title: SS2_16_364_J18

description: counts.csv


title: SS2_16_364_J16

status: Public on Feb 13 2019

type: SRA

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

description: counts.csv

library_source: transcriptomic

data_processing:
Individual Fastq files were aligned to the mouse Genome (Gencode M11 / GRCm38) using the STAR aligner version 2.5.2b with parameters STAR --runThreadN <cpu> --genomeDir <index> --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn <fastq> --readFilesCommand zcat --outFileNamePrefix <sampleID> --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate
Gene counts were obtained from BAM files using featureCounts v1.5.1 with parameters -a <Gencode_vM11.gtf> -G <GRCm38.primary_assembly.genome.fa> -o counts.txt -F GTF -R -g gene_id -t exon -T 12 --largestOverlap <bamfiles>
single cell RNAseq analysis and clustering was performed using RaceId/StemId2 (Grün, D., L. Kester, and A. van Oudenaarden. 2014. “Validation of noise models for single-cell transcriptomics.” Nat. Methods 11 (6): 637–40.). Cells with less than 500 detected genes, less than 5000 aligned reads or more than 700 000 aligned reads were discarded. Only genes with a count of 5 in at least a single cell were used for analysis.
Genome_build: Gencode M11 / GRCm38
Supplementary_files_format_and_content: comma separated (csv) file with gene counts per sample

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
After transcardial perfusion with PBS, brains were roughly minced and homogenized with a potter in HBSS containing 15 mM HEPES buffer and 0.54 % Glucose. Whole-brain homogenate was separated by 70/37/30 % layered Percoll gradient centrifugation at 800 g for 30 min at 4 °C (no brake). The CNS macrophages containing interphase was then collected and washed once with PBS containing 2% FCS and 10mM EDTA before staining. Cells were stained with primary antibodies directed against CD11b (M1/70, BioLegend), CD45 (30-F11, BD Biosciences), Ly6C (AL-21, BD Biosciences) and Ly6G (1A8, BD Biosciences) for 20 min, and CD206 (C068C2, BioLegend) for 45 min at 4 °C. After washing, cells were analyd using a MoFlo Astrios (Beckman Coulter). microglia were FACS-sorted from six different CNS regions of healthy and diseased brains (see gating strategy shown in supplementary Fig.2) into a 384-well plate containing a lysis buffer.
Single cell RNAseq libraries were generated following the published SmartSeq2 protocol (Picelli et al. Nature Metods 2013)

tag: strain

tag: tissue

value: Hippocampus

tag: treatment

tag: age

value: 16 weeks


title: SS2_16_364_J22

description: counts.csv


title: SS2_16_364_J17

description: counts.csv


title: SS2_16_364_J15

description: counts.csv


title: SS2_16_364_J12

description: counts.csv

source_name: Cortex

value: Cortex


title: SS2_16_364_J7

description: counts.csv


title: SS2_16_364_J10

description: counts.csv


title: SS2_16_364_I8

description: counts.csv


title: SS2_16_364_J14

description: counts.csv


title: SS2_16_364_J11

description: counts.csv


title: SS2_16_364_I4

description: counts.csv


title: SS2_16_364_I24

description: counts.csv


title: SS2_16_364_I20

description: counts.csv


title: SS2_16_364_I22

description: counts.csv


title: SS2_16_364_I7

description: counts.csv


title: SS2_16_364_J1

description: counts.csv


title: SS2_16_364_I9

description: counts.csv


title: SS2_16_364_I6

description: counts.csv


title: SS2_16_364_I21

description: counts.csv


title: SS2_16_364_I19

description: counts.csv


title: SS2_16_364_I16

description: counts.csv


title: SS2_16_364_I13

description: counts.csv


title: SS2_16_364_I5

description: counts.csv


title: SS2_16_364_J13

description: counts.csv


title: SS2_16_364_I23

description: counts.csv


title: SS2_16_364_I15

description: counts.csv


title: SS2_16_364_I18

description: counts.csv


title: SS2_16_364_I14

description: counts.csv


title: SS2_16_364_I12

description: counts.csv


title: SS2_16_364_I3

description: counts.csv


title: SS2_16_364_I11

description: counts.csv


title: SS2_16_364_I1

description: counts.csv


title: SS2_16_364_H9

description: counts.csv


title: SS2_16_364_I10

description: counts.csv


title: SS2_16_364_H4

description: counts.csv


title: SS2_16_364_H7

description: counts.csv


title: SS2_16_364_H8

description: counts.csv


title: SS2_16_364_H6

description: counts.csv


title: SS2_16_364_H22

description: counts.csv


title: SS2_16_364_I2

description: counts.csv


title: SS2_16_364_H5

description: counts.csv


title: SS2_16_364_H18

description: counts.csv


title: SS2_16_364_H17

description: counts.csv


title: SS2_16_364_H3

description: counts.csv


title: SS2_16_364_I17

description: counts.csv


title: SS2_16_364_H24

description: counts.csv


title: SS2_16_364_H10

description: counts.csv


title: SS2_16_364_G8

description: counts.csv


title: SS2_16_364_G6

description: counts.csv


title: SS2_16_364_G7

description: counts.csv


title: SS2_16_364_G3

description: counts.csv


title: SS2_16_364_G5

description: counts.csv


title: SS2_16_364_H12

description: counts.csv


title: SS2_16_364_H23

description: counts.csv


title: SS2_16_364_H21

description: counts.csv


title: SS2_16_364_G24

description: counts.csv


title: SS2_16_364_G23

description: counts.csv


title: SS2_16_364_H15

description: counts.csv


title: SS2_16_364_G22

description: counts.csv


title: SS2_16_364_H19

description: counts.csv


title: SS2_16_364_H2

description: counts.csv


title: SS2_16_364_H16

description: counts.csv


title: SS2_16_364_G20

description: counts.csv


title: SS2_16_364_G2

description: counts.csv


title: SS2_16_364_H14

description: counts.csv


title: SS2_16_364_H13

description: counts.csv


title: SS2_16_364_G16

description: counts.csv


title: SS2_16_364_H11

description: counts.csv


title: SS2_16_364_G14

description: counts.csv


title: SS2_16_364_G9

description: counts.csv


title: SS2_16_364_G4

description: counts.csv


title: SS2_16_364_H1

description: counts.csv


title: SS2_16_364_G11

description: counts.csv


title: SS2_16_364_H20

description: counts.csv


title: SS2_16_364_G21

description: counts.csv


title: SS2_16_364_G1

description: counts.csv


title: SS2_16_364_G19

description: counts.csv


title: SS2_16_364_F9

description: counts.csv


title: SS2_16_364_F8

description: counts.csv


title: SS2_16_364_G17

description: counts.csv


title: SS2_16_364_G15

description: counts.csv


title: SS2_16_364_F7

description: counts.csv


title: SS2_16_364_G13

description: counts.csv


title: SS2_16_364_G10

description: counts.csv


title: SS2_16_364_G12

description: counts.csv


title: SS2_16_364_G18

description: counts.csv


title: SS2_16_364_F4

description: counts.csv


title: SS2_16_364_F5

description: counts.csv


title: SS2_16_364_F6

description: counts.csv


title: SS2_16_364_F3

description: counts.csv


title: SS2_16_364_F24

description: counts.csv


title: SS2_16_364_F23

description: counts.csv


title: GLUT1 KO M0.4

type: RNA

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

country: USA

institute: UTHSC

description: replicate 4

hyb_protocol: hybridized to SurePrint G3 Mouse GE 8x60K microarrays (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: bone marrow derived macrophage

label_protocol: Samples (2 µL) were Cy3-labeled with the Agilent Low-Input Quick Amp Labeling kit

growth_protocol: BMDMs were generated by culturing marrow cells in 10 cm non-tissue culture-treated dishes for 6 days with 20 ng/ml M-CSF  in RPMI-1640 supplemented with 10% FBS, 1X L-glutamine, and 1X penicillin/streptomycin antibiotic mix.

extract_protocol: mRNA was isolated using Qiagen’s RNeasy mini kit. The RNA quantity and quality were determined using Nanodrop (Thermo Fisher Scientific). RNA sample quality was assessed using the RNA ScreenTape assay (Agilent, Santa Clara, CA)

treatment_protocol: BMDMs were left untreated as naïve M0 Unstimulated MФs or activated using 5ng/ml LPS and 10 ng/ml IFNγ (M1-like) or 10 ng/ml IL-4 (M2-like) for 24 hours.

tag: genotype

value: myeloid GLUT1 deficient are KO or Slc2a1M-/- (LysMCre X Slc2a1fl/fl)

value: 24 hour untreated, naïve M0 Unstimulated MФs


title: GLUT1 WT M1.3

description: replicate 3

value: WT or Slc2a1 fl/fl floxed control

value: 24 hour treated:5ng/ml LPS and 10 ng/ml IFNγ (M1)


title: GLUT1 WT M2.3

description: replicate 3

value: 24 hour treated:10 ng/ml IL-4 (M2)


title: SS2_16_364_F22

description: counts.csv


title: GLUT1 KO M2.2

description: replicate 2


title: GLUT1 KO M2.4

description: replicate 4


title: GLUT1 WT M1.4

description: replicate 4


title: GLUT1 KO M1.3

description: replicate 3


title: SS2_16_364_F21

description: counts.csv


title: GLUT1 WT M0.4

description: replicate 4


title: GLUT1 WT M2.4

description: replicate 4


title: GLUT1 KO M2.3

description: replicate 3


title: GLUT1 KO M1.4

description: replicate 4


title: SS2_16_364_F18

description: counts.csv


title: GLUT1 KO M1.2

description: replicate 2


title: SS2_16_364_F20

description: counts.csv


title: GLUT1 WT M2.2

description: replicate 2


title: SS2_16_364_F19

description: counts.csv


title: SS2_16_364_F2

description: counts.csv


title: GLUT1 WT M1.2

description: replicate 2


title: SS2_16_364_F17

description: counts.csv


title: SS2_16_364_F16

description: counts.csv


title: SS2_16_364_F15

description: counts.csv


title: GLUT1 KO M0.3

description: replicate 3


title: SS2_16_364_F13

description: counts.csv


title: GLUT1 WT M0.3

description: replicate 3


title: GLUT1 KO M1.1

description: replicate 1


title: SS2_16_364_F10

description: counts.csv


title: SS2_16_364_F12

description: counts.csv


title: 0N1

city: Shenzhen

first: Giles

last: Hu

address: Dapeng

country: China

institute: YJY

description: mRNA sequencing approach for library contructions

data_processing:
Basecalls performed using CASAVA
RNA reads are removed adaptor sequences and low quality sequences using software SOAPnuke version 1.0.1 with parameters by default aligned to the genome hg19 using hisat version 2.0.12  with default parameters, and Fragments per kilobase of exon per million fragments mapped (FPKM) are caculated.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm files were generated using hisat

organism: Homo sapiens

source_name: mucosa

growth_protocol: Fresh tissue specimens of OSCC (n=8), OSF (n=8), and normal oral mucosa (n=2) were obtained at the time of surgical resection at Xiangya Second Hospital and Xiangya Hospital, Central South University (Changsha, China) and Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine (Shanghai, China) from January 2016 to June 2017. The patients’ informed consents had been obtained under a protocol reviewed and approved by the Institutional Review Boards of the Xiangya School of Medicine or Shanghai Jiaotong University School of Medicine. 2 normal specimens were obtained from healthy oral mucosa. OSF is diagnosed excluding OSCC or neoplastic disease.

extract_protocol:
Total RNA was isolated using TRIzol reagent (MRI, USA), and then measured by using Nanodrop 2.0.
Epicentre Ribo-ZeroTM kit was used to remove rRNA. Subsequently, the fragmentation buffer was used to break the RNA into short fragments of 150-200 bp, which was used as a template to synthesize cDNA using random hexamers. After purification, the double-stranded cDNA was subjected to terminal repair; a tail was added, and the sequencing linker was ligated, and finally cDNA library of total RNA was obtained by PCR enrichment.

value: oral

tag: Sex

value: female

tag: condition

value: N


title: 08N

treatment_protocol: Fresh tissue specimens of OSCC (n=8), OSF (n=8), and normal oral mucosa (n=2) were obtained at the time of surgical resection at Xiangya Second Hospital and Xiangya Hospital, Central South University (Changsha, China) and Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine (Shanghai, China) from January 2016 to June 2017. The patients’ informed consents had been obtained under a protocol reviewed and approved by the Institutional Review Boards of the Xiangya School of Medicine or Shanghai Jiaotong University School of Medicine. 2 normal specimens were obtained from healthy oral mucosa. OSF is diagnosed excluding OSCC or neoplastic disease.

value: OSF


title: 08T

value: OSCC


title: ON2


title: 07N


title: 07T


title: SS2_16_364_F1

description: counts.csv


title: SS2_16_364_E9

description: counts.csv


title: GLUT1 WT M0.2

description: replicate 2


title: 06T


title: 05T


title: SS2_16_364_F14

description: counts.csv


title: SS2_16_364_E8

description: counts.csv


title: 05N


title: GLUT1 KO M2.1

description: replicate 1


title: SS2_16_364_E7

description: counts.csv


title: GLUT1 KO M0.1

description: replicate 1


title: SS2_16_364_E6

description: counts.csv


title: GLUT1 WT M2.1

description: replicate 1


title: 03T


title: GLUT1 WT M0.1

description: replicate 1


title: SS2_16_364_F11

description: counts.csv


title: 025N


title: SS2_16_364_E5

description: counts.csv


title: GLUT1 WT M1.1

description: replicate 1


title: SS2_16_364_E4

description: counts.csv


title: 024N


title: SS2_16_364_E3

description: counts.csv


title: SS2_16_364_E23

description: counts.csv


title: SS2_16_364_E24

description: counts.csv


title: 013T


title: SS2_16_364_E21

description: counts.csv


title: SS2_16_364_E22

description: counts.csv


title: 011N


title: SS2_16_364_E2

description: counts.csv


title: 01N


title: 011T


title: 01T


title: SS2_16_364_E19

description: counts.csv


title: SS2_16_364_E18

description: counts.csv


title: SS2_16_364_E20

description: counts.csv


title: SS2_16_364_E17

description: counts.csv


title: SS2_16_364_E15

description: counts.csv


title: SS2_16_364_E16

description: counts.csv


title: 013N


title: SS2_16_364_E14

description: counts.csv


title: SS2_16_364_E13

description: counts.csv


title: SS2_16_364_E12

description: counts.csv


title: SS2_16_364_E11

description: counts.csv


title: SS2_16_364_E10

description: counts.csv


title: SS2_16_364_E1

description: counts.csv


title: SS2_16_364_D8

description: counts.csv


title: SS2_16_364_D9

description: counts.csv


title: SS2_16_364_D7

description: counts.csv


title: SS2_16_364_D6

description: counts.csv


title: SS2_16_364_D5

description: counts.csv


title: SS2_16_364_D3

description: counts.csv


title: SS2_16_364_D23

description: counts.csv


title: SS2_16_364_D22

description: counts.csv


title: SS2_16_364_D21

description: counts.csv


title: SS2_16_364_D20

description: counts.csv


title: Adult satellite cells microarray rep1

city: Minneapolis

first: Tania

last: Incitti

state: Minnesota

address: 2231 6th Street SE

institute: University of Minnesota

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 4 x 44K using Agilent’s recommended hybridization chamber and oven. Microarrays were then washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). Finally, the Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing:
Microarrays were analyzed in R (3.4.3) using the limma package. First, background correction was performed on each microarray using “normexp” method. Then we performed quantile normalization between all microarrays before performing differential expression analysis.  Filtering on microarray was conducted by retaining only the probes that were above background in at least 4 arrays.
For differential expression analysis, we first fitted a linear model on the normalized microarray expression and then used an empirical Bayes moderation approach to calculate the statistical significance. The differentially expressed genes are defined as fold change over 2 and false-discovery-rate adjusted p-value less than 0.05. Hierarchical clusterings were performed using correlation as similarity metric and average-link method in R.

source_name: Adult satellite cells

label_protocol: RNA was amplified and retrotranscribed according to SuperAmp™ Preparation kit’s instruction. cDNA was quantified and analyzed on a Agilent 2100 Bioanalyzer platform (AgilentTechnologies). 250 ng of each cDNA were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: 1500 cells isolated from 3 mice/line in 3 independent experiments were sorted directly into the SuperAmp™ lysis buffer (Miltenyi Biotech)

value: Tibialis anterior

tag: cell type

value: satellite cells

value: 3 months-old


title: iPax7 re-isolated microarray rep2

source_name: iPax7 re-isolated

value: mononucleated cells


title: Adult satellite cells microarray rep3


title: Adult satellite cells microarray rep2


title: iPax3 re-isolated microarray rep2

source_name: iPax3 re-isolated


title: iPax7 re-isolated microarray rep1


title: iPax7 re-isolated microarray rep3


title: iPax3 re-isolated microarray rep3


title: SS2_16_364_D2

description: counts.csv


title: SS2_16_364_D19

description: counts.csv

value: Hippocampus


title: SS2_16_364_D18

description: counts.csv

value: 16 weeks


title: SS2_16_364_D24

description: counts.csv


title: SS2_16_364_D4

description: counts.csv

value: Cortex


title: SS2_16_364_D16

description: counts.csv


title: SS2_16_364_D14

description: counts.csv


title: SS2_16_364_D15

description: counts.csv


title: SS2_16_364_D13

description: counts.csv


title: SS2_16_364_D12

description: counts.csv


title: SS2_16_364_D10

description: counts.csv


title: SS2_16_364_D1

description: counts.csv


title: SS2_16_364_D11

description: counts.csv


title: Primary hippocampal cultures_GYKI-52466 + MK-801 26h_R3

city: Coimbra

first: Joana

middle: Filipa

last: Fernandes

state: -- Please Select --

address: Rua Larga, Faculdade de Medicina 2º andar, lab 206A Coimbra

department: Life Sciences

country: Portugal

institute: Center for Neuroscience and Cell Biology

description: Gene expression of hippocampal cultures treated with AMPARs and synaptic NMDARs antagonists _ 26h

hyb_protocol: Hybridizations were carried out following Agilent Technologies instructions for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Santa Clara, CA, USA), using whole-genome Rat GE 4x44K v3 Microarrays.

scan_protocol: Images were obtained using Agilent G2565AA microarray scanner and fluorescence quantization was performed using Agilent Feature Extraction 10.5.1.1 software and GE1_105_Dec08 protocol.

data_processing: The signal intensity was aligned and normalized between microarrays by centering the median of the signal distribution using BRB-ArrayTools v3.8.1.

organism: Rattus norvegicus

source_name: Primary cultures of hippocampal neurons, GYKI-52466 + MK-801, 26h

label_protocol: Equal amounts of RNA extract (200 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies), according to manufecturer's instructions.

growth_protocol: Primary cultures of hippocampal neurons were prepared from embryonic day (E) 18 Wistar rats. The cultures were mantained in Neurobasal medium [supplemented with SM1 neuronal supplement (1:50), glutamine (0.5mM), gentamycin (0.12 mg/ml) and glutamate (25 μM, first week in culture)] and kept in a humidified incubator at 37º with 5% CO2/95% air, for 14-15 day.

extract_protocol: Total RNA from three independent rat hippocampal neuronal cultures subjected either to chronic synaptic activity blockade for 9h or 26h, or under control conditions was extracted using TRIzol (according to manufecturer's instructions).

treatment_protocol: Hippocampal cultures were treated with 50 μM GYKI-52466 and 10 μM MK-801 for 9 or 26 hours or kept in control conditions.

value: Wistar

tag: tissue type

value: Primary cultures of hippocampal neurons

tag: days in vitro (div)


title: SS2_16_364_C9

description: counts.csv


title: iPax3 re-isolated microarray rep1


title: 17921_Pdgfra-KO rep1

city: Los Angeles

first: Fremont

last: Gao

state: California

address: 2011 Zonal Ave, HMR 903

institute: USC

data_processing:
The unaligned raw reads were processed on PartekFlow platform.
Reads alignment and gene annotation & quantification were based on mouse genome (mm10) and transcriptome (GENECODE genes-release 7); Tophat2 and Upper Quartile were algorithms used for mapping and normalization; Differential Gene Expression was done with PartekFlow’s Gene Specific Analysis (GSA).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene ID, total counts, FDR, Fold change

extract_protocol:
Lungs were dissected from mouse pups at PN14; cells were separated using gentleMACS dissociator; GFP+ cells were collected by FACs; RNA was extracted using Qiagen RNeasy micro kit; total RNA was sent to the sequencing facility at Caltech for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: post natal day 14

tag: genotype/variation

value: Lung

value: GFP+ cells; secondary crest myofibroblasts (SCMF)


title: 17924_Pdgfra-KO rep2


title: SS2_16_364_D17

description: counts.csv


title: 17928_WT rep2

value: wild type; Gli1creERT:mTmG


title: 17927_WT rep1


title: SS2_16_364_C7

description: counts.csv


title: Primary hippocampal cultures_GYKI-52466 + MK-801 26h_R2


title: Primary hippocampal cultures_GYKI-52466 + MK-801 26h_R1


title: SS2_16_364_C6

description: counts.csv


title: Primary hippocampal cultures_Ctrl 26h_R1

description: Gene expression of non-treated hippocampal cultures _ 26h

source_name: Primary cultures of hippocampal neurons, Ctrl 26h

value: non-treated _ 26h


title: Primary hippocampal cultures_Ctrl 26h_R2


title: Primary hippocampal cultures_GYKI-52466 + MK-801 9h_R3

description: Gene expression of hippocampal cultures treated with AMPARs and synaptic NMDARs antagonists _ 9h

source_name: Primary cultures of hippocampal neurons, GYKI-52466 + MK-801, 9h


title: Primary hippocampal cultures_Ctrl 9h_R2

description: Gene expression of non-treated hippocampal cultures _ 9h

source_name: Primary cultures of hippocampal neurons, Ctrl 9h

value: non-treated _ 9h


title: Primary hippocampal cultures_GYKI-52466 + MK-801 9h_R1


title: SS2_16_364_C5

description: counts.csv


title: Primary hippocampal cultures_GYKI-52466 + MK-801 9h_R2


title: CcncKO#3

city: Stratford

first: David

last: Stieg

state: NJ

address: 42 E. Laurel Rd

department: Molecular Biology

institute: Rowan Graduate School of Biomedical Sciences

data_processing:
The paired-end reads were mapped to the Ensembl Mus_musculus (GRCm38) cDNA FASTA file downloaded from UCSC. Mapping was performed with Bowtie2 using default settings
To generate count tables from the reads uniquely mapped to annotated genes, featureCounts was performed on each sample using the GRCm38 annotation gtf file. The featureCounts data were filtered for protein coding genes and aggregated for gene level analysis.
Genome_build: mm10
Supplementary_files_format_and_content: featureCount data for each sample representing reads mapped uniquely to protein coding genes.

growth_protocol: Ccnc+/+ (WT) and Ccnc−/− immortalized MEF cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C and 5% CO2. Replicate WT and Ccnc-/- MEF cultures were grown to 80% confluence.

extract_protocol:
Total RNA was prepared from the cell samples using mechanical disruption and the QIAGEN® RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Oxidative stressed cells were exposed to 0.4 mM H2O2 in DMEM without FBS or antibiotics for 4 h.

value: Ccnc-/-

value: immortalized embryonic fibroblasts cells


title: Primary hippocampal cultures_Ctrl 26h_R3


title: Primary hippocampal cultures_Ctrl 9h_R1


title: SS2_16_364_C3

description: counts.csv


title: SS2_16_364_C4

description: counts.csv


title: 19016_WT rep3


title: SS2_16_364_C23

description: counts.csv


title: WT#2Stress

value: Ccnc+/+ (WT)

value: 0.4 mM H2O2 for 4hrs


title: CcncKO#1


title: CcncKO#2


title: WT#3Control


title: SS2_16_364_C8

description: counts.csv


title: WT#1Stress


title: SS2_16_364_C22

description: counts.csv


title: SS2_16_364_C24

description: counts.csv


title: SS2_16_364_C2

description: counts.csv


title: WT#2Control


title: WT#1Control


title: SS2_16_364_C20

description: counts.csv


title: SS2_16_364_C19

description: counts.csv


title: SS2_16_364_C18

description: counts.csv


title: SS2_16_364_C17

description: counts.csv


title: SS2_16_364_C16

description: counts.csv


title: Primary hippocampal cultures_Ctrl 9h_R3


title: MC38

city: Chiyoda

first: Ranmaru

last: Shimoda

state: Tokyo

address: 3F Yayoi Bldg., 3-7-4 Iwamotocho

country: Japan

institute: Rhelixa, Inc.

data_processing:
Samples were sequenced using Illumina HiSeq2500 instrument with paired-end 2 x 125-bp cycle
Base calls were performed on CASAVA 1.8.2. pipeline
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.36 with LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 as command option. Fastq reads were generated using BCL2FASTQ Conversion Software1.8.4; First line begins with a '@' character and is followed by a sequence identifier. Second line represent raw nucleotide sequence letters. The last line encodes the quality values for the sequence.
Mapping of sequence reads using TopHat version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: only bam files were generated to compare the allele imbalance among samples and available as SRA records.

source_name: colon epithelial cell

growth_protocol: EL4 or MC38 (1 × 10^6 cells/well/6 well plate) were cultured for 24 h in RPMI1640 supplemented with 10%FBS.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Libraries were prepared for sequencing using library creation kits (TruSeq Stranded mRNA sample prep kit, Illumina, San Diego, CA, USA)

tag: cell line

value: colon adenocarcinoma


title: EL4

source_name: thymocyte

value: thymoma


title: SS2_16_364_C14

description: counts.csv

value: Hippocampus


title: SS2_16_364_C15

description: counts.csv

value: 16 weeks


title: GLUT1 KO M0.2

description: replicate 2

value: myeloid GLUT1 deficient are KO or Slc2a1M-/- (LysMCre X Slc2a1fl/fl)

value: 24 hour untreated, naïve M0 Unstimulated MФs


title: IFN-alpha-pMC_right_02

data_processing:
Samples were sequenced using Illlumina HiSeq2500 instrument with paired-end 2 x 100-bp cycle
Base calls were performed on CASAVA 1.8.2. pipeline
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.36 with LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 as command option. Fastq reads were generated using BCL2FASTQ Conversion Software1.8.4; First line begins with a '@' character and is followed by a sequence identifier. Second line represent raw nucleotide sequence letters. The last line encodes the quality values for the sequence.
Mapping of sequence reads using Hisat2 version 2.1.0
Raw read counts were determined using HT-Seq Count version 0.10.0 with -m union -r pos -t exon --stranded=no as options
Differentially expressed genes were identified using DESeq2 version 1.20.0 (log fold change x>1, x<-1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including read counts from HTSeq-count

treatment_protocol: C57BL/6 mice were inoculated subcutaneously with tumor cells (MO4; an ovalbumin (OVA)-expressing B16F10 melanoma cell line of C57BL/6 origin) into the right and left hindlimb simultaneously (1 × 10^5) on day 0. On day 5, when tumors were palpable, mice were treated peritumorally with iPSC-pMCs or IFN-α-iPSC-pMCs (1 × 10^6) into the right hindlimb on days 5, 6, and 7. Total RNA from tumor tissue was extracted on day 11. Tumor tissue samples with no treatment were served as references.

value: melanoma

value: IFN-α-iPSC-pMCs

value: treated tumor (right)


title: IFN-alpha-pMC_right_03


title: IFN-alpha-pMC_left_01

value: distant tumor (left)


title: IFN-alpha-pMC_left_02


title: SS2_16_364_C13

description: counts.csv


title: IFN-alpha-pMC_right_01


title: SS2_16_364_C12

description: counts.csv

value: Cortex


title: pMC_left_03

value: iPSC-pMCs


title: SS2_16_364_C21

description: counts.csv


title: SS2_16_364_C10

description: counts.csv


title: SS2_16_364_C11

description: counts.csv


title: pMC_right_03


title: IFN-alpha-pMC_left_03


title: SS2_16_364_B9

description: counts.csv


title: pMC_right_02


title: SS2_16_364_C1

description: counts.csv


title: pMC_left_01


title: pMC_left_02


title: SS2_16_364_B8

description: counts.csv


title: control_left_03

value: none (control)


title: SS2_16_364_B7

description: counts.csv


title: SS2_16_364_B5

description: counts.csv


title: control_right_03


title: SS2_16_364_B6

description: counts.csv


title: control_left_02


title: SS2_16_364_B3

description: counts.csv


title: SS2_16_364_B23

description: counts.csv


title: control_right_01


title: SS2_16_364_B22

description: counts.csv


title: IFN-alpha-pMC_01

data_processing:
Samples were sequenced using Illumina HiSeq2500 instrument with paired-end 2 x 100-bp cycle
Base calls were performed on CASAVA 1.8.2. pipeline
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.36 with LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 as command option. Fastq reads were generated using BCL2FASTQ Conversion Software1.8.4; First line begins with a '@' character and is followed by a sequence identifier. Second line represent raw nucleotide sequence letters. The last line encodes the quality values for the sequence.
Mapping of sequence reads using TopHat version 2.1.1
Raw read counts were determined using Cufflinks version 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: IFN-α-transuduced iPSC-pMCs

growth_protocol: iPSC-pMCs or IFN-α- iPSC-pMCs (2 × 10^6 cells/well/6 well plate) were cultured for 24 h in RPMI1640 supplemented with 10%FBS. iPSC-pMCs stimulated with recombinant IFN-α (10^4 U/mL) were served as a reference.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Libraries were prepared using (TruSeq Stranded mRNA sample prep kit, Illumina, San Diego, CA, USA)

value: iPSC-derived myeloid cells

value: IFN-alpha-pMC


title: pMC_02

source_name: iPSC-pMCs

value: pMC


title: pMC+rIFN-alpha_01

source_name: IFN-α-treated iPSC-pMCs

value: pMC+rIFN-alpha


title: pMC+rIFN-alpha_02


title: control_right_02


title: IFN-alpha-pMC_02


title: SS2_16_364_B2

description: counts.csv


title: Ptenbraf peptide2

first: Sathi

last: Wijeyesinghe

state: MN

description:
Ex vivo culture ptenbraf - peptide
Ptenbraf ReSeq Unnormalized Counts.csv

data_processing:
Quality control of FastQ files - FastQC
Low quality segments and adapters trimmed - Trimmomatic
Aligned to relevant reference genome - HiSat2
Differentially expressed genes were quantified - DESeq2
Genome_build: GRCm38; GRCh38
Supplementary_files_format_and_content: .csv files with normalized and unnormalized abundance measurements

source_name: Ptenbraf tumor

extract_protocol:
RNA was isolated using TRIZOL and further purified using the QIAGEN RNA Cleanup Kit
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Library Prep Kit)

tag: peptide

value: Relevant viral peptide

tag: peptide therapy

value: Ex vivo peptide culture w/ tumor slice


title: SS2_16_364_B24

description: counts.csv

source_name: Hippocampus

value: Hippocampus


title: SS2_16_364_B15

description: counts.csv

value: 16 weeks


title: pMC_right_01


title: Ptenbraf peptide1


title: SS2_16_364_B19

description: counts.csv


title: SS2_16_364_B18

description: counts.csv


title: SS2_16_364_B21

description: counts.csv


title: SS2_16_364_B17

description: counts.csv


title: SS2_16_364_B4

description: counts.csv

source_name: Cortex


title: Ptenbraf control3

description:
Ex vivo culture ptenbraf - control
Ptenbraf ReSeq Unnormalized Counts.csv

value: Irrelevant control peptide


title: SS2_16_364_B16

description: counts.csv


title: Ptenbraf peptide3


title: SS2_16_364_B14

description: counts.csv


title: SS2_16_364_B13

description: counts.csv


title: B16 peptide2

description:
In vivo B16 peptide therapy - peptide
B16 Unnormalized Counts.csv

source_name: B16 tumor

value: In vivo peptide injected intratumorally


title: pMC_01


title: Ptenbraf control2


title: SS2_16_364_B20

description: counts.csv


title: SS2_16_364_B12

description: counts.csv


title: Ptenbraf control1


title: SS2_16_364_A9

description: counts.csv


title: SS2_16_364_B11

description: counts.csv


title: B16 control3

description:
In vivo B16 peptide therapy - control
B16 Unnormalized Counts.csv


title: B16 control2


title: B16 control1


title: SS2_16_364_A8

description: counts.csv


title: SS2_16_364_A6

description: counts.csv


title: Nr4aTKO CAR-T cells rep2 tr2 (rna-seq)

city: Denver

first: James

last: Scott-Browne

state: Colorado

address: 1400 Jackson St, K806

institute: National Jewish Health

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARNr4aTKO_rep2

data_processing:
Basecalls and demultiplexing performed in illumina basespace
Single-end 50 bp were trimmed of adapters and to a minimal length of 36nt with TrimGalore v0.4.5
RNA-seq reads from technical replicates were merged into biological replicates
RNA-seq reads were aligned to the mm10 genome assembly using STAR v2.5.3a
Reads aligning to mm10 annotated exon features were counted using the summarizeOverlaps function of the Bioconductor package GenomicAlignments v1.10.1.
The DESeq2 package v1.14.1 was used to normalize the raw counts and identify differentially expressed genes.
Genes with less than 10 reads total were pre-filtered in all comparisons as an initial step.
Transformed values (rlog) were calculated within DESeq2 for data visualization.
Genome_build: mm10
Supplementary_files_format_and_content: tsv containing RNA-seq rlog values

source_name: B16-OVA-hCD19 tumor infiltrating lymphocytes

extract_protocol:
Total RNA was isolated from FACS sorted cells with Qiagen RNA Micro
SMARTseq2

value: CD8+ T cell

value: RV_Cre, RV_CAR-T


title: Nr4aTKO CAR-T cells rep2 tr1 (rna-seq)


title: SS2_16_364_A7

description: counts.csv


title: SS2_16_364_A5

description: counts.csv


title: SS2_16_364_A4

description: counts.csv


title: Nr4aTKO CAR-T cells rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARNr4aTKO_rep1


title: Nr4aTKO CAR-T cells rep1 tr1 (rna-seq)


title: B16 peptide1


title: CAR-T cells, PD1hiTIM3hi rep2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARPD1hiTIM3lo_rep2


title: CAR-T cells, PD1hiTIM3lo rep2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARPD1hiTIM3hi_rep2


title: SS2_16_364_A23

description: counts.csv


title: Endogenous T cells, PD1loTIM3lo rep2 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1loTIM3lo_rep2


title: Endogenous T cells, PD1hiTIM3lo rep2 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1hiTIM3lo_rep2


title: SS2_16_364_A21

description: counts.csv


title: SS2_16_364_A22

description: counts.csv


title: Endogenous T cells, PD1loTIM3lo rep2 tr1 (rna-seq)


title: Endogenous T cells, PD1hiTIM3hi rep2 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1hiTIM3hi_rep2


title: SS2_16_364_A19

description: counts.csv


title: Endogenous T cells, PD1hiTIM3lo rep2 tr1 (rna-seq)


title: SS2_16_364_A20

description: counts.csv


title: SS2_16_364_A2

description: counts.csv


title: B16 peptide3


title: CAR-T cells, PD1hiTIM3lo rep1 tr1 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARPD1hiTIM3lo_rep1


title: SS2_16_364_A3

description: counts.csv


title: Endogenous T cells, PD1hiTIM3hi rep2 tr1 (rna-seq)


title: CAR-T cells, PD1hiTIM3lo rep1 tr2 (rna-seq)


title: SS2_16_364_A16

description: counts.csv


title: SS2_16_364_B1

description: counts.csv


title: SS2_16_364_A24

description: counts.csv


title: SS2_16_364_A18

description: counts.csv


title: CAR-T cells, PD1hiTIM3hi rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARPD1hiTIM3hi_rep1


title: SS2_16_364_A14

description: counts.csv


title: Endogenous T cells, PD1loTIM3lo rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1loTIM3lo_rep1


title: WT#3Stress

value: Ccnc+/+ (WT)

value: immortalized embryonic fibroblasts cells

value: 0.4 mM H2O2 for 4hrs


title: CAR-T cells, PD1hiTIM3hi rep1 tr1 (rna-seq)


title: SS2_16_364_A13

description: counts.csv


title: SS2_16_364_A12

description: counts.csv

value: Cortex


title: Endogenous T cells, PD1loTIM3lo rep1 tr1 (rna-seq)


title: SS2_16_364_A10

description: counts.csv


title: Endogenous T cells, PD1hiTIM3lo rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1hiTIM3lo_rep1


title: Endogenous T cells, PD1hiTIM3lo rep1 tr1 (rna-seq)


title: SS2_16_364_A17

description: counts.csv


title: 1862091118_F11

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read were removed.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position. Cells were rejected if the showed less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: comma separated file containing gene counts per sample

source_name: Amygdala

extract_protocol:
The tissue pieces were dissociated using the Papain dissociation system (Worthington) following manufacturers recommendations, adjusting incubation time based on tissue piece size to 25-45 mins. Using glass pipettes of increasingly smaller tip diameter, the cell suspension was then filtered with 20um filter (Partec) and cells kept in N2 media, and cells loaded into C1 chips for cell capture.
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C using the тАЬCell Load (1772x/1773x) script. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave 3тАЩ fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 µl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.


title: SS2_16_364_A11

description: counts.csv


title: Endogenous T cells, PD1hiTIM3hi rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1hiTIM3hi_rep1


title: 1862091114_G01


title: 1862091118_A02


title: CAR-T cells, PD1hiTIM3hi rep3 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARPD1hiTIM3hi_rep3


title: Endogenous T cells, PD1hiTIM3hi rep3 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1hiTIM3hi_rep3


title: Endogenous T cells, PD1hiTIM3hi rep1 tr1 (rna-seq)


title: CAR-T cells, PD1hiTIM3lo rep3 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARPD1hiTIM3lo_rep3


title: 1862091105_A01


title: 1862091105_H06


title: Endogenous T cells, PD1loTIM3lo rep3 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1loTIM3lo_rep3


title: 1862091110_D03


title: Endogenous T cells, PD1hiTIM3lo rep3 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8PD1hiTIM3lo_rep3


title: 1862091053_B04


title: Nr4aWT CAR-T cells rep2 tr1 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARNr4aWT_rep2

value: RV_Empty, RV_CAR-T


title: Nr4aWT CAR-T cells rep2 tr2 (rna-seq)


title: 1862091053_F11


title: Nr4aWT CAR-T cells rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
B16OVAhCD19_CD8CARNr4aWT_rep1


title: 1862091049_D05


title: Nr4aWT CAR-T cells rep1 tr1 (rna-seq)


title: SS2_16_364_A1

description: counts.csv


title: 1862091041_C05


title: RV HA-Nr4a3, in vitro rep2 tr2 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvNR4A3_rep2

source_name: spleen and peripheral lymph nodes


title: RV HA-Nr4a3, in vitro rep2 tr1 (rna-seq)


title: 1862091037_F04


title: RV HA-Nr4a2, in vitro rep2 tr2 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvNR4A2_rep2


title: RV HA-Nr4a1, in vitro rep2 tr2 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvNR4A1_rep2


title: RV HA-Nr4a2, in vitro rep2 tr1 (rna-seq)


title: 1862091035_H12


title: 1862091035_A04


title: RV HA-Nr4a1, in vitro rep2 tr1 (rna-seq)


title: RV Empty vector, in vitro rep2 tr1 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvEmpty_rep2

value: RV_Empty vector


title: 1862091032_A03


title: RV Empty vector, in vitro rep2 tr2 (rna-seq)


title: RV HA-Nr4a3, in vitro rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvNR4A3_rep1


title: 1862091037_H06


title: RV HA-Nr4a3, in vitro rep1 tr1 (rna-seq)


title: 1862091032_B05


title: 1862091031_B06


title: RV HA-Nr4a2, in vitro rep1 tr2 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvNR4A2_rep1


title: 1862091030_C05


title: 1862091030_D11


title: RV Empty vector, in vitro rep1 tr1 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvEmpty_rep1


title: RV HA-Nr4a1, in vitro rep1 tr1 (rna-seq)

description:
RNArlog_summary.tsv
invitro_CD8rvNR4A1_rep1


title: RV HA-Nr4a1, in vitro rep1 tr2 (rna-seq)


title: RV HA-Nr4a2, in vitro rep1 tr1 (rna-seq)


title: 1862091029_D04


title: RV Empty vector, in vitro rep1 tr2 (rna-seq)


title: 1862091029_B08


title: 1862091029_A02


title: 1862091024_H04


title: invitro 10U rep1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8Resting

library_source: genomic

data_processing:
Basecalls and demultiplexing performed in illumina basespace
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie v 1.0
Unmapped reads were trimmed of adapters and to a length of 36nt with trim_galore and remapped and merged with first bam file
Merged duplicate
bam files were filtered to extract fragments less than 100 nt, and peak summits were called using MACS2 with parameters
Peak summits from individual replicates were expanded to region of 500bp and overlapping regions from all samples were merged
Tn5 insertions sites per peak were computed for all replicates using all reads and normalized with limma/voom
Genome_build: mm10
Supplementary_files_format_and_content: tsv containing ATAC-seq density

molecule: genomic DNA

source_name: spleen

extract_protocol:
Isolated cells were lysed in 10 mM Tris pH 7.5, 10 mM NaCl, 3mM MgCl2, 0.1% NP-40
Lysed cells were treated with Nextera transposase for 30 minutes at 37°C, followed by PCR amplification.


title: invitro 10U PMAIono rep1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8PMAIono

value: PMAIono


title: 1772099200_C07

source_name: DentGyr


title: 1772099199_G09


title: 1862091028_G05


title: invitro 10U rep2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8Resting


title: 1862091024_G09


title: invitro 10U PMAIono rep2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8PMAIono


title: 1862091020_D02


title: 1862091030_F01


title: 1862091028_F11


title: 1862091019_H01


title: 1862091031_C08


title: naive rep4 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
naive_CD8


title: control_left_01

value: melanoma

value: none (control)

value: distant tumor (left)


title: naive rep3 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
naive_CD8


title: 1772099191_D12

source_name: bone marrow


title: naive rep2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
naive_CD8


title: naive rep1 tr1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
naive_CD8


title: 1772099197_H10


title: naive rep1 tr2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
naive_CD8


title: invitro Mock rep2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvMock


title: 1772099191_B02


title: invitro NFAT CARIT rep2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNFATCARIT


title: invitro NFAT CARIT rep1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNFATCARIT


title: 1862091036_A07


title: 1772099087_E11

source_name: ZonaIncerta


title: 1772099154_C01

source_name: dorsal horn


title: 1772099087_C03


title: 1772099087_C09


title: 1772099086_D03


title: exhausted rep4 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVCl13_CD8PD1hiTIM3hi

value: LCMV Cl13, d20


title: memory rep1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVArm_CD8Memory

value: LCMV Arm, d35


title: exhausted rep1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVCl13_CD8PD1hiTIM3hi


title: 1772099086_G07


title: 1772099086_E10


title: exhausted rep3 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVCl13_CD8PD1hiTIM3hi


title: invitro Mock rep1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvMock


title: effector rep1 tr2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVArm_CD8Effector

value: LCMV Arm, d8


title: 1772099085_G02


title: effector rep2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVArm_CD8Effector


title: 1772099084_B04


title: 1772099085_A08


title: RV Empty vector, in vitro rep2 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvEmpty


title: 1772099083_G10


title: RV HA-Nr4a3, in vitro rep2 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A3


title: effector rep1 tr1 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVArm_CD8Effector


title: 1772099084_A05


title: 1772099083_D05


title: RV Empty vector, in vitro rep2 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvEmpty


title: RV HA-Nr4a2, in vitro rep2 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A2


title: 1772099083_C08


title: 1772099083_D08


title: RV HA-Nr4a3, in vitro rep2 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A3


title: 1772099086_F09


title: 1772099083_A02


title: RV HA-Nr4a1, in vitro rep2 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A1


title: SS2_16_364_B10

description: counts.csv

value: 16 weeks


title: memory rep2 (re-analyzed) (atac-seq)

description:
ATACdensity.tsv
LCMVArm_CD8Memory


title: RV Empty vector, in vitro rep1 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvEmpty


title: RV HA-Nr4a1, in vitro rep2 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A1


title: 1772099080_C04


title: RV HA-Nr4a3, in vitro rep1 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A3


title: RV HA-Nr4a3, in vitro rep1 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A3


title: 1772099078_H08


title: 1772099075_D09


title: 1772099073_B02


title: RV HA-Nr4a2, in vitro rep1 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A2


title: SS2_16_364_A15

description: counts.csv

value: Hippocampus


title: 1772099072_F03


title: 1772099078_D06


title: RV HA-Nr4a2, in vitro rep2 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A2

value: CD8+ T cell


title: RV HA-Nr4a1, in vitro rep1 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A1


title: 1772099072_D05


title: CAR-T cells, in vitro rep5 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8CAR


title: RV HA-Nr4a1, in vitro rep1 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A1


title: CAR-T cells, in vitro rep4 tr1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8CAR


title: CAR-T cells, in vitro rep4 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8CAR


title: 1772099081_C06


title: 1772099072_A03


title: 1772099071_C08


title: 1772099057_G02


title: 1772099058_F05


title: CAR-T cells, in vitro rep3 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8CAR


title: RV Empty vector, in vitro rep1 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvEmpty


title: 1772099057_D12


title: 1772099081_G05


title: CAR-T cells, in vitro rep2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8CAR


title: CAR-T cells, in vitro rep1 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8CAR


title: 1772099056_B04


title: RV HA-Nr4a2, in vitro rep1 tr2 (atac-seq)

description:
ATACdensity.tsv
invitro_CD8rvNR4A2


title: 1772099056_C05


title: Endogenous T cells, PD1loTIM3lo rep8 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8PD1loTIM3lo


title: 1772099054_C10


title: 1772099054_B09


title: Endogenous T cells, PD1loTIM3lo rep7 (atac-seq)


title: Endogenous T cells, PD1loTIM3lo rep6 tr1 (atac-seq)


title: Endogenous T cells, PD1loTIM3lo rep5 (atac-seq)


title: 1772099052_B12


title: 1772099052_F05


title: 1772099050_D04


title: Endogenous T cells, PD1loTIM3lo rep4 (atac-seq)


title: Endogenous T cells, PD1loTIM3lo rep2 (atac-seq)


title: 1772099048_A06


title: 1772099048_H10


title: Endogenous T cells, PD1loTIM3lo rep1 (atac-seq)


title: 1772099046_D09

source_name: SN-VTA


title: Endogenous T cells, PD1loTIM3lo rep3 (atac-seq)


title: Endogenous T cells, PD1hiTIM3lo rep2 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8PD1hiTIM3lo


title: Endogenous T cells, PD1hiTIM3lo rep1 tr2 (atac-seq)


title: 1772099046_A04


title: Endogenous T cells, PD1hiTIM3lo rep1 tr1 (atac-seq)


title: Endogenous T cells, PD1hiTIM3hi rep7 tr1 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8PD1hiTIM3hi


title: Endogenous T cells, PD1hiTIM3lo rep3 (atac-seq)


title: 1772099045_H11


title: 1772099046_G08


title: 1772099044_E12


title: Endogenous T cells, PD1hiTIM3hi rep8 (atac-seq)


title: Endogenous T cells, PD1loTIM3lo rep6 tr2 (atac-seq)


title: Endogenous T cells, PD1hiTIM3hi rep6 tr1 (atac-seq)


title: Endogenous T cells, PD1hiTIM3hi rep7 tr2 (atac-seq)


title: 1772099047_G04


title: 1772099049_C03


title: Endogenous T cells, PD1hiTIM3hi rep4 (atac-seq)


title: Endogenous T cells, PD1hiTIM3hi rep5 (atac-seq)


title: Endogenous T cells, PD1hiTIM3hi rep3 (atac-seq)


title: 1772099038_F03


title: M8_M. bovis

city: Dublin

first: Thomas

last: Hall

state: Select One

address: 2, Taney Grove

department: Vet sciences

country: Ireland

institute: UCD

data_processing:
Stringent adapter trimming (overlap ≥ 1 bp at the 3’ end of each read), and quality trimming (Phred ≤ 20 from the 3’ end of each read) were performed using Trim Galore! [version 0.4.1].
Bisulfite-treated libraries were aligned using Bismark [version 0.15.2] and the Bowtie2 aligner [version 2.2.6] in strand-specific (directional) mode to computationally bisulfite-converted copies of the top and bottom strands of the Bos taurus UMD 3.1 genome.
Paired-end alignments where both mates aligned to the same position in the genome were removed from the Bismark alignment output using the deduplicate_bismark script to mitigate the impact of duplicate DNA fragments sequenced.
The bismark_methylation_extractor script was used in a two-pronged approach. First, methylation calls extracted from the full sequence of aligned read pairs were used to evaluate M-bias across the aligned mates.
After analysis of the M-bias plots generated in the first pass, the second call to the bismark_methylation_extractor script was set to ignore the first 7 bases at the 5’ end of both read mates.
Genome_build: Bos taurus UMD 3.1
Supplementary_files_format_and_content: Bismak genome-wide cytosine reports were generated using bismark_methylation_extractor. They contain seven columns: chromosome, position, strand, count methylated, count non-methylated, C-context, trinucleotide context.

organism: Bos taurus

source_name: Alveolar macrophages

growth_protocol: total lung cells were harvested by pulmonary lung lavage with Hank’s Balanced Salt Solution (Invitrogen, Life Technologies) following the removal of lungs from eight unrelated Holstein-Friesen male calves. Total lung cells were washed and cultured for 24 h at 37 °C in R10+ media (RPMI 1640 medium supplemented with antibiotics [Invitrogen]). After incubation, cells were prepared for infection by dissociation and seeding at 5 × 105, for each biological replicate. The purity of the seeded macrophages was confirmed by flow cytometry using anti-CD14 antibody.

extract_protocol:
DNA was extracted from M. bovis-infected and control bAM, isolated from eight animals, using the DNeasy kit (Qiagen)
Genomic DNA (50 ng) isolated from M. bovis-infected or non-infected bAM (24 hpi) was bisulfite-modified (EZ Methylation-Direct Kit, Zymo)
Libraries were prepared for WGBS using the post–bisulfite conversion library preparation method for methylation analysis (EpiGnome™ Methyl-Seq Kit, Epicentre, Illumina)

treatment_protocol: Macrophages were infected with M.bovis strain AF2122/97 at a multiplicity of infection (MOI) of 10 bacilli per alveolar macrophage

tag: animal

value: M. bovis

tag: barcode

value: ACAGTG


title: 1772099038_H07


title: 1772099036_D12


title: 1772099044_G02


title: M7_M. bovis

value: CGATGT


title: Endogenous T cells, PD1hiTIM3hi rep1 (atac-seq)

tag: strain


title: 1772099040_B12


title: 1772099040_D12


title: OT-I T cells, PD1hiTIM3hi rep1 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8OTIPD1hiTIM3hi

value: OT-I TCR Tg


title: OT-I T cells, PD1hiTIM3hi rep2 (atac-seq)


title: 1772099033_C06


title: 1772099031_C07


title: CAR-T cells, PD1hiTIM3lo rep2 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8CARPD1hiTIM3lo


title: M5_M. bovis

value: ACTTGA


title: 1772099033_G09


title: M12_M. bovis

value: GGCTAC


title: 1772099026_G03


title: 1772099026_G12


title: 1772099044_A08


title: 1772099003_B04


title: Endogenous T cells, PD1hiTIM3hi rep2 (atac-seq)


title: M11_M. bovis


title: M1_M. bovis


title: M4_M. bovis


title: M6_M. bovis


title: CAR-T cells, PD1hiTIM3lo rep1 tr2 (atac-seq)


title: 1772099026_H09


title: CAR-T cells, PD1hiTIM3lo rep1 tr1 (atac-seq)


title: 1772099014_E02


title: C8_Control

value: Control

value: TGACCA


title: 1772099002_D03


title: 1772099001_D08


title: C7_Control

value: ATCACG


title: 1772099001_D06


title: CAR-T cells, PD1hiTIM3hi rep5 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8CARPD1hiTIM3hi


title: 1772096151_D05


title: CAR-T cells, PD1hiTIM3hi rep4 tr2 (atac-seq)


title: CAR-T cells, PD1hiTIM3hi rep3 tr2 (atac-seq)


title: C5_Control

value: CAGATC


title: 1772096149_B06


title: C6_Control

value: TAGCTT


title: CAR-T cells, PD1hiTIM3hi rep3 tr1 (atac-seq)


title: 1772096149_B02


title: 1772099002_C12


title: C4_Control


title: CAR-T cells, PD1hiTIM3hi rep4 tr1 (atac-seq)


title: 1772096149_A05


title: 1772099002_G10


title: 1772096172_C03

source_name: hypothalamus


title: CAR-T cells, PD1hiTIM3hi rep2 tr2 (atac-seq)


title: 1772099001_C04


title: 1772096144_G11


title: C12_Control


title: 1772096148_C05


title: 1772096144_B03


title: CAR-T cells, PD1hiTIM3hi rep2 tr1 (atac-seq)


title: C11_Control


title: CAR-T cells, PD1hiTIM3hi rep1 tr2 (atac-seq)


title: 1772096123_C11


title: 1772096123_C10


title: 1772096122_B05


title: 1772096120_F12


title: C1_Control


title: 1772096120_H12


title: 1772096121_E04


title: CAR-T cells, PD1hiTIM3hi rep1 tr1 (atac-seq)


title: 1772096116_A04


title: 1772096120_D05


title: Nr4aTKO CAR-T cells rep1 tr2 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8CARNr4aTKO

value: RV_Cre, RV_CAR-T


title: 1772096121_A10


title: 1772096131_B07


title: Nr4aTKO CAR-T cells rep2 tr1 (atac-seq)


title: 1772096115_A12

source_name: ventral midbrain


title: 1772096101_C10


title: 1772096101_A12


title: Nr4aWT CAR-T cells rep2 tr2 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8CARNr4a3WT

value: RV_Empty, RV_CAR-T


title: Nr4aTKO CAR-T cells rep2 tr2 (atac-seq)


title: 1772096099_D11


title: Nr4aWT CAR-T cells rep2 tr1 (atac-seq)


title: 1772096100_F11


title: 1772096099_A01


title: 1772099045_A08


title: 1772094174_B10


title: 1772094175_D05


title: Nr4a3KO CAR-T cells rep2 (atac-seq)

description:
ATACdensity.tsv
B16OVAhCD19_CD8CARNr4a3KO


title: 1772094162_G01


title: 1772094173_B03


title: 1772094162_G03


title: 1772096100_C02


title: 1772094158_F03


title: pol2-wt-2: wild-type Rpb1 ChIP-Seq 2

city: Boston

first: Rajaraman

last: Gopalakrishnan

state: MA

address: NRB 239, 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: ChIP-Seq of Rpb1 in a wild-type S. cerevisiae strain grown at 30ºC

data_processing:
Reads were trimmed using cutadapt (base quality threshold of 20)
Reads were aligned to a combined S. cerevisiae + S. pombe genome using Bowtie2
Average fragment size of DNA molecules sequenced was determined by cross-correlation (done in R using the SPP package)
Reads mapping to S. cerevisiae genome were separated from the reads mapping to the S. pombe genome
Coverage files (wig format) were produced using the igvtools count function, extending reads by (length of fragment sizes - average read length) for each library.
wig format files were converted to the bedgraph format
Spike in normalization was done as described previously(Orlando et al., 2014), correcting for variations in the input samples.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: The bedGraph files contain spike-in normalized coverage of DNA fragments obtained after immunoprecipitation. Average fragment length determined using cross-correlation

organism: Saccharomyces cerevisiae

source_name: log phase S. cerevisiae

growth_protocol: S.cerevisiae cells were grown to OD600 ≈ 0.6 (~2x107 cells) in YPD at 30ºC

extract_protocol:
Cultures were cross-linked by the addition of formaldehyde to a final concentration of 1% followed by incubation with shaking at room temperature for 20 minutes. Glycine was added to a final concentration of 125 mM and the incubation was continued for 10 minutes. The cells were pelleted and washed twice with cold 1x TBS (100mM Tris, 150 mM NaCl, pH 7.5) and once with cold water. The cell pellets were then suspended in 800 µl cold LB140 buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1x cOMPLETE Protease Inhibitor tablet (Roche)). One ml of glass beads was added and the cells were lysed by bead beating for 8 minutes at 4oC with incubation on ice for 3 minutes after every one minute. The lysate was collected and centrifuged at 12,500 rpm for 5 minutes and the resulting pellet was washed once with 800 µl cold LB140 buffer. The pellet was resuspended in 580 µl cold LB140 buffer and sonicated in a QSonica Q800R machine for 20 minutes (30 seconds on, 30 seconds off, 70% amplitude). The sonicated samples were centrifuged at 12,500 rpm for 30 minutes and the resulting supernatant was taken for the immunoprecipitation step. 300-500 µg of S. cerevisiae chromatin was mixed with 33-55 µg (10%) of S. pombe chromatin and the volume was brought up to 800 µl with WB140 buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate). This was used as the input for the immunoprecipitation reaction. Antibody was added to the input and the samples incubated overnight at 4oC with end-over-end rotation. Fifty µl of Protein G sepharose beads (GE healthcare) pre-washed twice in WB140 was added to the IPs and samples were incubated for 4 hours at 4oC with end-over-end rotation. . The beads were washed twice with WB140, twice with WB500 (50 mM HEPES-KOH, pH 7.5, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), twice with WBLiCl (10 mM Tris pH 7.5, 250 mM LiCl, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) for two minutes each and once with TE (10 mM Tris pH 7.4, 1 mM EDTA) for five minutes. The immunoprecipitated material was eluted twice with 100 µl TES (50 mM Tris pH 7.4, 1 mM EDTA, 1% SDS) at 65oC for 30 minutes. The eluates were incubated at 65oC overnight to reverse the crosslinking. Two hundred µl of TE was added to the eluates followed by RNase A/T1 to a final concentration of 0.02 µg/µl. The samples were incubated at 37oC for 2 hours. Proteinase K was added to a final concentration of 0.4 mg/ml and samples were incubated at 42oC for 2 hours. DNA was purified using Zymo DCC (for ChIP-Seq).
The library preparation was done as described in Wong et al., 2013.

tag: temperature

tag: tissue

value: log phase S. cerevisiae


title: Nr4a3KO CAR-T cells rep1 tr2 (atac-seq)

tag: treatment


title: 1772094158_B01

tag: age


title: pol2-spt6-set2-2: spt6-1004 SET2-H366N Rpb1 ChIP-Seq 2

description: ChIP-Seq of Rpb1 in a spt6-1004 SET2-H366N mutant S. cerevisiae strain grown at 30ºC


title: 1772096088_E11


title: Nr4aTKO CAR-T cells rep1 tr1 (atac-seq)


title: pol2-wt-1: wild-type Rpb1 ChIP-Seq 1


title: 1772094154_D02


title: 1772094155_F09


title: Nr4a3KO CAR-T cells rep1 tr1 (atac-seq)


title: 1772099035_B02


title: pol2-spt6-2: spt6-1004 Rpb1 ChIP-Seq 2

description: ChIP-Seq of Rpb1 in a spt6-1004 mutant S. cerevisiae strain grown at 30ºC


title: pol2-spt6-set2-1: spt6-1004 SET2-H366N Rpb1 ChIP-Seq 1


title: 1772094148_G03

source_name: striatum


title: 1772094155_E04


title: Nr4aWT CAR-T cells rep1 tr1 (atac-seq)


title: 1772094147_C03


title: Nr4aWT CAR-T cells rep1 tr2 (atac-seq)


title: 1772094146_C08


title: 1772094144_F02


title: iPax3 single-cell RNA-Seq, 2

data_processing:
Illumina Casava 1.8 software used for basecalling.
libraries were aggregated and normalized via cellranger aggr function (--id=cellranger-aggr --csv=metadata.csv) using cellranger version 2.2.0. The output cloupe.cloupe file was imported into Loupe? Cell Browser (10X Genomics) version 2.0.0 and clusters were classified based on cell type.
Differential gene expression was determined via two methods: 1) Globally Distinguishing: for each selected cluster or group in a category, genes that distinguish that cluster from every other cell in the dataset were identified and 2) Locally Distinguishing: for each checked cluster or group, genes that distinguish that cluster from the other currently checked clusters in that category.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include aggregated gene expression matrix and differential gene expression results.

source_name: PSC-derived myogenic progenitors

growth_protocol: iPax3/iPax7 myogenic progenitors were generated thorugh sorting of Vcam1+Flk1- cells from EBs, plated and expanded upon Dox and bFGF administration for 3 passages, then collected with PBS-based dissociation buffer and submitted for downstream analyses.

extract_protocol: Libraries were prepared using Illumina standard protocols (RNA-Seq); Chromium Single Cell 3’ Reagent kit 10X Genomics (single-cell RNA-Seq)

value: ES-derived myogenic progenitors


title: pol2-spt6-1: spt6-1004 Rpb1 ChIP-Seq 1


title: pol2-set2-2: SET2-H366N Rpb1 ChIP-Seq 2

description: ChIP-Seq of Rpb1 in a SET2-H366N S. cerevisiae strain grown at 30ºC


title: 1772094142_D11


title: 1772094142_D02


title: iPax3 single-cell RNA-Seq

description: single-cell iPax3

extract_protocol:
Cultured Cells and freshly sorted tissue-derived cells were lysated with buffer RA1+TCEP of kit RNA XS (Machirey-Nagel) and RNA was extracted according to manufacturer's instructions.
Libraries were prepared using Illumina standard protocols (RNA-Seq); Chromium Single Cell 3’ Reagent kit 10X Genomics (single-cell RNA-Seq)


title: 1772094141_A12


title: Adult satellite cells single-cell RNA-Seq

description: single-cell Sat

source_name: mouse Tibialis anterior

value: mouse myogenic progenitors

value: 3 months-old


title: 1772094155_C12


title: input-wt-2: wild-type Input ChIP-Seq 2

description: ChIP-Seq of Input in a wild-type S. cerevisiae strain grown at 30ºC


title: 1772094135_A03


title: input-wt-1: wild-type Input ChIP-Seq 1


title: pol2-set2-1: SET2-H366N Rpb1 ChIP-Seq 1


title: 1772094141_E07


title: jac_NASH-150

city: College Station

first: Ivan

last: Rusyn

address: Department of Veterinary Integrative Biosciences  College of Vet Medicine & Biomedical Sciences  4458 TAMU Texas A&M University

institute: Texas A&M University

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings
Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
Trimmomatic used to trim adapter sequences and low quality bases
TopHat v.2.0.13 was used to map to GRcm38/mm10 assembly
HTSeq was used to generate read counts per gene using the intersection-nonempty parameter to account for ambiguous read mappings
DESeq2 was used to generate normalized counts for each gene (using the parameter normalized=TRUE)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample.

source_name: Kidney

extract_protocol:
Total RNA was extracted from pulverized kidney tissue using Qiagen miRNEasy kits.
Libraries were prepared according to Illumina's instructions accompanying the commercial-available kit (Illumina Truseq stranded mRNA HT kit cat# RS-122-2103)

tag: diet group

value: LFD

value: Vehicle

tag: dose

value: Repeated


title: jac_NASH-149

department: Department of Veterinary Integrative Biosciences


title: 1772094132_F02


title: 1772094133_F06


title: 1772094134_E04


title: input-spt6-set2-2: spt6-1004 SET2-H366N Input ChIP-Seq 2


title: 1772094134_D05


title: 1772094131_E07


title: jac_NASH-148

value: PERC


title: input-spt6-set2-1: spt6-1004 SET2-H366N Input ChIP-Seq 1


title: input-spt6-2: spt6-1004 Input ChIP-Seq 2


title: 1772094125_H09


title: 1772094124_G07


title: 1772094125_G08


title: 1772094141_H07


title: 1772094124_E08


title: input-spt6-1: spt6-1004 Input ChIP-Seq 1


title: input-set2-2: SET2-H366N Input ChIP-Seq 2


title: jac_NASH-090

value: HFD


title: 1772094124_D05


title: jac_NASH-088

value: MCD


title: 1772094121_H03


title: jac_NASH-092


title: input-set2-1: SET2-H366N Input ChIP-Seq 1


title: 1772094122_D03


title: Endogenous T cells, PD1hiTIM3hi rep6 tr2 (atac-seq)

source_name: B16-OVA-hCD19 tumor infiltrating lymphocytes

tag: cell type

value: CD8+ T cell


title: ha-wt-2: wild-type Set2-HA ChIP-Seq 2

description: ChIP-Seq of HA tagged Set2 in a wild-type S. cerevisiae strain grown at 30ºC


title: 1772094124_A03


title: jac_NASH-086


title: 1772099044_D03


title: jac_NASH-147


title: 1772099036_D09


title: 1772094118_G11


title: ha-wt-1: wild-type Set2-HA ChIP-Seq 1


title: ha-spt6-set2-2: spt6-1004 SET2-H366N Set2-HA ChIP-Seq 2

description: ChIP-Seq of HA tagged Set2 in a spt6-1004 SET2-H366N mutant S. cerevisiae strain grown at 30ºC


title: jac_NASH-146


title: ha-spt6-set2-1: spt6-1004 SET2-H366N Set2-HA ChIP-Seq 1


title: 1772092312_C06


title: jac_NASH-144


title: ha-spt6-2: spt6-1004 Set2-HA ChIP-Seq 2

description: ChIP-Seq of HA tagged Set2 in a spt6-1004 mutant S. cerevisiae strain grown at 30ºC


title: jac_NASH-091


title: jac_NASH-087


title: 1772094111_D10


title: 1772094111_F11


title: 1772094108_D01


title: 1772094111_H06


title: 1772094111_E04


title: 1772099035_C06


title: jac_NASH-089


title: jac_NASH-085


title: ha-set2-2: SET2-H366N Set2-HA ChIP-Seq 2

description: ChIP-Seq of HA tagged Set2 in a SET2-H366N S. cerevisiae strain grown at 30ºC


title: ha-spt6-1: spt6-1004 Set2-HA ChIP-Seq 1


title: 1772092308_F09


title: 1772092309_B04


title: jac_NASH-084


title: 1772092305_G04


title: 1772092308_B10


title: 1772092295_A10


title: 1772092305_F06


title: 1772092307_G07


title: 1772092307_G05


title: 1772092305_D11


title: 1772092296_H10


title: 1772092294_F06


title: jac_NASH-082


title: jac_NASH-080


title: h3-wt-2: wild-type H3 ChIP-Seq 2

description: ChIP-Seq of H3 in a wild-type S. cerevisiae strain grown at 30ºC


title: 1772092293_A04


title: jac_NASH-078


title: ha-set2-1: SET2-H366N Set2-HA ChIP-Seq 1


title: h3-spt6-set2-1: spt6-1004 SET2-H366N H3 ChIP-Seq 1


title: 1772092293_C01


title: h3-wt-1: wild-type H3 ChIP-Seq 1


title: 1772092290_G04


title: 1772092290_E09


title: h3-spt6-2: spt6-1004 H3 ChIP-Seq 2


title: 1772092290_E12


title: 1772092290_E07


title: 1772092290_A02


title: 1772092289_G01


title: h3-set2-2: SET2-H366N H3 ChIP-Seq 2


title: h3-set2-1: SET2-H366N H3 ChIP-Seq 1


title: jac_NASH-142


title: 1772092269_G07


title: jac_NASH-083


title: jac_NASH-143


title: 1772092270_H10


title: 1772092287_E04


title: jac_NASH-140


title: 1772092277_D04


title: 1772092269_E04


title: jac_NASH-145


title: 1772092293_E04


title: h3-spt6-set2-2: spt6-1004 SET2-H366N H3 ChIP-Seq 2


title: 1772092260_C09


title: 1772092260_C04


title: h3k36me3-wt-1: wild-type H3K36me3 ChIP-Seq 1

description: ChIP-Seq of H3K36me3 in a wild-type S. cerevisiae strain grown at 30ºC


title: h3k36me3-wt-2: wild-type H3K36me3 ChIP-Seq 2


title: 1772092008_F10


title: 1772092288_E11


title: jac_NASH-079


title: 1772092009_A01


title: h3-spt6-1: spt6-1004 H3 ChIP-Seq 1


title: jac_NASH-077


title: 1772092007_D06


title: 1772092007_C09


title: h3k36me3-spt6-set2-2: spt6-1004 SET2-H366N H3K36me3 ChIP-Seq 2


title: jac_NASH-081


title: 1772092008_F05


title: 1772092006_H03


title: h3k36me3-spt6-2: spt6-1004 H3K36me3 ChIP-Seq 2


title: jac_NASH-076


title: 1772092006_G06


title: h3k36me3-spt6-1: spt6-1004 H3K36me3 ChIP-Seq 1


title: jac_NASH-074


title: 1772092005_F06


title: 1772092005_E01


title: jac_NASH-141


title: 1772092004_E09


title: 1772089202_H04


title: 1772089201_B07


title: h3k36me3-spt6-set2-1: spt6-1004 SET2-H366N H3K36me3 ChIP-Seq 1


title: h3k36me3-set2-2: SET2-H366N H3K36me3 ChIP-Seq 2


title: h3k36me2-wt-2: wild-type H3K36me2 ChIP-Seq 2

description: ChIP-Seq of H3K36me2 in a wild-type S. cerevisiae strain grown at 30ºC


title: h3k36me3-set2-1: SET2-H366N H3K36me3 ChIP-Seq 1


title: 1772089200_F10


title: jac_NASH-073


title: 1772089200_E05


title: jac_NASH-075


title: 1772089200_A04


title: 1772089186_G10


title: 1772089200_F03


title: 1772089190_B08


title: jac_NASH-138


title: 1772089186_G06


title: jac_NASH-072


title: jac_NASH-071


title: 1772089190_A08


title: h3k36me2-wt-1: wild-type H3K36me2 ChIP-Seq 1


title: h3k36me2-spt6-set2-2: spt6-1004 SET2-H366N H3K36me2 ChIP-Seq 2

description: ChIP-Seq of H3K36me2 in a spt6-1004 SET2-H366N mutant S. cerevisiae strain grown at 30ºC


title: 1772078032_H08


title: 1772084017_G12


title: 1772078031_F01


title: jac_NASH-070


title: jac_NASH-139


title: 1772078028_H12


title: h3k36me2-spt6-1: spt6-1004 H3K36me2 ChIP-Seq 1

description: ChIP-Seq of H3K36me2 in a spt6-1004 mutant S. cerevisiae strain grown at 30ºC


title: 1772078023_E04


title: h3k36me2-spt6-2: spt6-1004 H3K36me2 ChIP-Seq 2


title: h3k36me2-set2-2: SET2-H366N H3K36me2 ChIP-Seq 2

description: ChIP-Seq of H3K36me2 in a SET2-H366N S. cerevisiae strain grown at 30ºC


title: 1772078019_C11


title: 1772078018_B02


title: jac_NASH-066


title: 1772078017_A10


title: 1772078016_C10


title: 1772078013_H05


title: h3k36me2-spt6-set2-1: spt6-1004 SET2-H366N H3K36me2 ChIP-Seq 1


title: jac_NASH-137


title: 1772078014_F01


title: Chae rep1

city: Istanbul

first: Tugba

last: Bagci-Onder

state: Sariyer

address: Koc University School of Medicine

department: School of Medicine

country: Turkey

institute: Koc University

data_processing:
a soft adapter trimming was applied to low quality ends of all samples with using cutadapt with - -quality-cutoff=5. The trimmed fastqs were aligned to human genome GRCh37.75 using TopHat2 with default parameters only adding --library-type=fr-unstranded --num-threads=8 –no-mixed –no-coverage-search. Tophat-recondition is used to restore correct and restore unmapped reads with default parameters. Samtools is used to merge the two BAM files.
Raw read counts are generated using feautureCounts with -s 0 parameter.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: Tab delimeted text files with raw counts for all samples.

source_name: GBM cells

growth_protocol: U87MG cells were seeded to 6 well tissue culture plates with DMEM supplemented with 10% FBS and 1% pen/Strep at300.000 cell/well density and incubated for 24 hr until cells were fully attached.

extract_protocol:
High quality total RNA was extracted from samples using Nucleospin RNA kit of Macherey-Nagel and eluted in RNAse free water.
Library preparation was performed by the Functional Genomics Laboratory (FGL),  a QB3-Berkeley Core Research Facility at UC Berkeley. mRNA enrichment was performed on total RNA using polyA selection with the Invitrogen Dynabeads mRNA Direct kit. Subsequent library preparation steps of enzymatic fragmentation, adapter ligation and cDNA synthesis were done on the enriched RNA on an Apollo 324™ liquid handling system, with PrepX™ RNAseq Library Prep Kits (WaferGen/now TakaraBio). 15 cycles of PCR amplification was used for index addition and library fragment enrichment. Libraries were sequenced on an Illumina HiSeq4000 by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant.

treatment_protocol: Cells were treated with Chaetocin at 50 nM concentration (in DMSO) for 24h.Control cells were left untreated.

value: GBM

tag: passages

tag: genotype

value: wild type


title: Chae rep2


title: jac_NASH-069


title: jac_NASH-135


title: Control rep2


title: jac_NASH-068


title: 1772075310_D02


title: 1772078013_D03


title: Control rep1


title: jac_NASH-067


title: 1772075304_A02


title: 1772078018_C03


title: 1772075302_F08


title: jac_NASH-136


title: h3k36me2-set2-1: SET2-H366N H3K36me2 ChIP-Seq 1


title: jac_NASH-064


title: 1772072246_E05


title: 1772078013_B09


title: 1772072246_A01


title: LO3

city: Fort Collins

first: Ahmed

last: Gad

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Information of adapter and UMI in raw reads was extracted using Cutadapt
The output from cutadapt is used to remove adapter sequences and reads ≥18 nucleotides were analyzed for the presence of Unique Molecular Indices (UMIs). All reads containing identical insert sequence and UMI sequence (insert-UMI pair) were collapsed into a single read.
Sequence reads were mapped to Sus scrofa reference genome (release Sscrofa10.2) using Bowtie2 (2.2.2)
Mapped reads were used for annotation against both mature and precursor miRNAs of porcine and all other organism listed in the mirBase database (release 21)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization)
The differential expression analysis was done using TMM in the EdgeR statistical software package
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Tab separated values file include TPM values for each sample

organism: Sus scrofa

source_name: Oocyte

extract_protocol:
Total RNA enriched with miRNA was isolated from denuded oocytes of different groups using mirVana™ miRNA Isolation Kit (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instruction.
MicroRNA library preparation was done using the QIAseq miRNA Library Kit (QIAGEN) according to the Illumina small RNA sample preparation protocol.

treatment_protocol: Porcine ovaries were collected from prepubertal gilts at a local abattoir and transported to our laboratory in flask within 3 h after slaughter. Ovaries were washed three times with saline solution. COCs were aspirated from small follicles with diameter <2 mm (SO) using a 23-gauge needle attached to a 5 mL syringe or from large follicles with diameter from 3 to 6 mm (LO) using 20-gauge needle attached to a 10 mL syringe.

tag: animal reproductive stage

value: Prepubertal gilts

tag: follicle size

value: Large (3-6 mm)


title: SO1

value: Small (<2 mm)


title: 1772072246_C05


title: 1772075319_E09


title: 1772071055_G05

source_name: cortex S1


title: SO3


title: SO2


title: jac_NASH-061


title: 1772075304_G10


title: 1772071055_C08


title: 1772071068_B07

source_name: epidermis (dorsal)


title: jac_NASH-065


title: LO1


title: jac_NASH-062


title: 1772072247_G07


title: 1772071055_E02


title: 1772071053_G04


title: 1772072246_H07


title: IPO-3

city: Changsha

first: Pengpeng

last: Zhang

state: Hunan

address: No.138 Tongzipo Road

institute: The Third Xiangya Hospital of Central South University

data_processing:
Subsequent data processing was performed to use the R software Ballgown package
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: IPO, liver

extract_protocol:
liver samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina KAPA Stranded RNA-Seq Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: post natal 8 weeks

value: IPO


title: jac_NASH-130

value: Single


title: 1772071053_D05


title: IPO-2


title: 1772071053_D04


title: jac_NASH-125


title: LO2


title: 1772071053_A02


title: 1772071046_C12


title: IPO-1


title: I-R-3

source_name: I/R, liver

value: I/R


title: 1772071055_B10


title: 1772071044_B03

source_name: hippo CA1


title: 1772067094_C07


title: jac_NASH-060


title: 1772067096_G06


title: jac_NASH-063


title: jac_NASH-129

value: LFD


title: jac_NASH-120


title: I-R-2


title: 1772067092_C11


title: 1772071053_H01


title: jac_NASH-059

value: Vehicle


title: jac_NASH-046


title: I-R-1


title: 1772067070_C02


title: 1772067074_D04


title: N-3

source_name: N, liver

value: sham


title: 1772067064_D12


title: 1772067064_B09


title: N-2


title: jac_NASH-045

value: PERC


title: 1772071046_D06


title: N-1


title: jac_NASH-055


title: 1772067078_B07


title: 1772067057_B09


title: 1772066104_B07


title: 1772067057_G11


title: jac_NASH-040

value: HFD


title: 1772066096_E03


title: jac_NASH-115


title: 1772066098_G07


title: 1772066095_G07


title: 1772066096_B02


title: 1772066095_B12


title: jac_NASH-058


title: jac_NASH-054

value: MCD


title: 1772066096_G06


title: 1772066090_B06


title: jac_NASH-053


title: jac_NASH-128


title: 1772066090_E08


title: 1772067058_C04


title: 1772066087_E02


title: H522U48

city: Tampa

first: Eric

last: Welsh

state: FL

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center

description: H522 cells untreated for 48 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The images were analyzed with the Affymetrix GCOS 1.4 software, then normalized using IRON against A549T2 as the reference sample

label: biotin

source_name: H522 lung cancer cells

label_protocol: Biotinylated cRNA was prepared according to the Ambion Message Amp Premier protocol using 100 ng of total RNA (Ambion).

growth_protocol: The NSCLC cell lines were grown in RPMI-1640, supplemented with 10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, and 1 mM glutamine. The cell lines were maintained in a humid incubator at 37°C and 5% CO2.

extract_protocol: Isolation of total RNA was performed using the Qiagen RNEasy column according to the manufacturer's instructions.

treatment_protocol: NSCLC cell lines were treated with TGFβ-1 (5 ng/mL). Untreated and treated cells were harvested at various times (0, 24, 48, and 120 hours). Media was aspirated and cells were dissolved in Tryzol, then transferred to a 15 mL conical tube for storage at -20°C.

tag: cell line

value: NSCLC

value: Untreated

tag: time point (hours)

tag: condition

tag: phenotype

value: Epitheleal

tag: will transition

value: NoEMT

tag: sample batch date


title: 1772066101_E10

first: Ori

last: Staszewski


title: jac_NASH-035

tag: strain


title: jac_NASH-110


title: H441T48

description: H441 cells untreated for 48 hours

source_name: H441 lung cancer cells

value: TGFB


title: 1772066084_B04

source_name: ventral midbrain


title: 1772067070_C04


title: H522U0

description: H522 cells untreated for 0 hours


title: 1772066090_D03


title: jac_NASH-030


title: 1772066080_F07


title: 1772066084_A07


title: H358T48

description: H358 cells untreated for 48 hours

source_name: H358 lung cancer cells

value: Mesenchymal

value: EMT


title: H358T120

description: H358 cells untreated for 120 hours


title: jac_NASH-025


title: 1772063078_G02


title: 1772063078_A09


title: 1772063078_E10


title: 1772066077_B04


title: H358U0

description: H358 cells untreated for 0 hours


title: 1772063077_D08


title: 1772063077_D09


title: jac_NASH-020


title: 1772066076_A07


title: H358U120

description: H358 cells untreated for 120 hours


title: 1772063079_A05


title: H292T120

description: H292 cells untreated for 120 hours

source_name: H292 lung cancer cells


title: 1772063074_G02


title: jac_NASH-105


title: 1772066084_E02


title: jac_NASH-126


title: 1772063077_E03


title: 1772063074_E07


title: H292U120

description: H292 cells untreated for 120 hours


title: H522T48

description: H522 cells untreated for 48 hours


title: H322T48

description: H322 cells untreated for 48 hours

source_name: H322 lung cancer cells


title: 1772063077_D12


title: jac_NASH-056


title: jac_NASH-127


title: 1772063074_B12


title: jac_NASH-015


title: H292T2

description: H292 cells untreated for 2 hours


title: H322U0

description: H322 cells untreated for 0 hours


title: H292U0

description: H292 cells untreated for 0 hours


title: H292T48

description: H292 cells untreated for 48 hours


title: jac_NASH-057


title: 1772063070_C07


title: 1772063074_H12


title: 1772063063_H11


title: 1772063063_E05


title: 1772063062_G08


title: jac_NASH-052


title: 1772063074_F08


title: 1772063074_C03


title: jac_NASH-051


title: 1772063061_H11


title: 1772063061_F10


title: H23T48

description: H23 cells untreated for 48 hours

source_name: H23 lung cancer cells


title: 1772062128_H04


title: H292U48

description: H292 cells untreated for 48 hours


title: 1772063061_E08


title: 1772063074_B06


title: 1772063074_B03


title: 1772062128_E12


title: 1772062128_D02


title: H2347T120

description: H2347 cells untreated for 120 hours

source_name: H2347 lung cancer cells


title: jac_NASH-010

source_name: Kidney


title: jac_NASH-005


title: 1772062128_B03


title: H2347U120

description: H2347 cells untreated for 120 hours


title: 1772063062_D07


title: 1772062118_H06


title: 1772063063_A03


title: 1772062118_F11


title: 1772062118_F04


title: 1772062128_F05


title: 1772063061_C11


title: H2122U120

description: H2122 cells TGFB treated for 120 hours

source_name: H2122 lung cancer cells


title: H1648T120

description: H1648 cells TGFB treated for 120 hours

source_name: H1648 lung cancer cells


title: H2122T120

description: H2122 cells TGFB treated for 120 hours


title: 1772062118_D03

source_name: cortex S1


title: H23U0

description: H23 cells untreated for 0 hours


title: 1772062118_A11


title: 1772062116_G09


title: 1772062128_C02


title: H1944T48

description: H1944 cells TGFB treated for 48 hours

source_name: H1944 lung cancer cells


title: 1772062128_A07


title: H1944U120

description: H1944 cells TGFB treated for 120 hours


title: 1772062116_D02


title: 1772062116_B06


title: 1772062118_H03


title: H1944T120

description: H1944 cells TGFB treated for 120 hours


title: H1944U0

description: H1944 cells TGFB treated for 0 hours


title: 1772062118_E06


title: 1772062118_H01


title: H1437T120

description: H1437 cells TGFB treated for 120 hours

source_name: H1437 lung cancer cells


title: 1772062118_D09


title: 1772062118_F03


title: 1772062115_C02


title: 1772062118_B06


title: H1437U120

description: H1437 cells TGFB treated for 120 hours


title: H1648U120

description: H1648 cells TGFB treated for 120 hours


title: Calu6T48

description:
constitutively mesenchymal
Calu6 cells TGFB treated for 48 hours

source_name: Calu6 lung cancer cells


title: A549T120

description: A549 cells TGFB treated for 120 hours

source_name: A549 lung cancer cells


title: 1772062111_G10


title: 1772062116_A09


title: 1772062115_A07


title: 1772062115_H11


title: H1395T48

description: H1395 cells TGFB treated for 48 hours

source_name: H1395 lung cancer cells


title: 1772062111_E11


title: H1395U0

description: H1395 cells TGFB treated for 0 hours


title: 1772062116_E04


title: 1772062111_F12


title: A549T48

description: A549 cells TGFB treated for 48 hours


title: 1772062113_E05


title: 1772062113_A11


title: 1772062111_H06


title: Calu6U0

description:
constitutively mesenchymal
Calu6 cells TGFB treated for 0 hours


title: A549U120

description: A549 cells TGFB treated for 120 hours


title: A549T24

description: A549 cells TGFB treated for 24 hours


title: 1772062111_G09


title: 1772062111_G08


title: A549T2

description: A549 cells TGFB treated for 2 hours


title: A549U48

description: A549 cells TGFB treated for 48 hours

value: Epithelial


title: 1772062111_G06


title: 1772062111_D12


title: A549U0

description: A549 cells TGFB treated for 0 hours


title: H441U0

description: H441 cells untreated for 0 hours


title: 1772062111_A05


title: 1772062109_F11


title: 1772062109_F04


title: 1772062111_C05


title: 1772062109_G05


title: 1772062109_D12


title: 1772062109_D10


title: 1772062111_C12


title: 1772062109_D06


title: 1772062109_D01


title: 1772062109_E12


title: 1772062109_C12


title: 1772062109_C06


title: 1772062109_C05


title: 1772062109_A06


title: 1772062109_A11


title: 1772062109_E05


title: 1772060240_H11


title: 1772063077_F06


title: 1772060240_H10


title: 1772062109_B11


title: P22_Infected

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

hyb_protocol: Nine µg labeled cRNA were hybridized onto Human Genome U133 Plus 2.0 GeneChips (Affymetrix), revealed and washed using FS450 fluidic station.

scan_protocol: GeneChips were scanned using a 3000 scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

data_processing: The MAXRS algorithm was used to summarize probe information into probesets. Then, dataset was normalized using Tukey median polish algorithm.

source_name: Nasal swab

label_protocol: cRNA labelling was performed after a 3-step amplification protocol, according to Affymetrix specifications

growth_protocol: Nasal wash samples were collected in RNAlater® Stabilization Solution (Thermo Fisher Scientific).

extract_protocol: Total RNA was extracted using RNeasy Micro kit, Qiagen following the manufacturer’s instructions. RNA quality was assessed using a Bioanalyzer2100 (Agilent technologies, Inc, Palto Alto, CA, USA).

treatment_protocol: Samples were stored at -80°C until extraction

tag: patient id

tag: status

value: Infected


title: TCR_spleen_02

data_processing:
Data processing, assignment, and data aggregation were automatically performed using repertoire analysis software originally developed by Repertoire Genesis.
Sequence reads were used for repertoire analysis of T cell receptor beta locus
Genome_build: Mouse TRB
Supplementary_files_format_and_content: tab-delimited text files including TRBV/TRBJ , amino acid sequence, read counts

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Total RNA was converted to complementary DNA (cDNA) with Superscript III reverse transcriptase (Invitrogen, Carlsbad, California, USA). Then, double strand (ds)-cDNA was synthesized and an adaptor was ligated to the 5′ end of the ds-cDNA and cut with SphI restriction enzyme. For TCRβ, PCR was performed with a P20EA adaptor primer and a TCRβ-chain constant region-specific primer (mCB1). The second PCR was performed with mCB2 and P20EA primers using the same PCR conditions. After Tag PCR amplification, index (barcode) sequences were added by amplification with a Nextera XT Index Kit v2 setA (Illumina, San Diego, California, USA). Sequence was done with the Illumina MiSeq paired-end platform (2 × 300 base pairs (bp)).

treatment_protocol: C57BL/6 mice were inoculated subcutaneously with tumor cells (MO4; an ovalbumin (OVA)-expressing B16F10 melanoma cell line of C57BL/6 origin) into the right and left hindlimb simultaneously (1 × 10^5) on day 0. On day 5, when tumors were palpable, mice were treated peritumorally with IFN-α-iPSC-pMCs (1 × 10^6) into the right hindlimb on days 5, 6, 7, 12, and 13. Total RNA from tumor tissue was extracted on day 14.

tag: tissue

value: spleen


title: P47_Cured

value: Cured


title: 1772062109_B10

city: Freiburg

address: Breisacher Str. 64

institute: University Medical Center Freiburg

tag: age


title: P8_Infected


title: TCR_distant_tumor_02

value: melanoma

value: distant tumor


title: TCR_spleen_01


title: 1772060226_G10


title: P24_Cured


title: P19_Cured


title: P48_Infected


title: P48_Cured


title: P46_Cured


title: P24_Infected


title: 1772060226_E03

source_name: sscortex


title: 1772060240_F05


title: 1772060226_H12


title: P17_Cured


title: 1772060225_F12


title: TCR_treated_tumor_02

value: IFN-α-iPSC-pMC-treated tumor


title: 1772060226_H02


title: Ramos640

city: Shanghai

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCh37  genome using Mapsplice v2.1.6 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
read count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Ramos640 cells

growth_protocol: Ramos and Ramos640 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: Ramos640 cells were treated with 640 mg/mL Rituximab and 20% NHS every 21 days to maintain resistance.

value: Rituximab-resistant Burkitt's lymphoma cells

value: derived from Ramos


title: 1772060226_A10


title: P17_Infected


title: 1772060226_D02


title: 1772060226_A08


title: 1772060225_F05


title: TCR_treated_tumor_01


title: Ramos

source_name: Ramos cells

value: Burkitt's lymphoma cell line

value: Ramos


title: 1772060226_F12


title: P16_Cured


title: P16_Infected


title: P46_Infected


title: TCR_distant_tumor_01


title: 1772060224_H07


title: 1772060224_F07


title: 1772060224_D03


title: P14_Cured


title: OVK18_WRN3A

first: Edmond

last: Chan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
Data was processed using Illumina Bcl2fastq v2.18
Sequencing reads were aligned to hg19 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: comma seperated value (CSV) files for all samples. STAR_Gene_Counts.csv reports raw counts. Cuff_Gene_Counts.csv reports FPKM.

extract_protocol:
Total RNA was purified according to the Qiagen RNeasy Mini Kit protocol
Libraries were prepared using Roche Kapa mRNA Hyper sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol

treatment_protocol: Cas9 expressing SW48 and OVK18 cells were transduced with indicated sgRNA 72 hours before harvesting

tag: sgrna transduction

tag: replicate

value: A


title: OVK18_WRN3B

value: B


title: P19_Infected


title: 1772060226_A06


title: 1772060224_G02


title: P14_Infected


title: 1772060224_B12


title: OVK18_WRN2B


title: 1772060224_B07


title: P10_Cured


title: 1772060224_A06


title: OVK18_WRN2A


title: 1772058177_G04


title: OVK18_Ch2-2B


title: 1772058177_F07


title: UT286 peptide3

institute: University of Minnesota

description:
Ex vivo culture human tumor - peptide
Human 2 Unnormalized Counts.csv

source_name: endometrial tumor

extract_protocol:
RNA was isolated using TRIZOL and further purified using the QIAGEN RNA Cleanup Kit
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Library Prep Kit)

tag: peptide

value: Relevant viral peptide

tag: peptide therapy

value: Ex vivo peptide culture w/ tumor slice


title: P9_Cured


title: UT286 peptide2


title: 1772058177_E03


title: P10_Infected


title: 1772058177_D11


title: 1772058177_D10


title: SW48_WRN3A


title: OVK18_Ch2-2A


title: 1772060225_E03


title: 1772058177_C03


title: UT286 control3

description:
Ex vivo culture human tumor - control
Human 2 Unnormalized Counts.csv

value: Irrelevant control peptide


title: P9_Infected


title: SW48_WRN2B


title: 1772058177_A07


title: 1772058171_F11


title: 1772058177_F04


title: 1772058177_A12


title: UT286 control2


title: 1772058177_A09


title: 1772058177_E01


title: 1772058171_F04


title: UT286 control1


title: 1772058177_B11


title: SW48_Ch2-2A


title: SW48_Ch2-2B


title: SW48_WRN3B


title: UT286 peptide1


title: 1772058148_F06


title: 1772058148_D12


title: UT241 control3


title: UT241 peptide2


title: 1772058171_C05


title: SW48_WRN2A


title: UT241 control2


title: 1772058148_E12


title: 1772058148_A05