title: ID8 Day21_1

value: tumor-associated macrophages injected with ID8

value: Day 21


title: Ctrl _shRNA 2 [9031313088_F]

status: Public on Feb 06 2019

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Melanoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell line

tag: cell type

value: melanoma

tag: genotype/variation

value: control


title: Spleen_178_NK_B

type: SRA

city: Cambridge

first: Christian

middle: Thomas

last: Covington

state: Massachusetts

address: 415 Main St.

department: Infectious Disease and Microbiome

country: USA

institute: Broad Institute

description: counts.txt

library_source: transcriptomic

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to hg19 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by gene ID) in each sample. Four samples are missing due to low read counts.

source_name: Spleen

extract_protocol:
Tissue digestion as described in STAR methods
SmartSeq2

value: natural killer cells

tag: tissue

value: Spleen


title: Spleen_201_ILC1_A

description: counts.txt


title: Spleen_178_NK_C

description: counts.txt


title: ID8 Day21_2

city: Heidelberg

first: Juan

last: Rodriguez-Vita

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: Samples were prepared and were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays according to Affymetrix specifications

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only.
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.

organism: Mus musculus

source_name: Cell sorting by flow cytometry

label_protocol: end-labelling

extract_protocol: Tumor associated macrophages were isolated from tumor bearing mice. Cells were sorted with the following sorting strategy: CD45.2+, CD19-, CD11b+, CD115+, F4/80+

tag: time point


title: naïve_1

value: peritoneal macrophages

value: Day 0


title: ID8 Day5_1

value: Day 5


title: Spleen_178_NK_A

description: counts.txt


title: Spleen_178_ILC3_B

description: counts.txt


title: ID8 Day5_2


title: Ctrl _shRNA 1 [9031313088_B]


title: Ctrl _shRNA 1 [9031313088_A]


title: Spleen_178_ILC3_C

description: counts.txt


title: Ctrl _shRNA 2 [9031313088_E]


title: Ctrl _shRNA 2 [9031313088_D]


title: Spleen_178_ILC1_C

description: counts.txt


title: Spleen_178_ILC1_B

description: counts.txt


title: dal80_Glu_1

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
B126T5
dal80-delta cells in glutamine-containing medium

data_processing:
Reads were mapped to the S. cerevisiae  reference genome using the version 2.0.6 of TopHat, with no mismatch in seed alignment (of size 22) anda tolerance of 3 mismatches in read length, a minimum and a maximum size for introns of 5 bp and 5kb, respectively.
Tags densities were normalized on the total number of reads uniquely mapped on ORFs.
Genome_build: Yeast saccharomyces_cerevisiae R64-1-1
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for all annotated genes, in each sample.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

extract_protocol:
Total RNA was extracted using standard hot-phenol procedure
Ribosomal RNAs were depleted from total RNA using the RiboMinus Eukaryote v2 Kit (Life Technologies). Strand-specific total RNA-Seq libraries were prepared from 125 ng of rRNA-depleted RNA using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Paired-end sequencing (2 x 50 nt) of the libraries was performed on a HiSeq 2500 sequencer.

tag: growth protocol

value: grown in  glutamine-containing medium

tag: biological replicate


title: gat1_Pro_1

description:
B126T4
gat1-delta cells in proline-containing medium

value: grown in  proline-containing medium


title: gat1_Pro_2

description:
B126T10
gat1-delta cells in proline-containing medium


title: Spleen_178_ILC3_A

description: counts.txt


title: Spleen_178_ILC1_A

description: counts.txt


title: gat1_Glu_2

description:
B126T9
gat1-delta cells in glutamine-containing medium


title: Lung_223_ILC2_B

description: counts.txt

source_name: Lung

value: Lung


title: dal80_Glu_2

description:
B126T11
dal80-delta cells in glutamine-containing medium


title: Lung_217_NK_A

description: counts.txt


title: WT_Glu_2

description:
B126T7
Wild-type cells in glutamine-containing medium

value: Wild-type


title: Lung_217_ILC3_B

description: counts.txt


title: WT_Glu_1

description:
B126T1
Wild-type cells in glutamine-containing medium


title: Lung_223_ILC2_A

description: counts.txt


title: Lung_217_ILC2_D

description: counts.txt


title: Lung_217_ILC3_A

description: counts.txt


title: Lung_217_ILC2_B

description: counts.txt


title: Lung_217_ILC2_A

description: counts.txt


title: Lung_217_ILC2_C

description: counts.txt


title: Jejunum_223_NK_C

description: counts.txt

source_name: Jejunum

value: Jejunum


title: prem-input

city: Badalona

first: Jeannine

last: Diesch

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Research

country: Spain

institute: Josep Carreras Leukaemia Research Institute

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the mm9 genome assembly containing one rDNA copy using bowtie with default parameters
Remove duplicate reads using picard (version 1.110) MarkDuplicates
Read coverage was determined using Bed tools package
peaks were called using SPP peak caller version 1.11
Genome_build: mm9
Supplementary_files_format_and_content: peaks called by SPP
Supplementary_files_format_and_content: narrowPeak (i.e. bed6+4)

molecule: genomic DNA

source_name: primary preB cells

growth_protocol: Eμ-Myc mice were maintained as heterozygote on a C57BL/6 background

extract_protocol:
Primary pre-B cells were purified from bone marrow of wt, prem and mal mice on the basis of high B220, low IgM and low IgD surface marker expression by flow cytometry.
Libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics Inc.)

treatment_protocol: Wt and prem mice were sacrificed at age 4-6 weeks and mal mice as soon as they established spontaneous lymphoma (age 10-20 weeks)

tag: strain

value: primary preB cells from bone-marrow

tag: genotype

value: premalignant

tag: chip antibody


title: mal-UBTF replicate 1

value: malignant

value: UBTF


title: mal-input


title: Jejunum_223_NK_B

description: counts.txt


title: Jejunum_223_NK_A

description: counts.txt


title: miRNA_Patient10 cancer tissue

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

country: China

institute: Soochow university

description:
microRNA
S10_2

hyb_protocol: not provided

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: Tissue specimen

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: patient id

value: colorectal cancer

tag: gender

value: female

tag: age


title: prem-UBTF replicate 2


title: prem-UBTF replicate 1


title: wt-input

value: wild type


title: gat1_Glu_1

description:
B126T3
gat1-delta cells in glutamine-containing medium


title: miRNA_Patient9 cancer tissue

description:
microRNA
S9_2

value: male


title: wt-UBTF replicate 2


title: miRNA_Patient8 cancer tissue

description:
microRNA
S8_2


title: Jejunum_223_ILC3_B

description: counts.txt


title: wt-UBTF replicate 1


title: mal-UBTF replicate 2


title: Jejunum_223_ILC3_A

description: counts.txt


title: miRNA_Patient5 cancer tissue

description:
microRNA
S5_2


title: miRNA_Patient4 cancer tissue

description:
microRNA
S4_2


title: miRNA_Patient6 cancer tissue

description:
microRNA
S6_2


title: miRNA_Patient7 cancer tissue

description:
microRNA
S7_2


title: Jejunum_223_ILC1_C

description: counts.txt


title: Gata2 +9.5(Ets)-/- + 5-FU, replicate 3

city: Madison

first: Emery

middle: H.

last: Bresnick

state: WI

address: 4009 WIMR 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

description:
0507J
Gata2 +9.5(Ets)-/- + 5-FU

data_processing:
Read quality was checked for each sample using FastQC v0.11.2.
High quality reads were imported into the RSEM v1.3.1 for alignment using STAT v2.6.1b as aligner. Also, read enrichment measurement was calculated for each gene using rsem-calculate-expression command.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files include expected count, TPM and FPKM values for each gene across different conditions and replicates.

source_name: bone marrow LSK cells

growth_protocol: 8-14 week old mice (C57BL/6J background).

extract_protocol:
RNA was purified using RNeasy Micro Kit (Qiagen, Cat. 74004) as per manufacturer instructions.
Libraries were prepared with the NuGEN Ovation Ultralow Library System as per manufacturer instructions.

treatment_protocol: Bone marrow from 5-FU- or PBS-treated animals (10 days post-treatment) was dissociated, resuspended in IMDM with 10% FBS and passed through 25 μm cell strainers to obtain single-cell suspensions prior to antibody staining. LSK cells (B220-,CD3-,CD4-,CD5-,CD8-,Sca1+,c-Kit+; 3,000-10,000 per replicate) were collected on a FACSAria II cell sorter (BD Bioscience).

tag: strain/background

value: Bone marrow LSK cells

tag: treatment


title: miRNA_Patient3 cancer tissue

description:
microRNA
S3_2


title: Gata2 +9.5(Ets)-/- + 5-FU, replicate 2

description:
0507F
Gata2 +9.5(Ets)-/- + 5-FU


title: Jejunum_223_ILC1_B

description: counts.txt


title: miRNA_Patient2 cancer tissue

description:
microRNA
S2_2


title: Lung_223_ILC2_C

description: counts.txt


title: Jejunum_223_ILC1_A

description: counts.txt


title: Jejunum_223_ILC3_C

description: counts.txt


title: miRNA_Patient1 cancer tissue

description:
microRNA
S1_2


title: WT + 5-FU, replicate 3

description:
715E
WT + 5-FU

value: WT


title: miRNA_Patient10 corresponding normal-appearing tissue

description:
microRNA
S10_1

value: normal-appearing colorectal tissue


title: WT (replicate 3)

city: Pozuelo de Alarcón

first: Pedro

last: Crevillén

state: Madrid

address: Campus de Montegancedo

institute: CBGP (UPM-INIA)

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GENECHIP MODEL). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

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

data_processing: GeneChip intensities were background-corrected, normalized and summarized by RMA method, using the “Affy” package from Bioconductor.

label: Biotin

organism: Arabidopsis thaliana

source_name: 20-day-old seedlings, short-days, ZT8

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip 3' IVT Express Kit).

growth_protocol: Plants were grown on agar plates under short-day conditions (8 hours light:16 dark) for 20 days at 22°C and samples were collected at the end of the light period (ZT8). Each sample contained about 250 mg of seedlings. Three biological replicates were processed.

extract_protocol: RNA was extracted using E.Z.N.A.® Plant RNA Kit – Omega Bio-tek.

tag: accession/ecotype/background

value: Seedlings

value: 20 days

tag: collection time


title: Jejunum_217_ILC3_C

description: counts.txt


title: yaf9a yaf9b (replicate 2)

value: yaf9a yaf9b mutant


title: yaf9a yaf9b (replicate 1)


title: WT + 5-FU, replicate 1

description:
509F
WT + 5-FU


title: yaf9a yaf9b (replicate 3)


title: Jejunum_217_NK_C

description: counts.txt

value: natural killer cells


title: Gata2 +9.5(Ets)-/- + 5-FU, replicate 1

description:
0507E
Gata2 +9.5(Ets)-/- + 5-FU


title: WT (replicate 1)


title: miRNA_Patient7 corresponding normal-appearing tissue

description:
microRNA
S7_1


title: Gata2 +9.5(Ets)-/- + PBS, replicate 5

description:
707E
Gata2 +9.5(Ets)-/- + PBS

value: PBS


title: WT (replicate 2)


title: Jejunum_217_ILC3_B

description: counts.txt

value: Jejunum


title: Gata2 +9.5(Ets)-/- + PBS, replicate 3

description:
0702A
Gata2 +9.5(Ets)-/- + PBS


title: Jejunum_217_NK_B

description: counts.txt


title: WT + 5-FU, replicate 2

description:
509K
WT + 5-FU


title: Jejunum_217_NK_A

description: counts.txt


title: M2PerMixedS1

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0, 10X Genomics), we used the “--force-cells 6000” option to get a “loose” upper bound on the number of cells that could be recovered
Genome_build: We used a custom assembled transcriptome based on NCBI transcriptome for M. fascicularis (annotation release 101)
Supplementary_files_format_and_content: Csv files including gene expression matrix from each macaque by different sorting methods

organism: Macaca fascicularis

source_name: Macaque 6 retina

extract_protocol:
Peripheral retinal pieces were dissected and pooled from all quadrants of the retina. Single cell suspensions were dissociated as described for fovea. Dissociated cells were stained incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102) to deplete rods. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Single cell suspensions were diluted at a concentration of 500-1800 cells/mL in 0.04% BSA/Ames for loading into 10X Chromium Single Cell A Chips.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.

treatment_protocol: Eyes from male and female macaques (Macaca fascicularis) of 3-9 years of age were generously provided by Biomere (Worcester, MA), Mikhail Papisov,Curtis Cetrulo, or Tatsuo Kawai (Massachusetts General Hospital) or purchased from Toxikon Corporation (Bedford, MA). For sequencing and labeling, macaque eyes were collected either under deep anesthesia or 15-45 min postmortem, then immediately stored as either whole globes in ice-cold Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) or as posterior poles in room temperature Ames solution following a rapid hemisection to remove the vitreous and the anterior chamber. Retinas were dissected free from the posterior pole, following hemisection in the case whole globes, and then stored in ice-cold Ames solution. Experiments described below commenced within 8 hours (depending on travel time from provider sites).

value: Peripheral retina

tag: sorting

value: CD90 enrichment + Nonenrichment


title: miRNA_Patient6 corresponding normal-appearing tissue

description:
microRNA
S6_1


title: M4Fovea3

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0, 10X Genomics), we used the “--force-cells 6000” option to get a “loose” upper bound on the number of cells that could be recovered
Genome_build: We used a custom assembled transcriptome based on NCBI transcriptome for M. fascicularis (annotation release 101)
Supplementary_files_format_and_content: Csv files including gene expression matrix from each macaque

source_name: Macaque 4 retina

extract_protocol:
0.5-1.5 mm diameter foveal tissues centering on the foveal pit were dissected out from four macaque eyes. Foveal tissues were digested with 200 units papain (Worthington, LS003126). Foveas M1 and M2 foveas were digested at 37 °C; M3 and M4 foveas were digested at 22 °C). Following digestion, retinas were and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames solution for loading into 10X Chromium Single Cell A Chips.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.

value: Fovea retina


title: M1CD90PNA

source_name: Macaque 5 retina

value: CD90 + PNA enrichment


title: M4Fovea2


title: miRNA_Patient9 corresponding normal-appearing tissue

description:
microRNA
S9_1


title: miRNA_Patient8 corresponding normal-appearing tissue

description:
microRNA
S8_1


title: M4Fovea1


title: miRNA_Patient4 corresponding normal-appearing tissue

description:
microRNA
S4_1


title: Gata2 +9.5(Ets)-/- + PBS, replicate 4

description:
707D
Gata2 +9.5(Ets)-/- + PBS

tag: cell type


title: Jejunum_217_ILC1_B

description: counts.txt


title: M3PerCD90S2

source_name: Macaque 7 retina

value: CD90 enrichment


title: Jejunum_217_ILC1_A

description: counts.txt


title: Gata2 +9.5(Ets)-/- + PBS, replicate 2

description:
0507H
Gata2 +9.5(Ets)-/- + PBS

tag: genotype/variation


title: Jejunum_217_ILC1_C

description: counts.txt

tag: tissue


title: M3PerCD90S3


title: M2PerCD90S2


title: miRNA_Patient2 corresponding normal-appearing tissue

description:
microRNA
S2_1


title: Gata2 +9.5(Ets)-/- + PBS, replicate 1

description:
0507G
Gata2 +9.5(Ets)-/- + PBS


title: miRNA_Patient1 corresponding normal-appearing tissue

description:
microRNA
S1_1


title: miRNA_Patient5 corresponding normal-appearing tissue

description:
microRNA
S5_1


title: M2PerCD90S1


title: Jejunum_216_NK_B

description: counts.txt


title: miRNA_Patient3 corresponding normal-appearing tissue

description:
microRNA
S3_1

value: female


title: WT + PBS, replicate 2

description:
0607F
WT + PBS


title: M1PerCD90S3


title: Jejunum_217_ILC3_A

description: counts.txt


title: WT + PBS, replicate 4

description:
715C
WT + PBS


title: Jejunum_216_NK_A

description: counts.txt


title: WT + PBS, replicate 3

description:
0629A
WT + PBS


title: Q11 input

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.2
Alignment: BWA v0.7.5a with options "-q 15 -n 10"
Peaks calling: R package SPP against their own control input samples to remove background signal at FRD 5%
Differentially binding sites identification: R bioconductor package Diffbind
Identified binding sites annotation: R bioconductor package Chipseeker within a window defined as 0.5kb upstream to 15kb downstream regions of transcription start sites (TSS)
Motif finding: Homer wrapper program - findMotifsGenome.pl
Genome_build: UCSC rn5
Supplementary_files_format_and_content: peak calling results from SPP are presented in bed format for each IP samples, peaks presented in Q11 samples only in compared with EV were extracted and annotated with ChIPseeker are presented in txt format

organism: Rattus norvegicus

growth_protocol: PC12 cells (rat pheochromocytoma) stable expressing pCDNA3 or alpha1ACT were cultured in F-12K medium (ATCC, Manassas) supplemented with 10% horse serum and 2.5% FBS in a 37 ºC, 5% CO2 incubator. The medium were changed every 2-3 days.

extract_protocol:
Anti-FLAG chromatin-IP (ChIP) was performed as Magna ChIP protocol described (Millipore, Billerica, MA, USA). Target cells were crosslinked by adding of 1% (v/v) of formaldehyde to a cell monolayer in growth medium followed by incubation for 10 min at 37°C. The crosslinking reaction was stopped by addition of 11% of the suspension volume of an ice cold 1 M solution of glycine.Media was removed and cells were washed twice with cold 1 × PBS buffer. The cells were spun down immediately (4 min, 2000 g, 4°C) and resuspended in cell lysis buffer (Millipore, Billerica, MA, USA, 2 × 107 cells per 500 μl) with protease inhibitor and incubated for 15 min on ice with vortex briefly every 5 min. To shear the chromatin into pieces of a few hundred base pairs, the cell lysate was sonicated using a vibra cell sonifier (Thermo Fisher Scientific, Waltham, MA, USA). The immunoprecipitation reaction was set up by combining 50 μl sonicated cell supernatant 10-fold in ChIP dilution buffer, 10 μg anti-FLAG M2 antibody and 20 μl of Protein G Magnetic beads for one ChIP reaction. This reaction was incubated overnight at 4°C. The beads were washed five times with wash buffer and TE-buffer using a magnetic particle concentrator (Millipore, Billerica, MA, USA). The bound chromatin was eluted twice by addition of 50 μl of ChIP elution buffer to the beads followed by centrifugation. Candidate DNA sequences were subsequently recovered by reverse crosslink and proteinase K treatment.
Extracted DNAs were analyzed by Agilent Bio-analyzer and submitted to University of Chicago Functional genomic facility for library preparation (TruSeq ChIP Library Preparation Kit, IP-202-1012) and sequencing (HiSEQ2500).

tag: cell line

value: neural crest origin pheochromocytoma

tag: passages

value: stable expression human alpha1ACT


title: Q11 treated with 1804 antibody


title: Q11 treated with M2 antibody


title: Jejunum_216_ILC1_C

description: counts.txt


title: Jejunum_216_NK_C

description: counts.txt


title: WT + PBS, replicate 1

description:
0607E
WT + PBS

value: Bone marrow LSK cells


title: M1PerCD90S2


title: M3PerCD90S1


title: Jejunum_216_ILC1_B

description: counts.txt


title: EV treated with 1804 antibody

value: stable expression pCDNA3 vector


title: Jejunum_216_ILC1_A

description: counts.txt


title: EV input


title: M4PerCD73S2

value: CD73 depletion


title: Jejunum_201_NK_C

description: counts.txt


title: M1PerCD90S4


title: EV treated with M2 antibody


title: Jejunum_201_NK_B

description: counts.txt


title: M4PerCD73S1


title: Jejunum_201_NK_A

description: counts.txt


title: Jejunum_201_ILC3_C

description: counts.txt


title: Q11_10D_2

description: paired-end 100bp sequenced in 3 lanes

data_processing:
Raw sequencing QC assessement: FastQC v0.11.2
Alignment: Tophat v2.0.10
Post alignement QC assessment: RSeQC and Picard tools v1.117
Gene transcripts assembly: htseq-count 0.5.4p5
Differentially expressed genes analysis: edgeR
Genome_build: NCBI rn5
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by htseq-count for each Sample.

extract_protocol:
Total  cellular  RNA from PC12 cell lines expressing pcDNA3 (EV) and expressing pcDNA3-α1ACT(α1ACT) was isolated by RNeasy mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer’s instructions at expected time points.
PC12 cell lines expressing pcDNA3 (EV) and expressing pcDNA3-α1ACT at 4 different time points (6h, 24h, 3d, 10d) were analyzed by Agilent Bio-analyzer and submitted to university of Chicago Functional genomic facility for library preparation (TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold, RS-122-2301) and sequencing on Illumina HiSeq2500 platform, with 3 biological replicates for each condition.

tag: time point

value: 10 days


title: Q11_10D_3

description: paired-end 100bp sequenced in 3 lanes


title: M2PerCD73S1


title: Q11_10D_1

description: paired-end 100bp sequenced in 3 lanes


title: WT + PBS, replicate 5

description:
715D
WT + PBS

value: WT


title: Jejunum_201_ILC3_B

description: counts.txt


title: M1PerCD73S2


title: Jejunum_201_ILC3_A

description: counts.txt


title: P_10D_1

description: paired-end 100bp sequenced in 3 lanes


title: M1PerCD73S1


title: P_10D_3

description: paired-end 100bp sequenced in 3 lanes


title: M1PerCD90S1


title: Jejunum_178_NK_B

description: counts.txt


title: Jejunum_178_NK_C

description: counts.txt


title: Q11_3D_2

description: paired-end 100bp sequenced in 3 lanes

value: 3 days


title: Q11_3D_1

description: paired-end 100bp sequenced in 3 lanes


title: M3Fovea2

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0, 10X Genomics), we used the “--force-cells 6000” option to get a “loose” upper bound on the number of cells that could be recovered
Genome_build: For the crab-eating macaque data, we used a custom assembled transcriptome based on NCBI transcriptome for M. fascicularis (annotation release 101)
Genome_build: For the human data, we used GRCh38 as reference for reads alignment
Supplementary_files_format_and_content: Csv files including gene expression matrix from each macaque/human

source_name: Macaque 3 retina

extract_protocol:
0.5-1.5 mm diameter foveal tissues centering on the foveal pit were dissected out from four macaque eyes. Foveal tissues were digested with 200 units papain (Worthington, LS003126). Foveas M1 and M2 foveas were digested at 37 °C; M3 and M4 foveas were digested at 22 °C). Following digestion, retinas were and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames solution. Peripheral retinal pieces were dissected and pooled from all quadrants of the retina. Single cell suspensions were dissociated as described for fovea. Dissociated cells were stained incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102) to deplete rods. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Single cell suspensions were diluted at a concentration of 500-1800 cells/mL in 0.04% BSA/Ames for loading into 10X Chromium Single Cell A Chips.  Human cells were dissociated and treated with anti-CD73 as above.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA)


title: Jejunum_178_ILC1_C

description: counts.txt


title: M3Fovea1


title: M2PerCD73S2


title: Q11_3D_3

description: paired-end 100bp sequenced in 3 lanes


title: M2Fovea8

source_name: Macaque 2 retina


title: P_3D_3

description: paired-end 100bp sequenced in 3 lanes


title: Jejunum_178_ILC1_B

description: counts.txt


title: P_3D_2

description: paired-end 100bp sequenced in 3 lanes


title: Jejunum_178_ILC1_A

description: counts.txt


title: M2Fovea7


title: Q11_24H_3

description: paired-end 100bp sequenced in 3 lanes

value: 24 hours


title: P_10D_2

description: paired-end 100bp sequenced in 3 lanes


title: Q11_24H_2

description: paired-end 100bp sequenced in 3 lanes


title: M3Fovea3


title: M2Fovea4


title: M2Fovea3


title: Jejunum_178_NK_A

description: counts.txt

value: natural killer cells


title: mcsf_day6_donor2

first: Brian

last: Hie

address: 77 Massachusetts Ave

institute: MIT

data_processing:
Raw sequencing data was converted to demultiplexed FASTQ files using bcl2fastq2 based on Nextera N700 indices corresponding to individual samples/arrays.
Reads were then aligned to the hg19 genome using the Galaxy portal maintained by the Broad Institute for Drop-Seq alignment using standard settings.
Individual reads were tagged according to the 12-bp barcode sequence and the 8-bp UMI contained in Read 1 of each fragment. Following alignment, reads were binned onto 12-bp cell barcodes and collapsed by their 8-bp UMI.
Digital gene expression matrices for each sample were obtained from quality filtered and mapped reads, with an automatically determined threshold for cell count.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited cell-by-gene expression matrix with digital gene expression values corresponding to unique molecule counts

source_name: CD14+ monocytes + M-CSF (6 days)

growth_protocol: Human monocytes were isolated from human buffy coats purchased from the Massachusetts General Hospital blood bank using a standard Ficoll gradient and subsequent CD14+ cell positive selection (Stemcell Technologies).

extract_protocol:
SeqWell analysis was performed as described in Gierahn et al. (Nature Methods, 2017) Briefly, at the respective timepoint, cells were detached using trypsin, spun down, and counted. Approximately 12,000 cells were loaded on each array for each timepoint and condition to minimize doublet-loading. The arrays were sealed with a semi-permeable membrane prior to cell lysis and hybridization to single-cell beads. Beads were subsequently pooled for reverse transcription and whole transcriptome amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Selected monocytes were cultured in ultra low-adherence flasks (Corning) for 0, 3, or 6 days with RPMI media (Invitrogen) supplemented with 10% FBS (Invitrogen) and 50 ng/mL human M-CSF (Biolegend).

tag: donor id

value: peripheral blood

value: CD14+ monocytes

value: 50 ng/mL human M-CSF

tag: adapter

value: CGTACTAG

tag: sequencing run


title: 697_TPA_RNA_Rep1

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG19 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best". RNA-seq reads were alined to the HG19 human genome sequence using TopHat with the default parameters.
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq ; "-z 5 -w 10" for RNA-seq.
The gene expression profiling was analyzed by HOMER software
Genome_build: HG19
Supplementary_files_format_and_content: Tiled data files (TDF) and tab-delimited text files include RPKM values for each RNA-seq samples.

source_name: pre-B leukemic 697 cells

growth_protocol: The human pre-B leukemia 697 cell line was grown in RPMI1640 (Sigma) supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Total RNAs were extrated using Rneasy Mini kit (Qiagen)
Multiplexing libraries were prepared for sequencing using Illumina standard protocol.

treatment_protocol: The cells were treated with 0.5 ug/ml TPA for 0~ 24 hr before DNA or RNA extraction.

value: pre-B leukemic cell line

value: parental 697


title: 697_Ctrl_RNA_Rep2


title: M2Fovea2

value: Fovea retina


title: Q11_24H_1

description: paired-end 100bp sequenced in 3 lanes

value: neural crest origin pheochromocytoma


title: mcsf_day6_donor1

value: TAAGGCGA


title: P_24H_3

description: paired-end 100bp sequenced in 3 lanes


title: 697_Ctrl_RNA_Rep1


title: M2Fovea1


title: 697_TPA_H1_ChIPSeq

extract_protocol:
Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with antibody.
Multiplexing libraries were prepared for sequencing using Illumina standard protocol.

value: Inducible 697 expressing FH-NAP1

tag: chip antibody

value: anti-HA (ab9110, Abcam)


title: P_24H_2

description: paired-end 100bp sequenced in 3 lanes

value: stable expression pCDNA3 vector


title: mcsf_day3_donor2

source_name: CD14+ monocytes + M-CSF (3 days)

value: TAGGCATG


title: 697_Ctrl_H1_ChIPSeq


title: M2Fovea6


title: 697_TPA_RNA_Rep2


title: mcsf_day3_donor1

value: GGACTCCT


title: M2Fovea5


title: monocyte_donor4

source_name: CD14+ monocytes

value: TCCTGAGC


title: Q11_6H_3

description: paired-end 100bp sequenced in 3 lanes

value: 6 hours

value: stable expression human alpha1ACT


title: 697_input_DNA_Rep2


title: 697_TPA_CTCF_ChIPSeq

value: anti-CTCF (17-10044, Millipore)


title: P_3D_1

description: paired-end 100bp sequenced in 3 lanes

value: 3 days


title: M1Fovea8

source_name: Macaque 1 retina


title: monocyte_donor3

value: peripheral blood

value: CD14+ monocytes

value: AGGCAGAA


title: Q11_6H_2

description: paired-end 100bp sequenced in 3 lanes


title: M1Fovea5


title: 697_Ctrl_CTCF_ChIPSeq

value: pre-B leukemic cell line

value: parental 697


title: M1Fovea6

value: Fovea retina


title: monocyte_donor2

value: CGTACTAG


title: Q11_6H_1

description: paired-end 100bp sequenced in 3 lanes

value: neural crest origin pheochromocytoma


title: M1Fovea4


title: monocyte_donor1

value: TAAGGCGA


title: 697_input_DNA_Rep1


title: M1Fovea3


title: P_6H_2

description: paired-end 100bp sequenced in 3 lanes

value: stable expression pCDNA3 vector


title: M1Fovea2


title: M1Fovea1


title: P_6H_1

description: paired-end 100bp sequenced in 3 lanes


title: Arg2_4

city: St. Louis

middle: Jesse

last: DeBosch

state: MO

address: 660 S. Euclid Ave, Box 8208

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
To enhance the biological interpretation of the large set of transcripts, grouping of genes/transcripts based on functional similarity was achieved using the R/Bioconductor packages GAGE and Pathview.
GAGE and Path-view were also used to generate pathway maps on known signaling and metabolism pathways curated by KEGG.
Genome_build: NCBI GRCm38.p2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: liver

growth_protocol: Primary murine hepatocytes were equilibrated in regular growth media (See DeBosch et al 2014 J Biol Chem) overnight following collagenase digestion.

extract_protocol:
Total RNA was extracted using Trizol Reagent precisely per manufacturer protocol.
Library preparation was performed with 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.  Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

treatment_protocol: Hepatocytes were transfected with adenovirus at approximately 10^6 viral particles per million cells for 24hr prior to RNA collection.

value: primary hepatocytes

tag: strain

value: db/db

value: liver

value: 10 weeks

value: infection with adeno-associated virus 8 (AAV8) encoding ARG2


title: Arg2_5

tag: age


title: P_24H_1

description: paired-end 100bp sequenced in 3 lanes

value: 24 hours


title: M1Fovea7


title: Arg2_1


title: Arg2_3


title: Arg2_2


title: GFPpN10

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray analysis was performed using Affymetrix Mouse Gene 2.1 arrays on two conditions GFP+ and GFP-. For each condition, total RNA was extracted from three biological replicates. Data normalization and analysis were performed using the R software (version 3.3.0) and Bioconductor packages. Arrays were normalized using the Robust Multi-Array (RMA) procedure (R package affy 1.5.2), then annotated using Mus musculus mogene21st annotation library (19.0.2).

source_name: Intestinal crypt cells

label_protocol: standard Affymetrix protocol

growth_protocol: No growth protocol was applied.

extract_protocol: Tumors/Crypt cells were dissociated and total RNA was extracted from sorted GFPpos (Notch1+ cells) and GFPneg (non-marked cells) using the Micro RNeasy Extraction kit (QIAGEN).

treatment_protocol: Mice were induced with a single dose of tamoxifen 24h prior analysis

value: Epithelial intestinal crypt cells

tag: developmental stage

value: Adults


title: GFPpN12


title: MeV-IC323-mCherry-uN genomes passaged 14x on Granta cells (L14-2nd)

city: Rochester

first: Ryan

last: Donohue

state: Minnesota

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

description:
total viral genomic RNA
derived from CsCl density gradient purification

data_processing:
Base-calling was performed using Illumina’s RTA version 1.18.54.
Raw BAM files were converted to FASTQ files (SAM-to-FASTQ v. 1.56.0), generating two FASTQ files for each data set (split by read group)
Adapter sequences were clipped (FASTX Toolkit), using Illumina adapter recognition sequences GATCGGAAGA GCACACGTCT GAACT (read 1 files) or AGATCGGAAG AGCGTCGTGT AGGGA (read 2 files), quality-trimmed (3’ ends, sliding window 1, step size 1, quality score ≥20) and quality-filtered (35-301 nt length; discard reads with N;  >95% of nucleotides with quality scores >30).
The resulting FASTQ files were aligned against a custom built genome containing sequences of the Chlorocebus sabaeus genome, hsa-45S-pre-rRNA, and MeV-IC323 using Bowtie2 (v. 2.2.6; sensitive end-to-end), generating aligned BAM files.
Count tables of BAM alignments (WIG) were generated using IGVTools (count --bases -w 1)
Genome_build: custom-built genome consisting of the Chlorocebus sabaeus genome (GCA_000409795.2), 45S-pre-rRNA (accession: NR_046235) and MeV-IC323-mCherry (or MeV-IC323-mCherry-uN) derived from IC323-EGFP (accession: LC420351.1)
Supplementary_files_format_and_content: Each custom genome has 3 parts:
Supplementary_files_format_and_content: (1) the Chlorocebus sabaeus genome (GCA_000409795.2),
Supplementary_files_format_and_content: (2) hsa-45S-pre-rRNA (accession: NR_046235.3), and
Supplementary_files_format_and_content: (3) either the MeV-IC323-mCherry-uN genome or the MeV-IC323-mCherry genome, which are ~16kB measles virus genomes.
Supplementary_files_format_and_content: The only difference between the two builds is in part (3). Both MeV-IC323 genomes are identical to the published IC323-EGFP (accession LC420351.1), except the EGFP additional transcription unit sequence was replaced with a transcription unit containing an mCherry-NLS reporter gene (MeV-IC323-mCherry-uN); or in the case of MeV-IC323-mCherry, the EGFP transcription unit sequence was replaced with the same mCherry-NLS transcription unit and also moved downstream of the H gene.
Supplementary_files_format_and_content: All downstream analyses (ie: the WIG files) were performed using reads aligned to only part (3) of the custom build.
Supplementary_files_format_and_content: *.WIG, IGVTools base count file (tab delimited, LC420351.1)

organism: Measles morbillivirus

source_name: Vero hSLAM cells

growth_protocol: Cells were cultivated in 10x 150 mm dishes per sample in D-MEM +10% FBS + 1% Penicillin/Streptomycin

extract_protocol:
Viral ribonucleocapsids were purified from cellular RNA through CsCl density gradient centrifugation. Viral genomic RNA was extracted from ribonucleocapsids with phenol:chloroform:isoamyl alcohol (25:24:1) and then ethanol-precipitated.
0.5 μg viral genomic RNA was fragmented for 7 min using the Ambion Fragmentation Reagent according to the manual. Fragmented RNA was purified by phenol:chloroform:isoamyl alcohol phase separation and precipitated using ethanol/sodium-acetate. RNA pellets were washed with 70% (w/v) ethanol, dried and resuspended in 11 μl nuclease-free water. The concentration and integrity of the RNA was assessed on an Agilent Bioanalyzer DNA 100 chip (Agilent, Santa Clara, CA). cDNA libraries were generated using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. 300 x 2 paired end sequencing of each library was performed on an Illumina MiSeq using MiSeq v2 sequencing kit and MCS v2.6.2.1 collection software. Base-calling was performed using Illumina’s RTA version 1.18.54.

treatment_protocol: Vero hSLAM cells were infected with half of the inoculum harvested from passaged MeV. To prevent premature cell lysis, 20 μg/ml of fusion inhibitory peptide (Z-D-Phe-Phe-OH) (Bachem California Inc., Torrance, CA) was added 24 h post infection and the infection was moved from 37°C to 32°C until harvest. Harvest was performed at maximum infection as detected by mCherry-NLS expression, which typically occured 72 to 96 h post infection.

tag: original inoculum

tag: passage type

value: 14 passages on Granta-519 lymphocytes


title: MeV-IC323-mCherry-uN genomes passaged 14x on H358 cells (E14-2nd)

value: 14 passages on H358 epithelial cells


title: GFPpN8


title: MeV-IC323-mCherry genomes passaged 14x on H358 cells (E14)


title: MeV-IC323-mCherry genomes passaged 7x on H358 cells (E7)

value: 7 passages on H358 epithelial cells


title: GFPmN11


title: MeV-IC323-mCherry-uN genomes passaged 1x on Granta cells (L1-2nd)

value: 1 passage on Granta-519 lymphocytes


title: GFPmN13


title: GFPmN9


title: GFPmT5

source_name: Intestinal tumor cells

value: GFP-

value: Epithelial intestinal tumor cells


title: Gfp_5

value: infection with adeno-associated virus 8 (AAV8) encoding eGFP


title: CTD1uM-24h-2

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed and stained  in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: human neuroblastoma

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip WT PLUS Reagent Kit (Affymetrix).

growth_protocol: Human neuroblastoma SH-SY5Y cells (ECACC, No. 94030304) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin at 37 °C in humidified air with 5% CO2.

extract_protocol: RNA was extracted from cells using a NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >5.0 were considered acceptable.

treatment_protocol: Semi-confluent cells were exposued to 1uM of CTD or vehicle (0.1%DMSO) dossolved in medium for 24 hours.

value: female

value: 4 years

value: bone marrow

value: SH-SY5Y cells (ECACC, No. 94030304)

tag: treatment


title: Gfp_4

value: primary hepatocytes

value: db/db

value: liver


title: MeV-IC323-mCherry genomes passaged 14x on Granta cells (L14)


title: MeV-IC323-mCherry-uN genomes passaged 1x on H358 cells (E1-2nd)

value: 1 passage on H358 epithelial cells


title: GFPpT6

tag: sorting

value: GFP+


title: Gfp_1

tag: cell type

value: 10 weeks


title: GFPmT3

value: Adults


title: GFPmT1


title: MeV-IC323-mCherry genomes passaged 7x on Granta cells and 7x on H358 cells (S14)

value: 7 passages on Granta-519 lymphocytes, and 7 passages on H358 epithelilal cells


title: CTD1uM-24h-1


title: CSF1R+ CD11c+ cells [9B]

status: Public on Feb 05 2019

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Basecalling using Illumina software
Sequencing reads were processed using the community developed next generation sequencing analysis pipeline bcbio-nextgen (blue collar bioinformatics, https://github.com/chapmanb/bcbio-nextgen). First, the Illumina adapter sequences were trimmed with cutadapt, RNA-seq reads were mapped to the mouse genome (UCSC mm10) assembly using STAR with default parameters. Post alignment quantification was performed with featureCount.
Read count data were then transformed with the variance stabilizing method from DESeq2 and differentially expressed genes were identified.
Genome_build: mm10
Supplementary_files_format_and_content: csv fiile with raw counts

source_name: Liver

extract_protocol:
In anesthetized (Ketamine/Xylazine (87.5/12.5 mg/Kg)) C57BL/6 mice, the inferior vena cava was catheterized (BD auto guard, 22G) aseptically to perfuse the liver by draining through the portal vein. A steady-state perfusion of the liver was performed first with 1x PBS (4mL/min for 5 minutes), then Liver Perfusion Medium (4mL/min for 3 minutes, Gibco), and finally Liver Digest Medium (4mL/minute for 5 minutes, Gibco) and the perfusate was collected. Digested liver was excised and a single cell suspension made and resuspended in a wash solution of 10% FBS (Sigma-Aldrich) in DMEM (Gibco). Hepatocytes were pelleted and separated from the single cell suspension above by centrifugation at 60g, 3 mins. The supernatant and the whole perfusates were combined and purified using 35% Percoll (GE Healthcare) in HBSS (Gibco). These cells were further negatively enriched by magnetic bead isolation with AutoMacs (Miltenyi Biotec). APC conjugated antibodies against CD3e, CD19, NK1.1, and Ter119 were used to negatively enrich DCs, before separating the CSF1R+ subsets within, using positive enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection

value: Plasmodium yoelii

tag: time point post infection

value: dendritic cells


title: CSF1R- CD11c+ cells [8C]

tag: tissue


title: CSF1R+ CD11c+ cells [8B]


title: CSF1R- CD11c+ cells [7C]


title: Ctrl(DMSO)-24h-2

tag: cell line

value: DMSO


title: Ctrl(DMSO)-24h-1


title: CSF1R- CD11c+ cells [6C]


title: Gfp_2

tag: genotype/variation


title: MeV-IC323-mCherry genomes passaged 7x on Granta cells (L7)

value: 7 passages on Granta-519 lymphocytes


title: CSF1R+ CD11c+ cells [6B]


title: MeV-IC323-mCherry genomes unpassaged (p1)

value: unpassaged


title: Heart_Healthy_rep3

city: Beijing

first: Wenxi

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent Fragmentation Buffer and 10x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with 37 °C Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction software to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Heart, Healthy, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male 7-week-old DSS rats were randomly classified into a HS diet group to induce HFpEF at 14-week-old, or into a low-salt (LS) diet group as shams. Diastolic dysfunction symptoms were detected by echocardiography and electrocardiograph. Hearts from different groups were washed by injecting PBS into left ventricular in vivo.

value: heart

tag: gender

value: male

tag: diet

value: low salt


title: Heart_HFpEF_rep3

source_name: Heart, HFpEF, replicate 3

value: high salt


title: Gfp_3

value: primary hepatocytes

value: infection with adeno-associated virus 8 (AAV8) encoding eGFP


title: CSF1R+ CD11c+ cells [7B]

value: liver


title: Heart_Healthy_rep1

source_name: Heart, Healthy, replicate 1


title: P0 mouse brain cortex, rep 1, RNA-seq

city: La Jolla

first: Song

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

data_processing:
Basecalls performed using bcl2fastq v2.17
Reads with less than five T bases in the last nine bases of read 1 or a poor quality score (<10) were filtered out
Cell barcode and UMI information were inferred from the first 20 bases of read 1.
STAR v2.5 was used to align cDNA reads with reference genome.
Encode ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) was used to trim and call peaks with paired-end chromatin reads as input.
Peak files were converted to Picard style interval_list file and overlapped with each mapped reads to assign reads with peak region.
Digital accessibility matrix or expression matrix was then generated with peak region or gene name as rows and cell barcodes as columns.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Tab-delimited text files include count values for cell line mixture experiment. Sparse matrix with expression and accessibility counts values and tab-delimited text files showing barcodes and gene/peak names files for mouse brain cortex experiment.

molecule: polyA RNA

source_name: mouse brain

growth_protocol: BJ and K562 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum. GM12878 cells were maintained in 1640 medium supplemented with 15% fetal bovine serum. H1 human embryonic stem cell line was maintained in feeder-free mTeSR medium and passaged with ReLeSR according to manufacturer’s instruction.

extract_protocol:
Nuclei were extracted from human cell line mixture and mouse brain cortex by 0.1% Triton-X and Nuclei EZ Prep kit respectively.
RNA libraries were prepared for sequencing using standard Dropseq protocol. ATAC-seq libraries were prepared by amplifying beads captured chromatin fragments with dropseq P5_Tso and nextera index1 primers and gel size-selected for bands in the range of 225 bp and 1000 pb.

value: brain

value: postnatal day 0

tag: type

value: Nuclei


title: P0 mouse brain cortex, rep 1, ATAC-seq


title: P0 mouse brain cortex, rep 4, RNA-seq


title: P0 mouse brain cortex, rep 4, ATAC-seq


title: P0 mouse brain cortex, rep 2, ATAC-seq


title: P0 mouse brain cortex, rep 3, ATAC-seq


title: P0 mouse brain cortex, rep 3, RNA-seq


title: P0 mouse brain cortex, rep 2, RNA-seq


title: Foxp3WT_Th1_r2

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description:
160330_160420_combined_d_s05
RNA-Seq_R23-R70_rpkm.xlsx
R67

data_processing:
base calling was carried out using CASAVA1.8.2/bcl2fastq1.8.4
ATAC-seq, alignment: PE reads were mapped to the mouse genome (mm9 assembly) using Bowtie 1.1.1.
ATAC-seq, peak calling: Redundant reads were removed using Fastquniq. Uniquely mapped reads from fragments less than 175 bp were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
RNA-seq, alignment: SE reads were mapped to the mouse genome mm9 using TopHat 2.1.0
RNA-seq, RPKM calculation RNA-seq: RPKMs were calculated using Partek6.6
ChIP-seq, alignment: SE reads were aligned to the mouse genome build mm9 with Bowtie 1.1.1
ChIP-seq, peak calling: Non-redundant and Uniquely mapped reads were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
Genome_build: mm9
Supplementary_files_format_and_content: peak bed files for ATAC-seq & ChIP-seq generated by MACS1.4.2; RPKM files for RNA-seq generated by Partek 6.6

source_name: Rag2 OT-II (WT) Th1 cells

extract_protocol:
For in vitro polarized cells, total RNA was prepared from approximately 500,000 cells using an Ambion mirVana miRNA isolation kit following the manufacturer’s protocol (ThermoFisher AM1560). For in vivo IL-9 producing cells and other subsets, total RNA was prepared from approximately 2,000-10,000 cells using a Trizol-based extraction technique following the manufacturer’s protocol (ThermoFisher 15596026).
Total RNA was subsequently processed to mRNA-seq library using NEBNext Poly(A) mRNA Magnetic Isolation followed by either Ultra II Directional RNA Library Prep kit for Illumina (NEB E7490,  E7760, E7335); or Mondrian Ovation Ultralow according to the vendor’s manual for the Illumina platform (Cat#0344; NuGEN).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2500 following the manufacturer's protocols.

value: Spleen and lymph nodes

tag: culture condition

value: in vitro culture for 72 hours with anti CD3/28 and Th1-promoting cytokines/antibodies

tag: chip antibody


title: Foxp3Sf_Th1_r2

description:
160330_160420_combined_d_s07
RNA-Seq_R23-R70_rpkm.xlsx
R69

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th1 cells

tag: strain


title: P0 mouse brain cortex, rep 5, RNA-seq

tag: developmental stage


title: GFPpT4

value: GFP+

value: Epithelial intestinal tumor cells

value: Adults


title: Heart_Healthy_rep2

source_name: Heart, Healthy, replicate 2

tag: age


title: Heart_HFpEF_rep2

source_name: Heart, HFpEF, replicate 2


title: Heart_HFpEF_rep1

source_name: Heart, HFpEF, replicate 1


title: GFPpT2


title: Foxp3Sf_Th1_RA_r2

description:
160330_160420_combined_d_s08
RNA-Seq_R23-R70_rpkm.xlsx
R70

source_name: Rag2 OT-II Foxp3Sf (Scurfy) Th1 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28, Th1-promoting cytokines/antibodies, and retinoic acid


title: Foxp3WT_Th1_RA_r2

description:
160330_160420_combined_d_s06
RNA-Seq_R23-R70_rpkm.xlsx
R68

source_name: Rag2 OT-II (WT) Th1 cells treated with retinoic acid


title: P0 mouse brain cortex, rep 5, ATAC-seq


title: Foxp3Sf_Th1_RA_r1

description:
160330_160420_combined_d_s04
RNA-Seq_R23-R70_rpkm.xlsx
R66


title: Th2-YFP_1

description:
180314_0462_s02
RNA-Seq_R01-R16_rpkm.xlsx
R02

source_name: in vivo Th2 cells

value: Lung

tag: surface marker

value: ex vivo, sensitized to papain


title: Th17-YFP_1

description:
180314_0462_s04
RNA-Seq_R01-R16_rpkm.xlsx
R04

source_name: in vivo Th17 cells


title: Th1-YFP_1

description:
180314_0462_s01
RNA-Seq_R01-R16_rpkm.xlsx
R01

source_name: in vivo Th1 cells


title: WT_iTreg_rep1

description: 150512_SN7001365_0238_AHLVWFADXX_iTreg (s07)

source_name: WT iTreg cells

extract_protocol:
cell isolation protocol: Cells from spleen and lymph nodes were obtained by mechanical disruption. Cells from lung were isolated after incubating lung fragments with 100U collagenase for 1 hour and 10 min, followed by filtering with 100 μm cell strainer.  Naïve CD4+/CD25-/CD44lo/CD62Lhi mouse T cells were isolated by cell sorting from spleen and lymph nodes to >95% purity using a FACSAria III Cell Sorter, after magnetic enrichment (StemCell Technologies or Miltenyi Biotec). In vivo Th subsets were isolated from lungs of papain-sensitized mice and further sorted as based on their surface markers.
in vitro culture protocol: All in vitro cultured cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). For in vitro Th cultures, naive T cells were plated at a density of 0.5x106/mL and activated with 10 micrograms/mL plate bound anti-CD3/ anti-CD28 for 72h in the presence of polarizing cytokines and antibodies, with or without 1 micromolar retinoic acid, to promote the differentiation of Th0 (none), Th1 (10ng/mL IL-12, 10 micrograms/mL anti-IL-4), Th2 (20 ng/mL IL-4, 10 micrograms/mL anti-IFN-gamma, Th9 (20ng/mL IL-4, 10 micrograms/mL anti-IFN-gamma, 2.5 ng/mL TGF-beta, 100 units/mL hIL-2), Th17 (10ng/mL IL-6, 10 micrograms/mL anti- IFN-gamma, 10 mg/mL anti-IL-4, 2.5ng/mL TGF-beta), iTreg (10ng/mL TGF-beta, 100 units/mL hIL-2).
Papain sensitization protocol: Mice of at least 8 weeks of age were anaesthetized with isoflurane and exposed intranasally to 25 micrograms papain (Calbiochem) in 30 microliters PBS on day 0, 3, 6 and 14. 12-16 hours after the last challenge, cells were isolated from lung
Approximately 50,000 cells were isolated, washed with cold PBS, and lysed for 10 minutes in cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After pelleting the nuclei by centrifugation (500×g for 10 min), pellets were resuspended in a 40-ul transposition reaction with 2 ul Tn5 transposase (FC-121-1030; Illumina) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37°C, 400 rpm for 30 min; DNA was then purified using a MinElute kit (QIAGEN) and amplified with 8-12 cycles of PCR based on the amplification curve. After purification using a QIAquick PCR cleanup kit (QIAGEN) and Ampure XP beads (Beckman Coulter) , samples were sequenced for 75 cycles (paired-end reads) on a Illumina HiSeq 2500.

value: in vitro culture for 72 hours with anti CD3/28 and iTreg-promoting cytokines/antibodies


title: Foxp3WT_Th1_r1

description:
160330_160420_combined_d_s01
RNA-Seq_R23-R70_rpkm.xlsx
R63


title: Th9-YFP_1

description:
180314_0462_s03
RNA-Seq_R01-R16_rpkm.xlsx
R03

source_name: in vivo Th9 cells (YFP reporter)


title: Foxp3Sf_Th1_r1

description:
160330_160420_combined_d_s03
RNA-Seq_R23-R70_rpkm.xlsx
R65


title: WT_Th9_RA_rep1

description: 150512_SN7001365_0238_AHLVWFADXX_Th9_RA (s06)

source_name: WT Th9 cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28, Th9-promoting cytokines/antibodies, and retinoic acid


title: WT_iTreg_RA_rep2

source_name: WT iTreg cells treated with retinoic acid

value: in vitro culture for 72 hours with anti CD3/28,  iTreg-promoting cytokines/antibodies, and retinoic acid


title: WT_iTreg_rep2


title: WT_Th2_rep1

description: 150512_SN7001365_0238_AHLVWFADXX_Th2  (s03)

source_name: WT Th2 cells

value: in vitro culture for 72 hours with anti CD3/28 and Th2-promoting cytokines/antibodies


title: WT_Th9_rep1

description: 150512_SN7001365_0238_AHLVWFADXX_Th9 (s05)

source_name: WT Th9 cells

value: in vitro culture for 72 hours with anti CD3/28 and Th9-promoting cytokines/antibodies


title: WT_Th2_rep2


title: RARAdCD4_Th9_RA_rep2

source_name: RARa f/f Cd4 Cre (RARA knockout) Th9 cells treated with retinoic acid


title: WT_Th9_rep2


title: RARA_flox_CD4_WT_Th9_RA_rep2

source_name: RARA f/f (WT) Th9 cells treated with retinoic acid


title: RARAdCD4_Th9_rep2

source_name: RARa f/f Cd4 Cre (RARA knockout) Th9 cells


title: RARA_flox_CD4_WT_Th9_rep1

source_name: RARA f/f (WT) Th9 cells


title: RARA_flox_CD4_WT_Th9_rep2


title: RARAdCD4_Th9_rep1


title: WT_Th9_RA_rep2


title: Foxp3WT_Th1_RA_r1

description:
160330_160420_combined_d_s02
RNA-Seq_R23-R70_rpkm.xlsx
R64


title: RARA_flox_CD4_WT_Th9_RA_rep1


title: WT_iTreg_RA_rep1

description: 150512_SN7001365_0238_AHLVWFADXX_iTreg_RA (s08)


title: WT_Th9RA_input_r2

extract_protocol:
Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody. Aliquots of genomic DNA (input) and immunoprecipitated samples were treated with proteinase K, heated to induce de-cross linking, and purified using columns (D4014, Zymo).
After recovering purified DNA, 5ng or more of DNA was used to generate libraries according to the vendor’s manual for the Illumina platform (Cat#0344; NuGEN).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq  2500 following the manufacturer's protocols.


title: WT_Th9_H3K4M1_r2

value: AbCam ab8895


title: WT_Th9_H3K4M3_r2

value: AbCam ab8580


title: WT_Th9RA_H3K4M1_r2


title: WT_Th9RA_H3K4M3_r2


title: WT_Th9_input_r2


title: Input_RARA_flox_CD4_WT_RA_Th9_2


title: Input_RARAdCD4_RA_Th9_2


title: Input_RARA_flox_CD4_WT_Th9_2


title: Input_RARAdCD4_Th9_2


title: Input_RARA_flox_CD4_WT_RA_Th9_1


title: RARAdCD4_Th9_RA_rep1


title: Input_RARAdCD4_RA_Th9_1


title: K4M3_RARA_flox_CD4_WT_RA_Th9_2


title: Input_RARAdCD4_Th9_1


title: WT_Th9RA_H3K27Ac_r2

value: AbCam ab4729


title: Input_RARA_flox_CD4_WT_Th9_1


title: K4M3_RARAdCD4_RA_Th9_2


title: K4M3_RARAdCD4_Th9_2


title: K4M3_RARA_flox_CD4_WT_Th9_1


title: K4M3_RARA_flox_CD4_WT_RA_Th9_1


title: K4M3_RARA_flox_CD4_WT_Th9_2


title: WT_Th9_H3K27Ac_r2


title: TRS_3

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
mapped to hg19 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using a edgeR v.3.12.1. The CPM values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Embryonic kidney cells

growth_protocol: HEK293 cells were routinely passaged by re-plating culture vessel (normally 1 X 107 in 150 mm dish)

extract_protocol: The RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA). RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: derivation

value: Embryonic kidney 293 cells containing SV40 T-antigen

tag: molecular subtype

value: Immunoprecipitated RNA

tag: antibody

value: TRS (Santa Cruz Biotechnology, sc-166146)


title: PRS_2

value: PRS (Santa Cruz Biotechnology, sc-393505)


title: IRS_2

value: IRS (Santa Cruz Biotechnology, sc-271826)


title: IgG_4

value: IgG (Santa Cruz Biotechnology, sc-3877)


title: TRS_4


title: IRS_1


title: PRS_1


title: AGS_sh4B_Hp_6h

city: Hsinchu city

first: Meng-Chen

last: Wu

address: 101, Section 2 Kuang Fu Road

department: Institute of Molecular and Cellular Biology

institute: National Tsing Hua University

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45°C on the Affymetrix GeneChip Human Gene 2.0 ST Array using Affymetrix hybridization kit materials. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000

data_processing: Data were processing using Transcriptome Analysis Console (TAC) Software. Robust Multi-array Average (RMA) method was used to background correction and normalization.

label_protocol: Biotin

growth_protocol: AGS cells (A) were cultured in Ham's F-12K medium contained with 10% fetal bovine serum at 37°C in 5% CO2. H. pylori 26695 (ATCC 700392) was routinely cultured on brucella agar plates contained with 2.8% Brucella powder, 0.2% β-cyclodextrin, 0.1% yeast extract, 1.5% agar, 1% isovitalex, and 10% sheep blood in a microaerophilic atmosphere (5% O2, 10% CO2, and 85% N2) at 37°C for 2 days.

extract_protocol: Total RNAs were extracted with TRIzol reagent following manufacturer's instructions.

treatment_protocol: pLKO or shKDM4B cells were uninfected or infected with H. pylori at an moi of 50 for 6 hours.

value: AGS (ATCC number:CRL-1739)

tag: cell type

value: Caucasian gastric adenocarcinoma

value: control

tag: treatment

value: infected by H. pylori at an moi of 50 for 6 h


title: K4M3_RARAdCD4_RA_Th9_1

tag: tissue

value: Spleen and lymph nodes

value: in vitro culture for 72 hours with anti CD3/28, Th9-promoting cytokines/antibodies, and retinoic acid


title: AGS_sh4B_Hp_no

tag: cell line

value: uninfected


title: IgG_3


title: K4M3_RARAdCD4_Th9_1

value: in vitro culture for 72 hours with anti CD3/28 and Th9-promoting cytokines/antibodies


title: K4M1_RARA_flox_CD4_WT_Th9_2

value: AbCam ab8895


title: K4M1_RARA_flox_CD4_WT_RA_Th9_2


title: AGS_pLKO_Hp_no

tag: genotype/variation

value: KDM4B knockdown


title: NLW36a

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: paired end scRNASeq data

data_processing:
The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
Sequence aligned using Star
Next, using the tools embedded in Picard tools (picard-tools-1.115) and the DropSeq analysis pipeline developed by the McCarroll lab (http://mccarrolllab.com/dropseq/), the fastq files were processed and the data matrix table containing the gene expression of the barcoded cells was generated. Individual cells were labeled with barcodes, and transcripts within each cell were tagged with distinct UMIs (Unique Molecular Identifiers) in order to determine absolute transcript abundance.
Genome_build: GRCh38
Supplementary_files_format_and_content: Data matrix table is in text format

source_name: Organoid

extract_protocol:
Organoids were grown on a 6 well tissue culture dish for 18-30 days, washed twice with ice-cold PBS, scraped off and transferred to 1 ml cold active protease solution (PBS, 5 mg of Bacillus Licheniformis protease [Sigma, #P5380], 5 mM CaCl2, 20 U DNAse I [Roche, #4716728001]). Organoid tissue was incubated in a 2 ml reaction tube for 10-25 min on a slow moving shaker (nutator) in a coldroom at 4°C with repeated trituration steps for 10 seconds every 5 minutes. Single cell dissociation was confirmed with a hemocytometer under the microscope. The dissociation was stopped with 1 ml ice cold PBS supplemented with 10% fetal bovine serum (FBS). Afterwards the cells were immediately pelleted at 300x g for 5 min at 4°C. Subsequently, the supernatant was discarded and cells were suspended in 2 ml PBS/10%FBS and pelleted again at 300x g for 5 min at 4°C. Then cells were suspended in PBS/0.04%BSA and pelleted again (300x g for 5 min at 4°C), suspended in 1 ml PBS/0.04%BSA, and passed through a 30 µM filter mesh (Miltenyi MACS smart strainer). Viability was then investigated with the Trypan-blue exclusion test and cell concentration was determined with a hemocytometer and adjusted to 200,000 cells/ml for Drop-seq.
Uniformly dispersed 1 nl-sized droplets were generated using self-built polydimethylsiloxane (PDMS) microfluidic co-flow devices on the basis of the AutoCAD design provided by the McCarroll group. The devices were treated with a water repellant solution (Aquapel) to create a hydrophobic channel surface. Drop-Seq runs followed closely the procedure published by Macosko et al. (Online Dropseq protocol v. 3.1 http://mccarrolllab.com/dropseq/). Barcoded beads (ChemGenes Corp., Wilmington, MA), suspended in lysis buffer, were co-flown with a single cell suspension and a droplet generation mineral oil (QX200, Bio-Rad Laboratories). Resulting droplets were collected in a 50 ml tube and immediately disrupted after adding 30 ml high-salt saline-sodium citrate buffer (6xSSC) and 1 ml perfluoro-octanol. Subsequently, captured mRNA’s were reverse transcribed for 2 hours using 2,000 U of the Maxima H Minus Reverse Transcriptase (ThermoFisher) followed by an exonuclease treatment for 45 minutes to remove unextended primers. After two washing steps with 6xSSC buffer about 70,000 remaining beads (60% of input beads) were aliquoted (5,000 beads per 50 µl reaction) and PCR-amplified (5 cycles at 65˚C and 12 cycles at 67˚C annealing temperature). Aliquots of each PCR reaction were pooled and double-purified using 0.5x volume of Agencourt AMPure XP beads (# A63881, Beckman Coulter) and finally eluted in 10 µl EB buffer. Quality and quantity of the amplified cDNAs were analyzed on a BioAnalyzer High Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). About 600 pg cDNA was fragmented and amplified (17 cycles) to generate a next-generation sequencing library by using the Nextera XT DNA sample preparation kit (Illumina).
The libraries were purified, quantified (Agilent High sensitivity DNA chip), and then sequenced (paired end 26x115 bases) on an Illumina HiSeq2500 platform (Rapid mode). Custom primer (5’-GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC-3’) was used for the first sequence read to identify all different cell barcodes und unique molecular identifier (UMI) sequences.

tag: sample type

value: whole well extract

tag: time point

value: Harvested day 19


title: NLW39

description: paired end scRNASeq data

value: singly picked organoid

value: Harvested day 20


title: K4M1_RARA_flox_CD4_WT_RA_Th9_1


title: K4M1_RARAdCD4_RA_Th9_2


title: NLW36b

description: paired end scRNASeq data


title: NLW35b

description: paired end scRNASeq data


title: AGS_pLKO_Hp_6h


title: K4M1_RARAdCD4_RA_Th9_1


title: K4M1_RARA_flox_CD4_WT_Th9_1


title: NLW34b

description: paired end scRNASeq data


title: NLW33

description: paired end scRNASeq data

value: Harvested day 21


title: K27Ac_RARA_flox_CD4_WT_Th9_2

value: AbCam ab4729


title: K4M1_RARAdCD4_Th9_2


title: K27Ac_RARA_flox_CD4_WT_RA_Th9_2


title: K4M1_RARAdCD4_Th9_1


title: K27Ac_RARAdCD4_Th9_2


title: K27Ac_RARAdCD4_RA_Th9_2


title: NLW34a

description: paired end scRNASeq data


title: K27Ac_RARA_flox_CD4_WT_Th9_1


title: K27Ac_RARAdCD4_RA_Th9_1


title: K27Ac_RARAdCD4_Th9_1


title: NLW35a

description: paired end scRNASeq data


title: RARA_flox_CD4_WT_Th9_Rep3

description:
171129_0104_s24
RNA-Seq_R17-R22_rpkm.xlsx
R20


title: RARA_flox_CD4_WT_Th9_Rep2

description:
171129_0104_s20
RNA-Seq_R17-R22_rpkm.xlsx
R19


title: RARAdCD4_Th9_Rep2

description:
171129_0104_s26
RNA-Seq_R17-R22_rpkm.xlsx
R21


title: RARAdCD4_Th9_Rep3

description:
171129_0104_s30
RNA-Seq_R17-R22_rpkm.xlsx
R22


title: K27Ac_RARA_flox_CD4_WT_RA_Th9_1


title: RARAdCD4_Th9_Rep1

description:
171129_0104_s08
RNA-Seq_R17-R22_rpkm.xlsx
R18


title: RARA_flox_CD4_WT_Th9_Rep1

description:
171129_0104_s04
RNA-Seq_R17-R22_rpkm.xlsx
R17


title: H576

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

description: Exon expression data from diffuse large B-cell lymphoma samples

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were analyzed using Partek Genomics Suite version 6.6. The .CEL-files were pre-processed using the Robust Multichip Average procedure (RMA) as implemented in the Partek software. The .CEL files were analyzed by the alternative splice analysis of variance (asANOVA) incorporated in Partek Genomics.
HuEx-1_0-st-v2.pgf
HuEx-1_0-st-v2.mpf

source_name: Primary diffuse large B-cell lymphoma tissue

label_protocol: Combination of WT Expression Kit (Ambion) and Affymetrix GeneChip WT Terminal Labeling Kit

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using a modified protocol combining Trizol reagent (Invitrogen) and mirVana microRNA isolation kit (Ambion/ThermoFisher Scientific)

treatment_protocol: The tumor sample was after removal snap frozen and stored in OCT at -80ºC. From each OCT block, a small fraction of the sample was removed using a scalpel, washed twice in PBS, and homogenized using the TissueLyser II (Qiagen).

value: Fludarabin

tag: ipi


title: Th17-YFP_2

description:
180515_0136_s09
RNA-Seq_R01-R16_rpkm.xlsx
R13

value: Lung

tag: culture condition

value: ex vivo, sensitized to papain


title: H578

value: Rituximab


title: H572

value: R-CHOP


title: H581

value: CHOP


title: Th17-YFP_3

description:
180515_0136_s12
RNA-Seq_R01-R16_rpkm.xlsx
R16

tag: chip antibody


title: Th2-YFP_3

description:
180515_0136_s11
RNA-Seq_R01-R16_rpkm.xlsx
R15

tag: strain


title: H575


title: H573


title: Th1-YFP_2

description:
180515_0136_s07
RNA-Seq_R01-R16_rpkm.xlsx
R11


title: non-Th9_GFP_2

description:
180515_0136_s06
RNA-Seq_R01-R16_rpkm.xlsx
R10

source_name: in vivo non-Th9 cells


title: H560


title: H574


title: H564


title: H563


title: H565


title: P_6H_3

description: paired-end 100bp sequenced in 3 lanes

extract_protocol:
Total  cellular  RNA from PC12 cell lines expressing pcDNA3 (EV) and expressing pcDNA3-α1ACT(α1ACT) was isolated by RNeasy mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer’s instructions at expected time points.
PC12 cell lines expressing pcDNA3 (EV) and expressing pcDNA3-α1ACT at 4 different time points (6h, 24h, 3d, 10d) were analyzed by Agilent Bio-analyzer and submitted to university of Chicago Functional genomic facility for library preparation (TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold, RS-122-2301) and sequencing on Illumina HiSeq2500 platform, with 3 biological replicates for each condition.

tag: passages

value: neural crest origin pheochromocytoma

value: 6 hours

value: stable expression pCDNA3 vector


title: H558


title: H570


title: Th1-YFP_3

description:
180515_0136_s10
RNA-Seq_R01-R16_rpkm.xlsx
R14


title: H561


title: H566


title: H557


title: H562

value: R-O


title: non-Th9_GFP_1

description:
180515_0136_s05
RNA-Seq_R01-R16_rpkm.xlsx
R09


title: human cell line mixture, RNA-seq

source_name: cell line

value: cell line mixture (BJ, GM12878, H1, K562)

tag: developmental stage

tag: type

value: Nuclei


title: H559


title: Th9_YFP_3

description:
180515_0136 & 180531_0139 combined_s04
RNA-Seq_R01-R16_rpkm.xlsx
R08

tag: surface marker


title: H569


title: Th9_GFP_2

description:
180515_0136 & 180531_0139 combined_s02
RNA-Seq_R01-R16_rpkm.xlsx
R06

source_name: in vivo Th9 cells (GFP reporter)


title: Th9_YFP_2

description:
180515_0136 & 180531_0139 combined_s03
RNA-Seq_R01-R16_rpkm.xlsx
R07


title: Th9_GFP_1

description:
180515_0136 & 180531_0139 combined_s01
RNA-Seq_R01-R16_rpkm.xlsx
R05


title: ChIPseq-Input-DNA-Th2-WT-experiment2

city: Toulouse

first: Veronique

last: Adoue

address: CHU Purpan

institute: CNRS

data_processing:
Trimming of adaptor sequences and removal of low-quality bases (−q value, <15) (Cutadapt).
BWA mem (alignment).
H3K4me1, H3K27ac and ATAC-seq peaks were detected by using the ‘broad’ option of MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include ChIP-seq peaks coordinates for each histone mark or ATAC-seq peaks.

source_name: Spleen CD4+ T cells

growth_protocol: Naïve CD4 T cells were cultured for three days in 96-well flat bottom plates coated with 10 ug/mL anti-CD3epsilon antibody (145-2C11, InVivoMabTM, BioXcell) in RPMI 1640 GlutamaxTM supplemented with 1 mM sodium pyruvate, non-essential amino acids, 10 mM HEPES, 100 units/mL penicillin, 100 ug/mL streptomycin, 50 mM 2beta-mercaptoethanol, 10% fetal calf serum (all from Thermo Fischer Scientific) and 1 ug/mL anti-CD28 antibody (37.51, InVivoMabTM, BioXcell). Th2 medium contained 50 ng/mL recombinant mouse IL-4 (R&D systems) and 10 ug/mL anti-IFNgamma neutralizing antibody (XMG1.2, InVivoMabTM, BioXcell). At day 3, the cells were re-plated in the same conditioning medium but without the anti-CD3epsilon and anti-CD28 antibodies and with 30 IU/mL recombinant IL-2 (Proleukin).

extract_protocol:
DNA purification was performed by column (MinElute PCR purification kit, Qiagen).
Libraries were prepared for sequencing using standard TruSeq Illumina protocols (ChIP-seq) and Nextera DNA Library Prep Kit Illumina (ATAC-seq).

value: Th2 T lymphocytes

tag: number of culture days

value: C57BL/6 Setdb1+/+


description: ChIPseq-Th2-Setdb1-KO-H3K27ac-experiment2-peaks.bed

value: C57BL/6 Setdb1-/-

tag: antibody

value: H3K27ac (ab4729 from Abcam; lot GR228556-1)


title: ChIPseq-Th2-WT-H3K4me1-experiment2

description: ChIPseq-Th2-WT-H3K4me1-experiment2-peaks.bed

tag: cell type

value: H3K4me1 (ab8895 from Abcam; lot GR324268-2)


title: ChIPseq-Input-DNA-Th2-Setdb1-KO-experiment2


title: KS31

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter masked fastq files were generated.
Unique molecular indices were removed using Trimmomatic (Galaxy version 0.36.3)
Read alignment using RNA STAR (Galaxy version 2.5.2b-0). BAM files were generated.
Reads were counted using HTSeq-Count set to union mode with a minimum alignment quality of 10 (Galaxy version 0.6.1galaxy3).
Genome_build: hg19
Supplementary_files_format_and_content: text file of raw read counts

source_name: full-thickness sigmoid colon tissue

extract_protocol:
Surgical specimens were transferred immediately from the operating room to the surgical pathology lab where a section of full-thickness sigmoid colon was obtained away from sites of active inflammation and stored in RNAlater. RNA was extracted from tissue samples using trizol reagent followed by purification with the Qiagen RNeasy Mini Kit.
The cDNA libraries were prepared using the NEXTflex® Rapid Directional qRNA-Seq™ Kit (24 barcodes) (BioO Scientific) as per the manufacturer’s instructions. The final product was assessed for its size distribution using the Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Six libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).

value: sigmoid colon

tag: Sex

value: Female

tag: family history of diverticular disease

value: No

tag: race

value: White, Not Hispanic

tag: smoking status

value: Former Smoker

tag: perforation/abscess

value: Yes

tag: fistula

value: Colovesical

tag: bmi

tag: age of diagnosis

tag: age of surgery

tag: surgery timing

value: Elective


title: KS26

tag: tissue

value: Current Smoker


title: KS27

value: Never Smoked


title: ChIPseq-Th2-WT-H3K27ac-experiment2

description: ChIPseq-Th2-WT-H3K27ac-experiment2-peaks.bed

tag: strain


description: ChIPseq-Th2-Setdb1-KO-H3K4me1-experiment2-peaks.bed


title: KS25


title: KS21


title: KS19


title: KS16


title: KS12

value: Male

value: Enterocolonic


title: KS24


title: Th2-YFP_2

description:
180515_0136_s08
RNA-Seq_R01-R16_rpkm.xlsx
R12

source_name: in vivo Th2 cells

value: Lung

tag: culture condition

value: ex vivo, sensitized to papain

tag: chip antibody


title: H553

description: Exon expression data from diffuse large B-cell lymphoma samples

tag: treatment

value: R-CHOP

tag: ipi


title: H552


title: KS10

value: Urgent


title: H551

value: R-CVP


title: KS08

value: sigmoid colon


title: KS07

value: Female


title: H484


title: H548


title: H479


title: H545


title: H550


title: KS23

value: No

value: Colovaginal


title: H554


title: H555


title: H543


title: H344


title: KS20

value: White, Not Hispanic

value: Former Smoker

value: Enteroenteric


title: H333


title: H473


title: KS13

value: Yes

value: Elective


title: H544


title: KS14

value: Current Smoker

value: Colovesical


title: KS11

value: Male


title: H330


title: KS17


title: KS15

value: Never Smoked


title: KS06


title: KS09


title: WT4

city: Heidelberg

first: Juan

last: Rodriguez-Vita

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 90 bp bandwidth and perfect match only.
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.

source_name: Cell sorting by flow cytometry

extract_protocol: Tumor associated macrophages were isolated from tumor bearing mice. Cells were sorted with the following sorting strategy: CD45.2+, CD19-, CD11b+, CD115+, F4/80+

tag: genotype/variation

value: wild type

tag: tumor stage

value: 4 Weeks post tumor implantation


title: p110d-/- chimeric3


title: p110d-/- chimeric2


title: p110d-/- chimeric4


title: w1118 (Ctrl HttQ138)

city: South San Francisco

first: Imilce

middle: A

last: Rodriguez-Fernandez

state: CA

address: 103 DNA WAY, BUILDING 12, OFFICE 12-232-13

department: Immunology Discovery

institute: Genentech, Inc

description: 24387 sorted cells

data_processing:
standard Tuxedo suite pipeline
Genome_build: Reads were mapped to the Drosophila genome (release 5.75)
Supplementary_files_format_and_content: FPKM (Fragments Per Kilobase per Million reads) values were recorded for each gene.

organism: Drosophila melanogaster

source_name: escargot-positive cells (ISCs/EBs)

growth_protocol: Flies were grown under normal conditions and placed at 29C for the indicated time above (characteristics: knockdown)

extract_protocol:
Total RNA was isolated from sorted cells using Trizol reagent, and used as template to generate RNA-seq libraries for Illumina MiSeq sequencing (150bp paired-end reads were obtained).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: genotype

value: esgGal4ts > +

tag: age

value: 7 days old

tag: knockdown

value: 2d at 29C


title: CncCRNAi

description: 34129 sorted cells

value: esgGal4ts > CncCRNAi


title: KS03

value: sigmoid colon

tag: Sex

value: Female

tag: family history of diverticular disease

value: No

tag: race

tag: smoking status

tag: perforation/abscess


title: p110d-/- chimeric1


title: attP2 (Ctrl Rpn3RNAi)

description: 62921 sorted cells

value: attP2, esgGal4ts > +

value: 4d at 29C


title: WT3


title: KS04

value: Yes

value: White, Not Hispanic

tag: fistula

tag: bmi

tag: age of diagnosis

tag: age of surgery

tag: surgery timing


title: HttQ138

description: 16611 sorted cells

value: esgGal4ts > HttQ138


title: human cell line mixture, ATAC-seq

tag: tissue

value: cell line mixture (BJ, GM12878, H1, K562)

tag: strain

tag: developmental stage

tag: type

value: Nuclei


title: WT2

tag: genotype/variation

tag: tumor stage


title: Rpn3RNAi

description: 34986 sorted cells

tag: genotype

value: attP2, esgGal4ts > Rpn3RNAi

tag: age

tag: knockdown


title: KS02

tag: Sex

value: Male

tag: family history of diverticular disease

tag: race

value: Current Smoker

value: Elective


title: H556

tag: treatment

value: Cyclophoshamide

tag: ipi


title: CncCRNAi HttQ138

description: 37452 sorted cells

value: esgGal4ts > CncCRNAi and HttQ138

value: 7 days old

value: 2d at 29C


title: WT1

value: wild type

value: 4 Weeks post tumor implantation


title: KS01

value: sigmoid colon

tag: smoking status

tag: perforation/abscess

tag: fistula

tag: bmi

tag: age of diagnosis


title: KS22

tag: tissue

value: Never Smoked

value: Colovesical

tag: age of surgery

tag: surgery timing


title: MRA6MR NICD-2

city: MADISON

first: Vijayasaradhi

last: Setaluri

address: 1300 University Avenue

department: Dermatology

institute: University of Wisconsin-Madison

description:
MRA6MR.data.NICD.D2.16
MRA6-MR-NICD-D2-16_S2_L003_R1_001.fastq

data_processing:
Raw FASTQ files were analyzed for quality using FASTQC, and low quality reads and adaptors were filtered and trimmed using cut-adapt. RSEM was used to map the reads to transcripts from human genome version hg19 and call isoform level expression.
Genome_build: hg19
Supplementary_files_format_and_content: Text File: Contains Reads per Million,  Differential expression and fold change for gene expression

source_name: Metastatic tumor

growth_protocol: Cells were maintained and passaged in DMEM, high glucose, pyruvate medium supplemented with 10% FBS and 1% penicillin-streptomycin. BRAF mutation was confirmed by genomic DNA PCR and western blotting for expression of BRAF(V600E) protein. The cell cultures were maintained in a CO2 (5%) incubator at 37oC.

extract_protocol:
RNA samples were extracted and purified using the miRNeasy Mini Kit (#217004, Qiagen, Germany). The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). 1ug of Total RNA was used as starting material to construct RNA Seq library using Illumina's Truseq Stranded Total RNA Library preparation kit as per the instructions. First the total RNA is Ribo depleted to remove rRNA from total RNA. The remaining non-rRNA is fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR. Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were plated on 6-well plates. After attachment, cells were transduced with equal amounts of either the NICD expression or control lentiviruses.  30 hours after transduction RNA was extracted.

tag: cell type

value: melanoma

value: BRAF(V600E)/WT NRAS

tag: transduced with

value: NICD

tag: phenotype

value: Acquired resistance to MEKi


title: MRA6MR NICD-1

description:
MRA6MR.data.NICD.D1.15
MRA6-MR-NICD-D1-15_S5_L005_R1_001.fastq

tag: genotype


title: Liver_exercised_slaughter_rep14

city: Zaragoza

first: Jorge

middle: H

last: Calvo

address: Avd. Montañana 930

department: Producción y Sanidad animal

institute: CITA

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol using GCOS

data_processing: Expression data were generated with GeneChip Operating Software (GCOS, Affymetrix) and normalization was carried out with Robust Multi-Array Average (RMA) algorithm with quantile normalization.

organism: Ovis aries

source_name: Liver, exercised, slaughter

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

growth_protocol: 7 single reared male lambs were weaned at 48.28 ± 0.85 days of age, and therfore they were fed a basal concentrate from weaning to slaughter. Another group of 7 lambs continuously grazed on alfalfa pasture with their dams. Lambs suckled their mothers, grazed, and received the same basal concentrate.

extract_protocol: RNeasy Tissue isolation kit (QIAGEN, Madrid, Spain)

treatment_protocol: Liver tissue samples obtained at slaughter were mantained at -80ºC until processing for RNA extraction

tag: gender

value: male

value: Liver

tag: breed

value: Rasa Aragonesa

value: Basal concentrate


title: Liver_exercised_slaughter_rep10


title: Liver_exercised_slaughter_rep13


title: MRA6MR Empty Vector-1

description:
MRA6MR.data.EMPTY.D1.7
MRA6-MR-EMPTY-D1-7_S2_L004_R1_001.fastq

value: empty vector


title: Liver_exercised_slaughter_rep11


title: MRA6MR Empty Vector-2

description:
MRA6MR.data.EMPTY.D2.8
MRA6-MR-EMPTY-D2-8_S3_L004_R1_001.fastq


title: MRA6BR NICD-2

description:
MRA6BR.data.NICD.D2.14
MRA6-BR-NICD-D2-14_S4_L005_R1_001.fastq

value: Acquired resistance to BRAF(V600E)i


title: Liver_exercised_slaughter_rep9


title: Liver_exercised_slaughter_rep5

value: Alfalfa grazing


title: Liver_exercised_slaughter_rep4


title: Liver_exercised_slaughter_rep8


title: MRA6BR NICD-1

description:
MRA6BR.data.NICD.D1.13
MRA6-BR-NICD-D1-13_S4_L004_R1_001.fastq


title: Liver_exercised_slaughter_rep3


title: FB_P28_1 3'SAGE-seq

city: Noda, Chiba

first: Kazushige

last: Shiraishi

address: Yamasaki 2669

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by Trimommatic-0.33 and PRINSEQ-0.20.4. Trimmed reads were mapped to the Refseq mm10 by using Bowtie2-2.2.5. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Total tag number was adjusted to 1 million tags, and between-sample normalization was performed by using R-3.4.0 and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized tag-count values for each sample

source_name: Lung fibroblasts

extract_protocol:
Epithelial cells and fibroblasts from various developmental stages (E18.5, P0.5, P2, P7, P28, and P56) were isolated from C57BL/6 mice. Lungs were cut into small pieces and digested enzymatically using collagenase (Wako, Osaka, Japan), Dispase II (Roche, Basel, Switzerland), and DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Single-cell suspended lung cells were first stained with anti-mouse CD31, CD45, Ter119, CD146, and Epcam antibodies. Cells were next stained with Streptavidin-APC, followed by anti-APC microbeads (Miltenyi). Labeled cells were magnetically depleted. Finally, lineage (CD31, CD45, Ter119, and CD146)– propidium iodide– GFP– Epcam+ live epithelial cells and lineage (CD31, CD45, Ter119, and CD146)– propidium iodide– Epcam– GFP+ fibroblasts were sorted with a MoFlo Astrios flow cytometer (Beckman Coulter).
polyA RNAs were isolated and amplified from donor epithelial cells and fibroblasts according to the protocol described in (Huang H, Nucleic Actd Res, 2014) with some modifications. 3'SAGE-seq libraries were constructed according to the protocol described in (Matsumura H, Methods Mol Biol, 2012) with some modifications. Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

value: lineage (CD31, CD45, CD146 and Ter119) negative, Epcam negative, Col1a2-GFP positive fibroblasts

tag: strain

value: lung

tag: developmental stage

value: Postnatal day 28

value: Col1a2-GFP Transgenic


title: Liver_exercised_slaughter_rep1

tag: treatment


title: Liver_exercised_slaughter_rep6


title: FB_P0.5_2 3'SAGE-seq

value: Postnatal day 0.5


title: Liver_exercised_slaughter_rep7


title: FB_P28_2 3'SAGE-seq


title: FB_P7_1 3'SAGE-seq

value: Postnatal day 7


title: FB_P7_2 3'SAGE-seq


title: MRA6 NICD-2

description:
MRA6.data.NICD.D2.12
MRA6-NICD-D2-12_S3_L005_R1_001.fastq

value: melanoma

value: MAPKi Sensitive


title: Liver_exercised_slaughter_rep2


title: MRA6BR Empty Vector-2

description:
MRA6BR.data.EMPTY.D2.6
MRA6-BR-EMPTY-D2-6_S1_L004_R1_001.fastq

value: BRAF(V600E)/WT NRAS


title: FB_P2_1 3'SAGE-seq

value: Postnatal day 2


title: FB_P0.5_1 3'SAGE-seq


title: FB_E18.5_1 3'SAGE-seq

value: Embryonic day 18.5


title: Liver_exercised_slaughter_rep12

value: male

value: Liver


title: FB_P2_2 3'SAGE-seq


title: MRA6 NICD-1

description:
MRA6.data.NICD.D1.11
MRA6-NICD-D1-11_S2_L005_R1_001.fastq

value: NICD


title: H345

value: R-CHOP

tag: ipi


title: FB_P56_1 3'SAGE-seq

value: Postnatal day 56


title: Epi_P28_1 3'SAGE-seq

source_name: Lung epithelial cells

value: lineage (CD31, CD45, CD146 and Ter119) negative, Col1a2-GFP negative, Epcam positive epithelial cells


title: Epi_P7_2 3'SAGE-seq


title: FB_E18.5_2 3'SAGE-seq

value: lineage (CD31, CD45, CD146 and Ter119) negative, Epcam negative, Col1a2-GFP positive fibroblasts


title: bisulphite converted DNA from control placenta PL60

type: genomic

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

hyb_protocol: bisulphite converted DNAs were amplified, fragmented and hybridised to Illumina HumanMethylationEPIC and HumanMethylation450 Beadchips using standard Illumina protocol

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

data_processing: Minfi package for the R statistical software and in-house R scripts

label: Cy5 and Cy3

source_name: PL60 triplet placenta

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from placenta samples using standard phenol/chloroform extraction protocol

value: placenta

tag: gestation

value: D

tag: test

value: opposite sides / triplets


title: Epi_P2_2 3'SAGE-seq

value: lung

value: Col1a2-GFP Transgenic


title: Epi_P28_2 3'SAGE-seq

value: Postnatal day 28


title: Epi_P0.5_1 3'SAGE-seq

value: Postnatal day 0.5


title: MRA6 Empty Vector-1

description:
MRA6.data.EMPTY.D1.3
MRA6-EMPTY-D1-3_S2_L007_R1_001.fastq

value: melanoma

value: BRAF(V600E)/WT NRAS

value: empty vector

value: MAPKi Sensitive


title: Epi_P7_1 3'SAGE-seq

value: Postnatal day 7