title: LX2_TGFβ_2

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
The original FASTQ read files were trimmed and cleaned using fastp, then quality analysis was performed using FastQC
The trimmed fastq files were aligned by HISAT2 to human GENCODE v38 genome reference.
The aligned reads were calculated by featureCounts and differential expression genes (DEGs) were analyzed by R package DESeq2/3.1.0
Assembly: GENCODE v38
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

source_name: LX-2 Cell Line

extract_protocol:
The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: TGFBeta

value: LX-2Cell Line


title: LX2_TGFβ_3

status: Public on Jul 03 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment

tag: cell line


title: K562_polysome_WT_120min_rep2

city: Boston

first: Brendan

middle: Michael

last: Smalec

state: MA

address: 77 Avenue Louis Pasteur, Rm 356

department: Genetics

institute: Harvard Medical School

description:
U5-poly
K562_polysome_WT_rep2.tsv

data_processing:
Read trimming with cutadapt v2.5 (see Churchman lab github for complete steps)
Alignment with STAR v2.7.0a (see Churchman lab github for complete steps)
Conversion to .cit format with GRAND-SLAM v2.0.5d (see Churchman lab github for complete steps)
Estimation of fraction new RNA with GRAND-SLAM v2.0.5d (see Churchman lab github for complete steps)
Assembly: K562 data: hg38; NIH-3T3 data: mm10
Supplementary files format and content: .tsv files containing fraction new RNA estimates from GRAND-SLAM

molecule: cytoplasmic RNA

extract_protocol:
RNA was extracted from subcellular fractions with Trizol LS according to the manufacturer's protocol.
2.5ug purified RNA was subjected to TimeLapse chemistry (Schofield et al., 2018) and then 1ug was used for library preparation with the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) according to the manufacturer's protocol.


title: LX2_TGFβ_1


title: hIAPP429

city: Los Angeles

first: Montgomery

last: Blencowe

address: 610 Charles E Young Drive East

institute: UCLA

data_processing:
Illumina’s NextSeq 500 platform was used to generate 75 bp, paired-end reads (260 ± 6M reads per sample).
Short reads were aligned to the mouse reference genome build GRCm38 (mm10) using the STAR aligner
The HT-Seq package 25260700 was used to count the number of fragments aligned to known exonic regions.
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Islet

growth_protocol: We used control wild-type FVB mice, beta cell specific human-IAPP expressing mice, and beta cell specific rodent-IAPP expressing mice bred at UCLA. Animals were maintained on a 12-h day/night cycle with Harlan Teklad Rodent Diet 8604 and water ad libitum.

extract_protocol:
RNA was extracted from islet samples (165±6 islets per mouse) were using the RNeasy Mini Kit (Qiagen). RNA integrity was confirmed using the Agilent Bioanalyzer 2100 (RIN score range: 8.4–9.5)
RNA-seq libraries were prepared using the TruSeq with Ribo-Zero treatment (Illumina, San Diego, CA, USA) to deplete rRNA.

tag: tissue

value: Islet

tag: strain background

value: FVB

tag: genotype

value: hIAPP

tag: age


title: K562_polysome_WT_60min_rep2

description:
U4-poly
K562_polysome_WT_rep2.tsv


title: Testis, group A, fish 190

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Testis

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon post smolts were kept in tanks with brackish water within a flow-through system, with an average salinity of 20 ± 0.4 ppt and mean temperature of 12.1 ± 0.2°C

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Various light treatments were explored, including continuous exposure (Group A), increasing exposure (Group B), and decreasing exposure (Groups C, D and E) were investigated on growth and sexual maturation, sampling was performed after 18 weeks to assess gonadal growth and blood steroid hormone levels. All groups were provided with the same feed, except for Group E, which received a low-fat diet.

tag: developmental stage of testis

value: Stage IV

value: Testis

tag: group

value: group A

tag: FISH id

value: fish 190


title: hIAPP409


title: K562_polysome_WT_30min_rep2

description:
U3-poly
K562_polysome_WT_rep2.tsv


title: LX2_Solvent_3

value: Solvent


title: Testis, group A, fish 188

value: Stage I

value: fish 188


title: Testis, group A, fish 184

value: fish 184


title: hIAPP402


title: LX2_Solvent_2


title: Adipose, group E, fish 236

source_name: Adipose

tag: immune activity

value: Low immune activity

value: Adipose

value: group E

value: fish 236


title: Adipose, group E, fish 240

value: fish 240


title: LX2_Solvent_1

value: LX-2Cell Line


title: hIAPP388

value: Islet


title: PHSC_TGFβ_3

source_name: Priamry Hepatic Stellate Cells

value: TGFBeta

value: Priamry Hepatic Stellate Cells


title: hIAPP387

value: FVB

value: hIAPP


title: K562_polysome_WT_15min_rep2

description:
U2-poly
K562_polysome_WT_rep2.tsv


title: K562_polysome_WT_0min_rep2

description:
U1-poly
K562_polysome_WT_rep2.tsv


title: K562_cytoplasm_WT_120min_rep2

description:
U5-cyto
K562_cytoplasm_WT_rep2.tsv


title: WT426

value: WT


title: WT425


title: PHSC_TGFβ_1


title: K562_cytoplasm_WT_60min_rep2

description:
U4-cyto
K562_cytoplasm_WT_rep2.tsv


title: Adipose, group E, fish 211

value: fish 211


title: PHSC_TGFβ_2


title: K562_cytoplasm_WT_30min_rep2

description:
U3-cyto
K562_cytoplasm_WT_rep2.tsv


title: Adipose, group D, fish 255

value: High immune activity

value: group D

value: fish 255


title: Adipose, group E, fish 233

value: fish 233


title: PHSC_Solvent_2

value: Solvent


title: WT408


title: K562_cytoplasm_WT_15min_rep2

description:
U2-cyto
K562_cytoplasm_WT_rep2.tsv


title: PHSC_Solvent_1


title: WT407


title: K562_cytoplasm_WT_0min_rep2

description:
U1-cyto
K562_cytoplasm_WT_rep2.tsv


title: Adipose, group D, fish 193

value: Adipose

value: fish 193


title: WT383


title: PHSC_Solvent_3


title: Adipose, group D, fish 198

value: fish 198


title: Nitrofen_CDH_AF-EV_6

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database allowing up to two base mismatches.
Assembly: miRbase 21
Supplementary files format and content: txt files of raw read counts of each samples

organism: Rattus norvegicus

source_name: amniotic fluid-derived EV

growth_protocol: Three pregnant Sprague-Dawley rats were purchased from Japan SLC Inc. (Hamamatsu, Japan). All rats were maintained on a 12 h light/ 12 h dark lighting schedule (lights on 9:00 a.m., off at 9:00 p.m.), and allowed free access to water and standard chow.

extract_protocol:
On day 21 of the pregnancy, the rats were sacrificed. After uterine incision, amniotic fluid was collected using cellulose nanofiber-based EV sheets. we checked for the presence of a diaphragm in all fetuses by thoracolaparotomy. Next, lung tissues were collected in GentleMACS M tubes (Miltenyi Biotec, Bergisch Gladbach, Germany) containing 1.5 mL of QIAzol buffer (Qiagen, Hilden, Germany). Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

treatment_protocol: Two rats received 100 mg of nitrofen (2,4-dichlorophenyl-p-nitrophenylether) dissolved in 1 mL of olive oil and one rat received olive oil alone through the gastric tube on pregnancy day 9.

tag: embryonic day

value: amniotic fluid-derived EV

value: Nitrofen


title: WT382

value: Islet


title: K562_nuclear_WT_120min_rep2

description:
U5-nuc
K562_nuclear_WT_rep2.tsv

molecule: nuclear RNA


title: K562_nuclear_WT_60min_rep2

description:
U4-nuc
K562_nuclear_WT_rep2.tsv


title: Adipose, group D, fish 180

value: fish 180


title: Nitrofen_CDH_AF-EV_5


title: K562_nuclear_WT_30min_rep2

description:
U3-nuc
K562_nuclear_WT_rep2.tsv


title: Nitrofen_CDH_AF-EV_4


title: K562_nuclear_WT_15min_rep2

description:
U2-nuc
K562_nuclear_WT_rep2.tsv


title: PD-1-Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 3

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

state: PA

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

data_processing:
STAR aligned RNA-seq data, using ENSEMBLE annotations
Read count extraction and normalization were performed using DESeq2
Assembly: mm10
Supplementary files format and content: CSV document containing TPM counts, with each sample contained in a separate column

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Spleens were removed from infected mice, single-cell suspensions were prepared by mechanically disrupting tissue using double frosted slide, followed by red blood cell lysis with RBC Lysis Buffer , and stained with fluorescently labeled CD8, CD45.1, CD45.2, CD44 and PD-1 and Tim-3 antibodies. Then different subsets of Live CD8+T cells were sorted with help of fluorescence assisted cell sorter directly into lysis buffer.
SmartSeq cDNA / Nextera XT libraries

value: Spleen

tag: cell type

value: P14 CD8+T cells

tag: time

value: Day 8 post LCMV CL13 infection

value: tamoxifen prior to infection


title: Nitrofen_CDH_AF-EV_3


title: Adipose, group B, fish 213

value: group B

value: fish 213


title: Adipose, group D, fish 176

value: High immune activity

value: group D

value: fish 176


title: K562_nuclear_WT_0min_rep2

description:
U1-nuc
K562_nuclear_WT_rep2.tsv


title: PD-1+Tim-3+ P14 T cells isolated from Treg-specific Tim-3 KO mouse replicate 2


title: Adipose, group B, fish 203

value: fish 203


title: Nitrofen_CDH_AF-EV_2


title: K562_chromatin_WT_120min_rep1

description:
T5-chr
K562_chromatin_WT_rep1.tsv


title: PD-1+Tim-3+ P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 3


title: PD-1+Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 2


title: Adipose, group B, fish 202

value: Adipose

value: fish 202


title: K562_chromatin_WT_30min_rep1

description:
T3-chr
K562_chromatin_WT_rep1.tsv


title: Nitrofen_No-CDH_AF-EV_6


title: PD-1+Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 3


title: K562_chromatin_WT_60min_rep1

description:
T4-chr
K562_chromatin_WT_rep1.tsv


title: PD-1+Tim-3+ P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 1


title: PD-1-Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 2


title: Adipose, group B, fish 160

value: fish 160


title: K562_chromatin_WT_15min_rep1

description:
T2-chr
K562_chromatin_WT_rep1.tsv


title: PD-1+Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 1


title: Nitrofen_No-CDH_AF-EV_5

value: amniotic fluid-derived EV


title: Adipose, group B, fish 211

value: fish 211


title: Nitrofen_No-CDH_AF-EV_4

value: Nitrofen


title: Adipose, group A, fish 245

value: group A

value: fish 245


title: PD-1-Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 1

value: Spleen

value: P14 CD8+T cells


title: Adipose, group A, fish 190

value: fish 190


title: Nitrofen_No-CDH_AF-EV_3


title: Adipose, group A, fish 188

value: fish 188


title: Adipose, group A, fish 250

value: fish 250


title: K562_chromatin_WT_0min_rep1

description:
T1-chr
K562_chromatin_WT_rep1.tsv


title: PD-1+Tim-3+ P14 T cells isolated from Cre-only mouse, replicate 3

value: Day 8 post LCMV CL13 infection

value: tamoxifen prior to infection


title: K562_total_WT_120min_rep1

description:
T5-tot
K562_total_WT_rep1.tsv


title: L1_DP_AID_Auxin_300mM_biol_rep3

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

description: RNA-seq from L1 hatched larvae

data_processing:
For all of the library, normalized bigwig files were generated from the mapping results using millions of non-structural mappers as a normalization factor. This normalized coverage information was computed for 10 bp bins using the bedtoolsand bedopsv.2.4.26 packages.
Assembly: ce11 C. elegans Sequencing Consortium WBcel235
Supplementary files format and content: normalized big wig files will be provided for each libraries

organism: Caenorhabditis elegans

source_name: Hatched L1 larvae

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
To obtain synchronized non-starved L1, we used the NemaSync C. elegans synchronizer model 5000. L1 larvae were frozen in dry ice with TRIzol Reagent (Invitrogen), and after six repetitions of freeze and thaw, RNA was extracted using the Direct-zol RNA Microprep kit (ZymoResearch, R2062). The small RNA fragments (17 to 200 nucleotides) were separated from the large RNAs (>200 nucleotides) using the Quick-RNA MicroPrep kit (ZymoResearch, R1051). The large RNA was DNAse treated using the reagent provided along with the Quick-RNA Microprep kit. Using these size separation kits, we were able to sequence both the small RNA and the mRNA coming from the same samples. An Agilent 2200 TapeStation System was used to evaluate the RIN indexes of the large RNAs (>200 nucleotides), and only samples with RNA integrity number RIN  > 8 were used for RNA-seq. For 2-cell embryo RNA extraction, precisely staged 2-cell embryos were obtained by alkaline hypochlorite treatment of synchronized gravid adult hermaphrodites, and fifty 2-cell embryos were collected using a mouth pipet. Embryos were lysed for 10min at 65˚C and 1min at 85˚C in a lysis solution containing Tris pH8 5mM final, EDTA 0.25mM final, Triton 100X 0.5%, Tween 20 0.5%, Proteinase K 0.5% and Water. The lysates were subjected to RNA purification using the Quick-RNA MicroPrep kit (ZymoResearch, R1051), and small RNAs (RNA fraction from 17 to 200 nucleotides) and mRNAs (RNA fraction >200 nucleotides) were collected separately. The RNA fraction > 200 nucleotides were used for preparing RNA-seq libraries.
DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. Ribosomal and mitochondrial rRNAs were depleted using a custom RNAse-H-based method to degrade rRNAs using complementary oligos as described in42.Strand-specific RNA libraries were prepared using at least 100 ng of rRNA-depleted RNAs using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S). RNA libraries were analysed on Agilent 2200 TapeStation System using high sensitivity D1000 screentapes and quantified using the Qubit Fluorometer High Sensitivity dsDNA assay kit (Thermo Fisher Scientific, Q32851). Multiplexed libraries were sequenced on a NextSeq 2000 Illumina platform.

treatment_protocol: To induce the degradation of DROSHA and PASHA in C. elegans intestine, we used the AID degron system. Mothers were treated with Auxin at L3 stages and embryos or hatched L1 were collected for the RNA-seq experiment. 250 mM auxin stock solution was prepared in ethanol and stored at 4 °C. Auxin plates or ethanol plates were prepared by the addition of auxin or only ethanol to NGM plates (final concentration: 500 µM auxin, 0.2% ethanol for auxin plates and 0.2% ethanol for ethanol plates). Plates were seeded with OP50 Escherichia coli.

value: Hatched L1 larvae

value: MHE229 (Drosha Pasha intestinal degron)

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)

value: mothers exposed to 300mM NaCl and Auxin


title: Nitrofen_CDH_AF-EV_1


title: Nitrofen_No-CDH_AF-EV_2


title: Nitrofen_No-CDH_AF-EV_1


title: L1_DP_AID_Auxin_300mM_biol_rep2

description: RNA-seq from L1 hatched larvae


title: K562_total_WT_60min_rep1

description:
T4-tot
K562_total_WT_rep1.tsv


title: PD-1+Tim-3- P14 T cells isolated from Cre-only mouse, replicate 3


title: Adipose, group A, fish 184

value: Adipose

value: fish 184


title: K562_total_WT_30min_rep1

description:
T3-tot
K562_total_WT_rep1.tsv


title: Ctrl_AF-EV_3

value: amniotic fluid-derived EV

value: Olive oil


title: PD-1-Tim-3- P14 T cells isolated from Cre-only mouse, replicate 3


title: L1_DP_AID_Auxin_300mM_biol_rep1

description: RNA-seq from L1 hatched larvae


title: K562_total_WT_15min_rep1

description:
T2-tot
K562_total_WT_rep1.tsv


title: K562_total_WT_0min_rep1

description:
T1-tot
K562_total_WT_rep1.tsv


title: PD-1+Tim-3- P14 T cells isolated from Cre-only mouse, replicate 2


title: L1_DP_AID_Auxin_50mM_biol_rep2

description: RNA-seq from L1 hatched larvae

value: mothers exposed to 50mM NaCl and Auxin


title: Ctrl_AF-EV_1


title: K562_polysome_WT_120min_rep1

description:
T5-poly
K562_polysome_WT_rep1.tsv


title: PD-1-Tim-3- P14 T cells isolated from Cre-only mouse, replicate 2


title: K562_polysome_WT_60min_rep1

description:
T4-poly
K562_polysome_WT_rep1.tsv


title: Nitrofen_CDH_fetal-lung_6

source_name: fetal lung

value: fetal lung

value: Nitrofen


title: L1_DP_AID_EtOH_300mM_biol_rep3

description: RNA-seq from L1 hatched larvae

value: mothers exposed to 300mM NaCl and EtOH


title: PD-1+Tim-3+ P14 T cells isolated from Cre-only mouse, replicate 1

value: Spleen

value: P14 CD8+T cells


title: Nitrofen_CDH_fetal-lung_5


title: PD-1+Tim-3- P14 T cells isolated from Cre-only mouse, replicate 1


title: K562_polysome_WT_30min_rep1

description:
T3-poly
K562_polysome_WT_rep1.tsv


title: Nitrofen_CDH_fetal-lung_4


title: Ctrl_AF-EV_2


title: Cut and Run TAC2_CX3CR1neg_IgG

city: San Francisco

first: Michael

last: Alexanian

state: CA

address: 1650 Owens Street

institute: Gladstone Institutes

description:
TAC2_CX3CR1neg_IgG
IgG control CUT&RUN from Cx3cr1-sorted cells from TAC mouse heart

library_source: genomic

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed with Illumina bcl2fastq v2.20.0.422
Demultiplexed reads were aligned, read normalized and quantified with the nfcore/cutandrun pipeline v2.0 (https://nf-co.re/cutandrun) via Nextflow and Singularity using standard settings
Assembly: Mm10
Supplementary files format and content: Genomic coverage tracks in bigWig format

molecule: genomic DNA

source_name: Heart Tissue (ventricles)

extract_protocol:
Whole hearts were obtained from Brd4 flag/flag animals that underwent Sham or TAC surgeries and were subjected to Langendorff perfusion to obtain suspensions of cardiac cells. The non-CM population was purified by serial differential centrifugation and size-exclusion filtering steps followed by CX3CR1 antibody staining and sorting by flow cytometry (mCx3cr1-APC; Biolegend; 1:100). CX3CR1-positive cells were subjected to CUT&RUN using the CUTANATM ChIC/CUT&RUN kit (Epicypher) using an anti-FLAG antibody (Sigma M2 #1804) following manufacturer instructions with included positive and negative controls. Purified fragmented DNA was quantified using a Qubit 2.0 fluorometer (ThermoFisher Scientific) using the dsDNA HS Assay Kit.
Paired-end Illumina sequencing libraries were prepared from CUT&RUN enriched DNA using the NEBNext UltraTM II DNA Library Prep Kit (New England Biolabs) and sequenced on a NextSeq 500 (Illumina).

value: Sorted Cx3cr1-positive cells from cardiac ventricles in the adult heart

value: Heart Tissue (ventricles)

tag: strain

value: 3-5 months

tag: cut&run antibody

value: anti-FLAG antibody (Sigma M2 #1804)


title: Nitrofen_CDH_fetal-lung_3


title: Nitrofen_CDH_fetal-lung_1


title: L1_DP_AID_EtOH_300mM_biol_rep1

description: RNA-seq from L1 hatched larvae

value: Hatched L1 larvae

value: MHE229 (Drosha Pasha intestinal degron)


title: K562_cytoplasm_WT_120min_rep1

description:
T5-cyto
K562_cytoplasm_WT_rep1.tsv


title: PD-1-Tim-3- P14 T cells isolated from Cre-only mouse, replicate 1

value: Day 8 post LCMV CL13 infection

value: tamoxifen prior to infection


title: Nitrofen_CDH_fetal-lung_2


title: L1_DP_AID_Auxin_50mM_biol_rep3

description: RNA-seq from L1 hatched larvae

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)


title: PD-1+Tim-3+ P14 T cells isolated from Cre-only mouse, replicate 2


title: L1_DP_AID_EtOH_50mM_biol_rep1

description: RNA-seq from L1 hatched larvae

value: mothers exposed to 50mM NaCl and EtOH


title: L1_DP_AID_EtOH_50mM_biol_rep2

description: RNA-seq from L1 hatched larvae


title: K562_polysome_WT_15min_rep1

description:
T2-poly
K562_polysome_WT_rep1.tsv


title: K562_cytoplasm_WT_60min_rep1

description:
T4-cyto
K562_cytoplasm_WT_rep1.tsv


title: Cut and Run Sham_CX3CR1pos_FLAG

description:
Sham_CX3CR1pos_FLAG
Anti-FLAG CUT&RUN from Cx3cr1-sorted cells from Sham control mouse heart


title: Nitrofen_No-CDH_fetal-lung_5


title: K562_polysome_WT_0min_rep1

description:
T1-poly
K562_polysome_WT_rep1.tsv


title: Cut and Run TAC2_CX3CR1pos_FLAG

description:
TAC2_CX3CR1pos_FLAG
Anti-FLAG CUT&RUN from Cx3cr1-sorted cells from TAC mouse heart


title: Nitrofen_No-CDH_fetal-lung_6


title: K562_cytoplasm_WT_15min_rep1

description:
T2-cyto
K562_cytoplasm_WT_rep1.tsv


title: L1_DP_AID_EtOH_50mM_biol_rep3

description: RNA-seq from L1 hatched larvae


title: PA14_plus_CA_38_6

city: Uxbridge

first: Ronan

last: McCarthy

address: Kingston Ln

country: United Kingdom

institute: Brunel University London

data_processing:
Raw fastq files were obtained from the sequencing facility. Adapter and quality trimming was performed by MiGS using bcl2fastq.
Reads and their quality was assessed with fastqc and visualised through multiqc (Andrews S, 2010, Ewels et al., 2016)
Read mapping was performed with hisat2 with ‘--very-sensitive’ parameter (Kim et al., 2019)
Read quantification was performed with featureCounts available within the Subread package (Liao et al., 2014).
Read normalisation was performed using the edgeR package in R with the Trimmed Mean of M values algorithm (Robinson et al., 2010).
Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups.
All quantified genes were subset by log-fold change (logFC) > |1| and p-value < 0.05 to create a list of differentially expressed genes.
All quantified genes were visualised in a volcano plot in ggplot2 R package.
Assembly: Pseudomonas_aeruginosa_UCBPP-PA14_109.gff downloaded from www.pseudomonas.com
Supplementary files format and content: hisat2_counts.tsv contains feature counts per sample
Supplementary files format and content: alighnment.tsv contains the number of reads per sample
Supplementary files format and content: All quantified genes.tsv contain the results of edgeR analysis.

organism: Pseudomonas aeruginosa PA14

growth_protocol: P. aeruginosa PA14 was grown in the overnight tube at 37°C at 180 rpm. Cultures were then adjusted to OD=0.1 with LB and added in proportion 1:1 to TSB or the supernatant of C. acnes CCUG 38584 to be grown to OD600=0.6-0.7 at 37°C at 180 rpm.

extract_protocol:
Upon reaching the desired optical density, 1 ml of the cultures was aliquoted and spun down at 5000 rpm for 10 mins, the supernatant was discarded, and the pellets were resuspended in the RNAlater buffer (ThermoFischer). The resuspended cells were stored in the buffer at 4°C overnight. RNA extraction procedure was performed with RNeasy Mini Kit (Qiagen). Extracted RNA was quantified using Nanodrop.  The quality of the extraction was assessed with Bioanalyser. Samples were stored at -20°C until shipment to the sequencing facility.
Illumina sequencing was performed by Microbial Genome Sequencing Centre (MiGS).

value: WT

value: C. acnes CCUG 38584 supernatant.


title: K562_chromatin_WT_60min_rep2

description:
U4-chr
K562_chromatin_WT_rep2.tsv


title: Nitrofen_No-CDH_fetal-lung_4

value: fetal lung


title: L1_DP_AID_Auxin_50mM_biol_rep1

description: RNA-seq from L1 hatched larvae

value: mothers exposed to 50mM NaCl and Auxin


title: L1_DP_AID_EtOH_300mM_biol_rep2

description: RNA-seq from L1 hatched larvae

value: mothers exposed to 300mM NaCl and EtOH


title: Cut and Run TAC1_CX3CR1pos_FLAG

description:
TAC1_CX3CR1pos_FLAG
Anti-FLAG CUT&RUN from Cx3cr1-sorted cells from TAC mouse heart


title: Nitrofen_No-CDH_fetal-lung_3

value: Nitrofen


title: K562_cytoplasm_WT_0min_rep1

description:
T1-cyto
K562_cytoplasm_WT_rep1.tsv


title: PA14_plus_CA_38_1


title: K562_cytoplasm_WT_30min_rep1

description:
T3-cyto
K562_cytoplasm_WT_rep1.tsv


title: EXO2

city: Shanghai

first: Zheyu

last: Zhang

address: Yueyang Road

country: China

institute: CAS

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads.
Cutadapt was used to trim the adapters for short reads.
miRDeep2 was used for the prediction of new miRNAs and the quantification of miRNAs.
Based on CPM standardized miRNAs, the DE miRNAs were calculated and screened by R software edgeR.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

growth_protocol: BV-2 cells weremaintained in high glucose-DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C in a humidified atmosphere containing 5% CO2. BV-2 cells were passaged three times per week.

extract_protocol: Total RNA was extracted from BV-2 cells using Trizol reagent (Ambion, Austin, TX, USA) according to the manufacturer's instructions.

treatment_protocol: BV-2 cells were pre-incubated with hUC-MSCs-Exo (1ug/ml) for 24 h, and then the cells were washed twice with PBS, followed by exposure to 1 µg/mL LPS for 6 h.

value: Microglial cells

value: LPS+MSCs-Exo


title: Nitrofen_No-CDH_fetal-lung_2


title: PA14_plus_CA_TSB_6

value: Untreated control


title: PA14_plus_CA_TSB_5


title: PA14_plus_CA_38_4


title: K562_nuclear_WT_60min_rep1

description:
T4-nuc
K562_nuclear_WT_rep1.tsv


title: EXO3


title: K562_nuclear_WT_30min_rep1

description:
T3-nuc
K562_nuclear_WT_rep1.tsv


title: EXO1


title: K562_nuclear_WT_15min_rep1

description:
T2-nuc
K562_nuclear_WT_rep1.tsv


title: Nitrofen_No-CDH_fetal-lung_1


title: PA14_plus_CA_TSB_4


title: con3

value: control


title: Ctrl_fetal-lung_2

value: Olive oil


title: Marcela 23

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

country: Canada

institute: Université Laval

data_processing:
Trimgalore / cutadapt
STAR
featurecounts
DESEQ2
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw counts for each sample in .csv file
Supplementary files format and content: NDA

organism: Bos taurus

source_name: oocyte

growth_protocol: Cumulus-oocyte complexes (COCs) were obtained by aspiration of 2-4 mm follicles from bovine slaughterhouse-derived ovaries. COCs were selected and washed three times in collection media (tissue culture medium 199 (TCM-199) with 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 10% fetal bovine serum (FBS), 0.2 mM pyruvate and  50 µg/mL gentamicin). Only Grade I and II COCs (Sarwar, et al., 2020) were selected and IVM was performed in groups of 25 COCs in 90 µL droplets of maturation medium (TCM-199 with bicarbonate supplemented with 10% FBS, 10 µg/mL FSH (FolltropinV; Bioniche), 10 µg/mL human chorionic gonadotropin (hCG; Chorulon; Merck Animal Health) and 1 µg/mL estradiol) under mineral oil at 38.5oC with 5% CO2 in air and high humidity

extract_protocol:
First, the CCs were removed by denudation and only oocytes with the presence of the first polar body (matured) were used in this analysis. cDNA synthesis and amplification from denuded oocytes were performed using the SMART-Seq HT Kit (Takara Bio Inc) and pools of 5 oocytes (~0.1 ng of total RNA) per group per replicate (3 replicates), following the manufacturer's recommendation. Next, cDNA was purified using AMPure XP Beads (Beckman Coulter), and cDNA concentration and profile were determined using Qubit dsDNA High Sensitivity (ThermoFisher Scientific) and Bioanalyzer High Sensitivity DNA Kit (Agilent), respectively.
Libraries were prepared using the Nextera XT DNA Library Prep (Illumina) as recommended by the SMART-Seq HT kit. Libraries were assessed using Qubit and Bioanalyzer, before sequencing on the NextSeq (Illumina) considering 100 bp paired-end reads.

treatment_protocol: Bovine COCs were submitted to IVM in medium supplemented with 0.1 mM, 0.5 mM, 1.5 mM and 5 mM of DCA and 0.1 µM, 0.5 µM, 1.5 µM and 5 µM of IA for 24 h.

value: oocyte

value: CTRL


title: Marcela 22


title: Ctrl_fetal-lung_3


title: NC_3

city: Shenyang

first: Shengjun

last: Dong

address: No.120 Dongling Road, Shenhe District, Shenyang, Liaoning Province, P.R.China.

institute: Shenyang Agricultural University

data_processing:
The sequencing-obtained raw image data were converted to sequence reads using CASAVA.
The raw data was filtered by R language, and finally the clean reads for subsequent analysis were obtained.
Trinity v2.4.0 program was used to stitch and assemble clean reads of all samples. Redundancy was removed by clustering with Corset hierarchy, The longest transcript of each gene was selected as Unigene for subsequent analysis.
The transcript sequence obtained by splicing with Trinity was used as a reference sequence. RSEM software (version v1.2.15) (bowtie2, mismatch=0) (bowtie2 default parameters, mismatch = 0)was used to compare clean reads of each repeated sample with reference sequences, and the readcount of each gene was counted and compared. FPKM (fragments per kilobase of exon per million mapped fragments) was used to standardize the readcount of genes.
The DEGseq R package (1.12.0) was used for differential expression analyses. The P-value was calculated based on a negative binomial distribution model. P-values was adjusted using the Benjamini-Hochberg mothed (Benjamini and Hochberg, 1995). Genes with an adjusted P-value < 0.05 and log2(Fold change) > 1 were assigned as differentially expressed.
Genome_build: Prunus armeniaca
Supplementary_files_format_and_content: FPKM file includes gene ID and expression for each sample.

organism: Prunus sibirica

source_name: Floral organ

extract_protocol:
Select the natural frost-damaged Prunus sibirica flower organs, use the kit method to extract RNA, and use the Illumina sequencing platform to construct a sequencing library to extract RNA
The six RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultiva

value: Prunus sibirica clone

value: Floral organ

value: weak frost resistance clone

tag: developmental stage

value: Blooming stage


title: Ctrl_fetal-lung_1

tag: treatment


title: K562_nuclear_WT_0min_rep1

description:
T1-nuc
K562_nuclear_WT_rep1.tsv

tag: cell line


title: LPS2

value: LPS


title: NC_2

tag: tissue


title: K562_nuclear_WT_120min_rep1

description:
T5-nuc
K562_nuclear_WT_rep1.tsv


title: Marcela17

value: DCA


title: Marcela 24


title: con1


title: LPS1


title: con2


title: CR_3

value: strong frost resistance clone


title: LPS3


title: CR_2


title: KLF1 mommeD45 Input

city: Brisbane

first: Stephen

last: Huang

state: Queensland

address: 37 Kent Street Woolloongabba

department: Mater Research institute

country: Australia

institute: University of Queensland

data_processing:
ChIP-Seq:
Base calling was performed with RTAv2
Bowtie2 was used to mapped PE sequencing reads with default parameters to the reference genome (mm9)
Duplicate reads were removed using Picard with the MarkDuplicates function
ChIP-seq peaks were called with MACS2 using uniquely mapped ChIP and input sequence alignments.
---------------
RNA-Seq
Base calling was performed with Torrent Suite v4.0.1
Tophat2 (v2.0.10) was used to perform spliced alignment to the reference transcriptome and genome (mm9; ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz) using default options with the following additional parameters: -g 3, --library-type fr-firststrand.
Unaligned sequences were subsequently remapped using TMAP (v3.0.1) with the following options: -o 1, map4.
Successful alignments were merged back into the Tophat2 SAM file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between replicate groups was performed with Cuffdiff2 using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited genelist of FPKM output from CuffDiff2
Supplementary_files_format_and_content: excel file of peaks called from MACS2 for both wildtype and mutant ChIPseq

source_name: 14.5DPC fetal liver

extract_protocol:
Fetal Liver lysates were clarified from sonicated DNA and KLF1 bound DNA complexes were isolated with antibody
Sequencing libraries were generated from 2 pooled replicates using the NEBNext ChIPseq library kit (E6200S) with multiplex adaptors (E7335S)

value: Fetal Liver


title: Marcela16


title: KLF1 mommeD45 ChIPseq

tag: chip antibody

value: KLF1 Antibody

tag: chip antibody reference

value: Perkins, A. C., Sharpe, A. H. & Orkin, S. H. Lethal beta-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF. Nature 375, 318–322 (1995).


title: Marcela12

value: IA


title: KLF1 wiltype Input


title: Marcela11


title: KLF1 wildtype ChIPseq


title: B602-03

city: Madison

first: Aicha

last: Quamine

state: WI

address: 1111 highland ave

institute: University of Wisconsin Madison

description: Total RNA from isolated murine NK cells

hyb_protocol: Purified RNA samples were hybridized for 16 to 24 hours at 65°C according to  NanoString nCounter hybridization protocol. Each hybridization reaction consisted of 10 μL Master Mix, 5 μL purified RNA sample, and 3 μL Capture ProbeSet.

scan_protocol: standard NanoString protocol

data_processing: Raw gene expression data were processed using NanoString Technologies' NanoTube Bioconductor package, including quality control, normalization, and analysis steps according to standard nSolver procedures. Differential expression analysis was conducted using the limma R package, defining significantly differentially expressed genes with log fold-change (FC) ≥ 2 and q value ≤ 0.05.

label: TRIzol

source_name: Purified NK Cells

label_protocol: cDNA synthesis was performed using Bio-Rad iScript Reverse Transcription Supermix. Gene expression was detected using qRT-PCR with specific primers for human and mouse gene targets on Applied Biosystems Veriti 96-Well PCR Thermal Cycler.

growth_protocol: NK cells were cultured at a density of 0.1E6 cells/mL and were activated with irradiated (100 Gy) AgN2a-4P cells at a 1:1 ratio. Medium was refreshed every 2 days with additional 10 ng/mL IL-15/IL-15Rα conjugate and 5 mL of fresh RPMI medium. NK cells were expanded for a total of 12 days, and cell density and viability were monitored daily using a hemocytometer.

extract_protocol: NK cells were isolated from culture using Miltenyi Biotec NK cell isolation kit on AutoMACS Pro. RNA was extracted from purified NK cells using QIAGEN RNeasy Mini Kit following manufacturer’s protocol. RNA purity and concentration were assessed with NanoDrop 1000.

treatment_protocol: NK cells were harvested at day 12 and exposed to anti-TIM-3 or IgG2a isotype control antibody for 4 hours. Prior to RNA isolation, NK cells  were purified using the AutoMACS pro-separator (Miltenyi Biotec, San Jose, CA). Total RNA was isolated from purified NK cells using an RNA isolation kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s protocol.

tag: gender

value: Femaie

tag: expansion method


title: B603-03

description: Total RNA from isolated murine NK cells


title: B601-04

description: Total RNA from isolated murine NK cells

value: Anti-TIM-3 antibody


title: B602-04

description: Total RNA from isolated murine NK cells


title: B603-02

description: Total RNA from isolated murine NK cells


title: Marcela18


title: SH18, DKO41-N

status: Public on Jul 02 2024

city: St. Louis

first: Christina

last: Stallings

state: MO

address: 425 South Euclid ave

institute: Washington University in Saint Louis

data_processing:
Base calls and demultiplexing were performed using Illumina bcl2fast
Reads were aligned to Ensemble release 76 primary assembly with STAR 2.5.1a
Counts were obtained using Subread:featureCount and Salmon 0.8.2
Sequencing QC was performed using RSeQC 2.6.2
Assembly: GENCODE M3 (GRCm38.p3)
Supplementary files format and content: raw-delimited text file includes raw counts for each sample

source_name: bone marrow

extract_protocol:
Cells were lysed using TRIzol reagent (Invitrogen) and RNA was isolated using a phenol/chloroform and isopropanol precipitation with high salt.
Library preparation conducted by the Washington University in St. Louis Genome Technology Access Center (GTAC).

value: bone marrow

tag: genotype

value: DKO

value: N


title: Marcela10

value: oocyte


title: SH18, DKO25-HK

value: HK


title: NC_1

value: Prunus sibirica clone

value: Floral organ

tag: group


title: SH18, DKO28-HK


title: SH18, DKO25-N


title: B601-02

description: Total RNA from isolated murine NK cells


title: Mycobacteirophage Adephagia lysogen in Mycobacterium smegmatis mc2 155

first: Krista

middle: G.

last: Freeman

address: 4249 Fifth Avenue

department: Biological Sciences

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.17 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.3.4.2
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.9
BAM format was converted to BED format using bedtools version 2.27.1
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.27.1
Assembly: Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Assembly: Genome_build: JF704105 (Adephagia)
Supplementary files format and content: bedgraph formatted files containing strand-specific ("plus" and "minus" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycolicibacterium smegmatis

source_name: bacterial

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using Ribo-Zero (Illumina)
Libraries were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

value: bacterial

tag: phage

value: mycobacteriophage Adephagia

tag: infection timepoint

value: no exogenous phage added


title: SH18, KO23-M

value: KO

value: M


title: SH18, DKO25-M


title: SH10, KO2-M


title: SH18, KO23-N


title: Mycobacterium smegmatis infected with mycobacteriophage Adephagia for 210min

tag: cell type

value: 210 minutes


title: Mycobacterium smegmatis infected with mycobacteriophage Adephagia for 30min

value: 30 minutes


title: SH18, DKO41-HK


title: SH10, WT1-N

value: WT


title: SH08, WT1-N


title: SH18, DKO28-N


title: SH10, WT1-HK


title: SH08, WT3-N


title: CR_1

value: strong frost resistance clone

value: Blooming stage


title: SH10, WT1-M

value: bone marrow


title: SH04, KO89-HK


title: SH04, DKO47-M

value: DKO


title: SH04, KO90-HK


title: SH04, DKO51-M


title: SH08, KO1-N

value: N


title: SH02, KO2-HK


title: SH04, WT0-HK


title: SH01, WT1-M


title: SH02, KO3-M


title: SH02, WT1-HK


title: SH02, WT2-M


title: Brain Sample4

city: Shenzhen

first: Gaowei

last: Chen

address: 1056 Xueyuan avenue

institute: ShenZhen Institute of Advanced technology Chinese Academy of sciences

library_source: transcriptomic single cell

data_processing: The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells

source_name: brain

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: brain

value: wild type

tag: brain area

value: septal area


title: Brain Sample5


title: Brain Sample6


title: Brain Sample2


title: SH08, KO3-N


title: Brain Sample1


title: KO_7d_Rec_rep4

city: Philadelphia

first: Mohit

middle: K.

last: Midha

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
RNA-seq reads were aligned to UCSC mouse genome, mm9, using STAR aligner. Only uniquely aligned reads were retained for downstream analysis. Read count for each gene and samples were counted using FeatureCounts. Differential analysis was performed using EdgeR.
Assembly: mm9
Supplementary files format and content: EdgeR_results

source_name: interscapular BAT

growth_protocol: Male HDAC3 floxed and Ucp1-cre HDAC3 floxed mice on a C57BL/6 background maintained on a 12 hour dark /light cycle and were sacrificed at 5PM (ZT10) at 10-12 weeks of age for the collection of interscapular brown adipose tissue.

extract_protocol:
Total RNA was extracted from snap-frozen BAT using TRIzol reagent (Thermo Fisher Scientific, 15596026) followed by RNeasy Mini Kit (QIAGEN, 74104).
Total RNA was isolated from mouse interscapular BAT of 10-12-week old mice. 250 ng of total RNA from biological replicates were DNase-treated prior to rRNA removal completed with a Ribo-Zero Magnetic kit (Illumina, MRZH11124) per standard protocol. The RNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, RS-122-2001) according to the standard Illumina protocol.

treatment_protocol: Male mice housed at 22C were subjected to cold exposure to 15C for 24 hours in environmental rodent incubator maintained on the same 12:12 hour dark/light cycle. After that, they were housed at 22C for 1 or 7 days. Room temperature (22C) cohorts were maintained in standard housing room.

value: interscapular BAT

value: Ucp1-cre HDAC3 floxed on C57BL/6J, male

value: Following cold exposure to 15C for 24 hr, mice were housed at 22C for 7 days


title: KO_7d_Rec_rep3


title: Control_7d_Rec_rep1

value: HDAC3 floxed on C57BL/6J, male


title: KO_24h_Rec_rep2

value: Following cold exposure to 15C for 24 hr, mice were housed at 22C for 1 day


title: KO_24h_Rec_rep1


title: KO_7d_Rec_rep2


title: Control_24h_Rec_rep4


title: Control_24h_Rec_rep2


title: Control_24h_Rec_rep1


title: Control_7d_Rec_rep4


title: Brain Sample3


title: KO_22C_rep4

value: Room Temperature 22C


title: KO_7d_Rec_rep1


title: Control_7d_Rec_rep3


title: Control_7d_Rec_rep2


title: KO_24h_Rec_rep4


title: KO_24h_Rec_rep3


title: Control_22C_rep2


title: Control_22C_rep3


title: Control_22C_rep1


title: Control_24h_Rec_rep3


title: BAT_WT_22C

data_processing:
Adapter sequence and low-quality bases were trimmed from sequencing reads using Cutadapt. Reads with >= 25 bp were subject to alignment to UCSC mouse genome, mm9, using bowtie with options “-q -S --best --strata --fullref -m 1 -v 3”. Highly abundant rRNA, tRNA, or snRNA were filtered out before downstream analysis. eRNA was called by peak calling routine in Homer in a strand-specific manner.
BigWig genome browser tracks were made similarly to ChIP-seq data but in a strand-specific manner.
Assembly: mm9
Supplementary files format and content: bigWig format
Library strategy: GRO-seq

extract_protocol:
Ten genotype confirmed mice per group per experimental condition were utilized for each experiment. Ten interscapular BAT pads from each HDAC3 KO and control littermate groups were quickly dissected, pooled and then minced in ice-cold nuclei isolation buffer A (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In), a cold swelling buffer, and filtered through a 100 um cell strainer. All GRO-seq steps including tissue harvest, nuclei isolation, nuclear run-on reactions, immunoprecipitations, library preparation, and sequencing were performed in parallel to reduce batch effects. Nuclei Isolation: Nuclei were isolated by dounce homogenization conducted on ice. Filtered lysate in buffer A was centrifuged at 400 x g for 10 min and resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% Igepal). Lysis buffer containing sample were incubated on ice for 5 min, and nuclei washed twice with lysis buffer. Nuclei pellet was washed twice with lysis buffer. Nuclei were resuspended at a final concentration of 10 x 107 nuclei/ml in freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA).  Nuclear Run-on reaction: 40 million nuclei were utilized for each nuclear run-on reaction. The nuclei were thawed on ice and mixed with 1:1 volume of ice-cold run-on buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 200 U/ml Superase-In, 1% Sarkosyl, 500 uM ATP, GTP and Br-UTP, 2 uM CTP). The run-on reaction was incubated at 30C for 7 minutes and terminated by addition of Trizol with 5 minute incubation at room temperature. RNA was extracted from Trizol, treated with DNAse, prior to 10 minute RNA hydrolysis fragmentation reaction, purified over a Micro Bio-Spin P30 column and treated with T4 polynucleotide kinase at 37C for 1 hour, treated with additional T4 polynucleotide kinase and heat inactivated for 5 minutes at 75C.  NRO-RNA Immunoprecipitation: Blocked Anti-BrdU agarose beads (Santa Cruz Biotechnology, sc-32323 AC), rotated for 1h in blocking buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20, 0.1% PVP, and 0.1% BSA) were used for immunoprecipitation. Labeled-RNA was incubated and rotated with beads for 1h at room temperature, followed by washing beads twice in binding buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20), twice in low salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20, 138 mM NaCl), and twice in TET buffer (TE pH 7.4, 0.05% Tween-20). BrdU-labeled RNA was eluted from the anti-BrdU agarose beads four separate times using 10 min incubation with 100 ul preheated (42C) elution buffer. RNA precipitation was performed using 300 mM NaCl, 1 ul of glycogen and 2.5 volumes of ethanol and an overnight incubation at −20C, followed by 30 minute centrifugation at 4C. RNA pellet was resuspended in water (with 1 U/μl Superase-In and 0.05% Tween-20), denatured for 3 min at 65C, placed on ice, and subsequently treated with E.coli poly(A)-polymerase for 30 min at 37C.
cDNA synthesis was completed utilizing entire volume of E.coli poly(A)-polymerase reaction with previously reported oNTI223 primer (5′-/5′ phosphorylation/GA TCG TCG GAC TGT AGA ACT CT/abasic dSpacer furan/CAA GCA GAA GAC GGC ATA CGA TTT TTT TTT TTT TTT TTT TT/ degenerate nucleotides /-3′) using Superscript III RT (Thermo Fisher Scientific, 18080-051) in reaction mix for 40 min at 48C. cDNA reaction was incubated with exonuclease I for 15 min at 37C, then inactivated using 100 mM NaOH for 20 min at 98C, and neutralized with 100 mM HCl. Denatured cDNA was run on a 10% TBE-urea 10-well gel, gel stained with SYBR-gold, and gel extracted 105-400 nucleotides size were excised, eluted from shredded gel pieces in TE + 0.1% Tween for 4 hours at room temperature and then ethanol precipitated. cDNA was resuspended and circularized with CircLigase for 1 hr at 60C, denatured for 10 min at 80C, and relinearized with relinearization mix (25 mM KCl, 500 μM DTT) plus 15 unites APE I enzyme. PCR amplification was conducted with Phusion Hot Start II Kit (Thermo Fisher Scientific, F-549L), according to manufacturer’s instructions. PCR amplification was performed using primers oNTI200 (5′-CAA GCA GAA GAC GGC ATA-3′) and oNTI201 (5′-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC G-3′). PCR amplified product was run on a 10% TBE gel and products ranging from 150-305 nucleotides were gel extracted and eluted from gel pieces using 4 h in TE + 0.1% Tween + 150 mM NaCl. Gel isolated PCR products in elution buffer were purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research, 11-379). Libraries were sequenced on an Illumina HiSeq2000 with sequencing primer 5′-CGA CAG GTT CAG AGT TCT ACA GTC CGA CGA TC-3′.

treatment_protocol: Male mice housed at 22C were subjected to cold exposure to 15C for 24 hours in environmental rodent incubator maintained on the same 12:12 hour dark/light cycle.  Room temperature (22C) cohorts were maintained in standard housing room.


title: BAT_hKO_22C

value: Adiponectin-cre HDAC3 floxed on C57BL/6J, male


title: KO_22C_rep2


title: KO_22C_rep1


title: Control_22C_rep4


title: KO_22C_rep3


title: BAT_HDAC3_5pm_RT_34408

data_processing:
ChIP-seq reads were aligned to UCSC mouse genome, mm9, using STAR aligner.
Only uniquely aligned reads were retained for downstream analysis. Redundant reads were deduplicated.
Peak calling was performed against matching input control using Homer , and 1 RPM cut off was subsequently applied to retain stringent peaks.
De novo motif search was performed using Homer within 200 bp window. BigWig files were generated using bedtools and bedGraphToBigWig from UCSC toolkit in RPM scale.
BigWig data profiles for all high throughput sequencing data were extracted using bwtool and visualized using R.
Assembly: mm9
Supplementary files format and content: bigWig format

growth_protocol: Male wild-type mice on a C57BL/6 background maintained on a 12 hour dark /light cycle and were sacrificed at 5PM (ZT10) at 10-12 weeks of age for the collection of interscapular brown adipose tissue.

extract_protocol:
Interscapular BAT pads (two lobes) were minced and cross-linked in 1X PBS/1% formaldehyde at room temperature for 20 min. The cross-linking was stopped by adding glycine at a final concentration of 125 mM. After 5-min incubation at room temperature, the BAT pieces were washed three times with ice-cold 1X PBS. Cross-linked BAT pieces were suspended in ice-cold ChIP dilution buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1.1% Triton X-100, 0.11% sodium deoxycholate, 0.1% SDS) with cOmpleteProtease Inhibitor Cocktail (Roche), and Phosphatase Inhibitor Cocktail 2 (Sigma-Aldrich), and sonicated (3 times for 10 s each with a 60-s interval at 10% amplitude, followed by 3 times for 10 s each with a 60-s interval at 15% amplitude) with probe sonication (Fisher Scientific, FB705 Sonic Dismembrator). Lysates were centrifuged at 20,817 rpm for 15 min at 4°C to remove lipid. After centrifugation, chromatin lysates were brought to 1 ml with ChIP dilution buffer and an aliquot was saved as 5% input sample. After the addition of 50 ml of Pierce ChIP-grade Protein A/G Magnetic Beads (Thermo Fisher Scientific, 26162), samples were incubated at 4°C for 1 h. The precleared samples were divided into 2 tubes and subjected to immunoprecipitation at 4°C overnight with 3-5 mg of antibodies
ChIP-seq libraries were prepared from independent formaldehyde-crosslinked biological replicates of interscapular BAT from dissected from independent mice. Replicates were pooled on a PCR cleanup column prior to sequencing library generation. Libraries were generated according to Illumina ChIP-seq guide, utilizing Illumina adapter oligos and primer sequences for all library construction and amplification steps. Enzymes for library generation were from New England Biolabs. Size selection of adaptor ligated DNA was performed prior to PCR library amplification using Agencourt AMPure XP Beads (Beckman Coulter, A63881) and subsequently purified with a MinElute PCR Purification kit (QIAGEN, 28004). Next-generation sequencing was performed utilizing with the Illumina HiSeq2000.

treatment_protocol: Male mice housed at 22C were subjected to cold exposure to 4C for 24 hours in environmental rodent incubator maintained on the same 12:12 hour dark/light cycle. Room temperature (22C) cohorts were maintained in standard housing room.


title: BAT_ERRa_5pm_RT_34410

value: ERRa


title: BAT_WT_15C

value: Cold exposure to 15C for 24 hr


title: HDAC3_KO_7d_Rec

data_processing:
ATAC-seq reads were aligned to UCSC mouse genome, mm9, using STAR aligner with an option “--outFilterMultimapNmax 1 --alignIntronMax 1 --alignMatesGapMax 2000”. Only uniquely aligned reads were retained and deduplicated for downstream analysis. Given that TF-binding open chromatin regions yield short fragments, reads pairs with fragment length < 120bp were selected for downstream analysis. Peak calling and de novo motif search were performed using Homer
Assembly: mm9
Supplementary files format and content: bigWig format

extract_protocol:
Interscapular BAT was harvested from individual mice and snap frozen in liquid nitrogen. For each genotype and condition, three biological replicates (individual mouse BAT pads) were thawed on ice and quickly pooled in ice-cold celling buffer A and nuclei isolated on ice by dounce homogenization per GRO-seq nuclei isolation protocol. 5 x 104 isolated nuclei were then washed in ice-cold 1ml of 1x Tagmentation Buffer (2x 20 mM Tris (hydroxymethyl)-aminomethane, 10mM MgCl2, 20% (vol/vol) dimethylformamide, pH 7.6) and resuspended in 50 ml 1x TD buffer prior to the transposition assay. The Nextera DNA Library Prep Kit (Illumina, FC-121-1030) was used for the transposition reaction. The nuclei pellet was resuspended and incubated with transposition reaction mix at 37°C for 30 minutes. DNA was isolated using MinElute Reaction Cleanup kit and eluted in elution buffer (EB).
Libraries were generated using the Ad1_noMX and Ad2.1–2.4 barcoded primers and were amplified for 7-9 total cycles. The libraries were purified with AMPure beads (to remove primer-dimers and >1,000 bp DNA fragments) by manufacturer protocol. The library was assessed on an Agilent High Sensitivity DNA Bioanalysis chip and quantitated with the Qubit dsDNA high-sensitivity Assay kit (Thermo Fisher Scientific, Q32851). Libraries were sequenced on an Illumina HiSeq 2000 using 50 bp paired-end (50PE) sequencing.


title: BAT_CEBPb_5pm_4C_34415

value: CEBPb

value: Cold exposure 4C


title: BAT_hKO_15C


title: BAT_CEBPb_5pm_RT_34414


title: HDAC3_Control_22C


title: HDAC3_Control_24h_Rec


title: HDAC3_KO_22C


title: EFL-3_NanoDam_C-t_dam-only_Rep1

city: London

first: Michalis

last: Barkoulas

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

description: amplicons of GATC-6mA-methylated genomic DNA fragments

data_processing:
Sequencing data were fully processed using the automated pipeline defined by the perl script damidseq_pipeline v1.4.5 (Marshall and Brand, 2015) (available at https://github.com/owenjm/damidseq_pipeline). The pipeline  was used calling Bowtie 2 v2.3.4 (Langmead and Salzberg, 2012) for alignment to C. elegans bowtie indices from genome assembly WBcel235 (available from illumina® iGenomes page), Samtools v1.9 (Li et al., 2009) for alignment manipulations and generation of BAM files. Using a GATC fragment file with the coordinates of all GATC fragments across the C. elegans genome in gff format, built from a WBcel235 FASTA file (available at https://www.ensembl.org/Caenorhabditis_elegans/Info/Index) using the gatc.track.marker.pl script (available at https://github.com/owenjm/damidseq_pipeline), the pipeline calculated genome-wide log2(EFL-3:GFP, GFP-nanobody:dam/GFP-nanobody:dam) signal enrichment scores per GATC fragment of the genome as gff files from pairs of BAM files from EFL-3:GFP, GFP-nanobody and GFP-nanobody samples.
Using damidseq_pipeline v1.4.5 all pairwise calculations of log2(EFL-3:GFP, GFP-nanobody:dam/GFP-nanobody:dam) scores between pairs of EFL-3:GFP, GFP-nanobody:dam and GFP-nanobody:dam sample replicates were performed producing 4 independet bedgraph signal files.
The 4 bedgraph signal files were normalised by quantile normalisation and averaged arithmetically per GATC fragment of the genome to genarate the single averaged signal bedgraph for each C-t and N-t GFP-nanobody:dam configuration.
Statistically significant enrichment peaks with an FDR<0.05 were identified from the averaged profiles using the the perl script find_peaks (available at https://github.com/owenjm/find_peaks) which generated peak interval gff files
Assembly: WBcel235
Supplementary files format and content: bedgraph interval files representing coordinates of GATC fragments of the genome with a log2(EFL-3:GFP, GFP-nanobody:dam/GFP-nanobody:dam) score each
Supplementary files format and content: bed files representing statistically singificant peaks (FDR<0.05)
Library strategy: DamID-seq

source_name: Epidermis - wrt-2p expression domain

growth_protocol: For each replicate of each strain used for NanoDam nine 55 mm NGM plates seeded with dam-/dcm- bacterial lawns and fully populated by gravid adults were used for large-scale egg preparation with isolated embryos seeded in new dam-/dcm- plates that were incubated at 20 °C. The resulting synchronised populations were collected in a 15 ml centrifuge tube after 48 hours, at the L4 stage. All collected populations pellets (~100 μl) underwent extensive washing with 10 ml M9 at least 5 times and were frozen at -20C.

extract_protocol:
gDNA for each sample was extracted by lysing animal pellets with Cell Lysis Solution (QIAGEN) containing Proteinase K. RNA was removed by treating with RNase A  and DNA was isolated after treatment with Protein precipitation solution (QIAGEN) by percipitating in isopropanol and washing with 70% ethanol. gDNA was redissolved in water. For isolation and amplification of the GATC methylated gDNA fragments the protocol followed was an adapted version of the one presented in (Marshall et al., 2016).
Amplicon sonication and library preparation was outsourced to GENEWIZ which used illumina protocols for sequencing on the Illumina HiSeq 2x150 platform

value: Epidermis - wrt-2p expression domain

tag: strain

tag: biological replicate

value: Replicate 1

value: icbSi252[pDK179(ttTi5605_right::wrt-2p::wcherry::Dam:linker:egl-13NLS:vhhGFP4::unc-54 3'UTR::unc1193'UTR::unc-119::punc119::ttTi5605_left)] I; unc-119(ed3) III


title: EFL-3_NanoDam_C-t_efl-3:gfp_Rep2

value: Replicate 2

value: icbSi252[pDK179(ttTi5605_right::wrt-2p::wcherry::Dam:linker:egl-13NLS:vhhGFP4::unc-54 3'UTR::unc1193'UTR::unc-119::punc119::ttTi5605_left)] I; unc-119(ed3) III; efl-3(syb5037[efl-3::GFP::AID] II


title: EFL-3_NanoDam_N-t_dam-only_Rep2


title: HDAC3_KO_24h_Rec


title: EFL-3_NanoDam_N-t_dam-only_Rep1


title: EFL-3_NanoDam_C-t_efl-3:gfp_Rep1


title: EFL-3_NanoDam_N-t_efl-3:gfp_Rep1

value: icbSi251[pDK175(ttTi5605_right::wrt-2p::wcherry::egl-13NLS:vhhGFP4:linker:Dam::unc-54 3'UTR::unc1193'UTR::unc-119::punc119::ttTi5605_left)] I; unc-119(ed3) III; efl-3(syb5037[efl-3::GFP::AID] II


title: HDAC3_Control_7d_Rec

value: interscapular BAT


title: PX_23

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

data_processing: Data was preprocessed using NSolver software. Background was corrected with the method “background thresholding” using the mean plus two standard deviations of the negative control counts as threshold. The geometric mean of the Positive Control and Housekeeping genes were used to normalize and a reference sample was used to normalize across different CodeSets (codeset calibration).

source_name: primary cervical cancer

label_protocol: 275 ng of total RNA was processed.

extract_protocol: On average, 5, 10 um-thick, cryostat sections were prepared for the extraction of total RNA from cervical cancer biopsies using High pure FFPET RNA Isolation Kit of Roche.

value: primary cervical cancer

tag: age

value: 48 years

tag: histology

value: SCC

tag: Stage

value: immunotherapy

tag: clinical outcome

value: Complete Response


title: PX_24

tag: tissue

value: 77 years

value: IVB

tag: treatment

value: Partial Response


title: PX_21

value: 52 years

value: IIB

value: Progressive Disease


title: EFL-3_NanoDam_C-t_dam-only_Rep2

value: Epidermis - wrt-2p expression domain

tag: developmental stage


title: EFL-3_NanoDam_N-t_efl-3:gfp_Rep2


title: PX_20

value: 46 years

value: Stable Disease


title: PX_18

value: 61 years


title: PX_12

value: 41 years


title: PX_19

value: 32 years


title: PX_10

value: primary cervical cancer

value: 55 years


title: PX_7

value: 48 years

value: SCC

value: EIVB


title: PX_14

value: immunotherapy


title: PX_8

value: 34 years

value: IVB


title: PX_22

value: 44 years


title: PX_16

value: 79 years

value: Complete Response


title: PX_15

value: 43 years

value: IIB


title: PX_4

value: 37 years

value: Progressive Disease


title: PX_3


title: PX_17

value: 38 years


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1152

city: Foster City

first: Ruidong

last: Li

address: 324 Lakeside Drive

department: Research Data Sciences

institute: Gilead Sciences, Inc.

description:
Seurat_Object_HT_SS3.rds
TraCeR_filtered_cell_data_HT_SS3.csv
TraCeR_filtered_recombinants_HT_SS3.txt

data_processing:
Demultiplexed FASTQ files for cells on each plate were first merged using the merge_demultiplexed_fastq.R script provided in the zUMIs tool (v2.9.7). Then, the zUMIs.sh script was used to execute a series of steps - filtering, mapping, counting, and summarizing - to generate the gene expression count matrices and summary statistics.
The source code in the runfeatureCountFun.R script within zUMIs was modified to exclude multi-mappers (countMultiMappingReads=FALSE) and fragments that were not successfully mapped to both ends (requireBothEndsMapped=TRUE) from quantification. The read count matrix for both exonic and intronic mapping was used for downstream analysis.
To ensure consistency for benchmarking, the same genome reference sequence (genome.fa) and gene annotation information (genes.gtf) provided in cellranger reference index refdata-gex-GRCh38-2020-A was used for Smart-seq3 data analysis
Seurat (v5.0.0) was used for quality control and downstream analysis of gene expression data
To reconstruct TCR sequences from HT Smart-seq3 RNA sequencing data, we utilized the Docker image of the TraCeR tool (v0.6.0) in Docker Hub. The assemble module within TraCeR was first used to reconstruct TCR sequences for each individual cell, and the summarise module was subsequently used to generate the summary statistics and detailed information for all cells
Assembly: GRCh38
Supplementary files format and content: RDS file includes Seurat object for all cells
Supplementary files format and content: CSV file includes cell data output from TraCeR summarise analysis for all cells
Supplementary files format and content: tab-delimited TXT file includes recombinants output from TraCeR summarise analysis for all cells

source_name: PBMC

extract_protocol:
PBMCs from healthy donors were isolated by SepMateTM tubes (STEMCELL Technologies, Catalog#85450), following manufacturer’s instruction, and resuspended in RPMI 1640 medium (Gibco, Catalog#11875093) containing 5% human serum (Sigma, Catalog# H3667-100ML) and 1% penicillin-streptomycin and cultured in 6-well plates (3 mL/well). After overnight culture, the PBMC was resuspended and cultured at 5 × 106 cells/ml in 48-well plate and treated immediately with DMSO or phorbol-12-myristate-13-acetate (PMA) plus ionomycin (PMA/Ionomycin) cocktail (Cell stimulation cocktail, eBioscience, Catalog#00-4970) for 3 h. Then, PBMC was stained with APC mouse anti-human CD4 (SK3, BD Biosciences, Catalog#340443) and Alexa Fluor 488 mouse anti-human CD3 (UCHT1, BioLegend, Catalog#300454) before sorting. The dead cells were gated out after staining with viability dye eFluor 780 (Invitrogen, Catalog#65-0865-14). The live and single CD4+ T-cells were sorted into 96-well plates containing lysis buffer using SH800S cell sorter (Sony Biotechnology Inc, San Jose, CA) with a 100-μm nozzle.
The Smart-seq3 library preparations were performed as previously described [Hagemann-Jensen et al., Nat Biotechnol, 2020, 38:708-714] with some modifications. In addition, we developed and optimized an automated sample handling process for most steps of the Smart-seq3 protocol, including single-cell lysis, reverse transcription, and library construction by using Integra Biosciences VIAFLO 96 electronic pipetting system and Mantis liquid handler (Formulatrix, Bedford, MA, USA).

value: PBMC

value: CD4+ T cells

tag: donor id

value: Donor 2

tag: plate

value: Plate 18

tag: disease

value: Healthy

value: PMA/Ionomycin


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1150


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1151


title: PX_2

value: primary cervical cancer

value: 39 years

value: SCC

value: immunotherapy


title: PX_1

value: 65 years

value: EIVB

value: Stable Disease


title: PX_11

value: 67 years


title: PX_9

value: 49 years

value: IVB


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1149


title: PX_13

value: 54 years

value: Partial Response


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1148

value: PBMC

value: CD4+ T cells


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1146

value: Donor 2

value: Plate 18


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1147

value: Healthy

value: PMA/Ionomycin


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1145


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1144


title: PX_5

value: primary cervical cancer

value: 42 years

value: IIIA

value: Progressive Disease


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1143


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1142


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1140


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1141


title: PX_6

value: SCC

value: IVA

value: immunotherapy


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1137


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1139


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1138


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1130


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1128


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1131


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1127


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1135


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1134


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1136


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1133


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1121


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1132


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1129


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1126


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1125


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1124


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1120


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1123


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1122


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1119


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1117


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1118


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1116


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1114


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1113


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1112


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1111


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1109


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1110


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1106


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1105


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1108


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1104


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1102


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1103


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1107


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1100


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1099


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1101


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1097


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1096


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1098


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1093


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1092


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1095


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1094


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1091


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1089


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1090


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1086


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1081


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1088


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1080


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1084


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1079


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1083


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1076


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1077


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1078


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1087


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1074


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1070


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1082


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1072


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1071


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1075


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1069


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1067


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1062


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1066


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1064


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1065


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1063


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1061


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1085


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1059


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1115


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1058


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1073


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_956


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_958


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_957


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1057


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_960


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_959


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_955


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_953


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_954


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1068


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_950


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_947


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_949


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_948


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_952


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_951


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_946


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_945


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_1060


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_943


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_944


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_942


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_938


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_941


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_939


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_936


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_935


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_940


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_932


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_937


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_927


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_934


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_929


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_930


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_931


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_922


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_921


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_928


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_918


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_926


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_925


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_920


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_924


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_923


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_919


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_915


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_914


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_916


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_933


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_913


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_911


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_909


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_908


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_905


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_907


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_904


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_903


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_902


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_901


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_900


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_897


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_895


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_917


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_891


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_892


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_912


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_888


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_887


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_889


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_884


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_906


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_880


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_883


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_899


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_875


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_896


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_870


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_894


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_873


title: Donor2_PMA/Ionomycin_HT SS3_Plate18_890


title: Donor2_DMSO_HT SS3_Plate18_1151

value: DMSO


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title: Donor2_DMSO_HT SS3_Plate18_1144


title: Donor2_DMSO_HT SS3_Plate18_1145


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title: Donor2_DMSO_HT SS3_Plate18_1140


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title: Donor2_DMSO_HT SS3_Plate18_1137


title: Donor2_DMSO_HT SS3_Plate18_1138


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title: Donor2_PMA/Ionomycin_HT SS3_Plate18_866


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title: Donor2_DMSO_HT SS3_Plate18_878


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1055

value: Plate 17


title: Donor2_DMSO_HT SS3_Plate18_879


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1052


title: Donor2_DMSO_HT SS3_Plate18_877


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1051


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1050


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1029


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1031


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1028


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1039


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1026


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1038


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1037


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1018


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1017


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1034


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1030


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1015


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1027


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1012


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1010


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1022


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1006


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1019


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1002


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1004


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1035


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1020


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_997


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_987


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1011


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1009


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1007


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_1003


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_978


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title: Donor2_PMA/Ionomycin_HT SS3_Plate17_826


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_799


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_798


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_817


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_797


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_796


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_789


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_790


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_794


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_787


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_785


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_805


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_782


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_781


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_804


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_783


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_778


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_777


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_775


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_801


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_780


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_774


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_802


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_793


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_791


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_779


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_769


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_772


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_773


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_788


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_771


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_770


title: Donor2_DMSO_HT SS3_Plate17_1054


title: Donor2_PMA/Ionomycin_HT SS3_Plate17_786


title: Donor2_DMSO_HT SS3_Plate17_1052


title: Donor2_DMSO_HT SS3_Plate17_1055


title: Donor2_DMSO_HT SS3_Plate17_1053


title: Donor2_DMSO_HT SS3_Plate17_1051


title: Donor2_DMSO_HT SS3_Plate17_1045


title: Donor2_DMSO_HT SS3_Plate17_1044


title: Donor2_DMSO_HT SS3_Plate17_1049


title: Donor2_DMSO_HT SS3_Plate17_1042


title: Donor2_DMSO_HT SS3_Plate17_1036


title: Donor2_DMSO_HT SS3_Plate17_1034


title: Donor2_DMSO_HT SS3_Plate17_1039


title: Donor2_DMSO_HT SS3_Plate17_1050


title: Donor2_DMSO_HT SS3_Plate17_1046


title: Donor2_DMSO_HT SS3_Plate17_1035


title: Donor2_DMSO_HT SS3_Plate17_1038


title: Donor2_DMSO_HT SS3_Plate17_1041


title: Donor2_DMSO_HT SS3_Plate17_1031


title: Donor2_DMSO_HT SS3_Plate17_1030


title: Donor2_DMSO_HT SS3_Plate17_1029


title: Donor2_DMSO_HT SS3_Plate17_1027


title: Donor2_DMSO_HT SS3_Plate17_1022


title: Donor2_DMSO_HT SS3_Plate17_1023


title: Donor2_DMSO_HT SS3_Plate17_1025


title: Donor2_DMSO_HT SS3_Plate17_1026


title: Donor2_DMSO_HT SS3_Plate17_1021


title: Donor2_DMSO_HT SS3_Plate17_1019


title: Donor2_DMSO_HT SS3_Plate17_1014


title: Donor2_DMSO_HT SS3_Plate17_1018


title: Donor2_DMSO_HT SS3_Plate17_1017


title: Donor2_DMSO_HT SS3_Plate17_1015


title: Donor2_DMSO_HT SS3_Plate17_1012


title: Donor2_DMSO_HT SS3_Plate17_1033


title: Donor2_DMSO_HT SS3_Plate17_1010


title: Donor2_DMSO_HT SS3_Plate17_999


title: Donor2_DMSO_HT SS3_Plate17_1004


title: Donor2_DMSO_HT SS3_Plate17_1003


title: Donor2_DMSO_HT SS3_Plate17_1006


title: Donor2_DMSO_HT SS3_Plate17_1011


title: Donor2_DMSO_HT SS3_Plate17_1007


title: Donor2_DMSO_HT SS3_Plate17_1002


title: Donor2_DMSO_HT SS3_Plate17_1001


title: Donor2_DMSO_HT SS3_Plate17_990


title: Donor2_DMSO_HT SS3_Plate17_1009


title: Donor2_DMSO_HT SS3_Plate17_993


title: Donor2_DMSO_HT SS3_Plate17_982


title: Donor2_DMSO_HT SS3_Plate17_996


title: Donor2_DMSO_HT SS3_Plate17_1020


title: Donor2_DMSO_HT SS3_Plate17_991


title: Donor2_DMSO_HT SS3_Plate17_986


title: Donor2_DMSO_HT SS3_Plate17_989


title: Donor2_DMSO_HT SS3_Plate17_988


title: Donor2_DMSO_HT SS3_Plate17_979


title: Donor2_DMSO_HT SS3_Plate17_980


title: Donor2_DMSO_HT SS3_Plate17_983


title: Donor2_DMSO_HT SS3_Plate17_981


title: Donor2_DMSO_HT SS3_Plate17_977


title: Donor2_DMSO_HT SS3_Plate17_974


title: Donor2_DMSO_HT SS3_Plate17_997


title: Donor2_DMSO_HT SS3_Plate17_975


title: Donor2_DMSO_HT SS3_Plate17_987


title: Donor2_DMSO_HT SS3_Plate17_971


title: Donor2_DMSO_HT SS3_Plate17_969


title: Donor2_DMSO_HT SS3_Plate17_966


title: Donor2_DMSO_HT SS3_Plate17_978


title: Donor2_DMSO_HT SS3_Plate17_970


title: Donor2_DMSO_HT SS3_Plate17_963


title: Donor2_DMSO_HT SS3_Plate17_962


title: Donor2_DMSO_HT SS3_Plate17_965


title: Donor2_DMSO_HT SS3_Plate17_967


title: Donor2_DMSO_HT SS3_Plate17_961


title: Donor2_DMSO_HT SS3_Plate17_863


title: Donor2_DMSO_HT SS3_Plate17_862


title: Donor2_DMSO_HT SS3_Plate17_861


title: Donor2_DMSO_HT SS3_Plate17_859


title: Donor2_DMSO_HT SS3_Plate17_857


title: Donor2_DMSO_HT SS3_Plate17_860


title: Donor2_DMSO_HT SS3_Plate17_855


title: Donor2_DMSO_HT SS3_Plate17_854


title: Donor2_DMSO_HT SS3_Plate17_852


title: Donor2_DMSO_HT SS3_Plate17_850


title: Donor2_DMSO_HT SS3_Plate17_849


title: Donor2_DMSO_HT SS3_Plate17_853


title: Donor2_DMSO_HT SS3_Plate17_973


title: Donor2_DMSO_HT SS3_Plate17_847


title: Donor2_DMSO_HT SS3_Plate17_844


title: Donor2_DMSO_HT SS3_Plate17_843


title: Donor2_DMSO_HT SS3_Plate17_845


title: Donor2_DMSO_HT SS3_Plate17_846


title: Donor2_DMSO_HT SS3_Plate17_842


title: Donor2_DMSO_HT SS3_Plate17_841


title: Donor2_DMSO_HT SS3_Plate17_836


title: Donor2_DMSO_HT SS3_Plate17_834


title: Donor2_DMSO_HT SS3_Plate17_838


title: Donor2_DMSO_HT SS3_Plate17_830


title: Donor2_DMSO_HT SS3_Plate17_831


title: Donor2_DMSO_HT SS3_Plate17_833


title: Donor2_DMSO_HT SS3_Plate17_851


title: Donor2_DMSO_HT SS3_Plate17_835


title: Donor2_DMSO_HT SS3_Plate17_827


title: Donor2_DMSO_HT SS3_Plate17_819


title: Donor2_DMSO_HT SS3_Plate17_818


title: Donor2_DMSO_HT SS3_Plate17_822


title: Donor2_DMSO_HT SS3_Plate17_820


title: Donor2_DMSO_HT SS3_Plate17_825


title: Donor2_DMSO_HT SS3_Plate17_821


title: Donor2_DMSO_HT SS3_Plate17_815


title: Donor2_DMSO_HT SS3_Plate17_817


title: Donor2_DMSO_HT SS3_Plate17_813


title: Donor2_DMSO_HT SS3_Plate17_812


title: Donor2_DMSO_HT SS3_Plate17_807


title: Donor2_DMSO_HT SS3_Plate17_809


title: Donor2_DMSO_HT SS3_Plate17_806


title: Donor2_DMSO_HT SS3_Plate17_804


title: Donor2_DMSO_HT SS3_Plate17_839


title: Donor2_DMSO_HT SS3_Plate17_805


title: Donor2_DMSO_HT SS3_Plate17_803


title: Donor2_DMSO_HT SS3_Plate17_828


title: Donor2_DMSO_HT SS3_Plate17_801


title: Donor2_DMSO_HT SS3_Plate17_798


title: Donor2_DMSO_HT SS3_Plate17_802


title: Donor2_DMSO_HT SS3_Plate17_799


title: Donor2_DMSO_HT SS3_Plate17_791


title: Donor2_DMSO_HT SS3_Plate17_797


title: Donor2_DMSO_HT SS3_Plate17_795


title: Donor2_DMSO_HT SS3_Plate17_794


title: Donor2_DMSO_HT SS3_Plate17_793


title: Donor2_DMSO_HT SS3_Plate17_787


title: Donor2_DMSO_HT SS3_Plate17_788


title: Donor2_DMSO_HT SS3_Plate17_782


title: Donor2_DMSO_HT SS3_Plate17_781


title: Donor2_DMSO_HT SS3_Plate17_785


title: Donor2_DMSO_HT SS3_Plate17_780


title: Donor2_DMSO_HT SS3_Plate17_789


title: Donor2_DMSO_HT SS3_Plate17_783


title: Donor2_DMSO_HT SS3_Plate17_786


title: Donor2_DMSO_HT SS3_Plate17_777


title: Donor2_DMSO_HT SS3_Plate17_779


title: Donor2_DMSO_HT SS3_Plate17_778


title: Donor2_DMSO_HT SS3_Plate17_775


title: Donor2_DMSO_HT SS3_Plate17_770


title: Donor2_DMSO_HT SS3_Plate17_769


title: Donor2_DMSO_HT SS3_Plate17_772


title: Donor2_DMSO_HT SS3_Plate17_771


title: Donor2_DMSO_HT SS3_Plate17_774


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_768

value: Plate 16


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_764


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_765


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_762


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_761


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_763


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_760


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_759


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_758


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_757


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_754


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_755


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_756


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_753


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_752


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_750


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_749


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_748


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_745


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_744


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_747


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_746


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_741


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_742


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_739


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_735


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_732


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_734


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_733


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_738


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_736


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_729


title: Donor2_PMA/Ionomycin_HT SS3_Plate16_730