title: gastrocnemius muscle, isolated from muscle-specific Sel1L-deficient mouse, replicate 2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.54.1).

source_name: gastrocnemius muscle, isolated from 8-wk old female muscle-specific Sel1L-deficient mouse

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Muscle-specific SEL1L (Sel1LMLC) deficient mice were generated by crossing Sel1Lf/f mice with mice expressing Cre driven by the myosin light chain-promoter (MLC), mice that were Cre-negative were used as controls. All mice strains used were on C57BL/6J background and were  fed a regular chow diet (13% fat, 57% carbohydrate, and 30% protein; LabDiet 5L0D) with free access to water.

extract_protocol: RNA was extracted using RNeasy micro kit (Qiagen) including a column for elimination of genomic DNA as per manufacturer’s instructions. RNA concentration was determined using NanoDrop 2000 UV-Vis Spectrophotometer. The quality and concentration were determined using the RNA 6000 Nano kit on an Agilent 2100 bioanalyser.

treatment_protocol: Gastrocnemius muscles were harvested from 8-week-old female control (WT) and muscle-specific Sel1L deficient (KO) Mice.

value: Muscle-specific Sel1L KO

tag: age of mice (wks)

value: female


title: Ascl1 Tcf7l1-KO Day0 RepC4

status: Public on Jul 17 2023

type: SRA

city: Vienna

first: Gintautas

last: Vainorius

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

library_source: transcriptomic

data_processing:
Reads were trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
Read mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCm38/mm10 assembly obtained from Mus musculus Ensembl release 94. Reads were aligned to the genome using star v2.6.0c
Reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Differential expression analysis and variance stabilized transformation for PCA analysis was performed using R package Deseq2
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files with RPM normalized values

molecule: total RNA

organism: Mus musculus

source_name: mESC

growth_protocol: mESC grown in Serum-LIF; Differentiation is done in Neurobasal, DMEM-F12, N2 supplement, B27 supplement, L-Glutamate, Na-Pyruvate, Penicilin-Streptomycin, Non-essential amino acids, 20 µg/ml Insulin. Cells were grown at 37 ºC, 5% CO2.

extract_protocol:
Cells were washed with PBS and processed using the Qiagen RNeasy mini kit. RNA was additionally treated with TURBO DNA-free™ kit (Invitrogen) according to the manufacturer’s protocols. Integrity of RNA was measured using Fragment Analyzer™.
RNAseq-Libraries were prepared using QuantSeq 3` mRNA-Seq Library Prep Kit (Lexogen GmbH).
Quantseq

treatment_protocol: 1 day of 1 µg/ml Doxyciclin.

tag: cell type

value: mESC

tag: genotype

value: Tcf7l1 knockout

tag: treatment

value: mESC before Ascl1 induction


title: bulk RNA-seq, C9-FTD donor F4, Frontal cortex, Other glia

city: New York

first: Stella

last: Dracheva

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

country: USA

institute: Icahn School Of Medicine at Mount Sinai

data_processing:
FastQC (v0.11.8) was used to examine the quality of the RNA-seq reads.
Reads were then trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 20) using Trim Galore (v0.5.0) in paired-end mode. The first 3 bp from the 5′ end of read 1 were also removed.
Trimmed reads were then mapped to the human hg38 genome and the GENCODE annotated transcriptome (release V35) with STAR (v2.7.1a). Gene expression was estimated using RSEM (v1.2.30).
Gene-level ‘expected count’ from the RSEM results were rounded and fed into edgeR (v3.34.1) to perform differential expression tests separately for each sorted population in each brain region. Only genes that were expressed (with CPM > 2) in at least six samples were kept.
The read counts of the remaining genes were then normalized using the TMM method, and DEGs were called in the quasi-likelihood F-test mode with a cutoff of FDR < 0.05.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw counts or TPM (Transcripts per million) values for each sample.

molecule: nuclear RNA

organism: Homo sapiens

source_name: frontal cortex

extract_protocol:
The isolation of brain nuclei prior to the flow cytometry separation was performed mostly as previously described in Kozlenkov et al. (Sci Adv. 2018). Tissue (~300 mg) was homogenized in ice-cold lysis buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton X-100, 1 mM DTT, 1 U/µl Recombinant RNase Inhibitor (RRI; Takara, Cat. # 2313A), and 10mM Tris-HCl, pH 8.0), underlaid with the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, 0.4 U/µl RRI, and 10 mM Tris-HCl pH 8.0), and centrifuged for 1h at 24,000 rpm. The nuclear pellets were then resuspended in the antibody-incubation buffer (0.5% BSA, 3mM MgCl2, 1 U/µl RRI, and 10 mM Tris-HCl, pH 8.0) and incubated with antibodies against NeuN and SOX10 for 1 hr at 4°C. Fluorescence-activated nuclei sorting (FANS) was then used to isolate neurons (NeuN+SOX10- population), oligodendrocyte lineage cells (NeuN-SOX10+ population), consisting of mature oligodendrocytes and a smaller population of OPCs, and a third population (NeuN-SOX10-; hereafter “other glia”) that mostly consisted of astrocytes and microglia. Alexa488-conjugated anti-NeuN antibodies (1:1000 dilution, Millipore, Cat. # MAB377x) and anti-SOX10 antibodies (R&D Systems, Cat. # AF2864) that were custom conjugated to Alexa647 (1:150 dilution, Cat# FCMAB317PE, Millipore) were used. DNA stain DAPI was used to label intact nuclei. From each sample, 250-300K nuclei of neurons, 250-300K of oligodendrocytes, and 150-200K nuclei of other glia were collected. Nuclei were collected directly to the lysis buffer from PicoPure RNA Isolation Kit (ThermoFisher Scientific, Cat. # KIT024), which was then used for RNA isolation.
RNA-seq libraries were prepared with the SMARTer Stranded Total RNA-seq Kit, Pico-Input v2 (Takara, Cat. # 634414) from 10ng of the RNA. Libraries were sequenced on a NovaSeq 6000 instrument (Illumina), using paired-end 100 cycles protocol to an average of 120 million read pairs per sample.

tag: tissue

value: frontal cortex

value: other glia (NeuN-SOX10-)

tag: donor id

tag: disease

tag: Sex

value: Male


title: Ascl1 Ctrl Day1 Rep3

value: WT

value: Ascl1 overexpression for 1 day


title: DT 6 [PLUS6_S15]

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the mouse transcriptome and genome version GRCm39 with annotations from Ensembl release 106 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCm39 with annotations from Ensembl release 106
Supplementary files format and content: Each row in the file contains a certain ensembl Gene ID, Symbol, name and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).

source_name: Gingival epithelium

extract_protocol:
RNA was extracted using Rneasy Micro Kit (Qiagen) following manufacturer protocol
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421). In brief, 1µg was used for the library construction; library was eluted in 20µl of elution buffer. All DNA samples libraries were pooled to 10nM sample. Multiplex samples Pool were loaded on NovaSeq 6000, using NovaSeq 6000 SP Reagent Kit v1.5 100 cycles (cat# 20028401), with 122 cycles

treatment_protocol: the samples are mice gingival epithelium samples taken from Langerin-DTR mice that were injected with either PBS or Diphtheria toxin, and therefore are either depleted (DT) or non depleted (PBS) of Langerhans cells.

value: Gingival epithelium

value: Langerin-DTR mice

value: injected with Diphtheria toxin


title: Patient 1 CD8+ [Pt01_CD8]

city: Aurora

first: Ann

last: Strange

state: CO

address: 12801 E. 17th Ave, 8th floor

department: Division of Medical Oncology

institute: CU Anschutz

description: HistonePath

library_source: genomic

data_processing:
Sequence quality and adapter contamination in the ChIP-seq libraries were evaluated with FASTQC
Reads were trimmed using “Trim Galore!”.
Reads were aligned to the human genome (GRCH38) using bowtie2.
Multimapping and duplicate reads removed with SAMtools and Picard tools.
Only analyze files containing CD8 in the filename, as CD4 is a different cell population and did not appear to be powereed in our analysis.
Assembly: ChIP enrichment peaks were called using macs28 and differential ChIP peaks identified with DiffBind
Supplementary files format and content: NCBI GRCh38 p14
Supplementary files format and content: count matrix

molecule: genomic DNA

source_name: TIL ACT Product

extract_protocol: 5µg of chromatin was extracted from CD4+ and CD8+ sorted TIL and subjected to immunoprecipitation using 4µl of a H3 pan-acetyl antibody (Active Motif, cat #23139), per Active Motif’s standard protocols. Pooled, unprecipitated genomic DNA was used as an input control. These libraries were then sequenced on the Illumina NextSeq 500 v2 sequencer with a 75-base paired-end run in order to generate 30-40 million read pairs per sample.

value: TIL ACT Product

tag: cell line

value: Expanded TIL

tag: chip antibody

value: H3 pan-acetyl

tag: dataset

tag: trial

tag: response

value: PD

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8

tag: gender

value: M

value: TIL ACT


title: Patient 10 CD4+ [Pt10_CD4]

description: HistonePath

tag: tissue

tag: cell type

value: F

tag: treatment


title: gastrocnemius muscle, isolated from wildtype mouse, replicate 3

type: RNA

label: biotin

source_name: gastrocnemius muscle, isolated from 8-wk old female wildtype (C57BL/6J) mouse

tag: genotype

value: wildtype (C57BL/6J)

tag: age of mice (wks)

tag: Sex

value: female


title: 8K_M_1531

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: Ascl1 Ctrl Day1 Rep2

value: mESC


title: Patient 1 CD4+ [Pt01_CD4]

description: HistonePath

tag: cell line

tag: chip antibody

tag: dataset

tag: trial

tag: response

tag: pfs months


title: gastrocnemius muscle, isolated from wildtype mouse, replicate 2


title: Patient 9 CD8+ [Pt09_CD8]

description: HistonePath

value: PR

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8


title: Naïve (CD44loCD62Lhi) rep2

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
FASTQ files were aligned to the mouse genome (GRCm38) with the STAR aligner using the GeneCounts QuantMode.
Assembly: GRCm38
Supplementary files format and content: Gene counts (.txt)

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Qiagen AllPrep Kit
poly(A) selection

tag: tissue

value: Spleen

tag: cell type

value: PD-1+ CD8 T cells

tag: genotype

value: WT (C57BL/6J)

tag: treatment


title: Ascl1 Ctrl Day1 Rep1

value: WT

value: Ascl1 overexpression for 1 day


title: bulk RNA-seq, C9-FTD donor F5, Frontal cortex, Other glia

value: frontal cortex

value: other glia (NeuN-SOX10-)

tag: donor id

tag: disease

tag: Sex

value: Male


title: Ascl1 Ctrl Day0 Rep3

value: mESC before Ascl1 induction


title: bulk RNA-seq, C9-FTD donor F5, Motor cortex, Oligodendrocyte lineage cells

source_name: motor cortex

value: motor cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: gastrocnemius muscle, isolated from wildtype mouse, replicate 1

tag: age of mice (wks)


title: Naïve (CD44loCD62Lhi) rep1


title: bulk RNA-seq, C9-FTD donor F3, Motor cortex, Oligodendrocyte lineage cells


title: RNASeq, HEK293T cells, EZH2 H689A/F667I, replicate 2

city: Columbus

first: Julian

last: Aldana

state: Ohio

address: 460 W 12th Ave

institute: Ohio State University

data_processing:
RNA-Seq reads were trimmed using TrimGalore v.0.6.5
RNA-Seq reads were aligned to the human genome assembly (GRCh38/hg38) using STAR v.2.7.9a
Transcript abundance was estimated with salmon v.1.2.0
Read counts and normalization were estimated using edgeR v3.16
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicilin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
Total RNA was harvested using Total RNA Purification Plus Kit (Norgen Biotech) following manufacturer’s protocol.
RNA-Seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer’s protocol. Libraries were amplified using 16 cycles in a Real-Time PCR System.

tag: cell line

value: Human embryonic kidney


title: Patient 6 CD8+ [Pt06_CD8]

description: HistonePath

value: TIL ACT Product

value: Expanded TIL

tag: chip antibody

value: H3 pan-acetyl

tag: dataset

tag: trial

tag: response

tag: gender

value: F

value: TIL ACT


title: bulk RNA-seq, C9-FTD donor F5, Frontal cortex, Oligodendrocyte lineage cells


title: Ascl1 Ctrl Day0 Rep2

value: mESC


title: Patient 5 CD8+ [Pt05_CD8]

description: HistonePath

value: PD

tag: pfs months

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

value: M


title: bulk RNA-seq, C9-FTD donor F3, Motor cortex, Neurons

tag: tissue

tag: cell type

value: neurons (NeuN+SOX10-)

tag: genotype


title: Patient 24 CD8+ [Pt24_CD8 RNA-seq]

data_processing:
After merging lanes, sequence quality and adapter contamination in the RNA-seq reads were evaluated by FASTQC
Reads were aligned to the human genome (GRCH38) using HISAT2
Differential gene expression tests were performed with DESeq2
Assembly: NCBI GRCh38 p14
Supplementary files format and content: count matrix

extract_protocol:
Total RNA was extracted from CD4+ and CD8+ sorted TIL with the Qiagen RNEasy Mini Kit.
100ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol (NuGEN Technologies, Inc., San Carlos, CA). These libraries were then sequenced on the Illumina NextSeq 500 v2 sequencer with a 75-base paired-end run in order to generate 30-40 million read pairs per sample.

value: PR

tag: infusion percent_cd4

tag: infusion percent_cd8

tag: treatment


title: bulk RNA-seq, C9-FTD donor F4, Motor cortex, Other glia

tag: donor id

tag: disease

tag: Sex


title: bulk RNA-seq, C9-FTD donor F3, Frontal cortex, Oligodendrocyte lineage cells

value: frontal cortex


title: Patient 22 CD8+ [Pt22_CD8 RNA-seq]

tag: cell line

tag: trial


title: bulk RNA-seq, C9-FTD donor F3, Frontal cortex, Neurons


title: gastrocnemius muscle, isolated from muscle-specific Sel1L-deficient mouse, replicate 3

value: Muscle-specific Sel1L KO

tag: age of mice (wks)

value: female


title: RNASeq, HEK293T cells, EZH2 Y641F, replicate 3

value: EZH2 Y641F


title: Patient 22 CD4+ [Pt22_CD4 RNA-seq]

tag: response

tag: pfs months

tag: gender


title: Patient 3 CD8+ [Pt03_CD8]

description: HistonePath

tag: chip antibody

tag: dataset

value: CR

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor


title: PBS 2 [MINUS2_S5]

tag: tissue

value: Gingival epithelium

tag: genotype

value: Langerin-DTR mice

value: injected with PBS


title: bulk RNA-seq, C9-FTD donor F4, Frontal cortex, Oligodendrocyte lineage cells

tag: cell type

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Male


title: Patient 2 CD4+ [Pt02_CD4]

description: HistonePath

value: TIL ACT Product

value: Expanded TIL

value: H3 pan-acetyl

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8

tag: treatment


title: bulk RNA-seq, C9-FTD donor F2, Motor cortex, Oligodendrocyte lineage cells

value: motor cortex

tag: donor id

tag: disease

tag: Sex

value: Female


title: PBS 3 [MINUS3_S6]


title: gastrocnemius muscle, isolated from muscle-specific Sel1L-deficient mouse, replicate 1

tag: age of mice (wks)


title: PBS 1 [MINUS1_S4]


title: bulk RNA-seq, C9-FTD donor F4, Frontal cortex, Neurons

value: neurons (NeuN+SOX10-)


title: RNASeq, HEK293T cells, EZH2 Y641F, replicate 2

tag: cell line

value: Human embryonic kidney


title: bulk RNA-seq, C9-FTD donor F3, Motor cortex, Other glia

value: other glia (NeuN-SOX10-)


title: Patient 21 CD4+ [Pt21_CD4 RNA-seq]

tag: trial

tag: response

value: PR

tag: pfs months

tag: gender

value: F

value: TIL ACT


title: RNASeq, HEK293T cells, EZH2 H689A/F667I, replicate 3


title: Patient 24 CD4+ [Pt24_CD4 RNA-seq]

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor


title: RNASeq, HEK293T cells, EZH2 Y641F, replicate 1

tag: cell type

tag: genotype

value: EZH2 Y641F


title: anti-PD-1 treated, stem-like, rep2

tag: tissue

value: Spleen

value: PD-1+ CD8 T cells

value: WT (C57BL/6J)

value: anti PD-1 antibody


title: RNASeq, HEK293T cells, EZH2 H689A/F667I, replicate 1


title: Patient 23 CD4+ [Pt23_CD4 RNA-seq]

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8

value: M


title: Patient 22 CD4+CD8+ [Pt22_DP RNA-seq]

value: TIL ACT Product

value: PD

tag: treatment


title: RNASeq, HEK293T cells, EZH2 WT, replicate 3

value: WT


title: bulk RNA-seq, C9-FTD donor F3, Frontal cortex, Other glia

value: frontal cortex

tag: donor id

tag: disease

tag: Sex

value: Male


title: RNASeq, HEK293T cells, EZH2 A677G, replicate 3

tag: cell line

value: EZH2 A677G


title: Patient 20 CD8+ [Pt20_CD8 RNA-seq]

value: Expanded TIL

tag: trial

tag: response


title: anti-PD-1 treated, stem-like, rep1


title: RNASeq, HEK293T cells, EZH2 A677G, replicate 2

value: Human embryonic kidney


title: anti-PD-1 treated,  terminally differentiated rep1


title: anti-PD-1 treated,  terminally differentiated rep2


title: Isotype treated, stem-like, rep2

value: Isotype antibody


title: bulk RNA-seq, C9-FTD donor F2, Motor cortex, Other glia

value: motor cortex

value: other glia (NeuN-SOX10-)

value: Female


title: Patient 21 CD4+CD8+ [Pt21_DP RNA-seq]

value: PR

tag: pfs months

tag: gender

value: F

value: TIL ACT


title: Cytokine hashtags for samples 44

city: Cambridge

first: Ang

last: Cui

state: MA

address: 415 Main St.

institute: Broad Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw bcl sequencing data was processed using the Cell Ranger (version 3.0) Gene Expression pipeline (10x Genomics), including demultiplexing and alignment.
Sequencing reads were aligned to the mm10 mouse reference genome (version 3.0.0) and transcriptomic count matrices were assembled.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Single-cell suspensions of freshly collected lymph nodes were generated using enzymatic digestion with Collagenase IV, Dispase, and DnaseI in RPMI. To rebalance cell types, a biotinylated anti-CD3 and anti-CD19 antibody cocktail was incubated with the cells, then streptavidin beads were added and the samples were processed using MACS MS columns according to the manufacturer’s protocol. After cell sorting, a small fraction of the CD3+ or CD19+ cells was pooled with CD3-/CD19- cells for optimal representation of all cell types, and proceeded immediately to scRNA-seq. Cell hashing was used to combine multiple samples into the same single-cell emulsion channel.
The lymph node cells were stained with TotalSeq antibodies (BioLegend anti-mouse Hashtags), washed 5 times and pooled in ice-cold PBS with 0.04% BSA according to the manufacturer's protocol. Next, 55,000 cells were loaded onto a 10x Genomics Chromium instrument (10x Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium Single Cell 3’ Library & Gel Bead v3 Kit (10x Genomics) with BioLegend's protocol for generating hashtag libraries. Quality control for amplified cDNA libraries and final sequencing libraries was performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). scRNA-seq and hashing libraries were normalized to 4nM concentration and pooled. The pooled libraries were sequenced on the NovaSeq S4 platform for gene expressions, targeting an average sequencing depth of 20,000 reads per cell for gene expression libraries. Hashtag libraries were sequenced on NovaSeq S4 or SP targeting 5,000 reads per cell.

treatment_protocol: For each cytokine, 5μg in 100μl sterile PBS were injected into each animal. Cytokines were injected under the skin (50% subcutaneous, 50% intradermal) bilaterally in the abdominal flank of each mouse. Bilateral skin-draining inguinal lymph nodes were harvested 4 hours post-injection at 6am-8am and pooled for each mouse for downstream processing.

value: Lymph node

tag: strain

tag: age

value: 11-15 weeks old

value: Cytokine injection


title: Isotype treated, terminally differentiated, rep2

value: Spleen

tag: cell type

value: PD-1+ CD8 T cells

value: WT (C57BL/6J)


title: RNASeq, HEK293T cells, EZH2 A677G, replicate 1

tag: genotype


title: Patient 21 CD8+ [Pt21_CD8 RNA-seq]

tag: tissue

value: TIL ACT Product

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor


title: bulk RNA-seq, C9-FTD donor F2, Motor cortex, Neurons

value: neurons (NeuN+SOX10-)


title: Isotype treated, stem-like rep1

tag: treatment


title: Isotype treated, terminally differentiated rep1


title: Patient 20 CD4+CD8+ [Pt20_DP RNA-seq]

value: Expanded TIL

value: PD

tag: number til_infused

tag: infusion percent_cd4

tag: infusion percent_cd8

value: M


title: bulk RNA-seq, C9-FTD donor F2, Frontal cortex, Other glia

value: frontal cortex

tag: donor id

tag: disease

tag: Sex


title: GBM827 cells naïve

city: Cleveland

first: Jeongwu

last: Lee

state: OH

address: 9500 Euclid Ave

department: Cancer Biology

institute: Lerner Research Institute, Cleveland Clinic

description:
Lee7
PolyA RNA
Sc-RNA-seq
827timecourse.xlsx

data_processing:
For cells processed with the 10X platform, we excluded the sequenced cells whose number of detected genes was less than half or more than twice the mean number of genes detected across cells coming from the same tumor.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.tar: Tar archives include barcodes.tsv, genes.tsv, and matrix.mtx files.
Supplementary_files_format_and_content: 131timecourse.xlsx: Excel file containing TPM values (transcript-per-million reads) for across about 80,000 glioma cells with the 10X platform; Mesenchymal and senescence signature gene expression levels in Lee S1, S2, S3 and S4.
Supplementary_files_format_and_content: 022timecourse.xlsx: Excel file containing TPM values (transcript-per-million reads) for across about 80,000 glioma cells with the 10X platform; Mesenchymal and senescence signature gene expression levels in Lee S5 and S6.
Supplementary_files_format_and_content: 827timecourse.xlsx: Excel file containing TPM values (transcript-per-million reads) for across about 80,000 glioma cells with the 10X platform; Mesenchymal and senescence signature gene expression levels in Lee S7 and S8.

source_name: patient-derived glioblastoma

growth_protocol: Cells were cultured in standard neural stem cell media.

extract_protocol:
RNA from the single cells was isolated, following the 10X protocol.
Single cells were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell Library, following the manufacturer’s protocol.

treatment_protocol: In vitro irradiation (10 Gy) was performed on day 0 of the indicated cells and various times after irradiation. Cells were harvested and processed for single cell seq.

value: Glioblastoma

tag: time point

value: 0 days


title: bulk RNA-seq, C9-FTD donor F2, Frontal cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Female


title: RNASeq, HEK293T cells, EZH2 WT, replicate 2

tag: cell line

value: Human embryonic kidney

value: WT


title: Cytokine hashtags for samples 45

description: 10x Genomics

value: Lymph node

tag: strain

value: 11-15 weeks old


title: bulk RNA-seq, C9-FTD donor F1, Motor cortex, Neurons

value: motor cortex


title: Cytokine hashtags for samples 43

description: 10x Genomics

tag: age

value: Cytokine injection


title: bulk RNA-seq, C9-FTD donor F2, Frontal cortex, Neurons

tag: cell type


title: RNASeq, HEK293T cells, EZH2 WT, replicate 1

tag: genotype


title: Cytokine hashtags for samples 41

description: 10x Genomics

tag: tissue


title: Cytokine hashtags for samples 42

description: 10x Genomics


title: bulk RNA-seq, C9-FTD donor F1, Motor cortex, Other glia

value: other glia (NeuN-SOX10-)


title: Patient 18 CD4+CD8+ [Pt18_DP RNA-seq]

value: TIL ACT Product

tag: trial

tag: response

tag: pfs months

tag: pfs censor_at_12_months

tag: gender

value: F

value: TIL ACT


title: Patient 20 CD4+ [Pt20_CD4 RNA-seq]

value: Expanded TIL

value: PD

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

tag: treatment


title: GBM022 cells naïve

description:
Lee5
PolyA RNA
Sc-RNA-seq
022timecourse.xlsx

tag: time point


title: Cytokine hashtags for samples 39

description: 10x Genomics

tag: Sex


title: GBM827 cells RT 2 days

description:
Lee8
PolyA RNA
Sc-RNA-seq
827timecourse.xlsx

value: Irradiation

value: 2 days


title: Patient 18 CD8+ [Pt18_CD8 RNA-seq]

tag: cell line

tag: infusion percent_cd8


title: Cytokine hashtags for samples 38

description: 10x Genomics

tag: strain

tag: age


title: bulk RNA-seq, C9-FTD donor F1, Frontal cortex, Neurons

tag: tissue

value: frontal cortex

tag: cell type

value: neurons (NeuN+SOX10-)

tag: genotype

tag: donor id

tag: disease


title: bulk RNA-seq, C9-FTD donor F1, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Female


title: Patient 18 CD4+ [Pt18_CD4 RNA-seq]

tag: trial

tag: response

tag: pfs months

tag: pfs censor_at_12_months

tag: gender


title: GBM022 cells RT 2 days

description:
Lee6
PolyA RNA
Sc-RNA-seq
022timecourse.xlsx

value: Glioblastoma

tag: treatment


title: bulk RNA-seq, C9-ALS donor A6, Motor cortex, Other glia

value: Male


title: Patient 15 CD4+CD8+ [Pt15_DP RNA-seq]

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4

value: M


title: bulk RNA-seq, C9-ALS donor A6, Motor cortex, Oligodendrocyte lineage cells

value: motor cortex

tag: Sex


title: bulk RNA-seq, C9-FTD donor F1, Frontal cortex, Other glia


title: GBM131 cells naïve

description:
Lee1
PolyA RNA
Sc-RNA-seq
131timecourse.xlsx

tag: time point

value: 0 days


title: Patient 16 CD8+ [Pt16_CD8 RNA-seq]

tag: tissue

tag: cell line

value: PR

tag: infusion percent_cd8


title: Cytokine hashtags for samples 35

description: 10x Genomics

value: Lymph node

tag: strain

tag: genotype

value: WT

tag: age

value: 11-15 weeks old

value: Cytokine injection


title: Cytokine hashtags for samples 34

description: 10x Genomics


title: bulk RNA-seq, C9-FTD donor F1, Frontal cortex, Oligodendrocyte lineage cells

tag: cell type

tag: donor id

tag: disease


title: GBM131 cells RT 3 weeks

description:
Lee4
PolyA RNA
Sc-RNA-seq
131timecourse.xlsx

value: 3 weeks


title: bulk RNA-seq, C9-ALS donor A6, Frontal cortex, Other glia

value: other glia (NeuN-SOX10-)


title: Patient 16 CD4+ [Pt16_CD4 RNA-seq]

value: TIL ACT Product

value: Expanded TIL

tag: trial

tag: response

tag: pfs months

tag: pfs censor_at_12_months

tag: gender

value: F

value: TIL ACT


title: GBM131 cells RT 5 days

description:
Lee3
PolyA RNA
Sc-RNA-seq
131timecourse.xlsx

tag: treatment

value: Irradiation

value: 5 days


title: Cytokine hashtags for samples 37

description: 10x Genomics

tag: Sex

value: Female


title: Patient 11 CD8+ [Pt11_CD8 RNA-seq]

value: PD

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd4


title: GBM131 cells RT 2 days

description:
Lee2
PolyA RNA
Sc-RNA-seq
131timecourse.xlsx

value: Glioblastoma

tag: time point

value: 2 days


title: 2KR_rescue_rep3

city: Oslo

first: Roza Berhanu

last: Lemma

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: rescue of endogenos c-Myb KD with 2KR-Myb

data_processing:
Basecalls were performed using bcl2fastq v2.18.0.12.
Low quality reads and adaptors were trimmed/removed using Trimmomatic v0.36
Illumina spike-in PhiX were removed using BBMap v37.4
Cleaned reads were aligned against Homo sapiens GRCh38 ensembl release-90 using Tophat2 v2.1.1 with ‘--library-type fr-firststrand --no-mixed --no-novel-juncs' as parameters
Differential expression was calculated using cufflinks in cuffdiff suite v2.2.1 and viewed using cummeRbund v2.16 R package
Genome_build: GRCh38 release-90
Supplementary_files_format_and_content: Replicate FPKM table from cummeRbund

source_name: human erythroleukemic cell line

growth_protocol: K-562 cells were cultivated in IMDM (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptamycin. Selection of stable cell lines was achieved with the addition of 200 µg/ml G418 to the medium.

extract_protocol:
RNeasy Mini kit (Qiagen, 74104)
TruSeq stranded RNA library prep, poly(A) selection (Illumina)

treatment_protocol: No treatment

tag: cell line

tag: stably expressing

tag: sirna


title: Cytokine hashtags for samples 40

description: 10x Genomics

tag: tissue

tag: strain

tag: genotype

tag: age


title: Patient 15 CD4+ [Pt15_CD4 RNA-seq]

tag: cell type

tag: trial

tag: response

tag: pfs months

tag: infusion percent_cd8

value: M


title: Cytokine hashtags for samples 36

description: 10x Genomics

value: Lymph node

tag: Sex

tag: treatment


title: Patient 11 CD4+ [Pt11_CD4 RNA-seq]

tag: pfs censor_at_12_months

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: gender


title: Patient 14 CD8+ [Pt14_CD8 RNA-seq]

tag: cell line

value: CR

tag: infusion percent_cd4


title: bulk RNA-seq, C9-ALS donor A5, Motor cortex, Other glia

tag: tissue

value: motor cortex

tag: donor id

tag: disease

value: Male


title: Cytokine hashtags for samples 31

description: 10x Genomics

tag: strain

tag: genotype

value: WT

tag: age

value: 11-15 weeks old

value: Cytokine injection


title: Patient 9 CD4+CD8+ [Pt09_DP RNA-seq]

value: TIL ACT Product

value: Expanded TIL

tag: cell type

tag: trial

tag: response

value: PR

tag: pfs months


title: Patient 16 CD4+CD8+ [Pt16_DP RNA-seq]

tag: pfs censor_at_12_months

tag: infusion percent_cd8

value: F

tag: treatment

value: TIL ACT


title: Patient 9 CD8+ [Pt09_CD8 RNA-seq]

tag: overall survival_months

tag: survival censor

tag: number til_infused


title: bulk RNA-seq, C9-ALS donor A6, Motor cortex, Neurons

value: neurons (NeuN+SOX10-)

tag: Sex


title: bulk RNA-seq, C9-ALS donor A6, Frontal cortex, Oligodendrocyte lineage cells

tag: tissue

value: frontal cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: ANAA_rescue_rep1

description: rescue of endogenos c-Myb KD with ANAA-Myb

tag: cell line

tag: stably expressing

tag: sirna


title: Patient 11 CD4+CD8+ [Pt11_DP RNA-seq]

value: PD

tag: infusion percent_cd4

tag: gender


title: Cytokine hashtags for samples 33

description: 10x Genomics

value: Female

tag: strain

tag: genotype

tag: age


title: ANAA_rescue_rep3


title: 2KR_rescue_rep2


title: bulk RNA-seq, C9-ALS donor A6, Frontal cortex, Neurons

tag: cell type

tag: donor id

tag: disease


title: Patient 14 CD4+ [Pt14_CD4 RNA-seq]

tag: trial

tag: response

tag: pfs months

tag: pfs censor_at_12_months

tag: infusion percent_cd8

tag: treatment


title: bulk RNA-seq, C9-ALS donor A5, Frontal cortex, Other glia

tag: tissue

value: other glia (NeuN-SOX10-)

tag: Sex


title: Patient 8 CD4+CD8+ [Pt08_DP RNA-seq]

tag: cell line

tag: overall survival_months

tag: survival censor

tag: number til_infused


title: Cytokine hashtags for samples 26

description: 10x Genomics

value: Lymph node

tag: strain

tag: genotype


title: bulk RNA-seq, C9-ALS donor A5, Frontal cortex, Oligodendrocyte lineage cells

tag: cell type


title: Cytokine hashtags for samples 30

description: 10x Genomics

tag: age


title: bulk RNA-seq, C9-ALS donor A5, Frontal cortex, Neurons

tag: donor id

tag: disease


title: bulk RNA-seq, C9-ALS donor A5, Motor cortex, Oligodendrocyte lineage cells

value: motor cortex


title: bulk RNA-seq, C9-ALS donor A5, Motor cortex, Neurons

value: Male


title: 2KR_rescue_rep1

tag: stably expressing

tag: sirna


title: Cytokine hashtags for samples 29

description: 10x Genomics

value: WT


title: ANAA_rescue_rep2


title: Patient 9 CD4+ [Pt09_CD4 RNA-seq]

tag: trial

tag: response

tag: pfs months

tag: pfs censor_at_12_months

tag: infusion percent_cd4

tag: gender

value: M


title: Cytokine hashtags for samples 32

description: 10x Genomics

tag: tissue

tag: Sex

value: 11-15 weeks old

tag: treatment

value: Cytokine injection


title: α-synuclein 0.5 mg/mL pull-down by anti-α-synuclein antibody

city: Kumamoto

first: Yasushi

last: Yabuki

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Genomic neurology

country: Japan

institute: Kumamoto University

library_source: other

data_processing:
library strategy: RNA Bind-n-Seq
Fastq files were processed for quality check and adapter trimming (24-mer sequences) with the Trimgalore! (v0.6.6).
Random 500000 sequences of 24-mer RNAs were extracted from trimed files and enriched 12-mer motifs compared to input sequences  were detected by the MERMADE program (Kashiwazaki G et al., 2016: doi: 10.1002/cbic.201600282.).
Supplementary files format and content: Enriched sequences, a: Number of enriched sequence in BG4 (or αSyn 0-1.0 mg/mL), b: Number of enriched sequence in input, Enrichment ((a + 1)/(b + 1))  and Enrichment Score (-Log10 p-value).

molecule: other

organism: synthetic RNA

source_name: Synthesized random RNA pool

extract_protocol:
Bound RNAs were extracted from the protein by phenol/chloroform isolation and ethanol precipitation.
RNAs were reverse-transcribed into cDNA using Superscript III (Invitrogen) according to manufac-turer’s instructions together with the following primer: 5'-GCCTTGGCACCCGAGAATTCCA-3'. To control for any nucleotide biases in the input random library, the input RNA pool (0.5 pmol) was also reverse-transcribed and Illumina sequencing library prep was followed by 8–10 cycles of PCR using High Fidelity Phusion (New England Biolabs). All libraries were barcoded in the PCR step, pooled together,

tag: rip antibody

value: anti-α-synuclein antibody (ab212184, Abcam)

value: Synthesized random RNA pool


title: α-synuclein 1.0 mg/mL pull-down by anti-α-synuclein antibody


title: BG4 0.32 μM pull-down by anti-DYKDDDDK tag antibody

value: BG4 scFV & anti-DYKDDDDK tag (14793S, Cell Signaling Technology)


title: Cytokine hashtags for samples 28

description: 10x Genomics

tag: strain

tag: genotype


title: Patient 8 CD4+ [Pt08_CD4 RNA-seq]

value: TIL ACT Product

tag: cell line

value: Expanded TIL

tag: cell type

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd8

value: F

value: TIL ACT


title: α-synuclein 0.1 mg/mL pull-down by anti-α-synuclein antibody


title: Cytokine hashtags for samples 25

description: 10x Genomics

tag: age


title: Patient 7 CD8+ [Pt07_CD8 RNA-seq]

tag: trial

tag: response

value: PD

tag: pfs months


title: α-synuclein 0.05 mg/mL pull-down by anti-α-synuclein antibody


title: Cytokine hashtags for samples 24

description: 10x Genomics

value: Female


title: Patient 7 CD4+CD8+ [Pt07_DP RNA-seq]

tag: pfs censor_at_12_months

tag: infusion percent_cd4

tag: gender


title: α-synuclein 0.01 mg/mL pull-down by anti-α-synuclein antibody


title: Patient 7 CD4+ [Pt07_CD4 RNA-seq]

tag: tissue

tag: treatment


title: Cytokine hashtags for samples 23

description: 10x Genomics

tag: Sex

tag: strain


title: Cytokine hashtags for samples 27

description: 10x Genomics

tag: genotype


title: bulk RNA-seq, C9-ALS donor A4, Motor cortex, Neurons

tag: cell type

value: neurons (NeuN+SOX10-)

tag: donor id

tag: disease


title: α-synuclein 0 mg/mL pull-down by anti-α-synuclein antibody

tag: rip antibody


title: Patient 3 CD8+ [Pt03_CD8 RNA-seq]

tag: cell line

value: CR

tag: overall survival_months

tag: survival censor

tag: number til_infused

tag: infusion percent_cd8


title: Cytokine hashtags for samples 22

description: 10x Genomics

value: Lymph node

tag: age


title: bulk RNA-seq, C9-ALS donor A4, Frontal cortex, Oligodendrocyte lineage cells

value: frontal cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: bulk RNA-seq, C9-ALS donor A4, Frontal cortex, Neurons


title: BMM9-Benign-immune

city: Boston

first: Shenglin

last: Mei

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

description: Benign bone marrow from hip-replacement surgery; enriched for immune cell markers by FACS.

data_processing:
Demultiplexing of bcl files into .fastq files was performed using cellranger 3.0.1 mkfastq software (10x Genomics) and alignments to the human (GRCh38) genome reference sequences were performed using cellranger count. The reference included all protein coding genes as well as mitochondrial genes for downstream analysis.
Assembly: GRCh38/hg38
Supplementary files format and content: count matrix in csv

source_name: Bone Marrow

extract_protocol:
10X Genomics Single cell 3' gene expression V2
We collected unique sets of tissue fractions from each patient: solid metastatic tissue (Tumor fraction), liquid bone marrow at the site of the metastasis (Involved), liquid bone marrow from a vertebral body distant from the tumor site (Distal/Noninvolved), as well as bone marrow from hip-replacement surgery (Benign). Cells were washed once with 2% FBS-PBS (v/v) followed by DAPI staining (1 ug/ml). Flow sorting for live and non-erythroid cells (DAPI-neg/CD235-neg) was performed on a BD FACS Aria III equipped with a 100um nozzle (BD Biosciences, San Jose, CA) instrument.

tag: patient id

tag: prior systemic therapies

value: Benign

value: Bone marrow (enriched for immune cell markers)


title: Cytokine hashtags for samples 20

description: 10x Genomics

tag: tissue

value: WT

value: 11-15 weeks old

value: Cytokine injection


title: BMM8-Benign-immune


title: Cytokine hashtags for samples 21

description: 10x Genomics

tag: treatment


title: BMM6-Benign-immune


title: Cytokine hashtags for samples 19

description: 10x Genomics

tag: Sex


title: bulk RNA-seq, C9-ALS donor A3, Motor cortex, Other glia

value: motor cortex

value: other glia (NeuN-SOX10-)


title: bulk RNA-seq, C9-ALS donor A4, Motor cortex, Other glia


title: bulk RNA-seq, C9-ALS donor A4, Motor cortex, Oligodendrocyte lineage cells


title: Cytokine hashtags for samples 18

description: 10x Genomics

tag: strain


title: rat lung, MWCNT treated-3, Year 2

city: Tokyo

first: Motoki

last: Hojo

address: 3-24-1 Hyakunincho, Shinjuku-kuku

department: Department of Pharmaceutical and Environmental Sciences

institute: Tokyo Metropolitan Institute of Public Health

description:
M3-4_FRAS210026666-1r
Gene expression_Y-2_MWCNT vs Control.txt

data_processing:
CLC Genomic Workbench v22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomic Workbench (Quality score limit 0.05)
Trimmed sequence reads were mapped to Rnor_6.0/rn6  using CLC Genomic Workbench (parameters: mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8, and auto-detect paired distances (max. no. of hits for a read: 10)
Read count extraction and normalization were performed using CLC Genomic Workbench
Assembly: Rnor_6.0
Supplementary files format and content: Tab-deliminated text files include raw counts, RPKM, TPM, and CPM for each sample

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Total RNA was harvested using Rneasy mini kit (Qiagen).
RNA-seq libraries were prepared using NEB Next Ultra II RNA Library Prep Kit for Illumina (New England Biolabs)

value: lung

value: MWCNT suspension


title: rat lung, MWCNT treated-1, Year 2

description:
M3-1_FRAS210026664-1r
Gene expression_Y-2_MWCNT vs Control.txt


title: rat lung, MWCNT treated-3, Year 1

description:
M2-4_FRAS210026654-1r
Gene expression_Y-1_MWCNT vs Control.txt


title: BMM4-Benign-immune


title: bulk RNA-seq, C9-ALS donor A3, Motor cortex, Oligodendrocyte lineage cells

tag: genotype


title: bulk RNA-seq, C9-ALS donor A3, Motor cortex, Neurons

tag: cell type


title: Cytokine hashtags for samples 17

description: 10x Genomics


title: rat lung, MWCNT treated-2, Year 2

description:
M3-3_FRAS210026665-1r
Gene expression_Y-2_MWCNT vs Control.txt


title: BMM3-Benign-immune


title: rat lung, MWCNT treated-2, Year 1

description:
M2-3_FRAS210026653-1r
Gene expression_Y-1_MWCNT vs Control.txt


title: bulk RNA-seq, C9-ALS donor A3, Frontal cortex, Other glia

tag: donor id


title: bulk RNA-seq, C9-ALS donor A4, Frontal cortex, Other glia

tag: disease


title: Cytokine hashtags for samples 16

description: 10x Genomics


title: BMM7-Benign-stroma

description: Benign bone marrow from hip-replacement surgery; enriched for stroma markers by FACS.

value: Bone marrow (enriched for stroma markers)


title: rat lung, MWCNT treated-1, Year 1

description:
M2-2_FRAS210026652-1r
Gene expression_Y-1_MWCNT vs Control.txt


title: Input from random library

tag: rip antibody

value: none (Rabbit IgG)

value: Synthesized random RNA pool


title: rat lung, MWCNT treated-2, Year 0.5

description:
M1-2_FRAS210026647-1r
Gene expression_Y-0.5_MWCNT vs Control.txt


title: rat lung, MWCNT treated-1, Year 0.5

description:
M1-1_FRAS210026646-1r
Gene expression_Y-0.5_MWCNT vs Control.txt


title: BMM9-Benign-stroma


title: Cytokine hashtags for samples 13

description: 10x Genomics

value: Female


title: BMM5-Benign-immune


title: Cytokine hashtags for samples 15

description: 10x Genomics


title: Cytokine hashtags for samples 11

description: 10x Genomics


title: bulk RNA-seq, C9-ALS donor A2, Motor cortex, Other glia


title: rat lung, vehicle control-3, Year 2

description:
C3-3_FRAS210026669-1r
Gene expression_Y-2_MWCNT vs Control.txt

value: Vehicle


title: BMM6-Benign-stroma


title: BMM2-Benign-immune


title: rat lung, MWCNT treated-3, Year 0.5

description:
M1-4_FRAS210026648-1r
Gene expression_Y-0.5_MWCNT vs Control.txt


title: bulk RNA-seq, C9-ALS donor A2, Motor cortex, Neurons

value: neurons (NeuN+SOX10-)


title: bulk RNA-seq, C9-ALS donor A3, Frontal cortex, Neurons

value: frontal cortex


title: Cytokine hashtags for samples 14

description: 10x Genomics

value: Lymph node


title: bulk RNA-seq, C9-ALS donor A3, Frontal cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: BMM5-Benign-stroma

value: Benign


title: bulk RNA-seq, C9-ALS donor A2, Frontal cortex, Other glia


title: bulk RNA-seq, C9-ALS donor A2, Motor cortex, Oligodendrocyte lineage cells


title: BMM8-Benign-stroma


title: BMM4-Benign-stroma


title: rat lung, vehicle control-2, Year 2

description:
C3-2_FRAS210026667-1r
Gene expression_Y-2_MWCNT vs Control.txt


title: bulk RNA-seq, C9-ALS donor A2, Frontal cortex, Oligodendrocyte lineage cells


title: Cytokine hashtags for samples 10

description: 10x Genomics

value: WT


title: rat lung, vehicle control-3, Year 1

description:
C2-4_FRAS210026657-1r
Gene expression_Y-1_MWCNT vs Control.txt


title: rat lung, vehicle control-1, Year 2

description:
C3-1_FRAS210026668-1b
Gene expression_Y-2_MWCNT vs Control.txt


title: Cytokine hashtags for samples 09

description: 10x Genomics

value: 11-15 weeks old


title: BMM3-Benign-stroma


title: bulk RNA-seq, C9-ALS donor A2, Frontal cortex, Neurons


title: Cytokine hashtags for samples 07

description: 10x Genomics

value: Cytokine injection


title: Cytokine hashtags for samples 06

description: 10x Genomics


title: bulk RNA-seq, C9-ALS donor A1, Motor cortex, Other glia

value: motor cortex

value: Male


title: rat lung, vehicle control-1, Year 1

description:
C2-1_FRAS210026655-1r
Gene expression_Y-1_MWCNT vs Control.txt

value: lung


title: rat lung, vehicle control-2, Year 1

description:
C2-2_FRAS210026656-1r
Gene expression_Y-1_MWCNT vs Control.txt


title: bulk RNA-seq, C9-ALS donor A1, Motor cortex, Oligodendrocyte lineage cells


title: BMM1-Benign-stroma


title: Cytokine hashtags for samples 05

description: 10x Genomics


title: Cytokine hashtags for samples 04

description: 10x Genomics


title: bulk RNA-seq, C9-ALS donor A1, Motor cortex, Neurons


title: rat lung, vehicle control-2, Year 0.5

description:
C1-3_FRAS210026650-1r
Gene expression_Y-0.5_MWCNT vs Control.txt


title: Cytokine hashtags for samples 08

description: 10x Genomics


title: RCC-BM9-Tumor

value: Renal cell carcinoma, bone metastatic tumor

value: Bone Marrow


title: bulk RNA-seq, C9-ALS donor A1, Frontal cortex, Other glia

value: other glia (NeuN-SOX10-)


title: rat lung, vehicle control-1, Year 0.5

description:
C1-1_FRAS210026649-1r
Gene expression_Y-0.5_MWCNT vs Control.txt


title: Cytokine hashtags for samples 02

description: 10x Genomics


title: bulk RNA-seq, C9-ALS donor A1, Frontal cortex, Oligodendrocyte lineage cells


title: BMM2-Benign-stroma

value: Bone marrow (enriched for stroma markers)


title: RCC-BM9-Involve


title: AG-221-treated replicate3

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
Cluster generation was performed with 2 nM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 SR Cluster Kit reagents and sequenced on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents for 150 cycles (single read). Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina).
Sequencing reads were pre-processed and aligned to the mouse genome using the RNA-seq method of the bcbio-nextgen pipeline (v. 20.11). The reads were first trimmed for quality and adapter using Atropos (v. 1.1.28).
Trimmed reads were aligned to the Mus musculus genome (mm10) using hisat2 (v. 2.2.1). Numbers of reads were summarized at the gene level per sample using htseq-count function of HTSeq (v. 0.9.1).
Genome_build: mm10
Supplementary_files_format_and_content: The csv file contains htseq-counts output. The first 2 columns contain the Ensembl gene ID and the gene symbol, and the last 6 columns contain raw counts per sample. The first row contains the column names, with treatment of each sample (Idh2i or DMSO)  indicated within the sample names.

source_name: Splenic CD8 T cells

growth_protocol: Splenocytes were cultured in RPMI medium (Gibco 61870-01) supplemented with 10% FBS, (Gibco 10270-106), 1% Penicillin/Streptomycin (Gibco 15070-063), 50µM ß-mercaptoethanol, 1% HEPES (Gibco 15630-080), 1x Non-essential amino acids (Gibco 11140-035), 1% L-glutamine (Gibco 25030-081) and 1mM Sodium Pyruvate (Gibco 11360-039). Cells were additionally supplemented with recombinant human (rh) IL-2 100IU/ml (in house) and ovalbumin peptide (SIINFEKL) 1µg/ml and either with 20 µM UK5099 (Sigma Aldrich) or with their solvent DMSO as a control. Splenocytes were collected at day 3, washed and split, and cells were cultured for 4 additional days with 100U/ml rhIL-2 and 10ng/ml rhIL-7 (Peprotech 200-07) without small molecule inhibitor.

extract_protocol:
RNA was collected using Qiagen RNA extraction kit
RNA quality was assessed on a Fragment Analyzer (Agilent Technologies). All RNAs had an RQN between 9.4 and 10. RNA-seq libraries were prepared from 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer). Libraries were quantified by a fluorometric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies).

treatment_protocol: T cells were treated for 7 days with either DMSO or 5µM AG-221

value: Splenic CD8 T cells


title: Cytokine hashtags for samples 01

description: 10x Genomics

value: Female


title: RCC-BM9-Noninvolved


title: bulk RNA-seq, C9-ALS donor A1, Frontal cortex, Neurons

value: neurons (NeuN+SOX10-)


title: RCC-BM2-Noninvolved


title: AG-221-treated replicate2


title: AG-221-treated replicate1


title: RCC-BM2-Involve


title: ChIP-seq Input, Control donor C9, Motor cortex, Oligodendrocyte lineage cells

data_processing:
Raw sequencing data were pre-processed to remove adapters and low-quality sequences with the HTStream tool.
Reads were mapped to the human hg38 genome build with BWA-MEM2 and filtered to remove multi-mapping reads and low-quality alignments using Samtools.
Reads mapping to ENCODE-blacklisted genomic regions were excluded using BEDTools.
H3K27ac-enriched peaks were detected using MACS2, including input controls for each cell type and condition.
Differential peaks between C9-ALS and control for each FANS-sort population were identified using DiffBind in edgeR mode. Peaks with FDR < 0.05 were called significant.
Assembly: hg38
Supplementary files format and content: bigWig, H3K27ac signal normalized to 1 million reads (except for Input sample)
Supplementary files format and content: tab-delimited text files, broad peaks output from MACS2 (except for Input sample)

extract_protocol:
The isolation of brain nuclei prior to the flow cytometry separation was performed mostly as previously described in Kozlenkov et al. (Sci Adv. 2018). Tissue (~300 mg) was homogenized in ice-cold lysis buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 0.1% Triton X-100, 1 mM DTT, 0.1 mM benzamidine, 0.1 mM phenylmethylsulfonyl fluoride (PMSF), and 10mM Tris-HCl, pH 8.0), underlaid with the sucrose buffer (1.8 M Sucrose, 3 mM Mg(Ac)2, 1 mM DTT, and 10 mM Tris-HCl pH 8.0), and centrifuged for 1h at 24,000 rpm. The nuclear pellets were then resuspended in the antibody-incubation buffer (0.5% BSA, 3mM MgCl2, and 10 mM Tris-HCl, pH 8.0) and incubated with antibodies against NeuN, SOX10 and IRF5 for 1 hr at 4°C. Fluorescence-activated nuclei sorting (FANS) was then used to isolate neurons (NeuN+SOX10- population), oligodendrocyte lineage cells (NeuN-SOX10+ population), consisting of mature oligodendrocytes and a smaller population of OPCs, microglia (NeuN-SOX10-IRF5+ population) and the remaining population (NeuN-SOX10-IRF5-) that mostly consisted of astrocytes. Alexa488-conjugated anti-NeuN antibodies (1:1000 dilution, Millipore, Cat. # MAB377x), Alexa488-conjugated anti-IRF5 antibodies (1:200 dilution, R&D Systems, Cat. # IC4508G), and anti-SOX10 antibodies (R&D Systems, Cat. # AF2864) that were custom conjugated to Alexa647 (1:150 dilution, Cat# FCMAB317PE, Millipore) were used. DNA stain DAPI was used to label intact nuclei. From each sample and population, 100-150K nuclei were collected.
We employed the native ChIP protocol (N-ChIP) in which chromatin fragmentation is performed using micrococcal nuclease (MNase) without crosslinking proteins to DNA (Sci Adv. 2018). We used anti-H3K27ac antibodies from Active Motif (Cat# 39133; rabbit polyclonal, 3 µg per sample). ChIP-Seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Cat. # E7645). The resulting libraries were sequenced on a NovaSeq 6000 instrument (Illumina), using paired-end 100 cycles protocol, to an average of 60 million read pairs per sample. For each diagnostic group, three input control samples obtained from MNAse-digested DNA were prepared and sequenced.

value: Control

tag: chip antibody


title: Cytokine hashed samples 45

description: 10x Genomics

value: Lymph node


title: RCC-BM2-Tumor


title: rat lung, vehicle control-3, Year 0.5

description:
C1-5_FRAS210026651-1r
Gene expression_Y-0.5_MWCNT vs Control.txt

value: Vehicle


title: Cytokine hashed samples 44

description: 10x Genomics


title: Cytokine hashtags for samples 03

description: 10x Genomics


title: Cytokine hashed samples 43

description: 10x Genomics


title: DMSO-treated replicate3

value: DMSO


title: RCC-BM1-Noninvolved


title: ChIP-seq H3K27ac, Control donor C9, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: H3K27ac (Active Motif #39133)


title: ChIP-seq Input, Control donor C9, Motor cortex, Neurons

value: neurons (NeuN+)


title: Cytokine hashed samples 42

description: 10x Genomics

value: WT

value: 11-15 weeks old

value: Cytokine injection


title: ChIP-seq H3K27ac, Control donor C9, Motor cortex, Neurons

value: motor cortex


title: DMSO-treated replicate1


title: RCC-BM1-Involve

value: Bone Marrow


title: RCC-BM1-Tumor

value: Renal cell carcinoma, bone metastatic tumor


title: Cytokine hashed samples 41

description: 10x Genomics


title: ChIP-seq Input, Control donor C9, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: Peripheral white blood cells, Subfertile, 32

city: Auburn

first: Paul

middle: W

last: Dyce

state: Alabama

address: 559 Devall Dr,

department: Animal Science

institute: Auburn University

data_processing:
Raw sequencing data were subjected to a quality check using FastQC v0.11.9 and MultiQC v1.12. The 3’ adapter sequence was trimmed using Cutadapt with the following parameters: -a TGGAATTCTCGGGTGCCAAGG -minimum length 23. The reads were further trimmed using Cutadapt to remove four bases from either side of each read following the small RNA trimming instructions (cutadapt -u 4 -u -4) (recommended by NEXTflex small RNA-Seq kit v3 (Perkin Elmer)). Trimmed Fastq files were checked for quality control with FastQC v0.11.9 and MultiQC v1.12. To profile both novel and known miRNA expression in the samples from the cleaned sequence data, the trimmed reads were processed using the miRDeep2 analysis workflow. Sequences were aligned to Ensembl's ARS-UCD 1.2 Bos taurus reference genome using the mapper.pl module in miRDeep2 and were further aligned with Bos taurus precursor and matured miRNAs extracted from miRBase v22.1 producing raw read counts for each sample. The read counts were transformed to counts per million (CPM) using edgeR v3.28.1. For quality control, raw counts with CPM < 1 in 50% of the samples were filtered out. The differentially expressed miRNAs were identified using DESeq2 v1.26.0.
Assembly: ARS UCD1.2 Bos taurus
Supplementary files format and content: Matrix table with raw counts for all miRNAs and samples in miRNA_raw_counts.txt
Supplementary files format and content: Normalized counts for all miRNAs and samples in miRNA_Normalized.csv

organism: Bos taurus

source_name: Blood

extract_protocol:
Total RNA was isolated from 14 heifers using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following standard procedures. RNA purification and DNase digestion were done using an RNA clean and concentrator kit (Zymo Research, Irvine, CA, USA). RNA was quantified using a Qubit RNA broad-range assay kit (Eurogene, OR) on a Qubit fluorometer. The RNA integrity was assessed using the Agilent Bioanalyzer and the Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). The quality of small RNAs was determined using the Agilent 2100 Bioanalyzer Small RNA kit (Agilent, Santa Clara, CA, USA)
The total RNA of each sample was diluted with RNase-free water to obtain a final concentration of 1 mg as a starting material. This diluted total RNA was used to prepare libraries using the protocols by NEXTflex small RNA-Seq kit v3 (Perkin Elmer). Following the protocol from the kit, the 5’ and 3’ adapters were ligated to the RNA fragments, which were then reverse-transcribed and amplified (18 cycles) to generate cDNA libraries with a unique barcode primer. Libraries were cleaned up using NEXTflex Cleanup beads (gel-free protocol), and the size distribution of the final library was assessed by Agilent Bioanalyzer high-sensitivity DNA assay (Agilent, Santa Clara, CA, USA). The quality-checked libraries were pooled and sequenced in the NextSeq 500 using the single-end 50 bp chemistry at Discovery Life Sciences (Hudson Alpha Institute of Biotechnology, Huntsville, AL, USA).

value: Blood

tag: pregnancy outcome

value: Subfertile (Not pregnant to AI)

value: Peripheral white blood cells

tag: breed

value: Angus-Simmental crossbred


title: Cytokine hashed samples 40

description: 10x Genomics

value: Lymph node

value: Female


title: ChIP-seq H3K27ac, Control donor C9, Motor cortex, Microglia

value: Control


title: RCC-BM8-Tumor


title: Peripheral white blood cells, Fertile, 31

value: Fertile (Pregnant to AI)


title: RCC-BM7-Tumor


title: Cytokine hashed samples 39

description: 10x Genomics


title: ChIP-seq Input, Control donor C9, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)


title: RCC-BM5-Tumor


title: ChIP-seq H3K27ac, Control donor C9, Motor cortex, Astrocytes

value: H3K27ac (Active Motif #39133)


title: Cytokine hashed samples 37

description: 10x Genomics

value: WT


title: Peripheral white blood cells, Fertile, 29


title: Peripheral white blood cells, Subfertile, 30


title: Peripheral white blood cells, Subfertile, 28


title: RCC-BM4-Tumor

value: Pazopanib, sorafenib + radium-223 (last 3/2016), axitinib


title: ChIP-seq H3K27ac, Control donor C8, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: RCC-BM3-Tumor


title: ChIP-seq H3K27ac, Control donor C8, Motor cortex, Neurons

value: motor cortex

value: neurons (NeuN+)


title: Peripheral white blood cells, Fertile, 27


title: Cytokine hashed samples 35

description: 10x Genomics

value: 11-15 weeks old

value: Cytokine injection


title: ChIP-seq H3K27ac, Control donor C8, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: RCC-BM10-Noninvolved

value: Bone Marrow


title: Cytokine hashed samples 38

description: 10x Genomics


title: RCC-BM10-Involve


title: DMSO-treated replicate2

value: Splenic CD8 T cells

value: DMSO


title: Peripheral white blood cells, Subfertile, 26

value: Blood

value: Subfertile (Not pregnant to AI)

value: Peripheral white blood cells

value: Angus-Simmental crossbred


title: ChIP-seq H3K27ac, Control donor C8, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

value: Control

value: Female


title: Cytokine hashed samples 34

description: 10x Genomics

value: Lymph node

value: WT


title: Peripheral white blood cells, Fertile, 25

value: Fertile (Pregnant to AI)


title: Cytokine hashed samples 33

description: 10x Genomics


title: RCC-BM10-Tumor

value: Renal cell carcinoma, bone metastatic tumor


title: Cytokine hashed samples 32

description: 10x Genomics

value: 11-15 weeks old


title: UIinput

city: Ramat Gan

first: Dror

last: Avni

address: Derech Shiba, 2

department: Department of Medicine C

institute: Weizmann InstituteSheba Medical Center -Tel Hashomer

data_processing:
Reads were demultiplexed
Adapters were trimmed using the cutadapt tool
The reads were aligned uniquely to the human genome (hg19) using bowtie
Bound regions were detected using MACS2 (version 2.0.10.20131216)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak Macs2 files (bed)

source_name: psoriasis non-lesion biopsies

extract_protocol:
Skin biopsies were snap-frozen and stored in liquid nitrogen. Before thawing, epidermal layers were separated from adipose tissues using scalpel. Tissues were crosslinked with 1% formaldehyde at 37° for 10 min, neutralized by adding 1.25 M glycine for 5 min. Crosslinked tissues were washed with 1 ml of ice-cold PBS, then grinded using mortar and dry ice-cooled pestle. Pellets were wash with two buffers sequentially: buffer I (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5), and buffer II (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5), each step followed by centrifugation for 5 min at 4°C. Next, the pellets  were re-suspended in 0.12 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.1, 1× protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN) and sonicated using Covaris microTUBE (duty cycle 10%, Peak power 165, 200 cycles per burst, 180 s cycle time, 4 cycles), followed by centrifugation for 10 min. Supernatants were collected and diluted in buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1). Sheared chromatin was incubated with anti-H3K27ac antibody (ab4729, Abcam), pre-coupled to magnetic protein G dynabeads (1004D, Invitrogen™), overnight at 4°C. Beads were extensively washed with RIPA buffer (×2), high salt RIPA buffer, LiCl buffer and finally softly with 10mM Tris-HCl, pH 8. Samples were treated with RNase A for 30 min at 37°C. Crosslinking was reversed by proteinase K and elution buffer (5 mM Tris-HCl, NaCl 150mM, SDS 0.5%, EDTA 1mM). DNA was purified using SPRI beads (Beckman Coulter). DNA fragments were checked for the proper size range using Agilent 4200 TapeStation system.
All 12 samples were treated in the same day to avoid batch effects. From each sample, 2.4-20 ng of purified ChIP DNA fragments were used to generate libraries for deep sequencing. Sequencing libraries were constructed with barcodes to allow multiplexing of 12 samples on one lane. Between 16-44 million single-end 75-bp reads were sequenced per sample.

tag: antibody

value: Input

tag: sample type

value: 3-mm punch biopsies

tag: disease state

value: psoriasis non-lesion


title: ChIP-seq Input, Control donor C7, Motor cortex, Oligodendrocyte lineage cells

value: motor cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: Peripheral white blood cells, Fertile, 24

value: Blood


title: ChIP-seq H3K27ac, Control donor C7, Motor cortex, Oligodendrocyte lineage cells

value: H3K27ac (Active Motif #39133)


title: Peripheral white blood cells, Fertile, 22

value: Peripheral white blood cells


title: Ninput

source_name: healthy skin biopsies

value: healthy skin


title: Cytokine hashed samples 29

description: 10x Genomics

tag: age

value: Cytokine injection


title: ChIP-seq Input, Control donor C7, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)

value: Control


title: Peripheral white blood cells, Subfertile, 23

value: Subfertile (Not pregnant to AI)

value: Angus-Simmental crossbred


title: Cytokine hashed samples 30

description: 10x Genomics

value: Lymph node

value: Female

value: WT


title: Peripheral white blood cells, Subfertile, 21


title: UI4


title: ChIP-seq H3K27ac, Control donor C7, Motor cortex, Neurons

value: neurons (NeuN+)


title: Cytokine hashed samples 31

description: 10x Genomics

value: 11-15 weeks old


title: Cytokine hashed samples 36

description: 10x Genomics


title: Cytokine hashed samples 28

description: 10x Genomics


title: Peripheral white blood cells, Subfertile, 17


title: ChIP-seq Input, Control donor C7, Motor cortex, Neurons


title: Cytokine hashed samples 27

description: 10x Genomics


title: UI2

value: 3-mm punch biopsies

value: psoriasis non-lesion


title: ChIP-seq Input, Control donor C7, Motor cortex, Astrocytes

value: motor cortex

value: astrocytes (NeuN-SOX10-IRF5-)


title: Peripheral white blood cells, Fertile, 20

value: Blood

value: Fertile (Pregnant to AI)


title: Pinput

source_name: psoriasis lesion biopsies

value: Input

value: psoriasis lesion


title: Cytokine hashed samples 26

description: 10x Genomics

value: Cytokine injection


title: UI1


title: ChIP-seq H3K27ac, Control donor C7, Motor cortex, Astrocytes

value: Control

value: H3K27ac (Active Motif #39133)


title: P4


title: Cytokine hashed samples 25

description: 10x Genomics


title: ChIP-seq H3K27ac, Control donor C15, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Male


title: UI3


title: ChIP-seq H3K27ac, Control donor C7, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)

value: Female


title: VZN, SC, F2, Synergy, rep2

city: Madrid

first: Odei

last: Barreñada

address: C/ Ramiro de Maeztu 9

country: Spain

institute: CIB Margarita Salas - CSIC

description:
Total RNA < 100 bp length
VS2-Sy-R

data_processing:
From the raw data, adaptor sequences are removed, poor quality reads are filtered out (sequences below the Phred score of 32) and poorly expressed sequences (under 10 CPM, counts per million) were removed.
To speed up the analysis and sequencing process, we used a software called FASTX-Toolkit (available at http://hannonlab.cshl.edu/fastx_toolkit/)
To identify small RNA molecules,miRNAs or piRNAs, we compared them to publicly available databases that contain these sequences. We utilized a sequence aligner called Bowtie v 1.3.1, allowing for one mismatch between the query sequence and the database sequence. For identifying miRNAs, we used the miRNA database called miRBase v22. To identify piRNA sequences, we utilized piRNA-IPdb.
Assembly: mm39
Supplementary files format and content: Processed data are sequences identified as miRNAs or piRNAs in fasta format. The identic reads are collapsed in one unique sequence with the number of detected sequences after "_" symbol.
Supplementary files format and content: Aditionaly, the complete matrix of counts is uploaded with detected miRNAs or piRNAs in each sample.

source_name: Gonad

growth_protocol: Pathogen-free (SPF), temperature (22°C ± 1°C), humidity (50%-55%). All animals were housed on a 12 h light/dark cycles with ad libitum access to food and water.

extract_protocol:
Early ovaries were isolated from embryos obtained from pregnant females at E13.5. The mesonephros was removed before the purification of germ and somatic cells. PGCs and somatic cells were purified using a paramagnetic technology according to Brieño-Enriquez et al. 2015. Briefly, groups of about 80 gonads were incubated in 0.25% trypsin-EDTA during 15 minutes at 37ºC, washed followed by incubation with PGC-specific antibodies (anti-CD15) bound to paramagnetic-microbeads. Finally, PGCs were isolated from somatic stromal cells by a magnetic column (miniMAcs) and stained both separated fractions with the naphtol AS-MX/ FAST-RED (Sigma-Aldrich) (PGC specific) to determine the level of enrichment of cell populations. In all cases, the enrichment of the PGCs was 93-96%. Similarly, the purity of somatic cells was over 90% in all samples. RNA was extracted using minipreps (Directzol DNA/RNA Miniprep de Zymo Research) following standar guidelines. The quality and quantity of RNA was using Bioanalyzer 2100 (Agilent Technologies). Always best quality samples were prioritized and no samples under 8 RIN were used for sequencing.
Sequencing library was constructed from more than 1ug  of total RNA by BGI sequencing service

treatment_protocol: Pregnant animals were exposed to different endocrine disruptores via drinking water during the first 13 days of pregnancy. Three exposure groups were made: i) unexposed or control group, which were administered only the vehicle, DMSO, at a final solution of 0.3% (v/v); ii) VZN group, corresponding to mice exposed to 50 mg/kg bw/day VZN (using the same amount of DMSO as in the control group); iii) MEHP group, to which 35 mg/kg bw/day MEHP (and same amount of DMSO) was administered. Estimated intakes were calculated from mean drinking and body weight measurements recorded in previous experiments conducted in the laboratory and according to literature data.

value: Gonad

value: Early ovary somatic cell

tag: developmental stage

value: WT

tag: generations since_exposure

tag: exposure

value: Vinclozolin


title: VZN, SC, F3, rep1

description:
Total RNA < 100 bp length
VS3

tag: tissue

tag: Sex


title: VZN, SC, F3, rep2

description:
Total RNA < 100 bp length
VS3-R

tag: strain

tag: genotype


title: Cytokine hashed samples 24

description: 10x Genomics

value: Lymph node

value: 11-15 weeks old

tag: treatment


title: ChIP-seq H3K27ac, Control donor C15, Motor cortex, Neurons

value: motor cortex

tag: cell type

value: neurons (NeuN+)

tag: donor id

tag: disease


title: P3

value: 3-mm punch biopsies


title: Cytokine hashed samples 23

description: 10x Genomics


title: P2

value: psoriasis lesion


title: ChIP-seq H3K27ac, Control donor C15, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

tag: chip antibody


title: ChIP-seq H3K27ac, Control donor C15, Motor cortex, Microglia

value: Control


title: VZN, SC, F1, rep2

description:
Total RNA < 100 bp length
VS1-R


title: VZN, SC, F2, rep2

description:
Total RNA < 100 bp length
VS2-R


title: N3

value: healthy skin


title: P1


title: Cytokine hashed samples 22

description: 10x Genomics

value: Cytokine injection


title: N2

value: 3mm biopsies


title: VZN, SC, F2, rep1

description:
Total RNA < 100 bp length
VS2


title: Cytokine hashed samples 21

description: 10x Genomics


title: ChIP-seq Input, Control donor C14, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Male


title: N4


title: Cytokine hashed samples 20

description: 10x Genomics

value: Female


title: Cytokine hashed samples 18

description: 10x Genomics


title: ChIP-seq H3K27ac, Control donor C14, Motor cortex, Oligodendrocyte lineage cells

value: H3K27ac (Active Motif #39133)


title: VZN, SC, F1, rep1

description:
Total RNA < 100 bp length
VS1

value: Gonad

value: Early ovary somatic cell

value: WT


title: VZN, SC, F2, Synergy, rep1

description:
Total RNA < 100 bp length
VS2-Sy

value: Vinclozolin


title: VZN, PGC, F2, Synergy, rep2

description:
Total RNA < 100 bp length
VP2-Sy-R

value: Primordial germ cell


title: VZN, PGC, F2, Synergy, rep1

description:
Total RNA < 100 bp length
VP2-Sy


title: ChIP-seq Input, Control donor C14, Motor cortex, Neurons

value: motor cortex

value: neurons (NeuN+)


title: Cytokine hashed samples 19

description: 10x Genomics

value: Lymph node

value: 11-15 weeks old


title: VZN, PGC, F3, rep1

description:
Total RNA < 100 bp length
VP3


title: ChIP-seq H3K27ac, Control donor C14, Motor cortex, Neurons

value: Control


title: ChIP-seq H3K27ac, Control donor C14, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: Cytokine hashed samples 17

description: 10x Genomics

value: Cytokine injection


title: Cytokine hashed samples 16

description: 10x Genomics


title: Cytokine hashed samples 15

description: 10x Genomics


title: N1

value: 3mm biopsies

value: healthy skin


title: VZN, PGC, F3, rep2

description:
Total RNA < 100 bp length
VP3-R


title: VZN, PGC, F2, rep1

description:
Total RNA < 100 bp length
VP2


title: Th0-2

city: Bethesda

first: Chuan

last: Wu

state: MD

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

data_processing:
All analyses were performed in Partek® Flow® software, version 5.0 (Copyright 2016, Partek Inc., St. Louis, MO).
FASTQ files were uploaded into Partek Flow software for processing, aligned using STAR aligner, and quantified to transcriptome (Partek E/M using mm10 – Ensembl Transcripts release 94 as the reference index)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: in vitro differentiated pTreg cells with or without TGFb under anti-CD3/28 sitmulation in  DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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 were prepared for sequencing using standard Illumina protocols

value: Spleen

value: CD4+ T cells

value: in vitro differentiation without TGFb


title: ChIP-seq H3K27ac, Control donor C14, Motor cortex, Astrocytes

city: New York

first: Stella

last: Dracheva

address: 1 Gustave L. Levy Pl

institute: Icahn School Of Medicine at Mount Sinai

value: astrocytes (NeuN-SOX10-IRF5-)

value: Male

value: H3K27ac (Active Motif #39133)


title: ChIP-seq Input, Control donor C14, Motor cortex, Microglia


title: VZN, PGC, F2, rep2

description:
Total RNA < 100 bp length
VP2-R

value: Gonad

value: Female

value: WT

value: Vinclozolin


title: Cytokine hashed samples 11

description: 10x Genomics

value: Lymph node


title: Cytokine hashed samples 14

description: 10x Genomics

value: 11-15 weeks old


title: CTSW KO pTregs-1

growth_protocol: in vitro differentiated pTreg cells with TGFb in  DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: pTreg cells

value: CTSW KO

value: in vitro differentiation with TGFb


title: pTreg-1


title: Th0-1


title: CTSW KO pTregs-2


title: Cytokine hashed samples 13

description: 10x Genomics

value: Cytokine injection


title: VZN, PGC, F1, rep2

description:
Total RNA < 100 bp length
VP1-R

value: Primordial germ cell


title: ChIP-seq H3K27ac, Control donor C13, Motor cortex, Neurons

value: motor cortex

value: neurons (NeuN+)

value: Control


title: ChIP-seq H3K27ac, Control donor C13, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: VZN, PGC, F1, rep1

description:
Total RNA < 100 bp length
VP1


title: ChIP-seq Input, Control donor C14, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

value: Male


title: WT pTregs-1

value: Spleen


title: WT pTregs-2


title: Cytokine hashed samples 10

description: 10x Genomics

value: Female


title: MEHP, SC, F3, rep2

description:
Total RNA < 100 bp length
MS3-R

value: Gonad

value: Early ovary somatic cell

value: WT

value: MEHP


title: Cytokine hashed samples 09

description: 10x Genomics

value: Lymph node

value: 11-15 weeks old


title: ChIP-seq H3K27ac, Control donor C12, Motor cortex, Neurons

value: H3K27ac (Active Motif #39133)


title: ChIP-seq H3K27ac, Control donor C12, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: DR29_m

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

data_processing:
Raw-DNA-reads have been quality controlled and processed using Trimgalore v0.4.2, FastQC v0.11.5, Bismark v0.17.08 and MethPipe v3.4.2.
Assembly: Reference genome file was generated by combining GRCm38.68 B6 reference and GRCm38p4 SNP file in order to exchange all B6 to NZO high quality SNPs. Non-symmetric CpGs have been withdrawn, p-values have been calculated using log-likelihood ratio test.
Supplementary files format and content: sites_CpG.adjusted.bed: statistic values (pval, neighbors,fdr) of all found CpGs merged by groups of all DNA samples
Supplementary files format and content: proportion_table_CpG.txt: propotion values (found CpGs, methylated CpGs) for all DNA samples seperated

source_name: liver

extract_protocol:
Genomic DNA was isolated with using Invisorb® Genomic DNA Kit II according to the manufacturer’s protocol.
Genomic DNA from each sample was bisulfite-converted using Zymo EZ DNA Methylation-Gold kit

value: liver

value: NZO/HIBomDife

value: female

value: 10 weeks

tag: sample group

value: diabetes resistant (DR)


title: ChIP-seq H3K27ac, Control donor C12, Motor cortex, Microglia

value: motor cortex

value: microglia (NeuN-SOX10-IRF5+)

value: Control


title: DR7_m


title: Cytokine hashed samples 08

description: 10x Genomics

value: Female

value: Cytokine injection


title: MEHP, SC, F2, Synergy, rep2

description:
Total RNA < 100 bp length
MS2-Sy-R

value: Gonad

value: Early ovary somatic cell


title: DR26_m


title: ChIP-seq H3K27ac, Control donor C12, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

value: Male


title: Cytokine hashed samples 07

description: 10x Genomics

value: Lymph node

value: WT

value: 11-15 weeks old


title: Cytokine hashed samples 06

description: 10x Genomics


title: MEHP, SC, F2, Synergy, rep1

description:
Total RNA < 100 bp length
MS2-Sy

value: MEHP


title: Cytokine hashed samples 05

description: 10x Genomics


title: MEHP, SC, F2, rep2

description:
Total RNA < 100 bp length
MS2-R


title: ChIP-seq H3K27ac, Control donor C11, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: H3K27ac (Active Motif #39133)


title: DR25_m

value: liver

value: NZO/HIBomDife

value: female

value: 10 weeks


title: DR18_m

value: diabetes resistant (DR)


title: MEHP, SC, F2, rep1

description:
Total RNA < 100 bp length
MS2

value: Female


title: ChIP-seq H3K27ac, Control donor C13, Motor cortex, Astrocytes

value: motor cortex

value: Control


title: MEHP, SC, F3, rep1

description:
Total RNA < 100 bp length
MS3

value: Gonad

value: Early ovary somatic cell


title: ChIP-seq H3K27ac, Control donor C11, Motor cortex, Neurons

value: neurons (NeuN+)


title: Cytokine hashed samples 03

description: 10x Genomics

value: Lymph node

value: Cytokine injection


title: MEHP, SC, F1, rep2

description:
Total RNA < 100 bp length
MS1-R

value: WT


title: Cytokine hashed samples 04

description: 10x Genomics

value: 11-15 weeks old


title: DR12_m


title: ChIP-seq H3K27ac, Control donor C11, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: Cytokine hashed samples 02

description: 10x Genomics


title: MEHP, SC, F1, rep1

description:
Total RNA < 100 bp length
MS1

value: MEHP


title: DP9_m

value: liver

value: diabetes prone (DP)


title: ChIP-seq H3K27ac, Control donor C11, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

value: H3K27ac (Active Motif #39133)


title: MEHP, PGC, F3, rep2

description:
Total RNA < 100 bp length
MP3-R

value: Primordial germ cell


title: DP5_m

value: NZO/HIBomDife

value: female

value: 10 weeks


title: Cytokine hashed samples 01

description: 10x Genomics

value: Female


title: SCI3

city: Beijing

first: Junhao

last: Deng

state: Beijing

address: Fuxing Road,  Beijing, 100853, People’s Republic of China.

country: China

institute: Chinese PLA General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: spinal cord

extract_protocol:
Total RNAs in each group were isolated and extracted using TRIzol reagents following the manufacturer’s protocol.RNA integrity was evaluated using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Once the RNA were collected and integrity was confirmed, they would be prepared for cDNA amplification, library construction, and quality control. Once the quality of cDNA library was confirmed, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions (from Beijing Novel Bioinformatics Co., Ltd. (https://en.  novogene.com/)). After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: spinal cord

value: without rotarod training

tag: time point

value: 28 days post training


title: MEHP, PGC, F3, rep1

description:
Total RNA < 100 bp length
MP3

value: Gonad


title: SCI2


title: ChIP-seq H3K27ac, Control donor C10, Motor cortex, Neurons

value: motor cortex

value: neurons (NeuN+)

value: Control


title: DP27_m


title: ChIP-seq H3K27ac, Control donor C10, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: MEHP, PGC, F2, Synergy, rep2

description:
Total RNA < 100 bp length
MP2-Sy-R

value: WT

value: MEHP


title: MEHP, PGC, F2, Synergy, rep1

description:
Total RNA < 100 bp length
MP2-Sy


title: SCI1


title: SCIT3

value: rotarod training


title: DP24_m

value: liver

value: diabetes prone (DP)


title: MEHP, PGC, F2, rep2

description:
Total RNA < 100 bp length
MP2-R

value: Primordial germ cell


title: ChIP-seq H3K27ac, Control donor C10, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

value: H3K27ac (Active Motif #39133)


title: DP14_m

value: NZO/HIBomDife

value: female

value: 10 weeks


title: SCIT2

value: spinal cord

value: 28 days post training


title: ChIP-seq H3K27ac, Control donor C10, Motor cortex, Oligodendrocyte lineage cells

value: motor cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Female


title: ChIP-seq H3K27ac, C9-ALS donor A9, Motor cortex, Oligodendrocyte lineage cells

value: Male


title: SCIT1


title: MEHP, PGC, F2, rep1

description:
Total RNA < 100 bp length
MP2

value: Gonad

value: WT


title: ChIP-seq H3K27ac, C9-ALS donor A9, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: DP9_FPKM

data_processing:
Raw-RNA-reads have been quality controlled and processed using Trimgalore v0.4.2, FastQC v0.11.5, Hisat2 v2.1.0, Cufflinks v2.2.1.
Raw-Read-Files of DP24 have been merged before QC and further processing
Assembly: Reference genome file was generated by combining GRCm38.68 B6 reference and GRCm38p4 SNP file in order to exchange all B6 to NZO high quality SNPs. Non-symmetric CpGs have been withdrawn, p-values have been calculated using log-likelihood ratio test.
Supplementary files format and content: FPKM tracking of all transcripts

extract_protocol:
RNAeasy kit according to manufacturer`s protocol
done by company GATC (Eurofins)

value: liver


title: DP31_m

value: diabetes prone (DP)


title: MEHP, PGC, F1, rep2

description:
Total RNA < 100 bp length
MP1-R

value: Primordial germ cell

value: MEHP


title: DP5_FPKM


title: ChIP-seq H3K27ac, C9-ALS donor A9, Motor cortex, Neurons

value: neurons (NeuN+)

value: H3K27ac (Active Motif #39133)


title: DP31_FPKM

value: NZO/HIBomDife

value: female


title: donor library, biol rep 1, E. coli MDFpir

city: Paris

first: David

last: Bikard

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

description:
plasmid
MG1655 RP4-2-Tc::[ΔMu1::aac(3)IV-ΔaphA-Δnic35-ΔMu2::zeo] ΔdapA::(erm-pir) Δrec

data_processing:
custom script (fastq2counts.py)
Supplementary files format and content: tsv file with counts data. Columns are: target, counts
Library strategy: CRISPR-seq

organism: Escherichia coli

source_name: MDFpir

growth_protocol: LB +  1 µM aTc + 50 µg/ml Kanamycin

extract_protocol:
Plasmid extraction
Amplicon library

tag: cell line

value: MDFpir

value: MG1655 RP4-2-Tc::[deltaMu1::aac(3)IV-deltaaphA-deltanic35-deltaMu2::zeo] deltadapA::(erm-pir) deltarec


title: MEHP, PGC, F1, rep1

description:
Total RNA < 100 bp length
MP1


title: DP27_FPKM

value: 10 weeks


title: Library

city: Vienna

first: Gintautas

last: Vainorius

address: Dr. Bohr-Gasse 3

institute: Institute of Molecular Biotechnology

description:
amplicons
CRISPR-UMI reference library

data_processing:
First 20nt of Read1 sequences were mapped using Bowtie v1.1.2
Samples were demultiplexed and guides, barcodes were summed using custom Python scripts.
Supplementary files format and content: tab-delimited text files with RPM normalized values
Library strategy: CRISPR-UMI

source_name: Escherichia coli

extract_protocol:
Genomic DNA isolation was extracted using Phenol-Chlorophorm followed by Isopropanol precipitation. Chromatin was fragmented and sgRNA fragments were excised by PacI digestion (NEB). Size selection was performed using Speed Beads (GE45152105050250; Sigma-Aldrich) . sgRNA sequences were PCR amplified with AATGATACGGCGACCACCGAGATCTACAC-NNNNNN-CGAGGGCCTATTTCCCATGATTCCTTC, where the 6-bp NNNNNN sequence represents specific experimental indices used for demultiplexing samples after NGS, and CAAGCAGAAGACGGCATACGAGATACCGTTGATGAGTAG. NGS was performed using custom primer (CGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCG) instead of standard illumina primer. For more detail see Michlits et. al. 2017.
Read 1: custom primer (first 20bp are sgRNA Sequence) index read1: UMI (first 10bp random nucleotides used as unique molecular identifiers) index read2: 6bp sequences for demultiplexing (see Michlits et al., 2017)

treatment_protocol: 6 day of 1 µg/ml Doxyciclin. Neurons were enriched by cytosine β-D-arabinofuranoside (AraC) and Puromycin treatment; iTrophoblasts were enriched via differential plating; iNSC were enriched by passaging cells in medium containing Fgf2 and Egf.

value: Escherichia coli


title: ChIP-seq H3K27ac, C9-ALS donor A8, Motor cortex, Oligodendrocyte lineage cells

source_name: motor cortex

value: motor cortex

value: oligodendrocyte lineage cells (NeuN-SOX10+)

value: Female


title: Control, SC, F3, rep1

description:
Total RNA < 100 bp length
CS3

value: Gonad

value: Early ovary somatic cell

value: WT

value: Control


title: DP24_FPKM

value: liver

value: diabetes prone (DP)


title: ChIP-seq H3K27ac, C9-ALS donor A8, Motor cortex, Neurons

value: neurons (NeuN+)


title: donor library, biol rep 2, E. coli MDFpir


title: Control, SC, F2, Synergy, rep2

description:
Total RNA < 100 bp length
CS2-Sy-R


title: ChIP-seq H3K27ac, C9-ALS donor A9, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

value: Male

value: H3K27ac (Active Motif #39133)


title: DP14_FPKM

value: NZO/HIBomDife

value: female


title: Control, SC, F2, Synergy, rep1

description:
Total RNA < 100 bp length
CS2-Sy


title: DR7_FPKM

value: 10 weeks

value: diabetes resistant (DR)


title: OSE_230_9

city: NANTES

first: Isabelle

last: Girault

state: PAYS-DE-LA-LOIRE

address: 22 BOULEVARD BENONI GOULIN

institute: OSE IMMUNOTHERAPEUTICS

description: lungs were harvested when mice were euthanized and digested into single cell for RNA extraction

hyb_protocol: Followed NanoString nCounter XT gene expression assay protocol

scan_protocol: Raw counts of mRNA hybridized to oligos were counted using the NanoString nCounter instrument.

data_processing: Data from the NanoString nCounter system was standardized to the internal positive controls and housekeeping genes using the recommended settings in the nSolver 4.0 software normalization module (NanoString Technologies). Standardized not log2 transformed data was exported and differential expression analysis was performed using DESEq2 R package  for the R programming language.

label: Capture probe-3'biotin, Reporter probe-5' barcode signal

growth_protocol: 4T1-luc2 cell line (from ATCC) was cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 2mM L-glutamine and 1% penicillin/Streptomycin and 5% FCS at 37°C and 5% CO2

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen)

treatment_protocol: Mice were treated with antiChemR23 or hIgG1 mAbs intraperitoneally at 1mg/kg 3 times a week for 3 weeks from day 7 to day 28. At day 13, primary tumors were surgically removed from mammary glands


title: DR29_FPKM


title: ChIP-seq H3K27ac, C9-ALS donor A8, Motor cortex, Astrocytes

value: motor cortex


title: DR26_FPKM


title: Control, SC, F3, rep2

description:
Total RNA < 100 bp length
CS3-R


title: ChIP-seq H3K27ac, C9-ALS donor A7, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: Control, SC, F2, rep1

description:
Total RNA < 100 bp length
CS2

value: Female


title: Control, SC, F1, rep2

description:
Total RNA < 100 bp length
CS1-R

value: Gonad


title: OSE_230_16

label_protocol: Capture probe-3'biotin, Reporter probe-5' barcode signal


title: OSE_230_14


title: OSE_230_15


title: DR25_FPKM


title: ChIP-seq H3K27ac, C9-ALS donor A7, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: OSE_230_13


title: ChIP-seq H3K27ac, C9-ALS donor A8, Motor cortex, Microglia


title: DR18_FPKM


title: ChIP-seq H3K27ac, C9-ALS donor A7, Motor cortex, Astrocytes


title: Control, SC, F2, rep2

description:
Total RNA < 100 bp length
CS2-R

value: Early ovary somatic cell

value: WT


title: Ascl1 Ngn2 CRISPR-UMI Screen

description:
amplicons
Screen Samples

source_name: mESC, iNeurons, iTrophoblasts, iNSC

value: mESC, iNeurons, iTrophoblasts, iNSC


title: Control, PGC, F3, rep2

description:
Total RNA < 100 bp length
CP3-R

value: Primordial germ cell

value: Control


title: OSE_230_10


title: ChIP-seq H3K27ac, C9-ALS donor A7, Motor cortex, Neurons

value: neurons (NeuN+)


title: Control, PGC, F3, rep1

description:
Total RNA < 100 bp length
CP3


title: Ngn2 Rep2.Input

description: Input

data_processing:
ChIP-seq reads were trimmed using trim-galore v0.4.4 and thereafter aligned to the mm10 reference genome using bwa mem v0.7.17.
Duplicated reads were removed using Picard MarkDuplicates (v2.23.4.).
To generate bigwig files from corresponding bam files, we used deepTools bamCoverage (v 3.5.0), with parameter -normalizeUsing RPKM.
Peak calling from the sorted BAM files was done using MACS2 (v2.1.1).
Peaks in blacklist regions were identified using bedtools intersect (v2.27.1) and mm10.blacklist.bed.gz v1.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: N2 supplement, B27 supplement, Neurobasal, DMEM-F12, L-Glutamate, Na-Pyruvate, Penicilin-Streptomycin, Non-essential amino acids, 20 µg/ml Insulin. Cells were grown at 37 ºC, 5% CO2.

extract_protocol:
Cells were collected 24h after induction, washed with PBS and fixed with 1% freshly prepared formaldehyde FA solution in PBS for 7 min at room temperature. Fixation was then quenched and cells were lysed. Chromatin was sheared using Covaris E220 High  Performance Focused Ultrasonicator. IP was performed using FLAG M2 antibody (Sigma, F1804) overnight at 4C. Samples were washed, reverse criss-linked overnight, RNase treated and NGS libraries were prepared from the isolated DNA.
ChIP libraries were prepared using NEBNext Ultra-II kit (New England Biolabs) following manufacturer’s protocol. Quality of the libraries was assessed with Fragment Analyzer™

value: mESC

value: anti-FLAG (Sigma F2426)


title: Control, PGC, F2, Synergy, rep2

description:
Total RNA < 100 bp length
CP2-Sy-R


title: ChIP-seq Input, C9-ALS donor A3, Motor cortex, Oligodendrocyte lineage cells


title: ChIP-seq H3K27ac, C9-ALS donor A3, Motor cortex, Oligodendrocyte lineage cells

value: H3K27ac (Active Motif #39133)


title: Ngn2 Rep2.2

description: IP


title: hIgG1_8


title: ChIP-seq Input, C9-ALS donor A3, Motor cortex, Neurons


title: ChIP-seq Input, C9-ALS donor A3, Motor cortex, Microglia


title: Control, PGC, F2, rep2

description:
Total RNA < 100 bp length
CP2-R


title: Control, PGC, F2, Synergy, rep1

description:
Total RNA < 100 bp length
CP2-Sy


title: hIgG1_7


title: Control, PGC, F2, rep1

description:
Total RNA < 100 bp length
CP2


title: 16 hours, biol rep 2, K. pnuemoniae strain KPPR1

description: plasmid

organism: Klebsiella pneumoniae


title: hIgG1_4


title: hIgG1_6


title: Ngn2 Rep1.2

description: IP


title: ChIP-seq H3K27ac, C9-ALS donor A3, Motor cortex, Neurons


title: ChIP-seq Input, C9-ALS donor A3, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)


title: Ngn2 Rep1.1

description: IP


title: 16 hours, biol rep 1, K. pnuemoniae strain KPPR1

description: plasmid


title: Control,  PGC, F1, rep2

description:
Total RNA < 100 bp length
CP1-R


title: hIgG1_3


title: Ngn2 Rep2.1

description: IP


title: Control, PGC, F1, rep1

description:
Total RNA < 100 bp length
CP1


title: Ngn2 Rep1.Input

description: Input


title: Ascl1 Rep2.Input

description: Input


title: 16 hours, biol rep 2, K. pnuemoniae strain NTUH-K2044

description: plasmid


title: 16 hours, biol rep 1, K. pneumoniae strain NTUH-K2044

description: plasmid


title: Ascl1 Rep2.2

description: IP


title: 16 hours, biol rep 2, K. pneumoniae strain SB5442

description: plasmid


title: ChIP-seq Input, C9-ALS donor A11, Motor cortex, Oligodendrocyte lineage cells

value: Male


title: pTreg-2

source_name: Spleen

value: Spleen

value: CD4+ T cells

value: in vitro differentiation with TGFb


title: Ascl1 Rep2.1

description: IP


title: Control, SC, F1, rep1

description:
Total RNA < 100 bp length
CS1

value: Female


title: ChIP-seq H3K27ac, C9-ALS donor A3, Motor cortex, Microglia

value: motor cortex


title: ChIP-seq H3K27ac, C9-ALS donor A11, Motor cortex, Oligodendrocyte lineage cells

value: oligodendrocyte lineage cells (NeuN-SOX10+)


title: Ascl1 Rep1.Input

description: Input


title: 16 hours, biol rep 1, K. pneumoniae strain SB5442

description: plasmid


title: NC(dsGFP)

city: harbin

first: rui

last: cheng

address: 92 Xidazhi Street

institute: Harbin Institute of Technology

description: dsGFP

data_processing:
The raw reads were trimed using trim_galore
The clean reads were mapped to mouse genome (GRCm38) using HISAT with default parameter.
The reads of each gene were counted by Htseq-count.
Assembly: GRCm38
Supplementary files format and content: xls files include count and fpkm value for each samples

source_name: embryo

extract_protocol:
RNA-sequencing of fifty dsGFP- or dsNat10-injected morulae were performed by Beijing Genomics Institute (Shenzhen, China).
The library preparation was performed following the SMARTseq2 protocol.

value: embryo

value: ICR

value: morula

value: dsGFP


title: Ascl1 Rep1.2

description: IP


title: 3 hours, biol rep 2, K. pnuemoniae strain KPPR1

description: plasmid

value: WT


title: KD(dsNat10)


title: ChIP-seq H3K27ac, C9-ALS donor A11, Motor cortex, Neurons

value: neurons (NeuN+)


title: ChIP-seq Input, C9-ALS donor A11, Motor cortex, Microglia

value: microglia (NeuN-SOX10-IRF5+)


title: Ascl1 Rep1.1

description: IP

value: mESC

value: anti-FLAG (Sigma F2426)


title: 3 hours, biol rep 1, K. pnuemoniae strain KPPR1

description: plasmid


title: 3 hours, biol rep 2, K. pnuemoniae strain NTUH-K2044

description: plasmid


title: ChIP-seq H3K27ac, C9-ALS donor A3, Motor cortex, Astrocytes

value: astrocytes (NeuN-SOX10-IRF5-)

value: H3K27ac (Active Motif #39133)