title: MMWL48hInternode rep8

city: Dalian

first: Changqing

last: Tong

state: Liaoning

address: Heishijiao Str.

department: College of Food science and Engineering

institute: Dalian Ocean University

data_processing:
The initial read quality assessment with FastQC.
Sequence trimming using TrimGalore (https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md).
rRNA removal via SortMeRNA.
Read mapping and read-group annotation using STAR (Dobin et al., 2013).
Alignment quality control with RSeQC (Wang et al., 2012) and Preseq ( https://smithlabresearch.org/software/preseq/).
PCR duplicate detection employing Sambamba MarkDup (Tarasov et al., 2015)
Gene expression and biotype quantification through featureCounts (Liao et al., 2014).
Assembly: The sequences were mapped against ITAG4.1 annotation of tomato reference genome SL4.1 https://solgenomics.net/organism/Solanum_lycopersicum/genome.
Supplementary files format and content: tab-delimited text file that includes the raw counts for each sample

organism: Solanum lycopersicum

source_name: Internode

growth_protocol: We germinated Solanum lycopersicum seeds (cv Moneymaker (obtained from Intratuin B.V) and M82 (obtained from Tomato Genetics Resource Center)) for one week in sealed plastic boxes padded with a paper towel soaked with tap water. After one week, similarly sized seedlings were transferred to a 7 cm square pot filled with sieved Primasta ® soil. One week after transfer, plants were randomly separated into two groups and put into far-red or white light treatment. We grew the seedlings grown at 20C, 70% humidity, 16/8 hour light/ dark cycle in white light conditions for 7 days before the start of the light treatments.

extract_protocol:
We prepared RNA-seq libraries according to the random-primer primed method published originally in (Townsley et al., 2015) with modifications from Kajala et al., 2021. Tissue samples were ground by hand and immediately incubated in 250 μL lysis buffer (LBB: 100 mM Tris-HCl, 1000 mM LiCl, 10 mM EDTA, 1% SD, 5 mM DTT, Antifoam A) supplemented with 5 μ l/ml β-mercaptoethanol before use. The samples were transferred to 2ml tubes and the tubes were beat 2 times for 1min at 30 Hz. The samples were incubated at room temperature for 10 min and spun down at 13,000 rpm for 10 min. One uL of 12.5 μM biotin-20nt-dT(Table 3.1) oligo was mixed into 200 μL of lysate in PCR tubes and incubated  at room temperature for 10 min. Then, we added 20 μL Biolabs® streptavidin beads per reaction for incubation. The mRNA from samples binds the oligo through the polyA tail, and the biotin in the oligo binds the streptavidin on the beads. This allows pulling down only the mRNA and washing the rest of the material off. So, the samples were separated into magnetic bead-bound mRNA and supernatant by 96 well Magwell® magnetic separator. The bead pellets were washed with 200 μl washing buffer series: washing buffer A (WBA; 10 mM Tris-HCl, 150 mM LiCl, 1 mM EDTA, 0.1% SDS), washing buffer B (WBB; 10 mM Tris-HCl, 150 mM LiCl,1mM EDTA), and low salt buffer LSB (20 mM Tris-HCl,150 mM NaCl, 1 mM EDTA). The mRNA was eluted in 16 uL Tris-HCl with 80C. These pulldown and washing steps were repeated a second time to remove non-specifically associating rRNA from the samples.
We prepared RNA-seq libraries according to the random-primer primed method published originally in (Townsley et al., 2015) with modifications from Kajala et al., 2021. RNA fragmentation was carried out by preparing 10 μL mixtures of 1.5 μl 5X Thermo Scientific RT buffer, 0.5 μl Invitrogen ® random primers, 8 μl mRNA from the above elution. The mixtures were put into thermocycler for temperature-induced fragmentation and priming of 1st strand of cDNA (25°C 1 sec, 94°C 1.5 min, 4°C 5 min, 4°C hold).cDNA synthesis. We prepared first strand master mixture as following: 1.5 μL 5X Thermo Scientific RT buffer, 1.5 μL 0.1M DTT, 1 μL H2O, 0.5 μL 25mM dNTPs, 0.5 μL RevertAid H minus reverse transcriptase enzyme (Thermo Scientific). The mixture was added onto the samples and incubated in thermocycler: 25°C 10min, 42°C 50min, 50°C 10min, 70°C 10min, 4°C hold. The second strand synthesis, end repair, and A-tailing were performed by adding a 5 μL mixture to the first strand, consisting of 1.5 μL H2O, 0.4 μL 25mM dNTPs, 1 μL DNA polymerase I (Thermo Fisher), 0.1 μL RNaseH (NEB), 0.4 μL NEBNext® End Repair Module enzyme mix, 0.2 μL Taq, and 1.4 μL. This mixture was incubated in a thermocycler following these temperature and time settings: 16°C for 20 minutes, 20°C for 20 minutes, 72°C for 20 minutes, and held at 4°C. Subsequently, the reaction mixture was left at room temperature for 5 minutes with a mix of Beckman® Ampure XP beads at 1.5 times the volume, followed by two washes with 200 μL of 80% ethanol each, until the beads were completely dry. Adapter ligation: The dry beads were mixed with 3 ul of annealed 1 μM universal adapter primers (8μL of 100μM each primer was combined with 784 μL of H2O and cooled through the program: 94°C 1min, (94°C 10sec) * 60 cycles -1°C /cycle, 20°C 1min, 4°C hold). Then, 7 μL ligase mixture (5 μL Enzymatics 2X Rapid T4 ligation buffer, 0.25 μL Biolabs® DNA ligase) was added for 15-min room temperature incubation. We added 10 μL of 50 mM EDTA and 25 μL Ampure XP Bead Resuspension buffer (15% PEG 8000, 2.5M NaCl) to each sample, washed with 80% EtOH twice, and eluted the ligated DNA fragments with 20-22 μL 10mM Tris.  Enrichment, indexing and quantification We used 10 μl of cDNA into enrichment mixed with 4 μL 5X Phusion HF (Thermo Fisher) buffer,2.6 μL H2O, 1 μL 2 μM PE1 primer, 1 μl 8 μM each EnrichS1 + S2 primers (Table 3.1), 0.2 μl 25mM dNTPs, and 0.2 μl Phusion Polymerase (Thermo Fisher). Each sample used 1 μl of appropriate unique indexed enrichment oligo (Townsley et al., 2015). The mixture was heated in thermocycler with the following program: 98°C 30 sec,  (98 °C 10 sec, 65 °C 30 sec, 72 °C 30 sec) *12 cycles, 72 °C 5 min, 10 °C hold. We cleaned the enriched libraries according to Bailey-Serres lab protocol: 1.1 volume of well-resuspended Ampure beads are mixed well with the samples, followed by washing twice by 200 μl of 80% EtOH and resuspending in 10 μl 10mM Tris pH 8.0.  One μl of the samples were used for quality check by Bioanalyzer High Sensitivity DNA Analysis kit, and we selected cleaned library of 200-350 bps based on the peaks. Libraries were pooled together for sequencing with the same target concentration. A final clean-up was done with 0.8 volumes of Ampure beads and elution to the final target volume.

treatment_protocol: For this experiment two treatments with different light conditions were used: white light (WL) and far-red (WL+FR). WL light intensity was 200 PAR (photosynthetically active radiation). WL+FR condition light intensity was 200 PAR white light supplemented with additional FR to reach R:FR (red-light: far-red light = 0.21). The first internode (between the cotyledons and first true leaf) or its innermost cell type pith was harvested. Each group of internodes were collected at 6, 24, 30, 48 hours after treatment start. In the end, samples were collected for two light treatments (WL and WL+FR), two cultivars, four timepoints and two tissues with at least 4 biological replicates per group. Samples were placed immediately into liquid nitrogen until mRNA isolation.

tag: cultivar

value: MM

value: Internode

tag: genotype

value: Wildtype

tag: treatment

value: FR


title: P62-3

status: Public on Feb 29 2024

type: SRA

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

country: USA

institute: New York University Grossman School of Medicine

library_source: transcriptomic

data_processing:
Sequencing reads were mapped using STAR against the human genome reference (hg19), and gene level quantification was performed with featureCounts. Total counts mapped to protein-coding genes were used for downstream analysis.
Assembly: hg19
Supplementary files format and content: Comma-separated values (CSV) file with featureCounts for protein-coding genes

molecule: total RNA

organism: Homo sapiens

source_name: Plasma extracellular vesicles

growth_protocol: Not applicable

extract_protocol:
RNA was isolated using Invitrogen total exosome RNA & Protein Isolation kit according to the manufacturer protocol
SMART-Seq® v4 Ultra® low input RNA kit followed by Illumina Nextera XT DNA Library Preparation

treatment_protocol: Not applicable

tag: tissue

value: Plasma extracellular vesicles

tag: disease stage

value: Metastatic colorectal cancer

tag: disease status

value: No evidence of disease (NED2)


title: PI-32_(Clariom_S_Human)_G1

type: RNA

city: Bergen

first: Harleen

last: Grewal

address: The Laboratory Building, 5th floor, 5021

department: Department of Clinical Science

country: Norway

institute: University of Bergen

hyb_protocol: 2.3 µg of fragmented and labeled ss-cDNA was hybridized to the Clariom S Assay Human in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression using Transcriptome Analysis console software version 4.0.2 (Affymertix, USA) . QC passed CEL files were further analyzed using TAC software. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

label: biotin

source_name: Whole blood

label_protocol: 100ng of total RNA was used for cRNA amplification with GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. After 16h of In vitro transcription cRNA synthesis, cRNA was purified using magnetic beads and 15µg of purified cRNA was used to prepare ss-cDNA, then 5.5 µg of ss-cDNA was fragmented with fragmentation buffer then labeled using DNA labeling reagent.

extract_protocol: Total RNA extracted from whole blood using PAXgene blood RNA kit

tag: gender

value: Female


title: Pt04 - Day 4 - Arm A [S065]

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

library_source: genomic

data_processing:
library strategy: Cut&Run
Raw reads in the FASTQ files were trimmed using trimmomatic (v0.36) and aligned to human reference genome (GRCh38) using bowtie2 (v2.2.9).
Duplicated reads were marked using Picard (v2.8.0).
Peaks were called using macs2 (v2.1.1.20160309).
Assembly: GRCh38

molecule: genomic DNA

source_name: PBMC

extract_protocol:
Briefly, isolated CD4T cells from 17 study participants in the ACTIVATE clinical trial were bound to concanavalin A-coated magnetic beads (Bangs Laboratories), followed by cell permeabilization using 0.01% digitonin (Millipore) in wash buffer. Primary antibodies against intracellular H3K27ac and H3K27me3 (Cell Signaling Technology) were added and cells were incubated at 4oC for overnight. Guinea pig anti-rabbit IgG antibody (Antibodies-online) was used as a negative control. The next day, fusion protein CUTANA pA/G-MNase (20x) (Epicypher) was added and cells were incubated at 4oC for 1 hour, followed by chromatin digestion using 100mM CaCl2 (Fisher Scientific). Stop buffer was then added to stop the chromatin digestion. DNA fragments were extracted using phenol chloroform (Invitrogen) and the extracted DNA was eluted in 1mM Tris-HCl pH 8.0 (Fisher Scientific) + 0.1 mM EDTA (Sigma Aldrich).
The DNA library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).

value: PBMC

tag: cell type

value: CD4 T cells

tag: time

value: Day 4

tag: participant id

tag: histone mark

tag: group

value: Arm A

tag: participant treatment

value: panobinostat


title: lncRNA_skin tissues, healthy,E56_3

city: Ya'an

first: Xinyue

last: Zhang

state: Sichuan

address: Xinkang street num 46

department: Department of Zoology,College of Life Science

country: China

institute: Sichuan Agricultural University

description:
sow
IncRNA_processed data.tar.gz

data_processing:
Data filtering: SOAPnuke (v1.5.6)
Sequence matching：For mRNAs and lncRNAs, their sequence alignment was performed using HISTA2 (v2.1.0) [79] software to align clean data to the reference genome sequence (Sus scrofa, GCF_000003025.6_Sscrofa11.1)；And circRNA uses Bowtie2 (v2.2.5) to compare clean data into CircBase
Data quantification：For mRNA and lncRNA, gene expression quantification was performed using RSEM (v1.3.1) software. For circRNAs, circRNAs were quantified using reads spanning the junction site (the first and last junctions of the circRNA sequence) with at least 10 bp coverage at both ends.
Assembly: Reference Genome Version: GCF_000003025.6_Sscrofa11.1
Supplementary files format and content: tar.gz. files include all processed data

organism: Sus scrofa

source_name: dorsal skin

extract_protocol:
The removed tissues were snap-frozen and the total RNA of the skin was extracted using the Trizol method kit.
Two RNA libraries were constructed for four types of RNA from the dorsal skin of the Chenghua pig at four time points, of which the mRNA, lncRNA and circRNA were unified to construct the DNBSEQ LncRNA-Seq library, and the miRNA was constructed separately as the DNBSEQ Small RNA library for high-throughput sequencing.

value: dorsal skin

tag: breed

value: Chenghua pig

tag: Sex

value: female

tag: disease state

value: healthy

value: 56-day embryo


title: lncRNA_skin tissues, healthy,E105_1

description:
sow
IncRNA_processed data.tar.gz

value: 105-day embryo


title: P63-3


title: MMWL48hPith rep6

molecule: polyA RNA

source_name: Pith

value: MM

value: Pith

value: Wildtype


title: P62-2

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: No evidence of disease (NED1)


title: lncRNA_skin tissues, healthy,E56_2

description:
sow
IncRNA_processed data.tar.gz


title: Pt08 - Day 28 - Arm B [S059]

value: PBMC

value: Day 28

value: Arm B

value: panobinostat + IFN-alpha2A


title: PI-30_(Clariom_S_Human)_G2

value: Male


title: MMWL30hPith rep6

value: FR


title: P62-1

value: At the time of surgery (hepatectomy)


title: Pt08 - Day 28 - Arm B [S058]

value: CD4 T cells


title: lncRNA_skin tissues, healthy,E56_1

description:
sow
IncRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig

value: female

value: healthy


title: circRNA_skin tissues, healthy,D3_3

description:
sow
circRNA_processed data.tar.gz

value: Day 3


title: P60-4

value: Recurrence


title: MMWL48hInternode rep7

value: MM

value: Internode

value: Wildtype


title: Pt08 - Day 4 - Arm B [S057]

value: PBMC

value: Day 4

value: IgG


title: MMWL30hPith rep5

value: Pith


title: P60-3

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: No evidence of disease (NED2)


title: Pt08 - Day 4 - Arm B [S056]

value: CD4 T cells

value: Arm B

value: panobinostat + IFN-alpha2A


title: P60-2

value: No evidence of disease (NED1)


title: Pt08 - Day 28 - Arm B [S060]

value: Day 28


title: MMWL30hInternode rep5

value: FR


title: P60-1

value: At the time of surgery (hepatectomy)


title: Pt08 - Day 4 - Arm B [S055]


title: circRNA_skin tissues, healthy,D3_2

description:
sow
circRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig

value: female

value: healthy

value: Day 3


title: Pt08 - Day 0 - Arm B [S054]

value: PBMC

value: Day 0

value: IgG


title: circRNA_skin tissues, healthy,E105_3

description:
sow
circRNA_processed data.tar.gz

value: 105-day embryo


title: MMWL06hInternode rep5

value: MM

value: Internode

value: Wildtype


title: circRNA_skin tissues, healthy,D3_1

description:
sow
circRNA_processed data.tar.gz


title: P59-4

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: Recurrence


title: Pt08 - Day 0 - Arm B [S053]

value: CD4 T cells

value: Arm B

value: panobinostat + IFN-alpha2A


title: circRNA_skin tissues, healthy ,E105_2

description:
sow
circRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig


title: MMWL48hPith rep4

value: Pith

value: FR


title: P59-3

value: No evidence of disease (NED2)


title: MMWL30hInternode rep4


title: Pt08 - Day 0 - Arm B [S052]

value: PBMC

value: Day 0


title: circRNA_skin tissues, healthy,E105_1

description:
sow
circRNA_processed data.tar.gz

value: female

value: healthy

value: 105-day embryo


title: P59-2

value: No evidence of disease (NED1)


title: 72 hours_2

city: Manchester

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

country: United Kingdom

institute: University of Manchester

description: single cell RNA

library_source: transcriptomic single cell

data_processing:
For FASTQ generation and alignments, illumina basecall files (*.bcl) were converted to FASTQs using bcl2fastq
Gene counts were generated using CellRanger for single cell RNAseq (v.6.0.0)
Mapping strategy was conducted on CellRanger or SpaceRanger against a combined Homo sapiens (Hg38) transcriptome reference
After alignment, reads were grouped based on barcode sequences and demultiplexed using the Unique Molecular Identifiers (UMIs)
Assembly: Hg38
Supplementary files format and content: .h5 files were generated as outputs from CellRanger.

source_name: Human brain organoids

growth_protocol: We performed single cell gene expression profiling analysis using data obtained from RNA-seq of iPSC-derived human brain organoids co-cultured with T. brucei gambiense for 24 and 72 hours, and included untreated controls.

extract_protocol:
Single cell suspensions were obtained from human brain organoids using enzymatic dissociation, followed by library preparation using the 10X Chromium platform.
Illumina compatible, RNA libraries were prepared with the 10X Chromium technolgy

treatment_protocol: Two biological replicates per time point (untreated, 24, and 72 hours in culture with trypanosomes) for single cell transcriptomics.

tag: cell line

value: Induced pluripotent embryonic stem cells

value: Wild type

value: 72h co-culture with T. b. gambiense


title: MMWL48hInternode rep3

tag: cultivar

value: MM

value: Internode

value: Wildtype


title: circRNA_skin tissues, healthy,E76_2

description:
sow
circRNA_processed data.tar.gz

value: dorsal skin

value: 76-day embryo


title: circRNA_skin tissues, healthy,E76_3

description:
sow
circRNA_processed data.tar.gz

value: Chenghua pig


title: 24 hours_2

description: single cell RNA

tag: genotype

value: 24h co-culture with T. b. gambiense


title: P58-3

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: No evidence of disease (NED2)


title: circRNA_skin tissues, healthy,E76_1

description:
sow
circRNA_processed data.tar.gz

value: female


title: MMWL24hInternode rep5

tag: treatment

value: FR


title: MMWL48hPith rep2

tag: tissue

value: Pith


title: circRNA_skin tissues, healthy,E56_3

description:
sow
circRNA_processed data.tar.gz

value: healthy

value: 56-day embryo


title: MMWL30hPith rep2


title: P58-2

tag: disease stage

value: No evidence of disease (NED1)


title: Untreated_2

description: single cell RNA

value: Induced pluripotent embryonic stem cells

value: Wild type

value: Untreated


title: circRNA_skin tissues, healthy,E56_2

description:
sow
circRNA_processed data.tar.gz


title: MMWL30hInternode rep2

value: MM

value: Internode

value: Wildtype


title: 24 hours_1

description: single cell RNA


title: Untreated_1

description: single cell RNA


title: circRNA_skin tissues, healthy,E56_1

description:
sow
circRNA_processed data.tar.gz

value: dorsal skin

value: Chenghua pig


title: MMWL24hInternode rep2


title: P57-2

value: Plasma extracellular vesicles

tag: disease status


title: MMWL06hInternode rep2


title: 72 hours_1

description: single cell RNA

value: 72h co-culture with T. b. gambiense


title: MMWL30hInternode rep3


title: P59-1

value: Metastatic colorectal cancer

value: At the time of surgery (hepatectomy)


title: MMWL48hInternode rep1

value: FR


title: P56-2


title: MMWL24hInternode rep1


title: P56-1


title: P58-1


title: EndoC-βH1 HNF4A8 WT FLAG biological replicate 2 - input

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Sequencing adapters were trimmed using BBDuk from the BBMap toolkit [v38.59] (https://sourceforge.net/projects/bbmap)
Trimmed reads were aligned to GRCh38 with Bowtie2 version 2.2.5 and reads non-uniquely mapped were discarded.
Filtering of unmapped and duplicate aligned reads were performed using samtools 1.12 and sambamba 0.8.0
Peaks were called using MACS2 version 2 2.7.1 against input control library with default q-value (minimum FDR) cutoff of 0.1
Assembly: GRCh38
Supplementary files format and content: peak bed files

source_name: EndoC-βH1 beta cell line

growth_protocol: hPSC-derived pancreatic progenitors (PP), endocrine progenitors (EP), beta-like cells and hepatoblasts were generated from H9 hESCs following the differentiation protocols previously described in Ng et al., 2019. (doi: 10.1016/j.isci.2019.05.032)

extract_protocol:
Cells were dissociated using TrypLE, cross-linked, and extracted for nuclear lysates. The lysates were sonicated (from which input DNA was obtained as control) and incubated with the respective ChIP antibodies. Immunoprecipitation was performed and the genomic DNA was extracted and purified for sequencing analysis.
Library preparation was done using a commercially available kit, NEB# E7645 NEBNext Ultra II DNA Library Prep Kit for Illumina KIT® following the manufacturer’s protocol. During the library construction, the ChIP-ed DNA underwent End Repair, Adapter ligation, size selection (for ~150bp insert)  and 16 cycles PCR enrichment to generate the final sequencing ready library. The quality of the library was checked using Agilent D1000 ScreenTape. The final library should have a fragment size of ~270bp insert plus adaptor and PCR primer sequences). The quality of the library was checked using Agilent D1000 ScreenTape. A single peak was expected and was observed indicating that the library was good and suitable for sequencing.

treatment_protocol: EndoC-βH1 cells stably overexpressing HNF4A8 WT/variant were generated using lentiviral vectors followed by puromycin selection.

value: EndoC-betaH1 beta cell line

tag: chip antibody

value: None (control)

value: Stably overexpressing HNF4A8 WT


title: EndoC-βH1 GFP (Empty) FLAG biological replicate 2 - input

tag: cell type

value: Stably overexpressing empty vector


title: EndoC-βH1 HNF4A8 T117I FLAG biological replicate 1 - input

value: Stably overexpressing HNF4A8 T117I


title: P57-3

value: No evidence of disease (NED2)


title: MMFR48hInternode rep8


title: P55-3


title: P55-2

value: No evidence of disease (NED1)


title: MMFR24hInternode rep6

value: MM


title: EndoC-βH1 HNF4A8 WT FLAG biological replicate 1 - input


title: EndoC-βH1 HNF4A8 T117I FLAG biological replicate 2 - input


title: MMFR06hInternode rep6

value: Internode


title: EndoC-βH1 GFP (Empty) FLAG biological replicate 1 - input


title: D35 beta-like cells HNF4A H1415 - input

source_name: Beta-like cells

value: hESC-derived beta-like cells

value: untreated


title: P55-1


title: P56-3


title: MMFR48hInternode rep7

value: Wildtype


title: P54-3

value: Plasma extracellular vesicles


title: D20 EP HNF4A H1415 - input

source_name: Endocrine progenitor cells

value: hESC-derived endocrine progenitor cells


title: J1 (ES), biological replicate 1

city: Pohang, Kyungbuk

first: Sojeong

last: Yun

address: Hyoja-dong,Nam-gu

department: IBIO

country: South Korea

institute: POSTECH

description: The J1 ES line was derived from a male agouti 129S4/SvJae embryo [PubMed: 1606615].

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadScan 500 System.

data_processing: The data were quantile-normalized using R (version 2.9.1) with BeadArray (version 1.12.1).

organism: Mus musculus

source_name: ESC

label_protocol: Refer to the Illumina Gene Expression System Manual.

growth_protocol: Media: DMEM, 4.5g/L D-Glucose, 110mg/L Sodium Pyruvate,15% Defined fetal bovine serum, 2-Mercaptoethanol and MEM Non-essential amino acid solution 100X.

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment.

value: mouse embryonic stem cell (ESC)


title: L3 (KU-iN2), biological replicate 2

description:
Line3 (Konkuk university-iPS cells generated using magneto-Nanoparticle 2; Ku-iN2), biological replicate 2.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.

source_name: iPSC, KU-iN2

value: induced pluripotent stem (iPS) cell

tag: transfected genes

value: oct4, sox2, klf4, C-myc


title: L3 (KU-iN2), biological replicate 1

description:
Line3 (Konkuk university-iPS cells generated using magneto-Nanoparticle 2; Ku-iN2), biological replicate 1.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.


title: P54-2

value: Metastatic colorectal cancer


title: MMFR48hPith rep5

value: Pith

value: FR


title: J1 (ES), biological replicate 2


title: MMFR30hPith rep5


title: D14 PP HNF4A H1415 biological replicate 2 - input

source_name: Pancreatic progenitor cells

value: hESC-derived pancreatic progenitor cells

value: None (control)


title: L1 (KU-iN1), biological replicate 2

description:
Line1 (Konkuk university-iPS cells generated using magneto-Nanoparticle 1; Ku-iN1), biological replicate 2.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.

source_name: iPSC, KU-iN1


title: L3 (KU-iN2), biological replicate 3

description:
Line3 (Konkuk university-iPS cells generated using magneto-Nanoparticle 2; Ku-iN2), biological replicate 3.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.


title: E1 (KU-iN3), biological replicate 3

description:
Experiment1 (Konkuk university-iPS cells generated using magneto-Nanoparticle 3; Ku-iN3), biological replicate 3.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.

source_name: iPSC, KU-iN3


title: L1 (KU-iN1), biological replicate 1

description:
Line1 (Konkuk university-iPS cells generated using magneto-Nanoparticle 1; Ku-iN1), biological replicate 1.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.


title: P53-3

value: No evidence of disease (NED2)


title: MMFR30hInternode rep5


title: HepG2 HNF1A ab96777 - input

source_name: HepG2 hepatoma cell line

value: HepG2 hepatoma cell line


title: P53-2

value: No evidence of disease (NED1)


title: Islets HNF1A ab96777 - input

source_name: Human islets

value: Primary human islets


title: MMFR48hInternode rep5

source_name: Internode

value: MM

value: Internode


title: E1 (KU-iN3), biological replicate 1

description:
Experiment1 (Konkuk university-iPS cells generated using magneto-Nanoparticle 3; Ku-iN3), biological replicate 1.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.


title: E1 (KU-iN3), biological replicate 2

description:
Experiment1 (Konkuk university-iPS cells generated using magneto-Nanoparticle 3; Ku-iN3), biological replicate 2.

Generated from mouse embryonic fibroblast cell by Magneto-nanofection with the transcription factors Oct4, Sox2, Klf4, and c-Myc.


title: D20 EP HNF1A ab96777 - input

value: untreated


title: MMFR06hInternode rep5

value: Wildtype


title: SCF6X12 - 2 CL (Contra)

city: Duarte

first: Margarita

last: Gutova

state: California

address: 1500 East Duarte Road

institute: City of Hope

description: tissue lysates

hyb_protocol: RNA was hybridized with the Codeset from the gene panel at 65°C for 16 h. The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, and all data analyses were performed on nSolver (NanoString Technologies).

scan_protocol: Scanning was done using NanoString nCounter system, following manufacturer's instructions.

data_processing: All raw data were first normalized with internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Statistically significant (p<0.05) and < 2-fold up- or down- regulated genes were analyzed and clustered as described below.

organism: Rattus norvegicus

source_name: rat brain

label_protocol: Brain tissue isolated from TBI site were labeled SCF6X2TBI_01 to SCF6X2TBI_10 and brain tissue from contralateral site were labeled SCF6X2TBICL_01 to SCF6X2TBICL_10 accordingly

growth_protocol: Brain tissue was dissected, and RNA was isolated from snap frozen tissues according to a diagram in figure S7 and half was used for Nanostring analysis and half for protein ELISA assays.

treatment_protocol: RNA expression in the ipsilateral and contralateral hemispheres of NSC and VEH-treated TBI brains was analyzed using the NanoString nCounter platform (NanoString Technologies) by digitally detecting and counting RNA expression in a single reaction without amplification.

value: brain

tag: region

value: Contra


title: SCF6X11 - 2 CL (Contra)

description: tissue lysates

extract_protocol: RNA was isolated from snap frozen tissues according to a diagram in figure S7 and half was used for Nanostring analysis and half for protein ELISA assays.


title: P53-1

source_name: Plasma extracellular vesicles

value: Plasma extracellular vesicles

value: At the time of surgery (hepatectomy)


title: P52-3

value: Metastatic colorectal cancer


title: D8 Hep HNF4A H1415 - input

source_name: Hepatoblasts

value: hESC-derived hepatoblasts


title: Islets HNF4A H1415 - input


title: P54-1


title: SCF6X10 - 2 CL (Contra)

description: tissue lysates


title: P52-2


title: SCF6X8 - 2 CL (Contra)

description: tissue lysates


title: MMFR30hPith rep4

value: Pith

value: FR


title: P52-1


title: MMFR48hInternode rep4


title: P51-3


title: HepG2 HNF4A H1415 - input

value: None (control)


title: MMFR24hInternode rep5


title: EndoC-βH1 HNF4A H1415 - input

value: EndoC-betaH1 beta cell line


title: MMFR24hInternode rep4

description:
MF4-2
raw data not provided for this record


title: SCF6X6 - 2 CL (Contra)

description: tissue lysates


title: HepG2 HNF4A sc-8987 - input

value: HepG2 hepatoma cell line


title: MMFR06hInternode rep4


title: P51-2

value: No evidence of disease (NED1)


title: HepG2 HNF4A ab41898 - input


title: EndoC-βH1 HNF1A sc-6547 - input


title: P51-1


title: SCF6X5 - 2 CL (Contra)

description: tissue lysates


title: MMFR48hPith rep4


title: P50-3

value: No evidence of disease (NED2)


title: EndoC-βH1 HNF4A sc-8987 - input


title: SCF6X2 - 2 CL (Contra)

description: tissue lysates


title: D14 PP HNF4A H1415 biological replicate 1 - input

value: hESC-derived pancreatic progenitor cells


title: SCF6X3 - 2 CL (Contra)

description: tissue lysates


title: MMFR30hPith rep3

value: MM


title: P50-1


title: SCF6X7 - 2 CL (Contra)

description: tissue lysates


title: SCF6X12 - 2 TBI (Ipsi)

description: tissue lysates

value: Ipsi


title: P50-2


title: P49-2


title: SCF6X10 - 2 TBI (Ipsi)

description: tissue lysates


title: P49-3


title: SCF6X11 - 2 TBI (Ipsi)

description: tissue lysates


title: MMFR48hPith rep3

value: Wildtype


title: EndoC-βH1 GFP (Empty) FLAG biological replicate 2 - chip

value: FLAG M2 (Sigma Aldrich, F1804)

value: Stably overexpressing empty vector


title: SCF6X4 - 2 CL (Contra)

description: tissue lysates

value: brain

value: Contra


title: EndoC-βH1 HNF4A8 T117I FLAG biological replicate 1 - chip

value: Stably overexpressing HNF4A8 T117I


title: MMFR06hInternode rep3

value: Internode


title: SCF6X8 - 2 TBI (Ipsi)

description: tissue lysates


title: P49-1

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: At the time of surgery (hepatectomy)


title: MMFR48hPith rep1

value: Pith

value: FR


title: P48-3


title: EndoC-βH1 HNF4A8 WT FLAG biological replicate 1 - chip

value: EndoC-betaH1 beta cell line

value: Stably overexpressing HNF4A8 WT


title: MMFR48hInternode rep3


title: MMFR30hPith rep1


title: SCF6X7 - 2 TBI (Ipsi)

description: tissue lysates


title: EndoC-βH1 HNF4A8 T117I FLAG biological replicate 2 - chip


title: P48-1


title: D35 beta-like cells HNF4A H1415 - chip

value: hESC-derived beta-like cells

value: HNF4A (R&D Systems, H1415)

value: untreated


title: MMFR30hInternode rep3

value: MM

value: Wildtype


title: P48-2

value: No evidence of disease (NED1)


title: MMFR24hInternode rep3


title: EndoC-βH1 GFP (Empty) FLAG biological replicate 1 - chip

value: FLAG M2 (Sigma Aldrich, F1804)

value: Stably overexpressing empty vector


title: MMFR48hInternode rep1


title: EndoC-βH1 HNF4A8 WT FLAG biological replicate 2 - chip


title: SCF6X5 - 2 TBI (Ipsi)

description: tissue lysates

value: brain

value: Ipsi


title: MMFR30hInternode rep1

value: Internode


title: P47-3

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: No evidence of disease (NED2)


title: MMFR24hInternode rep1

value: FR


title: D20 EP HNF4A H1415 - chip

value: hESC-derived endocrine progenitor cells


title: P47-2


title: SCF6X4 - 2 TBI (Ipsi)

description: tissue lysates


title: SCF6X3 - 2 TBI (Ipsi)

description: tissue lysates


title: MMFR06hInternode rep1


title: P46-7


title: D8 Hep HNF4A H1415 - chip

value: hESC-derived hepatoblasts


title: SCF6X2 - 2 TBI (Ipsi)

description: tissue lysates


title: D14 PP HNF4A H1415 biological replicate 2 - chip

value: hESC-derived pancreatic progenitor cells


title: P46-6

value: No evidence of disease (NED3)


title: SCF6X6 - 2 TBI (Ipsi)

description: tissue lysates


title: M82WL48hPith rep6

value: Pith

value: WL


title: P46-5

description: other label: P61-4


title: HepG2 HNF1A ab96777 - chip

value: HepG2 hepatoma cell line

value: HNF1A (Abcam, ab96777)

value: untreated


title: M82WL30hInternode rep6

value: Wildtype


title: Islets HNF1A ab96777 - chip

value: Primary human islets


title: M82WL48hPith rep5


title: M82WL06hInternode rep5


title: P46-3

description: other label: P61-2

value: No evidence of disease (NED1)


title: M82WL48hPith rep4


title: P46-2

value: Residual disease (responding)


title: D14 PP HNF4A H1415 biological replicate 1 - chip

value: HNF4A (R&D Systems, H1415)


title: D20 EP HNF1A ab96777 - chip


title: HepG2 HNF4A H1415 - chip


title: Islets HNF4A H1415 - chip


title: P46-1

description: other label: P61-1

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: At the time of surgery (hepatectomy)


title: M82WL30hPith rep4


title: M82WL48hInternode rep4

value: Internode


title: P46-4

description: other label: P61-3

value: No evidence of disease (NED2)


title: EndoC-βH1 HNF4A H1415 - chip

value: EndoC-betaH1 beta cell line


title: P45-5

value: Progression


title: P45-4

value: At the time of surgery (hepatectomy2)


title: HepG2 HNF4A sc-8987 - chip

value: HNF4A (Santa Cruz, sc-8987)


title: M82WL30hInternode rep4

value: WL


title: P45-3


title: M82WL30hPith rep3

value: Pith


title: HepG2 HNF4A ab41898 - chip

value: HepG2 hepatoma cell line

value: HNF4A (Abcam, ab41898)

value: untreated


title: M82WL48hInternode rep3

value: Wildtype


title: PLAP preGDM_high_HOMA%β_index_pool2

city: Mexico City

first: Melissa

last: Razo-Azamar

address: Calz. de los Tenorios 235 Col. Rinconada de las Hadas, Alcaldía Tlalpan, Ciudad de México

department: Centro de Investigación sobre el Envejecimiento

country: Mexico

institute: Instituto Nacional de Medicina Genómica (INMEGEN)

description: miRNA expression data from early pregnancy serum placental exosomes from preGDM women with high HOMA%β index

hyb_protocol: 150 ng of cRNA were hybridized for 18 hr at 48°C on GeneChip miRNA 4.0 Array in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the GenChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Expression and differential expression of miRNA profiles among study subgroups using Affymetrix Transcriptome Analysis Console (TAC) Software version 4.0.1 (Affymetrix, Applied Biosystems). Briefly, the raw data obtained from the Affymetrix GeneChip Scanner was pre-processing (normalization, quality checking and statistical analysis) using the Affymetrix Expression Console, The resulting files were analyzed in order to identify differentially expressed miRNAs (DEmiRNAs) between the subgroups The DEmiRNAs were then identified using the Affymetrix Transcriptome Analysis Console (TAC) Software version 4.01 (Affymetrix, Applied Biosystems) in accordance with the software's instructions. The results were preprocessed at RMA+DABG-NONORM-Human-only setting

source_name: Early pregnancy serum placental exosomes from preGDM women with high HOMA%β index

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Serum maternal or placental total RNA

extract_protocol: Maternal and placental total exosomal RNA isolation was performed using QIAGEN’s exoRNeasy Midi Kit (Cat. No. ID 77144) commercial kit according to the manufacturer’s instructions. The total RNA yield quality was analyzed using NanoDrop 2000 spectrophotometer (NanoDrop, Wilmington, USA). The maternal and placental exosomal miRNA expression profiles were analyzed using the Affymetrix Gene-Chip miRNA 4.0 Array (Applied Biosystems, Affymetrix Inc., Santa Clara, CA, USA) following the manufacturer’s protocol.

treatment_protocol: Serum maternal or placental exosomes of control and preGDM samples were isolated using the QIAGEN exoRNeasy midi Kit (Cat. Number 77144) according to the manufacturer's instructions. Placental exosomes were selected via immunoprecipitation following the protocol by Lai et al (Lai, A., et al., Optimized Specific Isolation of Placenta-Derived Exosomes from Maternal Circulation. Methods Mol Biol, 2018).

value: serum placental exosomes

tag: gender

value: female

tag: weeks of gestation (weeks.days)

value: pregnant women 13.2 weeks of gestation


title: P45-2

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: Residual disease


title: PLAP preGDM_low_HOMA%β_index_pool1

description: miRNA expression data from early pregnancy serum placental exosomes from preGDM women with low HOMA%β index

source_name: Early pregnancy serum placental exosomes from preGDM women with low HOMA%β index

value: pregnant women 12.7 weeks of gestation


title: PLAP control_high_HOMA%β_index_pool4

description: miRNA expression data from early pregnancy serum placental exosomes from control women with high HOMA%β index

source_name: Early pregnancy serum placental exosomes from control women with low HOMA%β index

value: pregnant women 13.1 weeks of gestation


title: PLAP preGDM_high_HOMA%β_index_pool3

description: miRAN expression data from early pregnancy serum placental exosomes from preGDM women with high HOMA%β index


title: PLAP preGDM_low_HOMA%β_index_pool2

value: pregnant women 12.2 weeks of gestation


title: PLAP preGDM_high_HOMA%β_index_pool1


title: PLAP preGDM_low_HOMA%β_index_pool3

value: pregnant women 12.6 weeks of gestation


title: PLAP control_high_HOMA%β_index_pool3

source_name: Early pregnancy serum placental exosomes from control women with high HOMA%β index

value: pregnant women 12.3 weeks of gestation


title: EndoC-βH1 HNF1A sc-6547 - chip

source_name: EndoC-βH1 beta cell line

value: EndoC-betaH1 beta cell line

value: HNF1A (Santa Cruz, sc-6547)


title: M82WL30hInternode rep3

value: Internode

value: WL


title: PLAP control_low_HOMA%β_index_pool3

description: miRNA expression data from early pregnancy serum placental exosomes from control women with low HOMA%β index


title: P45-1

value: At the time of surgery (hepatectomy1)


title: P44-3

value: Progression


title: PLAP control_high_HOMA%β_index_pool2

value: serum placental exosomes

value: pregnant women 14.3 weeks of gestation


title: M82WL06hInternode rep3

value: Wildtype


title: EndoC-βH1 HNF4A sc-8987 - chip

value: HNF4A (Santa Cruz, sc-8987)

value: untreated


title: P44-2

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: Residual disease


title: M82WL48hPith rep2

source_name: Pith

value: Pith


title: M82WL30hPith rep2


title: P44-1

value: At the time of surgery (hepatectomy)


title: LDKO 2

city: Boston

first: rongya

last: tao

state: Ma

address: 300 longwood ave

institute: Boston children's hospital

data_processing:
NGS 4.0
Assembly: mm10
Supplementary files format and content: table-delimited xlsx file including the raw counts

source_name: Skeletal muscle

extract_protocol:
Total RNAs were isolated from  tissues using TRI Reagent (Sigma).
SMARTER Mrna-aeq library prep kit

value: Skeletal muscle

value: male

value: LDKO

value: High fat diet


title: LTKOFstL/L 2

value: LTKOFstL/L


title: LTKOFstL/L 1


title: MAT preGDM_high_HOMA%β_index_pool2

description: miRNA expression data from early pregnancy serum maternal exosomes from preGDM women with high HOMA%β index

source_name: Early pregnancy serum maternal exosomes from preGDM women with high HOMA%β index

value: serum maternal exosomes

value: female

value: pregnant women 13.2 weeks of gestation


title: PLAP control_low_HOMA%β_index_pool1

value: serum placental exosomes

value: pregnant women 14.3 weeks of gestation


title: M82WL48hInternode rep2

value: Internode

value: Wildtype

value: WL


title: M82WL30hInternode rep2


title: PLAP control_low_HOMA%β_index_pool4

value: pregnant women 14.1 weeks of gestation


title: P43-4

description: other label: P66-4

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer

value: Recurrence


title: LDKO 1

value: Skeletal muscle


title: P43-3

description: other label: P66-3

value: No evidence of disease (NED2)


title: M82WL24hInternode rep2


title: Control 2

value: male

value: Control


title: P43-2

description: other label: P66-2

value: No evidence of disease (NED1)


title: PLAP control_high_HOMA%β_index_pool1

value: pregnant women 15.1 weeks of gestation


title: Control 1

value: High fat diet


title: M82WL06hInternode rep2


title: PLAP control_low_HOMA%β_index_pool2

value: female

value: pregnant women 14.4 weeks of gestation


title: P43-1

description: other label: P66-1

value: At the time of surgery (hepatectomy)


title: P42-1


title: MAT preGDM_low_HOMA%β_index_pool1

description: miRNA expression data from early pregnancy serum maternal exosomes from preGDM women with low HOMA%β index

source_name: Early pregnancy serum maternal exosomes from preGDM women with low HOMA%β index

value: serum maternal exosomes

value: pregnant women 12.7 weeks of gestation


title: MAT control_high_HOMA%β_index_pool4

description: miRNA expression data from early pregnancy serum maternal exosomes from control women with high HOMA%β index

source_name: Early pregnancy serum maternal exosomes from control women with low HOMA%β index

value: pregnant women 13.1 weeks of gestation


title: M82WL30hPith rep1

value: Pith

value: Wildtype

value: WL


title: Custom Cell Hashing Library

city: Los Angeles

first: Fremont

address: 2011 Zonal Ave, HMR 903

institute: USC

description: 10x Genomics

data_processing:
Sample demultiplexing was carried out with reference to the 10x Genomics community-developed protocol: Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags. The usual Cell Ranger pipeline was then invoked to deconvolute raw base call (BCL) files into FASTQ files, perform alignment and filtering, decode cellular barcodes, count UMIs, normalize counts, and generate feature-barcode matrices. The derived matrices were further processed in Seurat for dimensionality reduction, cell clustering, cell type classification, cell counting, and gene expression comparative analysis.
Assembly: mm10
Supplementary files format and content: sample hashtag reference csv file, sequencing results summary http file, and feature barcode matrix file

source_name: Lung

growth_protocol: Wild type and Pdlim2 myeloid KO mice were bred and maintained as regulated by IACUC.

extract_protocol:
Lungs freshly dissected from euthanized mice at 48 hours after LPS treatment were dissociated into single cell suspension. The cell samples from each group were stained with TotalSeq CD45 antibody conjugated with unique oligo barcodes purchased from BioLegend. All hashtagged samples were pooled together for GEM partitioning and library construction using 10x genomics single cell 5’ kit.
The gene expression and cell hashing libraries were constructed according to the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User Guide with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping (10× Genomics, CG000330 Rev A).

treatment_protocol: Mice of 6-8-week-old were intratracheally instilled with LPS (4 mg/g body weight, Sigma-Aldrich) or phosphate-buffered saline (PBS) followed by daily body weight monitoring.

value: Lung

value: mouse primary cell

value: wild type and Pdlim2 myeloid KO mice of FVB/N background

value: PBS or LPS intratracheal instillation


title: P41-1

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer


title: Single Cell 5’ Gene Expression Library

description: 10x Genomics


title: MAT preGDM_high_HOMA%β_index_pool1


title: EIC with S120 mice [81-EIC-S120]

city: Birmingham

first: Colin

middle: Robert

last: Reily

state: Alabama

department: Medicine

institute: University of Alabama at Birmingham

description:
Raw counts for EIC animals with S120
EIC_with_S120_raw_counts.csv

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: GRCm38
Supplementary files format and content: Raw counts

source_name: kidney

extract_protocol:
Kidney tissues were harvested, stored I RNA Later at -80C. RNA was extracted by GeneWiz using Qiagen mRNA extraction kits.
GeneWiz uses a Poly(A) selection method for cDNA construction

treatment_protocol: As outlined I the protocol, animals were injected with EIC (immune complex) with or without sparsentan treatment at two different doses.

value: kidney

value: NCr nude

value: EIC + S120


title: MAT control_low_HOMA%β_index_pool3

description: miRNA expression data from early pregnancy serum maternal exosomes from control women with low HOMA%β index

value: female


title: EIC with S120 mice [78-EIC-S120]


title: M82WL30hInternode rep1

value: Internode


title: EIC with S120 mice [79-EIC-S120]


title: P39-1

value: At the time of surgery (hepatectomy)


title: EIC with S120 mice [80-EIC-S120]


title: P38-1


title: M82WL48hInternode rep1


title: MAT preGDM_high_HOMA%β_index_pool3

value: serum maternal exosomes


title: M82WL06hInternode rep1


title: P40-1


title: M82WL24hInternode rep1


title: P37-1


title: M82FR06hInternode rep5

value: FR


title: M82WL48hPith rep1

value: Pith


title: EIC with S60 mice [75-EIC-S60]

description:
Raw counts for EIC animals with S60
EIC_with_S60_raw_counts.csv

value: EIC + S60


title: M82FR48hPith rep4

value: Wildtype


title: EIC with S120 mice [77-EIC-S120]


title: EIC with S60 mice [74-EIC-S60]


title: MAT preGDM_low_HOMA%β_index_pool2

value: pregnant women 12.2 weeks of gestation


title: M82FR48hInternode rep4


title: MAT control_high_HOMA%β_index_pool1

source_name: Early pregnancy serum maternal exosomes from control women with high HOMA%β index

value: pregnant women 15.1 weeks of gestation


title: P34-1


title: MAT control_high_HOMA%β_index_pool2

value: pregnant women 14.3 weeks of gestation


title: MAT control_high_HOMA%β_index_pool3

value: pregnant women 12.3 weeks of gestation


title: MAT control_low_HOMA%β_index_pool4

value: pregnant women 14.1 weeks of gestation


title: EIC with S60 mice [73-EIC-S60]


title: P33-1

value: Plasma extracellular vesicles

value: Metastatic colorectal cancer


title: EIC with S60 mice [72-EIC-S60]

value: kidney

value: NCr nude


title: M82FR30hInternode rep4

source_name: Internode


title: P36-1

description: other label: P78-1


title: EIC with S60 mice [71-EIC-S60]


title: MAT control_low_HOMA%β_index_pool2

value: female

value: pregnant women 14.4 weeks of gestation


title: d7_daf16_daf2_3

city: Shanghai

first: Zhifei

address: NO.1239 Siping Road

institute: Tongji university

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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 directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample.

organism: Caenorhabditis elegans

source_name: the proximal region of the somatic gonad (PSG) cells

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
The SMARTer amplification was performed based on the instruction of SMARTer® Ultra® Low RNA kit (Takara, Janpan, Catalog #: 634936).

value: untreated


title: P31-1

source_name: Plasma extracellular vesicles

value: At the time of surgery (hepatectomy)


title: P32-1


title: M82FR30hInternode rep3

value: Internode

value: FR


title: M82FR48hInternode rep3


title: P30-1


title: MAT preGDM_low_HOMA%β_index_pool3

value: serum maternal exosomes

value: pregnant women 12.6 weeks of gestation


title: P35-1


title: d7_daf2_3

value: the proximal region of the somatic gonad (PSG) cells


title: EIC only mice [67-EIC]

description:
Raw counts for EIC animals
EIC_raw_counts.csv

value: EIC


title: P29-1


title: d7_daf2_2


title: M82FR24hInternode rep3

value: Wildtype


title: M82FR48hPith rep2

value: Pith


title: EIC only mice [66-EIC]


title: d7_daf2_1


title: M82FR48hInternode rep2


title: d7_daf16_daf2_2


title: EIC only mice [69-EIC]


title: P27-1


title: EIC only mice [65-EIC]


title: Control mice [655-CONTROL]

description:
Raw counts for control animals
Control_raw_counts.csv

value: control


title: M82FR30hInternode rep2


title: P26-1

value: Plasma extracellular vesicles


title: d1_daf16_daf2_2


title: EIC only mice [68-EIC]


title: M82FR24hInternode rep2


title: Library 11 mRNA

city: Leuven

first: Bart

last: De Strooper

address: Herestraat 49 box 602

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

description:
10x Genomics
Mancuso2022_RNAcounts.mtx.gz
Mancuso2022_RNAcounts_genes.txt
Mancuso2022_RNAcounts_cellbarcodes.txt
Mancuso2022_NormExpr.mtx.gz
Mancuso2022_NormExpr_genes.txt
Mancuso2022_NormExpr_cellbarcodes.txt

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: Genome build: Human reference, hg19 (Ensembl 87), downloaded from 10x Genomics pre-built Cell Ranger reference packages (3.0.0).
Supplementary files format and content: *.mtx.gz: Raw or SCT normalised gene expression counts per cell in a gzipped tab-separated values file.
Supplementary files format and content: *genes.txt: row names (genes) for raw or SCT normalised gene expression matrices, in txt files.

source_name: Brain

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F, Apphu/hu or AppNL-G-FApoE-/-  mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. Of note, 5 μM Actinomycin D was kept during collection, dissociation and washing and was removed afterwards to avoid cellular toxicity. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with mouse FcR blockers (1:10 in FACS Buffer, Miltenyi, Cat#130- 092-575) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
In this manuscript, we generated a total of 20 libraries containing 95 biological replicates for single cell RNA sequencing. In brief, we sorted 15000-20000 alive human microglia (CD11b+, hCD45+) per mouse and adjusted the final concentration to 1000 cells/µl. Out of each mouse, 2000 sorted cells were loaded into the Chromium Next GEM Chip G (PN #2000177). Since all the individual replicates were hashed using TotalSeqTM-A cell hashing antibodies, we pooled different samples into the same library. Libraries were prepared using manufacturer’s instructions (CG000204 Chromium Next GEM Single Cell 3’ Reagent Kits v3.1). For hashtag oligo libraries, we followed manufacturers’ instructions (BioLegend - TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol) using 16 cycles for the index PCR. Libraries were sequenced on a HiSeq4000 or NovaSeq6000 (Illumina) platform with the recommended read lengths by 10X Genomics workflow targeting 90% mRNA and 10% hashtag library (50,000 reads/cell).

value: Brain

value: Microglia

tag: mouse host genotype

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F ApoE-/-

tag: human cells gender

value: male

tag: mouse host gender

value: female and male

tag: timepoint

value: 6 months

tag: injection

tag: multiplexed samples

tag: samples used for this study


title: Control mice [654-CONTROL]

value: kidney

tag: genotype

value: NCr nude

tag: treatment


title: MAT control_low_HOMA%β_index_pool1

tag: tissue

value: female

value: pregnant women 14.3 weeks of gestation


title: d1_daf16_daf2_1

value: untreated


title: Library 9 mRNA

tag: cell line

value: Rag2-/- Il2r{gamma}-/- hCSF1KI AppNL-G-F


title: d1_daf2_3

value: the proximal region of the somatic gonad (PSG) cells


title: M82FR06hInternode rep2

tag: cultivar

value: Internode

value: Wildtype

value: FR


title: Control mice [653-CONTROL]

value: control


title: P28-1

value: Plasma extracellular vesicles

tag: disease stage

value: Metastatic colorectal cancer

tag: disease status

value: At the time of surgery (hepatectomy)


title: M82FR48hPith rep1

value: Pith


title: d1_daf2_2


title: Control mice [652-CONTROL]


title: M82FR30hPith rep1


title: Library 8 mRNA

value: Brain

tag: cell type

value: Microglia

value: female and male

value: all


title: Control mice [651-CONTROL]

value: kidney

value: NCr nude


title: Library 7 mRNA

value: male

value: 6 months


title: d1_daf16_daf2_3

value: the proximal region of the somatic gonad (PSG) cells

value: untreated


title: PLUS6

status: Public on Feb 28 2024

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description: ATACseq

data_processing:
Fastq files were analyzed using ENCODE’s ATAC-seq-pipeline for single end reads with default parameters
Assembly: GCA_000002445.1_ASM244v1 Genome fasta file was processed by the build_genome_data.sh script (which is supplied with the ATAC-seq pipeline) and used for the analysis

organism: Trypanosoma brucei brucei

source_name: UMSBP2 knock down

growth_protocol: Procyclic T. brucei cells were grown in Beck's Medium.

extract_protocol:
ATAC-seq dna extraction was performed following manufacturer (Diagenode ATAC-seq kit, Cat. No. C01080002) instructions.
ATAC-seq sequences library was generated following manufacturer (Diagenode ATAC-seq kit, Cat. No. C01080002) instructions.

treatment_protocol: UMSBP2 gene was knockdown through RNAi under tetracycline induction.

value: one complete parasite per sample

tag: Stage

value: parasite was collected from host at procyclic stage

value: UMSBP2 knock down


title: M82FR06hInternode rep1

value: Internode

value: Wildtype

value: FR


title: PLUS5

description: ATACseq


title: PLUS4

description: ATACseq


title: MINUS3

description: ATACseq

source_name: Wild type

value: Wild type


title: MINUS2

description: ATACseq


title: MINUS1

description: ATACseq


title: Wistar_129PBMC

type: genomic

first: Michael

last: Corley

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

description: DNAPBMC

hyb_protocol: Illumina Infinium HumanMethylationEPIC protocol. Scanned using Illumina HiScan System.

scan_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

data_processing:
IDAT Data loaded into R using Minfi and normalized using noob method.
Normalized average beta

label: Cy5 and Cy3

source_name: PBMC

label_protocol: Illumina Infinium protocol. Cy5 and Cy3

extract_protocol: Genomic DNA was extracted using a Qiagen kit according to manufacturer's instructions. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

tag: Sex

value: Male

value: PBMC

tag: disease state

value: HIV


title: Wistar_134PBMC

description: DNAPBMC

value: Female

value: Control


title: Wistar_131PBMC

description: DNAPBMC


title: WT-M.tb (THP-1), rep2

city: Alar

first: Aikebaier

last: Reheman

address: Tarim Avenue, Alar City

institute: Tarim University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol: The libraries were generated with VAHTS Universal V6 RNA-seq Library Prep Kit for MGI (Vazyme, NRM604)

value: macrophage

value: WT


title: Rv1476-OE (THP-1), rep2


title: Wistar_133PBMC

description: DNAPBMC


title: Rv1476-OE (THP-1), rep1


title: Wistar_132PBMC

description: DNAPBMC


title: Wistar_130PBMC

description: DNAPBMC


title: Wistar_128PBMC

description: DNAPBMC


title: Wistar_127PBMC

description: DNAPBMC


title: Wistar_122PBMC

description: DNAPBMC


title: Wistar_126PBMC

description: DNAPBMC


title: Wistar_123PBMC

description: DNAPBMC


title: Wistar_125PBMC

description: DNAPBMC


title: Wistar_124PBMC

description: DNAPBMC


title: d1_daf2_1


title: WT-M.tb (THP-1), rep1


title: Wistar_120PBMC

description: DNAPBMC


title: Wistar_121PBMC

description: DNAPBMC


title: Wistar_119PBMC

description: DNAPBMC


title: Wistar_114PBMC

description: DNAPBMC


title: Wistar_116PBMC

description: DNAPBMC


title: Wistar_112PBMC

description: DNAPBMC


title: Wistar_113PBMC

description: DNAPBMC


title: Wistar_111PBMC

description: DNAPBMC


title: Wistar_110PBMC

description: DNAPBMC


title: Wistar_109PBMC

description: DNAPBMC


title: Wistar_108PBMC

description: DNAPBMC


title: Wistar_107PBMC

description: DNAPBMC


title: Wistar_100PBMC

description: DNAPBMC


title: Wistar_106PBMC

description: DNAPBMC


title: Wistar_101PBMC

description: DNAPBMC


title: Wistar_103PBMC

description: DNAPBMC


title: Wistar_99PBMC

description: DNAPBMC


title: Wistar_102PBMC

description: DNAPBMC


title: Wistar_98PBMC

description: DNAPBMC


title: Wistar_96PBMC

description: DNAPBMC


title: Wistar_93PBMC

description: DNAPBMC


title: Wistar_91Ileum

description: DNAIleum

source_name: Ileum

value: Ileum


title: Wistar_92Ileum

description: DNAIleum


title: Wistar_97PBMC

description: DNAPBMC


title: Wistar_95PBMC

description: DNAPBMC


title: Wistar_90Ileum

description: DNAIleum


title: Wistar_88Ileum

description: DNAIleum


title: Wistar_86Ileum

description: DNAIleum


title: Wistar_87Ileum

description: DNAIleum


title: Wistar_85Ileum

description: DNAIleum


title: Wistar_89Ileum

description: DNAIleum


title: Wistar_81Ileum

description: DNAIleum


title: Wistar_82Ileum

description: DNAIleum


title: Wistar_105PBMC

description: DNAPBMC


title: Wistar_104PBMC

description: DNAPBMC


title: Wistar_80Ileum

description: DNAIleum


title: Wistar_79Ileum

description: DNAIleum


title: Wistar_76Ileum

description: DNAIleum


title: Wistar_78Ileum

description: DNAIleum


title: Wistar_72Ileum

description: DNAIleum


title: Wistar_75Ileum

description: DNAIleum


title: Wistar_73Ileum

description: DNAIleum


title: Wistar_74Ileum

description: DNAIleum


title: Wistar_94PBMC

description: DNAPBMC


title: Wistar_70Ileum

description: DNAIleum


title: Wistar_69Ileum

description: DNAIleum


title: Wistar_68Ileum

description: DNAIleum


title: Wistar_67Ileum

description: DNAIleum


title: Wistar_84Ileum

description: DNAIleum


title: Wistar_71Ileum

description: DNAIleum


title: Wistar_64Ileum

description: DNAIleum


title: Wistar_63Ileum

description: DNAIleum


title: Wistar_62Ileum

description: DNAIleum


title: Wistar_61Ileum

description: DNAIleum


title: Wistar_83Ileum

description: DNAIleum


title: Wistar_60Ileum

description: DNAIleum


title: Wistar_58Ileum

description: DNAIleum


title: Wistar_59Ileum

description: DNAIleum


title: Wistar_57Ileum

description: DNAIleum


title: Wistar_77Ileum

description: DNAIleum


title: Wistar_53Ileum

description: DNAIleum


title: Wistar_55Ileum

description: DNAIleum


title: Wistar_56Ileum

description: DNAIleum


title: Wistar_52Ileum

description: DNAIleum


title: Wistar_48Ileum

description: DNAIleum


title: Wistar_54Ileum

description: DNAIleum


title: Wistar_66Ileum

description: DNAIleum


title: Wistar_50Ileum

description: DNAIleum


title: Wistar_51Ileum

description: DNAIleum


title: Wistar_47Colon

description: DNAColon

source_name: Colon

value: Colon


title: Wistar_49Ileum

description: DNAIleum


title: Wistar_46Colon

description: DNAColon


title: Wistar_65Ileum

description: DNAIleum


title: Wistar_44Colon

description: DNAColon


title: Wistar_45Colon

description: DNAColon


title: Wistar_42Colon

description: DNAColon


title: Wistar_38Colon

description: DNAColon


title: Wistar_37Colon

description: DNAColon


title: Wistar_40Colon

description: DNAColon


title: Wistar_36Colon

description: DNAColon


title: Wistar_39Colon

description: DNAColon


title: Wistar_34Colon

description: DNAColon


title: Wistar_32Colon

description: DNAColon


title: Wistar_31Colon

description: DNAColon


title: Wistar_29Colon

description: DNAColon


title: Wistar_27Colon

description: DNAColon


title: Wistar_28Colon

description: DNAColon


title: Wistar_24Colon

description: DNAColon


title: Wistar_25Colon

description: DNAColon


title: Wistar_22Colon

description: DNAColon


title: Wistar_43Colon

description: DNAColon


title: Wistar_20Colon

description: DNAColon


title: Wistar_18Colon

description: DNAColon


title: Wistar_19Colon

description: DNAColon


title: Wistar_17Colon

description: DNAColon


title: Wistar_41Colon

description: DNAColon


title: Wistar_21Colon

description: DNAColon


title: Wistar_23Colon

description: DNAColon


title: Wistar_16Colon

description: DNAColon


title: Wistar_35Colon

description: DNAColon


title: Wistar_12Colon

description: DNAColon


title: Wistar_33Colon

description: DNAColon


title: Wistar_11Colon

description: DNAColon


title: Wistar_10Colon

description: DNAColon


title: Wistar_15Colon

description: DNAColon


title: Wistar_9Colon

description: DNAColon


title: Wistar_14Colon

description: DNAColon


title: Wistar_30Colon

description: DNAColon


title: Wistar_8Colon

description: DNAColon


title: Wistar_26Colon

description: DNAColon


title: Wistar_7Colon

description: DNAColon


title: M82FR30hPith rep3

city: Dalian

first: Changqing

address: Heishijiao Str.

institute: Dalian Ocean University

data_processing:
The initial read quality assessment with FastQC.
Sequence trimming using TrimGalore (https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md).
rRNA removal via SortMeRNA.
Read mapping and read-group annotation using STAR (Dobin et al., 2013).
Alignment quality control with RSeQC (Wang et al., 2012) and Preseq ( https://smithlabresearch.org/software/preseq/).
PCR duplicate detection employing Sambamba MarkDup (Tarasov et al., 2015)
Gene expression and biotype quantification through featureCounts (Liao et al., 2014).
Assembly: The sequences were mapped against ITAG4.1 annotation of tomato reference genome SL4.1 https://solgenomics.net/organism/Solanum_lycopersicum/genome.
Supplementary files format and content: tab-delimited text file that includes the raw counts for each sample

source_name: Pith

extract_protocol:
We prepared RNA-seq libraries according to the random-primer primed method published originally in (Townsley et al., 2015) with modifications from Kajala et al., 2021. Tissue samples were ground by hand and immediately incubated in 250 μL lysis buffer (LBB: 100 mM Tris-HCl, 1000 mM LiCl, 10 mM EDTA, 1% SD, 5 mM DTT, Antifoam A) supplemented with 5 μ l/ml β-mercaptoethanol before use. The samples were transferred to 2ml tubes and the tubes were beat 2 times for 1min at 30 Hz. The samples were incubated at room temperature for 10 min and spun down at 13,000 rpm for 10 min. One uL of 12.5 μM biotin-20nt-dT(Table 3.1) oligo was mixed into 200 μL of lysate in PCR tubes and incubated  at room temperature for 10 min. Then, we added 20 μL Biolabs® streptavidin beads per reaction for incubation. The mRNA from samples binds the oligo through the polyA tail, and the biotin in the oligo binds the streptavidin on the beads. This allows pulling down only the mRNA and washing the rest of the material off. So, the samples were separated into magnetic bead-bound mRNA and supernatant by 96 well Magwell® magnetic separator. The bead pellets were washed with 200 μl washing buffer series: washing buffer A (WBA; 10 mM Tris-HCl, 150 mM LiCl, 1 mM EDTA, 0.1% SDS), washing buffer B (WBB; 10 mM Tris-HCl, 150 mM LiCl,1mM EDTA), and low salt buffer LSB (20 mM Tris-HCl,150 mM NaCl, 1 mM EDTA). The mRNA was eluted in 16 uL Tris-HCl with 80C. These pulldown and washing steps were repeated a second time to remove non-specifically associating rRNA from the samples.
We prepared RNA-seq libraries according to the random-primer primed method published originally in (Townsley et al., 2015) with modifications from Kajala et al., 2021. RNA fragmentation was carried out by preparing 10 μL mixtures of 1.5 μl 5X Thermo Scientific RT buffer, 0.5 μl Invitrogen ® random primers, 8 μl mRNA from the above elution. The mixtures were put into thermocycler for temperature-induced fragmentation and priming of 1st strand of cDNA (25°C 1 sec, 94°C 1.5 min, 4°C 5 min, 4°C hold).cDNA synthesis. We prepared first strand master mixture as following: 1.5 μL 5X Thermo Scientific RT buffer, 1.5 μL 0.1M DTT, 1 μL H2O, 0.5 μL 25mM dNTPs, 0.5 μL RevertAid H minus reverse transcriptase enzyme (Thermo Scientific). The mixture was added onto the samples and incubated in thermocycler: 25°C 10min, 42°C 50min, 50°C 10min, 70°C 10min, 4°C hold. The second strand synthesis, end repair, and A-tailing were performed by adding a 5 μL mixture to the first strand, consisting of 1.5 μL H2O, 0.4 μL 25mM dNTPs, 1 μL DNA polymerase I (Thermo Fisher), 0.1 μL RNaseH (NEB), 0.4 μL NEBNext® End Repair Module enzyme mix, 0.2 μL Taq, and 1.4 μL. This mixture was incubated in a thermocycler following these temperature and time settings: 16°C for 20 minutes, 20°C for 20 minutes, 72°C for 20 minutes, and held at 4°C. Subsequently, the reaction mixture was left at room temperature for 5 minutes with a mix of Beckman® Ampure XP beads at 1.5 times the volume, followed by two washes with 200 μL of 80% ethanol each, until the beads were completely dry. Adapter ligation: The dry beads were mixed with 3 ul of annealed 1 μM universal adapter primers (8μL of 100μM each primer was combined with 784 μL of H2O and cooled through the program: 94°C 1min, (94°C 10sec) * 60 cycles -1°C /cycle, 20°C 1min, 4°C hold). Then, 7 μL ligase mixture (5 μL Enzymatics 2X Rapid T4 ligation buffer, 0.25 μL Biolabs® DNA ligase) was added for 15-min room temperature incubation. We added 10 μL of 50 mM EDTA and 25 μL Ampure XP Bead Resuspension buffer (15% PEG 8000, 2.5M NaCl) to each sample, washed with 80% EtOH twice, and eluted the ligated DNA fragments with 20-22 μL 10mM Tris.  Enrichment, indexing and quantification We used 10 μl of cDNA into enrichment mixed with 4 μL 5X Phusion HF (Thermo Fisher) buffer,2.6 μL H2O, 1 μL 2 μM PE1 primer, 1 μl 8 μM each EnrichS1 + S2 primers (Table 3.1), 0.2 μl 25mM dNTPs, and 0.2 μl Phusion Polymerase (Thermo Fisher). Each sample used 1 μl of appropriate unique indexed enrichment oligo (Townsley et al., 2015). The mixture was heated in thermocycler with the following program: 98°C 30 sec,  (98 °C 10 sec, 65 °C 30 sec, 72 °C 30 sec) *12 cycles, 72 °C 5 min, 10 °C hold. We cleaned the enriched libraries according to Bailey-Serres lab protocol: 1.1 volume of well-resuspended Ampure beads are mixed well with the samples, followed by washing twice by 200 μl of 80% EtOH and resuspending in 10 μl 10mM Tris pH 8.0.  One μl of the samples were used for quality check by Bioanalyzer High Sensitivity DNA Analysis kit, and we selected cleaned library of 200-350 bps based on the peaks. Libraries were pooled together for sequencing with the same target concentration. A final clean-up was done with 0.8 volumes of Ampure beads and elution to the final target volume.

value: Pith


title: d7_daf16_daf2_1

value: the proximal region of the somatic gonad (PSG) cells

value: untreated


title: Wistar_4Colon

city: New York

description: DNAColon


title: Wistar_3Colon

description: DNAColon


title: Wistar_2Colon

description: DNAColon


title: C364, hippocampus, MiSeq

city: Santa Barbara

first: Kenneth

middle: S

last: Kosik

state: CA

address: 5165 Biology II

department: Molecular, Cellular, and Developmental Biology

institute: University of California Santa Barbara

description:
C364_c12
10X Genomics
Visium Spatial Gene Expression

data_processing:
The Space Ranger pipeline (v1.3.1) for processing of Visium Spatial Gene Expression (GEX) data with brightfield images to align reads and generate Feature Barcode (FB) matrices was used (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger).
Downstream analysis was performed using Seurat 4.1.1 (https://satijalab.org/seurat/index.html).
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: filtered feature barcoded matrix is a spaceranger output .h5 file with counts for every spot.
Supplementary files format and content: tissue low resolution image is a spaceranger output .png file for projecting gene expression values onto
Supplementary files format and content: metadata .csv file includes all demographic and tissue spot information; C140, C363 and C364 are donor ids.

source_name: Brain (hippocampus)

extract_protocol:
Hippocampal and frontal cortical samples were cryosectioned at -20°C. The 10 μm sections were placed on a Visium Tissue Optimization Slide (10x Genomics, #3000394) and Visium Spatial Gene Expression Slide (10x Genomics, #2000233). By following the Visium Spatial Tissue Optimization User Guide (10x Genomics, #CG000238 Rev E), the optimal permeabilization time was determined to be twelve minutes. The gene expression slides underwent methanol fixation, Hematoxylin & Eosin (H&E) staining, and brightfield imaging using a 10x objective on a Nikon Eclipse Ti2-E (10x Genomics, #CG000160 Rev C).
Immediately after imaging, the tissues were permeabilized and the remaining steps for library construction were completed according to the user guide (10x Genomics, #CG000239 Rev F).

value: Brain (hippocampus)

value: diverse brain cell types

tag: disease

value: Healthy Control

value: no treatment

value: male

tag: donor


title: C363, hippocampus, MiSeq

description:
C363_c12
10X Genomics
Visium Spatial Gene Expression

value: Autosomal dominant Alzheimer's Disease

value: PSEN1 E280A

value: female


title: graft_after.treatment_patMa.Em

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: Transciptomic signature of chronic antibody-mediated kidney rejection

hyb_protocol: 300 ng total RNA was hybridized to gene-specific probes at 65ÀöC for 18 hours and then purified and deposited onto glass cartridges using the high sensitivity setting on the nCounter Prep Station

scan_protocol: The number of barcodes hybridized to specific RNA targets on cartridges were directly counted by the nCounter Digital Analyzer with 555 fields of view setting.

data_processing: Data weer processed in nSolver 4.0.70 as manufacturer recommandations.

source_name: Frozen

label_protocol: using the nCounter® Human Organ Transplant Panel, as manufacturer recommandations.

extract_protocol: RNA was isolated and extracted using the tissue RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany), and then concentration was assessed with the NanoDrop spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). 300ng of total RNA from each sample was then hybridized to the nCounter® Human Organ Transplant Panel (NanoString Technologies, Seattle, WA, USA).

treatment_protocol: Ten-µm-thick sections were obtained from frozen (2/16) or alcohol-formalin-acetic acid (AFA) fixed-paraffin embedded (14/16) tissue-block to collect the 300 ng of RNA required for analyses.

value: graft biopsy


title: graft_after.treatment_patMa.Do

source_name: AFA


title: graft_before.treatment_patMa.Em


title: Wistar_13Colon

description: DNAColon

value: Male

value: HIV


title: graft_after.treatment_patHe


title: C140, hippocampus, MiSeq

description:
C140_c12
10X Genomics
Visium Spatial Gene Expression


title: graft_before.treatment_patMa.Do


title: graft_after.treatment_patCa


title: Eso26_ctl_rep1 RNA-Seq

first: Qian

last: Yang

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
Single-end and pair-end  reads were aligned to the hg19 reference genome using Bowtie. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR.
Adaptors were removed using Trim galore software. Each replicate, the raw reads were aligned to masked version of the reference human genome hg19.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Assembly: hg19
Supplementary files format and content: bigwig files representing signal normalized to per million reads

source_name: Esophageal Adenocarcinoma cell line

growth_protocol: ESO26 and SKGT4 cells were grown in RPMI-1640 medium (Corning, 45000-396), supplemented with 10% FBS (Omega Scientific, FB-02) and 1% penicillin-streptomycin sulfate (Gibco, 10378016).

extract_protocol:
Sonicated nuclei were used to generate lysates, and protein-DNA complexes were subsequently isolated using antibodies. Total RNA was then extracted from these complexes using the RNeasy Mini Kit (QIAGEN) following the manufacturer's instructions.
Standard Illumina library preparation protocol

treatment_protocol: ESO26 cells were treated with 1uM Afatinib (Sigma,#SML3109) or DMSO for 24 hours.  ESO26 cells were transfected with non-silencing siRNA or siFOXM1 (Horizon Discovery, 009762-00-0005) using Lipofectomine RNAiMAX (Thermo Fisher, #13778150).

value: Esophageal adenocarcinoma cell line


title: Eso26_siFOXM1_rep2 RNA-Seq


title: Eso26_siFOXM1_rep1 RNA-Seq


title: Eso26_ctl_rep2 RNA-Seq


title: graft_after.treatment_patLo


title: Wistar_5Colon

description: DNAColon

value: Control


title: graft_after.treatment_patCr


title: Wistar_6Colon

description: DNAColon

value: Colon


title: graft_before.treatment_patCr


title: SKGT4_FOXM1 ChIIP-Seq

value: Esophageal Adenocarcinoma cell line


title: graft_before.treatment_patCa


title: graft_before.treatment_patLo


title: Wistar_1Colon

description: DNAColon


title: ESO26_FOXM1 ChIIP-Seq


title: M_JC-C-C_Ab

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

library_source: other

data_processing:
library strategy: CITE-seq
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference
QC and Filtering and Unsupervised Clustering: Seurat V3/V4
Assembly: GRCh38 V3.0.0
Supplementary files format and content: .rds objects

molecule: protein

source_name: heart

extract_protocol:
Freshly isolated hearts from 16-week-old WT, Dsg2mut/mut and Dsg2mut/mut x Ccr2-/- mice (n=3 per group) were minced on ice with a razor blade, transferred to a 15 mL conical tube containing 3mL DMEM with 170uL collagenase IV (250U/mL final concentration), 35uL DNAse1 (60U/mL), and 75uL hyaluronidase (60U/mL), and incubated at 37 °C for 45 min with agitation. Thereafter, the digestion reaction was quenched with 5 mL of HBB buffer (2% FBS and 0.2% BSA in HBSS), passed through 40-µm filters into a 50 mL conical tube and transferred back into a 15 mL conical tube to obtain tighter pellets. Samples were then spun down at 4°C, 1200rpm for 5 min and the supernatant was discarded. Pellets were resuspended in 1 mL ACK Lysis buffer (Gibco A10492-01)    and incubated at room temperature for 5 min, followed by the addition of 9 mL DMEM and centrifugation (4°C, 5 min, 1200 rpm). Supernatant was discarded and the pellets were resuspended in 2 mL FACS buffer (2% FBS and 2mM EDTA in calcium/magnesium free PBS); centrifugation was repeated in above conditions and supernatant aspirated. The TotalSeq A 277 panel (BioLegend) antibody cocktail was resuspended in 100 µL of FACS buffer and added to each sample. The combined 100 µL were used to resuspend the pellet with the addition of 1 µL of DRAQ5 (5mM solution Thermo Fisher Scientific, 564907) and incubated on ice for 30 min. Solution was washed 3x with FACS buffer following same centrifugation as above and then resuspended in 300 µL of FACS buffer and 1 uL DAPI (BD Biosciences, 564907) and filtered into filter top FACS tubes. First singlets were gated and subsequent DRAQ5+/DAPI- events were collected in 300 µL cell resuspension buffer (0.04% BSA in PBS) – collected cells were centrifuged as above and resuspended in collection buffer to a target concentration of 1,000 cells/µL. Cells were counted on a hemocytometer before proceeding with the 10x protocol.    Sample preparation for single nuclei RNA-seq (snRNA-seq): Frozen hearts from 16-week-old WT, Dsg2mut/mut and Dsg2mut/mut x Ccr2-/- mice (n=3 per group) were minced with a razor blade and transferred into a 5 mL Dounce homogenizer containing 1–2 mL chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40 in nuclease-free water). Samples were homogenized gently using five passes without rotation, and then incubated on ice for 15 min. Lysate was gently passed through a 40-μm filter into 50-mL conical tube, followed by rinsing the filter once with 1 ml lysis buffer and transfer of lysate to a new 15-mL conical tube. Nuclei were then centrifuged at 500g for 5 min at 4°C, followed by resuspension in 1 mL Nuclei Wash Buffer (2% BSA and 0.2 U /µL RNase inhibitor in 1× PBS) and filtered through a 20-μm pluristrainer into a fresh 15-mL conical tube. Centrifugation was repeated according to the above parameters. Supernatant was then removed, and    nuclei were resuspended in 300 µL Nuclei Wash Buffer and transferred to a 5-mL tube for flow sorting. Then, 1 µl DRAQ5 (5 mM solution; Thermo Fisher, cat. no. 62251) was added, mixed gently and allowed to incubate for 5 min before sorting. DRAQ5+ nuclei were sorted into Nuclei Wash Buffer. Recovered nuclei were centrifuged again under the above parameters and were gently resuspended in Nuclei Wash Buffer to a target concentration of 1,000 nuclei/µL. Nuclei were counted on a hemocytometer.
Chromium Single Cell 5ʹ Reagent v1.1 kit from 10X Genomics and Chromium Single Cell 3ʹ Reagent v1.1 kit from 10X Genomics

value: heart


title: graft_before.treatment_patDu2


title: M_JC-C-C


title: graft_before.treatment_patDu1


title: M_JC-D-D_Ab


title: qT1qF11qF17_5DPI_B

city: Beaucouzé

first: Laure

last: Perchepied

address: 42 rue Georges Morel

institute: INRAE

data_processing:
The sequenced reads (ranging from 29.3 to 41 million read pairs per sample) were mapped on the reference transcriptional units from GDDH13 v1.1 using Salmon software (Patro et al., 2017)
Identification of differentially expressed genes (DEGs) was performed with DESeq2, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) (Love et al., 2014)
Assembly: GDDH13v1.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios of the 16 comparisons

organism: Malus domestica

source_name: leaf

growth_protocol: Plants were grown in individual pots (8 x 5.5 x 7 cm) under greenhouse conditions (natural photoperiod supplemented with artificial light if needed, 17°C night and 20–23°C day)

extract_protocol:
RNA was harvested using NucleoSpin RNA Plant (Macherey Nagel)
Libraries were generated using the Illumina mRNA Stranded protocol

treatment_protocol: Plants received water treatment two days before scab inoculation, and sampling for RNAseq analysis occurred on non inoculated plants at day of inoculation with the EU-B04 strain of Venturia inaequalis (0DPI) and on inoculated plant 5 days post inoculation (5DPI).  For the scab inoculation, monoconidial suspensions were prepared from diseased dry leaves at a concentration of 2.5 × 10exp5 conidia.ml−1 and sprayed on grafted trees, incubated thereafter 2 days at 17°C under a plastic sheet to maintain a high humidity, according to the conditions described by Caffier et al. (2010).

value: leaf

value: Pool of  F072, F073, F081 and F259 genotypes

value: Venturia inaequalis strain EU-B05


title: graft_before.treatment_patHe


title: M_JC-W-W_Ab

value: WT


title: qT1qF11qF17_5DPI_A

value: Venturia inaequalis strain EU-B04


title: graft_after.treatment_patBo


title: qT1qF11qF17_0DPI_B

value: Water


title: M_JC-Dsg-x-CCR2-16wk-7-lib1

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference
QC and Filtering and Unsupervised Clustering: Seurat V3/V4
Assembly: GRCh38 V3.0.0
Supplementary files format and content: .rds objects


title: graft_before.treatment_Bo.


title: M_JC-W-W


title: qT1qF11qF17_0DPI_A


title: qF11qF17_5DPI_B

value: Pool of F135, F139, F171 and F336 genotypes


title: M_JC-D-D


title: qF11qF17_5DPI_A


title: M_JC-Dsg-16wk-6-lib1


title: qF11qF17_0DPI_B


title: qF11qF17_0DPI_A


title: qT1_5DPI_B

value: Pool of  F064, F117, F207 and F244 genotypes


title: M_JC-WT-16wk-5-lib1


title: M_JC-Dsg-6wk-2-lib1


title: qT1_5DPI_A


title: qT1_0DPI_B


title: M_JC-Dsg-x-CCR2-6wk-3-lib1


title: NoscabQTL_5DPI_B

value: Pool of F025, F138, F193 and F233 genotypes


title: hfCas13d_2

first: Zilong

last: Geng

address: 800 Dongchuan Rd, Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

description:
hfCas13d.csv
hfCas13d_DEG.csv

data_processing:
The resulting FASTQ files were aligned to the human reference genome (hg38) using HISAT2
mRNA abundance was quantified in counts per million (CPM) by HTseq
Differential expression analysis was conducted using DESeq2
Assembly: hg38
Supplementary files format and content: All processed files are in CSV format, containing the results of transcriptomic differential analysis statistics.

source_name: cultured cell

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics humidified with atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was then extracted and purified using the RNAprep Pure Micro Kit (TIANGEN).
mRNA enrichment was performed using the TIANSeq mRNA Capture Kit (TIANGEN), and the libraries were constructed using the TIANSeq Fast RNA Library Kit (TIANGEN ).

treatment_protocol: 3 μg of Cas13d-T2A-GFP-U6-gRNA plasmids targeting PPIA and RPL4 were transfected  into HEK293T cells cultured in 6-well plates.

value: cultured cell

value: transfectedwith hfCas13d agaist PPIA


title: hfCas13d_1

description:
hfCas13d.csv
hfCas13d_DEG.csv


title: hpCas13d_2

description:
hpCas13d.csv
hpCas13d_DEG.csv

value: transfectedwith hpCas13d agaist PPIA


title: NoscabQTL_5DPI_A


title: NoscabQTL_0DPI_B


title: wtCas13d_1

description:
wtCas13d.csv
wtCas13d_DEG.csv

value: transfectedwith wtCas13d agaist PPIA


title: qT1_0DPI_A


title: wtCas13d_2

description:
wtCas13d.csv
wtCas13d_DEG.csv


title: M_JC-WT-6wk-1-lib1


title: NoscabQTL_0DPI_A


title: dCas13d_2

description:
wtCas13d.csv
wtCas13d_DEG.csv
hpCas13d.csv
hpCas13d_DEG.csv
hfCas13d.csv
hfCas13d_DEG.csv

value: transfectedwith dCas13d


title: dCas13d_1


title: Discordant

type: protein

city: New Orleans

first: Eric

last: Dumonteil

state: LA

address: 1440 Canal st.

department: Tropical Medicine

institute: Tulane University

description: A pool of IgG from 11 subjects serodiscordant for T. cruzi infection was incubated with an overlapping peptide array of the Trypanosoma cruzi conserved proteome.

hyb_protocol: Microarrray slides were deprotected in TFA EDT H20 for 3h at room temperature and blocked overnight in 0.1% BSA, 0.1% Tween-20 in PBS. After blocking, slides were incubated for 1h at RT with one of the IgG probes (100 µg/ml IgG in 0. 1% BSA, 0.1% Tween-20 in PBS), washed 3 x 20 min with 0.1% BSA, 0.1% Tween-20 in PBS and incubated for 1h at RT with Cy3- goat anti-Human IgG (1 µg/ml in 0.1% B SA, 0.1% Tween-20 in PBS). Slides were washed 3 x 20 min with 0.1% BSA in PBS, dried

scan_protocol: Scanned using a laser scanner with 1 µm resolution

data_processing: Statistics assuming normal distribution of signals from fields with no sequence (= blanks): signal-µblanks = signal from peptide minus mean of blank fields in the sector indicated.

label: Cy3 goat anti-Human IgG

source_name: Purified IgG

label_protocol: none provided

extract_protocol: IgG antibodies were purified from human plasma samples using Thermo Scientific™ Melon™ Gel IgG Spin Purification Kit

tag: status

value: Serodiscordant for T. cruzi infection

tag: sample type

value: Pool of IgG from 11 subjects


title: A. wentii 'c gfdB NaCl + sorbitol 1

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A nidulans FGSC A4 or A. wentii CBS141173 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/fasta/data/FungiDB-65_AnidulansFGSCA4_Genome.fasta; https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/gff/data/FungiDB-65_AnidulansFGSCA4.gff; https://fungidb.org/common/downloads/release-65/AwentiiDTO134E9/fasta/data/FungiDB-65_AwentiiDTO134E9_Genome.fasta; https://fungidb.org/common/downloads/release-65/AwentiiDTO134E9/gff/data/FungiDB-65_AwentiiDTO134E9.gff
Supplementary files format and content: excell file includes count and RPKM values for each Sample

organism: Aspergillus wentii

source_name: mycelium

growth_protocol: Barratt’s minimal broth (100 mL in 500 mL Erlenmeyer flask) inoculated with 1x108 conidia was incubated in a rotary shaker at 25 °C, 220 rpm (approx. 3.7 Hz). A. nidulans mycelia were harvested after 36 h (THS30) or 38 h (ΔgfdB), meanwhile A. wentii mycelia were harvested after 65 h (both CBS141173 and 'c gfdB) cultivation. Different incubation times were used in order we collect exponentially phase mycelia with similar physiological conditions in the case of each strain

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Mycelia were collected, washed and then transferred into 100 mL fresh Barratt’s minimal broth or Barratt’s minimal broth supplemented with 2 M sorbitol, 1 M NaCl, or 1 M NaCl + 2 M sorbitol. Cultures were further incubated at 25 °C and 220 rpm and samples were taken after 0.5 h for RNA isolation.

value: mycelium

value: 'c gfdB mutant expressing A. nidulans gfdB

value: NaCl+sorbitol treated


title: Negative

description: A pool of IgG from 10 subjects negative for T. cruzi infection was incubated with an overlapping peptide array of the Trypanosoma cruzi conserved proteome.

value: Negative for T. cruzi infection

value: Pool of IgG from 10 subjects


title: Positive

description: A pool of IgG from 9 subjects positive for T. cruzi infection was incubated with an overlapping peptide array of the Trypanosoma cruzi conserved proteome.

value: Positive for T. cruzi infection

value: Pool of IgG from 9 subjects


title: A. wentii 'c gfdB NaCl + sorbitol 3


title: A. wentii 'c gfdB NaCl + sorbitol 2


title: A. wentii 'c gfdB NaCl 3

value: NaCl treated


title: A. wentii 'c gfdB NaCl 2


title: hpCas13d_1

description:
hpCas13d.csv
hpCas13d_DEG.csv

value: WT


title: DLBCL tissue PDX intermediate passage 24 rep2 RNA [PDX_24_SC_int-2 ]

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

description:
PDX_24_SC_int-2
logCPM_Normalized_human_PDX.csv

data_processing:
Illumina Casava-1.8.2 software used for basecalling
STAR v2.6.1a was used to align
XenofilteR v0.99 used to deconvolute PDX samples
Salmon v1.3.0 used for quantification post deconvolution
Assembly: hg38, mm10 (for PDX TME reads)
Supplementary files format and content: csv file includes Salmon TPM values

source_name: DLBCL

extract_protocol:
Qiagen total RNA
TruSeq mRNA
polyA selection and stranded RNA-seq

value: DLBCL

tag: tissue type

value: DLBCL tissue PDX intermediate passage


title: DLBCL tissue PDX intermediate passage 20 RNA [PDX_20_RN_int ]

description:
PDX_20_RN_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 22 RNA [PDX_22_AD_int ]

description:
PDX_22_AD_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 25 RNA [PDX_25_BH_int ]

description:
PDX_25_BH_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 18 RNA [PDX_18_KK_int ]

description:
PDX_18_KK_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 19 RNA [PDX_19_RRR_int ]

description:
PDX_19_RRR_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 16 RNA [PDX_16_RR_int ]

description:
PDX_16_RR_int
logCPM_Normalized_human_PDX.csv


title: A. wentii 'c gfdB NaCl 1


title: DLBCL tissue PDX intermediate passage 24 rep1 RNA [PDX_24_SC_int-1 ]

description:
PDX_24_SC_int-1
logCPM_Normalized_human_PDX.csv


title: A. wentii 'c gfdB sorbitol 2

value: sorbitol treated


title: A. wentii 'c gfdB sorbitol 3


title: DLBCL tissue PDX intermediate passage 14 RNA [PDX_14_YLL_int ]

description:
PDX_14_YLL_int
logCPM_Normalized_human_PDX.csv


title: A. wentii 'c gfdB sorbitol 1


title: A. wentii 'c gfdB untreated 3

value: untreated


title: DLBCL tissue PDX intermediate passage 12 RNA [PDX_12_CR_int ]

description:
PDX_12_CR_int
logCPM_Normalized_human_PDX.csv


title: A. wentii 'c gfdB untreated 2


title: DLBCL tissue PDX intermediate passage 8 RNA [PDX_8_TA23_int ]

description:
PDX_8_TA23_int
logCPM_Normalized_human_PDX.csv


title: A. wentii 'c gfdB untreated 1


title: DLBCL tissue PDX intermediate passage 7 RNA [PDX_7_WA_int ]

description:
PDX_7_WA_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 11 RNA [PDX_11_FE_int ]

description:
PDX_11_FE_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 6 RNA [PDX_6_RE_int ]

description:
PDX_6_RE_int
logCPM_Normalized_human_PDX.csv


title: A. wentii CBS141173 NaCl + sorbitol 3

value: CBS141173 reference strain


title: A. wentii CBS141173 NaCl + sorbitol 2


title: DLBCL tissue PDX intermediate passage 5 RNA [PDX_5_TE_int ]

description:
PDX_5_TE_int
logCPM_Normalized_human_PDX.csv


title: A. wentii CBS141173 NaCl 3


title: DLBCL tissue PDX intermediate passage 3 RNA [PDX_3_AL_int ]

description:
PDX_3_AL_int
logCPM_Normalized_human_PDX.csv


title: DLBCL tissue PDX intermediate passage 2 RNA [PDX_2_PA_int ]

description:
PDX_2_PA_int
logCPM_Normalized_human_PDX.csv


title: A. wentii CBS141173 sorbitol 3


title: A. wentii CBS141173 sorbitol 2


title: A. wentii CBS141173 NaCl 1


title: DLBCL tissue PDX intermediate passage 15 RNA [PDX_15_BSE_int ]

description:
PDX_15_BSE_int
logCPM_Normalized_human_PDX.csv


title: A. wentii CBS141173 NaCl 2


title: DLBCL tissue PDX intermediate passage 1 RNA [PDX_1_CJ_int ]

description:
PDX_1_CJ_int
logCPM_Normalized_human_PDX.csv


title: A. wentii CBS141173 untreated 3


title: A. wentii CBS141173 untreated 2


title: A. wentii CBS141173 sorbitol 1


title: A. wentii CBS141173 untreated 1


title: 12astroko

first: Oded

last: Behar

address: Ein Kerem. P.O. Box 12271, The Hebrew University Faculty ,, building 3, floor 2, room 3213

department: Developmental Biology and Cancer Research

institute: The Hebrew University

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt (54); resulting reads shorter than 30bp were discarded. Reads were mapped to the M. musculus GRCm38 reference genome using STAR (55), supplied with gene annotations downloaded from Ensembl release 92 (STAR was run with EndToEnd option and outFilterMismatchNoverLmax 0.04). Expression levels for each gene were quantified using htseq-count (56). Differentially expressed genes were identified using DESeq2 (57) with the betaPrior, cooksCutoff and independent filtering parameters set to False. The pipeline was run using snakemake (58).
Assembly: Mus_musculus.GRCm38.dna
Supplementary files format and content: Immune cell fraction Sema4B-/- versus Sema4B+/- upregulated genes. Xlsx file
Supplementary files format and content: Astrocyte cell fraction Sema4B-/- versus Sema4B+/- upregulated genes. Xlsx file

source_name: brain (cortex)

extract_protocol: To test the changes in gene expression systematically and within specific cell types, Sema4B+/- and Sema4B -/- mice inflicted cortical injury. A 3x3mm square around the injured site was dissected out 12h after injury and dissociated into cells. Using immunopanning astrocytes (collecting the cells adhering to the Acsa-2 plate isolate) and immune cells (collecting cells adhering to a secondary-only plate and CD45 plate). The isolated cell populations were used to extract RNA and perform RNAseq.

value: brain (cortex)

value: astrcocytes

value: cortical injury


title: 11astroko