title: Mouse_basal_stim_IFNA_5_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.29
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A12

status: Public on Apr 23 2020

type: SRA

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

country: Belgium

institute: Université Libre de Bruxelles (ULB)

description:
single-cell smartSeq2 RNAseq
single-cell RNA

library_source: transcriptomic

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw comma-separated file containing raw expression matrix and Seurat R data object file

molecule: total RNA

organism: Mus musculus

source_name: Mammary Gland Epithelium

growth_protocol: Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

extract_protocol:
Samples were incubated in 250µl of 2% FBS/PBS with fluorochrome-conjugated primary antibodies for 30 minutes, with shaking every 10 minutes. Primary antibodies were washed with 2% FBS/PBS, and cells were resuspended in 2.5mg/ml DAPI (Invitrogen D1306) before analysis. The following primary antibodies were used: APC-conjugated anti-CD45 (1:100, clone 30-F11, eBiosciences), APC-conjugated anti-CD31 (1:100, clone 390, eBiosciences), APC-conjugated anti-CD140a (1:100, cloneAPA5, eBiosciences), PE-Cy7-conjugated anti-CD24 (1:100, clone M1/69, BD), FITC-conjugated anti-CD29 (1:100, clone Ha2/5, BD Biosciences),APC-Cy7-conjugated anti Epcam (1:100, clone G8.8, Biolegend). Data analysis andcell sorting were performed on a FACSAria sorter using the FACS DiVa software (BDBiosciences). Dead cells were excluded with DAPI; CD45+, CD31+ and CD140a+ cells excluded (Lin+) before analysis of the Tomato+ cells
scRNA-seq was performed using a modified Smartseq-2 protocol. 1µL lysis buffer in384 well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer,2.5mM dNTPs and 2.5µM oligo-dT30-VN. Reverse transcription and PCR was performed according to the Smartseq-2 protocol with reduced volumes: 1µl of reverse241 transcription mix instead of 5.7µl and 3µl PCR Master mix instead of 15µl. cDNA was amplified for 23 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8x ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 30µl buffer EB (Qiagen) and transferred to 384_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermofisher) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit. Next-generation sequencing library preparation was performed using a Nextera XT DNA library preparation kit with volumes reduced by one-tenth (Illumina) using an acoustic dispenser. In brief, 100pg of cDNA in a volume of 500nL was tagmented by adding 1.5µl Tn5-buffer mix and incubating for 10 min at 55°C. Tagmented samples were barcoded with Nextera index sets A - D and amplified with 12 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6x ratio. Library pools were eluted in buffer EB and quality control performed using an Agilent 2100 BioAnalyser and High Sensitiviy DNA chip before adjusting to a concentration of 4nM. The diluted pools were quantified using a KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before a final dilution to 2nM. The pool of 384 samples was sequenced on 2 lanes of a HiSeq4000 with 1x51bp read length

treatment_protocol: For the ablation condition, mice were anesthetized (5% xylazine, 10% ketamine in PBS), abdominal skin removed with depilatory cream and the nipple region disinfected with ETOH 70%. The intraductal injection of 0.2 mg doxycycline was performed using a stereoscope. One week after injection the mice have been sacrificed and the epithelial cells of the mammary gland FACS sorted into a 384 wells PCR plate.

tag: strain

value: K8rtta/TetO-DTA/K5CreER/Rosa-Tomato mice, mixed background

tag: treatment

value: Wild-type single-cell

tag: cell-type

value: Luminal cell


title: GC059869_A11


title: GC059869_A10

description:
single-cell smartSeq2 RNAseq
Negative control

value: Negative control


title: Mouse_basal_stim_IFNA_5_REP1

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

country: USA

institute: MIT

description: Mouse basal cells from the trachea three replicates of each stimulation with IFNA, IFNB, or IFNG, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.28
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

molecule: polyA RNA

source_name: tracheal basal cells

growth_protocol: placed into culture at a number of 10,000 cells seeded at passage 5 (e.g. 5 weeks ex vivo) and cultured at confluence in 96 well flat-bottom collagen-coated tissue culture plates (Corning 3596) for 48 hours in Pneumacult-Ex serum-free media (Stemcell Technologies)

extract_protocol: Bulk RNA-seq (Ordovas-Montanes et al., 2018)

tag: agent

value: IFNA

tag: dose

tag: cell type

value: tracheal basal cells


title: Mouse_basal_stim_IFNB_2_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.26
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

value: IFNB


title: Mouse_basal_stim_IFNB_2_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.27
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNB_2_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.25
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNB_1_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.23
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A07


title: Mouse_basal_stim_IFNB_1_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.22
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A08


title: GC059869_A06


title: GC059869_A05

description:
single-cell smartSeq2 RNAseq
multicell RNA

value: Doxycycline treatment Multicell control

value: Hybrid cell


title: Mouse_basal_stim_IFNB_5_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.34
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A17


title: Mouse_basal_stim_IFNA_2_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.21
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A15


title: Mouse_basal_stim_IFNA_2_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.20
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A04


title: GC059869_A03

value: Basal cell


title: Mouse_basal_stim_IFNA_2_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.19
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A02

value: Wild-type Multicell control


title: Mouse_basal_stim_IFNA_1_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.18
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A01


title: Mouse_basal_stim_IFNA_1_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.17
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Ngn3Cre_STZ_M2_NoIns_1

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

data_processing:
The fastq file for each single-cell sample was split based on 8-bp cell-specific barcode sequences included in Read2.
The 8bp unique molecular identifiers (UMIs) included in Read1 were added into the corresponding read 1.
The polyA sequences in Read1 were trimmed.
We aligned preprocessed Read1 reads to the mouse genome (mm10) with TopHat (v2.1.0).
Mapped reads were annotated to genes using featureCounts (v1.5.3), so the gene ID was appended as XT tag in the bam file.
We sorted and indexed the bam file with samtools (v.1.3.1).
We quantified the unique molecular identifiers (UMIs) of each gene with umi_tools (v0.5.0) using the following parameters: “count --per-gene --gene-tag=XT --method unique -I indexed_sorted_bam -S out_file”.
The UMI matrix was transformed to transcripts per 0.1 million (TP0.1M). To eliminate the influence of individual genes on the transcriptome, we ignored extremely highly expressed genes (Ins1, Ins2, Gcg, Sst, Ppy, Pyy, Iapp, and Yam1) in our total transcripts calculations.
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include UMI and TP0.1M values for each sample

source_name: Pancreas

extract_protocol:
Library preparation was conducted following the modified STRT-seq protocol (Dong et al., 2018, Genome biology). Briefly, after cell sorting, single Ins1-RFP+ or Ngn3-Cre; Rosa-RFP+ cells were transferred quickly into lysis buffer by mouth pipette. Next, we reverse-transcribed the RNA and amplified the resulting cDNA over 18 cycles of PCR. The quality of the cDNA was assessed by qPCR of the housekeeping gene Gapdh. cDNA of single cells with good quality was pooled together and purified. Biotinylated pre-indexed primers were added to the cDNA during an additional 4 cycles of PCR. Approximately 300 ng of purified PCR product was sheared to approximately 300 bp by sonication.
Sequencing libraries were prepared using the Kapa Hyper Prep Kit (KK8502, Kapa Biosystems).

treatment_protocol: STZ was dissolved in 50 mM sodium citrate buffer (pH 4.5) and injected within 15 minutes of preparation. Two-month-old male mice were injected intraperitoneally with a single dose of STZ (200 mg/kg, Sigma, V900890) after an overnight fast. Age-matched male mice injected with an equal volume of sodium citrate buffer served as controls.

value: Ngn3-Cre; Rosa-RFP

value: STZ

tag: insulin implants

value: No

tag: time after stz

tag: age

value: Adult

tag: batch


title: GC059869_A09


title: Mouse_basal_stim_IFNB_0.5_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.15
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNB_1_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.24
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNB_0.5_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.13
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Ngn3Cre_P12_2


title: Ngn3Cre_P12_1


title: Ngn3Cre_STZ_D12_2

value: Yes


title: Ngn3Cre_P21_1


title: Mouse_basal_stim_IFNB_0.1_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.12
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Ngn3Cre_P3_1


title: Mouse_basal_stim_IFNB_0.1_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.11
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNA_0.5_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.9
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: d7 WT CT rep5

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description:
mRNA
processed data file: Raw_counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1.
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads.
Genome_build: GRCm38.89
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts.

source_name: Ear Skin

extract_protocol:
mRNA was prepared from ears of Aldara-treated mice with the mirVana kit (InVitrogen #AM1560, ThermoFisher Scientific) following the manufacturer’s instructions. RNA clean-up was performed with RNA Clean XP beads (Beckman Coulter #A66514, Indianapolis, IND, USA). RNA quantification was performed with a Qubit fluorimeter (Life Technologies, Thermo Fisher Scientific) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies, Santa Clara, CAL, USA). The TruSeq mRNA stranded kit from Illumina was used for the library preparation with 500 ng of total RNA as input.
The 34 and 40 libraries were pooled at 2 nM and loaded for clustering on 4 and 5 lanes respectively of a single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.
Libraries were sequenced using single-end reads (100 nt-long) on an Illumina HiSeq4000.

tag: mouse line

tag: tissue

value: Ear skin

tag: ear treatment

tag: time point


title: GC059869_F02

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw comma-separated file containing raw expression matrix and Seurat R data object file

value: K8rtta/TetO-DTA/K5CreER/Rosa-Tomato mice, mixed background

value: Doxycycline treatment single-cell


title: d7 WT CT rep4


title: d7 WT CT rep3


title: Mouse_basal_stim_IFNA_0.5_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.7
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNA_0.5_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.8
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: d7 WT CT rep2


title: Mouse_basal_stim_IFNA_0.1_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.6
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: d7 WT CT rep1


title: d7 WT AL rep5

value: Aldara


title: Ngn3Cre_STZ_M2_NoIns_2


title: Mouse_basal_stim_IFNA_1_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.16
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNB_0.5_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.14
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNA_0.1_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.4
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNA_0.1_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.5
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: d7 WT AL rep3


title: Mouse_Nasal_Saline_M2_1

description: Nasal mucosa of mice stimulated with saline intranasally, Mouse 2 replicate 1

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: Nasal Epithelium

extract_protocol: Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well S^3 method (Hughes et al., BioRxiv 2019)

value: saline

value: Nasal mucosa


title: Mouse_Nasal_Saline_M2_2


title: d7 WT AL rep2


title: Mouse_Nasal_Saline_M1_2

description: Nasal mucosa of mice stimulated with saline intranasally, Mouse 1 replicate 2


title: d7 WT AL rep1


title: Mouse_Nasal_Saline_M1_1

description: Nasal mucosa of mice stimulated with saline intranasally, Mouse 1 replicate 1


title: Mouse_basal_stim_IFNB_0.1_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.10
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

value: tracheal basal cells


title: d7 KO CT rep3


title: Mouse_Nasal_IFNA_High_M2_2

description: Nasal mucosa of mice stimulated with 200 ng IFNA intranasally, Mouse 2 replicate 1

value: IFNA


title: d7 KO CT rep4


title: d7 KO CT rep1


title: Mouse_Nasal_IFNA_High_M1_1

description: Nasal mucosa of mice stimulated with 200 ng IFNA intranasally, Mouse 1 replicate 1


title: Mouse_Nasal_IFNA_High_M1_2

description: Nasal mucosa of mice stimulated with 200 ng IFNA intranasally, Mouse 1 replicate 2


title: d7 KO CT rep2


title: d7 KO AL rep3


title: d7 KO AL rep4


title: HATX PARIS 1

city: Stanford

first: Zhipeng

last: Lu

state: CA

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

data_processing:
remove 5' and 3' adapters using trimmomatic-0.32.jar SE -threads 16 -phred33
removed PCR duplicates using splitFastqLibrary (in the icSHAPE pipeline)
mapped reads using STAR, version 2.4, with the following parameters: --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --runThreadN 16
secondary mappings were removed using samtools
Genome_build: mm10 and mmXist
Supplementary_files_format_and_content: Processed data are in bed format and contains the starts and ends of RNA duplexes identified by PARIS.

source_name: mouse HATX ES cells

growth_protocol: All mES cells were maintained on 0.2% gelatin coated plates at 37C with mES media, which was changed daily: Knockout DMEM + 10% FBS + 1% MEM NEAA + 1% GlutaMax + 1% Pen Strep + 0.2% BME and 0.01% LIF.

extract_protocol:
Cells were digested with S1 nuclease, proteinase K and RNA was extracted using TRIzol.
See previous publication for the protocol (PMID: 25799993)

treatment_protocol: 1ug/ml Dox for 48 hours, with daily changes of media

value: mouse embryonic stem cells (mES)


title: mES KI17_2 IP

data_processing:
Reads are aligned to mm10 genome using STAR
Reads mapped to the two strands are separated using samtools
Coverage in the Xist region is converted to a custom mini-genome for the mature Xist transcript
m6A modification levels are calculated by normalization against input and again against internal regions of the large RNA domains
To visualize the bedgraph files in IGV, means were taken in 50 nt windows to minimize file size.
Genome_build: mm10 and custom build mmXist for the Xist mini-genome
Supplementary_files_format_and_content: bedgraph for the mmXist region alone and counts

source_name: mouse ES cells

extract_protocol:
Standard Trizol extraction
Total mES RNA was subjected to one round of Poly(A)Purist MAG treatment to enrich for polyadenylated RNAs as per manufacturer’s instructions (Ambion). RNA was then fragmented to 100nt median sized fragments using RNA Fragmentation Reagents (Ambion) and subjected to one round of m6A immunoprecipitation. For immunoprecipitation of RNA, 5 ug of m6A antibody (Millipore) was coupled to 40 ul Protein A Dynabeads (Novex) in 100 ul 1X IPP Buffer (50mM Tris-HCl, pH 7.5; 150mM NaCl; 0.1% NP-40; 5mM EDTA) overnight at 4C. Beads were then washed twice in 1X IPP Buffer. Fragmented RNA was denatured at 70C for 2 min, cooled on ice, and bound to antibody-beads in 185 ul 1X IPP Buffer for 3h at 4C. Beads were then washed sequentially with (2x) 500 ul 1X IPP Buffer, (2x) 500 ul Low Salt Buffer (0.25X SSPE; 1mM EDTA; 0.05% Tween-20; 37.5mM NaCl), (2x) 500 ul High Salt Buffer (0.25X SSPE; 1mM EDTA; 0.05% Tween-20; 137.5mM NaCl), (1x) 500 ul TET Buffer (10mM Tris-HCl, pH 8.0; 1mM EDTA; 0.05% Tween-20). Beads were eluted with 50 ul RLT Buffer (Qiagen RNeasy Mini Kit) and incubated at 25C for 5 min, and recovered with RNeasy Mini Kit followed by concentrating with Zymo RNA Clean & Concentrator in 10 ul water. 10 ng of input RNA (before immunoprecipitation) and 10 ng of immunoprecipitated RNA were then used to prepare sequencing libraries using SMARTer Stranded RNA-Seq Kit - Pico Input Mammalian (Clontech #634411), as per manufacturer’s instructions. Sequencing libraries were pooled and sequenced on the Illumina MiSeq (files named *apr26*, including the following samples: ) and NextSeq (files named *jun24*, including the following samples).

treatment_protocol: Cells were cultured and treated for 48h with 4 ug/ml doxycycline before RNA collection

tag: antibody

value: Millipore m6A antibody (ABE572)


title: mES KI17_2 input


title: d7 FL CT rep3

value: Il36rfl/fl (FL)


title: d7 KO AL rep2


title: d7 KO AL rep1


title: d7 FL CT rep4


title: d7 WT AL rep4


title: d7 FL CT rep1


title: d7 FL CT rep2


title: d7 FL AL rep4


title: donor_17

city: Iowa City

first: Andrew

last: Voigt

state: Iowa

address: 375 Newton Road

institute: University of Iowa

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Reads were mapped to the human genome hg19 with STAR (version = 020201) and quantified with the featureCounts function from the Rsubread package (version = 1.28.1).
Differential expression analysis between infant and adult libraries was performed with edgeR (version = 3.26.8).
Genome_build: hg 19
Supplementary_files_format_and_content: Processed TPMs for all 17 samples are provided in a single supplemental spreadsheet

organism: Homo sapiens

source_name: RPE/choroid

extract_protocol:
A central punch of RPE/choroid was acquired from seventeen human donors. After dissection away from the retina and sclera, the RPE/choroid was flash frozen in liquid nitrogen. Total RNA was extracted from frozen RPE/choroidal tissue (Qiagen RNeasy kit).
RNeasy kit (Qiagen, Valencia, CA), Illumina TruSeq RNA Sample Preparation v2 library preparation kit (Illumina, San Diego, CA)

value: adult


title: donor_14


title: donor_15


title: donor_16


title: donor_12


title: donor_13


title: donor_11


title: Mouse_Nasal_IFNA_High_M2_1


title: d7 FL AL rep2


title: d7 FL AL rep1


title: donor_10


title: d7 DK CT rep4

description:
Il36rΔK (DK)
mRNA
processed data file: Raw_counts.txt

value: Il36r<delta>K (DK)


title: donor_9


title: d7 DK CT rep3


title: d7 DK CT rep2


title: donor_8


title: donor_6


title: donor_7


title: d7 DK CT rep1


title: d7 DK AL rep4


title: d7 FL AL rep3


title: donor_4

value: infant


title: d7 DK AL rep3


title: donor_2


title: donor_3


title: d7 DK AL rep2


title: d7 DK AL rep1


title: donor_1


title: d3 WT CT rep5


title: Day16_Rep2

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

description:
Day16.bw
DESeq_Read_Counts.txt.gz

data_processing:
Sequenced reads were mapped to hg38 with Hisat2 version 2.0.3
Transcript quantification was performed with featureCounts of the Rsubread package version 1.14.2 to hg38 RefSeq genes
Differential analysis was performed with DESeq
Genome_build: hg38
Supplementary_files_format_and_content: Text file contains number of read counts per gene as tabulated by featureCounts of the Rsubread package. WIG files represent the scaled mapped reads coverage of the RNA-Seq across the genome. The files were generated using the BEDTools suite and UCSC genome browser standalone tools for Unix from the aligned reads output of HISAT. Replicates from the same sample were merged together.

source_name: Umbilical cord blood

growth_protocol: described in Palii et al. (doi: 10.3791/2813. J Vis Exp. 53, 2011)

extract_protocol:
Qiagen RNA extraction Kit including the DNA digestion step
mRNA enrich KAPA stranded RNA library
Illumina Hiseq 2000 paired-end 50 cycles

value: CD34+ cells were subjected to ex vivo erythropoiesis according to the protocol described in Palii et al. (doi:10.3791/2813. J Vis Exp. 53, 2011)

tag: days of differentiation


title: donor_5


title: d3 WT CT rep4


title: Day16_Rep1

description:
Day16.bw
DESeq_Read_Counts.txt.gz

treatment_protocol: described in Palii et al. (doi: 10.3791/2813. J Vis Exp. 53, 2011)


title: d3 WT CT rep3


title: Day14_Rep2

description:
Day14.bw
DESeq_Read_Counts.txt.gz


title: d3 WT CT rep2


title: Day14_Rep1

description:
Day14.bw
DESeq_Read_Counts.txt.gz


title: d3 WT CT rep1


title: Day12_Rep2

description:
Day12.bw
DESeq_Read_Counts.txt.gz


title: d3 WT AL rep5


title: Day12_Rep1

description:
Day12.bw
DESeq_Read_Counts.txt.gz


title: d3 WT AL rep4


title: Day11.5_Rep2

description:
Day11_5.bw
DESeq_Read_Counts.txt.gz


title: d3 WT AL rep3


title: Day11.5_Rep1

description:
Day11_5.bw
DESeq_Read_Counts.txt.gz


title: high-grade adenoma 20

type: genomic

first: Jian

last: Fan

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v1.8

label: Cy5 and Cy3

molecule: genomic DNA

source_name: high-grade adenoma 20

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from colorectal adenoma and adjacent normal samples using Qiagen DNA mini Kit according to standard instructions

tag: gender

value: male

tag: disease

value: high-grade adenoma

value: colorectal


title: low-grade adenoma 17

source_name: low-grade adenoma 17

value: low-grade adenoma


title: high-grade adenoma 21

source_name: high-grade adenoma 21


title: low-grade adenoma 18

source_name: low-grade adenoma 18


title: high-grade adenoma 22

source_name: high-grade adenoma 22


title: low-grade adenoma 15

source_name: low-grade adenoma 15


title: normal 18

source_name: normal 18

value: normal


title: low-grade adenoma 16

source_name: low-grade adenoma 16


title: Day11_Rep2

description:
Day11.bw
DESeq_Read_Counts.txt.gz


title: high-grade adenoma 16

source_name: high-grade adenoma 16


title: d3 WT AL rep2

value: Ear skin

value: Aldara


title: high-grade adenoma 17

source_name: high-grade adenoma 17


title: high-grade adenoma 18

source_name: high-grade adenoma 18


title: Day11_Rep1

description:
Day11.bw
DESeq_Read_Counts.txt.gz


title: normal 16

source_name: normal 16


title: normal 19

source_name: normal 19


title: low-grade adenoma 14

source_name: low-grade adenoma 14


title: high-grade adenoma 19

source_name: high-grade adenoma 19


title: high-grade adenoma 15

source_name: high-grade adenoma 15


title: Day10.5_Rep2

description:
Day10_5.bw
DESeq_Read_Counts.txt.gz

source_name: Umbilical cord blood


title: normal 20

source_name: normal 20


title: low-grade adenoma 13

source_name: low-grade adenoma 13

value: female


title: low-grade adenoma 10

source_name: low-grade adenoma 10


title: low-grade adenoma 12

source_name: low-grade adenoma 12


title: normal 17

source_name: normal 17


title: d3 WT AL rep1

source_name: Ear Skin


title: d3 KO CT rep5


title: d3 KO CT rep3


title: Day10_Rep2

description:
Day10.bw
DESeq_Read_Counts.txt.gz


title: high-grade adenoma 14

source_name: high-grade adenoma 14


title: normal 15

source_name: normal 15


title: low-grade adenoma 9

source_name: low-grade adenoma 9


title: low-grade adenoma 11

source_name: low-grade adenoma 11


title: Day10.5_Rep1

description:
Day10_5.bw
DESeq_Read_Counts.txt.gz


title: Sample 14 (TdTomato +ve)

city: St Louis

first: Vijay

last: Samineni

state: MO

address: 4940 Parkview Place, Room 5539 Department of Anesthesiology

institute: Washington university St. louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: Central Amygdala

extract_protocol: Clontech SMARTer v1

tag: strain

value: Central Amygdala

value: CeA TdTomato+ve Neurons

tag: cell population

value: Facs amygdala cells after FosTRAP

tag: genotype

value: cFos Cre Mice X TdTomato (Ai9) Mice


title: normal 13

source_name: normal 13


title: normal 14

source_name: normal 14


title: d3 KO CT rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1.
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads.
Genome_build: GRCm38.89
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts.


title: Day10_Rep1

description:
Day10.bw
DESeq_Read_Counts.txt.gz


title: Sample 13 (TdTomato +ve)


title: Day08.5_Rep2

description:
Day08_5.bw
DESeq_Read_Counts.txt.gz


title: d3 KO CT rep1


title: Sample 12 (TdTomato +ve)


title: high-grade adenoma 12

source_name: high-grade adenoma 12


title: high-grade adenoma 13

source_name: high-grade adenoma 13


title: d3 KO AL rep5


title: Day08.5_Rep1

description:
Day08_5.bw
DESeq_Read_Counts.txt.gz


title: Sample 11 (TdTomato +ve)


title: Day08_Rep2

description:
Day08.bw
DESeq_Read_Counts.txt.gz


title: Sample 10 (TdTomato -ve)

value: CeA TdTomato-ve Neurons


title: Day08_Rep1

description:
Day08.bw
DESeq_Read_Counts.txt.gz


title: d3 KO AL rep3


title: Sample 9 (TdTomato +ve)


title: d3 KO AL rep2


title: Day07.5_Rep2

description:
Day07_5.bw
DESeq_Read_Counts.txt.gz


title: d3 KO AL rep4


title: Sample 7 (TdTomato -ve)


title: low-grade adenoma 8

source_name: low-grade adenoma 8


title: d3 KO AL rep1


title: d3 FL CT rep5

value: Il36rfl/fl (FL)


title: Day07.5_Rep1

description:
Day07_5.bw
DESeq_Read_Counts.txt.gz

source_name: Umbilical cord blood


title: Day06_Rep2

description:
Day06.bw
DESeq_Read_Counts.txt.gz


title: Sample 6 (TdTomato +ve)


title: d3 FL CT rep4


title: normal 12

source_name: normal 12


title: normal 11

source_name: normal 11


title: Day06_Rep1

description:
Day06.bw
DESeq_Read_Counts.txt.gz


title: d3 FL CT rep3


title: high-grade adenoma 8

source_name: high-grade adenoma 8


title: high-grade adenoma 11

source_name: high-grade adenoma 11


title: Sample 8 (TdTomato -ve)


title: d3 FL CT rep1


title: Day04_Rep1

description:
Day04.bw
DESeq_Read_Counts.txt.gz


title: Day02_Rep2

description:
Day02.bw
DESeq_Read_Counts.txt.gz


title: high-grade adenoma 7

source_name: high-grade adenoma 7


title: d3 FL AL rep5

source_name: Ear Skin


title: high-grade adenoma 9

source_name: high-grade adenoma 9


title: Day02_Rep1

description:
Day02.bw
DESeq_Read_Counts.txt.gz


title: d3 FL AL rep4


title: normal 9

source_name: normal 9


title: low-grade adenoma 6

source_name: low-grade adenoma 6


title: d3 FL AL rep3


title: Day00_Rep1

description:
Day00.bw
DESeq_Read_Counts.txt.gz


title: Day00_Rep2

description:
Day00.bw
DESeq_Read_Counts.txt.gz


title: high-grade adenoma 10

source_name: high-grade adenoma 10


title: d3 FL AL rep1


title: d3 DK CT rep6

value: Il36r<delta>K (DK)


title: normal 10

source_name: normal 10


title: mES KI17_1 IP

source_name: mouse ES cells

value: mouse embryonic stem cells (mES)

value: Millipore m6A antibody (ABE572)


title: d3 DK CT rep5


title: Day04_Rep2

description:
Day04.bw
DESeq_Read_Counts.txt.gz

value: CD34+ cells were subjected to ex vivo erythropoiesis according to the protocol described in Palii et al. (doi:10.3791/2813. J Vis Exp. 53, 2011)


title: mES KI17_1 input


title: Over19

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

data_processing:
Basecalls performed using CASAVA version 1.4
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
RNA-seq reads were aligned to the mm9 genome assembly using TopHat2
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: AML12 hepatocyte

growth_protocol: The nontumorigenic mouse hepatocyte cell line AML12 was maintained in DMEM/F12 medium (Invitrogen) containing 10% fetal calf serum, 1×ITS (insulin-transferrin-sodium selenite media supplement, Sigma-Aldrich), dexamethasone (40 ng/ml), penicillin (100 units/ml), and streptomycin (100 μg/ml). All cells were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from AML12 subline cells with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate the AML12 cells that stably express H19, AML12 cells were infected with the recombinant lentivirus expressing H19 (Lv-H19) or the control virus (Lv-NC) respectively. After lentivirus infection, the stable cell lines were selected using 0.5 mg/ml of puromycin. The stable lines were maintained in DMEM supplemented with 10% FBS and 0.25 mg/ml of puromycin. The stable expression of H19 was confirmed by qRT-PCR

value: hepatocyte

tag: passages


title: d3 DK CT rep4


title: high-grade adenoma 6

source_name: high-grade adenoma 6

value: male

value: high-grade adenoma

value: colorectal


title: normal 8

source_name: normal 8

value: normal


title: Ctrl

tag: cell type


title: d3 KO CT rep4

value: Ear skin


title: SEM sh5-3

city: Staten Island

first: Joanna

last: Pierro

state: NY

address: 550 1st Avenue

institute: NYU Langone Health

data_processing:
adapters and low quality bases were trimmed using trimmomatic
data was aligned to reference genome (hg19) using STAR
Genes-samples count matrices were generated using featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: xls files presenting normalized counts

source_name: B-ALL cell line

growth_protocol: The B-lineage leukemia cell lines RS4;11, Reh (ATCC, Manassas, VA), KOPN8, 697, RCH-ACV (DSMZ, Braunschweig, Germany), and SEM (kindly gifted by Jun Yang, St. Jude Children’s Hospital) were grown in RPMI1640 medium. HEK293T (ATCC) cells were grown in DMEM medium. All media were supplemented with 10% FBS, 1% penicillin/streptomycin under 5% CO2 at 37°C. No cell lines were used beyond passage 20.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini Kit and quality was verified by an Agilent Bioanalyzer 2100 (PICO chip).
RNAseq libraries were generated using TruSeq stranded total RNA, with RiboZero Gold. RNA-seq libraries were sequenced using 54 base pair reads on the Illumina Genome Analyzer GAIIx.

value: bone marrow


title: mES KI14 IP


title: SEM sh5-2


title: mES KI14 input


title: d3 DK CT rep2


title: mES KI5 IP


title: low-grade adenoma 7

source_name: low-grade adenoma 7

value: low-grade adenoma


title: normal 7

source_name: normal 7


title: SEM sh5-1


title: d3 DK AL rep6

value: Aldara


title: normal 5

source_name: normal 5


title: SEM sh2-2


title: low-grade adenoma 4

source_name: low-grade adenoma 4

value: female


title: normal 6

source_name: normal 6


title: SEM sh2-3


title: mES KI5 input


title: d3 DK CT rep3


title: d3 DK AL rep5


title: normal 4

source_name: normal 4


title: SEM sh2-1


title: mES ΔSX input


title: d3 DK AL rep4

source_name: Ear Skin


title: d3 DK CT rep1


title: high-grade adenoma 4

source_name: high-grade adenoma 4


title: SEM NT3


title: low-grade adenoma 3

source_name: low-grade adenoma 3


title: d3 DK AL rep3


title: mES WT IP


title: mES WT input


title: d3 DK AL rep2


title: SEM NT2


title: high-grade adenoma 3

source_name: high-grade adenoma 3


title: SEM NT1


title: mES ΔSX IP


title: 12 week old NOD Islet - sample 6

type: RNA

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

description:
Gene expression in pancreatic islets of a 12 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
12WK-6

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)

data_processing: Data were processed using Genespring 12.6.1

source_name: pancreatic islet

label_protocol: 300 ng of total RNA from each individual  NOD mouse, or 300 ng of total RNA from a pool of 6  NOD.B10 mice were labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: NOD and NOD.B10 mice were bred at the Stanford School of Medicine Animal facility.  All mice were maintained under pathogen-free conditions according to institutional guidelines under approved protocols in the Stanford Medical Center’s Department of Comparative Medicine.

extract_protocol: Total RNA was extracted from NOD and NOD.B10 islets using Trizol (Invitrogen) combined with the RNeasy micro kit (Qiagen).

treatment_protocol: Islets  were isolated by collagenase digestion, and islets from each individual mouse was resuspended in 0.5ml Trizol Reagent (Invitrogen).

value: NOD

value: 12 weeks old

tag: Sex

value: pancreatic islet

source_name: Pancreatic islet


title: high-grade adenoma 5

source_name: high-grade adenoma 5


title: low-grade adenoma 5

source_name: low-grade adenoma 5


title: d3 DK AL rep1

value: Il36r<delta>K (DK)


title: RCH sh5-2


title: Ngn3Cre_STZ_M9_1

data_processing:
The fastq file for each single-cell sample was split based on 8-bp cell-specific barcode sequences included in Read2.
The 8bp unique molecular identifiers (UMIs) included in Read1 were added into the corresponding read 1.
The polyA sequences in Read1 were trimmed.
We aligned preprocessed Read1 reads to the mouse genome (mm10) with TopHat (v2.1.0).
Mapped reads were annotated to genes using featureCounts (v1.5.3), so the gene ID was appended as XT tag in the bam file.
We sorted and indexed the bam file with samtools (v.1.3.1).
We quantified the unique molecular identifiers (UMIs) of each gene with umi_tools (v0.5.0) using the following parameters: “count --per-gene --gene-tag=XT --method unique -I indexed_sorted_bam -S out_file”.
The UMI matrix was transformed to transcripts per 0.1 million (TP0.1M). To eliminate the influence of individual genes on the transcriptome, we ignored extremely highly expressed genes (Ins1, Ins2, Gcg, Sst, Ppy, Pyy, Iapp, and Yam1) in our total transcripts calculations.
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include UMI and TP0.1M values for each sample

tag: genotype/variation

value: Ngn3-Cre; Rosa-RFP

value: Adult

tag: treatment

value: STZ

tag: insulin implants

value: Yes, discontinuous insulin implant in the last 2 months before sacrifice

tag: time after stz

value: pancreas


title: normal 3

source_name: normal 3

tag: age

tag: tissue


title: 12 week old NOD Islet - sample 3

description:
Gene expression in pancreatic islets of a 12 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
12WK-3


title: RCH sh5-1


title: 12 week old NOD Islet - sample 2

description:
Gene expression in pancreatic islets of a 12 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
12WK-2


title: 12 week old NOD Islet - sample 4

description:
Gene expression in pancreatic islets of a 12 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
12WK-4


title: Ngn3Cre_STZ_M2_1

value: Yes

tag: batch


title: normal 2

source_name: normal 2

value: colorectal


title: RCH sh2-3

source_name: B-ALL cell line


title: low-grade adenoma 2

source_name: low-grade adenoma 2


title: RCH sh2-1


title: Ngn3Cre_STZ_D12_1


title: Ngn3Cre_STZ_D42_1


title: Ngn3Cre_STZ_M5_1


title: 12 week old NOD Islet - sample 5

description:
Gene expression in pancreatic islets of a 12 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
12WK-5


title: Ngn3Cre_STZ_D6_1


title: RCH NT3


title: RCH sh2-2


title: Ngn3Cre_STZ_D30_1


title: RCH NT2


title: RS411 sh5-3


title: Ngn3Cre_Control_3

value: Control


title: Ngn3Cre_Control_2


title: Ngn3Cre_Control_1


title: RS411 sh5-1


title: 4 week old NOD Islet - sample 6

description:
Gene expression in pancreatic islets of a 4 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
4WK-6

value: 4 weeks old


title: low-grade adenoma 1

source_name: low-grade adenoma 1


title: RS411 sh5-2

value: bone marrow


title: RS411 sh2-3


title: NO2 mRNAseq

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4
cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs
Genome_build: MM10
Supplementary_files_format_and_content: FPKM

source_name: skin tissue from nonirradiated area

growth_protocol: SPF condition for the growth of C57 mice.

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
RNA-seq.10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: Male C57 mice (4 weeks old) were irradiated with a single 35-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues were then collected 24 h after radiation.

tag: stress

value: control

value: skin


title: NO3 mRNAseq


title: NO4 mRNAseq


title: RS411 sh2-2


title: 10 day old NOD Islet - sample 5

description:
Gene expression in pancreatic islets of a 10 day old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
10D-5

value: 10 days old

value: female


title: 10 day old NOD Islet - sample 4

description:
Gene expression in pancreatic islets of a 10 day old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
10D-4

value: NOD


title: normal 1

source_name: normal 1

value: normal


title: 10 day old NOD Islet - sample 6

description:
Gene expression in pancreatic islets of a 10 day old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
10D-6

value: pancreatic islet


title: 4 week old NOD Islet - sample 3

description:
Gene expression in pancreatic islets of a 4 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
4WK-3


title: high-grade adenoma 1

source_name: high-grade adenoma 1

value: high-grade adenoma


title: 4 week old NOD Islet - sample 4

description:
Gene expression in pancreatic islets of a 4 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
4WK-4


title: 4 week old NOD Islet - sample 5

description:
Gene expression in pancreatic islets of a 4 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
4WK-5


title: RS411 sh2-1


title: 4 week old NOD Islet - sample 1

description:
Gene expression in pancreatic islets of a 4 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
4WK-1


title: 12 week old NOD Islet - sample 1

description:
Gene expression in pancreatic islets of a 12 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
12WK-1

value: 12 weeks old


title: 10 day old NOD Islet - sample 2

description:
Gene expression in pancreatic islets of a 10 day old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
10D-2


title: 10 day old NOD Islet - sample 3

description:
Gene expression in pancreatic islets of a 10 day old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
10D-3


title: 4 week old NOD Islet - sample 2

description:
Gene expression in pancreatic islets of a 4 week old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
4WK-2


title: 10 day old NOD Islet - sample 1

description:
Gene expression in pancreatic islets of a 10 day old NOD mouse compared to a pool of 6 age-matched NOD.B10 islets
10D-1


title: RS411 NT3


title: IR3 mRNAseq

source_name: skin tissue with 35 Gy radiation

value: 35 Gy radiation


title: NO1 mRNAseq


title: Mesa 911GH

city: Düsseldorf

first: Agatha

middle: Alexandra

last: Walla

address: Universitätsstraße 1

department: Institut of Plant Genetics

country: Germany

institute: Heinrich-Heine-University

data_processing:
BWA-MEM (version  0.7.15) was used for alingment of the reads, Salmon was used to extract transcript per million (TPM) values.
Log fold change values comparing mutant versus wildtype at different developmental stages were obtained using Limma-Voom (compare to van Esse et al., 2017).
Variant calling was performed with GATK UnifiedGenotyper (Version 3.6) on processed alignment files (compare to van Esse et al., 2017).
Genome_build: A combined set of High Confidence (HC) and Low confidence (LC) predicted coding sequences of barley cv. Morex (Mascher et al., 2017) as reference was used.
Supplementary_files_format_and_content: Processed data for this sample are included in the vcf file with variant information.

organism: Hordeum vulgare

source_name: enriched shoot apex material

growth_protocol: Plants were grown under long day conditions (16h, 22°C day; 8h, 18°C night).

extract_protocol:
Enriched inflorescence tissue was isolated at Waddington stage W2.0, W3.5 and 5.0 and frozen in liquid nitrogen. Tissue was ground, dissolved in 500 mL TRIzol reagent (Invitrogen), incubated for 5 min at room temperature after which, 100 mL of chloroform was added. The sample was homogenized, incubated for 2 min, and centrifuged for 15 min at 4°C followed by phase separation (keeping the aqueous phase). Next, isopropanol was added and incubated for 10 min at room temperature and further purified using an RNA easy Micro Kit (Qiagen). Residual DNA was removed using a DNA-free kit (Ambion). The quality of the RNA was tested using a bio analyzer (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: shoot apex

tag: developmental stage

value: Waddington stage 1.0

tag: genetic background

value: cv. Mesa

value: wild-type


title: mnd1.a 1328BZ

data_processing:
BWA-MEM (version  0.7.15) was used for alingment of the reads, Salmon was used to extract transcript per million (TPM) values.
Log fold change values comparing mutant versus wildtype at different developmental stages were obtained using Limma-Voom (compare to van Esse et al., 2017).
Variant calling was performed with GATK UnifiedGenotyper (Version 3.6) on processed alignment files (compare to van Esse et al., 2017).
Genome_build: A combined set of High Confidence (HC) and Low confidence (LC) predicted coding sequences of barley cv. Morex (Mascher et al., 2017) as reference was used.
Supplementary_files_format_and_content: Excel sheet with log fold changes comparing the different stages, vcf file with variant information.

source_name: enriched inflorescence material

value: inflorescence

value: Waddington stage 5.0

value: cv. Bowman

value: mnd1.a (GSHO2038)


title: RS411 NT1

value: bone marrow


title: RS411 NT2


title: mnd1.a 1328BY


title: IR1 mRNAseq

value: skin


title: CC_S4

city: Kunming

first: Tianqing

last: Li

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: Kunming University of Science and Technology

data_processing:
The sequencing qualities of 21 RNA-seq profiles were examined with the FASTQC
HISAT2 (v 2.1.0) was used to align the RNA-seq profiles to the human genome.
The alignment results of HISAT2 in the SAM format were converted to BAM format and sorted with SAMTools (v 1.1).
Stringtie (v 1.3.4) was used to calculate the abundances of genes (in FPKM) annotated in GENCODE (v29) using the options of "-G gencode.v29.gtf -B -e –v".
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: fibroblasts

growth_protocol: Conventional human ESC lines H9 and hES1 and human iPSC line S4 were maintained on mouse embryonic fibroblast (Millipore, PMEF-CFL) feeder cells (hereafter referred to as feeders) inactivated by mitomycin C (Sigma, M0503) and passaged enzymatically with 1 mg/ml Collagenase type IV (Thermo Fisher Scientific, 17104-019).     iPSC S4 were generated by reprogramming human fibroblasts from one 8-year-old girl with Sendai Reprogramming Kit (Thermo Fisher Scientific, A16518) according to the manufacturer’s instructions The culture medium of conventional human ESCs and iPSCs is hPSC medium (hPSM). hPSM was mixed with PSGro Human iPSC/ESC Growth Medium (StemRD, PGroF-500) and common hPSC culture medium according to the 1:4 ratio as reported    Conventional-culture hPSCs were digested into single cells with 50% TrypLE and inoculated at a density of 3×104 cells per 3.5 cm dish onto feeders or Matrigel  (Corning, 354277) or Vitronectin (thermofisher, A14700) coated plates in the AIC medium with 5μM Y27632. 24 hours later, the media were replaced with the fresh  media without Y27632. The AIC medium consisted of modified N2B27 medium supplemented with 10 ng/ml Activin A (Peprotech, 120-14E), 2 μM IWP-2 (Selleck,  S7085) and 0.6 μM CHIR99021 (Selleck, S2924). AIC-hPSCs cultured on feeder or matrix were routinely passaged every 3-4 days at a ratio from 1:5 to 1:10 by single-cell dissociation.    AIC-hPSCs in suspension culture were expanded on Ultra-Low Attachment 6-well plate by passaging every 4 days at the ratio of 1:25.

extract_protocol:
Isolation of cells samples. The ES cells were washed in PBS for 2times, incubated with tryple (TrypLE™ Express Enzyme (1X), phenol red,12605028) for around 3 min at 37 °C.
Total RNA was isolated from hPSCs cultured in conversional medium and AIC medium using the TRIzol Reagent (Thermo Fisher Scientific, 15596018). RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB England BioLabs, E7530L). The fragmented and randomly primed 2×150-bp paired end libraries were sequenced using an Illumina HiSeq X Ten.

treatment_protocol: Screen culture system of hPSCs  CC-hPSCs were dissociated into single cells with 50% TrypLE (Thermo Fisher  Scientific, 12605-028) and seeded at a density of 1500 cells per individual well of  96-well plate on feeders in different culture media based on modified N2B27 medium  supplemented with 5 μM Y27632. 48 hours later, Y27632 was withdrawal  from the media. 96 hours later, cells were fixed in 4% PFA, immune-stained and  imaged. A total of 500 ml of modified N2B27 medium was composed of 240 ml  DMEM/F12 (Thermo Fisher Scientific, 10565-018), 240 ml Neurobasal (Thermo  Fisher Scientific, 21103-049), 5 ml N2 supplement (Thermo Fisher Scientific,  17502-048), 10 ml B27 supplement (Thermo Fisher Scientific, 17504-044), 0.5%  GlutaMAX (Thermo Fisher Scientific, 35050-061), 1% nonessential amino acids  (Thermo Fisher Scientific, 11140-050), 0.1 mM β-mercaptoethanol (Sigma, M7522),  50 μg/ml L-ascorbic acid 2-phosphate (Sigma, A8960), 0.5 ml Chemically Defined  Lipid Concentrate (Thermo Fisher Scientific, 11905-031), 12.5 μg/ml Insulin (Roche,  11376497001), 1.25 ml Sodium Pyruvate (Thermo Fisher Scientific, 11360-070), 0.02μg/ml Progesterone (Sigma, P8783). During the course of screening culture systems,  different dosages and combinations of Activin-A (0-50 ng/ml, Peprotech, 120-14E),  IWP-2 (0-5 μM, Selleck, S7085) and CHIR-99021 (0-3 μM, Selleck, S2924) were  added into modified N2B27 media.      Derivation of new hESC lines from blastocysts in conventional conditions.  10 frozen-thawed human blastocysts (5-6 days post-fertilization) were  transiently treated by 0.5% protease (Sigma, P8811) to remove the zona pellucida.  Whole blastocyst was seeded on feeders in hPSM supplemented by 10 μM Y27632.  hPSM was pre-warmed in a humidified incubator under 20% O2 and 5% CO2 at 37℃  for at least one hour before the embryos were seeded. 72 hours later, the embryo  attached to feeder cell layer and the medium was completely replaced by fresh hPSM  medium including 5 μM Y27632. Henceforth, the medium was replaced every 2 days  until hESC-like outgrowth was visible. Generally, hESC-like outgrowth became  evident on Day 4-7. After treating the embryo for about 10 min with 1 mg/ml  Collagenase type IV, the outgrowth was mechanically picked, dissociated into smallclumps, and seeded onto fresh feeder cell layer in hPSM with 5 μM Y27632. After 3-5  days, the outgrowth displayed typical conventional hESC colony morphology and  could be passaged and expanded with Collagenase type IV as CC-hPSC    Derivation of new hESC lines from blastocysts in AIC medium.  Five frozen-thawed human blastocysts (5-6 days post-fertilization) were  transitorily treated by 0.5% protease (Sigma, P8811) solution to remove the zona  pellucida. Whole blastocyst was seeded on Matrigel-coated 96-well plate and cultured  in 150 μl of the AIC medium with 10 μM Y27632. The AIC medium was pre-warmed  in a humidified incubator under 20% O2 and 5% CO2 at 37℃ for at least one hour  before the embryos were seeded. After 48 hours, hESC-like outgrowths became  visible in the attached embryos, was mechanically picked into 50% TrypLE and  incubated for 5-10 min at 37℃. Next, the digested hESC-like outgrowth (or whole  embryo) was transferred into a drop of AIC medium and dissociated into single cells  by mildly pipetting up and down for mechanical separation by a finely drawn Pasteur  pipette. Alternatively, if the hESC-like outgrowth was invisible, the whole attached  embryo was dissociated into single cells with 50% TrypLE for 5-10 min at 37℃.  Single cells were re-seeded on Matrigel-coated 96-well plate and cultured in 150 μl of  AIC medium including 10 μM Y27632. The culture medium was replaced every two  days. On Day 2-4 following dissociation, proliferating AIC-hESC colonies were  evident and further dissociated into single cells by 50% TrypLE treatment on Day 5-7.  After that, the newly established AIC-hESC lines were routinely passaged every 3-4  days at a 1:5 to 1:10 split ratio.

tag: cell line

value: induced pluripotent stem cell

tag: condition

value: bFGF/KSR (Feeders)

tag: passage


title: IR2 mRNAseq

tag: strain


title: IR4 mRNAseq


title: 697 WT2


title: mnd1.a 1328BW

tag: genotype


title: mnd1.a 1327BS

value: Waddington stage 3.5


title: 697 WT1


title: AIC_S4_F4_S15

tag: cell type

value: AIC (suspension)


title: CC_H9

source_name: blastocyst

value: embryonic stem cell


title: CC_H1


title: mnd1.a 1328BX


title: mnd1.a 1327BR


title: 697 EV3


title: high-grade adenoma 2

source_name: high-grade adenoma 2

tag: gender

value: male

tag: disease

value: high-grade adenoma

value: colorectal


title: AIC_S4_F7_M19

value: AIC (Matrigel)


title: mnd1.a 1327BQ


title: RCH sh5-3


title: AIC_S4_F8

value: AIC (Feeders)


title: 697 EV2


title: mnd1.a 1328AR

value: Waddington stage 2.0


title: 697 EV1


title: AIC_H9_F8_M9_S5


title: 697 WT3


title: mnd1.a 1328AS

value: inflorescence


title: AIC_H9_F8_M6_S13


title: 697 EK3


title: mnd1.a 1328AQ


title: 697 EK2


title: Bowman 1327H

value: Waddington stage 5.0

value: wild-type


title: AIC_H9_F8_M15


title: AIC_H9_F8_M10


title: Bowman 1327G

value: cv. Bowman


title: 697 EK1

value: bone marrow


title: REH EK_2


title: Bowman 1327F


title: AIC_h3_M8_S7


title: AIC_h3_M10


title: REH WT_2


title: Bowman 1327D


title: AIC_h2_M8_S5


title: REH WT_1


title: AIC_h2_M8


title: REH EV_2


title: AIC_h1_M8_S5


title: AIC_H1_F18_S5


title: Bowman 1327B


title: Bowman 1327C


title: Bowman 1327A


title: Bowman 1328BA


title: Inflorescence, stk ces-4 bee1 bee3 rep3

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
reads were mapped to the reference  A. thaliana TAIR 10 transcriptome using bowtie2
gene expression levels were estimated by the means of RSEM
reads counts were normalized using the TMM normalization as implemented by edgeR
differentially expressed genes were identified by using the edgeR quasi-likelihood F-test
Genome_build: TAIR10
Supplementary_files_format_and_content: gene expression values in logCPM and adjusted p-values for differential expression

organism: Arabidopsis thaliana

source_name: Inflorescence, stk ces-4 bee1 bee3

growth_protocol: Arabidopsis thaliana seeds were stratified for 2 days at 4°C after sowing. Plants were grown at 22°C under long day conditions (LD)

extract_protocol:
Total RNA was extracted from three biological replicates (1 gr) from both wild-type and stk ces-4 bee1 bee3, using the Macherey Nagel ‘Nucleospin RNA Plant’ according to the manufacturer’s instructions
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA library Prep Kit for illumina (NEB) according to the manufacture’s instruction

value: inflorescence till stage 12

value: stk ces-4 bee1 bee3


title: Bowman 1328AZ


title: AIC_h1_M9


title: Inflorescence, stk ces-4 bee1 bee3 rep2


title: REH EK_1


title: Inflorescence, stk ces-4 bee1 bee3 rep1


title: AIC_H9_F11


title: Inflorescence, Col-0 rep3

source_name: Inflorescence Col-0

extract_protocol:
Total RNA was extracted from three biological replicates (1 gr) from both wild-type and stk ces-2 bee1 bee3, using the Macherey Nagel ‘Nucleospin RNA Plant’ according to the manufacturer’s instructions
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA library Prep Kit for illumina (NEB) according to the manufacture’s instruction

value: wild type


title: Bowman 1328AY


title: AIC_H1_F18_M19


title: Bowman 1327E


title: AIC_H1_F14


title: Inflorescence, Col-0 rep2


title: Inflorescence, Col-0 rep1


title: Wildtype TDP43 8

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

description:
microRNA
WT8

hyb_protocol: Performed according to the manufacturer's instructions (nanoString Technologies). Nanostring product used was the Nanostring nCounter Human V3A miRNA Expression Assay Kit

data_processing: nSolver Analysis Software 3.0 (NanoString Technologies) was used to background subtract and normalize the top 100 miRNA counts. Fold-change differences for WT-TDP43- or ∆NLS-TDP43-associated miRNAs relative to control (eGFP-His) were identified using P<0.05 as the significance cutoff.

source_name: HeLa cells

label_protocol: Total RNA from the cytoplasmic fractions pulled-down with Ni2+-beads for WT-TDP43-eGFP-His, ∆NLS-TDP43-eGFP-His, and eGFP-His lines (n=4 for each line) was performed.

growth_protocol: HeLa cells were grown following standard protocols and transiently transfected with 100 ng of the pLVX-TRE3G-eGFP-His, pLVX-TRE3G-WT-TDP43-eGFP-His, or pLVX-TRE3G-∆NLS-TDP43-eGFP-His constructs along with pLVX-EF1a-Tet3G (Clontech, Takara Bio USA) using Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s protocol. Following a 6 h incubation, wells were rinsed and replenished with growth media containing the selection antibiotics puromycin (1 µg/ml; #P8833, Sigma, St. Louis, MO) and geneticin (1 µg/ml; G418; #10131-035, Gibco) for 48 h. Doxycycline (1 µg/ml; #PHR1145, Sigma) was then added to the media to induce protein expression and confirm transfection, and stable lines were generated using a serial dilution protocol in 96-well plates (Corning Inc., Corning, NY). Single colonies were grown to confluence, induced with doxycycline, and eGFP-positive clones were selected for expansion. Multiple clones were generated that varied modestly in the level of WT-TDP43-eGFP-His, ∆NLS-TDP43-eGFP-His, or eGFP-His expression, and those with the most optimal eGFP level (high expression with normal cellular morphology and survival) were selected for further experiments.

extract_protocol: Fractionation was used to examine subcellular localization of TDP43 variant expression per established protocols (Barmada et al., 2010 J. Neurosci; Archbold et al., 2018 Sci Rep). WT-TDP43-eGFP-His, ∆NLS-TDP43-eGFP-His, and control eGFP-His were then pulled down via their His tags from the subcellular fractions using nickel-agarose (Ni2+) beads (Qiagen) (Figueroa-Romero et al., 2009 FASEB J). To extract associated miRNAs, bead aliquots from the cytoplasmic fractions were washed twice with 1X PXL (0.1% SDS, 0.5% Triton X-100, 0.5% deoxycholate in 1x PBS) and twice with 5X PXL. Samples were then boiled for 3 min to reverse cross-linking (King et al., 2014 J Biol Chem), and QIAzol (Qiagen) was added and samples were stored at -80 oC. Next, a miRNeasy Mini Kit (cat# 217004, Qiagen) was used to extract total RNA, enriched in cyTDP43-bound miRNAs. Purified RNA was treated with RNase-free DNase and stored at -80 oC until required for miRNA profiling.

treatment_protocol: Doxycycline (1 µg/ml; #PHR1145, Sigma) was added to the media to induce protein expression.

tag: transfected with

value: eGFP-His Wildtype

value: HeLa


title: REH EV_1


title: Wildtype TDP43 6

description:
microRNA
WT6

scan_protocol: Performed according to the manufacturer's instructions (nanoString Technologies)


title: AIC_H1_F19_S16

value: embryonic stem cell

value: AIC (suspension)


title: Mycobacterium smegmatis infected with mycobacteriophage Wildcat for 150 minutes

city: Pittsburgh

first: Graham

middle: F.

last: Hatfull

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.17 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.3.4.2
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.9
BAM format was converted to BED format using bedtools version 2.27.1
Expression levels were computed as reads mapped per base pair per strand ("plus" and "minus") using the genomecov tool of bedtools version 2.27.1
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: DQ398052 (Wildcat)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("plus" and "minus" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycolicibacterium smegmatis

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using Ribo-Zero (Illumina)
Libraries were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: host strain

tag: agent

value: mycobacteriophage Wildcat

tag: infection timepoint

value: 150 minutes


title: Mycobacterium smegmatis infected with mycobacteriophage Wildcat for 30 minutes

value: 30 minutes


title: C23_MX2_dox0_6hr_rep3

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling and The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Additional quality control was performed by the MultiQC RNA-Seq module
Quasi-mapping algorithm Salmon was used to provide fast and bias-aware quantification of transcript expression using Gencode human transcripts database (release 29 based on GRCh38.p12)
differentially expressed genes (DEGs) were calculated with DESeq2 adjusting for cell line, biological replicate, and library construction batch.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files of Salmon quantificiation include normalized TPM and read count values for each Sample.

source_name: Primary cultured melanocytes

growth_protocol: Melanocytes were grown in Medium M254 with supplements (Invitrogen) at 37C with 5% CO2, and infected with the lentiviral system using MX2 cDNA cloned into pINDUCER20, followed by drug selection (1mg/ml Geneticin)

extract_protocol:
Total RNA was isolated using a miRNeasy Mini kit (217004, Qiagen). To reduce melanin carryover, cell lysate in QIAzol reagent was heated at 65°C for 5 minutes before the addition of chloroform and phase separation.
Sequencing library was constructed following Illumina TruSeq Standard mRNA Library protocol for 151bp paired-end sequencing

treatment_protocol: Following drug selection, cells were treated with 0 or 100ng/ml doxycycline for 6hr and 72hrs before being harvested for RNA isolation.

tag: individual id

tag: lentiviral vector

value: pINDUCER20-MX2 cDNA

tag: doxycycline

value: 0 ng/ml

tag: time


title: C23_MX2_dox100_72hr_rep3

value: 100 ng/ml


title: deltaNLS-TDP43 8

description:
microRNA
Mutant8

value: eGFP-His-deltaNLS


title: Wildtype TDP43 3

description:
microRNA
WT3


title: deltaNLS-TDP43 3

description:
microRNA
Mutant3


title: Wildtype TDP43 4

description:
microRNA
WT4


title: C23_MX2_dox0_72hr_rep2


title: C23_MX2_dox100_6hr_rep3


title: deltaNLS-TDP43 6

description:
microRNA
Mutant6


title: Control 8

description:
microRNA
Ctrl8

value: EmptyVector


title: C23_MX2_dox100_72hr_rep2


title: Control 6

description:
microRNA
Ctrl6


title: deltaNLS-TDP43 4

description:
microRNA
Mutant4


title: C23_MX2_dox0_72hr_rep3


title: C23_MX2_dox0_6hr_rep2


title: C23_MX2_dox100_6hr_rep2


title: Control 4

description:
microRNA
Ctrl4


title: Control 3

description:
microRNA
Ctrl3


title: 07_celastrol_male3

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

description: Gene expression of whole brain treated with celastrol

hyb_protocol: Labeled cRNA was purified with RNeasy mini spin columns (QIAGEN) and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: After washing with Gene Expression Wash Buffer (Agilent Technologies), the slide glass was scanned on a Microarray Scanner (Agilent Technologies).

data_processing: Microarray data were analyzed using the GeneSpring software (Agilent Technologies).

organism: Oryzias latipes

source_name: celastrol treatment_whole brain

label_protocol: cDNA synthesis and cRNA labeling reactions were performed with the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Medaka fish (Oryzias latipes) were obtained from a local dealer and kept outdoors.

extract_protocol: Total RNA was prepared from each fish using an RNeasy tissue kit (QIAGEN).

treatment_protocol: Adult male medaka kept under SC conditions were treated with DMSO or celastrol. Twenty-four hours after the treatment, whole brains were collected in the middle of the light phase.

tag: Sex

value: male

tag: developmental stage

value: adult

tag: treatment

value: celastrol

tag: tissue

value: whole brain


title: 06_celastrol_male2


title: 10_LWtoSC_SC_male5

description: Gene expression of whole brain under SC conditions

source_name: SC conditions, whole brain, replicate 5

treatment_protocol: Adult male medaka kept under LW conditions either reimained in LW or were transferred into SC conditions. Two weeks after transfer, whole brains were collected in the middle of the light phase.

value: SC (short-day and cool temperature conditions:10 h light/14 h dark and 10 °C)


title: 02_DMSO_male2

description: Gene expression of whole brain treated with DMSO

source_name: DMSO treatment_whole brain

value: DMSO


title: 08_celastrol_male4


title: C23_MX2_dox100_72hr_rep1


title: 05_celastrol_male1


title: 09_LWtoSC_SC_male4

source_name: SC conditions, whole brain, replicate 4


title: 04_DMSO_male4


title: C23_MX2_dox0_6hr_rep1


title: 03_DMSO_male3


title: C23_MX2_dox0_72hr_rep1


title: 01_DMSO_male1


title: C23_MX2_dox100_6hr_rep1


title: RCH sh2

library_source: genomic

data_processing:
Aigned to reference genome (hg19) using Bowtie2
Filtering of duplicate reads by Sambamba
Peak-calling conducted with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files consisting of peak calls for each sample with 2replicates, bigwig files consisiting of peak information for visualization

source_name: B-ALL cell line

extract_protocol:
Cells were lysed via centrifugation for 1 minute at 500xg. Nuclei were tagmented using Nextera (Illumina) Tagmentation DNA buffer and enzyme.
libraries were prepped according to protocol by Buenrostro et al. Briefly, PCR was performed using barcoded primers that recongizne the adapter sequences inserted during the transpase reaction.

treatment_protocol: Not applicable

value: bone marrow


title: RCH NT


title: RCH NT1


title: SEM NT


title: SEM sh2


title: Oocyte, replicate 2

city: Nouzilly

first: Svetlana

last: UZBEKOVA

address: PRC INRA

country: France

institute: INRA

description: Gene expression in immature oocyte

hyb_protocol: Hybridization was performed using 600 ng of Cy3-labeled cRNA with specific activity > 6.0 pmol of Cy3/μg of cRNA during 17 hours at 65°C, following the manufacturer’s protocol (http://crb-gadie.inra.fr/).

scan_protocol: The slides were scanned immediately after washing using a G2565CA Scanner System with one color scan setting for 8×60k array slides (Agilent Technologies)

data_processing: The resulting images were analysed using the Feature Extraction Software v10.7.3.1 (Agilent Technologies).

organism: Bos taurus

source_name: Bovine oocytes, immature, repl 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared with 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit following the recommended protocol (Agilent Technologies, SantaClara, CA, USA)

growth_protocol: Antral follicles were punctioned from bovine ovaries after slaughting, cumulus-oocyte complexes and granulosa cells were separated. Thcea cells were srabbed from folliular walls. Trizol was added and samples  frosen at -80°C

extract_protocol: Total RNA was extracted using Trizol Reagent(Invitrogen, Cergy Pontoise, France)  and then and treated using RQ1 DNAse (Promega, Frace) according to manufacturer's instructions.

treatment_protocol: IVM was performed during 4 hours, the CC were detached, washed in cold PBS and put into Trizol reagent, kept at -80°C

value: female gamete

tag: Stage

value: immature


title: 07_LWtoSC_SC_male2

source_name: SC conditions, whole brain, replicate 2


title: 05_LWtoSC_LW_male5

description: Gene expression of whole brain under LW conditions

source_name: LW conditions, whole brain, replicate 5

value: LW (long-day and warm temperature conditions:14 h light/10 h dark and 26 °C)


title: Oocyte, replicate 3

description: Gene expression in immature oocyte

source_name: Bovine oocytes, immature, repl 3


title: Cumulus cells, 4h IVM, replicate 3

description: Gene expression in cumulus cells, after 4h IVM

source_name: Bovine cumulus cells aftre 4h IVM, repl 3

value: ovarian cumulus cells

value: 4h in vitro maturation


title: RS411 sh2


title: RS411 NT


title: Oocyte, replicate 4

description: Gene expression in immature oocyte

source_name: Bovine oocytes, immature, repl 4


title: 06_LWtoSC_SC_male1

source_name: SC conditions, whole brain, replicate 1


title: 03_LWtoSC_LW_male3

source_name: LW conditions, whole brain, replicate 3


title: Oocyte, replicate 1

description: Gene expression in immature oocyte

source_name: Bovine oocytes, immature, repl 1


title: 02_LWtoSC_LW_male2

source_name: LW conditions, whole brain, replicate 2


title: donor_25_mac_CD31_neg

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
The sixteen samples (paired samples from eight single-cell donors, including 4 previously described donors in GSE135922) were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.
Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 1100 (to remove cells with poor read quality) or greater than 10000 (to remove cells likely to be doublets) were removed. Cells with greater than 30% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-")
For each of the sixteen libraries, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands: my_choroid_object <- NormalizeData(my_choroid_object, normalization.method = "LogNormalize", scale.factor = 10000), my_choroid_object <- FindVariableFeatures(my_choroid_object, selection.method = “vst”, nfeatures = 2000)
Integration anchors from the first 25 dimensions of the canonical correlation analysis were used to integrate data with the following commands: choroid.anchors <- FindIntegrationAnchors(object.list = my_choroid_object_list, dims=1:25), choroid.combined <- IntegrateData(anchorset = choroid.anchors, dims = 1:25)
Data scaling, principal component analysis, and clustering were performed with the following commands: CD31.combined <- ScaleData(CD31.combined, verbose = FALSE), CD31.combined <- RunPCA(CD31.combined, npcs = 30, verbose = FALSE), CD31.combined <- RunUMAP(CD31.combined, reduction = "pca", dims = 1:23), CD31.combined <- FindNeighbors(CD31.combined, reduction = "pca", dims = 1:23), CD31.combined <- FindClusters(CD31.combined, resolution = 0.35)
Genome_build: hg 19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format for count(*_count.tsv) and processed/normalized (*_processed) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: RPE/choroid

extract_protocol:
A 12-mm macular centered punch of RPE/choroid was acquired from four human donors (Donors 8-11). After dissection away from the retina and sclera, the RPE/choroid was finely diced into small squares (approximately 1 mm x 1 mm) with a razor blade. The resulting suspension was dissociated in 450 units/mL of collagenase II (Gibco, Grand Island NY) reconstituted in Hank’s Balanced Salt Solution containing calcium chloride and magnesium chloride (Life technologies, Grand Island NY). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Cryopreserved cells from single-cell donors 22-25 were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) into CD31+ and CD31-cell fractions. Sequencing of both CD31-positive and CD31-negative fractions was performed on pooled libraries using the Illumina NovaSeq platform (San Diego, CA).
Single-cell RNA-Seq

tag: region

value: macula

value: negative

tag: age

value: infant


title: Cumulus cells, 4h IVM, replicate 2

source_name: Bovine cumulus cells aftre 4h IVM, repl 2


title: donor_24_mac_CD31_neg


title: donor_24_mac_CD31_pos

value: positive


title: 12_SCtoLW_LW_male6

source_name: LW conditions, whole brain, replicate 6

treatment_protocol: Adult male medaka kept under SC conditions either reimained in SC or were transferred into LW conditions. Two weeks after transfer, whole brains were collected in the middle of the light phase.

tag: gender


title: Cumulus cells, replicate 2

description: Gene expression in cumulus cells, before IVM

source_name: Bovine cumulus cells, immature, repl 2


title: Cumulus cells, 4h IVM, replicate 1

source_name: Bovine cumulus cells aftre 4h IVM, repl 1


title: 01_LWtoSC_LW_male1

source_name: LW conditions, whole brain, replicate 1


title: 09_SCtoLW_LW_male3


title: 04_LWtoSC_LW_male4

source_name: LW conditions, whole brain, replicate 4


title: donor_23_mac_CD31_neg


title: 11_SCtoLW_LW_male5


title: Cumulus cells, replicate 1

source_name: Bovine cumulus cells, immature, repl 1


title: 08_LWtoSC_SC_male3

source_name: SC conditions, whole brain, replicate 3


title: 10_SCtoLW_LW_male4


title: Cumulus cells, replicate 4

source_name: Bovine cumulus cells, immature, repl 4


title: donor_25_mac_CD31_pos


title: Granulosa cells, replicate 4

description: Gene expression in granulosa cells

source_name: Bovine granulosa cells, repl 4

value: ovarian granulosa cells


title: 07_SCtoLW_LW_male1

value: male


title: Granulosa cells, replicate 2

description: Gene expression in granulosa cells

source_name: Bovine granulosa cells, repl 2


title: Cumulus cells, replicate 3

source_name: Bovine cumulus cells, immature, repl 3


title: Ileal Small Intestine enterocytes

city: Cambridge

first: Alex

last: Shalek

address: 45 Carleton Street

institute: MIT

description:
Pinch biopsies from human ileal tissue from 13 pediatric donors
Human_Ileum_absorptiveAndCryptentero_dge.csv

data_processing:
Reads aligned and pre-processed using CellRanger v 2.2.0
Normalization and variable gene selection was processed with SCTransform (https://github.com/ChristophH/sctransform). Clustering was processed using the Seurat R package v3.1.0 (https://github.com/satija.lab/seurat). Clusters were annotated based on the identification of highly expressed genes and cells identified as enterocytes were included in these matrices.
GRCh38
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: Ileal Small Intestine enterocytes

extract_protocol: Single-cell RNA capture, barcoding, and multiplexing according to the 10X 3' v2 sequencing

tag: cell type

value: Ileal Small Intestine enterocytes


title: donor_22_mac_CD31_neg

first: Andrew

last: Voigt

address: 375 Newton Road

value: adult


title: HeLa-Met-mRNA rep1

status: Public on Apr 22 2020

city: Hangzhou

first: Jie

last: Cao

address: Zheda Road 38

department: Department of Polymer Science and Engineering

institute: Zhejiang University

description:
processed data file: HeLa_counts.txt
processed data file: HeLa.DEseq2.results.xls

data_processing:
Adapter, low quality reads and short reads were trimmed with fastp v0.19.7 with following parameters: -f 10 -F 10 -x --detect_adapter_for_pe -l 25
Clean reads were aligned with hg38 genome using hisat2 v2.1.0 with parameters: --rna-strandness RF
Mutation was called by samtools mpileup v1.9 with parameters: -BQ 0 -d 10000000 -l HEK293T.allyl.peaks.bed
RNA-seq from HeLa cells were counted with featureCounts and analyzed with DESeq2 for differential gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files contain a6A and m6A peak regions in a6A/m6A-IP product relative to input samples in our method, Excel files contain mutations called from a6A-IP-cyclized samples using samtools and RNA differential gene analysis, txt file contains counts.

source_name: HeLa cells

growth_protocol: HEK293T and HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/high-glucose media (HyCloneSH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco 10270), 1% 100× Pen Strep (HyClone SV30010) at 37 °C with 5 % CO2.

extract_protocol:
Total RNA was extracted with Trizol Reagent (Invitrogen), mRNA was extracted with GenElute™ Direct mRNA Miniprep Kits (Sigma), IP and cyclized products were precipitated with isopropanol.
Libraries were constructed following Illumina's instructions except using HIV/RevertAid Reverse Transcriptase for reverse transcription in a6A-associated sequencing, Superscript II was used for m6A-seq of HEK293T cells and RNA-seq of HeLa cells.

treatment_protocol: HEK293T cells were starved in methionine deficient medium supplemented with 1 mM L-cysteine for 30min then treated with 1mM allyl-L-selenohomocysteine for 16h. For RNA-seq, HeLa cells were starved in methionine deficient medium supplemented with 1 mM L-cysteine for 30min then treated with 1mM normal methionine and allyl-L-selenohomocysteine for 16h, respectively.

tag: reverse transcriptase

value: SuperScript II

value: HeLa


title: HEK293T-cyclized a6A-IP mRNA

source_name: HEK293T cells

value: HIV


title: 08_SCtoLW_LW_male2

source_name: LW conditions, whole brain, replicate 2

value: whole brain


title: HeLa-Met-mRNA rep2


title: 05_SCtoLW_SC_male5

source_name: SC conditions, whole brain, replicate 5

value: SC (short-day and cool temperature conditions:10 h light/14 h dark


title: Theca cells, replicate 4

description: Gene expression in theca cells

source_name: Bovine theca cells, repl 4

value: ovarian theca cells

value: immature


title: 06_SCtoLW_SC_male6

source_name: SC conditions, whole brain, replicate 6


title: 03_SCtoLW_SC_male3


title: Granulosa cells, replicate 1

description: Gene expression in granulosa cells

source_name: Bovine granulosa cells, repl 1


title: HEK293T-m6A-IP mRNA


title: 04_SCtoLW_SC_male4

source_name: SC conditions, whole brain, replicate 4


title: Theca cells, replicate 2

description: Gene expression in theca cells

source_name: Bovine theca cells, repl 2


title: Granulosa cells, replicate 3

description: Gene expression in granulosa cells

source_name: Bovine granulosa cells, repl 3


title: HEK293T-m6A-input mRNA


title: HEK293T-a6A-IP mRNA

value: RevertAid Reverse Transcriptase


title: HEK293T-a6A-input mRNA


title: 02_SCtoLW_SC_male2

source_name: SC conditions, whole brain, replicate 2


title: HeLa-Allyl-mRNA rep2


title: 01_SCtoLW_SC_male1

source_name: SC conditions, whole brain, replicate 1


title: Theca cells, replicate 3

description: Gene expression in theca cells

source_name: Bovine theca cells, repl 3


title: Theca cells, replicate 1

description: Gene expression in theca cells

source_name: Bovine theca cells, repl 1


title: HeLa-Allyl-mRNA rep1


title: 293T.2.m6A.seal.ip.500ng

city: Los Angeles

first: Ye

last: Wang

state: California

address: 611 Charles E Young Dr E

department: Bioinformatics

institute: UCLA

description: No antibody(chemical assisted enrichment)

data_processing:
Library strategy: m6A-SEAL
Single-end and paired-end sequencing data were trimmed by single-end and paired-end model of cutadapt (v1.18) software respectively. Reads longer than 20 bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 (v2.1.0) software using the default parameter for single or pair-end model
Peakcalling were performed by macs2(v3.8), the enrichment fold threshold is 1, FDR threshold is 0.05.
Comparision of m6A sites from MeRIP-m6A-seq and m6A-SEAL are performed by intersectBed in BEDtools.
Peaks from input and IP samples in both MeRIP-m6A-seq and m6A-SEAL are converted to bigwig files by bamCoverage script in deepTools for visualization and analysis.
Genome_build: hg38

growth_protocol: HEK293T cell were cultured by DMEM medium(10% FBS) and 1% Penicillin Streptomycin in 15cm dish under 37℃, 5%CO2.   Rice were cultivated in a half-strength Kiruma B solution (pH 5.6, changed every two days.) at 28℃ and 80% relative humidity for 15 days.

extract_protocol:
Total RNA was first extracted from HEK293T cells or rice tissue by Trizol reagent, The polyA RNA was then purified with oligo d(T)25 magnetic beads
PolyA RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module. A portion of fragmented RNA was reserved as m6A input sample.For MeRIP-m6A-seq,  the left RNA was incubated with anti-m6A antibody and then eluted to get the m6A IP sample. For m6A-SEAL, the left RNA was enzymatically oxidized by FTO and then conjugated with biotin by dithiothreitol under acidic aqueous solution. The biotinylated RNA are enriched by streptavidin beads and then eluted by dithiothreitol to get m6A IP sample. Both input and m6A IP samples were prepared for next-generation sequencing library by standard protocol of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.
m6A-SEAL and MeRIP-m6A-seq. Library was sequenced in PE150 model on Illumina X-Ten platform or in SR75 model on Illumina NextSeq 500 platform.

tag: cell line

value: HEK293T cells


title: 293T.2.m6A.seal.input


title: 293T.1.m6A.seal.input.500ng


title: 293T.1.m6A.seal.input


title: 293T.1.m6A.seal.ip.500ng


title: 293T.2.m6A.seal.ip


title: Case1_paracancerous

city: Nantong

first: Liang

last: Han

state: Jiangsu

address: 30.tongyang road

department: 1Department of Head and Neck Surgery

institute: Nantong Tumor Hospital

description: All.counts.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: paracancerous of tongue cancer

extract_protocol:
Total RNA was extracted from tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: paracancerous of tongue cancer

tag: tumor stage

tag: differentiation

value: well-differentiated

tag: type

value: ulcerative infiltrating


title: Case4_cancer

description: All.counts.txt

source_name: cancer tissue of tongue cancer

value: cancer tissue of tongue cancer


title: Case3_cancer

description: All.counts.txt

value: moderately differentiated


title: Case2_paracancerous

description: All.counts.txt

value: exogenous


title: Case4_paracancerous

description: All.counts.txt


title: 293T.1.m6A.seal.ip


title: Case1_cancer

description: All.counts.txt


title: MS male inject dCA3 mouse 99

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

data_processing:
After sequencing with the MiSeq Sequencer (V3 chemistry for 150 cycles), sequencing quality was analyzed with FastQC. Low-quality reads with phred scores lower than 20 or a length smaller than 25 bp were removed using PRINSEQ (PReprocessing and INformation of SEQuence data) lite Version 0.20.4. Subsequently, the reads were aligned with Burrows-Wheeler Aligner (BWA) Version 0.7.12 with default settings (allowing a maximum of three mismatches) and the manifest file provided by Illumina as reference. Gene expression quantification was inferred from the alignment. Genes with low overall coverage, i.e. <2000 reads across all samples, were excluded from further analysis (n = 5). The data were then normalized using DESeq2. Finally, surrogate variable analysis (SVA) from the R/Bioconductor package sva was applied to identify hidden technical batches.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including expression values for each sample.

extract_protocol:
Frozen micropunches were lysed quickly in 500 µl Trizol (QIAzol) reagent and homogenized by repeated passing through an insulin syringe (29G). Subsequently, samples were kept at room temperature for at least 3 min before adding 100 µl chloroform. The remaining steps were conducted according to the miRNeasy Mini Kit (Qiagen, Hilden, Germany) protocol. Elution was performed with 30 µl RNAse-free water with a second round using the eluate from the first round.
TruSeq Targeted RNA sequencing (Illumina, San Diego, USA) was carried out according to the manufacturer’s protocol.

tag: strain

value: Male Balb/c mice

value: post natal day 9

tag: animal

tag: status

tag: injection


title: MS male inject PVN mouse 99

source_name: PVN

value: PVN


title: MS male inject vCA3 mouse 99


title: MS male inject PFC mouse 99

source_name: PFC

value: PFC


title: MS male inject vCA1 mouse 99


title: MS male inject CER mouse 99

source_name: CER

value: CER


title: MS male inject BNST mouse 99

source_name: BNST

value: BNST


title: MS male inject vDG mouse 99

source_name: vDG

value: vDG


title: MS male inject AMY mouse 99

source_name: AMY

value: AMY


title: MS male inject vDG mouse 97


title: MS male inject vCA1 mouse 97


title: MS male inject vCA3 mouse 97


title: MS male inject Pit mouse 97

source_name: Pit

value: Pit


title: MS male inject PFC mouse 97


title: Case3_paracancerous

description: All.counts.txt


title: MS male inject dDG mouse 97

source_name: dDG

value: dDG


title: Case2_cancer

description: All.counts.txt


title: MS male inject Pit mouse 99


title: MS male inject PVN mouse 97


title: MS male inject CER mouse 97


title: MS male inject AMY mouse 97


title: MS male inject dDG mouse 99


title: MS male inject BNST mouse 97


title: MS male inject vCA3 mouse 95


title: MS male inject dCA1 mouse 97


title: MS male inject vDG mouse 95


title: MS male inject dCA3 mouse 97


title: MS male inject dDG mouse 95


title: MS male inject CER mouse 95


title: MS male inject Pit mouse 95


title: MS male inject PFC mouse 95


title: MS male inject dCA1 mouse 95


title: MS male inject PVN mouse 95

description: sample has no processed data


title: MS male inject dCA3 mouse 95


title: MS male inject dCA1 mouse 99


title: MS male inject AMY mouse 95


title: MS male inject BNST mouse 95


title: MS male inject vDG mouse 93


title: MS male inject vCA1 mouse 93


title: MS male inject vCA3 mouse 93


title: MS male inject Pit mouse 93


title: MS male inject PVN mouse 93


title: MS male inject dDG mouse 93


title: MS male inject PFC mouse 93


title: MS male inject dCA3 mouse 93


title: MS male inject dCA1 mouse 93


title: MS male inject CER mouse 93


title: MS male naive PVN mouse 91


title: MS male naive vDG mouse 91


title: MS male inject vCA1 mouse 95


title: MS male inject BNST mouse 93


title: MS male inject AMY mouse 93


title: MS male naive vCA3 mouse 91


title: MS male naive Pit mouse 91


title: MS male naive dCA3 mouse 91


title: MS male naive PFC mouse 91


title: MS male naive dDG mouse 91


title: MS male naive AMY mouse 91


title: MS male naive CER mouse 91


title: MS male naive vDG mouse 89


title: MS male naive BNST mouse 91


title: MS male naive vCA3 mouse 89


title: MS male naive vCA1 mouse 89


title: MS male naive Pit mouse 89


title: MS male naive dCA3 mouse 89


title: MS male naive vCA1 mouse 91


title: MS male naive PVN mouse 89


title: MS male naive dCA1 mouse 89


title: MS male naive PFC mouse 89


title: MS male naive CER mouse 89


title: MS male naive dDG mouse 89


title: MS male naive BNST mouse 89


title: Cumulus cells, 4h IVM, replicate 4

source_name: Bovine cumulus cells aftre 4h IVM, repl 4

value: ovarian cumulus cells

value: 4h in vitro maturation


title: MS male naive vDG mouse 87


title: MS male naive PVN mouse 87


title: MS male naive vCA3 mouse 87


title: MS male naive vCA1 mouse 87


title: MS male naive PFC mouse 87


title: MS male naive Pit mouse 87


title: MS male naive dCA1 mouse 91


title: MS male naive dCA1 mouse 87


title: MS male naive CER mouse 87


title: MS male inject vCA3 mouse 85


title: MS male naive BNST mouse 87


title: MS male inject vCA1 mouse 85


title: MS male naive AMY mouse 87


title: MS male inject vDG mouse 85


title: MS male inject PVN mouse 85


title: MS male inject PFC mouse 85


title: MS male inject Pit mouse 85


title: MS male naive AMY mouse 89


title: MS male inject dDG mouse 85


title: MS male inject dCA1 mouse 85


title: MS male naive dDG mouse 87


title: MS male inject vCA3 mouse 83


title: MS male inject AMY mouse 85


title: MS male inject vDG mouse 83


title: MS male inject BNST mouse 85


title: MS male inject dCA3 mouse 85


title: MS male inject Pit mouse 83


title: MS male naive dCA3 mouse 87


title: MS male inject dDG mouse 83


title: MS male inject CER mouse 85


title: MS male inject dCA3 mouse 83


title: MS male inject PFC mouse 83


title: MS male inject dCA1 mouse 83


title: MS male inject CER mouse 83


title: MS male inject vCA1 mouse 83


title: MS male inject BNST mouse 83


title: MS male inject vDG mouse 81


title: MS male inject vCA3 mouse 81


title: MS male inject PVN mouse 81


title: MS male inject PFC mouse 81


title: MS male inject vCA1 mouse 81


title: MS male inject Pit mouse 81


title: MS male inject dDG mouse 81


title: MS male inject dCA3 mouse 81


title: MS male inject CER mouse 81


title: MS male inject dCA1 mouse 81


title: MS male inject BNST mouse 81


title: MS male inject PVN mouse 83


title: MS male inject AMY mouse 81


title: MS male inject vCA3 mouse 79


title: MS male inject vDG mouse 79


title: MS male inject PFC mouse 79


title: MS male inject Pit mouse 79


title: MS male inject dCA1 mouse 79


title: MS male inject PVN mouse 79


title: Co male inject vDG mouse 267


title: MS male inject dDG mouse 79


title: MS male inject vCA1 mouse 79


title: MS male inject dCA3 mouse 79


title: MS male inject AMY mouse 83