title: Lateral rectus muscle, H3K4me3_18hpi

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

description:
H3K4me3_18hpi_intervals.txt
H3K4me3_active_regions.txt

data_processing:
Basecalling was performed by Illumina's RTA2.
Reads were mapped to the danRer10 reference genome using BWA (defaul settings).
Read duplicates were filtered and uniquely-mapping reads (mapping quality > 25), downsampled to smallest library, and saved to BAM format.
Coverage files in BigWig format were generated from extended reads (150-250 nt, depending on average fragment length).  BigWig binsize was set to 35 nt.
For H3K27Ac and H3K4me3, peaks ("intervals") were called using MACS v2.1.0 and cutoff p-value of 1×10e-7.  For H3K27me3, intervals were called using SICER v12.1 and cutoff FDR of 1×10-10. and a gap size of 200 nt.
For each histone modification, overlapping intervals were merged into common regions ("active regions").
Genome_build: danRer10
Supplementary_files_format_and_content: BigWig coverage files were generated using in silico-extended reads (to 150-250 nt) and binsize set to 35 nt.
Supplementary_files_format_and_content: interval files contain genomic coordinates of peaks called by MACS or SICER as well as measurements and gene annotation.  Column definitions: sample - sample name; interval_id - id in the form "interval_#####"; chr/start/end - genomic coordinates; length - interval length; peak_summit - position of the summit; peak_val - fragment density of bin at summit; avg_val - mean of bined fragment densities within the interval; bin_count - number of bins in the interval; cgi_island_count - number of CpG islands in the interval; promoter_count - number of annotated promoters within the interval; gene_count - number of genes within 10kb of the interval; genes - comma-delimited list of genes within 10kb of the interval.
Supplementary_files_format_and_content: active regions files contain genomic coordinates of regions of overlap in the intervals for three conditions (Control, 9 hpi, and 18 hpi) for the given histone modification.  Column definitions: active_region_id - id in the form "active_region_#####"; chr/start/end - genomic coordinates; length - active region length; inbterval_count - number of intervals comprising the active region; avg_val_control/9hpi/18hpi - the average of binned fragment densities within the active region for condition; peak_val_control/9hpi/18hpi - fragment density of bin at summit for condition; cgi_island_count - number of CpG islands in the active region; promoter_count - number of annotated promoters within the active region; gene_count - number of genes within 10kb of the active region; genes - comma-delimited list of genes within 10kb of the active region.

source_name: lateral rectus muscle

growth_protocol: Sexually mature adult (4-18 months of age) wild-type and transgenic (α-actin::EGFP) zebrafish were spawned in our fish facility and raised according to standard protocol at 28°C with a 14 hour light:10 hour dark cycle.

extract_protocol:
Chromatin was disrupted using a dounce homogenizer in resence of lysis buffer. The product was sonicated and the DNA sheared to fragments of 300-500 base pairs. Input genomic DNA was prepared by treating with RNase, proteinase K with heat, and ethanol precipitation. For ChIP samples, chromatin were precleared with protein A agarose beads (Invitrogen), immunoprecipitated with indicated antibodies, beads washed, eluted with SDS, and treated with RNAse and proteinase K.  Crosslinking was reversed by overnight incubation at 65°C and DNA purified via phenol-chloroform extraction and ethanol precipitaiton.
DNA libraries were performed using end-polishing, dA-addition, and adaptor ligation before sequencing.

treatment_protocol: Adult zebrafish were anesthetized using 0.05% tricaine methanosulfate (Tricaine-S; Western Chemical, Ferndale, WA) with 0.05% sodium bicarbonate buffer and placed on moist Kimwipes (Fisher Scientific, Cat. No. 06-666) under a stereomicroscope with GFP fluorescence illumination. Both eyes were adducted in turn with a thin blunt probe and a 0.5- to 1.0-mm segment (approximately 50%) of lateral rectus (LR) muscle was excised. 100-300 mg tissue was harvested from multiple specimens --119 fish for Control, 192 fish for 9 hpi, and 200 fish for 18 hpi.

value: lateral rectus muscle

tag: cell type

value: adult muscle cells

value: injury

tag: chip antibody

value: H3K4me3 (rabbit polyclonal; Active Motif cat # 39159)


title: 170227_s12

status: Public on Dec 06 2019

type: SRA

city: Vienna

first: Loan

last: Vulliard

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM

library_source: transcriptomic

data_processing:
Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0.
Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
Read counts per exon were obtained in R 3.4.0 with Rsubread_1.26.1, with the featureCount function, either allowing or not both parameters allowMultiOverlap and countMultiMappingReads.
Genome_build: mm9
Supplementary_files_format_and_content: Feature counts with and without multimapping reads, in two objects called respectively fcMulti and fcStrict, were exported as binary file using R's save function.

molecule: total RNA

organism: Mus musculus

source_name: Preosteoclasts

growth_protocol: Bone marrow was culutred for three days with 100 ng/ml M-CSF, scratched and replated in 30 ng/ml M-CSF and/or 50 ng/ml RANKL and  for 24 hours

extract_protocol:
RNA-seq was performed as described previously with slight modification (Hirahara et al., Immunity 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol  following manufacture’s protocol (Life Technologies).
Total RNA was subsequently processed to mRNA-seq library using NeoPrep Library Prep System and TruSeq Stranded mRNA Library Prep Kit for NeoPrep (Illumina).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

treatment_protocol: Cells were either plated on day 3 either with M-CSF, M-CSF+RANKL, M-CSF+RANKL+recArg1 (MCSF+RANKL+recArg1) in full medium or with M-CSF (M-CSF+depl), MCSF+arginine (MCSF+rescue), MCSF+RANKL (MCSF+RANKL+depl), MCSF+RANKL+arginine (MCSF+RANKL+rescue) in arginine-free medium

tag: condition

value: MCSF+rescue

tag: mouse


title: 170227_s13


title: Lateral rectus muscle, H3K4me3_9hpi

country: USA

description:
H3K4me3_9hpi_intervals.txt
H3K4me3_active_regions.txt

library_source: genomic

molecule: genomic DNA

organism: Danio rerio

tag: tissue

tag: treatment

tag: time


title: Patient with MI 1

type: RNA

city: Moscow

first: German

last: Osmak

address: 3-ya Cherepkovskaya

country: Russia

institute: National Medical Research Center for Cardiology

description: Gene expression data from patients with MI

hyb_protocol: Following fragmentation, 5.5 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip™ Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Computational analysis of the microarray data files was performed using R programming language version 3.5.1. Data processing was carried out based on the affy package written in R [Gautier L, Cope L, Bolstad BM, Irizarry RA (2004). “affy—analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics, 20(3), 307–315. ISSN 1367-4803, doi: 10.1093/bioinformatics/btg405]. A biomaRt package was used to annotate the obtained data [Durinck S. et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis //Bioinformatics. – 2005. – Т. 21. – №. 16. – С. 3439-3440].

label: biotin

organism: Homo sapiens

source_name: Blood sample from patient with MI

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (GeneChip™ WT PLUS Reagent Kit Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Array User Guide, 2018, Thermo Fisher Scientifi).

growth_protocol: Six patients with first ST-segment elevation myocardial infarction (MI) were enrolled in this study. All patients were diagnosed at the National Medical Scientific Center for Cardiology (Moscow, Russia) based on symptoms of myocardial ischemia, increase of high-sensitivity cardiac troponin I (hs-cTn-I) and/or emergence of new or presumed new ST-segment elevation, new left bundle branch block or development of pathological Q waves in accordance with Third Universal Definition of MI. Hs-cTn-I was measured during the initial patient assessment (from 1 to 18 h after the onset of disease symptoms). All patients underwent coronary angiography on admission. All patients and were treated according to contemporary guidelines. A total of 6 healthy controls (HCs) (all men, mean age 51.0 ± 7.1 years) with normal electrocardiogram, no history of cardiovascular diseases (CVD) and diabetes mellitus were included in the study; healthy controls (HCs characteristics by smoking status and body mass index were compatible to MI patients. All participants lived in European Russia.

extract_protocol: Blood samples were collected from MI patients 24-36 h after the disease onset and from HCs in the morning. PBMCs were isolated using Ficoll-Hypaque density gradient method (Sigma-Aldrich, St. Louis, MO, USA) within 3 h of sampling. Total RNA including small RNA was extracted using miRNeasy Mini Kit (Qiagen, Hildren, Germany) following the manufacturer's instructions. The RNA quantity was measured using the NanoDropTM spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA); the RNA integrity was assessed by QIAxcel Advanced System (Qiagen, Hilden, Germany). Samples with a RNA integrity number (RIN) value above eight were included in subsequent experiments.

tag: subject group

value: patient with Myocardial infarction (MI)

tag: gender

value: male

tag: subject status

value: Increase of high-sensitivity cardiac troponin I (hs-cTn-I) and new ST-segment elevation

value: blood


title: Col-0_L-Glu_06_h_rep2 time course

city: Yokohama

first: Yukihisa

last: Goto

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

data_processing:
The 50 bp single-end reads were sequenced on an Illumina Hiseq 4000 platform. The Fastx toolkit 0.0.13.2 (http://hannonlab.cshl.edu/fastx_toolkit/) was used for quality filtering. The first 6 bp sequences were trimmed to remove barcode sequences. Low-quality nucleotides (<30 quality score) were removed from the 3’ ends and short reads (<39 bp) and reads showing at least 95 % of nucleotides with less than 20 quality score were removed.
Filtered reads were mapped to Arabidopsis genome TAIR10.30 by tophat v2.1.0 (Trapnell et al., 2009)　(https://ccb.jhu.edu/software/tophat/index.shtml).
Read counts were extracted by HTSeq version 0.6.0 (Anders et al., 2015) (https://htseq.readthedocs.io/)
Read counts were filtered such that there was at least one count per million in at least half of the samples and subsequently normalized using the trimmed mean of M-values (TMM) method in the Bioconductor package edgeR 3.22.3 (Robinson et al., 2010).
Genome_build: Arabidopsis genome TAIR10.30
Supplementary_files_format_and_content: comma separated text files includeTMM-normalized expression

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis ecotype Columbia (Col-0) was sown on soil or half-strength Murashige-Skoog media containing 1 % sucrose. After a 2 day cold treatment to break seed dormancy, Liquid culture seedlings were grown under continuous-light at 23℃.

extract_protocol:
Sample preparation was performed using a High-throughput RNA-Seq method as described previously (Kumar et al., 2012)
RNA-Seq library preparation was also carried out using a High-throughput RNA-Seq method (Kumar et al., 2012)

treatment_protocol: The 14-day-old Arabidopsis seedlings were treated with 20 mM urea, 20 mM L-Glu, or 1mM SA after 6 h, 12 h, 24 h, and 48 h

value: L-Glu

tag: ecotype

value: 6 h


title: 170227_s11

value: MCSF+depl


title: Organoid_irradiated_96h_rep4

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

hyb_protocol: We hybrized the samples at 48 degrees celcius, which is what Nugen recommends in the manual of the Encore BiotinIL Module.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: small intestinal organoid, irradiated, t=96h

label_protocol: Biotinylated cDNA was created using Nugen Ovation Pico SL kit and after that the Nugen Encore BiotinIL Module.

growth_protocol: Small intestinal organoids were isolated from C57BL/6 mice and were cultured in ENR medium, containing Advanced DMEM medium (Invitrogen/Thermo Fisher, Waltham, MA, USA) supplemented 1% Penicillin/Streptomycin, 1% HEPES buffer and 1% Glutamax, 50 ng/ml EGF, 20% Noggin conditioned medium, 10% R-spondin conditioned medium, 1X B-27 supplement, 1X N-2 supplement (all from Invitrogen) and 1.25 mM n-Acetyl Cysteine (Sigma).

extract_protocol: RNA was extracted from the organoids using the Isolate II RNA Mini Kit (Bioline, London, K) following the manufacturer’s instructions.

treatment_protocol: 3 days after reseeding the organoids, they were irradiated with 6Gy gamma-irradiation. Controls were not irradiated.

value: small intestinal organoid

value: irradiated

tag: time point

value: 96h after irradiation


title: Lateral rectus muscle, H3K4me3_Control

description:
H3K4me3_Control_intervals.txt
H3K4me3_active_regions.txt

value: Control


title: Col-0_L-Glu_06_h_rep1 time course


title: 170227_s10


title: Lateral rectus muscle, H3K27me3_18hpi

description:
H3K27me3_18hpi_intervals.txt
H3K27me3_active_regions.txt

value: H3K27me3 (rabbit polyclonal; Millipore cat # 07-449)


title: 170227_s09

value: MCSF


title: Organoid_irradiated_96h_rep2


title: Organoid_control_96h_rep3

source_name: small intestinal organoid, non-irradiated, t=96h

value: control


title: Organoid_irradiated_96h_rep3


title: Tissue_treated1_60d_rep1

city: 兰州

first: 佳佳

last: 刘

state: 甘肃

address: 城关区定西东路35号

country: China

institute: 甘肃中医药大学

description: Gene expression of the liver after metformin treatment

hyb_protocol: The labeled and concentrated RNA product was adjusted to 17 μL with water, and other ingredients were added and heated at 100 ° C for 5 min. Then transfer to the ice bath; assemble the hybridization device, add 45 μL of the hybridization solution to the hybrid cover slip; place the hybridization device in the Agilent hybridization oven for overnight hybridization (about 16 hr, 20 rpm);

scan_protocol: After the hybridization, the chip is removed, first Wash in 0.2% SDS, 2×SSC lotion I for 5 min at 42 °C, then wash in 0.2×SSC lotion II at room temperature for 5 min. After the slide is dried, it can be used for scanning; use Agilent chip Scanner (G2565CA) scans the cleaned chip

data_processing: Hybrid images were analyzed and extracted using Agilent Feature Extraction (v10.7) software. The analysis was then performed using the Boo Expression Profiling Chip Analyzer software (CBC Analyzer, an expression profiling process based on R Bioconductor and Perl).

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation And cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from each group of mice was extracted using a Trizol kit and then processed using FeatureExtraction software to obtain raw data files (.txt). Import the raw data file (.txt) into GeneSpring software and write parameter information such as grouping. Data normalization and QC analysis were performed for each sample.

treatment_protocol: The liver tissues of each group were derived from natural aging mice, aging diabetic mice, mice treated with metformin in aging diabetes, and mice treated with astragalus polysaccharide and metformin in the treatment of aging diabetes.

tag: group

value: aging diabetes model with metformin treatment

tag: disease state

value: type 2 aging diabetes model

value: Whole liver


title: Organoid_control_96h_rep1


title: Tissue_treated2_60d_rep1

description: Gene expression of liver in the treatment of astragalus polysaccharide combined with metformin

value: aging diabetes model with astragalus polysaccharide and metformin treatment


title: Tissue_unprocessed_60d_rep1

description: Gene expression of liver without drug treatment

value: aging control

value: natural aging

value: male


title: Col-0_urea_48_h_rep2 time course

value: urea


title: Lateral rectus muscle, H3K27me3_9hpi

description:
H3K27me3_9hpi_intervals.txt
H3K27me3_active_regions.txt

value: lateral rectus muscle

value: adult muscle cells

value: injury


title: Organoid_irradiated_96h_rep1

value: small intestinal organoid

value: irradiated


title: Organoid_control_96h_rep4


title: Tissue_modeled_60d_rep1

description: Gene expression of the liver after modeling

value: aging diabetes model


title: 170227_s08


title: Organoid_control_96h_rep2


title: Lateral rectus muscle, H3K27me3_Control

description:
H3K27me3_Control_intervals.txt
H3K27me3_active_regions.txt

value: Control

value: H3K27me3 (rabbit polyclonal; Millipore cat # 07-449)


title: Organoid_irradiated_48h_rep3

source_name: small intestinal organoid, irradiated, t=48h

value: 48h after irradiation


title: Col-0_urea_48_h_rep1 time course


title: 170227_s06


title: Lateral rectus muscle, H3K27Ac_18hpi

description:
H3K27Ac_18hpi_intervals.txt
H3K27Ac_active_regions.txt

value: H3K27Ac (rabbit polyclonal; Active Motif cat # 39133)


title: Organoid_irradiated_48h_rep4


title: Col-0_urea_24_h_rep3 time course


title: Lateral rectus muscle, H3K27Ac_9hpi

description:
H3K27Ac_9hpi_intervals.txt
H3K27Ac_active_regions.txt


title: Small intestine, Hnf4aKO_rep8

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: small intestine, Hnf4a knockout

label_protocol: Biotinylated cRNA were prepared with the Invitrogen Illumina Totalprep RNA amplification kit for Illumina arrays

growth_protocol: VillinCreERT2+-Hnf4afl/fl mice and VillinCreERT2--Hnf4afl/fl mice were given 1 mg of tamoxifen (Sigma, Saint Louis, MO, USA) administered by oral gavage for 5 consecutive days.

extract_protocol: The intestinal tissue RNA was extracted with TRI Reagent (Sigma-Aldrich) and RNA clean-up was performed with the RNeasy kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 3 weeks after tamoxifen-induced Cre recombination, the animals were treated with 14 Gy whole-body γ-irradiation and sacrificed 96 hours afterwards.

value: small intestine

tag: genotype

value: 96h after irradiation


title: Organoid_irradiated_48h_rep1


title: 170227_s02

value: MCSF+RANKL+depl


title: Lateral rectus muscle, H3K27Ac_Control

description:
H3K27Ac_Control_intervals.txt
H3K27Ac_active_regions.txt


title: Lateral rectus muscle, input


title: Col-0_urea_24_h_rep1 time course


title: Organoid_control_48h_rep4

source_name: small intestinal organoid, non-irradiated, t=48h

value: control


title: Col-0_urea_12_h_rep3 time course


title: Organoid_irradiated_48h_rep2


title: Organoid_control_48h_rep3


title: Col-0_urea_12_h_rep2 time course


title: Organoid_control_48h_rep2


title: Organoid_control_48h_rep1


title: Col-0_urea_12_h_rep1 time course


title: HXH-B2-D230

city: Wenzhou

first: Mei-Ling

last: Gao

state: Zhejiang

address: N0.207, West Xueyuan Road

department: Division of Ophthalmic Genetics

institute: Wenzhou Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence (GRCh38_release95). Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow: $$FPKM = {cDNA Fragments \over {Mapped Fragments(Millions) * TranscriptLength(kb)}}$$
For the samples without biological replicates: Differential expression analysis of two samples was performed using the EBseq.The FDR < 0.01 & |log2（foldchange）| ≥2 was set as the threshold for significantly differential expression.
Supplementary_files_format_and_content: tab-delimited text file includes raw count and RPKM values for each Sample

source_name: retinal organoids

growth_protocol: Retinal organoids were generated from iPSCs following a published method with slight modification. Briefly, iPSCs were dissociated into single cells and resuspended in retinal differentiation medium I. Approximately 12,000 cells in 100 μl were added to each well and reaggregated in a V-bottom low-cell-adhesion 96-well plate. The differentiation starting day was defined as day 0; 20 μM Y-27632 was added to the retinal differentiation medium I on day 0, and half the medium was exchanged with fresh retinal differentiation medium I on day 6. From day 2 to day 18, Matrigel was added in a final proportion of 1% v/v. On day 12, the cell aggregates were transferred to petri dishes in retinal differentiation medium II. From day 18, the cell aggregates were maintained in neural retina culture medium.The medium was changed weekly.

extract_protocol:
RNA was harvested using Trizol reagent.A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations .

value: iPSC-derived retinal organoids

value: PDE6B mutation

tag: developmental stage

value: late-stage

tag: differentiation day


title: C3

city: Changchun

first: Xin

last: Wen

address: Ziqiang Stree No.218

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of the original data was statistically analyzed, and the sequencing data quality of the samples was visually evaluated by FastQC.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, HISAT2 was used to compare the quality-controlled sequencing sequence with the reference genome, and the results were statistically compared by RSeQC.
Fragments Per Kilobase of exon transcript per Million fragments mapped reads(FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Cervical squamous cell carcinoma

growth_protocol: The SiHa cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimitotic solution. All cells were maintained at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
The transfected cells were digested with trypsin and washed three times with PBS, and total RNA was harvested using Trizol reagent. Hieff NGS MaxUp Dual-mode mRNA Library Prep Kit for Illumina (Cat#12301ES96) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The SiHa cells were transfected with GV230-BRCA1 or GV230 plasmid using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis.

tag: cell line

value: SiHa cell

tag: trasfection

value: Transfection with GV230 plasmid


title: HXH-B2-D180

value: mid-stage


title: HXH-B2-D151


title: C2


title: 170227_s04

tag: condition

value: MCSF+RANKL+rescue


title: Organoid_irradiated_24h_rep3

source_name: small intestinal organoid, irradiated, t=24h

value: small intestinal organoid

value: irradiated

value: 24h after irradiation


title: Col-0_urea_06_h_rep3 time course

value: urea

value: 6 h


title: HXH-B2-D90


title: A3

value: Transfection with GV230-BRCA1 plasmid


title: Organoid_irradiated_24h_rep2


title: CZJ-B2-D230

value: non-phenotype control


title: Col-0_urea_06_h_rep2 time course


title: Col-0_urea_06_h_rep1 time course


title: Col-0_SA_06_h_rep1 time course

value: SA


title: Organoid_irradiated_24h_rep4


title: A2


title: CZJ-B2-D180


title: A1


title: HXH-B2-D123


title: Organoid_control_24h_rep4

source_name: small intestinal organoid, non-irradiated, t=24h


title: CZJ-B2-D150


title: C1


title: Col-0_mock_0_h_rep3 time course

value: mock

value: 0 h


title: Col-0_urea_48_h_rep3 time course


title: CZJ-B2-D120

value: iPSC-derived retinal organoids


title: Col-0_mock_0_h_rep1 time course


title: CZJ-B2-D90


title: U87MG cells, shcon

city: Dalian

first: dapeng

last: Liang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

data_processing:
clean reads were retained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw fastq data using in-house perl scripts
RNASeq reads were aligned to the hg38 genome assembly using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to generate gene-level count matrix as input for edgeR’s statistical model
Differential expression analysis between shTRIP13 and shControl cells was performed using the edgeR package
Genome_build: hg38
Supplementary_files_format_and_content: txt file includes FPKM expression value and gene annotation

source_name: U87MG cell

growth_protocol: U87MG cells were cultured for one week under stem cell culture conditions

extract_protocol:
Total RNA was extracted from cells by TRIZOL
The sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions.

treatment_protocol: U87MG cells were infected with pGIPZ-CTRL and TRIP13-shRNA lentiviruses, and stable clones were selected using puromycin.

value: brain

tag: cell type

value: Glioma spheres

value: control


title: Hela-rep1-pyr

status: Public on Dec 05 2019

city: Wuhan

first: Yinsheng

last: Wu

state: Hubei

address: No.368,Youyi Avenue

department: School of life science

institute: Hubei University

description: pyruvate treatment

data_processing:
CASAVA(v1.8.2) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat(v2.0.14)(Nat Methods.2015 Apr; Kim D,et al.) with default parameter
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi,2008 with Htseq software(V0.6.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: cervix

extract_protocol:
HeLa cells were treated with pyruvate for 24h.And then total RNA was extracted using TRIzol from control and pyruvate treatment samples.And the quality was examined using Agilent Bioanalyzer according to the manufacturer’s instructions. Library   construction, sequencing and bioinformatics analysis were done by GENEWIZ Inc
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa

tag: age

tag: Sex

value: female


title: Hela-rep2-pyr

description: pyruvate treatment


title: Hela-rep3-control

description: no treatment


title: Organoid_irradiated_24h_rep1

tag: tissue


title: Organoid_control_24h_rep1


title: U87MG cells, shTRIP13

tag: treatment

value: TRIP13 knockdown


title: Col-0_mock_0_h_rep2 time course

tag: time


title: Hela-rep3-pyr

description: pyruvate treatment


title: Hela-rep2-control

description: no treatment


title: MM.MCF7-TRβ_2

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G from Affymetrix

data_processing: RMA

source_name: Mammospheres from MCF7 cell line transduced with TRβ gene replicate 2

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

growth_protocol: Mammospheres were grown in Ultralow attachment plates (Corning) in Dulbecco's Modified Eagle Medium GlutaMAX™  (Gibco-BRL Life Technologies) supplemented with 1% penicillin/streptomycin (Gibco-BRL Life Technologies), 2% B27  (Gibco), 10 ng/ml FGFb (PeproTech) and 20 ng/ml EGF (PeproTech) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted from cells using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: When indicated, T3 was added to a final concentration of 25 nM.

value: mammospheres made from luminal breast cancer cell line


title: MM.MCF7-TRβ + T3_3

source_name: Mammospheres from MCF7 cell line transduced with TRβ gene and treated with T3 (25 nM) replicate 3


title: MM.MCF7-TRβ + T3_2

source_name: Mammospheres from MCF7 cell line transduced with TRβ gene and treated with T3 (25 nM) replicate 2


title: MM.MCF7-TRβ_1

source_name: Mammospheres from MCF7 cell line transduced with TRβ gene replicate 1


title: MCF7-TRβ + T3_3

data_processing: Expression data were normalized, background and batch corrected using the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) implemented in the Transcriptome Analysis Console software version 4.0 (TAC 4.0).

source_name: MCF7 cell line transduced with TRβ gene and treated with T3 (25 nM) replicate 3

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Transcript WT Expression Arrays, Affymetrix).

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium GlutaMAX™ supplemented with 1% L-glutamine (Gibco-BRL Life Technologies), 10% fetal bovine serum (Sigma) and 1% penicillin/streptomycin (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.

value: Luminal breast cancer cell line


title: MM.MCF7 Control_2

source_name: Mammospheres from MCF7 cell line transduced with a selector Neo gene replicate 2


title: MM.MCF7 + T3_2

source_name: Mammospheres from MCF7 cell line transduced with a selector Neo gene and treated with T3 (25 nM) replicate 2


title: MM.MCF7 + T3_3

source_name: Mammospheres from MCF7 cell line transduced with a selector Neo gene and treated with T3 (25 nM) replicate 3


title: MCF7-TRβ + T3_1

source_name: MCF7 cell line transduced with TRβ gene and treated with T3 (25 nM) replicate 1


title: MM.MCF7 Control_1

source_name: Mammospheres from MCF7 cell line transduced with a selector Neo gene replicate 1


title: MM.MCF7-TRβ_3

source_name: Mammospheres from MCF7 cell line transduced with TRβ gene replicate 3


title: MCF7 + T3_3

source_name: MCF7 cell line transduced with a selector Neo gene and treated with T3 (25 nM) replicate 3


title: MM.MCF7 Control_3

source_name: Mammospheres from MCF7 cell line transduced with a selector Neo gene replicate 3


title: MCF7-TRβ_2

source_name: MCF7 cell line transduced with TRβ gene replicate 2


title: MCF7-TRβ + T3_2

source_name: MCF7 cell line transduced with TRβ gene and treated with T3 (25 nM) replicate 2


title: MM.MCF7 + T3_1

source_name: Mammospheres from MCF7 cell line transduced with a selector Neo gene and treated with T3 (25 nM) replicate 1


title: MCF7 Control_3

source_name: MCF7 cell line transduced with a selector Neo gene replicate 3


title: MCF7-TRβ_3

source_name: MCF7 cell line transduced with TRβ gene replicate 3


title: JunB.ECKO.rep3.428

city: Boston

first: Eric

last: Engelbrecht

state: MA

address: 1 Blackfan Street

department: Vascular Biology Program

institute: Boston Children's Hospital

description:
JunB.ECKO.rep3.428
processed data file:
GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx
JunB.ECKO.428.429.431.merged.RNA.bw.gz

data_processing:
ATAC-seq: Read alignment to the MGSCv37 (mm9) genome assembly was performed with bowtie2 (Langmead & Salzberg, 2012) and the options: --very-sensitive –X 2000 –no-mixed –no-discordant. Duplicated fragments were removed using the Picard “MarkDuplicates” script with the options: Remove_Duplicates=true Validation_stringency=lenient (http://broadinstitute.github.io/picard/).   Paired-end reads were separated, centered on Tn5 cut sites, and trimmed to 10 bp using a custom in-house script. Peaks were called using the MACS2 “callpeak” script (Zhang et al., 2008) with options: -B –keep-dup all –nomodel –nolambda –shift -75 –extsize 150. Reads mapping to murine blacklisted regions and mitochondrial DNA were masked out of peak lists using the Bedtools “intersect -v” script (Quinlan & Hall, 2010).   Replicates from each biological group were merged using the bedops “merge” script to generate one high-confidence peak set for each of the two biological groups (Control and gTKO) (Neph et al., 2012). These two peak sets were then merged to generate a final merged peak set of 62,748 peaks. For each replicate, reads covering consensus peak intervals were counted using the Bedtools “coverage” script with the “-counts” option (Quinlan & Hall, 2010). The resultant count table was input to edgeR (M. D. Robinson et al., 2010) to determine differentially accessible peaks (DAPs), which can be found in the excel file “GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx”. HOMER results from different peak inputs are in the excel file “GEO_retina_ATACseq_HOMER_results.xlsx”.
Base calls were performed using Illumina CASAVA 1.8.2
bigWig files:  Nucleotide-resolution coverage (bigWig) tracks were generated by first combining trimmed reads from each replicate, then inputting the resultant .bam files to the DeepTools (Ramirez et al., 2016) “bamCoverage” script with options “—normalizeUsing RPGC –binSize 1”.
bulk RNA-seq: Reads from each sample were aligned to the MGSCv37 (mm9) genome assembly using STAR (Dobin et al., 2013) with the options: --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM. Gene-level counts over UCSC annotated exons were calculated using the Rsubread package and “featureCounts” script (Liao, Smyth, & Shi, 2013) with options: -M –O –p –d 30 –D 50000. The resultant count table was input to edgeR (M. D. Robinson, McCarthy, & Smyth, 2010) for differential gene expression analysis.
bulk RNA-seq: The .bam files from STAR were input to the RSEM (B. Li & Dewey, 2011) script “rsem-calculate-expression” with default parameters to generate FPKMs for each replicate. FPKMs are located in the excel files called "GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx" and “GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx”.
Genome_build: mm9
Supplementary_files_format_and_content: The excel files "GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx" and “GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx” include RSEM-generated FPKMs and the edgeR output for RNA-seq experiments.     The excel file “GEO_retina_ATACseq_S1PR.gTKO_edgeR.xlsx” includes the edgeR output for the ATAC-seq experiment. HOMER results from different peak inputs are in the excel file “GEO_retina_ATACseq_HOMER_results.xlsx”.     All 58,311 and 50,178 merged Control and gTKO peaks, respectively, are included in the .bed files “retina.Control_peaks.narrowPeak.bed”, and “retina.gTKO_peaks.narrowPeak.bed”. The bigWig files were generated as described in "data processing".

molecule: polyA RNA

growth_protocol: Mice were housed in our animal facility with food ad libitum and 12 hr light/dark cycles. Animals were used in accordance with protocols approved by the Institutional Animal Care and Use Committees (IACUC) of Boston Children’s Hospital and the French Department of Education.

extract_protocol:
bulk RNA-seq: Cells were sorted into either 0.1% FAF-BSA/PBS or buffer RLT (Qiagen) supplemented with beta-mercaptoethanol for ATAC-seq and RNA-seq, respectively. Cells sorted into buffer RLT were subjected to total RNA extraction using the RNeasy Micro Kit (Qiagen).
ATAC-seq: ATAC-seq libraries were prepared according to the previously described fast-ATAC protocol (Corces et al., 2016). Briefly, 5,000-8,000 FACS-isolated cells in 0.1% FAF-BSA/PBS were pelleted by centrifugation at 400 xg at 4 ˚C for 5 min. Supernatant was carefully removed to leave the cell pellet undisturbed, then cells were washed once with 1 mL ice-cold PBS. The transposition mix [25 µL buffer TD, 2.5 µL TDE1 (both from Illumina FC-121-1030), 1 µL of 0.5% digitonin (Promega, G9441) and 16 µL nuclease-free water] was prepared and mixed by pipetting, then added to the cell pellet. Pellets were disrupted by gently flicking the tubes, followed by incubation at 37 ˚C for 30 minutes in an Eppendorf ThermoMixer with constant agitation at 300 rpm. Tagmented DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, 28204), and subjected to cycle-limiting PCR as previously described (Buenrostro et al., 2013). Transposed fragments were purified using the MinElute PCR Purification Kit (Qiagen, 28004) and Agilent DNA Tapestation D1000 High Sensitivity chips (Agilent) were used to quantify libraries.
RNA-seq: Double-stranded cDNA was synthesized from 5-10 ng RNA using the SMART-Seq2 v4 Ultra Low RNA Kit for Sequencing (Takara) according to the manufacturer’s instructions.

treatment_protocol: "Control" and "gTKO" pups were given intraperitoneal injections of tamoxifen (100 ug) from P1-P3. "JunB.Control" and "JunB.ECKO" pups were given subcutaneous injections of 4-hydroxytamoxifen (50 ug) from P1-P3.

tag: strain background

tag: genotype/variation

value: Junbflox/flox  Cdh5-CreERT2

value: postnatal day 6

value: FACS-sorted adult mouse retinal endothelial cells


title: MCF7 + T3_1

source_name: MCF7 cell line transduced with a selector Neo gene and treated with T3 (25 nM) replicate 1


title: MCF7-TRβ_1

source_name: MCF7 cell line transduced with TRβ gene replicate 1


title: MCF7 Control_2

source_name: MCF7 cell line transduced with a selector Neo gene replicate 2


title: JunB.ECKO.rep2.429

description:
JunB.ECKO.rep2.429
processed data file:
GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx
JunB.ECKO.428.429.431.merged.RNA.bw.gz


title: MM.MCF7-TRβ + T3_1

source_name: Mammospheres from MCF7 cell line transduced with TRβ gene and treated with T3 (25 nM) replicate 1


title: MCF7 + T3_2

source_name: MCF7 cell line transduced with a selector Neo gene and treated with T3 (25 nM) replicate 2


title: JunB.Control.rep2.425

description:
JunB.Control.rep2.425
processed data file:
GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx
JunB.WT.423.425.430.merged.RNA.bw.gz

value: Junbflox/flox


title: JunB.ECKO.rep1.431

description:
JunB.ECKO.rep1.431
processed data file:
GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx
JunB.ECKO.428.429.431.merged.RNA.bw.gz


title: CD20Cre.C45p.3

city: Philadelphia

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p9

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: Xbp1_PC_stim.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Xbp1_PC_stim.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol

source_name: Cre control, 5th division, CD138+ CpG-+IL-4,5stimulated B cell

growth_protocol: B6.Xbp1flox and B6.hCD20-TamCre mice were maintained in UPENN SPF facilities.

extract_protocol:
Spleens were harvested at time of saccrifice and lypmhocytes were stained and FACS sorted directly into TRIZOL reagent as follows:  follicular B cell: live, singlet, CD19+, CD93-, CD23+, CD21/35int.  marginal zone B cell: live, singlet, CD19+, CD93-, CD23-, CD21/35high.  In-vitro cultured were FACS sorted by live, singlet, CTV dilution and CD138 expression.
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech smarter v4 kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.

treatment_protocol: In-vivo samples are untreated from SPF mice.  In-vitro cultures from these mice were prepared from follicular B cells stimulated for  72 hours  with CpG DNA (ODN1826) with and without IL-4 and IL-5.

tag: strain

value: Xbp1 wt

value: 12 weeks

value: Spleen

value: in-vitro cultured primary B cell


title: CD20Cre.C45p.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p7


title: CD20Cre.C45p.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p6


title: JunB.Control.rep3.423

description:
JunB.Control.rep3.423
processed data file:
GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx
JunB.WT.423.425.430.merged.RNA.bw.gz


title: Col-0_urea_24_h_rep2 time course

source_name: seedlings

value: urea

tag: ecotype


title: Xbp1flox.C45p.5

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p5

source_name: Xbp1 null, 5th division, CD138+ CpG+IL-4,5-stimulated B cell

value: Xbp1 null


title: Organoid_control_24h_rep2

source_name: small intestinal organoid, non-irradiated, t=24h

value: small intestinal organoid

tag: time point


title: RNA.rep4.gTKO.170

description:
RNA.rep4.gTKO.170.KY6
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CrePos.retina.168.170.172.174.176.merged.sorted.bw.gz

value: S1pr3-/- S1pr1flox/flox S1pr2flox/flox Rosa26-CreERT2


title: JunB.Control.rep1.430

description:
JunB.Control.rep1.430
processed data file:
GEO_JunB.RNAseq_edgeR.and.RSEM_FPKMs.xlsx
JunB.WT.423.425.430.merged.RNA.bw.gz


title: RNA.rep3.gTKO.172

description:
RNA.rep3.gTKO.172.KY8
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CrePos.retina.168.170.172.174.176.merged.sorted.bw.gz


title: RNA.rep5.gTKO.168

description:
RNA.rep5.gTKO.168.KY4
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CrePos.retina.168.170.172.174.176.merged.sorted.bw.gz


title: Xbp1flox.C45p.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p1

tag: genotype


title: Xbp1flox.C45p.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p2


title: CD20Cre.C45n.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n9

source_name: Cre control, 4th division, CD138- CpG-+IL-4,5stimulated B cell


title: CD20Cre.C45n.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n6


title: Xbp1flox.C45p.4

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p4


title: CD20Cre.C45n.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n7


title: RNA.rep2.gTKO.174

description:
RNA.rep2.gTKO.174.KY10
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CrePos.retina.168.170.172.174.176.merged.sorted.bw.gz


title: RNA.rep1.gTKO.176

description:
RNA.rep1.gTKO.176.KY12
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CrePos.retina.168.170.172.174.176.merged.sorted.bw.gz


title: RNA.rep1.Control.175

description:
RNA.rep1.Control.175.KY11
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CreNeg.retina.167.169.171.173.175.merged.sorted.bw.gz

value: S1pr3-/- S1pr1flox/flox S1pr2flox/flox


title: RNA.rep4.Control.169

description:
RNA.rep4.Control.169.KY5
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CreNeg.retina.167.169.171.173.175.merged.sorted.bw.gz


title: RNA.rep2.Control.173

description:
RNA.rep2.Control.173.KY9
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CreNeg.retina.167.169.171.173.175.merged.sorted.bw.gz


title: RNA.rep5.Control.167

description:
RNA.rep5.Control.167.KY3
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CreNeg.retina.167.169.171.173.175.merged.sorted.bw.gz


title: RNA.rep3.Control.171

description:
RNA.rep3.Control.171.KY7
processed data file:
GEO_Retina_S1PR.gTKO.edgeR_RNAseq.xlsx
RNA.CreNeg.retina.167.169.171.173.175.merged.sorted.bw.gz


title: MCF7 Control_1

source_name: MCF7 cell line transduced with a selector Neo gene replicate 1


title: Xbp1flox.C45p.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45p3


title: Xbp1flox.C45n.5

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n5

source_name: Xbp1 null, 4th division, CD138- CpG+IL-4,5-stimulated B cell


title: Xbp1flox.C45n.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n2


title: CD20Cre.CpGn.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn6

source_name: Cre control, 4th division, CD138- CpG-stimulated B cell


title: Xbp1flox.C45n.4

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n4


title: Xbp1flox.CpGn.5

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn5

source_name: Xbp1 null, 4th division, CD138- CpG-stimulated B cell


title: CD20Cre.CpGn.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn9


title: Xbp1flox.C45n.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n1


title: CD20Cre.CpGn.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn7


title: Xbp1flox.CpGn.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn3


title: Xbp1flox.CpGn.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn1


title: Xbp1flox.MZ_B.5

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ5

source_name: Xbp1 null marginal zone B cell

value: Splenic B cell


title: Xbp1flox.MZ_B.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ3


title: Xbp1flox.CpGn.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn2


title: CD20Cre.MZ_B.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ7

source_name: Cre control marginal zone B cell


title: CD20Cre.MZ_B.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ6


title: Xbp1flox.C45n.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-C45n3


title: Xbp1flox.MZ_B.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ1


title: Xbp1flox.MZ_B.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ2


title: Xbp1flox.FO_B.5

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO5

source_name: Xbp1 null follicular B cell


title: CD20Cre.MZ_B.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ9


title: Xbp1flox.MZ_B.4

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-MZ4


title: CD20Cre.FO_B.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO9

source_name: Cre control follicular B cell


title: Xbp1flox.CpGn.4

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-CPGn4


title: Xbp1flox.FO_B.4

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO4


title: CD20Cre.FO_B.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO7


title: CD20Cre.FO_B.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO6


title: Xbp1flox.FO_B.3

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO3


title: Xbp1flox.FO_B.2

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO2


title: Xbp1flox.FO_B.1

description:
processed data file:
Xbp1_PC_stim.normExp.txt, Xbp1_PC_stim.rawTPM.txt
116-FO1


title: MZ.Rp.0h.neg.3

description:
processed data file:
Raptor_PC_stim.normExp.txt, Raptor_PC_stim.rawTPM.txt

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: Raptor_PC_stim.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Raptor_PC_stim.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol

source_name: Rptor null marginal zone B cell

treatment_protocol: In-vivo samples are untreated from SPF mice.  In-vitro cultures from these mice were prepared from follicular B cells stimulated for 24, 48 and 72 hours with CpG DNA (ODN1826) with  IL-4 and IL-5.

value: Rptor null


title: MZ.Cr.0h.neg.1

source_name: Rptor wt marginal zone B cell

value: Rptor wt


title: MZ.Cr.0h.neg.2


title: MZ.Rp.0h.neg.1


title: MZ.Rp.0h.neg.2


title: MZ.Cr.0h.neg.3


title: FO.Cr.72h.pos.3

source_name: Rptor null, CD138+, 72h CpG-stimulated follicular B cell


title: FO.Cr.72h.pos.2


title: FO.Cr.72h.pos.1


title: FO.Cr.72h.neg.3

source_name: Rptor wt, CD138-, 72h CpG-stimulated follicular B cell


title: FO.Cr.72h.neg.1


title: FO.Cr.72h.neg.2


title: FO.Rp.72h.pos.2


title: FO.Rp.72h.pos.1


title: FO.Rp.72h.neg.3

source_name: Rptor null, CD138-, 72h CpG-stimulated follicular B cell


title: FO.Cr.48h.neg.2

source_name: Rptor wt, CD138-, 48h CpG-stimulated follicular B cell


title: FO.Rp.48h.neg.2

source_name: Rptor null, CD138-, 48h CpG-stimulated follicular B cell


title: FO.Rp.48h.neg.3


title: FO.Cr.48h.neg.1


title: FO.Rp.48h.neg.1


title: FO.Rp.72h.neg.2


title: FO.Cr.48h.neg.3


title: FO.Cr.24h.neg.3

source_name: Rptor wt, CD138-, 24h CpG-stimulated follicular B cell


title: FO.Cr.24h.neg.1


title: FO.Rp.24h.neg.3

source_name: Rptor null, CD138-, 24h CpG-stimulated follicular B cell


title: FO.Rp.72h.pos.3


title: FO.Rp.24h.neg.2


title: FO.Rp.0h.neg.3

source_name: Rptor null follicular B cell


title: FO.Cr.0h.neg.1

source_name: Rptor wt follicular B cell


title: FO.Rp.24h.neg.1


title: FO.Cr.0h.neg.3


title: Hela-rep1-control

description: no treatment

source_name: cervix

value: HeLa

value: female


title: FO.Rp.72h.neg.1


title: FO.Rp.0h.neg.2


title: FO.Cr.0h.neg.2


title: FO.Rp.0h.neg.1


title: NP_LPS.Bcell.3

description:
NP_BC3
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of 4 lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
data was analysed both before and after being filtered to remove immunoglobulin transcripts prior to further analysis
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: NPLPS_PC_stim.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: NPLPS_PC_stim.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: NPLPS_PC_stim_noIg.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts
Supplementary_files_format_and_content: NPLPS_PC_stim_noIg.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts

growth_protocol: B6.Blimp1+/GFP mice were maintained in UPENN SPF facilities.

extract_protocol:
Spleens were harvested at time of saccrifice and lypmhocytes were stained and FACS sorted directly into TRIZOL reagent as follows: naïve B cell: live, singlet, Dump(CD4, CD8a, Ter-119, F4-80)-, IgDhigh, B220+, NP-; activated B cell: live, singlet, IgD-, Dump-, GFP(Blimp1)-, CD138-, B220+, NP+; plasma cell: live, singlet, IgD-, Dump-, GFP(Blimp1)+, CD138+, B220+/-, NP+.
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech smarter v4 kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.

treatment_protocol: Mice were immunized I.P. 4 days prior to saccrifice with 50 μg NP-LPS

value: NP-binding activated B cell


title: NP_LPS.Bcell.2

description:
NP_BC2
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt


title: Organoid_control_24h_rep3

source_name: small intestinal organoid, non-irradiated, t=24h

value: control


title: NP_LPS.PC.3

description:
NP_PC3
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt

value: NP-binding plasma cell


title: Naive.Bcell.2

description:
IgD_BC2
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt

value: Naive B cell


title: Naive.Bcell.1

description:
IgD_BC1
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt

value: 12 weeks


title: NP_LPS.PC.2

description:
NP_PC2
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt

value: Spleen


title: NP_LPS.PC.1

description:
NP_PC1
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt


title: NP_LPS.Bcell.1

description:
NP_BC1
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt


title: mGst-LfngT2AVenus-SC-p11-exp2-seqrun1

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institue

description: mRNA

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Genome_build: Ensembl version 93 of the mouse genome
Supplementary_files_format_and_content: Tabular-separated file indicating number of transcripts per cell obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell.

source_name: mouse gastruloid

growth_protocol: 120h Mouse gastruloids from IB10 or LfngT2AVEnus mESCs were generated as described previously (van den Brink et al., Development, 2014; Baillie-Johnson et al., 2014), with the following modifications: After neutralization of trypsin with ESLIF, cells were washed with PBS twice. Next cells, were resuspended in N2B27 medium, and the concentration was determined while cells were already in N2B27. Cells were then diluted in N2B27 to a concentration of 7.5 cells/µl (37.500 cells in 5 ml of N2B27 for a full 96-wells plate), and 40 µl (300 cells) of this suspension was transferred to each well of a U-bottomed 96-wells plate. N2B27 was ordered by Takara (NDiff 227 medium, 500 ml, Y40002) and was thawed and aliquotted to prevent the formation of protein aggregates.

extract_protocol:
Gastruloids were dissociated by carefully washing them with PBS 2x, adding 50 μl Trypsin-EDTA to the well, incubating at 37 °C for 5 min 162 until they start to fall apart. Then we dissociate by pipetting up and down with a p200 pipette, inactivate Trypsin with 100 μl ESLIF, spin ~170 x g for 3 min, remove supernatant and resuspend in PBS with 10% serum. 164 Prior to FACS, DAPI (Thermo Fisher) was added to assess cell viability, and cells were sorted in the individual wells of a 384-well plate as described previously (Muraro, M. J. et al. Cell Syst 3, 385– 394.e3 (2016)) using a BD FACSJazz Cell Sorter 166 (BD Biosciences) that was equipped with BD FACS software (version 1.2.0.124). scRNA-seq on cells that were sorted was performed using the CEL-Seq2-based SORT-Seq method (Muraro, M. J. et al. Cell Syst 3, 385– 394.e3 (2016)). Bulk gastruloid A is a mix of 10 gastruloids dissociated together. Gastruloids B-J have been dissociated individually.
Celseq2 runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode.
Illumina TruSeq adapaters.

tag: sample

tag: experiment

value: single cell

tag: protocol/barcodes

tag: days after aggregation

tag: sequencing runs

value: 1 from 1

tag: plates

tag: gastruloid barcodes

value: bulk, 30 pooled gastruloids, also sequenced with 10x Genomics (batch1)


title: mGst-LfngT2AVenus-SC-p12-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p10-exp2-seqrun1

description: mRNA

value: bulk, 30 pooled gastruloids, also sequenced with 10x Genomics (batch2)


title: mGst-LfngT2AVenus-SC-p14-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p13-exp2-seqrun1

description: mRNA


title: FO.Cr.24h.neg.2

tag: age

tag: cell type

value: in-vitro cultured primary B cell


title: mGst-LfngT2AVenus-SC-p09-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p08-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p06-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p07-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p05-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p04-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p03-exp2-seqrun1

description: mRNA


title: Naive.Bcell.3

description:
IgD_BC3
processed data file:
NPLPS_PC_stim.normExp.txt, NPLPS_PC_stim.rawTPM.txt, NPLPS_PC_stim_noIg.normExp.txt, NPLPS_PC_stim_noIg.rawTPM.txt

tag: tissue


title: mGst-LfngT2AVenus-SC-p05-exp1-seqrun1

description: mRNA

value: bulk, 15 pooled gastruloids


title: mGst-LfngT2AVenus-SC-p01-exp2-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p06-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p14-exp3-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p03-exp1-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p02-exp1-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p07-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p10-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p05-exp3-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p02-exp2-seqrun1

description: mRNA


title: mGst-LfngT2AVenus-SC-p04-exp1-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p12-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p11-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p13-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p03-exp3-seqrun1

description: mRNA

value: 1 from 2


title: mGst-E14IB10-SC-p04-exp3-seqrun1

description: mRNA

value: 2 from 2


title: mGst-E14IB10-SC-p01-exp3-seqrun1

description: mRNA


title: mGst-Lfng-10x-B2B

description: mRNA

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Genome_build: Ensembl version 93 of the mouse genome
Supplementary_files_format_and_content: Tabular-separated files indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell.

growth_protocol: 120h Mouse gastruloids from LfngT2AVenus mESCs line were generated as described previously (van den Brink et al., Development, 2014; Baillie-Johnson et al., 2014), with the following modifications: After neutralization of trypsin with ESLIF, cells were washed with PBS twice. Next cells, were resuspended in N2B27 medium, and the concentration was determined while cells were already in N2B27. Cells were then diluted in N2B27 to a concentration of 7.5 cells/µl (37.500 cells in 5 ml of N2B27 for a full 96-wells plate), and 40 µl (300 cells) of this suspension was transferred to each well of a U-bottomed 96-wells plate. N2B27 was ordered by Takara (NDiff 227 medium, 500 ml, Y40002) and was thawed and aliquotted to prevent the formation of protein aggregates. To dissociate gastruloids for scRNA-seq, gastruloids were washed with PBS 2x, incubated in Trypsin-EDTA at 37 °C for 5 min and titrated with a p200 pipette, after which ESLIF (see above) was added to neutralize the Trypsin. After centrifugation (170 x g, 3 min), cells were resuspended in PBS with 10% serum and filtered through a 35 μm filter (Falcon, 352235). Prior to FACS, DAPI (Thermo Fisher) was added to assess cell viability. For SORT-seq, individual live cells were sorted into the wells of a 384-well plate as described previously34 using a BD FACSJazzTM Cell Sorter (BD Biosciences) that was equipped with BD FACS software (version 1.2.0.124). For 10x Genomics scRNA-seq, washes were done using PBS0 (PBS without calcium and magnesium), and 100,000 live cells were sorted into 1.5 ml DNA lowbind tubes (Eppendorf, 022431021) that were pre-filled with 50 μl PBS0, after which cells were centrifuged for 3 min at 200 x g, resuspended in 80 μl PBS0 containing 5-10% serum, and filtered through a 35 μm filter (Falcon, 352235). After resuspension and filtering, the cell concentration was determined using a counting chamber (Bürker-Türk, Marienfeld). For 10x Genomics scRNA-seq, two batches were used: B1 is made of old LfngT2AVenus cells, and B2 is made from freshly thawed LfngT2AVenus cells. For each batch, two replicates were processed (denoted by A or B) concentrations of fetal calfs serum). Each sample contains 2,000-4,000 cells from a pool of 25 gastruloids.

extract_protocol:
After cryosectioning, sections are sorted into 96 well plates containing mineral oil, and uniquely barcoded cell specific primers (celseq1 or celseq2 barcodes) for mRNA detection, Spike-in controls inhibitor.
Tomo-seq-celseq: celseq1 runs contain the cell-specific barcode in the first 8 nucleotides in Read 1, followed by the 4-nucleotide long UMI. Celseq2 runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode. 10x Genomics follows the standard 10X library contrustion protocol.
Illumina TruSeq adapaters

value: 10x Genomics

value: 10x barcode


title: mGst-Lfng-10x-B2A

description: mRNA


title: mGst-Lfng-10x-B1B

description: mRNA


title: mGst-LfngT2AVenus-SC-p01-exp1-seqrun1

description: mRNA


title: mGst-Lfng-02-seqrun2

description: SvdB-Lfng2-Tomo-F8-11-20um-FullGastruloid-Run2

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Genome_build: Ensembl version 93 of the mouse genome
Supplementary_files_format_and_content: Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell.

growth_protocol: 120h Mouse gastruloids from Lfng mESCs were generated as described previously (van den Brink et al., Development, 2014; Baillie-Johnson et al., 2014), with the following modifications: After neutralization of trypsin with ESLIF, cells were washed with PBS twice. Next cells, were resuspended in N2B27 medium, and the concentration was determined while cells were already in N2B27. Cells were then diluted in N2B27 to a concentration of 7.5 cells/µl (37.500 cells in 5 ml of N2B27 for a full 96-wells plate), and 40 µl (300 cells) of this suspension was transferred to each well of a U-bottomed 96-wells plate. N2B27 was ordered by Takara (NDiff 227 medium, 500 ml, Y40002) and was thawed and aliquotted to prevent the formation of protein aggregates

extract_protocol:
After cryosectioning, sections are sorted into 96 well plates containing mineral oil, and uniquely barcoded cell specific primers (celseq1 or celseq2 barcodes) for mRNA detection, Spike-in controls inhibitor.
Tomo-seq-celseq: celseq1 runs contain the cell-specific barcode in the first 8 nucleotides in Read 1, followed by the 4-nucleotide long UMI. Celseq2 runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode
Illumina TruSeq adapaters

value: tomo-seq

tag: section thickness

value: from 13 to 61


title: mGst-Lfng-03-seqrun1

description: SvdB-Lfng2-Tomo-B10-12-20um-FullGastruloid-Run1

value: from 14 to 59


title: mGst-E14IB10-SC-p15-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p09-exp3-seqrun1

description: mRNA


title: mGst-Lfng-03-seqrun2

description: SvdB-Lfng2-Tomo-B10-12-20um-FullGastruloid-Run2


title: mGst-Lfng-02-seqrun1

description: SvdB-Lfng2-Tomo-F8-11-20um-FullGastruloid-Run1


title: mGst-E14IB10-SC-p08-exp3-seqrun1

description: mRNA


title: mGst-E14IB10-SC-p02-exp3-seqrun1

description: mRNA


title: mGst-Lfng-01-seqrun2

description: SvdB-Lfng2-Tomo-E8-10-20um-FullGastruloid-Run2

value: from 14 to 69


title: mGst-Lfng-01-seqrun1

description: SvdB-Lfng2-Tomo-E8-10-20um-FullGastruloid-Run1


title: mGst-E14IB10-SC-p13-exp2-seqrun1

growth_protocol: 120h Mouse gastruloids from IB10 mESCs were generated as described previously (van den Brink et al., Development, 2014; Baillie-Johnson et al., 2014), with the following modifications: After neutralization of trypsin with ESLIF, cells were washed with PBS twice. Next cells, were resuspended in N2B27 medium, and the concentration was determined while cells were already in N2B27. Cells were then diluted in N2B27 to a concentration of 7.5 cells/µl (37.500 cells in 5 ml of N2B27 for a full 96-wells plate), and 40 µl (300 cells) of this suspension was transferred to each well of a U-bottomed 96-wells plate. N2B27 was ordered by Takara (NDiff 227 medium, 500 ml, Y40002) and was thawed and aliquotted to prevent the formation of protein aggregates

extract_protocol:
Gastruloids were dissociated by carefully washing them with PBS 2x, adding 50 μl Trypsin-EDTA to the well, incubating at 37 °C for 5 min 162 until they start to fall apart. Then we dissociate by pipetting up and down with a p200 pipette, inactivate Trypsin with 100 μl ESLIF, spin ~170 x g for 3 min, remove supernatant and resuspend in PBS with 10% serum. 164 Prior to FACS, DAPI (Thermo Fisher) was added to assess cell viability, and cells were sorted in the individual wells of a 384-well plate as described previously (Muraro, M. J. et al. Cell Syst 3, 385– 394.e3 (2016)) using a BD FACSJazz Cell Sorter 166 (BD Biosciences) that was equipped with BD FACS software (version 1.2.0.124). scRNA-seq on cells that were sorted was performed using the CEL-Seq2-based SORT-Seq method (Muraro, M. J. et al. Cell Syst 3, 385– 394.e3 (2016)). Bulk gastruloid A is a mix of 10 gastruloids dissociated together. Gastruloids B-J have been dissociated individually.
Celseq2 runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode
Illumina TruSeq adapaters

value: mouse gastruloid


title: RNA-seq wildtype replicate 5 [TA RNA-seq]

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

description:
W384-Mu-2-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using Tophat 2 with Bowtie 2.
FPKM values were generated using Cufflinks.
Ingenuity Pathway Analysis was run using a differential expression list generated by Cufflinks filtered for p < 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx: Excel file includes FPKM values for each sample.

source_name: Tibialis anterior muscle homogenate

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology.

extract_protocol:
Whole TA muscles were homogenized in RNAzol lysis reagent and further processed as per manufacturer's instructions to obtain RNA for library preparation and subsequent NGS.
TruSeq stranded mRNA.

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before a 1 year experimental period before harvest of TA muscles.

value: Whole TA muscle


title: RNA-seq wildtype replicate 2 [MP RNA-seq]

description:
ws25
WT;Hic1F/F 2
processed data file: Supplemental_Table_2_RNA-seq_Hic1_10d_cKO_MP_gene_expression.xlsx

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using Tophat 2 with Bowtie 2.
FPKM values were generated using Cufflinks.
Ingenuity Pathway Analysis was run using a differential expression list generated by Cufflinks filtered for p < 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Supplemental_Table_2_RNA-seq_Hic1_10d_cKO_MP_gene_expression.xlsx: Excel file includes FPKM values for each sample.

source_name: Mesenchymal Progenitors

extract_protocol:
FACS purified cells were centrifuged, resuspended in RNAzol lysis reagent and further processed as per manufacturer's instructions to obtain RNA for library preparation and subsequent NGS.
TruSeq stranded mRNA.

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before experiments were performed.

value: Whole hindlimb muscle

value: Mesenchymal progenitors


title: RNA-seq wildtype replicate 3 [MP RNA-seq]

description:
ws29
WT;Hic1F/F 3
processed data file: Supplemental_Table_2_RNA-seq_Hic1_10d_cKO_MP_gene_expression.xlsx


title: RNA-seq knockout replicate 3 [MP RNA-seq]

description:
ws26
UBC-CreERT2;Hic1F/F 3
processed data file: Supplemental_Table_2_RNA-seq_Hic1_10d_cKO_MP_gene_expression.xlsx


title: RNA-seq knockout replicate 5 [TA RNA-seq]

description:
W382-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq wildtype replicate 6 [TA RNA-seq]

description:
W385-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq knockout replicate 3 [TA RNA-seq]

description:
73-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq wildtype replicate 7 [TA RNA-seq]

description:
W388-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq knockout replicate 2 [TA RNA-seq]

description:
62-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq knockout replicate 1 [MP RNA-seq]

description:
ws28
UBC-CreERT2;Hic1F/F 1
processed data file: Supplemental_Table_2_RNA-seq_Hic1_10d_cKO_MP_gene_expression.xlsx


title: RNA-seq knockout replicate 9 [TA RNA-seq]

description:
W391-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq wildtype replicate 4 [TA RNA-seq]

description:
40-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq wildtype replicate 2 [TA RNA-seq]

description:
18-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq knockout replicate 6 [TA RNA-seq]

description:
W383-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq wildtype replicate 3 [TA RNA-seq]

description:
29-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq knockout replicate 2 [MP RNA-seq]

description:
ws30
UBC-CreERT2;Hic1F/F 2
processed data file: Supplemental_Table_2_RNA-seq_Hic1_10d_cKO_MP_gene_expression.xlsx


title: RNA-seq knockout replicate 1 [TA RNA-seq]

description:
51-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq knockout replicate 7 [TA RNA-seq]

description:
W389-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq wildtype replicate 1 [TA RNA-seq]

description:
7-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: RNA-seq knockout replicate 8 [TA RNA-seq]

description:
W390-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: GP33_day8

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Demultiplexing was performed using the mkfastq function in Cell Ranger (version 1.3.1) (10x Genomics)
Alignment and generation of gene-barcode matrix was performed using the count function in Cell Ranger (version 1.3.1) (10x Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx: filtered gene-barcode matrix in MEX format

extract_protocol: CD8+ CD44+ gp33+ cells from the spleen of C57BL/6 mice on day 8 or day 30 p.i. with LCMV Clone 13 were sorted by flow cytometry, then single cell libraries were prepared according the the 10x Genomics Chromium Single Cell 3' Reagent Kit protocol.

tag: strain background

value: day 8 p.i.

value: spleen

value: CD8 T cells

tag: cell subset


title: mGst-E14IB10-SC-p12-exp2-seqrun1

value: single cell

value: 1 from 1


title: Single cell ATAC-seq tdTomato MPs quiescent

description: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP Quiescent

data_processing:
Samples were demultiplexed using cellranger-atac 1.1.0 mkfastq with bcl2fastq.
Samples were aligned and output matrices generated using cellranger-atac 1.1.0 count for alignment and peak calling to cell clustering.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak matrices, cell barcode and peak list are included as .mtx, .tsv and .bed files, respectively.

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium nuclei preparation pipeline.
Nuclei were lysed for five minutes according to 10x standard protocol and subjected to the transposition reaction followed by library preparation pipeline and subsequent NGS.
Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 Rev B).
2 x 75 PE kit to produce 2 X 50 reads.

tag: strain

value: Mesenchymal Progenitors


title: mGst-Lfng-10x-B1A

description: mRNA


title: RNA-seq knockout replicate 4 [TA RNA-seq]

description:
W381-Mu-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx


title: mGst-E14IB10-SC-p11-exp2-seqrun1


title: mGst-E14IB10-SC-p10-exp2-seqrun1


title: RNA-seq wildtype replicate 1 [MP RNA-seq]

description:
ws27
WT;Hic1F/F 1
processed data file: Supplemental_Table_2_RNA-seq_Hic1_10d_cKO_MP_gene_expression.xlsx


title: GP33_day30

value: day 30 p.i.


title: mGst-E14IB10-SC-p09-exp2-seqrun1


title: mGst-E14IB10-SC-p06-exp2-seqrun1


title: mGst-E14IB10-SC-p06-exp1-seqrun2

description:
SvdB12f2-6-CELSEQ2-5dAA-Bulk-mGstrlds-Run1-2_cbc_trimmed_star_ie_spliced.coutb.tsv
SvdB12f2-6-CELSEQ2-5dAA-Bulk-mGstrlds-Run1-2_cbc_trimmed_star_ie_spliced.coutc.tsv
SvdB12f2-6-CELSEQ2-5dAA-Bulk-mGstrlds-Run1-2_cbc_trimmed_star_ie_spliced.coutt.tsv

value: 2 from 2


title: mGst-E14IB10-SC-p07-exp1-seqrun1

description:
SvdB12f2-7-CELSEQ2-5dAA-Bulk-mGstrlds-Run1-2_cbc_trimmed_star_ie_spliced.coutb.tsv
SvdB12f2-7-CELSEQ2-5dAA-Bulk-mGstrlds-Run1-2_cbc_trimmed_star_ie_spliced.coutc.tsv
SvdB12f2-7-CELSEQ2-5dAA-Bulk-mGstrlds-Run1-2_cbc_trimmed_star_ie_spliced.coutt.tsv

value: 1 from 2


title: mGst-E14IB10-SC-p04-exp2-seqrun1


title: mGst-E14IB10-SC-p08-exp2-seqrun1


title: mGst-E14IB10-SC-p07-exp1-seqrun2


title: mGst-E14IB10-SC-p05-exp2-seqrun1


title: mGst-E14IB10-SC-p01-exp2-seqrun1


title: mGst-E14IB10-SC-p07-exp2-seqrun1


title: mGst-E14IB10-01-seqrun1

description:
mG01_trim_star_spliced.coutb.tsv
mG01_trim_star_spliced.coutc.tsv
mG01_trim_star_spliced.coutt.tsv

value: tomo-seq


title: mGst-E14IB10-SC-p06-exp1-seqrun1


title: mGst-E14IB10-04-seqrun1

description:
mG04_trim_star_spliced.coutb.tsv
mG04_trim_star_spliced.coutc.tsv
mG04_trim_star_spliced.coutt.tsv

value: 1 from 3


title: mGst-E14IB10-01-seqrun2


title: mGst-E14IB10-02-seqrun1

description:
mG02_trim_star_spliced.coutb.tsv
mG02_trim_star_spliced.coutc.tsv
mG02_trim_star_spliced.coutt.tsv


title: mGst-E14IB10-03-seqrun1

description:
mG03_trim_star_spliced.coutb.tsv
mG03_trim_star_spliced.coutc.tsv
mG03_trim_star_spliced.coutt.tsv


title: mGst-E14IB10-03-seqrun2


title: mGst-E14IB10-02-seqrun2


title: mGst-E14IB10-05-seqrun2

description:
mG05_trim_star_spliced.coutb.tsv
mG05_trim_star_spliced.coutc.tsv
mG05_trim_star_spliced.coutt.tsv

value: 2 from 3


title: mGst-E14IB10-04-seqrun2


title: mGst-E14IB10-05-seqrun1


title: mGst-E14IB10-05-seqrun3

value: 3 from 3


title: Single cell RNA-seq tdTomato MPs 14 day post notexin injury

description: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 14DPI

data_processing:
Samples were demultiplexed using cellranger mkfastq with bclfastq2.
Samples were aligned and output matrices generated using cellranger count for alignment.
cellranger aggregate for alignment, matrix etc
Genome_build: mm10 with appended tdTomato and EGFP sequences
Supplementary_files_format_and_content: gene matrices, cell barcode and gene list are included as .mtx, .csv and .csv files, respectively

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium library preparation pipeline and subsequent NGS.
10X Chromium Single Cell 3' v2

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before experments were performed.

tag: time

value: 14 day post notexin injury


title: Single cell RNA-seq tdTomato MPs 2 day post notexin injury

description: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 2DPI

value: 2 day post notexin injury


title: Single cell RNA-seq tdTomato MPs 1 day post notexin injury

description: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 1DPI

value: Whole hindlimb muscle

value: 1 day post notexin injury


title: Single cell RNA-seq tdTomato MPs quiescent

value: quiescent


title: mGst-E14IB10-SC-p02-exp2-seqrun1

value: mouse gastruloid


title: mGst-E14IB10-04-seqrun3


title: RNA-seq tdTomato MPs 10 day post injury

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 10DPI
10 DPI tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using Tophat 2 with Bowtie 2.
FPKM values were generated using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology

extract_protocol:
FACS purified cells were centrifuged, resuspended in RNAzol lysis reagent and further processed as per manufacturers instructions to obtain RNA for library preparation and subsequent NGS.
tru seq stranded mRNA

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before experments were performed

value: 10 day post notexin injury


title: Single cell RNA-seq tdTomato MPs 4 day post notexin injury

description: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 4DPI

value: 4 day post notexin injury


title: RNA-seq tdTomato MPs 7 day post injury

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 7DPI
7 DPI tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx

value: 7 day post notexin injury


title: RNA-seq tdTomato MPs 5 day post injury

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 5DPI
5 DPI tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx

value: Mesenchymal Progenitors

value: 5 day post notexin injury


title: RNA-seq tdTomato MPs 4 day post injury

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 4DPI
4 DPI tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx


title: mGst-E14IB10-SC-p03-exp2-seqrun1

value: single cell

value: 1 from 1


title: RNA-seq tdTomato MPs 3 day post injury

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 3DPI
3 DPI tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx

value: 3 day post notexin injury


title: Lineage negative Sca1 negative fraction replicate 4

description:
Lin - Sca1 - 4
Lin - Sca1 - 4.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

data_processing:
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using Tophat 2 with Bowtie 2.
FPKM values were generated using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample.

source_name: lineage negative sca1 negative mononuclear cell fraction

tag: cell population


title: Lineage negative fraction replicate 3

description:
Lin - 3
Lin - 3.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

source_name: lineage negative mononuclear cell fraction


title: Lineage negative Sca1 negative fraction replicate 1

description:
Lin - Sca1 - 1
Lin - Sca1 - 1.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

value: lineage negative sca1 negative mononuclear cell fraction


title: RNA-seq tdTomato MPs 2 day post injury

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 2DPI
2 DPI tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx


title: RNA-seq tdTomato MPs 1 day post injury

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP NTX 1DPI
1 DPI tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx


title: Lineage negative Sca1 positive fraction replicate 1

description:
Lin - Sca1 + 1
Lin - Sca1 + 1.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

source_name: mesechymal progenitor fraction

value: mesechymal progenitor fraction


title: Lineage negative fraction replicate 4

description:
Lin - 4
Lin - 4.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

value: lineage negative mononuclear cell fraction


title: Lineage negative Sca1 positive fraction replicate 3

description:
Lin - Sca1 + 3
Lin - Sca1 + 3.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: Lineage positive fraction replicate 4

description:
Lin + 4
Lin + 4.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

source_name: endothelial and blood dervived mononuclear cell fraction


title: Lineage positive fraction replicate 3

description:
Lin + 3
Lin + 3.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

value: endothelial and blood dervived mononuclear cell fraction


title: RNA-seq tdTomato MPs quiescent

description:
Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MP Quiescent
Quiescent tdTomato MPs.FPKM
Supplemental_Table_4_RNA-seq_MP_muscle_injury.xlsx


title: Lineage negative Sca1 positive fraction replicate 2

description:
Lin - Sca1 + 2
Lin - Sca1 + 2.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: Lineage positive fraction replicate 2

description:
Lin + 2
Lin + 2.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: Lineage negative Sca1 negative fraction replicate 2

description:
Lin - Sca1 - 2
Lin - Sca1 - 2.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: Lineage positive fraction replicate 1

description:
Lin + 1
Lin + 1.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: Lineage negative fraction replicate 1

description:
Lin - 1
Lin - 1.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: Lineage negative fraction replicate 2

description:
Lin - 2
Lin - 2.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: Whole muscle mononuclear cell suspension replicate 2

description:
Whole muscle 2
Whole Muscle2.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

source_name: muscle all mononuclear cells

value: muscle all mononuclear cells


title: Whole muscle mononuclear cell suspension replicate 3

description:
Whole muscle 3
Whole Muscle3.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

value: Whole hindlimb muscle


title: Whole muscle mononuclear cell suspension replicate 1

description:
Whole muscle 1
Whole Muscle1.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: RNAPII_ChIA-PET_ZnSO4 Treatment

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

description: RNAPII_ChIA-PET_ZnSO4 Treatment

data_processing:
Library strategy: ChIA-PET
Filtering linker sequence using in-house script
Mapping to reference genome using BWA MEM
Deduplicating reads using Picard (MarkDuplicates)
Peak-calling using MACS (v1.4)
2D contact map using Juicer tool
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt format for peak (bed), loop (bedpe), binary data format for Juicebox (hic)

growth_protocol: Both U937-PR9 and NB4 cells were cultured in RPMI 1640 (ThermoFisher, A10491), supplemented with 10% fetal bovine serum (ThermoFisher, 10082147). These cells were cultured at 37 ℃ , 5% CO2, and ambient oxygen levels.

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 ×150bp) was used for ChIA-PET libraries  with Illumina Hiseq 2500 or Illumina Nextseq 500.

treatment_protocol: The U937-PR9 cells were treated with 100 μM ZnSO4 (Sigma, Z0251) for 4 hours for ChIA-PET and ChIP-Seq experiment. The U937-PR9 cells were treated with 100 μM ZnSO4  and then collected these cells at 4, 6, 12, 24 hours for RNA-Seq experiment. These cells was preincubated with 100 μM ZnSO4 for 4 hours and then treated with ATRA (Sigma, R2625) for 24 and 48 hours used for RNA-Seq experiment. NB4 cells were treated with ATRA for 24 and 48 hours used for RNA-Seq experiment.

tag: method

value: ChIA-PET

tag: factor

value: RNAPII (Biolegend, catalog# 920102)

tag: molecule subtype

value: nuclear chromatin


title: CTCF_ChIA-PET_Control

value: CTCF (Abcam, catalog# ab70303)


title: RARA_ChIA-PET_ZnSO4 Treatment

description: RARA_ChIA-PET_ZnSO4 Treatment

value: RARA (Santa Cruz, catalog# sc-551X)


title: Lineage negative Sca1 negative fraction replicate 3

description:
Lin - Sca1 - 3
Lin - Sca1 - 3.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx


title: hGst02-ChiSB43-seqrun1

description:
mRNA
processed data file: SvdB13a1-2-Tomo-120hAA-hGstrlds79-19052018-ChiSB43_cbc_trimmed_star_ie2_spliced.coutb.tsv.gz
processed data file: SvdB13a1-2-Tomo-120hAA-hGstrlds79-19052018-ChiSB43_cbc_trimmed_star_ie2_spliced.coutc.tsv.gz
processed data file: SvdB13a1-2-Tomo-120hAA-hGstrlds79-19052018-ChiSB43_cbc_trimmed_star_ie2_spliced.coutt.tsv.gz

data_processing:
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the human genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Genome_build: Ensembl version 93 of the human genome
Supplementary_files_format_and_content: Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell.

source_name: human gastruloid

growth_protocol: The SB43 pre-treated gastruloids for tomo-sequencing were made with RUES2-GLR cells pretreated in Nutristem with 3.25 μM Chiron and 10 μM SB431542 (1614). They were then aggregated in E6 with 3 μM Chiron and ROCK inhibitor. Subsequent media changes were performed daily with E6 alone.

extract_protocol:
After cryosectioning, sections are sorted into 96 well plates containing mineral oil, and uniquely barcoded cell specific primers (celseq1 or celseq2 barcodes) for mRNA detection, Spike-in controls inhibitor.
Tomo-seq-celseq: celseq1 runs contain the cell-specific barcode in the first 8 nucleotides in Read 1, followed by the 4-nucleotide long UMI. Celseq2 runs contain the 6-nucleotide long UMI in the first nucleotides of Read 1, followed by the 8-nucleotide long cell-specific barcode.
Illumina TruSeq adapaters

tag: sample

tag: experiment

value: tomo-seq

tag: protocol/barcodes

value: 1 from 2


title: hGst01-ChiSB43-seqrun1

description:
mRNA
processed data file: SvdB13a1-1-Tomo-120hAA-hGstrlds10-19052018-ChiSB43_cbc_trimmed_star_ie2_spliced.coutb.tsv.gz
processed data file: SvdB13a1-1-Tomo-120hAA-hGstrlds10-19052018-ChiSB43_cbc_trimmed_star_ie2_spliced.coutc.tsv.gz
processed data file: SvdB13a1-1-Tomo-120hAA-hGstrlds10-19052018-ChiSB43_cbc_trimmed_star_ie2_spliced.coutt.tsv.gz

tag: days after aggregation

tag: sequencing runs

tag: plates


title: hGst01-ChiSB43-seqrun2

value: 2 from 2

tag: gastruloid barcodes


title: hGst02-ChiSB43-seqrun2


title: Whole muscle mononuclear cell suspension replicate 4

description:
Whole muscle 4
Whole Muscle4.FPKM
Supplemental_Table_1_RNA-seq_Mononuclear_fractions.xlsx

tag: tissue


title: hGst02-Chi-seqrun2

growth_protocol: Human gastruloids at 72 hours after aggregation were made from the RUES2-GLR line. After pre-treatment for 24 hours in 3.25 mM CHIR99021 (‘Chiron’; Tocris Biosciences, 4423), cells were dissociated using 0.5 mM EDTA in PBS-/- (Invitrogen, 15575-038) and washed in PBS-/- . The cell suspension was then counted and resuspended at 10 cells per 1 ml in basal differentiation medium, Essential 6 (‘E6’; ThermoFisher, A15165-01) supplemented with 1:2000 Y-27632 (‘ROCK inhibitor’; Sigma Aldrich, Y0503) and 0.5 mM Chiron. 40 ml of this cell suspension was then added to each well of an ultra-low adherence 96-well plate (CellStar, 650970). The cell suspension was centrifuged using a benchtop plate centrifuge at 700 rpm for 2 minutes. The following day, 150 ml fresh E6 medium was added to each well. Medium was exchanged for fresh E6 medium daily following this timepoint.

value: human gastruloid

tag: section thickness


title: hGst02-Chi-seqrun1


title: hGst01-Chi-seqrun2


title: 200iPD_A

city: Los Angeles

first: Samuel

middle: A

last: Sances

state: CA

address: 8500 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars Sinai

data_processing:
RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0) (Dobin A et al., 2013) / RSEM (version 1.2.25) (Li B and Dewey CN, 2011) with default parameters, using a custom human GRCh38 (or mouse CRCm38)
Expression counts for each gene (TPM: transcripts per million) in all samples were normalized

extract_protocol: Illumina TruSeq Stranded mRNA library preparation kit

tag: cell type

value: iPSC-mDA Neurons

tag: disease state

value: Parkinson's Disease

tag: cell line


title: 00iCTR_C

value: Control


title: 190iPD_A


title: 194iPD_B


title: hGst01-Chi-seqrun1


title: 194iPD_A


title: WP3iCTR_C

source_name: CSWPiCTR

value: CSWPiCTR


title: 194iPD_C


title: WP3iCTR_A


title: 200iPD_B


title: WP3iCTR_B


title: 190iPD_B


title: 200iPD_C


title: 02iCTR_C


title: 02iCTR_A


title: 02iCTR_B


title: 190iPD_C