title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice,  Tumor stroma, biological replica 2

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

institute: Centre Léon Bérard

description:
TS_2
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

data_processing: Data processing was performed in collaboration with the platform of Bioinformatics Gilles Thomas. Bcl2fastq v.2.20 was used for demultiplexing data as well as for converting BCL files to FASTQ files. Quality controls were performed using FastQC-0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Trimmomatic-0.36 was used to remove adapters from our sequence data. Reads were mapped to the reference mouse genome GRCm38.p6 using STAR-2.5.1b. Qualimap v2.2.1 and Samtools-1.6 (algorithm: ‘flagstat’) were used for aligned reads quality checks of our BAM files. To identify differential gene expression changes during oral tumorigenesis we have used HTSeq-0.10.0 (algorithm: ‘HTSeq-count’). It creates a count matrix using the number of the reads from each bam file that map to the genomic features of mouse genome (gencode.vM17.annotation.gtf). Transcript and gene expression matrices (normalized in Transcripts Per Million) were generated using Salmon-0.9.1 (algorithm: ‘quant’) for the transcript quantification and tximport R package v1.8.0 for the Gene-level summarization. Human ortholog genes were identified for each gene (http://www.informatics.jax.org/orthology.shtml).

source_name: CBA mice (Mus musculus)

extract_protocol:
To ensure RNase-free conditions, only RNase-free solutions and materials were allowed. RNAse-free MembraneSlide1.0 PEN (Zeiss®) for preparation of FFPE-samples were used. To overcome the hydrophobic nature of the membrane, the MembraneSlide were initially irradiated with UV light at 254 nm for 30 min (in a cell culture hood), in order to improve FFPE-sections adhesions. Positive side effects were sterilization and destruction of potentially contaminating nucleic acids5. Unstained 3-µm sections were then mounted onto MembraneSlides the same way as routinely done using glass slides. Four to six sections were mounted on the same membrane slide for reasons of simplicity, efficiency and expediency (Supplementary Figure 2). The slides were let dry overnight in a drying oven at 56°C. To allow laser cutting and lifting, a coverslip and standard mounting medium was not applied.  Laser capture microdissection (LCM) was performed the following day. Because paraffin reduces laser efficiency (sometimes completely inhibiting cutting and lifting), we removed the paraffin before staining, laser cutting and lifting. Our deparaffinization protocol of unstained sections was the following: xylene 1.30 minute, 100% then 96% to finish 70% ethanol each 1 minute. After deparaffinization, the mounting sections were stained with RNAse free cresyl violet to preserve RNA quality (cresyl violet for 15 seconds, removing excess stain, 70% ethanol 30 sec and 100% ethanol 30 sec). After drying for 2 minutes, membrane slides were immediately used to avoid RNA degradation of deparaffinized samples. The selection of epithelial cells as well as the underlying stroma and muscle of interest was performed according to the mapping provided by the pathologist (A.T). Microdissection should be performed at least at a magnification of about 10× to respect histologic details. The energy cut should be among 50 to 60% to allow efficient cutting without risk of burning of the targeted tissue. Microdissection of the stroma should always be realized before the epithelium to avoid stromal damages (Supplementary Video). One hour of LCM allows the capture of 1mm2 and 0.3 mm2 of epithelium and stroma respectively. Microdissected specimens were collected in Adhesive Cap500® tube.
We performed total RNA extraction using QIAGEN RNeasy® FFPE-kit. At the end of the extraction protocol, aliquots of 2µL were used to control quantity as well as to assess the RNA purity (Thermo-Scientific™ NanoDrop 2000). Other aliquots of 2μL were submitted to the High Sensitivity RNA Screen system (Agilent 2200 Tapestation®) allowing measurement of the RNA integrity number (RIN) and the percentage of RNA fragments >200 nucleotides (DV200) which is a more reliable determinant of RNA quality for library preparation (TruSeq stranded total RNA Library Preparation Kit with Ribo-Zero Illumina®). RNA samples with DV200 < 30% were not sequenced. After the quality control steps (qPCR, Tapestation®), sequencing was performed using the NextSeq 550 system (Illumina®).
After total RNA extraction (QIAGEN RNeasy® FFPE-kit), samples (n=13 epithelial and n=13 stromal, subsequently referred as E-samples and S-samples respectively) were sequenced (NextSeq 550 Illumina®) (quality controls in Supplementary Table 1).

value: Stroma

tag: Histology type

value: Tumor

tag: age of mice at sacrifice (weeks)

tag: gender

tag: rnaseq run number

value: CBA mice (Mus musculus)


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice,  Tumor stroma, biological replica 3

status: Public on Jan 11 2022

type: SRA

country: France

description:
TS_3
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: group

value: male

tag: strain


title: IL-4/IL-13 L49348_M2_2_05_C01

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

description:
IL-4/IL-13
IL-4/IL-13

data_processing:
Bbasecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
Read alignment: Fragments were aligned to the mouse reference genome mm10 using the aligner gsnap (2019-06-10) with Ensembl 98 splice sites as support (parameters: --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0  --action-if-cigar-error noprint).
Counts per feature: Uniquely mapped fragments were compared based on their overlap to Ensembl 98 gene annotations using featureCounts (v1.6.3) to create a table of counts per gene and cell (parameters:  -a EnsemblGene-98.mm10.TR.gtf -s 0 -p -o bfx1341.mm10.e98.txt -Q 1).
Samples were processed and analyzed in R (4.0.0) using Seurat (v3)
Genes from specific metabolic pathways were retrieved from KEGG
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells.

source_name: Bone marrow

growth_protocol: In the presence of M-CSF

extract_protocol:
Wild-type BMDMs were stimulated with 10ng/ml IL4, IL13 and TNF. Cells were scraped and stained for live/dead staining with LDFA. Single cells were flow-sorted into 384-well plates containing nuclease-free water with 0.2% Triton X-100 and 1 U murine RNase inhibitor, centrifuged, and frozen at −80°C. After thawing, the primer mix and 1 U murine RNase inhibitor was added to each well. The reverse transcription reaction was performed, cDNA was amplified and purified. The concentration of samples was measured using a plate reader (Infinite 200 PRO, Tecan).
Then, pre-amplified cDNA was used for library preparation (TruePrep DNA library preparation kit V2 for Illumina, Vazyme) in a 1-μL reaction volume. Illumina indices were added during the PCR reaction with 1 × KAPA Hifi HotStart Ready Mix and dual indexing primers. After PCR, the libraries were quantified with AccuBlue Broad Range kit, pooled in equimolar amounts, and purified twice with Sera-Mag SpeedBeads. The libraries were sequenced on the Novaseq 6000 Illumina platform to obtain 50 bp paired-end reads aiming at an average sequencing depth of 0.5 million reads per cell.
Single Cell RNA seq

treatment_protocol: 10ng/ml IL4, IL13 and/or TNF

tag: cell type

value: BMDM

tag: treatment


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice,  Tumor epithelium, biological replica 1

description:
TE_1
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

value: Epithelium


title: IL-4/IL-13 L49347_M2_2_05_B24

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice,  Tumor stroma, biological replica 1

description:
TS_1
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: iATSKO - 30 days [60_CRE-Tamox_1mois]

city: Nantes

first: Xavier

last: Prieur

address: 8 quai Moncousu

institute: INSERM

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1)
Genome_build: Mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iATSKO - 30 days

growth_protocol: 8 weeks-old mice were injected with Tamoxifen or vehicle and killed 15 days, 30 days or 90 days after the first injection.

extract_protocol:
Total RNA from tissues was purified using Trizol (Life technology, les Ulis, France) according to the manufacturer’s instructions. Total RNA from cell samples were purified with the NucleoSpin RNA II (Macherey Nagel, Hoerdt, France).
the libraries was prepared from 10 ng of total RNA. 15 RNA samples were extracted from hiPS. The mRNA poly(A) tail was tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples were then pooled, amplified and tagmented using a transposon-fragmentation approach, which enriches for 3’ends of cDNA. 100ng of full-length cDNAs was used as input to the Nextera DNA Sample Prep kit (ref FC-121-1030, Illumina), which enriches for 3′ends of cDNA. Size library is controlled on 2200 Tape Station Sytem (Agilent Technologies). A library of 350-800bp was run on an Illumina HiSeq 2500 using a HiSeq Rapid SBS Kit v2 (50 cycles; FC-402-4022) and a HiSeq Rapid PE Cluster Kit v2 (PE-402-4002) according to manufacturer’s protocol (Denaturing and Diluting Libraries for the HiSeq® and GAIIx, Part # 15050107 v03 protocol, Illumina).

treatment_protocol: No othe treament has been applied

tag: strain background

tag: Sex

tag: age

value: 12 weeks-old

tag: genotype/time point

value: iATSKO - 30 days

tag: tissue

value: inguinal white adipose tissue


title: iATSKO - 30 days [59_CRE-Tamox_1mois]


title: IL-4/IL-13 L49350_M2_2_05_C03

description:
IL-4/IL-13
IL-4/IL-13


title: Liver sample from sASH group (SL2)

type: RNA

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Liver sample from sASH group

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor environment (v3.1) in R.3.6.3

label: biotin

organism: Homo sapiens

source_name: liver biopsy sample

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: disease state

value: silent alcoholic steatohepatitis (sASH)

value: liver


title: IL-4/IL-13 L49345_M2_2_05_B22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49349_M2_2_05_C02

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice,  Tumor epithelium, biological replica 3

description:
TE_3
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: iATSKO - 30 days [58_CRE-Tamox_1mois]


title: IL-4/IL-13 L49346_M2_2_05_B23

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice,  Tumor epithelium, biological replica 2

description:
TE_2
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: IL-4/IL-13 L49343_M2_2_05_B20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49342_M2_2_05_B19

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia stroma, biological replica 3

description:
DPS_3
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

value: Dysplasia


title: IL-4/IL-13 L49341_M2_2_05_B18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49340_M2_2_05_B17

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia stroma, biological replica 1

description:
DPS_1
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Bscl2lox/lox+ tamoxifen -30 days [56_Ctl-Tamox_1mois]

source_name: Bscl2lox/lox+ tamoxifen -30 days

value: Bscl2lox/lox+ tamoxifen -30 days


title: Bscl2lox/lox+ tamoxifen -30 days [55_Ctl-Tamox_1mois]


title: IL-4/IL-13 L49337_M2_2_05_B14

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [54_Ctl-Tamox_1mois]


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia stroma, biological replica 4

description:
DPS_1B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: IL-4/IL-13 L49338_M2_2_05_B15

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia stroma, biological replica 2

description:
DPS_2B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: IL-4/IL-13 L49335_M2_2_05_B12

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [52_Ctl-Tamox_1mois]


title: IL-4/IL-13 L49336_M2_2_05_B13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49344_M2_2_05_B21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49331_M2_2_05_B08

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen -30 days [53_Ctl-Tamox_1mois]


title: IL-4/IL-13 L49334_M2_2_05_B11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49333_M2_2_05_B10

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia epithelium, biological replica 4

description:
DPE_1
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: IL-4/IL-13 L49332_M2_2_05_B09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49330_M2_2_05_B07

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia epithelium, biological replica 1

description:
DPE_1B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Bscl2lox/lox+ tamoxifen -30 days [51_Ctl-Tamox_1mois]


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia epithelium, biological replica 3

description:
DPE_3B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Bscl2lox/lox+ tamoxifen -30 days [50_Ctl-Tamox_1mois]


title: iATSKO - 30 days [57_CRE-Tamox_1mois]


title: IL-4/IL-13 L49328_M2_2_05_B05

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Dysplasia epithelium, biological replica 2

description:
DPE_2
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: IL-4/IL-13 L49327_M2_2_05_B04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49326_M2_2_05_B03

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [49_CRE-Vhcl_1mois]

source_name: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days

value: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Hyperplasia stroma, biological replica 3

description:
HPS_3
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

value: Hyperplasia


title: IL-4/IL-13 L49325_M2_2_05_B02

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [48_CRE-Vhcl_1mois]


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [47_CRE-Vhcl_1mois]


title: IL-4/IL-13 L49324_M2_2_05_B01

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Hyperplasia stroma, biological replica 2

description:
HPS_2B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: IL-4/IL-13 L49322_M2_2_05_A23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49323_M2_2_05_A24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49321_M2_2_05_A22

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [46_CRE-Vhcl_1mois]


title: IL-4/IL-13 L49329_M2_2_05_B06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49317_M2_2_05_A18

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [44_CRE-Vhcl_1mois]


title: IL-4/IL-13 L49320_M2_2_05_A21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49319_M2_2_05_A20

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Hyperplasia epithelium, biological replica 2

description:
HPE_2B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [45_CRE-Vhcl_1mois]


title: Bscl2lox/lox -ERT2-Adipoq-CRE -30 days [43_CRE-Vhcl_1mois]


title: IL-4/IL-13 L49315_M2_2_05_A16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49318_M2_2_05_A19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49339_M2_2_05_B16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49314_M2_2_05_A15

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Hyperplasia epithelium, biological replica 1

description:
HPE_1
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Normal  stroma, biological replica 3

description:
NS_3
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

value: Normal


title: Bscl2lox/lox-30 days [42_Ctl-Vhcl_1mois]

source_name: Bscl2lox/lox-30 days

value: Bscl2lox/lox-30 days


title: IL-4/IL-13 L49312_M2_2_05_A13

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Normal  stroma, biological replica 2

description:
NS_2
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

value: Stroma


title: IL-4/IL-13 L49311_M2_2_05_A12

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-30 days [41_Ctl-Vhcl_1mois]


title: IL-4/IL-13 L49310_M2_2_05_A11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49308_M2_2_05_A09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49309_M2_2_05_A10

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Normal epithelium, biological replica 3

description:
NE_2
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Bscl2lox/lox-30 days [40_Ctl-Vhcl_1mois]


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Hyperplasia stroma, biological replica 1

description:
HPS_1B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Normal  stroma, biological replica 1

description:
NS_1B
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Hyperplasia epithelium, biological replica 3

description:
HPE_3
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice


title: IL-4/IL-13 L49307_M2_2_05_A08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49306_M2_2_05_A07

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-30 days [37_Ctl-Vhcl_1mois]


title: Bscl2lox/lox-30 days [38_Ctl-Vhcl_1mois]


title: IL-4/IL-13 L49304_M2_2_05_A05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49316_M2_2_05_A17

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-30 days [39_Ctl-Vhcl_1mois]


title: G6

city: Kunming

first: Honglei

last: Zhang

address: 1076 Yuhua Road, Chenggong District, Kunming, Yunnan Province

country: China

institute: Yunnan university of Chinese Medicine

data_processing:
Raw mRNA-Seq reads were aligned to the GRCm38 mouse genome with STAR
Gene expression was summaried with featureCouts
Genome_build: GRCm38
Supplementary_files_format_and_content: RAT-COAL.txt

organism: Rattus norvegicus

source_name: Lung tissue

extract_protocol:
mRNA isolation
Illumina Mranseq

value: Lung tissue

tag: protocol

value: smoky coal


title: IL-4/IL-13 L49301_M2_2_05_A02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49313_M2_2_05_A14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49303_M2_2_05_A04

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Normal epithelium, biological replica 1

description:
NE_1
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

value: male

value: CBA mice (Mus musculus)


title: IL-4/IL-13 L49302_M2_2_05_A03

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L49278_B_M2_04_P03

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-30 days [35_Ctl-Vhcl_1mois]

value: 12 weeks-old


title: IL-4/IL-13 L49305_M2_2_05_A06

description:
IL-4/IL-13
IL-4/IL-13


title: Microdissected paraffin-embedded (FFPE) tongues of CBA mice, Normal epithelium, biological replica 2

description:
NE_3
RNAseq data from microdissected paraffin-embedded (FFPE) tongues of CBA mice

value: Epithelium


title: IL-4/IL-13 L49107_M2_2_04_H24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49105_M2_2_04_H22

description:
IL-4/IL-13
IL-4/IL-13


title: G3


title: IL-4/IL-13 L49106_M2_2_04_H23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49104_M2_2_04_H21

description:
IL-4/IL-13
IL-4/IL-13


title: G2


title: IL-4/IL-13 L49102_M2_2_04_H19

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 15 days [33_CRE-Tamox_2sem]

source_name: iATSKO - 15 days

value: 10 weeks-old

value: iATSKO - 15 days

value: inguinal white adipose tissue


title: iATSKO - 15 days [32_CRE-Tamox_2sem]


title: Bscl2lox/lox-30 days [34_Ctl-Vhcl_1mois]


title: IL-4/IL-13 L49103_M2_2_04_H20

description:
IL-4/IL-13
IL-4/IL-13


title: G1


title: IL-4/IL-13 L49101_M2_2_04_H18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49100_M2_2_04_H17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49300_M2_2_05_A01

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 15 days [31_CRE-Tamox_2sem]


title: IL-4/IL-13 L49099_M2_2_04_H16

description:
IL-4/IL-13
IL-4/IL-13


title: C6


title: Bscl2lox/lox-30 days [36_Ctl-Vhcl_1mois]


title: IL-4/IL-13 L49098_M2_2_04_H15

description:
IL-4/IL-13
IL-4/IL-13


title: G5


title: iATSKO - 15 days [30_CRE-Tamox_2sem]


title: IL-4/IL-13 L49096_M2_2_04_H13

description:
IL-4/IL-13
IL-4/IL-13


title: C5


title: iATSKO - 15 days [29_CRE-Tamox_2sem]


title: IL-4/IL-13 L49095_M2_2_04_H12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49097_M2_2_04_H14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49094_M2_2_04_H11

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 15 days [28_CRE-Tamox_2sem]


title: C3


title: IL-4/IL-13 L49093_M2_2_04_H10

description:
IL-4/IL-13
IL-4/IL-13


title: G4


title: IL-4/IL-13 L49092_M2_2_04_H09

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 15 days [27_CRE-Tamox_2sem]


title: IL-4/IL-13 L49091_M2_2_04_H08

description:
IL-4/IL-13
IL-4/IL-13


title: C2


title: IL-4/IL-13 L49090_M2_2_04_H07

description:
IL-4/IL-13
IL-4/IL-13


title: iATSKO - 15 days [26_CRE-Tamox_2sem]


title: IL-4/IL-13 L49088_M2_2_04_H05

description:
IL-4/IL-13
IL-4/IL-13


title: C1


title: Bscl2lox/lox+ tamoxifen - 15 days [25_Ctl-Tamox_2sem]

source_name: Bscl2lox/lox+ tamoxifen - 15 days

value: Bscl2lox/lox+ tamoxifen - 15 days


title: B6


title: IL-4/IL-13 L49086_M2_2_04_H03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49087_M2_2_04_H04

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen - 15 days [24_Ctl-Tamox_2sem]


title: B5


title: IL-4/IL-13 L49084_M2_2_04_H01

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49085_M2_2_04_H02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49083_M2_2_04_G24

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen - 15 days [23_Ctl-Tamox_2sem]


title: B4


title: IL-4/IL-13 L49082_M2_2_04_G23

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen - 15 days [22_Ctl-Tamox_2sem]


title: IL-4/IL-13 L49081_M2_2_04_G22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49080_M2_2_04_G21

description:
IL-4/IL-13
IL-4/IL-13


title: B3


title: Bscl2lox/lox+ tamoxifen - 15 days [21_Ctl-Tamox_2sem]


title: C4


title: B2


title: IL-4/IL-13 L49079_M2_2_04_G20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49078_M2_2_04_G19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49077_M2_2_04_G18

description:
IL-4/IL-13
IL-4/IL-13


title: B1


title: IL-4/IL-13 L49076_M2_2_04_G17

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox+ tamoxifen - 15 days [19_Ctl-Tamox_2sem]


title: IL-4/IL-13 L49075_M2_2_04_G16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49089_M2_2_04_H06

description:
IL-4/IL-13
IL-4/IL-13


title: A6


title: Bscl2lox/lox+ tamoxifen - 15 days [18_Ctl-Tamox_2sem]


title: A5


title: Bscl2lox/lox+ tamoxifen - 15 days [17_Ctl-Tamox_2sem]


title: IL-4/IL-13 L49071_M2_2_04_G12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49072_M2_2_04_G13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49073_M2_2_04_G14

description:
IL-4/IL-13
IL-4/IL-13


title: A4


title: Bscl2lox/lox+ tamoxifen - 15 days [16_Ctl-Tamox_2sem]


title: IL-4/IL-13 L49070_M2_2_04_G11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49069_M2_2_04_G10

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days [15_CRE-Vhcl_2sem]

source_name: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days

value: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days


title: A3


title: IL-4/IL-13 L49067_M2_2_04_G08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49068_M2_2_04_G09

description:
IL-4/IL-13
IL-4/IL-13


title: A2


title: IL-4/IL-13 L49066_M2_2_04_G07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49064_M2_2_04_G05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49065_M2_2_04_G06

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days [14_CRE-Vhcl_2sem]


title: A1


title: Bscl2lox/lox+ tamoxifen - 15 days [20_Ctl-Tamox_2sem]


title: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days [12_CRE-Vhcl_2sem]


title: IL-4/IL-13 L49061_M2_2_04_G02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49060_M2_2_04_G01

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days [11_CRE-Vhcl_2sem]


title: IL-4/IL-13 L49062_M2_2_04_G03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49074_M2_2_04_G15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49058_M2_2_04_F23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49057_M2_2_04_F22

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days [10_CRE-Vhcl_2sem]


title: IL-4/IL-13 L49055_M2_2_04_F20

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-15 days [8_Ctl-Vhcl_2sem]

source_name: Bscl2lox/lox-15 days

value: Bscl2lox/lox-15 days


title: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days [9_CRE-Vhcl_2sem]


title: IL-4/IL-13 L49053_M2_2_04_F18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49056_M2_2_04_F21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49054_M2_2_04_F19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49052_M2_2_04_F17

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-15 days [7_Ctl-Vhcl_2sem]


title: Bscl2lox/lox-15 days [6_Ctl-Vhcl_2sem]


title: IL-4/IL-13 L49049_M2_2_04_F14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49051_M2_2_04_F16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49048_M2_2_04_F13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49046_M2_2_04_F11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49047_M2_2_04_F12

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox -ERT2-Adipoq-CRE -15 days [13_CRE-Vhcl_2sem]


title: IL-4/IL-13 L49063_M2_2_04_G04

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-15 days [4_Ctl-Vhcl_2sem]


title: Bscl2lox/lox-15 days [3_Ctl-Vhcl_2sem]


title: Bscl2lox/lox-15 days [2_Ctl-Vhcl_2sem]


title: IL-4/IL-13 L49045_M2_2_04_F10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49059_M2_2_04_F24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49042_M2_2_04_F07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49043_M2_2_04_F08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49044_M2_2_04_F09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49040_M2_2_04_F05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49041_M2_2_04_F06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49038_M2_2_04_F03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49039_M2_2_04_F04

description:
IL-4/IL-13
IL-4/IL-13


title: Bscl2lox/lox-15 days [1_Ctl-Vhcl_2sem]


title: immortalized, replicate 3

first: Fatima

last: Gebauer

address: C/Dr. Aiguader, 88

department: Gene Regulation, Stem cells and Cancer Programme

institute: Centre for Genomic Regulation (CRG)

data_processing:
Basecalling with Illumina bcl2fastq version 2.17.1.14
STAR v2.5.3a mapping to Mus musculus Ensembl release 88 (mm10) with –quantMode geneCounts option to get raw counts per gene and per sample
Differential expression analysis is performed with the DESeq2 R/Bioconductor package
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text files: raw counts per gene obtained by STAR mapper’s –quantMode GeneCounts parameter (4th column: reverse stranded protocol)

molecule: polyA RNA

source_name: Primary mouse keratinocytes

growth_protocol: Primary mouse keratinocytes (PMK) were isolated from newborn mice (1-2 days old). Briefly, pups were sacrificed and the skins were dissected. For epidermis-dermis separation, the skin was incubated with dispase II at 4 ºC overnight. The epidermis was separated from the dermis and chopped using scissors and a blade. Skins were incubated under stirring with EMEM complete media during 40 minutes at room temperature. Using a cell strainer of 70 μm the cell suspension was filtered and centrifuged. Cell pellets were resuspended in the desired volume of EMEM complete media, and plated in collagen-treated plates. Cells were incubated for 24 hours at 37ºC in a CO2 incubator, and washed several times with PBS before adding new CnT prime media.

extract_protocol:
Cells were collected at the appropriate time points and RNA was isolated by Trizol extraction.
Truseq total RNA-seq protocol with rRNA depletion

treatment_protocol: PMK were infected with the supernatant of retrovirus-producing Phoenix E cells 48 hours after seeding, following three rounds of 2 hours incubation. Polybrene was added to viral supernatant to enhance retroviral infection. Cells were split 24 hours after the last infection and selected first with 1 μg/ml of puromycin for 48 hours and then with 25  μg/ml hygromycin. Cells were maintained in CnT media and collected at 7 and 12 days post-infection.

value: Primary mouse keratinocytes

tag: time

tag: shRNA treatment

value: UNR


title: IL-4/IL-13 L49037_M2_2_04_F02

description:
IL-4/IL-13
IL-4/IL-13


title: immortalized, replicate 2


title: IL-4/IL-13 L49034_M2_2_04_E23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49036_M2_2_04_F01

description:
IL-4/IL-13
IL-4/IL-13


title: immortalized, replicate 1


title: IL-4/IL-13 L49032_M2_2_04_E21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49050_M2_2_04_F15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49031_M2_2_04_E20

description:
IL-4/IL-13
IL-4/IL-13


title: sh-ctrl 12dpi, replicate 3

value: control


title: Bscl2lox/lox-15 days [5_Ctl-Vhcl_2sem]


title: IL-4/IL-13 L49030_M2_2_04_E19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49028_M2_2_04_E17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49029_M2_2_04_E18

description:
IL-4/IL-13
IL-4/IL-13


title: sh-UNR 7dpi, replicate 3


title: IL-4/IL-13 L49027_M2_2_04_E16

description:
IL-4/IL-13
IL-4/IL-13


title: sh-ctrl 7dpi, replicate 3


title: IL-4/IL-13 L49025_M2_2_04_E14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49024_M2_2_04_E13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49026_M2_2_04_E15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49023_M2_2_04_E12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49020_M2_2_04_E09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49021_M2_2_04_E10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49035_M2_2_04_E24

description:
IL-4/IL-13
IL-4/IL-13


title: sh-ctrl 12dpi, replicate 2


title: sh-UNR 7dpi, replicate 2


title: IL-4/IL-13 L49019_M2_2_04_E08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49018_M2_2_04_E07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49017_M2_2_04_E06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49015_M2_2_04_E04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49033_M2_2_04_E22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49016_M2_2_04_E05

description:
IL-4/IL-13
IL-4/IL-13


title: sh-ctrl 7dpi, replicate 2


title: IL-4/IL-13 L49014_M2_2_04_E03

description:
IL-4/IL-13
IL-4/IL-13


title: sh-UNR 12dpi, replicate 3


title: IL-4/IL-13 L49012_M2_2_04_E01

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49013_M2_2_04_E02

description:
IL-4/IL-13
IL-4/IL-13


title: sh-ctrl 12dpi, replicate 1


title: IL-4/IL-13 L49011_M2_2_04_D24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49010_M2_2_04_D23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49009_M2_2_04_D22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49007_M2_2_04_D20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49022_M2_2_04_E11

description:
IL-4/IL-13
IL-4/IL-13


title: H-ras infected, RNA-Seq, replicate 3

extract_protocol:
Not-infected (NI), Empty Vector-infected (EV) and H-Ras-infected (Ras) PMK were cross-linked on ice at 0.15 J cm−2 with UV light at 254 nM. Immediately after irradiation, cells were lysed in 1 mL of lysis buffer (50 mM Tris-HCl, pH 7.4; 100 mM NaCl; 1% NP-40; 0.1% SDS; 0.5% sodium deoxycholate). Cell extracts were sonicated using a bioruptor (Digenode) for 10 cycles of 30 seconds, level L at 4ºC, then they were cleared by centrifugation at 10'000 rpm for 10 min at 4°C. RNA was isolated from the extracts by phenol:chloroform extraction.
Truseq total RNA-seq protocol with rRNA depletion

treatment_protocol: PMK were infected with the supernatant of retrovirus-producing Phoenix E cells 48 hours after seeding, following three rounds of 2 hours incubation. Polybrene was added to viral supernatant to enhance retroviral infection. Cells were split 24 hours after the last infection and selected with 1 μg/ml of puromycin for 48 hours. Cells were maintained in CnT media and collected at 7 days post-infection.

tag: infection

value: H-ras infected

tag: crosslink

value: crosslink


title: IL-4/IL-13 L49006_M2_2_04_D19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49008_M2_2_04_D21

description:
IL-4/IL-13
IL-4/IL-13


title: sh-UNR 12dpi, replicate 2


title: H-ras infected, RNA-Seq, replicate 2


title: IL-4/IL-13 L49005_M2_2_04_D18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49004_M2_2_04_D17

description:
IL-4/IL-13
IL-4/IL-13


title: H-ras infected, RNA-Seq, replicate 1


title: IL-4/IL-13 L49003_M2_2_04_D16

description:
IL-4/IL-13
IL-4/IL-13


title: Not infected, RNA-Seq, replicate 3

value: not infected


title: IL-4/IL-13 L49002_M2_2_04_D15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49001_M2_2_04_D14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48996_M2_2_04_D09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L49000_M2_2_04_D13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48999_M2_2_04_D12

description:
IL-4/IL-13
IL-4/IL-13


title: sh-UNR 12dpi, replicate 1


title: Not infected, RNA-Seq, replicate 1


title: IL-4/IL-13 L48997_M2_2_04_D10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48994_M2_2_04_D07

description:
IL-4/IL-13
IL-4/IL-13


title: sh-ctrl 7dpi, replicate 1


title: Empty Vector, RNA-Seq, replicate 3

value: EV


title: IL-4/IL-13 L48995_M2_2_04_D08

description:
IL-4/IL-13
IL-4/IL-13


title: Empty Vector, RNA-Seq, replicate 2


title: sh-UNR 7dpi, replicate 1


title: IL-4/IL-13 L48993_M2_2_04_D06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48990_M2_2_04_D03

description:
IL-4/IL-13
IL-4/IL-13


title: shUNR poly 12dpi, replicate4

data_processing:
Basecalling with Illumina bcl2fastq version 2.17.1.14
STAR v2.5.3a mapping to Mus musculus Ensembl release 88 (mm10) with –quantMode geneCounts option to get raw counts per gene and per sample
Mode of regulation with Anota2seq R package
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text files: raw counts per gene obtained by STAR mapper’s –quantMode GeneCounts parameter (4th column: reverse stranded protocol)

extract_protocol:
Polysome Profiling was adapted from Liang S. et al, 2017. Media was discarded from shCTRL and shCSDE1 cells (12 dpi – one 100 mm plate per condition), plates were placed on ice and immediately washed in an ice-cold solution of 1x phosphate-buffered saline (PBS) and cycloheximide (100 ug/mL, Sigma-Aldrich). Cells were then lysed in 200 ul hypotonic lysis buffer (5 mM Tris–HCl, pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 ug/mL cycloheximide, 2 mM DTT, 0.5% Triton, 0.5% sodium deoxycholate) and left on ice for 10 min. Extracts were cleared by centrifugation at 16’000 rcf for 7 min and the OD was measured (between 2.5 and 4 OD per experiments were loaded onto the gradient). Samples were brought to a final volume of 300 ul if necessary with lysis buffer and loaded on a non-linear sucrose gradient prepared by layering different percentage of sucrose solutions (5%, 34% and 55%) into an Open-Top Thinwall Ultra-Clear Tube (Beckman, 344059). A 5X gradient buffer (100 mM HEPES pH 7.6, 500 mM KCl, 25 mM MgCl2) was used to prepare sucrose solutions (1x final concentration of gradient buffer [v/v] adjusted with water). The samples were centrifuged at 36’000 rpm for 2 hrs at 4ºC in a SW 41 Ti rotor and a Beckman Coulter Ultracentrifuge Optima L-90K. Samples were eluted using the gradient station (BioComp) and fractions (1-6 for monosomal RNA and 11 and 12 for polysomal RNA) were collected with Gradient Fractionator (BioComp) coupled with a fraction collector (Gilson). The precise location of the fractions along the UV-tracing was monitored using the gradient profiler v1.25 (BioComp) software. TRIzol reagent (Invitrogen) was immediately added to each fraction and the RNA was extracted according to the protocol of the manufacturer.
Poly-A RNA selection protocol

treatment_protocol: PMK were infected with the supernatant of retrovirus-producing Phoenix E cells 48 hours after seeding, following three rounds of 2 hours incubation. Polybrene was added to viral supernatant to enhance retroviral infection. Cells were split 24 hours after the last infection and selected first with 1 μg/ml of puromycin for 48 hours and then with 25  μg/ml hygromycin. Cells were maintained in CnT media and collected at 12 days post-infection.


title: IL-4/IL-13 L48991_M2_2_04_D04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48989_M2_2_04_D02

description:
IL-4/IL-13
IL-4/IL-13


title: Empty Vector, RNA-Seq, replicate 1


title: IL-4/IL-13 L48988_M2_2_04_D01

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48992_M2_2_04_D05

description:
IL-4/IL-13
IL-4/IL-13


title: shCTRL poly 12dpi, replicate 4


title: IL-4/IL-13 L48986_M2_2_04_C23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48984_M2_2_04_C21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48987_M2_2_04_C24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48985_M2_2_04_C22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48998_M2_2_04_D11

description:
IL-4/IL-13
IL-4/IL-13


title: Not infected, RNA-Seq, replicate 2


title: shUNR poly 12dpi, replicate2


title: IL-4/IL-13 L48981_M2_2_04_C18

description:
IL-4/IL-13
IL-4/IL-13


title: shCTRL poly 12dpi, replicate 2


title: shCTRL poly 12dpi, replicate 3


title: IL-4/IL-13 L48979_M2_2_04_C16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48980_M2_2_04_C17

description:
IL-4/IL-13
IL-4/IL-13


title: shUNR poly 12dpi, replicate3


title: IL-4/IL-13 L48977_M2_2_04_C14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48976_M2_2_04_C13

description:
IL-4/IL-13
IL-4/IL-13


title: shCTRL poly 12dpi, replicate 1


title: shUNR poly 12dpi, replicate1


title: IL-4/IL-13 L48975_M2_2_04_C12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48973_M2_2_04_C10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48974_M2_2_04_C11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48971_M2_2_04_C08

description:
IL-4/IL-13
IL-4/IL-13


title: shUNR mono 12dpi, replicate4


title: shCTRL mono 12dpi, replicate 4


title: IL-4/IL-13 L48972_M2_2_04_C09

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Spleen_non-dox_1025

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

country: USA

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie v4.4.1 against the GENCODE Basic gene model on the mouse genome assembly GRCm38.
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV count matrices

source_name: Old mouse spleen

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Mice treated with doxycycline (1 mg/ml) in drinking water for 2-days to induce 4F overexpression followed by 5 days of withdraw per week for 10 months.

value: Male

value: 25 months

value: Spleen


title: B6_Spleen_non-dox_1031


title: shUNR mono 12dpi, replicate3


title: B6_Spleen_dox-treated_1037

value: Doxycycline-induced 4F


title: IL-4/IL-13 L48968_M2_2_04_C05

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L48983_M2_2_04_C20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48967_M2_2_04_C04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48966_M2_2_04_C03

description:
IL-4/IL-13
IL-4/IL-13


title: shUNR mono 12dpi, replicate2


title: shCTRL mono 12dpi, replicate 3


title: IL-4/IL-13 L48969_M2_2_04_C06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48965_M2_2_04_C02

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Skin_non-dox_1027

source_name: Old mouse skin

value: Skin


title: B6_Skin_non-dox_1033


title: IL-4/IL-13 L48964_M2_2_04_C01

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Skin_dox-treated_1045


title: IL-4/IL-13 L48963_M2_2_04_B24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48962_M2_2_04_B23

description:
IL-4/IL-13
IL-4/IL-13


title: shCTRL mono 12dpi, replicate 2


title: shUNR mono 12dpi, replicate1


title: IL-4/IL-13 L48961_M2_2_04_B22

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Skin_dox-treated_1039


title: shCTRL mono 12dpi, replicate 1


title: IL-4/IL-13 L48960_M2_2_04_B21

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Spleen_dox-treated_1043


title: IL-4/IL-13 L48959_M2_2_04_B20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48970_M2_2_04_C07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48958_M2_2_04_B19

description:
IL-4/IL-13
IL-4/IL-13


title: H-ras infected, replicate 3

data_processing:
Library strategy: iCLIP-seq
iCLIP data was processed following the iCount Primary Analysis (Consensus mapping) pipeline from the iMaps website (https://imaps.genialis.com/iclip). Briefly, fastq files were demultiplexed and Cutadapt was used to trim off adapter sequences.
Reads were first mapped to tRNA/rRNA reference. Unmapped reads where then mapped to the mouse genome (GRCm38/mm10) using the STAR aligner with default options.
iCount xlsites was used to determine the number of unique crosslinked sites (unique cDNA molecules) for any given position with default options.
iCount peaks was used to find positions with high density of cross-linked sites. Only peaks showing an FDR < 0.05 were considered significant and taken for subsequent steps.
iCount RNA-maps was used to examine all cross-links that are located in vicinity of genomic landmarks.
Genome_build: GRCm38/mm10

source_name: Primary Mouse Keratinocytes

extract_protocol:
Not-infected (NI), Empty Vector-infected (EV) and H-Ras-infected (Ras) PMK were cross-linked on ice at 0.15 J cm−2 with UV light at 254 nM. Immediately after irradiation, cells were lysed in 1 mL of lysis buffer (50 mM Tris-HCl, pH 7.4; 100 mM NaCl; 1% NP-40; 0.1% SDS; 0.5% sodium deoxycholate). Cell extracts were sonicated using a bioruptor (Digenode) for 10 cycles of 30 seconds, level L at 4ºC, then they cleared by centrifugation at 10'000 rpm for 10 min at 4°C. RNA was then partially digested by adding 10 μl of 1:200 dilution of RNase I (Ambion, AM2295), as well as 2 μl of Turbo DNase (Ambion, AM 2238) and incubating for 3 min at 37°C under shaking at 1100 rpm. CSDE1 protein was then captured by incubation with an affinity purified CSDE1 antibody conjugated to protein A Dynabeads for 4 h, 4°C, gentle rotation. Beads were then washed 2x with 900 μl high-salt buffer (50 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA; 1% NP-40; 0.1% SDS; 0.5% sodium deoxycholate), 1x with 900 μl PNK wash buffer (20 mM Tris-HCl, pH 7.4; 10 mM MgCl2; 0.2% Tween-20) and resuspended in 40 μl of PNK mix (30 μl water; 8 μl 5x PNK pH 6.5 buffer [350 mM Tris-HCl, pH 6.5; 50 mM MgCl2; 5 mM dithiothreitol]; 1 μl PNK enzyme; 0.5 μl RNasin; 0.5 ul of FastAP alkaline phosphatase) and incubated 40 min at 37°C 1100 rpm. Beads were washed 1x with 900 μl of ligation buffer (50 mM Tris-HCl, pH 7.5; 10 mM MgCl2) and resuspended in 25 μl of ligation mix (6.8 μl water; 2.5 μl 10X ligation buffer; 0.8 ul 100% DMSO; 2.5 ul T4 RNA ligase I – high concentration [NEB]; 0.4 μl RNasin; 0.5 ul PNK enzyme; 2.5 μl pre-adenylated adaptor L3-App [1 uM] conjugated to an infrared-dye [IRdye-800CW-DBCO (LICOR, cat# 929-50000)]; 9 ul 50% PEG8000). Ligation was performed at room temperature for 75 minute flicking the tubes every 10 min. Beads were washed 2x with high-salt buffer, 1x with PNK wash buffer and resuspended in 20 ul of loading buffer and run on a 4-12% NuPAGE Bis-Tris gel (Invitrogen) in MOPS buffer according to the manufacturer's instructions. Protein-RNA complexes were transferred to a nitrocellulose membrane. Protein-infrared-RNA complexes were visualized at Odissey machine setting 1.5 intensity for both 700 nm and 800 nm channel.
RNA-protein complexes were isolated and treated with 200 μl PK buffer (10 mM Tris-HCl pH 7.4; 100 mM NaCl; 1 mM EDTA; 0.2% SDS) and 10 μl proteinase K (Roche, 03115828001) for 1 hr minutes at 1100 rpm and 50°C. Solution was collected and RNA was isolated by phenol:chloroform extraction and ethanol precipitation over night at -20°C. RNA pellet was resuspended in 7 μl RNA/primer mix (5.5 μl water; 1 μl irCLIP_ddRT_## primer; 0.5 μl dNTP mix [10mM]) and incubated at 65°C for 5 min. RNA was retrotranscribed by addition of 3 μl of RT mix (2 μl 5x SSIV buffer (Invitrogen); 0.5 μl 0.1 M DTT; 0.25 μl Superscript IV reverse transcriptase [Invitrogen]; 0.25 ul of RNasin) and incubation for 5 min at 25°C, 5 min at 50°C and 5 min at 55°C. cDNA was gel-size selected by running samples on a precast 6% TBE-urea gel 180V for 40 min and isolating a region between 75 and 200 nt. Gel slices were submerged and crushed in TE buffer, incubated 1 h at 37°C 1100 rpm, flash frozen, and incubated again for 1 h at 37°C 1100 rpm. cDNA was isolated by phenol:chloroform extraction and ethanol precipitation over night at -20°C. cDNA was resuspended in 7 μl of water and then 8 ul of CircLigase II mix (5 μl water; 1.5 μl 10x CircLigase Buffer II; 0.75 μl 50 mM MnCl2; 0.75 μl Circligase II [Epicentre]) were added. Samples were incubated for 1 h at 60°C for circularization and cDNA was isolated by phenol:chloroform extraction and ethanol precipitation over night at -20°C. Pellets were resuspended in 10 μl of H20. Amplification was performed using 4 μl cDNA; 1 μl primer mix P5/P3 solexa, 10 μM each; 20 μl Phusion HF Master mix [NEB], 15 μl H20 and the following PCR programme: 98°C for 40 sec, [98°C for 20 sec, 65°C for 30 sec, 72°C for 45 sec]x18 cycles, 72°C for 3 min, 4°C. Libraries were loaded on a precast 6% TBE gel (Invitrogen) and run at 180V for 30 min. Gel was stained with Sybrgreen I (Invitrogen) and a region between 150-300 nt was excised. Gel slices were submerged in Crush-Soak Gel buffer (500 mM NaCl; 1 mM EDTA; 0.05% SDS) and incubated at 65ºC for 2 hours with thermomixer settings of 15 sec at 1000 rpm, 45 sec rest. cDNA was isolated by phenol:chloroform extraction and ethanol precipitation over night at -20°C and resuspended in 10 ul of water. Libraries were sequenced using Illumina HiSeq 2500 sequencers (50 bp single-end reads).

value: Primary Mouse Keratinocytes


title: B6_Skeletal_Muscle_non-dox_1034

source_name: Old mouse skeletal muscle

value: Skeletal Muscle


title: IL-4/IL-13 L48956_M2_2_04_B17

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Skeletal_Muscle_non-dox_1028


title: IL-4/IL-13 L48955_M2_2_04_B16

description:
IL-4/IL-13
IL-4/IL-13


title: H-ras infected, no crosslink, replicate 3

value: no crosslink


title: IL-4/IL-13 L48957_M2_2_04_B18

description:
IL-4/IL-13
IL-4/IL-13


title: H-ras infected, replicate 2


title: IL-4/IL-13 L48952_M2_2_04_B13

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Skeletal_Muscle_dox-treated_1040


title: IL-4/IL-13 L48982_M2_2_04_C19

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Skeletal_Muscle_dox-treated_1046


title: IL-4/IL-13 L48953_M2_2_04_B14

description:
IL-4/IL-13
IL-4/IL-13


title: H-ras infected, no crosslink, replicate 2


title: IL-4/IL-13 L48951_M2_2_04_B12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48950_M2_2_04_B11

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Lung_non-dox_1035

source_name: Old mouse lung

value: Lung


title: IL-4/IL-13 L48949_M2_2_04_B10

description:
IL-4/IL-13
IL-4/IL-13

source_name: Bone marrow


title: H-ras infected, replicate 1


title: B6_Lung_non-dox_1029


title: H-ras infected, no crosslink, replicate 1


title: IL-4/IL-13 L48946_M2_2_04_B07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48948_M2_2_04_B09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48945_M2_2_04_B06

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Liver_non-dox_1030

source_name: Old mouse liver

value: Liver


title: IL-4/IL-13 L48940_M2_2_04_B01

description:
IL-4/IL-13
IL-4/IL-13


title: Not infected, replicate 3


title: IL-4/IL-13 L48939_M2_2_04_A24

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48944_M2_2_04_B05

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Lung_dox-treated_1041


title: B6_Liver_dox-treated_1042


title: Not Infected, no crosslink, replicate 3


title: Not infected, replicate 1


title: IL-4/IL-13 L48943_M2_2_04_B04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48937_M2_2_04_A22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48942_M2_2_04_B03

description:
IL-4/IL-13
IL-4/IL-13


title: Not infected, replicate 2


title: B6_Liver_dox-treated_1036


title: IL-4/IL-13 L48954_M2_2_04_B15

description:
IL-4/IL-13
IL-4/IL-13


title: Not Infected, no crosslink, replicate 2


title: IL-4/IL-13 L48934_M2_2_04_A19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48947_M2_2_04_B08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48932_M2_2_04_A17

description:
IL-4/IL-13
IL-4/IL-13


title: Not Infected, no crosslink, replicate 1


title: IL-4/IL-13 L48936_M2_2_04_A21

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Liver_non-dox_1024


title: IL-4/IL-13 L48941_M2_2_04_B02

description:
IL-4/IL-13
IL-4/IL-13


title: B6_Lung_dox-treated_1047


title: IL-4/IL-13 L48933_M2_2_04_A18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48935_M2_2_04_A20

description:
IL-4/IL-13
IL-4/IL-13


title: Empty Vector, replicate 2

value: EV infected


title: B6_Kidney_dox-treated_1044

source_name: Old mouse kidney

value: Kidney


title: B6_Kidney_non-dox_1026


title: B6_Kidney_dox-treated_1038


title: B6_Kidney_non-dox_1032


title: Empty Vector, no crosslink, replicate 3


title: IL-4/IL-13 L48931_M2_2_04_A16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48928_M2_2_04_A13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48926_M2_2_04_A11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48938_M2_2_04_A23

description:
IL-4/IL-13
IL-4/IL-13


title: Empty Vector, replicate 3


title: Empty Vector, no crosslink, replicate 2


title: IL-4/IL-13 L48927_M2_2_04_A12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48930_M2_2_04_A15

description:
IL-4/IL-13
IL-4/IL-13


title: Empty Vector, replicate 1


title: IL-4/IL-13 L48925_M2_2_04_A10

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Spleen_non-dox_1013

value: 4F het; R26::rtTA het C57BL/6

value: Female

value: 22 months


title: IL-4/IL-13 L48923_M2_2_04_A08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48924_M2_2_04_A09

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Spleen_non-dox_1007


title: IL-4/IL-13 L48922_M2_2_04_A07

description:
IL-4/IL-13
IL-4/IL-13


title: Empty Vector, no crosslink, replicate 1


title: IL-4/IL-13 L48921_M2_2_04_A06

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Spleen_dox-treated_1001


title: IL-4/IL-13 L48920_M2_2_04_A05

description:
IL-4/IL-13
IL-4/IL-13


title: WT_media_3_1

city: Cambridge

first: Ayshwarya

last: Subramanian

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

data_processing:
Bcl2Fastq
RSEM Gene quantification V1.2.8
Genome_build: mm10

source_name: BMDC

growth_protocol: Bone marrow derive dendritic cells were routinely generated by re-plating d9 bone marrow cell differentiation cultures (typically 2–3 × 106 cells into 100mm diameter dish) on uncoated plastic in complete RPMI1640 (Gibco) supplemented with  20 ng/ml of GM-CSF (PeproTech).

extract_protocol:
BMDCs were harvest, live CD11c hi BMDCs were sorted into lysis buffer, flash frozen on dry ice. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Five biological replicates with treatments for 8 hours.

value: BMDC

tag: genotype

value: wild type

value: medium


title: IL-4/IL-13 L48919_M2_2_04_A04

description:
IL-4/IL-13
IL-4/IL-13


title: WT_media_2_1


title: 4F_Spleen_dox-treated_0995

value: Spleen


title: WT_media_1_1


title: IL-4/IL-13 L48917_M2_2_04_A02

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Spleen_dox-treated_0989

value: Male

value: Doxycycline-induced 4F


title: IL-4/IL-13 L48978_M2_2_04_C15

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L48916_M2_2_04_A01

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48894_B_M2_03_P03

description:
IL-4/IL-13
IL-4/IL-13


title: WT_Tol_3_1

value: IL10 + TGF-β


title: IL-4/IL-13 L48929_M2_2_04_A14

description:
IL-4/IL-13
IL-4/IL-13


title: WT_Tol_2_1


title: IL-4/IL-13 L48722_M2_1_03_H23

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Skin_non-dox_1021

value: Skin


title: 4F_Skin_non-dox_1015


title: IL-4/IL-13 L48723_M2_1_03_H24

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Spleen_non-dox_1019


title: IL-4/IL-13 L48720_M2_1_03_H21

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Skin_non-dox_1009


title: IL-4/IL-13 L48718_M2_1_03_H19

description:
IL-4/IL-13
IL-4/IL-13


title: WT_TolLPS_3_1

value: LPS + IL10 + TGF-β


title: IL-4/IL-13 L48719_M2_1_03_H20

description:
IL-4/IL-13
IL-4/IL-13


title: WT_Tol_1_1


title: 4F_Skin_dox-treated_1003


title: IL-4/IL-13 L48717_M2_1_03_H18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48716_M2_1_03_H17

description:
IL-4/IL-13
IL-4/IL-13


title: WT_TolLPS_2_1


title: 4F_Skin_dox-treated_0997


title: WT_TolLPS_1_1


title: IL-4/IL-13 L48715_M2_1_03_H16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48714_M2_1_03_H15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48713_M2_1_03_H14

description:
IL-4/IL-13
IL-4/IL-13


title: WT_LPS_3_1

value: LPS


title: IL-4/IL-13 L48918_M2_2_04_A03

description:
IL-4/IL-13
IL-4/IL-13


title: WT_LPS_2_1


title: 4F_Skeletal_Muscle_non-dox_1022

value: Skeletal Muscle


title: IL-4/IL-13 L48710_M2_1_03_H11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48711_M2_1_03_H12

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Skeletal_Muscle_non-dox_1016


title: IL-4/IL-13 L48708_M2_1_03_H09

description:
IL-4/IL-13
IL-4/IL-13


title: WT_LPS_1_1


title: 4F_Skeletal_Muscle_non-dox_1010


title: IL-4/IL-13 L48709_M2_1_03_H10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48707_M2_1_03_H08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48721_M2_1_03_H22

description:
IL-4/IL-13
IL-4/IL-13


title: Bat3cKO_media_3_1

value: Bat3 fl/fl CD11c Cre


title: IL-4/IL-13 L48705_M2_1_03_H06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48704_M2_1_03_H05

description:
IL-4/IL-13
IL-4/IL-13


title: Bat3cKO_media_2_1


title: 4F_Skeletal_Muscle_dox-treated_1004


title: 4F_Skeletal_Muscle_dox-treated_0998


title: IL-4/IL-13 L48703_M2_1_03_H04

description:
IL-4/IL-13
IL-4/IL-13


title: Bat3cKO_media_1_1


title: IL-4/IL-13 L48702_M2_1_03_H03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48701_M2_1_03_H02

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Skeletal_Muscle_dox-treated_0992


title: IL-4/IL-13 L48700_M2_1_03_H01

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Skin_dox-treated_0991


title: IL-4/IL-13 L48712_M2_1_03_H13

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Lung_non-dox_1023

value: Lung


title: IL-4/IL-13 L48697_M2_1_03_G22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48699_M2_1_03_G24

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Lung_non-dox_1017

value: 4F het; R26::rtTA het C57BL/6


title: IL-4/IL-13 L48695_M2_1_03_G20

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Lung_non-dox_1011

value: Female


title: IL-4/IL-13 L48696_M2_1_03_G21

description:
IL-4/IL-13
IL-4/IL-13


title: 4PBA-KO_5

data_processing:
Bcl2Fastq
RSEM Gene quantification


title: IL-4/IL-13 L48694_M2_1_03_G19

description:
IL-4/IL-13
IL-4/IL-13


title: Bat3cKO_LPS_1_1


title: Bat3cKO_LPS_2_1


title: 4F_Lung_dox-treated_1005

value: 22 months


title: IL-4/IL-13 L48692_M2_1_03_G17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48693_M2_1_03_G18

description:
IL-4/IL-13
IL-4/IL-13


title: 4PBA-KO_4


title: 4F_Lung_dox-treated_0999


title: IL-4/IL-13 L48698_M2_1_03_G23

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48706_M2_1_03_H07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48690_M2_1_03_G15

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Lung_dox-treated_0993


title: 4PBA-KO_2


title: IL-4/IL-13 L48689_M2_1_03_G14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48688_M2_1_03_G13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48687_M2_1_03_G12

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Liver_non-dox_1018

value: Liver


title: Bat3cKO_LPS_3_1

value: BMDC


title: 4PBA-KO_1


title: 4F_Liver_non-dox_1012


title: IL-4/IL-13 L48685_M2_1_03_G10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48684_M2_1_03_G09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48686_M2_1_03_G11

description:
IL-4/IL-13
IL-4/IL-13


title: 4U8C-KO_5


title: 4F_Liver_non-dox_1006


title: 4U8C-KO_4


title: IL-4/IL-13 L48682_M2_1_03_G07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48681_M2_1_03_G06

description:
IL-4/IL-13
IL-4/IL-13


title: 4U8C-KO_3


title: 4F_Liver_dox-treated_1000


title: IL-4/IL-13 L48680_M2_1_03_G05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48679_M2_1_03_G04

description:
IL-4/IL-13
IL-4/IL-13


title: 4PBA-KO_3


title: IL-4/IL-13 L48691_M2_1_03_G16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48678_M2_1_03_G03

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Liver_dox-treated_0988


title: IL-4/IL-13 L48677_M2_1_03_G02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48676_M2_1_03_G01

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Kidney_non-dox_1020

value: Kidney


title: IL-4/IL-13 L48675_M2_1_03_F24

description:
IL-4/IL-13
IL-4/IL-13


title: 4U8C-KO_1


title: 4F_Kidney_non-dox_1014


title: IL-4/IL-13 L48673_M2_1_03_F22

description:
IL-4/IL-13
IL-4/IL-13


title: LPS-KO_5


title: IL-4/IL-13 L48674_M2_1_03_F23

description:
IL-4/IL-13
IL-4/IL-13


title: LPS-KO_4


title: 4F_Kidney_non-dox_1008


title: LPS-KO_3


title: IL-4/IL-13 L48670_M2_1_03_F19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48672_M2_1_03_F21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48671_M2_1_03_F20

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Kidney_dox-treated_1002


title: IL-4/IL-13 L48683_M2_1_03_G08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48669_M2_1_03_F18

description:
IL-4/IL-13
IL-4/IL-13


title: LPS-KO_2


title: IL-4/IL-13 L48668_M2_1_03_F17

description:
IL-4/IL-13
IL-4/IL-13


title: LPS-KO_1


title: 4F_Kidney_dox-treated_0996


title: 4F_Liver_dox-treated_0994


title: IL-4/IL-13 L48666_M2_1_03_F15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48665_M2_1_03_F14

description:
IL-4/IL-13
IL-4/IL-13


title: 4F_Kidney_dox-treated_0990


title: 4U8C-KO_2


title: medium-KO_5

value: medium


title: Young_Spleen_non-dox_5285

source_name: Young mouse spleen

treatment_protocol: Mice treated with doxycycline (1 mg/ml) in drinking water for 2-days to induce 4F overexpression followed by 5 days of withdraw per week for 1 months.

value: 3 months

value: Spleen


title: medium-KO_4


title: Young_Spleen_non-dox_5279


title: IL-4/IL-13 L48663_M2_1_03_F12

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: medium-KO_3


title: Young_Spleen_non-dox_5273

value: Male


title: IL-4/IL-13 L48659_M2_1_03_F08

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48660_M2_1_03_F09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48661_M2_1_03_F10

description:
IL-4/IL-13
IL-4/IL-13


title: medium-KO_2


title: IL-4/IL-13 L48657_M2_1_03_F06

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48658_M2_1_03_F07

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Skin_non-dox_5287

source_name: Young mouse skin

value: Skin


title: IL-4/IL-13 L48654_M2_1_03_F03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48653_M2_1_03_F02

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48656_M2_1_03_F05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48655_M2_1_03_F04

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48667_M2_1_03_F16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48652_M2_1_03_F01

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Skin_non-dox_5281


title: IL-4/IL-13 L48664_M2_1_03_F13

description:
IL-4/IL-13
IL-4/IL-13


title: Rapamycin-WT_4

value: wild type

value: Rapamycin


title: Rapamycin-WT_3


title: IL-4/IL-13 L48650_M2_1_03_E23

description:
IL-4/IL-13
IL-4/IL-13


title: Rapamycin-WT_5


title: Young_Skin_non-dox_5275


title: IL-4/IL-13 L48649_M2_1_03_E22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48662_M2_1_03_F11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48651_M2_1_03_E24

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Skin_non-dox_5269


title: IL-4/IL-13 L48648_M2_1_03_E21

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Muscle_non-dox_5288

source_name: Young mouse muscle

value: Muscle


title: Young_Spleen_non-dox_5267


title: Rapamycin-WT_2


title: Rapamycin-WT_1


title: Young_Muscle_non-dox_5276


title: Young_Muscle_non-dox_5282


title: medium-KO_1

value: Bat3 fl/fl CD11c Cre


title: 4PBA-WT_4


title: IL-4/IL-13 L48642_M2_1_03_E15

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48644_M2_1_03_E17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48643_M2_1_03_E16

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48645_M2_1_03_E18

description:
IL-4/IL-13
IL-4/IL-13


title: 4PBA-WT_3


title: 4PBA-WT_2


title: IL-4/IL-13 L48641_M2_1_03_E14

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48639_M2_1_03_E12

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48640_M2_1_03_E13

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48638_M2_1_03_E11

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48636_M2_1_03_E09

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48635_M2_1_03_E08

description:
IL-4/IL-13
IL-4/IL-13


title: 4PBA-WT_1


title: IL-4/IL-13 L48646_M2_1_03_E19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48637_M2_1_03_E10

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48647_M2_1_03_E20

description:
IL-4/IL-13
IL-4/IL-13


title: 4U8C-WT_5


title: 4PBA-WT_5


title: IL-4/IL-13 L48633_M2_1_03_E06

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Muscle_non-dox_5270


title: Young_Lung_non-dox_5283

source_name: Young mouse lung

value: Lung


title: Young_Lung_non-dox_5271

value: 4F het; R26::rtTA het C57BL/6


title: Young_Lung_non-dox_5277


title: Young_Lung_non-dox_5289

value: Female


title: IL-4/IL-13 L48634_M2_1_03_E07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48632_M2_1_03_E05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48630_M2_1_03_E03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48631_M2_1_03_E04

description:
IL-4/IL-13
IL-4/IL-13


title: 4U8C-WT_3


title: 4U8C-WT_2


title: 4U8C-WT_4


title: Young_Liver_non-dox_5278

source_name: Young mouse liver


title: IL-4/IL-13 L48627_M2_1_03_D24

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Kidney_non-dox_5286

source_name: Young mouse kidney


title: Young_Liver_non-dox_5272


title: IL-4/IL-13 L48624_M2_1_03_D21

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48628_M2_1_03_E01

description:
IL-4/IL-13
IL-4/IL-13


title: 4U8C-WT_1


title: Young_Liver_non-dox_5266


title: IL-4/IL-13 L48625_M2_1_03_D22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48623_M2_1_03_D20

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48626_M2_1_03_D23

description:
IL-4/IL-13
IL-4/IL-13


title: LPS-WT_5

value: LPS


title: Young_Kidney_non-dox_5280


title: LPS-WT_4


title: LPS-WT_3


title: IL-4/IL-13 L48622_M2_1_03_D19

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48621_M2_1_03_D18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48629_M2_1_03_E02

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Liver_non-dox_5284

value: Liver


title: IL-4/IL-13 L48620_M2_1_03_D17

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48619_M2_1_03_D16

description:
IL-4/IL-13
IL-4/IL-13


title: Young_Kidney_non-dox_5274


title: LPS-WT_2


title: LPS-WT_1


title: Young_Kidney_non-dox_5268


title: Old_Spleen_non-dox_5243

value: 26 months


title: medium-WT_5


title: M2T_1

library_source: genomic

data_processing:
Sequenced samples were trimmed with Trimmomatic and mapped using Bowtie2. Only fragments with less than 150bp were kept.
Open chromatin was detected with MACS2, while differences between treatments was determined using DiffBind with at lest 2 fold change in accessibility and a false discovery rate lower than 0.05.
For visualization only, replicate mapped files were merged with SAM tools and coverage files were generated with deepTools and visualized alongside coverage files on IGV.
Bed files were analyzed with Bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files showing normalized filtered mapped reads.

molecule: genomic DNA

extract_protocol:
BMDMs treated as described were washed in PBS and then lysed in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630 (all Sigma). Nuclei were then spun down and then resuspend in 25 l TD (2x reaction buffer), 2.5 L TDE1 (Nextera Tn5 Transposase) and 22.5 L nuclease-free water, incubated for 30 min at 37°C. DNA was purified with the Qiagen MinElute PCR Purification Kit (Thermo Fisher Scientific).
Libraries were prepared using the Nextera DNA library Prep Kit (Illumina) adapting a published protocol (Buenrostro et al., 2015). PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol.


title: M2T_2


title: M2T_3


title: IL-4/IL-13 L48618_M2_1_03_D15

description:
IL-4/IL-13
IL-4/IL-13


title: M2_3


title: IL-4/IL-13 L48617_M2_1_03_D14

description:
IL-4/IL-13
IL-4/IL-13


title: M2_2


title: Old_Spleen_non-dox_5231


title: medium-WT_4


title: IL-4/IL-13 L48616_M2_1_03_D13

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Spleen_dox-treated_5261

value: Doxycycline-induced 4F


title: Old_Spleen_non-dox_5237


title: IL-4/IL-13 L48615_M2_1_03_D12

description:
IL-4/IL-13
IL-4/IL-13


title: medium-WT_3

value: medium


title: M2_1


title: Old_Spleen_dox-treated_5255


title: M0_3


title: medium-WT_2


title: IL-4/IL-13 L48614_M2_1_03_D11

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Spleen_dox-treated_5249


title: M0_2


title: IL-4/IL-13 L48613_M2_1_03_D10

description:
IL-4/IL-13
IL-4/IL-13


title: medium-WT_1


title: dLNT_cells_ctrl

data_processing:
Cellranger 2.0 aligned to mm10
Genome_build: mm10
Supplementary_files_format_and_content: h5 Expression Matrices

source_name: classical dendritic cells

extract_protocol: Collagenase IV, Dnase I digestion, sorting

value: classical dendritic cells

value: EAE

value: WT


title: IL-4/IL-13 L48611_M2_1_03_D08

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: CNS_T_cells_Bat3_cko

value: Bat3fl/fl CD11cCre


title: M0_1


title: IL-4/IL-13 L48612_M2_1_03_D09

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Skin_non-dox_5245

value: Skin


title: Old_Skin_non-dox_5239

value: Male


title: dLNT_cells_Bat3_cko


title: Old_Skin_non-dox_5233


title: CNS_T_cells_ctrl


title: IL-4/IL-13 L48610_M2_1_03_D07

description:
IL-4/IL-13
IL-4/IL-13


title: dendritic cells donor 4

city: Leipzig

first: Manuela

last: Rossol

address: Liebigstr. 19

institute: University of Leipzig

description:
dendritic cells
donor 4

hyb_protocol: Standard Illumina protocol (Illumina Hybridiation Oven Model 5521)

scan_protocol: Illumina iScan scanner

data_processing: The data were background corrected and quantile normalized using the neqc function from the limma R package (v3.46.0).

source_name: blood

label_protocol: Standard Illumina protocol

growth_protocol: Human monocytes were isolated from the blood using Milteny negative separation kit. Monocytes were differentiated into macrophages and dendritic cells for 7 days.

extract_protocol: RNA was isolated using Trizol and further precipitated using ammonium acetate.

treatment_protocol: On day 7, cells were activated by 10 ng/ml lipopolysaccharide (LPS).

tag: stimulation

value: LPS-stimulated


title: Old_Skin_dox-treated_5257


title: Old_Skin_dox-treated_5263


title: IL-4/IL-13 L48608_M2_1_03_D05

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Skin_dox-treated_5251


title: dendritic cells donor 1

description:
dendritic cells
donor 1


title: IL-4/IL-13 L48607_M2_1_03_D04

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Muscle_non-dox_5246

source_name: Old mouse muscle

value: Muscle


title: dendritic cells donor 2

description:
dendritic cells
donor 2


title: IL-4/IL-13 L48606_M2_1_03_D03

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48609_M2_1_03_D06

description:
IL-4/IL-13
IL-4/IL-13


title: Evolved cells, repl2

city: Madrid

first: Antonio

middle: David

last: Moreno

address: Avda. Complutense 40

department: Department of Energy

institute: CIEMAT

description: Gene expression data from evolved cells collected after 4 h of fermentation in presence of insoluble solids and lignocellulose-derived inhibitors

hyb_protocol: Labeled cDNAs were processed with GeneChip® IVT PLUS Reagent Kit (Affymetrix®) and hybridized with GeneChip™ Yeast Genome 2.0 Array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix®)

data_processing:
Raw data were processed with RMA algorithm included in Affymetrix® Expression Console™ for normalization and gene level analysis. Fold changes between experimental conditions were calculated as a quotient between the mean of the gene expression signals. Statistical analysis was performed with LIMMA package included in Babelomics software package
logFC_data.txt: Raw data were processed with Bioconductor online Piano software, using FDR for multiple testing adjustment and a P-value cuttoff of 0.05; Summary topTable() with False Discovery Rate adjustment

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Evolved cells

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol

growth_protocol: Fermentation was performed in YNB medium (Conda, Cat.1553.00) supplemented with 20 g/L glucose and 7.5 g/L (NH4)2SO4 in presence of 40% (w/w) insoluble solids and a inhibitory mix (2.1 g/L furfural, 0.3 g/L 5-HMF, 13.4 g/L acetic acid, 10.5 g/L formic acid, 0.4 g/L ferulic acid, 0.2 g/L syringaldehyde, and 0.1 g/L vanillin).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: evolved


title: IL-4/IL-13 L48604_M2_1_03_D01

description:
IL-4/IL-13
IL-4/IL-13


title: Evolved cells, repl1


title: dendritic cells donor 3

description:
dendritic cells
donor 3


title: M-CSF donor 4

description:
M-CSF
donor 4


title: M-CSF donor 3

description:
M-CSF
donor 3


title: M-CSF donor 1

description:
M-CSF
donor 1


title: Old_Muscle_non-dox_5240

value: 4F het; R26::rtTA het C57BL/6


title: IL-4/IL-13 L48603_M2_1_03_C24

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Muscle_non-dox_5234


title: shup_91_r2

city: beijing

first: mayun

last: mayun

state: beijing

address: NO.1 West Beichen Road, Chaoyang District

institute: institute of microbiology

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and then mapped to hg38 whole genome
Reads Per Kilo bases per Million reads (RPKM) were calculated and analyzed using samtools v0.1.19
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: chronic myeloid leukemia cells

extract_protocol:
RNA was isolated with TRIzol RNA Isolation Reagents (Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: K562 cells stably expressing control (sh-luc) or lncRNA-up91 shRNA (sh-up91)

value: Knockdown lncRNA-up91

tag: cell line


title: Old_Muscle_dox-treated_5258

tag: strain


title: IL-4/IL-13 L48602_M2_1_03_C23

description:
IL-4/IL-13
IL-4/IL-13

tag: cell type


title: IL-4/IL-13 L48601_M2_1_03_C22

description:
IL-4/IL-13
IL-4/IL-13

tag: treatment


title: Evolved cells, repl3

tag: strain background


title: IL-4/IL-13 L48600_M2_1_03_C21

description:
IL-4/IL-13
IL-4/IL-13


title: Parental cells, repl3

description: Gene expression data from parental cells collected after 4 h of fermentation in presence of insoluble solids and lignocellulose-derived inhibitors

source_name: Parental cells

value: parental


title: Parental cells, repl1


title: Parental cells, repl2


title: shluc_r2

value: Control


title: Old_Lung_non-dox_5241

source_name: Old mouse lung

tag: Sex

value: 26 months

value: Lung


title: GM-CSF donor 3

description:
GM-CSF
donor 3


title: GM-CSF donor 2

description:
GM-CSF
donor 2


title: GM-CSF donor 4

description:
GM-CSF
donor 4


title: Old_Muscle_dox-treated_5264

value: Female

tag: age

value: Doxycycline-induced 4F


title: GM-CSF donor 1

description:
GM-CSF
donor 1


title: IL-4/IL-13 L48599_M2_1_03_C20

description:
IL-4/IL-13
IL-4/IL-13

source_name: Bone marrow


title: shluc_r1


title: shup_91_r1


title: Old_Lung_dox-treated_5265


title: Old_Muscle_dox-treated_5252


title: RNA-D7-1-0

city: Rochester

first: Zachary

middle: C

last: Murphy

state: NY

address: 601 Elmwood Ave box 703

institute: University of Rochester

data_processing: none provided by the submitter

source_name: CD34 cells

growth_protocol: CD34 cells grown through published methods in Gauthier et al. 2016. Semi-synchrnouse erythroid cells isolated on Day 7 and Day 10 for analysis.

extract_protocol: RNA was extracted using Qiagen RNeasy per manufacterurs protocol

value: erythroid


title: shup_91


title: Old_Lung_non-dox_5247


title: Old_Lung_dox-treated_5259


title: Old_Lung_dox-treated_5253


title: IL-4/IL-13 L48595_M2_1_03_C16

description:
IL-4/IL-13
IL-4/IL-13


title: RNA-D10-2-0


title: IL-4/IL-13 L48598_M2_1_03_C19

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Lung_non-dox_5235


title: IL-4/IL-13 L48597_M2_1_03_C18

description:
IL-4/IL-13
IL-4/IL-13


title: shluc


title: RNA-D10-1-0


title: Ortho_H3K27me3_R13_treat_pileup

data_processing:
Single end raw reads were processed for quality and residual adapter sequencing using fastp v0.19.6 (--trim_poly_g -x --cut_window_size 4 -3 -l 35)
Quality reads were aligned to the hg19 reference genome using bowtie2 and filtered for quality based on MAPQ > 10.
Significantly enriched histone modifications were identified using MACS2 (--broad --broad-cutoff 0.1 -f BAM -B --SPMR -g hs) with each biological replicate and the corresponding IgG control.
replicated regions were also identified by providing MACS2 with all biological replicates for each mark to generate continuous coverage and enrichments for each condition
Genome wide distribution of significantly enriched regions was evaluated using CEAS (v1.0.2).
Genome_build: hg19

growth_protocol: Cell were grown according to Schulz et al 2019, Cell Reports

extract_protocol: Library construction and strategy according to Schulz et al 2019, Cell Reports


title: Old_Liver_non-dox_5242

source_name: Old mouse liver

value: Liver


title: Ortho_H3K27me3_R31_treat_pileup


title: IL-4/IL-13 L48593_M2_1_03_C14

description:
IL-4/IL-13
IL-4/IL-13

data_processing:
Bbasecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
Read alignment: Fragments were aligned to the mouse reference genome mm10 using the aligner gsnap (2019-06-10) with Ensembl 98 splice sites as support (parameters: --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-98.ss.mm10.iit -N 0  --action-if-cigar-error noprint).
Counts per feature: Uniquely mapped fragments were compared based on their overlap to Ensembl 98 gene annotations using featureCounts (v1.6.3) to create a table of counts per gene and cell (parameters:  -a EnsemblGene-98.mm10.TR.gtf -s 0 -p -o bfx1341.mm10.e98.txt -Q 1).
Samples were processed and analyzed in R (4.0.0) using Seurat (v3)
Genes from specific metabolic pathways were retrieved from KEGG
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells.

extract_protocol:
Wild-type BMDMs were stimulated with 10ng/ml IL4, IL13 and TNF. Cells were scraped and stained for live/dead staining with LDFA. Single cells were flow-sorted into 384-well plates containing nuclease-free water with 0.2% Triton X-100 and 1 U murine RNase inhibitor, centrifuged, and frozen at −80°C. After thawing, the primer mix and 1 U murine RNase inhibitor was added to each well. The reverse transcription reaction was performed, cDNA was amplified and purified. The concentration of samples was measured using a plate reader (Infinite 200 PRO, Tecan).
Then, pre-amplified cDNA was used for library preparation (TruePrep DNA library preparation kit V2 for Illumina, Vazyme) in a 1-μL reaction volume. Illumina indices were added during the PCR reaction with 1 × KAPA Hifi HotStart Ready Mix and dual indexing primers. After PCR, the libraries were quantified with AccuBlue Broad Range kit, pooled in equimolar amounts, and purified twice with Sera-Mag SpeedBeads. The libraries were sequenced on the Novaseq 6000 Illumina platform to obtain 50 bp paired-end reads aiming at an average sequencing depth of 0.5 million reads per cell.
Single Cell RNA seq

value: BMDM


title: IL-4/IL-13 L48592_M2_1_03_C13

description:
IL-4/IL-13
IL-4/IL-13


title: M-CSF donor 2

description:
M-CSF
donor 2


title: IL-4/IL-13 L48596_M2_1_03_C17

description:
IL-4/IL-13
IL-4/IL-13


title: RNA-D7-2-0


title: IL-4/IL-13 L48594_M2_1_03_C15

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Liver_non-dox_5236


title: IL-4/IL-13 L48591_M2_1_03_C12

description:
IL-4/IL-13
IL-4/IL-13


title: Ortho_H3K36me3_R15_treat_pileup


title: IL-4/IL-13 L48590_M2_1_03_C11

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Liver_dox-treated_5254


title: Ortho_H3K36me3_R33_treat_pileup


title: calcium donor 3

description:
calcium
donor 3


title: calcium donor 2

description:
calcium
donor 2


title: Old_Liver_dox-treated_5248


title: Old_Liver_non-dox_5230


title: calcium donor 4

description:
calcium
donor 4


title: calcium donor 1

description:
calcium
donor 1


title: EB_H3K36me3_R106_treat_pileup


title: EB_H3K36me3_R98_treat_pileup


title: IL-4/IL-13 L48588_M2_1_03_C09

description:
IL-4/IL-13
IL-4/IL-13


title: 10006031017_J: 7 days macrophage (LPS)

growth_protocol: Human monocytes were isolated from the blood using Milteny negative separation kit. Monocytes for cultured for the indicated times in the presence of a danger signal to monitor macrophage differentiation.

treatment_protocol: On day 7, macrophages were also activated by 10 ng/ml lipopolysaccharide (LPS).

value: macrophage

tag: donor

value: donor 4


title: IL-4/IL-13 L48589_M2_1_03_C10

description:
IL-4/IL-13
IL-4/IL-13


title: 3999970005_C: 7 days macrophage (LPS)

value: donor 3


title: IL-4/IL-13 L48587_M2_1_03_C08

description:
IL-4/IL-13
IL-4/IL-13


title: 10002121075_K: 7 days macrophage (LPS)

value: LPS-stimulated

value: donor 2


title: Old_Kidney_non-dox_5244

source_name: Old mouse kidney

tag: tissue

value: Kidney


title: 10006031017_I: 7 days macrophage

value: unstimulated


title: 10002121075_L: 7 days macrophage


title: Old_Kidney_non-dox_5232

value: 4F het; R26::rtTA het C57BL/6

value: Male


title: 10006031017_D: 7 days macrophage


title: Old_Kidney_non-dox_5238


title: EB_H3K27me3_R96_treat_pileup


title: EB_H3K27me3_R104_treat_pileup


title: 10002121075_E: 7 days macrophage

value: donor 1


title: 10002121075_F: 7 days macrophage (LPS)


title: IL-4/IL-13 L48585_M2_1_03_C06

description:
IL-4/IL-13
IL-4/IL-13


title: Old_Kidney_dox-treated_5262

value: 26 months


title: 10006031017_H: 4 days macrophage


title: Old_Kidney_dox-treated_5256


title: 10006031017_C: 4 days macrophage


title: IL-4/IL-13 L48584_M2_1_03_C05

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48586_M2_1_03_C07

description:
IL-4/IL-13
IL-4/IL-13


title: Rpb1-ChIP-D7-1-0

data_processing:
none provided by the submitter
Genome_build: hg19
Supplementary_files_format_and_content: bigwig


title: Old_Kidney_dox-treated_5250


title: IL-4/IL-13 L48583_M2_1_03_C04

description:
IL-4/IL-13
IL-4/IL-13


title: Spleen_Control_6524

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie v4.2.1 against the GENCODE Basic gene model on the mouse genome assembly GRCm38.
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV count matrices

source_name: Old mouse spleen

treatment_protocol: Mice treated with doxycycline (1 mg/ml) in drinking water for 2-days to induce 4F overexpression followed by 5 days of withdraw per week for 7 months.

value: 22 months

value: Spleen

value: Control


title: Rpb1-ChIP-D10-1-0

value: erythroid


title: Old_Liver_dox-treated_5260

value: Female

value: Liver

value: Doxycycline-induced 4F


title: Spleen_Control_6523


title: 10002121075_J: 4 days macrophage

value: macrophage


title: IL-4/IL-13 L48581_M2_1_03_C02

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: Rpb1-ChIP-D10-2-0


title: 10002121075_D: 4 days macrophage


title: Spleen_Control_6522


title: 10006031017_G: 2 days macrophage

value: donor 4


title: Rpb1-ChIP-D10-TI-0


title: 10006031017_B: 2 days macrophage

value: donor 3


title: Spleen_Control_6521


title: Rpb1-ChIP-D7-2-0


title: 10002121075_C: 2 days macrophage


title: IL-4/IL-13 L48579_M2_1_03_B24

description:
IL-4/IL-13
IL-4/IL-13


title: 10006031017_F: 1 day macrophage


title: 10002121075_I: 2 days macrophage

value: donor 2


title: IL-4/IL-13 L48578_M2_1_03_B23

description:
IL-4/IL-13
IL-4/IL-13


title: Rpb1-ChIP-D7-TI-0


title: IL-4/IL-13 L48582_M2_1_03_C03

description:
IL-4/IL-13
IL-4/IL-13


title: 10006031017_A: 1 day macrophage

value: unstimulated


title: IL-4/IL-13 L48605_M2_1_03_D02

description:
IL-4/IL-13
IL-4/IL-13


title: 10002121075_H: 1 day macrophage


title: RWP-1 shSOX9 3

city: Donostia

first: Estefania

last: Carrasco-Garcia

state: Guipúzcoa

address: Dr. Begiritsain s/n

department: Oncology

institute: Biodonostia

description: Gene expression data from RWP-1 cells cells transduced with shSOX9 plasmid

hyb_protocol: Following fragmentation, 3.5 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 System of Affymetrix.

data_processing: The samples were analyzed using Affymetrix RMA default analysis settings and global scaling as normalization method. The genes used for exploration are those with P-VALUE lower than 0.05 and value of the log Fold Change is greater than |0.6| (increase or decrease of 1.5).

source_name: cells transduced with shSOX9 plasmid

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng of total RNA

growth_protocol: Transduced cells were selected using puromycin 2 ug/mL for 48 hours under standard culture conditions.

treatment_protocol: Cells were harvested using Trypsin EDTA, washed with PBS and lysed with Trizol for RNA isolation.

value: pancreatic cancer cell line (liver metastasis)


title: IL-4/IL-13 L48576_M2_1_03_B21

description:
IL-4/IL-13
IL-4/IL-13


title: Spleen_4F_6528

value: 4F het; R26::rtTA het C57BL/6


title: IL-4/IL-13 L48575_M2_1_03_B20

description:
IL-4/IL-13
IL-4/IL-13


title: Spleen_4F_6527


title: RWP-1 pLKO 3

description: Gene expression data from RWP-1 cells cells transduced with pLKO control plasmid


title: IL-4/IL-13 L48580_M2_1_03_C01

description:
IL-4/IL-13
IL-4/IL-13


title: RWP-1 pLKO 2

source_name: cells transduced with pLKO control plasmid


title: Spleen_4F_6526

value: Male


title: Spleen_4F_6525


title: Spleen_Control_6520


title: RWP-1 shSOX9 1


title: 3999970001_K: monocytes

value: monocyte


title: IL-4/IL-13 L48574_M2_1_03_B19

description:
IL-4/IL-13
IL-4/IL-13


title: 10006031017_E: monocytes


title: Spleen_4F_6529

value: 22 months


title: IL-4/IL-13 L48577_M2_1_03_B22

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48573_M2_1_03_B18

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48572_M2_1_03_B17

description:
IL-4/IL-13
IL-4/IL-13


title: Skin_Control_6544

source_name: Old mouse skin

value: Skin


title: IL-4/IL-13 L48571_M2_1_03_B16

description:
IL-4/IL-13
IL-4/IL-13


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 28 replicate 3

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and quality, then mapped to mm10 whole genome using tophat2 v2.0.11 with default parameters, except --no-novel-juncs was used and mate inner distance (-r) and standard deviation (--mate-std-dev) were estimated for each sample individually.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cerebellum

extract_protocol:
Total RNA was isolated from dissected cerebella using TRIzol Reagent, and further purified to remove any organic carryover using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA library prep kit, and standard protocols.

value: FVB

value: cerebellum

value: post natal week 28


title: 10002121075_G: monocytes


title: Skin_Control_6542

value: Control


title: Skin_Control_6543


title: IL-4/IL-13 L48570_M2_1_03_B15

description:
IL-4/IL-13
IL-4/IL-13


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 28 replicate 2


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 12 replicate 3

value: post natal week 12


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 28 replicate 1


title: Skin_Control_6540


title: 10002121075_A: monocytes

value: donor 1


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 12 replicate 2


title: IL-4/IL-13 L48569_M2_1_03_B14

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L48568_M2_1_03_B13

description:
IL-4/IL-13
IL-4/IL-13


title: RWP-1 pLKO 1


title: Control_Ly6c_L1

city: Philadelphia

first: Hong

last: Wang

state: PA

address: 3500 N Broad St. MERB1060

department: CMDR

institute: Temple University Lewis Katz School of Medicine

data_processing:
Flow cytometry sorted CD11b+Ly6G-Ly6Chigh and CD11b+Ly6G-Ly6Clow cells from control and ApoE-/- WBC (200000/MC subset) were collected in 1400 μL QIAzol Lysis Reagent (Qiagen, Germantown, MD) for total RNA extraction.
Samples were quality checked on an Agilent Bioanalyzer 2100 using pico RNA chip for RNA integrity number.
Total RNA (50-100 ng/sample) were used for cDNA library construction after ribosomal cDNA depletion using Takara pico-input kit.
Pooled samples were run for sequencing analysis in duplication on Illumina NextSeq 500 (CT) and Illumina Hiseq 4000 sequencer (ApoE-/-).
The processed data were generated by mapping the raw read to the mouse reference transcriptome (mouse cDNA FASTA from ensembl, website http://uswest.ensembl.org/info/data/ftp/index.html) using Kallisto.
Supplementary_files_format_and_content: tab-delimited text files include count per million (CPM) values for each Sample

source_name: Ly6Clow monocyte

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood monocyte

tag: monocyte subset

value: Ly6Clow monocyte

value: wild type

value: 22 weeks


title: IL-4/IL-13 L48567_M2_1_03_B12

description:
IL-4/IL-13
IL-4/IL-13


title: Skin_4F_6548

value: Female

value: Doxycycline-induced 4F


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 12 replicate 1


title: Skin_4F_6549

value: 4F het; R26::rtTA het C57BL/6


title: Skin_4F_6547


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 5 replicate 3

value: post natal week 5


title: IL-4/IL-13 L48566_M2_1_03_B11

description:
IL-4/IL-13
IL-4/IL-13


title: Skin_Control_6541

value: Male

value: 22 months


title: Skin_4F_6546

value: Skin


title: Control_Ly6c_H1

source_name: Ly6Chigh monocyte

value: Ly6Chigh monocyte


title: Skin_4F_6545


title: JnkIn8_TNF_3

description: wild-type

data_processing:
Quality check of the raw files using FastQC (v. 0.7.11)
After sequencing raw reads were filtered to discard reads with contaminations, low quality or adapter residues
The raw file were mapped to the mouse genome build GRCm38 using the STAR aligner (v. 2.7.4a)
the reads were counted per gene using the featureCounts tool from the SubRead package (v. 2.0.1)
differentail expression analysis was done using DESeq2 (v. 1.30.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample; Matrix table of normalized gene counts after filtering nd DESeq2 normalization

source_name: JnkIn8 TNF 6h BMDMs

extract_protocol:
RNA was harvested using Trizol reagent. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/μl before checking insert size on an Agilent 2100 and  quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10µM SP600125, 20µM Jnk-In-8 or DMSO; 10ng/ml IL4, IL13 and/or TNF

value: bone marrow

value: 8-10 weeks old


title: IL-4/IL-13 L48564_M2_1_03_B09

description:
IL-4/IL-13
IL-4/IL-13


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 5 replicate 2

value: FVB

value: cerebellum


title: Control_Ly6c_H2


title: JnkIn8_TNF_2

description: wild-type


title: IL-4/IL-13 L48563_M2_1_03_B08

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: IL-4/IL-13 L48565_M2_1_03_B10

description:
IL-4/IL-13
IL-4/IL-13


title: Cerebellum Cck-/- week 28 replicate 3

value: Cck-/-

value: post natal week 28


title: Cerebellum Cck-/- week 28 replicate 2


title: JnkIn8_IL4IL13_TNF_3

description: wild-type

source_name: JnkIn8 IL4/IL13+TNF 6h BMDMs


title: IL-4/IL-13 L48562_M2_1_03_B07

description:
IL-4/IL-13
IL-4/IL-13


title: IL-4/IL-13 L48561_M2_1_03_B06

description:
IL-4/IL-13
IL-4/IL-13


title: JnkIn8_TNF_1

description: wild-type


title: Skeletal_Muscle_Control_6554

source_name: Old mouse muscle

value: Muscle

value: Control


title: Skeletal_Muscle_Control_6552


title: IL-4/IL-13 L48560_M2_1_03_B05

description:
IL-4/IL-13
IL-4/IL-13


title: Cerebellum Cck-/- week 12 replicate 3

value: post natal week 12


title: Skeletal_Muscle_Control_6551


title: Skeletal_Muscle_Control_6553


title: JnkIn8_IL4IL13_TNF_2

description: wild-type


title: IL-4/IL-13 L48559_M2_1_03_B04

description:
IL-4/IL-13
IL-4/IL-13


title: JnkIn8_IL4IL13_TNF_1

description: wild-type


title: Cerebellum Cck-/- week 28 replicate 1


title: Cerebellum ATXN1[30Q]D776/Cck-/- week 5 replicate 1


title: IL-4/IL-13 L48558_M2_1_03_B03

description:
IL-4/IL-13
IL-4/IL-13


title: JnkIn8_IL4IL13_3

description: wild-type

source_name: JnkIn8 IL4/IL13 6h BMDMs


title: Skeletal_Muscle_Control_6550


title: Cerebellum Cck-/- week 12 replicate 2


title: Control_Ly6c_L2

value: Peripheral blood monocyte

value: Ly6Clow monocyte

value: wild type

value: 22 weeks


title: Cerebellum Cck-/- week 12 replicate 1


title: Skeletal_Muscle_4F_6559

value: 4F het; R26::rtTA het C57BL/6

value: Female

value: 22 months

value: Doxycycline-induced 4F


title: JnkIn8_IL4IL13_2

description: wild-type

value: bone marrow

value: 8-10 weeks old


title: Cerebellum Cck-/- week 5 replicate 3

value: FVB

value: cerebellum

value: post natal week 5


title: JnkIn8_IL4IL13_1

description: wild-type


title: IL-4/IL-13 L48556_M2_1_03_B01

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: Cerebellum Cck-/- week 5 replicate 2

value: Cck-/-


title: Cerebellum Cck-/- week 5 replicate 1


title: Skeletal_Muscle_4F_6557

value: Muscle


title: IL-4/IL-13 L48554_M2_1_03_A23

description:
IL-4/IL-13
IL-4/IL-13


title: JnkIn8_Ctrl_2

description: wild-type

source_name: JnkIn8 Ctrl BMDMs


title: SHR34 carotid body right

city: Bristol

first: Audrys

middle: G

last: Pauza

state: Somerset

address: University of Bristol, The Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School (THS)

country: United Kingdom

institute: University of Bristol

data_processing:
Original .fastq files were inspected using FastQC. As all samples passed initial QC no further trimming was applied
.fastq were aligned to the rat reference genome (Rn6) using RNA-STAR mapper
Reads were counted using featureCounts at a gene level
Differential expression analysis was performed using DEseq2
Genome_build: Rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Carotid body

extract_protocol:
Animals were euthanised with pentobarbital sodium (euthatal) and intracardially perfused with ice-cold PBS. Carotid bodies were excised from the common carotid artery bifurcation under the dissecting microscope and immediately snap-frozen in liquid nitrogen. Tissue was homogenized using QIAzol lysis reagent. Total RNA was extracted using phenol:chloroform phase separation method and isolated using ZYMO direct-zol RNA microprep kit following manufacturers instructions.
Illumina TruSeq® Stranded mRNA library preparation kit (20020594, Illumina)

value: SHR/NHsd

value: Carotid body

tag: gender

value: male

value: 12-14 weeks old


title: Skeletal_Muscle_4F_6556

value: Male


title: IL-4/IL-13 L48553_M2_1_03_A22

description:
IL-4/IL-13
IL-4/IL-13

source_name: Bone marrow


title: Skeletal_Muscle_4F_6555

value: 4F het; R26::rtTA het C57BL/6


title: SHR34 carotid body left


title: IL-4/IL-13 L48552_M2_1_03_A21

description:
IL-4/IL-13
IL-4/IL-13


title: SP600125_TNF_3

description: wild-type

source_name: SP600125 TNF 6h BMDMs


title: SHR37 carotid body right


title: Lung_Control_6564

source_name: Old mouse lung

value: Female

value: Lung

value: Control


title: 10002121075_B: 1 day macrophage

source_name: blood

value: macrophage

value: unstimulated

value: donor 1


title: IL-4/IL-13 L48551_M2_1_03_A20

description:
IL-4/IL-13
IL-4/IL-13


title: SP600125_TNF_2

description: wild-type

value: bone marrow

value: 8-10 weeks old


title: Lung_Control_6563

value: 22 months


title: SHR37 carotid body left


title: IL-4/IL-13 L48557_M2_1_03_B02

description:
IL-4/IL-13
IL-4/IL-13

value: BMDM


title: Skeletal_Muscle_4F_6558

value: Muscle

value: Doxycycline-induced 4F


title: SP600125_TNF_1

description: wild-type


title: IL-4/IL-13 L48555_M2_1_03_A24

description:
IL-4/IL-13
IL-4/IL-13


title: JnkIn8_Ctrl_3

description: wild-type


title: Lung_Control_6561


title: IL-4/IL-13 L48549_M2_1_03_A18

description:
IL-4/IL-13
IL-4/IL-13


title: SHR36 carotid body left

value: SHR/NHsd

value: Carotid body