title: rrAML180

tag: vital status

value: Alive

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: cytogenetic risk

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: dna methylation type

value: Intemediate


title: rrAML177

status: Public on Aug 06 2019

type: SRA

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

country: USA

institute: Coriell Institute for Medical Research

library_source: genomic

data_processing:
library strategy: Digital restriction enzyme analysis of methylation (DREAM)-seq
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let m be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and u be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(m+0.5)/(c*(m+0.5)+u+0.5)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated plain text files

molecule: genomic DNA

organism: Homo sapiens

source_name: AML patient peripheral blood cells

extract_protocol:
DNA isolation: Pretreated whole-blood genomic DNA was purified with the QIAamp DNA Blood mini Kit (Qiagen) and QIAcube automated sample preparation system (Qiagen).
Two micrograms of genomic DNA spiked with 5 methylation standards with defined methylation levels of 0, 25, 50, 75, and 100% were digested with 50 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 50 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'>5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments.
Ends of restriction fragments were repaired using Klenow exo- DNA polymerase. NEBNext adaptors for Illumina were ligated to the fragments. Size selected fragments were amplified with barcoded NEBNext oligos for Illumina.

value: Dead

tag: overall survival days

value: F

value: Intermediate Risk

tag: best response

value: NR

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

value: negative

tag: kras mutation

tag: dnmt3a mutation

tag: npm1 mutation

tag: cell type

value: AML patient peripheral blood cells


title: pre_Blood_CD4_0010

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

library_source: transcriptomic

data_processing:
Adapter sequences and low-quality reads were trimmed using cutadapt-v1.11 and PRINSEQ-0.20.4. Filtered reads were processed using “analyze amplicon” command of MiXCR-3.0.2 with following high-level options: -s = hsa, -starting-material = rna, -5-end = no-v-primers, -3-end = c-primers, -adapters = no-adapters, -receptor-type = trb, -region-of-interest = CDR3. In alignment to ImMunoGeneTics (IMGT) reference human TCR V/D/J sequences, we used the following parameters: -OvParameters.geneFeatureToAlign = VTranscript -OvjAlignmentOrder = JThenV. In assembling identical sequences into clones with PCR and sequencing error correlations, we used the following parameters: -ObadQualityThreshold=10, -OseparateByV=true. Only clones with productive CDR3 sequences were analyzed using VDJtools (ver 1.2.1.). Then, the sequencing coverage of samples, which was defined as the ratio of total reads to the starting number of T cells, was normalized to ×5 using the “DownSample” command in VDJtools. After coverage normalization, clones with lead count less than sequencing coverage were excluded as sequencing noise. Finally, for PBMC sample, we identified clones shared between CD4+ and CD8+ T cell repertoire as contamination, and separated these shared clones into CD4+ or CD8+ repertoire by their frequency in CD4+ or CD8+, because these shared clones were very few and their frequencies were biased to either CD4+ or CD8+ (Data not shown)
Genome_build: IMGT reference sequences of human TRB
Supplementary_files_format_and_content:  text files in VDJtools format include read count and frequency, complementarity determining region 3 (CDR3) nucleotide and amino acid sequences, Variable(V)/ Diversity(D)/ Joining(J) segment names, and V, D and J segment boundaries within CDR3 nucleotide sequence of individual clones

molecule: total RNA

source_name: CD4+ peripheral blood T cells

extract_protocol:
For bulk biopsy samples, total RNA was extracted using a RNA easy mini extraction kit (Qiagen) according to standard protocol, and diluted with Lysis buffer (100 mM Tris-HCl pH7.5, 500 mM LiCl, 10 mM EDTA, 5 mM DTT). For sorted CD4+ and CD8+ T cells, cells were collected directry into the Lysis buffer.
TCR sequencing libraries for next generation sequencing were prepared according to the previous report (Aoki, et al, GSE115425) with some modifications. PolyA RNAs were isolated and amplified from sorted T cells according to a previous report (Shichino, et al, GSE110711). To amplify the TCR cDNA containing complementarity determining region 3 (CDR3), nested PCR of the TCR locus was performed as follows. The first PCR mixture comprised 0.4 μL of 10 μM primer mix (5′ WTA and Trbc_ex), 4.6 μL of template, and 5 μL of KAPA Hifi Hotstart ReadyMix (KAPA Biosystems). The thermal cycling conditions were programmed as follows: denaturation at 95°C for 3 min, 10 cycles of denaturation for 20 sec at 98°C, annealing for 15 sec at 58°C and extension for 30 sec at 72°C, followed by final extension at 72°C for 2 min. Next, 10 μL of the first-PCR products was used for purification with an Agencort AM Pure XP kit (Beckman Coulter) at a 0.7:1 ratio of beads to sample, and eluted with 12 μL of DW. The second PCR mixture consisted of 1.25 μL of 10 μM primer mix (5′ WTA and Trbc_in-Bio), 11.25 μL of template and 12.5 μL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were same as the first PCR except the cycle number; 13 cycles. Next, 25 μL of the second-PCR products were purified using Agencort AM Pure XP kit (Beckman-Coulter) at a 0.8:1 ratio of beads to sample, and eluted in 15 μL of DW. The purified PCR products were sheared randomly using NEBNext dsDNA fragmentase (New England Biolabs). The fragmentation reaction mix consisted of 6 μL of DW, 2 μL of 10X Fragmentase Reaction Buffer v2, 10 μL of PCR product, and 2 μL of fragmentase. The fragmentation reaction was incubated at 37°C for 30 min, and then 5 μL of 0.5 M EDTA was added to stop the reaction on ice. The sheared PCR product was then purified and subjected to size selection using the Agencort AM Pure XP kit (Beckman Coulter) at a 0.8:1 ratio of beads to sample to remove large fragments, a 0.8:1 ratio of beads to sample to remove the smaller fragments, and eluted with 20 μL of Tris-HCl (pH 8.0). To capture the TCR cDNA containing the end of Constant region, the purified PCR products were incubated with 10 μL of Dynabeads M-270 Streptavidin (Thermo Fisher Scientific) for 30 min at room temperature (r.t.), washed 3 times with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], and once with Tris-HCl (pH 8.0), and DW. The captured TCR cDNA was repaired using NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs). The repair reaction mix contained 1.2 μL of reaction buffer, 8.3 μL of beads re-suspended with DW, and 0.5 μL of enzyme mix. The repair reaction was incubated at 20°C for 30 min, then washed once with lysis buffer [1% LiDS, 100 mM Tris-HCl (pH 7.5), 500 mM LiCl, 10 mM EDTA, and 5 mM DTT], 3 times with B&W-T buffer, and once with Tris-HCl (pH 8.0). The repaired TCR cDNA was attached to the sequencing adaptor using the DNA Ligation Kit ＜Mighty Mix＞ (TaKaRa Bio). The ligation reaction mix consisted of 1 μL of 10 μM P1 adaptor, 6.5 μL of beads re-suspended in Tris-HCl (pH 8.0), and 15 μL of enzyme mix. The ligation reaction was incubated at 16°C for 60 min using a thermal cycler with the cover open, washed once with lysis buffer, 3 times with B&W-T buffer, and once with Tris-HCl (pH 8.0). The third PCR were carried out using barcoded primers to enrich the TCR cDNA flanked with sequencing adapters. The third PCR mixture consisted of 0.35 μL of 10 μM trP1 primer, 1 μL of 3.5 μM IonA-BC-Trbc primer, 3.65 μL of beads resuspended in DW and 5 μL of KAPA Hifi Hotstart ReadyMix. The thermal cycling conditions were same as the first PCR except the cycle number; 12 cycles. The PCR product was purified and subjected to size selection using Agencort AM Pure XP kit (Beckman Coulter,) at a 0.75:1 ratio of beads to sample to remove large fragments, a 0.65:1 ratio of beads to sample to remove smaller fragments, and eluted with 20 μL of Tris-HCl (pH 8.0). Amplified TCR libraries were quantified using a KAPA Library Quantification Kit ((KAPA Biosystems) and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific). Final TCR libraries, whose lengths were 200–300 base pairs, were pooled and sequenced using an Ion Hi-Q Chef kit, an Ion PI v3 Chip kit, and an Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacturer’s instructions, except the input library concentration (100 pM) and flow number (550).

treatment_protocol: Patients with advanced solid tumors for whom no standard therapy was available, were treated with intravenous infusion of IT1208 at dose of 0.1 or 1.0 mg/kg. First patient in each cohort was treated as a single administration and other patients received two administrations of IT1208 on day 1 and 8 followed by safety and efficacy assessment with DLT evaluation period as 4 weeks.

value: CD4+ CD8- T cells

tag: age

tag: Sex

value: male

tag: cancer type

value: colorectal

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ

value: peripheral blood


title: post1_Blood_CD4_0010


title: rrAML171

tag: vital status

tag: clinical trial (p1/p2)

tag: gender

value: M

tag: age (years)

tag: cytogenetic risk

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: dna methylation type

value: CIMP-like


title: post2_Blood_CD4_0009

tag: cell type

value: gastric


title: rrAML169

tag: overall survival days

value: Unevaluable

tag: best response

value: CRp

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

value: positive

tag: kras mutation

tag: dnmt3a mutation

tag: npm1 mutation


title: post1_Blood_CD4_0009

tag: age

tag: Sex

tag: cancer type

tag: dose level

tag: agent

tag: organ


title: rrAML167

tag: vital status

value: Dead

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: idh1 mutation

tag: idh2 mutation

tag: dna methylation type

value: Normal-like


title: rrAML168

tag: overall survival days

value: F

tag: best response

value: NR

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: npm1 mutation

tag: cell type

value: Intemediate


title: rrAML163

tag: vital status

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

value: Intermediate Risk

value: negative

value: AML patient peripheral blood cells


title: rrAML154

tag: cytogenetic risk

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: idh1 mutation


title: rrAML159

tag: overall survival days

tag: best response

tag: idh2 mutation

tag: dna methylation type


title: rrAML162

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation


title: rrAML187

tag: kras mutation

tag: dnmt3a mutation

tag: npm1 mutation

tag: cell type


title: pre_Blood_CD4_0008

value: CD4+ CD8- T cells

tag: age

tag: Sex

value: male

tag: cancer type

value: gastro-esophageal

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ


title: pre_Blood_CD4_0009

value: gastric

value: peripheral blood


title: pre_Blood_CD4_0007


title: post1_Blood_CD4_0006

value: female

value: colorectal


title: post1_Blood_CD4_0007


title: pre_Blood_CD4_0006


title: rrAML147

tag: vital status

value: Alive

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: M

tag: age (years)

tag: cytogenetic risk

tag: best response

value: CR

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: idh1 mutation


title: rrAML152

value: Poor Risk

tag: peripheral blasts (%)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: idh2 mutation

value: positive

tag: npm1 mutation

tag: cell type

tag: dna methylation type


title: rrAML148

tag: vital status

value: Dead

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: CRi

value: Intemediate


title: rrAML149

tag: age (years)

tag: cytogenetic risk

value: Unevaluable

tag: best response

value: NR

tag: bone marrow blasts (%)

value: negative

value: AML patient peripheral blood cells

value: CIMP-like


title: pre_Blood_CD4_0005

value: CD4+ CD8- T cells

tag: age

tag: Sex

tag: cancer type

value: gastric

tag: dose level

value: 1.0 mg/kg

tag: agent

tag: organ


title: post1_Blood_CD4_0005

value: female

value: peripheral blood


title: rrAML144

value: M

tag: peripheral blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation


title: rrAML141

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: age (years)

tag: cytogenetic risk

tag: best response

tag: bone marrow blasts (%)

tag: cell type

tag: dna methylation type


title: rrAML138

value: CR

tag: peripheral blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

value: Normal-like


title: post1_Blood_CD4_0008

tag: age

tag: Sex

value: male

tag: cancer type

value: gastro-esophageal

tag: dose level

tag: agent

tag: organ


title: rrAML132

tag: vital status

value: Dead

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

tag: nras mutation

tag: kras mutation

value: positive

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation


title: rrAML137

tag: age (years)

tag: cytogenetic risk

value: Poor Risk

tag: best response

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: cell type

tag: dna methylation type


title: post2_Blood_CD4_0003

tag: age

tag: Sex

tag: cancer type

value: esophageal

tag: dose level

tag: agent

tag: organ


title: pre_Blood_CD4_0004

value: colorectal


title: rrAML131

tag: vital status

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: F

value: Intermediate Risk

value: CRi

tag: nras mutation

value: negative

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: AML patient peripheral blood cells


title: rrAML130

tag: age (years)

tag: cytogenetic risk

tag: best response

value: NR

tag: peripheral blasts (%)

tag: bone marrow blasts (%)

tag: platelets (x10^9/l)

tag: neutrophils (x10^9/l)

tag: hemoglobin in (g/dl)

tag: cell type

tag: dna methylation type

value: CIMP-like


title: HET Day14_1

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

description:
Chemically reprogrammed HET MEFs at Day14
connective tissue - MEFs

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Mus musculus GRCm38.p4 genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Genome_build: Mus musculus GRCm38.p4 genome version
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Mus musculus

source_name: Reprogrammed HET MEFs at Day14

growth_protocol: The β-actin+/+ (WT),  β-actin+/- (HET) and β-actin−/− MEFs (KO) from Dr. Christophe Ampe, University of Gent, Belgium, were cultured in DMEM with high glucose, 10% fetal bovine serum, and 100 U/ml penicillin and 100 µg/ml streptomycin (all from Millipore-Sigma), in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: OsteoMax-XF differentiation medium (EMD Millipore) was used as the osteogenesis induction medium, with the following supplements: GlutaMAX (1X), penicillin-streptomycin (100 μg/ml), Non-essential Amino Acid (1X) and Trace element B (1X). In addition, Small chemical molecules were dissolved and diluted in DMSO and used at the following final concentrations: Dexamethasone (Dex) 5 mM; Forskolin (F) 5mM. MEFs were seeded to a Matrigel-coated plate (1:30 dilution in pre-cold PBS, coated overnight at 4deg, at a density of 60,000 cells/well in a 24-well plate. The MEFs were cultured in DMEM until confluent. Once confluent, the DMEM was replaced with an osteo induction medium containing the small molecules (OsteoMax + Dex/F); this is considered day 0. The osteo medium was then changed every two days upto 14 days. Total RNA of each sample was collected on Day 4 and day14 for RNA-seq analysis,

tag: strain

value: BALB/c

tag: age

value: 10.5 day old embryos

value: chemically reprogrammed osteoblasts

tag: time

value: Day 14

tag: genotype

value: beta-actin heterozygote


title: pre_Blood_CD4_0001

value: CD4+ CD8- T cells

tag: Sex

value: male

tag: cancer type

value: gastric

tag: dose level

tag: agent

tag: organ

value: peripheral blood


title: post2_Blood_CD4_0004

value: female

value: colorectal


title: HET Day14_3


title: post1_Blood_CD4_0004


title: rrAML143

tag: vital status

value: Dead

tag: overall survival days

tag: clinical trial (p1/p2)

tag: gender

value: M

tag: age (years)

tag: cytogenetic risk

value: Intermediate Risk

tag: best response

tag: nras mutation

tag: kras mutation

tag: dnmt3a mutation

tag: idh1 mutation

tag: idh2 mutation

tag: npm1 mutation

value: Normal-like


title: post2_Blood_CD4_0002

tag: cell type

tag: age

tag: Sex

tag: cancer type


title: pre_Bulk_0011 [3'SAGE-seq]

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Trimommatic-v0.36 and PRINSEQ-0.20.4. Filtered reads were mapped to Refseq hg38 by using Bowtie2-2.2.5 with the following parameters: -t -p 11 -N 1 -D 200 -R 20 -L 20 -i S,1,0.50 --norc. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Between-sample normalization was performed by using Microsoft R Open 3.5.0 and TCC package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized tag-count values for each sample

source_name: biopsy of liver metastasis of pancreatic cancer

extract_protocol:
For bulk biopsy samples, total RNA was extracted using a RNA easy mini extraction kit (Qiagen) according to standard protocol, and diluted with Lysis buffer (100 mM Tris-HCl pH7.5, 500 mM LiCl, 10 mM EDTA, 5 mM DTT).
PolyA RNAs were isolated and amplified from each RNA samples according to the protocol described in (Shichino, S et al, GSE110711).
3'SAGE-seq libraries were constructed according to the protocol described in (Shichino, S et al GSE110711). Briefly, 150 ng of the whole-transcript library was restriction digested with NlaIII (New England Biolabs, Ipswich, MA, USA) for 2 h at 37ºC, and biotinylated 3′-tail transcripts were immobilized on Dynabead M-280 streptavidin beads (Thermo Fisher Scientific). Beads were washed, and 10 pmol of the CS1-EcoP15I-NlaIII adapter was ligated using a DNA ligation kit (Mighty Mix; Takara) for 30 min at 16ºC. Beads were washed three times with B&W-T buffer, once with 10 mM Tris-HCl (pH 8.0), suspended in 200 μL of EcoP15I digestion mix [1× NEBuffer 3.1, 1 mM ATP, and 0.2 U EcoP15I (New England Biolabs)], and digested for 16 h at 37ºC in a tightly sealed screw-cap tube with gentle rotation. Supernatant was purified using a Nucleospin Gel&PCR clean-up kit (Takara) and eluted twice with 12.5 μL of nuclease-free water. End-repair/polyA-tailing/ligation reactions were performed using NEBNext Ultra II modules (New England Biolabs) and 1.875 pmol of CS2-adapter according to manufacturer instructions. Reaction products were purified using a Qiagen MinElute Column (Qiagen, Hilden, Germany) and eluted with 13 μL of nuclease-free water. Barcoding mix [14.25 μL; 1× KAPA Hifi ReadyMix (KAPA Biosystems), 0.614 µM IonA-BC[N]-CS1-primer, and 0.614 µM Ion-trP1-CS2 primer] was added into 10.75 μL of elutant, and PCR enrichment was performed using the following program: 98ºC for 45 s, nine cycles of 98ºC for 15 s, 65ºC for 30 s, and 72ºC for 90 s, followed by 72ºC for 1 min and a hold at 4ºC. Reaction products were purified using double-size selection of AmPure XP beads (0.8× → 0.8×) and eluted with 10 μL of Tris-HCl (pH 8.0). The size distribution of each library was analyzed using an Agilent DNA high-sensitivity kit (Agilent Technologies, Santa Clara, CA, USA), and library concentration was quantified using a KAPA library quantification kit for Ion Torrent (KAPA Biosystems). Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

treatment_protocol: Patients with advanced solid tumors for whom no standard therapy was available, were treated with intravenous infusion of IT1208. Four and seven patients were assigned to dose levels 1 (0.1mg/kg) and 2 (1.0 mg/kg), having gastric or gastro-esophageal (n=6), colorectal (n=3), esophageal (n=1) and pancreatic cancer (n=1, also having simultaneous colon cancer). First patient in each cohort was treated as one dose of IT1208 on day 1 and other patients received two doses of IT1208 on day 1 and 8. Tumor biopsy for transcriptomic analysis were collected before and after the initiation of IT1208 from all patients (n=11).

value: bulk biopsy

value: colorectal and pancreas

tag: dose level

value: 1.0 mg/kg

tag: organ

value: liver metastasis of pancreatic cancer

tag: agent


title: post1_Bulk_0011 [3'SAGE-seq]


title: KO Day14_3

description:
Chemically reprogrammed KO MEFs at Day14
connective tissue - MEFs

source_name: Reprogrammed KO MEFs at Day14

tag: strain

value: BALB/c

value: 10.5 day old embryos

value: chemically reprogrammed osteoblasts

tag: time

tag: genotype

value: beta-actin knockout


title: KO Day14_1

value: Day 14


title: post1_Blood_CD4_0001

value: CD4+ CD8- T cells

value: male

value: gastric


title: pre_Bulk_0010 [3'SAGE-seq]

value: colorectal


title: pre_Blood_CD4_0002

value: peripheral blood


title: KO Day14_2


title: pre_Blood_CD4_0003

value: esophageal


title: pre_Bulk_0009 [3'SAGE-seq]

source_name: biopsy of gastric cancer

value: gastric cancer


title: post1_Bulk_0009 [3'SAGE-seq]


title: pre_Bulk_0008 [3'SAGE-seq]

source_name: biopsy of gastro-esophageal cancer

value: gastro-esophageal

value: gastro-esophageal cancer


title: WT Day14_3

description:
Chemically reprogrammed WT MEFs at Day14
connective tissue - MEFs

source_name: Reprogrammed WT MEFs at Day14

value: beta-actin wild type


title: KO Day4_1

description:
Chemically reprogrammed KO MEFs at Day4
connective tissue - MEFs

source_name: Reprogrammed KO MEFs at Day4

value: Day 4


title: KO Day4_2


title: post1_Blood_CD4_0002


title: post1_Bulk_0008 [3'SAGE-seq]

value: bulk biopsy

value: 1.0 mg/kg


title: HET Day14_2

value: BALB/c

value: 10.5 day old embryos

value: beta-actin heterozygote


title: WT Day14_2

value: chemically reprogrammed osteoblasts

value: Day 14


title: post1_Bulk_0010 [3'SAGE-seq]

value: male

value: liver metastasis of pancreatic cancer


title: WT Day14_1


title: pre_Bulk_0007 [3'SAGE-seq]


title: KO Day4_3

value: beta-actin knockout


title: WT Day4_1

description:
Chemically reprogrammed WT MEFs at Day4
connective tissue - MEFs

source_name: Reprogrammed WT MEFs at Day4


title: post1_Bulk_0007 [3'SAGE-seq]


title: WT Day4_3


title: pre_Bulk_0005 [3'SAGE-seq]

source_name: biopsy of stomach with no cancer

value: female

value: gastric

value: stomach with no cancer


title: pre_Bulk_0006 [3'SAGE-seq]

source_name: biopsy of skin metastasis of colorectal cancer

value: colorectal

value: skin metastasis of colorectal cancer


title: pre_Bulk_0004 [3'SAGE-seq]

source_name: biopsy of bronchus metastasis of colorectal cancer

value: 0.1 mg/kg


title: LLC cachectic 2

city: Charleston

first: Erin

last: Talbert

state: SC

address: 70 President Street

department: Pediatrics

institute: Medical University of South Carolina

description:
LLC mouse 2
DG-22

data_processing:
Illumina HiSeq4000 were used for sequencing
Sequence reads were mapped to GRCM38 V83 using tophat2v2.1.0 with default parameters
Sequences from 2 lanes were combined for each sample.
Raw counts were calculated using featureCounts v1.4.5
Genome_build: ensembl GRCm38 v83
Supplementary_files_format_and_content: Excel Worksheet file includes normalized voom counts values for each sample

source_name: tibalis anterior muscle

extract_protocol:
Total RNA was purified from snap-frozen muscle using Trizol reagent. 200 ng of rRNA-depleted RNA was used for the construction of the library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: tibalis anterior muscle


title: post1_Bulk_0004 [3'SAGE-seq]

value: bulk biopsy

value: bronchus metastasis of colorectal cancer


title: post1_Blood_CD4_0003

value: CD4+ CD8- T cells

value: esophageal

value: peripheral blood


title: WT Day4_2

value: BALB/c

value: 10.5 day old embryos

value: chemically reprogrammed osteoblasts

value: Day 4

value: beta-actin wild type


title: LLC control 1

description:
control 1 for LLC model
DG-19


title: C26 cachectic 2

description:
C26 mouse 2
DG-18


title: pre_Bulk_0003 [3'SAGE-seq]

source_name: biopsy of esophagus with no cancer

value: male

value: esophagus with no cancer


title: post1_Bulk_0003 [3'SAGE-seq]


title: LLC cachectic 1

description:
LLC mouse 1
DG-21


title: C26 cachectic 1

description:
C26 mouse 1
DG-17


title: post1_Bulk_0006 [3'SAGE-seq]

value: female

value: 1.0 mg/kg


title: post1_Bulk_0002 [3'SAGE-seq]

value: gastric

value: gastric cancer


title: Stromadip43

type: RNA

city: RENNES

first: vonick

last: sibut

address: avenue du Prof Leon BERNARD

country: France

description: Gene expression data from BM_MSC cells

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human HuGene-1_0-st arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: The data were analyzed with R package Limma v3.32.10 and GCRMA normalization.

label: biotin

source_name: BM_MSC cells

label_protocol: Biotinylated cRNA were amplified according to the IVT Express labeling protocol (Affymetrix, Santa Clara, CA)

growth_protocol: ASCs were obtained from lipoaspirate of abdominal fat layer, after digestion with collagenase, filtration, and centrifugation to obtain the stromal vascular fraction (SVF) (Bourin et al., 2011), SVF was then seeded onto closed cell culture chambers. Paired BM-MSCs were produced in parallel from unprocessed bone marrow seeded in the same culture dishes and in the same medium as those used for ASC. Medium was renewed twice weekly until cells reached confluence (end of passage 0 (P0)). Cells were then detached using trypsin, reseeded until near confluence (end of P1) and subsequently harvested and cryopreserved until use.

extract_protocol: RNA extraction was  performed using RNEasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions

tag: origin


title: C26 control 2

description:
control 2 for C26 model
DG-16

value: tibalis anterior muscle


title: Stromadip55

description: Gene expression data from ASC cells

source_name: ASC cells

value: ASC


title: KPC cachectic 2

description:
KPC mouse 2
DG-14

value: mixed


title: Stromadip42

description: Gene expression data from BM_MSC cells


title: Stromadip40

description: Gene expression data from BM_MSC cells


title: LLC control 2

description:
control 2 for LLC model
DG-20


title: human iduced pluripotent stem cell, biological replicate 2

city: Solna

first: Pierre

last: Sabatier

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from human induced plutipotent stem cell

hyb_protocol: Hybridization on Affymetrix Gene Chip Human Transcriptome Array 2.0 microarrays, array washing, staining, and scanning were performed according to the manufacturer protocol.

scan_protocol: Scans of the microarrays were converted into CEL files using the scanner software, and were then processed using the Transcriptome Analysis Console 3.0.

data_processing: Processed using the Transcriptome Analysis Console 3.0

source_name: human induced pluripotent stem cells reprogrammed from the human foreskin fibroblast cell line

label_protocol: Procedures for cDNA synthesis, target DNA fragmentation, and labelling were carried out according to the GeneChip WT PLUS Reagent Kit (Applied Biosystems) using 500 ng of total RNA as the starting material.

growth_protocol: HFF (ATCC® CRL-2429™) were grown in IMDM medium (Biowest) supplemented with 10% Gibco™ Fetal Bovine Serum, Qualified, US Origin, Standard (Sterile-Filtered) (Gibco). IPSCs were grown in Nutristem (Biowest) on Laminin-521 (BioLamina) coated dish. Both cell lines mentioned below were cultured at 37◦C and 5% CO2 in a humidified Forma Steri-cycle i160 CO2 incubator (Thermo Fischer Scientific).

extract_protocol: The RNA isolation had been performed using the miRNeasy mini kit (Qiagen) according to the manufacturer’s protocol with DNaseI (Qiagen) treatment.

treatment_protocol: Cells were washed twice in PBS and then scraped and pelleted. Cell lysis was performed using miRNeasy mini kit (Qiagen) according to manufacturer's instructions.

tag: cell line

value: human induced pluripotent stem cell


title: Stromadip41

description: Gene expression data from ASC cells


title: human iduced pluripotent stem cell, biological replicate 3


title: C26 control 1

description:
control 1 for C26 model
DG-15


title: KPC cachectic 1

description:
KPC mouse 1
DG-13


title: Genomic DNA from MDA-MB-453 cell line

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

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

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: breast cell line from ATCC

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Minfi R package standard protocol

label: Cy5 and Cy3

source_name: breast cell line

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: sample type

value: breast

tag: gender

value: Female


title: Genomic DNA from normal healthy human tissue NB10

description:
Genomic DNA from normal healthy human tissue
Normal breast tissue sample from a healthy individual

source_name: Normal breast


title: human iduced pluripotent stem cell, biological replicate 1


title: Stromadip38

description: Gene expression data from BM_MSC cells


title: Genomic DNA from normal healthy human tissue NB11


title: KPC control 2

description:
control 2 for KPC model
DG-12


title: Genomic DNA from MDA-MB-436 cell line

description: breast cell line from ATCC


title: pre_Bulk_0002 [3'SAGE-seq]

value: bulk biopsy

value: 0.1 mg/kg


title: KPC control 1

description:
control 1 for KPC model
DG-11


title: Genomic DNA from MCF7 cell line

description: breast cell line from ATCC


title: KPP cachectic 2

description:
KPP cachectic 2
DG-10


title: Genomic DNA from normal healthy human tissue NB7


title: Stromadip39

description: Gene expression data from ASC cells


title: Genomic DNA from normal healthy human tissue NB6


title: Genomic DNA from normal healthy human tissue NB4


title: Genomic DNA from normal healthy human tissue NB12


title: Genomic DNA from normal healthy human tissue NB5


title: Stromadip37

description: Gene expression data from BM_MSC cells


title: human foreskin fibroblast, biological replicate 2

description: Gene expression data from human foreskin fibroblast

source_name: human foreskin fibroblast

value: human foreskin fibroblast


title: human foreskin fibroblast, biological replicate 3


title: Methylation profile of OVCA429 shNon control, replicate 2

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing: The dat file was processed using R bioconductor  version 3.6, Chip Analysis Methylation pipeline for illumina HumanMethylation450 and EPIC package, v1.2.8

label: Cy3, Cy5

source_name: ovarian cancer cell line

label_protocol: Standard Illumina Protocol

growth_protocol: Cell lines were grown in media as detailed in sample table. OVCA429 control and shGRHL2 cells were grown in DMEM supplemented with 10% FBS and 2 μg/ml puromycin.

extract_protocol: Genomic DNA samples were purified using standard phenol-chloroform DNA extraction or AquaPure Genomic DNA Kit (Bio-rad).

tag: media

value: DMEM, 10% FBS


title: Stromadip36

description: Gene expression data from ASC cells


title: KPP cachectic 1

description:
KPP cachectic 1
DG-09


title: 72hr_hpi_b3

city: Fort Collins

first: Jeffrey

last: Wilusz

state: CO

address: 1682 Campus Delivery

institute: Colorado State University

data_processing:
FastQC v0.11.5 was utilized to assess the quality of sequence reads. Reads were trimmed of adapter sequences and filtered for low-complexity or low-quality reads using Trimmomatic v0.32 (Bolger et al., 2014). rRNA reads were filtered out using Bowtie2 v2.3.4.3 (Langmead and Salzberg, 2012) and a reference fasta file of mature 5S, 18S and 28S rRNA sequence obtained from NCBI RefSeq (mature_rRNA.fasta.gz). The slamdunk package (Herzog et al., 2017) was used to map reads to the hg19 genome, call single nucleotide polymorphisms (SNPs), and count relevant statistics for the 3’ UTRs of genes. Base transversion ratios for each sample were calculated using the alleyoop rates command. Mean base transversion ratios were calculated for 12 and 72 hpi and reported. All analysis using the slamdunk package was performed in accordance with published protocols (Herzog et al., 2017).
Genome_build: hg19
Supplementary_files_format_and_content: .tsv files: tab separated files with the overall conversions rates for individual samples. hg19_3UTR.bed.gz:  Gene annotation file of 3’ UTRs used to call SNPs and count relevant statistics.  mature_rRNA.fasta.gz: Fasta file containing the mature rRNA sequences used for rRNA filtering.

molecule: polyA RNA

growth_protocol: Human choriocarcinoma (JAR) cells were maintained in RPMI1640 (Corning) supplemented with 10% newborn calf serum (Peak Serum), 1% streptomycin/penicillin (Fisher Scientific-Hyclone), 0.5% L-glutamine (Fisher Scientific-Hyclone) and incubated at 37oC in the presence of 5% CO2.

extract_protocol:
Total RNA extractions were performed in accordance with recommended protocols (Invitrogen, #15596026).
Libraries were constructed from 500 ng of total RNA using the SMARTer™ PCR cDNA Synthesis Kit (Clontech, #634926) and Advantage 2 PCR kit (Clontech, #639207) followed by Tn5-mediated tagmentation (see Methods and Materials for an in-depth protocol).

treatment_protocol: JAR cells were infected with Zika virus (moi = 10). After 12 and 72 hours of infection, cellular RNAs were labeled with the uridine analog 4-thiouridine (4SU) at a concentration of 400mM.  Total RNA was collected 65 minutes after addition of 4SU in TRIzol and stored at -80°C.

value: JAR

value: choriocarcinoma cell

tag: tissue source

value: Placenta

tag: infection

value: Zika Virus

tag: treatment

value: 72 hours infection


title: human foreskin fibroblast, biological replicate 1


title: Genomic DNA from MDA-MB-231 cell line

description: breast cell line from ATCC


title: 72hr_hpi_b2

tag: cell type


title: Genomic DNA from normal healthy human tissue NB1


title: KPP control 2

description:
control 2 for KPP model
DG-08


title: Genomic DNA from normal healthy human tissue NB8


title: 72hr_hpi_b1


title: KPP control 1

description:
control 1 for KPP model
DG-07


title: KO_4

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

institute: cea

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped to reference genome mm9 using Bowtie v1.0.0 with default parameters except for “-p 3 -m 1 -X2000”.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Normalized BigWig files were generated using HomermakeUC- SCfile v4.9.1 with the following parameter ’-norm 4e7 -style dnase’.

source_name: Bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells were cultured in IMDM supplemented with 10% FCS (Invitrogen) 10μM thioglycerol (Sigma) and 25ng/ml mouse CSF1 (Milteny Biotech).

extract_protocol: Nuclei were isolated from 50.000 BMDM with lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Igepal) and resuspended in Tn5 transposase mixture (Nextera Tn5 Transposase, 1xTagment DNA buffer (Illumina), and 0.2mg/ml digitonin (Promega). The tagmentation reaction was carried out for 30 minutes at 37°C followed by DNA purification using the MinElute Reaction Cleanup kit (Qiagen). Tagmented DNA was amplified with NEBNext High-Fidelity PCR Master Mix (NEB) and sequencing primers Ad1_noMX and Ad2.1-4 indexing primers. Libraries were cleaned and size-selected using Spriselect beads (Beckman).

tag: genotype/variation

value: Bone marrow-derived macrophages


title: Methylation profile of OVCA429 shGRHL2, replicate 2

description: 429sh12_2 (429shGRHL2_2)


title: Stromadip20

description: Gene expression data from ASC cells


title: Genomic DNA from normal healthy human tissue NB9


title: Genomic DNA from normal healthy human tissue NB2


title: Methylation profile of OVCA429 shNon control, replicate 1


title: 12hr_hpi_b2

value: 12 hours infection


title: 12hr_hpi_b1


title: Genomic DNA from normal healthy human tissue NB3


title: KO_3


title: TD rep2

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

data_processing:
Quality of sequenced reads was checked using FastQC (v0.11.8). Adapter sequences and  low-quality sequences in reads were eliminated using BBMap (v38.50b).
Trimmed fastq files were aligned to GRCh37 genome using STAR aligner(v2.7.1a).
Read counts per gene were calculated using HTseq (v0.11.2) with Gencode v19 annotation GTF.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values per transcript for each sample.

source_name: Lung cancer

growth_protocol: Parental A549 and TD cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% FBS, gentamycin (50ug/ml), at 37 °C in humidified atmosphere of 5% CO2 in air. TD cell lines were maintained with treatment of TGFβ at 2 ng/ml concentration in every 3days.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
For library construction, we used the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Briefly, the steps of strand-specific protocol are: first strand cDNA synthesis; second strand synthesized using dUTPs instead of dTTPs; end repair, A-tailing, and adaptor ligation; PCR amplification. Then, each library was diluted to 8 pM for 76 cycles of paired-read sequencing (2 X 75bp) on the Illumina NextSeq 500 per the manufacturer’s recommended protocol.

treatment_protocol: TD cell lines were treated TGFβ (2 ng/ml) in every 3 days.

value: Lung

value: Non-small cell lung cancer cell line

tag: morphology

value: TGF-β induced mesenchymal like

value: A549 cells


title: Stromadip18

description: Gene expression data from ASC cells

value: ASC


title: WT_2

value: Wild type


title: Stromadip35

description: Gene expression data from ASC cells


title: WT_1


title: Stromadip17

description: Gene expression data from ASC cells


title: Methylation profile of UWB1.289, replicate 2


title: Stromadip15

description: Gene expression data from BM_MSC cells


title: A549 rep2

value: Epithelial


title: Stromadip16

description: Gene expression data from BM_MSC cells


title: A549 rep1


title: Tfhs hashtag library

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
AW18002
PolyA RNA
Single-cell RNA-seq

data_processing:
FASTQ files corresponding to AW18001 and AW18002 were generated and demultiplexed using Illumina bcl2fastq 2.18.0.12. Similarly, FASTQ files for AW19003 and AW19004 were generated and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For samples AW18001 and AW18002, R1 contains a 16bp cell barcode + 10bp UMI barcode. For samples AW19003 and AW19004, R1 contains a 16bp cell barcode + 12bp UMI barcode. For all samples, R2 contains the biological reads.
The barcodes in AW18001/AW18002 correspond to the same cells, similarly for AW19003/AW19004. Note that gene expression barcodes (AW18001 and AW19003) have a "-1" appended to each barcode that is not present in the hashtag barcodes (AW18002 and AW19003).
A filtered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mm10 reference build (version 2.1.0, GRCm38.84) using 10X Genomics CellRanger count version 2.2.0 for AW18001 and version 3.0.2 for AW19003.
A digital counts matrix was generated for each hashtag library using CITE-Seq-Count (https://github.com/Hoohm/CITE-seq-Count), version 1.3.3 for AW18002 and version 1.4.1 for AW19004. This produces a matrix of counts with hashtag labels for rows (available via BioLegend https://www.biolegend.com/totalseq) and cell barcodes for columns.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market CSR format. Rows correspond to genes in the order provided in genes.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.
Supplementary_files_format_and_content: AW18001_barcodes.tsv: Column labels (cell barcodes) of gene expression counts matrix.
Supplementary_files_format_and_content: AW18001_genes.tsv: Row labels (genes) of gene expression counts matrix.
Supplementary_files_format_and_content: AW18001_matrix.mtx: Digital counts matrix for gene expression (matrix market format).
Supplementary_files_format_and_content: AW18002_hto_counts.csv: Digital counts matrix for HTOs (including row and column labels).
Supplementary_files_format_and_content: AW19003_barcodes.tsv.gz: Column labels (cell barcodes) of gene expression counts matrix.
Supplementary_files_format_and_content: AW19003_features.tsv.gz: Row labels (genes) of gene expression counts matrix.
Supplementary_files_format_and_content: AW19003_matrix.mtx.gz: Digital counts matrix for gene expression (matrix market format).
Supplementary_files_format_and_content: AW19004_hto_barcodes.tsv.gz: Column labels (cell barcodes) of HTO counts matrix.
Supplementary_files_format_and_content: AW19004_hto_features.tsv.gz: Row labels (genes) of HTO counts matrix.
Supplementary_files_format_and_content: AW19004_hto_matrix.mtx.gz: Digital counts matrix for HTOs (matrix market format).

source_name: Sorted Tfh cells (TCRβ+ CD4+ CD44+ PD-1+ CXCR5+)

extract_protocol:
Sorted cells from each mouse sample were labeled with cell hashing antibodies (BioLegend TotalSeq anti-mouse Hashtag #3-6). 12,000 cells (4000 cells from each hashtagged mouse) were loaded into one lane of a 10X Chromium microfluidic chip. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform, version 2 chemistry for the Tfh sort and version 3 chemistry for the IL-4 4Get+ sort. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and pooled using a ratio of 95% gene expression library and 5% hashtag library before sequencing, one on a single lane of an Illumina HiSeq4000 and the other on 16.67% of lane of an Illumina NovaSeq 6000 S2 flow cell, both targeting 6,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.
Chromium System (10X Genomics) v2 or v3 chemistry.

treatment_protocol: Mice were immunized with Alternaria alternata extract (10μg) + NP-OVA (25μg) intranasally and day 7 mediastinal lymph node Tfh cells or IL-4+ activated CD4 T cells were sorted and stimulated with PMA and Ionomycin for 30 min and then subjected to single-cell RNA sequencing using the 10X platform and the reads were analyzed.

tag: strain/background

value: Immunization with lternaria alternata + NP-OVA

value: Mediastinal Lymph Node

value: Tfh cells


title: Tfhs gene expression library

description:
AW18001
PolyA RNA
Single-cell RNA-seq


title: Stromadip14

description: Gene expression data from ASC cells


title: Stromadip13

description: Gene expression data from BM_MSC cells


title: TD rep1


title: POLII_KO

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: bone marrow derived macrophages (BMDM)

extract_protocol: Cells were fixed with 1% formaldehyde for 10 min at 37 °C, lysed in SDS lysis buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS, protease inhibitor cocktail (Roche)) and sonicated. Supernatant was diluted 10 times in IP dilution buffer (16.7 mM Tris pH8, 167 mM NaCl, 1.2 mM EDTA, 1.1% TritonX-100, 0.01% SDS, protease inhibitor cocktail (Roche)) and immunoprecipitations were carried out overnight with specific antibodies. Immunoprecipitated chromatin was collected using Protein A Agarose/Salmon Sperm DNA beads (Millipore) and, after washing and elution, reverse cross-linking was carried out with 0.2 M NaCl at 65 °C overnight. The chromatin was then digested by 20 mg of Proteinase K (Invitrogen) for 1 h at 45 °C and isolated by phenol–chloroform extraction.

value: bone marrow derived macrophages (BMDM)

tag: chip antibody

value: anti-POLII (Santa Cruz, sc-9001X)


title: Methylation profile of UWB1.289, replicate 1


title: Stromadip19

description: Gene expression data from BM_MSC cells


title: clindamycin-hi rep5

city: Cambridge

first: Jemila

last: Kester

state: MA

address: 32 Vassar Street, Bldg 16, Rm 436

institute: MIT

data_processing:
Post-sequencing, quality-control on each of the libraries was performed to assess coverage depth, enrichment for messenger RNA (exon/intron and exon/intergenic density ratios), fraction of rRNA reads and number of detected genes using bespoke scripts.
The sequencing reads were mapped to hg38 reference using star/2.5.3a.
Gene expression counts were further estimated using ESAT v137.
Genome_build: GRCH38
Supplementary_files_format_and_content: normalized abundance measurements of each treatment condition to its relative control using DEseq2, text file

source_name: colon tissue

growth_protocol: Caco2 (clone: C2BBe1, passage 48–58, ATCC, Manassas, VA) and HT29-MTX (passage 20–30, Sigma–Aldrich, St. Louis, MO) were maintained in DMEM (Gibco, Gaithersburg, MD) supplemented with 10% heat-inactivated FBS (Atlanta Biologicals, Flowery Branch, GA), 1% GlutaMax (Gibco), 1% Non-Essential Amino Acids (NEAA, Gibco), and 1% Penicillin/Streptomycin (P/S). Both cell lines were passaged twice post thawing before their use for transwell seeding. Briefly, the apical side of transwell membrane were coated with 50mg/mL Collagen Type I (Corning Inc., Corning, NY) overnight at 4[Symbol]C. Caco2 at 80–90% confluence and HT29-MTX at 90-95% confluence were harvested using 0.25% Trypsin-EDTA and mechanically broken up into single cells. 9:1 ratio of C2BBe1 to HT29-MTX was seeded onto 12-well 0.4mm pore polyester transwell inserts (Corning, Tewksbury, MA) at a density of 105 cells/cm2. Seeding media contained 10% heat inactivated FBS, 1x GlutaMax and 1% P/S in Advanced DMEM (Gibco). Seven days post seeding, the media was switched to a serum-free gut medium by replacing FBS with Insulin-Transferrin-Sodium Selenite (ITS, Roche, Indianapolis, IN) and the epithelial cultures were matured for another 2 weeks. P/S was left out of media during experimental procedures.

extract_protocol:
RNA was prepared using PureLink RNA Mini Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. DNA removal was done on column with PureLink DNase (Invitrogen). cDNA synthesis using High-Capacity RNA-to-cDNA Kit (Applied Biosystems, Foster City, CA) according to product insert. qPCR was completed using TaqMan® assays with Fast Advanced Master Mix (Applied Biosystems) as per manufacturer’s guidelines.
RNA samples were quantified and quality assessed using an Advanced Analytical Fragment Analyzer. 20ng of totalRNA was used for library preparation with ERCC Spike-in control Mix A (Ambion 10-6 final dilution). All steps were performed on a Tecan EVO150. 3’DGE-custom primers 3V6NEXT-bmc#1-24 are added to a final concentration of 1.2uM. (5'-/5Biosg/ACACTCTTTCCCTACACGACGCTCTTCCGATCT[BC6]N10T30VN-3' where 5Biosg = 5’ biotin, [BC6] = 6bp barcode specific to each sample/well, N10 = Unique Molecular Identifiers, Integrated DNA technologies). After addition of the oligonucleotides, samples were denatured at 72C for 2 minutes followed by addition of SMARTScribe RT per manufacturer’s recommendations with Template-Switching oligo5V6NEXT (12uM, [5V6NEXT : 5’-iCiGiCACACTCTTTCCCTACACGACGCrGrGrG-3’ where iC: iso-dC, iG: iso-dG, rG: RNA G ]) and incubation at 42C for 90’ followed by inactivation at 72C for 10’. Following the template switching reaction, cDNA from 24 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 90 ul of water followed by digestion with Exonuclease I at 37C for 45 minutes, inactivation at 80C for 20 minutes. Single stranded cDNA was then cleaned using RNA Ampure beads at 1.0X and eluted in 50ul of water. Second strand synthesis and PCR amplification was done using the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer (10 pmol, Integrated DNA Technologies 5’-/5Biosg/ACACTCTTTCCCTACACGACGC-3’ ). 12 cycles of PCR was performed followed by clean up using regular SPRI beads at 1.0X, and was eluted with 20ul of EB. Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries are then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer (25μM, Integrated DNA Technologies, (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T*-3’ where * = phosphorothioate bonds. ) in place of the normal N500 primer. Final libraries were cleaned using SPRI beads at 1X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500.

treatment_protocol: 24hr basal application of antibiotics prior to lysis. Antibiotics used: Clindamycin, ciprofloxacin, tigecycline. Clindamycin and ciprofloxacin compared to untreated, while tigecycline compared to DMSO. 6 replicates per condition. Hi: Clindamycin 300ug/ml, Ciprofloxacin 200ug/ml, tigecycline 20ug/ml. Low: Clindamycin 3ug/ml, ciprofloxacin 5ug/ml, tigecycline 1ug/ml

tag: cell lines

value: 9:1 ratio of Caco2 :HT29 MTX cells

value: colon


title: SPT16_KO

value: anti-SPT16 (Santa Cruz, sc-28734X)


title: clindamycin-hi rep4


title: POLII_WT

value: wild type


title: Stromadip12

description: Gene expression data from ASC cells


title: Methylation profile of OVCA429 shGRHL2, replicate 1

description: 429sh12_1 (429shGRHL2_1)

value: DMEM, 10% FBS


title: Stromadip11

description: Gene expression data from BM_MSC cells


title: clindamycin-hi rep3


title: Methylation profile of SKOV3, replicate 2


title: Methylation profile of SKOV3, replicate 1


title: SPT16_WT


title: Methylation profile of TOV112D, replicate 1


title: clindamycin-hi rep2


title: Stromadip7

description: Gene expression data from BM_MSC cells


title: Methylation profile of TYKNu, replicate 2

value: TYKNu


title: Methylation profile of PEO1, replicate 2


title: H3K36me3_KO

value: anti-H3K36me3 (Abcam, ab9050)


title: clindamycin-hi rep1


title: Stromadip6

description: Gene expression data from ASC cells


title: Methylation profile of PEO1, replicate 1


title: ciprofloxacin-hi rep6


title: Methylation profile of TOV112D, replicate 2


title: Methylation profile of TYKNu, replicate 1


title: Stromadip5

description: Gene expression data from BM_MSC cells


title: ciprofloxacin-hi rep5


title: Stromadip8

description: Gene expression data from ASC cells


title: Methylation profile of OVCAR5, replicate 1

value: RPMI 1640, 10% FBS, 10 µg/ml insulin


title: H3K36me3_WT


title: Methylation profile of OVCAR3, replicate 2

value: RPMI 1640, 20% FBS, 10 µg/ml insulin


title: ciprofloxacin-hi rep4


title: Methylation profile of OVCAR5, replicate 2


title: INPUT_KO


title: Methylation profile of OVCAR3, replicate 1


title: ciprofloxacin-hi rep2


title: ciprofloxacin-hi rep3


title: RNA-seq-LA-24h-rep4

city: Chicago

first: Di

last: Zhang

state: IL

address: 929 E 57th GCIS, W403R

institute: the University of Chicago

description:
Mi-LA-24h_4
processed data file: RNA-seq_DE.txt

data_processing:
Base called by Real-Time Analysis (RTA).
ChIP-seq: Reads were mapped to reference genome of Illumina iGenomes UCSC mm10 using Bowtie version 2.2.6, and only uniquely mapped reads were retained. RNA-seq reads were mapped to reference genome of Illumina iGenomes UCSC mm10 using HISAT2 version 2.1.0.
ChIP-seq: SAMtools version 0.1.19 was used to convert files to bam format, sort, and remove PCR duplicates.
ChIP-seq: Peaks were called using MACS version 2.2.1 under q value = 0.01. RNA-seq: Differential expression analysis was implemented using edgeR version 3.16.540, after retaining only the genes of which counts per million (cpm) is larger than one in all four replicates.
ChIP-seq: Uniquely mapped reads of each gene were counted by featureCounts version 1.5.0-p1, and normalized by corresponding uniquely mapped spiked-in ChIP read counts. RNA-seq: Normalizing the library sizes across samples using the TMM method of edgeR package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_peaks.broadPeak: Tab-delimited text files include peaks.
Supplementary_files_format_and_content: ChIP-seq_normalization.txt: Tab-delimited text file.
Supplementary_files_format_and_content: RNA-seq_DE.txt: Tab-delimited text file.

source_name: Primary mouse bone marrow derived macrophages (BMDM)

extract_protocol:
Chromatin was digested with MNase, enriched with indicated antibodies, and purified with QIAquick PCR purification kit (Qiagen, #28106). Total RNAs were prepared by following protocols from RNeasy Plus Mini Kit (Qiagen, 74134).
ChIP-seq libraries were constructed with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. The libraries were then amplified and assessed for fragment size using TapeStation (Agilent) and quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). RNA-seq libraries were constructed with Illumina TruSeq Stranded mRNA Library Prep Kit Set A (Illumina, RS- 122-2101). The libraries’ size was selected by using the Agencourt AMPure XP beads (Beckman Coulter, A63882), with average size 400bps.

treatment_protocol: Primary mouse bone marrow-derived macrophages (BMDM) were either unstimulated or stimulated with LPS (5ng/ml) and IFNg (12ng/ml) for indicated period of time. LA samples were treated with LA 4h after LPS/IFNg treatment.

value: LPS/IFNg, lactic acid (LA)

tag: time after lps/ifng treatment

tag: spike-in information


title: ciprofloxacin-hi rep1

tag: tissue


title: Stromadip4

description: Gene expression data from ASC cells

tag: origin

value: ASC


title: H3K79me2_WT

tag: genotype

value: anti-H3K79me2 (Abcam, ab3594)


title: Stromadip1

description: Gene expression data from BM_MSC cells


title: Stromadip3

description: Gene expression data from BM_MSC cells


title: RNA-seq-LA-24h-rep3

description:
Mi-LA-24h_3
processed data file: RNA-seq_DE.txt

value: Primary mouse bone marrow derived macrophages (BMDM)


title: untreated rep6


title: Stromadip2

description: Gene expression data from ASC cells


title: H3K79me2_KO


title: clindamycin-hi rep6


title: RNA-seq-LA-24h-rep2

description:
Mi-LA-24h_2
processed data file: RNA-seq_DE.txt


title: untreated rep5


title: Gene expression of UWB1.289 rep2

description: Gene expression of UWB1.289, replicate 2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fragmented and biotin labeled cDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays for 18 hours at 45C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0002 fluidics protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalization using R package Affy 1.42.3
HuGene-1_0-st.pgf
HuGene-1_0-st.mps

source_name: Ovarian cancer cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the NuGEN Applause WT-Amp ST System and Encore Biotin Module.

growth_protocol: Cell lines were grown in media as detailed in samples description.

extract_protocol: Total RNA was extracted by Qiagen miRNEasy Mini kit according to the manufacturer's instructions.

tag: cell line

tag: media condition


title: RNA-seq-LA-24h-rep1

description:
Mi-LA-24h_1
processed data file: RNA-seq_DE.txt


title: RNA-seq-LA-16h-rep4

description:
Mi-LA-16h_4
processed data file: RNA-seq_DE.txt


title: untreated rep4


title: Gene expression of UWB1.289 rep1

description: Gene expression of UWB1.289, replicate 1


title: untreated rep3


title: Methylation profile of OVCAR2, replicate 1

tag: media


title: Methylation profile of OVCAR2, replicate 2


title: RNA-seq-LA-16h-rep3

description:
Mi-LA-16h_3
processed data file: RNA-seq_DE.txt


title: Gene expression of TYKNU rep2

description: Gene expression of TYKNU, replicate 2

value: TYKNU


title: Methylation profile of OVCA433, replicate 2


title: RNA-seq-LA-16h-rep2

description:
Mi-LA-16h_2
processed data file: RNA-seq_DE.txt


title: Methylation profile of OVCA433, replicate 1


title: untreated rep1


title: untreated rep2


title: Gene expression of TYKNU rep1

description: Gene expression of TYKNU, replicate 1


title: RNA-seq-LA-16h-rep1

description:
Mi-LA-16h_1
processed data file: RNA-seq_DE.txt


title: DMSO-lo rep3


title: Gene expression of TOV112D rep2

description: Gene expression of TOV112D, replicate 2


title: Methylation profile of OVCA432, replicate 2


title: Gene expression of SKOV3 rep2

description: Gene expression of SKOV3, replicate 2


title: RNA-seq-LA-8h-rep4

description:
Mi-LA-8h_4
processed data file: RNA-seq_DE.txt


title: Gene expression of TOV112D rep1

description: Gene expression of TOV112D, replicate 1


title: INPUT_WT


title: Gene expression of SKOV3 rep1

description: Gene expression of SKOV3, replicate 1


title: Methylation profile of OVCA429, replicate 2


title: Methylation profile of OVCA432, replicate 1


title: DMSO-lo rep2


title: RNA-seq-LA-8h-rep2

description:
Mi-LA-8h_2
processed data file: RNA-seq_DE.txt


title: Gene expression of PEO1 rep1

description: Gene expression of PEO1, replicate 1


title: RNA-seq-LA-8h-rep3

description:
Mi-LA-8h_3
processed data file: RNA-seq_DE.txt


title: DMSO-lo rep1


title: tigecycline-lo rep6


title: Methylation profile of OVCA420, replicate 1


title: Methylation profile of OVCA420, replicate 2


title: Methylation profile of OVCA429, replicate 1


title: RNA-seq-LA-8h-rep1

description:
Mi-LA-8h_1
processed data file: RNA-seq_DE.txt


title: RNA-seq-24h-rep4

description:
24h_4
processed data file: RNA-seq_DE.txt

value: LPS/IFNg


title: Gene expression of OVCAR5 rep2

description: Gene expression of OVCAR5, replicate 2


title: RNA-seq-24h-rep3

description:
24h_3
processed data file: RNA-seq_DE.txt


title: Methylation profile of OV56, replicate 2

value: DMEM/F12 (1:1), 5% FBS, 0.5 µg/ml hyrocortisone, 10 µg/ml insulin


title: Gene expression of OVCAR3 rep2

description: Gene expression of OVCAR3, replicate 2


title: Methylation profile of OV7, replicate 1


title: Gene expression of OVCAR3 rep1

description: Gene expression of OVCAR3, replicate 1


title: RNA-seq-24h-rep2

description:
24h_2
processed data file: RNA-seq_DE.txt


title: tigecycline-lo rep3


title: RNA-seq-24h-rep1

description:
24h_1
processed data file: RNA-seq_DE.txt


title: tigecycline-lo rep2


title: Methylation profile of OV17R, replicate 2

value: DMEM/F12 (1:1), 5% FBS, 0.4 µg/ml hyrocortisone, 10 µg/ml insulin


title: tigecycline-lo rep4

value: 9:1 ratio of Caco2 :HT29 MTX cells


title: Gene expression of OVCAR2 rep2

description: Gene expression of OVCAR2, replicate 2


title: Gene expression of PEO1 rep2

description: Gene expression of PEO1, replicate 2


title: RNA-seq-16h-rep4

description:
16h_4
processed data file: RNA-seq_DE.txt


title: Methylation profile of OV7, replicate 2


title: Methylation profile of OV17R, replicate 1


title: tigecycline-lo rep5

value: colon


title: Methylation profile of OV56, replicate 1


title: Gene expression of OVCAR2 rep1

description: Gene expression of OVCAR2, replicate 1


title: Gene expression of OVCA433 rep2

description: Gene expression of OVCA433, replicate 2


title: Gene expression of OVCA433 rep1

description: Gene expression of OVCA433, replicate 1


title: Methylation profile of OAW42, replicate 2

value: DMEM, 10% FBS, 0.7 µg/ml insulin


title: p63 OE_overexpression

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

description:
p63_OE.txt.gz
p63_OE

data_processing:
For ChIP-seq, peakcalls performed with cisGenome
ChIP-seq reads were aligned to the hg19 genome allowing 1 mismatch.
peaks were called using cisGenome with the following setting:  Enrichment Fold (3), P value (10^-5)).
The expression levels were calculated using TopHat and Cufflinks followed by the annotation references of Refseq and Ensemble transcript databases with the genome releases: Homo sapiens, hg19. The differentially analyses were determined by DEseq2 with the corresponding cutoff (P value <0.001, |log2(fold change)).
Genome_build: hg19

source_name: Cervical cancer cell lines

growth_protocol: SiHa and ME-180 cells (ATCC, Manassas, VA, USA) were maintained in DMEM (Hyclone, Logan, UT, USA) or McCoy's 5A Medium (Gibco) with 10% (v/v) fetal bovine serum (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) respectively, containing 100 units/ml penicillin and 100 mg/ml streptomycin (Hyclone).

extract_protocol: ChIP DNAs were isolated with antibody from whole cell lystaes. Total RNA was isolated from cells or tissues by TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.

value: SiHa

value: overexpression

tag: passages


title: RNA-seq-16h-rep3

description:
16h_3
processed data file: RNA-seq_DE.txt


title: RNA-seq-16h-rep2

description:
16h_2
processed data file: RNA-seq_DE.txt


title: RNA-seq-16h-rep1

description:
16h_1
processed data file: RNA-seq_DE.txt


title: Methylation profile of OAW28, replicate 2


title: p63 KD_knockdown

description:
p63_KD.txt.gz
shp63

value: knockdown


title: tigecycline-lo rep1


title: Methylation profile of OAW42, replicate 1


title: Methylation profile of OAW28, replicate 1


title: p63 KD_control

description:
p63_KD.txt.gz
plko

value: control


title: p63_ChIPSeq

tag: antibody


title: RNA-seq-8h-rep3

description:
8h_3
processed data file: RNA-seq_DE.txt

tag: treatment


title: p63_input

value: none (input)


title: RNA-seq-8h-rep4

description:
8h_4
processed data file: RNA-seq_DE.txt

tag: cell type


title: RNA-seq-8h-rep2

description:
8h_2
processed data file: RNA-seq_DE.txt


title: Gene expression of OVCA432 rep1

description: Gene expression of OVCA432, replicate 1

value: DMEM, 10% FBS


title: p63 OE_vector

description:
p63_OE.txt.gz
vector

tag: genotype/variation

value: vector


title: Methylation profile of JHOS4, replicate 2


title: Gene expression of OVCA429 rep2

description: Gene expression of OVCA429, replicate 2


title: Methylation profile of JHOS3, replicate 2


title: Gene expression of OVCA420 rep2

description: Gene expression of OVCA420, replicate 2


title: Methylation profile of JHOS3, replicate 1


title: UMC901 TP3

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Basecalling with NextSeq Control/RTA v2 and FastQ conversion with Bcl2fastq v2.20.0.422
Adapter clipping and trimming with cutadapt 2.1.
Mapping to RefSeq GRCh38.p12 Human genome with STAR version 2.6.1a_08-27 and raw read counting with featureCounts v1.6.3 using the RefSeq annotation.
Differential Expression analysis with DESeq2_1.22.2
Genome_build: human NCBI genome build 38
Supplementary_files_format_and_content: CSV: Raw read table

source_name: Myeloma cell line

growth_protocol: AMO1 WT and UMC901 cells were seeded at an initial density of 100000 cells/ml.

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen, Hilden, Germany) following manufacturer’s instructions and eluted in 30µl high purity H2O.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA kit (Illumina) with 500 ng total RNA as input for mRNA capture with oligo-dT beads.

treatment_protocol: On day 3 cells were counted and a cell pellet was generated containing 2 million cells for each sample. This process was repeated 3 times to obtain a sufficient number of replicates. Cell pellets were immediately stored at -80°C.

tag: condition

value: p53 mutant

value: TP53 del/mut

tag: gender

value: female

value: Myeloma cell line

value: UMC901 (derived from AMO1)


title: Gene expression of OVCA429 rep1

description: Gene expression of OVCA429, replicate 1


title: UMC901 TP2


title: RNA-seq-4h-rep4

description:
4h_4
processed data file: RNA-seq_DE.txt

tag: strain/background

value: Primary mouse bone marrow derived macrophages (BMDM)

value: LPS/IFNg


title: Methylation profile of JHOS4, replicate 1


title: RNA-seq-8h-rep1

description:
8h_1
processed data file: RNA-seq_DE.txt


title: UMC901 TP1


title: Gene expression of OV7 rep2

description: Gene expression of OV7, replicate 2

value: DMEM/F12 (1:1), 5% FBS, 0.5 µg/ml hyrocortisone, 10 µg/ml insulin


title: RNA-seq-4h-rep3

description:
4h_3
processed data file: RNA-seq_DE.txt


title: Methylation profile of JHOS2, replicate 2


title: RNA-seq-4h-rep2

description:
4h_2
processed data file: RNA-seq_DE.txt


title: AMO1 TP2

value: TP53 wt/wt


title: Gene expression of OVCA420 rep1

description: Gene expression of OVCA420, replicate 1


title: RNA-seq-4h-rep1

description:
4h_1
processed data file: RNA-seq_DE.txt


title: AMO1 TP3


title: Gene expression of OV7 rep1

description: Gene expression of OV7, replicate 1


title: RNA-seq-0h-rep4

description:
0h_4
processed data file: RNA-seq_DE.txt


title: AMO1 TP1


title: Gene expression of OVCAR5 rep1

description: Gene expression of OVCAR5, replicate 1

value: RPMI 1640, 10% FBS, 10 µg/ml insulin


title: Gene expression of OV56 rep1

description: Gene expression of OV56, replicate 1


title: Gene expression of OVCA432 rep2

description: Gene expression of OVCA432, replicate 2


title: ICH13359_Lin+MNC

city: Oxford

first: Sorcha

last: O'Byrne

state: Oxford

address: MRC MHU and WIMM, John Radcliffe Hospital

department: Department of Paediatrics

country: United Kingdom

institute: University of Oxford

data_processing:
Mapping and filtering according to Hay D, Hughes JR, Babbs C, et al. Genetic dissection of the alpha-globin super-enhancer in vivo. Nat Genet. 2016;48(8):895-903.
Normalised by scaling to 1x10^6 read counts
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files of normalised and filtered (for mitochondrial reads and blacklisted regions) samples.

source_name: Fetal bone marrow

extract_protocol:
The protocol for ATAC-Sequencing was adapted for small cell number from Corces et al26. 2000 PreProB and ProB-progenitors (n=3); and 5000 Lin+ mononuclear cells were sorted directly into 25uL of transposase mix (Tn5 enzyme, 2X TD buffer and 0.01% digitonin, Promega) at 4°C. Immediately following sorting, samples were incubated at 37°C for 30 minutes at 300 rpm agitation. Transposed DNA was immediately purified using a Qiagen MinElute kit and eluted in 10uL pre-warmed EB.
Transposed fragments were amplified by PCR as previously described27. Libraries were quantified by qPCR (NEBNext Library Quant for Illumina kit) before sequencing using a 75-cycle paired-end kit on the NextSeq Illumina platform.

tag: gestational age

value: 14 weeks

value: fetal bone marrow

tag: population

value: Lin2+ Mononuclear Cells


title: Gene expression of OV56 rep2

description: Gene expression of OV56, replicate 2


title: Methylation profile of JHOS2, replicate 1


title: Methylation profile of HEYC2, replicate 2


title: ICH13423_ProB

value: 17 weeks

value: ProB-progenitors


title: Gene expression of OV17R rep2

description: Gene expression of OV17R, replicate 2

value: DMEM/F12 (1:1), 5% FBS, 0.4 µg/ml hyrocortisone, 10 µg/ml insulin


title: RNA-seq-0h-rep3

description:
0h_3
processed data file: RNA-seq_DE.txt

tag: time after lps/ifng treatment

tag: spike-in information


title: Gene expression of OV17R rep1

description: Gene expression of OV17R, replicate 1


title: Methylation profile of HEYA8, replicate 1


title: Methylation profile of HEYC2, replicate 1


title: ICH13475_ProB

value: 19 weeks

tag: tissue


title: Gene expression of OAW42 rep2

description: Gene expression of OAW42, replicate 2

value: DMEM, 10% FBS, 0.7 µg/ml insulin


title: RNA-seq-0h-rep1

description:
0h_1
processed data file: RNA-seq_DE.txt


title: Methylation profile of HEY, replicate 2

value: HEY


title: ICH13195_ProB

value: 22 weeks


title: ChIP-seq-M1-H3K18ac

description:
M1 macrophages
processed data file: ChIP-seq_normalization.txt:

tag: chip antibody

value: spike-in chromatin (Active motif, Catalog No. 53083), spike-in antibody (Active motif, Catalog No. 61686)


title: ICH13423_PreProB

value: PreProB-progenitors


title: RNA-seq-0h-rep2

description:
0h_2
processed data file: RNA-seq_DE.txt

value: Primary mouse bone marrow derived macrophages (BMDM)


title: Gene expression of OAW42 rep1

description: Gene expression of OAW42, replicate 1

tag: cell line


title: ChIP-seq-M1-H3K18la

description:
M1 macrophages
The anti-H3K18la antibody was generated by PTM biolabs. The process for generating antibodies were described similarly in Cell, 2011. 146: p. 1016-1028. Mol Cell, 2015. 58(2): p. 203-15. Nat Chem Biol, 2014. 10(5): p. 365-70. except for using different immunogens.
processed data file: ChIP-seq_normalization.txt:

value: LPS/IFNg

value: H3K18la (PTM biolabs) (please see description field)


title: ICH13475_PreProB


title: Gene expression of OAW28 rep2

description: Gene expression of OAW28, replicate 2

tag: media condition


title: Gene expression of OAW28 rep1

description: Gene expression of OAW28, replicate 1


title: Methylation profile of HEYA8, replicate 2

tag: media


title: ChIP-seq-M0-H3K18ac

description:
M0 macrophages
processed data file: ChIP-seq_normalization.txt:


title: ChIP-seq-M1-Input


title: OVCA429 with shGRHL2 rep4

description:
OVCA429sh12_L004
GRHL2 knockdown

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg19 using STAR v2.4.2a with default parameters settings
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were computed using RSEM v1.2.25 and Gencode v19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

growth_protocol: Cells were grown in 6cm dishes in DMEM supplemented with 10% FBS and 2 μg/ml puromycin.

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries, using Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201).
Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries according to manufacturer's protocol.

tag: shconstruct

tag: genotype

value: GRHL2 knockdown


title: Gene expression of JHSO4 rep2

description: Gene expression of JHSO4, replicate 1


title: ChIP-seq-M0-H3K18la

description:
M0 macrophages
The anti-H3K18la antibody was generated by PTM biolabs. The process for generating antibodies were described similarly in Cell, 2011. 146: p. 1016-1028. Mol Cell, 2015. 58(2): p. 203-15. Nat Chem Biol, 2014. 10(5): p. 365-70. except for using different immunogens.
processed data file: ChIP-seq_normalization.txt:

tag: treatment


title: ICH13195_PreProB


title: OVCA429 with shGRHL2 rep3

description:
OVCA429sh12_L003
GRHL2 knockdown


title: Methylation profile of HEY, replicate 1


title: ChIP-seq-M0-Input

tag: cell type


title: Gene expression of JHOS4 rep1

description: Gene expression of JHOS4, replicate 2


title: Methylation profile of FUOV1, replicate 2


title: OVCA429 with shGRHL2 rep2

description:
OVCA429sh12_L002
GRHL2 knockdown


title: Gene expression of JHOS3 rep1

description: Gene expression of JHOS3, replicate 1


title: Methylation profile of DOV13, replicate 2

value: DMEM, 10% FBS


title: Methylation profile of EFO21, replicate 1

value: RPMI 1640, 20% FBS, 1x NEAA


title: Methylation profile of EFO21, replicate 2


title: Untag_wt_IP

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

institute: CABIMER-CSIC

description: Chromatin inmunoprecipitated

hyb_protocol: 7.5μg of DNA labelled was hybridized to Affymetrix GeneChip®  S.cerevisiae Tiling 1.0R Array for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven 450.

scan_protocol: Arrays were scanned following Manufacturer´s instruction in a GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
The signal intensity and pvalue data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using these parameters:quantile normalization, one side upper, PM/MM, scale intensity 500 and band-width 150bp
The BAR files were generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using these parameters:quantile normalization, one side upper, PM/MM, scale intensity 500 and band-width 150bp

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae yeast cells

label_protocol: Samples were prepared and labelled according to Affymetrix specifications for  GeneChip S.cerevisiae Tiling 1.0R Arrays

growth_protocol: Indicated strains were synchronised in G1 with alpha factor (0.5 o 1.0 µg/ml) for 3:00-3:30 hours at 30ºC in the presence of 5µg/ml of doxycicline in minimal complete media (SC). Cells were then washed three times with prewarmed rich media (YPAD, 37ºC) and  released in this media at 37ºC with 50µg/ml of pronase (eliminate remaining alpha factor) until all of them reached a G2/M state determined by FACS profile.

extract_protocol: ChIP samples were obtained breaking cells with a homogenizer (Multibeads shocker, Yasui Kikai) during 1 hour at 2500 rpm (30 sec on/30 sec off intervals) in lysis buffer (50mM HEPES, 140mM NaCl, 1mM EDTA, 1%Triton, 0.1% Sodium deoxycolate, 1mM PMSF) supplemented with protease cocktail inhibitors (Roche). Supernatant was transferred to new tubes by soft centrifugation piercing the bottom of the tube with a G25 needle, and chromatin was further concentrated by centrifugation. Chromatin was sheared via sonication to a size between 200 and 600 bp using a sonicator (REF SONICADOR). 10 µl of the supernatant were kept in ice and used as the input DNA control. The rest was incubated overnight with 1µg of HA antibody (3F10, Roche) overnight. All samples were immunoprecipitated using magnetic Protein G Dynabeads (referencia lab FX) for 90 minutes. After immunoprecipitation, samples were washed twice with 1 ml of the following solutions: lysis buffer, lysis buffer 0.5M NaCl, wash buffer (0.25M LiCl 10mM Tris HCl 1mM EDTA 0.5% NP-40 0.5% Sodium deoxycolate) and TE 1x. Samples were then eluted from magnetic beads with a 1% SDS TE solution, incubated overnight at 65ºC to reverse crosslinking, treated with 0.15mg of Proteinase K, and extracted using a standard phenol/clorophorm DNA purification and additionally purified through a DNA purification column (QIAGEN).

treatment_protocol: Cells at the indicated conditions were fixed for 15 minutes with 1% formaldehyde. Glycine was added to quench the reaction at a final concentration of 125 mM. Cells were sedimented, washed twice with cold TBS and stored at -80ºC until use.

tag: strain

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 bar1∆NAT

tag: antibody

value: H3F10, rat monoclonal (Roche)


title: OVCA429 with shGRHL2 rep1

description:
OVCA429sh12_L001
GRHL2 knockdown


title: Methylation profile of FUOV1, replicate 1


title: Gene expression of JHOS2 rep2

description: Gene expression of JHOS2, replicate 2


title: Methylation profile of DOV13, replicate 1


title: t::HHF2_input

description: input

value: t:HHF2 Scc1-HA DMY3

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11,15 RAD5 hhf1Δ::hphMX4 hhf2Δ::kanMX4 (p413TAR-tet:HHF2) bar1Δ::natMX4 SCC1-6HA:hphMX4


title: OVCA429 with shLuciferase rep4

description:
OVCA429shLuc_L004
Control

value: shLuciferase

value: control


title: t::HHF2_IP_rep2

description: Chromatin inmunoprecipitated

value: t:HHF2 Scc1-HA DMY4


title: OVCA429 with shLuciferase rep3

description:
OVCA429shLuc_L003
Control


title: Methylation profile of COLO720E, replicate 1


title: t::HHF2_IP_rep1

description: Chromatin inmunoprecipitated


title: Gene expression of JHOS2 rep1

description: Gene expression of JHOS2, replicate 1


title: wt_input

description: input

value: Scc1-HA DMY13-1

value: MATa leu2-3,112 trp1-1 ura3-1 ade2-1 can1-100 his3-11 RAD5 bar1∆NAT SCC1-6HA:hphMX4


title: Methylation profile of CH1, replicate 2


title: Methylation profile of CAOV3, replicate 2


title: OVCA429 with shLuciferase rep1

description:
OVCA429shLuc_L001
Control


title: CAL-27 shXBP-1s-3

city: New York

first: Xinyuan

last: Lei

state: New York

address: E5310 Melville library

department: Molecular and Cellular Biology

institute: Stony Brook University

description: Gene expression data

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

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

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: Human tongue cancer CAL-27 cell line

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

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

tag: transfection

value: shXBP


title: CAL-27 shXBP-1s-1

description: Gene expression data


title: CAL-27 shXBP-1s-2

description: Gene expression data


title: Methylation profile of CAOV3, replicate 1


title: Gene expression of HEYC2 rep2

description: Gene expression of HEYC2, replicate 2


title: Gene expression of HEY rep2

description: Gene expression of HEY, replicate 2

value: HEY


title: wt_IP_rep2

description: Chromatin inmunoprecipitated

value: Scc1-HA DMY13-3


title: wt_IP_rep1

description: Chromatin inmunoprecipitated


title: OVCA429shGRHL2 with H3K27me3 ChIP

description: OVCA429shGRHL2 with H3K27me3 ChIP-seq

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg19 using Novoalign v3.02.06 with default parameters settings
Peaks were called using MACS2 v2.1.0.20150731
Genome_build: hg19
Supplementary_files_format_and_content: chip-seq signal in bigwig for each sample

growth_protocol: PEO1 and HEYA8 cells were grown in RPMI supplemented with 10% FBS. OVCA429 and SKOV3 cells were grown in DMEM supplemented with 10% FBS. OVCA429 control and shGRHL2 cells were grown in DMEM supplemented with 10% FBS and 2 μg/ml puromycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed from the ChIP-DNA using Illumina TruSeq ChIP Sample Prep kit (IP-202-1012), with 15 to 18 cycles of PCR amplification. DNA size selection was performed using AMPure XP beads.

value: H3K27me3 (07-449, Millipore)


title: Gene expression of HEYC2 rep1

description: Gene expression of HEYC2, replicate 1


title: OVCA429shGRHL2 with H3K9me3 ChIP

description: OVCA429shGRHL2 with H3K9me3 ChIP-seq

value: H3K9me3 (ab8898, Abcam)


title: Methylation profile of COLO720E, replicate 2


title: CAL-27 shCtrl-2

description: Gene expression data

value: shCtrl


title: CAL-27 shCtrl-3

description: Gene expression data


title: OVCA429shGRHL2 with H3K27ac ChIP

description: OVCA429shGRHL2 with H3K27ac ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: Gene expression of HEY rep1

description: Gene expression of HEY, replicate 1


title: IL-4+ hashtag library

description:
AW19004
PolyA RNA
Single-cell RNA-seq

source_name: Sorted IL-4 4GET+ Activated CD4 T cells

tag: strain/background

value: C57BL/6 4GET IL-4 Reporter

value: Immunization with lternaria alternata + NP-OVA

value: Mediastinal Lymph Node

value: IL-4+ activated CD4 T cells


title: Gene expression of FUOV1 rep2

description: Gene expression of FUOV1, replicate 2


title: IL-4+ gene expression library

description:
AW19003
PolyA RNA
Single-cell RNA-seq


title: Methylation profile of A2780, replicate 2


title: OVCA429shGRHL2 with H3K4me1 ChIP

description: OVCA429shGRHL2 with H3K4me1 ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: Methylation profile of CH1, replicate 1

value: DMEM, 10% FBS


title: B7-H3 CAR-T SAHA-3

description: Gene expression of B7-H3 CAR-T after 5 days treatment of 0.5 μM SAHA

source_name: T cell

tag: agent

value: SAHA

value: B7-H3 CAR-T


title: 98PROL

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Nextpresso 1.9  was used for RNAseq analysis (http://bioinfo.cnio.es/nextpresso/) (DOI: 10.2174/157489361266617081015385)
Nextpresso use tophat for alignments with these parameters useCuffmergeAssembly="false" nThreads="1" outputFormat="simple-table" libraryNormalizationMethod="geometric"   Seed="123L" normalization="compatibleHits" reportSecondaryAlignments="false" bowtie="1"   ReadEditDist="2" readGapLength="2" referenceIndexing="false"
Nextpresso use cufflinks for measure abundance  with these parameters useGTF="true" nThreads="1" fragBiasCorrect="true" multiReadCorrect="false" libraryNormalizationMethod="classic-fpkm" maxBundleFrags="500000" normalization="compatibleHits" noEffectiveLengthCorrection="true" noLengthCorrection="false"
Nextpresso use cuffquant for measure abundance  with these parameters useCuffmergeAssembly="false" nThreads="1" fragBiasCorrect="true" multiReadCorrect="false" seed="123L" maxBundleFrags="500000" noEffectiveLengthCorrection="true" noLengthCorrection="false" normalization="compatibleHits" noEffectiveLengthCorrection="true" noLengthCorrection="false"
Nextpresso use cuffnorm for measure abundance  normalized for library size  with these parameters useCuffmergeAssembly="false" nThreads="1" fragBiasCorrect="true" multiReadCorrect="false" seed="123L" maxBundleFrags="500000" noEffectiveLengthCorrection="true" noLengthCorrection="false" normalization="compatibleHits" noEffectiveLengthCorrection="true" noLengthCorrection="false"
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample from cuffnorm ; bigwig were generated with nextpresso  1.9

source_name: urothelial organoid

growth_protocol: Normal mouse urothelial organoids (NMU-o) were maintained in culture with complete medium (proliferation condition), containing: Advanced DMEM/F12, 1x penicillin/streptomycin, 1x HEPES, 1x GlutaMAX, 50% WNT3A conditioned medium, 5% human RSPO1 conditioned medium, 1x N2 (Gibco, Cat. No. 17502048), 1x B27 (Gibco, Cat. No. 12587010), 50ng/mL human recombinant EGF (Invitrogen, Cat. No. PHG0311L), 1mM N-acetylcysteine (Sigma-Aldrich, Cat. No. 616-91-1), 50μg/mL human Noggin (Peprotech, Cat. No. 120-10C) and 1μM LY-2157299 (AxonChem, Cat. No. 700874-72-2). The ROCK inhibitor Y-27632 (Sigma-Aldrich, Cat. No. 129830-38-2) (10μM) was added during the first 3 days of culture.

extract_protocol:
RNA was isolated from Matrigel drops containing organoid-cultured cells using TRI Reagent® (Sigma-Aldrich, Cat. No. T9424) followed by the PureLinkTM RNA Mini Kit (Life Technologies, Cat. No. 12183020), according to manufacturer’s instructions. For 2D culture, RNA was extracted using ReliaPrepTM RNA Cell Miniprep System Kit (Promega, Cat. No. TM370). Samples were treated with DNase before reverse transcription (Life Technologies, Cat. No. AM1906).
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in “TruSeq Stranded mRNA Sample Preparation Guide” ( Part #15031047 Rev. E).  Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on a NovaSeq 6000- by following manufacturer's protocols.

treatment_protocol: For differentiation experiments, NMU-o were cultured for the first 7 days in complete medium, reseeded (without disaggregation) in fresh Matrigel, and cultured either with complete medium or with differentiation medium (lacking WNTA3A and RSPO-1 conditioned medium, EGF, LY-2157299 and Noggin) for the following 7 days.

value: bladder

value: urothelial organoid

tag: sampleID


title: 97PROL


title: OVCA429shGRHL2 with H3K4me3 ChIP

description: OVCA429shGRHL2 with H3K4me3 ChIP-seq

value: H3K4me3 (CS-003-100, Diagenode)


title: OVCA429shGRHL2 input DNA

description: input DNA for OVCA429shGRHL2 histone ChIP-seq


title: 60PROL


title: 98DIFF


title: globular stage suspensor

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Laser capture microdissected (LCM) suspensor at globular stage

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads were quality-filtered. Reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to TAIR10 genome using HISAT2 (version 2.0.6) {Kim, 2015} with the default parameters.
Read counts for each gene model were computed using HTSeq (version 0.6.1) {Anders, 2015}. Only uniquely mapped reads were used.
Reads per kilobase per million (RPKM) value was calculated according to Mortazavi et al. (Mortazavi et al., 2008) with the length of coding seuqeuences.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including gene model and normalized RPKM value in embryo proper and suspensor

organism: Arabidopsis thaliana

source_name: Arabidopsis globular stage suspensor captured by LCM

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

extract_protocol:
Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with 150 ng double-stranded cDNA using Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, starting at Day 2. The following modifications were done: the Illumina TruSeq DNA Sample preparation kit adapters were used (1/25 dilution) and the Agilent Pfu Turbo Cx hotstart DNA polymerase was used for the PCR enrichment step (15 cycles). Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.

treatment_protocol: Siliques with length between 1.1 and 1.4 cm containing globular stage seeds were collected from 38-46 day old plants. Seeds were either dissected out of siliques or left in sub-divided siliques and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on 5 or 7 um sections using a Leica LMD6000 system. Compartments were only captured from seeds with globular embryos 24-32 um in diameter, as determined by a medial section through the embryo proper.

tag: Stage

value: globular stage

value: suspensor


title: Methylation profile of A2780, replicate 1

data_processing: The dat file was processed using R bioconductor  version 3.6, Chip Analysis Methylation pipeline for illumina HumanMethylation450 and EPIC package, v1.2.8

source_name: ovarian cancer cell line

extract_protocol: Genomic DNA samples were purified using standard phenol-chloroform DNA extraction or AquaPure Genomic DNA Kit (Bio-rad).


title: globular stage embryo proper

description: Laser capture microdissected (LCM) embryo proper at globular stage

source_name: Arabidopsis globular stage embryo proper captured by LCM

value: embryo proper


title: Gene expression of JHOS3 rep2

description: Gene expression of JHOS3, replicate 2


title: 60DIFF


title: Mnase-seq: tHHF2 scc1-73 rep2

description: Mononucleosomes purified from DNA digested with MNaseI

data_processing:
reads mapping by Bowtie2 at galaxy.org
aboundance (occupancy value in wig file) calculated by DANPOS (Dpos funtion)
Dynamic nucleosome were selected with point_diff_log10pval>-15
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files report nucleosome occupancy data (the content is reads density)

source_name: S. cerevisiae yeast cells

growth_protocol: The four genetic backgrounds indicated previously were synchronised in G1 with alpha factor (0.5 o 1.0 µg/ml) for 3:00-3:30 hours at 30ºC in the presence of 5µg/ml of doxycicline in minimal complete media (SC). Cells were then washed three times with prewarmed rich media (YPAD, 37ºC) and  released in this media at 37ºC with 50µg/ml of pronase (eliminate remaining alpha factor) and 15 µg/ml of Nocodazole (block cells at the G2/M transition) until all of them reached a G2/M state determined by FACS profile.

extract_protocol:
Extracts for MNase were resuspended in 1M sorbitol and digested 1 hour with 4.5 mg of Zymoliase 20T (AmsBio 120491-1). Samples were then washed with 1 M sorbitol and 1M sorbitol PMSF 0.1mM, suspended gently in solution II (20mM Tris HCl 2mM EDTA 0.15M NaCl 0.1mM PMSF 0.2 % Triton), and treated 30 minutes with different concentrations of MNase (SIGMA N3755). The reaction was then stopped adding SDS (0.4%) and EDTA (8.5mM). Samples were incubated for 90 minutes at 37ºC with proteinase K and overnight at 65ºC for reversal crosslinking. DNA was extracted from samples using a standard phenol-chloroform extraction, treated with RNase A and loaded in a 1% agarose gel to check MNase digestion. MNase digestions enriched in mononucleosomes were loaded in a 1% agarose gel, and the DNA corresponding to mononucleosomes was purified with a DNA purification kit (Qiagen). The DNA size and quality was confirmed by an electropherogram analysis.
Libraries were generated using the Ion Plus Fragment Library Kit (4471252, Thermofisher) with 100ng input DNA. DNA fragments were size-selected around 230 bp after ligation of  adapters. Emulsion PCR allow enrich monocloning libraries

treatment_protocol: Samples for Mnase were fixed with formaldehyde (CF 0.5 %) for 15 minutes. Glycine (CF 125mM) was added after to quench the formaldehyde and end the cross-linking. After crosslinking and quenching cells were sedimented, washed twice with cold TBS and stored at -80ºC until use.

value: t:hhf2 scc1-73 SUP2-1

value: whole organism

value: MATa leu2-3,112 ura3-1 ade2-1 can1-100 his3-11,15 RAD5 hhf1<delta>hphMX4 hhf2<delta> kanMX4 (p413TAR-tet:HHF2) bar1<delta>natMX4 scc1-73


title: Gene expression of FUOV1 rep1

description: Gene expression of FUOV1, replicate 1


title: CAL-27 shCtrl-1

description: Gene expression data

value: shCtrl


title: Mnase-seq: tHHF2 scc1-73 rep1

value: t:hhf2 scc1-73 9b


title: B7-H3 CAR-T mock-3

description: Gene expression of B7-H3 CAR-T

value: mock


title: Gene expression of COLO720E rep1

description: Gene expression of COLO720E, replicate 1


title: OVCA429shLuc with H3K4me1 ChIP

description: OVCA429shLuc with H3K4me1 ChIP-seq


title: OVCA429shLuc with H3K27me3 ChIP

description: OVCA429shLuc with H3K27me3 ChIP-seq

value: H3K27me3 (07-449, Millipore)


title: Gene expression of CH1 rep2

description: Gene expression of CH1, replicate 2


title: Gene expression of EFO21 rep2

description: Gene expression of EFO21, replicate 2

value: RPMI 1640, 20% FBS, 1x NEAA


title: B7-H3 CAR-T mock-1

description: Gene expression of B7-H3 CAR-T


title: B7-H3 CAR-T SAHA-1