title: SP600125_IL4IL13_TNF_3

description: wild-type

source_name: SP600125 IL4/IL13+TNF 6h BMDMs


title: Lung_Control_6560

status: Public on Jan 11 2022

type: SRA

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

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Old mouse lung

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 7 months.

tag: strain

tag: Sex

value: Male

tag: age

value: 22 months

tag: tissue

value: Lung

tag: treatment

value: Control


title: JnkIn8_Ctrl_1

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

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 Ctrl BMDMs

growth_protocol: In the presence of M-CSF

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 L48548_M2_1_03_A17

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

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


title: Lung_4F_6569

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

value: Female

value: Doxycycline-induced 4F


title: SP600125_IL4IL13_TNF_2

description: wild-type


title: IL-4/IL-13 L48547_M2_1_03_A16

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


title: Lung_4F_6568


title: SP600125_IL4IL13_TNF_1

description: wild-type


title: SHR33 carotid body left

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

molecule: polyA RNA

organism: Rattus norvegicus

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: SP600125_IL4IL13_3

description: wild-type

source_name: SP600125 IL4/IL13 6h BMDMs


title: Lung_Control_6562


title: SHR31 carotid body right


title: IL-4/IL-13 L48546_M2_1_03_A15

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


title: IL-4/IL-13 L48550_M2_1_03_A19

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


title: SHR31 carotid body left


title: Lung_4F_6567


title: Lung_4F_6566


title: SP600125_IL4IL13_2

description: wild-type


title: IL-4/IL-13 L48545_M2_1_03_A14

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


title: SHR36 carotid body right


title: IL-4/IL-13 L48544_M2_1_03_A13

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


title: SHR30 carotid body right


title: SP600125_IL4IL13_1

description: wild-type


title: SP600125_Ctrl_3

description: wild-type

source_name: SP600125 Ctrl BMDMs


title: Lung_4F_6565


title: IL-4/IL-13 L48543_M2_1_03_A12

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


title: SHR30 carotid body left


title: SP600125_Ctrl_2

description: wild-type


title: IL-4/IL-13 L48542_M2_1_03_A11

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


title: SHR33 carotid body right


title: Liver_Control_6514

source_name: Old mouse liver

value: Liver


title: WKY41 carotid body right

value: WKY/NHsd


title: Liver_Control_6513


title: IL-4/IL-13 L48541_M2_1_03_A10

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


title: SP600125_Ctrl_1

description: wild-type


title: WKY41 carotid body left


title: IL-4/IL-13 L48540_M2_1_03_A09

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


title: DMSO_TNF_2

description: wild-type

source_name: DMSO TNF 6h BMDMs


title: WKY36 carotid body right


title: DMSO_TNF_3

description: wild-type


title: Liver_Control_6511


title: Liver_Control_6512


title: IL-4/IL-13 L48539_M2_1_03_A08

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


title: WKY36 carotid body left


title: IL-4/IL-13 L48537_M2_1_03_A06

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


title: Liver_Control_6510


title: WKY37 carotid body left


title: IL-4/IL-13 L48536_M2_1_03_A05

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


title: Liver_4F_6518


title: DMSO_TNF_1

description: wild-type


title: DMSO_IL4IL13_TNF_2

description: wild-type

source_name: DMSO IL4/IL13+TNF 6h BMDMs


title: Liver_4F_6519


title: IL-4/IL-13 L48538_M2_1_03_A07

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


title: WKY34 carotid body right


title: DMSO_IL4IL13_TNF_3

description: wild-type


title: IL-4/IL-13 L48535_M2_1_03_A04

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


title: Liver_4F_6517


title: WKY34 carotid body left


title: Liver_4F_6516


title: DMSO_IL4IL13_TNF_1

description: wild-type


title: DMSO_IL4IL13_3

description: wild-type

source_name: DMSO IL4/IL13 6h BMDMs


title: IL-4/IL-13 L48534_M2_1_03_A03

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


title: WKY33 carotid body right


title: Liver_4F_6515


title: IL-4/IL-13 L48533_M2_1_03_A02

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


title: WKY37 carotid body right


title: DMSO_IL4IL13_2

description: wild-type


title: WKY33 carotid body left


title: Kidney_Control_6534

source_name: Old mouse kidney

value: Kidney


title: IL-4/IL-13 L48532_M2_1_03_A01

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


title: DMSO_IL4IL13_1

description: wild-type


title: WKY32 carotid body right


title: IL-4/IL-13 L48510_B_M2_02_P03

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


title: WKY32 carotid body left


title: DMSO_Ctrl_3

description: wild-type

source_name: DMSO Ctrl BMDMs


title: DMSO_Ctrl_2

description: wild-type


title: Kidney_Control_6533

value: Male


title: Kidney_Control_6532

value: 22 months


title: Kidney_Control_6531


title: IL-4/IL-13 L48338_M2_1_02_H23

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


title: IL-4/IL-13 L48339_M2_1_02_H24

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


title: 87-rmec-10_ATCACG

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N Orchard St

department: Wisconsin Institute For Discovery

institute: University of Wisconsin-Madison

data_processing:
Merge/Aggregate data from 2 independent runs on the same samples
TPM computed with RSEM v1.2.22
edgeR, EBSeq and DESeq2 were used for differential expression analysis
Genome_build: rn5

source_name: Mammary epithelial cells

extract_protocol:
Cell pellets were collected by centrifugation and resuspended in 5 mL DMEM/F12. The suspension was loaded onto a 40μm nylon filter to eliminate stromal cells and collect mammary ductal fragments, consisting of an enriched mammary epithelial cell population. To isolate RNA, cells were homogenized in TRI Reagent (Ambion), followed by RNA extraction using the MagMAX-96 for Microarrays Total RNA kit (Ambion). RNA was extracted using the RNeasy Mini Kit (Qiagen).
The fastq files were processed by the UW Biotech center.

treatment_protocol: Mammary epithelial cell isolation began with fresh abdominal and inguinal mammary glands with lymph nodes removed that were finely minced and digested for 2 hours at 37°C in 10 mL of GIBCO Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12; Life Technologies) containing 0.01 g/mL of type III collagenase (Worthington).

value: Wistar-Furth

value: Mammary epithelial cells


title: DMSO_Ctrl_1

description: wild-type

value: bone marrow


title: 85-rmec-10_ACTGAT


title: Kidney_Control_6530

value: Control


title: IL-4/IL-13 L48337_M2_1_02_H22

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

value: BMDM


title: 83-rmec-10_CGTACG


title: Kidney_4F_6539

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


title: 81-rmec-10_GTTTCG


title: Testis, BaP, 3-7

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

data_processing:
FASTQ files were QC-filtered (Q>30) and adaptor sequence-trimmed using Trim Galore!
Filtered and trimmed FASTQ files were mapped to mouse genome reference sequence using the STAR aligner.
BAM files generated by STAR were subjected to feature (protein-coding gene) counting using Rsubread R/Bioconductor package.
Counted reads were normalized using normalized using the negative binominal, trimmed mean of M-values (TMM) method implemented by the Bioconductor package edgeR.
The General Linear Model (GLM) Likelihood Ratio Test (LRT) was performed using edgeR to identify Differentially Expressed Genes (DEGs) where the mean expression value of a gene in any group is significantly different from other sample groups. The obtained p-values were corrected by the Benjamini–Hochberg method to obtain False Discovery Rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: Count files generated using R/Bioconductor Rsubread.

source_name: embryonic testis

growth_protocol: Female mice were timed-mated, and exposed to oil or BaP. Emryos were collected at E13.5, and their gonads were collected by dissection.

extract_protocol:
Total gonads were subjected to total RNA isolation using QIAGEN RNeasy kit.
cDNA was synthesized from total RNA using Takara SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing with oligo(dT) priming. Libraries were prepared from sonicated cDNA using Takara Low Input Library Prep Kit.

treatment_protocol: Pregnant mice were exposed to 0 or 3.33 mg/kg BaP orally between E6.5 - E11.5.

tag: developmental stage

tag: exosure

value: BaP


title: Testis, BaP, 3-8


title: Testis, oil, 3-6

value: oil


title: 78-rmec-10_GTGAAA


title: IL-4/IL-13 L48335_M2_1_02_H20

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


title: Kidney_4F_6537

value: Female

value: Doxycycline-induced 4F


title: IL-4/IL-13 L48334_M2_1_02_H19

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


title: Testis, oil, 3-5


title: 74-rmec-10_CCGTCC


title: Kidney_4F_6536


title: Ovary, BaP, 3-4

source_name: embryonic ovary


title: IL-4/IL-13 L48333_M2_1_02_H18

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


title: 72-rmec-10_ATGTCA


title: ApoE_Ly6c_L2

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

tag: genotype

value: ApoE-/-

value: 22 weeks


title: Kidney_4F_6535

value: Kidney


title: IL-4/IL-13 L48332_M2_1_02_H17

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


title: 84-rmec-6_GAGTGG


title: 86-rmec-6_ATTCCT


title: Ovary, oil, 3-2


title: IL-4/IL-13 L48331_M2_1_02_H16

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


title: Ovary, oil, 3-1


title: IL-4/IL-13 L48330_M2_1_02_H15

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


title: Ovary, BaP, 3-3


title: ApoE_Ly6c_L1


title: Kidney_4F_6538


title: Testis, BaP, 2-7


title: 80-rmec-6_GTGGCC


title: ApoE_Ly6c_H1

source_name: Ly6Chigh monocyte

value: Ly6Chigh monocyte


title: 75-rmec-6_GTCCGC


title: ApoE_Ly6c_H2


title: KO_TGF_73

city: San Francisco

first: Ivan

last: Osokine

state: California

address: 513 Parnassus Avenue S1058

department: Laboratory Medicine

institute: University of California, San Francisco

data_processing:
Reads were aligned  to the mouse genome using the Splice-aware STAR aligner STAR_2.5.2b
Raw counts were determined using STAR_2.5.2b
Reads uniquely mapped to known mRNAs were used to identify genes with differential expression (FDR<0.05) using DESeq2 R v1.16.1 software. two separate analyses were performed: one comparing control and Ezh2 cKO DSCs both cultured without TGF-beta1 (i.e., comparing their “baseline expression”), and one comparing, in a paired fashion, each control or Ezh2 cKO sample cultured without TGF-beta1 to its biological replicate cultured with TGF-beta1.
Genome_build: Ensembl Mouse GRCm38.87
Supplementary_files_format_and_content: tab-delimited text file of raw counts

source_name: Decidual stromal cells

extract_protocol:
RNA was isolated with QIAGEN Mini reagents and kit according to manufacturer's instructions. DNAse digestion and RNA cleanup was performed using the RNase-Free DNase set (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared according to Illumina's instructions, using a Smartseq/NexteraXT  kit.

treatment_protocol: Decidual Stromal Cells were cultured in either with or without 2 ng/ml of TGF-beta1 for 24 hours

value: Pgr(cre/+) Ezh2(fl/fl) ("Ezh2 cKO")

value: Decidua

value: Decidual stromal cell

value: 2 ng/ml transforming growth factor beta 1.


title: Testis, BaP, 2-8


title: Testis, oil, 2-6


title: IL-4/IL-13 L48336_M2_1_02_H21

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


title: IL-4/IL-13 L48327_M2_1_02_H12

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


title: 70-rmec-6_AGTCAA

value: Wistar-Furth

value: Mammary epithelial cells


title: KO_TGF_72


title: Testis, oil, 2-5


title: IL-4/IL-13 L48325_M2_1_02_H10

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

value: BMDM


title: KO_TGF_71


title: IL-4/IL-13 L48326_M2_1_02_H11

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


title: Ovary, Bap, 2-4

value: BaP


title: KO_TGF_62


title: W48_12wk

library_source: genomic

data_processing:
Hi-C reads were processed using HiCPro version 2.7 with the default BowTie2 parameters (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder). Digestion paramters: LIGATION_SITE = GAATAATC,GAATACTC,GAATAGTC,GAATATTC,GAATGATC,GACTAATC,GACTACTC,GACTAGTC,GACTATTC,GACTGATC,GAGTAATC,GAGTACTC,GAGTAGTC,GAGTATTC,GAGTGATC,GATCAATC,GATCACTC,GATCAGTC,GATCATTC,GATCGATC,GATTAATC,GATTACTC,GATTAGTC,GATTATTC,GATTGATC, MIN_FRAG_SIZE = 10, MAX_FRAG_SIZE = 100000, MIN_INSERT_SIZE = 100, MAX_INSERT_SIZE = 1000
Removal of singleton reads, multi-mapped read-pairs and duplicates set to true
10kb contact maps generated with HiCPro 2.7
6wk samples were aggregated (sum), and 12 wk samples were similarly aggregated. ICED normalization was perfomed on both aggregated matrices (default HiCPro).
Genome_build: rn6
Supplementary_files_format_and_content: .matrix

molecule: genomic DNA

extract_protocol:
Centrifugation was used to remove fat and collect the cell pellets.  Individual cell pellets were washed and resuspended in DMEM/F12 media.  Each cell suspension was filtered using 40μm nylon to enrich the mammary ductal fragments and remove stromal cells.  The filter was inverted and rinsed to collect the fragments, and the resulting cell pellet containing mammary epithelial cells was diluted in PBS and treated for 10 minutes with 1.5% formaldehyde for DNA/chromatin fixation.  After a series of washes, the final cell pellets were collected using centrifugation and stored at -80oC.
A total of 6 samples were sent to Arima Genomic, Inc. (n=3 from each age group) for Arima HiC Service, consisting of complete sample processing for Arima-HiC and library preparation, Illumina Next-Generation sequencing and data upload.

treatment_protocol: Fresh mammary glands from the abdominal/inguinal regions of 6-week-old and 12-week-old female rats were individually collected, scissor minced and digested for 2 hours at 37°C in 10 mL of GIBCO Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12; ThermoFisher) containing 0.005 g/mL of type 3 collagenase (Worthington-Biochem).


title: Ovary, BaP, 2-3


title: IL-4/IL-13 L48323_M2_1_02_H08

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


title: KO_TGF_55


title: W16_12wk


title: Ovary, oil, 2-2

value: oil


title: IL-4/IL-13 L48329_M2_1_02_H14

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


title: 71-rmec-6_AGTTCC


title: IL-4/IL-13 L48328_M2_1_02_H13

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


title: Ovary, oil, 2-1


title: KO_TGF_53


title: IL-4/IL-13 L48322_M2_1_02_H07

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


title: W45_6wk


title: KO_BL_73


title: W47_6wk


title: IL-4/IL-13 L48321_M2_1_02_H06

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


title: Testis, BaP, 1-8


title: W43_6wk


title: Testis, oil, 1-6


title: KO_BL_71


title: IL-4/IL-13 L48324_M2_1_02_H09

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


title: IL-4/IL-13 L48320_M2_1_02_H05

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


title: KO_BL_72


title: KO_BL_62


title: Testis, oil, 1-5


title: IL-4/IL-13 L48319_M2_1_02_H04

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


title: IL-4/IL-13 L48318_M2_1_02_H03

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


title: IL-4/IL-13 L48316_M2_1_02_H01

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


title: WT_TGF_192

value: Pgr(+/+) Ezh2(fl/fl) ("Control")


title: Ovary, BaP, 1-4


title: WT_TGF_187


title: IL-4/IL-13 L48317_M2_1_02_H02

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


title: RNA Extracted from FRCs treated with B16.F10 TCM , replicate 2

city: Würzburg

first: Angela

last: Riedel

address: Josef-Schneider-Straße 2

department: Mildred-Scheel-Nachwuchszentrum (MSNZ) für Krebsforschung

institute: University Hospital Würzburg

data_processing:
the reads were aligned to ENSEMBL GRCm38 (mm10) Mus Musculus’s genome version 100 using STAR (2.7.0a) applying the default parameters
FeatureCounts (Subread package 2.0.1) was used to quantify the reads that were mapped to each gene and to generate count matrices.
The differenial  analysis was performed using DEseq2 R package (1.32.0).To exclude low quality genes, genes that were detected in less than 2 samples and those who have less than 10 reads were removed
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Row_Counts.csv is comma seperated file containing raw counts with genes as rows and samples as columns as for Normalized_counts_DESeq2.csv, it is comma seperated file containing normalized and filtered counts  with genes as rows and samples as columns

source_name: Fibroblastic reticular cell - cell line

extract_protocol:
Total RNA was isolated for each sample using Rneasy micro kit (QIAGEN) according to the manufacturer instructions
libraries were processed using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB #E7490)  as recommended by the manufacturer ,Poly A mRNA was isolated from 500 ng of total RNA by means of NEBNext Poly(A) mRNA Magnetic Isolation Module. Subsequently, the isolated poly mRNA was fragmented with the help of temperature and the preparation continued following the recommendation of the manufacturer. The quantity and the quality of the libraries were assessed using Bioanalyzer High Sensitivity DNA Analysis. Finally, The libraries were sequenced using Illumina NextSeq500

value: Lymph node


title: LTL331_CX

type: RNA

city: Vancouver

first: Yuzhuo

state: BC

address: 2660 Oak Street

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

hyb_protocol: Samples were hybridized on Agilent SurePrint G3 Human GE 8 x 60K Microarray

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3-um scan resolution

data_processing: Data were processed with Agilent Feature Extraction 10.10. Processed signal was quantile normalized with Agilent GeneSpring 11.5.1

organism: Homo sapiens

source_name: Prostate Tumor

label_protocol: For gene expression, total RNA samples were prepared following Agilent's One-Color Microarray-Based Gene Expres-  sion Analysis Low Input Quick Amp Labeling v6.0. An input of 100 ng of total RNA was used to generate cyanine-3–labeled cRNA.

growth_protocol: Tissues of patient-derived prostate cancer xenografts were grafted at the sub-renal capsule grafting sites of NGF mice.

extract_protocol: RNA from the snap-frozen PDX tissues was isolated using the mirVana Isolation Kit from Ambion (AM 1560).

treatment_protocol: Pre-castration PDX tissues were harvested without host castration. For PDX tissues of post-castration 12-week timepoint, hosts were surgically castrated by removing testes and testosterone pellets and the PDX tissues were harvested at Week 12 post-castration.

tag: tissue type

value: prostate cancer tumor

tag: tumor foci

value: Patient Derived Xenograft

tag: sample/cell line

value: Castrated LTL331


title: LTL484_CX

value: Castrated LTL484


title: Ovary, BaP, 1-3


title: WT_TGF_60


title: LTL467_CX

value: Castrated LTL467


title: KO_BL_53


title: WT_TGF_54


title: LTL418_CX

value: Castrated LTL418


title: Ovary, oil, 1-2


title: IL-4/IL-13 L48315_M2_1_02_G24

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

source_name: Bone marrow


title: Ovary, oil, 1-1


title: RNA Extracted from  FRCs treated with 15mM lactic acid , replicate 1


title: IL-4/IL-13 L48314_M2_1_02_G23

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


title: W44_12wk


title: WT_TGF_186


title: IL-4/IL-13 L48313_M2_1_02_G22

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


title: IL-4/IL-13 L48312_M2_1_02_G21

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


title: RNA Extracted from FRCs treated with B16.F10 TCM , replicate 1


title: IL-4/IL-13 L48310_M2_1_02_G19

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


title: RNA Extracted from FRCs treated with 15mM lactic acid , replicate 2


title: LTL556_CX

value: Castrated LTL556


title: LTL508_CX

value: Castrated LTL508


title: LTL412_CX

value: Castrated LTL412


title: IL-4/IL-13 L48309_M2_1_02_G18

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


title: KO_BL_55

value: Pgr(cre/+) Ezh2(fl/fl) ("Ezh2 cKO")

value: Decidua

value: Decidual stromal cell


title: WT_TGF_51

value: 2 ng/ml transforming growth factor beta 1.


title: IL-4/IL-13 L48311_M2_1_02_G20

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

value: BMDM


title: RNA Extracted from  FRCs treated with water as the vehicle control for lactate, replicate 2


title: IL-4/IL-13 L48308_M2_1_02_G17

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


title: LTL471_CX

value: Castrated LTL471


title: IL-4/IL-13 L48307_M2_1_02_G16

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


title: LTL313H_CX

value: Castrated LTL313H


title: RNA Extracted from  FRCs treated with control conditioned media, replicate 2

value: Lymph node


title: WT_BL_192

value: Pgr(+/+) Ezh2(fl/fl) ("Control")


title: WT_BL_187


title: RNA Extracted from FRCs treated with control conditioned media , replicate 1


title: WT_BL_186


title: LTL467_PRE

value: prostate cancer tumor

value: Patient Derived Xenograft

value: Parental LTL467 patient derived xenograft line


title: LTL484_PRE

value: Parental LTL484 patient derived xenograft line


title: WT_BL_60


title: RNA Extracted from FRCs treated with water as the vehicle control for lactate, replicate 1


title: Mouse inguinal white adipose 12-1

city: Boston

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

data_processing:
In Drop-Seq data, the cDNA read is single-ended (read 2); read 1 contains cell and UMI barcodes pertaining to the read
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Digital expression matrices were generated from the FASTQ files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Adjustments were made to the cell-tagging functions of this pipeline to account for the structure of the 10X barcode read: “BASE_RANGE=1-16” and “BASE_RANGE=17-28”, for the cell and UMI barcodes, respectively. The 10X TSO was provided to the starting sequence trimmer (“SEQUENCE=AAGCAGTGGTATCAACGCAGAGTACATGGG”); this is a minor deviation from the assumed TSO. Reads from were aligned with STAR (version 2.7.3) against the GRCm38 and GRCh38 genome assemblies for mouse and human, respectively. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 16 of the GENCODE mouse annotation or release 27 of the human annotation.
CellBender (Fleming, et. al 2019) version 0.2.0 was used to remove background/ambient signal from the mouse DGE matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: Digital gene expression matrices (“dge.tsv.gz” files): gene-by-cell UMI counts.

source_name: inguinal fat pad

extract_protocol:
Nuclei were isolated from frozen mouse and human adipose tissue samples for 10x snRNA-seq using a slightly modified approach to what was previously described50–52. Samples were kept frozen on dry ice until immediately before nuclei isolation, and all sample handling steps were performed on ice. Each flash-frozen adipose tissue sample was placed into a gentleMACS C tube (Miltenyi Biotec) with 2 mL freshly prepared TST buffer (0.03% Tween 20 [Bio-Rad], 0.01% Molecular Grade BSA [New England Biolabs], 146 mM NaCl [ThermoFisher Scientific], 1 mM CaCl2 [VWR International], 21 mM MgCl2 [Sigma Aldrich], and 10 mM Tris-Hcl pH 7.5 [ThermoFisher Scientific] in Ultrapure water [ThermoFisher Scientific]) with or without 0.2 U/ µL of Protector RNase Inhibitor (Sigma Aldrich). gentleMACS C tubes were then placed on the gentleMACS Dissociator (Miltenyi Biotec) and tissue was dissociated by running the program “mr_adipose_01” twice, and then incubated on ice for 10 minutes. Lysate was passed through a 40 µm nylon filter (CellTreat) and collected into a 50 mL conical tube (Corning). Filter was rinsed with 3 mL of freshly prepared ST buffer buffer (146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2; 10 mM Tris-Hcl pH 7.5) with or without 0.2 U/µL RNase Inhibitor, and collected into the same tube. Flow-through was centrifuged at 500 x g for 5 minutes at 4ºC with brake set to low. Following centrifugation, supernatant was removed, and the nuclear pellet was resuspended in 50 - 200 µl PBS pH 7.4 (ThermoFisher Scientific) with 0.02% BSA, with or without 0.2U/µL RNase Inhibitor. In order to reduce ambient mRNA, the nuclear pellets of some samples were washed 1-3 times with 5 mL of PBS-0.02% BSA before final resuspension. An aliquot of nuclei from each sample was stained with NucBlue (Thermofisher Scientific), counted in a hemocytometer using fluorescence to identify intact nuclei, and then immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol.
For each sample, 10,000-16,500 nuclei were loaded in one channel of a Chromium Chip (10x Genomics). The Single Cell 3’ v3.1 chemistry was used to process all samples. cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent).
cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (ThermoFisher Scientific). Gene expression libraries were multiplexed and sequenced on the Nextseq 500 (Illumina) with a 75-cycle kit and the following read structure: Read 1: 28 cycles, Read 2: 55 cycles, Index Read 1: 8 cycles.
OTHER: 10X Chromium Single-Cell 3’ (v3 Chemistry)

value: white adipose tissue

tag: mouse strain

value: male

tag: diet

value: HFD


title: LTL313B_CX

value: Castrated LTL313B


title: WT_BL_54


title: IL-4/IL-13 L48305_M2_1_02_G14

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


title: IL-4/IL-13 L48304_M2_1_02_G13

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


title: WT_BL_51


title: cKO_Myo_M3

data_processing:
Reads were aligned  to the mouse genome using the Splice-aware STAR aligner STAR_2.4.2a
Raw counts were determined using STAR_2.4.2a
Reads uniquely mapped to known mRNAs were used to identify genes with differential expression (FDR<0.05) using DESeq2 R v1.16.1 software. Two analyses were performed to compare contro decidua to Ezh2 cKO decidua and cpntrol myometrium  to Ezh2 cKO myometrium. Decidual and myometrial samples were not directly compared.
Genome_build: Ensembl Mouse GRCm38.87
Supplementary_files_format_and_content: tab-delimited text file of raw counts

source_name: Homogenized whole tissue myometrium

extract_protocol:
Implantation sites at E7.5 were dissected to separate the decidua from overlying myometrium and each layer was washed in cold PBS and homogenized in TRIzol (Thermo Fisher Scientific), for a total of n=4 wild-typecontrol and n=3 Ezh2 cKO isolates. RNA was subsequently purified by phenol chloroform extraction. DNAse digestion and RNA cleanup was performed using the RNase-Free DNase set (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared according to Illumina's instructions, using a TruSeq mRNA kit.

value: Pgr(cre/+) Ezh2(fl/fl) ("Ezh2 cKO")

value: Myometrium


title: Mouse inguinal white adipose 11-1

value: NCD


title: IL-4/IL-13 L48303_M2_1_02_G12

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


title: Mouse inguinal white adipose 10-2


title: LTL418_PRE

value: Parental LTL418 patient derived xenograft line


title: LTL508_PRE

value: Parental LTL508 patient derived xenograft line


title: Mouse inguinal white adipose 10-1


title: IL-4/IL-13 L48302_M2_1_02_G11

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

value: BMDM


title: cKO_Myo_M2


title: cKO_Myo_M1


title: LTL310_CX

value: Castrated LTL310


title: LTL412_PRE

value: Parental LTL412 patient derived xenograft line


title: LTL556_PRE

value: Parental LTL556 patient derived xenograft line


title: IL-4/IL-13 L48301_M2_1_02_G10

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


title: Mouse epididymal white adipose 19-1

source_name: epididymal fat pad


title: cKO_Dec_M3

source_name: Homogenized whole tissue decidua

value: Decidua


title: Mouse inguinal white adipose 13-1


title: IL-4/IL-13 L48300_M2_1_02_G09

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


title: IL-4/IL-13 L48306_M2_1_02_G15

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


title: LTL471_PRE

value: prostate cancer tumor

value: Patient Derived Xenograft

value: Parental LTL471 patient derived xenograft line


title: cKO_Dec_M2


title: IL-4/IL-13 L48299_M2_1_02_G08

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


title: cKO_Dec_M1


title: Mouse epididymal white adipose 17-1

value: white adipose tissue


title: LTL331_PRE

value: Parental LTL331 patient derived xenograft line


title: IL-4/IL-13 L48298_M2_1_02_G07

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


title: Mouse epididymal white adipose 14-1

value: male

value: HFD


title: LTL310_PRE

value: Parental LTL310 patient derived xenograft line


title: Ctrl_Myo_M3

value: Pgr(+/+) Ezh2(fl/fl) ("Control")

value: Myometrium


title: LTL313B_PRE

value: Parental LTL313B patient derived xenograft line


title: Mouse epididymal white adipose 12-1


title: Deg_MUT_mRNA_2

city: Poughkeepsie

first: Colin Echeverría

last: Aitken

state: NY

address: 124 Raymond Ave., Box 731

institute: Vassar College

description:
Mutant (eIF3a/b Degron) Total mRNA Replicate 2
Total mRNA collected fromeIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
mRNA

data_processing:
Basecalling with Illumina Casava 1.8 software.
3' adapter trimming with FastX-toolkit.
rRNA alignment with bowtie2 v2.2.6.0.
Transcriptome alignment with TopHat v2.1.0.
Read quantitation using custom scripts.
Analysis of reads using DESeq2.
Genome_build: sacCer3
Supplementary_files_format_and_content: .csv files containing combined accepted read counts (after alignment and filtering) for each mutant and WT control, as well as combined .csv file containing ∆TE and padj values calculated using DESeq2.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells

growth_protocol: We grew two biological replicates of each strain and its matching isogenic WT strain under permissive conditions before harvesting and adding to pre-warmed restrictive media for a duration resulting in an ~90% decrease in bulk translation (as judged by polysome:monosome ratios) and a final cell density at mid-log phase (OD600 = ~0.6).

extract_protocol:
We added cycloheximide to a final concentration of 100 µg/mL 2 min prior to harvesting by filtration through a Kontes filtration apparatus and flash freezing in liquid nitrogen with 2 mL of ribosome footprinting buffer (20 mM Tris pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 1% Triton, 100 μg/mL cycloheximide).
We generated sequencing libraries of ribosome footprints and total mRNA as previously described (Ingolia, 2010; Sen et al., 2015, 2016). Briefly, we lysed cells using a freezer mill and then prepared lysates by centrifuging 5 min at 3000 x g, collecting the supernatant and then centrifuging 12 min at >20,000 x g. We then collected the supernatant and flash-froze in 30 OD260 aliquots. We purified ribosome footprints by adding 5 µL RNase1 to one aliquot of purified lysate and incubating 60 min at 26 ºC with mixing at 700 rpm. We then added 5 µL SuperAsin (Thermo Fisher) and loaded on a 10-50% sucrose gradient and centrifuged at 40,000 rpm for 3 h and then collected the monosome peak using a gradient fractionator. We then purified RNA from purified monosomes via hot phenol extraction. We purified total mRNA from one 30 OD260 aliquot of purified lysate using the miRNeasy mini kit (Qiagen) per the vendor’s instructions and then randomly fragmented at 70 ºC for 8 min using Fragmentation Reagent (Invitrogen). We then performed subsequent steps (size selection, linker ligation, reverse transcription, circularization, rRNA subtraction, and PCR amplification) as previously described and had libraries sequenced using an Illumina HiSeq system.

treatment_protocol: We grew eIF3a/b degron cells at 25 ºC in SCRaff + Cu2+ before shifting them to pre-warmed SCRaff/Gal + BCS at 36 ºC for 90 min. We grew eIF3i DDKK at 30 ºC in SC media before shifting them to pre-warmed SC media at 37 ºC for 30 min.

value: YAJ34 cells

value: SCRaff/Gal + BCS at 36 ºC for 90 min

value: MATa trp1<delta>? leu2-3,112 ura3-52 gcn2?::hisG PGAL1-myc-UBR1::TRP1::ubr1 PCUP1H$%-UBI-R-HA-tif32td::URA3::tif32 PCUP1-UBI-R-DHFRts-HA-prt1td::URA3::prt1


title: Ctrl_Myo_M1


title: Deg_WT_mRNA_2

description:
WT (eIF3a/b Degron) Total mRNA Replicate 2
Total mRNA collected from isogenic WT control for eIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
mRNA

value: YAJ3 cells

value: MATa trp1<delta>? leu2-3,112 ura3-52 gcn2?::hisG PGAL1-myc-UBR1::TRP1::ubr1 pRS316 [URA3]


title: Deg_MUT_FT_2

description:
Mutant (eIF3a/b Degron) Ribosome Footprint Replicate 2
Ribosome-protected fragments collected fromeIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
ribosome-protected RNA

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software.
3' adapter trimming with FastX-toolkit.
rRNA alignment with bowtie2 v2.2.6.0.
Transcriptome alignment with TopHat v2.1.0.
Read quantitation using custom scripts.
Analysis of reads using DESeq2.
Genome_build: sacCer3
Supplementary_files_format_and_content: .csv files containing combined accepted read counts (after alignment and filtering) for each mutant and WT control, as well as combined .csv file containing ∆TE and padj values calculated using DESeq2.


title: IL-4/IL-13 L48296_M2_1_02_G05

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

value: BMDM


title: Ctrl_Myo_M2


title: Deg_WT_FT_2

description:
WT (eIF3a/b Degron) Ribosome Footprint Replicate 2
Ribosome-protected fragments collected from isogenic WT control for eIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
ribosome-protected RNA


title: Mouse epididymal white adipose 11-1

value: NCD


title: Ctrl_Dec_M4

value: Decidua


title: IL-4/IL-13 L48295_M2_1_02_G04

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


title: IL-4/IL-13 L48294_M2_1_02_G03

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


title: LTL313H_PRE

value: prostate cancer tumor

value: Patient Derived Xenograft

value: Parental LTL313H patient derived xenograft line


title: Ctrl_Dec_M3


title: IL-4/IL-13 L48293_M2_1_02_G02

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


title: Mouse epididymal white adipose 10-1

value: white adipose tissue

value: male


title: Deg_WT_mRNA_1

description:
WT (eIF3a/b Degron) Total mRNA Replicate 1
Total mRNA collected from isogenic WT control for eIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
mRNA


title: IL-4/IL-13 L48292_M2_1_02_G01

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


title: Deg_MUT_FT_1

description:
Mutant (eIF3a/b Degron) Ribosome Footprint Replicate 1
Ribosome-protected fragments collected fromeIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
ribosome-protected RNA


title: hepatocyte mCherry CUT&RUN rep2

description: biological replicate

data_processing:
Library strategy: CUT&RUN
RNA-seq:
RNA-seq data were mapped and quantified using Salmon (Patro et al., 2017).
Gene abundances were summarized from transcript abundances using the tximport package for R (Soneson et al., 2015).
Low expressed genes (log2 CPM≥1) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥1 and log2 false discovery rate (FDR)≤0.05 using EdgeR (Robinson et al., 2010).
Pathway analysis was performed using DAVID. Morpheus (https://software.broadinstitute.org/morpheus/) was used to visualize heatmaps.
CUT&RUN:
CUT&RUN data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by samtools (Li et al., 2009).
Peaks were called by MACS2 (Zhang et al., 2008).
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. We used the cutoffs of log2CPM≥1, log2FC≥0.5, FDR≤0.05 for IRF3-OE CUT&RUN.
For CUT&RUN track visualization, reads were processed to the bigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed bigWig files were viewed in UCSC Genome Browser (Kent et al., 2002).
ChIP-seq peak heatmaps and distribution plots were generated with the normalized bigWig files within 5kb genomic regions surrounding peaks by using deepTools (Ramirez et al., 2016).
Intersecting peaks were determined using bedtools, and peaks were assigned to genes using GenomicRanges (Lawrence et al., 2013).
Motif analysis was conducted using the MEME Suite package (Grant et al., 2011) with the HOCOMOCO database (Kulakovskiy et al., 2012).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.tsv: Tab-separated text files include raw counts.
Supplementary_files_format_and_content: *.bw: bigWig files.

source_name: Ex vivo cultured primary hepatocytes

growth_protocol: Primary hepatocytes were isolated from mice containing a constitutively active IRF3 allele (IRF3-2D) that was placed within the Rosa26 locus downstream of a lox-stop-lox cassette, allowing Cre-dependent expression. Hepatocytes were cultured in serum-free Williams' E medium.

extract_protocol:
mRNA was isolated from total RNA using the Ribo-Zero Magnetic Gold Kit, and nuclei were isolated for IRF3 CUT&RUN.
IRF3 CUT&RUN library preparation was performed using the NEB Ultra II kit, and RNA-Seq library preparation was performed using the TruSeq RNA kit.

treatment_protocol: Hepatocytes were infected with Cre- or mCherry-expressing adenovirus at an MOI of 5 for 16 hours.

value: hepatocyte

tag: perturbation

value: mCherry


title: IL-4/IL-13 L48291_M2_1_02_F24

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

tag: strain


title: IL-4/IL-13 L48297_M2_1_02_G06

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


title: Mouse epididymal white adipose 10-2

tag: Sex

value: HFD


title: Ctrl_Dec_M1

value: Pgr(+/+) Ezh2(fl/fl) ("Control")


title: Deg_WT_FT_1

description:
WT (eIF3a/b Degron) Ribosome Footprint Replicate 1
Ribosome-protected fragments collected from isogenic WT control for eIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
ribosome-protected RNA


title: Mouse epididymal white adipose 13-1

tag: age


title: Ctrl_Dec_M2

tag: tissue


title: hepatocyte mCherry CUT&RUN rep1

description: biological replicate


title: IL-4/IL-13 L48290_M2_1_02_F23

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

tag: treatment


title: DK_MUT_mRNA_2

description:
Mutant (eIF3i DDKK) Total mRNA Replicate 2
Total mRNA collected from eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
mRNA

value: H450 cells transformed with YCp-i/TIF34-D207K-D224K-HA

value: 37 ºC for 30 min

value: MATa leu2-3,-112 ura3-52::GCN2 trp1<delta> tif34<delta> hc TIF34 URA3 transformed with YCp-i/TIF34-D207K-D224K-HA


title: DK_WT_mRNA_2

description:
WT (eIF3i DDKK) Total mRNA Replicate 2
Total mRNA collected from isogenic WT control for eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
mRNA

value: H450 cells transformed with YCp-i/TIF34-HA

value: MATa leu2-3,-112 ura3-52::GCN2 trp1<delta> tif34<delta> hc TIF34 URA3 transformed with YCp-i/TIF34-HA


title: hepatocyte IRF3-2D CUT&RUN rep2

description: biological replicate

tag: cell type


title: hepatocyte IRF3-2D CUT&RUN rep1

description: biological replicate


title: IL-4/IL-13 L48289_M2_1_02_F22

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

value: BMDM


title: IL-4/IL-13 L48288_M2_1_02_F21

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


title: ZF_WT_24_Untreated_1

city: Edinburgh

first: E. Elizabeth

last: Patton

address: Institute of Genetics and Cancer, Crewe Road South

institute: MRC Human Genetics Unit, University of Edinburgh

description: Library prepared with Chromium Single Cell 3’ Library & Gel Bead Kit v2

data_processing:
Illumina  software used for basecalling.
Sequence quality was checked using FastQC (version 0.11.7)
Reads from each library were aligned to the zebrafish genome (GRCz11) using the CellRanger pipeline (v.2.1.1)
Libraries were aggregated using the CellRanger pipeline (v.2.1.1, CellRanger aggregate)
The gene-cell aggregated matrix  was subjected standard quality control with the Scater package (v.1.12.2). Only cells with total features >700, log10 total counts > 3.0, and mitochondrial gene counts (%) < 10 were considered as high quality and kept
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: zf_WT_24hpf_Unt-vs-ErbBi.csv: Gene-cell aggregated matrix BEFORE filtering;comma separated (csv) file of raw counts at gene level for each cell
Supplementary_files_format_and_content: zf_WT_24hpf_Unt-vs-ErbBi_filtered.csv: Gene-cell aggregated matrix AFTER filtering; comma separated (csv) file of raw counts at gene level for each cell

organism: Danio rerio

source_name: mitfa:GFP+/crestin:mCherry+ cells sorted from untreated 24hpf-old zebrafish embryos

extract_protocol:
polyA selection
Chromium Single Cell 3’ Library & Gel Bead Kit v2
scRNA-seq, paired end reads

value: AB (WT)

value: 24 hpf

value: Untreated


title: hepatocyte mCherry mRNA rep 3

description:
biological replicate
translating mRNA

data_processing:
RNA-seq:
RNA-seq data were mapped and quantified using Salmon (Patro et al., 2017).
Gene abundances were summarized from transcript abundances using the tximport package for R (Soneson et al., 2015).
Low expressed genes (log2 CPM≥1) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥1 and log2 false discovery rate (FDR)≤0.05 using EdgeR (Robinson et al., 2010).
Pathway analysis was performed using DAVID. Morpheus (https://software.broadinstitute.org/morpheus/) was used to visualize heatmaps.
CUT&RUN:
CUT&RUN data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by samtools (Li et al., 2009).
Peaks were called by MACS2 (Zhang et al., 2008).
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. We used the cutoffs of log2CPM≥1, log2FC≥0.5, FDR≤0.05 for IRF3-OE CUT&RUN.
For CUT&RUN track visualization, reads were processed to the bigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed bigWig files were viewed in UCSC Genome Browser (Kent et al., 2002).
ChIP-seq peak heatmaps and distribution plots were generated with the normalized bigWig files within 5kb genomic regions surrounding peaks by using deepTools (Ramirez et al., 2016).
Intersecting peaks were determined using bedtools, and peaks were assigned to genes using GenomicRanges (Lawrence et al., 2013).
Motif analysis was conducted using the MEME Suite package (Grant et al., 2011) with the HOCOMOCO database (Kulakovskiy et al., 2012).
Genome_build: GRCm38
Supplementary_files_format_and_content: *.tsv: Tab-separated text files include raw counts.
Supplementary_files_format_and_content: *.bw: bigWig files.


title: DK_MUT_FT_2

description:
Mutant (eIF3i DDKK) Ribosome Footprint Replicate 2
Ribosome-protected fragments collected from eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
ribosome-protected RNA


title: Deg_MUT_mRNA_1

description:
Mutant (eIF3a/b Degron) Total mRNA Replicate 1
Total mRNA collected fromeIF3a/b Degron cells upon addition of BCS and temperature shift to 36 ºC for 90 min.
mRNA

value: YAJ34 cells

value: SCRaff/Gal + BCS at 36 ºC for 90 min

value: MATa trp1<delta>? leu2-3,112 ura3-52 gcn2?::hisG PGAL1-myc-UBR1::TRP1::ubr1 PCUP1H$%-UBI-R-HA-tif32td::URA3::tif32 PCUP1-UBI-R-DHFRts-HA-prt1td::URA3::prt1


title: IL-4/IL-13 L48287_M2_1_02_F20

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


title: hepatocyte mCherry mRNA rep 2

description:
biological replicate
translating mRNA


title: HeLa_siVIM-270_2-8

city: Tokyo

first: Yoshiaki

last: Kobayashi

address: 2-11-16 Yayoi, Bunkyo-ku

country: Japan

institute: The University of Tokyo

description: Gene expression

hyb_protocol: Cy3-labeled RNAs were fragmented using the Gene Expression Hybridization Kit (Agilent Technologies) and hybridized to a SurePrint G3 Human GE Microarray (version 3, 8 × 60 K) (Agilent Technologies) at 65ºC for 17 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (one color, scan resolution 3um, dye channel is set to Green).

data_processing: Signals were quantified by Feature Extraction version 12.1.1.1 (Agilent Techinologies).

label_protocol: cDNA and Cy3-labeled RNA were synthesized using the Quick Amp Labeling kit for One Color (Agilent Technologies).

growth_protocol: A HeLa cell suspension (0.5 × 10^5 cells/mL) was inoculated into a well of 24-well culture plate 1 day before transfection.

extract_protocol: Total RNA was purified using FastGene RNA Premium Kit (NIPPON Genetics) and the quality of the total RNA was confirmed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and a Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were transfected with 100 nM of each siRNA using Lipofectamine 2000 (Thermo Fisher Scientific). At 24 h post-transfection, cells were harvested from three wells per one sample.

tag: cell line

value: HeLa

value: cervical cancer cells

tag: gender

value: female


title: IL-4/IL-13 L48286_M2_1_02_F19

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.


title: DK_MUT_mRNA_1

description:
Mutant (eIF3i DDKK) Total mRNA Replicate 1
Total mRNA collected from eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
mRNA


title: DK_WT_mRNA_1

description:
WT (eIF3i DDKK) Total mRNA Replicate 1
Total mRNA collected from isogenic WT control for eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
mRNA


title: hepatocyte mCherry mRNA rep 1

description:
biological replicate
translating mRNA

value: hepatocyte

value: mCherry


title: IL-4/IL-13 L48285_M2_1_02_F18

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


title: hepatocyte IRF3-2D mRNA rep 2

description:
biological replicate
translating mRNA


title: hepatocyte IRF3-2D mRNA rep 3

description:
biological replicate
translating mRNA


title: HeLa_siVIM-270_6-8

description: Gene expression


title: IL-4/IL-13 L48284_M2_1_02_F17

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


title: DK_MUT_FT_1

description:
Mutant (eIF3i DDKK) Ribosome Footprint Replicate 1
Ribosome-protected fragments collected from eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
ribosome-protected RNA

value: H450 cells transformed with YCp-i/TIF34-D207K-D224K-HA


title: DK_WT_FT_1

description:
WT (eIF3i DDKK) Ribosome Footprint Replicate 1
Ribosome-protected fragments collected from isogenic WT control for eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
ribosome-protected RNA

value: 37 ºC for 30 min


title: AB9915

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: A*.txt file:  includes mRNA molecule count values for each Sample (single cell expression matrix)
metadata_q.txt:  Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: C57BL/6, TCR-transgenic OT-II, and OVA-expressing B16 cell line

growth_protocol: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
[human samples]  Samples of tumor and adjacent normal lung tissues were obtained from treatment-naive surgical specimens of NSCLC patients undergoing resection at the Mount Sinai Medical Center (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}
single cell RNA-seq for gene expression quantitation

treatment_protocol:
(1) Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
(2) mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

tag: organ

value: cervical lymph node

value: T cells

tag: selection marker

value: TCRb+

tag: time point

value: day 17 post tumor injection

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection

tag: patient id

tag: replicate id

tag: mouse age

value: 6-8 weeks


title: IL-4/IL-13 L48282_M2_1_02_F15

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

value: BMDM


title: ZF_WT_24_ErbBi_2

description: Library prepared  with Chromium Single Cell 3’ Library & Gel Bead Kit v2

source_name: mitfa:GFP+/crestin:mCherry+ cells sorted from ErbBi-treated 24hpf-old zebrafish embryos

value: AB (WT)

tag: developmental stage

value: 24 hpf

value: ErbBi


title: AB9914

value: Myeloid cells


title: HeLa_siVIM-270_2-5

description: Gene expression

value: HeLa

value: cervical cancer cells


title: IL-4/IL-13 L48281_M2_1_02_F14

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


title: genomic DNA from PBMC_HC12

type: genomic

city: Guangzhou

first: Min

last: Xiao

state: Guangdong

address: 600 Tianhe Road

country: China

institute: Third Affiliated Hospital of Sun Yat-sen University

description: Health control sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The raw intensity data were loaded to a biocondutor package “minfi”. The raw data were normalized using the subset-quantile within array normalization (SWAN) method and probes with a detection p-value >= 0.01 in at least one sample were excluded from further analysis. Methylation values, referred to as β-values, were calculated as the ratio of the methylated signal intensity to the sum of the methylated and unmethylated signals after background subtraction. The β-values were reported as a DNA methylation score ranging from 0 (completely unmethylated) to 1 (fully methylated).

label: Cy3, Cy5

source_name: Health control sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: healthy

value: PBMC


title: IL-4/IL-13 L48280_M2_1_02_F13

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

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


title: HeLa_mock

description: Gene expression

value: female

value: mock


title: DK_WT_FT_2

description:
WT (eIF3i DDKK) Ribosome Footprint Replicate 2
Ribosome-protected fragments collected from isogenic WT control for eIF3i DDKK cells upon temperature shift to 37 ºC for 30 min.
ribosome-protected RNA

value: H450 cells transformed with YCp-i/TIF34-HA

value: 37 ºC for 30 min

tag: genotype

value: MATa leu2-3,-112 ura3-52::GCN2 trp1<delta> tif34<delta> hc TIF34 URA3 transformed with YCp-i/TIF34-HA


title: AB9913

tag: strain

value: cervical lymph node

value: Doublets of T cells and myeloid cells

value: day 17 post tumor injection


title: genomic DNA from PBMC_HC10

description: Health control sample


title: IL-4/IL-13 L48278_M2_1_02_F11

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

value: BMDM


title: IL-4/IL-13 L48283_M2_1_02_F16

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


title: AB9911

value: T cells

value: TCRb+

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection

value: 6-8 weeks


title: IL-4/IL-13 L48277_M2_1_02_F10

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


title: hepatocyte IRF3-2D mRNA rep 1

description:
biological replicate
translating mRNA

value: hepatocyte

tag: perturbation


title: genomic DNA from PBMC_HC8

description: Health control sample


title: genomic DNA from PBMC_HC7

description: Health control sample


title: HeLa_siVIM-270

description: Gene expression

value: HeLa

value: cervical cancer cells


title: IL-4/IL-13 L48276_M2_1_02_F09

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


title: AB9910

value: Myeloid cells


title: IL-4/IL-13 L48275_M2_1_02_F08

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


title: AB9909


title: IL-4/IL-13 L48274_M2_1_02_F07

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


title: genomic DNA from PBMC_HC6

description: Health control sample

value: healthy

value: PBMC


title: IL-4/IL-13 L48272_M2_1_02_F05

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


title: IL-4/IL-13 L48273_M2_1_02_F06

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


title: genomic DNA from PBMC_HC5

description: Health control sample


title: genomic DNA from PBMC_HC4

description: Health control sample


title: AB9906

value: tumor draining lymph node

value: OT-II T cells


title: AB9902

value: tumor


title: genomic DNA from PBMC_HC3

description: Health control sample


title: IL-4/IL-13 L48279_M2_1_02_F12

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


title: genomic DNA from PBMC_HC11

description: Health control sample


title: genomic DNA from PBMC_HC9

description: Health control sample


title: AB9912

value: cervical lymph node


title: genomic DNA from PBMC_HC2

description: Health control sample


title: IL-4/IL-13 L48271_M2_1_02_F04

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


title: genomic DNA from PBMC_HC1

description: Health control sample


title: AB9901


title: AB9900


title: IL-4/IL-13 L48270_M2_1_02_F03

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


title: IL-4/IL-13 L48269_M2_1_02_F02

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


title: AB9908


title: genomic DNA from PBMC_AS11

description: AS patients sample

source_name: AS patients sample

value: ankylosing spondylitis


title: AB9907

value: day 17 post tumor injection


title: AB9899

value: Doublets of T cells and myeloid cells


title: IL-4/IL-13 L48267_M2_1_02_E24

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

value: BMDM


title: AB9897


title: genomic DNA from PBMC_AS10

description: AS patients sample


title: IL-4/IL-13 L48268_M2_1_02_F01

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


title: genomic DNA from PBMC_AS12

description: AS patients sample


title: IL-4/IL-13 L48265_M2_1_02_E22

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


title: AB9896

value: T cells

value: TCRb+


title: AB9895

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection

value: 6-8 weeks


title: genomic DNA from PBMC_AS9

description: AS patients sample


title: genomic DNA from PBMC_AS8

description: AS patients sample


title: IL-4/IL-13 L48264_M2_1_02_E21

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


title: AB9894


title: genomic DNA from PBMC_AS7

description: AS patients sample


title: AB9893

value: in vitro

tag: co-culture conditions

value: B16-OVA + OT-II T cells + B6 DC co-culture

value: 20 hours


title: IL-4/IL-13 L48263_M2_1_02_E20

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


title: AB9898


title: IL-4/IL-13 L48262_M2_1_02_E19

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


title: genomic DNA from PBMC_AS6

description: AS patients sample


title: AB9890

value: OT-II T mono-culture


title: AB9892


title: IL-4/IL-13 L48261_M2_1_02_E18

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


title: genomic DNA from PBMC_AS1

description: AS patients sample

value: PBMC


title: genomic DNA from PBMC_AS4

description: AS patients sample


title: genomic DNA from PBMC_AS5

description: AS patients sample


title: genomic DNA from PBMC_AS2

description: AS patients sample


title: AB9888

value: B16-OVA + OT-II T cells co-culture


title: IL-4/IL-13 L48259_M2_1_02_E16

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


title: genomic DNA from PBMC_AS3

description: AS patients sample


title: IL-4/IL-13 L48257_M2_1_02_E14

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


title: AB9887


title: IL-4/IL-13 L48256_M2_1_02_E13

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


title: IL-4/IL-13 L48266_M2_1_02_E23

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


title: AB9891


title: IL-4/IL-13 L48260_M2_1_02_E17

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


title: Mouse epididymal white adipose 18-1

tag: tissue

value: white adipose tissue

tag: mouse strain

tag: Sex

value: male

tag: age

tag: diet

value: NCD


title: AB9884

tag: organ

tag: cell type


title: AB9889

tag: selection marker

tag: time point


title: IL-4/IL-13 L48254_M2_1_02_E11

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

tag: treatment


title: AB9885

value: Myeloid cells

tag: patient id

tag: replicate id

tag: mouse age


title: AB9886


title: AB9883


title: IL-4/IL-13 L48253_M2_1_02_E10

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


title: Control 4

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR aligner (version 2.4.2a)68 with modified parameter settings (--twopassMode=Basic) and UCSC knownGene annotation
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values were calculated using custom scripts
Differential expression analysis was performed using the R Bioconductor package DESeq2
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bam files were generated using STAR
Supplementary_files_format_and_content: text files were generated with HTSeq-count

source_name: Heart

extract_protocol:
Left ventricular myocardial tissue was snap frozen in liquid nitrogen and RNA was isolated using the AllPrep RNA Kit (Qiagen).
For library preparation, 1 ug of RNA was poly(A) selected, fragmented and reverse transcribed with the Elute, Prime, Fragment Mix (Illumina). A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Prep Guide (Illumina).

tag: disease

value: Ventricular septal defect (VSD)

value: left ventricular myocardium

tag: genotype


title: Control 3


title: NS-CM 5

value: Cardiomyopathy associated with Noonan syndrome (NS-CM)


title: AB9882

tag: strain

value: Doublets of T cells and myeloid cells


title: IL-4/IL-13 L48252_M2_1_02_E09

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

value: BMDM


title: HCM 2

value: Hypertrophic cardiomyopathy (HCM)


title: IL-4/IL-13 L48251_M2_1_02_E08

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


title: AB9881

tag: co-culture conditions

value: 6-8 weeks


title: Control 2

tag: tissue


title: IL-4/IL-13 L48250_M2_1_02_E07

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


title: Control 1


title: IL-4/IL-13 L48249_M2_1_02_E06

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


title: IL-4/IL-13 L48248_M2_1_02_E05

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


title: NS-CM 4


title: NS-CM 3

value: 1 y


title: IL-4/IL-13 L48247_M2_1_02_E04

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


title: AB9880

value: in vitro

value: T cells

value: TCRb+

value: B16-OVA + OT-II T cells + B6 DC co-culture


title: AB9878

value: 20 hours


title: AB9877

value: tumor

value: OT-II T cells

value: day 10 post tumor injection

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection


title: NS-CM 2


title: IL-4/IL-13 L48246_M2_1_02_E03

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


title: Wilms tumor (array)

city: Valencia

first: Jaime

last: Font de Mora Sain

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Oncology

country: Spain

institute: Instituto de Investigación Sanitaria La Fe

description: Hybridized to CytoScan HD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: Biotin

source_name: Wilms tumor A6130

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Wilms tumor was obtained at surgery from patient.

extract_protocol: Genomic DNA was extracted from pathologist supervised Wilms tumor sample using standard proteinase K and phenol-chloroform extraction protocol. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Primary Wilms tumor

value: de novo germline mutation in CTCF


title: IL-4/IL-13 L48245_M2_1_02_E02

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


title: NS-CM 1

value: Cardiomyopathy associated with Noonan syndrome (NS-CM)

value: left ventricular myocardium


title: AB9875

value: cervical lymph node


title: Neuron_6

first: Songlei

last: Liu

address: 77 Avenue Louis Pasteur

institute: Harvard University

description:
iNeuron with iEndo PGP1 2D co-culture - replicate 2
Neuron.Endo

data_processing:
A human genome reference index was built by Salmon 1.4.0 using genome primary assembly ( https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/GRCh38.primary_assembly.genome.fa.gz) and annotation file (https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.primary_assembly.annotation.gtf.gz) from GENCODE.
Read alignment and quantification were performed using salmon quant -i $transcriptome \  -p $cores \  -l A \  -1 $R1 \  -2 $R2 \  -o $salmon_out \  --seqBias \  --numBootstraps 30 \  --validateMappings \  --useVBOpt
Genome_build: GRCh38 GENCODE release 38
Supplementary_files_format_and_content: quant.sf text file

source_name: PGP1 iPSC

extract_protocol:
RNA extraction was performed utilizing the Ambion PureLink RNA mini kit. Extracted RNA samples were validating utilizing an Agilent 2200 TapeStation for RIN score quantification with all samples utilized validated to be above 8.7.
Library preparation was performed utilizing SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara, #634894) per manufacture's instructions. Library QC and Sequencing was performed by Harvard Biopolymers Facility.
Stranded poly(A) RNA-seq

value: Brain

value: Neuron

tag: growth protocol

value: iNeuron with iEndo PGP1 2D co-culture


title: Neuron_8

description:
iNeuron with WT PGP1 2D co-culture - replicate 3
Neuron.WT

value: iNeuron with WT PGP1 2D co-culture


title: Neuron_9

description:
iNeuron with iEndo PGP1 2D co-culture - replicate 3
Neuron.Endo


title: Neuron_4

description:
iNeuron cell line 2D culture - replicate 2
Neuron

value: iNeuron cell line 2D culture


title: Neuron_7

description:
iNeuron cell line 2D culture - replicate 3
Neuron


title: Neuron_11

description:
iNeuron with WT PGP1 2D co-culture - replicate 4
Neuron.WT


title: IL-4/IL-13 L48258_M2_1_02_E15

first: Assa

address: Am Klopferspitz 18

institute: Max-Planck-Institute for biochemistry

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

value: BMDM


title: AB9879

value: in vitro

value: T cells

value: B16-OVA + OT-II T cells + B6 DC co-culture

value: 6-8 weeks


title: IL-4/IL-13 L48244_M2_1_02_E01

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


title: Neuron_10

description:
iNeuron cell line 2D culture - replicate 4
Neuron


title: Neuron_3

description:
iNeuron with iEndo PGP1 2D co-culture - replicate 1
Neuron.Endo


title: Neuron_2

description:
iNeuron with WT PGP1 2D co-culture - replicate 1
Neuron.WT


title: AB9873

value: OT-II T cells

value: day 10 post tumor injection


title: NuTxMet_untreated_control [NuTxMet 525]

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description: untreated

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
creation of a homo sapiens/mus musculus multi-species reference using the cellranger function mired: mired -genome=hg38 --fasta=/ref/cellranger/hg38/refdata-gex-GRCh38-2020-A/fasta/genome.fa --genes=/ref/cellranger/hg38/refdata-gex-GRCh38-2020-A/genes/genes.gtf \  --genome=mm10 --fasta=/ref/cellranger/mm10/refdata-gex-mm10-2020-A/fasta/genome.fa --genes=/ref/cellranger/mm10/refdata-gex-mm10-2020-A/genes/genes.gtf
alignment of sequences using STAR against human/mouse multi-species reference --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos. Only counts of reads that were aligned against Hg38 were considered for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Mouse xenograft tumors were generated by a single subcutaneous injection  417 of 50 μl growth factor reduced matrigel (Thermo Scientific) containing 0.5 x 106 cells onto the hind limb of 418 immunodeficient NMRI nude mice with subsequent incubation for 3-5 days before tumor volumes of 419 approximately 100 mm3 were reached and treatments were started.

extract_protocol:
RNA of tumor explants was extracted using Trizol  36 reagent (Thermo Scientific).
RNA libraries were prepared for sequencing using the Lexogen Quantseq 3'-sequencing kit

treatment_protocol: Mice were randomized in different 420 treatment groups, and irradiation was applied under isoflurane (2-3%) anesthesia in daily fractions of 2 Gy 421 in 5 mm tissue depth using a collimated beam (17 × 22 mm2) with an RS320 X-ray cabinet (X-Strahl, 422 300 kV, 10 mA, 0.5 mm Cu-filter, ∼1.53 Gy/min) 53. Metformin was administered intraperitoneally at 423 250 μg/g in 100-150 μl PBS at the indicated time points. PBS injection served as vehicle control.

value: head and neck cells


title: AB9876

value: TCRb+

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection


title: Neuron_1

description:
iNeuron cell line 2D culture - replicate 1
Neuron


title: NuTxMet_XRT_only [NuTxMet 523]

description: XRT


title: Neuron_12

description:
iNeuron with iEndo PGP1 2D co-culture - replicate 4
Neuron.Endo


title: AB9871

value: Myeloid cells


title: IL-4/IL-13 L48242_M2_1_02_D23

last: Yeroslaviz

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


title: HCM 1

value: Hypertrophic cardiomyopathy (HCM)

value: left ventricular myocardium


title: IL-4/IL-13 L48240_M2_1_02_D21

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


title: AB9869

value: cervical lymph node

value: Doublets of T cells and myeloid cells


title: Endo_11

description:
iEndo with WT PGP1 2D co-culture - replicate 4
Endo.WT

value: Vascular

value: Endothelium

value: iEndo with WT PGP1 2D co-culture


title: IL-4/IL-13 L48238_M2_1_02_D19

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

value: BMDM


title: AB9870

value: T cells


title: Endo_12

description:
iEndo with iNeuron PGP1 2D co-culture - replicate 4
Endo.Neuron

value: iEndo with iNeuron PGP1 2D co-culture


title: IL-4/IL-13 L48239_M2_1_02_D20

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


title: NuTxMet_XRT_only [NuTxMet 524]

description: Met


title: NuTxMet_XRT_plus_Metformin [NuTxMet 521]


title: AB9868

value: 6-8 weeks


title: Endo_9

description:
iEndo with iNeuron PGP1 2D co-culture - replicate 3
Endo.Neuron


title: NuTxMet_XRT_plus_Metformin [NuTxMet 522]


title: Endo_10

description:
iEndo cell line 2D culture - replicate 4
Endo

value: iEndo cell line 2D culture


title: NuTxMet_untreated_control [NuTxMet 519]

description: untreated


title: AB9872

value: tumor

value: OT-II T cells

value: day 10 post tumor injection


title: IL-4/IL-13 L48237_M2_1_02_D18

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


title: AB9867

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection


title: NuTxMet_untreated_control [NuTxMet 520]

description: untreated

value: head and neck cells


title: Endo_8

description:
iEndo with WT PGP1 2D co-culture - replicate 3
Endo.WT


title: IL-4/IL-13 L48236_M2_1_02_D17

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


title: AB9866

value: TCRb+


title: NuTxMet_untreated_control [NuTxMet 518]

description: untreated


title: IL-4/IL-13 L48243_M2_1_02_D24

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


title: Endo_7

description:
iEndo cell line 2D culture - replicate 3
Endo


title: IL-4/IL-13 L48235_M2_1_02_D16

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


title: NuTxMet_XRT_only [NuTxMet 516]

description: XRT


title: IL-4/IL-13 L48234_M2_1_02_D15

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


title: AB9865


title: NuTxMet_XRT_only [NuTxMet 517]

description: XRT


title: Endo_6

description:
iEndo with iNeuron PGP1 2D co-culture - replicate 2
Endo.Neuron


title: Endo_5

description:
iEndo with WT PGP1 2D co-culture - replicate 2
Endo.WT


title: NuTxMet_XRT_only [NuTxMet 515]

description: XRT


title: AB9864


title: IL-4/IL-13 L48232_M2_1_02_D13

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


title: AB9863

value: tumor draining lymph node

value: Myeloid cells


title: IL-4/IL-13 L48233_M2_1_02_D14

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


title: IL-4/IL-13 L48231_M2_1_02_D12

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


title: NuTxMet_XRT_only [NuTxMet 513]

description: XRT


title: Endo_3

description:
iEndo with iNeuron PGP1 2D co-culture - replicate 1
Endo.Neuron


title: AB9862


title: Endo_2

description:
iEndo with WT PGP1 2D co-culture - replicate 1
Endo.WT


title: NuTxMet_untreated_control [NuTxMet 511]

description: untreated


title: IL-4/IL-13 L48230_M2_1_02_D11

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


title: AB9861

value: Doublets of T cells and myeloid cells


title: Endo_4

description:
iEndo cell line 2D culture - replicate 2
Endo

value: Vascular


title: NuTxMet_untreated_control [NuTxMet 512]

description: untreated


title: AB9860


title: Endo_1

description:
iEndo cell line 2D culture - replicate 1
Endo

value: Endothelium


title: AB9859


title: NuTxMet_XRT_only [NuTxMet 510]

description: Met


title: IL-4/IL-13 L48229_M2_1_02_D10

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


title: NuTxMet_XRT_only [NuTxMet 509]

description: Met


title: CSS2_B2

description: Multi-Core Shell Organoid - Replicate 2, Batch 2

data_processing:
Cellranger 5.0.0 was used for generating the processed files
This step was performed by the Bauer Core Facility at Harvard University
Each sample was aligned individually with the following code
#!/bin/bash
#SBATCH --time=4-18:00:00
#SBATCH --nodes=1
#SBATCH --mem=0
#SBATCH --partition=bos-info_priority
#SBATCH --job-name=count_10x.210120_A00794_0355_BHM3L3DSXY_CSS1_B1
#SBATCH --output=log/count_10x.CSS1_B1-%j.out
#SBATCH --error=log/count_10x.CSS1_B1-%j.err
#SBATCH --exclusive
#SBATCH --chdir=/n/boslfs02/LABS/informatics/Lab/sequencing/analysis/210120_A00794_0355_BHM3L3DSXY
#SBATCH --nice=2147483645
ulimit -u $(ulimit -Hu)
exit_code=0
mkdir -p /sequencing/analysis/210120_A00794_0355_BHM3L3DSXY/count/CSS1_B1
find /scratch -maxdepth 1 -name 'count_*' -user $(id -un) -exec rm -rf {} +
mkdir -p /scratch/count_210120_A00794_0355_BHM3L3DSXY_CSS1_B1_$SLURM_JOB_ID
cd /scratch/count_210120_A00794_0355_BHM3L3DSXY_CSS1_B1_$SLURM_JOB_ID
echo '{ "SC_RNA_COUNTER_CS.SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT": { "chunk.mem_gb": 64 } }' > count-overrides.json
env time -v cellranger count --project=SC_organoids_2021_01_06 --id=CSS1_B1 --transcriptome=/ref/refdata-gex-GRCh38-2020-A --sample=CSS1_B1 --overrides=count-overrides.json --fastqs=/sequencing/analysis/210120_A00794_0355_BHM3L3DSXY/fastq --localmem=$((9*$(ulimit -m)/10000000)) --localcores=$SLURM_JOB_CPUS_PER_NODE || exit_code=$?
env time -v cp -Rp CSS1_B1/*.mri.tgz CSS1_B1/outs /sequencing/analysis/210120_A00794_0355_BHM3L3DSXY/count/CSS1_B1/ || exit_code=$((exit_code | $?))
rm -rf /scratch/count_210120_A00794_0355_BHM3L3DSXY_CSS1_B1_$SLURM_JOB_ID
exit $exit_code
Genome_build: gencode.v32.primary_assembly.annotation (annotation gtf)
Supplementary_files_format_and_content: .h5 files that contains cell barcode, UMI and gene count information

extract_protocol:
WT iPSC, Mixed, and Multicore-shell cortical organoids were cultured using the previously described methods until day 25. Dissociation was performed using a previously described protocol (Velasco, S. et al. Nature, 2019).  Cell encapsulation (GEM generation) was performed using the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, PN-1000127) and accompanying Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.0 (10x Genomics, PN-1000128) on the 10x Chromium Controller (10x Genomics, PN-1000202).
Post GEM-RT Cleanup & cDNA Amplification was performed using the recommended protocols. cDNA QC was performed on the Qiagen Qubit 3.0 platform using the Qubit dsDNA HS Assay Kit (Thermofischer, Q32854), traces are provided in the supplemental. Quantification was performed using the Agilent High Sensitivity DNA Analysis Kit (Agilent, 5067-4626) on the Agilent 2100 Bioanalyzer Instrument (Agilent, G2939BA); traces are provided in the supplemental.  3’ Gene Expression Library Construction was performed, and samples were indexed using the Single Index Kit T Set A (10x Genomics, PN-1000213) using sample barcodes E2 – H3. Indexed samples were further validated for quality using Qubit and Bioanalyzer Kits and normalization of concentration was performed using the manual’s suggested methodology prior to pooling for submission for sequencing.
Stranded poly(A) RNA-seq

value: Brain Organoid

value: Brain

tag: organoid type

value: Multi-Core Shell Organoid


title: IL-4/IL-13 L48228_M2_1_02_D09

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

value: BMDM


title: AB9858

value: T cells

value: 6-8 weeks


title: IL-4/IL-13 L48227_M2_1_02_D08

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


title: CSS1_B2

description: Multi-Core Shell Organoid - Replicate 1, Batch 2


title: NuTxMet_XRT_plus_Metformin [NuTxMet 508]


title: AB9857


title: Mix2_B2

description: Mixed Organoid - Replicate 2, Batch 2

value: Mixed Organoid


title: IL-4/IL-13 L48226_M2_1_02_D07

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


title: AB9856

value: OT-II T cells


title: Mix1_B2

description: Mixed Organoid - Replicate 1, Batch 2


title: IL-4/IL-13 L48225_M2_1_02_D06

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


title: AB9855

value: day 10 post tumor injection


title: NuTxMet_XRT_only [NuTxMet 505]

description: Met


title: WT2_B2

description: Wild Type Organoid - Replicate 2, Batch 2

value: Wild Type Organoid


title: NuTxMet_XRT_plus_Metformin [NuTxMet 507]

value: head and neck cells


title: AB9854

value: TCRb+

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection


title: WT1_B2

description: Wild Type Organoid - Replicate 1, Batch 2


title: IL-4/IL-13 L48224_M2_1_02_D05

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


title: NuTxMet_XRT_only [NuTxMet 504]

description: Met


title: IL-4/IL-13 L48223_M2_1_02_D04

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


title: AB9853

value: tumor draining lymph node


title: CSS2_B1

description: Multi-Core Shell Organoid - Replicate 2, Batch 1


title: IL-4/IL-13 L48222_M2_1_02_D03

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


title: CSS1_B1

description: Multi-Core Shell Organoid - Replicate 1, Batch 1


title: AB9852


title: AB9851

value: Myeloid cells


title: Mix2_B1

description: Mixed Organoid - Replicate 2, Batch 1


title: NuTxMet_XRT_plus_Metformin [NuTxMet 502]


title: NuTxMet_XRT_plus_Metformin [NuTxMet 501]


title: IL-4/IL-13 L48221_M2_1_02_D02

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


title: NuTxMet_XRT_plus_Metformin [NuTxMet 506]


title: AB9850


title: AB9849

value: Doublets of T cells and myeloid cells


title: IL-4/IL-13 L48218_M2_1_02_C23

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


title: WT2_B1

description: Wild Type Organoid - Replicate 2, Batch 1


title: MCF7_L12KO_noE2_ER

city: La Jolla

first: Shenghong

last: Ma

address: 2880 TORREY PINES SCENIC DR, Sanford Consortium

institute: UCSD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v2.3.5.1 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
For RNA-seq data: Transcripts per Million (TPM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
For ATAC-seq data: peaks were called using Genrich version 0.6.1 with the following setting: -j -y -r -e chrM -v.Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
For ChIP-seq data: peaks were called using MACS3 version 3.0.0a6 with the following setting: -g hs -f BAM. Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
For CUT&Tag-seq data: peaks were called using SEACR version 1.3 with the following setting: -norm strigent. Bigwig file generated using bamCoverage version 3.3.2 with the following setting:  —binSize 20 —normalizeUsing BPM —smoothLength 60 —centerReads. Heatmap, genomic tracker and scatter map generated using EaSeq version 1.111.
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: For ATAC-seq, ChIP-seq and CUT&Tag-seq: bigwid files for display in hg38 genome browser track

source_name: MCF7 breast cancer cell lines

growth_protocol: DMEM with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The ChIP-seq DNA library construction was performed using the Rapid DNA Lib Prep Kit (ABclonal, #RK20200)

value: breast cancer cell line

tag: passage

tag: origin tissue

value: breast

tag: genotype/variation

value: LATS1 and LATS2 double knock-out

tag: chip antibody

value: anti-ER-alpha

tag: chip antibody vendor

value: Cell Signaling Technology

tag: chip antibody cat. #

tag: chip antibody lot/batch #

value: E2 starvation for 3 days


title: WT1_B1

description: Wild Type Organoid - Replicate 1, Batch 1

value: Brain Organoid

tag: cell type

value: Brain


title: Mix1_B1

description: Mixed Organoid - Replicate 1, Batch 1

value: Mixed Organoid


title: IL-4/IL-13 L48219_M2_1_02_C24

city: Martinsried

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

value: BMDM

tag: treatment


title: MCF7_L12KO_E2_ER

value: E2 starvation for 3 days, then treat with 100 nM E2 for 2 hours


title: MCF7_WT_E2_ER

value: wild type


title: Neuron_5

description:
iNeuron with WT PGP1 2D co-culture - replicate 2
Neuron.WT

value: Neuron

value: iNeuron with WT PGP1 2D co-culture


title: NuTxMet_XRT_only [NuTxMet 503]

description: Met

value: head and neck cells


title: IL-4/IL-13 L48217_M2_1_02_C22

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


title: AB9589

tag: organ

value: tumor draining lymph node

value: Myeloid cells

tag: selection marker

tag: time point

value: day 10 post tumor injection

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection

tag: patient id

tag: replicate id

tag: mouse age

value: 6-8 weeks


title: MCF7_WT_noE2_ER

value: breast cancer cell line

value: breast

value: anti-ER-alpha


title: Sample 201

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 9 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: metadata_q.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

growth_protocol:
Human samples: Samples of tumor and adjacent normal lung tissues were obtained from treatment-naive surgical specimens of NSCLC patients undergoing resection at the Mount Sinai Medical Center (New York, NY) after obtaining informed consent in accordance with a protocol reviewed and approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai
Mouse samples: 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were euthanized and auricular LNs were disected. Lymph nodes were digested in IMDM containing 100µg/mL Liberase TL and 100µg/mL DNase I for 20 minutes at 37°C. In the last 5 minutes of incubation, EDTA was added at a final concentration of 10mM. Cells were collected, filtered through a 70µm cell strainer, washed with IMDM and maintained strictly at 4°C. Cells were stained with FACS antibodies, then sorted into 384-well plates
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol:
treatment protocol (1): Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
treatment protocol (2): mice were treated with depleting or neutralizing antibodies or their isotype controls: Anti-NK1.1 (200 µg/dose), anti-IFNγ (500 µg/dose), Mouse IgG2a Isotype control and Rat IgG1 Isotype control were injected 24 hours prior to immunization and on the day of immunization

value: lung normal

value: T cells

tag: co-culture conditions


title: AB9588

tag: strain

value: TCRb+


title: IL-4/IL-13 L48216_M2_1_02_C21

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

value: BMDM


title: AB9587

value: Doublets of T cells and myeloid cells


title: Sample 200


title: IL-4/IL-13 L48220_M2_1_02_D01

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


title: IL-4/IL-13 L48215_M2_1_02_C20

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


title: AB9586

value: tumor

value: OT-II T cells


title: Sample 199


title: IL-4/IL-13 L48214_M2_1_02_C19

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


title: C0014G1

city: Paris

first: Jean-David

last: Bouaziz

address: Hôpital Saint-Louis 1, avenue Claude Vellefaux

department: Skin Research Center Service de Dermatologie

country: France

institute: INSERM U976

description: Control

data_processing:
Fastq files produced after RNA-seq sequencing have been processed by in-house CNRGH (Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France ) tools in order to assess quality of raw and genomic-aligned nucleotides
Quality control was performed on a random selection of 2 x 10 million reads, including the following steps: removal of adapters and poor-quality sequences to evaluate the % of usable reads (use of trimmomatic); alignment on the reference genome (Hisat2) as well as on the transcriptome and rRNAs (Bowtie2)
Use of rseqc and picardTools to evaluate the % of mapping on the genome and transcriptome, the % of duplicate sequences, the % of rRNA and the total number of usable sequences
Fastq files were aligned against the human GRCh38 genome assembly using STAR-2.6.0 according to author’s procedure (Dobin et al. 2016)
Genome_build: human GRCh38 genome assembly
Supplementary_files_format_and_content: table count

source_name: Skin biopsy

extract_protocol:
RNeasy Plus Universal Kit (Qiagen, Hilden, Germany)
Libraries have been prepared using the "TruSeq stranded mRNA” Kit from Illumina

tag: tissue

value: skin

tag: sample type (cgvhd or healthy)

value: Control

tag: age

tag: gender

value: F

tag: cohort

value: Local cohort - Saint-Louis Hospital


title: AB9874

value: cervical lymph node

value: day 10 post tumor injection


title: IL-4/IL-13 L48213_M2_1_02_C18

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

source_name: Bone marrow


title: AB9584

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection

value: 6-8 weeks


title: Sample 196

value: lung tumor


title: C0014FF

description: Control


title: IL-4/IL-13 L48211_M2_1_02_C16

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


title: Sample 197


title: Sample 198

value: doublets of T cells and myeloid cells


title: C0014FH

description: Control


title: C0014FE

description: Control

value: M


title: AB9585


title: IL-4/IL-13 L48210_M2_1_02_C15

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


title: AB9583

value: tumor draining lymph node

value: Myeloid cells


title: AB9582

value: T cells

value: TCRb+


title: AB9581

value: Doublets of T cells and myeloid cells


title: IL-4/IL-13 L48208_M2_1_02_C13

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

value: BMDM


title: IL-4/IL-13 L48255_M2_1_02_E12

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


title: C0014FY

description: Morphea

value: skin

value: morphea lesion of cGVHD


title: Sample 192


title: Sample 195


title: Sample 194


title: IL-4/IL-13 L48209_M2_1_02_C14

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


title: Sample 193


title: IL-4/IL-13 L48212_M2_1_02_C17

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


title: AB9580

value: OT-II T cells


title: AB9579


title: AB9578


title: IL-4/IL-13 L48207_M2_1_02_C12

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


title: C0014FW

description: Morphea

value: F

value: Local cohort - Saint-Louis Hospital


title: C0014FG

description: Control

value: Control


title: C0014FK

description: Control


title: IL-4/IL-13 L48205_M2_1_02_C10

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


title: IL-4/IL-13 L48204_M2_1_02_C09

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


title: C0014FX

description: Morphea


title: Sample 191


title: IL-4/IL-13 L48206_M2_1_02_C11

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


title: C0014FS

description: Morphea


title: Sample 188


title: IL-4/IL-13 L48203_M2_1_02_C08

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


title: AB9574

value: day 10 post tumor injection

value: B16-OVA subcutaneous injection; adoptive transfer of OT-II CD4+ T cells 6 days after tumor injection; OVA-vaccination 7 and 8 days after tumor injection


title: IL-4/IL-13 L48241_M2_1_02_D22

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


title: AB9577

value: 6-8 weeks


title: Sample 190

value: lung normal


title: AB9576


title: Sample 189

value: doublets of T cells and myeloid cells


title: C0014FM

description: Lichen planus

value: lichen planus lesion of cGVHD


title: AB9575

value: tumor draining lymph node


title: C0014G0

description: Lichen planus

value: M


title: IL-4/IL-13 L48201_M2_1_02_C06

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


title: C0014FQ

description: Morphea


title: C0014FZ

description: Lichen planus


title: IL-4/IL-13 L48202_M2_1_02_C07

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


title: Sample 186

value: lung tumor

value: T cells


title: C0014FV

description: Lichen planus


title: AB9572

value: TCRb+


title: AB9571

value: Doublets of T cells and myeloid cells


title: Sample 184

value: Myeloid cells


title: C0014FR

description: Lichen planus

value: skin


title: IL-4/IL-13 L48200_M2_1_02_C05

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

value: BMDM