title: Colorectal adenocarcinoma tumor 15

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample15

value: F

value: C


title: Differentiated stromal viscular cells

status: Public on Jun 05 2018

type: RNA

city: Gifu city

first: Shigeo

last: Takashima

state: Gifu

address: 1-1 Yanagido

department: Life Science Research Center

country: Japan

institute: Gifu University

description: Gene expression in SVC

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome ver.2.0 Microarrays (G2519F #26655) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then lightly dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_sep09 and Grid: 026655_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

organism: Mus musculus

source_name: Differentiated stromal viscular cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 30 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy mini kit purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoView spectrophotometer (General Electric).

extract_protocol: RNA was isolated using the Maxwell RSC Simply RNA Tissue Kit (Promega, Fitchburg, WI) following the manufacturer's instructions.  The quality of RNA was checked with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The concentration of the RNA solution was determined by NanoView spectrophotometer (General Electric, Boston, MA).

treatment_protocol: Epididymal fat from male C57/BL mice were digested with collagenase, and then centrifuged at 9 ×g for 1 sec. The floating cells were separated from the lower phase (SVC). The floating cell fraction was centrifugazed at 226 ×g for 3 min. The resultant floating cells and sediment cells were regarded as mature adipocytes (MA) and SPA, respectively. SVC and SPA were cultured in DMEM. When the cultured cells reached 90% confluency, they were incubated with differentiation medium containing insulin/dexamethasone/IBMX for 3 day followed by subsequent incubation with DMEM for 2 day. The cells were collected and RNA was extracted.

tag: Sex

value: male

tag: strain

tag: tissue

value: Adipose tissue


title: Colorectal adenocarcinoma tumor 14

type: genomic

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Insitute of Medical Reseach

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample14

hyb_protocol: Standard Illumina protocols for Human 610w-Quad chip

data_processing:
Log R ratio and B allele frequency were generated using using GenomeStudio (Illumina)
matrix_processed.txt is linked as a supplementary file on the Series record.  The file reports Genotype: AA,AB,BB,or NC (no call), GC_SCORE, Theta, R, B_Allele_Freq, Log_R_Ratio.
signal_intensities.txt is linked as a supplementary file on the Series record.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Colorectal adenocarcinoma

extract_protocol: AllPrep DNA/RNA Mini Kit (QUAGEN)

tag: gender

value: Colorectal adenocarcinoma

tag: disease state

value: Adenocarcinoma

tag: Stage

tag: site

value: Rectum

tag: estimated macrod2 status

value: Heterozygous deletion

tag: estimated chromosome segment number (ecsn)


title: UHR_6

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

country: USA

institute: Baylor College of Medicine

data_processing:
The dataset were normalized using NanoStringNorm function in the R NanoStringNorm package
genome build: UCSC hg19
Tab-deliminted raw counts for each gene across all the 24 samples

source_name: Universal Human Reference RNA (UHRR) from Stratagene (Agilent)

extract_protocol: Universal Human Reference RNA purchased as total RNA from Agilent Technologies; Human Brain Reference RNA purchased as total RNA from Thermo Fisher

tag: seqc sample

value: A

tag: sample type

value: 10 pooled human cell lines


title: HBR_6

source_name: Human Brain Reference RNA (HBRR) from Ambion (Life Tech)

value: B

value: Pooled brain tissue from 23 donors


title: HBR_4


title: HBR_5


title: Colorectal adenocarcinoma tumor 13

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample13

scan_protocol: Standard Illumina protocols for Human 610w-Quad chip

value: Right

value: Wild-type


title: A3 rep2

type: SRA

city: Grand Forks

first: Tim

last: Casselli

state: ND

address: UND School of Medicine & HS 1301 N Columbia Road Stop 9037

department: Basic Sciences

institute: University of North Dakota

description:
Other plasmids missing: lp5, cp9, lp38
countTable.csv

library_source: transcriptomic

data_processing:
SMRT sequencing: Basecalls and IPD values were generated using PacBio's PulseToBase pipeline.
SMRT sequencing: Alignment of sequences to the B. burgdorferi B31 genome,  modified base calling, and clustering of motifs were all determined using the RS_Modification_and_Motif_analysis tool from the SMRT analysis package 2.3.0 (http://www.pacb.com/devnet/).
Genome_build: SMRT sequencing: B. burgdorferi B31 consensus genome (NCBI)
Supplementary_files_format_and_content: SMRT sequencing: BigWig files for each sample of IPD for all bases (*.bw). Tab-delimited text files (*.gff) for called modified bases and sequence context for each sample.
RNA seq: Illumina Casava1.8 software used for basecalling.
RNA seq: Adapter sequences removed using Trimmomatic (Bolger et al., 2014) with parameters ILLUMINACLIP:2:30:10 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:2 MINLEN:25
RNA seq: Sequences aligned to B. burgdorferi reference transcriptome and counted using Salmon 0.81 with parameters quant -i  -1 A  --seqBias --gcBias
Genome_build: RNA seq: B. burgdorferi B31 consensus genome (NCBI) and ncRNAs (Arnold et al, 2016).
Supplementary_files_format_and_content: RNA seq: Comma delimited file of raw read counts for each sample.

organism: Borreliella burgdorferi

source_name: Log-phase in vitro bacterial culture

growth_protocol: All Borrelia burgdorferi clones were grown at 35°C under 5% CO2 in modified Barbour-Stoenner-Kelly medium (BSK) supplemented with 6% rabbit serum. Mutant strains were grown with kanamycin (200 µg/ml). Cell densities and growth phase were monitored by visualization under dark-field microscopy and counting using a Petroff-Hausser counting chamber. Cells were harvested for nucleic acid isolation during mid-late log phase (~3X107 cells / ml).

extract_protocol:
Three independent cultures of each of WT and MTase mutant strains were grown to mid-late log phase (3 X 107 cells / ml) for RNA isolation. RNA was isolated by first adding 20 ml RNAprotect (Qiagen) to 10 ml culture to stabilize transcripts during processing. Cells were collected by centrifugation, resuspended in 1 ml of pre-warmed (65°C) Trizol reagent (Invitrogen), and frozen at -80°C overnight. Cell suspensions were thawed at room temperature, and RNA was isolated using the Direct-zol RNA mini kit (Zymo Research) following the manufacturer’s instructions. RNA concentration was determined using using a Qubit® 2.0 Fluorometer (Life Technologies), and RNA integrity was verified using microfluidic-based capillary electrophoresis with an Agilent 2100 Bioanalyzer (RIN ≥ 9.8 for all samples).
Directional cDNA libraries were prepared from 5 μg of purified RNA using the ScriptSeq complete bacteria kit and SciptSeq index PCR primers (Illumina)  following the manufacturer’s instructions.

tag: isolate

tag: genotype

value: wild-type


title: A3 rep1


title: Colorectal adenocarcinoma tumor 12

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample12

label_protocol: Standard Illumina protocols for Human 610w-Quad chip


title: UHR_4


title: 5A18-NP1 rep3

description: countTable.csv

value: lp56-; {delta}bbe02


title: UHR_5


title: 5A18-NP1

library_source: genomic

extract_protocol:
DNA was isolated from a pool of three independent, late log-phase cultures (5 ml per culture) for each B. burgdorferi strain by standard phenol-chloroform extraction, concentrated by precipitation with isopropanol, and cleaned using Agencourt AMPure XP beads (Beckman Coulter).
Libraries were generated using a 20kb shear protocol, loaded onto one SMRT cell per sample, and sequenced on a PacBio RSII instrument using P6-C4 sequencing chemistry and a 360-minute data collection protocol.


title: Colorectal adenocarcinoma tumor 11

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample11

value: M


title: Colorectal adenocarcinoma tumor 18

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample18

value: F


title: A3-NP1

description: Other plasmids missing: lp5, cp9, lp38


title: Colorectal adenocarcinoma tumor 17

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample17

value: C


title: A3-NP1 rep1


title: Colorectal adenocarcinoma tumor 10

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample10


title: A3-NP1 rep2


title: Colorectal adenocarcinoma tumor 9

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample9


title: A3

description: Other plasmids missing: lp5, cp9, lp38


title: D_1

source_name: Mix of A and B (1:3)

value: D

value: Mixed human cancer cell lines and human brain tissue at a ratio of 1:3


title: Colorectal adenocarcinoma tumor 8

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample8

value: Colorectal adenocarcinoma

value: Left


title: C_2

source_name: Mix of A and B (3:1)

value: Mixed human cancer cell lines and human brain tissue at a ratio of 3:1


title: Colorectal adenocarcinoma tumor 7

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample7

value: Adenocarcinoma

value: Heterozygous deletion


title: C_1


title: C_3


title: Colorectal adenocarcinoma tumor 6

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample6


title: Colorectal adenocarcinoma tumor 5

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample5


title: HBR_3


title: D_2


title: Colorectal adenocarcinoma tumor 4

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample4

value: Rectum


title: HBR_1

value: B


title: HBR_2

value: Pooled brain tissue from 23 donors


title: Colorectal adenocarcinoma tumor 3

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample3


title: Colorectal adenocarcinoma tumor 2

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample2


title: Colorectal adenocarcinoma tumor 1

description:
Genomic DNA extracted from colorectal tumors was genotyped using Infinium Human 610w-Quad chip Genotyping BeadChips (Illumina).
Sample1


title: UHR_2

value: A

value: 10 pooled human cell lines


title: UHR_1


title: M. tuberculosis RNA_Experiment 1_3-dpi___rep1

city: Chandigarh

first: Indu

last: Verma

address: Research Block-A, Sector-12

department: Biochemistry

country: India

institute: PGIMER

description: Gene expression of intracellular M. tuberculosis isolated from infected ARPE-19 cells, 3-dpi

hyb_protocol: 1.0 µg of labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was used of each experimental and control sample for hybridization to microarray slides. cRNA was fragmented at 60°C for exactly 30 minutes in a reaction volume of 25µL containing 1X Gene Expression Blocking Agent and 1X Fragmentation Buffer, as per manufacturer’s instruction.  The fragmentation reaction was cooled for 1min., and 2X Hi-Hybridization buffer was added to stop the fragmentation reaction. The reaction was mixed well gently and loaded onto the array slides for hybridization to Agilent Whole M. tuberculosis Genome Oligo Microarrays (G2509F) for 17 hours at 65°C in a rotating (10rpm) Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with pre-warm (37°C) GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: The array slides were processed for scanning on the Agilent Sure Scan Microarray Scanner using one-color scan setting for 8X 15K array slides (Dye channel is set to green and Green PMT gain is set to 100%, Scan region/area 61 X 21.6 mm, Scan resolution 3µm and tiff file dynamic range is 20 bit)

data_processing: The scanned image (.tiff) was analyzed with Agilent Feature Extraction(FE) Software (version 12.0.3.1) using default parameters (protocol GE1_1200, Grid: 026323_D_F_20091124 and Saturation Value 776945 (green)) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The resulting text files (.txt) of control and experimental samples were analysed for data normalization, statistical significance and gene expression analysis using Agilent Technologies GeneSpring® GX software (version 14.9).  Significantly modulated genes were selected based on Benjamini-Hochberg procedure with a fold change > 2 and p < 0.05.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis RNA, Intracellular 3-dpi, Experiment 1, replicate 1

label_protocol: Input M. tuberculosis RNA (100ng) from experimental and control samples were amplified using T7 RNA polymerase and simultaneously labelled with Cyanine 3-CTP (Cy3) using One-Color Microarray-Based Low Input Quick Amp WT Labeling Protocol (Agilent Technologies) according to manufacturer’s instructions. Using RNeasy Mini kit the labeled/amplified cRNA samples were purified and quantified through NanoDrop ND-1000 UV-VIS Spectrophotometer. Cyanine 3 dye concentration (pmol/μL), RNA absorbance ratio (260 nm/280 nm) and cRNA concentration (ng/μL) were recorded to determine the yield and specific activity of each sample.

growth_protocol: H37Rv was grown in Sauton's medium and ARPE-19 cells were maintained in DMEM/F-12 medium, supplemented with 10% FBS

extract_protocol: After 3-day post-infection, euakrytoic RNA was removed by treating the infected ARPE-19 monolayer cells with GTC solution (4M guanidine thiocyanate, 0.5% sodium-N-lauryl sarcosine, 25mM tri-sodium citrate, 0.1M β-2-mercaptoethanol and 0.5% Trition-80) for 2-5 mins, lysate was centrifuged at 5000g for 20min at 4°C to collect the bacterial pellet to which 1-2mL of TRIzol solution was added and M. tuberculosis RNA was siolated with help of bead-beating (0.1 mm zirconia beads). Control M. tuberculosis RNA was  processed directly using TRIzol.

treatment_protocol: Single cell suspension of H37Rv was prepared before infection and ARPE-19 cells were infected with H37Rv at MOI of 10:1 (10 bacteria per cell)

tag: m. tuberculosis rna

value: 3-day post infection

tag: cell line

tag: condition

value: Intracellularly grown M. tuberculosis


title: A/HK68 Repeat MCK Passage 2 Replicate 1

city: New York

first: Peter

last: Palese

state: New York

address: 1 Gustave L. Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-H3-1_S4_L001

data_processing:
Illumina CasavaX.X software used for basecalling
A previously published script was used to filter and trim reads containing the transposon sequence marker (TGCGGCCGCA; contained in all insertion sites). Reads not containing the insertion sequence were placed in separate fastq file. Script found in
Reads with and without insertions were separately mapped to the influenza virus HA using Bowtie v2.
Statistics and visualization was performed with samtools and bedtools.
The total number of reads without inserts at each nucleotide position in the genome was counted to determine sequencing coverage, while the reads with inserts at each position in the genome were
The number of reads with insertions at each site was normalized to the sequencing coverage.
Then the total number of reads with insertions was normalized between the different samples.
The reads at each site in the passaged virus were divided by the total number of reads with insertions in the input.
Genome_build: A fasta file for the HA genomes (HAs.fasta)
Supplementary_files_format_and_content: The normalized transposon insertion frequency at each position of the ZIKV genome is provided. For the Sample 1: Input, the values are the normalized abundance of reads with inserts at each genomic position. For the rest of the samples, the fold over input value is provided at each genomic position.

organism: Influenza A virus

source_name: MDCK

extract_protocol:
RNA from the infected cells and eggs was extracted with TRIzol Plus RNA purification kit (Thermo Fisher Scientific). The RNA was subjected to RT-PCR with SuperScript III RT-PCR Platinum Taq High Fidelity kit (Thermo Fisher Scientific) and HA specific primers.
The cDNA and the plasmid input library were prepared with the NEB Next Ultra II kit and multiplex oligos (New England Biolabs) using the manufactures protocols.

tag: insertional mutant for

value: A/HK68 HA

tag: antigenic lineage

value: A/Hong Kong/1/68


title: A/PR8 Repeat MCK Passage 2 Replicate 3

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-H1-3_S3_L001

value: A/PR8 HA

value: A/Puerto Rico/8/1936


title: B/Ya88 plasmid input library

data_processing:
Illumina CasavaX.X software used for basecalling
A previously published script was used to filter and trim reads containing the transposon sequence marker (TGCGGCCGCA; contained in all insertion sites). Reads not containing the insertion sequence were placed in separate fastq file. Script found in
Reads with and without insertions were separately mapped to the influenza virus HA using Bowtie v2.
Statistics and visualization was performed with samtools and bedtools.
The total number of reads without inserts at each nucleotide position in the genome was counted to determine sequencing coverage, while the reads with inserts at each position in the genome were
The number of reads with insertions at each site was normalized to the sequencing coverage.
Then the total number of reads with insertions was normalized between the different samples.
The reads at each site in the passaged virus were divided by the total number of reads with insertions in the input.
Genome_build: A fasta file for the HA genomes are arrached
Supplementary_files_format_and_content: The normalized transposon insertion frequency at each position of the ZIKV genome is provided. For the Sample 1: Input, the values are the normalized abundance of reads with inserts at each genomic position. For the rest of the samples, the fold over input value is provided at each genomic position.

source_name: E. Coli

value: :A/PR8 HA

value: A/Puerto Rico/8/1934


title: B/Ya88 Repeat MCK Passage 2 Replicate 2

description:
processed data file: Repeat MDCK screen.xlsx
BF_13_S2_L001

organism: Influenza B virus

value: B/Ya88 HA


title: A/HK68 Repeat MCK Passage 2 Replicate 2

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-H3-2_S5_L001

value: A/Hong Kong/1/69


title: B/Ya88 Repeat MCK Passage 2 Replicate 3

description:
processed data file: Repeat MDCK screen.xlsx
BF_14_S1_L001


title: M. tuberculosis RNA_Experiment 3_3-dpi___rep1

source_name: M. tuberculosis RNA, Intracellular 3-dpi, Experiment 3, replicate 1

tag: strain


title: M. tuberculosis RNA_Experiment 2_3-dpi___rep1

source_name: M. tuberculosis RNA, Intracellular 3-dpi, Experiment 2, replicate 1


title: UHR_3


title: M. tuberculosis RNA_Experiment 1_3-dpi___rep2

source_name: M. tuberculosis RNA, Intracellular 3-dpi, Experiment 1, replicate 2


title: D_3

value: D

value: Mixed human cancer cell lines and human brain tissue at a ratio of 1:3


title: A/PR8 Repeat MCK Passage 2 Replicate 2

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-H1-2_S2_L001

value: A/Puerto Rico/8/1935


title: B/Ya88 Repeat MCK Passage 2 Replicate 1

description:
processed data file: Repeat MDCK screen.xlsx
BF_12_S3_L001


title: B/Mal04 Repeat MCK Passage 2 Replicate 3

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-Mal04-HA-3_S15_L001

value: B/Mal04 HA


title: A/PR8 Repeat MCK Passage 2 Replicate 1

description:
processed data file: Repeat MDCK screen.xlsx
pass2-H1-1_S1_L001


title: M. tuberculosis RNA_Experiment 2_3-dpi___rep2

source_name: M. tuberculosis RNA, Intracellular 3-dpi, Experiment 2, replicate 2


title: B/Mal04 Repeat MCK Passage 2 Replicate 2

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-Mal04-Ha-2_S14_L001


title: M. tuberculosis RNA_Control__rep2

description: Gene expression of M. tuberculosis from inoculum used during infection, repeat2

source_name: Inoculum M. tuberculosis RNA, Control, replicate 2

value: Log phase culture/Inoculum

value: Log phase M. tuberculosis Culture


title: M. tuberculosis RNA_Control__rep1

description: Gene expression of M. tuberculosis from inoculum used during infection, repeat1

source_name: Inoculum M. tuberculosis RNA, Control, replicate 1


title: M. tuberculosis RNA_Experiment 3_3-dpi___rep2

source_name: M. tuberculosis RNA, Intracellular 3-dpi, Experiment 3, replicate 2


title: MM at diagnosis, sample 30

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 2.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for gene annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/genecodeg.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Therefrom, the expression levels of Ensembl genes specific for 10138 unique lncRNAs were obtained.

label: biotin

source_name: Highly purified PCs from MM patient

label_protocol: Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

tag: cell type

value: Bone marrow plasma cells


title: MM at diagnosis, sample 29


title: MM at diagnosis, sample 28

description: hyperdiploid karyotype


title: A/HK68 Repeat MCK Passage 2 Replicate 3

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-H3-3_S6_L001

value: A/Hong Kong/1/70


title: MM at diagnosis, sample 26

description: MAF translocation


title: MM at diagnosis, sample 27


title: A/HK68 Egg

description:
processed data file: MDCK and Egg passages.xlsx
BF_10_S5_L001

source_name: Egg


title: MM at diagnosis, sample 25


title: B/Mal04 Repeat MCK Passage 2 Replicate 1

description:
processed data file: Repeat MDCK screen.xlsx
Pass2-Mal04-Ha-1_S13_L001


title: A/PR8 Egg

description:
processed data file: MDCK and Egg passages.xlsx
H1_EGG_S3_L001


title: B/Mal04 Egg

description:
processed data file: MDCK and Egg passages.xlsx
Mal1_EGG_S12_L001


title: B/Ya88 Egg

description:
processed data file: MDCK and Egg passages.xlsx
Ya1_EGG_S10_L001


title: A/PR8 MDCK P2

description:
processed data file: MDCK and Egg passages.xlsx
BF_7_S8_L001


title: New Library A/PR8 MDCK P2

description:
processed data file: MDCK and Egg passages.xlsx
BF_8_S7_L001


title: B/Mal04 MDCK P2

description:
processed data file: MDCK and Egg passages.xlsx
Mal1_MDCK_P2_S11_L001


title: B/Ya88 MDCK P2

description:
processed data file: MDCK and Egg passages.xlsx
Ya2_MDCK_P2_S14_L001


title: A/HK68 MDCK P2

description:
processed data file: MDCK and Egg passages.xlsx
BF_9_S6_L001


title: New A/PR8 plasmid input library

description:
processed data file: Input.xlsx
BF_11_S4_L001

tag: molecule subtype

value: DNA plasmid


title: B/Mal04 plasmid input library

description:
processed data file: Input.xlsx
Mal04-HA-Inputlib_S5_L001


title: A/HK68 plasmid input library

description:
processed data file: Input.xlsx
HK68-HA-Inputlib_S2_L001

value: A/HK68 HA


title: Adult_F_2

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

country: Spain

institute: Institute of Evolutionary Biology

data_processing:
Quality control with FastQC.
Read filtering and trimming with Trimmomatic.
Reads mapping with Bowtie.
Gene counts with FeatureCounts.
Genome_build: https://www.hgsc.bcm.edu/arthropods/german-cockroach-genome-project
Supplementary_files_format_and_content: mRNA_Counts_table_anotv2.txt,Tab-delimited text file includes counts.

organism: Blattella germanica

source_name: Whole body

growth_protocol: Blattella germanica specimens used for the whole transcriptome analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ÂºC and a commercial dog food diet.

extract_protocol:
GenElute ™ Mammalian Total RNA Miniprep Kit.
NEBNext® mRNA Library Prep master mix for Illumina®.

tag: developmental stage

value: Adult female

tag: tissue

value: Whole body


title: N6_2

value: Nymph 6


title: A/PR8 plasmid input library

description:
processed data file: Input.xlsx
PR8-HA-Inputlib_S1_L001

value: A/PR8 HA


title: Adult_F_1


title: MM at diagnosis, sample 23

description: hyperdiploid karyotype


title: MM at diagnosis, sample 20

description: hyperdiploid karyotype


title: MM at diagnosis, sample 24


title: N6_1


title: MM at diagnosis, sample 19


title: WT biological replicate 2 PAOG

city: Geneva

first: Hicham

last: CHAHTANE

address: 30, Quai Ernest-Ansermet

department: Department of Plant Biology

country: Switzerland

institute: University of Geneva

description:
PAO1 extract 0.7mg/mL + GA 10 μM
PAOG_COL

data_processing:
bcl2fastq2 Conversion Software v2.17 used to demultiplex data and convert BCL files to FASTQ files
Reads were mapped to Col-0 genome (TAIR10) with TopHap program.
Differential gene expression analysis was performed with Cuffdiff program by pooling the biological replicates
Genome_build: TAIR10
Supplementary_files_format_and_content: Cuffdiff output

organism: Arabidopsis thaliana

source_name: PAO1 extract 0.7mg/mL + GA 10 μM

growth_protocol: Wild-type (Col-0) and mutant (della quintuple) Arabidopsis seeds plated 20h on different conditions

extract_protocol:
Total RNA were isolated using phenol-chloroform method.
We used the TruSeq Stranded mRNA kit of Illumina according to manufcaturer's specifications.

treatment_protocol: MOCK (control line), Paclobutrazol 5 μM (PAC), Paclobutrazol 5 μM +GA 10 μM (PACG), PAO1 extract 0.7mg/mL (PAO), PAO1 extract 0.7mg/mL + GA 10 μM (PAOG)

tag: background ecotype

value: seeds

value: wild type

tag: age


title: della biological replicate 1 PAOG

description:
PAO1 extract 0.7mg/mL + GA 10 μM
PAOG_5D


title: MM at diagnosis, sample 21

description: hyperdiploid karyotype


title: N5_2

value: Nymph 5


title: WT biological replicate 1 PAOG


title: MM at diagnosis, sample 18


title: N5_1


title: della biological replicate 2 PAO

description:
PAO1 extract 0.7mg/mL
PAO_5D

source_name: PAO1 extract 0.7mg/mL


title: MM at diagnosis, sample 22

description: non-hyperdiploid karyotype, no major IgH (14q32) chromosomal translocations


title: MM at diagnosis, sample 16


title: MM at diagnosis, sample 15

description: MAF translocation


title: R10LB + 0.0625ug/mL Nafcillin Rep 3

city: La Jolla

first: Saugat

last: Poudel

address: 9500 Gilman Dr.

institute: University of California San Diego

data_processing:
Sequenced reads were aligned to TCH1516 genome (NC_010079.1) using bowtie-2 version 2.2.6 with parameters ’ -X 1000 -N 1 -3 3 ‘
Gene specific counts were generated from aligned reads with HTSeq version 0.9.1 using parameters ‘-s reverse -r pos’
Normalized TPM counts were generated with DESEq2 1.16.1
ComBat module in SVA package version 3.24.4 was used for batch correction of TPM data
Genome_build: NC_010079.1
Supplementary_files_format_and_content: Tab delimited file with read counts, normalized TPM counts and batch corrected TPM counts

organism: Staphylococcus aureus

source_name: Staphylococcus aureus

growth_protocol: Overnight cultures of CA-MRSA TCH1516 were diluted to a starting OD600 of 0.01 into fresh media and grown at 37C with stirring to OD600 of 0.4. This preculture was then diluted back to OD600 0.01 into fresh media containing no drug or sub-inhibitory concentrations of nafcillin relative for each media type. Growth was monitored by obtaining OD600 readings every 30 min and sample for RNA sequencing was taken at 2.5 hours.

extract_protocol:
After 2.5 hours of growth, 3 mL samples were taken for RNA sequencing and added to tubes containing 6 mL RNAprotect. After incubation, they were centrifuged to remove the supernatant. RNA was extracted from the pelleted cells using a ‘Quick RNA Fungal/Bacterial Microprep’ kit developed by Zymo Research. The cells were mechanically lysed with a Roche MagNa Lyzer instrument and DNA was removed with DNase I during the  RNA purification. RNA quality was checked with an Agilent Bioanalyzer instrument and ribosomal RNA was removed using an Illumina Ribo-Zero kit.
The remaining RNA was used to build a cDNA library for sequencing using a KAPA Stranded RNA-seq Library Preparation Kit. The kit was used for RNA fragmentation, sequencing adapter ligation, and library amplification. The generated cDNA libraries were sent for Illumina  sequencing on a HiSeq 4000.

tag: media

value: RPMI + 10 %LB (R10LB)

tag: nafcillin concentration (ug/ml)


title: R10LB + 0.0625ug/mL Nafcillin Rep 2


title: WT biological replicate 2 PAO

description:
PAO1 extract 0.7mg/mL
PAO_COL


title: della biological replicate 1 PAO

description:
PAO1 extract 0.7mg/mL
PAO_5D


title: MM at diagnosis, sample 14


title: R10LB + 0.0625ug/mL Nafcillin Rep 1


title: MM at diagnosis, sample 17


title: della biological replicate 2 PAOG


title: N1_2

description:
mRNA
Processed data file: mRNA_Counts_table_anotv2.txt

data_processing:
Quality control with FastQC.
Read filtering and trimming with Trimmomatic.
Reads mapping with Bowtie.
Gene counts with FeatureCounts.
Genome_build: https://www.hgsc.bcm.edu/arthropods/german-cockroach-genome-project
Supplementary_files_format_and_content: mRNA_Counts_table_anotv2.txt: Tab-delimited text file includes counts.

source_name: B. germanica nymph 1

growth_protocol: Blattella germanica specimens used for the whole transcriptome analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ºC and a commercial dog food diet.

value: Nymph 1


title: N3_1

source_name: B. germanica nymph 3

value: Nymph 3


title: N1_1


title: MM at diagnosis, sample 11

description: hyperdiploid karyotype


title: N3_2


title: MM at diagnosis, sample 13


title: MM at diagnosis, sample 12


title: MM at diagnosis, sample 10

description: MAF translocation


title: della biological replicate 2 PACG

description:
PAC 5 μM + GA 10 μM
PACG_5D

source_name: PAC 5 μM + GA 10 μM


title: ED13_2

source_name: B. germanica embryo day 13

value: Embryo day 13


title: WT biological replicate 1 PAO

description:
PAO1 extract 0.7mg/mL
PAO_COL


title: R10LB + 0ug/mL Nafcillin Rep 3


title: R10LB + 0ug/mL Nafcillin Rep 2


title: MM at diagnosis, sample 9

description: no information about hyperdiploid status, no major IgH (14q32) chromosomal translocations


title: ED13_1


title: R10LB + 0ug/mL Nafcillin Rep 1


title: WT biological replicate 2 PACG

description:
PAC 5 μM + GA 10 μM
PACG_COL


title: della biological replicate 1 PACG

description:
PAC 5 μM + GA 10 μM
PACG_5D


title: ED6_2

source_name: B. germanica embryo day 6

value: Embryo day 6


title: WT biological replicate 1 PACG

description:
PAC 5 μM + GA 10 μM
PACG_COL


title: MM at diagnosis, sample 8


title: CAMHB + 0.5 ug/mL Nafcillin Rep 2

value: CAMHB


title: MM at diagnosis, sample 7

value: Bone marrow plasma cells


title: CAMHB + 0.5 ug/mL Nafcillin Rep 3


title: ED6_1


title: CAMHB + 0.5 ug/mL Nafcillin Rep 1


title: della biological replicate 1 PAC

description:
PAC 5 μM
PAC_5D

source_name: PAC 5 μM


title: della biological replicate 2 PAC

description:
PAC 5 μM
PAC_5D


title: ED2_2

source_name: B. germanica embryo day 2

value: Embryo day 2


title: MM at diagnosis, sample 6

description: hyperdiploid karyotype


title: ED2_1


title: WT biological replicate 2 PAC

description:
PAC 5 μM
PAC_COL


title: ED1_2

source_name: B. germanica embryo day 1

value: Embryo day 1


title: MM at diagnosis, sample 5

description: hyperdiploid karyotype


title: CAMHB + 0.0625 ug/mL Nafcillin Rep 2


title: ED1_1


title: CAMHB + 0.0625 ug/mL Nafcillin Rep 3


title: CAMHB + 0.0625 ug/mL Nafcillin Rep 1


title: della biological replicate 2 MOCK

description:
MOCK control condition
MOCK_5D

source_name: MOCK control condition


title: ED0_2

source_name: B. germanica embryo day 0

value: Embryo day 0


title: CAMHB + 0 ug/mL Nafcillin Rep 3


title: MM at diagnosis, sample 3

description: hyperdiploid karyotype


title: ED0_1


title: della biological replicate 1 MOCK

description:
MOCK control condition
MOCK_5D


title: MM at diagnosis, sample 1


title: MM at diagnosis, sample 2

description: MAF translocation


title: CAMHB + 0 ug/mL Nafcillin Rep 2


title: Normal sample 4

description: normal karyotype

source_name: Highly purified PCs from healthy donor


title: Normal sample 3

description: normal karyotype


title: WT biological replicate 2 MOCK

description:
MOCK control condition
MOCK_COL


title: MM at diagnosis, sample 4

source_name: Highly purified PCs from MM patient


title: CAMHB + 0 ug/mL Nafcillin Rep 1


title: WT biological replicate 1 PAC

description:
PAC 5 μM
PAC_COL


title: WT biological replicate 1 MOCK

description:
MOCK control condition
MOCK_COL


title: NFE_1

source_name: B. germanica non-fecundated eggs

value: Non-fecundated eggs

value: Eggs


title: NFE_2


title: Normal sample 1

description: normal karyotype


title: Normal sample 2

description: normal karyotype


title: MSC44_O

status: Public on Jun 04 2018

city: Sacramento

first: Fernando

middle: A

last: Fierro

state: California

address: 2921 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

description: MSC44 Control (no FGF2)

data_processing:
Read basecalling was performed by BGI Americas
Reads were aligned to the human NCBI genome build 36 using CLC Bio WorkBench
The data were normalised using quantile normalisation with IlluminaGUI in R
Genome_build: human NCBI genome build 36

source_name: Mesenchymal Stem Cells

growth_protocol: Cells were isolated from human bone marrow aspirates. Cells were expanded to passage 3-4. The number (36, 42, 43 or 44) denotes the batch (cells derived from a donor). O means untreated, F means treated with FGF2

extract_protocol:
Total RNA was extracted using a Direct-zol RNA Mini-Prep kit (Zymo Research), following manufacturer’s instructions. RNA quality was determined using Agilent 2100. For all samples, RNA integrity number was above 8.0.
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Standard Illumina hybridization and scanning protocols

treatment_protocol: 24 hours with or without 10ng/ml FGF2

value: bone marrow derived stromal cells

tag: treatment


title: MSC42_F

description: MSC42 treated with FGF2

value: 10ng/ml Fibroblast Growth Factor 2


title: MSC43_O

description: MSC43 Control (no FGF2)


title: MSC44_F

description: MSC44 treated with FGF2


title: MSC43_F

description: MSC43 treated with FGF2


title: MSC36_O

description: MSC36 Control (no FGF2)


title: MSC42_O

description: MSC42 Control (no FGF2)


title: ChIP-seq BRD2 +JQ1 (spike in) replicate 2

city: TSURUMI WARD YOKOHAMA

first: Aki

last: Minoda

state: KANAGAWA

address: 230-0045, 1 CHOME-7-22 SUEHIROCHO

department: IMS

institute: RIKEN YOKOHAMA

data_processing:
the reads were aligned to hg19 using  bowtie: bowtie -v 2 -k 1 -S -p 10; samtools view -b; samtools sort; samtools index
the reads were aligned to dm3 using  bowtie: bowtie -v 2 -k 1 -S -p 10; samtools view -b; samtools sort; samtools index
read duplicates were removed: samtools rmdup -s
After mapping and alignment of the ChIP-seq reads to a human and Drosophila genome reference, differences in Drosophila read counts across samples were equalized or normalized. The human ChIP-seq read counts were subsequently normalized using the same ratio used to normalize the Drosophila reads.
H4K5ac8ac ChIP-seq peak call: macs2 callpeak -t -c --bw 400 --broad --broad-cutoff 0.00005 -g hs
BRD2 ChIP-seq peak call: macs2 callpeak -t -c --bw 350 -q 0.00005 -g hs --call-summits --slocal 2000
Genome_build: hg19, dm3
Supplementary_files_format_and_content: macs2 (see data processing step for parameter)

source_name: Non-small lung cancer cell

growth_protocol: H23 cell line (NCI-H23) was purchased from ATCC  (ATCC® CRL-5800™). Cells were cultured as recommended by ATCC in RPMI-1640 Medium containing 10% FBS and Penicillin/Streptomycin and sub-cultured every two days at the ratio of 1:3

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink reaction was stopped by addition of Glycin at the final concentration of 0.2M. H23 Chromatin extract was prepared as follows: the cell pellets were dissolved and incubated in the ice-cold 0.1% SDS lysis buffer (50 mM Hepes KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS, protease inhibitors) for 10 min on a rotation at 4°C. Following centrifugation, the cells were incubated in the ice-cold second lysis buffer (10 mM Tris-CL pH 8.0, 200 mM NaCl, 1 mM EDTA pH. 8.0, 0.5 mM EGTA pH 8.0, protease inhibitors) as described above. The cells were then dissolved in 0.5% SDS sonication buffer (3.106 cells per 135mg sonication buffer), directed to chromatin fragmentation by Covaris for 10 min
ChIP-seq library for sequencing was prepared as the manufacture's protocol: Mondrian™   SP+ Library Preparation (NuGen)

treatment_protocol:
48h prior to the treatment, H23 cells were cultured in a 15 cm plate at the density of 170,000 cells/mL (4 millions cells in one plate). On the day of treatment, the medium was replaced with the fresh medium containing 500nM JQ1 or an equivalent volume/percentage of DMSO, grown for 24h
spike in chip protocol: Anti H4K5acK8ac or BRD2 antibody and anti Drosophila H2Av antibody were mixed at the following ratio: H4K5acK8ac : H2Av = 4:2; BRD2 : H2Av = 10:4; and then incubated with the Dynabeads for overnight.  H23 chromatin extract and Drosophila chromatin extract were mixed at the ratio of 400 to 1 (mg) for H4K5acK8ac ChIP and 600 to 1 (mg)  for BRD2 ChIP.  Following overnight incubation of the mixed chromatin extract and the mix antibodies, the beads were subsequently washed using the above-mentioned conditions. The ChIP quality control was done as the manufacture’s protocol and ChIP-seq library preparation was done as above described.

tag: antibody

tag: antibody type

value: rabbit polyclonal

tag: 2nd antibody cat#, lot#

value: Cell Signalling, Cat# D89B4, Lot# 002

tag: 2nd antibody


title: ChIP-seq BRD2 + DMSO (spike in) replicate 1

value: DMSO 24g


title: ChIP-seq H4K5acK8ac + JQ1 (spike in) replicate 1

value: mouse monoclonal

value: self production/generation


title: ChIP-seq H4K5acK8ac + JQ1 (spike in) replicate 2


title: ChIP-seq BRD2 +JQ1 (spike in) replicate 1


title: HVS-transformed Saimiri T cells from Patient 4

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

hyb_protocol: 3,6 ug of Biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Clariom S Human (Affymetrix-Thermofisher) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The raw CEL files were imported and analyzed using 'affy' package in R language. Data was normalized using RMA normalization and log2 transformed.

label_protocol: 25 ng of total RNA is reverse transcribed  following the Ovation PicoSL V2 (Nugen). Briefly, the resulting double strand cDNA is used for SPIA amplification. 3,6 ug of amplified cDNA are fragmented and biotin labelled using Encore Biotin Module (Nugen).

extract_protocol: RNeasy Minikit Qiagen

treatment_protocol: Naive CD4+ T cells from patients or controls were stimulated with CD2/CD3/CD28-coated beads (Miltenyi) + IL-6 (100ng/mL). HVS-transformed Saimiri T cells were used without stimulation.

tag: subject status

value: patient with an autosomal recessive form of hyper-IgE syndrome (HIES)

value: blood

value: HVS-transformed Saimiri T cells


title: HVS-transformed Saimiri T cells from control 4

value: control


title: HVS-transformed Saimiri T cells from control 3


title: H23_DMSO_12h_R3

data_processing:
the reads were aligned to hg19 using BWA
Genome_build: hg19
Supplementary_files_format_and_content: reads within FANTOM5 promoters were counted using: samtools view -q 20 -F 768 -u bam_file |bamToBed -i stdin | intersectBed -s -c  -a FANTOM5/hg19.cage_peak_phase1and2combined_coord.bed -b stdin  |   awk 'OFS="\t" {print $1,$2,$3,$4,$10,$6}' > counts.bed
Supplementary_files_format_and_content: bed (expression counts saved in 5th column)

extract_protocol:
total RNA extraction
Deep Cap Analysis of Gene Expression (CAGE) (specifically nAnTi-CAGE protocol)

treatment_protocol: treatment with  500 nM JQ1 or an equivalent volume/percentage of DMSO.

value: (DMSO)


title: H23_DMSO_24h_R1


title: H23_DMSO_12h_R1


title: HVS-transformed Saimiri T cells from control 1


title: H23_DMSO_12h_R2


title: ChIP-seq BRD2 + DMSO (spike in) replicate 2


title: HVS-transformed Saimiri T cells from Patient 7


title: ChIP-seq H4K5acK8ac +DMSO (spike in) replicate 1

value: DMSO 24h


title: MSC36_F

description: MSC36 treated with FGF2


title: H23_DMSO_24h_R2


title: H23_DMSO_24h_R3


title: HVS-transformed Saimiri T cells from control 2


title: H23_DMSO_6h_R2


title: H23_DMSO_6h_R3


title: H23_DMSO_6h_R1


title: H23_JQ1_24h_R2

value: 500 nM JQ1 (DMSO)


title: H23_DMSO_3h_R1


title: H23_JQ1_24h_R3


title: H23_JQ1_6h_R3


title: H23_JQ1_12h_R2


title: H23_JQ1_6h_R1


title: H23_JQ1_3h_R2


title: H23_JQ1_3h_R3


title: H23_JQ1_6h_R2


title: H23_No_Treatment_R3


title: H23_DMSO_3h_R3


title: H23_JQ1_3h_R1


title: eWAT adoptive transfer, PBS, rep4

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description:
featureCount.AdoptiveTransfer.txt
PBS_DAH084_5

data_processing:
Bulk RNA-seq reads were aligned to UCSC mm9 genome using STAR aligner. Raw read counts were measured within RefSeq genes using featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: Raw tag count by featureCount

source_name: eWAT

growth_protocol: All experiments used male age-matched C57BL/6J mice housed at four or five animals per cage. High-fat diet studies were conducted by feeding mice a purified-ingredient diet composed of 60:20:20 kcal percentage of fat:carbohydrate:protein (Research Diets, D12492)

extract_protocol:
For bulk RNA-seq of sort-purified cell populations, libraries were prepared using the SMARTer Stranded RNA-seq kit (Clontech) and TruSeq RNA library prep kit (Illumina). For bulk RNA-seq of adipose tissue, total RNA was isolated from snap-frozen tissue samples. Tissues were mechanically homogenized in 500μL TRIzol (Life Technologies) in a TissueLyser (Qiagen) for 4 min, at a frequency of 22s−1. After homogenization, samples were centrifuged at 4°C and homogenates transferred to a fresh tube for RNA extraction with chloroform. Aqueous chloroform fractions were mixed with equal volumes of 70% ethanol/30% water and RNA further purified with RNeasy Mini spin columns (Qiagen) and oncolumn DNase-digestion (Qiagen). One microgram of purified DNase-treated total RNA from biological replicates was processed with a Ribo-Zero Magnetic rRNA removal kit (Epicentre, MRZH11124).
Bulk adipose RNA libraries were prepared using a TruSeq Stranded Total RNA Library Prep Gold (Illumina, 200020599) and standard Illumina protocol.

treatment_protocol: [ex-vivo macrophages] Epididymal white adipose tissue (eWAT) depots were isolated from mice. Adipose samples were placed in 1 mL of DMEM and individual depots were finely minced under sterile conditions with a razorblade prior to digestion in 5 mL DMEM with 6 mg/1 mL collagenase D (Roche) or 3 mg/1 mL collagenase IV (Gibco) at 37° C in a shaking incubator for 30 min. Cells were pelleted at 700g and adipocyte fraction removed. After resuspension of the stromal fraction in 5mL of MACS buffer (1x PBS, 2% calf serum, 25 mM HEPES, 2 mM EDTA) for cell sorting, cells were purified through a 100 μm filter (Falcon), pelleted at 700g, and re-suspended in 1 mL of RBC lysis buffer (0.15 M NH4Cl, .01 M NaHCO3, 0.0013 M EDTA) for 5 minutes at room temperature. Cells were washed again in MACS buffer prior to staining for sorting.  [BMDM] Bone marrow cells were isolated under sterile conditions and cultured in the presence of mCSF at a density of 5x106 cells/10 mL of complete media for a period of six days. On day six of culture, cells were re-plated at a density of 3x106 cells and cultured for a period of 24 hours in the presence of BSA (control), LPS (5 ng/mL), or IL-4 (10 ng/mL).  [Adoptive Transfer] 75-125K cells were sort-purified from obese, CD45.2+ donors and transferred via intraperitoneal injection three times over the course of one week into lean, CD45.1+ recipients. Recipient mice were allowed to rest 24-48 hours prior to sacrifice for subsequent eWAT RNA-seq.

tag: condition

value: PBS transfer

value: Epididymal white adipose tissue (eWAT)


title: eWAT adoptive transfer, PBS, rep3

description:
featureCount.AdoptiveTransfer.txt
PBS_DAH084_3


title: eWAT adoptive transfer, PBS, rep1

description:
featureCount.AdoptiveTransfer.txt
PBS_DAH084_1


title: K562_H4K5K8DiAc_R1

description: ChIP-seq with  anti-H4K5acK8ac antibody in H23 cells, replicate 1

data_processing:
the reads were aligned to hg19 using BWA
Genome_build: hg19
Supplementary_files_format_and_content: peak call MACS2
Supplementary_files_format_and_content: MACS2 narrow peaks, significance threshold: p-value = 0.01

source_name: immortalised myelogenous leukemia line

tag: antibody cat#, lot#


title: K562_Input_IN


title: GM12878_Input

source_name: lymphoblastoid cell line

tag: cell line


title: GM12878_H4K5K8Diac_R1


title: H23_No_Treatment_R2

tag: cell type


title: K562_H4K5K8DiAc_R2


title: eWAT adoptive transfer, Ly6c+ macrophage, rep4

description:
featureCount.AdoptiveTransfer.txt
Ly6c_DAH084_9

value: Ly6c+ macrophage transfer

tag: strain


title: GM12878_H4K5K8Diac_R2


title: eWAT adoptive transfer, PBS, rep2

description:
featureCount.AdoptiveTransfer.txt
PBS_DAH084_2


title: eWAT adoptive transfer, Ly6c+ macrophage, rep2

description:
featureCount.AdoptiveTransfer.txt
Ly6c_DAH084_6


title: H23_JQ1_12h_R3


title: H23_JQ1_12h_R1


title: ChIP-seq H4K5acK8ac +DMSO (spike in) replicate 2


title: H23_No_Treatment_R1


title: eWAT adoptive transfer, Cd9+ macrophage, rep4

description:
featureCount.AdoptiveTransfer.txt
CD9_DAH084_15

value: Cd9+ macrophage transfer


title: eWAT adoptive transfer, Cd9+ macrophage, rep3

description:
featureCount.AdoptiveTransfer.txt
CD9_DAH084_13


title: eWAT adoptive transfer, Cd9+ macrophage, rep2

description:
featureCount.AdoptiveTransfer.txt
CD9_DAH084_12


title: eWAT adoptive transfer, Cd9+ macrophage, rep1

description:
featureCount.AdoptiveTransfer.txt
CD9_DAH084_11


title: eWAT adoptive transfer, Ly6c+ macrophage, rep1

description:
featureCount.AdoptiveTransfer.txt
Ly6c_DAH084_10


title: eWAT adoptive transfer, Ly6c+ macrophage, rep3

description:
featureCount.AdoptiveTransfer.txt
Ly6c_DAH084_7


title: BMDM_LPS_r1

description:
featureCount.BMDM.txt
BMDM_LPS_r1

source_name: Bone marrow drived macrophage

value: LPS

value: Bone marrow

value: BMDM


title: BMDM_IL4_r1

description:
featureCount.BMDM.txt
BMDM_IL4_r1


title: BMDM_LPS_r2

description:
featureCount.BMDM.txt
BMDM_LPS_r2


title: eWAT macrophage, Ly6c+, rep2

data_processing:
ATAC-seq reads were aligned to UCSC mm9 genome in paired-end mode using STAR aligner. After removing chrM reads and discordantly aligned reads, PCR and optical duplicates were eliminated using Picard tools (http://broadinstitute.github.io/picard). Read-pairs of short fragments (<120bp) were selected as putative nucleosome-free reads for downstream analysis. A BigWig file was generated for each sample in RPM scale then one average BigWig file was generated for each macrophage population. Finally, median normalization performed.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file using nucleosome free reads in median-normalized RPM scale

source_name: eWAT macrophage

extract_protocol:
ATAC-seq was performed using a modified protocol based on the technique published by Buenrostro et al. Briefly, sort-purified cell populations were washed in PBS and lysed with lysis buffer (1 M Tris•Cl, pH 7.4, 5 M NaCl, 1 M MgCl2; 10% NP-40 in nuclease-free H2O) and gentle agitation prior to treatment with Tn5 transposase.
DNA was purified (Qiagen MinElute Reaction Cleanup Kit), and amplified with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs) using barcoded primers. DNA library was purified with AMPure XP beads, and library quality was assayed via Qubit and Agilent High Sensitivity DNA Bioanalysis chip. Libraries were sequenced via 40 bp paired-end sequencing using the Illumina NextSeq 500 platform.

treatment_protocol: Epididymal white adipose tissue (eWAT) depots were isolated from mice. Adipose samples were placed in 1 mL of DMEM and individual depots were finely minced under sterile conditions with a razorblade prior to digestion in 5 mL DMEM with 6 mg/1 mL collagenase D (Roche) or 3 mg/1 mL collagenase IV (Gibco) at 37° C in a shaking incubator for 30 min. Cells were pelleted at 700g and adipocyte fraction removed. After resuspension of the stromal fraction in 5mL of MACS buffer (1x PBS, 2% calf serum, 25 mM HEPES, 2 mM EDTA), cells were purified through a 100 μm filter (Falcon), pelleted at 700g, and re-suspended in 1 mL of RBC lysis buffer (0.15 M NH4Cl, .01 M NaHCO3, 0.0013 M EDTA) for 5 minutes at room temperature. Cells were washed again in MACS buffer prior to staining for sorting.

tag: diet

value: High fat diet

value: adipose tissue macrophage (ATM)

tag: cell sorting


title: BMDM_veh_r2

description:
featureCount.BMDM.txt
BMDM_veh_r2

value: Veh

tag: tissue


title: eWAT macrophage, Ly6c+, rep1


title: eWAT macrophage, Cd9+, rep2


title: eWAT macrophage, Ly6c+, rep3


title: eWAT macrophage, Cd9+, rep3


title: MC24h2

city: Edison

first: Ashutosh

last: Dharap

state: NJ

address: 65 James st

department: Neuroscience

institute: HackensackMeridian Health JFK Medical Center

data_processing:
Data analysis pipeline is based on the Tuxedo software package.
The sequencing reads were aligned to the mouse reference genome GRCm38 using TopHat (v2.0.11) and Bowtie2 (v. 2.2.2). Cufflinks (v2.2.2) was then used to assemble the aligned sequences into transcript isoforms and identify the transcription start sites using mouse transcript annotations from Ensembl 81 as a guide. Cuffdiff was used to calculate the FPKM values and test for differential expression and regulation among the assembled transcripts across the groups down to the isoform level.
Genome_build: mm10
Supplementary_files_format_and_content: gtf files containing the output from Cufflinks.

source_name: Cerebral cortex

extract_protocol:
Animals were euthanized and the infarcted ipsilateral cortical tissues were immediately harvested and snap-frozen in liquid nitrogen before storing in -80°C. Total RNA was then isolated from the tissues using the mirVana total RNA isolation kit, followed by Dnase I tratment. The RNA integrity was evaluated using Bioanalyzer.
Sequencing was performed on three independent replicate samples per group for the sham and reperfusion groups. RNA samples with RNA integrity number > 8 were used for library preparation using the TruSeq stranded total RNA sample preparation kit (Illumina Inc., USA). Starting material of 100 ng of total RNA was rRNA depleted followed by enzymatic fragmentation, cDNA synthesis and double-stranded cDNA purification (AMPure XP, Beckman Coulter, USA). The cDNA was end repaired, 3′ adenylated, Illumina sequencing adaptors ligated onto the fragments ends, and the stranded libraries were pre-amplified with PCR using AMPure XP. The libraries size distribution was validated and quality inspected on a Bioanalyzer high sensitivity DNA chip (Agilent Technologies, USA). High-quality libraries were quantified using qPCR, the concentration normalized and equal concentrations from the triplicate samples from each group were pooled. Optimal concentration of the library pool was used to generate the clusters on the surface of a flowcell before sequencing on Nextseq500 (High Output sequencing kit; 50 bp paired-end).

treatment_protocol: Transient focal ischemia was induced using the MCAO method. Mice were anesthetized with 5% isoflurane and a midline neck incision was made to expose the external carotid artery (ECA). A nick was made and a 6-0 silicon-coated filament was inserted and advanced through the internal carotid artery up to the middle cerebral artery (MCA) and left in place for 1 h to occlude blood flow into the MCA. Cerebral blood flow and body temperature were continuously monitored. The incision was sutured and the animals were returned to warm cages for recovery. After 1 h of occlusion, the filament was removed, the incision was sutured, and the mice were returned to their cages. Reperfusion was allowed for 6 h, 12 h or 24 h. For the sham cohort, midline neck incision was similarly done to expose the ECA; however, no filament was inserted to occlude the MCA.

value: Cerebral cortex

tag: age

value: 9 weeks

tag: gender

value: Male

tag: time point


title: MC24h3


title: MC24h1


title: MC6h3


title: MC6h1


title: MC6h2


title: MC12h2


title: eWAT macrophage, Cd9+, rep1


title: BMDM_veh_r1

description:
featureCount.BMDM.txt
BMDM_veh_r1


title: MC12h3


title: MC12h1


title: BMDM_IL4_r2

description:
featureCount.BMDM.txt
BMDM_IL4_r2


title: MCsham3


title: MCsham1


title: Negative Control TGCAGCTA-TTATGCGA

city: Bruxelles

first: Alexandra

last: Van Keymeulen

address: 808, route de Lennik CP602

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description: SmartSEQ2 scRNAseq

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated matrix containing raw transcript counts

source_name: No Cell

growth_protocol: E14 Lgr5-GFP embryos were collected and the whole skin containing the mammary buds was dissected. Female tissues were placed in HBSS + 300U/ml collagenase (Sigma) + 300μg/ml hyaluronidase (Sigma) and digested for 1h30 at 37°C under shaking. EDTA at a final concentration of 5mM was added for 3min to the resultant organoid suspension, followed by a wash in 10% FBS/PBS and labelling in 2% FBS/PBS before filtration through a 40μm mesh. Adult mammary glands were dissected and the lymph nodes removed. Tissues were briefly washed in HBSS, and chopped in 1mm3 pieces. Chopped tissues were placed in HBSS + 300 U/ml collagenase (Sigma) + 300μg/ml hyaluronidase (Sigma) and digested 2h at 37°C under agitation. Physical dissociation using a P1000 pipette was done every 15mins throughout the enzymatic digestion time. EDTA at a final concentration of 5mM was added for 5 min to the resultant organoid suspension, followed by 0,25% Trypsin-EGTA for 1 min before filtration through a 70-μm mesh, 2 successive washes in 2% FBS/PBS and labelling.

extract_protocol:
Samples were incubated in 250μl of 2% FBS/PBS with fluorochrome-conjugated primary antibodies for 30min, with shaking every 10min. Primary antibodies were washed with 2% FBS/PBS, and cells were resuspended in 2.5mg/ml DAPI (Invitrogen) before analysis. The following primary antibodies were used: APC-conjugated anti-CD45 (1:100, clone 30-F11, eBiosciences), APC-conjugated anti-CD31 (1:100, clone 390, eBiosciences), APC- conjugated anti-CD140a (1:100, clone APA5, eBiosciences) and PE-conjugated anti- CD49f (1:200, clone GoH3, eBiosciences) for embryos; PECy7-conjugated anti- CD24 (1:100, clone M1/69, BD Biosciences), APC-conjugated anti-CD29 (1:100, clone eBioHMb1-1, eBiosciences), PE-conjugated anti-CD45 (1:100, clone 30-F11, eBiosciences), PE-conjugated anti-CD31 (1:100, clone MEC 13.33, BD Biosciences), PE-conjugated anti-CD140a (1:100, clone APA5, eBiosciences) for adult MGs. Data analysis and cell sorting was performed on a FACSAria sorter using the FACS DiVa software (BD Biosciences). Dead cells were excluded with DAPI; CD45+, CD31+ and CD140a+ cells were excluded (Lin+) before analysis of the GFP+ cells.
Single cell transcriptomes were generated using a modified Smartseq-2 protocol74. 1μL lysis buffer in 384 well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer, 2.5mM dNTPs, 2.5μM oligo-dT30-VN and ERCC controls at a final dilution of 1:100 million. Reverse transcription and PCR was performed according to the Smartseq-2 protocol with reduced volumes: 1μl of reverse B372transcription mix instead of 5.7μl and 3μl PCR Master mix instead of 12.5μl. cDNA was amplified for 24 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8x ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 30μl buffer EB (Qiagen) and transferred to 384_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermofisher) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit. After initial quality control 24 samples were discarded with cDNA yields of less than 21ng. These samples were replaced with 24 cells from another 384 well plate from the same cell sort by plate reformatting with an acoustic dispenser (LabCyte Echo 525). Next generation sequencing library preparation was performed using a Nextera XT DNA library preparation kit with volumes reduced by one-tenth (Illumina) using an acoustic dispenser. In brief, 100pg of cDNA in a volume of 500nL was tagmented by adding 1.5μl Tn5-buffer mix and incubating for 10 min at 55°C. Tagmented samples were barcoded with Nextera index sets A - D and amplified with 11 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6x ratio. Library pools were eluted in buffer EB and quality control performed using an Agilent 2100 BioAnalyser and High Sensitiviy DNA chip before adjusting to a concentration of 4nM. The diluted pools were quantified using a KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before a final dilution to 2nM. The pool of 384 samples was sequenced on 2 lanes of a HiSeq2500 in high output mode v4 chemistry with 1x100bp read length.
scRNAseq

tag: library type

value: Nextera XT

tag: facs

value: No cell


title: Single Embryonal Progenitor Cell TACGCTGC-TTATGCGA

description: SmartSEQ2 scRNAseq

value: CD49f Hi/Lgr5 Hi


title: Single Embryonal Progenitor Cell ATGCGCAG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Negative Control CGATCAGT-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGGAGCCT-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTGAGCG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTCGCTA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGCGCTC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCGTAGTA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Negative Control CCTAAGAC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGAGCTAC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ATCTCAGG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: MCsham2


title: Single Embryonal Progenitor Cell GTAGAGGA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AAGAGGCA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGAGGCTG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCTCATGA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGACTCCT-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CTCTCTAC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGGCATG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TCCTGAGC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Negative Control TCGACGTC-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AGGCAGAA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAAGGCGA-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGTACTAG-TTATGCGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TCGACGTC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TGCAGCTA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGATCAGT-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ATGCGCAG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGCGCTC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TACGCTGC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGGAGCCT-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGAGCTAC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTCGCTA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ATCTCAGG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCTCATGA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AAGAGGCA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GTAGAGGA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGAGGCTG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCGTAGTA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGACTCCT-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: 30d_head_WT_ChIPseq_input_rep2

city: Shanghai

first: Hui

last: Wang

email: wanghuisimm@sioc.ac.cn, mazj@sioc.ac.cn

address: Qiuyue Road 26

country: China

institute: Chinese Academy of Science

data_processing:
For ChIP-Seq, Sequencing reads were mapped to reference genome dm6 or mm10 respectively with Bowtie2 by default parameter. The peak regions were identified by homer function findPeaks with parameter –style histone -F 2 -size 3000 -minDist 5000. The overlapped peaks of replicate data-sets were found using homer function mergePeaks by default parameter. Bedtools were used to compare the peaks between different genotypes and aging stages. To get inter-peak regions, we used Bedtools to subtracted the peak regions from whole genome.
Genome_build: dm6 and mm10
Supplementary_files_format_and_content: bigwig files were generated by deeptools.

organism: Drosophila melanogaster

source_name: fly head

growth_protocol: Flies were cultured in standard media at 25ºC with 60% humidity unless otherwise specified. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype male flies were collected at the day of eclosion and transferred to new vials every other day during aging process.

extract_protocol:
For ChIP-Seq, 5% mouse epigenome was used as internal control for H3K27me3 IP.
ChIP libraries were prepared according to instructions of NEB DNA library prep kit (NEB, E7370L). RNA libraries were prepared according to instructions of NEB Ultra RNA library prep kit (NEB, E7530L).

treatment_protocol: Flies were harvested at the given age.

value: head

value: 30 days

tag: genotype

tag: chip antibody


title: 3d_head_WT_ChIPseq_input_rep2

value: 3 days


title: 3d_head_Pcl_Su(z)12_ChIPseq_input_rep2

value: Pcl,Su(z)12 double mutant


title: Single Embryonal Progenitor Cell CGTACTAG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AGGCAGAA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: 30d_head_Pcl_Su(z)12_ChIPseq_input_rep2


title: Single Basal Cell CCTAAGAC-GAGCCTTA

description: SmartSEQ2 scRNAseq

source_name: Rosa-tdTomato


title: 3d_head_Pcl_Su(z)12_ChIPseq_rep2

value: H3K27me3 (Millipore 07-449)


title: Single Embryonal Progenitor Cell TAAGGCGA-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTGAGCG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: 30d_head_WT_ChIPseq_rep2


title: 3d_head_WT_ChIPseq_rep2


title: Single Embryonal Progenitor Cell TCGACGTC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGGCATG-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGATCAGT-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: 30d_head_Pcl_Su(z)12_ChIPseq_input_rep1


title: Single Embryonal Progenitor Cell CTCTCTAC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: 3d_head_Pcl_Su(z)12_ChIPseq_input_rep1


title: Single Luminal Cell TCCTGAGC-GAGCCTTA

description: SmartSEQ2 scRNAseq


title: 30d_head_Pcl_Su(z)12_ChIPseq_rep1


title: Single Embryonal Progenitor Cell TAGCGCTC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: 3d_head_WT_ChIPseq_input_rep1


title: 30d_head_Pcl_Su(z)12_ChIPseq_rep2


title: Single Embryonal Progenitor Cell CCTAAGAC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTGAGCG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ATGCGCAG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGGAGCCT-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCGTAGTA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTCGCTA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ATCTCAGG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGAGCTAC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: 3d_head_WT_ChIPseq_rep1


title: 3d_head_Pcl_Su(z)12_ChIPseq_rep1


title: Single Embryonal Progenitor Cell TACGCTGC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: 30d_head_WT_ChIPseq_rep1


title: Single Embryonal Progenitor Cell GCTCATGA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GTAGAGGA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TGCAGCTA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: 30d_head_WT_ChIPseq_input_rep1


title: Single Embryonal Progenitor Cell AAGAGGCA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGGCATG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CTCTCTAC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGAGGCTG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGACTCCT-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AGGCAGAA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGTACTAG-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TCCTGAGC-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CCTAAGAC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: H23_DMSO_3h_R2

tag: treatment

value: (DMSO)


title: Single Embryonal Progenitor Cell ACTGAGCG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGATCAGT-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TACGCTGC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ATGCGCAG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGGAGCCT-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGCGCTC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: H23_JQ1_24h_R1

value: 500 nM JQ1 (DMSO)


title: Single Embryonal Progenitor Cell ATCTCAGG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCTCATGA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCGTAGTA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGAGCTAC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AAGAGGCA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CTCTCTAC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ACTCGCTA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGGCATG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGACTCCT-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAAGGCGA-AAGGCTAT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TGCAGCTA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TCCTGAGC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TCGACGTC-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AGGCAGAA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGTACTAG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAAGGCGA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TCGACGTC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGAGGCTG-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GTAGAGGA-CTATTAAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TGCAGCTA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_815_NKT_uninf

city: Berlin

first: Jeroen

last: Maertzdorf

address: Chariteplatz 1

country: Germany

institute: MPIIB

description: natural killer T cells from uninfected lung tissue

data_processing:
Sequence reads were trimmed for adaptor sequence and mapped to hg19 human genome using STAR v2.5.3a
Read counts were calculated using htseq-count.
Expression analysis performed with edgeR v3.12.1
Genome_build: hg19
Supplementary_files_format_and_content: processed data files include raw counts of uniquely mapped sequence reads with ensemble transcript ID per sample.

source_name: Lung

extract_protocol:
Cells sorted into RLT buffer and RNA extracted with Qiagen micro RNA kit.
cDNA generation and amplification with SMartSeq v4 kit. Sequence libraries prepared with Nextera XT kit.

value: NKT

tag: infection

value: uninf


title: Sample_815_NK_Mtb

description: natural killer cells from Mtb infected lung tissue

value: NK

value: Mtb


title: Single Embryonal Progenitor Cell CGATCAGT-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CCTAAGAC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_815_NKT_Mtb

description: natural killer T cells from Mtb infected lung tissue


title: Sample_815_NK_uninf

description: natural killer cells from uninfected lung tissue


title: Single Embryonal Progenitor Cell TAGCGCTC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_815_MAIT_uninf

description: mucosal associated innate T cells from uninfected lung tissue

value: mait


title: Sample_815_AM_uninf

description: alveolar macrophages from uninfected lung tissue

value: AM


title: Sample_815_gd_uninf

description: gamma delta T cells from uninfected lung tissue

value: gd


title: Sample_815_gd_Mtb

description: gamma delta T cells from Mtb infected lung tissue


title: Single Embryonal Progenitor Cell ATGCGCAG-GCGTAAGA

description: SmartSEQ2 scRNAseq

value: Nextera XT


title: Sample_815_MAIT_Mtb

description: mucosal associated innate T cells from Mtb infected lung tissue


title: Sample_815_AM_Mtb

description: alveolar macrophages from Mtb infected lung tissue


title: Single Embryonal Progenitor Cell TACGCTGC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGGAGCCT-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_803_NKT_uninf


title: Single Embryonal Progenitor Cell GCGTAGTA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_803_NKT_Mtb


title: Sample_803_NK_uninf


title: Single Embryonal Progenitor Cell ACTCGCTA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGAGCTAC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell ATCTCAGG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_803_NK_Mtb


title: Sample_803_gd_uninf


title: Single Embryonal Progenitor Cell ACTGAGCG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCTCATGA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GTAGAGGA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AAGAGGCA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_803_epi_uninf

description: epithelial cells from uninfected lung tissue

value: epi


title: Single Embryonal Progenitor Cell CGAGGCTG-GCGTAAGA

description: SmartSEQ2 scRNAseq

value: CD49f Hi/Lgr5 Hi


title: Sample_803_gd_Mtb


title: Sample_803_epi_Mtb

description: epithelial cells from Mtb infected lung tissue


title: Single Embryonal Progenitor Cell TAGGCATG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_803_endo_Mtb

description: endothelial cells from Mtb infected lung tissue

value: endo


title: Single Embryonal Progenitor Cell CTCTCTAC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_803_endo_uninf

description: endothelial cells from uninfected lung tissue


title: Sample_803_AM_uninf


title: Single Embryonal Progenitor Cell TCCTGAGC-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGTACTAG-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_802_NKT_uninf


title: Single Embryonal Progenitor Cell TAAGGCGA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GGACTCCT-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell AGGCAGAA-GCGTAAGA

description: SmartSEQ2 scRNAseq


title: Sample_802_gd_uninf


title: Sample_802_NK_Mtb


title: Sample_802_gd_Mtb


title: Sample_802_NK_uninf


title: Sample_802_NKT_Mtb


title: Single Embryonal Progenitor Cell TGCAGCTA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TCGACGTC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_802_AM_uninf


title: Single Embryonal Progenitor Cell CGATCAGT-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_800_NKT_uninf


title: Single Embryonal Progenitor Cell ACTGAGCG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_802_AM_Mtb


title: Single Embryonal Progenitor Cell ATGCGCAG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TAGCGCTC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TACGCTGC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_803_AM_Mtb


title: Sample_800_NKT_Mtb


title: Sample_800_NK_Mtb


title: Single Embryonal Progenitor Cell CGGAGCCT-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell GCGTAGTA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_800_MAIT_Mtb


title: Sample_800_MAIT_uninf


title: Sample_800_NK_uninf


title: Sample_800_gd_uninf


title: Single Luminal Cell ACTCGCTA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GGAGCTAC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ATCTCAGG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CCTAAGAC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_800_gd_Mtb


title: Single Luminal Cell AAGAGGCA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_800_AM_uninf


title: Sample_800_epi_uninf


title: Single Luminal Cell GTAGAGGA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CTCTCTAC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGAGGCTG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_800_AM_Mtb


title: Sample_797_NKT_uninf


title: Sample_797_NKT_Mtb


title: Sample_797_NK_uninf


title: Single Luminal Cell TAGGCATG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_797_NK_Mtb


title: Single Luminal Cell GGACTCCT-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_797_MAIT_uninf


title: Single Luminal Cell TCCTGAGC-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell AGGCAGAA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_797_gd_uninf


title: Single Luminal Cell CGTACTAG-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_797_MAIT_Mtb


title: Single Luminal Cell TAAGGCGA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_797_gd_Mtb


title: Single Luminal Cell TCGACGTC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_800_epi_Mtb


title: Single Luminal Cell GCTCATGA-CCTAGAGT

description: SmartSEQ2 scRNAseq


title: Sample_797_epi_Mtb


title: Sample_797_epi_uninf


title: Single Luminal Cell TGCAGCTA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGATCAGT-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_797_endo_uninf


title: Single Luminal Cell CCTAAGAC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ACTGAGCG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TAGCGCTC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_797_AM_Mtb


title: Sample_797_endo_Mtb


title: Sample_797_AM_uninf


title: Single Luminal Cell ATGCGCAG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_796_NKT_uninf


title: Sample_796_NKT_Mtb


title: Single Luminal Cell TACGCTGC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGGAGCCT-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_796_NK_Mtb


title: Single Luminal Cell GCGTAGTA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_796_NK_uninf


title: Sample_796_MAIT_uninf


title: Sample_796_epi_uninf


title: Single Luminal Cell GGAGCTAC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ACTCGCTA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_796_epi_Mtb


title: Single Luminal Cell ATCTCAGG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GCTCATGA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GTAGAGGA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CTCTCTAC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_796_endo_uninf


title: Sample_796_endo_Mtb


title: Sample_796_AM_uninf


title: Single Luminal Cell AAGAGGCA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_796_AM_Mtb


title: Single Luminal Cell TAGGCATG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGAGGCTG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_795_NKT_uninf


title: Single Luminal Cell GGACTCCT-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_795_NKT_Mtb


title: Sample_795_MAIT_uninf


title: Single Luminal Cell AGGCAGAA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TCCTGAGC-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_795_MAIT_Mtb


title: Single Luminal Cell CGTACTAG-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_795_gd_uninf


title: Single Embryonal Progenitor Cell TAAGGCGA-TTCTAGCT

description: SmartSEQ2 scRNAseq


title: Sample_795_epi_uninf


title: Sample_796_MAIT_Mtb


title: Single Luminal Cell TGCAGCTA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_795_endo_uninf


title: Sample_795_gd_Mtb


title: Sample_795_endo_Mtb


title: Single Luminal Cell CCTAAGAC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGATCAGT-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_772_NKT_Mtb


title: Single Luminal Cell TAGCGCTC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_795_AM_uninf


title: Sample_795_AM_Mtb


title: Sample_772_NK_uninf


title: Single Luminal Cell ATGCGCAG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell TACGCTGC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGGAGCCT-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_772_NK_Mtb


title: Sample_772_MAIT_uninf


title: Sample_772_MAIT_Mtb


title: Single Luminal Cell TCGACGTC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_772_gd_uninf


title: Sample_795_epi_Mtb


title: Single Luminal Cell GCGTAGTA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ACTCGCTA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GCTCATGA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ATCTCAGG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_772_gd_Mtb


title: Single Luminal Cell GTAGAGGA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_772_endo_uninf


title: Single Luminal Cell ACTGAGCG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell AAGAGGCA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGAGGCTG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CTCTCTAC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_772_NKT_uninf


title: Sample_772_AM_Mtb


title: Single Luminal Cell TAGGCATG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GGAGCTAC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TCCTGAGC-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_944_susp_Mtb

description: whole cell suspension  from Mtb infected lung tissue

value: susp


title: Single Luminal Cell AGGCAGAA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_944_NK_uninf


title: Sample_944_NK_Mtb


title: Single Luminal Cell GGACTCCT-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TAAGGCGA-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGTACTAG-TCGACTAG

description: SmartSEQ2 scRNAseq


title: Sample_944_ILC3pos_Mtb

description: group 3 ILC (NKp44 positive) from Mtb infected lung tissue


title: Sample_944_susp_uninf

description: whole cell suspension from uninfected lung tissue


title: Sample_944_ILC3neg_uninf

description: group 3 ILC (NKp44 negative) from uninfected lung tissue


title: Sample_944_ILC2_uninf

description: group 2 ILC from uninfected lung tissue


title: Sample_944_ILC2_Mtb

description: group 2 ILC from Mtb infected lung tissue


title: Sample_772_endo_Mtb


title: Sample_944_ILC3neg_Mtb

description: group 3 ILC (NKp44 negative) from Mtb infected lung tissue


title: Sample_772_AM_uninf


title: Sample_944_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Single Luminal Cell TCGACGTC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CCTAAGAC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGATCAGT-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_944_ILC1_Mtb

description: group 1 ILC from Mtb infected lung tissue


title: Single Luminal Cell ACTGAGCG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_susp_uninf


title: Sample_923_susp_Mtb


title: Sample_944_ILC3pos_uninf

description: group 3 ILC (NKp44 positive) from uninfected lung tissue


title: Sample_923_NK_Mtb

description: natural killer cells from Mtb infected lung tissue


title: Single Luminal Cell ATGCGCAG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_NK_uninf

description: natural killer cells from uninfected lung tissue


title: Single Luminal Cell TACGCTGC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_ILC3pos_uninf


title: Single Luminal Cell CGGAGCCT-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GCGTAGTA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ACTCGCTA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TGCAGCTA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ATCTCAGG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_ILC3pos_Mtb


title: Single Luminal Cell GCTCATGA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GTAGAGGA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell AAGAGGCA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGAGGCTG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TAGCGCTC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_ILC3neg_Mtb


title: Sample_923_ILC3neg_uninf


title: Single Luminal Cell CTCTCTAC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_ILC2_uninf

description: group 2 ILC from uninfected lung tissue


title: Single Luminal Cell TAGGCATG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GGAGCTAC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TCCTGAGC-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_ILC2_Mtb


title: Single Luminal Cell GGACTCCT-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TAAGGCGA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell AGGCAGAA-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_923_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Single Luminal Cell TCGACGTC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TGCAGCTA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CCTAAGAC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ACTGAGCG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Sample_905_susp_Mtb


title: Single Luminal Cell TAGCGCTC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Sample_923_ILC1_Mtb


title: Single Luminal Cell ATGCGCAG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGTACTAG-TCTCTCCG

description: SmartSEQ2 scRNAseq


title: Sample_905_NK_Mtb


title: Single Luminal Cell GCGTAGTA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GGAGCTAC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGGAGCCT-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Sample_905_ILC3pos_uninf


title: Sample_905_susp_uninf


title: Single Luminal Cell ACTCGCTA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ATCTCAGG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: MMS_WT_animal 3

city: Guildford

first: Lisiane

middle: Borges

last: Meira

state: Surrey

address: University of Surrey

department: Clinical and Experimental Medicine

country: United Kingdom

institute: University of Surrey

description: Gene expression data from liver tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Applied Biosystems Gene Chip Scanner 3000.

data_processing: Data were analysed using R/Bioconductor. Raw data background correction (RMA method), normalization (qspline method), probe specific correction, and summary value computation were performed using the affy::expresso function

label: Biotin

source_name: MMS-treated Liver from wild-type mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C57Bl/6J mice, wild type or Aag knock-out, 6-8 weeks of age.

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

treatment_protocol: Mice were treated with a single intraperitoneal injection of methyl methane sulfonate (MMS) at 75 mg/kg.

value: 6-8 weeks

value: Liver

value: Wild-type


title: Sample_905_NK_uninf


title: MMS_KO_animal 2

description: Gene expression data from liver tissue

source_name: MMS-treated Liver from Aag knock-out mice

value: Aag knock-out


title: Control_KO_animal 1

description: Gene expression data from liver tissue

source_name: Control liver from Aag knock-out mice


title: Single Embryonal Progenitor Cell TACGCTGC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Sample_905_ILC3neg_uninf


title: Single Luminal Cell GCTCATGA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Sample_905_ILC3pos_Mtb


title: Single Luminal Cell GTAGAGGA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: MMS_WT_animal 2

description: Gene expression data from liver tissue


title: Control_WT_animal 2

description: Gene expression data from liver tissue

source_name: Control liver from wild type mice


title: MMS_WT_animal 1

description: Gene expression data from liver tissue


title: MMS_KO_animal 1

description: Gene expression data from liver tissue


title: MMS_KO_animal 3

description: Gene expression data from liver tissue


title: Single Luminal Cell AAGAGGCA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGAGGCTG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Control_KO_animal 3

description: Gene expression data from liver tissue


title: Single Luminal Cell TAGGCATG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CTCTCTAC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Sample_905_ILC3neg_Mtb


title: Basal-K5YFP-8w-2 [REANALYSIS]

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual.

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: All the results were normalized using the RMA normalization algorithm using R-bioconductor affy package with standard parameters. Cross experiment normalization was further performed to eliminate the batch effect using non-parametric empirical Bayes frameworks for adjusting data implemented in ComBat  function of the Surrogate Variable Analysis package (SVA) in R-bioconductor for the two different microarrays used here and then between this experiment and the previously published data under the accession number GSE69290.

source_name: YFP+ basal cells of K5CREERT2/RosaYFP mice 8w following tamoxifen administration

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Mice were maintained in a certified animal house according to European guidelines

extract_protocol: RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010).In brief, 813 or 2000 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 25 cycles when SYBR Green signal reached a plateau. cDNA was purified using Genelute PCR Clean-Up kit (Sigma Aldrich).

treatment_protocol: Pregnant females bearing Lgr5-IRES-GFP embryos were sacrificed at 14 days of gestation and E14 embryos were collected and epidermis + mammary gland were digested in Collagenase+hyaluronidase. Single cells were stained with the appropriate antibodies and FACS sorted.

value: Embryonic mouse mammary gland FACS purified cells


title: Sample_905_ILC2_uninf

description: group 2 ILC from uninfected lung tissue


title: Single Luminal Cell TCCTGAGC-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Sample_905_ILC2_Mtb


title: Single Luminal Cell AGGCAGAA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Control_WT_animal 3

description: Gene expression data from liver tissue


title: Control_KO_animal 2

description: Gene expression data from liver tissue


title: Sample_905_ILC1_uninf

description: group 1 ILC from uninfected lung tissue


title: Sample_905_ILC1_Mtb


title: Sample_903_susp_uninf


title: Control_WT_animal 1

description: Gene expression data from liver tissue


title: Basal-K5YFP-8w-1 [REANALYSIS]


title: Luminal-K8YFP-8w-1 [REANALYSIS]

source_name: YFP+ luminal cells of K8CREERT2/RosaYFP mice 8w following tamoxifen administration


title: Single Luminal Cell TAAGGCGA-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CCTAAGAC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Sample_903_susp_Mtb


title: Single Luminal Cell ACTGAGCG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TCGACGTC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGATCAGT-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Luminal-K8YFP-8w-2  [REANALYSIS]


title: CD49fHi Lgr5Hi biological replicate 3

description: Gene expression of 813 CD49fHi Lgr5Hi mammary cells from Lgr5-IRES-GFP female embryos isolated at E14, biological replicate 3


title: Single Embryonal Progenitor Cell GGACTCCT-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TAGCGCTC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Embryonal Progenitor Cell CGATCAGT-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: CD49fHi Lgr5Hi biological replicate 2

description: Gene expression of 2000 CD49fHi Lgr5Hi mammary cells from Lgr5-IRES-GFP female embryos isolated at E14, biological replicate 2


title: Single Luminal Cell CGTACTAG-CGTCTAAT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ATGCGCAG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell CGGAGCCT-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GCGTAGTA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: CD49fHi Lgr5Hi biological replicate 1

description: Gene expression of 2000 CD49fHi Lgr5Hi mammary cells from Lgr5-IRES-GFP female embryos isolated at E14, biological replicate 1


title: Single Luminal Cell TACGCTGC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell TGCAGCTA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Sample_903_NK_Mtb


title: Single Luminal Cell GGAGCTAC-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell ACTCGCTA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Sample_903_ILC3pos_uninf


title: Single Luminal Cell ATCTCAGG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Luminal Cell GCTCATGA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Sample_903_ILC3pos_Mtb


title: Single Luminal Cell GTAGAGGA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CGAGGCTG-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell AAGAGGCA-CTAAGCCT

description: SmartSEQ2 scRNAseq


title: Single Basal Cell CTCTCTAC-CTAAGCCT

description: SmartSEQ2 scRNAseq