title: RNA-Seq of Mus musculus: En1/2/3-KO-RA-1d rep-2


title: Hypoxia-ischemia vs naive mice + 3h  [RV PBS 3h c]

status: Public on Apr 16 2021

type: RNA

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

description: Biological replicate 3 of 3. 5 day-old brain harvested 3h after hypoxia-ischemia.

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for data extraction and LOWESS normalization.

molecule: total RNA

organism: Mus musculus

source_name: Brain Naive mice

label_protocol: Agilent Low input QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-2306) with 100ng  of total starting RNA.

growth_protocol: Naval Medical Resarch Institute (NMRI)-mice housed in our laboratory. Day of birth was noted 1.

extract_protocol: Total RNA from brain hemisphere (deleted of olfactory bulb and sectionned anterior to colliculus) were extracted using Nucleospin RNA plus kit (Ref 740984-250; Macherey-Nagel) following manufacturer's instructions. RNA Integrity Number was obtained by BioAnalyzer 2100 (Agilent).

treatment_protocol: Animals at day 5 received sub-cutaneous injection of MgSO4 (600 mg/kg) in Phosphate buffered saline or saline alone. Right carotid was ligatured permanently. After 1h30, 3h, 6h 12h or 24h 6 animals (3 males and 3 females) were sacrificed and forebrain tissues were collected. Controls were obtained from the same liters and were collected at the same time.

tag: strain

value: Naval Medical Resarch Institute (NMRI)-mouse

tag: treatment

value: PBS

tag: sublocalization

value: Forebrain

tag: time point

value: MgSO4 (600 mg/kg)

tag: hypoxia-ischemia (rv) or none

value: Hypoxia-ischemia (RV)

tag: delay for observation

tag: tissue

value: forebrain


title: MCF-7_DVL3

type: SRA

city: Lubbock

first: Kevin

last: Pruitt

state: Texas

address: 3601 4th Street

department: Immunology & Molecular Microbiology

country: USA

institute: Texas Tech University Health Sciences Center

library_source: genomic

data_processing:
Preprocessing : Qseq with DNASTAR/ArrayStar sofware from Lasergene genomics
ChIP-seq reads were aligned to the Human (GRCh38.p13)  genome assembly using DNASTAR from Lasegene genomics
Peak detection: MACS method; p vlaue cut off: 0.05; Mfold: 2; Lambsa set: 1000, 5000, 10000
Read assigment qualification options: Require at least 20 bases and at least 80% of the bases matching within each read. Mer length 15. Read technology Illumina
Filter out reads that match more than 25 places equally
Genome_build: Human (NCBI Genome Reference GRCh38.p13)
Supplementary_files_format_and_content: wig files were generated using DNASTAR/ArrayStar sofware from Lasergene genomics

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MDA-MB-468 cells were cultured in RPMI 1640 (Gibco) supplemented with 1% pen-strep and 10% fetal bovine serum (GIBCO)  and MCF7 cells were cultured in MEM (Gibco) media supplemented with 0.1% insulin,  1% pen-strep and 10% fetal bovine serum (GIBCO)  . Cells were plated for 72 hrs and the media was changed 24 hrs prior to the experiment.

extract_protocol:
The cells were subjected to 1% formaldehyde cross-linking (Sigma) for 8 minutes at room temperature. The cross-linking reaction was quenched by adding glycine (Sigma) to a final concentration of 0.125M for 5 minutes at room temperature. The medium was then removed and cells were washed twice with cold PBS containing protease inhibitor cocktail (Thermo Fisher Scientific). Cells were scraped in PBS and pelleted. Pellet was resuspended in SDS Lysis buffer (50mM Tris-HCl pH 8.0, 10mM 0.5M EDTA, and 1% SDS) with protease inhibitor cocktail and sonicated in a Diagenode Bioruptor sonicator. The soluble chromatin fraction was collected and incubated for 2 hrs at 4°C with antibody. Dynabeads Protein A (Invitrogen) were washed and then added to the chromatin-antibody mixture and nutated for 2 hrs at 4°C. Beads were washed with a low  salt  wash  buffer  (0.1%  SDS,  1%  Triton  X-100,  2mM EDTA, 20mM Tris HCl pH 8.1, and 150mM NaCl), a high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris HCl pH 8.1, and 500mM NaCl), and TE (1mM  EDTA  and  10mM  Tris  HCl  pH  8). Reverse-crosslinking was performed at 65°C overnight followed by treatment with RNaseA (Invitrogen) for 2 hrs at 37°C and proteinase K (Invitrogen) at 55°C for 2 hrs. The chromatin was eluted and purified using Qiaquick PCR purification kit (Qiagen)
Purified DNA were extracted and sent to GENEWIZ company for library construction and sequencing. Instrument/Configuration:   Illumina HiSeq 2x150bp SR

tag: cell type

value: Epithelium

value: Breast

tag: chip antibody

value: DVL3 (Sigma, SAB4200007)

value: untreated

tag: cell line


title: RNA-Seq of Mus musculus: En1/2/3-KO-RA-1d rep-1

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

country: China

institute: Nankai University

library_source: transcriptomic

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of Capture-C were cut into two pieces in the DpnII sites
All the reads were mapped to mm10 with Bowtie2(2.3.1)
Report all the reads that contains the Bait sequence
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values and Capture-C signal peaks for each Sample

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs E14 was cultured as the previous scheme with a few modifications. ESCs were grown in culture dishes coated with 0.1% gelatin (Sigma, Lot # SLBQ9498V) in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, Lot # 8119213) supplemented with 15% fetal bovine serum (FBS, AusGeneX, Lot # FBS00717-1), 100 nM nonessential amino acids (100x, Gibco, Lot # 2027433), 200 mM L-Glutamate (100x, Gibco, Lot # 2085472), 1% Penicillin-streptomycin (Gibco, Lot # 2029632), 50 μM β-mercaptoethanol (Sigma, Cas # 60-24-2), 10 ng/mL LIF (ESGRO, Lot # ESG1107), 1 μM PD0325901 (a MEK inhibitor, MedChemExpress, Lot # HY-10254) and 3 μM CHIR99021 (a GSK inhibitor, MedChemExpress, Lot # HY-10182). The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
1. For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions. 2. For Capture-C：Briefly, cells were fixed with 1% (vol/vol) formaldehyde for 10 min at room temperature, quenched with 125 mM glycine in PBS, and then lysed in cold lysis buffer (10 mM Tris–HCl, pH7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.2% NP-40, 1× complete protease inhibitor cocktail (Roche)). Chromatin was digested with DpnII (New England Biolabs) at 37°C overnight. Fragments were then diluted and ligated with T4 DNA ligase (Takara) at 16°C overnight. Cross-linking was reversed by overnight incubation at 60°C with proteinase K (Bioline). Then 3C libraries were purified by phenol-chloroform followed by chloroform extraction and ethanol-precipitated at −80°C overnight. Sequencing libraries were prepared from 10μg of the 3C library by sonication to an average size of 200 ~300 bp and indexed using NEBnext reagents (New England Biolabs), according to the manufacturer's protocol. Enrichment of 2μg of an indexed library incubated with 3uM of a pool of biotinylated oligonucleotides (probe sequences are listed in Supplementary Table 7) was performed using the SeqCap EZ Hybridization reagent kit (#05634261001, Roche/NimbleGen), following the manufacturer's instructions. Two rounds of capture employing 48~72 and 24 hr hybridizations, respectively, were used. Correct library size was confirmed by agarose gel electrophoresis, and DNA concentrations were determined using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). All sequencing was performed on Hi-Seq 2500 platforms using paired 150 bp protocols (Illumina).
The Capture-C libraray was constructed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: To induce ESCs differentiation, cells were gently washed with 1x phosphate buffer saline solution (PBS), dissociated and replanted at an appropriate density on gelatin-coated plates in LIF/2i withdrawal medium supplemented with 2µm RA (Solarbio®, Lot # 1108F031). The culture medium was replaced at the given point-in-time.

value: embryo, blastocyst embryo, blastocyst

value: Embryonic stem cell

value: RA induced differentiation


title: MCF-7_IgG

value: IgG (Sigma I5006)


title: Effect of MgSO4 + 24h [Mg 24h d]

description: Biological replicate 4 of 4. 5 day-old brain harvested 24h after treatment (control vs MgSO4 treatment).

source_name: 5 day-old brain harvested 24h after MgSO4 treatment


title: Hypoxia-ischemia vs naive mice + 3h  [RV PBS 3h b]

description: Biological replicate 2 of 3. 5 day-old brain harvested 3h after hypoxia-ischemia.


title: Hypoxia-ischemia vs naive mice + 3h  [RV PBS 3h a]

description: Biological replicate 1 of 3. 5 day-old brain harvested 3h after hypoxia-ischemia.


title: Mg-treated Hypoxia-ischemia vs Mg-treated naive mice + 3h  [RV Mg 3h b]

source_name: Brain Mg treated mice

source_name: 5 day-old brain harvested 3h after MgSO4-treated hypoxia-ischemia


title: Effect of MgSO4 + 24h [Mg 24h c]

description: Biological replicate 3 of 4. 5 day-old brain harvested 24h after treatment (control vs MgSO4 treatment).


title: RNA-Seq of Mus musculus: En2-KO-RA-1d rep-2


title: MDA-MB-468_DVL3


title: MDA-MB-468_IgG


title: Effect of MgSO4 + 24h [Mg 24h a]

description: Biological replicate 1 of 4. 5 day-old brain harvested 24h after treatment (control vs MgSO4 treatment).


title: Effect of MgSO4 + 12h [Mg 12h d]

description: Biological replicate 4 of 4. 5 day-old brain harvested 12h after treatment (control vs MgSO4 treatment).

source_name: 5 day-old brain harvested 12h after MgSO4 treatment


title: Effect of MgSO4 + 6h [Mg 6h g]

description: Biological replicate 7 of 7. 5 day-old brain harvested 6h after treatment (control vs MgSO4 treatment).

source_name: 5 day-old brain harvested 6h after MgSO4 treatment


title: Effect of MgSO4 + 12h [Mg 12h c]

description: Biological replicate 3 of 4. 5 day-old brain harvested 12h after treatment (control vs MgSO4 treatment).


title: Effect of MgSO4 + 12h [Mg 12h a]

description: Biological replicate 1 of 4. 5 day-old brain harvested 12h after treatment (control vs MgSO4 treatment).


title: Effect of MgSO4 + 12h [Mg 12h b]

description: Biological replicate 2 of 4. 5 day-old brain harvested 12h after treatment (control vs MgSO4 treatment).


title: Effect of MgSO4 + 6h [Mg 6h b]

description: Biological replicate 2 of 7. 5 day-old brain harvested 6h after treatment (control vs MgSO4 treatment).


title: Effect of MgSO4 + 6h [Mg 6h e]

description: Biological replicate 5 of 7. 5 day-old brain harvested 6h after treatment (control vs MgSO4 treatment).


title: SCR23 het

city: PARIS

first: Silvia

last: Cereghini

address: 9 Quai Saint Bernard BatC 7ET

department: Developmental Biology

institute: IBPS- UMR7622 CNRS -UPMC

data_processing:
RNA sequencing was performed on an Ion Proton™ System, according to the manufacturer's instructions.
The prepared libraries were quantified and pooled together in duplicates at the required concentration.
The library pools were then processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (ThermoFisher Scientific) and sequencing with the Ion PI™Sequencing 200 Kit on Ion Proton PI™ chips (ThermoFisher Scientific) according to commercial protocols.
The E17.5 libraries were sequenced on the Illumina HiSeq 2000
The resulting RNA-Seq BAM files were analyzed with the Bioconductor package metaseqR (Moulos and Hatsis, Nucleic Acids Res 43, e25 (2015) and applying the edgeR. (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) methodology for differential expression analysis with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: matrix table with Normalized counts for every gene and every sample at each stage (txt files)

source_name: Post natal P1 kidneys

extract_protocol:
RNA from microdissected kidneys was immediately extracted by Tryzol, using the miRNA mini kit Qiagen for the extraction of total and miRNAs. The quality of the RNA samples was assessed on the Agilent Bioanalyzer system using the Agilent RNA 6000 Nano Kit (Agilent Technologies) and RNA with a Ring higher than 8,5-9 was used.
1-2 μg of total RNA were used for mRNA isolation using the Dynabeads® mRNA DIRECT™ Micro Kit (ThermoFisher Scientific). mRNA was digested with RNase III, purified, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA‐Seq Kit v2 (ThermoFisher Scientific). The pools were then processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (ThermoFisher Scientific) and sequencing with the Ion PI™Sequencing 200 Kit on Ion Proton PI™ chips (ThermoFisher Scientific) according to commercial protocols. RNA sequencing from E17.5 embryo kidneys (SAMPLES 7 to 10) was performed by FASTERIS-Genome Analyzer Service (Switzerland). High-throughput DNA sequencing using Illumina technology consisted in processing in vitro samples to generate a library of short inserts (the DNA Colonies Template Library). The library was sequenced on the Illumina HiSeq 2000. For each lane 130-150 million DNA colonies producing pass filter sequences were assured. The read lengths are 1x50 or 1x100 base pairs (bp) for single-reads runs using the forward sequencing primer. The inserts can also be sequenced from both ends using a 'forward' and a 'reverse' sequencing primer, generating pairedreads of 2x100 bp. The data were processed using bioinformatics tools to extract biologically useful information.

tag: developmental stage

value: P1 (postnatal day 1)

tag: genotype

value: Hnf1b Sp2/+ (het)

value: kidney


title: RNA-Seq of Mus musculus: En1-KO-RA-1d rep-2


title: Effect of MgSO4 + 6h [Mg 6h c]

description: Biological replicate 3 of 7. 5 day-old brain harvested 6h after treatment (control vs MgSO4 treatment).

value: Naval Medical Resarch Institute (NMRI)-mouse


title: Effect of MgSO4 + 24h [Mg 24h b]

description: Biological replicate 2 of 4. 5 day-old brain harvested 24h after treatment (control vs MgSO4 treatment).

value: PBS


title: Effect of MgSO4 + 6h [Mg 6h d]

description: Biological replicate 4 of 7. 5 day-old brain harvested 6h after treatment (control vs MgSO4 treatment).

value: Forebrain


title: SCR22 het


title: RNA-Seq of Mus musculus: En2-KO-RA-1d rep-1


title: RNA-Seq of Mus musculus: En-WT-RA-1d rep-2


title: RNA-Seq of Mus musculus: En1-KO-RA-1d rep-1


title: SCR21 wt

value: wild type


title: RNA-Seq of Mus musculus: En-WT-RA-1d rep-1


title: Effect of MgSO4 + 6h [Mg 6h f]

description: Biological replicate 6 of 7. 5 day-old brain harvested 6h after treatment (control vs MgSO4 treatment).

value: MgSO4 (600 mg/kg)


title: Effect of MgSO4 + 6h [Mg 6h a]

description: Biological replicate 1 of 7. 5 day-old brain harvested 6h after treatment (control vs MgSO4 treatment).

value: forebrain


title: SCR20 wt


title: Effect of MgSO4 + 1h30 [Mg 1h30 c]

description: Biological replicate 3 of 4. 5 day-old brain harvested 1h30 after treatment (control vs MgSO4 treatment).

source_name: 5 day-old brain harvested 1h30 after MgSO4 treatment


title: Effect of MgSO4 + 3h [Mg 3h d]

description: Biological replicate 4 of 4. 5 day-old brain harvested 3h after treatment (control vs MgSO4 treatment).

source_name: 5 day-old brain harvested 3h after MgSO4 treatment


title: RNA-Seq of Mus musculus: WT-RA-0d rep-3

value: untreatment


title: SCR1 het

source_name: Embryonic kidneys


title: Effect of MgSO4 + 3h [Mg 3h b]

description: Biological replicate 2 of 4. 5 day-old brain harvested 3h after treatment (control vs MgSO4 treatment).


title: RNA-Seq of Mus musculus: WT-RA-0d rep-2


title: OVA_GCBcell_Ig_bulk_7dpi_4n

city: Hangzhou

first: Heping

last: Xu

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
immunization
Bulk Ig-seq
full-length immunoglobulin

data_processing:
Bulk Ig-seq: MIGEC 1.2.9 was used to perform sample demultiplexing, unique molecular identifiers extraction and reads assembly
Bulk Ig-seq: MiTools 1.5 was used to merge 5'- and 3'-end reads
Genome_build: mm10
Supplementary_files_format_and_content: For Bulk Ig-seq: annotation.csv, Igblast annotation result for high-quality IgH contig

source_name: spleen

growth_protocol: primary GC B cells

extract_protocol:
RNA were extracted from cells using RNAClean XP beads (Backman)
Bulk Ig-seq

tag: age

value: 8 weeks

tag: Sex

value: male

value: germinal center B cells


title: SCR2 wt


title: Effect of MgSO4 + 3h [Mg 3h a]

description: Biological replicate 1 of 4. 5 day-old brain harvested 3h after treatment (control vs MgSO4 treatment).


title: OVA_GCBcell_Ig_bulk_7dpi_3n


title: OVA_GCBcell_Ig_bulk_7dpi_4p


title: Effect of MgSO4 + 1h30 [Mg 1h30 d]

description: Biological replicate 4 of 4. 5 day-old brain harvested 1h30 after treatment (control vs MgSO4 treatment).


title: Effect of MgSO4 + 1h30 [Mg 1h30 b]

description: Biological replicate 2 of 4. 5 day-old brain harvested 1h30 after treatment (control vs MgSO4 treatment).


title: RNA-Seq of Mus musculus: WT-RA-0d rep-1

value: embryo, blastocyst embryo, blastocyst


title: Effect of MgSO4 + 3h [Mg 3h c]

description: Biological replicate 3 of 4. 5 day-old brain harvested 3h after treatment (control vs MgSO4 treatment).


title: SCR15-E145-7 het


title: OVA_GCBcell_Ig_bulk_7dpi_1p


title: Effect of MgSO4 + 1h30 [Mg 1h30 a]

description: Biological replicate 1 of 4. 5 day-old brain harvested 1h30 after treatment (control vs MgSO4 treatment).


title: T119_C3

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

data_processing:
Library strategy: Micro Capture-C (MCC)
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie.
CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: BigWig of data from multipul viewpoints

source_name: Spleen erythroid cells

growth_protocol: Erythroid cells were obtained from the spleen of mice treated with phenylhydrazine (40mg/g body weight x3 doses 12h apart; sacrificed on day 5). Phenylhydrazine causes haemolytic anaemia and marked erythroid expansion in the spleen so that >80% all cells are CD71+ Ter119+ erythroid precursors. Mouse ES cells (E14) were routinely cultured in Glasgow MEM x1 liquid (Gibco 21710-025) with 10% FCS (vol/vol) (Gibco), 1x Glutamine (Gibco 25030-024), 1 mM sodium pyruvate (Gibco 11360-039), 1x non-essential amino acids (Gibco 11140-035), mercaptoethanol (Gibco 31350010) and LIF (Thermo Fischer PMC9484) in gelatin (Gibco 10131-035) coated flasks. Cells were harvested when 80-95% confluent using trypsin (Sigma T-4049) and washed once prior to fixation. HUDEP-2 cells were cultured in expansion phase as previously described Canver, M. C. et al.,2015.

extract_protocol:
Qiagen DNeasy blood and tissue kit
7-10 µg of each 3C library was sonicated to a mean fragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (1-3 cycles of 60s: duty cycle 10%; intensity 5; cycles per burst 200). The library size was assessed using an Agilent TapeStation (DNA 1000) and an Ampure XP (Beckman Coulter) bead clean-up was performed once the sample had been adequately sonicated. To maximise library complexity three aliquots, each containing 2 µg sonicated 3C library, were processed in parallel for each sample to add sequencing adaptors. NEB Ultra II reagents were used following the standard protocol with the following modifications: first, additional adapter was added into the ligation reactions (7.5 µl rather than 2.5 µl); no size selection was performed (Ampure XP bead clean ups were always performed with a sample:bead ratio of 1:1.8) and the final PCR to add indices was amplified in triplicate from each aliquot using the Herculase II PCR kit (Agilent) to maximise DNA yield. All parallel library preparations and PCR reactions were pooled for each reaction. CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.

treatment_protocol: Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher). Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g). The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol). For standard nuclear preparation, the pellet was resuspended in 5ml cold lysis buffer (TRIS-HCl pH 8 10 mM, NaCl 10 mM, Igepal NP-40 (Sigma I8896) 0.2%, cOmplete proteinase inhibitor cocktail (PIC) (Roche 4693116001) (x1 tablet / 50 ml)) and incubated on ice for 20 min. The nuclei were centrifuged (300 g, 5 min) and resuspended in 1ml lysis buffer.

value: Spleen erythroid cells

tag: sample type


title: OVA_GCBcell_Ig_bulk_7dpi_2n


title: SCR12-E14-6 het


title: OVA_GCBcell_Ig_bulk_7dpi_2p


title: OVA_GCBcell_Ig_bulk_7dpi_1n


title: T119_C2


title: OVA_GCBcell_Ig_bulk_13dpi_4n


title: SCR13-E145-3 wt


title: OVA_GCBcell_Ig_bulk_13dpi_4p


title: T119_C1


title: OVA_GCBcell_Ig_bulk_13dpi_3p


title: OVA_GCBcell_Ig_bulk_7dpi_3p


title: OVA_GCBcell_Ig_bulk_13dpi_2n


title: SCR10-E145-4 wt


title: WFMD135B - Case

city: Hamilton

first: Jocelyn

middle: M

last: Wessels

state: Ontario

address: 1280 Main Street West

department: Obstetrics and Gynecology

country: Canada

institute: McMaster University

data_processing:
Paired-end alignment using PANDAseq
FASTQ Trimming using Cutadept/sickle
FASTQ Culling using Chimera checking
OTU picking - de novo (AbundantOTU+, CD-HIT, DNACLUST, UCLUST, UPARSE) and closed reference (BLAST, UCLUST-ref, UCLUST-ref-strict)
Genome_build: Taxon Assignment - assigment algorithm (BLAST, RDP) and reference database (Greengenes 2011, Greengenes 2013, Silva 111)
Supplementary_files_format_and_content: otu_table_rdp-training_gg2011_n1_noRoot_L6.xlsx (Relative abundance table)

source_name: Endometrial biopsy

extract_protocol:
Genomic DNA was extracted from the endometrial biopsies using the RNeasy Mini Kit (Qiagen, Hilden, Germany), omitting the DNase treatment, and following the manufacturer’s protocol. The quantity and purity of nucleic acids was assessed using the Nanodrop 2000. In order to retain bacterial DNA and eliminate the RNA that might inhibit the PCR reaction, RNase A (Qiagen Hilden, Germany) was added to the first PCR mastermix. The hypervariable V3 region of the 16S rRNA gene was amplified by using a two-stage (nested) PCR approach.
sl1p pipeline (Whenlan and Surette, 2017, BMC Microbiome)
16S rRNA gene sequencing

tag: group

value: endometriosis

value: Endometrial biopsy

tag: material sequenced

value: 16S rRNA gene


title: E14_S13 Micro Capture-C (MCC)

source_name: Embryonic stem cells

treatment_protocol: Cells were resuspended in aliquots of 1 x 107 in 10 ml media with 10% FCS in a 15-ml conical centrifuge tube using an automated cell counter (CountessII, Thermo Fisher).  Formaldehyde (37% (vol/vol)) was added to each aliquot to make a final concentration of 2% (vol/vol) and the cells were incubated on a roller mixer for 10 minutes at room temperature. The crosslinking reaction was quenched with cold 1 M glycine to a final concentration 130 mM and the sample was centrifuged (5 min at 220 g).  The supernatant was discarded and the cell pellet was washed with 10 ml cold Phosphate Buffered Saline (PBS) and reconstituted in 1 ml PBS. An automated cell count on was performed on 10 ml of the cell suspension to reconfirm the cell number. Digitonin (Sigma D-141) was prepared fresh for each experiment (0.5% in dimethylsulfoxide (DMSO) (wt/vol)). Each batch of digitonin was tested for its ability to permeabilise cells at a concentration of 0.005% (wt/vol). 10 ml digitonin was added to make a final concentration of 0.005% (wt/vol). For standard nuclear preparation, the pellet was resuspended in 5ml cold lysis buffer (TRIS-HCl pH 8 10 mM, NaCl 10 mM, Igepal NP-40 (Sigma I8896) 0.2%, cOmplete proteinase inhibitor cocktail (PIC) (Roche 4693116001) (x1 tablet / 50 ml)) and incubated on ice for 20 min. The nuclei were centrifuged (300 g, 5 min) and resuspended in 1ml lysis buffer.

value: Embryonic stem cells


title: OVA_GCBcell_Ig_bulk_13dpi_1p

tag: strain


title: OVA_GCBcell_Ig_bulk_13dpi_2p


title: p53 KO Clone414, 4th repeat

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

description:
RS216
p53KO2_rep4

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases  using Trimmomatic software before alignment with the reference genome (Human - hg19) .
Both the   normalized count and the raw count are provided as part of the data delivery.
Genome_build: hg19
Supplementary_files_format_and_content: The gene expression quantification analysis (RPKM) was normalized to the sequence reads.

source_name: MCF10A cells

growth_protocol: MCF10A cells were cultured in DMEM/F12 media supplemented with 5% horse serum, 10 µg/ml human recombinant insulin, 20 ng/ml human EGF, 500 ng/ml Hydrocortisone, 100ng/ml Cholera toxin and antibiotics.

extract_protocol:
RNA were extracted with Qiagen's Rneasey kit .
TruSeq mRNA Prep Kit  RS-122-2101
illumina TruSeq mRNA Prep Kit RS-122-  2101

value: MCF10A cells (ATCC CRL-10317)

tag: passages

value: fewer than 20

value: p53 KO


title: OVA_GCBcell_Ig_bulk_13dpi_3n


title: p53 KO Clone313, 4th repeat

description:
RS214
p53KO1_rep4


title: E14_S14 Micro Capture-C (MCC)


title: WFMD132A - Case


title: E14_S12 Micro Capture-C (MCC)


title: WFMD131B - Case


title: E14_S11 Micro Capture-C (MCC)


title: WFMD118B - Case


title: OVA_GCBcell_Ig_bulk_13dpi_1n


title: WT, 4th repeat

description:
RS212
p53WT_rep4

value: WT


title: p53 KO Clone414, 3rd repeat

description:
RS210
p53KO2_rep3


title: p53 KO Clone313, 3rd repeat

description:
RS208
p53KO1_rep3


title: WT, 3rd repeat

description:
RS206
p53WT_rep3


title: WFMD110A - Control

value: control


title: WFMD28B - Case


title: p53 KO Clone313, 2nd repeat

description:
RS202
p53KO1_rep2


title: E14_S10 Micro Capture-C (MCC)


title: E14_S5 Micro Capture-C (MCC)


title: WFMD25B - Case


title: WT, 2nd repeat

description:
RS200
p53WT_rep2


title: p53 KO Clone414, 1st repeat

description:
RS198
p53KO2_rep1


title: E14_S4 Micro Capture-C (MCC)


title: p53 KO Clone313, 1st repeat

description:
RS196
p53KO1_rep1


title: WFMD19B - Case


title: E14_S3 Micro Capture-C (MCC)


title: WT, 1st repeat

description:
RS194
p53WT_rep1


title: Tsga8-Y_adult_whole_testis_R3

city: Yokohama

first: Keisuke

last: Minamizawa

address: Kanazawa

country: Japan

institute: Yokohama city university

data_processing:
Sequence reads were checked for quality with FastQC and trimmed with Trim Galore! (version 0.4.0) with default parameters.
RNA-seq reads were mapped onto mm10 using Hisat2 (version 2.1.0) with default parameters.
Read counts and quantification were performed using SeqMonk (version 0.30.2)
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated using SeqMonk contain normalised RNA-seq read count (RPKM) for all genes.

source_name: Testis

extract_protocol:
Total RNA from whole testis was isolated using Isogen (Nippon Gene) according to the manufacturer's instructions. For the LCM samples, tissue lysate was used for RNA extraction using Isogen (Nippon Gene).
For the whole testis samples, purified RNA was used for library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) . For the LCM samples, purified total RNA was used to prepare RNA-seq libraries with the SMART-seq2 protocol.

value: adult whole testis

tag: gender


title: WFMD18B - Case


title: Tsga8-Y_adult_whole_testis_R2


title: E14_S6 Micro Capture-C (MCC)


title: E14_S2 Micro Capture-C (MCC)


title: Tsga8+Y_adult_whole_testis_R3


title: p53 KO Clone414, 2nd repeat

description:
RS204
p53KO2_rep2


title: E14_S1 Micro Capture-C (MCC)


title: Tsga8+Y_adult_whole_testis_R2


title: HUDEP_5882 Micro Capture-C (MCC)

source_name: Human Umbilical Cord Blood-Derived Erythroid Progenitor


title: Young 2 Post-differentiation

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

institute: Calico Life Sciences, LLC

data_processing:
Reads were demultiplexed using bcl2fastq.
Reads were aligned, assigned to cell barcodes, UMIs collapsed, and cell barcodes were filtered using 10X cellranger 3.
Cell barcodes were filtered if contained greater than 20% mitochondrial reads. Genes were removed if they were detected in fewer than 10 total cells.
Raw counts were normalized by the library sequencing depth to obtain counts per million and then natural log transformed with a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: h5ad, contains all normalized counts, gene annotations, and cell annotations

molecule: polyA RNA

source_name: Limb muscle

growth_protocol: Animals were maintained at Calico Life Sciences, LLC on ad libitum diet with a 12 hour light dark cycle.

extract_protocol:
Single cell suspensions were obtained from limb muscle tissue after mechanical digestion with scissors and enzymatic digestion with Collagenase II and Dispase. Suspensions were filtered through a 40 um filter before sorting for live cells via FACS. The populations of muscle stem cells and fibro/adipose progenitors were enriched by FACS to capture more of these rare cells. After differentiation in vitro, muscle stem cells and fibro/adipose progenitors were dissociated from culture wells and libraries were prepared from single cell suspensions.
Libraries were constructed following the 10X Genomics 3' Single Cell transcriptome v3 protocol.

treatment_protocol: Differentiation was performed on muscle stem cells and fibro/adipose progenitors by culturing cells on sarcoma-derived ECM coated well plates for 60 hours in DMEM + 10% horse serum.

value: 3 months

tag: time

value: Differentiated 60 hours

value: Limb muscle

value: Contains differentiated muscle stem cells and fibro/adipose progenitors


title: T119_S17 Micro Capture-C (MCC)


title: Aged 2 Post-differentiation

value: 20 months


title: T119_S16 Micro Capture-C (MCC)


title: HUDEP_5881 Micro Capture-C (MCC)

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor


title: Aged 1 Post-differentiation


title: Young 1 Pre-differentiation

value: Freshly-isolated 0 hours

value: Contains the total muscle mononuclear cell population


title: Young 2 Pre-differenitation


title: HUDEP_WT3 Micro Capture-C (MCC)


title: T119_S15 Micro Capture-C (MCC)

value: Spleen erythroid cells


title: HUDEP_WT2 Micro Capture-C (MCC)


title: Aged 1 Pre-differentiation


title: Tsga8-Y_adult_whole_testis_R1

value: male


title: WFMD13A - Case

value: endometriosis

value: Endometrial biopsy

value: 16S rRNA gene


title: T119_S13 Micro Capture-C (MCC)


title: T119_S14 Micro Capture-C (MCC)


title: Aged 2 Pre-differentiation


title: Pooled_Input

city: Montpellier

first: Mohammad

last: Salma

address: 1919 Route de Mende

institute: IGMM CNRS

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.3.4.3
Sam files were converted into bam format using Samtools (v1.9)
Mapped reads were transformed into a gnome-wide read density (covrage), in two steps: (1) by using makeUCSCfile from Homer suite (v4.10,5-16-2018) using the parameter -norm 20000000
(2) by using bedGraphToBigWig (v4) from UCSC
Peak calling was performed with Homer (v4.10,5-16-2018) with default parameters (-F 5 and -L 5)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig and bed

growth_protocol: Bone marrow MS5 cell line (CVCL_2128) were cultured in DMEM 10% CFS

extract_protocol:
Cells were were fixed in Formaldehyde (e.g. Sigma #F-8775) 1,1%.
ChIP were performed using anti c-Jun Ab (sc-1694) and anti-p300 Ab (sc-585)

treatment_protocol: Cells were treated during 5 hours with TGF-β1 (10 ng/mL, with or without pioglitazone (20 ng/Ml)

tag: treatment

value: Bone marrow stromal cells


title: Young 1 Post-differentiation


title: Tsga8+Y_adult_whole_testis_R1


title: TGF-B1_p300_ChIPSeq

value: without pioglitazone


title: TGF-B1-Pio_p300_ChIPSeq

value: pioglitazone (20 ng/mL)


title: T119_S12 Micro Capture-C (MCC)


title: TGF-B1-Pio_cJun_ChIPSeq

value: cJun, sc-1694 (SCBT)


title: HUDEP_5883 Micro Capture-C (MCC)


title: SpdefKO_GC_S7_bulkRNAseq

city: Gothenburg

first: Malin

middle: E. V.

last: Johansson

address: Medicinaregatan 9A

department: Department of Medical Biochemistry and Cell Biology

country: Sweden

institute: University of Gothenburg

data_processing:
Quality of the raw data was assessed with FastQC (version 0.11.2) looking at per base sequence quality and adapter contamination.
The reads were mapped using STAR version 2.4.0f
The number of the mapped reads was calculated using HTseq (version 0.6.1p1) with the stranded reverse protocol
Normalization of the data and differential expression were performed using DESeq2 (version 1.14)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts of sequencing reads and normalized counts by size.

source_name: Goblet cells

extract_protocol:
Freshly collected distal colons from SpdefKO_RedMUC298trTg and RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs and ECs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Sorted cells were pelleted and immediately resuspended in RLT buffer supplemented with β-merchaptoethanol. Samples were homogenized using QIAshredder columns (Qiagen) according to manufacturer’s instructions. Goblet cell lysates were loaded into RNeasy MinElute column and non-GC lysates into RNeasy Mini column (Qiagen). The columns were washed according to manufacturer’s instructions and the RNA was eluted with RNAse free H2O.
cDNA libraries were prepared with the TruSeq Stranded Total RNA Sample Preparation kit with Ribo Zero Gold (Rev. E; Illumina) according to manufacturer's protocol and sequenced via paired-end.

value: Distal colon

value: Goblet cells

value: 6-8 weeks old


title: SpdefKO_GC_S3_bulkRNAseq


title: SpdefKO_GC_S5_bulkRNAseq


title: T119_S4 Micro Capture-C (MCC)


title: T119_S5 Micro Capture-C (MCC)


title: SpdefKO_GC_S19_bulkRNAseq


title: SpdefKO_EC_S8_bulkRNAseq

source_name: Colonocytes

value: Colonocytes


title: T119_S3 Micro Capture-C (MCC)


title: HUDEP_WT1 Micro Capture-C (MCC)


title: SpdefKO_EC_S4_bulkRNAseq


title: T119_S2 Micro Capture-C (MCC)


title: SpdefKO_EC_S6_bulkRNAseq


title: SpdefKO_EC_S20_bulkRNAseq


title: TGF-B1_cJun_ChIPSeq


title: T119_S6 Micro Capture-C (MCC)


title: WT_GC_S11_bulkRNAseq


title: ABC-imKO9 Cisplatin it AIBP rep3 line 2

city: la Jolla

first: Juliana

middle: Maria

last: Navia-Pelaez

state: california

address: 9500 Gilman dr.

department: Medicine

institute: UCSD

description:
ABC-imKO9 sample technical replicate 3.  fastq read- pairs from lane 2
Y54_L002

data_processing:
Illumina Casava1.7 software used for basecalling and Illumina bcl2fastq Conversion Software was then used to convert bcl files to fastq format
Splice aware alignment of FASTQ data was done using STAR (Dobin et al., 2013)
Quality control of sequenced data and alignment was performed by FASTQC v0.11.17,  QoRTs v1.3.0, and MultiQC v1.7 ( pmid: 27312411 )
Counting of genes associated with the reads was performed using STAR v2.6.0a (Dobin et al., 2013)
Comparisons of experimental groups were performed with DEseq2 binomial modeling using Wald test and accounting for an FDR of 10%. Volcano plots include genes significantly different with a fold change >1.5.
Pathway enrichment and GO analysis were performed in metascape.org using a minimum of 3 genes and P<0.05 (Zhou et al., 2019).
genome build: GRCm38 from ENSEMBL
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: table with normalized counts for expressed genes

source_name: Microglia

extract_protocol:
Microglia cells were sorted directtly into lysis buffer buffer containing Triton X-100, RNase Inhibitor, and Oligo(dT)30-VN and vortexed. Then lysates were hybridized with oligo(dT)+ to the poly(A) tails of the mRNA. Reagents for reverse transcription were added to construct cDNA libraries following addition of reagents for PCR amplification (qPCR was not performed at this point). Libraries were quantified and QC was performed using TapeStation high sensitivity D5000 screentape in addition to Qubit double stranded high sensitivity assay. All samples were adjusted to 1ng of cDNA for input into NexteraXT protocol. QC check was performed with TapeStation high sensitivity D1000 screen tape in addition to Qubit double stranded high sensitivity assay. The samples were subjected to qPCR and pooling and loaded onto the NovaSeq for paired-end 50x50 reads using NovaSeq S1 100 cycle kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell suspentions from lumbar spinal cord were stained, filtered, and FACS-sorted to collect resident microglia

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  AIBP on day7


title: WT_GC_S18_bulkRNAseq


title: WT_GC_S13_bulkRNAseq


title: macrophage_infected_C24

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

description:
C24
200796210065_L

hyb_protocol: Standard Illumina protocol (Direct hybridization – BeadChip)

scan_protocol: Standard Illumina protocol on iScan Software

data_processing: Background correction (normal+exp conv. model) and between-array quantile normalization were computed with limma::neqc (v. 3.40.6).

label: biotin

source_name: macrophage, infected

label_protocol: Isolated RNA was labeled with Epicentre TargetAmp™ Nano Labeling Kit for Illumina® Expression BeadChip®

growth_protocol: PBCMs were purified using magnetic beads with anti-CD4 antibody. Monocytes were differentiated into macrophages by growing in Iscove’s modified Dubelcco’s medium, antibiotics, pooled human sera for 6 days at 37 °C in 5% CO2

extract_protocol: Cells were lysed with TRIzol reagent and RNA isolated with chloroform and isopropyl alcohol. RNA integrity was assessed with Agilent Bioanalyzer and purified using Rneasy MinElute Cleanup (Qiagen)

treatment_protocol: Live-Mycobacterium leprae m.o.i 10:1 (bacilli:macrophage) or mock

value: F

tag: individual

tag: ChIP

tag: lane

value: L

value: macrophage

value: infected


title: WT_GC_S9_bulkRNAseq

tag: tissue

tag: cell type


title: WT_EC_S17_bulkRNAseq


title: macrophage_control_C24

description:
C24
200796210065_J

source_name: macrophage, control

value: J

value: control


title: macrophage_infected_C21

description:
C21
200796210065_K

value: M

value: K


title: macrophage_control_C21

description:
C21
200796210065_I

value: I


title: macrophage_infected_C20

description:
C20
200796210065_G

value: G


title: ABC-imKO9 Cisplatin it AIBP rep3 line 1

description:
ABC-imKO9 sample technical replicate 3.  fastq read- pairs from lane 1
Y54_L001


title: WT_EC_S14_bulkRNAseq

value: Distal colon


title: ABC-imKO9 Cisplatin it AIBP rep2 line 2

description:
ABC-imKO9 sample technical replicate 2.  fastq read- pairs from lane 2
Y53_L002


title: WT_EC_S10_bulkRNAseq


title: ABC-imKO9 Cisplatin it AIBP rep2 line 1

description:
ABC-imKO9 sample technical replicate 2.  fastq read- pairs from lane 1
Y53_L001


title: E14_S7_Rad21 ChIP-seq

data_processing:
The raw fastq file is processed to reconstruct a single read from the paired end sequencing. This is then mapped to the 800bp sequence surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This allows the reads to be cut into ‘slices’ depending on whether they align to the sequence around the capture site. This strategy allows ligation junctions in the read to be determined with base pair accuracy. The resulting fastq file is aligned to the genome using bowtie.
CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: BigWig of data from multipul viewpoints

value: Embryonic stem cells

tag: chip antibody


title: ABC-imKO9 Cisplatin it AIBP rep1 line 2

description:
ABC-imKO9 sample technical replicate 1.  fastq read- pairs from lane 2
Y52_L002

tag: genotype


title: E14_S8_CTCF ChIP-seq

value: CTCF


title: ABC-imKO9 Cisplatin it AIBP rep1 line 1

description:
ABC-imKO9 sample technical replicate 1.  fastq read- pairs from lane 1
Y52_L001


title: T119_S10_NIPBL ChIP-seq

value: Spleen erythroid cells

value: NIPBL


title: T119_S1 Micro Capture-C (MCC)


title: ABC-imKO8 Cisplatin it AIBP rep3 line 2

description:
ABC-imKO8 sample technical replicate 3.  fastq read- pairs from lane 2
Y51_L002

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)


title: T119_S9_Rad21 ChIP-seq


title: T119_S11_NIPBL ChIP-seq


title: WT_EC_S12_bulkRNAseq

value: Colonocytes

tag: age

value: 6-8 weeks old


title: macrophage_control_C20

description:
C20
200796210065_E

tag: Sex

value: F

value: E

value: macrophage


title: T119_S8_CTCF ChIP-seq


title: T119_S7_CTCF ChIP-seq


title: macrophage_infected_C19

description:
C19
200796210065_C

value: C

value: infected


title: E14_S9_CTCF ChIP-seq


title: macrophage_control_C22

description:
C22
200796210065_B

value: B

value: control


title: macrophage_infected_C18

description:
C18
200796210050_L

value: L


title: macrophage_control_C19

description:
C19
200796210065_A

value: M

value: A


title: P1_rep2

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: transcriptional profiling (RNA sequencing)

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
The fastq files were mapped to the mm9 genome using TopHat v2.1.0 with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene is calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Htseq-count text file

source_name: Sorted small intesitinal crypt cells

extract_protocol:
Small intestinal crypts of EF1a-OSCAR mice were isolated and a single cell suspension derived by an 20min incubation with TrypLE at room temperature. Cells were stained with anti-EpCAM PE-Cy7 for 15mins on ice before washing and staining with Sytox Blue dead cell stain. FACS sorting was performed on a BD FACS ARIA III. 10.000 cells of each population were sorted and RNA extracted using TRIzol Reagent. Integrity and concentration of isolated RNA was determined using Qubit 4 Fluorometer (Thermo Fisher) and Fragment Analyzer (Agilent).
Poly-A library preparation was performed using TruSeq RNA Library Prep Kit V2 (Illumina) according to manual. Briefly, poly-A containg mRNA was enriched using magnetic beads, first strand synthesis of cDNA was done using SuperScript III Reverse Transcriptase (Thermo Fisher), second strand synthesis was performed using the second strand master mix (TruSeq RNA Library Prep Kit V2 (Illumina)) and the DNA was cleaned up using Agencourt AMPure XP Beads (Beckman Coulter). After end repair and dA tailing, adaptors were ligated and the library was further enriched using the PCR Master Mix (TruSeq RNA Library Prep Kit V2 (Illumina)). Quality and concentration of the library was determined using Qubit 4 Fluorometer (Thermo Fisher) and Fragment Analyzer (Agilent). cDNA libraries were pooled and 20pM loaded into the NextSeq 500 (Illumina) Sequencer using the NextSeq 500/550 High Output Kit v2.5 (75 cycles).

value: OSCARlow EF1alow


title: P1_rep1


title: macrophage_control_C23

description:
C23
200796210065_F


title: macrophage_control_C18

description:
C18
200796210050_J

value: J


title: P3_rep2

value: OSCARlow EF1ahigh


title: macrophage_infected_C15

description:
C15
200796210050_K

value: K


title: ABC-imKO8 Cisplatin it AIBP rep2 line 2

description:
ABC-imKO8 sample technical replicate 2.  fastq read- pairs from lane 2
Y50_L002

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  AIBP on day7


title: macrophage_control_C15

description:
C15
200796210050_I

value: I


title: P3_rep1


title: P2_rep1

value: OSCARhigh EF1alow


title: P4_rep1

value: OSCARmed EF1alow


title: ABC-imKO8 Cisplatin it AIBP rep2 line 1

description:
ABC-imKO8 sample technical replicate 2.  fastq read- pairs from lane 1
Y50_L001


title: P5_rep2

value: OSCARmed EF1ahigh


title: ABC-imKO8 Cisplatin it AIBP rep1 line 1

description:
ABC-imKO8 sample technical replicate 1.  fastq read- pairs from lane 1
Y49_L001


title: P4_rep2


title: P5_rep1


title: ABC-imKO8 Cisplatin it AIBP rep1 line 2

description:
ABC-imKO8 sample technical replicate 1.  fastq read- pairs from lane 2
Y49_L002


title: ABC-imKO7 Cisplatin it AIBP rep3 line 2

description:
ABC-imKO7 sample technical replicate 3.  fastq read- pairs from lane 2
Y48_L002


title: ABC-imKO8 Cisplatin it AIBP rep3 line 1

description:
ABC-imKO8 sample technical replicate 3.  fastq read- pairs from lane 1
Y51_L001


title: S07_AT2_Naive_ISRIB_R3

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

data_processing:
Reads were demultiplexed using bcl2fastq version 2.19.1
Quality of reads was assessed with FastQC and trimmed with Trimmomatic version 0.36
Trimmed reads were aligned to Mus musculus genome (mm10, version 78) with STAR version 2.6.0
Aligned reads were associated with genes and counted with HTSeq count version 0.11.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited table of gene counts

extract_protocol:
RNA was harvested following manufactures directions for Arcturus PicoPure RNA isolation kit (Applied Biosystems)
RNA-seq libraries were prepared from 3 ng total RNA using NEBNext RNA Ultra I kit (New England Biolabs, catalog number E7530L) with polyA mRNA isolation module (New England Biolabs, catalog number E7490S).

value: 2 months

value: Sorted Alveolar epithelial type 2 (AT2) cells

value: Integrated Stress Response inhibitor (ISRIB)

tag: condition

value: Naive


title: S06_AT2_Naive_ISRIB_R2


title: S08_AT2_Naive_ISRIB_R4


title: P2_rep2


title: ABC-imKO7 Cisplatin it AIBP rep3 line 1

description:
ABC-imKO7 sample technical replicate 3.  fastq read- pairs from lane 1
Y48_L001


title: S04_AT2_Naive_Saline_R4

value: Vehicle


title: S05_AT2_Naive_ISRIB_R1


title: macrophage_infected_C14

description:
C14
200796210050_G

value: F

value: G

value: macrophage

value: infected


title: macrophage_control_C14

description:
C14
200796210050_E

value: E

value: control


title: macrophage_control_C17

description:
C17
200796210050_F

value: M


title: macrophage_infected_C17

description:
C17
200796210050_H

value: H


title: S03_AT2_Naive_Saline_R3


title: macrophage_infected_C16

description:
C16
200796210050_D

value: D


title: macrophage_control_C16

description:
C16
200796210050_B

value: B


title: ABC-imKO7 Cisplatin it AIBP rep2 line 1

description:
ABC-imKO7 sample technical replicate 2.  fastq read- pairs from lane 1
Y47_L001

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  AIBP on day7


title: S01_AT2_Naive_Saline_R1

value: 2 months

value: Sorted Alveolar epithelial type 2 (AT2) cells


title: macrophage_control_C13

description:
C13
200796210050_A

value: A


title: S39_O_B_SFlow_ISRIB_R5

value: >18 months

tag: status

value: Bleomycin

value: Siglec F-low alveolar macrophages


title: ABC-imKO7 Cisplatin it AIBP rep2 line 2

description:
ABC-imKO7 sample technical replicate 2.  fastq read- pairs from lane 2
Y47_L002


title: S38_O_B_SFlow_ISRIB_R4


title: ABC-imKO7 Cisplatin it AIBP rep1 line 1

description:
ABC-imKO7 sample technical replicate 1.  fastq read- pairs from lane 1
Y46_L001


title: S34_O_B_SFlow_Saline_R5


title: S37_O_B_SFlow_ISRIB_R3


title: ABC-imKO6 Cisplatin it Saline rep3 line 2

description:
ABC-imKO6 sample technical replicate 3.  fastq read- pairs from lane 2
Y45_L002

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: S36_O_B_SFlow_ISRIB_R2


title: S33_O_B_SFlow_Saline_R4


title: ABC-imKO7 Cisplatin it AIBP rep1 line 2

description:
ABC-imKO7 sample technical replicate 1.  fastq read- pairs from lane 2
Y46_L002


title: S35_O_B_SFlow_ISRIB_R1


title: S31_O_B_SFlow_Saline_R2


title: ABC-imKO6 Cisplatin it Saline rep3 line 1

description:
ABC-imKO6 sample technical replicate 3.  fastq read- pairs from lane 1
Y45_L001


title: macrophage_infected_C30

description:
C30
200796210043_L

value: F

value: L

value: macrophage

value: infected


title: S32_O_B_SFlow_Saline_R3


title: ABC-imKO6 Cisplatin it Saline rep2 line 2

description:
ABC-imKO6 sample technical replicate 2.  fastq read- pairs from lane 2
Y44_L002


title: S02_AT2_Naive_Saline_R2

value: Vehicle

value: Naive


title: S30_O_B_SFlow_Saline_R1


title: macrophage_control_C30

description:
C30
200796210043_J

value: J

value: control


title: S29_Y_B_SFlow_ISRIB_R4

value: 8-12 weeks


title: macrophage_control_C27

description:
C27
200796210043_I

value: M

value: I


title: macrophage_infected_C29

description:
C29
200796210043_H

value: H


title: macrophage_infected_C27

description:
C27
200796210043_K

value: K


title: S28_Y_B_SFlow_ISRIB_R3


title: S26_Y_B_SFlow_ISRIB_R1


title: S27_Y_B_SFlow_ISRIB_R2


title: S23_Y_B_SFlow_Saline_R3


title: ABC-imKO6 Cisplatin it Saline rep2 line 1

description:
ABC-imKO6 sample technical replicate 2.  fastq read- pairs from lane 1
Y44_L001

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)


title: S22_Y_B_SFlow_Saline_R2

value: Bleomycin

value: Siglec F-low alveolar macrophages


title: S24_Y_B_SFlow_Saline_R4


title: ABC-imKO5 Cisplatin it Saline rep3 line 1

description:
ABC-imKO5 sample technical replicate 3.  fastq read- pairs from lane 1
Y42_L001

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: S21_Y_B_SFlow_Saline_R1


title: ABC-imKO6 Cisplatin it saline rep1 line 1

description:
ABC-imKO6 sample technical replicate 1.  fastq read- pairs from lane 1
Y43_L001


title: ABC-imKO5 Cisplatin it Saline rep2 line 2

description:
ABC-imKO5 sample technical replicate 2.  fastq read- pairs from lane 2
Y41_L002


title: S19_O_N_Mono_ISRIB_R4

value: >18 months

value: Naïve

value: Sorted lung monocytes


title: ABC-imKO6 Cisplatin it Saline rep1 line 2

description:
ABC-imKO6 sample technical replicate 1.  fastq read- pairs from lane 2
Y43_L002


title: ABC-imKO5 Cisplatin it Saline rep3 line 2

description:
ABC-imKO5 sample technical replicate 3.  fastq read- pairs from lane 2
Y42_L002


title: S18_O_N_Mono_ISRIB_R3


title: macrophage_infected_C26

description:
C26
200796210043_G

value: F

value: G

value: macrophage

value: infected


title: S15_O_N_Mono_Saline_R5


title: ABC-imKO5 Cisplatin it Saline rep1 line 2

description:
ABC-imKO5 sample technical replicate 1.  fastq read- pairs from lane 2
Y40_L002


title: S17_O_N_Mono_ISRIB_R2


title: macrophage_infected_C25

description:
C25
200796210043_C

value: C


title: S25_Y_B_SFlow_Saline_R5

value: 8-12 weeks


title: S13_O_N_Mono_Saline_R3


title: S20_O_N_Mono_ISRIB_R5


title: ABC-imKO5 Cisplatin it saline rep1 line 1

description:
ABC-imKO5 sample technical replicate 1.  fastq read- pairs from lane 1
Y40_L001


title: S12_O_N_Mono_Saline_R2


title: macrophage_control_C26

description:
C26
200796210043_E

value: E

value: control


title: S16_O_N_Mono_ISRIB_R1


title: macrophage_infected_C28

description:
C28
200796210043_D

value: D


title: macrophage_infected_C6

description:
C6
200796210020_L

value: L


title: macrophage_control_C25

description:
C25
200796210043_A

value: M

value: A


title: macrophage_control_C6

description:
C6
200796210020_J

value: J


title: macrophage_control_C28

description:
C28
200796210043_B

value: B


title: S11_O_N_Mono_Saline_R1

value: >18 months


title: S09_Y_N_Mono_ISRIB_R4

value: Naïve


title: ABC-imKO5 Cisplatin it Saline rep2 line 1

description:
ABC-imKO5 sample technical replicate 2.  fastq read- pairs from lane 1
Y41_L001

value: Spinal Cord

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: S08_Y_N_Mono_ISRIB_R3

value: Sorted lung monocytes


title: S10_Y_N_Mono_ISRIB_R5


title: ABC-imKO4 Cisplatin it Saline rep3 line 2

description:
ABC-imKO4 sample technical replicate 3.  fastq read- pairs from lane 2
Y39_L002


title: macrophage_infected_C5

description:
C5
200796210020_H

value: H

value: macrophage

value: infected


title: S14_O_N_Mono_Saline_R4


title: S07_Y_N_Mono_ISRIB_R2

value: 8-12 weeks


title: S06_Y_N_Mono_ISRIB_R1


title: S05_Y_N_Mono_Saline_R5


title: ABC-imKO4 Cisplatin it Saline rep2 line 1

description:
ABC-imKO4 sample technical replicate 2.  fastq read- pairs from lane 1
Y38_L001


title: S04_Y_N_Mono_Saline_R4


title: ABC-imKO4 Cisplatin it Saline rep2 line 2

description:
ABC-imKO4 sample technical replicate 2.  fastq read- pairs from lane 2
Y38_L002


title: S03_Y_N_Mono_Saline_R3


title: macrophage_infected_C2

description:
C2
200796210020_G

value: F

value: G


title: S02_Y_N_Mono_Saline_R2


title: S01_Y_N_Mono_Saline_R1


title: ABC-imKO4 Cisplatin it Saline rep3 line 1

description:
ABC-imKO4 sample technical replicate 3.  fastq read- pairs from lane 1
Y39_L001


title: ABC-imKO4 Cisplatin it Saline rep1 line 2

description:
ABC-imKO4 sample technical replicate 1.  fastq read- pairs from lane 2
Y37_L002


title: ABC-imKO4 Cisplatin it saline rep1 line 1

description:
ABC-imKO4 sample technical replicate 1.  fastq read- pairs from lane 1
Y37_L001


title: macrophage_control_C2

description:
C2
200796210020_E

value: E

value: control


title: macrophage_control_C5

description:
C5
200796210020_F

value: M


title: S24_O_A_SFlow_R4

source_name: Sorted lung macrophages

extract_protocol:
RNA was harvested following manufactures directions for AllPrep DNA/RNA Mini Kit (QIAGEN)
RNA-seq libraries were prepared from 30 ng total RNA using NEBNext RNA Ultra I kit (New England Biolabs, catalog number E7530L) with polyA mRNA isolation module (New England Biolabs, catalog number E7490S).

value: Asbestos

value: Siglec F-low alveolar macrophages


title: ABC-imKO3 Naïve rep3 line 1

description:
ABC-imKO3 sample technical replicate 3.  fastq read- pairs from lane 1
Y36_L001

value: naïve (no treatment)


title: S22_O_A_SFlow_R2

value: >18 months


title: ABC-imKO3 Naïve rep3 line 2

description:
ABC-imKO3 sample technical replicate 3.  fastq read- pairs from lane 2
Y36_L002

value: Spinal Cord


title: macrophage_control_C29

description:
C29
200796210043_F


title: S21_O_A_SFlow_R1


title: S20_O_A_SFhi_R4

value: Siglec F-high alveolar macrophages


title: macrophage_infected_C1

description:
C1
200796210020_C

value: C


title: macrophage_infected_C4

description:
C4
200796210020_D

value: D


title: S17_O_A_SFhi_R1


title: macrophage_control_C1

description:
C1
200796210020_A

value: A


title: S19_O_A_SFhi_R3


title: S16_Y_A_SFlow_R4

value: 8–12 weeks


title: ABC-imKO3 Naïve rep2 line 1

description:
ABC-imKO3 sample technical replicate 2.  fastq read- pairs from lane 1
Y35_L001

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)


title: ABC-imKO3 Naïve rep2 line 2

description:
ABC-imKO3 sample technical replicate 2.  fastq read- pairs from lane 2
Y35_L002


title: S18_O_A_SFhi_R2


title: macrophage_control_C4

description:
C4
200796210020_B

value: B

value: macrophage


title: ABC-imKO3 Naïve rep1 line 2

description:
ABC-imKO3 sample technical replicate 1.  fastq read- pairs from lane 2
Y34_L002


title: S23_O_A_SFlow_R3


title: S13_Y_A_SFlow_R1


title: S15_Y_A_SFlow_R3


title: S12_Y_A_Sfhi_R4


title: S14_Y_A_SFlow_R2


title: macrophage_infected_C9

description:
C9
200795790023_K

value: K

value: infected


title: S11_Y_A_Sfhi_R3


title: macrophage_infected_C12

description:
C12
200795790023_L

value: F

value: L


title: ABC-imKO3 Naïve rep1 line 1

description:
ABC-imKO3 sample technical replicate 1.  fastq read- pairs from lane 1
Y34_L001


title: S10_Y_A_Sfhi_R2

value: Asbestos


title: ABC-imKO2 Naïve rep3 line 2

description:
ABC-imKO2 sample technical replicate 3.  fastq read- pairs from lane 2
Y33_L002


title: ABC-imKO2 Naïve rep3 line 1

description:
ABC-imKO2 sample technical replicate 3.  fastq read- pairs from lane 1
Y33_L001


title: S08_O_N_Sfhi_R4

value: Naïve


title: S06_O_N_Sfhi_R2


title: S07_O_N_Sfhi_R3


title: S09_Y_A_Sfhi_R1


title: ABC-imKO2 Naïve rep2 line 2

description:
ABC-imKO2 sample technical replicate 2.  fastq read- pairs from lane 2
Y32_L002

value: naïve (no treatment)


title: S05_O_N_Sfhi_R1

value: >18 months


title: ABC-imKO2 Naïve rep2 line 1

description:
ABC-imKO2 sample technical replicate 2.  fastq read- pairs from lane 1
Y32_L001

value: Spinal Cord


title: S04_Y_N_Sfhi_R4

value: Siglec F-high alveolar macrophages


title: macrophage_infected_C8

description:
C8
200795790023_G

value: G


title: S03_Y_N_Sfhi_R3


title: S02_Y_N_Sfhi_R2


title: macrophage_control_C12

description:
C12
200795790023_J

value: J

value: control


title: ABC-imKO2 Naïve rep1 line 2

description:
ABC-imKO2 sample technical replicate 1.  fastq read- pairs from lane 2
Y31_L002


title: ABC-imKO2 Naïve rep1 line 1

description:
ABC-imKO2 sample technical replicate 1.  fastq read- pairs from lane 1
Y31_L001


title: ABC-imKO1 Naïve rep3 line 2

description:
ABC-imKO1 sample technical replicate 3.  fastq read- pairs from lane 2
Y30_L002


title: GZS36 het

tag: developmental stage

value: Hnf1b Sp2/+ (het)

value: kidney


title: macrophage_infected_C11

description:
C11
200795790023_H

value: M

value: H


title: GZS34 het

tag: strain


title: macrophage_control_C9

description:
C9
200795790023_I

value: I

value: macrophage


title: macrophage_control_C8

description:
C8
200795790023_E

value: F

value: E


title: macrophage_control_C11

description:
C11
200795790023_F


title: GZS35 wt

value: wild type


title: ABC-imKO1 Naïve rep3 line 1

description:
ABC-imKO1 sample technical replicate 3.  fastq read- pairs from lane 1
Y30_L001

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)


title: S01_Y_N_Sfhi_R1

value: 8–12 weeks

value: Naïve


title: macrophage_control_C10

description:
C10
200795790023_B

value: B


title: macrophage_infected_C10

description:
C10
200795790023_D

value: D

value: infected


title: GZS17 wt


title: Si8.GC_S4_bulkRNAseq

data_processing:
Quality of the raw data was assessed with FastQC (version 0.11.2) looking at per base sequence quality and adapter contamination.
If needed, the Fastq files were quality filtered using prinseq (version 0.20.3). Si8 Fastq files were filtered using the following parameters: -out_bad null -min_qual_mean 20 -ns_max_p 10 -trim_qual_right 3 -min_len 30  -no_qual_header
The reads were mapped using STAR (version 2.4.0f. for the DC and 2.5.2b for the Si8)
The number of the mapped reads was calculated using HTseq (version 0.6.1p1) with the stranded reverse protocol
Normalization of the data and differential expression were performed using DESeq2 (version 1.14)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts of sequencing reads and normalized counts by size.

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs and ECs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Sorted cells were pelleted and immediately resuspended in RLT buffer supplemented with β-merchaptoethanol. Samples were homogenized using QIAshredder columns (Qiagen) according to manufacturer’s instructions. Goblet cell lysates were loaded into RNeasy MinElute column and non-GC lysates into RNeasy Mini column (Qiagen). The columns were washed according to manufacturer’s instructions and the RNA was eluted with RNAse free H2O.
cDNA libraries were prepared with the TruSeq Stranded Total RNA Sample Preparation kit with Ribo Zero Gold (Rev. E; Illumina) according to manufacturer's protocol and sequenced via paired-end.

value: Goblet cells

value: 8th section of the small intestine

value: 6-8 weeks old


title: Si8.GC_S6_bulkRNAseq


title: ABC-imKO1 Naïve rep2 line 2

description:
ABC-imKO1 sample technical replicate 2.  fastq read- pairs from lane 2
Y29_L002

value: Spinal Cord

value: naïve (no treatment)


title: Si8.GC_S8_bulkRNAseq


title: Si8.EC_S5_bulkRNAseq

source_name: Enterocytes

value: Enterocytes


title: Si8.GC_S2_bulkRNAseq


title: Si8.EC_S7_bulkRNAseq


title: ABC-imKO1 Naïve rep2 line 1

description:
ABC-imKO1 sample technical replicate 2.  fastq read- pairs from lane 1
Y29_L001


title: Retinoblastoma_21

city: Birmingham

first: Carmel

last: McConville

state: UK

address: Vincent Drive

department: School of Cancer Sciences

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol

scan_protocol: Scanning was carried out using an Affymetrix GeneChip Scanner 3000 7G, with GCOS/GeneChip Command Console software.

data_processing: Affymetrix retinoblastoma data were extracted, normalised and summarised using the robust multi-average method implemented in the Affymetrix Expression Console. CEL files from the same Affymetrix array platform (Human Gene 1.0ST) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) for normal adult retina (GSM607947, GSM607948) and 96-day human fetal retina (GSM460264), and were normalised and summarised in parallel with retinoblastoma samples.

label: Biotin

source_name: Primary retinoblastoma tissue

label_protocol: Labelling was performed using the Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay

extract_protocol: Total RNA was isolated from retinoblastoma samples using Trizol extraction (Life Technologies Ltd, Paisley, UK), and additional purification was carried out using the Qiagen RNeasy system (Qiagen).

treatment_protocol: All samples are untreated tissues

value: Primary retinoblastoma tissue

value: Female

tag: Stage

tag: age (months)


title: ABC-imKO1 Naïve rep1 line 1

description:
ABC-imKO1 sample technical replicate 1.  fastq read- pairs from lane 1
Y28_L001


title: Si8.EC_S1_bulkRNAseq


title: macrophage_infected_C7

description:
C7
200795790023_C

value: M

value: C

value: macrophage


title: WT9 Cisplatin it AIBP rep3 line 2

description:
WT9 sample technical replicate 3.  fastq read- pairs from lane 2
Y27_L002

value: WT

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  AIBP on day7


title: WT9 Cisplatin it AIBP rep3 line 1

description:
WT9 sample technical replicate 3.  fastq read- pairs from lane 1
Y27_L001


title: DC.EC_S17_bulkRNAseq

value: Colonocytes

value: Distal colon


title: DC.GC_S13_bulkRNAseq


title: DC.GC_S18_bulkRNAseq


title: Retinoblastoma_19

tag: gender

value: E


title: ABC-imKO1 Naïve rep1 line 2

description:
ABC-imKO1 sample technical replicate 1.  fastq read- pairs from lane 2
Y28_L002

value: ABC-imKO (Abca1fl/fl Abcg1fl/fl Cx3cr1-CreERT2)

tag: treatment


title: Retinoblastoma_18

value: D


title: WT9 Cisplatin it AIBP rep2 line 2

description:
WT9 sample technical replicate 2.  fastq read- pairs from lane 2
Y26_L002


title: Si8.EC_S3_bulkRNAseq

value: 8th section of the small intestine


title: DC.EC_S12_bulkRNAseq

value: 6-8 weeks old


title: DC.EC_S14_bulkRNAseq


title: WT9 Cisplatin it AIBP rep2 line 1

description:
WT9 sample technical replicate 2.  fastq read- pairs from lane 1
Y26_L001

value: Spinal Cord


title: Retinoblastoma_17


title: DC.EC_S10_bulkRNAseq


title: DC.GC_S11_bulkRNAseq

value: Goblet cells


title: DC.GC_S9_bulkRNAseq


title: WT9 Cisplatin it AIBP rep1 line 2

description:
WT9 sample technical replicate 1.  fastq read- pairs from lane 2
Y25_L002


title: Retinoblastoma_20

value: Male


title: WT9 Cisplatin it AIBP rep1 line 1

description:
WT9 sample technical replicate 1.  fastq read- pairs from lane 1
Y25_L001


title: Retinoblastoma_14

value: Primary retinoblastoma tissue


title: Retinoblastoma_16

value: Female


title: Retinoblastoma_15


title: Hoxa-flox1

city: Nottingham

last: Thompson

address: University Park

department: Cancer and Stem Cells

institute: University of Nottingham

data_processing:
FASTQ Generation (Version: 1.0.0) in BaseSpace
FastQ files were aligned to mouse genome (GRCm38/mm10) using the STAR aligner
Transcripts were compiled from the alignments and differentially expressed genes identified using Cufflinks and Cuffdiff (version 2.2.2.20150701)
Reference annotation (Ensembl release 81) was used as a guide
Visualisation was performed using the cummeRbund package in R studio
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file matrix of FPKM values for all samples generated using Cufflinks

source_name: Leukemic Cells

growth_protocol: Leukemic cells were cultured overnight non-tissue culture treated petri dishes (P90) in RPMI 1640 with 10% FCS, 2 mM L-Glutamine , 10 ng/mL IL-3, 10 ng/mL IL-6, 10 ng/mL GM-CSF and 100 ng/mL SCF.

extract_protocol:
Total RNA was isolated using TRIzol® Reagent (Life Technologies).
Libraries were constructed using a stranded RNA-Seq Kit with RiboErase (Kapa Biosystems, London, UK), quantified using qPCR (KAPA Library Quantification Kit, Kapa Biosystems) and pooled and sequenced on a NextSeq 500 (Illumina, San Diego, CA, USA).

treatment_protocol: Leukemic cells were spinoculated with retroviral particles for control (GFP;flox) or Recombinase treatment (Cre;del) and sorted for high GFP expression using a FACSAria (BD Biosciences)

value: Bone marrow

value: Adult

value: Hoxa cluster floxed (Hoxa-flox)

value: Leukemic Cells


title: Hoxa-flox2


title: Hoxa-del2

value: Hoxa cluster deleted (Hoxa-del)


title: Hoxa-flox3


title: Hoxa-del3


title: Hoxa-del1


title: WT7 Cisplatin it AIBP rep3 line 2

description:
WT7 sample technical replicate 3.  fastq read- pairs from lane 2
Y21_L002

value: WT

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  AIBP on day7


title: Retinoblastoma_13

description: Expression data from this sample resembled that expected from normal retina

value: C


title: WT-Cre3

value: MA9-Hoxa-wild type (WT)


title: WT-Cre2


title: WT7 Cisplatin it AIBP rep3 line 1

description:
WT7 sample technical replicate 3.  fastq read- pairs from lane 1
Y21_L001


title: WT-Cre1


title: WT-GFP3


title: WT-GFP2


title: Retinoblastoma_12

value: D


title: WT-GFP1


title: WT7 Cisplatin it AIBP rep2 line 1

description:
WT7 sample technical replicate 2.  fastq read- pairs from lane 1
Y20_L001


title: Retinoblastoma_11

value: E


title: T24_R3

city: Oxford

first: Maria

last: Jakobsdottir

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics

institute: University of Oxford

data_processing:
Analysis of raw RNAseq data was carried out using version 3.0 of the nf-core/rnaseqpipeline developed by nf-core, within the nextflow framework (Nextflowversion 20.12.0-edge).   In  short,  quality  control  was  carried  out  using FastQCversion  0.11.9, unique molecular identifiers (UMIs) were extracted with UMI-tools, and adaptors were trimmed with version 0.6.6 of Trim Galore!.  Reads were aligned to hg19 (GRCH37) using version 2.6.1d of theSTAR aligner, and counted using version 1.4.0  of Salmon.   Alignments  were  sorted  and  indexed  using  version  1.10  of SAMtools,  de-duplicated  using UMI-tools,  and  duplicate  reads  were  marked using version 2.23.9 of picard MarkDuplicates.  Transcripts were assembled and quantified using StringTie version 2.1.4,  and bigWig coverage files were created using BEDTools version 2.29.2. Quality control was carried out using version 3.0.1 of RSeQC, version 2.2.2-dev of Qualimap, version 1.18.0 of dupRadar, version 2.0.3 of Preseq, version 1.28.0 of DESeq2, and aggregated using MultiQC.
Genome_build: GRCH37
Supplementary_files_format_and_content: Matrix of gene-level raw counts across all samples.

source_name: HCT116 Cells

growth_protocol: HCT116 cells were grown in high glucose DMEM medium supple-mented with 10% FBS, penicillin and streptomycin,  and L-glutamine.

extract_protocol:
Total RNA was extracted using the PARIS kit supplied by Life Technologies (AM1921).
Extracted RNA was treated with DNAse supplied by Life Technologies (AM1906), and checked for quality using RNA ScreenTapes on a 4200 TapeStation system (GS2991AA), both supplied by Agilent Technologies, before proceeding to cDNA synthesis.    cDNA was synthesised using the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads, following NEB's   Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490).    Sequencing libraries were prepared using the aforementioned kit and individual index primers for each sample (supplied by NEB).    Individual libraries were checked for quality using Qubit fluorometry (Life Sciences), as well as on the 4200 TapeStation using the High Sensitivity D1000 ScreenTape assay.    Libraries were sequenced using an Illumina NextSeq 500 sequencing machine.

treatment_protocol: HCT116 cells were seeded into 6 well plates and allowed to adhere overnight.  24 hours after seeding,  cells at the 0h time point were harvested and stored in RNAlater solution (AppliedBiosystems AM7020).  Alll other cells were infected with VSV-G pseudotyped HIV particles at an MOI of 1.  Infected cells were harvested and placed in RNAlater solution 6 hours 12 hours, and 24 hours after infection.

tag: hours post infection


title: WT7 Cisplatin it AIBP rep2 line 2

description:
WT7 sample technical replicate 2.  fastq read- pairs from lane 2
Y20_L002


title: WT7 Cisplatin it AIBP rep1 line 2

description:
WT7 sample technical replicate 1.  fastq read- pairs from lane 2
Y19_L002


title: T24_R2


title: Retinoblastoma_10


title: Retinoblastoma_09


title: A549-ONT-siPLANE-2

city: Zhengzhou

first: liu

last: Teng

address: No 7,Weiwu Road,Jinshui  District

department: Translational Research Institute

institute: Henan Provincial People’s Hospital and People’s Hospital of Zhengzhou University

data_processing:
Raw reads were first filtered with minimum average read quality score=7 and  minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA  database. Next, full-length, non-chemiric (FLNC) transcripts were determined by  searching for primer at both ends of reads. Clusters of FLNC transcripts were  obtained after mapping to reference genome with mimimap2, and consensus isoforms  were obtained after polishing within each cluster by pinfish.
Consensus sequences were mapped to reference genome using minimap2. Mapped  reads were further collapsed by cDNA_Cupcake package with min-coverage=85%  and min-identity=90%. 5’ difference was not considered when collapsing redundant  transcripts.
The criteria for fusion candidates is that a single transcript must: (1) must map to 2 or more loci,(2) minimum coverage for each loci is 5% and minimum coverage in bp is >= 1 bp,(3) total coverage is >= 95%,(4) distance between the loci is at least 10kb
Differential expression analysis of two samples was performed using the  EBSeq R package. The resulting FDR (false discovery rate) were adjusted using the  PPDE(posterior probability of being DE).The FDR < 0.05 and foldchange ≥ 1.5 was  set as the threshold for significantly differential expression.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file includes CPM values for each Sample,FDR,log2FC

source_name: Lung adinocarcinoma cell line

growth_protocol: cells were maintained in DMEM (Biological Industries, #01-052-1ACS; Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS, Biological Industries, #04-001-1A; Beit Haemek, Israel) and 1% penicillin-streptomycin (Biological Industries, #03-031-1BCS，Beit Haemek, Israel). Cells were cultured in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol™ Reagent(Catalog number: 15596026,ThermoFisher Scientific) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Oxford Nanopore Technologies protocols

treatment_protocol: A549 cells were seeded in 6-well plate (1.5X10^5/well). Transfections were performed after 24h by using Lipofectamine™ 3000 Transfection Reagent (Thermo Fisher, L3000-015) according to the manufacturer’s instructions.

tag: cell line

value: transfected with PLANE siRNA

tag: PLANE knockdown


title: A549-ONT-NC-2

value: transfected with negative control siRNA

tag: control


title: T24_R1


title: WT6 Cisplatin it Saline rep3 line 2

description:
WT6 sample technical replicate 3.  fastq read- pairs from lane 2
Y18_L002

tag: tissue

value: Spinal Cord

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: WT7 Cisplatin it AIBP rep1 line 1

description:
WT7 sample technical replicate 1.  fastq read- pairs from lane 1
Y19_L001


title: WT6 Cisplatin it Saline rep3 line 1

description:
WT6 sample technical replicate 3.  fastq read- pairs from lane 1
Y18_L001


title: A549-ONT-NC-1


title: Retinoblastoma_07

value: Primary retinoblastoma tissue


title: Retinoblastoma_06

value: Female


title: Retinoblastoma_08


title: T12_R2


title: WT6 Cisplatin it Saline rep2 line 2

description:
WT6 sample technical replicate 2.  fastq read- pairs from lane 2
Y17_L002


title: HEK293T-hACE2_cov rep1

city: Duarte

first: Guihua

last: Sun

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

data_processing:
Basecalls performed using CASAVA version 1.8
Subread 2.01 was used for alignment
featureCount was used to extract read count
Genome_build: hg38
Supplementary_files_format_and_content: gene count txt fule

source_name: HEK293T-hACE2 cell line

extract_protocol:
Trizol extractd total RNA
KAPA RNA HyperPrep with RiboErase

treatment_protocol: MOI=1, infect for 72 hours

value: stable hACE2 expression


title: Retinoblastoma_05

value: Male


title: HEK293T-hACE2_cov rep2


title: WT6 Cisplatin it Saline rep1 line 2

description:
WT6 sample technical replicate 1.  fastq read- pairs from lane 2
Y16_L002


title: HEK293T-hACE2_mock rep2

value: mock


title: T12_R1


title: WT6 Cisplatin it Saline rep2 line 1

description:
WT6 sample technical replicate 2.  fastq read- pairs from lane 1
Y17_L001


title: A549-ONT-siPLANE-1


title: Retinoblastoma_04


title: T6_R4


title: HEK293T-hACE2_mock rep1


title: Retinoblastoma_03


title: T12_R3


title: T12_R4


title: T6_R3


title: Spleen CD32+ T4 cells from AGM #3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

description:
SV.PvsM.complete.txt
AGMp3

data_processing:
Reads were cleaned of adapter sequences, and low-quality sequences were removed using cutadapt version 1.11.Only sequences ≥ 25 nucleotides (nt) in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene, -g ID and -s 1).
Data were analyzed using R version 3.4.3 and the Bioconductor package DESeq2 version 1.18.185. Normalization and dispersion estimation were performed with DESeq2, using the default parameters, and statistical tests for differential expression were performed by applying the independent filtering algorithm. A generalized linear model, including the monkey identifier as a blocking factor, was used to test for the differential expression between the biological conditions. For each pairwise comparison, raw p values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure86. Genes with an adjusted p value <0.05 were considered differentially expressed.
Genome_build: Chlorocebus sabaeus, and macaca fascicularis from Ensembl release 90
Supplementary_files_format_and_content: Matrix from DESeq2

organism: Chlorocebus sabaeus

source_name: Spleen from African green monkey

extract_protocol:
RNA was isolated from the sorted CD4 populations cells using the RNeasy® Mini Kit (205113, Qiagen)
RNA integrity was verified with the Agilent Bioanalyser. DNase-treated RNA was treated for library preparation using the Truseq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer’s instructions. An initial poly(A) RNA isolation step (included in the Illumina protocol) is performed on 10 ng of total RNA to keep only the polyadenylated RNA fraction and remove the ribosomal RNA. A step of fragmentation is then performed on the enriched fraction, by divalent ions at high temperature. The fragmented RNA samples were randomly primed for reverse transcription followed by second-strand synthesis to create double-stranded cDNA fragments. No end repair step was necessary. An adenine was added to the 3'-end and specific Illumina adapters were ligated. Ligation products were submitted to PCR amplification. The obtained oriented libraries were controlled by Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified by spectrofluorimetry (Quant-iT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen). Sequencing was performed on the Illumina Hiseq2500 platform to generate single-end 100 bp reads bearing strand specificity.

treatment_protocol: A 6-color panels was used to sort CD32+/- CD4+ T cells from the spleen of 3 chronically infected AGM and 3 chronically infected cynomolgus macaques. Cells were thawed in 20% FBS-containing media supplemented with benzonase nuclease, and counts and viabilities were performed (Life Technologies).  Cells were  incubated with Fcγ receptor blocker for 10 minutes. Antibody cocktail mix was added and incubated for 20 minutes. Following surface staining, cells were washed and resuspended in complete medium and kept in the dark at 4°C until acquisition. Cells were sorted on a FACSAria II (BD Biosciences)  in purity mode. For RNA extraction cells  were directly collected in a lysis buffer that contained TCEP. The purity of the cells was >97%.

tag: animal status

value: SIVagm.sab9018 chronically infected

value: spleen

tag: cell type

value: CD4+ T lymphocytes

tag: cell phenotype


title: tumor_566709

city: Tianjin

first: Yang

last: Qu

address: Huanhuxi Road, Tiyuanbei, Hexi District

department: Department of Gastrointestinal Cancer Biology

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Filter by read quality. Read pairs with low sequencing quality are first removed. This step reduces the influence of poor sequencing quality from the metrics that are specific to the BD Rhapsody Targeted assays.
Annotate R1 reads.The quality-filtered R1 reads are analyzed to identify the cell label section sequence (CLS), common sequences (L), Unique Molecular Identifier (UMI) sequence, and poly(T) tail.
Annotate R2 reads. The pipeline uses Bowtie2 version 2.2.9 to map the filtered R2 reads to the reference panel sequences.
Combine information from R1 and R2 annotations.Read pairs with a valid R1 read and a valid R2 read are retained for further analyses. A valid R1 read requires identified CLSs, a UMI sequence with non-N bases, and a poly(T) tail. A valid R2 read requires reads uniquely mapped to a gene in a panel with the correct PCR2 primer sequence at the start and an alignment of >60 bases in length.
Annotate molecules.Reads with the same cell label, same UMI sequence, and same gene are collapsed into a single raw molecule. The number of reads associated with each raw molecule is reported as the raw adjusted sequencing depth.
Putative cell identification using second derivative analysis (basic implementation). Removing false positives and false negatives (refined implementation)
Generate expression matrices. Reporting RSEC and DBEC metrics. RSEC-adjusted molecule counts and associated reads of each gene for each putative cell and DBEC-adjusted molecule counts and associated reads are presented in either .csv or .st format
Annotate SAM.The SAM file output by Bowtie2 is further annotated to summarize the results of the BD Rhapsody Analysis pipeline.
Generate metrics summary. A summary .csv file documenting the metrics of each of the analysis steps is generated.
Clustering analysis. The measured single cell gene expression profiles go through a clustering analysis pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tumor-infiltrating Tregs

extract_protocol:
Single-cell suspensions were loaded in the BD Rhapsody™ Cartridge, which could effectively capture and separate single cells. Then, we loaded magnetic beads carrying a cell-specific sequence and unique molecular index (UMI) into the cartridge. In each well, a single cell was lysed, and the released mRNA was captured by a barcoded bead.
All beads carrying mRNA were collected in an Eppendorf tube.Then we conducted cDNA synthesis, transcriptome amplification and library amplification via PCR with a cDNA kit. The libraries were analyzed on the Illumina HiSeq PE150 platform.

value: Tumor-infiltrating Tregs

tag: age

tag: tumor type

value: Gastric cancer

tag: tumor stage

value: III


title: WT5 Cisplatin it Saline rep3 line 2

description:
WT5 sample technical replicate 3.  fastq read- pairs from lane 2
Y15_L002

tag: genotype

value: WT


title: WT5 Cisplatin it Saline rep3 line 1

description:
WT5 sample technical replicate 3.  fastq read- pairs from lane 1
Y15_L001


title: Spleen CD32+ T4 cells from AGM #1

description:
SV.PvsM.complete.txt
AGMp1


title: tumour


title: blood_566709

source_name: Peripheral blood Tregs

value: Peripheral blood Tregs


title: WT5 Cisplatin it Saline rep2 line 2

description:
WT5 sample technical replicate 2.  fastq read- pairs from lane 2
Y14_L002


title: T0_R3

value: 0 hours/uninfected


title: Spleen CD32- T4 cells from AGM #3

description:
SV.PvsM.complete.txt
AGMm3


title: Spleen CD32- T4 cells from AGM #2

description:
SV.PvsM.complete.txt
AGMm2


title: T0_R1


title: T0_R2


title: WT6 Cisplatin it Saline rep1 line 1

description:
WT6 sample technical replicate 1.  fastq read- pairs from lane 1
Y16_L001


title: pbmc


title: WT5 Cisplatin it Saline rep2 line 1

description:
WT5 sample technical replicate 2.  fastq read- pairs from lane 1
Y14_L001


title: Spleen CD32- T4 cells from AGM #1

description:
SV.PvsM.complete.txt
AGMm1


title: N712


title: Retinoblastoma_02

value: E


title: p53_KO MCF10A, H3K4me3

description:
Abcam, ab8580, 5ug
CHNM64
CHNM64vs63_peaks.txt

data_processing:
Bascalling:Illumina RTA 2.4.6
Adapter removal: Cutadapt 1.18
Alignment: Bowtie2 2.2.6, -p 8 -x ref_genome -U read1.fastq
Processed files are peak files. Peak calling was performed using MACS2 (band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05)
Genome_build: hg38
Supplementary_files_format_and_content: txt file contains peak files from MACS

source_name: MCF10A cells

growth_protocol: DMEM/F12 media supplemented with 5% horse serum, 10 µg/ml human recombinant insulin (Sigma, Cat# 910077C), 20 ng/ml human EGF (PeproTech, Cat# AF100-15), 500 ng/ml hydrocortisone (Sigma, Cat# H0888g), 100 ng/ml cholera toxin (Sigma, Cat# C8052-5MG) and antibiotics.

extract_protocol:
ChIP DNA was extracted by standard phenol approach.
TruSeq ChIP Library Prep Kit (IP-202-1012)

treatment_protocol: No treatment

value: untreated

tag: repeat

value: p53 knockout

tag: chip antibody

value: H3K4me3 (Abcam, ab8580, 5ug)


title: N711

value: Female


title: T6_R2


title: WT4 Cisplatin it Saline rep3 line 2

description:
WT4 sample technical replicate 3.  fastq read- pairs from lane 2
Y12_L002

value: Spinal Cord

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: MCF10A, H3K4me3_2

description:
Abcam, ab8580, 5ug
CHNM63
CHNM64vs63_peaks.txt

value: wild type


title: SARS-CoV-2_3

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: processed data file: M0.MACROPHAGE.xlsx

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Transcript abundances was estimated in Fragments Per Kilobase of exon per Million mapped reads (FPKM) by using Cufflinks v2.1.1 package.
Raw reads counts were extracted using htseq-count v0.11.2.
Genome_build: hg19
Supplementary_files_format_and_content: txt file storing raw read counts; excel file storing FPKM values or TMM-based normalized counts per gene per sample

growth_protocol: For monolayer-based differentiation of cardiomyocytes (CMs), hPSCs were cultured between P20-P40 and seeded at a density of 3x105 cells/well of a 6-well plate and grown for 48 hr to 90% confluence in a humidified incubator with 5% CO2 at 37℃. On day 0, the medium was replaced with RPMI 1640 supplemented with B27 without insulin and 6 µM CHIR99021. On day 1, the medium was changed to RPMI 1640 supplemented with B27 without insulin for 48 hr. Day 3, medium was refreshed to RPMI 1640 supplemented with B27 without insulin and 2 µM C59 for another 48 hr. On day 5, the medium was changed back to RPMI-B27 without insulin for 48 hr, and then switched to RPMI 1640 plus normal B27 until day 12 with a medium change every 2 days. On day 12, the medium was transiently changed to RPMI 1640 without D-glucose containing ascorbic acid, human albumin and DL-Lactate for two days to allow metabolic purification of CMs. From that day on, fresh RPMI 1640-B27 was changed every two days; Macrophages were derived from hPSCs by adapting a previously reported protocol28. hPSCs were cultured between P20-P40. First, H9 or H1 cells were lifted with ReLeSR (STEMCELL Technologies) as small clusters onto Matrigel-coated 6-well plates at low density. On day 0, IF9S medium was supplemented with 50 ng/ml BMP-4, 15 ng/ml Activin A and 1.5 µm CHIR99021. On day 2, medium was refreshed with IF9S medium with 50 ng/ml VEGF, 50 ng/ml bFGF, 50 ng/ml SCF (R&D Systems) and 10 µm SB431542 (Cayman Chemical). On day 5 and da y7, medium was changed to IF9S with 50 ng/ml IL-6 (R&D Systems), 12 ng/ml IL-3 (R&D Systems), 50 ng/ml VEGF, 50 ng/ml bFGF, 50 ng/ml SCF and 50 ng/ml TPO (R&D Systems). On day 9, cells were dissociated with TrypLE (Life Technologies) and re-suspended in IF9S medium with 50 ng/ml IL-6, 12 ng/ml IL-3 and 80 ng/ml M-CSF (R&D Systems). On day 13 and day 15, medium was changed and supplemented with 50 ng/ml IL-6, 12 ng/ml IL-3 and 80 ng/ml M-CSF. All differentiation steps were cultured at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: To analyze the gene expression of CMs co-cultured with H9-derived macrophages using RNA-seq, we used trans-well plates. CMs were seeded on the lower plate of 24 well plates and macrophages were seeded onto the upper chamber. After 24 hr, drug treatments were done to CMs and macrophages in the upper chamber were infected with SARS-CoV-2 (MOI=0.1). The trans-well chamber will allow cytokines to go through but not macrophages. 24 hpi, CMs were collected to extract total RNA. For analyzing macrophages infected with virus, macrophages were seeded onto 24 well plates and infected with SARS-CoV-2 (MOI=0.1). 24 hpi, macrophages were collected for total RNA.

tag: tissue/cell type

value: human ES-derived macrophage

tag: virus

value: SARS-CoV-2 infected

value: No treatment


title: Spleen CD32+ T4 cells from AGM #2

description:
SV.PvsM.complete.txt
AGMp2

value: SIVagm.sab9018 chronically infected

value: spleen

value: CD4+ T lymphocytes


title: T6_R1


title: WT4 Cisplatin it Saline rep3 line 1

description:
WT4 sample technical replicate 3.  fastq read- pairs from lane 1
Y12_L001

value: WT

tag: treatment


title: Retinoblastoma_01

value: Primary retinoblastoma tissue

tag: gender

tag: Stage

tag: age (months)


title: RUNX1_KO MCF10A, H3K4me3

city: Bethesda

last: Huang

institute: National Cancer Institute

description:
Abcam, ab8580, 5ug
CHNM62
CHNM62vs60_peaks.txt

value: RUNX1 knockout


title: CSC

city: Kyoto

first: Tomoki

last: Konishi

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Division of Digestive Surgery

institute: Kyoto Prefectural University of Medicine

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Total RNA of PK59 CSCs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: We extracted total RNA by using an RNeasy kit (Qiagen, Valencia, CA)

treatment_protocol: Cells expressing high levels of ALDH1A1 were separated from PK59 cells using fluorescence-activated cell sorting (FACS) and then cultured in tumorsphere medium containing the following: RPMI-1640 with 100 U/ml penicillin, 100 μg/ml streptomycin, 2% B27 supplement (Gibco, Langley, OK, USA), 10 ng/ml epidermal growth factor (Invitrogen, Grand Island, NY, USA), and 10 ng/ml fibroblast growth factor (Invitrogen, Grand Island, NY, USA) for 7 days in ultra-low attachment 6-well plates (Corning International, Corning, NY, USA) (20). The presence of tumorspheres in plates was detected under an inverted microscope. Tumorspheres were recovered by centrifugation, counted, and dissociated into single cells by processing with trypsin-EDTA and gentle mechanical crushing using a glass pipette. The single cells obtained were re-plated to allow for the reformation of spheres. These spheres were passed on every 4-7 days when their diameter was approximately 100 μm.

value: pancreatic cancer

tag: cell line

tag: phenotype

value: CSC


title: non CSC

source_name: Total RNA of PK59 cells

tag: tissue

value: non-CSC


title: SARS-CoV-2_1

description: processed data file: M0.MACROPHAGE.xlsx


title: WT5 Cisplatin it Saline rep1 line 2

description:
WT5 sample technical replicate 1.  fastq read- pairs from lane 2
Y13_L002

source_name: Microglia


title: CBFB_KO MCF10A, H3K4me3

first: Jing

description:
Abcam, ab8580, 5ug
CHNM61
CHNM61vs60_peaks.txt

value: untreated

value: CBFB knockout

value: H3K4me3 (Abcam, ab8580, 5ug)


title: SARS-CoV-2_2

description: processed data file: M0.MACROPHAGE.xlsx


title: WT5 Cisplatin it Saline rep1 line 1

description:
WT5 sample technical replicate 1.  fastq read- pairs from lane 1
Y13_L001

value: Spinal Cord

value: i.p. injection of cisplatin on day1 and day3.  intrathecal (i.t.) injection of  saline on day 7


title: MCF10A, H3K4me3_1

description:
Abcam, ab8580, 5ug
CHNM60
CHNM61vs60_peaks.txt
CHNM62vs60_peaks.txt

value: wild type


title: Mock_3

description: processed data file: M0.MACROPHAGE.xlsx

source_name: Uninfected_ES-derived machrophage

value: human ES-derived macrophage

value: Uninfected


title: WT4 Cisplatin it Saline rep1 line 2

description:
WT4 sample technical replicate 1.  fastq read- pairs from lane 2
Y10_L002


title: Mock_2

description: processed data file: M0.MACROPHAGE.xlsx

value: No treatment


title: WT4 Cisplatin it Saline rep1 line 1

description:
WT4 sample technical replicate 1.  fastq read- pairs from lane 1
Y10_L001


title: Mock_1

description: processed data file: M0.MACROPHAGE.xlsx


title: Tofacitinib_3

description: processed data file: CM.expression.xls

source_name: SARS-CoV-2 infected_Tofacitinib treated_ES-derived cardiomyocyte

value: human ES-derived cardiomyocyte

value: SARS-CoV-2 infected

value: Tofacitinib treated


title: WT3 Naïve rep3 line 1

description:
WT3 sample technical replicate 3.  fastq read- pairs from lane 1
Y9_L001

value: WT

value: naïve (no treatment)


title: Tofacitinib_2

description: processed data file: CM.expression.xls


title: Tofacitinib_1

description: processed data file: CM.expression.xls


title: WT3 Naïve rep2 line 2

description:
WT3 sample technical replicate 2.  fastq read- pairs from lane 2
Y8_L002


title: WT4 Cisplatin it Saline rep2 line 2

description:
WT4 sample technical replicate 2.  fastq read- pairs from lane 2
Y11_L002


title: WT3 Naïve rep1 line 1

description:
WT3 sample technical replicate 1.  fastq read- pairs from lane 1
Y7_L001


title: WT4 Cisplatin it Saline rep2 line 1

description:
WT4 sample technical replicate 2.  fastq read- pairs from lane 1
Y11_L001