title: control-2w rep3

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M2w-C3


title: radiation-1d rep3

status: Public on Jun 10 2022

type: SRA

city: Guangzhou

first: Yanmei

last: Cui

address: Yuancun erheng Road

country: China

institute: Sun Yat-sen University

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M1d-R3

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts and fpkms for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: rectal tissue

extract_protocol:
Total RNA from the rectal tissues of mice in both irradiated and control group at 4 hours, 1 day, 3 days, 2 weeks and 8 weeks post-irradiation was extracted using Trizol reagent (Invitrogen, Carlsbad, CA). The mRNA was isolated by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, E7490).
The cDNA library was constructed following the manufacturer’s instructions of NEBNext Ultra RNA Library Prep Kit for Illumina（NEB, E7530）and NEBNext Multiplex Oligos for Illumina（NEB, E7500).

tag: strain

tag: tissue

value: rectal tissue

tag: treatment

value: 25Gy rectal radiation

tag: time


title: control-2w rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M2w-C2

value: sham-radiation


title: radiation-1d rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M1d-R2


title: radiation-4h rep3

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M4h-R3


title: control-4h rep3

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M4h-C3


title: control-3d rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M3d-C1


title: radiation-4h rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M4h-R1


title: NTC_rep1

first: Xiuling

last: Song

address: 1038 Shatai South Road

institute: Southern Medical University

data_processing:
The total reads were quality- and adapter-trimmed using bbduk and trimmomatic
The mouse transcriptome index was generated using the reference genome mm10 with Ensembl version 95 and the clean reads were aligned to mm10 transcriptome using RSEM integrated bowtie2.
Gene counts were calculated using RSEM
To ensure data quality, the low expressed genes which counts did not >=50 in at least two samples were discarded before downstream analysis.
R-Bioconductor package DESeq2 was used to normalized count data and calculated differentially expressed genes across different groups
Genome_build: mm10
Supplementary_files_format_and_content: text file

source_name: mouse spermatogonial stem cell line

growth_protocol: Spermaotogonial stem cells were inoculated in a culture dish with mitomycin C treated MEF as feeder cell. For the culture basic medium, StemPro-34 SFM (Invitrogen) with its supplement with 1% FBS, 0.1 mM NEAA, 1 mM sodium pyruvate, 2 mM GlutaMAX , 100 U/mL penicillin, 0.1 mg/mL streptomycin, 50 μM β-mercaptoethanol, 1 μL/mL DL-lactic acid, 1 × minimal essential medium (MEM) Vitamin Solution , 10 μg/mL biotin, 100 μM ascorbic acid, 60 ng/mL progesterone, 30 ng/mL β-estradiol, 6 mg/mL Glucose, 5 mg/mL Bovine Serum Albumin (BSA) and 1% N2 supplement. PTC group medium contain 10 ng/mL recombinant rat GDNF (R&D Systems, 512-GF), 10 ng/mL recombinant mouse EGF (R&D Systems, 2028-EG), 5000 U recombinant mouse LIF (Millipore, ESG1107) and 10 ng/mL recombinant mouse FGF2(R&D Systems, 3139-FB).  Change culture medium every other day and passage by 1:3-5 per week.

extract_protocol:
SSC samples were collected after 18 days cultured in different treatment.
Total RNA isolation and cDNA libraries generation were performed according to the manufacturer’s instructions of NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L). After purification of amplified cDNA products, the NGS libraries were prepared with the following procedures including end repair, adaptor ligation, size selection, PCR amplification, library purification and quality control. The constructed NGS libraries were sequenced with Illumina Hiseq XTEN platform at Novogene and sequencing strategy was paired-end 150 bp (PE150).

treatment_protocol: The difference between NTC and PTC group medium is the lack of GDNF. And LOVA group medium replace GDNF with 5 μM Lovastatin .

tag: cell type

value: mouse spermatogonial stem cells (mSSCs)

value: cultured in the medium without GDNF supplementary

tag: day of treatment

value: 18 days


title: yZSJ025-HiC-rep2

city: Tianjin

first: Zhou

last: Sijie

address: No.135 Yaguan road

institute: Tianjin Unversity

library_source: genomic

data_processing:
Sequencing was carried out using a 2×150 paired-end (PE) configuration; image analysis and base calling were conducted by the NovaSeq Control Software (HCS) + RTA 2.7 (Illumina) on the NovaSeq instrument
Call peaks on replicates, self-pseudoreplicates using MACS2 (3) (--nomodel --extsize 200 --shift -100)
HiC matrix was generated using HiC-Pro
HiC quality filtering using Trimmomatic (version 0.38)
The chromosomal 3D structure of the strain was inferred using the Pastis (v0.1) method. with a multidimensional scaling (MDS) model
Genome_build: yZSJ025.fa
Supplementary_files_format_and_content: *.treat_pileup.bware BigWig files containing the normalized ATAC signal；Saccharomyces_cerevisiae-all-MboI-10k_ICed.hm：A genome-wide corrected interaction matrix file of the sample at 10kb

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: ATAC-seq, Hi-C:Cells were grown to mid-log phase in YPD

extract_protocol:
ATAC-seq: 1,000,000 yeast cells were washed with 1mL RSB buffer (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) once and incubated for 60 min at 37 ℃ using zymolyase to digest cell walls (0.015 g/mL, Solarbio). Then the cell was resuspended in 1 mL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40, 0.1% Digitonin, 0.1% Tween-20, 1xProtease inhibitor) for 10 min at 4°C to lyse the yeast cell membrane to obtain the nucleus. Hi-C: Hi-C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocol(Rao et al., 2014). The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 150 bp high-throughput sequencing using illumina Nova-seq PE150 platform.
ATAC-seq: Immediately following the nuclei prep, the pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was carried out for 30 min at 37 °C. Tn5 transposed DNA were purified by AMPure DNA magnetic beads. A qPCR reaction was performed on a subset of the DNA to determine the optimum number of PCR cycles. The amplified libraries were run on an Agilent Tapestation 2100 (Agilent Technologies) to detect size distribution of library fragments. Biological replicates were performed in duplicate for all ATAC experiments. Hi-C: Restriction fragment ends were labeled with biotinylated cytosine nucleotides by biotin-14-dCTP (TriLINK) followed by ligation. Purified DNA was sheared to a length of ~400 bp. Point ligation junctions were pulled down with Dynabeads MyOne Streptavidin C1 (Thermofisher). The Hi-C library for Illumina sequencing was prepped by NEBNext Ultra II DNA library Prep Kit for Illumina (NEB) according to the manufacturers’ instructions. Fragments between 400 and 600 bp were paired-end sequenced on an illumina Nova-seq PE150 platform.

tag: disease state

tag: genotype

value: six synthetic chromosomes


title: radiation-1d rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M1d-R1


title: NTC_rep2


title: control-4h rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M4h-C2


title: radiation-3d rep3

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M3d-R3


title: control-3d rep3

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M3d-C3


title: LOVA_rep1

value: cultured in the medium with GDNF replaced by Lovastatin


title: control-3d rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M3d-C2


title: yZSJ025-ATACseq-rep1


title: yZSJ025-ATACseq-rep2


title: yZSJ025-HiC-rep1


title: LM3-CON_rep1

type: RNA

city: Wuhan

first: Xuewu

last: Zhang

address: Tongji Hospital, Jiefang Avenue

institute: Huazhong University of Science and Technology

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray (G2534A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

organism: Homo sapiens

source_name: LM3-CON control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low Input Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Stable cell lines were established by lentivirus-mediated transduction and puromycin selection. Cells were plated and cultured for  48 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the QIAGEN RNeasy Mini Kit following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatment

tag: cell line

value: hepatocellular carcinoma (HCC) cell line

tag: genotype/variation

value: control


title: PTC_rep2

value: cultured in the medium containing GDNF


title: radiation-4h rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M4h-R2


title: Old Microglia 4, AB42- [DH16b]

city: Cincinnati

first: Alyssa

last: Thomas

state: Ohio

address: 250 Albert Sabin Way

department: Immunobiology

country: USA

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequences were trimmed for adapter sequences/bad quality segments using FastQC v0.11.5, Trim Galore! v0.4.2, and cutadapt v1.9.1
Trimmed sequence reads were aligned to the reference mouse genome version mm10 with the program STAR v2.5.2a
Aligned reads were stripped of duplicate reads with picard tools v1.89
Read counting was done with Counts v1.6.2 from the Rsubread package
Raw counts were normalized as transcripts per million
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalizaed raw counts as transcripts per million for each sample

molecule: polyA RNA

source_name: microglia

extract_protocol:
RNA was harvested using Invitrogen's mirVana miRNA Isolation Kit
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep kit

treatment_protocol: Microglia were incubated in vitro with 2.5uM of amyloid-beta 1-42 for 2 hours

value: microglia

tag: age

value: Old

value: WT


title: 5 days HFHS diet, scRNAseq

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For the alignment of reads we used the sequences and annotation files for the Mouse genome (GRCm38) from Ensembl (release 100). The Cell Ranger software (from 10X Genomics, Pleasanton, CA, version 3.1.0) run with the command ‘cellranger mkref’ created an index of the genome. The Cell Ranger pipeline run with the command ‘cellranger count’ aligned the reads, generated QC metrics, estimated the number of valid barcodes and created the count matrices. The command was executed with standard parameters, except that we adjusted the number of expected cells and the chemistry parameter accordingly. AnnData objects of the raw and filtered count matrices were created using the Python package Scanpy, version 1.4.4). The alignment files (bam) were sorted by barcode using samtools ([2], version 1.10) and Velocyto ([3], version 0.17.17) was run using the ‘velocyto run’ command with the filtered barcodes list from the Cell Ranger run.
Assembly: GRCm38
Supplementary files format and content: Filtered feature barcode matrix

source_name: Brain, Arcuate nucleus of the hypothalamus (ARC)

growth_protocol: Mice were housed in groups under a 12-h light/12-h dark cycle at 22 +/- 2°C. All animals had free access to water and food.

extract_protocol:
ARCs were freshly collected by micropunching (1 mm diameter puncher on 1 mm thick brain section) into cold DMEM/F12 medium (Thermo Fisher Scientific Inc.; #11320033). The samples derived from 6 mice of the same experimental group were pooled together and washed once with cold D-PBS containing 0.05 g/ml of Trehalose (Sigma-Aldrich; #T0167). The buffer was then discarded and the samples incubated for 16 min at 37°C with 200 µl of 4 mg/ml collagenase/dispase solution (Sigma-Aldrich; #10269638001) supplemented with 0.05 g/ml of Trehalose. After the incubation period, the enzymatic solution was carefully removed and the tissue was incubated for 12 min at 37°C with 200 µl of papain/DNAse solution (prepared following steps 2 and 3 from the kit’s catalogue; Worthington Biochemical Corporation; #LK003150) supplemented with 0.05 g/ml of Trehalose. The enzymatic solution was then delicately removed and the tissue resuspended in 200 µl of D-PBS supplemented with 0.05 g/ml of Trehalose and RNAseOUT (1/1000; Thermo Fisher Scientific Inc.; #10-777-019), and gently tritured until the solution appeared milky and devoid of visible tissue pieces. The resulting cell suspension was filtered through a 40 µm cell strainer, and cells were pelleted by centrifugation for 8 min at 300 x g and 4°C in 40 ml of D-PBS containing 2% bovine serum albumin (BSA) (Miltenyi BioTec; #130-091-376). Cells were then washed one time by centrifugation (300 x g, 10 min, 4°C) in D-PBS containing 0.04% BSA, and resuspended in 40 µl of the same fresh solution. The final number and viability of the cells was assessed with a hemocytometer after staining with trypan blue. The final volume was adjusted to obtain a concentration of 1000 cells/µl.
Chromium Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics, #PN-1000121) was used to prepare libraries, according to the manufacturer’s instructions. Libraries were pooled and sequenced according to 10x Genomics’ recommendations on an Illumina NovaSeq6000 system with a target read depth of 50000 reads/cell.

treatment_protocol: At the weaning time, one group of mice was fed with SC diet (SC diet- control) for 15 days, the second group was fed with SC diet for 10 days, and switched successively to HFHS diet for 5 days (5d HFHS diet), and the third group received a HFHS diet for 15 days (15d HFHS diet).

value: Astrocytes, endothelial cells, ependymal cells, microglia, mural cells, neurons, oligodendrocytes, tanycytes, vascular leptomeningeal cells (VLMCs)

value: 5-6 weeks old

tag: Sex

value: male

tag: diet

value: High-fat high-sugar (HFHS) diet

value: 5 days


title: 15 days HFHS diet, scRNAseq

description: 10x Genomics

value: Brain, Arcuate nucleus of the hypothalamus (ARC)

value: 15 days


title: Old Microglia 4, AB42+ [DH15b]

value: 2.5uM of amyloid-beta 1-42 for 2 hrs


title: Old Microglia 3, AB42- [DH12b]


title: Old Microglia 2, AB42- [DH8b]


title: Old Microglia 2, AB42+ [DH7b]


title: SC diet, scRNAseq

description: 10x Genomics

value: Standard chow (SC) diet


title: Old Microglia 1, AB42- [DH4b]


title: Young Microglia 2, AB42- [DH6b]

value: Young


title: Young Microglia 3, AB42- [DH10b]


title: Young Microglia 4, AB42- [DH14b]


title: PTC_rep1

value: mouse spermatogonial stem cells (mSSCs)

value: 18 days


title: Young Microglia 3, AB42+ [DH9b]


title: Old Microglia 3, AB42+ [DH11b]


title: Nupr1, replicate 1, scRNAseq

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

institute: Xuanwu Hospital, Capital Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 5.0.1
Assembly: mm10
Supplementary files format and content: Processed data files included counts info for each replicate in csv format

source_name: caudal half

extract_protocol:
Cells from each E10 control and cKo caudal half were resuspended in 50 µL FACS-buffer (1× PBS with 1 % BSA). Sorting antibodies were prepared and added to the cell suspension, and incubated for 30 min at 4 °C. After washing, each oligo barcoded streptavidin with titrated dosage (0.125 μL for 1 million cells) were incubated with the stained cells for 20 min at 4 °C. After 3 washes, 10nmol/L Biotin was added to bind redundant streptavidin in the cell suspension, and incubated for about 5min at 4 °C. After 2 washes in 0.1 % BSA/PBS, staining with 7-AAD was performed for 5 min. Cells were sorted with gating strategy shown in Fig. 4B on BD FACS Aria II and harvested in 200 μL PCR tube. Cells from each tissue were pooled into one 1.5 mL centrifuge tube. Cells were collected at 400× g at 4 °C for 5 min, resuspend in 50 μL 0.04 % BSA/PBS to load into one lane of a 10× Chromium V3 chip.
The cDNA preparation was performed following the instruction manual, and the hashtag library was prepared following the BioLegend TotalSeq-B guide. The final cDNA library and tag library were both sequenced on NovaSeq 6000. Cells were sequenced to an average depth of 0.1 M per cell for cDNA and 0.01 M per cell for hashtags.

value: caudal half

value: WT and Nupr1 cKO


title: control-4h rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M4h-C1

value: rectal tissue

value: sham-radiation


title: Nupr1, replicate 2, scRNAseq

description: 10x Genomics


title: Young Microglia 1, AB42- [DH2b]

value: microglia

value: WT


title: LOVA_rep2

value: cultured in the medium with GDNF replaced by Lovastatin


title: Young Microglia 4, AB42+ [DH13b]


title: Young Microglia 2, AB42+ [DH5b]


title: C2C12, Lenti-dCas9-KRAB-En5, contr_rep1

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
We used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Sequence reads were aligned to the mouse reference genome (GRCm38/mm10) by HISAT2 (v2.2.1).
Sequence reads were quantified by featureCounts from Rsubread package (v2.8.1).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include count and TPM values for each Sample.

source_name: Muscle

growth_protocol: C2C12 mouse myoblast cells were maintained in DMEM (Gibco, USA) supplemented with 10% FBS (Gibco, USA) and 1% penicillin-streptomycin (Gibco, USA) at 37℃ under 5% CO2. The cells were confirmed without mycoplasma contamination using a PCR mycoplasma detection kit (TransGen, China). To induce differentiation, we cultured C2C12 cells in the differentiation medium consisting of 2% horse serum (HyClone, USA) when grown to 50–60% confluence. The differentiation medium was changed every 48h. Differentiated C2C12 cells are treated until day 5.

extract_protocol:
RNA was harvested using using HiPure Total RNA Mini Kit (Magen). 2 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse.

treatment_protocol: For transduction, C2C12 cells were seeded in a 12-well plate. When confluence reaches about 50%, the cells were infected with 1 mL lentiviruses medium containing dCas9-KRAB-sgRNA or dCas9-KRAB at multiplicity of infection (MOI) of 100. Cells that did not receive any treatment as a control. The day after transduction 24 hours, the medium was exchanged to remove the virus. At 48 hours post-infection, 2 µg/mL puromycin was used to select transduced cells. C2C12 cells were kept at ∼30% confluence during antibiotic selection. Untreated C2C12 and C2C12 stably expressing dCas9-KRAB-sgRNA or dCas9-KRAB were induced to differentiation with the differentiation medium consisting of 2% horse serum for 5 days.

value: Muscle

value: Myoblasts

value: Lentiviral transduction of the dCas9-KRAB-En5 system

tag: time point

value: myogenic differentiation day 5


title: C2C12, Lenti-dCas9-KRAB-En5, contr_rep2


title: Young Microglia 1, AB42+ [DH1b]


title: C2C12, Lenti-dCas9-KRAB, contr_rep3

value: Lentiviral transduction of the dCas9-KRAB system


title: Input-ChIP-biological replicate 1

city: shanghai

first: Yu

address: DongChuan Road No. 800

institute: Shanghai Jiaotong University

data_processing:
Low-quality and adapter sequences were trimmed from the reads using cutadapt (v1.18) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20, 20.
Then, the reads were mapped to the Arabidopsis thaliana TAIR10 genome using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal.
Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8).
Bam files were then converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalize using RPKM --binSize 25.
Assembly: TAIR10
Supplementary files format and content: bigWig(bigWig is the binary version of WIG or bedGraph. BigWig stores interval axis information. And correlation score (SCORE), mainly used to view continuous density maps of data in the Genome Browser)

organism: Arabidopsis thaliana

source_name: the 7-day-old whole seedlings

growth_protocol: Plants were grown at 21℃ on MS agar plates supplemented with 1.5% sucrose and 0.8% agar.

extract_protocol:
Briefly, 10 g fresh 7-day-old whole seedlings were cross-linked in the cross-link buffer (0.4 M sucrose, 10m M Tris-HCl (pH8.0), 1m M PMSF, 1 m M EDTA, 1% formaldehyde) for 3×5min using vacuum infiltration and the reaction was terminated in 2 M glycine.
After reverse cross-link, DNA was extracted by phenol-chloroform method and sheared to an average size of 300 bp using a sonicator.Sequencing library was constructed according to the standard Illumina protocol.First,the end was supplemented, adenine was added in the 3 'segment, and then PCR amplification technology was used to build the library.

value: the 7-day-old whole seedlings

tag: chip antibody


title: C2C12, Lenti-dCas9-KRAB, contr_rep2


title: C2C12, Lenti-dCas9-KRAB, contr_rep1


title: OQY-12-14

first: Chuyao

last: Wang

address: The Ninth People's Hospital, No. 639, Zhizaoju Road, Huangpu District, Shanghai

institute: shanghai ninth people hospital

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
OQY-12-14

data_processing:
Briefly, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer.
Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2).
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs.
The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Differentially expressed miRNAs between two samples were filtered through Fold change. Ddifferentially expressed miRNA between two groups were filtered by Fold Change and P-value.
Assembly: hg19
Supplementary files format and content: excel format
Supplementary files format and content: miRNA expression

extract_protocol:
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs).
The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina HiSeq sequencer following the manufacturer's instructions.

value: synovium

tag: organ

value: temporomandibular joint


title: XXF-12-14

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
XXF-12-14

source_name: Synovium,reducible anterior disc displacement,rep5


title: Old Microglia 1, AB42+ [DH3b]

value: Old

value: 2.5uM of amyloid-beta 1-42 for 2 hrs


title: LKK-11-18

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
LKK-11-18


title: CWH-11-18

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
CWH-11-18


title: C2C12, Lenti-dCas9-KRAB-En5, contr_rep3


title: HYX-11-23

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
HYX-11-23

source_name: Synovium,reducible anterior disc displacement,rep4


title: M-TC-LPS rep2

city: qingdao

first: qiaoling

last: song

address: Xiang Gang East Road NO.23

institute: Ocean University of China

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: Ensembl_release98
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: BMDM

growth_protocol: Bone marrow were isolated and routinely generated by 7-day GM-CSF or M-CSF treatment.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China)

treatment_protocol: GM-BMDMs or M-BMDMs were treated with LPS for 3 h.

value: bone marrow

value: 8 weeks

tag: agent

value: M-TC-LPS


title: ZXR-12-07

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
ZXR-12-07


title: M-TC-LPS rep1

tag: strain


title: SYL-12-07

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
SYL-12-07

source_name: Synovium,reducible anterior disc displacement,rep2

tag: tissue


title: M-TC rep2

value: M-TC


title: FJY-11-21

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
FJY-11-21

source_name: Synovium,reducible anterior disc displacement,rep1


title: SQ-12-14-Y

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
SQ-12-14-Y


title: M-TC rep1


title: SH_VMT2_02132019

city: Irvine

first: Stephanie

middle: Jeanelle

last: Hachey

state: CA

address: 2400 Biological Sciences III

institute: UC Irvine

description: 10x Genomics

data_processing:
After demultiplexing sequencing libraries to individual library FASTQ files, each library was aligned to an indexed GRCh38 reference genome using Cell Ranger (10X Genomics) Count 2.2.0. Aligned libraries are then normalized based on median reads per cell using Cell Ranger Aggr 2.2.0. Raw gene expression matrices were loaded into R (version 3.6.0) and converted to a Seurat object using the Seurat R package (version 2.3.4). From this, the data were log-transformed and corrected for unwanted sources of variation using the ScaleData function in Seurat. Gene expression matrices were then normalized to total cellular read count and to mitochondrial read count using linear regression as implemented in Seurat's RegressOut function. For quality control filtering, we excluded cells with less than 200 or more than 5000 genes detected, and over 15% UMIs (unique molecular identifiers) derived from mitochondrial genome. In addition, genes that were not detected in at least 3 cells after this trimming were also removed from further analysis.
Assembly: hg19/GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: SW480 CRC cells, NHLF, and EPC grown together in the VMT and harvested for scRNAseq (VMT = vascularized microtumor, 2 = biological replicate 2)

extract_protocol:
The PDMS membrane was carefully removed from the bottom of the platform to expose the VMT tissue chambers. Chambers were washed with HBSS before adding TrypLE express enzyme drop wise to each VMT unit and incubated at 37 °C for 5 minutes to loosen the extra-cellular matrix from the device. Chambers were flushed with a pipette to collect cells into a conical tube and washed once with EGM2 medium to stop the digestion reaction. Next, cells were subjected to centrifugation (340×g for 3 min) and briefly resuspended in an HBSS/collagenase type III solution (1 mg mL−1) to fully digest the matrix. Finally, the single cell suspension was washed with EGM2 and put through a 70 μm filter. Cells were processed for sorting within an hour and kept on ice. Sorting was performed on the BD flow assisted cell sorting (FACS) AriaII with BD FACS Diva software version 8.0.1. Samples were sorted using a 100 μm nozzle at 20 psi with a gating strategy to select for live cells. Flow cytometry sorted cells were washed in PBS with 0.04% BSA and re-suspended at a concentration of ∼1000 cell per μL. Cellular suspensions were loaded onto a Chromium Single Cell Instrument (10X Genomics) to generate single-cell gel beads in emulsion (GEMs).
Library construction was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). GEMs were processed to generate cDNA libraries by using 10X Genomics v2 chemistry according to the Chromium Single Cell 3' Reagents kits v2 user guide: CG00052 Rev B. Quantification of cDNA libraries was performed using Qubit dsDNA HS Assay kit (Life Technologies Q32851), high-sensitivity DNA chips (Agilent 5067-4626) and KAPA qPCR (Kapa Biosystems KK4824). Libraries were sequenced on an Illumina HiSeq4000 to achieve an average of 50 000 reads per cell.

value: HCT116 CRC cells, NHLF, and EPC

tag: growth condition

value: grown together in the VMT model


title: SH_S2_02132019

description: 10x Genomics

source_name: SW480 CRC cells grown as spheroids and harvested for scRNAseq (s = spheroid, 2 = biological replicate 2)

value: SW480 CRC cells

value: grown as spheroids


title: SH_VMT1_02132019

description: 10x Genomics

source_name: SW480 CRC cells, NHLF, and EPC grown together in the VMT and harvested for scRNAseq (VMT = vascularized microtumor, 1 = biological replicate 1)


title: SH_S1_02132019

description: 10x Genomics

source_name: SW480 CRC cells grown as spheroids and harvested for scRNAseq (s = spheroid, 1 = biological replicate 1)


title: M-noTC-LPS rep1

value: M-noTC-LPS


title: Input-ChIP-biological replicate 2


title: sh_hts_09192018

description: 10x Genomics

source_name: HCT116 CRC cells, NHLF, and EPC grown together in the VMT model, harvested and subjected to scRNAseq (hts = high throughput system)


title: SH_M1_02132019

description: 10x Genomics

source_name: SW480 CRC cells, NHLF, and EPC grown separately as monolayer cultures, harvested and combined for scRNAseq (m = monolayer, 1 = biological replicate 1)

value: grown separately as monolayer cultures


title: SH_M2_02132019

description: 10x Genomics

source_name: SW480 CRC cells, NHLF, and EPC grown separately as monolayer cultures, harvested and combined for scRNAseq (m = monolayer, 2 = biological replicate 2)


title: sh_f_09192018

description: 10x Genomics

source_name: HCT116 CRC cells, NHLF, and EPC grown separately as monolayer cultures, harvested and combined for scRNAseq (f = flask)


title: M-noTC rep1

value: M-noTC


title: GM-TC-LPS rep2

value: GM-TC-LPS


title: CLF-11-18

description:
miRNA_Expression.xlsx : Tag Counts of miRNAs in ten specimens
CLF-11-18

source_name: Synovium,reducible anterior disc displacement,rep3


title: GM-TC-LPS rep1


title: DBF4 patient

city: Cambridge

first: Adrian

last: Liston

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

data_processing:
Step1:  BCL to FASTQ file converter: bcl2fastq v2.20.0.422
Step2: cellranger count (Cell Ranger V.3.1, 10x Genomics)
Step 3: Quality control in each sample (keeping genes expressed in ≥5 cells, cells with gene count ≥200 and filtering out ribosomal genes, RPL and RPS). Further quality control (keeping cells with UMI counts≥500, gene counts<3000 and mitochondrial genes<15%) after merging all samples into one object using Seurat V3.1.5.
Genome_build: Human reference (GRCh38)
Supplementary_files_format_and_content: A matrix of UMI counts for each feature (i.e. gene; row) that are detected in each cell (column)  in each sample

source_name: Bone marrow

growth_protocol: Not applicable

extract_protocol:
RBC depletion using EasySep™ RBC Depletion Reagent (StemCell Technologies)
Single cell RNAseq libraries were generated using a commercial droplet platform (Chromium system; 10X Genomics). Briefly, the EasySep™ RBC Depletion Reagent (StemCell Technologies) was used to deplete erythrocytes from whole bone marrow samples collected in heparinised tubes according to manufacturer’s instructions. The cell count and the viability of the bone marrow cells were assessed using LUNA dual florescence cell counter (Logos Biosystems) and as per the 10X recommendations (Single cell 3’ reagent kits v2 user guide; CG00052 Rev B), we aimed at a target recovery of 6000 cells for all the samples. Post cell count and QC, the samples were immediately loaded individually onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturers recommendations, and at the different check points the library quality was assessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). With a sequencing coverage target of 50,000 reads per cell, single cell libraries were sequenced on Illumina HiSeq4000 platform using paired-end sequencing workflow and with recommended 10X; v3 read parameters (28-8-0-91 cycles).

treatment_protocol: Collection of whole bone marrow aspirate in heparanized tubes

tag: subject

value: patient


title: 8232_BZ_CTL-P28

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing, and gene counting were performed with Cell Ranger Single-Cell Software v.3.10 (https://support.10xgenomics.com/single-cell-gene expression/software). Reads were aligned to the Sscrofa11.1 pre-mRNA reference genome [78], and the pre-mRNA portion of the reference genome was extracted for single-nuclei UMI mapping with Cell Ranger mkref pre-mRNA
Only confidently mapped reads with valid barcodes and UMIs were used to generate the gene-barcode matrix. Cross-sample integration and quality-control were performed with the Seurat R package. Doublets were identified by using Seurat’s standard pipeline (https://satijalab.org/seurat/v3.2/pbmc3k_tutorial.html), and barcodes were removed if they had fewer than 500 UMIs, more than 30000 UMIs, or >5% mitochondrial UMIs
Nuclei were removed if they had <200 detected genes or if >25% of the transcripts were from mitochondrial genes. Mitochondrial genes and other transcript identifiers were removed without mapping to the official gene symbols from later analyses. Data were normalized as directed in the online Seurat tutorial (https://satijalab.org/seurat/v3.2/pbmc3k_tutorial.html); total expression was multiplied by a factor of 10,000 and then log-transformed
Assembly: Sscrofa11.1 pre-mRNA
Supplementary files format and content: Cell ranger output format (10X) for each sample

organism: Sus scrofa

source_name: Heart

extract_protocol:
Tissues were cut while submerged in cold phosphate-buffered saline (PBS) or UW solution, washed to remove blood, transferred into 1 mL lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet™ P40 Substitute, and 50 U/mL RNase inhibitor in DEPC-treated water), cut into smaller pieces, and aspirated with the lysis buffer into a 50-mL tube; then, 10 mL of lysis buffer was added, the tissues were ground for 20-30 seconds, and more lysis buffer was added. The mixture was placed on ice for 10 minutes, filtered with 100-μm and 70-μm strainers, and centrifuged for 5 minutes at 700 rcf and 4 °C; then, the supernatant was removed, and the pellet was resuspended in 10 mL nuclei wash and resuspension buffer (1× PBS, 1.0% bovine serum albumin [BSA], and 50 U/mL RNase inhibitor). The suspension was passed through a 40-μm strainer, and the nuclei were centrifuged again for 5 minutes at 700 rcf and 4 °C; then, the supernatant was removed, the pellet was resuspended in 1 mL nuclei wash and resuspension buffer, and the nuclei were centrifuged a third time for 5 minutes at 700 rcf and 4 °C. The supernatant was removed; then, the pellet was resuspended in 5 mL sucrose cushion buffer I (2.7 mL Nuclei PURE 2M Sucrose Cushion Solution and 300 μL Nuclei PURE Sucrose Cushion Buffer) and mixed with 10 mL sucrose buffer. The mixture was layered over 5 mL of sucrose cushion buffer in a second Eppendorf tube and then centrifuged for 60 minutes at 13000 g and 4 °C. All but 100 μL of the supernatant was removed, the nuclei were resuspended in nuclei wash and resuspension buffer, and the solution was passed through a 40-μm strainer; then, the nuclei concentration was determined with a cell counter or hemocytometer and adjusted to 1000 nuclei/μL
The nuclei were placed on ice, stained with propidium iodide for 5 minutes, and then immediately processed via the 10× Genomics® Single-Cell Protocol

tag: cell type

value: Cardiomyocyte (main focus) and other cardiac cell types (not being analyzed)

value: Heart

value: 28 day


title: 8233_BZ_CTL-P56

description: 10x Genomics

value: 56 day


title: 8234_BZ_CTL-P56

description: 10x Genomics


title: GM-TC rep1

value: bone marrow

value: GM-TC


title: 8210_BZ_MIp28-P42

description: 10x Genomics

value: 42 day


title: GM-noTC-LPS rep2

value: 8 weeks

value: GM-noTC-LPS


title: GM-TC rep2


title: M-noTC rep2


title: 8231_BZ_CTL-P28

description: 10x Genomics


title: 8205_BZ_MIp28-P35

description: 10x Genomics

value: 35 day


title: 8211_BZ_MIp28-P42

description: 10x Genomics


title: M-noTC-LPS rep2


title: GM-noTC-LPS rep1


title: 8179_BZ_MIp28-P35

description: 10x Genomics


title: Healthy gender-matched control for DBF4

value: control


title: LD3

city: Perth

first: Shamshad

middle: Ul

last: Hassan

state: Western Australia

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
The base-calling was done with an integrated software in DNBSeq platform.
The alignment of clean reads was done using STAR (v2.7.3a) aligner with default parameters.
The featureCounts function in the Subread (version 2.0.0) software was used to enumerate the number of reads mapping to each gene using the following parameters; -p --primary -t gene
DESeq2 R package was used to generate normalised abundance of genes in each sample.
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: tab-delimited text file includes raw gene counts for each gene in each sample
Supplementary_files_format_and_content: Matrix table with normalised gene counts for every gene and every sample.

organism: Ovis aries

source_name: Small Intestine

extract_protocol:
Total RNA was extracted using the RNeasy mini plus kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions with on column DNA digestion with DNase-I as an additional step.
RNA libraries were prepared for sequencing using standard DNBSeq protocols

value: duodenum

value: 1 year


title: LD4


title: GM-noTC rep1

value: GM-noTC


title: LD1


title: 8015_BZ_ARp1-P28

description: 10x Genomics


title: 8026_BZ_MIp28-P30

description: 10x Genomics

value: 30 day


title: 8030_CZ_ARp1-P28

description: 10x Genomics


title: GM-noTC rep2


title: Saline-Females (C76-SA-F)

city: Baton Rouge

first: Sonika

last: Patial

address: Baton Rouge, LA 70803

institute: Louisiana State University

description:
BL_FevsSA_Fe_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C76_SA_F

data_processing:
Reads were quality control by fastp 0.12.2
Reads were aligned to mm9 genome using hisat2 2.0.5
Quantification of the samples were performed using featureCounts 1.5.0-p3
Analysis of differential expressed genes were performed using DEseq2
Assembly: mm10
Supplementary files format and content: Matrix table with FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with fc/pvalue/padjust for every comparison groups

source_name: Saline-Females

extract_protocol:
Bronchoalveolar lavage was prepared and cells were isolated by standard methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Saline or bleomycin

value: female

value: Bronchoalveolar lavage cells

value: 8-10 weeks

tag: treatment

value: Saline


title: LD2


title: 8213_BZ_MIp28-P30

description: 10x Genomics

value: Cardiomyocyte (main focus) and other cardiac cell types (not being analyzed)

value: Heart


title: Saline-Females (C75-SA-F)

description:
BL_FevsSA_Fe_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C75_SA_F


title: Saline-Females (C74-SA-F)

description:
BL_FevsSA_Fe_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C74_SA_F


title: Saline-Males (C73-SA-M)

description:
BL_MalevsSA_Male_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C73_SA_M

source_name: Saline-Males

value: male


title: HD1


title: Saline-Males (C72-SA-M)

description:
BL_MalevsSA_Male_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C72_SA_M


title: HD4


title: hh_st3_rep1

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: JT Biohistory Research Hall

data_processing:
Base call and quality scoring were performed by the Real Time Analysis software application integrated in the Illumina sequencer.
Paired-end sequencing reads were trimmed for adaptor and primer sequences and low-quality sequences using Trim Galore! with default settings. Trimmed reads were then aligned to the version Ptep_2.0 of the Parasteatoda tepidariorum genome using bowtie2 v2.2.5 with default settings.
Reads mapped with low quality scores (less than 30) were filtered out. PCR duplicates were removed using Picard tools MarkDuplicates v2.23.4. The alignments of filtered reads to the genome were saved as bam files.
Peak calling was performed using the ATAC-seq mode of Genrich v0.6 to generate narrowPeak files from the bam files. These files were used to analyze differential accessibilities between the wild-type and fuchi or Pt-hh pRNAi stage 3 samples following the R workflow described in Reske et al. Epigenetics & Chromatin 13: 22 (2020).
The alignments in the bam format were converted into bigWig files using bamCoverage with the following parameter settings: binsize, 1; normalizeUsing, CPM.
Genome_build: Ptep_2.0
Supplementary_files_format_and_content: bigWig: Normalized read coverage (CPM)
Supplementary_files_format_and_content: narrowPeak: Information about peak regions

organism: Parasteatoda tepidariorum

growth_protocol: The timing of egg laying was determined by time-lapse recording (five min intervals). Embryos were incubated at 25˚C until they reached the appropriate stages.

extract_protocol:
Nuclei were extracted from 40 (for stage 3) or 200 (for stages 1 and 2) embryos in ATAC Lysis Buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, adjusted to pH 7.4 with HCl) containing 0.15 mM Spermidine and 0.1% NP-40, followed by tagmentation with the Tn5 transposase.
Transposed DNA was amplified with Illumina Nextera Transposase Adapters index PCR primers.

treatment_protocol: Mated adult females were injected with approximately 2 µl of dsRNA solution (2 µg/µl) three (for fuchi) or four (for Pt-hh) times at 2-3 days intervals. Embryos derived from egg sacs produced by the injected females 13-24 days after the first injection of the dsRNA were used for extraction of nuclei.

tag: isolate

value: Osaka

value: whole embryo

value: Pt-hh pRNAi

tag: developmental stage

value: stage 3 (18 h AEL)


title: 8217_BZ_ARp1-MIp28-P42

description: 10x Genomics

value: 42 day


title: fuchi_st3_rep2

value: fuchi pRNAi


title: Saline-Females (C77-SA-F)

description:
BL_FevsSA_Fe_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C77_SA_F


title: HD3

value: duodenum


title: OT-I T cells, 24h SIITFEKL + TGFb, biological rep. 4

city: Leeds

first: Robert

last: Salmond

address: Wellcome Trust Brenner Building, St James's University Hospital Trust

institute: University of Leeds

data_processing:
All data processing performed at Novogene. Raw data from Illumina transformed to sequence reads by base calling
Error rate calculated using Illumina CASAVA software
Reads with adaptor contamination, uncertain nucleotides >10% of either read or when low quality nucleotide (base quality <20) are >50% of read were discarded
Sequence aligned to reference genome using HISAT2
HTSeq software used to analyze gene expression levels, using union mode
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: OT-I TCR transgenic T cell

growth_protocol: OT-I T cells were harvested from mouse lymph nodes, single cell suspension were maintaned in IMDM/5% FCS/50uM 2-ME/pen-strep

extract_protocol:
RNA was harvested using Qiagen Rneasy kit at University of Leeds. QC by Nanodrop (UoL), agarose gel electrophoresis and Agilent 2100 at Novogene.
Libraries were constructed at Novogene. mRNA enriched using oligo(dT), cDNA synthesis by RT using random hexamers

treatment_protocol: Cells were activated for 24h with 10nM SIITFEKL ± 5ng/mL recombinant TGFb

tag: cell line

value: OT-I TCR transgenic T cell

value: CD8 T cell

tag: genotype

value: WT

value: Antigenic stimulation + cytokine


title: HD2

tag: age

value: 1 year


title: fuchi_st3_rep1


title: 8178_BZ_MIp28-P30

description: 10x Genomics

value: 30 day


title: Bleomycin-Females (C69-BL-F)

description:
BL_FevsSA_Fe_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C69_BL_F

source_name: Bleomycin-Females

tag: Sex

value: female

value: Bronchoalveolar lavage cells

value: 8-10 weeks

value: Bleomycin


title: 8215_BZ_ARp1-MIp28-P42

description: 10x Genomics

value: Cardiomyocyte (main focus) and other cardiac cell types (not being analyzed)

value: Heart


title: wild-type_st3_rep2

value: Osaka

value: whole embryo

value: wild-type


title: 8194_BZ_ARp1-MIp28-P35

description: 10x Genomics

value: 35 day


title: Bleomycin-Females (C68-BL-F)

description:
BL_FevsSA_Fe_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C68_BL_F


title: 8216_BZ_ARp1-MIp28-P30

description: 10x Genomics


title: hh_st3_rep2

value: Pt-hh pRNAi

value: stage 3 (18 h AEL)


title: OT-I T cells, 24h SIITFEKL, biological replicate 3

value: OT-I TCR transgenic T cell

value: CD8 T cell

value: Antigenic stimulation


title: OT-I T cells, 24h SIITFEKL, biological replicate 4

value: WT


title: Saline-Males (C71-SA-M)

description:
BL_MalevsSA_Male_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C71_SA_M

value: male

value: Saline


title: 8195_BZ_ARp1-MIp28-P30

description: 10x Genomics

value: 30 day


title: Bleomycin-Males (C67-BL-M)

description:
BL_MalevsSA_Male_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C67_BL_M

source_name: Bleomycin-Males

value: Bronchoalveolar lavage cells

value: 8-10 weeks


title: Saline-Males (C70-SA-M)

description:
BL_MalevsSA_Male_deg_all.txt
SA_MalevsSA_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C70_SA_M


title: wild-type_st1_rep1

value: stage 1 (9 h AEL)


title: OT-I T cells, 24h SIITFEKL + TGFb, biological rep. 3

value: Antigenic stimulation + cytokine


title: Bleomycin-Males (C66-BL-M)

description:
BL_MalevsSA_Male_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C66_BL_M

value: Bleomycin


title: OT-I T cells, 24h SIITFEKL, biological replicate 1


title: OT-I T cells, 24h SIITFEKL + TGFb, biological rep. 2


title: AML12 LL35 ASO 4

city: Moscow

first: Evgeniya

last: Shcherbinina

address: Bolshoy Boulevard 30, bld. 1

country: Russia

institute: Skolkovo Institute of Science and Technology

description: AML12cells_LL35knockdown_transcriptome.xls

data_processing:
For mapping samples, genome annotations were obtained from Ensembl, release 102.
Reads were mapped using STAR v2.5.3a with default settings except for the following one: –quantMode GeneCounts.
The resulting gene counts were further processed with R package DESeq2, where it was further normalized using RLE method.
To take into account unwanted variation in the data, we obtained by sva package additional variables and introduced them into design matrix to capture unwanted variations.
DESeq2 package were used for performing differential expression analysis based on Wald test. We defined genes as differentially expressed if they passed the thresholds: FDR < 0.05.
Assembly: Ensembl, release 102.
Supplementary files format and content: FC and adjusted p-value for knockdown samples versus control for AML12 cells, and control versus knockdown for liver samples

growth_protocol: Cultured in DMEM supplemented with Glutamax, 10% fetal bovine serum and 1% pen/strep

extract_protocol:
RNA was harvested using TRIzol Reagent (Thermo Fisher), 1 μg of total RNA was used for the construction of sequencing libraries.
Libraries were prepared with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB 7760, New England Biolabs, Ipswich, MA, USA), according to the manufacturer’s protocol.

treatment_protocol: LL35 knockdown in AML12 cells was performed using a mix of 5 ASOs at a final concentration of 20nM for each ASO. ASO specific to Firefly Luciferase gene was used as a control. For animal treatment GalNAc conjugated ASOs with the same core sequences, but with other types of chemical modifications, were used at a final concentration of 150mg/kg for each ASO. GalNAc conjugated ASO specific to Firefly Luciferase gene was used as a control.  1 mg/kg siRNA#5 and siRNA#7 were formulated in lipid nanoparticles and injected in murine tail vein for 6 and 13 days.

value: normal hepatocytes

value: mix of 5 LL35 ASOs, 2 days after transfection


title: OT-I T cells, 24h SIITFEKL + TGFb, biological rep. 1


title: Bleomycin-Females (C50-BL-F)

description:
BL_FevsSA_Fe_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C50_BL_F

value: female


title: wild-type_st3_rep1

value: Osaka

value: whole embryo

value: wild-type


title: Bleomycin-Females (C49-BL-F)

description:
BL_FevsSA_Fe_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C49_BL_F


title: CD4CD8RKFP2_3: CD4+CD8+ (Thpok-RKF+) replicate 3

city: Bethesda

first: Yayi

last: Gao

state: MD

address: 3016 Convert Drive

institute: National Cancer Institute

description: Mature CD4+CD8+ thymocytes from CD45.2+Thpokfl/flRunx3fl/dYFPCd4-Cre+Thpok-RKF+ from B2m-/- host.

data_processing:
Illumina RTA 3.4.4 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Raw RNAseq fastq reads were trimmed with Trimmomatic and aligned to mouse genome using STAR
Gene-assignment and count of RNA reads were performed with Htseq
Genome_build: mm39
Supplementary_files_format_and_content: count of RNA reads were performed with Htseq; FPM normalization was performed with the FPM function of the DEseq2 package

source_name: Thymus

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMARTer Ultra Low Input reagent (Takara)  was used for library.   Libraries were pooled and sequenced with paired-end reads of 101 bp on a Novaseq to reach 50 million read pairs per sample

tag: population

value: Mature CD4+CD8+ thymocytes


title: PDR Patient 4 [PDR_5]

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description: tsRNA and miRNA expression profile

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8
Sequencing quality are examined by FastQC and trimmed reads (trimmed 5‘,3’-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences
reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie
Raw reads were normalized by calculated CPM value
Assembly: hg19
Supplementary files format and content: The xlsx format file contains the CPM value of gene in every sample

source_name: vitreous humour from PDR patients

extract_protocol:
Total RNA was extracted from vitreous humour using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).Total RNA was pretreated to remove  some modification which interfere with small RNA-seq library construction(e.g. m1A).
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 134-160 bp PCR amplified fragments (corresponding to 14-40 nt small RNAs).

value: vitreous humour

tag: disease state

value: proliferative diabetic retinopathy (PDR)


title: PDR Patient 2 [PDR_3]

description: tsRNA and miRNA expression profile


title: wild-type_st2_rep1

value: stage 2 (12 h AEL)


title: wild-type_st1_rep2


title: Control Patient 4 [CON_4]

description: tsRNA and miRNA expression profile

source_name: vitreous humour from control (idiopathic macular hole) patients without diabetes mellitus

value: idiopathic macular hole (control)


title: CD4CD8RKFP2_1: CD4+CD8+ (Thpok-RKF+) replicate 1

value: CD45.2+Thpokfl/flRunx3fl/dYFPCd4-Cre+Thpok-RKF+ from B2m-/- host


title: Bleomycin-Males (C65-BL-M)

description:
BL_MalevsSA_Male_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C65_BL_M

value: male

value: Bronchoalveolar lavage cells


title: CD4CD8RKFN2_3: CD4+CD8+ (Thpok-RKF-) replicate 3

description: Mature CD4+CD8+ thymocytes from CD45.2+Thpokfl/flRunx3fl/dYFPCd4-Cre+Thpok-RKF- from B2m-/- host.


title: OT-I T cells, 24h SIITFEKL, biological replicate 2

value: OT-I TCR transgenic T cell

value: CD8 T cell

value: WT

value: Antigenic stimulation


title: AML12 Luc ASO 2

value: normal hepatocytes

value: luciferase ASO, 2 days after transfection


title: Bleomycin-Males (C33-BL-M)

description:
BL_MalevsSA_Male_deg_all.txt
BL_MalevsBL_Fe_deg_all.txt
BLvsSA_deg_all.txt
gene_count.txt
gene_fpkm.txt
C33_BL_M

value: 8-10 weeks

value: Bleomycin


title: Liver LL35 ASO 3

source_name: Liver

value: Liver

value: Balb/c

value: GalNAc-conjugated  mix of 5 LL35 ASOs, 5 days after injection


title: wild-type_st2_rep2

value: Osaka

value: whole embryo

value: wild-type


title: AML12 LL35 ASO 3

value: mix of 5 LL35 ASOs, 2 days after transfection


title: PDR Patient 3 [PDR_4]

description: tsRNA and miRNA expression profile

value: vitreous humour

value: proliferative diabetic retinopathy (PDR)


title: CD8RKFN2_3: CD8+ SP (Thpok-RKF-) replicate 3

description: Mature CD8+ SP thymocytes from CD45.2+Thpokfl/flRunx3fl/dYFPCd4-Cre+Thpok-RKF- from B2m-/- host.

value: Mature CD8+ SP thymocytes


title: CD8RKFN2_2: CD8+ SP (Thpok-RKF-) replicate 2

value: CD45.2+Thpokfl/flRunx3fl/dYFPCd4-Cre+Thpok-RKF- from B2m-/- host


title: AML12 LL35 ASO 2


title: AML12 LL35 ASO 1


title: Liver LL35 ASO 2


title: CD8RKFN2_1: CD8+ SP (Thpok-RKF-) replicate 1


title: CD4CD8RKFP2_2: CD4+CD8+ (Thpok-RKF+) replicate 2

value: CD45.2+Thpokfl/flRunx3fl/dYFPCd4-Cre+Thpok-RKF+ from B2m-/- host

value: Mature CD4+CD8+ thymocytes


title: PDR Patient 1 [PDR_1]

description: tsRNA and miRNA expression profile


title: Liver LL35 ASO 1


title: Control Patient 3 [CON_3]

description: tsRNA and miRNA expression profile

value: idiopathic macular hole (control)


title: AML12 Luc ASO 3

value: normal hepatocytes

value: luciferase ASO, 2 days after transfection


title: Control Patient 2 [CON_2]

description: tsRNA and miRNA expression profile


title: CD4CD8RKFN2_2: CD4+CD8+ (Thpok-RKF-) replicate 2


title: WTCD8_2: WT CD8+ SP replicate 2

description: Mature CD8+ SP thymocytes from CD45.1+ CD45.2+ competiters from Mixed Bone marrow chimara from I-Ab-/- host.


title: Liver Luc ASO 2

value: GalNAc-conjugated luciferase ASO, 5 days after injection


title: Control Patient 1 [CON_1]

description: tsRNA and miRNA expression profile


title: CD4CD8RKFN2_1: CD4+CD8+ (Thpok-RKF-) replicate 1


title: AML12 Luc ASO 1


title: Liver Luc ASO 1

value: Liver


title: Liver Luc ASO 3

value: Balb/c


title: WTCD4_3: WT CD4+ SP replicate 3

description: Mature CD4+ SP thymocytes from CD45.1+ CD45.2+ competiters from Mixed Bone marrow chimara from B2m-/- host.

value: Mature CD4+ SP thymocytes


title: WTCD8_3: WT CD8+ SP replicate 3


title: WTCD8_1: WT CD8+ SP replicate 1


title: MC3T3-E1 ChIP_Input_1

city: rochester

first: Roman

last: Thaler

state: MINNESOTA

address: 200 First street SW

institute: Mayo Clinic

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with BWA (version 0.7.15.1), PCR duplicates were removed with RmDup (version 2.0) and filtered to remove mitochondrial DNA and not properly aligned sequnces.
Peaks were called with MACS2 callpeak (version 2.1.1.20160309.6) and Bigwig files were created with multiBigwigSummary (version 3.1.2.0.0)
H3K9me3 and H3K27me3 coverage over defined regions was analyzed with the CEAS package (version 1.0.2)
Assembly: mm10

source_name: Bone

growth_protocol: Gulotm1Mae mice were kept on 3.3g/L vitamin C in drinking water (ad libitum), refreshed twice a week; cTet mice were grown until 11 weeks with a standard rodent diet;  MC3T3-E1 cells were grown in vitamin C free aMEM at 37ºC in a 5% CO2 humidified atmosphere and splitted around 70% confluence.

extract_protocol:
RNA and DNA was extraced with commercially available extraction kits (Zymo and Qiagen, respectively), chromatin for ChIP-Seq was extracted using standard protocols
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols; hMeDIP-seq: the libraries were prepared by the ACCEL-NGS® 1S Plus DNA library kit (Swift Bioscience, MI, Ann Arbor) following manufacturer’s instructions and sequenced to 51 base pairs from both ends. ChIP-Seq libraries were prepared using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) following the manufacturers instructions. All deep-sequncing runs were perfomed using the Illumina HiSeq 4000 instrument at the Mayo Clinic Medical Genome Facility Sequencing Core.

treatment_protocol: Gulotm1Mae mice were treated with vitamin C for 15 or 20 weeks at a concentration of 3.3g/L in drinking water ad libitum, refreshed twice a week; all mice were sacrificed at 20 weeks of age. MC3T3-E1 cells were cultured for 28 days in aMEM including 4 mM β-glycerophosphate and plus or minus 50 µg/ml vitamin C at 37ºC in a 5% CO2 humidified atmosphere.

tag: tissue/cell type

value: cell-line; calvarial osteoblasts

tag: passages


title: Q756

city: Fukuoka

first: Hiroo

last: Yamaguchi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurology

institute: Neurological Institute, Graduate School of Medical Sciences,  Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: brain, transgenic

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: brainstem/cerebellum

value: MSA Transgenic


title: MC3T3-E1 ChIP_Input_2


title: S2 Schneider cells — Zeste rep2

first: Marina

middle: Yu.

last: Mazina

address: Vavilova, 34/5

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to dm6 genome by bowtie2 v2.4.5 (usegalaxy.eu online tools). Aligned BAM files for replicate 1 and replicate 2 (for Combgap, Zeste, Psq ChIP-Seqs and Inputs) were merged by Merge BAM Files (Galaxy Version 1.2.0).
Bam files were filtered to MAPQ>5
BigWig files were generated using bamCoverage 3.5.1.0.0 with scores representing number of reads normalized by the size of the library. Final bigwig files were obtained using bigwigcompare 3.3.2.0.0 as ratio of ChIP signal to Input. Scores represent number of reads normalized by the size of the library.
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: bigwig

organism: Drosophila melanogaster

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider line 2 (S2-modencode) cells were maintained at 25°C in the Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine (crosslinking in Drosophila tissues was performed by 0,7% formaldehyde). After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 300-1000 bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

value: Primary culture of late stage (20-24 hours old) Drosophila melanogaster embryos

tag: chip antibody

value: The polyclonal antibodies against Zeste (full length, isoform PA) were raised in rabbits in current study

value: untreated


title: WTCD4_2: WT CD4+ SP replicate 2

tag: strain


title: S2 Schneider cells — Psq rep2

value: The polyclonal antibodies against Psq (amino acid (a.a.) residues 44–1065, PsqA, UniProtKB:Q9V5N1, GenBank:AAC47153.1) were raised in rabbits in current study


title: Q811

source_name: brain, wild-type

tag: tissue

value: wild type


title: WTCD4_1: WT CD4+ SP replicate 1


title: Q810


title: MC3T3-E1 VitC+ rep2 H3K27me3 ChIP-seq

tag: medip/chip antibody

value: H3K27me3 (Cell Signaling Technology, 9733BC)


title: Q757


title: MC3T3-E1 VitC+ rep1 H3K27me3 ChIP-seq


title: Q812


title: MC3T3-E1 VitC- rep2 H3K27me3 ChIP-seq


title: S2 Schneider cells — Input DNA rep1


title: S2 Schneider cells — Zeste rep1


title: ChIP-seq_HSF2_MEF_MD_Rep2

city: Turku

first: Samu

middle: Valtteri

last: Himanen

state: Varsinais-Suomi

address: Tykistökatu 6A

department: Cell Biology

country: Finland

institute: Åbo Akademi University

data_processing:
Adapters were removed using cutadapt (Marcel Martin, 2011).
The reads were mapped in paired-end mode to mm10 genome using Bowtie2 (Langmead et al., 2009) with parameters -q --sensitive-local --no-mixed --no-discordant --no-unal.
Mapped reads were processed to bed and bedgraph files.
Genome_build: mm10
Supplementary_files_format_and_content: Both replicates were combined to a single bedgraph file. bedgraph files which were normalized to total read counts.

source_name: MEF cell line

growth_protocol: MEFs were maintained at 37 °C in a humidified 5 % CO2 atmosphere and grown in Dulbecco's modified medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, 100 U/ml penicillin and non-essential amino acids (Gibco)

extract_protocol:
Cells were washed with PBS after treatments. Next, cells were lysed and chromatin was fragmented with sonicator (Bioruptor Pico). Protein-DNA complexes were isolated using protein G sepharose beads and antibodies against HSF1 (ADI-SPA-901, Enzo) and HSF2 (Östling et al., J. Biol. Chem. 282, 7077-7086). Normal rabbit IgG was used as a negative control. Chromatin extracted from heat-shocked human Hs578T cells was used as a spike-in for ChIP-seq.
Libraries were constructed using NEXTflex ChIP-seq kit (Perkin Elmer) and NEXTflex ChIP-seq barcodes (Perkin Elmer).

treatment_protocol: Oxidative stress was induced by adding 30 μM freshly prepared menadione solution to MEFs, after which the MEFs were grown for 2 h at 37 °C.  Heat shock was induced by submerging MEFs into 42 °C water bath for 1 h.

tag: cell line/type

value: mouse embryonic fibroblasts (MEFs)

value: menadione (30 μM, 2 h)


title: ChIP-seq_Input_MEF_MD_Rep2

value: none (input)


title: ChIP-seq_HSF1_MEF_MD_Rep2


title: S2 Schneider cells — Combgap rep2

tag: cell type

value: The rabbit polyclonal antibodies against Combgap (a.a. 31–269, isoform PF), described previously in PMID:34078365


title: ChIP-seq_IgG_MEF_MD_Rep2

tag: treatment

value: IgG


title: MC3T3-E1 VitC- rep1 H3K27me3 ChIP-seq


title: MC3T3-E1 VitC+ rep2 H3K9me3 ChIP-seq

value: H3K9me3 (Diagenode, C15410056)


title: MC3T3-E1 VitC+ rep1 H3K9me3 ChIP-seq


title: S2 Schneider cells — Psq rep1


title: ChIP-seq_Input_MEF_HS_Rep2

value: heat shock (42°C, 1 h)


title: S2 Schneider cells — Adf

value: The rabbit polyclonal antibodies against Adf1 (full length, isoform PC), described previously in PMID:28296955


title: ChIP-seq_IgG_MEF_HS_Rep2


title: S2 Schneider cells — Combgap rep1


title: Q809


title: MC3T3-E1 VitC- rep2 H3K9me3 ChIP-seq

value: cell-line; calvarial osteoblasts


title: ChIP-seq_HSF2_MEF_HS_Rep2


title: MC3T3-E1 VitC- rep1 H3K9me3 ChIP-seq


title: ChIP-seq_IgG_MEF_C_Rep2

value: control


title: fuchi_st2_rep2_d18

data_processing:
Base call and quality scoring were performed by the Real Time Analysis software application during Illumina's sequencing runs.
Sequence reads were trimmed for adaptor and primer sequences and low-quality sequences using the CLC Genomics Workbench 7.0.4 (Qiagen) with the following parameter settings for the quality trim: trim using quality scores, limit=0.05; trim ambiguous nucleotides, maximum number of ambiguities=2; filter on length, discard reads below length=30. Trimmed reads were then aligned to Ptep_1.0 genome assembly using the BLAT algorithm version 34 in the DDBJ Read Annotation Pipeline with default settings.
The output alignments were filtered based on quality, coverage, and uniqueness using a perl script filterPSL.pl available from the AUGUSTUS 3.0.1 scripts folder. The parameter settings were as follows: minimum coverage, 60%; minimum percent identity, 90%; unique threshold, 0.96. The filtered alignments were converted into sam and psl files with a custom perl script.
Using the sam files, abundance of mRNAs against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62) was calculated with htseq-count v. 0.6.1p1 in -s reverse, -m union settings and was normalized in Reads Per Kilobase of exon per Million reads (RPKM).
Based on the abundance of mRNAs against AUGUSTUS gene models, differentially expressed genes (DEGs) were estimated using EdgeR.
The alignments in the psl format were converted into wig files using a script aln2wig available from the AUGUSTUS 3.0.1 scripts folder, and the wig files were converted into bigWig files using the program wigToBigWig available from the ucsc directory.
Genome_build: Ptep_1.0
Supplementary_files_format_and_content: tab-delimited text file includes read counts for gene models and the features of the gene models.
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for gene models and the features of the gene models.
Supplementary_files_format_and_content: bigWig files ; Scores represent normalized read coverage (per 10 million reads).

growth_protocol: Embryos were incubated at 25˚C until they reached the appropriate stages.

extract_protocol:
Poly(A) mRNA was extracted using a Dynabeads mRNA DIRECT Kit (Ambion) from 50-100 embryos.
mRNA was fragmented using the NEBNext RNase III RNA Fragmentation Module (New England BioLabs). Sequencing libraries were constructed from fragmented RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England BioLabs).

treatment_protocol: Mated adult females were injected with approximately 1-2 µl of fuchi dsRNA solution (2µg/µl) four times at 2-3 days intervals. Embryos derived from egg sacs produced by the injected females 18-19 days after the first injection of the dsRNA were used for RNA extraction. Embryos from the same females 2 days before the first dsRNA injection were used as untreated samples.

tag: isolate

value: Osaka

value: whole embryo

value: fuchi pRNAi

value: stage 2


title: ChIP-seq_Input_MEF_C_Rep2


title: fuchi_st5e_rep2_d18

tag: developmental stage

value: early stage 5


title: Femur Input2

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with BWA (version 0.7.15.1), PCR duplicates were removed with RmDup (version 2.0) and filtered to remove mitochondrial DNA and not properly aligned sequnces.
Peaks were called with MACS2 callpeak (version 2.1.1.20160309.6) and Bigwig files were created with multiBigwigSummary (version 3.1.2.0.0)
5hmC coverage over defined regions was analyzed with the CEAS package (version 1.0.2)
Assembly: mm10

value: Femur


title: Femur cTet1_2 KO rep2 hMeDIP-seq

value: 5hmC (Active Motif, 39791)


title: ChIP-seq_HSF1_MEF_HS_Rep2

value: mouse embryonic fibroblasts (MEFs)

value: wild type


title: Femur Input1


title: fuchi_st3_rep2_d18

value: stage 3


title: ChIP-seq_HSF1_MEF_C_Rep2


title: Femur cTet1_2 KO rep3 hMeDIP-seq


title: fuchi_st5e_rep2_d00

value: untreated


title: Femur cTet WT rep3 hMeDIP-seq


title: ChIP-seq_Input_MEF_MD_Rep1

value: menadione (30 μM, 2 h)

value: none (input)


title: Femur cTet1_2 KO rep1 hMeDIP-seq


title: ChIP-seq_HSF2_MEF_C_Rep2


title: ChIP-seq_IgG_MEF_MD_Rep1

value: IgG


title: fuchi_st3_rep1_d19


title: Femur cTet1_2 KO rep3 RNA-seq

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with RNA STAR (version 2.6.0b-1)
Gene expression was qantified with featureCounts (version 1.6.3)
Differentially expressed genes were defined with DESeq2 (version 2.11.40.2)
Assembly: mm10


title: fuchi_st2_rep2_d00


title: fuchi_st5e_rep1_d19


title: ChIP-seq_HSF1_MEF_MD_Rep1


title: Femur cTet WT rep2 hMeDIP-seq


title: Femur cTet WT rep1 hMeDIP-seq


title: fuchi_st3_rep2_d00


title: ChIP-seq_HSF2_MEF_MD_Rep1


title: fuchi_st2_rep1_d00


title: fuchi_st2_rep1_d19


title: fuchi_st5e_rep1_d00


title: ChIP-seq_HSF2_MEF_HS_Rep1

value: heat shock (42°C, 1 h)


title: st5e_p1

data_processing:
Base call and quality scoring were performed by the Real Time Analysis software application during Illumina's sequencing runs.
Sequence reads were trimmed for adaptor and primer sequences, the first 3 bases derived from the SMARTer Stranded Oligo and low-quality sequences using the CLC Genomics Workbench 7.0.4 (Qiagen) with the following parameter settings for the quality trim: trim using quality scores, limit=0.05; trim ambiguous nucleotides, maximum number of ambiguities=2; filter on length, discard reads below length=30. Trimmed reads were then aligned to Ptep_1.0 genome assembly using the BLAT algorithm version 34 in the DDBJ Read Annotation Pipeline with default settings.
The output alignments were filtered based on quality, coverage, and uniqueness using a perl script filterPSL.pl available from the AUGUSTUS 3.0.1 scripts folder. The parameter settings were as follows: minimum coverage, 60%; minimum percent identity, 90%; unique threshold, 0.96. The filtered alignments were converted into sam and psl files with a custom perl script.
Using the sam files, abundance of mRNAs against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62) was calculated with htseq-count v. 0.5.4p5 in -s reverse, -m union settings and was normalized in Reads Per Kilobase of exon per Million reads (RPKM).
Based on the abundance of mRNAs against AUGUSTUS gene models, differentially expressed genes (DEGs) were estimated using EdgeR.
The alignments in the psl format were converted into wig files using a script aln2wig available from the AUGUSTUS 3.0.1 scripts folder, and the wig files were converted into bigWig files using the program wigToBigWig available from the ucsc directory.
Genome_build: Ptep_1.0
Supplementary_files_format_and_content: tab-delimited text file includes read counts for gene models and the features of the gene models.
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for gene models and the features of the gene models.
Supplementary_files_format_and_content: bigWig files ; Scores represent normalized read coverage (per 10 million reads).

source_name: wild-type spider embryo

extract_protocol:
Poly(A) mRNA was extracted using the Dynabeads mRNA DIRECT Kit (Ambion).
Sequencing libraries were constructed using the SMARTer Stranded RNA-Seq Kit (Clontech). Libraries were validated using the Agilent 2100 Bioanalyzer and Agilent High Sensitivity DNA Kit.

treatment_protocol: Approximately 10-100 cells were isolated from small regions (central [c], peripheral [p], and intermediate [i]) of radially symmetric forming/formed germ discs at stage 3 (st3, approximately 20 h after egg laying [AEL]), stage 4 (st4, approximately 28-29 h AEL), and early stage 5 (st5e, approximately 31-32 h AEL) using glass capillary.

value: cells from a peripheral region of a forming germ disc

tag: mother id


title: st5e_p2


title: ChIP-seq_Input_MEF_HS_Rep1

tag: genotype


title: Femur cTet2 KO rep1 RNA-seq


title: Femur cTet2 KO rep2 RNA-seq


title: Femur cTet1_2 KO rep1 RNA-seq


title: ChIP-seq_IgG_MEF_HS_Rep1


title: Femur cTet1_2 KO rep2 RNA-seq


title: Femur cTet1 KO rep3 RNA-seq


title: ChIP-seq_IgG_MEF_C_Rep1

value: control


title: Femur cTet2 KO rep3 RNA-seq


title: st4_p2

value: Osaka

value: stage 4


title: fuchi_st3_rep1_d00

value: whole embryo


title: ChIP-seq_Input_MEF_C_Rep1


title: PRO-seq_MEF_HSF2-KO_MD_Rep2

data_processing:
library strategy: PRO-seq
Adapters were removed using cutadapt (Marcel Martin, 2011).
Paired-end sequencing data is provided but only read1 was used in this study. The reads were mapped to mm10-dm3 genome using Bowtie2 (Langmead et al., 2009) with parameters --sensitive-local.
Reads that mapped only to mm10, were processed to bed and bedgraph files.
Genome_build: mm10-dm3
Supplementary_files_format_and_content: Both replicates were combined to a single normalized bedgraph file. Reads that mapped to spike-in genome (dm3) showed high variance between samples and, hereby, samples were normalized to total read counts and to genes whose expression level remained the same across all samples. Separate files are provided for plus and minus strands.

extract_protocol:
Cells were washed with PBS after treatments. Next, nuclei were isolated and run-on reactions were performed in the presence of biotinylated nucleotides as described by Mahat et al., Nat. Protocol 11, 1455–1476 (2016). An equal amount of Drosophila S2 cells were added to run-on reactions to provide whole-genome spike-in control for sample normalization.
Libraries were constructed using TruSeq small-RNA adaptors according to Mahat et al., Nat. Protocol 11, 1455–1476 (2016).

value: HSF2 knock out

tag: molecule type

value: nascent RNA


title: st5e_c1

value: cells from a central region of a forming germ disc

value: early stage 5


title: Femur cTet WT rep2 RNA-seq

value: Femur


title: Femur cTet1 KO rep2 RNA-seq


title: ChIP-seq_HSF1_MEF_HS_Rep1

value: mouse embryonic fibroblasts (MEFs)

value: wild type


title: ChIP-seq_HSF2_MEF_C_Rep1


title: st4_c2


title: PRO-seq_MEF_HSF2-KO_HS_Rep2


title: Femur cTet1 KO rep1 RNA-seq


title: st4_p1


title: st5e_c2


title: Femur cTet WT rep3 RNA-seq


title: PRO-seq_MEF_HSF1-KO_HS_Rep2

value: HSF1 knock out


title: PRO-seq_MEF_HSF1-KO_C_Rep2


title: PGCLC_3

city: La Jolla

first: Kun

last: Tan

address: 9500 Gilman Drive # 0695

department: Dept. of Obstetrics, Gynecology & Reproductive Science

institute: UCSD

data_processing:
Library strategy: SLAM-seq
Reads were filtered for quality and aligned with SLAM-DUNK (v0.4.3) (Neumann et al., 2019) against the full Mus musculus reference genome (mm10), reporting up to 100 alignments for multi-mappers and activating the multi-mapper retention strategy, filtering for variants with a variant fraction of 0.2. For each sample, reads of both steady-state and newly synthesis (transcription) were counted.
Gene and 3' UTR annotations were obtained from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables). T > C conversion rate was determined for each position along the custom defined counting windows by normalizing to genomic T content and coverage of each position and averaged per UTR.
Differential gene expression calling was performed on raw read counts with ≥2 T>C conversions using limma (v3.42.2) (Ritchie et al., 2015).
Genome_build: Mus musculus (mm10, GRCm38) genome.
Supplementary_files_format_and_content: SLAMseq_counts.xlsx: Matrix table with raw gene counts. For each sample, both steady-state and newly synthesis (transcription) were counted.

source_name: primordial germ cell-like cells

growth_protocol: Mouse ES cells were maintained on a 0.1% gelatin (Sigma)-coated dish, under 2i+LIF condition. Mouse ES cells were induced to differentiate into EpiLCs and PGCLCs, as previously described (Hayashi et al., 2011). Briefly, three hundred thousand cells were plated on six-well culture plates coated with 16.7 mg/ml fibronectin (Millipore Sigma) and grown in N2B27 medium supplemented with 1% knockout serum replacement (KSR; Gibco), bFGF (12 ng/ml; Life Technologies), and activin A (20 ng/ml; R&D Systems) for 2 days. The medium was changed every day. The PGCLCs were induced under a floating condition by plating two thousand day 2 EpiLCs in a single well from a 96-well Lipidure-Coat Plate (Amsbio) and grown in serum-free GK15 medium, BMP4 [500 ng/ml; Miltenyi Biotec], SCF [100 ng/ml; Miltenyi Biotec], BMP8b [500 ng/ml; R&D Systems], EGF [50 ng/ml; Pepprotech]) and LIF (Millipore Sigma) for 4 days. PGCLCs were purified by cell sorting stained with antibodies against ITGB3 (Biolegend) and SSEA1 (eBioscience) conjugated with PE and Alexa Fluor 647, respectively.

extract_protocol:
SLAMseq was performed as previously described (Herzog et al., 2017).
Libraries were prepared using Quant-seq mRNA 3′ end library preparation kit (Lexogen) according to the instructions of the manufacturer.

treatment_protocol: Before collecting samples, cells were pulse-treated with 400 μM s4U for 1 hr. After extracting total RNAs, carboxyamidomethylation was performed under standard conditions. The reaction was quenched by addition of 1 μl of 1M DTT. For negative controls, cells were pulse-treated with 400 μM s4U for 1 hr. RNAs were not treated with iodoacetamide (IAA).

value: ES-derived PGCLC cells


title: st3_p2

value: stage 3


title: st3_c2


title: st4_c1


title: PRO-seq_MEF_WT_MD_Rep2

value: menadione (30 μM, 2 h)


title: st3_c1


title: PRO-seq_MEF_HSF1-KO_MD_Rep2


title: PRO-seq_MEF_WT_HS_Rep2

value: heat shock (42°C, 1 h)


title: PGCLC_1


title: Negative_Ctrl_2

source_name: epiblast-like cells + primordial germ cell-like cells

value: ES-derived epiblast-like cells + ES-derived PGCLC cells


title: st3_i3

value: cells from an intermediate region of a forming germ disc


title: PRO-seq_MEF_HSF2-KO_C_Rep2

value: control


title: Negative_Ctrl_1

source_name: embryonic stem cells

value: ES cells


title: st3_i2

value: Osaka


title: PRO-seq_MEF_WT_C_Rep2


title: st3_p1

value: cells from a peripheral region of a forming germ disc


title: PGCLC_2


title: ChIP-seq_HSF1_MEF_C_Rep1


title: Femur cTet WT rep1 RNA-seq


title: EpiLC_2

source_name: epiblast-like cells

value: ES-derived epiblast-like cells


title: PRO-seq_MEF_HSF1-KO_MD_Rep1

value: nascent RNA


title: st3_p3


title: EpiLC_3


title: PRO-seq_MEF_HSF1-KO_HS_Rep1


title: ESC_1


title: PRO-seq_MEF_HSF2-KO_MD_Rep1

value: HSF2 knock out


title: WT scATACseq rep 2

first: Remy

last: Bosselut

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

data_processing:
Basecalling was performed using RTA 2.4.6
Barcode was demultiplexed allowing 1 mismatch with Bcl2fastq 2.17
The fastq files are processed through cellranger, including alignment, identification of cut sites, and peak calling.
Assembly: mm10
Supplementary files format and content: .h5 file of peak-by-barcode matrix

extract_protocol:
Nuclei were isolated following the recommended protocol from 10X Genomics. Transposition and scATACseq capture was performed with the 10X Chromium Single Cell ATAC Solution (v1.0) , following the manufacturer's recommended protocol
Libraries were run on a NextSeq, Parameters:50bp (Read1), 8bp (Index1), 16bp (Index2), 50bp (Read2)

value: Thpok fl/fl; Thpok-GFP

value: Mixture of Thpok-GFP+, CD8SP, and CD69- DP


title: KO scATACseq rep 2

value: CD4-Cre;Thpok fl/fl; Thpok-GFP

value: Mixture of Thpok-GFP+ and CD69- DP


title: PRO-seq_MEF_HSF2-KO_HS_Rep1

value: mouse embryonic fibroblasts (MEFs)


title: ESC_3


title: Aortic smooth muscle cell KO rep2

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

data_processing:
scRNA sequencing data was processed with Cell Ranger v 3.1.0. 62.7% of reads were confidently aligned to a modified version of the mouse transcriptome mm10 that includes the sequence for the gene ZsGreen1. The top cell barcodes selected by Cell Ranger were then utilized for downstream analysis.
Cell Barcode Clustering and Annotation: All analyses were performed in R version 3.6.1. Graph embedding and clustering were performed using the R package Seurat v.3.1.0. UMI counts were scaled to 10,000 UMIs per cell, then natural log transformed with a pseudo-count of one (log((TPM/100) + 1)). Feature selection, principal component analysis, neighbor embedding, and Louvain modularity clustering were recursively performed on the data for the purpose of identifying clusters of discretely identifiable cell populations. Clusters were then annotated as either a multiplet population or known cell type by expert curation of transcriptional marker genes. Multiplets were identified as cell populations whose transcriptomic profile resembled a combination of 2 or more cell populations found in the data. Uniform Manifold Approximation and Projection (UMAP) embedding was used to visualize gene expression.
Genome_build: mm10

source_name: Aortic smooth muscle cell

extract_protocol:
Aortas were harvested from WT/mTmG/ Myh11ERT2 and miR-21fl/flmTmG/Myh11ERT2 mice and digested in 1.5mg/ml collagenase A (10103578001, Roche) + 0.5mg/ml elastase (6365, Worthington) buffer supplemented with 0.1% actinomycin at 37oC for 1h with gentle shaking. Digested aortas were passed through a 70 μm Cell Strainer and stained with a live/dead viability dye eFluor 450 (Thermo Fisher Scientific).
The sorted eGFP+ (SMCs) and eGFP-/tdTomato+ (non-SMCs aortic cells) cells were mixed to represent complete profile of aortic cells and then encapsulated into droplets and processed following manufacturer’s specifications using 10X Genomics GemCode Technology. Equal numbers of cells per sample were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMs) at Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by cDNA generation using the Single Cell 3’ Reagent Kits v2 (10X Genomics). Libraries were sequenced on an Illumina HiSeq 4000 as 2 × 100 paired-end reads.

treatment_protocol: WT/mTmG/ Myh11ERT2 and miR-21fl/flmTmG/Myh11ERT2 littermates were injected Tamoxifen at 5weeks old for CRE recombination. Later received AAV8-PCSK9 injection then fed on western diet (1.25% cholesterol; D12108; Research Diets, Inc) for 20 weeks to induce atherosclerosis.

value: mTmG/ Myh11ERT2

value: Aorta

tag: age

value: 30-weeks old

tag: Sex

value: pooled male and female

tag: condition


title: KO scATACseq rep 1


title: PRO-seq_MEF_HSF1-KO_C_Rep1

value: HSF1 knock out


title: EpiLC_1


title: ESC_2


title: PRO-seq_MEF_HSF2-KO_C_Rep1

value: control


title: Aortic smooth muscle cell WT rep1

value: WT/mTmG/ Myh11ERT2


title: Input_DNA_MC3T3

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 instrument and Fastq file quality was checked with FastQC (version 0.72).
Quality and adapter trimming was performed with Trim Galore! (version 0.4.3.1)
Trimmed Fastq files were mapped to the mouse genome (mm10) with BWA (version 0.7.15.1), PCR duplicates were removed with RmDup (version 2.0) and filtered to remove mitochondrial DNA and not properly aligned sequnces.
Peaks were called with MACS2 callpeak (version 2.1.1.20160309.6) and Bigwig files were created with multiBigwigSummary (version 3.1.2.0.0)
5hmC coverage over defined regions was analyzed with the CEAS package (version 1.0.2)
Genome_build: mm10

growth_protocol: Gulotm1Mae mice were kept on 3.3g/L vitamin C in drinking water (ad libitum), refreshed twice a week. MC3T3-E1 cells were grown in vitamin C free aMEM at 37ºC in a 5% CO2 humidified atmosphere and splitted around 70% confluence.

value: cell-line; calvarial osteoblasts

tag: medip antibody

value: 5hmC (Active Motif, 39791)


title: D28_MC3T3-E1 VitC+ rep2 hMeDIP-seq

tag: passages


title: WT scATACseq rep 1


title: PRO-seq_MEF_WT_C_Rep1

value: wild type


title: D28_MC3T3-E1 VitC+ rep1 hMeDIP-seq


title: D28_MC3T3-E1 VitC- rep2 hMeDIP-seq


title: Myo_Aged_1_Msx1

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

address: 1170 Veterans Blvd

department: Computing

institute: Calico Life Sciences, LLC

description: processed data file: myo_msx1.h5ad

data_processing:
library demultiplexing: bcl2fastq
alignment: kallisto
cellular demultiplexing: bustools
normalization: scVI 0.8.1
feature barcode demultiplexing: kite
Genome_build: mm10
Supplementary_files_format_and_content: h5ad, cells-by-genes count matrices

source_name: Myogenic cells

growth_protocol: Adipogenic cells and MSCs were cultured in DMEM + 10%FBS, 1% Pen/Strep. Cells were passaged once after isolation prior to transduction with reprogramming factors. Myogenic cells were grown in F10 + 20% FBS, 1% Pen/Strep, 5 ng/mL FGF2 for a week prior to passaging and transduction.

extract_protocol: 10x Chromiums v3.1 NextGEM gene expression assay

treatment_protocol: SOKM experiments transduced cells with a polycistronic TetOn>SOKM casette, induced for three days, and chased for three days with doxycycline. Msx1 experiments followed the same protocol using a TetOn>Msx1 lentivirus. Pooled screening experiments transduced cells with pools of S, O, K, M lentiviruses carrying constituitively expressed barcodes to enable in silico demultiplexing. Pooled screens likewise performed a 3 day pulse, 3 day chase.

value: Aged

tag: cellt ype

value: Myogenic cells


title: st3_i1

value: Osaka

value: cells from an intermediate region of a forming germ disc

value: stage 3


title: Myo_Aged_1_Control

description: processed data file: myo_msx1.h5ad

value: Control


title: Thpok_CD4 replicate 2

description:
Mature CD4 thymocyte from recipient mice transplanted with Lz-Thpok transduced bone marrow
ThpokCD4_2

data_processing:
Illumina RTA 1.18.61 software used for basecalling.
Samples demultiplexed using Bcl2fastq 2.17 software
Raw RNAseq fastq reads were trimmed with Trimmomatic and aligned to mouse genome using STAR
Gene-assignment and count of RNA reads were performed with Htseq
Genome_build: mm10
Supplementary_files_format_and_content: count of RNA reads were performed with Htseq; FPM normalization was performed with the FPM function of the DEseq2 package

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMARTer Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina) were used for library.   Libraries were pooled and sequenced with paired-end reads of 75bp on a Nexseq to reach 70 million read pairs per sample

tag: strain

tag: cell population

value: Cd4 Cre+Thpokfl/fl transduced with retrovirus expressing Lz-Thpok


title: si8ME_C

city: Shanghai

first: Ran

last: Tong

address: 227 South Chongqing Road, Huangpu District

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p13 whole genome using hisat2(Version 2.1.0).
Transcripts Per Million were calculated by RSEM(Version 1.3.3) by default parameters.
Assembly: GRCh38.p13
Supplementary files format and content: gene.count.matrix.annot
Supplementary files format and content: gene.TPM.matrix.annot

source_name: Human embryonic stem cells

growth_protocol: SHhES8 were grown in mTeSR1 medium.

extract_protocol:
Cells were collected and total RNA was extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: SHhES8 cells were dissociated using Accutase (STEMCELL Technologies, Canada), and subsequently seeded at a density of around 4 × 105 cells per well in six-well plates in mTeSR1 medium. Transfection mixture that contains NT siRNA or HESX1 siRNAs was added to the well. After 24 hours of culture, the medium of siNT ME cells, siHESX1#1 ME cells and siHESX1#2 ME cells were changed to ME induction medium [E8 medium (STEMCELL Technologies, Canada) supplemented with 5 ng/mL BMP4 (PeproTech, America) and 25 ng/mL Activin A (PeproTech, America)] . 72 hours of culture after plating, cells were collected for further analysis.

tag: cell lines

value: SHhES8 hESC line

tag: culture medium

value: mTeSR1, ME medium


title: si8ME_B


title: Thpok_CD4 replicate 1

description:
Mature CD4 thymocyte from recipient mice transplanted with Lz-Thpok transduced bone marrow
ThpokCD4_1

source_name: Thymus


title: Myo_Aged_0_Msx1

description: processed data file: myo_msx1.h5ad


title: PRO-seq_MEF_WT_HS_Rep1

tag: cell line/type

value: mouse embryonic fibroblasts (MEFs)

value: heat shock (42°C, 1 h)

value: nascent RNA


title: D28_MC3T3-E1 VitC- rep1 hMeDIP-seq

tag: tissue


title: PRO-seq_MEF_WT_MD_Rep1

tag: treatment

value: menadione (30 μM, 2 h)


title: Input DNA Femur

value: Femur


title: Gulotm1Mae VitC+- rep3 hMeDIP-seq


title: si5ME_C


title: MSC_Aged_1_Screen

description: processed data file: msc_screen.h5ad

source_name: Muscle-derived mesenchymal stem cells

value: Muscle-derived mesenchymal stem cells

value: TetO-S-BC; TetO-O-BC; TetO-K-BC; TetO-M-BC


title: WT CD8 replicate 3

description:
Mature CD8 thymocyte from C57Bl/6 mice
WTCD8_3

value: WT


title: Thpok_CD4 replicate 3

description:
Mature CD4 thymocyte from recipient mice transplanted with Lz-Thpok transduced bone marrow
ThpokCD4_3


title: Gulotm1Mae VitC+- rep2 hMeDIP-seq

value: 5hmC (Active Motif, 39791)


title: Gulotm1Mae VitC+- rep1 hMeDIP-seq


title: MSC_Aged_0_ScreenCtrl

description: processed data file: msc_screen.h5ad

value: Aged


title: si5ME_B


title: Gulotm1Mae VitC+ rep3 hMeDIP-seq


title: NT_ME_B


title: MSC_Young_0_ScreenCtrl

description: processed data file: msc_screen.h5ad

value: Young


title: MSC_Young_1_Screen

description: processed data file: msc_screen.h5ad


title: MSC_Aged_0_Screen

description: processed data file: msc_screen.h5ad


title: NT_ME_C


title: si8mTe_C


title: Myo_Aged_0_Control

description: processed data file: myo_msx1.h5ad

value: Myogenic cells


title: WT CD8 replicate 2

description:
Mature CD8 thymocyte from C57Bl/6 mice
WTCD8_2