title: ATAC, E8.5 HE, rep 3

value: Hemogenic endothelium

value: 23GFP transgenic


title: SCC7-3

status: Public on Jun 30 2024

type: SRA

city: Wuhan

first: An

last: Song

address: Luoyu Road 237

country: China

institute: Wuhan University

library_source: transcriptomic

data_processing:
BGISEQ-500 sequencer
Clean reads were mapped to the reference genome using HISAT/Bowtie2tools.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

molecule: total RNA

organism: Mus musculus

growth_protocol: The SCC7  cells were grown in high glucose (Gibco) with 10% FBS.

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.
DNase I was used to digest double-stranded and single-stranded DNAin total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA

treatment_protocol: The SCC7  cells were received with radiotherapy in 9 Gy.

tag: cell line

tag: cell type

value: cancer cell

tag: treatment

tag: time

value: Day 0


title: SCC7-2


title: ATAC, E8.5 HE, rep 4

city: Oxford

first: Marella

last: de Bruijn

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Alignment, PCR duplicate filtering, and blacklist region filtering were performed using the NGseqBasic pipeline (Telenius et al. 2018).
Briefly, paired end reads were mapped using Bowtie (v1.0.0) to the mouse genome assembly (mm9).
Unmapped reads were trimmed using trim_galore (v0.3.1) and remapped. Short unmapped reads were combined using flash (v1.2.8) and remapped.
PCR duplicates were removed using samtools rmdup (v0.1.19). Reads mapping to Duke blacklisted regions (UCSC) were removed using BEDtools (v2.17.0).
BigWigs were created using DeepTools bamCompare (v3.0.1), and peaks were identified using MACS2 (v2.0.1) with parameters -BAMPE and -q 0.05.
Consensus peaks were generated using DiffBind (v1.14.6) and counts underlying each consensus peak were calculated using DiffBind dba.count with parameters bUseSummarizeOverlaps = T and score = DBA_SCORE_READS
Assembly: mm9
Supplementary files format and content: Output from DiffBind dba.count: TSV file including read counts over consensus peaks.

molecule: genomic DNA

source_name: E8.5 PAS+VU

extract_protocol:
1500 cells were sorted directly into 100% FCS, then nuclei were isolated by resuspending in  lysis buffer (10 mM Tris-HCl pH7.5; 10 mM NaC; 3 mM MgCl2; 10% IGEPAL CA-630; 0.1% TritoxX-100), and incubating 10 min on ice.
Protocol adapted from Buenrostro et al. 2015. Nuclei were resuspended in 10 uL tagmentation mix (0.35 uL Tn5 transposase; 5 uL 2X tagmentation buffer; 4.65 uL nuclease free water) (Illumina Nextera FC-121-1030), then incubated 37C for 30 min.
Tagmentation reaction was quenched using 1.1 uL 500 mM EDTA, and 10 uL 50 mM MgCl2 was added to the sample.
The library was amplified using 13 PCR cycles  on the thermocycler, then purified using a MinElute kit (Qiagen).

tag: tissue

value: E8.5 PAS+VU

tag: genotype


title: MPA-SiNCF2-2

city: Jinan

first: Yao

last: Liu

state: Shandong

address: Wenhuaxi Road 107#

institute: Qilu Hospital of Shandong University

data_processing:
Raw image data files obtained from high-throughput sequencing were processed by CASAVA for base calling, and transformed into raw sequencing data (Raw Data). The results are stored in the FASTQ format (commonly abbreviated as fq), which encompasses both the sequence information of the sequencing data and its corresponding quality information. Reads that pass filtering are termed "Clean Reads" and are saved in the FASTQ format.
Clean reads were aligned to the reference genome using HISAT2 (Kim D, et al. 2015).
Gene expression quantification was conducted using the StringTie software combined with the ballgown package in R. The results from StringTie were integrated using ballgown, and gene expression levels were represented by FPKM values.
Differential gene expression detection was carried out using algorithms DESeq2 (Michael I 2014), EBseq (Leng N 2013), NOIseq (Tarazona S 2011), and PossionDis (S 1997).
Assembly: RefSeq GRCh38
Supplementary files format and content: AllSamples.GeneExpression.Count.xls contains raw counts for each sample
Supplementary files format and content: A-VS-B.DEseq2.GeneDiffExpFilter.xls contains the differential gene expression profiles between the experimental and control groups.

organism: Homo sapiens

source_name: Ishikawa

extract_protocol:
RNA extraction：Cell toal RNA isolation kit(FOREGENE, Chengdu, China)RNA quality examination： The purity of the sample was determined by NanoPhotometer ®（IMPLEN, CA, USA）； RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies,  CA, USA)
After the total RNA samples were tested to be qualified, the MGIEasy RNA library preparation kit was used for library construction. Magnetic beads  with oligo (DT) were used for enrichment and purification; Fragment  buffer was added to the purified mRNA to make its fragment into a short  fragment; the fragment mRNA was used as a template for reverse  transcription into double stranded cDNA with six base random primers,  and then the product was purified. The purified double stranded cDNA was  subjected to end repair, addition of dA tail, linker connection and PCR  amplification. After the amplified product was qualified, it was denatured  and single stranded cyclized, and the cyclized product was inspected.

value: Ishikawa


title: SCC7-1


title: ATAC, E8.5 HE, rep 1


title: STARR_5bp_plDNA

city: Lausanne

first: Bart

last: Deplancke

address: SV Station 19

country: Switzerland

institute: EPFL

library_source: other

data_processing:
Insert seqeunes were mapped to the 12bp barcodes located at the 3 prime end with respect to the TSS using a custom script. STARR activity for each insert sequence was computed by taking the log2 ratio of mRNA over input DNA counts.
Library strategy: STARR-seq

molecule: other

growth_protocol: MEC1 cells were cultured in IMDM media (Gibco) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin.

extract_protocol: Cells were harvested 24h post transfection and lysed in Trizol. RNA was extracted by Chloroform extraction, followed by Isopropanol precipitation with a 1:1 ratio. RNA pellets were resuspended in RNAse-free water and digested with DNAseI for 20 min at room-temperature. DNAseI-treated RNA was purified with a RNA-clean&concentrator-25 kit (Zymo). A total of 10-12 μg RNA was reverse transcribed using the STARR-seq specific RT prime. For each μl of Maxima H minus RT 3 μg input was used. RT reactions were diluted 1:4 with RNAse & DNAse-free water before further amplification. The splice-junction PCR was run using the STARR-seq thio-splice-junction primer and a custom reverse primer spanning the SalI restriction site used for linearizing the STARR-seq vector and the read1 Nextera adapter sequence inserted with the library. About one third of the RT reaction was amplified for 19-22 cycles. Illumina barcodes were added by a final PCR with 8 cycles using the Illumina Nextera guidelines. After each amplification step, PCR products were cleaned up using AMPure XP magenetic beads (Beckman Coulter). Plasmid libraries were directly amplified with a 8-cycle PCR using NEXTERA-specific index primers.

treatment_protocol: Transfections of 5-bp and 10-bp libraries were done in duplicates using ~ 6 Mio cells and 30 μg plasmid per replicate. Transfections were carried out with the Neon Transfection System (Thermo Fisher) as follows: 3 pulses of 20 ms at 1200 V in R buffer using 100 ul tips.

value: CLL cell line

value: WT

value: not applicable


title: Lipid-laden monocyte-derived macrophages, mn:547

city: Amsterdam

first: Daan

middle: Juri

last: Kloosterman

address: Plesmanlaan 121

department: Tumor Biology & Immunology

country: Netherlands

institute: The Netherlands Cancer

data_processing:
The recorded ATAC-seq data were mapped to the mm10 reference genome with BWA-MEM (version 0.7.17-r1188).104 SAMtools (version 1.10)105 was used to discard the mapped reads with a mapping quality score <15, and PICARD tools (version 2.12.0) was applied to remove optical PCR duplicates. The coverage files were generated with the ‘normalize to 1× genome coverage’ methods in deepTools (version 3.5.1).106
Assembly: mm10
Supplementary files format and content: tab delimited tekst file with feature counts

source_name: Brain tumor

extract_protocol:
Nuclei of the FACS sorted cells were isolated, permeabilized and tagmented by using in-house-generated Tn5 transposase. The resulting DNA fragments underwent a first 9-cycle PCR amplifications using KAPA HiFi HotStart ReadyMix (7958935001, Roche), and we selected the fragments between 150 and 700 bp in size using with SPRI beads (A63881, Backman Coulter).
ATAC-seq libraries were prepared using an optimized protocol.103  The resulting DNA fragments underwent a first 9-cycle PCR amplifications using KAPA HiFi HotStart ReadyMix (7958935001, Roche), and we selected the fragments between 150 and 700 bp in size using with SPRI beads (A63881, Backman Coulter). The size-selected fragments were amplified for a second 9-cycle PCR reactions, and the resulted libraries were purified using SPRI beads.

value: Brain tumor

value: Lidid-Laden Monocyte-derived macrophage

value: Ink4a/ArfKO, PDGFB


title: Non-lipid-laden monocyte-derived macrophages, mn:547

value: Monocyte-derived macrophage


title: UPD sample 3 [patient C; CMA2022216]

type: genomic

city: Zhenjiang

first: Qi

last: Chen

address: 20 ZHENDONG ROAD

institute: Fourth affiliated hospital of Jiangsu University

description:
Hybridized to 750K
[CytoScan750K_Array] Affymetrix CytoScan 750K Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Amniotic fluid 3

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Amniotic fluid and peripheral blood were collected without growth

extract_protocol: Genomic DNA was extracted from amnoitic fluid obtained from preganant women using the Qiagen DNAiso Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: patient id

value: patient C

value: chromosome 14 UPD

tag: phenotype

value: Hypotonia, ARDS

tag: outcome

value: death

value: Amniotic fluid


title: UPD sample 2 [patient A; CMA2022324]

source_name: Amniotic fluid 2

value: patient A

value: chromosome 9 UPD

value: normal phenotype

value: alive


title: ATAC, E8.5 EC, rep 4

value: E8.5 PAS+VU

value: Endothelial cells

value: 23GFP transgenic


title: pESC-3

city: Hangzhou

first: Chengchen

last: Zhao

state: Zhejiang

address: Dunyu Road No.600, Xihu District

institute: Westlake University

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4)and then mapped to the susScr11 reference genome with HISAT2 (v2.2.1), and StringTie (v2.2.1) was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads).
GFOLD (v1.1.4) was used to perform differential expression analysis between conditions. The differentially expressed genes were identified with gfold value > 0.5.
Assembly: susScr11
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

molecule: polyA RNA

organism: Sus scrofa

growth_protocol: The pESCs were cultured in 4FIXY medium. Cells are collected after Tryple digestion.

extract_protocol:
Total RNAs were extracted by TRIZOL.
In brief, 1 μg total RNAs were used, library strategy are followed by mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611), library DNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411). High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150.

value: pESC


title: UPD sample 1 [patient B; CMA2021016]

source_name: Amniotic fluid 1

value: patient B

value: chromosome 2 UPD


title: pESC-2


title: ATAC, E8.5 EC, rep 3


title: pESC-1


title: ATAC, E8.5 EC, rep 2


title: Liver, SE-rGLU, rep7

city: Copenhagen

first: tik

last: muk

state: copenhagen

address: Dyrlægevej 68,1870 Frederiksberg C, Dyrlægevej 68, 1870 Frederiksberg C

country: Denmark

institute: University of Copenhagen

data_processing:
The libraries were sequenced on the Illumina NovaSeq 6000 S4 flowcell with PE150.
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using HISAT2
The annotated gene information of porcine genome was downloaded from Ensembl (release 99).
The script htseq-count was used to generate a gene-count matrix, followed by analyses of DEGs using DESeq2 .
Assembly: Sscrofa11.1
Supplementary files format and content: Processed data was formated as htseq.count files
Supplementary files format and content: Each file represent counting reads for genes in each sample with htseq-count

source_name: Liver

growth_protocol: Preterm pigs were gained by C-section and kept in NICU incubators for 15~20h.

extract_protocol:
Total RNA of homogenized liver tissues was extracted using RNeasy Mini Kit (Qiagen, Copenhagen, Denmark).
Construction of RNA-Seq libraries was done using Novogene NGS RNA Library Prep Set (PT042)

treatment_protocol: Preterm pigs were randomly allocated to sGAL/sGLU/rGLU-GAAs/rGLU groups and inoculated with live Staphylococcus epidermidis (SE) or saline control (CON)

value: Liver

value: SE, rGLU


title: ATAC, E8.5 EC, rep 1


title: Liver, SE-rGLU, rep6


title: ATAC, E8.5 HE, rep 2

value: Hemogenic endothelium


title: ATAC, E10.5 pre-HSC II, rep 4

source_name: E10.5 AGM+VU

value: E10.5 AGM+VU

value: pre-HSC II


title: ATAC, E10.5 pre-HSC II, rep 3


title: Liver, SE-rGLU, rep5


title: EXP2B-rep3-GRP158-HDOX-96 H

type: RNA

city: Córdoba

first: Jose

last: Echenique

state: Córdoba

address: Edificio Integrador, Medina Allende S/N, Ciudad Universitaria

department: Clinical Biochemistry

country: Argentina

institute: School of Chemistry Sciences, National University of Cordoba

description: replicate 3

hyb_protocol: Cyanine-3-labelled cRNA was hybridized on Agilent SurePrint G3 Human GE 8×60K Microarray v2.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner at a 3-um scan resolution

data_processing:
Image data were processed with Agilent Feature Extraction 11.0.1.1, and processed signals were quantile normalized with Agilent GeneSpring 12.0.
The normalized expression intensities for all probes were subjected to a two-way analysis of variance analysis (ANOVA).  Significantly differentially expressed genes were selected using criteria p-value (or FDR using the Benjimini-Hochberg method) < 0.05 and fold-change > 1.2.

source_name: human trabecular meshwork (HTM) cells.

label_protocol: cRNA was labelled with Cyanine-3

growth_protocol: TM-1 cells were seeded at 10'5/mL in the wells of 6-well plates. Cells were maintained in reduced serum (2.5%)

extract_protocol: Total RNA was extracted from each culture plate well using Aurum (Bio-Rad, Hercules, CA)

treatment_protocol:
Exp1: cells were treated with doxycycline at 100 ng/mL for 72 hours to induce GRP128.  Exp2A: cells were treated with doxycycline at 500 ng/mL for 24 hours. Exp2B: cells were  treated with doxycycline at 500 ng/mL for 96 hours.
Cells transfected with only lenti-vector were used as a negative control.

value: HTM cells transfected with TIGR/MYOC cDNA (TM-1).

value: human trabecular meshwork (HTM) cells

value: GRP158-HDOX-96 H


title: Liver, SE-rGLU-GAAs, rep18

value: SE, rGLU-GAAs


title: ATAC, E10.5 pre-HSC II, rep 2


title: EXP2B-rep1-GRP158-HDOX-96 H

description: replicate 1


title: EXP2B-rep2-GRP158-HDOX-96 H

description: replicate 2


title: Liver, SE-sGAL, rep17

value: SE, sGAL


title: EXP2B-rep3-GRP158-96 H

description: replicate 3


title: Liver, SE-sGLU, rep16

value: SE, sGLU


title: EXP2B-rep2-GRP158-96 H

description: replicate 2


title: Liver, SE-rGLU, rep4


title: DBA/2 CDH1+ spermatogonia

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

country: Japan

institute: Kyoto University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

label: biotin

source_name: wild-type, 12dpc testis

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Testes dissected from 12 dpc mice

extract_protocol: Testis cells were dissociated into single-cell suspension by two-step enzymatic digestion using collagenase type IV and trypsin. Testis cells were suspended in PBS/FBS with anti-Ecadherin(CDH1) antibody (clone ECCD2), and  incubated for 15 min on ice and washed three times with PBS/FBS. Goat anti-rat IgG microbeads (Miltenyi Biotech, Gladbach,Germany)  was added the cells were further incubated for 15 min and passed through an MS1 separation column (Miltenyi Biotec) to select cells, according to the manufacturer’s instructions.  Total RNA samples were extracted by using TRIzol solution (Invitrogen) and purified by the RNeasy cleanup system (QIAGEN, Valencia, CA). cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: not applicable

tag: strain

value: wild-type

value: 12dpc testis

value: Purified using anti-CDH1 antibody


title: ATAC, E10.5 pre-HSC I, rep 2

value: pre-HSC I

value: 23GFP transgenic


title: ATAC, E10.5 pre-HSC I, rep 3


title: EXP2B-rep1-GRP158-96 H

description: replicate 1


title: ATAC, E10.5 pre-HSC II, rep 1


title: ATAC, E10.5 pre-HSC I, rep 1


title: 129 CDH1+ spermatogonia


title: EXP2B-rep3-VECTOR-HDOX-96 H

description: replicate 3

value: VECTOR-HDOX-96 H


title: Liver, SE-rGLU-GAAs, rep16

value: Liver


title: B6 CDH1+ spermatogonia


title: ATAC, E10.5 pre-HSC I, rep 4


title: ATAC, E10.5 HE, rep 4


title: EXP2B-rep2-VECTOR-HDOX-96 H

description: replicate 2


title: Liver, SE-rGLU-GAAs, rep17


title: EXP2B-rep1-VECTOR-HDOX-96 H

description: replicate 1


title: Liver, SE-rGLU, rep3

value: SE, rGLU


title: Liver, SE-sGAL, rep16


title: Liver, SE-rGLU-GAAs, rep15


title: ATAC, E10.5 HE, rep 2

value: Hemogenic endothelium


title: EXP2B-rep3-VECTOR-96 H

description: replicate 3

value: VECTOR-96 H


title: ATAC, E10.5 HE, rep 1

value: E10.5 AGM+VU


title: Liver, SE-sGLU, rep15


title: EXP2B-rep1-VECTOR-96 H

description: replicate 1

value: HTM cells transfected with TIGR/MYOC cDNA (TM-1).


title: EXP2B-rep2-VECTOR-96 H

description: replicate 2

value: human trabecular meshwork (HTM) cells


title: Liver, SE-sGLU, rep14


title: ATAC, E10.5 HE, rep 3


title: ATAC, E10.5 EC, rep 4

value: Endothelial cells


title: Liver, SE-rGLU, rep2


title: ATAC, E10.5 EC, rep 3


title: EXP2A-rep3-GRP158-HDOX24 H

description: replicate 3

value: GRP158-HDOX24 H


title: Liver, SE-rGLU-GAAs, rep14

value: SE, rGLU-GAAs


title: ATAC, E10.5 EC, rep 2


title: Liver, SE-sGAL, rep15

value: SE, sGAL


title: EXP2A-rep2-GRP158-HDOX-24 H

description: replicate 2

value: GRP158-HDOX-24 H


title: kidney samples of controls [163]

city: zhengzhou

first: Guo

last: Jia

address: 1 Jianshe Dong Lu, Erqi District,

institute: The First Affiliated Hospital of Zhengzhou University

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.  The normalized_data.txt contains normalized signal intensity.

source_name: kidney samples of controls

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist (YY) using every 10th section stained by May-Giemsa. Careful attention was paid to the mi

treatment_protocol: three samples of DKDpatients and three samples of controls were performed the mircoassay analysis.

tag: gender

value: male

tag: subject status

value: control

value: kidney


title: kidney samples of controls [73]


title: EXP2A-rep1-GRP158-HDOX-24 H

description: replicate 1


title: ATAC, E10.5 EC, rep 1

value: 23GFP transgenic


title: EXP2A-rep3-GRP158-24 H

description: replicate 3


title: CT26_IMC_sgMen1-3_7

city: Shanghai

first: Yin

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

data_processing:
Single-cell library preparation was carried out using Chromium Single cell 3’ Reagent v2 Kits (10 × Genomics, USA) according to the manufacturer’s protocol. Cells were loaded on the Chromium Single Cell Controller Instrument to generate single cell gel beads in emulsions (GEMs). Next, reverse transcription was performed, cDNA was cleaned up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific, USA), and was then amplified by PCR with appropriate cycles. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor-ligated and subjected to library amplification.
Genome_build: mm10
Supplementary_files_format_and_content: featrues, barcodes,and mtx in zip

source_name: CT26 tumor

growth_protocol: CT26 cells were cultured in RPMI-1640 and supplemented with 10% fetal bovine serum (FBS).

extract_protocol: none provided by the submitter

treatment_protocol: We inoculated the transduced CT26 cells to BALB/C mice and harvested CT26 tumors at day 14.

value: colon

tag: growth

value: in vitro


title: Liver, SE-rGLU-GAAs, rep13

value: Liver


title: kidney samples of controls [71]


title: Liver, SE-rGLU, rep1

value: SE, rGLU


title: EXP2A-rep2-GRP158-24 H

description: replicate 2


title: CT26_IMC_sgMen1-3_6

value: in vivo


title: kidney samples of DKD [CK11]

source_name: kidney samples of DKD

value: DKD patient


title: Liver, SE-sGAL, rep14


title: EXP2A-rep3-VECTOR-HDOX-24 H

description: replicate 3

value: HTM cells transfected with TIGR/MYOC cDNA (TM-1).

value: VECTOR-HDOX-24 H


title: Liver, SE-sGLU, rep13

value: SE, sGLU


title: EXP2A-rep1-GRP158-24 H

description: replicate 1

value: human trabecular meshwork (HTM) cells


title: EXP2A-rep2-VECTOR-HDOX-24 H

description: replicate 2


title: Liver, SE-sGLU, rep12


title: CT26_IMC_sgMen1-1_3


title: kidney samples of DKD [CK10]


title: kidney samples of DKD [CK1]


title: CT26_IMC_sgMen1-1_1


title: CT26_IMC_sgEV_12


title: EXP2A-rep1-VECTOR-HDOX-24 H

description: replicate 1


title: Liver, SE-sGAL, rep13


title: Lung, hepatic ischemia-reperfusion, 6hours, rep1

city: Tianjin

first: Chen

last: Zhang

address: No. 22, Meteorological Observatory Road, Heping District, Tianjin

institute: Tianjin Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were compared to mouse genome mm10 with CellRanger version 6.0 (10× Genomics, USA).
Data were processed using Seurat R package 4.0 and Loupe browser 5.0.
Cells with less than 500 genes detected, more than 10% of mitochondrial genes or UMI <500 were excluded from the analysis.
The RNA reads section will be compared to the pre built reference genome database using STAR alignment software.
Based on the comparison results of STAR, combined with the information in the reference dataset (gtf/gff file), the read coverage information of each region on the genome can be calculated to obtain the proportion information of exons, introns, and inter gene regions compared, which serves as a reference indicator for data quality control.
Assembly: mm 10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Tab-separated matrix files

source_name: Lung

extract_protocol:
After anesthesia with sodium pentobarbital, the mice were executed by cervical dislocation. After exposure of the thorax, the lungs were excised, shredded, and transferred to 6-well plates containing enzyme solutions (type II collagenase (450 U/mL), elastase (4 U/mL) and DNase (1000 U/mL)). After incubation for 30 min at 37°C, DMEM-F12 medium was added to stop the enzymatic reaction. Subsequently, the cell suspension was passed through a 100 µm filter and transferred to a centrifuge tube at 500 × g for 5 min. erythrocytes were removed using erythrocyte lysis buffer (Sigma-Aldrich, USA). Live cells (>95%) were counted with a hemocytometer using the Taipan Blue exclusion method.
First, the extracted lung tissues were prepared as single cell suspensions, after which cell counts and cell viability tests were performed, and if the cell viability was 80%, the cell concentration was adjusted to 1000 cells/μl. The prepared cell suspensions were collected using microfluidic chips, and the beads with cell Barcode and cells were wrapped in droplets. In the droplet, the cells are lysed so that the mRNA in the cells is connected to the cell Barcode on the bead, forming Single Cell GEMs (Gel Bead-in-Emulsions), which are subjected to RT reaction in the droplet, followed by cDNA library construction. The cell Barcode on the library sequence distinguishes which cell the target sequence is from, and the sample Index on the sequence distinguishes which sample the target sequence is from. Cells and reaction reagents are placed in one lane on the microfluidic chip and beads in the other lane to form a GEM. Reverse transcription is performed independently in each GEM, after which the labeled cDNA is mixed and then amplified for library construction.

value: Lung

value: primary cell

value: mouse lung cell

value: Wild type

value: Hepatic ischemia-reperfusion


title: CT26_IMC_sgEV_9


title: EXP2A-rep3-VECTOR-24 H

description: replicate 3

value: VECTOR-24 H


title: Liver, CON-sGLU, rep6

value: CON, sGLU


title: EXP2A-rep2-VECTOR-24 H

description: replicate 2


title: E54-T1-47-AI: Conceptus_Endometrium Co-culture_Rep 8

city: Knoxville

first: Daniel

last: Mathew

state: TN

address: 2506 River Drive

department: Animal Science

country: USA

institute: University of Tennessee

data_processing:
The RNA-Seg raw sequences (fastq) underwent adaptor removal and quality trimming using Trimmomatic and quality reads were aligned to the bovine reference genome (ARS-UCD1.2.103) using the STAR aligner program for the endometrial sequences and Hisat2 mapper program for conceptus sequences (Dobin et al., 2013; Kim et al., 2015). The sorted binary alignment maps and the NCBI gene annotation assembly were subjected to FeatureCounts to quantify read counts of genes for each sample (Liao et al., 2014).
Assembly: ARS-UCD1.2.103
Supplementary files format and content: Gene FeatureCounts in Excel

organism: Bos taurus

source_name: Conceptus

extract_protocol:
Endometrial total RNA was extracted and analyzed using RNA-Sequencing (RNA-Seq). Endometrial total RNA extraction was achieved using 5 mm stainless steel beads (Qiagen) and a bead mill homogenizer (Bead Mill 4; ThermoFisher) and Trizol (Invitrogen) in combination with an on-column method (RNeasy Mini Kit; Qiagen) involving a DNase step as previously described by Mathew et al. 2019. The resulting RNA quality and quantity were assessed using the 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 (NanoDrop Technologies), respectively. Endometrial RNA integrity numbers (RIN) ranged from 5.2 – 9.3 and total endometrial RNA was analyzed using RNA-Sequencing (RNA-Seq) for the following culture tissues: 1) Endo (n=13; mono-culture); and 2) Endo-Conceptus Endo (n=15; co-culture). Conceptus RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) with the optional on-column DNase digestion step according to the manufacturer’s recommendations. The RNA quantity and quality were assayed using a NanoDrop 1000 and RNA Screen Tape (Agilent Technologies). The conceptus RIN ranged from 7.5 – 10. Conceptus section total RNA was assayed using RNA-Seq for the following culture tissues: Conceptus (n=8; mono-culture) and Endo-Conceptus Conceptus (n=9; co-culture).
Library preparation including poly (A) enrichment and RNA-Seq of the explant and conceptus total RNA was performed by the University of Missouri DNA Core facility (Columbia, MO). The cDNA libraries were prepared using the Stranded RNA Prep Ligation Kit (Illumina) as described by the manufacturer. The final amplified cDNA constructs were purified by addition of Axyprep Mag PCR Clean-up beads (Corning) and the final construct of each purified library was evaluated using a Fragment Analyzer automated electrophoresis system (Agilent), quantified using the Invitrogen Qubit HS dsDNA assay kit and Qubit fluorometer, and diluted according to Illumina’s standard protocol for sequencing on the NovaSeq 6000 (Illumina).

value: Conceptus

tag: Sex

value: Unknown

value: RPMI Medium + Endometrium


title: Liver, CON-sGLU, rep5

value: Liver


title: E39-T1-26-AI: Conceptus_Endometrium Co-culture_Rep 7


title: E70-R1-71-AI: Conceptus_Endometrium Co-culture_Rep 9


title: EXP2A-rep1-VECTOR-24 H

description: replicate 1


title: Lung, sham, rep1

description: 10x Genomics

value: Sham surgery


title: Liver, CON-sGAL, rep5

value: CON, sGAL


title: EXP1-rep3-GRP158-LDOX-72 H

description: replicate 3

value: HTM cells transfected with TIGR/MYOC cDNA (TM-1).

value: GRP158-LDOX-72 H


title: E38-T1-66-AI: Conceptus_Endometrium Co-culture_Rep 6


title: E38-R1-50-AI: Conceptus_Endometrium Co-culture_Rep 5


title: Tumor infiltrating lymphocytes, AB2

city: Cold Spring Harbor

first: Vyom

last: Shah

state: New York

address: 1 bungtown road

department: Beyaz Lab

institute: Cold Spring Harbor Laboratory

description: processed file is a count matrix

data_processing:
RNA-seq reads were implemented to trimming (cutadapt), mapping (STAR), and expression quantification (quantMode GeneCount), respectively.
Reads were mapped to GRCm38
Differential gene expression analyses were performed using DESeq2 ref. Lowly-expressed genes were filtered out from the differential expression analysis input matrix.
Limma (v3.46) was used to adjust for sequencing batch effects, prior to rlog normalisation of the size-factor normalized read counts.
Assembly: GRCm38
Supplementary files format and content: Comma-separated values version of raw counts of sequencing reads for all samples

source_name: Tumor infiltrating lymphocytes

extract_protocol: Samples were processed as/ the manufacturer’s instructions (Chromium single cell 3’ reagents, v3.1 chemistry) and libraries were sequenced using Illumina NovaSeq.

value: Tumor infiltrating lymphocytes

value: Sptlc1-KO + Sptlc1 cDNA


title: Tumor infiltrating lymphocytes, PMXS1

description: processed file is a count matrix


title: Tumor infiltrating lymphocytes, PMXS2

description: processed file is a count matrix


title: Tumor infiltrating lymphocytes, AB1

description: processed file is a count matrix


title: Liver, CON-sGAL, rep4


title: Liver, CON-rGLU-GAAs, rep5

value: CON, rGLU-GAAs


title: Liver, CON-rGLU-GAAs, rep4


title: EXP1rep-2-GRP158-LDOX-72 H

description: replicate 2

value: human trabecular meshwork (HTM) cells


title: E19-T1-47-AI: Conceptus_Endometrium Co-culture_Rep 4


title: Liver, CON-sGLU, rep4


title: EC, E13.5 mutant 3

city: New Haven

first: Jui

last: Dave

state: CT

address: 300 George St

department: Cardiovascular Research Center

institute: Yale University

description: E13.5 ECs Mut vs Con_processed data.txt

data_processing:
Data were analyzed using Partek Flow software.
BOWTIE2 was used to align trimmed reads to the reference genome (mm10).
Gene counts were normalized by Median ratio and differential analysis between controls and mutants was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: In general, controls and mutants are compared at specific conditions like timepoints and cell types. Processed data files contain gene name, pvalue, FDR, LSmean of controls, LS mean of mutants, ratio (mutant vs. control) and fold change (mutant vs control). Following datasets are compared for generating processed data files (1) PCs isolated at E11.5 from controls and mutants (2) PCs isolated at E13.5 from controls and mutants and (3) ECs isolated at E13.5 from controls and mutants. All features (genes) were included.

source_name: brain

growth_protocol: Cells were isolated from in vivo using FACS and directly utliized for RNA isolation

extract_protocol:
Total RNA was isolated using Direct-zol RNA MicroPrep (Zymo Research) kit and quantified by Agilent 2100 Bioanalyzer.
Samples with RIN values greater than 9 were used for library preparation. mRNA library was prepared from ~200 ng RNA using KAPA mRNA HyperPrep kit (Roche). Indexed libraries were quantified by KAPA Library Quantification kit (Roche), and insert size distribution was determined with the Agilent 2100 Bioanalyzer. Samples with a yield of  ≥ 0.5 ng/µl and a size distribution of 150-300 bp were used for sequencing using NovaSeq6000 sequencer (Illumina).

value: brain

value: endothelial cells

value: micorvascular endothelial cells

value: Pdgfrb-Cre, Alk5(flox/flox), Zs/+

tag: disease state

value: GMH-IVH


title: EXP1-rep1-GRP158-LDOX-72 H

description: replicate 1


title: EC, E13.5 mutant 2

description: E13.5 ECs Mut vs Con_processed data.txt


title: EXP1-rep2-GRP158-72 H

description: replicate 2


title: E14-T1-26-AI: Conceptus_Endometrium Co-culture_Rep 3

value: Conceptus


title: EXP1-rep3-GRP158-72 H

description: replicate 3


title: Liver, SE-rGLU-GAAs, rep12

value: SE, rGLU-GAAs


title: E69-V1-71-AI: Conceptus_Mono-culture_Rep 8

value: Unknown

value: RPMI Medium


title: E19-R1-22-AI: Conceptus_Endometrium Co-culture_Rep 2

value: RPMI Medium + Endometrium


title: EC, E13.5 control 3

description: E13.5 ECs Mut vs Con_processed data.txt

value: Pdgfrb-Cre, Alk5(flox/+), Zs/+

value: normal


title: EC, E13.5 control 5

description: E13.5 ECs Mut vs Con_processed data.txt


title: Liver, SE-rGLU-GAAs, rep11

value: Liver


title: Liver, SE-rGLU-GAAs, rep10


title: EXP1-rep1-GRP158-72 H

description: replicate 1

value: HTM cells transfected with TIGR/MYOC cDNA (TM-1).


title: E14-R1-8-AI: Conceptus_Endometrium Co-culture_Rep 1


title: Liver, SE-sGAL, rep12

value: SE, sGAL


title: EXP1-rep3-VECTOR-LDOX-72 H

description: replicate 3

value: VECTOR-LDOX-72 H


title: EC, E13.5 control 2

description: E13.5 ECs Mut vs Con_processed data.txt


title: EXP1-rep1-VECTOR-LDOX-72 H

description: replicate 1

value: human trabecular meshwork (HTM) cells


title: E38-V1-50-AI: Conceptus_Mono-culture_Rep 6


title: EC, E13.5 control 1

description: E13.5 ECs Mut vs Con_processed data.txt

value: brain


title: EXP1-rep2-VECTOR-LDOX-72 H

description: replicate 2


title: E38-X1-66-AI: Conceptus_Mono-culture_Rep 7


title: Liver, SE-sGAL, rep11


title: E14-X1-26-AI: Conceptus_Mono-culture_Rep 4


title: EC, E13.5 mutant 1

description: E13.5 ECs Mut vs Con_processed data.txt

value: endothelial cells


title: EXP1-rep3-VECTOR-72 H

description: replicate 3

value: VECTOR-72 H


title: Liver, SE-sGLU, rep11

value: SE, sGLU


title: EC, E13.5 control 4

description: E13.5 ECs Mut vs Con_processed data.txt

value: micorvascular endothelial cells


title: Liver, SE-sGAL, rep10


title: PC, E13.5 mutant 3

description: E13.5 PCs Mut vs Con_processed data.txt

value: pericytes

value: mesenchymal cells

value: Pdgfrb-Cre, Alk5(flox/flox), Zs/+

value: GMH-IVH


title: PC, E13.5 mutant 2

description: E13.5 PCs Mut vs Con_processed data.txt


title: E14-V1-8-AI: Conceptus_Mono-culture_Rep 2

value: Conceptus

value: Unknown

value: RPMI Medium


title: PC, E13.5 mutant 1

description: E13.5 PCs Mut vs Con_processed data.txt


title: PC, E13.5 mutant 4

description: E13.5 PCs Mut vs Con_processed data.txt


title: EXP1-rep2-VECTOR-72 H

description: replicate 2


title: Liver, SE-sGAL, rep9

value: Liver


title: R738 GBM OLIG2 ChIP

city: Albuquerque

first: Tou Yia

last: Vue

state: New Mexico

address: 915 Camino De Salud NE, Fitz Hall 145

department: Neurosciences

institute: University of New Mexico Health Sciences Center

data_processing:
Reads were mapped to hg19 assembly using bowtie2
Low quality reads were filtered using samtools
Removed duplicates using picard
Bigwig files contain ChIP signal normalized to 10M reads
Assembly: hg19
Supplementary files format and content: ChIP-seq signal in bedgraph format

source_name: gliomas

growth_protocol: PDX-GBMs were grown and dissected from brains of NOD-SCID mice.

extract_protocol:
Nuclear chromatin was pelleted, washed with cold PBS, and sonicated into 200–300 bp fragments using a Biorupter (Diagenode). A portion of the sheared chromatin (10%) was set aside as input DNA, while 100 μg was subjected to chromatin immunoprecipitation (ChIP) using 5 μg of mouse anti-ASCL1 (Mash1) antibody (BD Biosciences, 556604) or 5 μg rabbit ant-OLIG2 (Olig2) (Millipore, AB9610). Washes and reverse-crosslinking were performed using Dynabeads Protein G to elute the ChIP DNA for sequencing.
bowtie2 (v2.2.6) was used to aligned sequence reads to the human reference genome (hg19) and de novo motif analyses were performed using HOMER Software (v.4.7).

treatment_protocol: Cells were homogenized and fixed in 1% formaldehyde to crosslink proteins and DNA, followed by quenching with 0.125 M of glycine.

tag: host mouse_tissue

value: gliomas

value: NOD-SCID

tag: chip antibody

value: anti-OLIG2 (Millipore, AB9610)


title: PC, E13.5 control 4

description: E13.5 PCs Mut vs Con_processed data.txt

tag: cell line

value: Pdgfrb-Cre, Alk5(flox/+), Zs/+

value: normal


title: Liver, SE-rGLU-GAAs, rep9

value: SE, rGLU-GAAs


title: E19-X1-47-AI: Conceptus_Mono-culture_Rep 5


title: EXP1-rep1-VECTOR-72 H

description: replicate 1

value: HTM cells transfected with TIGR/MYOC cDNA (TM-1).

tag: cell type

value: human trabecular meshwork (HTM) cells

value: VECTOR-72 H


title: E19-V1-22-AI: Conceptus_Mono-culture_Rep 3

tag: treatment


title: R548 GBM OLIG2 ChIP

value: brain


title: E56-V1-5-AI: Conceptus_Mono-culture_Rep 1


title: PC, E13.5 control 3

description: E13.5 PCs Mut vs Con_processed data.txt

value: pericytes

value: mesenchymal cells

tag: time


title: Liver, SE-sGLU, rep10

tag: tissue

value: SE, sGLU


title: Liver, SE-rGLU-GAAs, rep7


title: Liver, SE-sGAL, rep8

value: SE, sGAL


title: RNA, E9.5 pro-HSC/HPC, rep 3

data_processing:
Paired end reads were mapped to the mouse genome assembly (mm9) using Tophat with default parameters
PCR duplicates and multi-mapping reads were removed using Samtools
Mapped reads over exons were quantified using subread featureCounts (v1.6.2)
Assembly: mm9
Supplementary files format and content: Output from featureCounts: TSV file including read counts over exons for each gene.

source_name: E9.5 PAS+VU

extract_protocol:
100 cells were sorted directly into 3.16 ul RNA lysis buffer (Clontech).
RNA libraries for RNA-seq were prepared using SMARTer Ultra Low Input RNA for Illumina Sequencing kit following manufacturer's protocols.

value: E9.5 PAS+VU

value: pro-HSC/HPC

tag: genotype

value: 23GFP transgenic


title: PC, E13.5 control 2

description: E13.5 PCs Mut vs Con_processed data.txt


title: PC, E13.5 control 1

description: E13.5 PCs Mut vs Con_processed data.txt


title: RNA, E9.5 pro-HSC/HPC, rep 2


title: PC, E11.5 mutant 4

description: E11.5 PCs Mut vs Con_processed data.txt

value: Pdgfrb-Cre, Alk5(flox/flox), Zs/+

value: GMH-IVH


title: Liver, SE-sGAL, rep7

value: Liver


title: Liver, SE-rGLU-GAAs, rep6


title: R738 GBM OLIG2 Input ChIP

value: gliomas

value: NOD-SCID


title: RNA, E9.5 pro-HSC/HPC, rep 1


title: RNA, E9.5 HE, rep 3

value: Hemogenic endothelium


title: Liver, SE-rGLU-GAAs, rep8

value: SE, rGLU-GAAs


title: Liver, SE-sGLU, rep8


title: PC, E11.5 mutant 3

description: E11.5 PCs Mut vs Con_processed data.txt


title: PC, E11.5 mutant 2

description: E11.5 PCs Mut vs Con_processed data.txt


title: RNA, E9.5 HE, rep 1


title: Liver, CON-rGLU-GAAs, rep3

value: CON, rGLU-GAAs


title: RNA, E9.5 EC, rep 3

value: Endothelial cells


title: R548 GBM OLIG2 Input ChIP

value: brain


title: Liver, SE-sGLU, rep7


title: Liver, SE-sGLU, rep9


title: PC, E11.5 control 3

description: E11.5 PCs Mut vs Con_processed data.txt

value: pericytes

value: Pdgfrb-Cre, Alk5(flox/+), Zs/+

value: normal


title: PC, E11.5 control 4

description: E11.5 PCs Mut vs Con_processed data.txt

value: mesenchymal cells


title: RNA, E9.5 HE, rep 2

value: E9.5 PAS+VU


title: PC, E11.5 mutant 1

description: E11.5 PCs Mut vs Con_processed data.txt


title: Liver, CON-sGAL, rep3

value: CON, sGAL


title: PC, E11.5 control 2

description: E11.5 PCs Mut vs Con_processed data.txt


title: Liver, CON-sGLU, rep3

value: CON, sGLU


title: PC, E11.5 control 1

description: E11.5 PCs Mut vs Con_processed data.txt


title: RNA, E9.5 EC, rep 1

value: 23GFP transgenic


title: Liver, CON-rGLU-GAAs, rep2


title: Liver, CON-sGAL, rep2


title: RNA, E8.5 HE, rep 3

source_name: E8.5 PAS+VU

value: E8.5 PAS+VU


title: Liver, CON-sGLU, rep2

value: Liver


title: RNA, E8.5 HE, rep 2


title: RNA, E8.5 HE, rep 1


title: Liver, CON-sGAL, rep1


title: Liver, CON-rGLU-GAAs, rep1


title: RNA, E8.5 EC, rep 3


title: BMDMs, IFN-γ, 3 h, rep2

city: Wuhan, China

first: Xiao

last: Yang

state: 湖北省

address: 武汉市江汉区马场路109号协和医院肿瘤中心

institute: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website (http:// ) directly. We selected Hisat2 as the mapping tool
The number of perfect clean tags for each gene was calculated and then normalized in fragments per kilo bases per million mapped Reads (FPKM) using the described method.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: macrophages

growth_protocol: For the generation of BMDMs, two million BM cells per well were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and mouse M-CSF (20 ng/mL, PeproTech). The culture media were replaced on day 3 and day 5.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen)
RNA sequencing libraries were generated using the KAPA Stranded mRNA-Seq Kit for illumina with multiplexing primers, according to the manufacturer’s protocol.

value: macrophages

value: WT

value: IFN-gamma


title: BMDMs, IFN-γ, 3 h, rep3

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: BMDMs, Untreated, 3 h, rep3

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: RNA, E9.5 EC, rep 2

city: Oxford

first: Marella

institute: University of Oxford


title: BMDMs, Untreated, 3 h, rep1

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: RNA, E8.5 EC, rep 2


title: Liver, SE-rGLU-GAAs, rep5

value: SE, rGLU-GAAs


title: RNA, E8.5 EC, rep 1


title: RNA, E8.5 HE, rep 4

value: Hemogenic endothelium


title: BMDMs, IFN-γ+4-OI, rep3

address: 武汉市江汉区马场路109号协和医院肿瘤中心

source_name: dendritic cells

growth_protocol: For the generation of BMDCs, two million BM cells per well were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and mouse GM-CSF (20 ng/mL, PeproTech). The culture media were replaced on day 3 and day 5.

value: dendritic cells


title: Liver, SE-rGLU-GAAs, rep3


title: BMDMs, IFN-γ+4-OI, rep2

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: RNA, E10.5 pre-HSC II, rep 3

value: E10.5 AGM+VU

value: pre-HSC II


title: RNA, E10.5 pre-HSC II, rep 2


title: RNA, E10.5 pre-HSC II, rep 1


title: BMDMs, IFN-γ+4-OI, rep1

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: Liver, SE-sGAL, rep5

value: SE, sGAL


title: BMDMs, IFN-γ, 3 h, rep1

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: Liver, CON-sGLU, rep1


title: BMDMs, IFN-γ, rep3

address: 武汉市江汉区马场路109号协和医院肿瘤中心

value: IFN-γ


title: RNA, E10.5 pre-HSC I, rep 3

value: pre-HSC I


title: BMDMs, IFN-γ, rep2

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: RNA, E10.5 pre-HSC I, rep 1


title: BMDMs, Untreated, 3 h, rep2

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: Liver, SE-rGLU-GAAs, rep4


title: RNA, E10.5 pre-HSC I, rep 2


title: Liver, SE-sGAL, rep4


title: BMDMs, IFN-γ, rep1

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: RNA, E10.5 HE, rep 3


title: Rare cell replicate 3

city: Qingdao

first: Xiaonan

last: Cui

address: 238 Songling Road

institute: The Ocean University of China

description: Different barcode represent different region of light illumination in RPE cells of mouse embryo （RPE（AAACCGG) NR（CAAGCCT））, replicate 3

data_processing:
Drop-seq core computational protocol (v.2.0.0)
DESeq2 package of the R project (version 4.1.2)
Assembly: Ensembl mm10 and hg18
Supplementary files format and content: tab-delimited text file includes matrix for each sample

source_name: embryo

extract_protocol:
Hela cells were cultured at 37 °C in a humidified 5 % CO2 atmosphere, in high-glucose DMEM (Gibco; 11965092) supplemented with 10 % calf serum (Gibco;10270-106), 1 % penicillin/streptomycin (Nacalai Tesque; 0503), and 1 % L-glutamine (Nacalai Tesque; 16948-04). For cell preparation, Poly-l-lysine-coated chambers were coated with sterile PDL (Sigma Aldrich cat. no. P6407) at 0.3 mg/ml overnight at 4 °C. Afterwards, the chamber was dried for 1 hour, washed with UltraPure water (Invitrogen; 10977023). Chambers were then seeded with cells per well and placed in an incubator (37 °C with 5 % CO2) two days for subcellar resolution validation.Fresh frozen tissue (moouse embryo E14.5 and mouse brain) were OCT embedded, and 10um fozen sections were cut with cryostat. FFPE tissue (mouse embryo E15.5) is sliced with 7um. Different barcode represent different region of light illumination. The library struction is "read2-7bp bar—32fix--8bp-UMI—22bp dTVN-cDNA-read1"
The library was performed by IVT and RT-PCR protocol. Briefly,The RT products (15 μl) were combined with PCR mix, and amplified by PCR . Fragments of 250–1000 bp were then purified and size-selected with Speedbead magnetic capboxylate. The quality of the resulting cDNA library was quantified using a Qubit dsDNA HS assay kit (Invitrogen, Q32854) with Qubit 3.0 Fluorometer (Invitrogen),before sequencing on the Illumina NovaSeq 6000.

value: embryo


title: Liver, SE-sGLU, rep5

source_name: Liver

value: SE, sGLU


title: Rare cell replicate 2

description: Different barcode represent different region of light illumination in RPE cells of mouse embryo （RPE（AAACCGG) NR（CAAGCCT））, replicate 2


title: Liver, SE-sGAL, rep6


title: Liver, SE-sGAL, rep3


title: Liver, SE-sGLU, rep4


title: RNA, E10.5 HE, rep 1

last: de Bruijn

address: MRC MHU, WIMM, John Radcliffe Hospital

source_name: E10.5 AGM+VU


title: Rare cell replicate 1

description: Different barcode represent different region of light illumination in RPE cells of mouse embryo （RPE（AAACCGG) NR（CAAGCCT））, replicate 1


title: RNA, E10.5 HE, rep 2


title: RNA, E10.5 EC, rep 3

value: Endothelial cells


title: Liver, SE-sGLU, rep3


title: RNA, E10.5 EC, rep 2

value: 23GFP transgenic


title: FFPE mouse embryo replicate 3

description: Different barcode represent different region of light illumination in FFPE mouse embryo（FFPE Eye （AAACCGG）FFPE viscus （CAAGCCT））, replicate 3


title: Liver, SE-sGLU, rep6


title: RNA, E10.5 EC, rep 1


title: FFPE mouse embryo replicate 1

description: Different barcode represent different region of light illumination in FFPE mouse embryo（FFPE Eye （AAACCGG）FFPE viscus （CAAGCCT））, replicate 1


title: Liver, SE-sGAL, rep2


title: C4-2 EV-RNA, enzalutamide 3

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

data_processing:
Sequence reads were scanned for rRNA contamination using bbduk, and trimmed for adaptor sequence/low-quality sequence using trim-galore
Trimmed reads were mapped to human genome GRCh38 using STAR-2.7.9a
Read count quantification was performed with featureCounts from subRead 2.0.3
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
Tumor RNA from cells  was harvested using RNeasy  kit (Qiagen).  EV-RNA from cells conditioned media was harvested using the ExoRNeasy kit.
RNA libraries for RNA-seq were prepared using a customized protocol named RExCuE, which is an adaptation of SmartSeq2 protocol

value: prostate cancer epithelial cells

value: enzalutamide (20uM)


title: Mito_BS_seq

city: Hefei

first: Yijie

last: Hao

address: Huangshan Road 443

institute: USTC

data_processing:
The qualified libraries were sequenced pair end PE150 on the illumina HiseqXten
Cutadapt was used to remove sequencens of adaptors, polymerase chain reaction(PCR) primers, reads with N bases more than 10% and bases with quality lower than 20 to obtain clean data.
Bismark was used to map clean data to reference genome, then call methylated cytosine (mC) by coverage2cytosine command.
Differentially methylated cytosines between the treatment and the control group were detected by methylKit. swDMR was used to reveal set of differentially methylated regions (DMR).
Assembly: hg19 ChM
Supplementary files format and content: bedGraph for BS-seq data

growth_protocol: DMEM supplemented with 10% FBS and 1% Pen/Strep. Cells were maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Mitochondria were purified usinga Dounce tissue grinder tube followed by centrifugations. mtDNA were further isolated from the purified mitochondira feactions.
Mitochondrial genomic DNA was randomly fragmented to <500 bp by sonication (Covaris S220). The fragments were treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by a T-A ligation to add Methylated adaptors to both ends. Then bisulfite conversion was performed using the related Kit. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The final library products for sequencing were then purified by beads, and the qualities were detected.

value: mtDNA were isolated from purified mitochondria from MDA-MB-468 cells.


title: Rare cell replicate 4

description: Different barcode represent different region of light illumination in RPE cells of mouse embryo （RPE（AAACCGG) NR（CAAGCCT））, replicate 4


title: FFPE mouse embryo replicate 2

description: Different barcode represent different region of light illumination in FFPE mouse embryo（FFPE Eye （AAACCGG）FFPE viscus （CAAGCCT））, replicate 2


title: C4-2 EV-RNA, enzalutamide 2

value: WT


title: Liver, SE-rGLU-GAAs, rep2

value: Liver


title: Liver, SE-sGLU, rep1


title: Liver, SE-sGAL, rep1


title: 12 HFD29 Mlkl-/- #1219

city: New York

first: Isabella

last: Kong

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The single-end 75 bp were demultiplexed using Casavav1.8.2 and Cutadapt (v1.9) was used for read trimming.
The trimmed reads were subsequently mapped to the mouse genome (mm10) using HISAT2.
FeatureCounts was used for read counting after which differential gene expression analysis was performed using Voom-LIMMA packages.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA extracted using Trizol RNA Isolation Reagents (Life Technologies) and purified using RNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
3’mRNA-sequencing libraries were prepared using 100 ng of total RNA using the QuantSeq 3’mRNA-Seq Library Prep (Lexogen) according to the manufacturer’s instructions and sequenced on the NextSeq 500 (Illumina).
3' mRNA-seq

value: Mlkl-/-

value: High fat diet (36% fat, 59% of total energy from lipid)

value: 25 weeks of diet


title: 11 HFD25 Mlkl-/- #915


title: Liver, SE-rGLU-GAAs, rep1

value: SE, rGLU-GAAs


title: C4-2 EV-RNA, vehicle 3

value: vehicle (DMSO)


title: Mouse embryo replicate 3

description: Different barcode represent different region of light illumination in mouse embryo （Eye （AAACCGG）Viscus （CAAGCCT））, replicate 3


title: C4-2 EV-RNA, enzalutamide 1


title: 10 HFD25 Mlkl-/- #910


title: 9 HFD29 WT #1231

value: wild-type


title: C4-2 EV-RNA, vehicle 2


title: Mouse embryo replicate 1

description: Different barcode represent different region of light illumination in mouse embryo （Eye （AAACCGG）Viscus （CAAGCCT））, replicate 1


title: Second_kidney_xeno_scRNA_seq_untransplanted

first: Weimin

state: NY

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

data_processing:
Raw single-cell sequencing data were processed with the CellRanger pipeline of 10X Genomics to generate single-cell raw gene expression matrices. Kidney single-cell sequencing data were separately mapped to both human genome (GRCh38) and porcine genome (Sscrofa11) to distinguish the species origin of cells, while recipient’s PBMC single cell data were mapped to human genome (GRCh38) only. Single-cell raw expression matrices were then processed and analyzed using Seurat v4.3.049. Cells with less than 500 expressed genes, 1000 UMI, or more than 8% of transcripts from mitochondrial genes were removed from the kidney single cells, resulting in a total of 23,868 cells. A library of homologous genes between human and pig, obtained from the HGD Database50, was used as a reference to subset the filtered gene expression data for downstream analyses. Within the scope of gene expression of human-porcine one-to-one homologous genes, single cells with greater proportion of transcripts mapped to the porcine genome than the human genome are identified to be porcine cells, and vice versa to be human cells.
Each filtered dataset obtained from the kidneys and PBMC samples were normalized using SCTransform v2 from Seurat followed by integration using most commonly deemed variable features within each dataset. Dimensionality reduction analyses were performed on integrated kidney and PBMC datasets separately using Principal Component Analysis (PCA: npcs = 30) and Uniform Manifold Approximation and Projection (UMAP: dims = 1:30). Cell clusters were generated using the original Louvain algorithm with a resolution of 0.7 for integrated kidney dataset and 0.5 for the integrated PBMC dataset. Individual clusters were annotated based on the expression of cell type-specific markers.
Assembly: sscrofa11, hg38
Supplementary files format and content: h5

source_name: kidney

extract_protocol:
Fresh kidney tissues were minced rapidly in a cell culture dish followed by washing with DPBS buffer. Minced tissue was resuspended in 5mL of 37°C pre-warmed 0.25% Trypsin for 20 min with mechanical dissociation using serological pipette every 5 min. Following digestion, dissociation mix was filtered through a 100µm strainer. The remaining large tissues on the strainer were further ground and washed to collect additional cells. Cell debris and dead cells were removed using Miltenyi Biotech Dead Cell Removal Kit before loading for 10X Genomics single-cell RNA-seq (v3.1 Chemistry). Longitudinal single-cell RNA-seq of the recipient’s PBMCs were prepared at the same time after collecting all samples across timepoints. Fresh PBMCs of each timepoint were first collected through gradient centrifugation, followed by cryopreservation of the prepared PBMCs according to the 10X Genomics protocol (protocol number: CG00039). Upon collecting all PBMC samples, the frozen cells were thawed at the same time, then loaded for 10X Genomics single-cell RNA-seq (v3.1 Chemistry).
prepared signle cells were sequenced using 10X Genomics single-cell RNA-seq (v3.1 Chemistry) following manufacturer's protocol.

value: kidney

value: Dissociated kidney cells

value: subject 2, untransplanted


title: Liver, SE-sGLU, rep2

first: tik

institute: University of Copenhagen

data_processing:
The libraries were sequenced on the Illumina NovaSeq 6000 S4 flowcell with PE150.
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using HISAT2
The annotated gene information of porcine genome was downloaded from Ensembl (release 99).
The script htseq-count was used to generate a gene-count matrix, followed by analyses of DEGs using DESeq2 .
Assembly: Sscrofa11.1
Supplementary files format and content: Processed data was formated as htseq.count files
Supplementary files format and content: Each file represent counting reads for genes in each sample with htseq-count

extract_protocol:
Total RNA of homogenized liver tissues was extracted using RNeasy Mini Kit (Qiagen, Copenhagen, Denmark).
Construction of RNA-Seq libraries was done using Novogene NGS RNA Library Prep Set (PT042)

value: SE, sGLU


title: Brain 4ROIs replicate 4

description: Different barcode represent different region of light illumination in mouse brain （CA1(AAACCGG）CA3（CAAGCCT）DG（CAGAGTG） RSP（CAGAGTG））, replicate 4

value: brain


title: C4-2 EV-RNA, vehicle 1


title: 8 HFD29 WT #1229


title: C4-2 Tumor RNA, enzalutamide 3


title: Mouse embryo replicate 2

description: Different barcode represent different region of light illumination in mouse embryo （Eye （AAACCGG）Viscus （CAAGCCT））, replicate 2

value: embryo


title: First_kidney_xeno_scRNA_seq_untransplanted_replicate_B

value: subject 1, untransplanted


title: 6 ND27 Mlkl-/- #1154

value: Normal chow diet


title: Brain 4ROIs replicate 1

description: Different barcode represent different region of light illumination in mouse brain （CA1(AAACCGG）CA3（CAAGCCT）DG（CAGAGTG） RSP（CAGAGTG））, replicate 1


title: 5 ND27 Mlkl-/- #1153


title: Second_kidney_xeno_scRNA_seq_transplanted

value: subject 2, transplanted


title: Brain 4ROIs replicate 2

description: Different barcode represent different region of light illumination in mouse brain （CA1(AAACCGG）CA3（CAAGCCT）DG（CAGAGTG） RSP（CAGAGTG））, replicate 2


title: 7 HFD25 WT #904


title: C4-2 Tumor RNA, enzalutamide 2

value: prostate cancer epithelial cells

value: WT

value: enzalutamide (20uM)


title: C4-2 Tumor RNA, vehicle 2


title: PDG-p53 Recurrent, replicate 2

city: Amsterdam

first: Daan

last: Kloosterman

address: Plesmanlaan 121

institute: The Netherlands Cancer

data_processing:
Libraries were loaded at a concentration of 250 pM (1% PhiX) and sequenced on a NovaSeq 6000 System (Illumina) using a NovaSeq SP Reagent Kit v1.5 (cat no. 20028401, Illumina), at a sequencing depth of approximately 40.000 to 50.000 read pairs per tissue covered spot. NovaSeq sequencing was performed using 28 cycles for Read 1, 10 cycles for each Read i7 and i5 and 90 cycles for Read 2. The Space Ranger software v1.0.0 (10X Genomics) was used to align the barcoded reads with the imaged tissue.
Assembly: mm10
Supplementary files format and content: visium_merged_complete.rds: compiled data contained both images, annotations and gene expression data

source_name: Brain tumor

extract_protocol:
For the Visium samples, libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG000239 RevD).
The Visium Spatial Gene Expression libraries of all 8 samples were pooled to create one sequencing pool. The sequencing pool was quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems).
Visium 10x

value: Brain tumor

value: 5 x 2Gy Irradiation


title: First_kidney_xeno_scRNA_seq_untransplanted_replicate_A


title: Brain 4ROIs replicate 3

description: Different barcode represent different region of light illumination in mouse brain （CA1(AAACCGG）CA3（CAAGCCT）DG（CAGAGTG） RSP（CAGAGTG））, replicate 3


title: C4-2 Tumor RNA, vehicle 3


title: First_kidney_xeno_scRNA_seq_transplanted_replicate_B

value: subject 1, transplanted


title: PDG-Ink4a Primary, replicate 4

value: No treatment


title: PDG-p53 Recurrent, replicate 3


title: pig_xeno_second_kidney_biopsy_bulk_RNA_seq_T48h

data_processing:
The bulk RNA-seq data across 0, 12, 24, and 48 hours pXTx was analyzed to understand the temporal changes in gene expression between the control and xenograft samples. Two technical replicates were conducted at 0 hours post-transplantation from the control kidneys. Gene expression at time 0 is calculated by the average value between the two replicates. The log2 fold change in gene expression was calculated for each gene across the different time points relative to the expression value at time 0. To calculate the human to pig raw count reads ratio (H/P Ratio), the absolute raw reads mapped to the human genome (hg38) for every gene at a specific time point is divided by the absolute raw reads mapped to the porcine genome (Sscrofa11).
Assembly: Sscrofa11, hg38
Supplementary files format and content: txt

source_name: Kidney

extract_protocol:
Kidney core biopsy samples were homogenized using a pestle homogenizer, total RNA was extracted from lysate using a QIAGEN RNeasy plus kit. Total RNA quality and quantity were examined using a Bioanalyzer (Agilent 2100, RNA 6000 nano kit)
Libraries were constructed by following the Illumina Ribo-Zero Plus rRNA Depletion Kit (20037135) protocol.

value: Kidney

tag: time point

value: xenotransplantation


title: 3 ND27 WT #1142

value: Liver

value: wild-type

value: 25 weeks of diet


title: First_kidney_xeno_scRNA_seq_transplanted_replicate_A

value: kidney

value: Dissociated kidney cells


title: C4-2 Tumor RNA, vehicle 1

value: vehicle (DMSO)


title: 2 ND23 WT #876

value: Normal chow diet


title: C4-2 Tumor RNA, enzalutamide 1


title: PDG-p53 Recurrent, replicate 1


title: 4 ND23 Mlkl-/- #859

value: Mlkl-/-


title: pig_xeno_second_kidney_biopsy_bulk_RNA_seq_T12h


title: SK-MES-1, FGF19 2

city: shanghai

first: Yanshuang

state: China

address: 1954 Huashan Road, Shanghai Jiao Tong University, Shanghai 200030, PR China

institute: Shanghai Jiao Tong University

data_processing:
Illumina San Diego, CA software used for basecalling.
Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
Gene expression values of the transcripts were computed by StringTie (version 1.3.3b).
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts, FPKMs, TPMs for every gene and every sample

extract_protocol:
RNA was harvested using RNAiso reagent. The Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit 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: Lung squamous cell carcinoma (LUSC)

value: Lung

value: FGF19 overexpression


title: pig_xeno_second_kidney_biopsy_bulk_RNA_seq_T0h_rep1

value: Control


title: SK-MES-1, FGF19 1


title: PDG-p53 Primary, replicate 3

value: Brain tumor


title: pig_xeno_second_kidney_biopsy_bulk_RNA_seq_T0h_rep2


title: PDG-p53 Primary, replicate 1


title: PDG-Ink4a Primary, replicate 3


title: aorta, 1 year-old rat, hyperoxia Aorta1013_S8

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

data_processing:
Alignment with RN6.0 genome build with Kallisto
Gene summarization and feature counts with tximport
Differental expression with DESeq2
Assembly: Rn6.0

organism: Rattus norvegicus

source_name: aorta

extract_protocol:
Total RNA was extracted from tissue homogenates with QIAGEN Rneasy kit per manufacturer's intructions
Afer polyA selection, paired-end RNA-sequencing with 150bp was done with a depth of 30M reads.
Library was generated at BGI Genomics

tag: breed

value: Sprague-Dawley

value: aorta

value: wild type

value: male

value: 85% oxygen postnatal day 1-14


title: PDG-p53 Primary, replicate 2

value: No treatment


title: SK-MES-1, FGF19 3


title: aorta, 1 year-old rat, hyperoxia Aorta1011_S6


title: SK-MES-1, Control 3

value: control


title: 1 ND23  WT #875

value: Liver

value: wild-type

value: 25 weeks of diet


title: PDG-Inka Recurrent, replicate 3

value: 5 x 2Gy Irradiation


title: SK-MES-1, Control 2


title: aorta, 1 year-old rat, hyperoxia Aorta1010_S5


title: aorta, 1 year-old rat, normoxia Aorta1006_S3

value: normoxia


title: nup1_S11_rep2

city: Shenzhen

first: Chuanlin

last: Shi

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

description: transcriptome profiling

data_processing:
Raw data were processed through in-house perl scripts by removing the 5’ adapter, reads with more than 10% N and reads with more than 50% nucleotides with Qphred <= 5.
Reads were mapped to the Oryza sativa v.7.0 genome sequences (MSU Rice Genome Annotation Project) using Hisat2
Gene expression level quantification and differential expression analysis (FDR < 0.01, FC > 2) were conducted using Cufflinks
Assembly: The clean reads were mapped to Oryza sativa v.7.0 genome sequences (MSU Rice Genome Annotation Project)
Supplementary files format and content: Tab-delimited text files include differentially expressed genes (DEGs) and their abundances (FPKM) in anther between wild-type and nup1 mutant

organism: Oryza sativa

source_name: anthers

extract_protocol:
Anthers at stages of 10 (S10) and 11 (S11) from wild-type and nup1 mutant were collected with three biological replicates. Total RNA was isolated and used for poly(A) RNA isolation with oligo(dT) beads.
Poly(A) RNA were then used for RNA-seq library construction using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), based on the manufacturer’s instructions.

value: anthers

value: nup1 mutant


title: nup1_S11_rep3

description: transcriptome profiling


title: SK-MES-1, Control 1

source_name: Lung

value: Lung squamous cell carcinoma (LUSC)

value: Lung


title: pig_xeno_second_kidney_biopsy_bulk_RNA_seq_T24h

value: Kidney

value: Dissociated kidney cells

value: xenotransplantation


title: lymphoid cell line, Input, replicate 1

city: Vienna

first: Thorsten

last: Klampfl

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Raw reads from the two lanes were merged and the file format was changed from bam to fastq
Raw and trimmed/filtered sequencing reads were quality controlled using the FASTQC software (version 0.11.5).
Trimmomatic (version 0.36) was used to perform adapter trimming and quality-based read filtering.
Filtered reads were mapped against the mm10 mouse reference genome (Gencode M13) using bwa-mem (v0.7.15) and blacklisted regions were removed with bedtools subtract (v2.26.0). Multimappers as well as reads with low mapping quality were removed using samtools (v1.3.1).
Peak calling was performed with MACS2 (v2.1.0) using default parameters.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input samples)

source_name: Pre/Pro-B-cells

extract_protocol:
Intracellular proteins were crosslinked with DSG (20 minutes, room temperature) and protein-DNA interactions were fixed with 1% formaldehyde (10 minutes, room temperature). Termination of the crosslinking procedure was performed using glycine. For immunoprecipitation, 70 μl Dynabeads Protein G magnetic beads (Invitrogen) were used.
Input DNA or DNA enriched through IP was subjected to sequencing library preparation using the NEBNext Ultra II chemistry (New England Biolabs)

value: Pre/Pro-B-cells


title: PDG-Inka Recurrent, replicate 2

value: Brain tumor


title: lymphoid cell line, Input, replicate 2


title: PDG-Inka Primary, replicate 2


title: WT_S11_rep3

description: transcriptome profiling


title: aorta, 1 year-old rat, normoxia Aorta1005_S2

value: Sprague-Dawley

value: aorta

value: wild type

value: male


title: aorta, 1 year-old rat, hyperoxia Aorta1012_S7

value: 85% oxygen postnatal day 1-14


title: aorta, 1 year-old rat, normoxia Aorta1004_S1


title: PDG-Inka Primary, replicate 1

value: No treatment


title: nup1_S11_rep1

description: transcriptome profiling


title: PDG-Inka Recurrent, replicate 1

value: 5 x 2Gy Irradiation


title: lymphoid cell line, HA-tagged CDK6-K43M, replicate 2

value: anti-HA (ab9110, abcam)


title: aorta, 1 year-old rat, normoxia Aorta1007_S4

value: normoxia


title: lymphoid cell line, HA-tagged CDK6-K43M, replicate 1


title: CD45-/CD45+, PDG-Ink4a Recurrent, c

data_processing:
NextSeq paired-end sequencing was performed using 28 cycles for Read 1, 8 cycles for Read i7 and 56 cycles for Read 2. Novaseq paired-end sequencing was performed using 26 cycles for Read 1, 10 cycles for each Read i7 and i5 and 90 cycles for Read 2.
Assembly: mm10
Supplementary files format and content: rds file containing all integrated and pre-processed samples with annotations

extract_protocol:
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 5’ Gene expression libraries were prepared according to the manufacturer’s protocol (CG000207 Rev E and CG000331 Rev A, 10X Genomics).
The Single Cell 5’ Gene Expression libraries were pooled to create three sequencing pools. The sequencing pools were quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems). The Single Cell 5’ Gene Expression libraries were sequenced on a NextSeq550 or NovaSeq 6000 system (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (cat. no. 20024906, Illumina) and NovaSeq SP Reagent Kit v1.5 (cat.no. 20028401, Illumina), at a sequencing depth of 20.000 reads pairs/cell.


title: WT_S11_rep2

description: transcriptome profiling

value: anthers

value: wild-type


title: kidney, 1 year-old rat, normoxia kidney1022

value: kidney


title: WT_S11_rep1

description: transcriptome profiling


title: kidney, 1 year-old rat, normoxia kidney1023


title: kidney, 1 year-old rat, normoxia kidney1020


title: kidney, 1 year-old rat, normoxia kidney1021


title: CD45-/CD45+, PDG-Ink4a Primary, c

value: No Treatment


title: lymphoid cell line, HA-tagged CDK6-WT, replicate 1


title: Prdx1_KO_RANKL_rep1

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

data_processing:
mRNA-Seq reads were mapped to reference mouse genome (mm10 assembly) using HISAT2 with default parameters.
RNA expression was quantified using analyzeRepeats.pl command in HOMER
DEGs was assessed with DESeq2 using getDiffExpression.pl in HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary cells

growth_protocol: Bone marrow (BM) cells were collected by flushing femurs and tibias from 6- to 8-week-old C57BL/6 mice. Cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml) for 16 h.  Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteoclast precursor cells depleted of PRDX1 were cultured in 48-well plates with 30 ng/mL of macrophage colony-stimulating factor (M-CSF) and 100 ng/mL of receptor activator of nuclear factor kappaB ligand (RANKL) for 48 h.

value: bone marrow cells

value: MCSF and RANKL


title: lymphoid cell line, HA-tagged CDK6-WT, replicate 2

value: Pre/Pro-B-cells


title: Prdx1_KO_RANKL_rep2


title: nup1_S10_rep2

description: transcriptome profiling

value: nup1 mutant


title: CD45-/CD45+, PDG-Ink4a Recurrent, b

value: Brain tumor


title: nup1_S10_rep1

description: transcriptome profiling


title: nup1_S10_rep3

description: transcriptome profiling


title: CD45-/CD45+, PDG-p53 Recurrent, a


title: Prdx1_KO_MCSF_rep1

value: MCSF


title: kidney, 1 year-old rat, hyperoxia kidney1013

value: Sprague-Dawley

value: wild type


title: kidney, 1 year-old rat, hyperoxia kidney1014

value: male

value: 85% oxygen postnatal day 1-14


title: Prdx1_WT_RANKL_rep2

value: WT


title: MG, Recurrent PDG-Ink4a

value: Microglia

value: 5 x 2Gy Irradiation


title: CD45-/CD45+, PDG-p53 Primary, a


title: CD45-/CD45+, PDG-Ink4a Primary, b


title: Prdx1_KO_MCSF_rep2


title: WT_S10_rep2

description: transcriptome profiling

value: anthers


title: Prdx1_WT_RANKL_rep1


title: kidney, 1 year-old rat, hyperoxia kidney1011


title: WT_S10_rep3

description: transcriptome profiling

value: wild-type


title: MG, Primary PDG-Ink4a


title: Prdx1_WT_MCSF_rep1


title: MDMs, Recurrent PDG-Ink4a

value: Monocyte-derived macrophages


title: MSCs from MCB, passage 3, donor 205, sequenced by RNAseq

city: Bogota

first: Cristian

middle: Camilo

last: Galindo

state: Bogota DC

address: Cra. 32 #12 - 81 Puente Aranda

country: Colombia

institute: Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud IDCBIS

description:
PA-CEM-GW-205
all_counts_merged.txt

data_processing:
Sequencing data from both RNA-seq and MACE-Seq were uploaded and analyzed on the GenXPro bioinformatics tools platform (https://tools.genxpro.net/).
Sequencing reads were adapter-trimmed, quality-trimmed, and cleaned from library-preparation artifacts using cutadapt (version 3.2).
Expression quantification was done using HTSeq (version 1.99.2) for MACE-Seq data and STAR for RNA-Seq data. QC was done using FASTQC (version 0.11.9), Samtools (version 1.12) and MultiQC (version 1.12).
Normalization and test for differential expression was performed in the statistical programming language R (www.rproject.org) with the DEseq2 package (version 1.34.0).
Assembly: Processed reads were mapped and annotated to the reference human genome GRCh38.p12 from ENSEMBL (version 102) using bowtie2 (version 2.4.3) for MACE-Seq data and using STAR (version 2.7.9a) for RNA-Seq data
Supplementary files format and content: Expression levels are given in transcripts per million (TPM)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Wharton's jelly from umbilical cord

growth_protocol: Wharton's jelly mesenchymal stromal cells were cultured in DMEM with low glucose an 10% human platelet lysate in a humidified atmosphere with CO2 at 37 °C

extract_protocol:
Cells were used and treated with the PureLink RNA Mini Kit (Thermo Fisher). The RNA concentration was measured with nanodrop (Thermo Fisher). Each sample was split into two tubes (25 ul each) and concentration varied between 50 and 2,760 ng/ml.
Conventional RNA-Seq libraries were prepared by Genwiz from Azenta Life Sciences an MACE-seq libraries were prepared by GenXPro GmbH MACE-Kit V2
RNA-seq
Massive Analysis of cDNA Ends (MACE-Seq)-RNA sequencing

treatment_protocol: Upon passage 1, cells were seeded at low (3000 - 4600 cells/cm2) or high denisity (4600 cm2) and expanded until reaching adequate number for cryopreservation

tag: passage

tag: donor

value: donor 205

value: Wharton's jelly from umbilical cord

value: Primary cells

value: Mesenchymal stromal cells

value: High seeding density


title: kidney, 1 year-old rat, hyperoxia kidney1012

value: kidney


title: Prdx1_WT_MCSF_rep2

value: bone marrow cells

value: MCSF


title: MSCs from MCB, passage 3, donor 203, sequenced by RNAseq

description:
PA-CEM-GW-203
all_counts_merged.txt

value: donor 203


title: MSCs from MCB, passage 3, donor 199, sequenced by RNAseq

description:
PA-CEM-GW-199R2
all_counts_merged.txt

value: donor 199


title: Denatonium_rep2

tag: strain

value: MCSF and RANKL with Denatonium


title: WT_S10_rep1

description: transcriptome profiling


title: Denatonium_rep1


title: MDMs, Primary PDG-Ink4a

value: Brain tumor

value: No Treatment


title: MSCs from MCB, passage 3, donor 197, sequenced by RNAseq

description:
PA-CEM-GW-197
all_counts_merged.txt

value: donor 197

value: WT


title: MDMs, Recurrent PDG-p53

value: 5 x 2Gy Irradiation


title: HK2_25mM GLU_003

city: guangzhou

first: Chun-Min

last: Kang

state: guangdong

address: No. 111, Dade Road, Yuexiu District

institute: The Second Clinical College of Guangzhou University of Chinese Medicine

description: Gene expression after 72hr in 25mM GLU

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.
Normalized signal intensity

label_protocol: RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.

treatment_protocol: Human renal tubular cells HK2 were cultured for 12 hours and then the cells were stimulated with new medium containing 25 mM glucose. Cultures were incubated for 72 h at 37 ºC in a humidified incubator with 5% CO2.

tag: cell

tag: dose


title: MSCs from MCB, passage 3, donor 190, sequenced by RNAseq

description:
PA-CEM-GW-190
all_counts_merged.txt

value: donor 190


title: MG, Non-tumor bearing

value: Microglia

value: Ink4a KO


title: MDMs, Primary PDG-p53

value: Monocyte-derived macrophages


title: RANKL_rep1

value: MCSF and RANKL


title: MSCs from MCB, passage 2, donor 206, sequenced by RNAseq

description:
PA-CEM-GW-206
all_counts_merged.txt

value: donor 206

value: Wharton's jelly from umbilical cord

value: Primary cells

value: Mesenchymal stromal cells

value: Low seeding density


title: MSCs from MCB, passage 3, donor 195, sequenced by RNAseq

description:
PA-CEM-GW-195
all_counts_merged.txt

value: donor 195

value: High seeding density


title: HK2_25mM GLU_001

description: Gene expression after 72hr in 25mM GLU


title: Dmel, IFM, tono[1], 48hAPF, biol rep 2

city: Marseille

first: Bianca

middle: Hermine

last: Habermann

address: Avenue de Luminy 163

country: France

institute: IBDM UMR7288

data_processing:
basecalling and demultiplexing by IMP sequencing core facility (Vienna, Austria) using Illumina software
quality assessment of the raw data using fastqc v.011.2
filtering and trimming of adapter residues and low quality reads with fthe FASTX toolkit v.0.0.14 and cutadapt v1.4.1
Sequenced reads were mapped to the Flybase 2015_04 genome assembly using STAR v2.4.2a
mapped reads were sorted and indexed using samtools v1.2
bam files were visualized in IGV or converted into bigwig for visualisation on the UCSC server
Mapped reads per feature were counted using featureCounts v1.4.2
differential gene expression analysis was performed with the RNfuzzyApp with TCC normalization and DESeq2
Assembly: Flybase 2015_04 genome assembly
Supplementary files format and content: tab delimited text files including raw counts for each sample
Supplementary files format and content: tab delimited text files including DEA results for both samples
Supplementary files format and content: excel file with annotated DEGs

organism: Drosophila melanogaster

source_name: indirect flight muscle

growth_protocol:
grown at 27C, staged 0h white pre-pupae
flies were grown on standard cornmeal-molasses medium using standard fly husbandry protocol at 27C, samples were staged as white pre-pupae at 0-2 h APF and aged on wetted filter paper in 60 mm dishes at 27C to the desired developmental timepoint

extract_protocol:
total RNA isolated in Tri-Pure reagent (phenol-choloform), mRNA selected via 3 passes over Invitrogen oligo-dT magnetic beads, mRNA was fragmented using heat and fragmentation buffer, RT was performed with Invitrogen SSIII first strand synthesis system and second-strand labeled with dUTP
RNA libraries were prepared for sequencing by the IMP sequencing core facility (Vienna, Austria) using standard Illumina protocols

treatment_protocol: IFM expressing Mef2-Gal4 > UAS-GFP-Gma were dissected from up to 10 flies in parallel under fluorescence for up to 30 min. in PBS, spun-down at 2000xg for 5 min. to remove buffer and stored in Tri-Pure (Roche) reagent at -80C until extraction

value: indirect flight muscle

value: tono[1]; Mef2-Gal4, UAS-GFP-Gma

tag: muscle type

value: fibrillar

tag: developmental stage

value: 48 h APF


title: MG, Primary PDG-p53

value: Brain tumor

value: No Treatment


title: HK2_25mM GLU_002

description: Gene expression after 72hr in 25mM GLU


title: MG, Recurrent PDG-p53

value: Microglia

value: 5 x 2Gy Irradiation


title: HK2_5.5mM GLU_003

description: Gene expression after 72hr in 5.5mM GLU


title: RANKL_rep2

value: bone marrow cells


title: MSCs from MCB, passage 2, donor 200, sequenced by RNAseq

description:
PA-CEM-GW-200
all_counts_merged.txt

value: donor 200

value: WT


title: Non-lipid-laden monocyte-derived macrophages, mn:718

data_processing:
A multiplex sequencing pool of all uniquely dual indexed RNA libraries was composed by equimolar pooling before sequencing on the NovaSeq 6000 Illumina sequencing platform. Paired-end sequencing was performed using 54 cycles for Read 1, 10 cycles for Read i7, 10 cycles for Read i5 and 54 cycles for Read 2, using a NovaSeq SP Reagent Kit v1.5 (cat no. 20028401, Illumina). This resulted in, on average, 20 M passing filter (PF) reads per sample.
Assembly: Mus musculus (mm10)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
For RNA-seq samples, FACS-purified (non-) LLMs from MG and MDMs from primary PDG-Ink4a tumors, dTomato+ BMDMs from ex vivo assays (4.000-20.000 cells) or MES-like tumor cells from in vitro assays (20.000-100.000 cells) were homogenized in RLT buffer (79216, Qiagen), total RNA was isolatedusing the RNeasy Micro Kit (74004, Qiagen), including an on-column DNase digestion (79254, Qiagen),according to the manufacturer’s instructions. Quality and quantity of the total RNA was assessed on the 2100 Bioanalyzer instrument following manufacturer’s instructions “Agilent RNA 6000 Pico” (G2938-90046, Agilent Technologies).In general RNA yields of 3-135 ng total RNA and RNA integrity numbers (RIN) above 8 were obtained. RNA samples were concentrated with Agencourt RNAClean XP beads (A63987), according to manufacturer’s instructions (Protocol 001298v001, Agencourt) with modifications. In short, 2.5-5 ng of total RNA for each sample was prepared in a volume of 30 μl by adding nuclease free water (AM9937, Ambion). 1.5 μl of Recombinant RNase inhibitor (2313A, Clontech) was added to each RNA sample. A 1.8x reaction volume RNAClean XP bead cleanup was performed, instead of adding 54 ul RNAClean XP bead suspension, 18 μl RNAClean XP bead suspension and 36 μl RNAClean XP bead buffer (same solution without the beads) were added to each RNA sample. After 3 times wash with 70% ethanol, the bead pellets were dried at 37 degrees Celsius for 3-5 minutes, untill bead pellet begins to show cracks. RNA was eluted by adding 4 μl of NF-H20 and mixing by vortexing. RNA library preparation was performed as previously described with modifications.96 In short, oligo dT primer hybridization was performed by the addition of Oligo dT mix (0.7ul H2O, 0.1 ul RNAse inhibitor (40U/ul), 0.1 ul dNTP mix (100mM) and 0.1 ul Oligo-dT30VN primer (100uM)) to the 4 ul sample-RNA bead suspension. Reverse transcription was performed as described but the MgCl2 concentration was adjusted to 10 mM. Template switching and 7-12 cycles pre-amplification of full length cDNAs with template switching oligo’s was performed using ISPCR primer at a final concentration of 0.08 uM.
The amplified full length cDNA was used for NGS library construction by Tagmentation for Illumina sequencing, using the Illumina Nextera XT DNA sample preparation kit (FC-131-1096, Illumina) and IDT® for Illumina Nextera DNA Unique Dual Indexes (20027216, Illumina). RNA sequencing libraries were quantified and normalized based library QC data generated on the Bioanalyzer system according to manufacturer’s protocols (G2938-90321, Agilent Technologies).

value: Monocyte-derived macrophage

value: Ink4a/ArfKO, PDGFB


title: Dmel, IFM, control, 48hAPF, biol rep 1

value: Mef2-Gal4, UAS-GFP-Gma


title: Week 48 LIDPAD 16

city: Singapore

first: Zun Siong

last: Low

address: 11 Mandalay Rd

country: Singapore

institute: Lee Kong Chian School of Medicine

data_processing:
Alignment done by HISAT2
Raw counts using featurecounts
DEGs determined using DESeq2 with cutoff of log2fc > ±1
Genome_build: grcm38
Supplementary_files_format_and_content: FPM

source_name: Mice from age of 8 weeks

extract_protocol:
TRIzol RNA extraction followed by E.Z.N.A.® HP Total RNA for purification, according to manufacturer’s protocol
Illumina library preparation done by NovogeneAIT

treatment_protocol: Mice from age of 8 weeks were fed either control or LIDPAD

value: Liver

tag: diet

value: LIDPAD

tag: diet duration (weeks)


title: Lipid-laden microglia, mn:718

value: Lipid-Laden Microglia


title: HK2_5.5mM GLU_002

description: Gene expression after 72hr in 5.5mM GLU


title: MCSF_rep2

value: MCSF


title: Week 48 LIDPAD 15


title: MSCs from MCB, passage 2, donor 198, sequenced by RNAseq

description:
PA-CEM-GW-198
all_counts_merged.txt

value: donor 198

value: Wharton's jelly from umbilical cord

tag: cell line

value: Primary cells

value: Mesenchymal stromal cells

value: Low seeding density


title: Dmel, IFM, tono[1], 48hAPF, biol rep 1

value: indirect flight muscle

value: tono[1]; Mef2-Gal4, UAS-GFP-Gma

value: fibrillar

value: 48 h APF


title: MSCs from MCB, passage 2, donor 202, sequenced by RNAseq

description:
PA-CEM-GW-202
all_counts_merged.txt

value: donor 202

tag: cell type

value: WT


title: MCSF_rep1

value: bone marrow cells

tag: treatment


title: Dmel, IFM, tono[1], 30hAPF, biol rep 2

value: 30 h APF


title: Non-lipid-laden monocyte-derived macrophages, mn:431

value: Brain tumor

value: Monocyte-derived macrophage

value: Ink4a/ArfKO, PDGFB


title: Lipid-laden monocyte-derived macrophages, mn:718

value: Lidid-Laden Monocyte-derived macrophage


title: Non-lipid-laden microglia, mn:718

value: Microglia


title: HK2_5.5mM GLU_001

description: Gene expression after 72hr in 5.5mM GLU


title: Dmel, IFM, control, 30hAPF, biol rep 2

value: Mef2-Gal4, UAS-GFP-Gma


title: Dmel, IFM, control, 48hAPF, biol rep 2


title: MSCs from MCB, passage 2, donor 199, sequenced by RNAseq

description:
PA-CEM-GW-199R1
all_counts_merged.txt

value: donor 199

value: Wharton's jelly from umbilical cord

value: Primary cells


title: Week 48 LIDPAD 12

value: Liver

value: LIDPAD


title: Non-lipid-laden microglia, mn:431


title: Week 48 LIDPAD 11


title: Week 48 LIDPAD 14


title: MSCs from MCB, passage 2, donor 196, sequenced by RNAseq

description:
PA-CEM-GW-196
all_counts_merged.txt

value: donor 196

value: Mesenchymal stromal cells

value: Low seeding density


title: Dmel, IFM, tono[1], 30hAPF, biol rep 1

value: indirect flight muscle

value: tono[1]; Mef2-Gal4, UAS-GFP-Gma

value: fibrillar


title: Lipid-laden microglia, mn:431

value: Brain tumor

value: Lipid-Laden Microglia


title: Week 48 LIDPAD 13


title: Lipid-laden monocyte-derived macrophages, mn:221

value: Ink4a/ArfKO, PDGFB


title: MSCs from MCB, passage 0, donor 205, sequenced by RNAseq

description:
BM-CEM-GW-205
all_counts_merged.txt

value: donor 205

value: WT


title: Dmel, IFM, control, 30hAPF, biol rep 1

value: Mef2-Gal4, UAS-GFP-Gma

value: 30 h APF


title: MSCs from MCB, passage 0, donor 206, sequenced by RNAseq

description:
BM-CEM-GW-206
all_counts_merged.txt

value: donor 206

value: Wharton's jelly from umbilical cord


title: MSCs from MCB, passage 0, donor 202, sequenced by RNAseq

description:
BM-CEM-GW-202
all_counts_merged.txt

value: donor 202

value: Primary cells


title: astrocyte-24 h after injury-4

city: Beijing

first: Tingting

last: Li

address: Beichen road

institute: Chinese Academy of Sciences

data_processing:
The remaining data was aligned against the UCSC D. melanogaster genome (dm6) using Hisat2 with the annotation file of the same version. On average, 92% of the initial reads were mapped to dm6. HTSeq was used to calculate the raw read counts of genes for each sample. DESeq2 was used to normalize the data. Transcripts were considered as significantly differentially expressed if their adjusted p values were less than 0.01 (p < 0.01) by the Benjamini-Hochberg method. Following normalization of the data, DESeq2 was used to perform pairwise comparisons between the control and experimental groups using parametric tests. Genes with absolute value of logarithmic fold change (log2FC) > 1.0 were qualified for the final set of DEGs. Volcano plots and heatmap were constructed for visualization of the resulting expression intensity data following the identification of DEGs and RNA-Seq data normalization by the adjusted p value calculations.
AnnotationHub 2.20.2 biomaRt 0.7 clusterProfiler 3.13 curl 4.3.2 DESeq2 1.30.1 DIOPT 8.0 dplyr 1.0.4 FastQC 0.11.7 ggplot2 3.3.5 ggrepel 0.9.1 org.Dm.eg.db 3.11.4 pheatmap 1.0.12 R 4.0.0 RSEM 1.3.1 RSeQC 2.5 STAR 2.6.0a Trimmomatic 0.39 VennDiagram 1.6.20
Assembly: dm6
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: brain

growth_protocol: Flies were maintained on standard cornmeal medium at 25°C otherwise indicated.

extract_protocol:
Brains from adult flies (R86E01-Gal4/UAS-Redstinger) with no injury, 4 h after injury and 24 h after injury were dissected out in freshly prepared adult hemolymph saline (AHS) buffer, as previously described (Yang et al., 2016). Briefly, a total of ∼50 brains for each group was immediately transferred to an Eppendorf tube (1.5 mL) containing 200 µL AHS with Pronase (1 mg/mL; P5147, SigmaAldrich) and Dispase (1 mg/mL; LS02104, Worthington Biochemical Corporation). After tissue digestion for 30 min at 25°C, the enzyme medium was removed, followed by two brief, gentle washes with fresh AHS containing 2% PBS. Brain samples were then triturated by gently pipetting in 1 mL AHS through four fire-polished Pasteur pipettes with descending pore sizes (400 μm, 300 μm, 200 μm, and 100 μm) for a total of ∼20 min. Next, the dissociated cells were centrifuged for 10 min at 100 × g and the AHS was replaced with the same buffer to minimize any RNA content released from damaged cells during the trituration process. Finally, dissociated tissues were filtered through 45 μm filter and then put on ice. FACS sorting was performed according to the following gating procedure with 70 μm nozzle by BD FACS Aria: (1) an initial SSC-A/FSC-A gate to minimize debris; (2) a SSC-A/pe-Texa Ted-A gate to choose only red fluorescence positive cells. At this step, 1600 cells were sorted directly into ice-cold cell lysis buffer (oligo-dT30VN primer, ribonuclease inhibitor, dNTP mix) and stored at -80°C until all samples were ready for RNA extraction and cDNA amplification.
Cell samples were sent to the Anoroad Company for RNA extraction. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step was used to purify the products. Briefly, Smart-Seq2 method was used to amplify cDNA. Concentration and integrity of cDNA was assessed using Qubit 3.0 Flurometer (Life Technologies) and Agilent 2100 Bioanalyzer (Agilent Technologies) to ensure the cDNA length was around 1-2 kbp. After quality control, 40 ng cDNA was used to be fragmented at 350 bp by Bioruptor® Sonication System (Diagenode Inc.). To construct Illumina library, end repair, 3’ ends A-tailing, adaptor ligation, PCR amplification and library validation were performed. PerkinElmer LabChip® GX Touch and Step OnePlus™ Real-Time PCR System were used for library quality inspection. Qualified libraries were loaded on Illumina Hiseq platform for PE150 sequencing.

treatment_protocol: Construction and use of the HIT device were described previously (Katzenberger et al., 2013). Deflection of the spring to 90° was the standard angle for strike. Flies were collected at 3 days after eclosion and treated with TBI.

value: brain

value: primary cell

value: astrocyte

value: 24 h after injury


title: Non-lipid-laden monocyte-derived macrophages, mn:221

value: Monocyte-derived macrophage


title: Week 48 LIDPAD 8

value: Liver

value: LIDPAD


title: MSCs from MCB, passage 0, donor 203, sequenced by RNAseq

description:
BM-CEM-GW-203
all_counts_merged.txt

value: donor 203

value: Mesenchymal stromal cells


title: astrocyte-24 h after injury-3


title: Non-lipid-laden microglia, mn:221

value: Brain tumor

value: Microglia

value: Ink4a/ArfKO, PDGFB


title: Week 48 LIDPAD 9


title: MSCs from MCB, passage 0, donor 200, sequenced by RNAseq

description:
BM-CEM-GW-200
all_counts_merged.txt

value: donor 200

value: WT


title: Lipid-laden microglia, mn:221

value: Lipid-Laden Microglia


title: MSCs from MCB, passage 0, donor 198, sequenced by RNAseq

description:
BM-CEM-GW-198
all_counts_merged.txt

value: donor 198

value: Wharton's jelly from umbilical cord


title: Week 48 LIDPAD 6


title: astrocyte-24 h after injury-2

value: brain


title: Week 48 LIDPAD 7


title: astrocyte-24 h after injury-5

value: primary cell


title: MSCs from MCB, passage 0, donor 196, sequenced by RNAseq

description:
BM-CEM-GW-196
all_counts_merged.txt

value: donor 196

value: Primary cells