title: Patient 6  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_14_barcodes.tsv.gz
MXMERZ002A_14_features.tsv.gz
MXMERZ002A_14_matrix.mtx.gz


title: Patient 14  apheresis  PB ADT

status: Public on Dec 15 2023

type: SRA

city: Leipzig

first: Maximilian

last: Merz

address: Liebigstr. 22

department: Department for Hematology, Cell Therapy and Hemostaseology

country: Germany

institute: University Hospital Leipzig

description:
10x Genomics
ADT
MXMERZ002A_12_barcodes.tsv.gz
MXMERZ002A_12_features.tsv.gz
MXMERZ002A_12_matrix.mtx.gz

library_source: other

data_processing:
The CAR sequences for Ide-cel and Cilta-cel were obtained from the respective patents. Two separate custom references for Cilta and Ide-cel have been created by adding the corresponding CAR sequences  to the reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cellranger v7.1.0. The Cellranger multi pipeline was used to process the single cell gene-expression, cell surface protein and V(D)J libraries. The feature reference CSV file, declaring Antibody Capture constructs and associated barcodes can be found in the supplementary files. The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: hg38
Supplementary files format and content: filtered and tab-separated value files and matrix files
Library strategy: ADT

molecule: protein

organism: Homo sapiens

source_name: Peripheral Blood

extract_protocol:
For single cell sequencing, mononuclear cells from bone marrow (BMMCs) and peripheral blood (PBMCs) were isolated following standardized operating procedures using Leucosep tubes (Greiner Bio One, Frickenhausen, Germany) with a Ficoll gradient (Ficoll-Paque™ PLUS, VWR Avantor, Spring House, Pennsylvania). Cells were frozen using a CoolCell LX container (Corning, USA) and stored in the vapour phase of liquid nitrogen in an Askion HS200S freezer (Askion, Gera, Germany). Prior to single cell staining and library construction, samples with initial viability < 80% were subjected to dead cell removal using Viahance™ from BioPAL, Inc. following the manufacturer’s instructions.
A custom panel of61oligonucleotide-coupled antibodies directed against cell surface proteins was used for surface proteome analyses. The oligonucleotides consist of a linker to the antibody, a polymerase chain reaction (PCR) handle, an antibody-specific barcode and a binding site for the cell identifying capture oligonucleotide. The antibody-oligonucleotide conjugate was afterwards incubated with the cells followed by the removal of unbound antibody. After single cell droplet encapsulation, the antibody-bound oligonucleotides act as synthetic transcripts and were then processed with 10x Genomics 5’ v2 chemistry to generate libraries for BCR, TCR, gene expression and surface protein expression.
scRNA + surface protein expression seq, BCRseq, TCRseq

tag: timepoint

value: time of leukapheresis

tag: cell type

value: PBMC

tag: tissue

value: Peripheral Blood

tag: patient sex

value: f

tag: patient age

tag: sample type

value: ADT


title: Patient 10  post CAR  BM ADT

description:
10x Genomics
ADT
MXMERZ002A_10_barcodes.tsv.gz
MXMERZ002A_10_features.tsv.gz
MXMERZ002A_10_matrix.mtx.gz

source_name: Bone Marrow

value: post CAR T cell infusion

value: BMMC

value: Bone Marrow

value: m


title: Patient 6  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_07_barcodes.tsv.gz
MXMERZ002A_07_features.tsv.gz
MXMERZ002A_07_matrix.mtx.gz


title: Patient 11  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_11_barcodes.tsv.gz
MXMERZ002A_11_features.tsv.gz
MXMERZ002A_11_matrix.mtx.gz


title: Patient 9  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_09_barcodes.tsv.gz
MXMERZ002A_09_features.tsv.gz
MXMERZ002A_09_matrix.mtx.gz


title: Patient 8  post CAR  BM ADT

description:
10x Genomics
ADT
MXMERZ002A_08_barcodes.tsv.gz
MXMERZ002A_08_features.tsv.gz
MXMERZ002A_08_matrix.mtx.gz


title: Patient 12  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_06_barcodes.tsv.gz
MXMERZ002A_06_features.tsv.gz
MXMERZ002A_06_matrix.mtx.gz


title: Patient 11  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_05_barcodes.tsv.gz
MXMERZ002A_05_features.tsv.gz
MXMERZ002A_05_matrix.mtx.gz


title: Patient 7  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_03_barcodes.tsv.gz
MXMERZ002A_03_features.tsv.gz
MXMERZ002A_03_matrix.mtx.gz


title: Patient 10  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_23_barcodes.tsv.gz
MXMERZ002A_23_features.tsv.gz
MXMERZ002A_23_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
The CAR sequences for Ide-cel and Cilta-cel were obtained from the respective patents. Two separate custom references for Cilta and Ide-cel have been created by adding the corresponding CAR sequences  to the reference genome (GRCh38, Ensembl release 98) and GENCODE v32 annotation using the mkref function from Cellranger v7.1.0. The Cellranger multi pipeline was used to process the single cell gene-expression, cell surface protein and V(D)J libraries. The feature reference CSV file, declaring Antibody Capture constructs and associated barcodes can be found in the supplementary files. The reference dataset required for the V(D)J contigs is provided by 10X Genomics (GRCh38 Human V(D)J Reference - 7.1.0 (December 7, 2022)).
Assembly: hg38
Supplementary files format and content: filtered and tab-separated value files and matrix files

molecule: total RNA

value: SC


title: Patient 10  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_22_barcodes.tsv.gz
MXMERZ002A_22_features.tsv.gz
MXMERZ002A_22_matrix.mtx.gz


title: Patient 7  post CAR BM ADT

description:
10x Genomics
ADT
MXMERZ002A_04_barcodes.tsv.gz
MXMERZ002A_04_features.tsv.gz
MXMERZ002A_04_matrix.mtx.gz


title: Patient 9  post CAR  BM SC

description:
10x Genomics
SC
MXMERZ002A_21_barcodes.tsv.gz
MXMERZ002A_21_features.tsv.gz
MXMERZ002A_21_matrix.mtx.gz


title: Patient 13  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_25_barcodes.tsv.gz
MXMERZ002A_25_features.tsv.gz
MXMERZ002A_25_matrix.mtx.gz


title: Patient 1  post CAR  BM ADT

description:
10x Genomics
ADT
MXMERZ002A_01_barcodes.tsv.gz
MXMERZ002A_01_features.tsv.gz
MXMERZ002A_01_matrix.mtx.gz


title: Patient 1  post CAR  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_02_barcodes.tsv.gz
MXMERZ002A_02_features.tsv.gz
MXMERZ002A_02_matrix.mtx.gz


title: Patient 8  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_20_barcodes.tsv.gz
MXMERZ002A_20_features.tsv.gz
MXMERZ002A_20_matrix.mtx.gz


title: Patient 14 post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_18_barcodes.tsv.gz
MXMERZ002A_18_features.tsv.gz
MXMERZ002A_18_matrix.mtx.gz


title: Patient 13 apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_17_barcodes.tsv.gz
MXMERZ002A_17_features.tsv.gz
MXMERZ002A_17_matrix.mtx.gz


title: Patient 9  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_15_barcodes.tsv.gz
MXMERZ002A_15_features.tsv.gz
MXMERZ002A_15_matrix.mtx.gz


title: Patient 12  post CAR  BM SC

description:
10x Genomics
SC
MXMERZ002A_16_barcodes.tsv.gz
MXMERZ002A_16_features.tsv.gz
MXMERZ002A_16_matrix.mtx.gz


title: Patient 1  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_13_barcodes.tsv.gz
MXMERZ002A_13_features.tsv.gz
MXMERZ002A_13_matrix.mtx.gz


title: Patient 8  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_19_barcodes.tsv.gz
MXMERZ002A_19_features.tsv.gz
MXMERZ002A_19_matrix.mtx.gz


title: Patient 6  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_14_barcodes.tsv.gz
MXMERZ002A_14_features.tsv.gz
MXMERZ002A_14_matrix.mtx.gz


title: Patient 14  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_12_barcodes.tsv.gz
MXMERZ002A_12_features.tsv.gz
MXMERZ002A_12_matrix.mtx.gz


title: Patient 11  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_11_barcodes.tsv.gz
MXMERZ002A_11_features.tsv.gz
MXMERZ002A_11_matrix.mtx.gz


title: Patient 1  apheresis  PB ADT

description:
10x Genomics
ADT
MXMERZ002A_13_barcodes.tsv.gz
MXMERZ002A_13_features.tsv.gz
MXMERZ002A_13_matrix.mtx.gz


title: Patient 10  post CAR  BM SC

description:
10x Genomics
SC
MXMERZ002A_10_barcodes.tsv.gz
MXMERZ002A_10_features.tsv.gz
MXMERZ002A_10_matrix.mtx.gz


title: Patient 9  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_09_barcodes.tsv.gz
MXMERZ002A_09_features.tsv.gz
MXMERZ002A_09_matrix.mtx.gz


title: Patient 8  post CAR  BM SC

description:
10x Genomics
SC
MXMERZ002A_08_barcodes.tsv.gz
MXMERZ002A_08_features.tsv.gz
MXMERZ002A_08_matrix.mtx.gz


title: Patient 6  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_07_barcodes.tsv.gz
MXMERZ002A_07_features.tsv.gz
MXMERZ002A_07_matrix.mtx.gz


title: Patient 12  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_06_barcodes.tsv.gz
MXMERZ002A_06_features.tsv.gz
MXMERZ002A_06_matrix.mtx.gz


title: Patient 11  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_05_barcodes.tsv.gz
MXMERZ002A_05_features.tsv.gz
MXMERZ002A_05_matrix.mtx.gz


title: Patient 7 post CAR BM SC

description:
10x Genomics
SC
MXMERZ002A_04_barcodes.tsv.gz
MXMERZ002A_04_features.tsv.gz
MXMERZ002A_04_matrix.mtx.gz


title: Patient 12  apheresis  PB SC

description:
10x Genomics
SC
MXMERZ002A_24_barcodes.tsv.gz
MXMERZ002A_24_features.tsv.gz
MXMERZ002A_24_matrix.mtx.gz


title: Patient 7 apheresis PB SC

description:
10x Genomics
SC
MXMERZ002A_03_barcodes.tsv.gz
MXMERZ002A_03_features.tsv.gz
MXMERZ002A_03_matrix.mtx.gz


title: Patient 1  post CAR  PB SC

description:
10x Genomics
SC
MXMERZ002A_02_barcodes.tsv.gz
MXMERZ002A_02_features.tsv.gz
MXMERZ002A_02_matrix.mtx.gz


title: Patient 1  post CAR  BM SC

description:
10x Genomics
SC
MXMERZ002A_01_barcodes.tsv.gz
MXMERZ002A_01_features.tsv.gz
MXMERZ002A_01_matrix.mtx.gz


title: Trigeminal ganglion (TG) cells, replicate 2, scRNAseq

status: Public on Dec 07 2023

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

country: USA

institute: UTHSA-GCCRI

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: trigeminal ganglion non-neuronal cells

extract_protocol:
Freshly collected trigeminal ganglia from wild-type untreated male C57black/B6 mice were treated by Librase (200ug/ml) and dispase II (300ug/ml) in Hanks for 60 min at 37 degree. Single cell susupension was generated by prituration of digested trigeminal ganglia. Suspension was filtered through 70um filter. Live cells were FACS sorted. Trigeminal ganglion cells were resuspended in DPBS supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Non-neuronal

value: trigeminal ganglia

tag: strain

tag: age

value: 6-8 weeks old


title: GSC11_Vehicle_2

status: Public on Dec 01 2023

description: Glioma stem cells treated with vehicle

library_source: transcriptomic

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the genes using htseq-count

source_name: glioma stem cells

growth_protocol: Primary GBM cells (GSC-111010) were subjected to CD133 sorting, and isolated CD133+ GSCs (GSC11) were treated with either vehicle or LY500307 (5 µM) for 24 h.  Cells were cultured as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL).

extract_protocol:
Cells were subjected to CD133 sorting and isolated CD133+ GSCs were treated with either vehicle or LY500307 (5 µM) for 24 h. Total RNA was isolated using RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from GSC11 after treatmet with either vehicle or LY500307 for 24 hours.

tag: treatment

value: Vehicle

value: Glioma stem cells


title: GSC11_LY500307_1

description: Glioma stem cells treated with ERβ agonist LY500307

value: ER[beta] agonist LY500307


title: Trigeminal ganglion (TG) cells, replicate 1, scRNAseq

description: 10x Genomics


title: GSC11_LY500307_2


title: spinal cord, CMT2A, day 30  [s_75]

status: Public on Nov 29 2023

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

description: bulk RNA

data_processing:
Bcl files were demultiplex to Fastq reads with bcl2fastq (v:2.20.0.422)
Fastq reads were mapped with STAR (v:2.7) with the following settings:  --quantMode GeneCounts --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outWigType wiggle --outWigStrand Stranded
resulting ReadsPerGene.out.tab were imported in R (v:4.1.1) and analyzed with edgeR (v:3.34.0)
Assembly: Mouse GRCm38.p6
Supplementary files format and content: Tab-delimited text files include count values for each sample (ReadsPerGene.out.tab output from STAR)

source_name: spinal cord

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit (Clontech) following manufacturer's protocols.

value: spinal cord

tag: genotype

tag: time

value: 30 days old


title: spinal cord, CMT2A, day 30  [s_74]

description: bulk RNA


title: spinal cord, CMT2A, day 30  [s_76]

description: bulk RNA


title: spinal cord, WT, day 30  [s_45]

description: bulk RNA


title: spinal cord, WT, day 30  [s_47]

description: bulk RNA


title: spinal cord, CMT2A, day 30  [s_43]

description: bulk RNA


title: spinal cord, CMT2A, day 30  [s_42]

description: bulk RNA


title: spinal cord, WT, day 30  [s_44]

description: bulk RNA


title: spinal cord, CMT2A, day 30  [s_41]

description: bulk RNA


title: L2/cgad-peig_ATC-_36hpi-2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
All RNA-seq Fastq reads were aligned with combined reference genome using STAR version 2.7.5a (parameters: --runThreadN 20)
Read count extraction was performed using htseq-count version 2.0.2 (parameters: -s no)
Assembly: Combined genome including Chlamydia trachomatis 434/Bu chromosome (GCF_000068585.1_ASM6858v1), C_trachomatis_pL2_plasmid_AM886278, and four genes cloned into the plasmid (ha-grgA, bla, tetR and mKate gene).
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

organism: Chlamydia trachomatis

growth_protocol: L2/cgad-peig-infected HeLa cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 0 or 1 nM ATC in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
RNA was harvested using Tri Reagent (MilliporeSigma). Genomic DNA was removed using RNase-free DNase I (New England Biolab).
2000 ng Total RNA was used for RNA-seq library preparation using Illumina TruSeq stranded mRNA-seq sample preparation protocol with the modifications to remove rRNAs from both host and bacteria, and mRNAs from host.

treatment_protocol: 0 or 1 nM ATC treatment started at the time of inoculation.

tag: cell line

value: 434/BU derivative

value: aadA::grgA, nh-grgA

value: 0 nM ATC

value: 36 hpi


title: L2/cgad-peig_ATC-_36hpi-3


title: spinal cord, CMT2A, day 30  [s_73]

description: bulk RNA


title: L2/cgad-peig_ATC-_36hpi-1


title: L2/cgad-peig_ATC-_24hpi-3

value: 24 hpi


title: L2/cgad-peig_ATC-_24hpi-1


title: L2/cgad-peig_ATC+_24hpi-2

value: 1 nM ATC


title: L2/cgad-peig_ATC+_18hpi-2

value: 18 hpi


title: L2/cgad-peig_ATC+_18hpi-1


title: L2/cgad-peig_ATC+_24hpi-3


title: L2/cgad-peig_ATC+_24hpi-1


title: GSC11_Vehicle_1

description: Glioma stem cells treated with vehicle


title: OVCAR3_Parental_INX_Rep3

status: Public on Nov 22 2023

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
trimmed reads were aligned using STAR (v2.7.5b) to the human reference genome (hg38)
Aligned reads were counted using featurecounts (v2.0.1) using annotations from GENCODE (gencode.vM25.basic.annotation.gtf)
Assembly: hg38
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

extract_protocol:
RNA was extracted from cell pellets using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using QuantSeq 3’ mRNA-Library Prep Kit FWD (Lexogen). RNA quantity and quality were assessed on TapeStation 4150 (Agilent). Reads were sequenced on NextSeq500 (Illumina) using 75-cycle High Output Reagent kits

treatment_protocol: OVCAR3 parental cells were treated with either control DMSO for 4 days or 300 nM INX-315 for 7 days. Cells were then colllected for RNA sequencing.

value: Ovarian Cancer

value: INX


title: OVCAR3_Parental_INX_Rep1


title: OVCAR3_Parental_INX_Rep2


title: OVCAR3_Parental_Control_Rep3

value: Untreated


title: OVCAR3_Parental_Control_Rep2


title: spinal cord, WT, day 30  [s_46]

description: bulk RNA


title: spinal cord, CMT2A, day 30  [s_72]

description: bulk RNA


title: CDK2i100mpkBID_2hrs_415_rep2

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
trimmed reads were aligned using STAR (v2.7.5b) to the human reference genome (hg38) and the mouse reference genome (mm10). Mouse reads were filtered out using XenofilteR (v1.6)
Aligned reads were counted using featurecounts (v2.0.1) using annotations from GENCODE (gencode.vM25.basic.annotation.gtf)
Assembly: hg38
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

source_name: Ovarian Cancer

extract_protocol:
RNA was extracted from crushed tumour pieces using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using QuantSeq 3’ mRNA-Library Prep Kit FWD (Lexogen). RNA quantity and quality were assessed on TapeStation 4150 (Agilent). Reads were sequenced on NextSeq500 (Illumina) using 75-cycle High Output Reagent kits

treatment_protocol: Tumour fragments from stock mice were harvested and implanted subcutaneously into the flank of NOD/SCID mice. Mice were treated by oral gavage with either control vehicle (PEG)200 mg/kg QD INX-315 or 100 mg/kg BID INX-315. After 40-50 days, tumors were harvested for RNA sequencing 2 hours post-final treatment.

tag: mouse number

value: NOD/SCID

tag: replicate


title: CDK2i100mpkBID_2hrs_442_rep3


title: CDK2i200mpkQD_2hrs_467_rep3


title: CDK2i200mpkQD_2hrs_446_rep2


title: CDK2i200mpkQD_2hrs_410_rep1


title: control_2hrs_455_rep5

value: control


title: control_2hrs_444_rep4


title: control_2hrs_429_rep3


title: control_2hrs_421_rep2


title: control_2hrs_416_rep1


title: T47D_LYFR_INX_rep3

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
trimmed reads were aligned using STAR (v2.7.5b) to the human reference genome (hg38)
Aligned reads were counted using featurecounts (v2.0.1)  using annotations from GENCODE (gencode.v35.annotation.gtf )
Assembly: hg38
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

treatment_protocol: Both parental (PAR) and abema-(LYR) or abema/fulvestrant-(LYFR) resistant MCF7 and T47D cells were treated with either control DMSO (+ abema or abema/fulv for resistant lines) for 7 days or 300 nM (MCF7) or 100 nM (T47D) INX-315 for 7 days. Cells were then colllected for RNA sequencing.

value: Breast Cancer

tag: condition

value: LYFR


title: L2/cgad-peig_ATC-_24hpi-2


title: L2/cgad-peig_ATC+_18hpi-3


title: T47D_LYFR_INX_rep2


title: T47D_LYFR_INX_rep1


title: T47D_LYFR_DMSO_rep1

value: DMSO


title: T47D_LYFR_DMSO_rep3


title: T47D_LYR_INX_rep3

value: LYR


title: T47D_LYR_INX_rep2


title: T47D_LYR_INX_rep1


title: T47D_LYFR_DMSO_rep2


title: T47D_LYR_DMSO_rep3


title: T47D_PAR_LY.INX_rep3

value: PAR


title: T47D_LYR_DMSO_rep2


title: T47D_PAR_LY.INX_rep2


title: OVCAR3_Parental_Control_Rep1


title: T47D_PAR_LY.INX_rep1


title: CDK2i100mpkBID_2hrs_406_rep1


title: T47D_PAR_INX_rep3


title: T47D_LYR_DMSO_rep1


title: T47D_PAR_INX_rep2


title: T47D_PAR_LY_rep3

value: LY


title: T47D_PAR_LY_rep1


title: T47D_PAR_DMSO_rep3


title: T47D_PAR_DMSO_rep2


title: T47D_PAR_INX_rep1


title: MCF7_LYFR_INX_rep2


title: MCF7_LYFR_INX_rep1


title: MCF7_LYFR_DMSO_rep2


title: MCF7_LYFR_INX_rep3


title: MCF7_LYFR_DMSO_rep3


title: MCF7_LYFR_DMSO_rep1


title: MCF7_LYR_INX_rep2


title: MCF7_LYR_INX_rep1


title: MCF7_LYR_INX_rep3


title: MCF7_LYR_DMSO_rep2


title: MCF7_LYR_DMSO_rep3


title: MCF7_PAR_LY.INX_rep2


title: MCF7_LYR_DMSO_rep1


title: MCF7_PAR_LY.INX_rep3


title: MCF7_PAR_LY.INX_rep1


title: MCF7_PAR_INX_rep3


title: MCF7_PAR_LY_rep3


title: MCF7_PAR_INX_rep1


title: MCF7_PAR_LY_rep1


title: MCF7_PAR_DMSO_rep3


title: MCF7_PAR_LY_rep2


title: MCF7_PAR_DMSO_rep2


title: MCF7_PAR_INX_rep2


title: T47D_PAR_LY_rep2


title: MCF7_PAR_DMSO_rep1


title: LYFR_INX_rep2

library_source: genomic

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
trimmed reads were aligned using BWA-MEM (v0.7.17) to the human reference genome (hg38)
Duplicate reads, blacklisted reads, chrM aligned reads and multimapping reads were filtered out using picard (v3.0.0; http://broadinstitute.github.io/picard/), samtools (v1.9) and bedtools (v2.27.1)
Peak calling was performed using Genrich with parameters “-a 100 -q 0.05 -g 1”. Bigwig files were made using deeptools (v3.5.0) with parameters “--binSize 1 --normalizeUsing RPGC --numberOfProcessors 5 –effectiveGenomeSize 2747877777”
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

extract_protocol: OmniATAC was performed on either fresh or cryopreserved cells using 50,000 nuclei per sample, using Illumina Tagment DNA enzyme and Buffer (Illumina, 20034197). qPCR side-reactions were performed to determine optimal PCR cycle number for each sample. Libraries were assessed using the TapeStation D1000 Assay and sequenced on the Illumina NextSeq 500 (75 bp paired end reads, approximately 30-40 million paired-end reads per sample).

treatment_protocol: MCF7 parental cells were treated for 7 days with either DMSO control, Abemaciclib (500nM), INX-315 (300nM) or both Abemaciclib and INX-315. MCF7 cells resistant to abemaciclib (500nM, LYR) or both abemaciclib and fulvestrant (500nM Abema, 100nM Fulvestrant, LYFR) were treated with DMSO (in combination to drugs the cells are resistant to) or 300nM INX-315 (in combination to drugs the cells are resistant to i.e. 100 nM Fulvestrant and/or 500nM Abema) for 7 days.

tag: resistance


title: T47D_PAR_DMSO_rep1


title: LYFR_DMSO_rep1


title: LYFR_DMSO_rep2


title: LYFR_INX_rep1


title: LYR_INX_rep2


title: LYR_DMSO_rep2


title: LYR_DMSO_rep1


title: Par_LYplusINX_rep2

value: LYplusINX


title: Par_LYplusINX_rep1


title: Par_INX_rep2


title: Par_DMSO_rep1


title: G2_0158_8hr_CDK2i_rep1

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
Trimmed reads were aligned using STAR (v2.7.5b) to the mouse reference genome (mm10)
Aligned reads were counted using featurecounts (v2.0.1) using annotations from GENCODE (gencode.vM25.basic.annotation.gtf)
Assembly: mm10
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

source_name: Gastric Cancer

treatment_protocol: Tumour fragments from stock mice were harvested and implanted subcutaneously into the flank of BALB/c nude mice. Mice were treated by oral gavage with either control vehicle (PEG) or 100 mg/kg BID INX-315. After 40-50 days, tumors were harvested for RNA sequencing either 2 hours or 8 hours  post-final treatment.

value: BALB/c nude

value: Gastric Cancer

tag: mouse


title: G2_0161_8hr_CDK2i_rep2


title: Par_LY_rep1


title: Par_LY_rep2


title: G2_0156_2hr_CDK2i_rep2


title: G1_0167_2hr_control_rep2

value: Vehicle


title: G2_0153_2hr_CDK2i_rep1


title: G1_0185_8hr_control_rep2


title: G1_0180_8hr_control_rep1


title: G1_0150_2hr_control_rep1


title: LY.INX_443_rep5

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were trimed using bbduk (v38.90) to remove adapter sequences and poor quality ends.
trimmed reads were aligned using STAR (v2.7.5b) to the mouse reference genome (mm10)
Aligned reads were counted using featurecounts (v2.0.1) using annotations from GENCODE (gencode.vM25.basic.annotation.gtf)
Assembly: mm10
Supplementary files format and content: csv file include raw count (non-normalised) values for each sample

source_name: Breast Cancer

extract_protocol:
RNA was extracted from crushed tumor samples using NucleoSpin® RNA plus kit (MachereyNagel, 40955) per manufacturers protocol.
Libraries were prepared using QuantSeq 3’ mRNA-Library Prep Kit FWD (Lexogen). RNA quantity and quality were assessed on TapeStation 4150 (Agilent). Reads were sequenced on NextSeq500 (Illumina) using 75-cycle High Output Reagent kits

treatment_protocol: Mice were treated with either control vehicle (PEG), Abemaciclib (50 mg/kg QD), INX-315 (50 mg/kg BID) or both for 7 days. Tumors were harvested at endpoint and crushed using liquid nitrogen.

tag: tumor number

value: MMTV-rtTA:+, tetO-HER2:+


title: LY.INX_443_rep3

tag: cell type


title: INX_395_rep4


title: INX_395_rep3


title: INX_395_rep1


title: LY.INX_443_rep2


title: LY.INX_443_rep4


title: LY_406_rep4


title: LY_406_rep5


title: LY_406_rep1


title: LY_406_rep3


title: LY_406_rep2


title: LYR_INX_rep1


title: Par_INX_rep1


title: Veh_426_rep5

value: Veh


title: Veh_426_rep4


title: INX_395_rep2


title: Par_DMSO_rep2


title: Veh_426_rep2


title: Veh_394_rep1


title: LY.INX_302_15days_rep1

treatment_protocol: Mice were treated with either control vehicle (PEG), Abemaciclib (50 mg/kg QD), INX-315 (50 mg/kg BID) or both for up to 23 days. Resistant tumors were harvested at endpoint and crushed using liquid nitrogen.


title: LY.INX_302_15days_rep2


title: LY.INX_306_7days_rep2


title: INX_307_23days_rep1


title: INX_307_23days_rep2


title: LY.INX_306_7days_rep1


title: LY.INX_443_rep1


title: LY.INX_306_7days_rep3


title: LY_311_9days_rep2


title: Veh_297_23days_rep1


title: LY_311_9days_rep1


title: LY_303_23days_rep2


title: LY_311_9days_rep3


title: Veh_309_9days_rep3


title: Veh_309_9days_rep4


title: LY_303_23days_rep1


title: Veh_309_9days_rep2


title: Veh_309_9days_rep5


title: Veh_309_9days_rep1


title: Veh_426_rep3


title: Male_paw_Veh_2

status: Public on Nov 17 2023

description: rRNA depleted RNA

data_processing:
Illumina bcl2fastq software used for base-calling.
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: UCSC mouse genome build mm9 (MGSCv37)
Supplementary_files_format_and_content: *_Genes_ReadCount.txt: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count.

source_name: hindpaw tissue

extract_protocol:
Fresh tissues were homogenized in RNeasy solution using Bead Mill Homogenizer (Omni International, Kennesaw, GA).
Approximately 500ng total RNA was used for RNA-seq library preparation by either following the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) sample preparation guide (Cat. No: KR1151, KAPA Biosystems, USA), or TruSeq stranded mRNA-seq library preparation kit (Cat. No: 20020595, Illumina, USA). Following rRNA removal or mRNA enrichment, the RNA was fragmented into small pieces using divalent cautions under elevated temperature and magnesium. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). The incorporation of dUTP in second strand synthesis effectively quenches the second strand during amplification, since the polymerase used in the assay will not incorporate past this nucleotide. These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-Seq library for sequencing by 50bp single-end protocol with Illumina HiSeq 3000 platform.

treatment_protocol: PBS single i.pl. injection; PBS 12d i.pl. injection (one per day); PRL (1ug) i.pl. injection; PRL (1ug) 12d i.pl. injection (one per day).

value: 10-12 weeks

tag: Sex

value: Male

tag: tissue

value: Hindpaw tissue


title: Male_paw_Veh_3

description: rRNA depleted RNA


title: Male_paw_PRL_3

description: rRNA depleted RNA

value: Prolactin


title: Male_paw_Veh_1

description: rRNA depleted RNA


title: Male_paw_PRL_1

description: rRNA depleted RNA


title: Male_paw_PRL_2

description: rRNA depleted RNA


title: Male_DRG_Veh_2

description: rRNA depleted RNA

source_name: dorsal root ganglion

value: Dorsal root ganglion


title: INX_331_8days_rep2

value: Breast Cancer

value: INX


title: INX_340_23days_rep1


title: INX_340_23days_rep2


title: Male_DRG_PRL_2

description: rRNA depleted RNA


title: INX_331_8days_rep1


title: Male_DRG_PRL_1

description: rRNA depleted RNA


title: Female_paw_Veh_3

description: rRNA depleted RNA

value: Female


title: Male_DRG_Veh_1

description: rRNA depleted RNA


title: Female_paw_Veh_2

description: rRNA depleted RNA


title: Male_DRG_PRL_3

description: rRNA depleted RNA


title: Female_paw_Veh_1

description: rRNA depleted RNA


title: Female_paw_PRL_Sh_1

description: mRNA


title: Female_paw_PRL_Sh_2

description: mRNA


title: Female_paw_PRL_3

description: rRNA depleted RNA


title: Female_paw_PRL_2

description: rRNA depleted RNA


title: Female_paw_PRL_Sh_3

description: mRNA


title: Female_DRG_Veh_3

description: rRNA depleted RNA


title: Female_DRG_Veh_1

description: rRNA depleted RNA


title: Female_DRG_PRL_Sh_3

description: mRNA


title: Female_paw_PRL_1

description: rRNA depleted RNA


title: Female_DRG_PRL_Sh_2

description: mRNA


title: Female_DRG_Veh_2

description: rRNA depleted RNA


title: Female_DRG_PRL_2

description: rRNA depleted RNA


title: ES2_KDM1A-KO+LY500307_2

status: Public on Oct 16 2023

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the genes using htseq-count

source_name: ovarian cancer cell line

growth_protocol: ES2 cells were cultured in McCoy's 5a Medium Modified, supplemented with 10% FBS.

extract_protocol:
ES2-control and ES2-KDM1A knockout cells were treated with vehicle or LY500307 (5 µM) for 48 hours. RNA was isolated using RNeasy mini kit and subjected to RNA-seq on illumina HiSeq 3000 system using Illumina TruSeq stranded mRNA-seq library preparation kit
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

value: ovarian cancer cell line

value: Knockout+Treatment

tag: group

value: ES2 KDM1A knockout cells treated with LY500307


title: ES2_KDM1A-KO+LY500307_1

treatment_protocol: ES2-control and ES2-KDM1A knockout cells were treated with vehicle or LY500307 (5 µM) for 48 hours.


title: ES2_Control+LY500307_2

value: Control+Treatment

value: ES2 control cells treated with LY500307


title: Female_DRG_PRL_1

description: rRNA depleted RNA


title: ES2_Control+LY500307_1


title: ES2_KDM1A-KO_2

value: Knockout

value: ES2 KDM1A knockout cells


title: ES2_KDM1A-KO_1


title: ES2_Control_1

value: Control

value: ES2 control cells


title: Male_DRG_Veh_3

description: rRNA depleted RNA

value: 10-12 weeks

value: Veh


title: SKBR3_rep3

status: Public on Oct 08 2023

city: Nanjing

first: Nignjun

last: Duan

address: 300 Guangzhou Road

country: China

institute: JSPH

data_processing:
RNA-seq reads were aligned to the hg38 build of the human genome reference using STAR 2.4.2a.
The GENCODE v19 annotation was used for the STAR alignment and all other quantifications.
Gene level read count values were calculated using RNA-SeQC v1.1.8.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: Breast; Mammary gland, epithelial


title: SKBR3_rep1


title: SKBR3_rep2


title: Sample_03_blood

status: Public on Oct 03 2023

data_processing:
Raw blc files were converted into fastq files using the Cell Ranger pipeline suite of 10X Genomics (version 3.0.2).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix starting from raw data.
Gene expression matrices were used as input for Seurat clustering (R version 3.6.1; Seurat version 3.1.1)
Genome_build: Pre-build Human genome (version GRCh38) was used as genome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell

source_name: CD3+ cells

extract_protocol:
Lymphoid cells sorted from blood of 3 CLM patients were subjected to scRNA-seq analysis. CD3+ FACS-sorted cells were counted with an automatic cell-counter (Countess II, Thermo Fisher) and loaded into one channel of the Single Cell Chip A using the Single Cell reagent kit v3 (10X Genomic) from gel bead emulsion generation.
Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol. 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq550 Illumina sequencing platform following 10xGenomics instruction for read generation, reaching at least 35000 reads as mean reads per cell.

value: Blood sample

tag: tissuee type

value: Blood samples from colon cancer metastatic patients


title: Sample_02_blood


title: sample.nalm6_no_rad_2

status: Public on Sep 27 2023

city: St. Louis

first: Carl

last: DeSelm

state: MO

address: 325 S. Euclid Ave

department: Radiation Oncology

institute: Washington University in St. Louis

data_processing:
Sequencing reads were mapped to the GRCh38/hg38 genome assembly by STAR (version 2.5.1a, RRID: SCR_004463) using ENSEMBL release 76 gene annotations
Gene expression was characterized using  featureCounts (v2.0.1) to obtain read counts
Counts were normalized for library sampling depth using size factor normalization in DESeq2 (RRID: SCR_015687)
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts in tab-delimitted text format
Supplementary files format and content: Tab-delimited matrix of size factor normalized expression values for all genes of all samples

source_name: Nalm6 cell line

extract_protocol:
Total RNA was isolated from 5 M Nalm6 cells by lysing with Trizol Reagent (Invitrogen Waltham, MA) followed by extraction with 24:1 chloroform:isoamyl alcohol (Sigma Aldrich St. Louis, MO). After separation by centrifugation, the aqueous phase was frozen in 100% isopropanol overnight, and then RNA was then precipitated and washed twice with 75% ethanol. RNA yield was quantified using an Epoch Microplate Spectrophotometer (Biotek Winooski, VT). From each isolate 10 µg of RNA was treated with 2 units of DNAse I for 10 minutes at 37 °C and purified on a Monarch RNA Cleanup Spin Column (New England Biolabs Ipswich, MA), all according to the manufacturer’s instructions.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was blocked using FastSelect reagents (Qiagen) during cDNA synthesis. RNA was fragmented in reverse transcriptase buffer with FastSelect reagent and heating to 94 degrees for 5 minutes, 75 degrees for 2 minutes, 70 degrees for 2 minutes, 65 degrees for 2 minutes, 60 degrees for 2 minutes, 55 degrees for 2 minutes, 37 degrees for 5 minutes, 25 degrees for 5 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

tag: dose

value: Pre-treatment

tag: batch


title: sample.6_8_7_3

value: Day 7


title: sample.6_8_7_1


title: sample.6_8_7_2


title: Female_DRG_PRL_3

description: rRNA depleted RNA

tag: strain

tag: age

value: Female

value: Dorsal root ganglion

tag: treatment

value: Prolactin


title: sample.6_8_24_2

tag: cell line

tag: time

value: 24 hrs


title: sample.6_8_24_4


title: sample.6_nr_24_1


title: Female_DRG_PRL_Sh_1

description: mRNA


title: sample.6_8_24_3


title: sample.6_8_24_1


title: ES2_Control_2

value: ovarian cancer cell line


title: sample.6_nr_24_2


title: sample.no_rad_d21

value: Day 21


title: sample.no_rad_24hrs


title: sample.1.8gy_d7


title: sample.1.8gy_24hrs


title: sample.6_nr_24_3


title: MISTRG6 scleroderma skin graft 6 [HSC-engrafted]

status: Public on Sep 20 2023

city: New Haven

first: Ian

last: Odell

state: CT

address: 330 Cedar St. LMP-5040

department: Dermatology

institute: Yale University

description: 10x Genomics

data_processing:
The 10x genomics Cell Ranger pipeline was used to align the reads, perform clustering and gene expression analysis, and aggregate the samples with normalized read counts. All 10x experiments were completed with the same 3’ chemistry and high-throughput sequencer to avoid batch effects. CellRanger was run 3 times using 3 different genomes: mm10, hg19, and a combined mm10 and GRCh38 genome. The analysis for the mm10, hg19, and combined mm10-GRCh38 genome was conducted separately but followed the same procedure. The raw matrices from Cell Ranger each of the genomes were processed and analyzed using Seurat version 3 R toolkit for single cell genomics (76, 77). For the matrices aligned to the mm10 genome and the combined mm10-GRCh38 genome, low quality cells with a high mitochondrial percentage of over 7.5% were filtered out. For the matrices aligned to the hg19 genome, low quality cells with a mitochondrial percentage of over 10% were filtered out. After initial filtering, the data was normalized (log normalized using the default scaling factor of 10000), scaled, principal components were calculated, and the data was visualized using a UMAP embedding of the data. After determining the clusters, canonical markers were used to identify the different cell types present. Once the canonical markers were identified, we used DAseq (27) to identify the regions that were differentially abundant between HSC engraftment and unengrafted samples. From DAseq, we were able to identify cell types that had differentially abundant regions and then looked at differential gene expression in those cell types using Seurat. After differential expression analysis, we performed pathway analysis of genes with adjusted p-value of less than 0.05 using Metascape (78) to identify pathways associated with genes upregulated in either the HSC or unengrafted samples
Assembly: GRCh38 and mm10
Supplementary files format and content: h5

organism:
Homo sapiens
Mus musculus

source_name: Skin

extract_protocol:
Skin grafts were incubated in RPMI 1640 medium (Gibco) containing 5% fetal bovine serum (5% FBS/RPMI) and 10 mg/ml Dispase II (Sigma D4693-1G) for 45 minutes at 37° C shaking at 200-250 rpm. The sample was then removed from the media and minced with sterile iris scissors, followed by digestion with Liberase TM (Sigma) 0.5 mg/ml and DNase I 30 Units/ml in 5% FBS/RPMI for 45 minutes at 37° C shaking at 200-250 rpm. The resulting single cell suspension was then filtered through a 70 mm nylon membrane and washed. Live cells were sorted on a FACSAria and their final concentration and viability quantified with Trypan blue on a hemacytomer. The cells were pelleted and suspended in phosphate buffered saline containing 0.04% bovine serum albumin between 500-1000 cells/ml. 3000-6000 cells with greater than 80% viability were submitted to the Yale DNA Sequencing facility for generation of single-cell cDNA libraries using the Chromium Single Cell Controller (10x Genomics).
per 10x Genomics protocol using Single Cell 3' v2. Each cDNA library was sequenced paired-end on 1 lane with 75 base-pair read length using the Illumina HiSeq 2500 System generating at least 75,000 reads per cell.

value: Skin

value: HSC engrafted


title: MISTRG6 scleroderma skin graft 3 [HSC-unengrafted]

description: 10x Genomics

value: no HSC


title: MISTRG6 scleroderma skin graft 2 [HSC-unengrafted]

description: 10x Genomics


title: MISTRG6 scleroderma skin graft 5 [HSC-engrafted]

description: 10x Genomics


title: MISTRG6 scleroderma skin graft 4 [HSC-engrafted]

description: 10x Genomics


title: MISTRG6 scleroderma skin graft 1 [HSC-unengrafted]

description: 10x Genomics


title: Sample_01_blood


title: Root-non_inoculated-control-3 [R-NI-C-3]

status: Public on Sep 12 2023

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description:
OZMYC47
This sample is from roots of plants with non-inoculated roots under control conditions . It is the third of four biological replicates used in this experiment.

data_processing:
Illumina software was used by the Genotoul sequencing facilities (Toulouse, France) to generate fastq raw data files
Raw reads were filtered and trimmed using erne-filter command (Erne v2.1.1, default parameters except --min-size=70;   Del Fabbro et al., 2013). Filtered reads from each library were aligned to P. trichocarpa (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1)  using TopHat2 v2.12 (Trapnell et al., 2009; D. Kim et al., 2013). The genome was indexed with the ‘bowtie-build’ command   from the genome sequence fasta file.   TopHat2 default parameters were used except: -r 60 --mate-std-dev 25 --read-mismatche 15 --read-gap-length 15 --read-edit-dist 30 -I 20000 -i 20 --read-realign-edit-dist 10 --max-insertion-length 19 --max-deletion-length 19 -g 10 --segment-mismatches 3 --segment-length 25 --min-segment-intron 20 --max-segment-intron 20000 --b2-very-sensitive.   Reads that mapped once were extracted from BAM files (accepted_hits.bam, TopHat2 output) using the NH:i:1 tag as   described by Loraine et al. (2013). We considered only genes that contained a minimum of 10 reads in the four replicates of a treatment as expressed genes.
DESEQ2 was used for normalisation of data and co-expression network analysis (WGCNA) to identify differentially expressed genes
Genome_build: reference genome sequence of Populus tricocarpa  (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1)
Supplementary_files_format_and_content: tab-delimited text file including aligned reads (raw counts) and normalised expression values (DESEQ2).nd; not used in DESEQ2 due to no or background expression.

organism: Populus trichocarpa

growth_protocol: Cuttings of the western poplar Populus trichocarpa (Washington clone 101-74) were rooted for two weeks in distillated water under climate-controlled greenhouse conditions, under a 16-h photoperiod and a temperature of 22°C (day). A random batch of young rooted poplars were then transplanted on well-dampened calcined attapulgite clay (Turf-Pro, Toul, France) and correspond to non-inoculated poplar roots (“NI” modality). Another random batch of poplar was transplanted in a mix of the ectomycorrhizal (ECM) fungal inoculum Laccaria bicolor into well dampened calcinated attapulgite clay (inoculated poplar roots “I” modality). The fungal inoculum was prepared as described in Plett et al., 2011. Regardless to the colonization modality, each pot was given 20 ml of a diluted nutrient solution (0.8 mM KNO3, 0.8 mM Ca (NO3)2, 4 H2O, 0.3 mM NaH2PO4, 0.3 mM MgSO4,7 H2O, and the commercial trace-element solution Kanieltra (CO- FAZ, BP 198-08, Paris, France). To allow plant rooting and symbiosis development, poplars were kept three months under climate-controlled greenhouse conditions, maintaining a 16-h photoperiod, with a photosynthetic photon flux density (PPFD) of 450–500 μmol m–2s-1 and a day temperature of 22°C. In June 2019, I and NI were transferred into phytotron chambers with a PPFD of 470–500 μmol m–2s-1 and a day temperature of 22°C for acclimation two weeks before the application of the short-term environmental challenges.

extract_protocol:
Total RNA of each sample was extracted separately. The RNA extraction was performed using the RNeasy Plant mini kit (Qiagen, Courtaboeuf, France) per the manufacturer’s instructions, with the addition of 25 mg of polyethylene glycol 8000 per milliliter of RLC buffer (RNeasy, Qiagen). A DNA digestion step with DNAse I (Ambion, Invitrogen) was also included to remove DNA contamination. RNA quality was verified by Nanodrop (Thermo Fisher Scientific) and Fragment Analyzer (Agilent, Santa Clara, USA).
Stranded cDNA sequencing libraries were generated from 1-3 µg of total pooled RNA following the manufacturer’s instructions (Illumina Inc., USA) followed by Illumina HiSeq 3000 mRNA sequencing   (RNA-Seq) at the Genotoul sequencing facilities (Toulouse, France).

treatment_protocol: Three treatments were applied on randomly assigned batch of inoculated and non-inoculated poplars. One third of trees were submitted to ozone exposure (“O” modality), or to stop watering (“SW” modality) while   the remaining trees were kept in the initial growth conditions (“C” modality). To ensure that trees were   submitted to only one treatment, O and C plants were watered to field capacity twice a day and SW and C plants   were cultivated under coal-filtered air. In details, O plants were exposed to 200 nmol mol-1 O3 using the control   device previously published (Dusart et al., 2019) during the 8 hours preceding the harvest (from 5h to 13h in the light time).   For SW plants, the watering was withheld 43h before harvest. At the end of treatments, trees were harvested   following a random sampling to avoid batch effects between inoculated or not (I or NI) control and treated poplars.   For the molecular analysis, two mature leaves per plant (9 and 10th from the apex) were sampled and immediately flash frozen.   Then, root system was rapidly washed; samples of bare fine roots and mycorrhizae-enriched fine roots (denoted “myc”)   were rapidly (in less than 30 min) sampled under binocular and flash-frozen in liquid nitrogen.    We pooled three or four plants per biological replicate and we made four replicates per modality.   The biological replicates were paired-distributed among organs (i.e. leaf, root or myc libraries with the same index   were constructed from the same pool of plants)."

tag: clone

tag: inoculation

value: Roots not inoculated

value: Control conditions

value: Roots


title: Root-non_inoculated-control-4 [R-NI-C-4]

description:
OZMYC48
This sample is from roots of plants with non-inoculated roots under control conditions . It is the fourth of four biological replicates used in this experiment.

value: Populus trichocarpa (Washington clone 101-74)


title: sample.6_8_7_4


title: sample.nalm6_no_rad_3


title: Root-non_inoculated-ozone-4 [R-NI-O-4]

description:
OZMYC44
This sample is from roots of plants with non-inoculated roots and treated with ozone . It is the fourth of four biological replicates used in this experiment.

value: Ozone treatment


title: Root-non_inoculated-control-2 [R-NI-C-2]

description:
OZMYC46
This sample is from roots of plants with non-inoculated roots under control conditions . It is the second of four biological replicates used in this experiment.


title: Root-non_inoculated-control-1 [R-NI-C-1]

description:
OZMYC45
This sample is from roots of plants with non-inoculated roots under control conditions . It is the first of four biological replicates used in this experiment.


title: Root-non_inoculated-ozone-3 [R-NI-O-3]

description:
OZMYC43
This sample is from roots of plants with non-inoculated roots and treated with ozone . It is the third of four biological replicates used in this experiment.


title: Root-non_inoculated-ozone-2 [R-NI-O-2]

description:
OZMYC42
This sample is from roots of plants with non-inoculated roots and treated with ozone . It is the second of four biological replicates used in this experiment.


title: Root-non_inoculated-stop_watering-4 [R-NI-SW-4]

description:
OZMYC40
This sample is from roots of plants with non-inoculated roots and stopped watering . It is the fourth of four biological replicates used in this experiment.

value: Stop watering


title: Root-non_inoculated-stop_watering-1 [R-NI-SW-1]

description:
OZMYC37
This sample is from roots of plants with non-inoculated roots and stopped watering . It is the first of four biological replicates used in this experiment.


title: Root-non_inoculated-stop_watering-2 [R-NI-SW-2]

description:
OZMYC38
This sample is from roots of plants with non-inoculated roots and stopped watering . It is the second of four biological replicates used in this experiment.


title: Root-non_inoculated-ozone-1 [R-NI-O-1]

description:
OZMYC41
This sample is from roots of plants with non-inoculated roots and treated with ozone . It is the first of four biological replicates used in this experiment.


title: sample.pre_radiation

value: Pre-treatment


title: Leaf-non_inoculated-control-2 [L-NI-C-2]

description:
OZMYC22
This sample is from leaves of plants with non-inoculated roots under control conditions . It is the second of four biological replicates used in this experiment.

value: Leaves


title: Root-non_inoculated-stop_watering-3 [R-NI-SW-3]

description:
OZMYC39
This sample is from roots of plants with non-inoculated roots and stopped watering . It is the third of four biological replicates used in this experiment.


title: Leaf-non_inoculated-control-4 [L-NI-C-4]

description:
OZMYC24
This sample is from leaves of plants with non-inoculated roots under control conditions . It is the fourth of four biological replicates used in this experiment.


title: Leaf-non_inoculated-ozone-4 [L-NI-O-4]

description:
OZMYC20
This sample is from leaves of plants with non-inoculated roots and treated with ozone . It is the fourth of four biological replicates used in this experiment.


title: Leaf-non_inoculated-ozone-2 [L-NI-O-2]

description:
OZMYC18
This sample is from leaves of plants with non-inoculated roots and treated with ozone . It is the second of four biological replicates used in this experiment.


title: Leaf-non_inoculated-control-3 [L-NI-C-3]

description:
OZMYC23
This sample is from leaves of plants with non-inoculated roots under control conditions . It is the third of four biological replicates used in this experiment.


title: Leaf-non_inoculated-ozone-3 [L-NI-O-3]

description:
OZMYC19
This sample is from leaves of plants with non-inoculated roots and treated with ozone . It is the third of four biological replicates used in this experiment.


title: Leaf-non_inoculated-ozone-1 [L-NI-O-1]

description:
OZMYC17
This sample is from leaves of plants with non-inoculated roots and treated with ozone . It is the first of four biological replicates used in this experiment.


title: Leaf-non_inoculated-control-1 [L-NI-C-1]

description:
OZMYC21
This sample is from leaves of plants with non-inoculated roots under control conditions . It is the first of four biological replicates used in this experiment.


title: Leaf-non_inoculated-stop_watering-4 [L-NI-SW-4]

description:
OZMYC16
This sample is from leaves of plants with non-inoculated roots and stopped watering . It is the fourth of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-control-4 [Myc-C-4]

description:
OZMYC60
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor under control conditions . It is the fourth of four biological replicates used in this experiment.

organism:
Populus trichocarpa
Laccaria bicolor

source_name: Mycorrhiza-inoculated-control

value: Populus trichocarpa (Washington clone 101-74)-Laccaria bicolor S238N

value: Roots inoculated with Laccaria bicolor


title: Leaf-non_inoculated-stop_watering-2 [L-NI-SW-2]

description:
OZMYC14
This sample is from leaves of plants with non-inoculated roots and stopped watering . It is the second of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-control-3 [Myc-C-3]

description:
OZMYC59
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor under control conditions . It is the third of four biological replicates used in this experiment.


title: Leaf-non_inoculated-stop_watering-1 [L-NI-SW-1]

description:
OZMYC13
This sample is from leaves of plants with non-inoculated roots and stopped watering . It is the first of four biological replicates used in this experiment.


title: Leaf-non_inoculated-stop_watering-3 [L-NI-SW-3]

description:
OZMYC15
This sample is from leaves of plants with non-inoculated roots and stopped watering . It is the third of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-control-2 [Myc-C-2]

description:
OZMYC58
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor under control conditions . It is the second of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-ozone-4 [Myc-O-4]

description:
OZMYC56
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the fourth of four biological replicates used in this experiment.

source_name: Mycorrhiza-inoculated-ozone


title: Mycorrhiza-inoculated-control-1 [Myc-C-1]

description:
OZMYC57
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor under control conditions . It is the first of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-ozone-2 [Myc-O-2]

description:
OZMYC54
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the second of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-ozone-1 [Myc-O-1]

description:
OZMYC53
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the first of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-stop_watering-2 [Myc-SW-2]

description:
OZMYC50
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the second of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-ozone-3 [Myc-O-3]

description:
OZMYC55
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the third of four biological replicates used in this experiment.


title: Root-inoculated-control-4 [R-I-C-4]

description:
OZMYC36
This sample is from roots of plants with roots inoculated with Laccaria bicolor under control conditions . It is the fourth of four biological replicates used in this experiment.

source_name: Root-inoculated-control


title: Mycorrhiza-inoculated-stop_watering-1 [Myc-SW-1]

description:
OZMYC49
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the first of four biological replicates used in this experiment.


title: Root-inoculated-control-2 [R-I-C-2]

description:
OZMYC34
This sample is from roots of plants with roots inoculated with Laccaria bicolor under control conditions . It is the second of four biological replicates used in this experiment.


title: Root-inoculated-control-1 [R-I-C-1]

description:
OZMYC33
This sample is from roots of plants with roots inoculated with Laccaria bicolor under control conditions . It is the first of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-stop_watering-4 [Myc-SW-4]

description:
OZMYC52
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the fourth of four biological replicates used in this experiment.


title: Root-inoculated-control-3 [R-I-C-3]

description:
OZMYC35
This sample is from roots of plants with roots inoculated with Laccaria bicolor under control conditions . It is the third of four biological replicates used in this experiment.


title: Root-inoculated-ozone-2 [R-I-O-2]

description:
OZMYC30
This sample is from roots of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the second of four biological replicates used in this experiment.

source_name: Root-inoculated-ozone


title: Root-inoculated-ozone-3 [R-I-O-3]

description:
OZMYC31
This sample is from roots of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the third of four biological replicates used in this experiment.


title: Root-inoculated-ozone-4 [R-I-O-4]

description:
OZMYC32
This sample is from roots of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the fourth of four biological replicates used in this experiment.


title: Root-inoculated-stop_watering-4 [R-I-SW-4]

description:
OZMYC28
This sample is from roots of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the fourth of four biological replicates used in this experiment.


title: Root-inoculated-stop_watering-2 [R-I-SW-2]

description:
OZMYC26
This sample is from roots of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the second of four biological replicates used in this experiment.


title: Root-inoculated-ozone-1 [R-I-O-1]

description:
OZMYC29
This sample is from roots of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the first of four biological replicates used in this experiment.


title: Root-inoculated-stop_watering-3 [R-I-SW-3]

description:
OZMYC27
This sample is from roots of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the third of four biological replicates used in this experiment.


title: Root-inoculated-stop_watering-1 [R-I-SW-1]

description:
OZMYC25
This sample is from roots of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the first of four biological replicates used in this experiment.


title: Leaf-inoculated-control-4 [L-I-C-4]

description:
OZMYC12
This sample is from leaves of plants with roots inoculated with Laccaria bicolor under control conditions . It is the fourth of four biological replicates used in this experiment.

source_name: Leaf-inoculated-control


title: Leaf-inoculated-control-2 [L-I-C-2]

description:
OZMYC10
This sample is from leaves of plants with roots inoculated with Laccaria bicolor under control conditions . It is the second of four biological replicates used in this experiment.


title: Leaf-inoculated-control-1 [L-I-C-1]

description:
OZMYC9
This sample is from leaves of plants with roots inoculated with Laccaria bicolor under control conditions . It is the first of four biological replicates used in this experiment.


title: Leaf-inoculated-ozone-3 [L-I-O-3]

description:
OZMYC7
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the third of four biological replicates used in this experiment.

source_name: Leaf-inoculated-ozone


title: Leaf-inoculated-ozone-4 [L-I-O-4]

description:
OZMYC8
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the fourth of four biological replicates used in this experiment.


title: Leaf-inoculated-ozone-2 [L-I-O-2]

description:
OZMYC6
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the second of four biological replicates used in this experiment.


title: Leaf-inoculated-ozone-1 [L-I-O-1]

description:
OZMYC5
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and treated with ozone . It is the first of four biological replicates used in this experiment.


title: Mycorrhiza-inoculated-stop_watering-3 [Myc-SW-3]

description:
OZMYC51
This sample is from ectomycorrhiza of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the third of four biological replicates used in this experiment.


title: Leaf-inoculated-stop_watering-3 [L-I-SW-3]

description:
OZMYC3
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the third of four biological replicates used in this experiment.


title: Leaf-inoculated-stop_watering-2 [L-I-SW-2]

description:
OZMYC2
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the second of four biological replicates used in this experiment.


title: Leaf-inoculated-stop_watering-4 [L-I-SW-4]

description:
OZMYC4
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the fourth of four biological replicates used in this experiment.


title: Leaf-inoculated-stop_watering-1 [L-I-SW-1]

description:
OZMYC1
This sample is from leaves of plants with roots inoculated with Laccaria bicolor and stopped watering . It is the first of four biological replicates used in this experiment.


title: FLOX-control_GCI_2 [Cont_GCI_21]

status: Public on Jul 13 2023

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: FLOX control mice

extract_protocol:
An astrocyte-specific aromatase knockout (GFAP-ARO-KO) mouse model was generated and utilized in this study. To conditionally delete locally synthesized aromatase in astrocyes in the brain, we generated Cyp19a1 Cre/LoxP conditional KO mice, under the control of the glial fibrillary acidic protein (GFAP) promoter, which expresses Cre exclusively in astrocytes. Ovariectomized female FLOX and GFAP-ARO-KO mice were subjected to two-vessel occlusion GCI and reperfusion for 24 hours. Bilateral ovariectomy of female mice was conducted one week prior to GCI surgery. For GCI, mice were anesthetized under isoflurane, and both common carotid arteries (CCAs) were isolated and occluded with clips for 20 minutes. Blood flow through the arteries was verified when the clips were removed. Total RNA was isolated from the hippocampi and subjected to RNA-seq analysis.
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from the hippocampi of FLOX and GFAP-ARO-KO mice that underwent 20 min CCA occlusion followed by 24 hours reperfusion and subjected to RNA-seq analysis.

tag: genotype/variation

value: FLOX-control

value: 20-minute CCA occlusion, followed by 24-hour reperfusion

value: hippocampus


title: FLOX-control_GCI_1 [Cont_GCI_20]


title: GFAP-ARO-KO_GCI_2 [GF_KO_GCI_24]

source_name: Astrocyte specific aromatase brain knock out mice

value: GFAP-ARO-KO


title: MDA-MB-231_CSCs_ KDM1A shRNA_1

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: MDA-MB-231 expressing KDM1A shRNA vector

growth_protocol: CSCs from MDA-MB-231 were FACS sorted using the ALDEFLUOR kit (StemCell Technologies, Seattle, WA). CSCs were cultured in MammoCult medium (StemCell Technologies, Seattle, WA).

extract_protocol:
CSCs transduced with lentiviral particles expressing either control shRNA or KDM1A shRNA vector and total RNA was isolated using RNeEasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 100bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from MDA-MB-231 CSCs stably expressing control shRNA or KDM1A shRNA and subjected to RNAseq analysis

value: breast cancer cell line

value: Knockdown


title: MDA-MB-231_CSCs_ control shRNA_2

source_name: MDA-MB-231 expressing control shRNA vector

value: Control


title: MDA-MB-231_CSCs_ KDM1A shRNA_2


title: MDA-MB-231_CSCs_ control shRNA_1


title: Leaf-inoculated-control-3 [L-I-C-3]

description:
OZMYC11
This sample is from leaves of plants with roots inoculated with Laccaria bicolor under control conditions . It is the third of four biological replicates used in this experiment.


title: anti MacroH2A1.2 Chromatin Immunoprecipitation, ESCs

status: Public on Jun 21 2023

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

description:
MacroH2A1.2_ESCs_IP
single-end

data_processing:
The quality of the generated fastq files was examined with the FASTQC software. FASTQ files were aligned against mm10 mouse genome with Bowtie2 aligner. The output file was filtered for low quality reads, duplicates, blacklist regions and mitochondrial genome entries with custom-made pipeline from Bedtools  and Samtools packages. Peak calling was performed with MACS2 with default parameters. Bigwig files were generated with BamCoverage from Deeptools.
Assembly: mm10
Supplementary files format and content: Regarding ChIPseq analysis, the .bw files contain the signal per sample as generated with bamCoverage command. The xlsx files contain the peaks generared with MACS2 compared to the respective Input file

growth_protocol: MEFs and HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich, Cat. No. D6429) supplemented with 10% heat-inactivated Fetal Bovine Serum (FBS), Penicillin/Streptomycin (100 ug/ml; Thermo Fischer Scientific, Cat. No. 15140122), 2 mM GlutaMAX (Gibco, Cat. No. 35-050-061) and 0.1 mM Non-Essential Amino Acids 100X (Gibco, Cat. No. 11140050), at 37°C and 5% CO2. Bruce4 ESCs were cultured in complete ESC medium [Knock Out DMEM (Gibco, Cat. No. 10829018), 20% ES-tested FBS (Pansera, Cat. No. P30-2602), Penicillin/Streptomycin 1X (Thermo Fischer Scientific, Cat. No. 15140122), GlutaMAX 1X (Gibco, Cat. No. 35-050-061). Non-Essential Amino Acids 1X (Gibco, Cat. No. 11140050) and mLIF 20ng/mL (Santa Cruz Biotechnology, sc-4378)

extract_protocol:
Nuclei extraction protocol as described in Ford et at. 2014 (Ford E, Nikopoulou C, Kokkalis A, Thanos D. A method for generating highly multiplexed ChIP-seq libraries. BMC Res Notes. 2014 May 22;7:312. doi: 10.1186/1756-0500-7-312. PMID: 24885602; PMCID: PMC4048252)
1-15 ng of “ChIPped” DNA was blunt-ended by End Repair Enzyme Mix (T4 DNA Polymerase, Klenow Fragment, T4 DNA Polynucleotide kinase), followed by “A”-tailing of 3΄-ends and ligation with the annealed TruSeq Adapters (Illumina). Conversion of the Y-shaped adapters to dsDNA occurred prior to the library size selection through 2.5% Metaphor/SeaKem LE (3:1 ratio) agarose gel electrophoresis. Each library was purified using miniElute columns (Qiagen) and then subjected to pre-amplification. The final quantification of DNA libraries was carried out according to the Quantification Standards of Illumina on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies).

value: Embryonic Stem Cells


title: anti MacroH2A1.2 Chromatin Immunoprecipitation, MEFs

description:
MacroH2A1.2_MEFs_IP
single-end

source_name: Mouse Embryonic Fibroblasts

value: Mouse Embryonic Fibroblasts

tag: genotype


title: Input, MEFs

description:
Input_MEFs
single-end


title: Input, ESCs

description:
Input_ESCs
single-end


title: CD45+ Sample_03_IM

status: Public on May 02 2023

data_processing:
Raw blc files were converted into fastq files using the Cell Ranger pipeline suite of 10X Genomics (version 3.0.2).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix starting from raw data.
Gene expression matrices were used as input for Seurat clustering (R version 3.6.1; Seurat version 3.1.1)
Assembly: Pre-build Human genome (version GRCh38) was used as genome reference.
Supplementary files format and content: UMI counts per gene per cell

source_name: CD45+ cells

growth_protocol: not applicable

extract_protocol:
Surgically resected CLM specimens were chopped into small fragments and subjected to GentleMACS (Miltenyi) dissociation in  Collagenase D solution for 35 min at 37°C. The resulting single cell suspension was filtered through a 100 µm cell strainer and erythrocytes were lysed with ACK. Cells were then stained for flow cytometry, sorted and resuspended in 0.5 ml PBS 1X plus 0.04% BSA and washed once by centrifugation at 450 rcf for 7min. Cells were then resuspended in 50 ml and counted with an automatic cell counter (Countess II, Thermo Fisher).
Approximately 10.000 cells for each sample were loaded into the Chromium Chip B using the Single Cell reagent kit v3 (10X Genomics) for Gel bead Emulsion generation into the Chromium system
Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol. 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq550 Illumina sequencing platform following 10xGenomics instruction for read generation, reaching at least 35000 reads as mean reads per cell.

treatment_protocol: not applicable

tag: condition

value: CLM

tag: tissue type

value: Invasive margin tissue


title: meta3,CRLM biopsy, Spatial transcriptomic

status: Public on May 16 2023

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting  were made using the Space Ranger software v1.2.2 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
The obtained count matrices were processed using R v4.0.5 and Seurat package v4.0.1.
Spots with too low or too high UMIs or features counts were removed and data were normalized using SCTransform function.
After remotion of spots overlapping hepatic tissue the dataset were merged with Seurat SCTransform integration workflow, using 3000 integration features and the clusters were found with Seurat FindCluster function
Assembly: hg38
Supplementary files format and content: raw_feature_bc_matrix.h5  (Matrix with raw counts for every gene and every spot)
Supplementary files format and content: filtered_feature_bc_matrix.h5  (Matrix with raw counts for every gene and every spot, filtered to include spots under tissue)
Supplementary files format and content: tif  (Hematoxylin and Eosin (HE) image in TIF format)
Supplementary files format and content: png  (Low resolution Hematoxylin and Eosin (HE) image in PNG format)
Supplementary files format and content: json  (Scalefactors in json format)
Supplementary files format and content: csv  (Table with array and pixel coordinates)
Library strategy: Visium 10x Spatial Transcriptomic

source_name: CRLM

extract_protocol:
We performed Visium Spatial Gene Expression protocol (CG000239) steps
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol

value: CRLM


title: CD45+ Sample_02_IM


title: CD45+ Sample_01_IM


title: CD45+ Sample_01_NA

value: Normal adjacent tissue


title: CD45+ Sample_03_NA


title: CD45+ Sample_02_NA


title: meta2,CRLM biopsy, Spatial transcriptomic

description: 10x Genomics


title: Sample_02_IM

source_name: CD163+CD66b- cells

tag: disease state

value: colo-rectal liver metastasis (CLM)


title: Sample_03_IM


title: GSC040815_RCN3 knockdown_3

status: Public on Apr 19 2023

description: GSCs transduced with RCN3 shRNA

source_name: patient derived glioma stem cell line

growth_protocol: Patient-derived primary GSCs were cultured as neurospheres in neurobasal medium supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL).

extract_protocol:
RNA was isolated using RNeasy mini kit and subjected to RNA-seq on illumina NextSeq 500 system using Illumina TruSeq stranded mRNA-seq library preparation kit
Total RNA samples about 500ng were used for sequencing library preparation according to NEB stranded mRNA-seq Sample Preparation Guide (NEB Cat. #: 7765). Each library was bar-coded and then pooled for cluster generation and sequencing run with 75bp single-end (SE) sequencing protocol.

treatment_protocol: Patient derived GSC040815 cells were transduced with either control shRNA or RCN3 shRNA.

value: knockdown


title: meta1,CRLM biopsy, Spatial transcriptomic

description: 10x Genomics

tag: tissue


title: GFAP-ARO-KO_GCI_1 [GF_KO_GCI_22]


title: Sample_02_NA


title: Sample_01_NA


title: Sample_03_NA


title: Sample_01_IM


title: GSC040815_control_2

description: GSCs transduced with control shRNA

value: control


title: GSC040815_RCN3 knockdown_1

description: GSCs transduced with RCN3 shRNA


title: GSC040815_RCN3 knockdown_2

description: GSCs transduced with RCN3 shRNA


title: GSC040815_control_3

description: GSCs transduced with control shRNA


title: P1_blood

status: Public on Apr 01 2023

type: genomic

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

description:
methylation profiling using bisulfite converted
platform name: Infinium MethylationEPIC

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing:
Genome-wide methylation analysis was performed by the Illumina Infinium methylation Epic array on bisulfite converted DNA extracted from the three tissues of the patient. Data were analyzed using R version 4.1.0. Beta values (Bvalues) were derived from “idat” files by the “champ.load” module of the “ChAMP” R package (v.2.22.0), with quality control options set as default and array type as “EPIC.” To adjust the Bvalues of type 2 probes, we applied BMIQ normalization with the default options for array type as “EPIC.”
normalized data files contain: BMIQ normalized matrix
signal intensities file contains: Unmethylated signal (B) and methylated signal (A) intensities

label: Cy5 and Cy3

source_name: Blood

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.

tag: gender

value: F

value: BWS-CRC

value: blood

value: A


title: Tumor, participant 128 and 129, ADT-derived cDNA

status: Public on Mar 01 2023

city: San Francisco

first: Matthew

last: Spitzer

state: CA

address: 513 Parnassus Ave.

institute: University of California, San Francicso

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
adata_ADT.h5ad

data_processing:
Alignment of raw sequencing results to generate count matrices was performed using Cell Ranger (v3.0.2 or v.6.0.2) with default settings and aligning to the hg38 genome build for gene expression or TotalSeq-C Feature Reference for ADT. The raw TCR fastq files for each participant from the lymph node and tumor were aligned to the vdj GRCh38 v.7.0.0 reference jointly in order to call shared clonotypes across the tissues using Cell Ranger v.7.0.0. The GEX BAM alignment files from each of the multiplexed libraries were used as the input for dsc-pileup v.0.1beta to generate pileup files which were then used as input for freemuxlet v.0.1beta for doublet identification, inferred genotypes for individuals in each library, and singlet assignment to those inferred genotypes. The percentage of shared single nucleotide polymorphism (SNP) assignments from the freemuxlet genotypes was used to match samples from the two individuals in the lymph node library and the tumor library to each other. The two samples in each pool were from a male and a female participant so the sex assignment (based on XIST expression and the percentage of total counts based on unique molecular identifiers (UMIs) mapping to Y chromosome genes) was used to match the freemuxlet IDs to the clinical trial participant IDs.
Further processing was done with scanpy v1.7.1 (cell and gene filtering, clustering, shared clones identification, and gene set scoring analysis).
Assembly: hg38
Assembly: TotalSeq-C Feature Reference
Assembly: vdj GRCh38 v.7.0.0
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated from gene expression data from all ten samples
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated gene expression data and TCR assignment from subsetted CD8+ T cells from all ten samples
Supplementary files format and content: h5ad file with raw ADT counts for filtered cells
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Library strategy: CITE-seq

source_name: Tumor

extract_protocol:
CD45+ and CD45- cells from paired HNSCC tumor and LN samples from five human participants were purified by flow cytometry. Purified cells were mixed in a 8:2 CD45+:CD45- ratio. For three of the participants, the resulting samples were then stained with a panel of 137 TotalSeq-C antibodes (Antibody Derived Tags) before loading into a Chromium Controller (10X Genomics). The samples from the other two participants were loaded directly on the Chromium Controller.
GEMs were prepared using Chromium Single Cell 5ʹ v1.1 protocol (10x Genomics) following manufacturer’s insturctions. The cDNA libraries for each sample were generated using all or a subset of Chromium Next GEM Single Cell 5' Library Kit (10X Genomics) for gene expression (GEX), Chromium Single Cell V(D)J Enrichment kit (10X Genomics) for T cell receptor (TCR), and Chromium Single Cell 5' Feature Barcode Library kit (10X Genomics) for antibody derived tag (ADT) according to the manufacturer’s instructions.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
OTHER: TCR-seq (V(D)J enrichment for immune profiling of human T cells)
OTHER: scRNA-seq (5' whole transcriptome gene expression of polyadenylated mRNA)

value: Tumor

tag: cell type

tag: library type

value: ADT

tag: antibodies/tags

value: 137 TotalSeqC antibodies


title: GSC040815_control_1

description: GSCs transduced with control shRNA


title: meta4,CRLM biopsy, Spatial transcriptomic

description: 10x Genomics


title: Tumor, participant 128 and 129, mRNA-derived cDNA

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
adata.h5ad
adata_CD8.h5ad

data_processing:
Alignment of raw sequencing results to generate count matrices was performed using Cell Ranger (v3.0.2 or v.6.0.2) with default settings and aligning to the hg38 genome build for gene expression or TotalSeq-C Feature Reference for ADT. The raw TCR fastq files for each participant from the lymph node and tumor were aligned to the vdj GRCh38 v.7.0.0 reference jointly in order to call shared clonotypes across the tissues using Cell Ranger v.7.0.0. The GEX BAM alignment files from each of the multiplexed libraries were used as the input for dsc-pileup v.0.1beta to generate pileup files which were then used as input for freemuxlet v.0.1beta for doublet identification, inferred genotypes for individuals in each library, and singlet assignment to those inferred genotypes. The percentage of shared single nucleotide polymorphism (SNP) assignments from the freemuxlet genotypes was used to match samples from the two individuals in the lymph node library and the tumor library to each other. The two samples in each pool were from a male and a female participant so the sex assignment (based on XIST expression and the percentage of total counts based on unique molecular identifiers (UMIs) mapping to Y chromosome genes) was used to match the freemuxlet IDs to the clinical trial participant IDs.
Further processing was done with scanpy v1.7.1 (cell and gene filtering, clustering, shared clones identification, and gene set scoring analysis).
Assembly: hg38
Assembly: TotalSeq-C Feature Reference
Assembly: vdj GRCh38 v.7.0.0
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated from gene expression data from all ten samples
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated gene expression data and TCR assignment from subsetted CD8+ T cells from all ten samples
Supplementary files format and content: h5ad file with raw ADT counts for filtered cells
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries

value: mRNA


title: Tumor, participant 126, ADT-derived cDNA


title: C57BL/6_R3__GEX

status: Public on Feb 24 2023

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: 10x Genomics

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v4.0.0) to perform quality control and sample de-multiplexing (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Single cell capture, cDNA and library preparations were performed with the Single Cell 3’ v3 Reagent Kit (10x Genomics) according to manufacturer’s instructions. GEX sequencing libraries were loaded on an Illumina NovaSeq with high output cycle kits and sequenced paired-end using the following read length: Read1-28 cycles / Read2-8 cycles / Read3-91 cycles. HTO libraries were prepared according to manufacturer instruction and loaded on an Illumina NextSeq 500 with high output cycle kits and sequenced paired-end using the following read length: Read1 28 cycles / Read2 8 cycles / Read3 56 cycles for HTO libraries. The first 15 bases of R3 represented HTO barcode sequence.
Samples were aligned to the UCSC mouse (mm10) genome using and expression of ensembl genes (v102) was quantified with "STARsolo" (version 2.7.9a) with recommended parameters (-- soloFeatures Gene GeneFull SJ Velocyto, --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB, --soloCBwhitelist 3M-february-2018.txt (provided by 10x), --soloCellFilter None) for all 6 samples. Additionally, the expression of Cre was quantified by including these sequences during mapping and quantification step.
Similarly, also hashtags-tags (HTO) were quantified with "STARsolo" after aligning the sample data only to HTO barcode sequences (with additional parameter: --clip3pNbases 41). The information obtained from HTO quantification was used only as additional annotation for cells (tissue of origin).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, RDS file with SingleCellExperiment
Supplementary files format and content: The raw_counts.mtx contains UMI counts (expression values), row names (ensembl gene ids) are stored in raw_genes.tsv and column names (cell barcodes) in raw_barcodes.tsv. The gene information is in raw_rowdata.tsv (rowData) and cell information in raw_coldata.tsv (colData). The raw_hto.mtx contains UMI counts for HTO, rownanes are stored in raw_hto.tsv.
Supplementary files format and content: The filtered dataset is stored in SingleCellExperiment.rds, with individual components: final_counts.mtx (UMI counts), final_logcounts.mtx (log2 UMI counts), column names in final_barcodes.tsv and row names in final_genes.tsv, gene annotation is stored in final_rowdata.tsv and cell information is in final_coldata.tsv.

source_name: spleen, skin draining lymph node (sLN), mesenteric lymp node (mLN)

extract_protocol:
Sort purified CD11c+ cells derived from C57BL/6 or Klf4fl/fl ItgaxCre+ spleens, sLNs and mLNs were multiplexed individually by labeling each sort purified cell suspension with a unique Hashtag (HTO) antibody. 10K sort purified CD11c+ cells from the spleen, sLN and mLN of either C57BL/6 or Klf4fl/fl ItgaxCre+ mice were mixed and loaded on a 10x Genomics Chromium Single Cell Controller.
Single cell capture, cDNA and library preparations were performed with the Single Cell 3’ v3 Reagent Kit (10x Genomics) according to manufacturer’s instructions. GEX sequencing libraries were loaded on an Illumina NovaSeq with high output cycle kits and sequenced paired-end using the following read length: Read1-28 cycles / Read2-8 cycles / Read3-91 cycles.
HTO libraries were prepared according to manufacturer instruction and loaded on an Illumina NextSeq 500 with high output cycle kits and sequenced paired-end using the following read length: Read1 28 cycles / Read2 8 cycles / Read3 56 cycles for HTO libraries. The first 15 bases of R3 represented HTO barcode sequence.

value: CD11c+ cells

tag: strain

value: wildtype

value: 6-14 weeks old

value: GEX -- gene expression


title: Tumor, participant 126, mRNA-derived cDNA


title: C57BL/6_R3__HTO

description: 10x Genomics

value: spleen, skin draining lymph node (sLN), mesenteric lymp node (mLN)

tag: age

value: HTO -- hash tags


title: C57BL/6_R1__GEX

description: 10x Genomics


title: C57BL/6_R2__HTO

description: 10x Genomics


title: C57BL/6_R2__GEX

description: 10x Genomics


title: Healthy control patient 5

status: Public on Dec 09 2022

description: 10x Genomics

data_processing:
The 10x genomics Cell Ranger pipeline was used to align reads, perform clustering and gene expression analysis, and aggregate the samples with normalized read counts
Assembly: GRCh3.0.0
Supplementary files format and content: h5

source_name: skin

extract_protocol:
6 mm punch biopsy specimen was first incubated in RPMI 1640 medium (Gibco) containing 5% fetal bovine serum (5% FBS/RPMI) and 10 mg/ml Dispase II (Sigma D4693-1G) for 45 minutes at 37° C shaking at 200-250 rpm. The sample was then removed from the media and minced with sterile iris scissors, followed by digestion with Liberase TM (Sigma) 0.5 mg/ml and DNase I 30 Units/ml in 5% FBS/RPMI for 45 minutes at 37° C shaking at 200-250 rpm. The resulting single cell suspension was then filtered through a 70 mm nylon membrane and washed. Live cells were sorted on a FACSAria and their final concentration and viability quantified with Trypan blue on a hemacytomer. The cells were pelleted and suspended in phosphate buffered saline containing 0.04% bovine serum albumin between 500-1000 cells/ml. 3000-6000 cells with greater than 80% viability were submitted to the Yale DNA Sequencing facility for generation of single-cell cDNA libraries using the Chromium Single Cell Controller (10x Genomics).
per 10x Genomics protocol using Single Cell 3' v2. Each cDNA library was sequenced paired-end on 1 lane with 75 base-pair read length using the Illumina HiSeq 2500 System generating at least 75,000 reads per cell.

value: all

value: skin

tag: individual

value: Healthy control patient 5


title: Healthy control patient 4

description: 10x Genomics

value: Healthy control patient 4


title: Healthy control patient 3

description: 10x Genomics

value: Healthy control patient 3


title: Healthy control patient 2

description: 10x Genomics

value: Healthy control patient 2


title: Healthy control patient 6 CD45 negative sorted cells

description: 10x Genomics

value: immune cells

value: Healthy control patient 6


title: Healthy control patient 1

description: 10x Genomics

value: Healthy control patient 1


title: SSc patient 2

description: 10x Genomics

value: SSc patient 2


title: SSc patient 4

description: 10x Genomics

value: SSc patient 4


title: BMDMs, KO 3

status: Public on Nov 29 2022

data_processing:
Bcl2fastq (v2.19.0.316) for demultiplexing and conversion to Fastq files
Single-end unstranded libraries (75bp) were first subjected to a quality check FastQC v0.11.8 and aligned to the to the reference genome assembly mm10 with the following settings (STAR --outFilterMultimapNmax 20 --alignSJoverhangMin 8 –alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD).   RNA-seq quality assessment was performed using RSeQC v3.0.1 tool. STAR's output in the format of tab files were used as input for expression analysis. Differential expression analysis was assessed with edgeR v3.30.0 R Bioconductor package (PMID: 19910308) and only genes with a cut-off expression > 1 CPM in at least three samples were included in the analysis. TMM method was applied to normalize gene counts and glmQLFTest function was used to perform differential analysis. Bigwig files were generated using the deepTools suite v3.5.1 (bamCoverage function).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts, bigWig files

source_name: Bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow-derived macrophages (BMDM) were obtained from suspensions of femoral BM and differentiated for 7 days in the presence of RPMI Medium supplemented with antibiotics, 10% fetal bovine serum and 100 ng/ml MCSF.

extract_protocol:
Total RNA from treated BMDM was isolated using Trizol reagent and RNeasy kits (QIAGEN).
Libraries for mRNA sequencing were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). Full-length cDNAs were processed using a Nextera XT DNA Library Preparation Kit (Illumina). Quality control was performed using a High Sensitivity DNA ScreenTape Assay with a 4200 TapeStation System (Agilent). Libraries were then multiplexed in an equimolar pool and sequenced using a NextSeq 550 Platform (Illumina).
mRNA sequecing

treatment_protocol: MCSF concentration in cell culture medium was decreased to 5 ng/ml for 48h to induce progressive synchronization of macrophages in G0 phase and cell cycle re-entry was induced by treatment with 100 ng/ml MCSF for 18h.

value: Bone marrow-derived macrophages (BMDM)

value: p53 ko


title: SSc patient 3

description: 10x Genomics

value: SSc patient 3


title: BMDMs, KO 2


title: BMDMs, KO 1


title: BMDMs, WT 2

value: p53 wt


title: RL_ADP3

status: Public on Nov 16 2022

description: RL95-2 cells incubated with serum-free RPMI+ADP-CM (1:1).

data_processing:
Illumina bcl2fastq software used for base-calling.
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene.
Gene count measurements were obtained using HTSeq-count.
Assembly: hg19
Supplementary files format and content: *_Genes_ReadCount.txt: The processed data files are in tabular format. The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count.

source_name: Endometrial cancer cell line-RL95-2

growth_protocol: RL95-2 cells were cultured in RPMI media supplemented with 10% FBS.

extract_protocol:
Total RNA from RL95-2 control, and ADP-CM cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing were done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide.

treatment_protocol: RL95-2 cells were incubated in serum-free RPMI medium with or without ADP-CM for 24 hrs.

tag: cell line

value: Endometrial cancer cell line

tag: treatment

value: ADP-CM


title: SSc patient 5

description: 10x Genomics

value: all

value: SSc patient 5


title: RL_ADP2


title: RL_ADP1


title: BMDMs, WT 1


title: C57BL/6_R1__HTO

description: 10x Genomics

value: spleen, skin draining lymph node (sLN), mesenteric lymp node (mLN)

value: CD11c+ cells

value: wildtype

value: 6-14 weeks old

value: HTO -- hash tags


title: RL_C3

description: RL95-2 cells incubated with serum-free RPMI+DMEM media (1:1).

value: Control


title: BMDMs, WT 3


title: Healthy control patient 6 CD45 positive sorted cells

description: 10x Genomics

value: mesenchymal cells

value: skin

value: Healthy control patient 6