title: RNA lungs, PRDM3/16KO, rep5

data_processing:
Quality was assessed with FastQC and reads were trimmed with TrimGalore (0.4.2)
Reads were aligned to mm10 reference genome with Bowtie2 (2.4.2) with options '-end-to-end' and '-sensitive'
Low quality alignments were removed with Samtools (1.10.0) and PCR duplicates were removed with Picard (2.18.22) MarkDuplicates
Raw count matrix was generated with HTSeq-count (2.0)
differential expression analysis done with DESeq2 using cutoffs: log2fold change > |0.58| and p.value < 0.05
Assembly: mm10
Supplementary files format and content: bulkRNA_raw_counts.txt, tab delimited file contains raw counts

source_name: lung

extract_protocol:
Lungs from E17.5 mice were harvested, minced, and incubated in RPMI media containing Liberase TM (Roche, 50ug/ml) and DNAse I (MilliporeSigma, 100ug/ml) at 37C for 30min. Tissues were dissociated with GentleMACS cell dissociator, then subjected to RBC lysis buffer for 2min on ice, followed by an incubation with FcR blocking reagent (Miltenyi: 130-092-575) on ice for 10min, followed by an incubation with CD326 anti-Mouse-EpCAM microbeads (Miltenyi: 130-105-958) at 4C for 15min. Cells were subjected to positive selection with EpCAM+ microbeads in an LS column and collected in MACS buffer (Miltenyi). Cells were quantified manually via hemacytometer with trypan blue.
RNA was isolated from selected cells using Qiagen's Rneasy Micro Plus kit following manufacturer's directions.
Collected RNA was sent to Genewiz for polyA enrichment, library construction, and sequencing.

value: lung

value: Epcam+ sorted Epithelial cells


title: Coral, col_L, temp_AMB, sym_RIC, rep_1

status: Public on Mar 01 2024

type: SRA

city: Parkville

first: Hugo

last: Scharfenstein

state: VIC

address: Grattan Street

country: Australia

institute: The University of Melbourne

description: Each sample was run on two NovaSeq 600 S4 lanes (L001 and L002)

library_source: transcriptomic

data_processing:
Quality of the raw sequences was verified using FastQC (version 0.12.0)
End-trimming of  sequences was carried out using fastp (version 0.23.2)
Concatanation of reads from lanes 1 and 2 for each sample and read direction
Trimmed sequences were first mapped to a P. daedalea reference genome using STAR (version 2.7.10b). This provided the gene count matrix for the coral host reads (processed file: "gene_counts_matrix_pdae.txt")
Unassigned sequences were then mapped to a C. proliferum reference genome using STAR (version 2.7.10b). This provided the gene count matrix for the photosymbiont reads (processed file: "gene_counts_matrix_cpol.txt")
Assembly: P. daedalea reference genome retrieved from: http://pdae.reefgenomics.org/. C. proliferum reference genome retrived from: https://espace.library.uq.edu.au/view/UQ:fba3259
Supplementary files format and content: Tab-delimited raw exon counts. Each column corresponds to a sample. One file for coral host reads, the second for photosymbiont reads.

molecule: polyA RNA

organism: Alveopora daedalea

source_name: P. daedalea colonies

extract_protocol:
Total RNA was isolated using a RNEasy Plant Mini Kit (Qiagen). The purified total RNA was normalised to a concentration of 50 ng/µl.
Messenger RNA libraries were constructed using Illumina Stranded mRNA Prep kit with 500 ng of starting input.

tag: cell type

value: P. daedalea colonies

tag: temperature treatment

value: Ambient

tag: coral genotype

value: Colony L

tag: inoculation treatment

value: RIC


title: As-50C-04

city: Ottawa

first: Santokh

last: Gill

state: Ontario

address: 251 SIR FREDERICK BANTING

department: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

description: DifferentialExpression_MicroPlastics_Astrocytes_Gill_50.tsv

data_processing:
Quality filtering and trimming Bbduk (38.84) maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment STAR (2.7.1a) OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting FeatureCounts (2.0.0) -p -Q=12 -C -t exon -g gene_id
Differential Expression calling DESeq2 (1.26.0) alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat fetal neural stem cell-derived Astrocyte

growth_protocol: Rat fetal neural stem cells (NSCs) were cultured in KnockOut DMEM/F12 supplemented with StemPro NSC SFM (2%), b-FGF and EGF (20ng/mL) (Peprotech, NJ, USA), GlutaMAX-1 (2mM) and 1% penicillin/streptomycin. These cells were culture on poly-L-ornithine (MilliporeSigma, ON, Canada) or Geltrex (ThermoFisher, ON, Canada) coated culture dishes. NSCs were differentiated into astrocytes with differentiation media consisting of D-MEM Medium with N-2 supplement (1%), 2mM GlutaMAX-1 supplement and 1% FBS, while plated on Geltrex coated plates.

extract_protocol:
Total RNA was extracted from cell culture samples using Qiagen miRNeasy kits. Subsequent steps were followed as per manufacture's instructions.
Polystyrene microsphere-treated astrocyte cDNA libraries were constructed using Illumina TruSeq Stranded mRNA protocol.

treatment_protocol: NSC-derived astrocytes were treated with non-fluorescent microspheres (Polybead®) 0-100 ug/ml for 7 days, with new microbeads in fresh media every 2-3 days.

tag: treatment

value: 10 µg/ml 50nm polystyrene microspheres


title: Coral, col_J, temp_AMB, sym_SS1, rep_1

value: Colony J


title: As-50C-03

value: Rat fetal neural stem cell-derived Astrocyte


title: 498MUS

city: Guangzhou

first: Liu

last: Yasong

address: Tianhe District Tianhe Road, No. 600

country: China

institute: Third Affiliated Hospital Of Sun Yat-Sen University

data_processing:
Illumina Casava 2.19 software was used for basecalling.
Clean reads were obtained by removing adapter, and excluded reads containing ploy-N and low-quality from raw data.
Reads were aligned to the mouse genome with Hisat2
For quantification of gene expression, only the reads aligned to exons, and with the mapping quality score larger than 10 were counted using the featureCounts v2.0.1
Assembly: GRCm38
Supplementary files format and content: text files include readcount values for each sample

organism: Mus musculus

source_name: MUS

extract_protocol:
Mice were monitored in the calorimetry chambers with recordings at 4-min intervals. After 30 min, ambient temperature of the chambers was lowered from 22°C to 4°C, and remained 4°C for 6 h. The mice were then quickly perfused with saline solution. Epididymal WAT, BAT, thigh skeletal muscle, and liver samples were collected and snap frozen in liquid nitrogen.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pre-diabetic obese mice with i.p. injected with KPT-330 (Selleck, 5 mg/kg) 30 min prior to acute cold stimulation; for vehicle control, mice were i.p. injected with equal amount of DMSO (1 ml/kg).

tag: tissue

value: MUS

tag: genotype

value: WT


title: RNA lungs, PRDM3/16KO, rep4

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

growth_protocol: Prdm3/16 double knockout mice were generated by crossing Prdm16 flox/flox ( Jackson Labs strain 024992) with Prdm3 flox/flox mice from the Mineo Kurokawa lab at the University of Tokyo and breeding in the ShhCre allele (Jackson laboratory strain  005622).  The cre allele was transmitted through the male germline from Prdm3fl/flPrdm16fl/wtShhCre+ animals bred to Prdm3fl/flPrdm16fl/fl females.

tag: time


title: B679MUS

value: DMSO


title: RNA lungs, PRDM3/16KO, rep2


title: 3MUS

value: CTRL


title: As-50C-02


title: RNA lungs, PRDM3/16KO, rep3


title: Coral, col_J, temp_AMB, sym_RIC, rep_1


title: Coral, col_I, temp_AMB, sym_RIC, rep_1

value: Colony I


title: 497MUS


title: As-500C-04

description: DifferentialExpression_MicroPlastics_Astrocytes_Gill_500.tsv

value: 10 µg/ml 500nm polystyrene microspheres


title: RNA lungs, PRDM3/16KO, rep1


title: As-50B-04

value: 1 µg/ml 50nm polystyrene microspheres


title: Coral, col_L, temp_AMB, sym_C, rep_2

value: C


title: 496MUS


title: RNA lungs, Control, rep5

value: lung

value: Control


title: Coral, col_L, temp_AMB, sym_C, rep_1

value: P. daedalea colonies


title: As-50B-03


title: As-50B-02


title: Coral, col_I, temp_AMB, sym_SS8, rep_2

value: Ambient


title: Coral, col_J, temp_AMB, sym_C, rep_2


title: Coral, col_I, temp_AMB, sym_RIC, rep_2


title: RNA lungs, Control, rep4

value: Epcam+ sorted Epithelial cells


title: RNA lungs, Control, rep3


title: RNA lungs, Control, rep2


title: Coral, col_J, temp_AMB, sym_C, rep_1


title: Coral, col_I, temp_AMB, sym_C, rep_1


title: As-50B-01


title: As-50C-01


title: S.rapa, without PQQ, rep3

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

description: srpqq.csv

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the streptomyces rapamycinicus NRRL5491(CP085193.1) and streptomyces griesus DSM 40236 (GCA_900105705.1) genome assembly using bowtie2（version: 2-2.0.5）.
Gene expression level was calculated by DESeq2 R package (v.1.20.0), displaying as average values of three clones from each group.
Assembly: streptomyces rapamycinicus NRRL5491(CP085193.1) and streptomyces griseus DSM 40236 (GCA_900105705.1)
Supplementary files format and content: csv files include values as follows: BaseMean (the average of the normalized counts for samples with and without PQQ operon); log2FoldChange (The log2-transformed fold change of averaged gene expression with and without PQQ operon); lfcSE (The standard error associated with the log2FoldChange): stat (The Wald test statistic for testing the null hypothesis that the log2FoldChange is equal to zero (i.e., no differential expression)); pvalue (The p-value associated with the Wald test).

organism: Streptomyces rapamycinicus

source_name: bacteria

extract_protocol:
The total RNA of each sample was extracted using Total RNA Extractor kit (B511311, Sangon, China) according to the manufacturer’s protocol. The extracted RNA was then sent to the Sangon Biotech (Shanghai) Co., Ltd. for library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bacteria

value: without PQQ operon


title: RNA lungs, Control, rep1


title: As-50A-03


title: male mouse, LC region

city: Seattle

first: Xiaonan

last: Fu

state: WA

address: 1705 NE Pacific St

department: Biochemistry

institute: University of Washington

description: Fresh Frozen spatial transcriptome sequencing (Pixel-seq)

data_processing:
Index map: in house basecalling for spatial indices
Index & gene extraction: Pixel-seq reads include two parts of information: The UMIs and spatial indices sequences were extracted from Read 1 using cutadaptv3.3. The read 2 were aligned to the GRCm38 genome assembly using STARv2.7.8a with the default configurations, featureCountsv1.6.0 was used to assign gene name to each reads with Mus_musculus.GRCm38.101.gtf as reference. Then they were integrated into a fasta file with header for gene mapping information and sequences as spatial indices.
Mapped reads: The spatial barcode sequencing mapping was performed by bowtie allowing up to 2 mismatches reporting the top alignment.
Segmentation: A customized method V-seg (Volume-distance based segmentation of mapped transcripts) was used to aggregate the profile for cellular level analysis, implemented in R
Clustering: The DGE matrix of segmented cells was analyzed in the Seurat v4.0.2 package. The SCTransform was used for normalization. The UMAP Clustering was performed on PCA reductions and optimal resolution.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file
Supplementary files format and content: seurat object file

source_name: Mouse brain LC region

extract_protocol:
Fresh frozen tissue were embedded in OCT,  brain region containing the LC and peri-LC was chosen at 10-μm sections
Spatial transcriptome libraries were constructed as Pixel-seq protocol
barcode sequence were contained in one end of the reads and the mRNA sequence were located in the other end

value: Mouse brain LC region

tag: Sex

value: male

value: wildtype


title: lungs, Wild Type C57Bl6, Rabbit IgG, rep2

library_source: genomic

data_processing:
Trimmomatic was used to remove adapter sequences and low quality base pairs
Reads were aligned with Bowtie2 to the mm10 reference genome using the --dovetail and --phred33 options
MACS2 was used to call peaks from bam files using -p 0.01 -B -f BAMPE --keep-dup all --SPMR options and the appropriate IgG control
Peaks were annotated and merged as needed with HOMER annotatePeaks.pl and mergePeaks
The bdgcmp function of MACS2 was used with -m FE (fold enrichment) option to generate a bedgraph, which was sorted and converted to a bigwig.
Assembly: mm10
Supplementary files format and content: big wig files for visulization
Supplementary files format and content: tab delimited narrowPeak files
Library strategy: Cut&Run

molecule: genomic DNA

extract_protocol:
100,000 EpCAM+ cells were bound to concanavalin A beads, then incubed with antibodies against PRDM16, NKX2-1, PRDM3, or H3K4me3. IgG controls with either a rabbit or sheep IgG were also generated.
Cells were incubated with pAG-Mnase to facilitate anitbody-guided DNA digestion. The extracted DNA was purified by phenol-chloroform-isoamyl alcohol (Invitrogen: 15593-031) extraction and  Phasemaker tubes (Invitrogen: A33248)
DNA was quantified using a Qubit (ThermoFisher) and libraries were constructed using the Illumina DNA Library Prep Kit (Cell Signaling Technology, 56795S) and Multiplexoligos (47538S). Libraries were sequenced for at least 15mil reads.
Libraries sequenced by Genewiz

treatment_protocol: Lungs from E17.5 Wild Type C57Bl6 mice were harvested, minced, and incubated in RPMI media containing Liberase TM (Roche, 50ug/ml) and DNAse I (MilliporeSigma, 100ug/ml) at 37C for 30min. Tissues were dissociated with GentleMACS cell dissociator, then subjected to RBC lysis buffer for 2min on ice, followed by an incubation with FcR blocking reagent (Miltenyi: 130-092-575) on ice for 10min, followed by an incubation with CD326 anti-Mouse-EpCAM microbeads (Miltenyi: 130-105-958) at 4C for 15min. Cells were subjected to positive selection with an LS column and collected in MACS buffer (Miltenyi). Cells were quantified manually via hemacytometer with trypan blue.

tag: antibody

value: Rabbit IgG

tag: antibody catalog_info

value: Vector Labs, BA-1000

value: Wild Type C57Bl6,


title: As-50A-01

value: Rat fetal neural stem cell-derived Astrocyte


title: As-50A-02


title: S.rapa, without PQQ, rep2

description: srpqq.csv


title: RNA lungs, Control, rep6


title: female mouse, LC region

value: female


title: Low-risk serrated lesions cfDNA pool  B9

type: genomic

city: Vigo

first: María

last: Gallardo-Gómez

address: Campus As Lagoas Marcosende

country: Spain

institute: Universidad de Vigo

description: Low-risk serrated lesions cfDNA pool  B9

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
Matrix_signal_intensities_serrated.txt file contains: Unmethylated and methylated signal intensities, Detection P-value

label: Cy3, Cy5

organism: Homo sapiens

source_name: serum

label_protocol: Standard Illumina labelling protocol

extract_protocol: Circulating cell-free DNA was isolated from serum samples by a phenol-chloroform protocol

value: serum

tag: pathology

value: LR-SL

tag: molecule subtype

value: circulating cell-free DNA


title: S.rapa, with PQQ, rep3

description: srpqq.csv

value: with PQQ operon


title: lungs, Wild Type C57Bl6, NKX2-1, rep2

value: lung

value: NKX2-1 Rabbit

value: Seven Hills Bioreagents, WRAB1231


title: As-50A-04

value: Control


title: Seq05_Tfh5_6

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

data_processing:
Fastq files were demultiplexes with Multi Demultiplex (Galaxy Version 1.0) using Illumina Index file
All raw fastq data were mapped to the mouse genome (mm10) using STAR 2.7.2b(Dobin et al., 2013)
Count matrices were generated using FeatureCount 1.6.4 (Liao et al., 2014) with the gene annotation file for mm10
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts

source_name: activated murine CD4 T cells in vitro

growth_protocol: Isolated naive CD4 T cells were cultured in 96-well flat-bottom plates in complete RPMI for 3.5 days

extract_protocol:
Cells were stained for flow cytometry and and sorted directly into Trizol LS. RNA was isolated using Chloroform-Extraction followed by a RNA-purification via spin-columns.
Libraries were generated according to manufacturer´s guidelines with the 3‘ mRNA-Seq Library Prep Kit FWD with Unique Dual Indices (Lexogen) using 50 ng total RNA as input.

treatment_protocol: The cells were activated with plate-bound anti-CD3 and anti-CD28 and differentiated in the indicated conditions

value: activated murine CD4 T cells in vitro

value: CD4Cre+ Maf fl/fl


title: Seq05_Tfh5_3


title: Coral, col_I, temp_AMB, sym_C, rep_2

value: P. daedalea colonies

value: Ambient

value: Colony I

value: C


title: Seq05_Tfh5_1


title: lungs, Wild Type C57Bl6, H3K4me3, rep3

value: H3K4me3 Rabbit

value: Cell Signaling, 9751

value: Epcam+ sorted Epithelial cells

value: Wild Type C57Bl6,


title: lungs, Wild Type C57Bl6, NKX2-1, rep3


title: lungs, Wild Type C57Bl6, H3K4me3, rep2


title: Seq05_Tfh1_1


title: S.rapa, without PQQ, rep1

description: srpqq.csv

value: bacteria

value: without PQQ operon


title: lungs, Wild Type C57Bl6, NKX2-1, rep1


title: Seq05_Tfh1_6


title: NaAC-CRP-E182D-3

city: Tianjin

first: Yangyang

last: Zheng

address: 135 Yaguan Road, Jinnan District, Tianjin

institute: Tianjin University

data_processing:
RNA sequencing of 6 samples was performed using an Illumina HiSeq platform.
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). The quantity and quality of the isolated RNA were determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), Nano Drop (Thermo Fisher Scientific Inc.) and 1% agarose gel electrophoresis.
The following library preparation required 1μg of total RNA with an RNA Integrity Number (RIN) value above 6.5. The NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England BioLabs, Ipswich, MA, USA) was used to construct next-generation sequencing libraries. The libraries sequencing was carried out on an Illumina HiSeq platform using a 2×150 paired-end (PE) configuration.
The sequences were processed and analyzed by GENEWIZ (Suzhou, China).
Assembly: Escherichia coli str. K-12 substr. MG1655, complete genome.
Supplementary files format and content: Fastq with raw gene counts for every gene and every sample

organism: Escherichia coli

growth_protocol: Mutant strain CRP-E182D was grown in the presence of 20 g/L sodium acetate and collected for transcriptome analysis. The wild-type strain MG1655 grown with 20 g/L sodium acetate was used as control.

extract_protocol:
RNA sequencing of 6 samples was performed using an Illumina HiSeq platform. The samples were collected during the mid-logarithmic phase, quickly frozen in liquid nitrogen and stored at -80 °C. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). The quantity and quality of the isolated RNA were determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), Nano Drop (Thermo Fisher Scientific Inc.) and 1% agarose gel electrophoresis. The following library preparation required 1μg of total RNA with an RNA Integrity Number (RIN) value above 6.5. The NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England BioLabs, Ipswich, MA, USA) was used to construct next-generation sequencing libraries. The libraries sequencing was carried out on an Illumina HiSeq platform using a 2×150 paired-end (PE) configuration.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: lungs, Wild Type C57Bl6, H3K4me3, rep1


title: S.rapa, with PQQ, rep2

description: srpqq.csv

value: with PQQ operon


title: NaAC-CRP-E182D-2


title: Seq05_Tfh1_3


title: lungs, Wild Type C57Bl6, Sheep IgG, rep1

value: lung

value: Sheep IgG

value: Jackson ImmunoResearch, 713-065-147


title: S.rapa, with PQQ, rep1

description: srpqq.csv


title: NaAC-CRP-E182D-1


title: Seq05_TfhA_3


title: lungs, Wild Type C57Bl6, Rabbit IgG, rep1

value: Rabbit IgG

value: Vector Labs, BA-1000


title: Wild type mouse HFSCs at PD 35, biological replicate 3

type: RNA

city: Navi Mumbai

first: SANJEEV

middle: K

last: WAGHMARE

state: MAHARASHTRA

address: Sector 22, Kharghar

department: STEM CELL BIOLOGY GROUP

country: India

institute: ACTREC, TATA MEMORIAL CENTRE

description: Gene expression data of wild type mouse hair follicle stem cells (HFSCs) isolated at postnatal day 35, i.e. telogen-anagen transition

hyb_protocol: The fragmented and labelled product was loaded onto GeneChip® MTA 1.0 array (Affymetrix, USA) and was hybridized using GeneChip® MTA 1.0 array (Affymetrix, USA).

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000. Streptavidin-Phycoerythrin (Molecular Probes) was used as the fluorescent conjugate to detect hybridized target sequences. Raw intensity data from the GeneChip array were analyzed by GeneChip Operating Software (Affymetrix).

data_processing: The raw signal intensity data (.CEL files) were obtained from the Affymetrix GeneChip® Command Console (AGCC) software. Normalization and summarization was done using the RMA sketch algorithm implemented in Expression Console to generate normalized intensity data (.CHP files)

label: Biotin

source_name: Wild type mouse skin at PD35

label_protocol: The fragmented cDNA was labelled by terminal deoxynucleotidyl transferase (TdT) by using the Affymetrix proprietary DNA Labelling Reagent that is covalently linked to biotin.

growth_protocol: Dab2 fl/fl mice and K14 Cre mice were imported from Jackson laboratories. Dab2 fl/ fl mice were crossed with K14 Cre for multiple generations to obtain K14 Cre- Dab2fl/fl (WT) and K14 Cre+ Dab2fl/fl (Dab2 cKO). To activate Cre expression, mice were treated with tamoxifen intraperitoneally for 5 consecutive days at 75mg/kg body weight per day.

extract_protocol: RNA extraction from FACS purified HFSCs was done using the absolutely RNA miniprep kit as described in the manufacturer’s procedure (Agilent technologies). The RNA quality was assessed by Agilent RNA 6000 Pico kit on the Agilent 2100 bioanalyzer. For microarray analysis, 1ng RNA was amplified by using the Gene Chip® WT Pico amplification Kit (Affymetrix, USA) as per manufacturer’s instruction. RNA was reverse transcribed to cDNA with T7 Oligo d (T) primer (Affymetrix). The cDNA was used for in vitro transcription reactions containing T7 RNA polymerase. Then sense-strand cDNA was synthesized by the reverse transcription of cRNA using 2nd-Cycle Primers followed by RNase H hydrolyzes the cRNA template leaving single-stranded cDNA. The purified, sense-strand cDNA was fragmented by uracil-DNA glycosylase (UDG) and a purinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues that break the DNA strand.

treatment_protocol: Dorsal skin sections of WT and Dab2 cKO mice at were collected at PD35 and incubated in 0.25% trypsin EDTA O/N. Next day, epidermis was separated from the dermis and single cell suspension was prepared.  The cells were centrifuged at 2000 rpm for five min. at 4°C. The cell pellet was washed by using ice-cold 1X 476 PBS and centrifuged again. The cell pellet was then dissolved in 750ul- 1ml of 5% chelated FBS in 1X PBS (FACS buffer) and stained with the anti- CD34 and anti-α6-Integrin to sort HFSCs using FACS Aria machine (BD Biosciences). The HFSCs were collected directly into 1.5 ml eppendorf tubes containing  into the RNA lysis buffer for RNA extraction.

value: Skin

value: WT

tag: gender

value: Female

tag: age

value: Postnatal day 35


title: Seq05_TfhA_1

value: activated murine CD4 T cells in vitro

value: CD4Cre+ Maf fl/fl


title: NaAC-Ctr-3

value: wild type


title: Homozygous Dab2 cKO mouse HFSCs at PD 35, biological replicate 3

description: Gene expression data of homozygous Dab2 cKO mouse hair follicle stem cells (HFSCs) isolated at postnatal day 35, i.e. late telogen

source_name: Homozygous Dab2 cKO skin at PD35

value: Homozygous Dab2 cKO


title: lungs, Wild Type C57Bl6, PRDM3, rep1

value: PRDM3 Rabbit

value: Cell Signaling, 2593

value: Epcam+ sorted Epithelial cells

value: Wild Type C57Bl6,


title: Homozygous Dab2 cKO mouse HFSCs at PD 35, biological replicate 1


title: Homozygous Dab2 cKO mouse HFSCs at PD 35, biological replicate 2


title: NaAC-Ctr-2


title: Wild type mouse HFSCs at PD 35, biological replicate 1


title: Wild type mouse HFSCs at PD 35, biological replicate 2


title: lungs, Wild Type C57Bl6, PRDM16, rep2

value: lung

value: PRDM16 Sheep


title: Seq05_TfhA_6


title: MNase Bud27 mutant rep2

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

institute: University of Seville

data_processing:
Sequencer Software HiSeq Control Software 2.2.58
AfterQC v0.9.6 was used with default parameters to do the quality control, filtering and trimming of the sequences
reads were mapped to the Saccharomyces cerevisiae reference genome version R64 (SacCer3) using Bowtie2 v2.3.3.1
DANPOS v2.2.2 was used to determine nucleosome positions
background correction with naked DNA data was from Begley et al. 2021 doi: 10.1080/15476286.2020.1845504
Supplementary files format and content: merged wig file generated by DANPOS

organism: Saccharomyces cerevisiae

source_name: bud27-delta from Euroscarf collection.

growth_protocol: YPAD medium

extract_protocol:
described in Begley et al. 2021 doi: 10.1080/15476286.2020.1845504
Standard Illumina 50 paired end HiSeq Sequencing v4 Chemistry

treatment_protocol: MNase digestion protocol was derived from Begley et al. 2021 doi: 10.1080/15476286.2020.1845504

tag: cell line

value: bud27-delta from Euroscarf collection.


title: HepG2 cells with hSPARC overexpression, replicate 3

city: Suzhou

first: Shan

last: Wan

address: Renai Road 199

department: Pathology

institute: Soochow University

data_processing:
Reads were normalized by edgeR according to Robinson et al., 2010.
Assembly: hg19
Supplementary files format and content: Excel file includes raw counts and counts normalized by edgeR for each Sample.

growth_protocol: HepG2 stable cell lines were cultured in a humidified incubator at 37℃ with 5% CO2. Cells were cultured in RPMI-1640 medium (Gibco, Cat. #11875-093) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
For isolation of RNA from cell lines, the NucleoSpin RNA Mini kit (Macherey-Nagel) was used according to the manufacturer’s instruction with a digestion step of genomic DNA. Concentrations of isolated RNA were determined by the Nanodrop One (Thermo Fisher Scientific, Cat. #840-317400).
RNA libraries were constructed using a Low Input RNA Library Prep Kit (GenSeq).

tag: cell type

value: liver cancer cells

value: SPARC overexpression


title: lungs, Wild Type C57Bl6, PRDM16, rep1

value: PRDM16 Rabbit

value: Harms, et. al. 2014 (see reference section)


title: NaAC-Ctr-1


title: ATAC lungs, Prdm3/16KO, rep5

data_processing:
Files were processed using the ENCODE pipeline for ATACSeq with replicates.
The IDR conservative peakset called by ENCODE pipeline defaults (MACS, p-value <0.01), along with the trimmed, sorted, deduplicated, no mitochondrial DNA bam file, were used for a DiffBind (v3)
Differential Accessibility Analysis done with DiffBind using cutoffs: log2 fold change > |0.58|, p.value < 0.05
Assembly: mm10
Supplementary files format and content: tab delimited narrowPeak file from MACS2 output
Supplementary files format and content: bigwigs normalized with deepTools bamCoverage RPKM

molecule: nuclear RNA

growth_protocol: Prdm3/16 double knockout mice were generated by crossing Prdm16 flox/flox (Jackson Labs strain 024992) with Prdm3 flox/flox mice from the Mineo Kurokawa lab at the University of Tokyo and breeding in the ShhCre allele (Jackson laboratory strain  005622).  The cre allele was transmitted through the male germline from Prdm3fl/flPrdm16fl/wtShhCre+ animals bred to Prdm3fl/flPrdm16fl/fl females.

extract_protocol:
Lungs from E17.5 mice were harvested, minced, and incubated in RPMI media containing Liberase TM (Roche, 50ug/ml) and DNAse I (MilliporeSigma, 100ug/ml) at 37C for 30min. Tissues were dissociated with GentleMACS cell dissociator, then subjected to RBC lysis buffer for 2min on ice, followed by an incubation with FcR blocking reagent (Miltenyi: 130-092-575) on ice for 10min, followed by an incubation with CD326 anti-Mouse-EpCAM microbeads (Miltenyi: 130-105-958) at 4C for 15min. Cells were subjected to positive selection with an LS column and collected in MACS buffer (Miltenyi). Cells were quantified manually via hemacytometer with trypan blue.
50,000 Epcam+ epithelial cells were captured and nuclei were isolated using lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were subjected to a transposition reaction with a Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) at 37C for 30m.
Transposed DNA fragments were quantified by qPCR and amplified with barcoded primers using the NEB Next High-Fidelity 2x PCR master mix.
Libraries sent to Genewiz for sequencing


title: Seq05_Tfh5_4

value: CD4Cre- Maf fl/fl


title: HepG2 cells with hSPARC overexpression, replicate 2


title: Seq05_Tfh5_5


title: MNase Bud27 mutant rep1


title: HepG2 cells with hSPARC overexpression, replicate 1


title: ATAC lungs, Prdm3/16KO, rep4


title: Seq05_Tfh5_2


title: MR-VL_FBO vs KOP8_rep3

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

description: Replicate 3 of 4 of MR-VL_FBO vs KOP8

hyb_protocol: Labeled cRNA were pooled and hybridized  on a custome-made Agilent 8x60k array using the Gene Expression Hybridization Kit (Agilent Technologies). Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: All arrays were scanned using an Agilent Microarray High Resolution Scanner (default settings for two-color GE micro-arrays).

data_processing: Raw data were extracted using Agilent Feature Extraction Software 10.5 (GE2_107_Sep09 protocol). Data were transferred to limma (Smyth, 2004) for statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was assessed using empirical Bayesian statistics.

organism: Tetranychus urticae

label_protocol: Cy5- and Cy3-labeled cRNA was synthesized from RNA following the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Mites were were maintained on bean (Phaseolus vulgaris cv. Prelude) in climatically controlled rooms at 25 ± 1°C, 60 % RH and 16:8 h light:dark photoperiod.

extract_protocol: T. urticae RNA was isolated with the Qiagen RNeasy Plus Mini kit using approximately 100-120 pooled female mites. Four RNA extractions were performed for each strain.

treatment_protocol: The MR-VL strain (described in Van Leeuwen et al. 2005, doi:10.1002/ps.1001) was grown on bean leaves sprayed with 200 mL of  1000 mg a.i./L fenbutatin oxide (Torque 550 g/L SC) until runoff, with sprayed leaves being refreshed weekly. The MR-VL strain was kept under fenbutatin oxide selection pressure for more than three years and subsequently renamed to MR-VL_FBO. Two weeks before RNA extraction for microarray experiments, MR-VL_FBO mites were grown on unsprayed bean leaves. The KOP8 strain was susceptible to fenbutatin oxide and has previously been described in Riga et al. 2016 (doi:10.1038/s41598-017-09054-y).

tag: developmental stage

value: adult

value: female

tag: colour morph

value: red


title: Seq05_Tfh1_4

value: activated murine CD4 T cells in vitro


title: MR-VL_FBO vs KOP8_rep4

description: Replicate 4 of 4 of MR-VL_FBO vs KOP8


title: ATAC lungs, Prdm3/16KO, rep3


title: MR-VL_FBO vs KOP8_rep2

description: Replicate 2 of 4 of MR-VL_FBO vs KOP8


title: Seq05_Tfh1_5


title: MR-VL_FBO vs KOP8_rep1

description: Replicate 1 of 4 of MR-VL_FBO vs KOP8


title: Seq05_Tfh1_2


title: HepG2 cells expressing empty vector, replicate 2

value: WT


title: HepG2 cells expressing empty vector, replicate 3


title: HepG2 cells expressing empty vector, replicate 1


title: ATAC lungs, Prdm3/16KO, rep1


title: ATAC lungs, Prdm3/16KO, rep2


title: Seq05_TfhA_4


title: ATAC lungs, Control, rep5

value: Control


title: ATAC lungs, Control, rep4


title: Seq05_TfhA_2


title: HUVEC_VEGF-0h_RNA-seq

city: Kumamoto

first: Shunsuke

last: Kamei

address: 2-2-1 Honjo

country: Japan

institute: Kumamoto University

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using RNA-specific STAR aligner.
Reads were further assigned to respective hg19 refseq of transcripts using the featureCounts tool.
Differential gene expression analysis to compare VEGF-treated for 18h samples with control VEGF-treated for 0h samples was performed using EBSeq.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw read counts and normalized counts (TPM) for each sample

source_name: HUVEC

growth_protocol: HUVEC cells were maintained in EGM-2 medium supplemented with 5% (v/v) fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using ISOSPIN Cell & Tissue RNA Kit (Nippon gene) according to the manufacturer's instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: HUVEC cells ware starved in EBM-2 basal medium with 0.5% (v/v) fetal bovine serum for 10h, treated with 20 ng/mL human recombinant VEGF-A165 for 0h or 18h.

value: HUVEC

value: Vascular endothelial cell

value: wild type

value: human recombiant VEGF-A


title: HUVEC_VEGF-18h_RNA-seq


title: HUVEC_siFOXO1_VEGF-18h_RNA-seq

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using RNA-specific STAR aligner.
Reads were further assigned to respective hg19 refseq of transcripts using the featureCounts tool.
Differential gene expression analysis to compare siFOXO1-treated samples with siControl-treated samples was performed using EBSeq.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw read counts and normalized counts (TPM) for each sample

treatment_protocol: HUVEC cells were treated with 20nM siRNA for 24h. After treated with siRNA, HUVEC cells ware starved in EBM-2 basal medium with 0.5% (v/v) fetal bovine serum for 10 h, treated with 20 ng/mL human recombinant VEGF-A165 for 18h.

value: Endothelial cell

value: FOXO1 knockdown


title: EB_D3_Zfp462_KO_rep2

city: chongqing

first: yu

last: meng

address: xinqiao street

institute: Army medical university

description: Zfp462 KO ESCs cultured in EB differentiation  for 3 days

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2.
featureCount software was used to calculate gene expression from aligned bam files
R statistical package DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: raw reads counts

growth_protocol: Mouse ESCs were cultured on 0.2% gelatin-coated plates in the indicated medium. LIF/serum culture: DMEM supplemented with 15% FBS, 2mM GlutaMAX, 1% MEM non-essential amino acids, 0.1mM β-mercaptoethanol (all from Invitrogen) and 10 ng/ml LIF (Millipore). For embryoid body differentiation, ESCs were trypsinized to single-cell suspensions and cultured in Petri dishes for 3 days.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library.
RNA-seq transcriptome libraries were prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA), using 1μg of total RNA. Shortly, messenger RNA was isolated with polyA selection by oligo(dT) beads and fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol.

value: embryoid differentiated cells

value: Zfp462 knockout


title: HUVEC_siControl_VEGF-18h_RNA-seq


title: EB_D3_Zfp462_KO_rep1


title: ATAC lungs, Control, rep3

value: lung

value: Epcam+ sorted Epithelial cells


title: ATAC lungs, Control, rep2


title: high-fat diet with mulberry leaf powder [QvsM], biological rep3

city: Kanagawa

first: Asuka

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

institute: Kanagawa Academy of Science and technology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip® Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using the DFW.

label: biotin

source_name: rat fed a high-fat diet with muberry leaf powder for 8 weeks

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip® 3' IVT Express kit, Affymetrix).

growth_protocol: Male Wistar rats (7 weeks old) were purchased from Japan SLC, Inc. (Shizuoka, Japan) and housed in a room that was maintained at 21 ± 1°C and 50 ± 10% relative humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). The rats were preliminary given a normal diet (CE-2, CLEA Japan, Kanagawa, Japan) for acclimation. After a week of acclimation, the rats were divided into three groups (n=10 each) and fed for 8 weeks on a high-fat diet (Quick fat, CLEA Japan, Kanagawa, Japan), a high-fat diet plus 1% mulberry leaf powder, or a normal diet. Mulberry leaf powder was obtained from Sagamihara chamber of commerce and industry (Kanagawa, Japan). The rats were given a specific diet and water for 24 h ad libitum. On day 56 after overnight fasting, the animals were euthanized under anesthesia to collect their blood.

extract_protocol: Total RNA was isolated using TRIzol LS reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Blood was collected, homogenated with TRIzol LS reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), and stored at -80˚C

value: Wistar

value: male

value: blood

tag: diet

value: high-fat diet with muberry leaf powder


title: high-fat diet with mulberry leaf powder [QvsM], biological rep4


title: high-fat diet with mulberry leaf powder [QvsM], biological rep2


title: ATAC lungs, Control, rep6


title: high-fat diet [QvsM], biological rep3

source_name: rat fed a high-fat diet for 8 weeks

value: high-fat


title: high-fat diet [QvsM], biological rep2


title: high-fat diet [QvsM], biological rep4


title: HUVEC_Ad-CA-FOXO1_RNA-seq

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using RNA-specific STAR aligner.
Reads were further assigned to respective hg19 refseq of transcripts using the featureCounts tool.
Differential gene expression analysis to compare Ad-CA-FOXO1-treated samples with Ad-Control-treated samples was performed using EBSeq.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw read counts and normalized counts (TPM) for each sample

treatment_protocol: HUVEC cells ware treated with MOI=100 of Ad-Control or Ad-CA-FOXO1 for 48h.

value: FOXO1 overexpression

tag: treatment


title: Seq05_TfhA_5

value: activated murine CD4 T cells in vitro

value: CD4Cre- Maf fl/fl


title: EB_D3_CTL_rep2

description: CTL ESCs cultured in EB differentiation  for 3 days

value: WT


title: high-fat diet with mulberry leaf powder [QvsM], biological rep1

tag: tissue


title: high-fat diet [QvsM], biological rep1


title: HUVEC_Ad-Control_RNA-seq

value: HUVEC

tag: genotype

value: wild type

value: Adeno Control (Adeno-IRES-EGFP)


title: ATAC lungs, Control, rep1

value: Control

tag: time


title: vitro_4T1-sgTsc1, rep2

city: Bethesda

first: Jae Young

last: So

state: MD

address: 37 Convent Drive, Rm 3134

department: LCBG

institute: NCI/NIH

data_processing:
FastQC/Preseq/Picard toos/RSeQC, trimm read by Cutadapt, mapping by STAR (v2.5.2b), differential gene analysis by Limma (v3.34.9)
Assembly: mm10
Supplementary files format and content: Vitro_RSEM.genes.TPM.all_samples.txt

extract_protocol:
RNA was extracted from cells by using the Rneasy Kit (QIAGEN, #74004)
TruSeq mRNA Prep Kit (RS-122-2101)

tag: growth protocol

value: in vitro cell culture

value: mammary tumor cell

value: TSC1 knockout


title: EB_D3_CTL_rep1

value: embryoid differentiated cells


title: vitro_4T1-sgTsc1, rep1


title: ESC_Zfp462_KO_rep1

description: Zfp462 KO ESCs cultured in LIF/Serum culture

value: mouse embryonic stem cells

value: Zfp462 knockout


title: ESC_Zfp462_KO_rep2


title: vitro_4T1-sgTgfbr2, rep2

value: TGFBR2 knockout


title: ESC_CTL_rep2

description: CTL ESCs cultured in LIF/Serum culture


title: HTR8/SVneo: Normal m6A IP

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

data_processing:
Library strategy: m6A-Seq
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg38).
Bioinformatic and motif enrichment analysis was performed as described previously(Liu, J., et al. (2018). "m(6)A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer." Nat Cell Biol 20(9): 1074-1083.)
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files containing the peak associated genes,location and enrichment of the peaks obtained from the m6A-seq experiments

growth_protocol: Cells were grown in RIPM-1640 media supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from normoxia or hypoxia HTR8 cell lines. Polyadenylated RNA was further enriched from total RNA using a Dynabeads mRNA purification kit (Invitrogen).
RNA fragmentation, m6A-IP and library preparation were carried out according to previously published protocols(Wang, X., et al. (2014). "N6-methyladenosine-dependent regulation of messenger RNA stability." Nature 505(7481): 117-120.)

treatment_protocol: HTR8/Svneo cells were treated with or without 2% O2 for 12 h

value: trophoblast

tag: m6a antibody

value: Synaptic Systems 202003


title: HTR8/SVneo: Normal input

value: none (input)


title: HTR8/SVneo: Hypoxia m6A IP


title: vitro_4T1-sgTgfbr2, rep1


title: HTR8/SVneo: Hypoxia input


title: high-fat diet [CvsQ], biological rep3

description: no additional information

value: Wistar

value: male

value: blood

value: high-fat


title: high-fat diet [CvsQ], biological rep1

description: no additional information


title: ESC_CTL_rep1

description: CTL ESCs cultured in LIF/Serum culture

value: WT


title: vitro_4T1-sgNf1, rep2

value: NF1 knockout


title: vitro_4T1-sgNf1, rep1


title: vitro_4T1-C1, rep2

value: control


title: ICSI_Eq_twin_131b, blastocyst, scRNA-seq

city: Muenster

first: Wojciech

last: Makalowski

address: Niels Stensen Strasse 14

department: Faculty of Medicine

institute: University of Muenster

description:
Smart-Seq2
plate2-M06-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

library_source: transcriptomic single cell

data_processing:
Reads were trimmed and adapters were removed using Trimmomatic (V.039).
Read quality was checked for each cell using FastQC (v0.12.1).
Reads were mapped to mm10, and expression of genes were quntified using STAR (2.7.10b) pipeline
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-seperated values files (features and barcodes) plus matrix files

source_name: preimplantation embryo Theiler stage 5

growth_protocol: In vitro culture of fertilized oocytes in KSOM medium supplemented with aminoacids, in pool (4-well plate) up to the 2-cell stage, then individually after bisection (one blastomere per well of 96-well plate), at 37 °C under 5% CO2 in air, as described (PMID 28811525).

extract_protocol:
Single blastomeres or single blastocysts were lysed in 10X Lysis Buffer from Takara (cat.no. 635013). Then the RNA was extracted by TaKaRa SMART-Seq Single Cell Kit (cat.no. 634470).
Total RNA was converted to cDNA using the TaKaRa SMART-Seq Single Cell Kit (cat.no. 634470) and sequencing libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit (cat.no. FC-131-1024). Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Sperm deposition by ICSI in three different ooplasmic locations (contralateral, isolateral or equatorial relative to meiotic spindle)

value: preimplantation embryo Theiler stage 5

value: blastocyst


title: ICSI_Eq_twin_132a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-M07-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: WT A3_2

city: Cleveland

first: JIAJIA

last: XI

address: 9620 Carnegie Avenue

department: Cancer Biology

institute: Cleveland Clinic

description: WT A3_2

data_processing:
The RNA-seq sequence data FASTQ files were first inspected by fastqc to ensure data quality.
The reads were trimmed of exogenous adapter sequences and low-quality bases were removed using cutadapt(version 2.8)
The trimmed reads were aligned to the mouse genome (ENSEMBL GRCm38)
Quantification of reads was performed to generate the gene level feature counts from the read alignment with STAR (version 2.7.5a)
Assembly: mm10(GRC38)
Supplementary files format and content: .xlsx file contains raw counts for each sample

source_name: Bone Marrow Drived Macrophages

growth_protocol: Mouse bone marrow was isolated from animals, and suspended 6- well plates with 2 mL DMEM+10% FBS containing 10 ng/mL M-CSF, medium was changed every 2 days.

extract_protocol:
Total mRNA was extracted with EZ-10 Spin Columns Total RNA Miniprepes Super Kit from Bio Basic accroding to manufacter's instruction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primer followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adpater ligation, size selection, ampification and purification.

treatment_protocol: On the 7th days after isolation, the cells were transfected with 2-5A or A3 or mock with lipofactamine for 2hs.

value: Bone Marrow Drived Macrophages

value: Primary cells

value: A3 transfected


title: vitro_4T1-C1, rep1

value: in vitro cell culture

value: mammary tumor cell


title: WT A3_1

description: WT A3_1


title: high-fat diet [CvsQ], biological rep2

description: no additional information


title: ICSI_Eq_twin_131a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-M05-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Cas_PT_4T1-sgTsc1, rep2

data_processing:
FastQC/Preseq/Picard toos/RSeQC, trimm read by Cutadapt, mapping by STAR (v2.5.2b), differential gene analysis by Limma (v3.34.9)
Assembly: mm10
Supplementary files format and content: Cas_PT_RSEM_Genes_TPM_AllSamples.txt

source_name: mammary tumor

value: mammary tumor

value: TSC1 knockout


title: WT 25A_2

description: WT 25A_2

value: 2-5A transfected


title: ICSI_Is_twin_130b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-M04-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Cas_PT_4T1-sgTsc1, rep1


title: HTR8/SVneo: Hypoxia_replicate2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2 v2.1.0
Stringtie v1.3.3b was used to calculate the FPKM of gene to represent their mRNA expresion level.
The pvalue were caculated by a negative binomial model using DEseq2 package.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files containing include RPKM values for each Sample

extract_protocol:
Total RNA was isolated from normoxia or hypoxia HTR8 cell lines using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: trophoblast


title: HTR8/SVneo: Normoxia_replicate2


title: HTR8/SVneo: Hypoxia_replicate1


title: Reads obtained from sequencing of sample Mice_DNA2

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human Saliva

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 268 --p-trunc-len-r 175 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x $BOWTIE2_DATABASE/INDEXED_GRCh38_analysis_set_BOWTIE2/GRCh38_noalt_as -U dna-sequences.fasta --al eucar_contaminant_ASV_1.fasta -S eucar_contaminants_ASV/bowtie2_HUMAN_SAM_output.txt -f -p 4
bowtie2 -x $BOWTIE2_DATABASE/INDEXED_mouse_GRCm39_BOWTIE2/GRCm39 -U dna-sequences.fasta --al eucar_contaminant_ASV_2.fasta -S eucar_contaminants_ASV/bowtie2_MICE_SAM_output.txt -f -p 4
qiime feature-classifier classify-consensus-vsearch --i-query clean_rep-seqs.qza --i-reference-reads ~/Scrivania/Tools/Database/silva-138-99-seqs.qza --i-reference-taxonomy ~/Scrivania/Tools/Database/silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza --o-search-results vsearch_hits.qza --verbose
R software (see the relative script publicly available at github.com/LeandroD94)
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundances of ASVs in each sample and the related taxonomic assignments
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

source_name: C2C12 culture

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

value: C2C12 culture

tag: sample id

tag: kit dna_extraction

tag: sample type

value: Control


title: HTR8/SVneo: Normoxia_replicate1


title: WT 25A_1

description: WT 25A_1


title: high-fat diet [CvsQ], biological rep4

description: no additional information

tag: strain

value: Wistar

value: male

value: blood

value: high-fat


title: ICSI_Is_twin_130a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-M03-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5


title: Cas_PT_4T1-sgTgfbr2, rep2

value: TGFBR2 knockout


title: Reads obtained from sequencing of sample Mice_DNA1


title: ICSI_Eq_twin_132b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-M08-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: blastocyst


title: normal diet [CvsQ], biological rep3

description: no additional information

source_name: rat fed a normal diet for 8 weeks

tag: gender

value: normal


title: normal diet [CvsQ], biological rep1

description: no additional information


title: VDJ-seq_Young_rep2

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
Hi-C, H3K27ac HiChIP,and capture Hi-C raw reads were processed to the mouse reference genome mm10 by HiCUP (v0.7.2) with the settings of Arima. High-quality and unique paired-end tags (PETs) from HiCUP were further processed to the HIC file through Juicer (v1.6.0) for visualization with Juicebox. These PETs were also processed with cLoops2 (v0.0.2) for quantifications. Chromosome X was excluded from the analysis.Replicates from H3K27ac HiChIP samples were combined and down-sampling equally to 39 million PETs for all following analysis.
ChIP-Seq raw reads were mapped to the mouse reference genome mm10 by Bowtie2 (v2.3.5) . Only non-redundant reads with MAPQ >=10 were saved as BED files for the following analysis. Bigwig tracks were generated by bamCoverage in deepTools (v3.3.0) with parameters of --ignoreDuplicates --minMappingQuality 10 --normalizeUsing CPM for visualization and quantification aggregation analysis.Visualization of ChIP-Seq tracks were performed by IGV or the cLoops2 plot module (v0.0.2) .ChIP-Seq peaks were identified using the cLoops2 callPeaks module. For transcription factor data, the key parameters -eps 150 -minPts 20,50 were employed. For H3K27ac data, the parameters -eps 150,300 -minPts 20,50 -sen were used. Peak identification was performed on each replicate individually, followed by the compilation of a union set encompassing both conditions (young and old) and overlapping replicates. Differential peaks were identified for young and old conditions using a Poisson test. The test utilized average counts from replicates for each peak and considered normalized total reads of 30 million. A p-value cutoff of <1e-5 and a fold change cutoff of >=2 were used to identify significant differential peaks. ChIP-seq peak or domain regions aggregation analyses, including heatmaps and average profile plots, were generated using the computeMatrix and plotHeatmap commands from the deepTools (v3.3.0) package.Quantification of ChIP-seq signals in Hi-C compartments was performed by the cLoops2 quant module. H3K27ac peak annotations were performed by the anoPeaks.py script in cLoops2 package. H3K27ac peaks within a 2 kb range upstream or downstream of the transcription start site (TSS) are annotated as promoters, while those outside this range are labeled as enhancers for the downstream analysis.
RNA-seq raw reads were mapped to mm10 by STAR (v2.7.3a) and quantified into RPKM with Cufflinks (v2.2.1).
VDJ-Seq analysis was performed using HTGTS-Rep.
Assembly: mm10
Supplementary files format and content: BEDPE files for capture Hi-C, Hi-C, HiChIP samples were provided for valid interactions.BED (BEDPE) files for single-end (paired-end) ChIP-seq samples were provided for processed high quality unqiue reads. TEXT files for processed VDJ-seq were provided. TEXT files for processed gene expression in FPKM from RNA-seq data were also provided.
Library strategy: VDJ-seq

source_name: progenitor B cells

growth_protocol:
Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+ and Rag2-/-Ebf1+/−Pax5+/− pro-B cell lines are cultured as previous described (Ramamoorthy et al., 2020).  The D345 cell line was maintained in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (FBS, Gemini) and a 1ⅹ penicillin-streptomycin solution (Gibco).  293T human embryonic kidney cells used for lentiviral expression was purchased from ATCC (Cat# CRL-3216) and cultured in DMEM (Gibco) with 10% FBS (Gemini) and 1ⅹ penicillin-streptomycin solution (Gibco).
The Platinum-E (Plat-E) cell line used for retroviral expression was purchased from Cell Biolabs (Cat# RV-101) and cultured in DMEM (Gibco) with 10% FBS (Gemini), 1ⅹpenicillin-streptomycin solution (Gibco), 10mM Hepes and 0.3 μg/mL L-glutamine. All cells were cultured at 37C in a humidified atmosphere with 5% CO2.

extract_protocol:
For Rag2-/- mice, total bone marrow was extracted from tibia and femurs and erythrocytes are lysed. Pro-B cells were purified by combining positive selection using CD19+ selective beads (Stem Cell Technology, Cat #18954) and sorting by CD19+ and B220+ markers.
For C57BL/6J mice, total bone marrow was extracted from tibia and femurs and erythrocytes are lysed. Cells were pre-purified using CD19+ selective beads (Stem Cell Technology, Cat#18954) and sorted with IgM-B220+CD43+ markers. Flow cytometry experiments were performed on BD FACSAria II Cell Sorter. Flowjo software was used for data analysis.
For the Hi-C libraries. Genome-wide in situ Hi-C was performed with Rag2-/- young and old primary pro-B cells, and Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+, Rag2-/-Ebf1+/−Pax5+/−, D345-BFP and D345-Wapl-BFP pro-B cell lines, using the Arima Hi-C Kit (Arima Genomics), including KAPA Hyper Prep indexing and library amplification (catalog no. KK8500, Roche Molecular Systems Inc) according to the manufacturer’s instructions. For each assay, 1-2×106 cells were used as the input materials and two biological replicates were performed for each group. Samples were sequenced 2×150 bp on an Illumina NovaSeq instrument at the Single Cell & Transcriptomics Core at Johns Hopkins University.
For the capture Hi-C libraries, whole genome Hi-C libraries were first generated as previously described. To enrich the IgH locus (mm10, chr12: 113,201,001 - 116,030,000), SureSelect Target Enrichment probes with 2× tiling density were designed and manufactured by Agilent (Agilent Technologies Inc.). Hi-C libraries were hybridized to probes as specified by the manufacturer. Enriched libraries were sequenced using Illumina NextSeq sequencer to generate paired-end 150-bp reads.
For the ChIP-seq libraries.For the chromatin immunoprecipitation (ChIP) of histone modifications, CTCF, and Rad21, both young and old primary Rag2-/- pro-B cells underwent crosslinking with 1% formaldehyde (Sigma) for 10 minutes at room temperature. The reaction was subsequently quenched with 125 mM glycine, and cell lysis was initiated in a buffer containing 1% SDS. Chromatin was then sheared using a Bioruptor (Diagenode) in cycles of 30 seconds on and 30 seconds off, totaling 15 minutes of shearing time. Immunoprecipitation was performed using specific antibodies, with 1×106 cells used for each assay, and antibody dilutions followed established protocols.
As for Brg1 and p300 ChIPs, we followed the protocol by Bossen et al., 2015, with some modifications. In this case,2×106 young and old primary Rag2-/- pro-B cells were first crosslinked with 1.5 mM EGS at room temperature with rotation for 15 minutes. Subsequently, the cells were fixed with 1% formaldehyde (Sigma) for 15 minutes at room temperature with rotation and quenched with 200 mM glycine. After two PBS washes, the cells were lysed in a buffer containing 1% SDS. Notably, we extended the sonication time to a total of 20 minutes of shearing time, while the subsequent steps of the protocol mirrored the previously mentioned procedure.
For the RNA-seq libraries.The RNA libraries for young and old Rag2-/- primary pro-B cells (four biological replicates for each group) were prepared using the NEXTFLEX Rapid Directional RNA-Seq Kit (PerkinElmer, Cat#NOVA-5138-07,) and sequenced 2×75 bp on an Illumina NovaSeq instrument at the Single Cell & Transcriptomics Core at Johns Hopkins University. RNA libraries for Rag2-/-Ebf1+/+Pax5+/+, Rag2-/-Ebf1+/-Pax5+/+, Rag2-/-Ebf1+/−Pax5+/− and D345-BFP and D345-Wapl-BFP pro-B cell lines (two replicates for each group) were prepared using SMARTer Stranded Total RNASeq Kit v2 (Takara, Cat# 634412) and sequenced 1×100 bp on an Illumina NovaSeq instrument at the Single Cell & Transcriptomics Core at Johns Hopkins University. RNA libraries for pro-B cells infected with Ebf1-GFP or GFP containing retrovirus were prepared using the SMART-Seq mRNA kit (Takara, Cat#634773) and sequenced 2×100 bp on an Illumina NovaSeq instrument at the Computational Biology and Genomics Core in NIA.
For the HiChIP libraries. The H3K27ac HiChIP procedure was executed employing the Arima Hi-C+ Kit (Arima Genetics Inc. Cat# A101020), strictly adhering to the manufacturer's guidelines outlined in the Arima-HiC+ documents A160168 v00 (HiChIP) and A160169 v00 (library preparation). In each sample, a total of 5×106 cells were utilized. These libraries were individually barcoded and then combined for sequencing on an Illumina NovaSeq instrument.
For the VDJ-Seq. It was performed following the HTGTS-Rep-Seq protocol by Hu et al., 2016. Briefly, 200 ng – 2 μg of genomic DNA isolated from primary pro-B cells sorted from young and old C57BL/6J mice was sonicated with Covaris using the setting of Durations 10s, Peak power 50, Duty Factor 20%, Cycles/ Burst 200. Sheared DNA was linearly amplified using a biotinylated JH1 primer and enriched with streptavidin C1 beads (Thermo Fisher Scientific). A bridge adaptor was ligated to enriched single stranded DNA to the 3’ end and then amplified by a nested primer set. Products were further amplified using P5-I5 and P7-I7 primers to be final libraries and sequenced by Illumina MiSeq sequencer to generate paired-end 250-bp reads.

treatment_protocol: Retrovirus was produced by transfection of Plat-E cells with retroviral plasmids containing Ebf1 cDNA and a selective GFP marker (pMYs-Ebf1-IRES-EGFP, as described in Treiber et al., 2010), or with GFP-only plasmids as the control (pMSCV-IRES-GFP, Addgene Cat# 20672). Supernatants were collected at both 48 and 72 hours post-transfection and subsequently concentrated using the Retro-X Concentrator (Takara, Cat#631456), following the manufacturer's instructions. Young and old Rag2-/- CD19+ cells were cultured with 2 ng/mL IL-7 for three days and then exposed to the resuspended virus with the supplement of 10 μg/ml polybrene. The cells were cultured for an additional 72 hours and subsequently sorted based on GFP expression before subsequent analysis. Lentivirus was produced by transfection of 293T cells with the pHIV-Wapl-IRES-BFP and pHIV-IRES-BFP plasmids. To make these plasmids, the BFP DNA fragment was amplified from plasmid pEJS614_pTetR-P2A-BFPnls/sgNS (Addgene, #108650), and then integrated into pHIV-IRES-Zsgreen (Addgene, #18121) using the NEBuilder® HiFi DNA Assembly Master Mix (New England Biolabs, #E2621S) as per the manufacturer's instructions, resulting in the generation of pHIV-IRES-BFP plasmids. Subsequently, Wapl cDNA was introduced into pHIV-IRES-BFP, creating the pHIV-Wapl-IRES-BFP. Supernatants were collected at both 48 and 72 hr post-transfection and subsequently concentrated using the Lenti-X Concentrator (Takara, Cat#631232). D345 cells were infected with the resuspended lentivirus with the addition of 8 μg/ml polybrene. After infection, the cells were cultured for 72 hr and sorted based on BFP expression. The sorted cells were then cultured for 2-3 additional days to obtain an increased number of BFP-positive cells for experimental purpose.

value: progenitor B cells

value: Bone marrow

value: WT C57BL/6J

value: B220+CD43+IgM- sorted primary pro-B cells


title: WT mock_2

description: WT mock_2

value: Bone Marrow Drived Macrophages

value: Primary cells

value: WT

value: Mock transfected


title: ICSI_Is_twin_129b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-M02-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: WT mock_1

description: WT mock_1


title: normal diet [CvsQ], biological rep4

description: no additional information


title: RKO A3_2

description: RKO A3_2

value: RNaseL KO

value: A3 transfected


title: normal diet [CvsQ], biological rep2

description: no additional information

value: Wistar

value: male


title: ICSI_Is_twin_129a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-M01-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Co_twin_128b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L10-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: VDJ-seq_Young_rep1


title: Cas_PT_4T1-sgNf1, rep1

value: mammary tumor

value: mammary tumor cell

value: NF1 knockout


title: Reads obtained from sequencing of sample E_Coli4

source_name: E coli culture

value: E coli culture

value: Control


title: RKO A3_1

description: RKO A3_1


title: Cas_PT_4T1-C1, rep2

value: control


title: Reads obtained from sequencing of sample E_Coli3


title: RKO 25A_1

description: RKO 25A_1

value: 2-5A transfected


title: RKO 25A_2

description: RKO 25A_2


title: Cas_PT_4T1-C1, rep1


title: ICSI_Co_twin_127b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L08-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5

value: blastocyst


title: Cas_PT_4T1-sgTgfbr2, rep1

value: TGFBR2 knockout


title: RKO mock_2

description: RKO mock_2

value: Bone Marrow Drived Macrophages

value: Primary cells


title: ICSI_Co_twin_127a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L07-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Co_twin_126b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L06-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: 45_M_H2AZ_KD+KQ

city: Mississauga

first: Iva

last: Zovkic

address: 3359 Mississauga Rd

department: Department of Psychology

institute: University of Toronto

description: Sample 45

data_processing:
Fastqc (v0.11.9), Rsubread (v2.12.3), R (4.2.3), DESeq2 (v1.38.3)
Sequence reads were quality controlled using fastqc
Sequence reads were aligned to the GRCm39/mm39 genome using Rsubread-align in R (softclipping, paired-end settings)
Read counts were generated using featureCounts in R part of Rsubread. Normalization was performed in R.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file containing the raw counts for each sample
Supplementary files format and content: tab-delimited text file containing the rpkm normalized counts for each sample

source_name: Male H2A.Z.1/H2A.Z.2 KD + H2A.Z.1 KQ overexpression

extract_protocol:
Total RNA was extracted from mouse hippocampal tissue using the RNeasy Mini Kit (Qiagen). 4ug of RNA per sample was sent to CD Genomics.
Samples were sent as total RNA on dry ice to CD Genomics (New York, United States of America)

value: Hippocampus

value: Male

value: H2A.Z.1 KQ Overexpression

value: Stereotaxic injection into hippocampus


title: ICSI_Co_twin_126a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L05-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: RKO mock_1

description: RKO mock_1

value: RNaseL KO

value: Mock transfected


title: 44_M_H2AZ_KD+KQ

description: Sample 44


title: Cas_PT_4T1-sgNf1, rep2

value: mammary tumor

value: mammary tumor cell


title: Fb3_1

city: Shanghai

first: Wei

last: Zhang

address: No.180 Fengling Road, Xuhui

department: Vascular Surgery

institute: Zhongshan Hospital, Fudan University

data_processing:
Reads that contained the sequence of adaptor, high content of unknown bases, and low-quality reads were filtered and stored in FASTQ format.
RNA-seq reads were aligned to mouse GRCm39_release-103 with Bowtie2 and then raw reads were obtained with RSEM.
The FPKM method was used to calculate gene expression for direct comparison among samples.
the DESeq2 method was used to screen differentially expressed genes (DEGs) between two groups according to the following default criteria: fold change ≥ 2 and Q value (adjusted P value) ≤ 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM for each samples

source_name: mouse aorta

growth_protocol: The mice were maintained in an SPF facility with a 12:12 h light/dark cycle for one week to acustomize the environment and then four weeks throughout the experiments.

extract_protocol:
Whole RNA was extracted using the TRIzol Plus RNA Purification Kit (Thermo Fisher Scientific) following the manufacturer’s protocol
SBS50 sequencing was performed at DNBSEQ using illumine HiseqTM 2000.

treatment_protocol: All mice were grouped by random number: (1) in the vehicle group (n=11), mice were fed water alone; (2) in the Fasudil group (n=10), mice were fed Fasudil dissolved in water at a dose of 150 mg/kg/day; (3) in the β-aminopropionitrile (BAPN) group (n=12), mice were fed BAPN dissolved in water at a concentration of 0.25%; and (4) in the BAPN+Fasudil group, mice were first fed BAPN (0.25% in water) for one week and then fed BAPN (0.25% in water) and Fasudil (150 mg/kg/day) together to induce AD.

value: mouse aorta

value: Fasudil,150mg/kg/d + BAPN, 0.25percent in water


title: Liver_WD_veh_rep2

city: Seoul

first: Haena

last: Choi

address: , Gwanak_1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Gene expression data from mouse liver tissue which was fed Western diet for 21 weeks with 5 week-oral administration of vehicle.
control-2

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

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

data_processing:
The data were analyzed with Robust Multichip Analysis (RMA) algorism of Affymetrix Power Tools (APT). The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
affymetrix-algorithm-name = rma-bg.quant-norm.pm-only.med-polish
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st

source_name: Western diet-fed without ODH-08 treatment mouse liver

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

extract_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

treatment_protocol: 7-week-old C57BL/6 male mice were fed a Western diet (WD) for 21 weeks. ODH-08 suspended in 0.5% carboxymethyl cellulose, was administered to mice for 5 weeks after 16 weeks of WD.

value: liver

value: male


title: primary KC, rep2

city: Minato

first: Yang

last: Li

state: Tokyo

address: Shirokanedai 4-6-1

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary files format and content: CSV files include read counts (RPM)  for each Sample

source_name: human iPSC; M48

extract_protocol:
RNA was isolated from samples using the PureLink RNA Mini Kit (Thermo Fisher Scientific).
RNA libraries were prepared using 100 ng of total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific).

value: human iPSC; M48

value: primary human Kupffer cells

value: WT


title: ICSI_Co_twin_125b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L04-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5

value: blastocyst


title: ICSI_Co_twin_128a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L09-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: 43_M_H2AZ_KD+KA

description: Sample 43

source_name: Male H2A.Z.1/H2A.Z.2 KD + H2A.Z.1 KA overexpression

value: Hippocampus

value: H2A.Z.1 KA Overexpression


title: primary KC, rep1


title: ICSI_Co_twin_125a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L03-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Liver_WD_ODH_rep2

description:
Gene expression data from mouse liver tissue which was fed Western diet for 21 weeks with 5 week-oral administration of ODH-08.
test-2

source_name: Western diet-fed with ODH-08 treatment mouse liver

value: Western diet-fed with ODH-08 treatment


title: 46_M_H2AZ_KD+WT

description: Sample 46

source_name: Male H2A.Z.1/H2A.Z.2 KD + H2A.Z.1 WT overexpression

value: Male

value: H2A.Z.1 WT Overexpression

value: Stereotaxic injection into hippocampus


title: Liver_WD_veh_rep1

description:
Gene expression data from mouse liver tissue which was fed Western diet for 21 weeks with 5 week-oral administration of vehicle.
control-1

value: Western diet-fed without ODH-08 treatment


title: ICSI_Co_twin_124b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L02-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Liver_WD_ODH_rep1

description:
Gene expression data from mouse liver tissue which was fed Western diet for 21 weeks with 5 week-oral administration of ODH-08.
test-1


title: EMP-KC, rep4

value: hiPSC-derived Kupffer cells


title: 41_M_Myc

description: Sample 41

source_name: Male Myc Overexpression


title: EMP-KC, rep3


title: B1_3

value: mouse aorta

value: BAPN,0.25percent in water


title: 40_F_H2AZ_KD+WT

description: Sample 40

source_name: Female H2A.Z.1/H2A.Z.2 KD + H2A.Z.1 WT overexpression

value: Female


title: ICSI_Co_twin_124a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-L01-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: B1_2


title: EMP-KC, rep2


title: ICSI_Co_twin_122b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K08-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: EMP-KC, rep1


title: 39_F_H2AZ_KD+WT

description: Sample 39


title: ICSI_Co_twin_122a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K07-ICSI_Co
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: 38_F_H2AZ_KD+KQ

description: Sample 38

source_name: Female H2A.Z.1/H2A.Z.2 KD + H2A.Z.1 KQ overexpression

value: H2A.Z.1 KQ Overexpression


title: CB-HSPC, rep2

value: human iPSC; M48

value: cord-blood hematopoietic stem and progenitor cells


title: F3_1


title: Fb2_1

value: Fasudil,150mg/kg/d + BAPN, 0.25percent in water


title: ICSI_Is_twin_121b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K06-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

source_name: preimplantation embryo Theiler stage 5

value: preimplantation embryo Theiler stage 5


title: 37_F_H2AZ_KD+KQ

description: Sample 37


title: 42_M_H2AZ_KD

description: Sample 42

source_name: Male H2A.Z.1/H2A.Z.2 KD


title: F2_1


title: Fb1_1


title: CB-HSPC, rep1

value: WT


title: 36_F_H2AZ_KD+KA

description: Sample 36

source_name: Female H2A.Z.1/H2A.Z.2 KD + H2A.Z.1 KA overexpression

value: Hippocampus


title: F1_1


title: ICSI_Is_twin_120b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K04-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: blastocyst


title: 35_F_H2AZ_KD+KA

description: Sample 35

value: H2A.Z.1 KA Overexpression


title: ICSI_Is_twin_120a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K03-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: hiPSC-EMP, rep2

value: erythro-myeloid progenitors


title: hiPSC-EMP, rep1


title: C4_1

value: Vehicle


title: C3_1


title: hiPSC, rep2

value: hiPSC


title: ICSI_Is_twin_119b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K02-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: C2_1


title: 34_F_H2AZ_KD

description: Sample 34

source_name: Female H2A.Z.1/H2A.Z.2 KD

value: Stereotaxic injection into hippocampus


title: B1_1


title: hiPSC, rep1


title: ICSI_Is_twin_119a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K01-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: 32_F_Myc

description: Sample 32

source_name: Female Myc Overexpression


title: 33_F_H2AZ_KD

description: Sample 33


title: KuLOs, recovery D3, rep2

value: human iPSC-derived liver organoids

value: remove LPS/IFNr

value: Day 19


title: Patient 110

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 110

hyb_protocol: Standard nanostring nCounter miRNA Hybridization Protocol; The final hybridization reaction contained the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet.

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer for image capture (555 fields of view).

data_processing: The miRNA data analysis was performed using nSolver Analysis (version 4·0) software. Each miRNA count data was subtracted from the geometric mean of the negative controls. Profiling data were then normalized by the geometric mean of the positive controls and the geometric mean of the top 100 most highly-expressed microRNAs.

source_name: grade 4

label_protocol: Standard nanostring miRNA protocols (nCounter Human v3 miRNA Expression Assays (NanoString Technologies,Seattle, USA))

extract_protocol: Total RNA was extracted from 400 mL of serum sample using miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s protocol.

tag: grade

value: grade 4 (CNS5 WHO)

tag: age

value: male

tag: ihd status


title: ICSI_Is_twin_118b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J10-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

tag: cell type


title: KuLOs, recovery D3, rep1

tag: cell line

value: human iPSC; M48


title: 31_F_Myc

description: Sample 31

value: Female


title: 30_M_H2AZ_KD+WT

description: Sample 30

value: Male

value: H2A.Z.1 WT Overexpression


title: ICSI_Is_twin_118a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J09-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5


title: ICSI_Is_twin_121a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-K05-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 109

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 109

value: WT


title: ICSI_Is_twin_117b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J08-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: blastocyst


title: KuLOs, recovery D2, rep2

value: Day 18


title: 29_M_H2AZ_KD+WT

description: Sample 29

value: Hippocampus


title: ICSI_Is_twin_117a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J07-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: KuLOs, recovery D2, rep1


title: Patient 108

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 108


title: 28_M_H2AZ_KD+KQ

description: Sample 28

value: H2A.Z.1 KQ Overexpression


title: KuLOs, recovery D1, rep2

value: Day 17


title: Patient 107

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 107

value: female


title: ICSI_Eq_twin_116b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J06-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 106

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 106


title: ICSI_Eq_twin_116a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J05-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: C1_1

value: mouse aorta

value: Vehicle


title: KuLOs, recovery D1, rep1

value: human iPSC-derived liver organoids

value: remove LPS/IFNr


title: Patient 105

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 105

value: grade 4 (CNS5 WHO)

value: male

value: MT


title: 25_M_H2AZ_KD+KA

description: Sample 25

value: Male

value: H2A.Z.1 KA Overexpression

value: Stereotaxic injection into hippocampus


title: ICSI_Eq_twin_115b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J04-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5


title: 26_M_H2AZ_KD+KA

description: Sample 26


title: Patient 103

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 103

value: WT


title: 22_M_Myc

description: Sample 22


title: KuLOs, Control, rep2

value: human iPSC; M48

value: Control

value: Day 14


title: KuLOs, septic, rep1

value: LPS/IFNr

value: Day 16


title: ICSI_Eq_twin_115a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J03-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: blastocyst


title: 23_M_Myc

description: Sample 23

value: Hippocampus


title: Patient 102

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 102


title: KuLOs, Control, rep1

value: human iPSC-derived liver organoids


title: 21_M_H2AZ_KD

description: Sample 21


title: ICSI_Eq_twin_114b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J02-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: 27_M_H2AZ_KD+KQ

description: Sample 27

value: H2A.Z.1 KQ Overexpression


title: Patient 100

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 100

value: grade 4 (CNS5 WHO)

value: female


title: Patient 101

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 101

value: male


title: EpoR- cDC1s, TLI/ATS_1

city: Palo Alto

first: Xiangyue

address: 3373 Hillview ave

institute: Stanford University

data_processing:
trimmomatic0.36 was used to trim low quality data and adaptor contamination;
hisat2 was applied to align reads onto mouse reference genome (https://cloud.biohpc.swmed.edu/index.php/s/grcm38_tran/download)
samtools was used for sam/bam file convertion and bam file sorting
stringtie/prepDE.pyor featureCounts were used to get the gene abundance from bam files
Assembly: grcm38
Supplementary files format and content: gene and count matix

source_name: XCR1+CD8a+ cDC1s

extract_protocol:
RNA was harvset using Rnaeasy mini plus kit (Qiagen). More than 1 ug of TOTAL RNA was used for constructing libaries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library following the manufacturer's protocols.

value: XCR1+CD8a+ cDC1s

value: EpoR-tdTomato

value: TLI/ATS


title: ICSI_Eq_twin_114a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-J01-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5


title: 20_F_H2AZ_KD+WT

description: Sample 20

value: Female

value: H2A.Z.1 WT Overexpression

value: Stereotaxic injection into hippocampus


title: ICSI_Eq_twin_112a, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I07-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: 19_F_H2AZ_KD+WT

description: Sample 19


title: Patient 104

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 104

value: WT


title: KuLOs, septic, rep2

value: human iPSC; M48

value: LPS/IFNr


title: EpoR- cDC1s, TLI/ATS_2


title: ICSI_Eq_intact_111, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I06-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: blastocyst


title: Patient 98

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 98

value: MT


title: 17_F_H2AZ_KD+KQ

description: Sample 17

value: Hippocampus


title: ICSI_Eq_twin_112b, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I08-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: EpoR+ cDC1s, TLI/ATS_2


title: EpoR+ cDC1s, TLI/ATS_1


title: ICSI_Eq_intact_110, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I05-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 99

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 99


title: 16_F_H2AZ_KD+KA

description: Sample 16

value: H2A.Z.1 KA Overexpression


title: Patient 97

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 97

value: grade 4 (CNS5 WHO)


title: ICSI_Eq_intact_109, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I04-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 96

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 96

value: female


title: 15_F_H2AZ_KD+KA

description: Sample 15


title: cDC1s, UNT_2

value: WT C57BL/6

value: no


title: ICSI_Eq_intact_108, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I03-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 95

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 95

value: male


title: 14_F_H2AZ_KD

description: Sample 14


title: cDC1s, TLI/ATS_2

value: XCR1+CD8a+ cDC1s

value: TLI/ATS


title: ICSI_Eq_intact_107, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I02-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5


title: Patient 94

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 94


title: Patient 93

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 93


title: cDC1s, TLI/ATS_1


title: 13_F_H2AZ_KD

description: Sample 13

value: Female


title: 10_M_H2AZ_KD+WT

description: Sample 10

value: Male

value: H2A.Z.1 WT Overexpression

value: Stereotaxic injection into hippocampus


title: 9_M_H2AZ_KD+WT

description: Sample 9


title: ICSI_Eq_intact_102, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H07-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Eq_intact_106, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-I01-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: ICSI_Eq_intact_105, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H10-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Cre_D6B_1

city: Chongqing

first: taiping

last: Liu

address: Gaotanyan zhengjie 30, Shapingba district, Chongqing

institute: Department of Pathogenic Biology, Army Medical University (Third Military Medical University)

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data by Trimmomatic.(parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Splenocytes

growth_protocol: For RNASeq analysis, CD11b+ cells  were isolated from splenocytes of P. yoelii 17XNL-infected mice at Day 0, Day 3 and Day 6 post-infection.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
P. yoelii 17XNL infection
CD11b+ cells isolated from splenocytes

value: Splenocytes

value: CD11b+ cells

value: ATG5fl-LysM Cre-

value: P. yoelii 17XNL infection

value: Day 6

tag: agent

value: P. yoelii 17XNL


title: Cre_D6B_3

tag: treatment


title: Patient 91

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 91

value: grade 4 (CNS5 WHO)

value: WT


title: Cre_D6B_2


title: Cre_D6A_3

value: ATG5fl-LysM Cre+


title: 11_F_Myc

description: Sample 11

tag: tissue

value: Hippocampus


title: 8_M_H2AZ_KD+KQ

description: Sample 8

source_name: Male H2A.Z.1/H2A.Z.2 KD + H2A.Z.1 KQ overexpression

tag: genotype

value: H2A.Z.1 KQ Overexpression


title: cDC1s, UNT_1

value: XCR1+CD8a+ cDC1s

value: WT C57BL/6

value: no

tag: time


title: ICSI_Eq_intact_101, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H06-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5

value: blastocyst


title: 5_M_H2AZ_KD+KA

description: Sample 5

value: Male

value: H2A.Z.1 KA Overexpression

value: Stereotaxic injection into hippocampus


title: Cre_D6A_1

value: Splenocytes

value: CD11b+ cells


title: Patient 90

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 90

value: female


title: ICSI_Eq_intact_98, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H03-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Patient 92

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 92


title: 3_M_H2AZ_KD

description: Sample 3


title: Patient 89

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 89

value: male


title: ICSI_Eq_intact_99, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H04-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx


title: Cre_D6A_2

value: P. yoelii 17XNL infection

value: Day 6

value: P. yoelii 17XNL


title: 4_M_H2AZ_KD

description: Sample 4

value: Hippocampus


title: Patient 88

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 88

value: grade 4 (CNS5 WHO)

value: MT


title: Cre_D3B_3

value: ATG5fl-LysM Cre-

value: Day 3


title: Patient 86

description:
miRNA
miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)
SAMPLE 86


title: ICSI_Is_intact_96, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H01-ICSI_Is
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: preimplantation embryo Theiler stage 5


title: ICSI_Eq_intact_100, blastocyst, scRNA-seq

description:
Smart-Seq2
plate2-H05-ICSI_Eq
Three output files that originated from analyzing all blastocysts together; barcodes_blastocysts.tsv, features_blastocysts.tsv, umiDedup-Exact_blastocysts.mtx

value: blastocyst