lobe


title: sncRNA organ atlas, Homo sapiens, gallbladder_4

value: gallbladder


title: sncRNA organ atlas, Homo sapiens, esophagus_5

value: esophagus


title: sncRNA organ atlas, Homo sapiens, liver_2

value: liver


title: sncRNA organ atlas, Homo sapiens, bowel-duodenum_5

value: bowel-duodenum


title: sncRNA organ atlas, Homo sapiens, brain-occipital lobe_2

source_name: brain-occipital lobe_2

value: brain-occipital lobe


title: sncRNA organ atlas, Homo sapiens, lung-bronchus_5

value: lung-bronchus


title: sncRNA organ atlas, Homo sapiens, liver_5


title: sncRNA organ atlas, Homo sapiens, brain-grey matter_2

source_name: brain-grey matter_2

value: brain-grey matter


title: sncRNA organ atlas, Homo sapiens, spleen_4

value: spleen