title: hMonocyte_Day6_AMTB_Donor5

first: Hamish

middle: W

last: King

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

data_processing:
Transcript counts were then generated using Salmon against the GRCh38 transcriptome (Ensembl release 92).
Tximport was used to collapse multiple transcripts per gene into a single expression estimate for each protein-coding gene.
Differential expression analysis was performed using DESeq2 with default settings.
Genome_build: GRCh38
Supplementary_files_format_and_content: DESeq2 results are provided (at gene level) in addition to individual transript abundance files from salmon.

source_name: Peripheral blood monocyte-derived macrophages

growth_protocol: CD14+ monocytes were isolated from the peripheral blood of healthy volunteers and differentiated into macrophages (Mo-M) in the presence of 100ng/ml M-CSF

extract_protocol:
RNA was isolated from CD14+ monocyte, Mo-M-DMSO and Mo-M-AMTB samples using an RNAeasy Mini kit PLUS (Qiagen)
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep Kit (NEBL)

treatment_protocol: Differentiation into Mo-M was done in the presence of 10μM AMTB or 0.01% DMSO (vehicle control)

tag: treatment

value: 10μM AMTB

tag: differentiation conditions

value: 100ng/ml M-CSF for 6 days


title: hMonocyte_Day0_Donor5

status: Public on May 16 2022

type: SRA

city: London

country: United Kingdom

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral blood monocytes


title: hMonocyte_Day6_AMTB_Donor4


title: Experiment 2, CellPlex_Pool3_part3

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
The Mesocricetus auratus genome MesAur 2.0 was downloaded from https://www.ncbi.nlm.nih.gov/genome/11998. The GFF file was converted to GTF, the generic gene names (LOCxxx) replaced with mouse-derived official gene symbols for several key genes, and 3'-UTRs extended as described previously (doi: 10.1101/2021.10.02.462569). Then, the SARS-CoV-2 genome annotation was merged.
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
For single-cell RNA-sequencing data, fastq files were processed using a the mergend MesAur2.0/SARS-CoV-2 genome with the GTF file provided here by applying CellRanger 6.0.2 with standard parameters
For single-cell RNA-sequencing data, fastq files were processed using a merged Roborvski hamster/SARS-CoV-2 genome by applying CellRanger 6.0.2 with standard parameters
Assembly: MesAur 2.0
Assembly: SARS-CoV-2 MN908947
Supplementary files format and content: GTF file
Supplementary files format and content: tab-separated values
Supplementary files format and content: h5 matrix

organism: Mesocricetus auratus

source_name: multiplexed sample

growth_protocol:
Hamsters were vaccinated intramuscularly with either an experimental adenovirus vector vaccine containing the whole SARS-CoV-2 spike (5 _ 108 infectious units (IFU) per animal) (PMID: 34835096), or BNT162b2 (5 ug per animal) or intranasally with 1x105 pfu of the live-attenuated SARS-CoV-2 vaccine candidate sCPD9 (PMID: 34320400, PMID: 34851677). For the prime-boost experiment, immunity was boosted by a second vaccination with the respective vaccines at the same dose 21 days after primary vaccination. In, one group, animals were primed with BNT162b2 and boosted with sCPD9, all other groups received a homologues boost.
Hamsters were weighted daily and monitored for signs of disease twice-daily. Hamsters were selected randomly for all scheduled take-out time points (day 2 and 5).
Euthanasia prior analysis occurred by cervical dislocation exsanguination under anesthesia as previously described (PMID 32698441, 33271063). Peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial as backup to repeat virological analyses as needed.

extract_protocol:
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits:
10xGenomics Chromium v3.1 single cell 3' gene expression kit
For isolation of single cells, the caudal lobe of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA) and counted via hemocytometer and trypan blue.
Then, 1,000,000 lung cells per sample were subjected to Cell Multiplexing Oligo (CMO) labeling according to the manufacturers’ instructions (3ʹ-CellPlex-Kit-Set-A, 10x Genomics). Labelled cells from 12 samples were pooled, filtered (40 µm) and counted. Pooled cells were adjusted to a final concentration of ~1,600 cells / μL and filtered with 40 µm FloMi filters (Merck) suitable for low volumes prior subjection to scRNA sequencing.
For Lung RNA Bulk sequencing the lobus medialis of the right lung lobe was removed carefully and homogenzied in Trizol reagent using a bead mill procedure (Speedmill, Analytic Jena), RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: 21 days following primary vaccination or 14 days following booster vaccination, hamsters were infected intranasally as previously described (PMID 32698441, 33271063). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 Variant Delta. [SARS-CoV-2, Human, 2021, Germany ex India, 20A/452R (B.1.617)] intranasally under anesthesia.

tag: first vaccination

value: Multiplexed sample (mixed treatments)

tag: second vaccination

tag: sampling timepoint


title: EPCR+CD45+ cells (HSC2) [SLX-9711.N703_S505]

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: University of Edinburgh

description:
SLX-9711
processed data file: Kapeni_etal_rawcounts.txt
processed data file: Kapeni_etal_logcounts.txt

data_processing:
Single-cell RNA-seq reads were quantified using the GRCm38 transcriptome and Kallisto version 0.43.1.
Data were filtered to remove poor quality cells & genes with low abundances.
Normalised using Scater ComputeSumFactors.
Genome_build: Ensembl 87
Supplementary_files_format_and_content: Kapeni_etal_rawcounts.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: Kapeni_etal_logcounts.txt: Tab-delimited text file includes normalised expression measurements.

molecule: total RNA

organism: Mus musculus

source_name: haematopoietic stem and progenitor cells

extract_protocol:
Cells were sorted from freshly isolated mouse embryos; dissected tissues were treated with collagenase and then stained with cell surface markers and directly sorted into lysis buffer.
SmartSeq2

tag: genotype/variation

value: Wild-type

tag: developmental stage

tag: tissue

value: aorta-gonads-mesonephros (AGM)

tag: cell type/region

value: HSC


title: hMonocyte_Day6_DMSO_Donor5


title: Sample 07670067C0011R (cancer pathways panel)

type: RNA

city: Waltham

first: Uma

last: Saxena

state: MA

address: 1000 Winter Street

country: USA

institute: Glaxosmithkline

hyb_protocol: Hybridization of biotinylated reporter probes was carried out according to the manufacturer's protocol

scan_protocol: Scanning was perfomred on the nCounter Digital Analyzer at 555 FOV.

data_processing:
The nSolver Analysis Software (NanoString Technologies) was used for the extraction of raw mRNA data.
Raw data extracted from the RCC files using the Nanostring nSolver software
The normalization for raw nCounter counts of expressed genes was separately done for QC-passed samples in PanCancer immune and PanCancer pathway panel using the R-package “NanoStringNorm” (R version 4.0.3) with a set of parameters; CodeCount = ‘geo.mean’, Background = ‘mean.2sd’, SampleContent = ‘housekeeping.geo.mean’, round.values = TRUE, take.log = TRUE.

source_name: Synovial Sarcoma tumor

label_protocol: RNA was analyzed and labeling was performed per manufacturer’s instructions of the NanoString nCounter system, with 2 sets of Nanostring assays (nCounter PanCancer Immune Profiling Panel and nCounter PanCancer Pathway Panel)

extract_protocol: RNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche). RNA extract was quantified (including assessment of RNA purity) using the Quant-iT RiboGreen RNA Reagent and Kit, and RNA quality was assessed using Agilent RNA Pico chip analysis.

treatment_protocol: Tumor biopsies were obtained prior to treatment with NY-ESO-1 TCR T cells or at the time of progression post treatment. Fresh biopsies were formalin fixed and paraffin embedded. For each sample, five 4-µm unstained slides were used for macrodissection and subsequent RNA extraction.

tag: sample note

value: Excluded from analysis:Progression after 2nd infusion


title: Experiment 2, GEX_Pool3_part3


title: hMonocyte_Day0_Donor4


title: Experiment 2, CellPlex_Pool3_part2


title: hMonocyte_Day6_DMSO_Donor4


title: Sample 07670064C0023R (cancer pathways panel)

tag: subject id

tag: timepoint

value: At Progression

tag: responder status

value: Non-responder

tag: progression free survival in weeks

tag: progression free survival status

value: Progressed or Died


title: Experiment 2, GEX_Pool3_part2


title: hMonocyte_Day6_AMTB_Donor3


title: Sample 07670062C0013R (cancer pathways panel)

value: Pre


title: Experiment 2, GEX_Pool3_part1


title: Experiment 2, CellPlex_Pool3_part1


title: Sample 07670059C0015R (cancer pathways panel)

value: Responder


title: hMonocyte_Day6_DMSO_Donor3


title: Sample 07670058C0013R (cancer pathways panel)


title: Sample 07670055C0013R (cancer pathways panel)

value: Excluded from analysis:Screening


title: hMonocyte_Day6_AMTB_Donor2


title: Experiment 2, CellPlex_Pool2_part3


title: Non-classical monocyte_6

city: New Delhi

first: Anmol

last: Chandele

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: International Center for Genetic Engineering and Biotechnology

data_processing:
RTA v2.7.7 was used for base calling and bcl2fastq v2.20.0.422 was used for demultiplexing
Quality of reads monitored by FastQC. Sequenced reads trimmed for adaptor sequences. Mapped to human GRCh38 whole genome using subread package.
Differential expression analysis done by DESeq2 package followed by removal of low count genes with raw counts < 10 in more than one sample of healthy subjects and in more than 3 samples of dengue subjects.
filter criteria: adjusted p value < 0.05; p value < 0.01; log2 fold change >= 1 (up); log2 fold change =< -1 (down)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
RNA isolated from sorted cell type of each patient using Qiagen Rneasy micro kit  with on-column DNase digestion. cDNA synthesized from 500 pg of total RNA using Clontech SMART-seq v4 ultra low input RNA kit as per the manufacturer's protocol.
Amplified cDNAs were appended with dual indexed barcodes using Nextera XT DNA library preperation kit (Illumina).

tag: cell type

value: Non-classical monocyte

tag: disease state

value: Dengue

tag: severity

value: DW


title: Sample 07670076C0023R (cancer pathways panel)


title: hMonocyte_Day6_DMSO_Donor2

tag: treatment

tag: differentiation conditions


title: HEK293T_Control_2

city: Riverside

first: feng

last: tang

state: CA

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

library_source: genomic

data_processing:
base calling analysis using the standard Illumina pipeline and sample de-multiplexing according to index read data
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
peaks were called using MACS2 with the following setting: macs2 callpeak -t -c -f BAM -g 2.7e+9 -n --outdir macs2
Assembly: hg19
Supplementary files format and content: bed files were genereated using bedtools by overlaping the peaks of two replicates
Supplementary files format and content: wig files were generated using deeptools

molecule: genomic DNA

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. For genomic DNA extraction, the cells were harvested at 80% confluence. Cell lines used in this study were examined for a mycoplasma contamination test using e-Myco Mycoplasma PCR Detection Kit (Bulldog Bio. Inc.).

extract_protocol:
Briefly, 2×107 cells were cross-linked by adding formaldehyde dropwise directly to the media for a final concentration of 1% and rotating gently at room temperature for 10 min. The reaction was quenched by adding 2.5 M glycine to the media for a final concentration of 125 mM and incubated with shaking for 5 min at room temperature. After washing with 1× PBS three times, the cells were resuspended in PBS. After centrifugation, the cell pellet was resuspended in RIPA buffer (50 mM Tris–HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% NP40, 0.5% Sodium Deoxycholate, 0.1% SDS and protease inhibitor cocktail) at 4 °C for 30 min with rotation. Chromatin was sheared using a Covaris S220 sonicator at 4°C for 10 min with a peak incident power of 140, a duty cycle of 10%, and 200 cycles per burst. After centrifugation at 16,000g for 15 min, the supernatant was incubated with pre-blocked anti-FLAG M2 affinity gel (Sigma) on a rotator at 4°C overnight. After washing, DNA was eluted from the beads with 120 µL 100 mM NaHCO3 and 1% SDS at 68 °C for 2 h. Cross-links were subsequently reversed by adding 4.8 µL of 5 M NaCl and 2 µL RNase A (10 mg/mL) and incubated with shaking at 65°C overnight. After reverse cross-links, proteins in the resulting DNA samples were removed with 2 µL proteinase K (20 mg/mL) and incubated while shaking at 60°C for 2 h. Finally, the DNA was purified using Cycle Pure Kit (omega). Purified DNA was quantified and verified on an Agilent 2100 Bioanalyzer.
The library was then constructed using NEBNext Ultra DNA Library Prep Kit (NEB, E7103S) following the manufacturer’s instructions. Subsequently, the purified DNA libraries were assessed using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on a HiSeq4000 system (Illumina).

tag: cell line

value: HEK293T cells

value: Human embryonic kidney

tag: genotype

value: WT


title: hMonocyte_Day0_Donor2


title: HEK293T_POLH_1

value: Tandem affinity tag was introduced to the C-terminus of endogenous Pol eta


title: hMonocyte_Day6_AMTB_Donor1

value: 10μM AMTB

value: 100ng/ml M-CSF for 6 days


title: HEK293T_Control_1


title: Non-classical monocyte_2

value: SD


title: Non-classical monocyte_3


title: Experiment 2, GEX_Pool2_part1

tag: first vaccination

value: Multiplexed sample (mixed treatments)

tag: second vaccination

tag: sampling timepoint


title: Experiment 2, CellPlex_Pool2_part1


title: Non-classical monocyte_5


title: Experiment 2, GEX_Pool2_part2


title: hMonocyte_Day0_Donor3


title: PBMCs [U2]

city: Tai'an

first: Zhenjie

last: Zhang

state: Shandong

address: 2 Yingsheng East

country: China

institute: Shandong First Medical University

data_processing:
Reads with low quality or adaptor contamination were filtered out.
The remaining data were mapped to the human genome GRCh38 using HISAT2 v2.1.015 with default parameters
Genes were quantified using the featureCounts program of the Subread package.
Differential gene expression analysis of the expression quantification results was conducted using R packages, including edgeR, limma-voom, and glimma.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: PBMCs

extract_protocol:
RNA was purified from peripheral blood mononuclear cells (PBMCs) of the participants using the RNeasy Plus Mini Kit (Qiagen, Cat.74134).
RNA libraries for RNA-seq were prepared  following manufacturer's protocols.
Transcriptome sequencing was performed on the Illumina HiSeq 4000 platform (Illumina, United Kingdom).

value: PBMCs

value: Bronchitis


title: HEK293T_POLH_2


title: Non-classical monocyte_4


title: Experiment 2, CellPlex_Pool2_part2


title: Non-classical monocyte_1

value: DI


title: PBMCs [T3]


title: Experiment 2, GEX_Pool2_part3


title: Experiment 2, GEX_Pool1_part2


title: hMonocyte_Day0_Donor1


title: Non-classical monocyte_10

value: Healthy


title: PBMCs [T2]


title: PBMCs [T1]


title: hMonocyte_Day6_DMSO_Donor1


title: Non-classical monocyte_8


title: Experiment 2, GEX_Pool1_part1


title: PBMCs [S6]


title: Non-classical monocyte_7


title: Experiment 2, CellPlex_Pool1_part1


title: Intermediate monocyte_6

value: Intermediate monocyte


title: CAIA biological rep4

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

description: Gene expression data from ankle tissue of mice treated with CAIA.

hyb_protocol: The labeled cRNA was then purified using the RNeasy Mini kit (Qiagen). The purified cRNAs were hybridized to GeneChip Mouse Genome 430 2.0 Arrays, washed and stained in the GeneChip Fluidics Station.

scan_protocol: Phycoerythrin-stained arrays were scanned to obtain digital image files

data_processing: Data were analyzed using GeneChip Operating Software (Affymetrix, USA)

label: biotin

source_name: Ankle from CAIA induced mice

label_protocol: Total RNA was reverse transcribed by SuperScript II (Invitrogen), converted into double-stranded cDNA, and purified using the MinElute Reaction Cleanup Kit (Qiagen). The purified double-stranded cDNA was transcribed and labeled in vitro using the BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, USA).

growth_protocol: At postnatal 7 weeks, female mice were subjected to collagen antibody induced arthritis (CAIA)

extract_protocol: ISOGEN and RNeasy was used for RNA extraction.

treatment_protocol: 5 mg of anti-collagen 2 monoclonal antibody cocktail (Chondrex, USA, Redmond) was administered on day 0, followed by 50 μg of LPS on day 3 i.p.

tag: strain

tag: Sex

value: female


title: PBMCs [S5]


title: Intermediate monocyte_5


title: CAIA biological rep3


title: PBMCs [S4]


title: Experiment 1, GEX_Pool4_part4


title: Experiment 1, CellPlex_Pool4_part4


title: Intermediate monocyte_4


title: Intermediate monocyte_3


title: Experiment 1, CellPlex_Pool4_part3


title: PBMCs [S2]


title: Experiment 2, CellPlex_Pool1_part2


title: PBMCs [S1]


title: Intermediate monocyte_2


title: Experiment 1, GEX_Pool4_part3


title: Intermediate monocyte_1


title: PBMCs [U1]

value: Pneumonia


title: Intermediate monocyte_10


title: Experiment 1, GEX_Pool4_part2


title: PBMCs [P6]


title: CAIA biological rep2


title: CAIA biological rep1


title: Intermediate monocyte_8


title: PBMCs [P5]


title: PBMCs [P4]


title: Experiment 1, CellPlex_Pool4_part1


title: Intermediate monocyte_7


title: PBMCs [U3]


title: LPS Control biological rep4

description: Gene expression data from ankle tissue of mice treated with LPS

source_name: Ankle from LPS control mice


title: LPS Control biological rep2


title: LPS Control biological rep1


title: Control biological rep4

description: Gene expression data from ankle tissue of control mice

source_name: Ankle from control mice


title: LPS Control biological rep3


title: Experiment 1, GEX_Pool4_part1


title: Classical monocyte_5

value: Classical monocyte

value: Dengue


title: Control biological rep2


title: Experiment 1, CellPlex_Pool3_part4


title: Experiment 1, GEX_Pool3_part4


title: ETV6-NCOA2_2

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description:
EN2_2
Human CD34 positive cord blood cells were retrovirally infected with MigR1-ETV6-NCOA2-IRES-GFP expression

data_processing:
Reads were aligned to the reference genome using TopHat
Differential expression analysis was performed using the DESeq package
Genome_build: GRCh38
Supplementary_files_format_and_content: RPKM

source_name: Cord blood progenitor cells

growth_protocol: The cells were cultured for five days in-vitro (SCF, Flt3L, and TPO) , sorted for GFP positive, and sent for bulk RNA-sequencing.

extract_protocol:
CD34 positive cord blood cells were isolated using magnetic beads from fresh cord blood (For each biological replicate, three different cord blood samples were mixed). The cell were retrovirally infected with ETV6-NCOA2 or empty vector and cultured in IMDM supplemented with hSCF, hTPO, hFlt3L (100 ng/ml) for 5 days. The positive cells were sorted (GFP). We extracted RNA from the samples and performed bulk RNA-sequencing.
RNA was purified, analyzed by bioanalyzer (Agilent 2100), cDNA libraries were prepared using Using PrepX mRNA Library kit (WaferGen), and Apollo 324 NGS automatic library prep system. Using the universal (SR) and index-specific primer with limited PCR cycle number (~13), a sample-specific index was added to each adaptor-ligated cDNA sample. Libraries were clustered onto Illumina’s TruSeq SR Cluster kit v3, and sequenced for 50 cycles using TruSeq SBS kit on Illumina HiSeq system

treatment_protocol: Each biological replicate composed of three different cord blood units

value: Cord blood progenitor cells

tag: sorted cells

value: CD34+ cells, GFP+

value: MigR1-ETV6-NCOA2-IRES-GFP expression


title: ETV6-NCOA2_3

description:
EN2_3
Human CD34 positive cord blood cells were retrovirally infected with MigR1-ETV6-NCOA2-IRES-GFP expression


title: Classical monocyte_6

value: DW


title: PBMCs [P3]


title: Experiment 1, CellPlex_Pool4_part2


title: PBMCs [P2]


title: Control biological rep1


title: Control biological rep3


title: Classical monocyte_4


title: ETV6-NCOA2_1

description:
EN2_1
Human CD34 positive cord blood cells were retrovirally infected with MigR1-ETV6-NCOA2-IRES-GFP expression


title: PBMCs [P1]


title: Experiment 1, GEX_Pool3_part3


title: Experiment 1, CellPlex_Pool3_part3


title: Empty vector_3

description:
EV_3
Human CD34 positive cord blood cells were retrovirally infected with MigR1-IRES-GFP expression

value: control


title: Classical monocyte_3


title: PBMCs [HC12]

value: Healthy Control (HC)


title: Empty vector_2

description:
EV_2
Human CD34 positive cord blood cells were retrovirally infected with MigR1-IRES-GFP expression


title: PBMCs [HC11]


title: Empty vector_1

description:
EV_1
Human CD34 positive cord blood cells were retrovirally infected with MigR1-IRES-GFP expression


title: Experiment 1, CellPlex_Pool3_part2


title: PBMCs [HC10]


title: Classical monocyte_2

value: SD


title: Classical monocyte_10


title: Classical monocyte_8


title: PBMCs [HC9]


title: PBMCs [HC8]


title: Experiment 1, GEX_Pool3_part1

value: Multiplexed sample (mixed treatments)


title: Experiment 1, GEX_Pool3_part2


title: Experiment 1, CellPlex_Pool3_part1


title: Classical monocyte_7


title: Experiment 1, GEX_Pool2_part4


title: NCI-H441 Input, 100nM dexamethasone, biol rep2

city: New York

first: Madeline

middle: Anne

last: Dorso

state: New York

address: 408 East 69th Street

department: Human Oncology and Pathogenesis

institute: Memorial Sloan Kettering Cancer Center

description: NCI-H441 Input

data_processing:
Peaks were called on ChIP-seq alignments from Genewiz using MACS combining both replicates and using a p-value of 0.001 to call peaks. Peaks that overlap the blacklist file from the Kundaje lab were removed
Each peak file was associated with a gene if the peak falls within the gene body or in 10kb upstream or downstream of any isoform from that gene. A gene is defined as shared between GRE and FOXA1 if that gene has an associated peak in both the GR and FOXA1 ChIP-seq data.
Assembly: hg38
Supplementary files format and content: bedGraph

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed  and extracts prepared according to the manufacturer's protocol (SimpleChIP Enzymatic Chromatin IP Kit, CST, #9005)
ChIP-seq libraries were prepared by Genewiz (Azenta)

treatment_protocol: Cells were treated with either 100nM dexamethasone or vehicle as indicated for 30 minutes.

value: Human papillary lung adenocarcinoma

tag: chip antibody

value: 100nM dexamethasone treatment, 30 mins.


title: A16_RNASeq, biological rep3

city: Göteborg

first: Xin

last: Chen

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_115

data_processing:
The raw reads from each sample were mapped to the CEN.PK 113-7D reference genome using TopHat (v 2.0.12), with 84.0—87.6% of the reads successfully mapped.
Cufflinks version 2.2.1 was used to calculate FPKM values, and the feature Counts module of the Subread package (v 1.4.6) was used to determine raw read counts.
Genome_build: CEN.PK 113-7D
Supplementary_files_format_and_content: raw read counts

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: shake flask 30 ˚C, 200rpm

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit with a FastPrep homogenizer to disrupt cells.
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.

treatment_protocol: Samples of cells were frozen rapidly in liquid nitrogen to prevent mRNA turnover.

tag: background strain


title: NCI-H441 Input, Vehicle, biol rep1

description: NCI-H441 Input

value: Vehicle, 30 mins.


title: PBMCs [HC6]

value: PBMCs


title: NCI-H441 IgG CST, Vehicle, biol rep2

description: NCI-H441 IgG CST

value: Normal Rabbit IgG (CST, #2729)


title: NCI-H441 Input, Vehicle, biol rep2

description: NCI-H441 Input


title: A16_RNASeq, biological rep2

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_114


title: PBMCs [HC5]


title: NCI-H441 Input, 100nM dexamethasone, biol rep1

description: NCI-H441 Input


title: Classical monocyte_1

value: DI


title: Experiment 1, GEX_Pool2_part3


title: NCI-H441 IgG CST, Vehicle, biol rep1

description: NCI-H441 IgG CST


title: PBMCs [HC4]


title: A16_RNASeq, biological rep1

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_113


title: NCI-H441 IgG CST, 100nM dexamethasone, biol rep2

description: NCI-H441 IgG CST


title: A08_RNASeq, biological rep3

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_112

value: lsm6-delta sin3-delta GCN4p-MDM34


title: PBMCs [HC7]


title: Experiment 1, CellPlex_Pool2_part4


title: PBMCs [HC3]


title: NCI-H441 IgG CST, 100nM dexamethasone, biol rep1

description: NCI-H441 IgG CST


title: Experiment 1, GEX_Pool2_part2


title: PBMCs [HC2]


title: NCI-H441 H3K27ac CST, Vehicle, biol rep2

description: NCI-H441 H3K27ac CST

value: Acetyl-Histone H3 (Lys27)(CST, #8173)


title: PBMCs [HC1]


title: Experiment 1, CellPlex_Pool2_part1


title: A08_RNASeq, biological rep1

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_110


title: A05_RNASeq, biological rep3

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_109

value: lsm6-delta sin3-delta


title: NCI-H441 H3K27ac CST, Vehicle, biol rep1

description: NCI-H441 H3K27ac CST


title: NCI-H441 H3K27ac CST, 100nM dexamethasone, biol rep2

description: NCI-H441 H3K27ac CST


title: Experiment 1, CellPlex_Pool2_part3


title: Experiment 1, CellPlex_Pool1_part4


title: Experiment 1, GEX_Pool1_part4


title: A05_RNASeq, biological rep2

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_108


title: NCI-H441 H3K27ac CST, 100nM dexamethasone, biol rep1

description: NCI-H441 H3K27ac CST


title: Experiment 1, CellPlex_Pool2_part2


title: A05_RNASeq, biological rep1

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_107


title: NCI-H441 FOXA1 CST, Vehicle, biol rep2

description: NCI-H441 FOXA1 CST


title: A02_RNASeq, biological rep3

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_106


title: A08_RNASeq, biological rep2

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_111


title: A02_RNASeq, biological rep2

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_105


title: Experiment 1, CellPlex_Pool1_part3


title: NCI-H441 FOXA1 CST, Vehicle, biol rep1

description: NCI-H441 FOXA1 CST


title: ISTB218.2vsCBS138.1

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

hyb_protocol: Six hundred nanograms of labelled cDNA were hybridized in the microarray. Hybridizations were carried out using Agilent gasket slides in a rotating oven for 17 h at 65°C.

scan_protocol: Slides were then washed following manufacturer’s instructions and scanned in an Agilent G2565AA microarrays scanner. Probes signal values were extracted using Agilent Feature Extraction Software.

data_processing:
Data were normalized using median centering of signal distribution with Biometric Research Branch BRB-Array tools v3.4.o software 36. Final statistical analysis was carried out using LIMMA package in MeV software (MultiExperiment Viewer 4.8.0) 36 with a cut-off p-value of 0.1.
Spots with both red and green signal intensities below 100 (the specified minimum) were excluded from the analysis, resulting in filtered out log-ratio value (FALSE). 8k probes out of 14k probes passed this filtering option.

organism: Nakaseomyces glabratus

label_protocol: cDNA synthesis, hybridization, and scanning were performed using the Agilent protocol for two-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 (Agilent Technologies), according to the manufacturer’s instructions. One hundred nanograms of total RNA of each isolate were used to synthesize labeled cDNA (with Cyanine 3-CTP and cyanine 5-CTP), using Agilent T7 Promoter Primer and T7 RNA polymerase Blend (Agilent Technologies, Cat.5190–2305).

growth_protocol: For the transcriptomic profiling an individual colony of the FFUL443, FFUL674 and ISTB218 isolates was inoculated in YPD at 30 ºC with orbital agitation (250 rpm) overnight and then re-inoculated (at an initial OD600nm of 0.1) in 150 mL of RPMI and left to grow at 30 ºC and 250 rpm orbital shake.

extract_protocol: RNA extraction was performed using the hot-phenol method. RNA extraction was performed using RiboPureTM RNA Isolation Kit (Ambion, Life Technologies, CA). The quality and integrity of the purified RNA was confirmed in a Bioanalyzer, and only samples with an RNA integrity number (RIN) > 7 were used.

treatment_protocol: When the OD600nm of the cultures achieved 2 (corresponding to mid-exponential phase) cells were harvested by centrifugation and immediately frozen at -80ºC until further use.

tag: carbon source

value: glucose 20g/L


title: Experiment 1, GEX_Pool1_part2


title: Experiment 1, GEX_Pool2_part1


title: NCI-H441 FOXA1 CST, 100nM dexamethasone, biol rep2

description: NCI-H441 FOXA1 CST


title: CBS138.2 vsFUL443.2


title: A02_RNASeq, biological rep1

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_104


title: Experiment 1, CellPlex_Pool1_part2


title: A01_RNASeq, biological rep3

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_103

value: control strain without metabolic engineering


title: NCI-H441 FOXA1 CST, 100nM dexamethasone, biol rep1

description: NCI-H441 FOXA1 CST


title: FFUL443.2vsCBS138.1


title: FFUL674.2vsCBS138.1


title: NCI-H441 GR CST, Vehicle, biol rep2

description: NCI-H441 GR CST


title: Experiment 1, GEX_Pool1_part1


title: ISTB218.2.1vsCBS138.1


title: A01_RNASeq, biological rep2

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_102


title: Experiment 1, CellPlex_Pool1_part1


title: A01_RNASeq, biological rep1

description:
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.
P19303_101


title: FFUL674.3vsCBS138.1


title: NCI-H441 GR CST, 100nM dexamethasone, biol rep2

description: NCI-H441 GR CST


title: Experiment 1, GEX_Pool1_part3


title: FFUL674.1vsCBS138.1


title: NCI-H441 GR CST, 100nM dexamethasone, biol rep1

description: NCI-H441 GR CST


title: u87_3009a_rep2

city: Birmingham

first: Anindya

last: Dutta

state: AL

address: 720 20th Street South, Kaul 230

department: Genetics

institute: University of Alabama at Birmingham

data_processing:
Kallisto was used to map reads to hg38 human genome build
Normalization and differential expression analysis performed with DESeq2
Genome_build: hg38

growth_protocol: U87 cells were obtained from ATCC and grown in Eagle's minimum essential medium modified to contain Earle's Balanced Salt Solution, non-essential amino acids, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate, 10% FBS, and penicillin/streptomycin

extract_protocol:
RNA was extracted using Trizol following manufacturer's protocol
250 or 500 ng total RNA was poly-A selected by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and then converted to libraries by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #7760) according to the manufacturer's protocol. The resulting libraries were quality checked for concentration and size distribution before pooling for paired-end sequencing on Illumina HiSeq by Novogene.

treatment_protocol: 50nM mimic transfected using lipofectamine 2000 for 48 hours

value: tRF-3009a mimic


title: u87_ssGL2_rep2


title: u87_ssGL2_rep1


title: NCI-H441 GR CST, Vehicle, biol rep1

description: NCI-H441 GR CST


title: CuONP 1

status: Public on May 15 2022

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

description: Processed_data_file_eco.xlsx, Processed_data_file_ppu.xlsx, Processed_data_file_rp4.xlsx

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (NC_00) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3  NC_002947.4
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

organism:
Plasmid RP4
Escherichia coli K-12
Pseudomonas putida KT2440

source_name: E. coli bacteria + P. putida bacteria + IncPα plasmid

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid were cultured in triplicate in the pressure of CuO NPs or Cu2+ at 25 °C, without shaking

tag: strain #1

value: E. coli K-12 LE392

tag: strain #2

value: P. putida KT2440

tag: strain #3

value: IncP{alpha} RP4 plasmid


title: CuONP 3


title: Cu2 3


title: Cu2 2


title: Day-10 from G85R mice-R#3

city: Vancouver

first: Honglin

last: Luo

state: British Columbia

address: Room 166, 1081 Burrard Street

country: Canada

institute: University of British Columbia

hyb_protocol: Hybridization of RNA with NanoString reporter codeset were performed according to manufacturer's recommended protocol

scan_protocol: After finishing the hybridization, samples were loaded into the designated cartridge, which is then installed into the digital analyzer together with the RLF file. Scanning was initiated as per manufacturer's suggestion.

data_processing: Data processing were performed by using NanoString nCounter Advanced Analysis Module (https://www.nanostring.com/products/ncounter-analysis-system/ncounter-consumables/)

source_name: whole brain homogenates_G85R

label_protocol: NanoString does not involved any labeling procedures

growth_protocol: This study involved direct used of mice organs and hence, no growth protocol were involved.

extract_protocol: Whole brain were homogenized with steel beads and digested with proteinase K to remove protein residuals. Homogenates were then lysed with lysis buffer & subjected to RNA extraction.

treatment_protocol: This study involved direct used of mice organs and hence, no treatment protocol were involved.

tag: strain background

tag: genotype/variation

value: SOD1-G85R transgenic

tag: tissue

value: whole brain


title: Day-10 from G85R mice-R#1


title: Cu2 1


title: FFUL443.1vsCBS138.1


title: Day-10 from WT mice-R#1

source_name: whole brain homogenates_WT

value: wild type


title: CuONP 2


title: control sample 2


title: control sample 3


title: 3DHS578T2

city: Mexico City

first: Yarely M.

last: Salinas-Vera

address: Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360 Mexico City, CDMX

department: Biochemistry

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del IPN

description: RMA expression value derived from Affymetrix GeneChip command console software v4.0.

hyb_protocol: Labeled samples were then hybridized with Affymetrix GeneChip miRNA 4.0 Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Samples were washed and stained with the Affymetrix GeneChip2 hybridization wash and stain kit, and then scanned with the Affymetrix GeneChip Scanner 3000 7G to generate fluorescent images, as described in the manufacturer’s protocol. For miRNA array analysis, CEL-files of the raw data were produced with Affymetrix GeneChip command console software v4.0.

data_processing:
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = miRNA-4_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: 3D cultures on matrigel

label_protocol: RNA was labeled with the flash tag biotin HSR kit (Genisphere, Hatfield, PA, USA) according to the manufacturer’s instructions for poly(A)-tailing.

growth_protocol: Establishment of 3D organotypic cultures of the Hs578T cell line grown on geltrex and 2D cultures of the Hs578T cell line.

extract_protocol: RNA was isolated from 2D and 3D cultures using the RNeasy plus mini kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

tag: cell line

tag: cell type

value: Triple-negative breast cancer cell line

tag: culture type

value: 3D cultures on matrigel


title: 3DHS578T3


title: 2DHS578T2

source_name: 2D cultures

value: 2D cultures


title: control sample 1


title: u87_3009a_rep1

tag: treatment


title: 3DHS578T1


title: Day-10 from WT mice-R#3


title: Day-10 from G85R mice-R#2


title: OPC Treatment, 5μM tunicamycin for 8hr, replicate 2

city: Louisville

first: Michal

last: Hetman

state: Kentucky

address: 511 South Floyd Street, MDR609A

department: Department of Neurological Surgery

institute: University of Louisville

data_processing:
Illumina FASTQ Generation version 1.0.0 used for basecalling
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1. The FastQC results indicated that all sequences were of high quality (>Q32), with the exception of the final base.
Sequences were directly aligned to the Rattus norvegicus  reference genome assembly (rn6.fa). A gene annotation file for rn6, was downloaded from Ensembl. The analysis was performed using Tophat (version 2.0.4), generating alignment files in bam format.
The aligned RNA-seq reads were assembled according to the rn6 gtf annotation file using Cufflinks V2.2.1.
Differentially expressed genes (DEGS) were identified for two pairwise comparisons (Treated vs. Untreated 2hr, Treated vs. Untreated 8hr) using Cuffdiff (version 2.1.1).
Genome_build: rn6
Supplementary_files_format_and_content: Tab-delimited cuffnorm normalized FPKM values

organism: Rattus norvegicus

source_name: oligodendrocyte precursor cells

growth_protocol: Total RNA for library construction was obtained from cultured rat oligodendrocyte precursor cells (OPCs) which are often used as a convenient model of oligodendrocytes. These cells were originally isolated from adult rat spinal cords by our collaborator Dr. Scott Whittemore. They were stored frozen. Only low passage cells were used (up to passage 6).

extract_protocol:
RNA from OPCs was obtained using commertially avaiable Rneasy MiniKit from Qiagen cat no 74104
Libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit-Set A (Cat # RS-122-2301) with Ribo-Zero Gold. Illumina NextSeq 500/550 model.

treatment_protocol: OPCs were treated with the ERSR inducer tunicamycin (0 or 5 µM) for 2- or 8h (4 samples from each experiment, 3 independent experiments were resulting in 12 samples, total).

value: oligodendrocyte precursor cells

tag: passages


title: OPC Control, 0μM tunicamycin for 8hr, replicate 2


title: OPC Control, 0μM tunicamycin for 8hr, replicate 3


title: OPC Treatment, 5μM tunicamycin for 8hr, replicate 1


title: OPC Treatment, 5μM tunicamycin for 8hr, replicate 3


title: Day-10 from WT mice-R#2


title: OPC Treatment, 5μM tunicamycin for 2hr, replicate 3


title: OPC Control, 0μM tunicamycin for 2hr, replicate 1


title: OPC Treatment, 5μM tunicamycin for 2hr, replicate 1


title: 2DHS578T1


title: Rag1 +/- Draining/Non-draining LN  1643-03

city: Boston

first: Margherita

last: Boieri

address: 55 Fruit Street

institute: Masachusetts General Hospital

description:
Rag1 +/-
Sample 9

data_processing:
Analysis done at Beijing Genomics Institute (BGI) pipeline version 5.0
Filtering was done using SOAPnuke
Mapping to mm10 using Bowtie/BWA
Gene/Transcript expression was done with RSEM
Differentially expressed gene screening was done with Poisson Distribution method/Noiseq package/EB Seq package
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Draining/Non-draining LN

growth_protocol: CD4+ T cells are sorted from lymph nodes of mice with terminal tumors

extract_protocol:
Stimulated CD4+ T cells were resuspended in RLT buffer with addition of 1% 2-mercaptoethanol and total RNA extracted using the  Rneasy Mini kit (QIAGEN, #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: K14-TSLP +/tg, TSLPR -/- mice were injected with PyMT tumors and Ly5.1 CD4+ T cells. TSLPR -/- mice were injected with PyMT tumors and TSLPRKO CD4+ T cells. MMTV-PyMT mice spontaneously develop breast tumor, and Rag1KO mice were injected with CD4+ T cells at 4 weeks of age. In all samples CD4+ T cells were sorted when the mouse had terminal tumors, stimulated in vitro with aCD3, aCD28, IL-2 and TSLP fror 5 hours.

tag: strain

value: Balb/c

tag: group

value: CONTROL

tag: sample number


title: K14-TSLP +/tg, MMTV-PyMT +/tg, TSLPR +/-  Draining/Non-draining LN  2953-23

description:
K14-TSLP +/tg, MMTV-PyMT +/tg, TSLPR +/-
Sample 6

value: TEST


title: K14-TSLP +/tg, MMTV-PyMT +/tg, Rag1 +/- Draining/Non-draining LN  3374-25

description:
K14-TSLP +/tg, MMTV-PyMT +/tg, Rag1 +/-
Sample 10


title: K14-TSLP +/tg, MMTV-PyMT +/tg, Rag1 -/- +CD4+ Draining/Non-draining LN  3365-02

description:
K14-TSLP +/tg, MMTV-PyMT +/tg, Rag1 -/- +CD4+
Sample 8


title: 2DHS578T3


title: K14-TSLP +/tg, MMTV-PyMT +/tg, TSLPR -/-  Spleen 2944-16

description:
K14-TSLP +/tg, MMTV-PyMT +/tg, TSLPR -/-
Sample 7

source_name: Spleen


title: TSLPR -/- + TSLPRKO CD4+ Draining/Non-draining LN  3584-77

description:
TSLPR -/- + TSLPRKO CD4+
Sample 4


title: K14-TSLP +/tg, TSLPR -/-  + Ly5.1 CD4+ Non-draining LN  3501-13, 3503-15

description:
K14-TSLP +/tg, TSLPR -/-  + Ly5.1 CD4+
Sample 5

source_name: Non-draining LN


title: TSLPR -/- + TSLPRKO CD4+ Draining LN 1784-19, 1788-61, 1789-62, 2517-32

description:
TSLPR -/- + TSLPRKO CD4+
Sample 3

source_name: Draining LN


title: OPC Control, 0μM tunicamycin for 8hr, replicate 1


title: OPC Treatment, 5μM tunicamycin for 2hr, replicate 2


title: OPC Control, 0μM tunicamycin for 2hr, replicate 2


title: K14-TSLP +/tg, TSLPR -/-  + Ly5.1 CD4+ Non-draining LN  3252-43, 1213-46, 3295-38, 3296-39

description:
K14-TSLP +/tg, TSLPR -/-  + Ly5.1 CD4+
Sample 2


title: OPC Control, 0μM tunicamycin for 2hr, replicate 3


title: hCG_5

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

institute: Fox Chase Cancer Center

hyb_protocol: Hybridization was performed as described in the GeneChip Expression Analysis (701021 Rev.5) protocol from Affymetrix, following the instructions for 49 format (standard)/64 format array.

scan_protocol: The scanner used was Affymetrix GeneChip® Scanner 3000 and the software used was Command Console.

data_processing: The data were 1) normalized using RMA; 2) The R version of the MAS5 algorithm was used to generate P/A/M calls (present, absent, marginal) for each probeset, and only probesets which were Present in at least 2/3 samples in either treated or control groups were kept; 3) Probesets which did not map to a valid Entrez ID were removed,  low intensity or low variability filters were not applied. 4) LIMMA package of Bioconductor under R environment was used to perform the differential expression analysis.  Cutoffs of 1.5 or 2.0 fold change and FDRp<0.05 were used to select the differentially expressed genes.

source_name: mammosphere culture

label_protocol: GeneChip Expression 3′-Amplification Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) was used for sample preparation following manufacturer's protocol.

growth_protocol: Female Sprague Dawley rats (Taconic Biosciences Inc., USA) at age 55 days were treated daily via intraperitoneal injection with 100 IU/day r-hCG (OVIDREL, 250 µg/0.5ml);  or vehicle control (phosphate buffered saline) for 21 days. Rat mammary gland 4&5 was resected 21 days after the last day of treatment. Mammary epithelial cell enriched single cells were plated in 6-well ultra-low attachment plate at a density of 25,000 cells/ml in complete EpiCult-B medium containing 10 ng/ml EGF, 10 ng/ml basic fibroblast growth factor (bFGF), 4 µg/ml Heparin and 1X Pen/Strep/ Fungizon. The formation of mammosphere was checked daily. After 7 days of culture,  the mammospheres were collected and used for RNA extraction.

extract_protocol: Primary mammospheres were collected by 40 µm cell strainer after 7 days of culture. Total RNA was extracted using RNAqueous Micro Scale RNA Isolation Kit (#AM1931, Invitrogen). RNA concentration was measured by Nanodrop 1000 spectrophotometer, and RNA quality was checked by RNA Pico assay using Agilent 2100 Bioanalyzer.

treatment_protocol: Female Sprague Dawley rats were treated daily via intraperitoneal injection with 100 IU/day r-hCG (OVIDREL, 250 µg/0.5ml);  or equivalent volume of vehicle (phosphate buffered saline) for 21 days.

tag: gender

value: female

value: Sprague Dawley

value: hCG


title: CTRL-T0-04

city: San Giuliano Terme

first: Paolo

last: Aretini

state: Pisa

address: Via Ferruccio Giovannini 13

country: Italy

institute: Fondazione Pisana per la Scienza

data_processing:
Basecalls were performed using NextSeq Control Software from Illumina
RNA-seq reads were aligned to the Mytilus Galloprovincialis genome assembly mg10 using Star 2.50
Differential Expression were performed using Cuffdiff 2.21
Genome_build: mg10 from https://denovo.cnag.cat/mussel_data
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files with differential expression results

organism: Mytilus galloprovincialis

source_name: M. galloprovincialis controls at time 0

extract_protocol:
hepatopancreas were removed, flash frozen on dry ice, and RNA was harvested using RNA-Later reagent.
The libraries were prepared following the protocol TruSeq® Stranded mRNA Sample Preparation kit (Illumina)

value: hepatopancreas

tag: genotype

value: wild

value: untreated

tag: time

value: time 0


title: K14-TSLPtg;PyMTtg;Rag1KO+CD4+ T cells rep1

data_processing:
Analysis done at Beijing Genomics Institute (BGI) pipeline version 5.0
Filtering was done using SOAPnuke
Mapping to mm10 using Bowtie/BWA
Gene/Transcript expression was done with RSEM
Differentially expressed gene screening was done with Poisson Distribution method/Noiseq package/EB Seq package
Genome_build: mm10

source_name: Breast tumor

growth_protocol: PyMT transgenic mice develop spontaneous breast tumors starting at ~4 weeks of age, these tumors are collected at endpoint (week 18-20)

extract_protocol:
Tumor tissue was isolated and homogenized in RLT buffer with addition of 1% 2-mercaptoethanol. Homogenized samples were stored in TriZol reagent and total RNA extracted using the  Rneasy Mini kit (QIAGEN, #74104)
RNA libraries were prepared for sequencing using standard Illumina protocols at BGI

treatment_protocol: PyMTtg;Rag1KO and K14-TSLPtg;PyMTtg;Rag1KO mice were injected with CD4+ T cells at the age of 4 weeks


title: PyMTtg;Rag1KO+CD4+ T cells rep2


title: K14-TSLPtg;PyMTtg;Rag1KO+CD4+ T cells rep2


title: K14-TSLPtg;PyMTtg;Rag1KO+CD4+ T cells rep3


title: Control_7

value: vehicle control (PBS)


title: PyMTtg;Rag1KO+CD4+ T cells rep1


title: hCG_7


title: PyMTtg;Rag1KO+CD4+ T cells rep3


title: Control_5


title: K14-TSLP +/tg, TSLPR -/-  + Ly5.1 CD4+ Draining LN 3252-43, 1213-46, 3295-38, 3296-39

description:
K14-TSLP +/tg, TSLPR -/-  + Ly5.1 CD4+
Sample 1


title: CTRL-T0-01


title: CTRL-T0-03


title: hCG_6


title: Control_6


title: CTRL-28gg-05

source_name: M. galloprovincialis controls at time 28 days

value: 28 days


title: CTRL-28gg-02


title: CTRL-28gg-03


title: CTRL-T0-02


title: CTRL-28gg-01


title: CTRL-28gg-04


title: CTRL-14gg-01

source_name: M. galloprovincialis controls at time 15days


title: CTRL-14gg-02


title: 5mgl-28gg-04

source_name: M. galloprovincialis treated at time 28 days

value: treated with EE2


title: CTRL-14gg-03


title: 5mgl-28gg-05


title: CTRL-14gg-04


title: 5mgl-28gg-03


title: 5mgl-28gg-02


title: 5mgl-14gg-05

source_name: M. galloprovincialis treated at time 15days


title: 5mgl-14gg-04


title: 5mgl-14gg-03


title: 5mgl-14gg-02


title: 5mgl-14gg-01


title: small RNAs from MTD-Gal4-driven rhino KD

city: Vienna

first: Lisa

last: Baumgartner

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 3 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: 25˚C, 12h dark/light

extract_protocol:
Argonaute-bound sRNAs were isolated according to Grentzinger et al. (2020)
Libraries were prepared by ligation of 3' and 5' barcoded adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.

value: ovary

value: w, MTD/+; MTD/+; MTD/pW20>rhi_sh[attP2]/;


title: MTD-Gal4 driven rhino KD input 2

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.3.0) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 3 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
ChIP-seq libraries were prepared using the NEB Next Ultra II DNA Library for Illumina (NEB).

tag: antibody


title: CG2678deltaZF4 input

description: CG2678 construct harboring a deletion of ZnF#4


title: MTD-Gal4 driven piwi KD input 2

value: w, MTD/+; MTD/+; MTD/pW20>piwi_sh2[attP2]/;


title: CG2678 homozygous KO delta1 H3K9me3-ChIP

value: anti-H3K9me3 antibody (active motif 39161)


title: MTD-Gal4 driven CG2678 KD input 2


title: MTD-Gal4 driven rhino KD CG2678-ChIP biological replicate 2


title: CG2678 homozygous KO delta1 Rhi-ChIP

value: anti-Rhi antibody (Rhino#1_3573gly)


title: small RNAs from MTD-Gal4-driven CG2678 KD


title: small RNAs from MTD-Gal4-driven control KD

value: w, MTD/+; MTD/+; MTD/pW20>w_sh[attP2]/;


title: CG2678 homozygous KO delta1 input


title: CG2678deltaZF4 FLAG-ChIP

description:
deltaZF4_in
CG2678 construct harboring a deletion of ZnF#4

value: anti-FLAG antibody (Sigma F1804-1MG)


title: MTD-Gal4 driven piwi KD H3K9me3-ChIP biological replicate 2


title: MTD-Gal4 driven rhino KD input 3


title: MTD-Gal4 driven rhino KD CG2678-ChIP biological replicate 1


title: MTD-Gal4 driven piwi KD H3K9me2-ChIP biological replicate 2

value: anti-H3K9me2 antibody (mAbcam 1220)


title: 5mgl-28gg-01


title: MTD-Gal4 driven CG2678 KD CG2678-ChIP biological replicate 2


title: MTD-Gal4 driven rhino KD Rhi-ChIP biological replicate 2


title: MTD-Gal4 driven CG2678 KD H3K9me3-ChIP biological replicate 2


title: MTD-Gal4 driven CG2678 KD Rhi-ChIP biological replicate 2


title: GFP-3xFLAG-HP1b input

description: endogenously tagged

value: w, 3xFLAG/V5/Precission/GFP-HP1b; ; ;


title: CG2678deltaZF4 Rhi-ChIP


title: MTD-Gal4 driven piwi KD Rhi-ChIP biological replicate 2


title: LaubLab_ChIPseq_antiFLAG_driD-3xFlag_minusvan

city: Cambridge

first: Kevin

last: Gozzi

address: 31 Ames St

institute: Massachusetts Institute of Techonology

description: cells were grown to mid exponential phase (in PYE at 30 degC) treated with or without DNA damage (zeocin to cause DSBs or vanillate to induce I-SceI) before DriD-3xFLAG-DNA complexes were extracted and immunoprecipitated with anti-FLAG beads

data_processing: For samples 1-6, paired-end reads were mapped to Caulobacter crescentus NC011916.1 using Bowtie2 (Langmead and Salzberg) with the following command: bowtie2 -x NA1000 -1 *sequence_1.fastq -2 *sequence_2.fastq -S output.sam. Subsequently, sam files were converted to bams samtools: samtools view -Sbo *.bam *.sam. Bam files were ordered with samtools: samtools sort *.bam _sorted.bam. Genome coverage and conversion to wig files were performed with custom python scripts. Final visualization was performed in MochiView, with read count normalized by total number of reads, relative to Sample 1.

organism: Caulobacter vibrioides

source_name: Caulobacter crecentus CB15N

growth_protocol: Cultures of Caulobacter crescentus were grown at 30oC in PYE to mid-exponential phase for all samples. Subsequently, formaldehyde was added to fix cells for ChIP-seq.

extract_protocol:
For samples 1-6, cultures were treated with formaldehyde to fix cells, and glycine was added to quench. Further washes and protein-DNA complex isolation was performed following protocols in the Methods.
Standard library construction for Illumina NextSeq500 sequencing platform.

treatment_protocol: For samples 2 and 4, 15ug/mL of zeocin was added to induced double strand breaks. For sample 6, 0.5mM vanillate was added to induce expression of the restriction enzyme I-SceI to cause a single double strand break at the engineered I-SceI site on the genome.

tag: growth phase

value: mixed population, mid-exponential phase

value: CB15N I-SceI, tet at ccna_00727; Pvan-I SceI, chl at Van locus,  hfaB::PdidA-lacZ (markerless); driD::driD-3xFlag

value: antiFLAG


title: GFP-3xFLAG-HP1b FLAG-ChIP

description:
GFPFLAGHP1b_in
endogenously tagged


title: LaubLab_ChIPseq_antiFLAG_driD-3xFlag_pluszeo

value: CB15N driD::driD-3xFlag

tag: agent

value: 15ug/mL zeocin


title: GFP-3xFLAG-HP1b Rhi-ChIP

description:
GFPFLAGHP1b_in
endogenously tagged


title: MTD-Gal4 driven piwi KD CG2678-ChIP biological replicate 2


title: LaubLab_ChIPseq_antiFLAG_WT_pluszeo

value: wildtype


title: GFP-3xFLAG-HP1b HP1

description:
GFPFLAGHP1b_in
endogenously tagged

value: anti-HP1 antibody (DSHB C1A9)


title: GFP-3xFLAG-HP1c FLAG

description:
GFPFLAGHP1c_in
endogenously tagged

value: w;; 3xFLAG/V5/Precission/GFP-HP1c ;


title: GFP-3xFLAG-HP1c H3K9me2-ChIP

description:
GFPFLAGHP1c_in
endogenously tagged

value: ovary


title: SDSD2

city: Shijiazhuang

first: Lei

last: Bao

address: Zhongshan road 361

institute: Hebei Medical University

description: peripheral blood

data_processing:
Sequencing data were filtered using SOAPnuke (BGI, Shenzhen, China)
Supplementary_files_format_and_content: txt

source_name: CD2+ T cell

extract_protocol:
Total DNA was isolated using the TIANamp™ Genomic DNA Kit (Tiangen Biotech, Beijing, China) according to manufacturer instructions.
For preparation of a TCR CDR3 library, multiplex polymerase chain reaction (PCR) was undertaken with the Multiplex PCR Kit (Qiagen, Hilden, Germany) using primers in the V region and reverse primers in the J region to amplify gDNA (400 ng). The target amplified product was purified by electrophoresis on a 2% agarose gel and sequenced with standard 2×150 paired-end reads on the Hiseq2000 platform (Illumina, San Diego, CA, USA).
Sequencing data were filtered using SOAPnuke (BGI, Shenzhen, China). Comparison of sequences was undertaken using BLAST Plus in the international ImMunoGeneTics information system (www.imgt.org/).

treatment_protocol: Mo-DCs exposed to ConA at the concentration of CV75 for 24 h. 4×106 CD2+ T cells (1×106 cells/mL) sorted from PBMCs were cultured in RPMI-1640 buffer (Gibco) containing 10% fetal bovine serum (Gibco) and were co-cultured with Mo-DCs exposed to ConA in proportion of 4:1 for 24 h.

value: CD2+ T cell incubated with Mo-DC exposed to SDS


title: GFP-3xFLAG-HP1c input

description: endogenously tagged


title: OSC WT input

description: parental OSC line

source_name: OSC

value: OSC

value: ovarian somatic stem cells

value: WT


title: LaubLab_ChIPseq_antiFLAG_WT_minuszeo


title: SDSD3

description: peripheral blood


title: OSC WT FLAG-ChIP

description:
OSCe9WT_in
parental OSC line


title: OSC ubi63E>FLAG-CG2678 FLAG-ChIP

description:
OSCd4_in
OSC cell line stably overexpressing internally 3xFLAG tagged CG2678 under the control of the ubi63E promoter


title: tbx5 enh knockout - diff rep 1 - cellplex

city: Dallas

first: Daniel

last: Armendariz

state: TX

address: 5323 Harry Hines Boulevard

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description:
Cellplex Library for tbx5 enh knockout - diff rep 1
KO_cmo_bc.csv
cellplex_library_assignments.csv

data_processing:
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 6.0.0, 10X Genomics). Cellplex barcodes and library assignments can be found in KO_cmo_bc.csv and cellplex_library_assignments.csv supplementary files respectively. Both knockout sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in KO_SC_DF.h5ad supplementary file.
processed data files format and content:CSV file containing Cellplex oligo barcodes used.
processed data files format and content:CSV containing Cellplex barcode library assignments.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.

source_name: H9-derived cardiomyocytes

growth_protocol: H9 ESCs were maintained feeder-free in mTeSR Plus (Stemcell Tech. 100-0276) according to suggested manufacturer’s instructions on Matrigel (Corning 354277) coated plates, passaged every 3-4 days with DPBS/0.5 mM EDTA and plated in 2 uM thiazovivin (Sigma SML1045) supplemented mTeSR Plus overnight.

extract_protocol:
Library prepared following 10x v3.1 Dual Index with Cell Multiplexing protocol.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.

treatment_protocol: At 80-90% confluency, media was replaced with 3 uM CHIR99021 (Tocris 4423) supplemented CDM3 (RPMI 1640, Sigma R8758; 0.5 mg/ml human albumin, ScienCell OsrHSA; 211 ug/ml L-ascorbic acid 2-phosphate, Sigma A8960) for 48 hours followed by 2 uM Wnt-C59 (Cayman 16644) supplemented CDM3 for 48 hours with subsequent media changes every 2 days with CDM3 alone.

tag: differentiation day


title: LaubLab_ChIPseq_antiFLAG_driD-3xFlag_minuszeo


title: GFP-3xFLAG-HP1c H3K9me3-ChIP

description:
GFPFLAGHP1c_in
endogenously tagged

value: anti-H3K9me3 antibody (active motif 39161)


title: tbx5 enh knockout - diff rep 2 - cellplex


title: DNCB3

description: peripheral blood

value: CD2+ T cell incubated with Mo-DC exposed to DNCB


title: OSC ubi63E>FLAG-CG2678 input

description: OSC cell line stably overexpressing internally 3xFLAG tagged CG2678 under the control of the ubi63E promoter


title: LaubLab_ChIPseq_antiFLAG_driD-3xFlag_plusvan

value: 0.5mM vanillate


title: rhino transheterozygous KO rhi18-7_rhig2m11 input 2


title: rhino transheterozygous KO rhi18-7_rhig2m11 H3K9me3-ChIP biological replicate 1


title: Cy3

description: peripheral blood

value: CD2+ T cell incubated with Mo-DC exposed to Cy


title: DNCB2

description: peripheral blood


title: SDSD1

description: peripheral blood


title: DNCB1

description: peripheral blood


title: MTD-Gal4 driven control KD input 4

value: w, MTD/+; MTD/+; MTD/pW20>w_sh[attP2]/;


title: MTD-Gal4 driven control KD H3K9me2-ChIP biological replicate 1

value: anti-H3K9me2 antibody (mAbcam 1220)


title: Control3

description: peripheral blood

value: CD2+ T cell incubated with Mo-DC


title: Cy2

description: peripheral blood


title: Cy1

description: peripheral blood


title: ConA2

description: peripheral blood

value: CD2+ T cell incubated with Mo-DC exposed to ConA


title: MTD-Gal4 driven control KD CG2678-ChIP biological replicate 2


title: Cim3

description: peripheral blood

value: CD2+ T cell incubated with Mo-DC exposed to Cim


title: Cim2

description: peripheral blood


title: MTD-Gal4 driven control KD H3K9me3-ChIP biological replicate 1


title: Control2

description: peripheral blood


title: ConA3

description: peripheral blood


title: rhino transheterozygous KO rhi18-7_rhig2m11 CG2678-ChIP biological replicate 2


title: DIPG13-KO_H33

first: Efrat

last: Shema

address: Herzl St 234

department: Department of Biological Regulation

data_processing:
Library strategy: CUT&RUN
Paiered-end reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 30 -m 20). Reads were mapped to human genome (hg19, UCSC) using Bowtie version 2.3.5.1 (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700).
Nucleosome fragments at the length >120bp were selected from the remaining unique reads using picard-tools, and broad peaks were called using MACS2 against the corresponding HRP samples as background control (parameters: -f BAMPE --SPMR --nomodel --extsize 100 --keep-dup auto -q 0.05).  MLL1 were called using narrow peaks. Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Assembly: hg19
Supplementary files format and content: Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Supplementary files format and content: Peaks files were constructed using MACS2 against the corresponding HRP samples as background control

source_name: Patient-derived DIPG cells (SU-DIPG13-CRISPR edited)

growth_protocol: DIPG cells were cultured in Tumor Stem Media (TSM) consisting of a 1:1 mixture of DMEM/F12 (Invitrogen) and Neurobasal (-A) (Invitrogen), with addition of B27(-A) (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah Biotechnology), human-EGF (20 ng/ml) (Shenandoah Biotechnology), human PDGF-AA (20 ng/ml) (Shenandoah Biotechnology), human PDGF-BB (20 ng/ml) (Shenandoah Biotechnology) and heparin (10 ng/ml) (Stemcell Technologies). Cells were passaged every week.

extract_protocol:
CUT&RUN assay was done as described in Skene et al (2017) with slight modifications as follows. Cells were harvested and counted with 200000 cells per reaction. Permeabilized cells, bound to Concanavalin A-coated beads were mixed with individual primary antibody (see antibody list) and incubated overnight at 4°C while rotating. Secondary antibody, anti-rabbit HRP was used as a negative control. pAG-MNase enzyme was added to each sample followed by incubation step of 1 hour at 4°C. Targeted digestion was done by 15 minutes incubation on ice block (0°C) under low salt conditions. DNA purification was done using Nucleospin gel and PCR clean-up kit (Machery-Nagel, 740609).
Libraries were prepared from 1-20ng of DNA as previously described by Blecher-Gonen et al (2013). Paired end sequencing was done on a Next-Seq 500 instrument (Illumina) using a V2 150 cycles mid output kit.

value: Brain

tag: part

value: Brainstem

tag: tumor

value: DIPG

tag: genotype/variation


title: DIPG13_K27M_3

data_processing:
library strategy: CUT&RUN
Paiered-end reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 30 -m 20). Reads were mapped to human genome (hg19, UCSC) using Bowtie version 2.3.5.1 (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700).
Nucleosome fragments at the length >120bp were selected from the remaining unique reads using picard-tools, and broad peaks were called using MACS2 against the corresponding HRP samples as background control (parameters: -f BAMPE --SPMR --nomodel --extsize 100 --keep-dup auto -q 0.05).  MLL1 were called using narrow peaks. Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Assembly: hg19
Supplementary files format and content: Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Supplementary files format and content: Peaks files were constructed using MACS2 against the corresponding HRP samples as background control

source_name: Patient-derived DIPG cells (SU-DIPG 13)

growth_protocol: HEK293 cells were cultured in DMEM supplemented with 10% FBS and 1% P/S. DIPG cells were cultured in Tumor Stem Media (TSM) consisting of a 1:1 mixture of DMEM/F12 (Invitrogen) and Neurobasal (-A) (Invitrogen), with addition of B27(-A) (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah Biotechnology), human-EGF (20 ng/ml) (Shenandoah Biotechnology), human PDGF-AA (20 ng/ml) (Shenandoah Biotechnology), human PDGF-BB (20 ng/ml) (Shenandoah Biotechnology) and heparin (10 ng/ml) (Stemcell Technologies). Cells were passaged every week.

treatment_protocol: Lentiviral (3rd generation) packaging was performed by jetPEI-mediated transfection of HEK293T with appropriate plasmids. Virus-containing supernatants were collected 48h following transfection, filtered, supplemented with 8µg/ml Polybrene, and added to HEK293 target culture. Infected cells were selected with 0.5mg/ml G418  and induced with .1 µg/ml doxycycline.

tag: cell type

value: Patient-derived DIPG cells (SU-DIPG 13)

tag: tissue

value: Brianstem


title: Gossypol, 10 µg/ml SAMPLE 65

city: New Orleans

first: Heping

last: Cao

state: LA

address: 1100 Robert E. Lee Blvd

department: Southern Regional Research Center

institute: USDA-ARS

description:
Gossypol, 10 µg/ml
Test

hyb_protocol: SYBR Green qPCR reaction mixtures contained 5 ng of total RNA-derived cDNAs, forward primer, reverse primer and 1X iQ SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA). The thermal cycle conditions were as follows: 3 min at 95°C, followed by 40 cycles at 95°C for 10 s, 65°C for 30 s and 72°C for 30 s. The qPCR reactions were performed in 96-well clear plates sealed by adhesives with a CFX96 real-time system-C1000 Thermal Cycler (Bio-Rad Laboratories).

data_processing:
Rpl32 mRNA was selected as the internal reference for qPCR analysis for this cell type (HKG).
1% DMSO treatment was used as sample control
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Gos normalized to Rpl32 and DMSO worksheet reports normalized signal (against housekeeping genes and sample control), where deltadeltaCt = delta(Ct_Target )− delta(Ct_DMSO)
Gos fold Change worksheet reports test/control (i.e., test/DMSO control) ratios. The 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.

label: SYBR Green

source_name: RAW264.7 cells

label_protocol: The cDNAs were synthesized from total RNA using SuperScript II reverse transcriptase (Life Technologies). The cDNA synthesis mixture (20 μl) contained 2.5 μg total RNA, 2.4 μg oligo(dT)12-18 primer, 0.1 μg random primers, 500 μM dNTPs, 10 mM DTT, 40 units RNaseOUT and 200 units SuperScript II reverse transcriptase in 1X first-strand synthesis buffer (Life Technologies). The cDNA synthesis reactions were incubated at 42°C for 50 min. The cDNA samples were stored in -80°C freezer and diluted with water to 1 ng/µl before qPCR analyses.

extract_protocol: Total RNA was extracted from mouse macrophages with Trizol reagent followed by DNase I treatment.

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.

tag: activation agent

value: Gossypol, 10 ug/ml


title: Gossypol, 5 µg/ml SAMPLE 63

description:
Gossypol, 5 µg/ml
Test

value: Gossypol, 5 ug/ml


title: Gossypol, 5 µg/ml SAMPLE 62

description:
Gossypol, 5 µg/ml
Test


title: Gossypol, 100 µg/ml SAMPLE 71

description:
Gossypol, 100 µg/ml
Test

value: Gossypol, 100 ug/ml


title: Gossypol, 100 µg/ml SAMPLE 72

description:
Gossypol, 100 µg/ml
Test


title: Gossypol, 50 µg/ml SAMPLE 68

description:
Gossypol, 50 µg/ml
Test

value: Gossypol, 50 ug/ml


title: Gossypol, 50 µg/ml SAMPLE 69

description:
Gossypol, 50 µg/ml
Test


title: Control1

description: peripheral blood

tag: treatment


title: Gossypol, 100 µg/ml SAMPLE 70

description:
Gossypol, 100 µg/ml
Test


title: Gossypol, 5 µg/ml SAMPLE 61

description:
Gossypol, 5 µg/ml
Test


title: Cim1

description: peripheral blood


title: Gossypol, 50 µg/ml SAMPLE 67

description:
Gossypol, 50 µg/ml
Test


title: DIPG13-KO_EZH2

city: Rehovot

institute: Weizmann Institute of Science

value: Patient-derived DIPG cells (SU-DIPG13-CRISPR edited)


title: Gossypol, 1 µg/ml SAMPLE 59

description:
Gossypol, 1 µg/ml
Test

value: Gossypol, 1 ug/ml


title: Gossypol, 10 µg/ml SAMPLE 66

description:
Gossypol, 10 µg/ml
Test


title: DIPG13_K27M_MLL1


title: KO-MLL1


title: DIPG13_HRP_3


title: DIPG13-KO_HRP


title: Gossypol, 10 µg/ml SAMPLE 64

description:
Gossypol, 10 µg/ml
Test


title: ConA1

description: peripheral blood


title: HEKwDox_EZH2

treatment_protocol: Lentiviral (3rd generation) packaging was performed by jetPEI-mediated transfection of HEK293T with appropriate plasmids. Virus-containing supernatants were collected 48h following transfection, filtered, supplemented with 8µg/ml Polybrene, and added to HEK293 target culture. Infected cells were selected with 0.5mg/ml G418  and induced with 1 µg/ml doxycycline.

value: Cell-line


title: HEK-Dox_EZH2


title: DIPG13-K27M_HRP


title: Gossypol, 0.1 µg/ml SAMPLE 54

description:
Gossypol, 0.1 µg/ml
Test

value: Gossypol, 0.1 ug/ml


title: Gossypol, 0.5 µg/ml SAMPLE 55

description:
Gossypol, 0.5 µg/ml
Test

value: Gossypol, 0.5 ug/ml


title: Gossypol, 0.1 µg/ml SAMPLE 53

description:
Gossypol, 0.1 µg/ml
Test


title: DIPG13-K27M_EZH2


title: DIPG17_K27M

source_name: Patient-derived DIPG cells (SU-DIPG 17)

value: Patient-derived DIPG cells (SU-DIPG 17)


title: DIPG13_K27M_4


title: HEKwDox_HRP


title: DIPG13_HRP_4


title: Gossypol, 0.5 µg/ml SAMPLE 57

description:
Gossypol, 0.5 µg/ml
Test


title: DMSO, 1% SAMPLE 51

description:
DMSO, 1%
Control

value: DMSO, 1%


title: HEK-Dox_HRP


title: Gossypol, 1 µg/ml SAMPLE 60

description:
Gossypol, 1 µg/ml
Test


title: DIPG17_MLL1

value: Brain


title: DMSO, 1% SAMPLE 49

description:
DMSO, 1%
Control


title: Gossypol, 0.5 µg/ml SAMPLE 56

description:
Gossypol, 0.5 µg/ml
Test


title: Gossypol, 0.1 µg/ml SAMPLE 52

description:
Gossypol, 0.1 µg/ml
Test


title: DIPG13_K36me2_4


title: Gossypol, 1 µg/ml SAMPLE 58

description:
Gossypol, 1 µg/ml
Test


title: DMSO, 1% SAMPLE 50

description:
DMSO, 1%
Control


title: Gossypol, 100 µg/ml SAMPLE 47

description:
Gossypol, 100 µg/ml
Test

value: 8 h


title: Gossypol, 100 µg/ml SAMPLE 46

description:
Gossypol, 100 µg/ml
Test


title: large screen - lane 1 - seq 1

description:
scRNA-seq
Large_SC_DF.h5ad
Large_CM_DF.h5ad

data_processing:
Provided datasets are for combined DAA243-250 scRNA-seq libraries.
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 3.1.0, 10X Genomics). All large screen sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Doublets were removed using the HTO libraries. HTO barcodes used can be found in Large_CM_bc.csv supplemental file. In short, we assigned HTO tags to cells using the saturation curve method described in Drop-seq (Macosko et al, 2015). Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in Large_SC_DF.h5ad supplementary file.
The Louvain clusters defining cardiomyocytes and mesoderm cells were isolated and re-clustered using Louvain. Clusters corresponding to cardiomyocyte and smooth muscle cells were selected and clustering above repeated to identify cardiomyocyte subpopulations. Dataset contained in Large_CM_DF.h5ad supplementary file.
processed data files format and content:H5AD file containing count matrix and cluster classifications for combined large screen scRNA-seq.
processed data files format and content:H5AD file containing count matrix and cluster classifications for CM subpopulations in combined large screen scRNA-seq.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.

extract_protocol:
Library prepared following 10x v3.1 gene expression protocol.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.

tag: strain


title: large screen - lane 1 - HTO

description: Cell Hashing HTO Library for large screen lane 1

data_processing:
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 3.1.0, 10X Genomics). All large screen sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Doublets were removed using the HTO libraries. HTO barcodes used can be found in Large_CM_bc.csv supplemental file. In short, we assigned HTO tags to cells using the saturation curve method described in Drop-seq (Macosko et al, 2015). Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in Large_SC_DF.h5ad supplementary file.
processed data files format and content:CSV file containing HTO antibody barcodes used.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.

extract_protocol:
Library prepared following the cell hashing protocol (Stoeckius et al, 2018). Briefly,  an additive primer was included to enrich HTO during cDNA amplification followed by HTO amplification and sequencing.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.


title: Gossypol, 50 µg/ml SAMPLE 45

description:
Gossypol, 50 µg/ml
Test


title: validation screen - lane 1

description: scRNA-seq

data_processing:
Provided datasets are for combined DAA189-190 scRNA-seq libraries.
scRNA-seq libraries were demultiplexed, mapped to the human reference genome (hg38), and aggregated by experiment using the Cellranger software (ver 3.1.0, 10X Genomics). Both validation screen sequencing lanes were combined using Cellranger aggr and normalized for sequencing. Scrublet was applied to remove doublets. Cells with higher than 20% mitochondrial content were removed, as well as genes with fewer than 1 counts. The count matrix was natural log transformed and saved as a separate layer for differential gene expression calling before scaling counts to unit variance and zero mean. Clusters were defined using the Louvain algorithm. Clusters which held fewer than 1% of all cells were removed. Dataset contained in Validation_SC_DF.h5ad supplementary file.
The Louvain cluster defining cardiomyocytes was isolated and re-clustered using Louvain. Clusters corresponding to cardiomyocyte and smooth muscle cells were selected and clustering above repeated to identify cardiomyocyte subpopulations. Dataset contained in Validation_CM_DF.h5ad supplementary file.
processed data files format and content: H5AD file containing count matrix and cluster classifications for combined validation screen scRNA-seq.
processed data files format and content:H5AD file containing count matrix and cluster classifications for CM subpopulations in combined validation screen scRNA-seq.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.


title: Gossypol, 50 µg/ml SAMPLE 44

description:
Gossypol, 50 µg/ml
Test


title: validation screen - sgRNA Amplicon Library for validation screen lane 1

description: sgRNA Amplicon Library for validation screen - lane 1

data_processing:
Provided datasets are for combined DAA197-198 sgRNA amplicon libraries.
sgRNA libraries were mapped using FBA count (Duan et al, 2021). Dataset contained in Focused_SG_DF.pkl supplementary file. We assigned sgRNA to cells using the saturation curve method described in Drop-seq (Macosko et al, 2015).
processed data files format and content:Pickle file containing dataframe with count matrix for sgRNA mapping.
Genome_build: hg38
Supplementary_files_format_and_content: KO_SC_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for combined knockout scRNA-seq.
Supplementary_files_format_and_content: KO_CM_DF_2.8.22.h5ad: H5AD file containing count matrix and cluster classifications for cardiomyocyte subpopulations in combined knockout scRNA-seq.

extract_protocol:
Library prepared by amplifiying sgRNA from cDNA.
On day 8 post-differentiation, samples were washed with DPBS and dissociated to single cells with Accutase (Sigma SCR005) and resuspended in CDM3.


title: Gossypol, 10 µg/ml SAMPLE 40

description:
Gossypol, 10 µg/ml
Test


title: Gossypol, 10 µg/ml SAMPLE 42

description:
Gossypol, 10 µg/ml
Test


title: WT_EZH2_S8

data_processing:
Library strategy: CUT&RUN
Paiered-end reads were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 30 -m 20). Reads were mapped to human genome (hg19, UCSC) using Bowtie version 2.3.5.1 (--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700).
Nucleosome fragments at the length >120bp were selected from the remaining unique reads using picard-tools, and broad peaks were called using MACS2 against the corresponding HRP samples as background control (parameters: -f BAMPE --SPMR --nomodel --extsize 100 --keep-dup auto -q 0.05).  MLL1 were called using narrow peaks. Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were constructed from BAM alignments using deepTools2 suite with bamCoverage, using RPKM-normalization in 10bp bins, and excluding ENCODE hg19 blacklist regions.
Supplementary_files_format_and_content: Peaks files were constructed using MACS2 against the corresponding HRP samples as background control

growth_protocol: HEK293 cells were cultured in DMEM supplemented with 10% FBS and 1% P/S.

tag: cell line


title: H31_EZH2_S12


title: WT_HRP_S7


title: DIPG13_H33_4

value: DIPG


title: Gossypol, 10 µg/ml SAMPLE 41

description:
Gossypol, 10 µg/ml
Test


title: Gossypol, 5 µg/ml SAMPLE 39

description:
Gossypol, 5 µg/ml
Test


title: Gossypol, 100 µg/ml SAMPLE 48

description:
Gossypol, 100 µg/ml
Test


title: db2

city: Guangzhou

first: SHENG

middle: TONG

last: HUANG

state: Guangdong

address: No. 74, Zhongshan 2nd Road, Guangzhou

institute: Sun Yat-Sen University

data_processing:
We use internal software SOAPnuke to filter reads, followed as:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases(N) are more than 10%;
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. For HISAT which is much faster, sensitive and high accuracy analysis software.
We mapped clean reads to reference using Bowtie2, v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Genome_build: mm9

source_name: kidney

extract_protocol:
kidney were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution.
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.

treatment_protocol: 50-weeks-old db/db mice that underwent 40 weeks atorvastatin treatment(10mg/kg.day)

value: C57 BLKS/L

tag: age

value: 50 weeks old

value: underwent 40 weeks normal saline treatment


title: db3


title: Gossypol, 5 µg/ml SAMPLE 38

description:
Gossypol, 5 µg/ml
Test

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.


title: Gossypol, 5 µg/ml SAMPLE 37

description:
Gossypol, 5 µg/ml
Test

value: Gossypol, 5 ug/ml


title: Gossypol, 1 µg/ml SAMPLE 36

description:
Gossypol, 1 µg/ml
Test


title: H31_HRP_S11


title: db1


title: DIPG6_MLL1_3

source_name: Patient-derived DIPG cells (SU-DIPG 6)

value: Brianstem


title: DIPG6_HRP_3


title: DIPG6_H3K4me3_3


title: Gossypol, 1 µg/ml SAMPLE 35

description:
Gossypol, 1 µg/ml
Test


title: DIPG6_H33_3


title: Gossypol, 50 µg/ml SAMPLE 43

description:
Gossypol, 50 µg/ml
Test

value: Gossypol, 50 ug/ml


title: KO_K27me3_S12

source_name: Patient-derived DIPG cells (CRISPR edited)

value: H3.3K27M KO


title: ato2

value: underwent 40 weeks atorvastatin treatment


title: CG2678 transheterozygous KO delta2_fs1 input

value: ovary


title: Gossypol, 0.5 µg/ml SAMPLE 33

description:
Gossypol, 0.5 µg/ml
Test


title: DIPG6_K27M_3


title: Gossypol, 0.5 µg/ml SAMPLE 32

description:
Gossypol, 0.5 µg/ml
Test


title: Gossypol, 1 µg/ml SAMPLE 34

description:
Gossypol, 1 µg/ml
Test

value: Gossypol, 1 ug/ml


title: Gossypol, 0.1 µg/ml SAMPLE 30

description:
Gossypol, 0.1 µg/ml
Test

value: Gossypol, 0.1 ug/ml


title: KO_K4me3_S13


title: Gossypol, 0.5 µg/ml SAMPLE 31

description:
Gossypol, 0.5 µg/ml
Test

value: Gossypol, 0.5 ug/ml


title: ato1


title: K27M_K4me3_S9


title: CG2678 transheterozygous KO delta2_fs1 Rhi-ChIP

value: anti-Rhi antibody (Rhino#1_3573gly)


title: K27M_K27M_S7

value: Brain


title: ato3


title: Gossypol, 0.1 µg/ml SAMPLE 29

description:
Gossypol, 0.1 µg/ml
Test

value: 8 h


title: Gossypol, 0.1 µg/ml SAMPLE 28

description:
Gossypol, 0.1 µg/ml
Test


title: KO_HRP_S11

value: DIPG


title: K27M_K27me3_S8


title: DIPG-6-2

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to hg19 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting was done using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file include raw counts, normalized abundance measurements and DESeq2 analysis

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel)
A bulk adaptation of the MARS-Seq protocol was used to generate RNA-Seq libraries for expression profiling.  30 ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.

treatment_protocol: no treatment

tag: region


title: GL>GFP-3xFLAG-HP1 input

tag: genotype


title: DIPG-6-1


title: K27M_HRP_S6


title: DIPG-48-2

source_name: Patient-derived DIPG cells (SU-DIPG 48)

value: WT


title: DMSO, 1% SAMPLE 27

description:
DMSO, 1%
Control

value: DMSO, 1%

tag: time


title: GL>GFP-3xFLAG-HP1 FLAG-ChIP

tag: antibody

value: anti-FLAG antibody (Sigma F1804-1MG)


title: DIPG-6-3


title: CG2678 transheterozygous KO delta1_fs1 Rhi-ChIP


title: DIPG-48-1


title: DMSO, 1% SAMPLE 26

description:
DMSO, 1%
Control

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.


title: Gossypol, 100 µg/ml SAMPLE 24

description:
Gossypol, 100 µg/ml
Test

value: Gossypol, 100 ug/ml

value: 2 h


title: CG2678 transheterozygous KO delta1_fs1 CG2678-ChIP


title: DIPG-48-3

value: Brianstem


title: DIPG-38-2

source_name: Patient-derived DIPG cells (SU-DIPG 38)


title: DIPG-38-3


title: DMSO, 1% SAMPLE 25

description:
DMSO, 1%
Control


title: DIPG-36-3

source_name: Patient-derived DIPG cells (SU-DIPG 36)


title: DIPG-38-1


title: CG2678 transheterozygous KO delta1_fs1 input


title: DIPG-36-2


title: Gossypol, 100 µg/ml SAMPLE 23

description:
Gossypol, 100 µg/ml
Test


title: DIPG-36-1


title: DIPG-13-2


title: MTD-Gal4 driven piwi KD input 1

value: w, MTD/+; MTD/+; MTD/pW20>piwi_sh2[attP2]/;


title: Gossypol, 100 µg/ml SAMPLE 22

description:
Gossypol, 100 µg/ml
Test


title: DIPG-13-1


title: DIPG-13-3


title: MTD-Gal4 driven rhino KD H3K9me2-ChIP biological replicate 1

value: w, MTD/+; MTD/+; MTD/pW20>rhi_sh[attP2]/;

value: anti-H3K9me2 antibody (mAbcam 1220)


title: DIPG6_H3K4me3_1


title: MTD-Gal4 driven CG2678 KD input 1

value: ovary


title: DIPG6_H3K27me3_1


title: Gossypol, 50 µg/ml SAMPLE 20

description:
Gossypol, 50 µg/ml
Test

value: Gossypol, 50 ug/ml


title: MTD-Gal4 driven rhino KD input 1


title: Gossypol, 50 µg/ml SAMPLE 19

description:
Gossypol, 50 µg/ml
Test


title: MTD-Gal4 driven piwi KD H3K9me2-ChIP biological replicate 1


title: DIPG6_K27M_1


title: DIPG48_HRP_1


title: MTD-Gal4 driven rhino KD H3K9me3-ChIP biological replicate 1

value: anti-H3K9me3 antibody (active motif 39161)


title: DIPG48_H3K4me3_1


title: DIPG48_H3K27ac_1


title: Gossypol, 10 µg/ml SAMPLE 18

description:
Gossypol, 10 µg/ml
Test

value: Gossypol, 10 ug/ml


title: Gossypol, 10 µg/ml SAMPLE 17

description:
Gossypol, 10 µg/ml
Test


title: Gossypol, 10 µg/ml SAMPLE 16

description:
Gossypol, 10 µg/ml
Test


title: Gossypol, 50 µg/ml SAMPLE 21

description:
Gossypol, 50 µg/ml
Test


title: MTD-Gal4 driven piwi KD H3K9me3-ChIP biological replicate 1


title: DIPG38_H3K4me3_1

value: Brain


title: DIPG6_HRP_1


title: DIPG38_H3K27me3_1


title: Gossypol, 5 µg/ml SAMPLE 15

description:
Gossypol, 5 µg/ml
Test

value: Gossypol, 5 ug/ml


title: DIPG6_K27ac_1

value: DIPG


title: DIPG38_H3K27ac_1


title: MTD-Gal4 driven CG2678 KD H3K9me2-ChIP biological replicate 1


title: MTD-Gal4 driven piwi KD Rhi-ChIP biological replicate 1

value: anti-Rhi antibody (Rhino#1_3573gly)


title: MTD-Gal4 driven CG2678 KD H3K9me3-ChIP biological replicate 1


title: DIPG38_K27M_1


title: DIPG36_H3K4me3_1


title: Gossypol, 5 µg/ml SAMPLE 14

description:
Gossypol, 5 µg/ml
Test


title: DIPG36_H3K27ac_1


title: MTD-Gal4 driven rhino KD Rhi-ChIP biological replicate 1


title: DIPG36_K27me3_1