title: nApoEC_HDF_3

first: Trevor

middle: R

last: Leonardo

state: Illinois

address: 801 South Paulina Street

department: Medicine

institute: University of Illinois at Chicago

data_processing:
Cutadapt and perl scripts in house (LC sciences, Houston, TX, USA) were used to remove any reads containing adapter contamination, low quality bases, and undetermined bases.
FastQC was used to verify sequence quality (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
HISAT2 was used to map reads to the mouse reference genome (ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/).
For each sample, mapped reads were assembled using StringTie (Pertea, M. et al. StringTie), which enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015), and transcriptomes were then merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
Assembly: ensembl release-96 mus_musculus (fasta)
Supplementary files format and content: tab-delimited text files include raw counts and FPKMs

source_name: Primary cells

growth_protocol: Fibroblasts were maintained in Dulbecco's Modified Eagle Medium with 10% FBS in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated and purified with a RNeasy Micro kit (QIAGEN) and treated with DNAse.
A poly (A) RNA-sequencing library was prepared by following the Illumina’s TruSeq-stranded-mRNA sample preparation protocol

treatment_protocol: Apoptotic human dermal microvascular endothelial cells expressing green fluorescent protein (GFP-HDMECs) were incubated with neonatal human dermal fibroblasts (HDFs). After incubation for 8 hours, HDFs were harvested and then sorted into two populations using fluorescent activated cell sorting (FACS). The populations were those that engulfed apoptotic GFP-HDMECs (eApoEC-HDF) and those that did not engulf apoptotic GFP-HDMECs (nApoEC-HDF). Normal untreated HDFs (N_HDF) were used as control.

value: Primary cells

value: neonatal human dermal fibroblasts

value: apoptotic human dermal microvascular endothelial cells

value: 8 hours

tag: product line

value: Cascade Biologics™

tag: catalog number

tag: sorted population


title: nApoEC_HDF_2

status: Public on Jun 01 2023

type: SRA

city: Chicago

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

tag: time

value: did not engulf apoptotic GFP-HDMECs (nApoEC-HDF)


title: ZT14-KO3-LI

city: Guangzhou

first: Min

last: Chen

state: Guangdong

address: No. 232, East Waihuan Street/Road

country: China

institute: Guangzhou university of Chinese medicine

data_processing:
Clean reads were obtained by removing those containing an adapter and ploy-N using FASTQ program, and aligned to mouse GRCm38/mm10 genome using HISAT2 v2.0.4 with default parameters.
Read counts were normalized to FPKM values using DESeq2 (v.1.16.1).
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38/mm10 genome
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: Liver

growth_protocol: 8- to 12-week-old male mice were used , and were maintained on a 12 h light/dark cycle (lights on at 7:00 AM, lights off at 7:00 PM) with free access to water and food.

extract_protocol:
RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) and its quality was checked using an Agilent 2100 Bioanalyzer (Santa Clara, CA).
Sequencing libraries were prepared using NEBNext Ultra RNA library Prep Kit for Illumina (Ipswich, MA). Sequencing was performed on an Illumina HiSeq X Ten for 150 bp length reads.

treatment_protocol: Not application.

tag: tissue

value: Liver

tag: Sex

value: male

tag: strain

tag: age

value: 8-12 weeks


title: 57878: Ileum_31_betaglucans_neonatal

type: RNA

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
201_201_2570_2

hyb_protocol: Hybridization was performed at 65°C for 17 h with head-over-head rotation. Microarrays were washed as recommended by the manufacturer.

scan_protocol: Microarrays were scanned using the Surescan high resolution scanner (Agilent Technologies) at a resolution of 3 µm, 20 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 color gene expression.

data_processing: The data were analyzed using R (v3.0.2) by executing different packages, including LIMMA and arrayQualityMetrics. The R package LIMMA from Bioconductor was used to correct for background (method=normexp and offset=1). Quantile normalization of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure: 1) select the highest of the dark spots to acquire a base value, 2) multiply by 1.1, 3) the gene/probe had to be expressed in each of the samples in the experimental condition.

organism: Sus scrofa

source_name: Ileum; 31; betaglucans; neonatal

label_protocol: Labelling of RNA was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling. 200 ng of total RNA was used as input, 600 ng of labelled cRNA was used to hybridize the porcine microarray (Agilent Technologies).

extract_protocol: Total RNA was extracted from 50 to 100 mg of mucosal scraping of jejunum, ileum, or colon tissue. Samples were homogenized using the TissuePrep Homogenizer Omni TP TH220P in 5 ml TRIzol reagent (Life Technologies). The homogenate was centrifuged for 5 min at 21,000 x g. 350 μl of supernatant was used to isolate RNA using the Direct-zol kit (Zymo Research) according to instructions of the manufacturer. Quality control was performed on the BioAnalyzer (Agilent Technologies), quantity of RNA was determined using the TapeStation (Agilent 2200 TapeStation, Agilent technologies).

value: Ileum

tag: gender

value: Female

tag: day

value: GOS

tag: route

value: neonatal

tag: animalid


title: ZT18-KO1-LI


title: 58075: Ileum_31_betaglucans_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
207_207_2394_4


title: 57883: Ileum_31_betaglucans_neonatal

value: Male


title: Liver, long-tailed macaque, rep 1

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample

organism: Macaca fascicularis

extract_protocol:
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)

treatment_protocol: The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).

value: adult

value: wild type


title: HSD 16h rep3

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

country: Finland

institute: University of Helsinki

description:
WT HSD 16h rep3
A027_27_S27_R1_001.fastq.gz

data_processing:
Sequenced reads were trimmed with Trimmomatic with parameters ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were mapped using TopHat (v2.1.0) to dmel R6.10 with parameter -p 4 and quantified with HTSeq (v2.7.6) with parameters -m HTSeq.scripts.count -m union -s reverse -a 10 -t exon -i Parent
Differentially expressed genes were calculated with R package limma with Benjamini-Hochberg correction, with genes with low counts (cpm<1 in more than one replicate) filtered
Assembly: dmel R6.10
Supplementary files format and content: Tab-delimited .xlxs file includes normalized read counts (CPM) for expressed genes for all samples and their statistics

organism: Drosophila melanogaster

source_name: whole larvae

growth_protocol: Control flies were kept in egg laying champers with apple juice plates and dry yeast for 24 h.

extract_protocol:
The larvae were homogenized with a disposable plastic pestle in lysis buffer. Total RNA was extracted using the Nucleospin RNA II kit (Macherey-Nagel) in accordance with the manufacturer’s instructions. Elution was done with water, and the samples were stored at -80 °C.
cDNA libraries were prepared from rRNA depleted samples using the TruSeq Stranded mRNA kit (Illumina). RNAseq (75 bp single end reads; reverse) was run on 2 technical replicates per sample with an average depth of 30 million reads per sample on the Illumina NextSeq500 using the 75bp cycle kit (Illumina).

treatment_protocol: First instar larvae were collected to plates with LSD (low sugar diet; 10% yeast) at a controlled density, and maintained at 25 ˚C for 24 h, after which early second instar larvae were transferred to plates containing either LSD (10% yeast) or HSD (high sugar diet; 10% yeast+15% sucrose) containing 2% blue food dye. After 4, 8 and 16 h, feeding larvae per sample were collected onto MQ/PBS plates to remove residual food from larval bodies, and snap-frozen in liquid nitrogen.

value: whole larvae

value: high sugar


title: NCI-H460 resistant #1 DMSO biol_rep_1

city: Freiburg im Breisgau

first: Sven

last: Diederichs

state: Baden Württemberg

address: Breisacherstrasse 115

department: ZTZ

country: Germany

institute: Universitätsklinikum Freiburg

description:
featureCounts on data 115 and data 124: Counts
DESeq2_normalized_counts_NCI_H460_resistant_vs_parental(DMSO_level).txt
Output_DESeq2_NCI_H460_resistant_vs_parental(DMSO_level).xlsx

data_processing:
RNA-seq data analysis was executed on the European Galaxy platform (https://usegalaxy.eu)
RNA-seq reads quality was assessed with FastQC and MultiQC. Reads were aligned to the GRCh38/hg38 human reference genome with STAR.
Aligned reads were counted using featureCounts and differentially expressed genes were identified using DESeq2.
Gene-set enrochment analysis was carried out using the DESeq2 normalized counts as the expression dataset examining the hallmark gene set collection (MSigDB, UC San Diego and Broad Institute) in the GSEA software (v4.2.3, Broad Institute).
Assembly: GRCh38/hg38
Supplementary files format and content: txt files with normalized counts
Supplementary files format and content: excel files containing DESeq2 differential gene expression analysis results of NCI-H460 resistant #1 and #2 cells compared to parental NCI-H460 cells (ATRA+DAChigh treated level or DMSO control level)

growth_protocol: NCI-H460 cells (both parental and resistant #1 and #2) were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
At 72 hours, cells were lysed and RNA was isolated using the RNeasy Mini kit (Qiagen) following the manufacturer’s quick-start protocol with the optional in-column DNase I (Qiagen) digestion step
RNA libraries for RNA-seq were prepared by the DKFZ Genomics and Proteomics Core Facility using TruSeq stranded mRNA sample prep kit (Illumina).

treatment_protocol: At the 0-hour time point, 1.5 x 105 NCI-H460 cells per well were seeded in 6-well plates (Greiner Bio-One). At 24 hours, cells were treated with 2 μM ATRA and 50 μM DAC or DMSO as control.

value: epithelial, adherent, large cell lung cancer cells

tag: cell population

value: NCI-H460 resistant #1

value: DMSO control (0.7% v/v in  RPMI-1640)

value: 72 hours


title: Cerebellum, long-tailed macaque, rep 1

source_name: Cerebellum

value: Cerebellum


title: ZT14-KO1-LI

value: Liver


title: ZT14-KO2-LI

value: male


title: Liver, long-tailed macaque, rep 2


title: nApoEC_HDF_1

value: Primary cells

value: neonatal human dermal fibroblasts

value: WT

value: apoptotic human dermal microvascular endothelial cells

value: 8 hours

tag: product line

value: Cascade Biologics™

value: did not engulf apoptotic GFP-HDMECs (nApoEC-HDF)


title: 58125: Jejunum_31_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
204_204_2613_1

source_name: Jejunum; 31; MCFA; neonatal

value: Jejunum

value: Male

value: GOS

value: neonatal


title: HSD 16h rep4

description:
WT HSD 16h rep4
A028_28_S28_R1_001.fastq.gz

value: whole larvae

value: high sugar


title: 58116: Jejunum_31_MCFA_neonatal

value: Female


title: N_HDF_3

value: No treatment

value: 0 hours

tag: catalog number

value: untreated HDFs (N_HDF) were used as control


title: N_HDF_2

value: Primary cells

tag: sorted population


title: ZT10-KO3-LI

value: Liver

value: male

value: 8-12 weeks


title: 57706: Jejunum_31_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
209_209_2411_4


title: HSD 16h rep2

description:
WT HSD 16h rep2
A026_26_S26_R1_001.fastq.gz

value: WT


title: HSD 16h rep1

description:
WT HSD 16h rep1
A025_25_S25_R1_001.fastq.gz


title: N_HDF_1

tag: cell line

value: neonatal human dermal fibroblasts

value: Cascade Biologics™


title: 57764: Jejunum_31_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
203_203_2484_3

value: Jejunum

value: betaglucans


title: ZT10-KO2-LI


title: ZT10-KO1-LI


title: eApoEC_HDF_3

tag: cell type

value: apoptotic human dermal microvascular endothelial cells

value: 8 hours

value: engulfed apoptotic GFP-HDMECs (eApoEC-HDF)


title: HSD 8h rep4

description:
WT HSD 8h rep4
A020_20_S20_R1_001.fastq.gz

value: whole larvae

tag: genotype

value: high sugar


title: 57778: Jejunum_31_MCFA_neonatal

value: Male

tag: treatment

value: neonatal


title: ZT6-KO3-LI

tag: time


title: HSD 8h rep3

description:
WT HSD 8h rep3
A019_19_S19_R1_001.fastq.gz


title: eApoEC_HDF_2


title: eApoEC_HDF_1


title: HSD 8h rep2

description:
WT HSD 8h rep2
A018_18_S18_R1_001.fastq.gz


title: ZT6-KO2-LI

tag: tissue


title: ZT6-KO1-LI

tag: Sex


title: HSD 8h rep1

description:
WT HSD 8h rep1
sample removed as outlier
A017_17_S17_R1_001.fastq.gz


title: CD4+, before, scRNAseq

city: Chiba

first: Takahiro

last: Kageyama

address: 1-8-1, Inohana

country: Japan

institute: Chiba University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequence reads from all samples were processed and aggregated using a Cell Ranger (version 6.0) (10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were freshly isolated by density gradient centrifugation from heparinized peripheral blood. Purified PBMCs were sorted into CD45+ leukocytes and CD4+ T cells fractions using a BD FACS Aria III (10,000 cells each, cell viability >98%). CD4+ T cells were stimulated with Phorbol 12-myristate 13-acetate (50 ng/ml) and ionomycin (500 nM) for 4 h in 1ml cultures.
Cells were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3.1’ Reagent Kits v3 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

value: PBMC

value: CD4+ T cells

value: before dupilumab

tag: disease state

value: Kimura disease


title: ZT2-KO3-LI

value: Liver

value: male

tag: strain

tag: age

value: 8-12 weeks


title: CD4+, after, scRNAseq

description: 10x Genomics

value: after dupilumab


title: ZT2-KO2-LI


title: CD45+, after, scRNAseq

description: 10x Genomics

value: CD45+ cells


title: 57696: Jejunum_31_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
202_202_2566_2

value: Jejunum

tag: gender

value: Female

tag: day

value: betaglucans


title: 57693: Jejunum_31_MCFA_neonatal

tag: route

tag: animalid


title: 57853: Ileum_31_CONTROL_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
107_107_2406_4

source_name: Ileum; 31; CONTROL; neonatal

value: Ileum


title: HSD 4h rep4

description:
WT HSD 4h rep4
A008_8_S8_R1_001.fastq.gz

value: whole larvae

value: WT


title: ZT2-KO1-LI


title: HSD 4h rep3

description:
WT HSD 4h rep3
A007_7_S7_R1_001.fastq.gz

value: high sugar


title: HSD 4h rep2

description:
WT HSD 4h rep2
sample removed as outlier
A006_6_S6_R1_001.fastq.gz


title: HSD 4h rep1

description:
WT HSD 4h rep1
A005_5_S5_R1_001.fastq.gz


title: ZT22-WT3-LI


title: CD45+, before, scRNAseq

description: 10x Genomics


title: LV-2

city: Lund

first: Yang

last: Liu

address: A12 BMC

country: Sweden

institute: Lund University, Stem Cell Center

data_processing:
The cell Ranger software pipeline (version 3.1.0) provided by 10x Genomic was used to demultiplex cellular barcodes, map reads to the human reference genome (refdata-cellranger-GRCh38-3.0.0) (command cellranger count).
Assembly: GRCh38 3.0.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: cord blood

extract_protocol:
The cDNA sample was prepared according to the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index), with using all the included reagents.
Indexed libraries were pooled at equimolarity and sequenced on an Illumina NovaSeq 6000 with read setup 28-10-10-90. Coverage of approximately 100,000 reads per single cells were obtained.

value: cord blood

value: CD34+ hematopoietic stem and progenitor cells

value: RPS19 transgene

value: Erythroid differentiation


title: LV-1


title: LSD 8h rep4

description:
WT LSD 8h rep4
A004_4_S4_R1_001.fastq.gz

value: low sugar


title: 58069: Ileum_31_CONTROL_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
106_106_2496_3

source_name: Ileum; 31; CONTROL; maternal

value: Male

value: MCFA

value: neonatal


title: 57829: Ileum_31_CONTROL_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
104_104_2609_1


title: 57857: Ileum_31_CONTROL_maternal


title: ZT22-WT2-LI

value: Liver

value: male

value: 8-12 weeks


title: 57841: Ileum_31_CONTROL_maternal


title: RPS19-D-2


title: LSD 8h rep3

description:
WT LSD 8h rep3
A003_3_S3_R1_001.fastq.gz


title: ZT22-WT1-LI


title: RPS19-D-1


title: 58062: Ileum_31_CONTROL_neonatal

value: Female


title: ZT18-WT3-LI


title: 57818: Ileum_31_CONTROL_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
101_101_2569_2


title: LSD 8h rep2

description:
WT LSD 8h rep2
A002_2_S2_R1_001.fastq.gz


title: Control


title: ZT18-WT2-LI


title: LSD 8h rep1

description:
WT LSD 8h rep1
A001_1_S1_R1_001.fastq.gz


title: ZT18-WT1-LI


title: MUT HSD rep4

data_processing:
Sequenced reads were trimmed with Trimmomatic with parameters ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36
Sequences were mapped using TopHat (v2.1.0) to dmel R6.10 with parameter -p 4 and quantified with HTSeq (v2.7.6) with parameters -m HTSeq.scripts.count -m union -s reverse -a 10 -t exon -i Parent
Differentially expressed genes were calculated with R package limma with Benjamini-Hochberg correction, with genes with low counts (cpm<1 in more than one replicate) filtered
Assembly: dmel R6.10
Supplementary files format and content: Excel (.xlxs file) includes normalized read counts (CPM) for expressed genes for all samples and their statistics

growth_protocol: Control and cwoB9 flies were kept in egg laying champers with apple juice plates and dry yeast for 24 h.

treatment_protocol: First instar larvae were collected to plates with LSD (low sugar diet; 10% yeast) at a controlled density, and maintained at 25 ˚C for 24 h, after which early second instar larvae were transferred to plates containing either LSD (10% yeast) or HSD (high sugar diet; 10% yeast+15% sucrose) containing 2% blue food dye. After 8h, feeding larvae per sample were collected onto MQ/PBS plates to remove residual food from larval bodies, and snap-frozen in liquid nitrogen.

value: CWO


title: 57760: Colon_31_CONTROL_neonatal

source_name: Colon; 31; CONTROL; neonatal

value: Colon

value: CONTROL


title: K30Nap

first: Yiqiu

last: Li

state: State...

address: College of Pharmacy, Sun Yat-sen University

institute: Sun Yat-sen University

data_processing:
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Assembly: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer??s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Kyse150 or Kyse30 cells were cultured in DMEM medium with 10% fetal bovine serum (FBS), 100IU/mL penicillin and 100 μg/mL streptomycin, in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Kyse150 or Kyse30 cells were infected by Fn (the MOI of 1:10) or treated with Fn-Dps (1 μM) for 48 h

value: esophageal carcinoma cells

value: WT

value: treated with Fn-Dps (1 μM) for 48 h


title: ZT14-WT3-LI


title: MUT HSD rep3

value: whole larvae

value: high sugar


title: ZT14-WT2-LI


title: MUT HSD rep2


title: K150Fn

value: infected by Fn (the MOI of 1:10) for 48 h


title: K30Con

value: without any treatment


title: ZT14-WT1-LI


title: MUT HSD rep1


title: K150Con


title: ZT10-WT3-LI


title: 57827: Ileum_31_CONTROL_maternal

value: Ileum

value: Male


title: 58069: Colon_31_CONTROL_maternal

source_name: Colon; 31; CONTROL; maternal

value: maternal


title: K30Fn


title: 57857: Colon_31_CONTROL_maternal


title: MUT LSD rep4

value: low sugar


title: radiation 2 week, 2 Gy rep3

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

description:
MSC_all_raw_counts.txt
MSC_2Gy_norm_counts_table.txt
MSC2GR3

data_processing:
Raw sequencing data were demuxed using bcl2fastq2 conversion software.
Raw paired-end sequencing reads were aligned to the human reference genome (hg38) using MapSplice version 2.2.2.
Gene read counts against GENCODE v28 basic gene models were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_id -s reverse
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Assembly: hg38
Supplementary files format and content: MSC_all_raw_counts.txt - tab-delimited text file of gene raw counts for all samples
Supplementary files format and content: MSC_1Gy_norm_counts_table.txt - tab-delimited text file of normalized gene read counts (DESeq size factor normalization) for 1Gy samples (controls and treated)
Supplementary files format and content: MSC_2Gy_norm_counts_table.txt - tab-delimited text file of normalized gene read counts (DESeq size factor normalization) for 2Gy samples (controls and treated)

source_name: bone marrow

growth_protocol: Human bone marrow mesenchymal stem cells (MSC) were purchased from Lonza (Morristown, NJ, USA) and cultured in mesenchymal stem cell growth medium (Lonza). Cells were used within seven passages for all experiments. For irradiations, cells were plated in 25 ml flasks or in Lab-Tek Flaskette Chamber slides (ThermoFisher Scientific, Waltham, MA), and grown to 60-70% confluence.

extract_protocol:
Immediately following irradiation, total RNA was isolated from MSC using the RNeasy Mini Kit with on-column DNase digestion (Qiagen) according to manufacturer’s protocol. RNA was quantified spectroscopically (ND-1000 Spectrophotometer, Nano-Drop, Wilmington, DE, USA).
Sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Samples were sequenced using a NovaSeq 6000 instrument (Illumina, San Diego, CA).

treatment_protocol: Cells were irradiated in the Armed Forces Radiobiology Research Institute (AFRRI) Low Level Cobalt Facility at 0.66 cGy/h to reach a total irradiation of 0.3, 0.7, 1, or 2 Gy. Dosimetry for Low Level Cobalt Facility was performed by preliminary mapping of irradiation field inside the cell culture incubator.

value: bone marrow

value: primary

value: mesenchymal stem cell

value: 2 Gy radiation, 2 week


title: ZT10-WT2-LI

value: Liver

value: male

value: 8-12 weeks


title: 57829: Colon_31_CONTROL_neonatal

value: Colon

value: Female

value: CONTROL

value: neonatal


title: 57827: Colon_31_CONTROL_maternal


title: 58062: Colon_31_CONTROL_neonatal


title: MUT LSD rep3

value: whole larvae

value: CWO


title: radiation 2 week, 2 Gy rep2

description:
MSC_all_raw_counts.txt
MSC_2Gy_norm_counts_table.txt
MSC2GR2


title: ZT10-WT1-LI


title: MUT LSD rep2


title: radiation 2 week, 2 Gy rep1

description:
MSC_all_raw_counts.txt
MSC_2Gy_norm_counts_table.txt
MSC2GR1


title: ZT6-WT3-LI


title: 57818: Colon_31_CONTROL_neonatal


title: MUT LSD rep1


title: control 2 week rep2

description:
MSC_all_raw_counts.txt
MSC_2Gy_norm_counts_table.txt
MSC2GC2

value: 2 Gy, 2 week control


title: control 2 week rep3

description:
MSC_all_raw_counts.txt
MSC_2Gy_norm_counts_table.txt
MSC2GC3


title: CTRL HSD rep3

value: CTRL

value: high sugar


title: ZT6-WT1-LI


title: CTRL HSD rep2


title: ZT2-WT3-LI


title: control 2 week rep1

description:
MSC_all_raw_counts.txt
MSC_2Gy_norm_counts_table.txt
MSC2GC1


title: radiation 1 week, 1 Gy rep3

description:
MSC_all_raw_counts.txt
MSC_1Gy_norm_counts_table.txt
MSC1GR3

value: 1 Gy radiation, 1 week


title: ZT2-WT2-LI


title: 57853: Jejunum_31_CONTROL_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
107_107_2406_4

source_name: Jejunum; 31; CONTROL; neonatal

value: Jejunum

value: maternal


title: CTRL HSD rep1


title: 57857: Jejunum_31_CONTROL_maternal

source_name: Jejunum; 31; CONTROL; maternal

value: Male


title: 58069: Jejunum_31_CONTROL_maternal


title: CTRL LSD rep4

value: low sugar


title: ZT2-WT1-LI

value: Liver


title: 57829: Jejunum_31_CONTROL_neonatal


title: CTRL LSD rep3


title: 57841: Jejunum_31_CONTROL_maternal


title: CTRL HSD rep4


title: control 1 week rep3

description:
MSC_all_raw_counts.txt
MSC_1Gy_norm_counts_table.txt
MSC1GC3

value: bone marrow

value: primary

value: mesenchymal stem cell

value: 1 Gy, 1 week control


title: Th2, Dopamine, rep2

first: Xingbin

last: Ai

state: MA

address: 55 Fruit St

department: Pediatrics

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
Raw reads were pre-processed using FastQC v.0.11.2 and mapped to the mouse genome (Mus musculus UCSC version mm10) using the TopHat version 2.0.13.
The read count table was produced using HTSeq v.0.6.
Differentially expressed genes were identified based on an adjusted p-value less than 0.05 using DESeq2 package in R-3.6.2.
Assembly: mm10
Supplementary files format and content: csv

source_name: Spleen

extract_protocol:
Total RNA isolation using a RNeasy kit (QIAGEN, Cat# 74106).
cDNA libraries were prepared with the TruSeq Stranded mRNA Library kit (Illumina, Cat# 20020594).

treatment_protocol: we apply bulk RNA-seq to test the transcriptome changes in mouse Th2 cells after dopamine treatment  (10μM).

value: Spleen

value: Th2 cell

value: Dopamine (10uM)


title: 58062: Jejunum_31_CONTROL_neonatal

value: Female

value: CONTROL

value: neonatal


title: ZT6-WT2-LI

value: male

value: 8-12 weeks


title: 57827: Jejunum_31_CONTROL_maternal

value: Jejunum


title: 57818: Jejunum_31_CONTROL_neonatal


title: control 1 week rep2

description:
MSC_all_raw_counts.txt
MSC_1Gy_norm_counts_table.txt
MSC1GC2


title: Th2, Dopamine, rep1


title: CTRL LSD rep1

value: whole larvae

value: CTRL


title: radiation 1 week, 1 Gy rep2

description:
MSC_all_raw_counts.txt
MSC_1Gy_norm_counts_table.txt
MSC1GR2

value: 1 Gy radiation, 1 week


title: Th2, PBS, rep1

value: PBS


title: 57964: Colon_1_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
709_709_2407_4

source_name: Colon; 1; GOS; maternal

value: Colon

value: Male

value: maternal


title: radiation 1 week, 1 Gy rep1

description:
MSC_all_raw_counts.txt
MSC_1Gy_norm_counts_table.txt
MSC1GR1

value: bone marrow

value: primary

value: mesenchymal stem cell


title: 57977: Colon_1_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
704_704_2565_2


title: Mutant replicate4

first: Yanhui

last: Hu

department: Genetics

institute: Harvard Medical School

description: Poly-A selected mRNA

data_processing:
FastQC was used for sequencing data quality control and MultiQC was used to aggregate the results.
Sequenced reads were aligned to the mm10 reference genome assembly and gene counts were quantified using STAR
Differential gene expression testing was performed by DESeq2
Genome_build: Flybase genome annotation version r6.30
Supplementary_files_format_and_content: text files include read counts for each sample

source_name: Adult thorax

growth_protocol: Crosses were kept at 18°C to avoid expression of REPTOR during development. Adult males were collected every 24-48 hours and incubated 3-4 days at 18°C before being shifted to 29°C

extract_protocol:
5-6 thoraces dissected out from the flies incubated for 4 days at 29°C, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eclosed male flies were incubated for 4 days at 29°C

value: tub-Gal80ts; dMef2-GAL4 x UAS-REPTOR[ACT]

value: thorax


title: Mutant replicate3

description: Poly-A selected mRNA


title: IL4_1_adipocyte_precursor_miRNAseq

city: Bongmyeongdong

first: Mihye

last: Lee

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

data_processing:
RNA-seq
From mRNA sequencing, low-quality raw sequence reads, reads with adapters, and reads with unknown bases were filtered by SOAPnuke software to yield clean reads.
Filtered clean reads were mapped into the reference mouse genome (mm10) using HISAT.
Novel genes predicted using StringTie and Cuffcompare to compare the reconstructed transcripts to the reference annotation and then used CPC tools to predict the novel transcripts.
Gene expression level for each sample was determined using the tools Bowtie2 and RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
miRNA-seq
Small RNA raw sequencing reads are filtered based on their quality.
The readings are aligned to the reference mouse genome (mm10) and miRBase v21 precursor miRNAs to find known and novel miRNAs.
The miRDeep2 algorithm is then used to predict potential hairpin structures.
Unique cluster reads are then sequentially matched against the reference mouse genome, miRBase v21, and the non-coding RNA database, Rfam9.1 to classify known miRNAs.
Read counts for each miRNA are extracted from mapped miRNAs to report the abundance of each miRNA.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Subcutaneous white adipose tissue

extract_protocol:
The total RNA of the samples was extracted with the Trizol (Invitrogen) reagent and used for construction of sequencing libraries.
miRNA libraries for miRNA-seq were prepared using TruSeq Small RNA Library Prep Kit following manufacturer's protocols.

value: Subcutaneous white adipose tissue

value: Adipocyte precursor

value: IL4 treatment


title: Mutant replicate2

description: Poly-A selected mRNA


title: control 1 week rep1

description:
MSC_all_raw_counts.txt
MSC_1Gy_norm_counts_table.txt
MSC1GC1

value: 1 Gy, 1 week control


title: Mutant replicate1

description: Poly-A selected mRNA


title: 21_FMOcm_SenNeur

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: human iPSC derived sensory neuorns, forskolin+mannose+oncomodulin

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mouse genome using STAR spliced read aligner
Count read using HT-seq with GRCh38 as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using egdeR.
Assembly: GRCh38
Supplementary files format and content: Counts

source_name: iPSC derived sensory neurons

growth_protocol: Human periphery blood monocytes (ATCC, Cat. # PCS-800-010) were culture with chemically defined monocyte attachment medium. Human iPSCs were maintained under feeder-free conditions in Essential 8(E8) cell culture medium and were differentiated into sensory neurons by treating with Noci-1, Noci-2 and Noci-3 medium, etc until maturation.

extract_protocol:
The total RNA was extracted from cell lysate in QIAzol® (Qiagen). Briefly, 180 ul chloroform was added to 800 – 900 ul of cell lysate and mixed. The mixture was centrifuged at 12,000 g for 15 minutes at 4 0C. The clear upper aqueous layer was transferred to a new tube and mixed with an equal volume of 70% ethanol. The extraction was continued using the RNeasy MinElu column (Qiagen). The extracted RNA was examined on High Sensitivity RNA Screen Tape (Agilent) before use.
The RNA-seq libraries were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) followed by Nextera XT DNA Library Preparation Kit (Illumina) according to manufactures’ instructions. Libraries were indexed and sequenced over 1 lane using S4 flowcell of NovaSeq 6000 (Illumina) with 2x100-bp paired end reads.

treatment_protocol: Human monocytes and sensory neurons were treated with control vehicle, forskolin, mannose and/or Ocm for 5 hours and 24 hours resepctively.

value: iPSC derived sensory neurons

value: F+M+oncomodulin


title: 24_FMOcm_SenNeur


title: CTRL LSD rep2

source_name: whole larvae

value: whole larvae

value: CTRL

value: low sugar


title: control_1_adipocyte_precursor_miRNAseq

value: control


title: 57947: Colon_1_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
710_710_2302_7

value: Colon

value: Male

value: CONTROL

value: neonatal


title: Th2, PBS, rep2

value: Spleen

value: Th2 cell

value: PBS


title: 58214: Ileum_1_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
701_701_2611_1

source_name: Ileum; 1; betaglucans; maternal

value: Ileum


title: 57680: Colon_1_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
708_708_2561_2

value: maternal


title: 22_FMOcm_SenNeur


title: 57790: Colon_1_GOS_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
705_705_2607_1


title: IL4_2_adipocyte_precursor_miRNAseq

value: Subcutaneous white adipose tissue

value: Adipocyte precursor

value: IL4 treatment


title: 58143: Ileum_1_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
702_702_2562_2

value: Female


title: Wild type replicate4

description: Poly-A selected mRNA

value: tub-Gal80ts; dMef2-GAL4 x w[1118]

value: thorax


title: 20_FM_SenNeur

description: human iPSC derived sensory neuorns, forskolin+mannose

value: iPSC derived sensory neurons

value: forskolin+mannose


title: 58192: Ileum_1_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
703_703_2464_3


title: Wild type replicate3

description: Poly-A selected mRNA


title: 23_FMOcm_SenNeur

value: F+M+oncomodulin


title: Wild type replicate2

description: Poly-A selected mRNA


title: 19_FM_SenNeur


title: control_2_adipocyte_precursor_miRNAseq

value: control


title: 57841: Colon_31_CONTROL_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
104_104_2609_1

value: Colon

value: Male

value: CONTROL


title: Wild type replicate1

description: Poly-A selected mRNA


title: 17_FM_SenNeur


title: NDRG1-EGFP LMNA KO [KO20424]

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

description:
KO20424
chromatin

library_source: genomic

data_processing:
Raw sequencing paired-end files were aligned by STAR (v2.7.0.e) (Dobin et al. 2013) to the mm10 reference genome using the following parameters: --alignIntronMax 1 --out FilterMismatchNmax 100 --alignEndsType EndToEnd --out FilterScoreMinOverLread 0.3 --out FilterMatchNminOverLread 0.3. This yielded for each sample a BAM file of mapped paired-end reads sorted by genomic coordinates. From these BAM-files, we removed reads that were mapped to multiple loci or to the mitochondrial genome using samtools (v0.1.19) (Li et al. 2009) as well as the duplicated reads using PICARD (v2.24; http://broadinstitute.github.io/picard). The read coverage files (bedGraph) were generated by genomeCoverageBed from BEDTools (v2.25.0) (Quinlan and Hall 2010) and converted to the indexed binary format files (bigWig) using bedGraphToBigWig. TSS enrichment was calculated by ataqv package (Orchard et al. 2020) using TSS positions of 2,816 housekeeping genes.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bigWig files

molecule: genomic DNA

source_name: sorted myelinating oligodendrocytes

growth_protocol: Mouse breeding scheme to obtain desired populations of sorted cells: The myelinating oligodendrocyte reporter line Ndrg1-EGFP mice (Marechal et al., 2021) were bred with Cnp-cre+/+;Lmnafl/fl mice to obtain NDRG1-EGFP LMNA WT or with Cnp-cre cre/+; Lmnafl/fl mice to obtain NDRG1-EGFP LMNA KO.

extract_protocol:
Sorting protocol: Oligodendrocytes were sorted from P8 weeks NDRG1_EGFP-LMNA WT and KO brains, using fluorescence-activated cell sorting as described (Moyon et al., 2021). Tissue was dissected in HBSS 1X (HBSS 10X (Invitrogen), 0.01 M HEPES buffer, 0.75% sodium bicarbonate (Invitrogen), and 1% penicillin/streptomycin) and mechanically dissociated. After an enzymatic dissociation step using papain (30 μg/ml in DMEM-Glutamax, with 0.24 μg/ml L-cysteine and 40 μg/ml DNase I), samples were layered over a pre-formed Percoll density gradient and then centrifuged for 15 min. Cells were then collected and stained with propidium iodide (PI) for 2 min at room temperature (RT) to exclude dead cells. In a second step, GFP-positive and PI-negative cells were sorted by fluorescence-activated cell sorting (FACS; Aria, Becton Dickinson) and collected in pure fetal bovine serum.
ATAC-seq reactions were performed using an established protocol (Buenrostro et al. 2013). Briefly, each sample consisted of 65000 oligodendrocyte cells sorted from the brain of NDRG1-EGFP LMNAWT or NDRG1-EGFP LMNAKO. To each cell pellet, added 25 ul of TD buffer ( 2X reaction buffer from Nextera Kit); 2.5 ul of TDE1 (Nextera TN5 Transposase from Nextera Kit) and 22.5 ul of Nuclease-free H2O. Keep at 37 degrees in gentle mixing for 30 minutes. DNA elution using Qiagen mini-elution kit.
To each 10 ul of transposed DNA, 10 ul of nuclease free H2O, 2.5 ul of 25uM PCR Primer 1, 2.5 ul od 25uM Barcoded PCR Primer 2 and 25ul of NEBNext High Fidelity 2x PCR Master mix, were added. Libraries were amplified using the Nextera index kit (Illumina Cat #FC-121-1011), under the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute for a total of 5 cycles. To avoid saturation due to over-amplification, a 10% aliquot of this reaction was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 90%. The additional number of cycles was determined as follows: (1) Plot linear Rn vs. Cycle (2) Calculate the # of cycles that corresponded to 1⁄4 of maximum fluorescent intensity. In general, we found adding 4 cycles to this estimate yielded optimal ATACseq libraries, as determined by analysis on Agilent D5000 screen tapes (Agilent Technologies Cat#5067-5588 and Cat#5067-5589). Libraries were amplified for a total of 13–15 cycles. Following PCR, ATACseq libraries were resolved on 2% agarose gels and fragments ranging in size from 100bp-1.5Kbp were excised and purified (Qiagen Minelute Gel Extraction Kit – Qiagen Cat#28604). Libraries were quantified by quantitative PCR (KAPA Biosystems Cat#KK4873) prior to sequencing. Libraries were sequenced on Hi-Seq2500 (Illumina) obtaining 2x50 paired-end reads.

value: NDRG1-EGFP LMNA KO

value: P8 weeks

value: sorted myelinating oligodendrocytes


title: NDRG1-EGFP LMNA KO [KO10424]

description:
KO10424
chromatin


title: NDRG1-EGFP LMNA KO [KO10523]

description:
KO10523
chromatin


title: NDRG1-EGFP LMNA KO [KO20523]

description:
KO20523
chromatin


title: T38R-yki

description: rRNA depletion

source_name: adult thorax

growth_protocol: Crosses were kept at 18°C to avoid expression of yki during development. Adult males were collected every 24-48 hours and incubated at 29°C to induce yki-tumors in the gut. For the recovery phase, flies were incubated at 29°C for 14 days and then shifted back to 18°C for several days.

extract_protocol:
8-10 thoraces dissected out from the flies either during the tumor induction phase (29°C) or tumor recovery (18°C) and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eclosed male flies were incubated at 29°C for tumor induction and then shifted back to 18°C for tumor shutdown

tag: time course

value: day38 recover


title: NDRG1-EGFP LMNA WT [WT30424]

description:
WT30424
chromatin

value: NDRG1-EGFP LMNA WT


title: T26R-yki

description: rRNA depletion

value: day26 recover


title: T20R-yki

description: rRNA depletion

value: day20 recover


title: 58039: Ileum_1_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
608_608_2495_3

value: Ileum

value: neonatal


title: 14_Ctrl_SenNeur

description: human iPSC derived sensory neuorns, control


title: 58006: Ileum_1_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
609_609_2606_1


title: 16_Ctrl_SenNeur


title: 12_FMOcm_PriMono

description: human primary monocytes, forskolin+mannose+oncomodulin

source_name: peripheral blood

value: peripheral blood

value: primary monocytes


title: 57811: Jejunum_1_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
602_602_2608_1

source_name: Jejunum; 1; MCFA; maternal

value: Jejunum

value: MCFA


title: NDRG1-EGFP LMNA KO [KO0227]

description:
KO0227
chromatin


title: T32R-yki

description: rRNA depletion

value: thorax

value: day32 recover


title: 13_Ctrl_SenNeur

value: iPSC derived sensory neurons

value: control


title: 15_Ctrl_SenNeur


title: NDRG1-EGFP LMNA WT [WT20523]

description:
WT20523
chromatin


title: 11_FMOcm_PriMono

value: F+M+oncomodulin


title: 18_FM_SenNeur

value: forskolin+mannose


title: 57940: Jejunum_1_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
603_603_2303_7

value: Male


title: T14-yki

description: rRNA depletion


title: T38R-wt

description: rRNA depletion

value: esg-Gal4, tub-Gal80ts, UAS-GFP/+

value: day38 recover


title: 10_FMOcm_PriMono


title: 57913: Jejunum_1_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
601_601_2395_4

value: betaglucans


title: NDRG1-EGFP LMNA WT [WT0227]

description:
WT0227
chromatin

value: NDRG1-EGFP LMNA WT

value: P8 weeks

value: sorted myelinating oligodendrocytes


title: 57758: Jejunum_1_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
108_108_2616_1

value: neonatal


title: 57924: Ileum_1_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
610_610_2365_5

value: Ileum

value: CONTROL

value: maternal


title: 58174: Jejunum_1_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
606_606_2510_3

value: Jejunum


title: NDRG1-EGFP LMNA WT [WT10523]

description:
WT10523
chromatin


title: T8-yki

description: rRNA depletion

value: thorax


title: NDRG1-EGFP LMNA WT [WT10424]

description:
WT10424
chromatin


title: 58185: Jejunum_1_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
605_605_2615_1


title: T2-wt

description: rRNA depletion


title: T14-wt

description: rRNA depletion


title: T2-yki

description: rRNA depletion


title: RAW264.7 cells Ti rep3

city: Jinan

first: yonghui

last: jiang

address: #44 Wenhuaxi Road

institute: Shandong University

data_processing:
The obtained clean reads were compared and analyzed by Hisat2 software.
Stringtie software was used to assemble the results of the comparison. After that, we use Cuffmerge software to merge and compare the transcripts obtained by the splicing of each sample.
Ensembl database was used to filter out the known transcripts, and the selected new transcripts without coding potential served as novel lncRNAs.
The circRNA was identified by using find_circ and CIRI. Finally, the candidate circRNA with read count greater than or equal to 2 was used as the identified circRNA.
Take the miRBase20.0 database as a reference, mirdeep2 was used to obtain the potential miRNA. miREvo and mirdeep2 were integrated to predict the novel miRNA.
Genome_build: mm9
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: macrophages

extract_protocol:
Total RNA was extracted from specific cultured RAW 264.7 cells using TRIzol reagent (Invitrogen, California, USA) according to the manufacturer’s instructions. RNA concentration was measured in Qubit 2.0 Flurometer (Life Technologies, CA, USA) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: macrophages

tag: background strain

value: Ti particles


title: RAW264.7 cells Ti rep2


title: RAW264.7 cells Ti rep1


title: NDRG1-EGFP LMNA WT [WT20424]

description:
WT20424
chromatin


title: AAV-Isl1 followed by noise exposure, (n=5), scRNA-seq

first: Volkan

last: Ergin

address: 243 Charles St.

department: Otolaryngology, Harvard Medical School

institute: Massachusetts Eye and Ear

description: 10x Genomics

data_processing:
Transcriptome sequencing analysis and read mapping were performed using CellRanger pipeline (v5.0; 10X Genomics) according to the manufacturer’s guidelines. Raw sequencing reads processed by CellRanger were demultiplexed and mapped to the mouse reference genome (mm10, GRCm38) using STAR. CellRanger-generated count matrices were loaded into Seurat v3.2.2 for downstream analysis.
Assembly: mm10, GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Inner ear cochlea

growth_protocol: In experimental group, we treated WT CBA/CaJ adult cochlear with the ISL1 (e12 GC/ml) followed by noise exposure. Two days later, we dissected sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. The untreated contralateral ears from the same mice were used as control group.

extract_protocol:
Sensory epithelium from cochlear explants was dissociated to single cells using 0.25% trypsin-EDTA for 15 min incubation at 37C. Tissues were gently singularized by P1000 pipette in a complete medium (DMEM/F12 medium containing 10% FBS). Cells were strained twice through 40 mm mesh into 5 ml medium, spun down for 5 min at 300 g to pellet, and resuspended in 50 ml of complete medium. Roughly 1600 cells were loaded onto a 10X Chip-G for a target recovery of 1000 cells. Single cells from NIHL-only (n=5) and AAV-Isl1-treated (n=5) groups were captured separately to prepare libraries.
Single-cell suspensions were immediately transferred to individual channels of the chip (Chromium Next GEM Chip G) to generate gel beads in emulsion together with reverse transcription master mix on the droplet-based high-throughput Chromium Controller (10X Genomics) allowing cell lysis, individual cell barcoding, and reverse transcription by Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000128). Briefly, single-cell library preparation was carried out by emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter, and Illumina sample index addition following the manufacturer's protocol. The single-cell derived cDNA libraries were then assessed with a bioanalyzer (High Sensitivity DNA Kit, Agilent 2100 Bioanalyzer) for quality control. Following library preparation, next-generation sequencing was performed with paired-end sequencing of 150 bp each end using Illumina HiSeqXTen (Novogene Inc.).

treatment_protocol: The intensity of 105dB, 1-20kHz noise was given to the mice for 2 hours.

value: Sensory epithelium

value: Inner ear cochlea

value: CBA/CaJ

value: 4-6 weeks old


title: 7_FM_PriMono

description: human primary monocytes, forskolin+mannose

value: peripheral blood

value: primary monocytes

value: forskolin+mannose


title: 9_FMOcm_PriMono

value: F+M+oncomodulin


title: 6_FM_PriMono


title: 5_FM_PriMono

description: human primary monocytes, forskolin+manose

value: forskolin+mannose (F+M)


title: 4_Ctrl_PriMono

description: human primary monocytes, control

value: control


title: 8_FM_PriMono


title: RAW264.7 cells Ctrl rep2

value: PBS


title: 57747: Jejunum_1_MCFA_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
604_604_2563_2

value: Male

value: MCFA

value: neonatal


title: RAW264.7 cells Ctrl rep3


title: RAW264.7 cells Ctrl rep1


title: Drug-treatment followed by noise exposure, (n=5), scRNA-seq

description: 10x Genomics

growth_protocol: In experimental group, we treated WT C57bl/6j adult cochleae with the Drug (90mg/ml) followed by noise exposure. Two days later, we dissected sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. The untreated contralateral ears from the same mice were used as control group (NIHL; Noise-only). NIHL (Noise-only; n=5) vs. Drug-NIHL (n=5).

extract_protocol:
Sensory epithelium from cochlear explants was dissociated to single cells using 0.25% trypsin-EDTA for 15 min incubation at 37C. Tissues were gently singularized by P1000 pipette in a complete medium (DMEM/F12 medium containing 10% FBS). Cells were strained twice through 40 mm mesh into 5 ml medium, spun down for 5 min at 300 g to pellet, and resuspended in 50 ml of complete medium. Roughly 20000 cells were recovered from both groups after 10X Chip-G running. Single cells from cochlea pretreated with Drug before noise exposure and untreated (noise-exposed-only) cochleae were captured separately to prepare cDNA libraries. NIHL (Noise-only; n=5) vs. Drug-NIHL (n=5).
Single-cell suspensions were immediately transferred to individual channels of the chip (Chromium Next GEM Chip G) to generate gel beads in emulsion together with reverse transcription master mix on the droplet-based high-throughput Chromium Controller (10X Genomics) allowing cell lysis, individual cell barcoding, and reverse transcription by Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000128). Briefly, single-cell library preparation was carried out by emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter, and Illumina sample index addition following the manufacturer's protocol. The single-cell derived cDNA libraries were then assessed with a bioanalyzer (High Sensitivity DNA Kit, Agilent 2100 Bioanalyzer) for quality control. Following library preparation, next-generation sequencing was performed with paired-end sequencing of 150 bp each end using Illumina HiSeqXTen (Novogene Inc.).

treatment_protocol: The intensity of 105dB, an octave band of 8-16kHz noise was given to the mice for 2 hours. Two days later, we dissected sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. The untreated contralateral ears from the same mice were treated as control group (NIHL; Noise-only).


title: Noise exposure-only, (n=5), scRNA-seq

description: 10x Genomics


title: 58227: Colon_1_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
206_206_2610_1

source_name: Colon; 1; GOS; neonatal

extract_protocol: Total RNA was extracted from 50 to 100 mg of mucosal scraping of jejunum, ileum, or colon tissue. Samples were homogenized using the TissuePrep Homogenizer Omni TP TH220P in 5 ml TRIzol reagent (Life Technologies). The homogenate was centrifuged for 5 min at 21,000 x g. 350 μl of supernatant was used to isolate RNA using the Direct-zol kit (Zymo Research) according to instructions of the manufacturer. Quality control was performed on the BioAnalyzer (Agilent Technologies), quantity of RNA was determined using the TapeStation (Agilent 2200 TapeStation, Agilent technologies).

value: Colon


title: 3_Ctrl_PriMono

description: human primary monocytes, control


title: Vehicle (sterile water)-treatment followed by ad.Atoh1 infection, (n=5), scRNA-seq

description: 10x Genomics

growth_protocol: The bulla was first removed from the skull and dipped in 75% ethanol for 3 mins before being placed in HBSS. Under a dissecting microscope, the vestibular region, the middle ear, vessels, and the debris were removed from the bulla. The bone covering the apical turn was removed, and round window and oval window membranes were opened to allow media exchange with the cochlear fluids. The ligament portion and Reissner’s membrane at each end of the cochlea were also removed to facilitate the access of the medium to the sensory epithelial region. The cochlea explants were maintained in DMEM/F12 medium supplemented with N2 and B27 over the course of the experiment.

extract_protocol:
Sensory epithelium from cochlear explants was dissociated to single cells using 0.25% trypsin-EDTA for 15 min incubation at 37C. Tissues were gently singularized by P1000 pipette in a complete medium (DMEM/F12 medium containing 10% FBS). Cells were strained twice through 40 mm mesh into 5 ml medium, spun down for 5 min at 300 g to pellet, and resuspended in 50 ml of complete medium. Roughly, 3000 cells of Dox, 1100 cells of Vehicle samples were recovered from 10X Chip-G. Single cells from cochlear cultures of Dox plus adAtoh1 (n=5) and Vechicle plus ad.Atoh1 (n=5) groups were captured separately to prepare NGS libraries for the samples.
Single-cell suspensions were immediately transferred to individual channels of the chip (Chromium Next GEM Chip G) to generate gel beads in emulsion together with reverse transcription master mix on the droplet-based high-throughput Chromium Controller (10X Genomics) allowing cell lysis, individual cell barcoding, and reverse transcription by Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000128). Briefly, single-cell library preparation was carried out by emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter, and Illumina sample index addition following the manufacturer's protocol. The single-cell derived cDNA libraries were then assessed with a bioanalyzer (High Sensitivity DNA Kit, Agilent 2100 Bioanalyzer) for quality control. Following library preparation, next-generation sequencing was performed with paired-end sequencing of 150 bp each end using Illumina HiSeqXTen (Novogene Inc.).

treatment_protocol: In the rtTA/tet-Myc/tet-NICD mouse model, cochlea explants were treated with Dox (2 μg/ml final concentration) or sterile water in complete medium for 4 days followed by ad.Atoh1 infection for 2 weeks.


title: Kidney, baboon, rep 6

organism: Papio anubis

source_name: Kidney

extract_protocol:
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)

value: Kidney

value: male

value: adult

value: wild type


title: 58149: Colon_1_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
110_110_2405_4

value: Female


title: Brain, baboon, rep 6

source_name: Brain

value: Brain


title: 58223: Colon_1_GOS_neonatal


title: 1_Ctrl_PriMono

description: human primary monocytes, control

value: peripheral blood


title: 58110: Colon_1_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
109_109_2476_3

value: CONTROL

value: maternal


title: Dox-treatment followed by ad.Atoh1 infection, (n=5), scRNA-seq

description: 10x Genomics

value: Sensory epithelium

value: Inner ear cochlea

value: 4-6 weeks old


title: 58025: Ileum_1_betaglucans_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
607_607_2346_6

value: Ileum


title: 2_Ctrl_PriMono

description: human primary monocytes, control

value: primary monocytes

value: control


title: 58100: Colon_1_GOS_neonatal

value: neonatal


title: Liver, baboon, rep 5

source_name: Liver

value: Liver


title: 58160: Colon_1_GOS_neonatal

value: Colon

value: Male


title: Kidney, baboon, rep 5

value: Kidney

value: male

value: adult


title: SUM149 xenograft tumor cell pool4

city: Portland

first: Xi

state: Oregon

address: 2730 SW Moody Ave

institute: Oregon Health & Science University

data_processing:
basecalls were done by Illumina Casava1.8 software
sequenced reads were demultiplexed by Cell Ranger v6.0.0
sequenced reads were mapped to GRCh38 whole genome with all transcripts by Cell Ranger v6.0.0 with default parameters
sequenced reads were mapped to GRCh38 whole genome with only exons by velocyto v0.17
raw reads were loaded, merged and filtered in Python using scVelo
Assembly: GRCh38
Supplementary files format and content: comma-delimited text files include CPM values of spliced RNA for each cells
Supplementary files format and content: comma-delimited text files include raw counts of spliced RNA for each cells

source_name: NSG mouse/breast cancer

growth_protocol: For xenograft assays 6 weeks old female NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice were purchased from Jackson Laboratory. Tumors were induced by unilateral orthotopic mammary fat pad injection of 2*106 SUM149 cells transfected with shCON or shCD9 lentivirus and suspended in 50 μL of culture medium/Matrigel Growth Factor Reduced Basement Membrane Matrix, Phenol Red-Free (Corning, CLS356231) in a 1:1 ratio. After 14 days, mice were randomized to treatment groups (n=8) based on tumor size.

extract_protocol:
tumor was harvested from NSG mouse mamary pad. Tumor tissue was dissociated with gentleMACS tissue dissociation kits (SUM149 xenograft tumors were disaggregated by gentleMACS kits (Miltenyi Biotec, #130-096-730), and incubated in TotelseqA hashtag antibodies (Biolegend, #394601, #394603, #394605, #394607, #394609, #394611, #394613, #394615) following the manufactural instructions. Live cells were isolated by EasySep Dead Cell Removal (Annexin V) Kit (STEMCELL Technologies, #17899). Single cell suspensions were processed according to 10xGenomics scRNAseq sample preparation protocol (Chromium Single Cell 3’ v3.1 Reagent Kit, 10xGenomics). 1000 cells were targeted for each sample.)
RNA libraries were prepared for sequensing using standard library construction protocol by 10x Genomics

treatment_protocol: Mice were administered with vehicle or JQ1 (25mg/kg, daily, Selleckchem, #S7110) for 30 days.

value: mammary pad

value: JQ1 25mg/kg/day


title: SUM149 xenograft tumor cell pool3


title: Cocktail (chemical reprogramming)-treatment followed by ad.Atoh1 infection, (n=5), scRNA-seq

description: 10x Genomics

extract_protocol:
Sensory epithelium from cochlear explants was dissociated to single cells using 0.25% trypsin-EDTA for 15 min incubation at 37C. Tissues were gently singularized by P1000 pipette in a complete medium (DMEM/F12 medium containing 10% FBS). Cells were strained twice through 40 mm mesh into 5 ml medium, spun down for 5 min at 300 g to pellet, and resuspended in 50 ml of complete medium. Roughly, 1400 cells of Cocktail, 1700 cells of Vehicle samples were recovered from 10X Chip-G. Single cells from cochlear cultures of Cocktail plus adAtoh1 (n=5) and Vehicle plus ad.Atoh1 (n=5) groups were captured separately to prepare NGS libraries for the samples.
Single-cell suspensions were immediately transferred to individual channels of the chip (Chromium Next GEM Chip G) to generate gel beads in emulsion together with reverse transcription master mix on the droplet-based high-throughput Chromium Controller (10X Genomics) allowing cell lysis, individual cell barcoding, and reverse transcription by Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000128). Briefly, single-cell library preparation was carried out by emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter, and Illumina sample index addition following the manufacturer's protocol. The single-cell derived cDNA libraries were then assessed with a bioanalyzer (High Sensitivity DNA Kit, Agilent 2100 Bioanalyzer) for quality control. Following library preparation, next-generation sequencing was performed with paired-end sequencing of 150 bp each end using Illumina HiSeqXTen (Novogene Inc.).

treatment_protocol: In chemical reprogramming group, we treated whole adult cochlear explants with VPA (1.5 mM), LiCl (8mM), FSK (20μM), siFIR (0.02 μM), and siMxi1 (0.02 μM) for 4 days, followed by 2 weeks ad.Atoh1 overexpression. In control group, we treated whole adult cochlear explants with sterile water supplemented with 0.1% DMSO in vitro for four days followed by ad.Atoh1 infection for the duration of 2 weeks. Vehicle_ad.Atoh1 group, n=5; Cocktail_ad.Atoh1 (chemical reprogramming) group, n=5.


title: 57903: Colon_1_GOS_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
205_205_2567_2

data_processing: The data were analyzed using R (v3.0.2) by executing different packages, including LIMMA and arrayQualityMetrics. The R package LIMMA from Bioconductor was used to correct for background (method=normexp and offset=1). Quantile normalization of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure: 1) select the highest of the dark spots to acquire a base value, 2) multiply by 1.1, 3) the gene/probe had to be expressed in each of the samples in the experimental condition.

value: CONTROL


title: SUM149 xenograft tumor cell pool2


title: Vehicle (sterile water containing 0.1% DMSO)-treatment followed by ad.Atoh1 infection, (n=5), scRNA-seq

description: 10x Genomics


title: Liver, baboon, rep 6

data_processing:
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample

value: wild type


title: Brain, baboon, rep 5

value: Brain


title: 57896: Colon_1_GOS_neonatal

value: Female


title: 58086: Ileum_1_betaglucans_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
207_207_2394_4

source_name: Ileum; 1; betaglucans; neonatal

value: maternal


title: scRNA_Th1_1

city: Cambridge

first: Pratiksha

middle: I

last: Thakore

address: 415 Main St

institute: Broad Institute

data_processing:
Basecalls performed by RTA v2.4.11.
RNA-seq: Fastq files were generated from bcl with CellRanger v2.2.0 with default parameters. ATAC-seq: Fastq files were generated from bcl with CellRanger-ATAC v1.0.1 with default parameters.
RNA-seq: Reads were mapped to mm10 and UMI count matrices were computed by CellRanger v2.2.0 with default parameters. ATAC-seq: Reads were mapped to mm10 and UMI count matrices were computed by CellRanger-ATAC v1.0.1.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (scRNA-seq) and barcodes.tsv, peaks.bed, and matrix.mtx (scATAC-seq) files together define a matrix of raw UMI counts

source_name: Sorted live cells polarized in Th1 conditions for 48 hours

growth_protocol: For the in vitro differentiation of naïve CD4+ T cells, naïve CD4+ CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines.

extract_protocol:
After 48h, live cells were sorted into PBS/2%FCS and were encapsulated into droplets and libraries were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.
ScRNA-seq library preparations were performed according to manufacturer’s instructions (10X Genomics, Chromium Single Cell 5’ Library & Gel Bead Kit). scATAC-seq library preparations were performed according to manufacturer's instructions (10X Genomics, Chromium Single Cell ATAC Library & Gel Bead Kit).

value: spleen and lymph nodes


title: 58076: Ileum_1_betaglucans_neonatal

first: Dirkjan

institute: Wageningen UR

value: Ileum


title: Liver, baboon, rep 4

first: Alexander

institute: Brigham & Women's Hospital, Harvard Medical School


title: Kidney, baboon, rep 4


title: scRNA_Th1_2


title: Brain, baboon, rep 4


title: scRNA_pTh17_1

source_name: Sorted live cells polarized in pTh17 conditions for 48 hours


title: scRNA_npTh17_2

source_name: Sorted live cells polarized in npTh17 conditions for 48 hours


title: scRNA_npTh17_1


title: SUM149 xenograft tumor cell pool1


title: 57719: Ileum_1_betaglucans_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
208_208_2483_3


title: 57876: Ileum_1_betaglucans_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
201_201_2570_2


title: Kidney, baboon, rep 3


title: Liver, baboon, rep 3


title: STAT6-D419N, IL-4, 72hr, N3

city: Montreal

first: Koren

middle: Kathleen

last: Mann

state: QC

address: 3755 Chemin de la Cote Sainte Catherine

country: Canada

institute: Lady Davis Institute

data_processing:
Data was processed using the STAR aligner to the HG38 build of the human genome
Duplicate reads were not removed. Raw counts were obtained using the HTSeq Software and were filtered for low read depth. Genes that had a total read count below 10 across all samples were removed.
Raw counts were normalized using the variance stabilizing transformation (‘vst’) function in the bioconductor package ‘DESEQ2’.
To remove batch effect, the ‘removeBatchEffect’ function from the bioconductor package ‘limma’ was used.
Differential Expression analysis was performed using the Bioconductor package ‘DESeq2’.
Assembly: HG38
Supplementary files format and content: csv files include readcounts for each sample

growth_protocol: OCI-Ly8 GCB-DLBCL cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted with the Absolutely Total RNA Purification Kit from Agilent
Libraries were prepared by Genome Quebec, prior to sequencing on an Illumina NovaSeq 6000 S2 PE100

treatment_protocol:
STAT6 was activated with either acute (3hr) IL-4 stimulation or chronic (72hr) IL-4 stimulation.
For acute IL-4 stimulation, 200pg/mL was added to tissue culture media for 3 hours. For chronic IL-4 stimulation, OCI-Ly8 cells were co-cultured with a stromal cell line which constituitively produces IL-4 for 72 hours.

value: GCB-Type DLBCL

value: 72 hr


title: STAT6-D419N, IL-4, 3hr, N3

value: 3 hr


title: STAT6-D419N, IL-4, 3hr, N2


title: STAT6-D419N, IL-4, 72hr, N1


title: STAT6-D419N, IL-4, 72hr, N2


title: Brain, baboon, rep 3


title: 57882: Ileum_1_betaglucans_neonatal

last: Schokker

address: Droevendaalsesteeg 1


title: 58118: Jejunum_1_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
204_204_2613_1

source_name: Jejunum; 1; MCFA; neonatal

value: Jejunum

value: neonatal


title: scRNA_pTh17_2


title: STAT6-D419N, IL-4, 3hr, N1


title: 58123: Jejunum_1_MCFA_neonatal

value: Male


title: 57775: Jejunum_1_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
203_203_2484_3

value: GOS


title: LB2T3

city: Taian

first: Qingqing

last: Wei

state: Shandong

address: 61 Daizong Street

institute: Shandong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with parameters -q --fr -p 8 --dta-cufflinks --summary-file
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. We use htseq-count to call the raw counts of each sample then calculate the RPKM  with the annotation gtf file via edgeR (R package).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: embryo

extract_protocol: Libraries for RNA sequencing (RNA-seq) were prepared with the SMARTer Ultra Low Input RNA Kit for sequencing (Clontech) and the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: siRNA specific for Tdgf1 and negative control were designed and synthesized by GenePharma company. GFP mRNA was injected with siRNA to zygotes as a marker for successful injection.

tag: developmental stage

value: late blastocyst

value: embryo

tag: sirna target


title: LB2NC

value: negative control


title: 57766: Jejunum_1_MCFA_neonatal

value: MCFA


title: Liver, baboon, rep 2

last: Tyshkovskiy

address: 77 Avenue Louis Pasteur

treatment_protocol: The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).

value: Liver

value: male

value: adult

value: wild type


title: LB1T3


title: 57729: Ileum_1_betaglucans_neonatal

value: CONTROL


title: Kidney, baboon, rep 2

value: Kidney


title: STAT6-D419N, control, N3

tag: cell line

tag: cell type

value: GCB-Type DLBCL

value: Control

value: 0 hr


title: LB1NC


title: 57690: Jejunum_1_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
202_202_2566_2

value: Jejunum

tag: treatment

value: betaglucans


title: STAT6-D419N, control, N2

tag: genotype

tag: time


title: STAT6-D419N, control, N1


title: EB2T3

value: early blastocyst

tag: tissue


title: Liver, baboon, rep 1

tag: Sex


title: STAT6-WT, IL-4, 72hr, N3

value: 72 hr


title: EB2NC

tag: strain


title: Kidney, baboon, rep 1

tag: age


title: EB1T3


title: Brain, baboon, rep 1

value: Brain


title: 57702: Jejunum_1_MCFA_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
209_209_2411_4

tag: gender

value: Female

value: neonatal


title: STAT6-WT, IL-4, 72hr, N2


title: STAT6-WT, IL-4, 72hr, N1


title: 57682: Jejunum_1_MCFA_neonatal

tag: day

value: GOS


title: EB1NC

value: embryo

value: negative control


title: PDX1-ESC-R2

first: Julian

last: Pulecio

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
4C processing was first carried out with pipe4C v1.0. Default settings were used for all analysis. After all reads were processed, the data was first re-binned into fixed bins of 2500 bp, and then a sliding window of 5 was used to aggregate counts. Smoothed counts were then used for subsequent analysis.
Assembly: hg19
Supplementary files format and content: Coverage track in bigWig format
Library strategy: 4C-Seq

growth_protocol: hESCs were cultured in Essential 8 (E8) medium (Thermo Fisher Scientific, A1517001) on vitronectin (VTN) (Thermo Fisher Scientific, A14700) pre-coated plates at 37 °C with 5% CO2. Medium was changed every day. Cells were passaged every 4-5 days at a ratio 1:15-20 using 0.5 mM EDTA (KD Medical, RGE-3130) or TrypLE Select (Gibco, 12563029) to dissociate cells. 5 μM Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Selleck Chemicals, S1049) was added into the E8 media when passaging or thawing hESCs.

extract_protocol:
10 million hESCs were  fixed with  1% formaldehyde (Thermo Scientific) in PBS without Ca+/Mg+ for 10 min at room temperature . After quenching with  glycine, tubes were centrifuged for 5 min 500g at 4°C. Cells were kept on ice, washed with PBS, centrifuged for 5 min 500g at 4°C, and pellets were frozen in liquid nitrogen and stored at −80°C. Next, cells were vigorously resuspended in 1 ml of ice-cold lysis buffer (10 mM tris (pH 8), 10 mM NaCl, 0.2% NP-40, and 1 tablet of complete protease inhibitor (Roche)], transferred to 9 ml of prechilled lysis buffer, and incubated for 15 min on ice. After centrifugation, cell pellets were resuspended in CutSmart buffer containing 0.5% SDS and incubated for 1 hr at 37°C while shaking at 750 rpm. After, samples were ready for enzymatic digestion.
Viewpoint primers were designed either around promoter of EOMES, GATA6, SOX17 and PDX1, depending on the availability of the nearest restriction enzyme sites. Library preparation was then performed using  the Expand Long Range PCR kit (Millipore) under specific PCR conditions (94 °C for 2 min, 16 cycles: 94 °C for 10 s; 59°C for 1 min; 68 °C for 3 min, final extension: 68 °C for 5 min). Amplified DNA was pooled, and primers were removed using AMPure beads (Beckman Coulter,). A second round of PCR was performed using the amplified DNA as a template and overlapping primers to add the P5/P7 sequencing primers and indexes (94 °C for 2 min, 20 cycles: 94 °C for 10 s; 60 °C for 1 min; 68 °C for 3 min and 68 °C for 5 min).

value: Embryonic Stem Cells

value: WildType


title: 57710: Jejunum_1_MCFA_neonatal

value: Male

value: CONTROL

tag: route


title: Brain, baboon, rep 2

value: male

value: adult

value: wild type


title: M2NC

value: morula


title: STAT6-WT, IL-4, 3hr, N2

value: GCB-Type DLBCL

value: 3 hr


title: 57846: Ileum_1_CONTROL_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
107_107_2406_4

source_name: Ileum; 1; CONTROL; neonatal

value: Ileum

tag: animalid


title: 58068: Ileum_1_CONTROL_maternal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
106_106_2496_3

source_name: Ileum; 1; CONTROL; maternal

value: betaglucans


title: 58063: Ileum_1_CONTROL_neonatal

value: Female

value: MCFA

value: maternal


title: STAT6-WT, IL-4, 3hr, N1


title: 57860: Ileum_1_CONTROL_maternal

value: GOS

value: neonatal


title: EOMES-ESC-R2

value: Embryonic Stem Cells


title: M1NC

value: embryo

value: negative control


title: STAT6-WT, control, N3

value: Control

value: 0 hr


title: M1T3


title: EOMES-ESC-R1

value: WildType


title: 57831: Ileum_1_CONTROL_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
104_104_2609_1


title: M2T3


title: 57843: Ileum_1_CONTROL_maternal

value: Male


title: SOX17-ESC-R2


title: PRO12-HUES8-WT

data_processing:
We performed Trim Galore (https://github.com/FelixKrueger/TrimGalore) to trim the adapters, and aligned all the clean reads to human reference genome hg19 using STAR 2.7.1.
We applied UMI-tools to remove the duplicated reads and the unique aligned reads were further converted to bigwig format normalized by FPKM using BamCoverage function in deepTools.
Assembly: hg19
Supplementary files format and content: Coverage track in bigWig format

molecule: nuclear RNA

source_name: Embryonic Stem Cells

extract_protocol:
Around 5 million  hESCs were swelled in swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 1XProteinase Inhibitor Cocktail, 10 U/ml Superase-In) for 10mins, then nuclei were extracted in swelling buffer added with 10% glycerol and 0.5% NP-40. The nuclei were resuspended in freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 1xPIC, 10U/100uL Superase-IN).
Total RNAs from the nuclei were immediately extracted by TRIzol LS, and the NRO RNAs from this mixture were purified by streptavidin C1 beads twice. The purified NRO RNAs were processed to sequencing library using a two rounds of adaptor ligation following eCLIP-seq method with 10nt UMI
PRO-seq


title: STAT6-WT, control, N2


title: 57821: Ileum_1_CONTROL_neonatal

description:
BirthLocation_AfterRelocation_SowNr_ParitySow:
101_101_2569_2


title: 57825: Ileum_1_CONTROL_maternal


title: SOX17-ESC-R1


title: STAT6-WT, IL-4, 3hr, N3


title: PDX1-ESC-R1


title: STAT6-WT, control, N1


title: GATA6-ESC-R2


title: GATA6-ESC-R1


title: 58068: Colon_1_CONTROL_maternal

source_name: Colon; 1; CONTROL; maternal

value: Colon


title: NS01

city: Seoul

first: Sejin

last: Oh

address: 81 Irwon-ro Gangnam-gu

institute: Samsung Medical Center

description: scRNA-seq

data_processing:
Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.
The 10x sequencing data was mapped to human reference genome (GRCh38; official Cell Ranger reference) for generating raw gene expression matrix.
Assembly: hg38
Supplementary files format and content: MTX

source_name: Skin

extract_protocol:
the keloid tissue was washed in phosphate-buffered saline (PBS). Excised keloids were immersed in physiological saline and immediately transferred to the lab. After sample was minced into small pieces with scalpel in a petri-dish, prepared dissociation solution (2 mg/ml Liberase TL in PBS, Sigma Aldrich) was used to digest at 37ºC for 60 min. The debris were filtered out with a 70-μm cell strainer (#352340, Corning). The remaining tissue were transferred into dissociation solution containing 0.25% Trypsin for a second round of dissociation. Subsequently, the live cells were resuspended in PBS-0.04% bovine serum albumin. Cells were pelleted by centrifuging at 500 x g for 5min.
To generate single-cell gel bead emulsions, suspensions of skin cells were immediately injected into the Chromium Controller (10x Genomics) targeting 9,000 cells, respectively. Following the manufacturer’s protocols, the Chromium Single Cell 3’ Reagent V2 Chemistry Kit(10x Genomics) was used to construct single cell libraries. Then, prepared libraries were sequenced on NovaSeq 6000 Sequencing System (Illumina, USA) or Illumina NextSeq 550 System targeting 50,000 raw reads per cell.

tag: pathology

value: Scar

tag: location

value: Neck


title: H3K27ac-2

data_processing:
Paired-end reads were mapped to hg19 reference genome with bowtie2(Langmead and Salzberg, 2012) using default parameters.
Peaks were called using macs2 (Model-based Analysis of ChIP-Seq (MACS) (Zhang et al., 2008)), with the options to filter duplicates using –keepdup auto with the permissive P-value threshold of 0.01.
Peaks were further filtered down using irreproducible discovery ratio (IDR) (Li et al., 2011) filter of 0.01.
Assembly: hg19
Supplementary files format and content: Coverage track in bigWig format

extract_protocol:
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
Libraries were generated by the NEBNext® Ultra II DNA Library Prep Kit (New England Biolabs; E7103S) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs Index Primers Set 1; NEB, E7335S). Samples were QC on a Bioanalyzer(Agilent) and sequenced on an Illumina Next Gen sequencer by the Integrated Genomic Operation(IGO) Core Facility at the MSKCC.

treatment_protocol: For FOXA2 expression in hESCs, 2x105 iSAM hESCs were transduced with two lentiviral gRNAS targeting the promoter region of the endogenous FOXA2 locus. After one day of recovery cells were cultured in E8 medium and treated with puromycin for three days. Doxycycline was added for an additional day ( no Doxycycline for the NODOX conditions)

tag: chip antibody

value: H3K27ac Active Motif 39134


title: 58063: Colon_1_CONTROL_neonatal

source_name: Colon; 1; CONTROL; neonatal

value: betaglucans


title: IC02

description: scRNA-seq

value: Keloid

value: Chest

value: Female


title: H3K27ac-1

value: H3K27ac Active Motif 39133


title: MS02

description: scRNA-seq


title: DOXFOXA2-2

value: FOXA2 R&D AF2400

value: CRISPRa mediated FOXA2 expression


title: sor405_3

city: Shenzhen

first: Conghui

last: You

address: 1068 Xueyuan Blvd.

institute: Shenzhen University

description:
Batch culture at 37°C, OD600≈0.4
sor405.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, poly-N and low-quality sequence, then mapped to NCM3722 whole genome using bowtie2 v2.2.3 with parameters -q --phred33 --sensitive -I 100 -X 500 --end-to-end --no-unal -p 4
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. To avoid counting reads from the neighbor genes, we use TMM to normalize the read count.
Genome_build: NCM3722 (NZ_CP011495.1 and NZ_CP011496.1)
Supplementary_files_format_and_content: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample

organism: Escherichia coli

source_name: E. coli

growth_protocol: in N-C- minimal medium supplemented with 20 mM sorbitol and 20 mM NH4Cl aerobically at 37°C water bath, 250rpm

extract_protocol:
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction. Total RNA was extract by RNAiso plus (Takara) and PureLink RNA Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: add 0.001g/L Ammonium ferric citrate(Fe)

tag: culture method

value: batch culture at 37C

tag: optical density (od600)

value: approximately 0.4


title: 57860: Colon_1_CONTROL_maternal

city: Wageningen

value: maternal


title: MS01

description: scRNA-seq

value: Back


title: IP01

description: scRNA-seq


title: 57831: Colon_1_CONTROL_neonatal


title: sor405_2


title: 57843: Colon_1_CONTROL_maternal


title: Noise exposure-only control, (n=5), scRNA-seq

city: Boston

description: 10x Genomics

source_name: Inner ear cochlea

tag: cell type

value: Sensory epithelium

value: Inner ear cochlea

value: CBA/CaJ

value: 4-6 weeks old


title: IP02

description: scRNA-seq


title: IC01

description: scRNA-seq

value: Male


title: 57825: Colon_1_CONTROL_maternal

value: Colon

tag: treatment

value: MCFA


title: DOXFOXA2-1

value: Embryonic Stem Cells

tag: cell line

tag: genotype

value: WildType


title: WT-SOX2-R2

tag: tissue


title: sor405_1


title: AP02

description: scRNA-seq

value: Keloid

value: Female


title: Fe405_3

description:
Batch culture at 37°C,add Fe, OD600≈0.4
Fe405.txt

value: added Fe


title: Fe405_1


title: WT-OCT4-R2

value: Oct4 Cell Signaling 5677s


title: sor3722_3

description:
Batch culture at 37°C, OD600≈0.4
sor3722.txt

value: batch culture at 37C

value: Wild Type


title: WT-OCT4-R1


title: 58068: Jejunum_1_CONTROL_maternal

source_name: Jejunum; 1; CONTROL; maternal

value: Jejunum

value: maternal


title: 57860: Jejunum_1_CONTROL_maternal


title: AP01

description: scRNA-seq

value: Chest


title: WT-SOX2-R1


title: 58063: Jejunum_1_CONTROL_neonatal

source_name: Jejunum; 1; CONTROL; neonatal


title: WT-NANOG-R2

value: NANOG R&D AF1997-SP


title: 57846: Jejunum_1_CONTROL_neonatal


title: sor3722_2

value: approximately 0.4


title: Fe405_2


title: sor3722_1


title: 57831: Jejunum_1_CONTROL_neonatal


title: pCCL-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [GFP_CD371N_HSPC_rep3]

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

data_processing:
All fastq files are mapped to the hg38 human genome using Hisat2 software to generate sam files.
Gene expression value (raw counts.txt) matrix are generated by Featurecount program derived from sam files.
Assembly: hg38
Supplementary files format and content: Hisat2_raw_counts.txt

source_name: cord blood

growth_protocol: CD34+HSPCs are isolated from human cord blood, and then infected by lentivirus after stimulating of 12 hours.

extract_protocol:
Two thousand of pCCL-L-ELK1-GFP, pCCL-S-ELK1-GFP, pCCL-GFP lentiviral transduced GFP+ CD34+CD123+CD38+CD371– HSPCs are sorted into 1.5 mL tube containing 200 μL 0.5% BSA-DPBS solution. The dsDNA and libraries are generated as previously described (PMID: 20203668).
DNA libraries are constructed using Vazyme TruePrepTM DNA library Prep Kit V2 from Illumina (TD-503) as previous reported (PMID: 29434353,32640500, 27720903,32725842) and sequenced using theIllumina NovaSeq 6000 system (Novogene Co., Ltd.).

treatment_protocol: pCCL-L-ELK1-GFP, pCCL-S-ELK1-GFP, pCCL-GFP lentivirus transudced CD34+CD123+CD38+CD371–  HSPCs are isolated 48 hour latter.

value: cord blood

value: lentiviral transduced for 48 hours

value: hematopoetic stem/progenitor cells

value: Control

value: pCCL-GFP lentiviral transduced


title: pCCL-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [GFP_CD371N_HSPC_rep2]


title: AC02

description: scRNA-seq

value: Back


title: hiPSCs, myogenic_diff, DMD, Day28, plate2

city: Nantes

first: Jean-Baptiste

last: Dupont

address: 22 boulevard Benoni Goullin

department: INSERM

country: France

institute: Nantes Université

description: sci-RNA-Seq

data_processing:
basecalling (bcl2fastq v 2.16.0.10)
demultiplexing based on the P5 barcode
adaptor trimming (trim_galore v 0.4.5)
alignment to the human genome (STAR v 2.5.2b)
demultiplexing based on RT barcodes
secondary analysis (monocle 2 and 3,as published by Qiu et al. 2017, Nature Methods, DOI: 10.1038/nmeth.4402; http://cole-trapnell-lab.github.io/monocle-release/)
Assembly: hg19
Supplementary files format and content: matrix of expression values aggregated in a csv (.csv) file
Supplementary files format and content: cell and feature (gene) informations providede as csv files

source_name: hiPSCs

growth_protocol: Myogenic differentiation protocol as published by Chal et al. 2016, Nature Protocols, DOI: 10.1038/nprot.2016.110

extract_protocol:
Cells were detached with Trypsin-EDTA + collagenase IV and resuspended in DPBS prior to fixation and permeabilization with pre-chilled 100 % methanol
single-cell combinatorial indexing RNA-Seq (sci-RNA-Seq) as published by Cao et al. (2017) Science (DOI: 10.1126/science.aam8940)

value: hiPSCs

tag: condition

value: DMD


title: Lin_neg_3mo_Tet2_KO_WGBS

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

institute: Albert Einstein College of Medicine

description: WGBS

data_processing:
For RNA-seq RNA was extracted using Qaigen RNeasy Total RNA kit I. Library preparation and mRNA sequencing were performed at Novogene using their Illumina Novoseq 6000 platform. Adaptors were trimmed using trim galore (v0.6.5) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.3a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with edgeR (FDR <0.05 and fold-change >1.0), following the standard package documentation.
For WGBS, DNA was extracted by Quick-DNA miniprep kit (Zymo, D3024) following the manufacturer’s instructions. Bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.4% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (v1.5.5) (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.22.3) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor.
Assembly: mm10

growth_protocol: Bone marrow was harvested and LSK (Lin-, Sca1+, cKit+) and Lin– (lineage negative) cells sorted by FACS.

extract_protocol:
For RNA-seq, RNA extraction was performed using Qaigen RNeasy Total RNA kit. For WGBS, DNA extraction was performed using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/).

tag: strain

value: Mixed 129/C57BL/6


title: Fe3722_3

description:
Batch culture at 37°C,add Fe, OD600≈0.4
Fe3722.txt

value: added Fe


title: pCCL-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [GFP_CD371N_HSPC_rep1]


title: Fe3722_2

value: batch culture at 37C


title: hiPSCs, myogenic_diff, DMD, Day22, plate2

description: sci-RNA-Seq


title: pCCL-S-ELK1-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [S-ELK1_CD371N_HSPC_rep3]

value: S-ELK1 overexpressing

value: pCCL-S-ELK1-GFP lentiviral transduced


title: Lin_neg_3mo_Tet2_Mut_WGBS

description: WGBS

tag: age


title: pCCL-S-ELK1-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [S-ELK1_CD371N_HSPC_rep2]


title: pCCL-S-ELK1-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [S-ELK1_CD371N_HSPC_rep1]


title: hiPSCs, myogenic_diff, DMD, Day14, plate2

description: sci-RNA-Seq


title: hiPSCs, myogenic_diff, DMD, Day18, plate2

description: sci-RNA-Seq


title: 57821: Jejunum_1_CONTROL_neonatal

value: Jejunum

tag: gender

value: Female

value: GOS

value: neonatal


title: Fe3722_1

value: approximately 0.4

value: Wild Type


title: AC01

description: scRNA-seq

value: Keloid

value: Chest

value: Male


title: hiPSCs, myogenic_diff, DMD, Day10, plate2

description: sci-RNA-Seq


title: LSK_3mo_Tet2_KO_WGBS

description: WGBS

source_name: LSK

value: LSK


title: Lin_neg_3mo_Tet2_WT_WGBS

description: WGBS


title: LSK_3mo_Tet2_Mut_WGBS

description: WGBS


title: WT-NANOG-R1

value: Embryonic Stem Cells

value: WildType

value: NANOG R&D AF1997-SP


title: 57843: Jejunum_1_CONTROL_maternal

tag: day


title: 57825: Jejunum_1_CONTROL_maternal

tag: route


title: pCCL-L-ELK1-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [L-ELK1_CD371N_HSPC_rep3]

value: cord blood

value: lentiviral transduced for 48 hours

value: hematopoetic stem/progenitor cells

value: L-ELK1 overexpressing

value: pCCL-L-ELK1-GFP lentiviral transduced


title: LSK_3mo_Tet2_WT_WGBS

description: WGBS

value: Mixed 129/C57BL/6


title: pCCL-L-ELK1-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [L-ELK1_CD371N_HSPC_rep2]


title: hiPSCs, myogenic_diff, DMD, Day4, plate2

description: sci-RNA-Seq

value: hiPSCs

value: DMD


title: hiPSCs, myogenic_diff, DMD, Day7, plate2

description: sci-RNA-Seq


title: pCCL-L-ELK1-GFP transduced CD34+CD123+CD38+CD371– HSPCs derived from cord blood CD34+HSPCs [L-ELK1_CD371N_HSPC_rep1]


title: Macrophage, mdx

city: Irvine

first: S.

middle: Armando

last: Villalta

state: California

address: 843 Health Sciences Rd

institute: University of California Irvine

description:
Integrated_WT_MDX_Figure1.rds
Integrated_B6_B10_MDX_B6AJ_SFigure10.rds

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: rms files

source_name: Muscle

extract_protocol:
WT C57BL/6, WT C57BL/10, mdx, B6A/J mice were humanely euthanized, perfused to clear circulating immune cells, and hind limb lymph nodes removed. Single-cell suspensions were prepared from healthy and dystrophic muscle by mechanical dissociation and enzymatic digestion with collagenase and DNase. Cell suspensions were washed and filtered sequentially through 70- and 40-micron cell strainers. Live muscle macrophages were FACS-sorted based on their expression of F4/80 and CD11b, and single-cell libraries constructed with the 10X Genomics platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Muscle

value: Macrophage

value: B10 mdx


title: hiPSCs, myogenic_diff, DMD, Day2, plate2

description: sci-RNA-Seq


title: Macrophage, B10_WT1

value: B10 WT


title: hiPSCs, myogenic_diff, DMD, Day0, plate2

description: sci-RNA-Seq


title: hiPSCs, myogenic_diff, DMD, Day1, plate2

description: sci-RNA-Seq


title: 4T1 cells - shDap5_heavy_rep3

first: Robert

middle: J

last: Schneider

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie used to align the reads to the reference, and the aligned reads were counted per gene.
DGE and translational efficiency were calculated using RIVET (Ernlund etal, BMC Gen, 2018)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: breast cancer cells

growth_protocol: Cells were passaged whenevr they reached 70% confluency.

extract_protocol:
Sucrose gradients were run; RNA was extracted using Trizol, heavy and light fractions were combined aacordinlgy and cleaned through Zymo clean and concentrate.
Illumina automated stranded RNA-seq library prep, polyA selection

treatment_protocol: Doxycycline (2ug/ml) induction for 6 days

value: 4T1 TNBC breast cancer cells

value: BALB/c

tag: molecule

value: heavy polysome fraction polyA RNA


title: 4T1 cells - shDap5_heavy_rep2


title: hiPSCs, myogenic_diff, DMD, Day28, plate1

description: sci-RNA-Seq


title: 4T1 cells - NSi_heavy_rep3