title: lung tumor_vehicle for continuous_biological rep4

first: Hyejin

last: Choi

address: 408 East 69th Street Z1525

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description:
LungTum_Vehicle_Conti_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

hyb_protocol: Following fragmentation, 5.5 ug of ss-cDNA were hybridized for 16 hr at 45C on Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed using the Summarization SST-RMA algorithm in the Transcriptome Analysis Console (TAC) software version 4.0.

source_name: mouse KC375

label_protocol: Biotinylated ss-cDNA were prepared according to the standard WT Pico protocol from 50 ng total RNA (Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays User Guide, 2017, Thermo Fisher Scientific).

growth_protocol: The lung tissue was harvested at the designed time point (when the treatment was complete) and fixed with formaldehyde, then embedded into paraffin and sectioned.

extract_protocol: RNA was extracted from 6-10 paraffin embedded tissue sections using QUICK RNA FFPE kit (ZYMO Research).

treatment_protocol: KRASG12C GEMM mice were treated with selumetinib continuously (daily for 3 weeks) or pulsatilely (1 cycle: 1 week ON + 1 week OFF, total 3 cycles) with their matched control (vehicles).

tag: strain

value: KRASG12C GEMM

value: Lung tumor

tag: treatment

value: Vehicle for continuous selumetinib group

tag: genotype/variation

value: Tumor cells harbor an activating mutation of the human version of KRAS (KRASG12C/+) at the collagen I locus.


title: lung tumor_vehicle for continuous_biological rep3

status: Public on Sep 11 2019

type: RNA

city: New York

state: NY

country: USA

description:
LungTum_Vehicle_Conti_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse KC374

tag: tissue


title: lung tumor_vehicle for continuous_biological rep2

description:
LungTum_Vehicle_Conti_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

source_name: mouse KC306


title: lung tumor_continuous_biological rep3

description:
LungTum_Continuous_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC174

value: Selumetinib, continuous


title: lung tumor_vehicle for continuous_biological rep1

description:
LungTum_Vehicle_Conti_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

source_name: mouse KC237


title: lung tumor_continuous_biological rep4

description:
LungTum_Continuous_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC344


title: Kasumi1_shScramble_rep7

type: SRA

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description:
Scr7
processed data file: RSEM.gene.counts.txt

library_source: transcriptomic

data_processing:
Base calling using Illumina RTA 2.4.11.
Sequenced reads were hard clipped 1 bp at the 5' and 3 bps at the 3' read ends. Using Skewer v0.2.2, reads were then trimmed of adaptor sequences and low 3' base quality (q20), while read pairs with reads 18 or smaller were filtered out.
Reads mapped to GRCh38.p7 transcriptome using STAR v2.5.3 and RSEMv1.3.0 with default parameters.
Counts were estimated using RSEM gene.results.
Genome_build: Ensembl 87: GRCh38.p7
Supplementary_files_format_and_content: RSEM.gene.counts.txt: Tab-delimited text file contains aggregated normalized expected counts for all samples.

organism: Homo sapiens

source_name: Kasumi-1, 5 days

growth_protocol: 20% FBS in RPMI 1640.

extract_protocol:
RNA was harvested using Qiagen RNeasy Plus Micro Kit (Cat#76034). NEBNext rRNA depletion Kit (E6310) and NEBNext Ultra directional RNA library prep Kit for Illumina (E7420) were used per manufacturer's instructions.
Libraries were prepared for sequencing using standard Illumina protocols.
Paired-end RNAseq for experiments A and C, and single-end RNAseq for Experiment B.

treatment_protocol: 20% FBS in RPMI 1640 for Lentivirus. Addition of DMSO or Bay-364 for Experiment C.

tag: cell line

tag: cell type

value: Acute Myeloid Leukemia

tag: virus

value: Lentiviral Constitutive

tag: shRNA

value: Scramble Control

tag: experiment

value: B


title: lung tumor_continuous_biological rep2

description:
LungTum_Continuous_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC159


title: Kasumi1_TAF1_sh2_rep2

description:
shTAF-2-2
processed data file: RSEM.gene.counts.txt

value: TAF1 shRNA #2

value: A


title: lung tumor_continuous_biological rep1

description:
LungTum_Continuous_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC158


title: lung tumor_vehicle for pulsatile_biological rep4

description:
LungTum_Vehicle_Pul_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC197

value: Vehicle for pulsatile selumetinib group


title: P151 [validation]

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

description: Total RNA was extracted from whole blood drawn from kidney transplant recipients at 3m post transplantation.

hyb_protocol: Hybridization was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Gene-level intensity data were extracted and normalized by RMA stretch in Affymetrix Expression Console. Data were then log2 transformed.
Core exons were included in the analysis. Transcript assignments are based on NetAffx build 28 (hg18/NCBI36).

source_name: whole blood

label_protocol: ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to samples to generate biotin-labeled RNA fragments for hybridization to the chip.

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted from blood samples obtained at 3 month after transplantation using All prep kit (QIAGEN-ALLprep kit, Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Not applicable.

value: Whole blood

tag: acr 3m

value: No


title: Kasumi1_TAF1_sh1_rep2

description:
shTAF-1-2
processed data file: RSEM.gene.counts.txt

value: TAF1 shRNA #1


title: P152 [validation]


title: P150 [validation]


title: P149 [validation]


title: Kasumi1_TAF1_sh1_rep1

description:
shTAF-1-1
processed data file: RSEM.gene.counts.txt


title: lung tumor_vehicle for pulsatile_biological rep1

description:
LungTum_Vehicle_Pul_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC258


title: P99 [validation]


title: Kasumi1_TAF1_sh2_rep1

description:
shTAF-2-1
processed data file: RSEM.gene.counts.txt


title: lung tumor_pulsatile_biological rep4

description:
LungTum_Pulsatile_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC244

value: Selumetinib, pulsatile


title: P148 [validation]


title: lung tumor_pulsatile_biological rep3

description:
LungTum_Pulsatile_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC241


title: P98 [validation]


title: Kasumi1_AE_sh1_rep2

description:
shAE1-2
processed data file: RSEM.gene.counts.txt

value: AE shRNA #1


title: Kasumi1_AE_sh1_rep1

description:
shAE1-1
processed data file: RSEM.gene.counts.txt


title: lung tumor_vehicle for pulsatile_biological rep3

description:
LungTum_Vehicle_Pul_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC515

value: KRASG12C GEMM


title: lung tumor_vehicle for pulsatile_biological rep2

description:
LungTum_Vehicle_Pul_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC274

value: Lung tumor


title: Kasumi1_shScramble_rep6

description:
Scr6
processed data file: RSEM.gene.counts.txt


title: P95 [validation]


title: lung tumor_pulsatile_biological rep2

description:
LungTum_Pulsatile_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC257


title: Kasumi1_shScramble_rep5

description:
Scr5
processed data file: RSEM.gene.counts.txt


title: DC_C_10

city: Lyngby

first: Pankaj

last: Arora

email: sbrix@dtu.dk, sbp@bio.dtu.dk, panar@dtu.dk, panar.arora@sund.ku.dk

address: Søltofts Plads - blg. 224 room 218, DK-2800 Kgs. Lyngby

department: Department of Biotechnology and Biomedicine

country: Denmark

institute: Technical University of Denmark

description:
processed data files:
ReadCount.gene.matrix_moDCs
FPKM.gene.matrix_moDCs
TPM.gene.matrix_moDCs
moDCs_don C

data_processing:
De-multiplexed raw data was provided by Novogene Corporation, China.
Cutadapt (v1.15) was used to remove sequencing adapters and low quality reads from the de-multiplexed raw data (cutadapt -j 1 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --mask-adapter --quality-base=33 --max-n=0.2 -o ....) . STAR (v2.6.0) and RSEM (Li nd Dewey BMC Bioinformatics 2011) were used to map and align the clean reads and perform transcript quantification, respectively.
After mapping transcripts to gene symbols, we obtained a gene count matrix with 17,220 genes and removed the least abundant transcripts for the 31 genes with duplicate gene symbols, resulting in a list of 17,189 genes. To remove low abundance transcripts, the dataset was filtered to only include genes that were present in at least three samples with at least five reads, resulting in a set containing 8,312 genes.
Differentially expressed genes were identified using SAM-seq v3.0 (Li and Tibshirani Stat Mehods 2013) using a two-class paired analysis with 20 resamples and 100 permutations. Pathway gene enrichment analysis was performed using the Reactome Pathway Database (Fabregat et al., Nucleic Acid Research 2018).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read count matrix, RPKM and TPM values for each sample

source_name: Blood

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats from human donors using Ficoll-Paque gradient centrifugation. CD14+ monocytes were isolated from PBMCs by magnetic-activated cells sorting (MACS) and were cultured in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-glutamine, 50 µM 2-Mercaptoethanol, 1% Penicillin-Streptomycin and 150 U/mL recombinant human IL-4 and 160 U/mL recombinant human GM-CSF at 37°C and 5% CO2 to obtain monocyte-derived dendritic cells (moDCs). Medium was replaced after 3 days of culturing and moDCs were used 6 days after the start of culture. Cells were harvested and rested for 1 hour at 37°C and 5% CO2 before stimulation.

extract_protocol:
RNA was extracted from 4 hrs stimulated cells. Total RNA concentration was measured, checked for quality and used for cDNA preparation by reverse transcription of 5.6 μL of purified RNA. cDNA was amplified using Smart-seq2 protocol (Picelli et al., Natue protocols 2014), purified, quantified, and checked for quality and library size.
Nextera XT DNA library preparation kit  (Illumina, FC-131-1096) was used with 1 ng purified cDNA for the construction of swquencing libraries.
cDNA libraries having insert sizes of 500-800 bp were used for paired-end sequencing on the Illumina NovaSeq 6000 sequencing platform (Novogene Corporation, China).

treatment_protocol: Cells were supplemented with (final concentrations) TSLP (25 ng/mL) , IL-25 (25 ng/mL),  TSLP+IL-25 (both 25 ng/mL), helminth PCF (100 μg dry matter/mL), bitter melon extract (BME) (100 μg dry matter/mL), butyrate (2 mM), and succinate (0.5 mM and 2 mM, di-sodium succinate hexahydrate). Afterwards, the medium containing Escherichia coli O26:B6 LPS (100 ng/mL) and IFN-γ (10 ng/mL) was added. Cells were stimulated for 4 or 20 h at 37°C, 5% CO2, and 95% humidity. The transcriptional profile of stimulated human moDCs was evaluated after 4 hours of stimulation and after stimulation for 20 hours, the cell-free culture supernatants were harvested and frozen at -80°C until further analysis and cells were immunoprofiled using flow cytometry.  The cell-free culture supernatants were harvested and frozen at -80°C until further analysis. IL-12p70 levels were determined using ELISA  according to the manufacturer’s protocol.

tag: donor

value: C

value: monocyte-derived dendritic cells

tag: stimulation reagent

value: LPS + IFN-gamma + Butyrate

tag: stimulation time

value: 4 hrs


title: Kasumi1_AE_sh2_rep2

description:
shAE2-2
processed data file: RSEM.gene.counts.txt

value: Acute Myeloid Leukemia

value: Lentiviral Constitutive

value: AE shRNA #2


title: DC_C_9

value: LPS + IFN-gamma + Succinate


title: Kasumi1_shScramble_rep4

description:
Scr4
processed data file: RSEM.gene.counts.txt

value: Scramble Control

value: A


title: DC_C_6

value: LPS + IFN-gamma + PCF


title: P93 [validation]

description: Total RNA was extracted from whole blood drawn from kidney transplant recipients at 3m post transplantation.

value: Whole blood

value: No


title: P8 [validation]


title: lung tumor_pulsatile_biological rep1

description:
LungTum_Pulsatile_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC217

value: Selumetinib, pulsatile

value: Tumor cells harbor an activating mutation of the human version of KRAS (KRASG12C/+) at the collagen I locus.


title: Bone marrow derived macrophages, miR-511-3p Media

city: Baltimore

first: Danh

middle: Cong

last: Do

state: MD

address: 5501 Hopkins Bayview Circle, 3A.4

department: Medicine

institute: Johns Hopkins University

description:
B6-b2-mi-511-M_3998719051
B6MM_3998719051G

hyb_protocol: Standard Illumina protocol. Each BeadChip has more than 48,000 probes derived from NCBI RefSeq Release 38 (November 7, 2009). The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting carried out by Johns Hopkins Sequencin Core.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Background were filtered out ( Illumina detection Pvalue of 0.02 and above) and all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std.

source_name: Bone marrow

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit and converted into single-stranded cDNA. cDNA was cleaned and concentrated with the supplied columns andsingle-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP

growth_protocol: Bone marrow stem cells from C57BL/6 were differentaited in DMEM contaning 10% FBS, 1% PenStrep, and 20 ng/mL of M-CSF.

extract_protocol: Total RNA was extracted using RNAeasy mini kit with on-column DNA I digestion.

treatment_protocol: miR-511-3p mimics were transfected using RNAiMax 48 h prior to 100ng/mL of LPS (M1) and 20ng/mL of IL-4 (M2) treatment for 6hr and 24hr, respectively

value: Bone marrow derived macrophage

tag: genotype

value: Wildtype

tag: transfection

tag: stimulation

value: Media


title: P6 [validation]


title: Kasumi1_shScramble_rep2

description:
Scr2
processed data file: RSEM.gene.counts.txt


title: Bone marrow derived macrophages, Mrc1-KO Media

description:
MR-b2-mi-neg-M_3998719051
MR_3998719051F

value: miRNA mock control


title: DC_C_2

value: C

value: monocyte-derived dendritic cells

value: LPS + IFN-gamma


title: Bone marrow derived macrophages, miR-511-3p LPS-treated

description:
B6-b2-mi-511-LPS_3998719051
B6MILPS_3998719051B

value: LPS


title: Bone marrow derived macrophages, Mrc1-KO miR-511-3p

description:
MR-b2-mi-511-M_3998719051
MM_3998719051H


title: P87 [validation]


title: P89 [validation]


title: Bone marrow derived macrophages, miR-511-3p IL4-treated

description:
B6-b2-mi-511-IL-4_3998719051
B6MIL4_3998719051D


title: Bone marrow derived macrophages, Control LPS-treated

description:
B6-b2-mi-neg-LPS_3998719051
B6RILPS_3998719051C


title: Bone marrow derived macrophages, Control Media

description:
B6-b2-mi-neg-M_3998719051
B6RM_3998719051A


title: DC_B_10

description:
processed data files:
ReadCount.gene.matrix_moDCs
FPKM.gene.matrix_moDCs
TPM.gene.matrix_moDCs
moDCs_don B

value: B

value: LPS + IFN-gamma + Butyrate

value: 4 hrs


title: Bone marrow derived macrophages, Control IL4-treated

description:
B6-b2-mi-neg-IL-4_3998719051
B6RIL4_3998719051E


title: Kasumi1_shScramble_rep3

description:
Scr3
processed data file: RSEM.gene.counts.txt

value: Acute Myeloid Leukemia

value: Lentiviral Constitutive

value: Scramble Control

value: A


title: P38 [validation]

value: Whole blood

value: No


title: Kasumi1-WT-input_rep6

library_source: genomic

data_processing:
Base calling using Illumina RTA 2.4.11.
Trimmed fastq files with cutadapt v.1.15 --nextseq-trim=20 -u 2 -u -2 -m 18.
Processed with Kundaje lab Aquas Pipeline (git commit SHA1: 5e0e6f119b70c6e7a0a2578d38847f30e200df95) with -peak_caller macs2 -species hg38.
For histones, used naïve overlap for peak file. For ETO peaks, used optimal replicate IDR < 0.05 for peaks. For TAF1, used optimal pseudo-replicate IDR < 0.05.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: .bw: bigWig files were generated as fc signal over input from MACS2.
Supplementary_files_format_and_content: *narrowPeak:

molecule: genomic DNA

source_name: Kasumi-1 Cells

growth_protocol: 20% FBS in RPMI1 1640.

extract_protocol:
SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology) was used for chromatin immunoprecipitation per manufacturer's instructions.
Libraries were prepared using E7645S NEBNext(r) Ultra(tm) II DNA Library Prep Kit for Illumina® according to manufacturer's instructions.

tag: chip antibody


title: D13.5placenta_40ppm_rep4

city: Athens

first: Christian

last: Andersen

state: Georgia

address: 501 D.W. Brooks Dr., Physiology and Pharmacology

department: Physiology and Pharmacology

institute: University of Georgia

hyb_protocol: none provided by the submitter

scan_protocol: Chip images were digitized and microRNA intensity values are generated. Background was subtracted from signal means and then normalized using a LOWESS filter (LC Sciences).

data_processing: The R package limma was employed for differential expression analysis. Signal intensity values were provided as input to limma.

source_name: D13.5 whole placenta, 40 ppm diet, 9 day exposure

label_protocol: none provided by the submitter

extract_protocol: D13.5 whole placentas were homogenized in liquid nitrogen for total RNA isolation using Trizol reagent (Invitrogen, ThermoFisher Scientific, #15596018). Total RNA was sent to LC Sciences for array services.

treatment_protocol: Mice were exposed to various levels of zearalenone through diet, from gestation day 5.5 through 13.5. D0.5 is the morning a plug is found.

tag: strain


title: D13.5placenta_40ppm_rep3


title: P35 [validation]


title: P33 [validation]


title: D13.5placenta_40ppm_rep2


title: DC_B_6

value: LPS + IFN-gamma + PCF


title: D13.5placenta_40ppm_rep1


title: Kasumi1_shScramble_rep1

description:
Scr1
processed data file: RSEM.gene.counts.txt


title: P32 [validation]


title: P5 [validation]


title: DC_B_2


title: DC_A_10

description:
processed data files:
ReadCount.gene.matrix_moDCs
FPKM.gene.matrix_moDCs
TPM.gene.matrix_moDCs
moDCs_don A


title: Kasumi1-WT-input_rep4


title: Kasumi1-WT-ETO_rep6

description: processed data file: Kasumi1-WT-ETO.filt.narrowPeak.gz

value: ETO (Diagenode, C15310197)


title: DC_A_9

value: LPS + IFN-gamma + Succinate


title: Kasumi1-WT-input_rep5


title: Kasumi1-WT-TAF1_rep5

description: processed data file: Kasumi1-WT-TAF1_rep5.filt.narrowPeak.gz

value: TAF1 (Millipore, 04-1525)


title: DC_A_6


title: D13.5placenta_4ppm_rep4

source_name: D13.5 whole placenta, 4 ppm diet, 9 day exposure


title: Kasumi1-WT-input_rep3


title: DC_B_9


title: D13.5placenta_4ppm_rep3


title: D13.5placenta_0ppm_rep4

source_name: D13.5 whole placenta, 0 ppm diet, 9 day exposure


title: D13.5placenta_4ppm_rep1


title: D13.5placenta_4ppm_rep2


title: Kasumi1-WT-TAF1_rep3

description: processed data file: Kasumi1-WT-TAF1_rep3.filt.narrowPeak.gz

value: TAF1 (Santa Cruz, sc-735)


title: P29 [validation]

description: Total RNA was extracted from whole blood drawn from kidney transplant recipients at 3m post transplantation.


title: P31 [validation]


title: mm10_J2_KO_H3K27me2

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
Align reads to reference genome (hg19) using bowite2 and the --very-sensitive-local parameter
Align reads to spike-in genome (mm9 or dm6) using bowtie2 and the --very-sensitive-local parameter
Convert sams to sorted bams using Samtools, and extract headers from both alignments for each of the 2 alignments (reference and spike-in)
Filter read ambiguosly aligned to both genomes using Picards FilterSamReads, mark duplicates using Picards MarkDuplicates and index the filtered, marked bam file with Samtools
The number of spike-in reads was used as a scale factor to generate normalised bigWigs using bamCoverage from the deeptools suite with a bin size of 10
Genome_build: hg19, mm9 & dm6
Supplementary_files_format_and_content: bigwig files of ChIP-Rx spike-in normalised tracks for each sample

organism:
Drosophila melanogaster
Mus musculus

source_name: Embryonic stem cell and S2 cell line

growth_protocol:
ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates.ChIPs for certain histone modification ChIP samples include a 2% spike in of Drosophila S2 chromatin that were cultured according to established protocols. ChIPs for PRC2 components and H2AK119ub1 include a 10% spike in of human NT2 chroamtin that were cultured according to established protocols .
Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). S2 cells were cultured in Schneider media supplemented with 10% Heat inactivated FBS

extract_protocol:
Embryonic stem cells were washed once with PBS before crosslinking for 10 minutes with PBS containing 1% formaldehyde (Sigma). Crosslinking was quenched with 0.125M Glycine for 5 minutes before two PBS washes. The crosslinked cells were lysed in 6mL of SDS-Lysis buffer (100mM NaCl, 50mM Tris pH8.1, 5mM EDTA pH 8.0, 0.02% NaN3, 0.5% SDS, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF). Chromatin was pelleted by centrifugation at 1200rpm for 5 minutes at room temperature. The supernatant was then discarded, and the chromatin was resuspended in 3mL of ChIP buffer (2:1 dilution of SDS-Lysis buffer: Triton dilution buffer [100mM Tris pH 8.6, 100mM NaCl, 5mM EDTA pH 8.0, 0.02% NaN3, 5% Triton X-100, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF]). Chromatin was sheared to approximately 200bp-600bp fragments by sonication on a Branson Sfx150 Sonifier for a total of 4min at 50% amplitude. Sonicated chromatin was incubated overnight with antibody while rotating at 4°C. Following clarification, the chromatin was incubated for 3 hours with 50µL of protein A or G Dyna beads (ThermoFisher) beads. After incubation, the beads were washed three times in Mixed Micelle Buffer (150mM NaCl, 20mM Tris pH 8.1, 5mM EDTA pH 8.0, 5.2% Sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), twice with Buffer 500 (0.1% Sodium Deoxycholate, 1mM EDTA pH 8.0, 50mM HEPES pH7.5, 1% Triton X-100, 0.02% NaN3), twice with LiCl detergent wash (0.5% Sodium Deoxycholate, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 10mM Tris pH 8.0, 0.02% NaN3) and finally one wash with TE. Immunoprecipitated material was eluted from the beads with Elution buffer (0.1M NaHCO3, 1% SDS) while shaking for 1 hour at 65°C. The supernatant was retained and incubated overnight at 65°C while shaking to reverse the crosslinks. The eluted complexes were then subject to RNase (Thermo Fisher) and Proteinase K (Sigma) treatment prior to DNA clean up (Qiagen Qiaquick PCR Purification Kit). ChIP enrichments were analysed by qPCR using the SYBR Green I detection chemistry (M3003E NEB) on an Applied Biosystems Quant Studio 3 platform.
Following the ChIP experiment, the precipitated DNA was quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Q32854). A Total of 2-10 ng of DNA from each ChIP-Rx experiment was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) and NEBNext Multiplex Oligos for Illumina (Set#1, NEB #7335). Following adaptor ligation, DNA was PCR amplified for 5-9 cycles, depending on amount of input DNA. DNA purification was then performed using NEBNext Sample Purification Beads (E7767S). The quality of DNA libraries was analysed on a High Senstivity D1000 Screen Tape (Agilent). The resulting libraries were then used for cluster generation and sequencing using an Illumina NextSeq 500 (ID: NB501524), with 75bp read length.

value: Embryonic stem cell and S2 cell line

value: Jarid2 KO

tag: antibody


title: D13.5placenta_0ppm_rep3


title: P30 [validation]


title: P25 [validation]


title: P22 [validation]


title: Kasumi1-WT-TAF1_rep4

description: processed data file: Kasumi1-WT-TAF1_rep4.filt.narrowPeak.gz


title: D13.5placenta_0ppm_rep2


title: P23 [validation]


title: Kasumi1-WT-H3K4me1_rep2

description: processed data file: Kasumi1-WT-H3K4me1.naive_overlap.filt.narrowPeak.gz

value: H3K4me1 (Diagenode, C15200150)


title: Fmn 10 c

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
Raw reads passing Illumina quality filters were cleaned of adapters, and mapped with STAR.
For each sample, between 4 and 15 millions reads were mapped at a unique location on the Mus musculus genome (mm10 GRCm38, with Ensembl83 annotation).
Read counts per gene were also generated by STAR, and the DESeq2 package was used for differential expression analysis.
Differentially expressed genes with an adjusted p-value threshold of 0.05 were selected for further analysis.
Genome_build: mm10 GRCm38, with Ensembl83 annotation
Supplementary_files_format_and_content: STAR raw read count files

source_name: fully grown competent oocytes

extract_protocol:
Oocytes were freshly collected as described in Verlhac et al, Development 120, 1017-1025 (1994). Total RNA was extracted from oocytes using the RNAqueous®-Micro Total RNA Isolation Kit (Thermofisher, Ref. AM1931). Oocytes were washed 3 times in PBS, resuspended in lysis buffer, freezed in liquid nitrogen and conserved at -80°C overnight. After unfreezing, RNA extraction was carried out following the manufacturer’s instructions.
Library preparation and Illumina sequencing were performed at the Ecole normale superieure Genomic Platform (Paris, France). 1 ng of total RNA were amplified and converted to cDNA using NuGEN’s Ovation RNA-Seq kit V2. Following amplification, 1 µg of cDNA was fragmented to ∼200 bps using Covaris S200.
The remainder of the library preparation was done using 200 ng of cDNA following TruSeq RNA Sample Prep v2 kit from the End Repair step.
Three runs were performed following the same design: libraries were multiplexed by 4 on 1 flow cell lane. A 50 bp read sequencing was performed on a HiSeq 1500 device (Illumina). A mean of 17,3 ± 3,9 million passing Illumina quality filter reads was obtained for each of the 4 samples.


title: D13.5placenta_0ppm_rep1


title: P12 [validation]


title: Fmn 10 b


title: P20 [validation]


title: DC_A_2

value: monocyte-derived dendritic cells

value: LPS + IFN-gamma


title: KO INPUT (+S2 Drospohila)

first: Darren

middle: John

last: Fitzpatrick

description: ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates.ChIPs for certain histone modification ChIP samples include a 1.67% spike in of Drosophila S2 chromatin that were cultured according to established protocols. ChIPs for PRC2 components and H2AK119ub1 include a 10% spike in of human NT2 chroamtin that were cultured according to established protocols .

data_processing:
Reads were alinged to the mouse reference genome (mm10) and the relevant spike-in genome (dm6 for S2 and hg38 for NT2) using bowtie2.
Bigwig files were generated at a resolution of 10bp using bamCoverage. Tracks were normalised using spike-in derived normalisation factors.
Genome_build: mm10

growth_protocol: Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). S2 cells were cultured in Schneider media supplemented with 10% Heat inactivated FBS

value: Pcl1-3 TKO

value: Input


title: Kasumi1-WT-input_rep1

value: Acute Myeloid Leukemia


title: WT INPUT (+S2 Drosophila)

value: Wild type


title: P1 [validation]


title: Kasumi1-WT-ETO_rep1


title: oral_mucosa_baseline

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

description: total RNA samples isolated from unwounded mouse oral mucosa

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

source_name: orla mucosa

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

extract_protocol: Qiagen miRNeasy kit was used for total RNA extraction following manufacturer's protocol.

value: oral mucosa (baseline unwounded)


title: Kasumi1-WT-input_rep2


title: Fmn 10 a


title: Fmn 9 c


title: TKO_H3K27me1


title: mm10_J2_KO_H3K27me3


title: Kasumi1-WT-H3K27ac_rep1

description: processed data file: Kasumi1-WT-H3K27ac.naive_overlap.filt.narrowPeak.gz

value: H3K27ac (Millipore, 07-360)


title: skin_baseline

description: total RNA samples isolated from unwounded mouse skin

source_name: skin

value: skin (baseline unwounded)


title: Kasumi1-WT-H3K4me1_rep1


title: TKO_H3K27me2


title: WT_H3K27me1


title: Fmn 9 a


title: Kasumi1-WT-H3K27ac_rep2


title: Fmn 8 c


title: Fmn 8 b


title: WT_H3K27me2


title: Fmn 9 b


title: WT_H3K27me3


title: Fmn 7 c


title: Fmn 8 a


title: Fmn 7 b


title: Fmn 7 a


title: Placebo Group

city: Silver Spring

first: Hang

last: Xie

state: Maryland

address: 10993 New Hampshire Ave WO 52/72 Rm 1324

institute: US Food and Drug Administration, Center for Biologics Evaluation and Research

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://dataanalysis.qiagen.com/pcr/arrayanalysis.php?wuid=b4d56157-c14b-4fd9-a99c-8ddecd502e64&logindata=&customerdata=&customeremail=&platform=catalogArray&format=X
For the normalization it uses the average of five housekeeping genes: B2M, GUSB, HSP90AB1, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., E2 group/Placebo group) ratios.

label: SYBR Green

source_name: Lung

label_protocol: PCR assays were performed using Profiler™ PCR Array Mouse Signal Transduction PathwayFinder™ kit (QIAgen) following the Manufacturer’s instructions. Reverse transcription was performed from 100 ng total RNA using RT2 Easy First Strand Kit (QIAgen). Quantitative real-time PCR were performed (Stratagene MX3000p) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: Whole lung homogenate

tag: activation agent

value: Placebo-implantation followed by H5N1 infection

tag: time

value: 7 days after implantation and 1 day after H5N1 infection


title: Lung graft, non-OB.3

city: Chiba

first: ATSUSHI

last: HATA

state: Chiba

address: 1-8-1, Inohana, Chuo-ku

department: Department of General Thoracic Surgery and Department of Molecular Oncology

country: Japan

institute: Graduate School of Medicine, Chiba University

description: Gene expression of OB transplanted from C57BL/10 to C57BL/6

hyb_protocol: A total of 0.6 ug of Cy3-labeled cRNA was then fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. After fragmentation, 25 ul of 2xAgilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression 8 60K arrays (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), followed by a 1 minute wash at 37°C with GE Wash buffer 2 (Agilent).

scan_protocol: Immediately after washing, the slides were scanned on an Agilent SureScan Microarray Scanner (G2600D) using the one color scan setting for 8 x 60k array slides (Scan Area, 61 x 21.6 mm; Scan resolution, 3 um; Dye channel, Green Photomultiplier tube is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using the default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were then normalized using the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and higher ends of the probe intensities and was then used to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, whereby the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: allograft, non-OB

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug of total RNA using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions. These labeled cRNAs were then purified with an RNeasy column (Qiagen, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Lung grafts were harvested on day 21 post-surgery. Only animals diagnosed histologically were subjected to the gene expression analysis for each group. All samples were immediately frozen at -80℃ with Allprotect Tissue Reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Total RNA from the samples was isolated by homogenization of the frozen tissue using TissueLyser II (Qiagen) and purified by NucleoSpin® RNA XS (MACHEREY-NAGEL) as described in the manufacturer’s protocol.

tag: donor strain

tag: tissue

value: Lung

tag: gender

value: male

tag: recipient strain

tag: treatment

value: allograft, non-OB


title: Estradiol Group

description: Test

value: Estradiol (E2)-implantation followed by H5N1 infection


title: TKO_H3K27me3

tag: cell type

value: Embryonic stem cell and S2 cell line


title: Lung graft, sham.3

source_name: sham

value: sham


title: Lung graft, sham.2


title: Lung graft, sham.1


title: Exp2_SF_A

status: Public on Sep 10 2019

city: Lausanne

first: Joanito

last: Liberti

address: Biophore

country: Switzerland

institute: University of Lausanne

description: Three pooled brains

data_processing:
Reads were processed with Trimmomatic to remove adapters and low quality bases using the following parameters: LEADING: 3 (trim the leading nucleotides until quality > 3), TRAILING: 3 (trim the trailing nucleotides until quality > 3), SLIDINGWINDOW: 4:15 (trim the window of size four for reads with local quality below a score of 15), and MINLEN: 36 (discard reads shorter than 36 bases).
Reads that matched ribosomal RNA sequences (rRNA) were removed using SortMeRNA
Reads were aligned with STAR v. 2.4.2a to the latest version of the honeybee genome (Apis mellifera assembly 4.5) available on BeeBase (http://hymenopteragenome.org/beebase/?q=download_sequences)
Mapped reads were converted into raw read counts with the htseq-count script (http://www.huber.embl.de/users/anders/HTSeq/doc/count.html)
DESeq2 v.1.10.1 was used to quantify differential gene expression between all pair-wise combinations of treatment groups for each experiment. P values of differential expression analyses were corrected for multiple testing with a false discover rate (FDR) of 10%.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Tab-delimited text files with read counts per gene for each sample

molecule: polyA RNA

organism: Apis mellifera

source_name: Seminal-fluid-inseminated queens

growth_protocol: We sampled honeybee (Apis mellifera ligustica) larvae at day four of their development (i.e. one day after hatching) from a single colony, transferred them into plastic queen cells (Ceracell, Aukland, NZ) and placed them into a queen-right cell-building colony, prepared 24 h in advance by moving two frames of uncapped brood above the queen excluder and placing the graft bar in between these brood frames. Ten days later we placed the resulting queen cells into 4-frame queen-less nucleus hives with queen excluders at the entrance to prevent natural mating flights and allowed them to hatch. Four days after hatching and one day before artificial inseminations, virgin queens were removed from their hives, caged, and exposed to CO2 for 1 minute to stimulate ovary activation. Five nurse bees were added to the cages and the caged queens were returned to their original nucleus hives.

extract_protocol:
Brains of queens were dissected with Inox 5 watchmaker forceps under an Olympus SZX10 stereo microscope in ice-cold sterile Hayes saline. Care was taken to remove brains intact, including the optic lobes, and to remove hypopharyngeal and other extraneous glandular material. We combined the brains from three individual queens to obtain enough RNA for Illumina TruSeq sequencing, froze these pooled brain samples in liquid nitrogen and immediately stored them at -80 °C. To extract RNA from pooled brain samples, we briefly thawed them on ice, placed them in 10 µl of 0.25 M Tris pH 7.5 and homogenized them with a plastic pestle. We then added 50 µl of Trizol to each sample, incubated samples on ice for 15 min, thoroughly vortexed and returned them to ice for another 15 min, followed by centrifugation at 20,000 g for 15 min at 4 °C. We collected the supernatant and added one volume isopropanol. Next, we briefly vortexed the samples and incubated them at room temperature for 20 min, followed by centrifugation at 20,000 g for 15 mins at 4 °C. After discarding the supernatants, we washed each pellet with 70% EtOH, followed by air-drying and resuspension in 20 µl of RNase-free H2O. To precipitate the RNA, we added 1.6 volumes of ice-cold 4 M LiCl and incubated samples on ice for 1 h, followed by centrifugation at 20,000 g for 15 min at 4 °C. After discarding the supernatants, each RNA pellet was washed with 500 µl 70% EtOH before resuspension in 10 µl RNase-free H2O.
Sequencing libraries were generated from 1 µg total input RNA using the TruSeq Stranded mRNA Sample Kit (Illumina, San Diego, CA)

treatment_protocol: For our first RNA-sequencing experiment we compared brain gene expression in queens that we artificially inseminated with either semen or pure seminal fluid with brain gene expression of queens for which all artificial insemination procedures were followed but no fluid was injected into the vaginal orifice. Virgin queens were sampled from their nucleus hives and randomly assigned to one of three experimental groups: (i) instrumentally inseminated with 6 µl of freshly collected semen pooled from approximately 10 males, (ii) instrumentally inseminated with 6 µl of seminal fluid after thawing previously prepared aliquots, and (iii) mock-inseminated without injecting any fluid. We then performed an additional RNA-sequencing experiment for which queens were once more randomly assigned to one of three experimental groups to be: (i) instrumentally inseminated with 6 µl of semen, (ii) instrumentally inseminated with 6 µl of seminal fluid, and (iii) instrumentally inseminated with 6 µl of Hayes saline (9 g NaCl, 0.2 g CaCl2, 0.2 g KCl and 0.1 g NaHCO3 in 1000 ml H2O, adjusted to pH 8.7 and sterilized by filtration through a 0.22 µm syringe-filter, Membrane Solutions). To artificially inseminate queens, we placed them inside their cages and sedated them with CO2, before placing them in a holder mounted onto a standard artificial insemination instrument (Schley, Germany) and inseminating them according to their planned treatments. Queens were allowed to recover for about 30 min before we returned them to their hives. We recollected queens after 24 h, anaesthetized them with CO2 and flash froze their heads in liquid nitrogen. All heads were then stored at -80 °C until further dissection.

value: Brain

tag: Sex

value: female


title: Exp2_SF_C

description: Three pooled brains


title: Exp2_SF_B

description: Three pooled brains


title: Lung graft, non-OB.2


title: Exp2_INS_A

description: Three pooled brains

source_name: Semen-inseminated queens


title: Mus musculus lung-24h-wsn(+)_rep3

city: Beijing

first: jing

last: ouyang

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of microbiology, Chinese Academy of Sciences

description: Gene expression after 24hours,with IAV infection

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) 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 dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: C57BL/6 mice were infected intranasally with A/WSN/33 influenza virus (PFU= 5×104 ) or PBS for 24 hours.Then the mice were euthanized and their lungs were removed for further analysis.

value: lung

tag: age


title: Lung graft, non-OB.1


title: Exp2_HS_C

description: Three pooled brains

source_name: Hayes-saline-inseminated queens


title: Mus musculus lung-24h-wsn(+)_rep2


title: Lung graft, OB.2

source_name: allograft, OB

value: allograft, OB


title: Exp1_SF_C

description: Three pooled brains


title: Exp2_HS_B

description: Three pooled brains


title: Exp2_HS_A

description: Three pooled brains


title: Lung graft, OB.3


title: Mus musculus lung-24h-wsn(+)_rep1


title: Exp1_SF_B

description: Three pooled brains


title: Exp2_INS_C

description: Three pooled brains


title: Exp1_INS_C

description: Three pooled brains


title: Exp1_INS_B

description: Three pooled brains


title: Mus musculus lung-24h-wsn(-)_rep3

description: Gene expression after 24hours,without IAV infection


title: Lung graft, OB.1


title: Exp2_INS_B

description: Three pooled brains


title: Mus musculus lung-24h-wsn(-)_rep1


title: Replicate 3, IL-10neg cells

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

description: 16h activated with CD3/CD28 beads

data_processing:
The RNA-Seq Alignment App (version 1.1.0) on Illumina Basespace was used for data-processing and read quantification as follows:
Basecalls were made using RTA v2.1. Demultiplexing was achieved using bcl2fastq2.
Alignment: STAR aligners version 2.5.0a
Quantification of gene expression was done with RnaReadCounter which is part of the IsisRNA tool (Version 2.6.25.18) in the RNA-Seq Alignement App. The raw gene counts generated by RnaReadCounter are saved in the 'processed data file'.
DESeq2 version 1.16 for R was used for analysis of differential gene expression with the raw counts (from the 'processed data file') as input.
Genome_build: Homo sapiens (PAR-masked)/hg19 reference sequence
Supplementary_files_format_and_content: Individuals counts.genes files for all 9 samples, raw data fastq.gz files downloaded from Illumina basespace

source_name: Peripheral Blood

growth_protocol: Stimulation protocol: CD4+ T cells were isolated using RosetteSep enrichment and centrifugation over Ficoll-Paque. Isolated cells were either left unstimulated or stimulated for 16h with CD3/CD28 beads. The Miltenyi IL-10 capture assay was used to sort IL-10+ (Tr1 cells) and IL-10neg cells. Matched Tregs were sorted from unstimulated cultures and stimulated for 16h with CD3/CD28 beads before cells collected for RNA extraction.

extract_protocol:
Expanded cells were centrifuged, resuspended in RNAzol lysis reagent and further processed as per manufacturers instructions to obtain RNA for library preparation and subsequent NGS.
Qualifying samples (RIN>8) were prepared using the TruSeq stranded mRNA library kit (Illumina) on the Illumina Neoprep automated nanofluidic prep instrument.

tag: subject id

value: Peripheral Blood

tag: activation

value: 16h CD3/CD28 bead activation


title: Mus musculus lung-24h-wsn(-)_rep2


title: Replicate 3, Tregs

description: 16h activated with CD3/CD28 beads

value: Treg


title: Exp1_MI_C

description: Three pooled brains

source_name: Mock-inseminated queens


title: Exp1_MI_B

description: Three pooled brains


title: Replicate 2, IL-10neg cells

description: 16h activated with CD3/CD28 beads


title: Replicate 2, Tregs

description: 16h activated with CD3/CD28 beads


title: Replicate 1, IL-10neg cells

description: 16h activated with CD3/CD28 beads


title: Replicate 1, Tregs

description: 16h activated with CD3/CD28 beads


title: Exp1_SF_A

description: Three pooled brains


title: Replicate 1, Tr1 cells

description: 16h activated with CD3/CD28 beads


title: Exp1_INS_A

description: Three pooled brains


title: Replicate 2, Tr1 cells

description: 16h activated with CD3/CD28 beads


title: AML_P16_Rel_RNA

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.1 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 40 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.5. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.
RNA-seq:  Sequencing reads were aligned on the human reference genome build hg38 from RefSeq with annotated transcripts  using HISAT2 version 2.0.5. Reads that mapped to multiple locations and duplicate reads were removed using Samtools version 1.5. Reads in genes were counted using HTSeq-counts in the union mode q.
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in _H3K27ac.bw; RNA-seq count values are in _RNA.count;

source_name: Bone marrow

extract_protocol: TruSeq Stranded mRNA Library Preparation (Illumina)

tag: time point

value: relapse

value: Bone marrow

tag: disease

value: acute myeloid leukemia


title: AML_P27_Rel_RNA


title: AML_P18_Dx_RNA

value: initial diagnosis


title: AML_P3_Dx_RNA


title: AML_P27_Dx_RNA


title: AML_P2_Dx_RNA


title: AML_P27_Dx_H3K27ac

extract_protocol: TruSeq DNA sample preparation kit (Illumina)


title: Replicate 3, Tr1 cells

description: 16h activated with CD3/CD28 beads


title: AML_P27_Rel_H3K27ac


title: AML_P26_Rel_H3K27ac


title: AML_P26_Dx_H3K27ac


title: AML_P25_Rel_H3K27ac


title: AML_P25_Dx_H3K27ac


title: AML_P24_Dx_H3K27ac


title: AML_P24_Rel_H3K27ac


title: AML_P23_Dx_H3K27ac


title: AML_P23_Rel_H3K27ac


title: AML_P22_Rel_H3K27ac


title: AML_P22_Dx_H3K27ac


title: AML_P21_Dx_H3K27ac


title: AML_P20_Rel_H3K27ac


title: AML_P21_Rel_H3K27ac


title: AML_P20_Dx_H3K27ac


title: AML_P25_Rel_RNA


title: AML_P17_Dx_H3K27ac


title: AML_P19_Rel_H3K27ac


title: AML_P16_Rel_H3K27ac


title: AML_P18_Dx_H3K27ac


title: AML_P13_Dx_H3K27ac


title: AML_P12_Dx_H3K27ac


title: AML_P16_Dx_H3K27ac


title: AML_P15_Dx_H3K27ac


title: AML_P14_Dx_H3K27ac


title: AML_P11_Dx_H3K27ac


title: AML_P10_Dx_H3K27ac


title: AML_P8_Dx_H3K27ac


title: AML_P9_Dx_H3K27ac


title: AML_P6_Dx_H3K27ac


title: AML_P7_Dx_H3K27ac


title: AML_P4_Dx_H3K27ac


title: AML_P5_Dx_H3K27ac


title: AML_P2_Dx_H3K27ac


title: AML_P1_Dx_H3K27ac


title: AML_P3_Dx_H3K27ac


title: edl_ATAC

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

institute: Northwestern University

data_processing:
Alignment:  Paired end sequence reads were obtained and mapped to the mouse mm10 genome using Bowtie 2.
Peaks: Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Peaks were identified with Homer findPeaks using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files with annotated peak lists, and bedgraphs

source_name: skeletal muscle - EDL

extract_protocol:
Skeletal muscle was dissected and snap frozen in liquid nitrogen.  ATAC-seq samples were cryo-pulverized and 30mg of powdered tissue was subjected to transposase reaction as per Buenrostro et al 2013.
ATAC-seq libraries were prepared as per Beunrostro et al 2013.

tag: genotype

value: wild type

value: skeletal muscle - EDL


title: quad_ATAC

source_name: skeletal muscle - quadricep

tag: strain

value: skeletal muscle - quadricep


title: ChIP-Seq Quad control_input_72hrRest

description: sedentary

data_processing:
Alignment:  Sequence reads were obtained and mapped to the mouse mm10 genome using Bowtie 1.2 with --best and -m 1  parameters.
Peaks: Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Homer getDifferentialPeaksReplicates.pl was used to call ChIP-seq peaks in comparison to input controls using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files containing annotated peaks

extract_protocol:
Skeletal muscle was dissected and finely minced. ChIP-seq samples were subjected to cross linking in 1% formaldehyde for 30 minutes and quenched with glycine. Tissue was dounced to release nuclei. Nuclei were sonicated to shear the chromatin and subjected to immunoprecipitation. Precipitates were washed and DNA was purified by column (Qiagen Min-Elute).
ChIP-seq libraries were prepared with the KAPA Hyper Prep Kit (Kapa Biosciences).
Kapa Hyper Prep

treatment_protocol: exercised mice were rested 72 hours before tissue harvest

tag: antibody

value: H3K27ac (Active Motif 31933)


title: ChIP-Seq Quad exercise_input_72hrRest

description: exercised/rested


title: diaphragm_ATAC

source_name: skeletal muscle - diaphragm

value: skeletal muscle - diaphragm


title: ChIP-Seq Quad ex1_72hrRest

description: exercised/rested


title: ChIP-Seq Quad ex2_72hrRest

description: exercised/rested


title: ChIP-Seq Quad control1_72hrRest

description: sedentary


title: ChIP-Seq Quad control2_72hrRest

description: sedentary


title: Spleen_DN_rep1

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.7).
Filtered adaptor and poor quality sequences, using cutadapt (v. 1.18) and trim_galore (minimum phred quality score = 20).
The reference genome (mm10) based alignment of clean reads were performed using STAR (v. 2.6.1a) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/1.6.2 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Genome_build: Mus musculus reference genome (mm10).
Supplementary_files_format_and_content: Tab-delimited text files include log2 normalized expression values for each Sample.

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
cDNA libraries were constructed using SMARTer low input kit for mRNA seq.

treatment_protocol: For mRNA sequencing analysis, B220 positive, CD73 positive MBCs were sorted as CD11b, CD11c double negative and CD11b, CD11c double positive. After the sort, the cells were spun down and washed with PBS and re-suspended in RLT+1% beta-mercaptoethanol.

value: Spleen

value: murine splenic memory B cells (B220+ CD73+)

tag: sorted population

value: CD11b, CD11c double negative (DN)


title: Spleen_DN_rep3


title: Liver_DN_rep2

value: Liver

value: murine hepatic memory B cells (B220+ CD73+)


title: Spleen_DP_rep2

value: CD11b, CD11c double positive (DP)


title: Spleen_DN_rep2


title: Liver_DP_rep2


title: Liver_DN_rep1


title: Spleen_DP_rep1


title: Spleen_DP_rep3


title: Liver_DP_rep1


title: Liver_DP_rep3


title: Liver_DN_rep3


title: ChIP_Soleus_Nfat

data_processing:
Alignment:  Sequence reads were obtained and mapped to the mouse mm10 genome using Bowtie 1.2 with --best and -m 1  parameters.
Peaks: Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Homer getDifferentialPeaksReplicates.pl was used to call ChIP-seq peaks in comparison to input controls using default settings. ATAC-seq peaks were called using the Homer findPeaks command, default settings.
Footprinting: ATAC-seq footprints were detected with RGT-HINT using the --atac-seq and --paired-end parameters. Differential motifs withing the footprints were detected using the rgt-motifanalysis and rgt-hint differential commands.
Genome_build: mm10 (footprinting done in mm9)
Supplementary_files_format_and_content: Tab-delimited text (txt) files with annotated peak lists

source_name: skeletal muscle - soleus

extract_protocol:
Skeletal muscle was dissected and finely minced. ChIP-seq samples were subjected to cross linking in 1% formaldehyde for 30 minutes and quenched with glycine. Tissue was dounced to release nuclei. Nuclei were sonicated to shear the chromatin and subjected to immunoprecipitation. Precipitates were washed and DNA was purified by column (Qiagen Min-Elute). ATAC-seq samples were cryo-pulverized and 30mg of powdered tissue was subjected to transposase reaction as per Buenrostro et al 2013.
ChIP-seq libraries were prepared with the KAPA Hyper Prep Kit (Kapa Biosciences). ATAC-seq libraries were prepared as per Beunrostro et al 2013.

value: skeletal muscle - soleus

tag: chip primary antibody

value: mouse monoclonal anti-Nfat (Millipore MABS409)


title: ChIP_Soleus_Med1

value: rabbit anti-Med1 (Bethyl A300-793A)


title: ChIP_Soleus_TFInput


title: ChIP_Quad_TFInput


title: ChIP_Quad_Nfat


title: ChIP_Quad_Med1

value: rabbit anti-Med1 (Bethyl Laboratories A300-793A)


title: soleus_ATAC


title: ChIP_Diaphram_TFInput

source_name: skeletal muscle - diaphram

value: skeletal muscle - diaphram


title: ChIP_EDL_Med1


title: ChIP_Diaphram_Med1


title: ATAC_Quad_PGC1-3


title: ATAC_Quad_PGC1-2


title: ATAC_Quad_PGC1-1


title: ATAC_Quad_ex2


title: ATAC_Quad_ex3


title: ATAC_Quad_ex1


title: PGC1transgenic_RNAseq_rep5

description:
mTgQuad_DifferentialGenes.xlsx
FpkmValues_AllSamples.xlsx

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using STAR
Differential Expression Analysis: differentially expressed RNAs were identified using DESeq2 (FDR-adjusted p-value <0.05).  STAR alignment and DESeq2 analysis were executed through the RNA-Seq Allignment v1.1.1 and Deseq2 v1.1.0  BaseSpace applications, respectively (Illumina).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) file with differential expression

extract_protocol:
Total RNA was isolated from skeletal muscle tissues using Trizol (ThermoFisher) and Rneasy columns (Qiagen).  RNA quality was assessed using a Bioanalyzer (Agilent).
TruSeq Stranded mRNA sample prep kit (Illumina).

value: PGC1a Tg(+)

value: sedentary


title: ExerciseQuad_RNAseq_rep3

description:
ExerciseQuad_DifferentialGenes.xlsx
FpkmValues_AllSamples.xlsx

value: wild type

value: exercise


title: PGC1transgenic_RNAseq_rep3

value: skeletal muscle - quadricep


title: PGC1transgenic_RNAseq_rep2


title: ExerciseQuad_RNAseq_rep4


title: ExerciseQuad_RNAseq_rep5


title: PGC1transgenic_RNAseq_rep4


title: PGC1transgenic_RNAseq_rep1


title: WtQuad_Input

data_processing:
Alignment:  Sequence reads were obtained and mapped to the mouse mm10 genome using Bowtie 1.2 with --best and -m 1  parameters.
Peaks. Tag directories were generated in HOMER using the -tbp 1 command to remove clonal reads. Homer getDifferentialPeaksReplicates.pl was used to call ChIP-seq peaks in comparison to input controls using default settings. ATAC-seq peaks were called using the Homer findPeaks command, default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text (txt) files with annotated peak lists


title: ATAC_Quad_ctr3


title: ATAC_Quad_ctr1


title: ControlQuad_RNAseq_rep3


title: ExerciseQuad_RNAseq_rep2


title: ControlQuad_RNAseq_rep4


title: ControlQuad_RNAseq_rep5


title: ATAC_Quad_ctr2


title: WtQuad_H3K27Ac_rep1

value: rabbit anti-H3K27Ac (Active Motif 39133)


title: WtQuad_H3K27Ac_rep2


title: ControlQuad_RNAseq_rep2


title: ControlQuad_RNAseq_rep1


title: ExerciseQuad_RNAseq_rep1


title: WtQuad_H3K4me2_rep1

value: rabbit anti-H3K4me2 (AbCam 32356)


title: Soleus_Input


title: Soleus_H3K4Me2_rep2


title: Soleus_H3K27Ac_rep1


title: Soleus_H3K27Ac_rep2


title: SedQuad_Me2Input


title: SedQuad_H3K27Ac_rep2


title: Soleus_H3K4Me2_rep1


title: SedQuad_H3K4me2_rep2


title: SedQuad_AcInput


title: SedQuad_H3K27Ac_rep1


title: Quad_Input_rep2


title: mTg_Quad_Input


title: Quad_H3K4me2_rep2


title: mTg_Quad_H3K27Ac_rep1

description:
mTgQuad_H3K27ac_peaks.txt
mTgQuad_HyperH3K27ac_Peaks.txt
mTgQuad_HypoH3K27ac_Peaks.txt


title: Quad_H3K27Ac_rep1


title: Quad_H3K4me2_rep1


title: ExerciseQuad_Me2Input


title: Quad_Input_rep1


title: ExerciseQuad_H3K27Ac_rep1

description:
ExerciseQuad_H3K27ac_peaks.txt
ExerciseQuad_HyperH3K27ac_Peaks.txt
ExerciseQuad_HypoH3K27ac_Peaks.txt


title: Quad_H3K27Ac_rep2


title: mTg_Quad_H3K27Ac_rep2


title: ExerciseQuad_H3K27Ac_rep2


title: ExerciseQuad_H3K4me2_rep2


title: ExerciseQuad_AcInput


title: ExerciseQuad_H3K4me2_rep1


title: EDL_H3K27Ac_rep2

value: skeletal muscle - EDL


title: ChIP_EDL_TFInput


title: SedQuad_H3K4me2_rep1


title: EDL_Input


title: EDL_H3K27Ac_rep1


title: EDL_H3K4me2_rep2


title: EDL_H3K4me2_rep1


title: mTg_Quad_H3K4me2_rep1


title: Diaphram_Input


title: mTg_Quad_H3K4me2_rep2


title: Diaphram_H3K27Ac_rep1


title: Diaphram_H3K4me2_rep1


title: Diaphram_H3K27Ac_rep2


title: AMI-5 3 (Am3)

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

country: Germany

institute: TU Dresden

data_processing:
Bcl2fastq 2.19.1 for Am samples, respetively bxl2fastq 1.8.4 for A samples
Alignment to mouse (mm10) reference with GSNAP (2018-05-30) and support of Ensembl 87 annotation to detect splice sites
FeatureCounts (1.6.2) was used to create fragment to gene counts; mm10 and Ensembl 87 annotation was used
Genome_build: mm10
Supplementary_files_format_and_content: tab separated file output of FeatureCounts; the first columns are geneid, chromosom, start, end, strand and length, followed by the raw counts for the 6 samples

source_name: embryonic pancreata at 14.5 dpc

growth_protocol: growth protocol described in Serafimidis et al, Plos Biology, 2017

extract_protocol:
RNAeasy
Strand specific RNA-Seq library preparation was performed with Ultra II, respectively Ultra I for A samples, Directional RNA Library Prep (New England Biolabs)

treatment_protocol: treatment protocol included in Giannios et al, under revision

value: pancreas

tag: developmental stage

value: 10 uM AMI-5


title: AMI-5 2 (Am2)

tag: tissue


title: AMI-5 1 (Am1)


title: Diaphram_H3K4me2_rep2


title: BMMs_TDB_IFNg_24h_3

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

hyb_protocol: Affymetrix GeneChip WT PLUS Reagent Kit

scan_protocol: GeneChip Scanner 3000 7G, AGCC 4.0

data_processing: Partek Genomics Suite 6.6, GC-RMA

source_name: bone marrow derived macrophages

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit

growth_protocol: Bone marrow derived macrophages (BMMs) from female C57BL/6 mice aged 6 to 8 weeks were stimulated in 12 well plates with 106 cells per well in 1 ml.

extract_protocol: Total RNA was prepared using Qiagen RNEasy Mini Kit, including DNAse treatment. Quality control on RNA samples was performed on an Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano protocol according to manufacturer’s instructions. Each sample had a RIN of 10 and a concentration of at least 50 ng/µl.

treatment_protocol: TDB and TDM were coated to the culture wells, IFN-gamma was added in solution. After 6 and 24 h, cells were harvested.

value: female

value: bone marrow derived macrophages (BMMs)

value: TDB

value: IFNg

tag: harvest time

value: 24 hrs


title: BMMs_TDM_IFNg_24h_3

value: TDM


title: BMMs_IFNg_mock_6h_3

value: mock

value: 6 hrs


title: BMMs_TDB_IFNg_6h_3


title: BMMs_TDB_mock_24h_3


title: BMMs_TDB_mock_24h_2


title: BMMs_mock_mock_6h_3


title: BMMs_Iso_mock_24h_3

value: Isopropanol


title: BMMs_Iso_mock_6h_3


title: BMMs_TDB_mock_6h_3


title: BMMs_mock_mock_24h_3


title: BMMs_TDM_mock_6h_3


title: BMMs_Iso_mock_24h_2


title: BMMs_TDM_mock_24h_3


title: BMMs_TDM_IFNg_24h_2


title: BMMs_TDM_IFNg_6h_3


title: BMMs_TDB_IFNg_24h_2


title: BMMs_IFNg_mock_24h_2


title: BMMs_TDM_mock_24h_2


title: BMMs_TDM_IFNg_6h_2


title: BMMs_mock_mock_24h_2


title: BMMs_TDB_mock_6h_2


title: BMMs_TDM_mock_6h_2


title: BMMs_TDB_IFNg_6h_2


title: BMMs_IFNg_mock_6h_2


title: WtQuad_H3K4me2_rep2

value: wild type

value: sedentary


title: WT-derived T-ALL 201 (Exome-seq)

city: Tarrytown

first: Qi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals Inc

data_processing:
Library strategy: Exome-seq
Exome-Seq reads were mapped to the mouse mm10 reference genome by OSA aligner implemented in ArrayStudio software from Qiagen
mutation frequency for identified somatic point mutations by comparing to the mm10 reference genome then removing strain-related SNPs downloaded from COSMIC_db
Genome_build: mm10
Supplementary_files_format_and_content: mutation frequency for identified somatic point mutations

source_name: WT-derived T-ALL

extract_protocol:
Total DNA was extracted
Whole exome capture was performed by using the Agilent Sure-Select Mouse All Exon 50 Mb kit

value: BALB/c

value: spleen

tag: disease state

value: tumor

tag: donor thymus genotype

value: Wild type


title: WT-derived T-ALL 128 (Exome-seq)


title: BMMs_mock_mock_6h_2

tag: cell type


title: BMMs_Iso_mock_6h_2

tag: Sex


title: WT-derived T-ALL 126 (Exome-seq)


title: WT-derived T-ALL 108 (Exome-seq)


title: WT-derived T-ALL 111 (Exome-seq)


title: Exp1_MI_A

description: Three pooled brains

value: Brain


title: WT-derived T-ALL 124 (Exome-seq)


title: BMMs_Iso_mock_24h_1


title: BMMs_TDB_IFNg_24h_1


title: BMMs_IFNg_mock_6h_1


title: BMMs_mock_mock_24h_1


title: BMMs_TDM_mock_6h_1


title: BMMs_IFNg_mock_24h_1


title: BMMs_TDB_mock_6h_1


title: BMMs_TDM_mock_24h_1


title: BMMs_TDB_IFNg_6h_1


title: BMMs_IFNg_mock_24h_3


title: BMMs_TDM_IFNg_24h_1


title: WT-derived T-ALL 204 (Exome-seq)


title: WT-derived T-ALL 203 (Exome-seq)


title: WT-derived T-ALL 202 (Exome-seq)


title: WT-derived T-ALL 120 (Exome-seq)


title: WT-derived T-ALL 110 (Exome-seq)


title: BMMs_mock_mock_6h_1


title: BMMs_TDB_mock_24h_1


title: BMMs_TDM_IFNg_6h_1


title: WT-derived T-ALL 36 (Exome-seq)


title: WT-derived T-ALL 13 (Exome-seq)


title: BMMs_Iso_mock_6h_1


title: WT-derived T-ALL 14 (Exome-seq)


title: WT-derived T-ALL 7 (Exome-seq)


title: WT-derived T-ALL 4 (Exome-seq)


title: WT-derived T-ALL 3 (Exome-seq)


title: 864: Lhx5-EGFP-Rpl10a-DT154 Hypothalamus Input Rep1

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description: 864_Lhx5_Hypothalamu_Input_Rep1_CTTGTA_L002

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Hypothalamus

growth_protocol: Not applicable

extract_protocol:
The hypothalamus was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Control mice only. No treatment

value: Hypothalamus

tag: animal line

value: Lhx5-TRAP DT154

tag: application

value: RNA-seq

tag: sample type

value: Unbound


title: 862: Lhx5-EGFP-Rpl10a-DT154 Hypothalamus IP Rep1

description: 862_Lhx5_Hypothalamus_IP_Rep1_GCCAAT_L002

value: Immunopurified (IP)


title: 875: Lhx5-EGFP-Rpl10a-DT154 Hypothalamus IP Rep3

description: 875_Lhx5_Hypothalamus_IP_Rep3_GCCAAT_L002


title: 25: Stard8-EGFP-Rpl10a-ES2342 UB2

source_name: Midbrain

extract_protocol:
The midbrain was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Midbrain

value: Stard8-TRAP ES2342


title: 23: Stard8-EGFP-Rpl10a-ES2342 UB1


title: 877: Lhx5-EGFP-Rpl10a-DT154 Hypothalamus Input Rep2

description: 877_Lhx5_Hypothalamu_Input_Rep2_CTTGTA_L004


title: 27: Stard8-EGFP-Rpl10a-ES2342 UB3


title: 863: Lhx5-EGFP-Rpl10a-DT154 Hypothalamus IP Rep2

description: 863_Lhx5_Hypothalamus_IP_Rep2_GCCAAT_L004


title: 28: Stard8-EGFP-Rpl10a-ES2342 IP4


title: 29: Stard8-EGFP-Rpl10a-ES2342 UB4


title: 878: Lhx5-EGFP-Rpl10a-DT154 Hypothalamus Input Rep3

description: 878_Lhx5_Hypothalamu_Input_Rep3_CTTGTA_L002


title: 872: Lhx5-EGFP-Rpl10a-DT154 Input Rep3

description: 872_Lhx5_Midbrain_Input_Rep3_CTTGTA_L001


title: WT-derived T-ALL 48 (Exome-seq)


title: 22: Stard8-EGFP-Rpl10a-ES2342 IP1


title: 861: Lhx5-EGFP-Rpl10a-DT154 Input Rep2

description: 861_Lhx5_Midbrain_Input_Rep2_CTTGTA_L003


title: 869: Lhx5-EGFP-Rpl10a-DT154 IP Rep3


title: WT-derived T-ALL 5 (Exome-seq)


title: 859: Lhx5-EGFP-Rpl10a-DT154 IP Rep2


title: 858: Lhx5-EGFP-Rpl10a-DT154 IP Rep1


title: Adipose gdT, KD_E_3

city: New Haven

first: Emily

middle: L

last: Goldberg

state: CT

address: 310 Cedar Street

institute: Yale

data_processing:
Bulk seq: Base-calling: Illumina HiSeq2500 software
Bulk seq: Btrim to trim reads; BWA for alignment to GRCm38 and TopHat2 for alignment for cellular gene analysis
Bulk Seq: Expression quantification was performed using RSEM
Bulk seq:DEseq2 was used to calculate differential gene expression
See detailed methods in Goldberg et al., Nature Metabolism 2019
Genome_build: GRCm38
Supplementary_files_format_and_content: excel spreadsheet ofcounts, fpkms

source_name: sorted gdT

extract_protocol:
Total RNA was extracted with RLT buffer
Bulk RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: treatment

value: ketogenic diet (KD)

value: visceral adipose tissue

value: gamma delta T cells


title: Adipose gdT, KD_E_1


title: Adipose gdT, KD_E_4


title: Adipose gdT, KD_E_2


title: Adipose gdT, Chow_E_1

value: control


title: Adipose gdT, Chow_E_2


title: 24: Stard8-EGFP-Rpl10a-ES2342 IP2


title: I3: CCR2-/- NMBA6

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

data_processing:
Illumina HiSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of mm10 using HISTA2. Transcript assembly were performed using Cufflink. DEG analyses were performed using DESeq2.
Genome_build: Mus_musculus.GRCm38.84.gtf.new.gtf

source_name: gavaged with NMBA

extract_protocol:
Forestomach were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kitwas used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild type and CCR2-/- C57 mice were gavaged with carboxyl methyl cellulose (1%) or N-nitrosomethylbenzylamine(NMBA) 0.25 mg/kg body weight (BW) twice per week for 5 weeks. At the end of Week 25, the forestomach were harvested to carry out RNA resequencing. We found that CCR2 mediated monocyte infiltration promoted tumor evasion through activating PD-1 signaling pahtway.

value: forestomach

value: male

tag: genotype/variation

value: esophageal cancer


title: O2: CCR2-/- NMBA2


title: I2: CCR2-/- NMBA5


title: O4: CCR2-/- NMBA3


title: C1: CCR2-/- CT1

source_name: gavaged with 1% CMC


title: G3: WT NMBA5

value: WT


title: C3: CCR2-/- CT3


title: Adipose gdT, Chow_E_4


title: A3: WT CT3


title: M2: WT NMBA1


title: G2: WT NMBA4


title: A2: WT CT2


title: M4: WT NMBA3


title: A1: WT CT1


title: Adipose gdT, Chow_E_3


title: Murine rechallenged MAIT 3

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

data_processing:
RNA-seq reads were aligned to reference genome sequences using STAR(Dobin et al., 2013) aligner software. Mapped reads were assigned to genomic features using Rsubread(Liao et al., 2013)  R package(Team, 2014).
Genes that were differentially expressed (>2 fold, P<0.01, FDR<0.05) between conditions and their normalised expression values, were generated with EdgeR R package(Robinson et al., 2010), Partek® Flow®, an online analysis platform for Next Generation Sequencing data (http://www.partek.com/partek-flow/).
RNA-seq data (logCPM) and ImmGen microarray data were integrated using a common set of Entrez(Maglott et al., 2011) annotated genes; batch effect removal was performed using ComBat algorithm in sva(Leek et al., 2012) R package. Hierarchical clustering analysis of transcription profiles was conducted in R employing highly variable genes (IQR >0.75(Gentleman et al., 2004)) and Euclidian distance.

source_name: Pulmonary lymphocytes

extract_protocol:
Cells were lysed in Agilent lysis buffer (Agilent Ltd., UK) containing 100 mM beta-mercaptoethanol and passed through a QIAshredder device (Qiagen, Valencia, US), then RNA extracted using the Absolutely RNA Nanoprep Kit according to the manufacturer’s instructions, including using of DNase I.
RNA libraries were prepared at the Melbourne Translational Genomics Platform, Department of Pathology (The University of Melbourne). Briefly, RNA quality and quantity were assessed using the Bioanalyzer 2100 RNA pico kit (Agilent technologies). The input total RNA was normalized to 250 pg per sample and median RIN was 9.7 (range 5.7-10.0). RNA was reverse transcribed and cDNA amplified by in vitro transcription with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). First strand cDNA synthesis and tailing by reverse transcription was performed using Clontech’s proprietary SMART (Switching Mechanism at 5’ End of RNA Template) technology. Following first strand synthesis, cDNA was amplified 12 cycles by LD PCR using blocked PCR primers. Amplified cDNA was purified using AMPure XP prior to QC using the bioanalyser 2100 HS DNA kit (Agilent technologies).
Library preparation of purified amplified cDNA was performed using Nextera XT library preparation (Illumina, AUS). Following QC, 150 pg of cDNA was tagmented (simultaneously fragmented with adaptors inserted) using Nextera transposons. Molecular barcodes were incorporated during 12 cycles of amplification followed by purification using AMPure XP. The libraries passed a quality checkpoint (Qubit and Bioanalyser HS DNA) prior to normalization and pooling before loading onto the HiSeq 2500 (Illumina, AUS) for paired end sequencing.

treatment_protocol: Single-cell suspensionswere generated from murine lungs which were finely chopped with a scalpel blade and treated with 3 mg.ml-1 collagenase III , 5ug/ml DNAse, and 2% foetal calf serum in RPMI for 90 min at 37'C with gentle shaking, and, where relevant, brefeldin A. Lung cells were then filtered (70 um) and washed with PBS/2% foetal calf serum. Red blood cells were lysed with hypotonic buffer TAC (Tris-based amino chloride) for 5 min at 37'C. Approximately 1.5x106 cells were filtered (40 um) and used for flow cytometric analysis. To obtain sufficient cells for sorting naïve CD8+CD44-CD62L+ cells from infection-naïve mice lungs from 2-3 mice per sample were pooled and stained with 0.18 ul anti-CD8-PE, then magnetically enriched using anti-PE beads (Miltenyi) prior to sorting. Human PBMC: cells were stained with surface antibodies (CD3-PE-CF594, CD8-PerCPCy5.5, CD45RA-FITC, TCR Va7.2-APC and FCg block for 15 mins at RT, followed by staining with MR1-5-OP-RU tetramer-PE for 20 mins at RT. Tetramer positive cells were positively selected using anti-PE microbeads (10 ul per 10-7 cells). Cells were sorted immediately into ice cold PBS with 10% FCS using an FACSAria III cell sorter selecting live CD3+TCR-Va7.2+MR1-5OP-RU-tetramer+ MAIT cells from the positive fraction and live CD3+CD8+CD45RA+MR1-Tetramer- cells from the negative fraction. The following day the remaining cells were stimulated for 6 h with 10 nM 5-OP-RU then magnetically enriched using MR1-5-OP-RU-tetramer-PE and anti-PE microbeads, and live CD3+TCR-Va7.2+MR1-5-OP-RU-tetramer+ MAIT cells sorted in the same manner. Purity was checked and with an average of 98%. Immediately after sorting cells were centrifuged at 400 g for 5 mins then resuspended in 100 uL of RNA lysis buffer (Agilent Ltd, UK) with 0.7uL beta-mercaptoethanol and stored at -80'C.

value: Pulmonary lymphocytes

value: 7 days post infection with 2x104 CFU L. longbeachae in mice previously infected at least 13 weeks prior with  1x104 CFU L. longbeachae


title: M3: WT NMBA2


title: C2: CCR2-/- CT2


title: Murine rechallenged MAIT 2


title: Murine rechallenged MAIT 1


title: I1: CCR2-/- NMBA4


title: Murine acute MAIT 1

value: 7 days post infection with 1x104 CFU L. longbeachae


title: Murine acute MAIT 2


title: Murine chronic MAIT 1

value: 12 weeks post infection with 1x104 CFU L. longbeachae


title: O1: CCR2-/- NMBA1


title: Murine chronic MAIT 2


title: G6: WT NMBA6


title: shPHF2 rep1 RNA-seq

city: Barcelona

first: Marian

last: Martínez-Balbás

state: Barcelona

address: C/ Baldiri Reixac 15-21

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

description:
Total RNA without ribosomal RNA
shPHF2rep1_23547_GCCAAT

data_processing:
Alignment was performed using HISAT2
Assignment of aligned reads to genes using HTSeq
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values (csv) generated using DESseq2 including log2FoldChange, pvalue and qvalue

source_name: Neural stem cells (NSCs)

growth_protocol: NSCs were cultured in a poly-D-lysine (5 mg/ml, 2 hours at 37°C) and laminin (5 mg/ml, 4 hours at 37°C) pre-coated dishes growing with a media comprising equal parts DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing penicillin/streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential amino acids (0.1 mM), sodium pyruvate (1 mM), Hepes (5 mM), heparin (2 mg/l), bovine serum albumin (25 mg/l) and -mercaptoethanol (0.01 mM). We added fresh recombinant human EGF (R&D Systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final, respectively

extract_protocol:
For RNA-seq, RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment.
Libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Human/Mouse/Rat Kit (ref. RS-122-2201/2, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA was used for ribosomal RNA depletion RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina High HiSeq 2500)

treatment_protocol: NSCs were infected with lentivirus expressing shRNA control (shControl) or shRNA specific for PHF2 (shPHF2)

value: Neural stem cells (NSCs)


title: shControl RNA-seq

description:
Total RNA without ribosomal RNA
shControl_23546_ACAGTG

value: shControl


title: CONTROL 2 (A2)

value: pancreas


title: CONTROL 3 (A3)


title: CONTROL 1 (A1)


title: Murine chronic MAIT 3


title: Murine naïveCD8+44lo62Hi 2

value: Naïve controls, uninfected, pooled from 3 mice


title: 860: Lhx5-EGFP-Rpl10a-DT154 Input Rep1

description: 860_Lhx5_Midbrain_Input_Rep1_CTTGTA_L006

value: Midbrain

value: Lhx5-TRAP DT154

value: RNA-seq

value: Unbound


title: Murine acute MAIT 3


title: Murine naïveCD8+44lo62Hi 3


title: shPHF2 rep2 RNA-seq

description:
Total RNA without ribosomal RNA
shPHF2rep2_23549_GTGAAA


title: L16569_M5-1m_09_G11

description: single cell

data_processing:
basecalling: bcl2fastq 2.17.1.14
alignment: alignment of single-end data against mm10 with gsnap version 2017-03-17; splice sites were supported by using Ensembl version 87 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-87.ss.mm10.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.5.2 (-a EnsemblGene-87.mm10.TR.gtf -s 2 -Q 1) and the Ensembl version 87 gtf file
quality filtering: qc was done with the scater package and cells removed based on various quality metrics (ERCC content, chrM, total Features, total Counts and cell cycle)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.mm10.e87.tsv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the sequenced single cell libraries
Supplementary_files_format_and_content: tab delimited file (scater.cpmlog10_counts.tsv.gz) created with the scater package; columns are the remaining cells and rows are genes

source_name: adult mouse pancreas

extract_protocol:
To isolate Aldh1b1 expressing cells and their progeny, 1 mg of corn oil dissolved tamoxifen (20 mg/ml; Sigma) was injected intraperitoneally in Aldh1b1CreERT2 / ROSA26 LSLtdTomato double heterozygous adult mice for 5 consecutive days. Aldh1b1 expressing cells and their early progeny were isolated one day later from pancreata dissociated into single cells by virtue of their tdTomato (PE-Texas Red channel) expression from the lineage tracing mouse pancreas by FACS.
Pancreata were dissociated into single cells and cells were FACsorted into a 96 well plate containing 2 ul of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. Lysis, reverse transcription of the RNA and cDNA amplification was performed according to the smartseq-2 protocol 6 with few modifications as detailed below. After thawing the samples, 2 ul of a primer mix (5 mM dNTP (Invitrogen), 0.5 uM dT-primer*, 4 U RNase Inhibitor (NEB)) was added. After filling up to 10 ul with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 uM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II, RNA was denatured for 3 minutes at 72°C and reverse transcription was performed at 42°C for 90 min. The reverse transcriptase was then inactivated at 70°C for 15 min. The cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab) at a final 1x concentration and 0.1 uM UP primer* under the following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA was purified using 1x volume of hydrophobic Sera-Mag SpeedBeads (GE Healthcare) and the DNA was eluted in 12 ul nuclease free water. The concentration of the samples was measured with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium). For library preparation 700 pg cDNA in 2 ul was mixed with 0.5 ul tagment DNA enzyme and 2.5 ul tagment DNA buffer (Nextera, Illumina) and tagmented at 55°C for 5 min. Subsequently, Illumina indices were added during PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 0.7 uM dual indexing primers. After PCR, libraries were quantified with AccuBlue Broad range chemistry, equimolarly pooled and purified twice with 1x volume Sera-Mag SpeedBeads. This was followed by Illumina sequencing on a Nextseq500 aiming at an average sequencing depth of 0.5 mio reads per cell. Primers were as follows: dT primer: Aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACT(30)VN; Template Switch Oligo (TSO) primer: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG; Universal Part (UP) primer: AAGCAGTGGTATCAACGCAGAGT.

tag: genotype

tag: age

value: 8 weeks


title: L16568_M5-1m_09_F11

description: single cell

tag: strain


title: L16573_M5-1m_09_C12

description: single cell


title: L16576_M5-1m_09_F12

description: single cell


title: L16578_M5-1m_09_H12

description: single cell


title: L16567_M5-1m_09_E11

description: single cell


title: L16574_M5-1m_09_D12

description: single cell


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description: single cell


title: L16566_M5-1m_09_D11

description: single cell


title: L16577_M5-1m_09_G12

description: single cell


title: L16565_M5-1m_09_C11

description: single cell


title: L16559_M5-1m_09_E10

description: single cell


title: L16564_M5-1m_09_B11

description: single cell


title: L16561_M5-1m_09_G10

description: single cell


title: L16560_M5-1m_09_F10

description: single cell


title: Murine naïveCD8+44lo62Hi 1


title: L16558_M5-1m_09_D10

description: single cell


title: L16575_M5-1m_09_E12

description: single cell


title: L16570_M5-1m_09_H11

description: single cell


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description: single cell


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description: single cell


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description: single cell


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description: single cell


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description: single cell


title: L16551_M5-1m_09_E09

description: single cell


title: L16552_M5-1m_09_F09

description: single cell


title: L16549_M5-1m_09_C09

description: single cell


title: L16562_M5-1m_09_H10

description: single cell


title: L16548_M5-1m_09_B09

description: single cell


title: L16555_M5-1m_09_A10

description: single cell


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description: single cell


title: L16537_M5-1m_09_G07

description: single cell


title: L16532_M5-1m_09_B07

description: single cell


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description: single cell


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description: single cell


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description: single cell


title: L16536_M5-1m_09_F07

description: single cell


title: L16546_M5-1m_09_H08

description: single cell


title: L16547_M5-1m_09_A09

description: single cell


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description: single cell


title: L16543_M5-1m_09_E08

description: single cell


title: L16542_M5-1m_09_D08

description: single cell


title: L16529_M5-1m_09_G06

description: single cell


title: L16540_M5-1m_09_B08

description: single cell


title: L16545_M5-1m_09_G08

description: single cell


title: L16525_M5-1m_09_C06

description: single cell


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description: single cell


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description: single cell


title: L16523_M5-1m_09_A06

description: single cell


title: L16520_M5-1m_09_F05

description: single cell


title: L16521_M5-1m_09_G05

description: single cell


title: L16528_M5-1m_09_F06

description: single cell


title: L16524_M5-1m_09_B06

description: single cell


title: L16516_M5-1m_09_B05

description: single cell


title: L16519_M5-1m_09_E05

description: single cell


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description: single cell


title: L16515_M5-1m_09_A05

description: single cell


title: L16517_M5-1m_09_C05

description: single cell


title: L16518_M5-1m_09_D05

description: single cell


title: L16514_M5-1m_09_H04

description: single cell


title: L16509_M5-1m_09_C04

description: single cell


title: L16512_M5-1m_09_F04

description: single cell


title: L16510_M5-1m_09_D04

description: single cell


title: L16513_M5-1m_09_G04

description: single cell


title: L16511_M5-1m_09_E04

description: single cell


title: L16503_M5-1m_09_E03

description: single cell


title: L16504_M5-1m_09_F03

description: single cell


title: L16502_M5-1m_09_D03

description: single cell


title: L16500_M5-1m_09_B03

description: single cell


title: L16507_M5-1m_09_A04

description: single cell


title: L16505_M5-1m_09_G03

description: single cell


title: L16506_M5-1m_09_H03

description: single cell


title: L16497_M5-1m_09_G02

description: single cell


title: L16496_M5-1m_09_F02

description: single cell


title: L16494_M5-1m_09_D02

description: single cell


title: L16495_M5-1m_09_E02

description: single cell


title: L16493_M5-1m_09_C02

description: single cell


title: L16492_M5-1m_09_B02

description: single cell


title: L16486_M5-1m_09_D01

description: single cell


title: L16489_M5-1m_09_G01

description: single cell


title: L16499_M5-1m_09_A03

description: single cell


title: L16487_M5-1m_09_E01

description: single cell


title: L16508_M5-1m_09_B04

description: single cell


title: L16498_M5-1m_09_H02

description: single cell


title: L16488_M5-1m_09_F01

description: single cell


title: L16484_M5-1m_09_B01

description: single cell


title: L16491_M5-1m_09_A02

description: single cell


title: L16485_M5-1m_09_C01

description: single cell


title: L16501_M5-1m_09_C03

description: single cell


title: L16479_M5-1m_08_E12

description: single cell


title: L16480_M5-1m_08_F12

description: single cell


title: L16478_M5-1m_08_D12

description: single cell


title: L16482_M5-1m_08_H12

description: single cell


title: L16481_M5-1m_08_G12

description: single cell


title: L16476_M5-1m_08_B12

description: single cell


title: L16471_M5-1m_08_E11

description: single cell


title: L16473_M5-1m_08_G11

description: single cell


title: L16472_M5-1m_08_F11

description: single cell


title: L16464_M5-1m_08_F10

description: single cell


title: L16477_M5-1m_08_C12

description: single cell


title: L16463_M5-1m_08_E10

description: single cell


title: L16467_M5-1m_08_A11

description: single cell


title: L16465_M5-1m_08_G10

description: single cell


title: L16475_M5-1m_08_A12

description: single cell


title: L16474_M5-1m_08_H11

description: single cell


title: L16468_M5-1m_08_B11

description: single cell


title: L16461_M5-1m_08_C10

description: single cell


title: L16466_M5-1m_08_H10

description: single cell


title: L16460_M5-1m_08_B10

description: single cell


title: L16470_M5-1m_08_D11

description: single cell


title: L16455_M5-1m_08_E09

description: single cell


title: L16469_M5-1m_08_C11

description: single cell


title: L16462_M5-1m_08_D10

description: single cell


title: L16457_M5-1m_08_G09

description: single cell


title: L16458_M5-1m_08_H09

description: single cell


title: L16456_M5-1m_08_F09

description: single cell


title: L16449_M5-1m_08_G08

description: single cell


title: L16452_M5-1m_08_B09

description: single cell


title: L16450_M5-1m_08_H08

description: single cell


title: L16454_M5-1m_08_D09

description: single cell


title: L16451_M5-1m_08_A09

description: single cell


title: L16459_M5-1m_08_A10

description: single cell


title: L16447_M5-1m_08_E08

description: single cell


title: L16453_M5-1m_08_C09

description: single cell


title: L16446_M5-1m_08_D08

description: single cell


title: L16448_M5-1m_08_F08

description: single cell


title: L16437_M5-1m_08_C07

description: single cell


title: L16441_M5-1m_08_G07

description: single cell


title: L16436_M5-1m_08_B07

description: single cell


title: L16433_M5-1m_08_G06

description: single cell


title: L16435_M5-1m_08_A07

description: single cell


title: L16442_M5-1m_08_H07

description: single cell


title: L16428_M5-1m_08_B06

description: single cell


title: L16444_M5-1m_08_B08

description: single cell


title: L16440_M5-1m_08_F07

description: single cell


title: L16429_M5-1m_08_C06

description: single cell


title: L16432_M5-1m_08_F06

description: single cell


title: L16443_M5-1m_08_A08

description: single cell


title: L16427_M5-1m_08_A06

description: single cell


title: L16434_M5-1m_08_H06

description: single cell


title: L16426_M5-1m_08_H05

description: single cell


title: L16424_M5-1m_08_F05

description: single cell


title: L16425_M5-1m_08_G05

description: single cell


title: L16423_M5-1m_08_E05

description: single cell


title: L16420_M5-1m_08_B05

description: single cell


title: L16421_M5-1m_08_C05

description: single cell


title: L16422_M5-1m_08_D05

description: single cell


title: L16419_M5-1m_08_A05

description: single cell


title: L16418_M5-1m_08_H04

description: single cell


title: L16417_M5-1m_08_G04

description: single cell


title: L16445_M5-1m_08_C08

description: single cell


title: L16414_M5-1m_08_D04

description: single cell


title: L16415_M5-1m_08_E04

description: single cell


title: L16416_M5-1m_08_F04

description: single cell


title: L16413_M5-1m_08_C04

description: single cell


title: L16408_M5-1m_08_F03

description: single cell


title: L16410_M5-1m_08_H03

description: single cell


title: L16411_M5-1m_08_A04

description: single cell


title: L16409_M5-1m_08_G03

description: single cell


title: L16407_M5-1m_08_E03

description: single cell


title: L16405_M5-1m_08_C03

description: single cell


title: L16399_M5-1m_08_E02

description: single cell


title: L16404_M5-1m_08_B03

description: single cell


title: L16402_M5-1m_08_H02

description: single cell


title: L16403_M5-1m_08_A03

description: single cell


title: L16401_M5-1m_08_G02

description: single cell


title: L16490_M5-1m_09_H01

description: single cell


title: L16396_M5-1m_08_B02

description: single cell


title: L16406_M5-1m_08_D03

description: single cell


title: L16394_M5-1m_08_H01

description: single cell


title: L16398_M5-1m_08_D02

description: single cell


title: L16397_M5-1m_08_C02

description: single cell


title: L16388_M5-1m_08_B01

description: single cell


title: L16390_M5-1m_08_D01

description: single cell


title: L16395_M5-1m_08_A02

description: single cell


title: L16389_M5-1m_08_C01

description: single cell


title: L16391_M5-1m_08_E01

description: single cell


title: L16392_M5-1m_08_F01

description: single cell


title: L16393_M5-1m_08_G01

description: single cell


title: L16412_M5-1m_08_B04

description: single cell


title: L16383_M4-1m_07_E12

description: single cell


title: L16400_M5-1m_08_F02

description: single cell


title: L16382_M4-1m_07_D12

description: single cell


title: L16380_M4-1m_07_B12

description: single cell


title: L16387_M5-1m_08_A01

description: single cell


title: L16375_M4-1m_07_E11

description: single cell


title: L16377_M4-1m_07_G11

description: single cell


title: L16374_M4-1m_07_D11

description: single cell


title: L16381_M4-1m_07_C12

description: single cell


title: L16378_M4-1m_07_H11

description: single cell


title: L16370_M4-1m_07_H10

description: single cell