title: planktonic cultures of S. acidocaldarius MW001 parent and Planktonic cultures of S. acidocaldarius Saci_1223 mutant

city: Raleigh

first: Robert

middle: M

last: Kelly

state: North Carolina

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

description:
Comparison of planktonic cultures of Sulfolobus acidocaldarius MW001 parent strain and Planktonic cultures of Sulfolobus acidocaldarius Saci_1223 mutant.
Data is comparing biofilm and planktonic cultures of Sulfolobus acidocaldarius MW001 parent strain and a Sulfolobus acidocaldarius Saci_1223 mutant.

hyb_protocol: Samples were then hybridized in a three-slide loop design, by methods described in Chharbra et al. 2003, with minor adjustments for long oligonucleotide platforms (Tachdjian S and Kelly RM 2006).

scan_protocol: Microarray slides were scanned with the Axon 400B (Molecular Devices, Sunnyvale, CA) microarray scanner and raw data were analyzed with GenePix Pro 6.0 (Molecular Devices, Sunnyvale, CA).

data_processing:
Data from each experiment were analyzed with JMP Genomics version 4.0 (SAS, Cary, NC), using a mixed linear analysis of variance model as described previously (Tachdjian S and Kelly RM 2006).
A ± 2.0-fold change (FC) or higher (where a log2 value of ± 1 equals a 2-FC) with significance values at or above the Bonferroni correction, which was 4.8 (equivalent to a p-value of 4.0 x 10– 6), defined differential expression for this data set.

organism: Sulfolobus acidocaldarius

source_name: Planktonic Sulfolobus acidocaldarius MW001

label_protocol: Labeled cDNA with Cy3 and Cy5.

growth_protocol: Biofilms and planktonic Sulfolobus acidocaldarius MW001 cultures were grown as described in Koerdt et al. 2011

extract_protocol: From each sample RNA was extracted using the Qiagen RNAqueous kit (Qiagen, Valencia, CA), following the manufacturer’s instructions. Equal amounts of RNA from the biological repeats were pooled and cDNA was synthesized

treatment_protocol: Biofilm and planktonic cultures of Sulfolobus acidocaldarius MW001 parent strain and a Sulfolobus acidocaldarius Saci_1223 mutant.

tag: growth condition

value: Planktonic cells

source_name: Planktonic Sulfolobus acidocaldarius Saci_1223


title: planktonic cultures and biofilm cells of a S. acidocaldarius MW001 parent strain.

status: Public on Mar 27 2023

type: RNA

country: USA

description:
Comparison of planktonic cultures and biofilm cells of a Sulfolobus acidocaldarius MW001 parent strain.
Data is comparing biofilm and planktonic cultures of Sulfolobus acidocaldarius MW001 parent strain and a Sulfolobus acidocaldarius Saci_1223 mutant.

molecule: total RNA

source_name: Biofilm Sulfolobus acidocaldarius MW001

tag: strain

value: Biofilm cells


title: biofilm cells of S. acidocaldarius MW001 parent and Planktonic cultures of S. acidocaldarius Saci_1223 mutant.

description:
Comparison of biofilm cells of Sulfolobus acidocaldarius MW001 parent strain and Planktonic cultures of Sulfolobus acidocaldarius Saci_1223 mutant.
Data is comparing biofilm and planktonic cultures of Sulfolobus acidocaldarius MW001 parent strain and a Sulfolobus acidocaldarius Saci_1223 mutant.

source_name: Biofilm Sulfolobus acidocaldarius Saci_1223


title: planktonic cultures and biofilm cells of a S. acidocaldarius Saci_1223 mutant.

description:
Comparison of planktonic cultures and biofilm cells of a Sulfolobus acidocaldarius Saci_1223 mutant.
Data is comparing biofilm and planktonic cultures of Sulfolobus acidocaldarius MW001 parent strain and a Sulfolobus acidocaldarius Saci_1223 mutant.


title: BAT, Musclin_Cold, rep1

type: SRA

city: Hangzhou

first: Lu

last: Jin

state: China

address: Yuhangtang Road

country: China

institute: Zhejiang Univeristy

description:
Fpkms_ BAT_MCK-Musclin&CTR.txt
Musclin_Cold_BAT1

library_source: transcriptomic

data_processing:
Raw reads were filtered with fastp (https://github.com/OpenGene/fastp) and bowtie2 (V 2.4.1) (https://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Filtered data were then aligned to mm10 reference genome (Mus_musculus.GRCm38.90) with HISAT2 (V2.1.0) .
The reads for each library were converted to FPKM (fragments per kilobase of exon per million fragments mapped) by running Cuffdiff 2.1.137 to determine gene expression
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Brown white adipose tissue

extract_protocol:
Total RNA from WAT and iWAT was isolated using a commercially available kit (TIANGEN Biotech, DP430). Total RNA from other tissues including skeletal muscle, liver, BAT, heart, brain and small intestine was isolated following the standard method using TRIzol.
RNA libraries for RNA-seq were prepared using SMART-RNAseq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: Brown white adipose tissue

tag: genotype

value: MCK-Musclin

tag: treatment

value: Cold exposure at 8C for 1 week


title: BAT, WT_Cold, rep3

description:
Fpkms_ BAT_MCK-Musclin&CTR.txt
WT_Cold_BAT3

value: Wild type


title: BAT, WT_Cold, rep2

description:
Fpkms_ BAT_MCK-Musclin&CTR.txt
WT_Cold_BAT2


title: BAT, WT_Cold, rep1

description:
Fpkms_ BAT_MCK-Musclin&CTR.txt
WT_Cold_BAT1


title: iWAT, Musclin_Cold, rep2

description:
Fpkms_ iWAT_MCK-Musclin&CTR.txt
Musclin_Cold_iWAT2

source_name: Inguinal white adipose tissue

value: Inguinal white adipose tissue


title: 237C-N-4

city: Philadelphia

first: Hunter

last: Reavis

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt
Read quality was checked for each sample using FastQC
Trimmed sequence reads were mapped to GRCh38 primary assembly using STAR aligner (default parameters)
Aligned reads were quantified at the gene-level using HTSeq-count
Gene counts were then normalized using varianceStabilizingTransform method from DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized log2 abundance values for each Sample

organism: Homo sapiens

extract_protocol:
RNA was harvested using Total RNA Purification Kit (Norgen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using th TruSeq Stranded Total RNA Library Kit (Illumina) following manufacturer's protocols.

tag: cell line

tag: cell type

value: immortalized fallopian tube epithelial cell

value: WT

value: 10 microM norepinephrine

tag: time


title: P2136_N707-S506

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

description:
Tetramer+ CD4+ T cells from BDC 2.5mi/IAg7-NP-treated NOD mice
Raw_counts_BDC_SMARTseq2.xlsx

data_processing:
Quality check with FastQC v0.11.8
Alignment to the mouse genome mm10 with STAR v2.5.4b
Gene expression estimation with RSEM v1.3.0
QC filtering of low quality cells
TCR sequences reconstructed to infer clonality with TraCeR v.0.5.1
Genome_build: mm10
Supplementary_files_format_and_content: xlsx (Raw counts for each cell)

source_name: Tetramer+ CD4+ T cells

extract_protocol:
Single-cell sorting in SMARTseq2 plates
Smart-seq protocol (Picelli et al., 2013)

treatment_protocol:
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.

value: NOD

value: T cell

value: pMHCII-NPs


title: BAT, Musclin_Cold, rep2

description:
Fpkms_ BAT_MCK-Musclin&CTR.txt
Musclin_Cold_BAT2


title: P2136_N707-S507


title: P2136_N707-S505


title: iWAT, WT_Cold, rep3

description:
Fpkms_ iWAT_MCK-Musclin&CTR.txt
WT_Cold_iWAT3


title: 237C-V-24

value: vehicle


title: iWAT, Musclin_Cold, rep1

description:
Fpkms_ iWAT_MCK-Musclin&CTR.txt
Musclin_Cold_iWAT1


title: iWAT, WT_Cold, rep2

description:
Fpkms_ iWAT_MCK-Musclin&CTR.txt
WT_Cold_iWAT2


title: BAT, Musclin_Cold, rep3

description:
Fpkms_ BAT_MCK-Musclin&CTR.txt
Musclin_Cold_BAT3


title: 237C-V-4


title: P2136_N707-S504


title: 237C-V-0


title: iWAT, WT_Cold, rep1

description:
Fpkms_ iWAT_MCK-Musclin&CTR.txt
WT_Cold_iWAT1


title: Brown adipose, WT

description:
Fpkms_7tissues_WT.txt
WT_Brown adipose

source_name: Brown adipose tissue

value: Brown adipose tissue


title: Liver, WT

description:
Fpkms_7tissues_WT.txt
WT_Liver

source_name: Liver

value: Liver


title: 237B-NP-24

value: 10 microM norepinephrine+10 microM propranolol


title: 237C-N-24


title: P2136_N707-S502


title: Tibialis anterior muscle, WT

description:
Fpkms_7tissues_WT.txt
WT_Tibialis anterior muscle

source_name: Muscle

value: Muscle


title: 237B-N-24


title: 237B-P-24

value: 10 microM propranolol


title: iWAT, Musclin_Cold, rep3

description:
Fpkms_ iWAT_MCK-Musclin&CTR.txt
Musclin_Cold_iWAT3


title: 237B-V-24


title: Ly/singlet/Foxp3+/Nrp1-/ITGB7- Treg cells, animal#11

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

data_processing:
Data processing was done by Novogene Co., Ltd., Beijing, China.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.14.1). Readcount was normalized with the DESeq method, and the Negative Binomial Distribution model was applied to calculate nominal alpha (p-values).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling False Discover Rate (FDR). Genes with an adjusted Pvalue < 0.05 found by ESeq2 were assigned as differentially expressed.
Assembly: Reference genome and gene model annotation files were downloaded from the Genome website directly. Index of the reference genome was built using hisat2 2.1.0 and paired-end clean reads were aligned to the reference genome using HISAT2
Supplementary files format and content: Single tab-delimited text file displaying data matrix consisting of the FPKM values of all samples

source_name: spleen

extract_protocol:
RNeasy Micro Kit Plus (Qiagen). RNA purity, integrity, and concentration were analyzed on RNA 6000 Pico Chips, with help of a 2100 Bioanalyzer (both from Agilent).
mRNA enrichment, library preparation and transcriptome profiling by NGS, 6Gb Pe150, Illumina Hiseq, were done by Novogene Co., Ltd. (Beijing, China).

value: spleen

tag: cell subtype

value: regulatory T cell

value: C57BL/6-Tg(CAG-OVAL)916Jen/J / B6.Cg Foxp3tm2(EGFP)Tch/J (Foxp3-GFP)


title: Heart, WT

description:
Fpkms_7tissues_WT.txt
WT_Heart

source_name: Heart

value: Heart

value: Wild type


title: P2136_N707-S503


title: Ly/singlet/Foxp3+/Nrp1-/OX40dim Treg cells, animal#6


title: Ly/singlet/Foxp3+/Nrp1-/ITGB7- Treg cells, animal#9


title: Small intestine, WT

description:
Fpkms_7tissues_WT.txt
WT_Small intestine

source_name: Small intestine

value: Small intestine


title: Ly/singlet/Foxp3+/Nrp1-/ITGB7- Treg cells, animal#8


title: P2136_N706-S506


title: Ly/singlet/Foxp3+/Nrp1-/ITGB7- Treg cells, animal#7


title: Ly/singlet/Foxp3+/Nrp1-/ITGB7- Treg cells, animal#10


title: Ly/singlet/Foxp3+/Nrp1-/OX40dim Treg cells, animal#4


title: P2136_N706-S507


title: 237B-V-4

value: immortalized fallopian tube epithelial cell

value: WT


title: Brain, WT

description:
Fpkms_7tissues_WT.txt
WT_Brain

source_name: Brain

value: Brain


title: P2136_N706-S505

value: NOD

value: T cell


title: Ly/singlet/Foxp3+/Nrp1-/ITGB7- Treg cells, animal#12


title: P2136_N706-S504

value: pMHCII-NPs


title: Ly/singlet/Foxp3+/Nrp1-/OX40dim Treg cells, animal#3


title: 237A-NP-24


title: Ly/singlet/Foxp3+/Nrp1-/OX40dim Treg cells, animal#2


title: White adipose, WT

description:
Fpkms_7tissues_WT.txt
WT_White adipose

source_name: White adipose tissue

value: White adipose tissue


title: Ly/singlet/Foxp3+/Nrp1-/OX40dim Treg cells, animal#5


title: 237B-V-0


title: P2136_N706-S517


title: Ly/singlet/Foxp3+/Nrp1+/ITGB7+ Treg cells, animal#12


title: P2136_N706-S508


title: P2136_N706-S503


title: 237B-N-4

value: 10 microM norepinephrine


title: Ly/singlet/Foxp3+/Nrp1+/ITGB7+ Treg cells, animal#11


title: Ly/singlet/Foxp3+/Nrp1+/ITGB7+ Treg cells, animal#9


title: Ly/singlet/Foxp3+/Nrp1+/ITGB7+ Treg cells, animal#7


title: Ly/singlet/Foxp3+/Nrp1+/OX40bright Treg cells, animal#6


title: Ly/singlet/Foxp3+/Nrp1-/OX40dim Treg cells, animal#1


title: P2136_N705-S507


title: 237A-P-24


title: P2136_N706-S502


title: 237A-N-24


title: Ly/singlet/Foxp3+/Nrp1+/ITGB7+ Treg cells, animal#10


title: P2136_N705-S517


title: Ly/singlet/Foxp3+/Nrp1+/ITGB7+ Treg cells, animal#8


title: P2136_N705-S508


title: 237A-N-4


title: 237A-V-24

value: vehicle


title: P2136_N705-S505


title: Ly/singlet/Foxp3+/Nrp1+/OX40bright Treg cells, animal#1


title: C28/I2 cells,mimics_NC, Day2 3

city: Shanghai

first: Yuxuan

last: Gao

state: Shanghai

address: Xinhua Hospital, kongjiang Road, Yangpu District, Shanghai

institute: Shanxi medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/CHM13 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: CHM13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cartilage

growth_protocol: C28/I2 cells were maintained in DMEM supplemented with 10% fetalbovineserum(FBS) and antibioticsin humidified atmosphere with 5%CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
PiR_019914_mimics was used to transfect C28/I2 cells to overexpress piR_019914.
1) the inoculated cells planted C28/I2 with 10000-50000 cells in a 24-well culture plate containing complete culture medium, set the group in advance to ensure that each transfection sample was provided with at least 3 multiple holes, and the cell density was observed the next day. 2) configuration reagent: take transfection mimic and siRNA as an example, add LipofectamineTMRNAiMAXReagent (3uL), Opti-MEMMedium (50uL) to No. 1 EP tube to mix, add mimic (6uL) or siRNA (6uL), Opti-MEMMedium (50uL) to No. 2 EP tube to mix, mix No. 1 tube and No. 2 tube at room temperature for 5 minutes, then mix them thoroughly with pipette, and rest at room temperature for 30 minutes. 3) during the transfection process, the cells were changed, and the complete medium without serum of 400uL was added. The static transfection reagent and the mixture of mimic were blown and mixed again, and then added to the cell culture medium, then moved into the cell incubator containing 5%CO2 at 37 ℃, and the medium was changed 6 hours later.

value: cartilage

value: C28/I2 cells,mimics_NC, Day2

value: chondrocytes

value: Day 2


title: C28/I2 cells,mimics_NC, Day2 2


title: 4T1_day_21

city: Rehovot

first: Ayelet

last: Erez

state: Please Select

address: CANDIOTTI 214

country: Israel

institute: WEIZMANN INSTITUTE

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Default 10x pipeline
mm10-3.0.0

extract_protocol:
RNA was extracted from dissociated liver NPCs following liver perfusion
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: 8 Weeks old female Balb\c mice were orthotopically injected with PBS or 4T1 BC cells for 4 or 21 days.

value: non parenchimal cells

value: Liver

value: Balb\c

tag: age

value: 11 weeks


title: Ly/singlet/Foxp3+/Nrp1+/OX40bright Treg cells, animal#4

value: spleen

value: regulatory T cell

value: C57BL/6-Tg(CAG-OVAL)916Jen/J / B6.Cg Foxp3tm2(EGFP)Tch/J (Foxp3-GFP)


title: P2136_N705-S506

value: NOD


title: 237A-V-4

value: immortalized fallopian tube epithelial cell

value: WT


title: Ly/singlet/Foxp3+/Nrp1+/OX40bright Treg cells, animal#5


title: Ly/singlet/Foxp3+/Nrp1+/OX40bright Treg cells, animal#3


title: 237A-V-0


title: Ly/singlet/Foxp3+/Nrp1+/OX40bright Treg cells, animal#2


title: P2136_N705-S502

value: T cell

value: pMHCII-NPs


title: P2136_N705-S504


title: P2136_N704-S517


title: C28/I2 cells, piR_019914_mimics, Day2 2

value: piR_019914 overexpression


title: P2136_N705-S503


title: 4T1_day_4

description: 10x Genomics

value: 8 weeks


title: P2136_N704-S508


title: mouse_leptomen_cancer_ifng RNA

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

data_processing:
Raw FASTQC files were pre-processed with SEQC with modified mouse reference genome mm10 that included GFP, RFP and AmCyan sequences, and pre-processed as human samples, with the exception that no batch correction was applied, and haemoglobin genes and CD41 protein signal (platelet marker) were filtered out. HTO and CITE-seq data were demultiplexed with CellRanger (10x Genomics)
RNA and protein data (HTO and CITE) were integrated with totalVI (default settings with top 4,000 HVG).
Assembly: mm10, customized
Supplementary files format and content: filtered and totalVI-integrated atlas in h5ad format

molecule: polyA RNA

source_name: mouse leptomeninges

extract_protocol:
Cells were isolated from transcardially perfused mice and processed as described in Remsik et al., 2022. Three libraries were constructed and sequenced: RNA, HTO, and CITE. Experiments were approved by MSKCC IACUC.
10x Chromium Single-cell 3'RNA-seq, HTO (barcode), CITE-seq (TotalSeqA panel)

tag: treatment 1

tag: treatment 2

value: LLC LeptoM


title: mouse_leptomen_cancer_ifng CITE


title: C28/I2 cells, piR_019914_mimics, Day2 3

value: cartilage

value: C28/I2 cells,mimics_NC, Day2

value: chondrocytes


title: Control

description: 10x Genomics

value: non parenchimal cells

value: Liver


title: mouse_leptomen_cancer_ifng HTO

library_source: other

molecule: protein


title: mouse_leptomen_cancer_egfp CITE


title: P2136_N704-S507


title: C28/I2 cells, piR_019914_mimics, Day2 1

value: Day 2


title: C28/I2 cells,mimics_NC, Day2 1


title: Human_TR1_rep3

description:
Human CD45RA-TCR+CD4+CD127-CD25-CCR5+PD1+ (TR1)
Human_Circulating_Tconv_TFH_TR1_Raw_counts.xlsx

data_processing:
Contaminant rRNA filtering with Bowtie2 (2.2.5)
Mouse samples: Alignment with STAR 2.5.3a to the GENCODE  release 16 of the Mus musculus genome (mm10 assembly)
Human samples: Alignment with STAR 2.5.3a to the GENCODE  release 29 of the Homo sapiens genome (hg38 assembly)
Raw count of reads per gene was obtained with Partek “Quantify to annotation model (Partek E/M)” tool
Counts were normalized by CPM
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheets (xlsx) containing raw counts

source_name: Human TR1

extract_protocol:
RNA purification using Rneasy Mini kit (QIAGEN)
TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer's protocol (Illumina, San Diego, CA)


title: mouse_leptomen_cancer_egfp HTO


title: Human_TR1_rep2


title: P2136_N704-S506


title: mouse_leptomen_cancer_egfp RNA


title: P2136_N704-S505


title: frh_1_day_14_rep_5

city: Düsseldorf

first: Natascia

last: Ventura

address: Auf'm Hennekamp 50

country: Germany

institute: Heinrich Heine University  and the IUF- Leibniz Research Institute for Environmental Medicine

description: extracted total RNA

hyb_protocol: Samples were prepared and hybridized to C. elegans Gene 1.0 ST Microarray according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing: RMA normalization; normalized also per gene to the median

label: Affymetrix labeling

organism: Caenorhabditis elegans

source_name: nematodes pellet, RNA extracted

growth_protocol: C. elegans strains were grown and mantained at 20°C.

extract_protocol: For each time point, worms were collected into nuclease-free water and frozen   at −80 °C for further processing. Worms lysates were prepared using the TissueLyser II   (Qiagen), briefly 2 stainless-steel beads (6 mm) were added to the worms´ pellet  containing the lysis buffer 1:1 v:v then 2 cycles of shaking (2 minutes at 30 Hz) were   performed on each samples. Total RNA was extracted using the RNeasy Mini Kit and   QIAshredder according to the manufacturer’s instructions (Qiagen-74104 and 79654).   5 different biological replicas were used for each condition.

treatment_protocol:
frataxin (frh-1) dsRNA  fed worms collected at day 14
Worms were fed with either an empty-vector control (pL4440) or vector-expressing dsRNA against nematode frataxin (frh-1) to induce mild mitochondrial stress, for 3 consecutive generation starting from eggs. ematodes were collected at day 4, 7 and 14 of   adulthood

value: frh-1 RNAi

value: 14 days


title: mouse_leptomen_naïve_ifng CITE

value: vehicle


title: Human_TR1_rep1


title: Human_TFH_rep3

description:
Human CD45RA-TCR+CD4+CXCR5+PD1+ (TFH)
Human_Circulating_Tconv_TFH_TR1_Raw_counts.xlsx

source_name: Human TFH


title: frh_1_day_14_rep_4

description: extracted total RNA

label_protocol: Samples were prepared and hybridized to C. elegans Gene 1.0 ST Microarray according to Affymetrix specifications.


title: P2136_N704-S502

value: NOD


title: P2136_N704-S503


title: Human_TFH_rep2


title: mouse_leptomen_naïve_ifng HTO


title: mouse_leptomen_naïve_ifng RNA


title: Human_TFH_rep1


title: P2136_N703-S517


title: mouse_leptomen_naïve_egfp CITE


title: P2136_N703-S508


title: frh_1_day_7_rep_5

description: extracted total RNA

treatment_protocol:
frataxin (frh-1) dsRNA  fed worms collected at day 7
Worms were fed with either an empty-vector control (pL4440) or vector-expressing dsRNA against nematode frataxin (frh-1) to induce mild mitochondrial stress, for 3 consecutive generation starting from eggs. ematodes were collected at day 4, 7 and 14 of   adulthood

value: 7 days


title: frh_1_day_14_rep_2

description: extracted total RNA


title: mouse_leptomen_naïve_egfp HTO


title: P2136_N704-S504


title: frh_1_day_14_rep_1

description: extracted total RNA


title: frh_1_day_7_rep_4

description: extracted total RNA


title: P2136_N703-S507


title: Human_Tconv_rep1

description:
Human CD45RA-TCR+CD4+CXCR5-PD1-CD127+CD25- (Tconv)
Human_Circulating_Tconv_TFH_TR1_Raw_counts.xlsx

source_name: Human Tconv


title: Human_Tconv_rep2


title: 3H5_Human_clone_rep3

description:
IL-10-producing CD4+ T-cell clone specific for the human pre-proinsulin (PPI)76-90/DRB1*0401 pMHCII stimulated with aCD3/CD8
Human_TR1_clones_Raw_counts.xlsx

source_name: IL-10-positive Human clone 3H5

growth_protocol: Human CD4+ T cells from peripheral blood of T1D patients have been peptide-challenged on pMHCII-coated plates to obtain peptide-specific clones

treatment_protocol: aCD3/CD28 stimulation

value: a-CD3/CD28 stimulation


title: mouse_leptomen_naïve_egfp RNA


title: frh_1_day_14_rep_3

description: extracted total RNA


title: P2136_N703-S506

value: T cell


title: frh_1_day_7_rep_3

description: extracted total RNA


title: frh_1_day_4_rep_5

description: extracted total RNA

treatment_protocol:
frataxin (frh-1) dsRNA  fed worms collected at day 4
Worms were fed with either an empty-vector control (pL4440) or vector-expressing dsRNA against nematode frataxin (frh-1) to induce mild mitochondrial stress, for 3 consecutive generation starting from eggs. ematodes were collected at day 4, 7 and 14 of   adulthood

value: 4 days


title: frh_1_day_4_rep_4

description: extracted total RNA


title: cortex and corpus callosum, Normal Trem2-/-, 3

city: Saint Louis

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Cell Ranger Software Suite (v5.0.0) from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cell Ranger count was used to align samples to the reference genome GRCm38 (mm10), quantify reads, and filter reads and barcodes. Downstream analysis was performed using the Seurat package.
Assembly: To include Clec7a gene, we built a custom reference genome by adding Clec7a cDNA to the pre-built mouse reference genome (mm10)
Supplementary files format and content: raw aligned barcode and feature count matrices from cellranger count (.h5)

source_name: cortex and corpus callosum

extract_protocol:
Flash frozen brain tissues were homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash buffer (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash buffer and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash buffer at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
Chromium Single Cell 5' Reagent Kit (v2)
single nucleus RNA sequencing

treatment_protocol: Eight-week-old male wild-type (WT) or Trem2 knockout mice were fed with 0.2% CPZ or regular chow and three experimental groups were set up in each genotype: a) demyelination (5-week CPZ treatment); b) remyelination (5-week CPZ treatment, followed by 2-week regular chow); c) control (regular chow throughout the time course)

value: cortex and corpus callosum

value: Eight-week-old

tag: Sex

value: male

value: Trem2 KO

value: regular chow


title: cortex and corpus callosum, Normal WT, 3

value: WT


title: 3H5_Human_clone_rep1


title: frh_1_day_7_rep_2

description: extracted total RNA


title: frh_1_day_4_rep_3

description: extracted total RNA


title: P2136_N703-S504

source_name: Tetramer+ CD4+ T cells

value: pMHCII-NPs


title: 3H5_Human_clone_rep2


title: 2G1_Human_clone

description:
IL-10-negative CD4+ T-cell clone specific for the human pre-proinsulin (PPI)76-90/DRB1*0401 pMHCII stimulated with aCD3/CD8
Human_TR1_clones_Raw_counts.xlsx

source_name: IL-10-negative Human clone 2G1


title: frh_1_day_7_rep_1

description: extracted total RNA


title: P2136_N703-S503


title: 2E5_Human_clone

source_name: IL-10-negative Human clone 2E5


title: cortex and corpus callosum, Demyelination Trem2-/-, 1

value: 5-week cuprizone


title: 1D7_Human_clone

source_name: IL-10-negative Human clone 1D7


title: cortex and corpus callosum, Demyelination Trem2-/-, 2


title: P2136_N702-S517


title: cortex and corpus callosum, Demyelination WT, 3


title: P2136_N703-S505


title: P2136_N702-S508


title: Ctrl_day_14_rep_5

description: extracted total RNA

treatment_protocol:
Empty-vector control (pL4440) fed worms collected at day 14
Worms were fed with either an empty-vector control (pL4440) or vector-expressing dsRNA against nematode frataxin (frh-1) to induce mild mitochondrial stress, for 3 consecutive generation starting from eggs. ematodes were collected at day 4, 7 and 14 of   adulthood

value: Empty vector (pL4440)


title: cortex and corpus callosum, Demyelination WT, 2


title: P2136_N703-S502


title: Ctrl_day_14_rep_3

description: extracted total RNA


title: P2136_N702-S507


title: eIF4E-BP1 Nav1.8 cKO BL [BP 3 IP]

city: Montreal

first: Arkady

last: Khoutorsky

address: McIntyre Medical Building, Room 1208

department: Department of Anesthesia and Faculty of Dentistry

country: Canada

institute: McGill University

data_processing:
RNA-seq read files (fastq files) were checked for quality by FastQC and read trimming was done based on the Phred score and per-base sequence content
Trimmed Reads were then mapped against the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR v2.2.1
Relative abundances in Transcripts Per Million (TPM) for every gene of every sample was quantified by stringtie v1.3.5
Assembly: Genome Reference Consortium Mouse Build 38 patch release 5
Supplementary files format and content: TAR packaging followed by a GNU zip (gzip), tab separated text files with columns for gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all genes

source_name: Dorsal root ganglia

growth_protocol: Transgenic mice expressing Cre recombinase under the control of the Scn10a (Nav1.8) promoter were obtained initially from Professor John Wood (University College London) but are commercially available from Infrafrontier (EMMA ID: 04582). Nav1.8cre mice on a C57BL/6J genetic background were injected at postnatal day 2-4 with AAV2/9-FLEX-eGFP-L10a virus to generate the Nav1.8-trap mice that express a fused EGFP-L10a protein in Nav1.8 expressing neurons. All experiments were carried out using male and female littermates aged 8 to 12 weeks old.

extract_protocol:
Direct-zol RNA kit (Zymo Research)
rRNA-depleted stranded (HMR)

value: Dorsal root ganglia

value: DRG Nav1.8 neurons

value: eIF4E-BP1 Nav1.8 cKO


title: eIF4E-BP1 Nav1.8 cKO BL [BP 2 IP]


title: eIF4E-BP1 Nav1.8 cKO BL [BP 1 IP]


title: cortex and corpus callosum, Demyelination WT, 1


title: Ctrl_day_14_rep_4

description: extracted total RNA

value: 14 days


title: frh_1_day_4_rep_2

description: extracted total RNA

value: frh-1 RNAi


title: frh_1_day_4_rep_1

description: extracted total RNA


title: cortex and corpus callosum, Demyelination Trem2-/-, 3


title: P2136_N702-S506

value: NOD


title: Ctrl_day_14_rep_1

description: extracted total RNA


title: P2136_N702-S505

value: T cell


title: cortex and corpus callosum, Remyelination Trem2-/-, 2

value: 5-week cuprizone, followed by 2-week regular chow


title: eIF4E-BP1 Nav1.8 cKO BL [BP 3 IN]

value: DRG neurons


title: Ctrl_day_7_rep_5

description: extracted total RNA

treatment_protocol:
Empty-vector control (pL4440) fed worms collected at day 7
Worms were fed with either an empty-vector control (pL4440) or vector-expressing dsRNA against nematode frataxin (frh-1) to induce mild mitochondrial stress, for 3 consecutive generation starting from eggs. ematodes were collected at day 4, 7 and 14 of   adulthood

value: 7 days


title: cortex and corpus callosum, Remyelination Trem2-/-, 3

value: cortex and corpus callosum

value: Eight-week-old

value: male


title: Ctrl_day_14_rep_2

description: extracted total RNA


title: Ctrl_day_7_rep_4

description: extracted total RNA


title: P2136_N702-S504


title: Ctrl_day_7_rep_3

description: extracted total RNA


title: eIF4E-BP1 Nav1.8 cKO BL [BP 2 IN]


title: cortex and corpus callosum, Remyelination Trem2-/-, 1

value: Trem2 KO


title: eIF4E-BP1 Nav1.8 cKO BL [BP 1 IN]


title: P2136_N702-S503

value: pMHCII-NPs


title: cortex and corpus callosum, Remyelination WT, 3

value: WT


title: Nav1.8 Control BL [WT 3 IP]

value: Nav1.8 Control


title: P2136_N702-S502


title: cortex and corpus callosum, Remyelination WT, 2


title: P2136_N701-S517


title: cortex and corpus callosum, Remyelination WT, 1


title: Nav1.8 Control BL [WT 2 IP]

value: Dorsal root ganglia


title: Nav1.8 Control BL [WT 1 IP]

value: DRG Nav1.8 neurons


title: cortex and corpus callosum, Normal Trem2-/-, 2

value: regular chow


title: P2136_N701-S508


title: P2136_N701-S507


title: Ctrl_day_4_rep_5

description: extracted total RNA

treatment_protocol:
Empty-vector control (pL4440) fed worms collected at day 4
Worms were fed with either an empty-vector control (pL4440) or vector-expressing dsRNA against nematode frataxin (frh-1) to induce mild mitochondrial stress, for 3 consecutive generation starting from eggs. ematodes were collected at day 4, 7 and 14 of   adulthood

value: Empty vector (pL4440)

value: 4 days


title: Ctrl_day_7_rep_1

description: extracted total RNA


title: Nav1.8 Control BL [WT 3 IN]


title: cortex and corpus callosum, Normal  Trem2-/-, 1


title: Ctrl_day_7_rep_2

description: extracted total RNA


title: P2136_N701-S506

value: NOD


title: Ctrl_day_4_rep_4

description: extracted total RNA


title: cortex and corpus callosum, Normal  WT, 2


title: Nav1.8 Control BL [WT 1 IN]


title: Ctrl_day_4_rep_3

description: extracted total RNA


title: P2136_N701-S505

value: T cell


title: cortex and corpus callosum, Normal  WT, 1


title: P2136_N701-S504


title: P2136_N701-S503


title: AFD, 15 degrees, rep3

city: Waltham

first: Nathan

last: Harris

state: MA

address: 415 South Street

institute: Brandeis University

description:
ribosome-associated RNA
AFD_15_3

data_processing:
Cutadapt 1.12, quality cutoff=20, minimum length=50
Mapping with STAR with GeneCounts option. Reference genome was WBcel235/ce11.
Assembly: WBcel235/ce11
Supplementary files format and content: tab-delimited text files include raw per gene read counts for each sample

source_name: AFD

growth_protocol: Animals were synchronized by bleaching then plated as L1s on HB101 bacteria and grown at 20 degrees celsius to the L4 stage.

extract_protocol:
AFD-specific RNA was obtained using Translating Ribosome Affinity Purification. Briefly, frozen worms samples were lysed by grinding. The lysates were either used in an anti-EGFP ribosome immunoprecipitation followed by Trizol extraction (AFD samples) or RNA was extracted directly from lysates using Trizol (whole animal samples). 10 ng of RNA was used for library construction.
Libraries were generated using the Smart-Seq v4 Ultra Low Input RNA kit followed by Nextera XT DNA Library Preparation Kit.

treatment_protocol: At the L4 stage, animals were shifted to either 15 or 25 degrees celsius overnight (~16 hours) and then collected (flash frozen) as adults.

value: AFD

value: 15 degrees celsius overnight


title: AFD, 25 degrees, rep3

description:
ribosome-associated RNA
AFD_25_3

value: 25 degrees celsius overnight


title: whole animal, 15 degrees, rep2

description:
total RNA
whole_15_2

source_name: whole animal

value: whole animal


title: Ctrl_day_4_rep_2

description: extracted total RNA


title: cortex and corpus callosum, Remye3

data_processing:
Cell Ranger Software Suite (v3.0.2) from 10X Genomics was used for sample demultiplexing, barcode processing, and single-cell counting. Cell Ranger count was used to align samples to the reference genome GRCm38 (mm10), quantify reads, and filter reads and barcodes. Downstream analysis was performed using the Seurat package.
Assembly: To include Clec7a gene, we built a custom reference genome by adding Clec7a cDNA to the pre-built mouse reference genome (mm10)
Supplementary files format and content: raw aligned barcode and feature count matrices from cellranger count (.h5)

extract_protocol:
Flash frozen brain tissues were homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash buffer (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash buffer and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash buffer at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
Chromium Single Cell 5' Reagent Kit (v1)
single nucleus RNA sequencing

treatment_protocol: Eight-week-old male wild-type (WT) mice were fed with 0.2% CPZ or regular chow and three experimental groups were set up: a) demyelination (5-week CPZ treatment); b) remyelination (5-week CPZ treatment, followed by 2-week regular chow); c) control (regular chow throughout the time course)

value: cortex and corpus callosum

value: Eight-week-old

value: 5-week cuprizone, followed by 2-week regular chow


title: cortex and corpus callosum, Remye2

value: male


title: s_EMT6_lucV5_BrM2_1

description:
Proj_09317_J
s_EMT6_lucV5_BrM2_1.bam

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Assembly: mm10
Supplementary files format and content: tab-delimited file containing normalized counts

source_name: brain parenchyma metastatic variant of EMT6

growth_protocol: Cells were derived and cultured as described in Remsik et al, 2022. Approximately 1x10*6 cells were seeded into 100 mm dish. Approximately 24 hours later, cells were lysed in RNA lysis buffer (RLT).

extract_protocol:
RNA was extracted from lysates using Rneasy Mini columns (Qiagen).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, #RS-122-2102), with 8 cycles of PCR.

tag: derivative

tag: primary tumor type

value: mouse mammary cancer


title: Ctrl_day_4_rep_1

description: extracted total RNA


title: whole animal, 25 degrees, rep2

description:
total RNA
whole_25_2


title: P2136_N701-S502

value: pMHCII-NPs


title: cortex and corpus callosum, Remye1

value: WT


title: Nav1.8 Control BL [WT 2 IN]

value: Dorsal root ganglia

value: DRG neurons

value: Nav1.8 Control


title: s_EMT6_lucV5_R3_IC_1

description:
Proj_09317_J
s_EMT6_lucV5_R3_IC_1.bam

source_name: leptomeningeal metastatic variant of EMT6

value: Par


title: P2120_N712-S508

value: NOD


title: AFD, 25 degrees, rep2

description:
ribosome-associated RNA
AFD_25_2


title: s_EMT6_lucV5_R3_IC_3

description:
Proj_09317_J
s_EMT6_lucV5_R3_IC_3.bam

value: LeptoM


title: cortex and corpus callosum, Demye2

value: 5-week cuprizone


title: whole animal, 15 degrees, rep1

description:
total RNA
whole_15_1

value: 15 degrees celsius overnight


title: cortex and corpus callosum, Demye1


title: P2120_N712-S517

value: T cell


title: s_EMT6_lucV5_Par_3

description:
Proj_09317_J
s_EMT6_lucV5_Par_3.bam

source_name: parental EMT6


title: AFD, 15 degrees, rep2

description:
ribosome-associated RNA
AFD_15_2

value: AFD


title: P2120_N712-S506


title: whole animal, 25 degrees, rep1

description:
total RNA
whole_25_1

value: whole animal

value: 25 degrees celsius overnight


title: cortex and corpus callosum, WT2

value: cortex and corpus callosum

value: Eight-week-old

value: regular chow


title: AFD, 15 degrees, rep1

description:
ribosome-associated RNA
AFD_15_1


title: P2120_N712-S505

value: pMHCII-NPs


title: cortex and corpus callosum, WT1

value: male

value: WT


title: AFD, 25 degrees, rep1

description:
ribosome-associated RNA
AFD_25_1


title: s_EMT6_lucV5_BrM2_2

description:
Proj_09317_J
s_EMT6_lucV5_BrM2_2.bam

value: mouse mammary cancer


title: s_EMT6_lucV5_Par_1

description:
Proj_09317_J
s_EMT6_lucV5_Par_1.bam


title: Tetramer-sorted CD4 T cells - Prdm1 KO [E_TR1_CreBlimp1_BDC]

first: Josep

last: Garnica

address: Rosselló, 149

data_processing:
Reads were aligned refdata-gex-mm10-2020-A transcriptome using Cellranger count version 5.0.0
Genome_build: mm10
Supplementary_files_format_and_content: barcodes of each cell
Supplementary_files_format_and_content: list of genes
Supplementary_files_format_and_content: gene count matrix

source_name: Tetramer-sorted CD4 T cells

growth_protocol: Sorting by tetramer of CD4 T cells from spleen.

extract_protocol:
10x Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead kit (PN-1000121)
10x Chromium Next GEM Chip G Single Cell Kit (PN-1000120)
10x Chromium i7 Sample Index (PN-120262)
NovaSeq 100 cycle S1

treatment_protocol: Mice were treated with BDC2.5/IAg7-NPs at 30ug/dose, 2 times a week for 5 weeks.

tag: celltype

value: Tetramer-sorted CD4 T cells

tag: genotype/variation

value: NOD.Prdm1 flox/floxCD4-Cre+


title: s_EMT6_lucV5_R3_IC_2

description:
Proj_09317_J
s_EMT6_lucV5_R3_IC_2.bam


title: P2120_N712-S503

value: NOD


title: cortex and corpus callosum, Demye3


title: Tetramer-sorted CD4 T cells - control [B_TR1_Blimp1_BDC]

value: NOD.Prdm1 flox/flox


title: P2120_N712-S507


title: s_EMT6_lucV5_BrM2_3

description:
Proj_09317_J
s_EMT6_lucV5_BrM2_3.bam


title: Flp-P63-d23-Live

city: CINCINNATI

first: Kang

state: OH

address: 3333 Burnet Ave, Cincinnati

institute: Cincinnati Children's Hospital Medical Center

data_processing:
10x single-cell RNA-sequencing data in Fastq files were aligned to transcripts using Cell Ranger 3.1.0 (https://www.10xgenomics.com/support/single-cell-gene-expression). Reference genome GRCh38 (Ensembl 93) was used as the reference genome. In the CellRanger count command, parameters chemistry and expected-cells were set as SC3Pv3 and 6000, respectively.
Cell Ranger output h5 files were loaded using Seurat 4 as the raw data. To reduce the impact of low-quality cells, we first removed cells with less than 1200 or more than 25,000 unique molecular identifiers (UMI). In addition, we removed cells with less than 600 or more than 6000 unique genes. Since low-quality or dying cells often exhibit extensive mitochondrial contamination, we removed cells with more than 10% mitochondrial transcripts.
Furthermore, we removed several clusters (details of the clustering will be mentioned later) of cells with low-sequencing depth to avoid the influence of poorly sequenced cells. Clusters with lower-than-normal distributions of the number of UMIs or unique genes were manually removed from the data. In the end, 9 lowly-sequenced clusters were removed from both donor-derived and engineered organoids single cell data (Figure S3). In addition, we utilized Scrublet investigate the doublets in the data. Only a small number of cells reached the threshold of doublets, indicating a low prevalence of doublets.
After the quality control, we finally harvested 33,538 genes and 141,039 high-quality cells, including 88,623 cells from 16 donor-derived organoid samples and 52,416 cells from 10 engineered organoid samples. Both original and processed data can be found in Data Availability. We normalized the total UMI counts per gene to 1 million (CPM) and applied log2(CPM+1) transformation for heatmap visualization and downstream differential gene expression analysis, which were conducted in Scanpy. In the following Seurat integration procedure, we applied the default normalization approach of Seurat.
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: 10x CellRanger h5 output

molecule: cytoplasmic RNA

source_name: brain organoid

growth_protocol: hESC and iPSCs were cultured on feeder-free conditions. In order to form serum-free floating embryoid body (EB) aggregates, hPSCs were dissociated into single cells using Accutase (Innovative Cell Technologies). Dissociated cells were then reaggregated in low adhesion microwell culture plates (AggreWell-800, Stem cell technologies). 3 million cells were plated per 2mL well in mTesR plus Y-27632 (1 μM, Axon Medchem). 24 hours after plating, aggregated EBs were transferred to ultra-low attachment 10cm petri dishes and cultured. Briefly, EBs in 10 cm dishes are cultured in E6 medium (ThermoFisher) for up to 6 days with SB431542 (10 μM, Peprotech) and dorsomorphin (5 μM, Peprotech) for dual SMAD inhibition, promoting neural stem cell differentiation. Following day 6, EBs were cultured in Neurobasal (ThermoFisher) containing B27 without vitamin A supplement, Glutamax (Life Technologies), Penicillin-Streptomycin (ThermoFisher) and the following morphogens at 20 ng/mL (Peprotech): human EGF, human FGF, human BDNF, and human NT3. At day 6-8, forebrain organoids were placed on an orbital shaker for gentle agitation to reduce spontaneous fusion. Starting at day 43, all morphogens were removed and brain organoids were cultured solely in B27 containing Neurobasal media.

extract_protocol:
Organoids were rinsed 3 times with HBSS (10X HBS salt, 1M HEPES, 0.004M NaHCO3 diluted to 1X), then minced into small pieces and transferred to a 15mL conical tube for incubation in digestion solution (consisting of HBSS, 1 mg/mL Papain, 0.5mM EDTA, and 1mM L-cysteine) for 15 minutes at 37°C. Upon incubation, digestion mixture containing organoids were gently triturated with DNase I (25 μg/mL, Worthington-Biochem) and subsequently incubated again for another 10 minutes at 37°C followed by filtration with 70uM and 30uM filters (Miltenyi Biotech). Cell mixture was then centrifuged and pelleted. Cell pellet was resuspended in Neurobasal media with B27. This step was done to help dilute any remaining enzyme, EDTA, and other components of the digest mix. After the final re-suspension in Neurobasal media (without supplements), single cell mix was filtered again using 40 μM FlowMi pipet (Milipore Sigma) to help remove debris.
Following isolation of single cells from brain organoids, cells were centrifuged at 300 g for 5 min and then re-suspended in 1 mL ice-cold Neurobasal media. Cell concentration and viability were determined using a hemocytometer with trypan blue dye exclusion and cell concentrations were adjusted to 700-1200 cells/μL for 10X single cell sequencing. For each sample, 9,600 cells were loaded into the 10X Chromium controller to target recovery of 6,000 cells and a Gel Beads in Emulsion (GEM) was generated. 10X Genomics 3’v3.1 chemistry was used. The samples were processed according to the protocol from 10X Genomics, using 14 cycles for cDNA amplification. Single cell libraries were sequenced using the Illumina NovaSeq 6000.

treatment_protocol: Lentiviral plasmid constructs used in this study for NRXN1 cKO hESC lines are Cre-recombinase and Flp-recombinase fused to EGFP driven by the ubiquitin-C promoter as previously described. For all lentiviral vectors, viruses were produced in HEK293T cells (ATCC, VA) by co-transfection with three helper plasmids (3.25 μg of pRSV-REV, 8.1 μg of pMDLg/pRRE and 10 μg of lentiviral vector DNA per 75 cm2 culture area using calcium phosphate transfection method90. Lentiviruses were harvested from the medium 48 hrs after transfection. Viral supernatants were then centrifuged at a high speed of 49,000 x g for 90 min and aliquoted for storage in −80C. Viral preparations that yielded 90% EGFP expression were assessed to be efficiently infected and used for experiments. All other iPSC lines were not treated with viruses.

value: brain organoid

value: neural progenitor cells and neurons

value: Flp

tag: time point

tag: cell line_(detailed)

value: NRXN1 cKO hESC

tag: procedure

value: live


title: P2120_N712-S502

tag: strain

value: T cell


title: s_EMT6_lucV5_Par_2

description:
Proj_09317_J
s_EMT6_lucV5_Par_2.bam

value: Par


title: Flp-P61-d50-Methanol

tag: tissue

tag: genotype


title: s_4T1_lucV5_R3_IC_2

description:
Proj_09317_I
s_4T1_lucV5_R3_IC_2.bam

source_name: leptomeningeal metastatic variant of 4T1

value: LeptoM


title: Tetramer-sorted CD4 T cells - control [A_TR1_CD4cre_BDC]

tag: treatment


title: P2120_N711-S517

tag: cell type


title: Bcl6_KO_S4

description: CD4+ IL-10+ cells from CD4.cre.Bcl6(fl/fl) NOD mice treated with anti-CD3e Ab

data_processing:
CellRanger counts
CellRanger aggr
Downstream analysis in Seurat (normalization, scaling and differential expression analysis)
Genome_build: mm10
Supplementary_files_format_and_content: One folder containing the aggregated files from CellRanger aggr (3 files: matrix, features and barcodes)

source_name: CD4+ IL-10+ cells

extract_protocol:
Partition of cell suspensions into Gel-Bead-In-Emulsions
10X Single-cell mRNA kit

treatment_protocol: Samples are obtained from mice that have received 2 IP injections of anti-CD3e Ab.

value: NOD CD4.cre.Bcl6(fl/fl)

value: anti-CD3e Ab


title: Flp-P61-d50-Live

tag: cell line


title: s_4T1_lucV5_Par_3

description:
Proj_09317_I
s_4T1_lucV5_Par_3.bam

source_name: parental 4T1


title: s_4T1_lucV5_Par_2

description:
Proj_09317_I
s_4T1_lucV5_Par_2.bam


title: Flp-P61-d112-Live


title: P2120_N711-S508

value: pMHCII-NPs


title: Flp-d100-Methanol


title: P2120_N711-S507


title: Bcl6_KO_S3


title: P2120_N712-S504


title: Cre-P63-d23-Live

value: Cre


title: s_4T1_lucV5_Par_1

description:
Proj_09317_I
s_4T1_lucV5_Par_1.bam

value: mouse mammary cancer


title: s_4T1_lucV5_BrM2_3

description:
Proj_09317_I
s_4T1_lucV5_BrM2_3.bam

source_name: brain parenchyma metastatic variant of 4T1


title: INS_Tet

description: Tet+ CD4+ T cells from pMHCII-NP-treated NOD mice

treatment_protocol: Samples are obtained from mice that have received intravenously 10 doses of pMHCII-NPs.


title: Cre-P61-d50-Methanol


title: P2120_N711-S505

description:
Tetramer+ CD4+ T cells from BDC 2.5mi/IAg7-NP-treated NOD mice
Raw_counts_BDC_SMARTseq2.xlsx

treatment_protocol:
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.
Treated samples are obtained from mice that have received intravenously 10 doses of BDC2.5mi/IAg7-NPs.


title: INS_Ctl

description: Conventional Tet- CD4+ T cells from pMHCII-NP-treated NOD mice

source_name: Conventional T cells


title: P2120_N711-S504

source_name: Tetramer+ CD4+ T cells


title: s_4T1_lucV5_R3_IC_1

description:
Proj_09317_I
s_4T1_lucV5_R3_IC_1.bam


title: P2120_N711-S503


title: Cre-P61-d50-Live


title: s_4T1_lucV5_BrM2_1

description:
Proj_09317_I
s_4T1_lucV5_BrM2_1.bam


title: BDC_Tet


title: P2120_N711-S502


title: BDC_Ctl


title: s_4T1_lucV5_R3_IC_3

description:
Proj_09317_I
s_4T1_lucV5_R3_IC_3.bam


title: Cre-P61-d112-Live


title: P2120_N711-S506


title: s_4T1_lucV5_BrM2_2

description:
Proj_09317_I
s_4T1_lucV5_BrM2_2.bam


title: P2120_N710-S508


title: s_Yumm52_BrM2_1

description:
Proj_09317_G
s_Yumm52_BrM2_1.bam

source_name: brain parenchyma metastatic variant of Yumm5.2

value: mouse melanoma


title: P2120_N710-S517


title: Hyperglycemia rep1

first: Bin

last: Chen

state: Zhejiang

address: Qingchun East Road 3

department: Assisted Reproduction Unit, Department of Obstetrics and Gynecology

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

description: Born from hyperglycemic oocyte.

library_source: genomic

data_processing:
Raw data was processed using skewer (0.2.2). After adaptor-trimming and low quality reads removing, high quality reads were generated.
High quality reads were aligned to mouse reference genome using bowtie2 (2.2.3) software with default parameters.
Peak calling was performed with MACS (2.1.0) software.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bw: Genome coverage bigWig files.

molecule: genomic DNA

source_name: Fetal pancreas

extract_protocol:
Fetal pancreas were removed, flash frozen on dry ice. Genomic DNA was isolated according to the manufacturer recommended protocol.
MeDIP DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pancreas

tag: age

value: Embryo day 18.5

tag: maternal diagnosis

value: Hyperglycemia


title: WT_S2

description: CD4+ IL-10+ cells from WT NOD mice treated with anti-CD3e Ab

value: NOD


title: Hyperglycemia rep2

description: Born from hyperglycemic oocyte.


title: s_Yumm52_R1_IC_3

description:
Proj_09317_G
s_Yumm52_R1_IC_3.bam

source_name: leptomeningeal metastatic variant of Yumm5.2


title: 4C-d100-Methanol

value: brain organoid

value: neural progenitor cells and neurons

value: control


title: 4N-d100-Methanol


title: WT_S1


title: P2120_N710-S507


title: N1884a-d50

value: live


title: s_Yumm52_Par_2

description:
Proj_09317_G
s_Yumm52_Par_2.bam

source_name: parental Yumm5.2


title: Control rep2

description: Born from control oocyte.

value: Control


title: N1884a-d22


title: Cre-d100-Methanol

value: NRXN1 cKO hESC


title: Control rep1

description: Born from control oocyte.


title: s_Yumm52_Par_3

description:
Proj_09317_G
s_Yumm52_Par_3.bam

value: Par


title: P2120_N710-S505

value: T cell


title: s_Yumm52_Par_1

description:
Proj_09317_G
s_Yumm52_Par_1.bam


title: N1884a-d101


title: C8905-d50


title: P2120_N710-S504


title: C8905-d22


title: s_Yumm52_BrM2_3

description:
Proj_09317_G
s_Yumm52_BrM2_3.bam


title: A41270 cells grown for 8h at 37ºC [1624.8h.d7855]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were aligned to a S. cerevisiae transcriptome with STAR version 2.5.3a and gene expression was quantified with RSEM version 1.3.0. Transcript per million (TPM) values were offset by +1 and transformed to log 2 space.
Assembly: SacCer3 plus spike-ins with an ensembl annotation
Supplementary files format and content: allegra_l2tpm.txt.gz is a tab-delimited text file of log2 tpm data

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Growth at 37ºC for 8 hours in YEPD after alpha-factor synchronization

extract_protocol:
RNeasy kit (Qiagen)
Illumina Truseq followed by Roche KAPA

value: yeast

tag: strain source

value: Amon Lab

tag: strain genotype

value: MATa, cdc28-13, ADE2, URA3, TRP1, HIS3, can1-100, GAL, psi+, cdc28-13, leu2::4xSTRE-GFP:LEU2

tag: temperature


title: P2120_N710-S503

data_processing:
Quality check with FastQC v0.11.8
Alignment to the mouse genome mm10 with STAR v2.5.4b
Gene expression estimation with RSEM v1.3.0
QC filtering of low quality cells
TCR sequences reconstructed to infer clonality with TraCeR v.0.5.1
Genome_build: mm10
Supplementary_files_format_and_content: xlsx (Raw counts for each cell)

extract_protocol:
Single-cell sorting in SMARTseq2 plates
Smart-seq protocol (Picelli et al., 2013)

value: pMHCII-NPs


title: A41270 cells grown for 6h at 37ºC [1624.6h.d7854]

growth_protocol: Growth at 37ºC for 6 hours in YEPD after alpha-factor synchronization


title: A41270 cells grown for 4h at 37ºC [1624.4h.d7853]

growth_protocol: Growth at 37ºC for 4 hours in YEPD after alpha-factor synchronization


title: C8905-d101


title: s_Yumm52_R1_IC_2

description:
Proj_09317_G
s_Yumm52_R1_IC_2.bam

tag: derivative

value: LeptoM

tag: primary tumor type

value: mouse melanoma


title: P2120_N710-S502


title: A17896 cells grown for 8h at 37ºC [1622.8h.d7851]


title: N9540a-d50


title: P2120_N709-S517


title: A41270 cells grown for 2h at 37ºC [1624.2h.d7852]

growth_protocol: Growth at 37ºC for 2 hours in YEPD after alpha-factor synchronization


title: P2120_N709-S508


title: s_Yumm52_BrM2_2

description:
Proj_09317_G
s_Yumm52_BrM2_2.bam


title: P2120_N710-S506


title: P2120_N709-S507


title: s_E0771_R3_IC_4

description:
Proj_09317_F
s_E0771_R3_IC_4.bam

source_name: leptomeningeal metastatic variant of E0771

value: mouse mammary cancer


title: N9540a-d101


title: A17896 cells grown for 4h at 37ºC [1622.4h.d7849]


title: N9540a-d22


title: s_E0771_R3_IC_1

description:
Proj_09317_F
s_E0771_R3_IC_1.bam


title: P2120_N709-S506


title: A17896 cells grown for 2h at 37ºC [1622.2h.d7848]


title: C9632-d22


title: s_Yumm52_R1_IC_1

description:
Proj_09317_G
s_Yumm52_R1_IC_1.bam


title: P2120_N709-S505


title: s_E0771_Par_3

description:
Proj_09317_F
s_E0771_Par_3.bam

source_name: parental E0771


title: A40501 cells grown for 6h at 37ºC [cdc15.2.BCY1.6h.d226047]

growth_protocol: Growth at 37ºC for 6 hours in YEPD + 0.0138% glacial acetic acid, 4 hours 500μM auxin treatment refreshed after 2 hours

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, cdc15-2, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: s_E0771_Par_2

description:
Proj_09317_F
s_E0771_Par_2.bam


title: P2120_N709-S504

value: NOD


title: s_E0771_BrM2_1

description:
Proj_09317_F
s_E0771_BrM2_1.bam

source_name: brain parenchyma metastatic variant of E0771


title: P2120_N709-S503


title: A17896 cells grown for 6h at 37ºC [1622.6h.d7850]


title: s_E0771_BrM2_2

description:
Proj_09317_F
s_E0771_BrM2_2.bam


title: P2120_N709-S502


title: 1N-d100-Methanol

value: brain organoid


title: 1C-d100-Methanol

value: neural progenitor cells and neurons


title: A40501 cells grown for 2h at 37ºC [cdc15.2.BCY1.2h.d226045]

growth_protocol: Growth at 37ºC for 2 hours in YEPD + 0.0138% glacial acetic acid


title: s_E0771_R3_IC_3

description:
Proj_09317_F
s_E0771_R3_IC_3.bam


title: P2120_N708-S517


title: s_E0771_Par_1

description:
Proj_09317_F
s_E0771_Par_1.bam


title: A2596 cells grown for 4h at 37ºC [cdc15.2.4h.d226043]

growth_protocol: Growth at 37ºC for 4 hours in YEPD + 0.0138% glacial acetic acid, 2 hours 500μM auxin treatment

value: Nasmyth Lab

value: MATa, cdc15-2, leu2-3, ura3, trp1-1, omns, ade1


title: C9632-d50

value: control

value: live


title: A2596 cells grown for 6h at 37ºC [cdc15.2.6h.d226044]


title: P2120_N708-S508


title: A2596 cells grown for 2h at 37ºC [cdc15.2.2h.d226042]


title: s_E0771_BrM2_3

description:
Proj_09317_F
s_E0771_BrM2_3.bam


title: A40499 cells grown for 6h at 37ºC [cdc20.1.BCY1.6h.d226041]

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, cdc20-1, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: P2120_N708-S507

value: T cell


title: A40501 cells grown for 4h at 37ºC [cdc15.2.BCY1.4h.d226046]

value: yeast


title: C9632-d101


title: Vancomycin-2

city: Changsha

first: Kun

last: Liu

address: Tongzipo road 138.

department: Pharmacy

institute: The Third Xiangya Hospital, Central South University

description: Sample 11

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Supplementary files format and content: tab-delimited text files include gene count for each Sample

growth_protocol: HK-2 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 ssay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: The first group was the control group, and water was the control lysozyme. The second group was iohexol induced-AKI. Iohexol (75 mg I/mL) was used to intervene HK-2 cells for 48h. The third group was the cisplatin induced-AKI group. The HK-2 cells were treated with cisplatin (5 μM) for 48h. The fourth group was vancomycin induced-AKI.Vancomycin (4 mM) was used to intervene HK-2 cells for 48h.

value: human renal proximal tubular epithelial

value: Vancomycin


title: Vancomycin-3

description: Sample 12


title: s_E0771_R3_IC_2

description:
Proj_09317_F
s_E0771_R3_IC_2.bam


title: Cisplatin-3

description: Sample 9

value: Cisplatin


title: Vancomycin-1

description: Sample 10


title: P2120_N708-S506

value: pMHCII-NPs


title: A40499 cells grown for 4h at 37ºC [cdc20.1.BCY1.4h.d226040]

value: Amon Lab


title: P2120_N708-S505


title: Cisplatin-2

description: Sample 8


title: A40499 cells grown for 2h at 37ºC [cdc20.1.BCY1.2h.d226039]


title: P2120_N708-S504


title: s_B16_R1_IC_4

description:
Proj_09317_D
s_B16_R1_IC_4.bam

source_name: leptomeningeal metastatic variant of B16

value: LeptoM

value: mouse melanoma


title: A937 cells grown for 6h at 37ºC [cdc20.1.6h.d226038]

value: MATalpha, cdc20-1, ura3, trp1, leu2,  his3 , ade2, can1


title: s_B16_Par_3

description:
Proj_09317_D
s_B16_Par_3.bam

source_name: parental B16

value: Par


title: Cisplatin-1

description: Sample 7


title: A937 cells grown for 4h at 37ºC [cdc20.1.4h.d226037]


title: Iohexol-3

description: Sample 6

value: Iohexol


title: s_B16_BrM2_3

description:
Proj_09317_D
s_B16_BrM2_3.bam

source_name: brain parenchyma metastatic variant of B16


title: s_B16_R1_IC_1

description:
Proj_09317_D
s_B16_R1_IC_1.bam


title: P2120_N708-S502

value: NOD


title: Iohexol-1

description: Sample 4


title: A937 cells grown for 2h at 37ºC [cdc20.1.2h.d226036]

value: Nasmyth Lab


title: P2120_N707-S517


title: s_E0771_R3_IC_5

description:
Proj_09317_F
s_E0771_R3_IC_5.bam

value: mouse mammary cancer


title: s_B16_Par_2

description:
Proj_09317_D
s_B16_Par_2.bam


title: s_B16_R1_IC_3

description:
Proj_09317_D
s_B16_R1_IC_3.bam


title: A40444 cells grown for 6h at 37ºC [cdc28.13.BCY1.6h.d226035]

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, cdc28-13::URA, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: P2120_N707-S508


title: Control-3

description: Sample 3


title: A40444 cells grown for 2h at 37ºC [cdc28.13.BCY1.2h.d226033]


title: Control-2

description: Sample 2


title: s_B16_Par_1

description:
Proj_09317_D
s_B16_Par_1.bam


title: P2120_N707-S507


title: P2120_N707-S506


title: A39000 cells grown for 6h at 37ºC [cdc28.13.6h.d226032]


title: A40444 cells grown for 4h at 37ºC [cdc28.13.BCY1.4h.d226034]


title: s_B16_BrM2_2

description:
Proj_09317_D
s_B16_BrM2_2.bam


title: P2120_N707-S505


title: Iohexol-2

description: Sample 5


title: P2120_N708-S503


title: P2120_N707-S504


title: Pt16Dx_ZRSR2.R126_XVseq

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

description: XV-seq

data_processing:
For demultiplexing, we used cellranger-7.0.0 mkfastq or bcl2fastq v2.20.0.422, with identical results.
For alignment of scRNA-seq data and to generate gene expression matrices, we used cellranger-7.0.0 count.
For the analysis of XV-seq data, we used IronThrone-GoT.
Assembly: hg38
Supplementary files format and content: counts.tsv: tab-separated transcript counts per cell
Supplementary files format and content: norm.tsv: tab-separated normalized transcript counts per cell
Supplementary files format and content: metadata.tsv: tab-separated metadata per cell
Supplementary files format and content: FilteredCells.txt: tab-separated number of UMIs with wildtype or mutant genotyping calls per cell
Library strategy: XV-seq

source_name: Bone marrow

extract_protocol:
mRNA was extracted and hybridized to polyT oligos on 10x Genomics or Seq-Well beads.
10x Genomics 3' v3 or v3.1, or Seq-Well S3 library construction methods were used to construct single-cell RNA-sequencing libraries. From the full-length cDNA, XV-seq was used to enrich and sequence mutation sites of interest (similar to Genotyping of Transcriptomes, GoT).

value: Bone marrow

tag: Sex

value: Male

tag: disease state

value: Diagnosis

tag: bone marrow_involvement

value: Yes


title: A39000 cells grown for 2h at 37ºC [cdc28.13.2h.d226030]

value: yeast


title: Pt16Dx_TET2.S794_XVseq

description: XV-seq


title: s_B16_BrM2_1

description:
Proj_09317_D
s_B16_BrM2_1.bam


title: P2120_N707-S503

value: T cell


title: A40439 cells grown for 6h at 37ºC [WT.BCY1.6h.d226029]

growth_protocol: Growth at 37ºC for 6 hours in YEPD + 0.0138% glacial acetic acid, 4 hours 500μM auxin treatment refreshed after 2 hours, kept between OD600 = 0.2 and OD600 = 0.8

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: Pt16Dx_TET2.Q876_XVseq

description: XV-seq


title: Pt16Dx_ASXL1.R693_XVseq

description: XV-seq


title: P2120_N707-S502

value: pMHCII-NPs


title: Control-1

description: Sample 1

value: human renal proximal tubular epithelial


city: Houston

first: Navin

last: Varadarajan

state: TX

address: 4722 Calhoun Rd

institute: University of Houston

description:
BD Rhapsody
SampleTag01_hs = MDAMB231-S
SampleTag02_hs = MDAMB231-NS
SampleTag03_hs = MDAMB231
SampleTag04_hs = MCF7
SampleTag05_hs = HCC70

data_processing:
We uploaded and analyzed the FASTQ files on Seven Bridges website (Seven Bridges Genomics) by running the “BD Rhapsody WTA Analysis Pipeline”.
We performed alignment, filtering, and sample tag detection by the "BD Rhapsody WTA Analysis Pipeline".
Cells with SampleTag01_hs, SampleTag02_hs, SampleTag03_hs, SampleTag04_hs and SampleTag05_hs are MDAMB231-S, MDAMB231-NS, MDAMB231, MCF7, and HCC70, respectively.
Assembly: GRCh38
Supplementary files format and content: CSV file format, molecules per gene per cell based on RSEC
Supplementary files format and content: CSV file format, assigned Sample Tag for each putative cell

source_name: multiplexed sample: pool of MDAMB231-S, MDAMB231-NS, MDAMB231, MCF7, and HCC70

extract_protocol:
We labeled HCC70, MCF7, MDAMB231, MDAMB231-S, and MDAMB231-NS cells separately with the Sample-Tags from the BD Human Immune Single-Cell Multiplexing Kit (BD Biosciences) as described in the manufacturer’s protocol.
We prepared a library from ~5000 cells (approximately 1000 cells from each group) using the BD Rhapsody System following the BD “mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol”.

value: multiplexed sample:pool of MDAMB231-S, MDAMB231-NS, MDAMB231, MCF7, and HCC70

value: Breast cancer cells


title: A40439 cells grown for 4h at 37ºC [WT.BCY1.4h.d226028]

growth_protocol: Growth at 37ºC for 4 hours in YEPD + 0.0138% glacial acetic acid, 2 hours 500μM auxin treatment, kept between OD600 = 0.2 and OD600 = 0.8

value: Amon Lab


title: Gingiva_vi

city: Guangzhou

first: Wejun

last: Zhu

state: Guangdong

address: 56th Lingyuan Road West

department: Periodontology

institute: Sun Yat-sen University

description: 10x Genomics

data_processing:
Single-cell FASTQ sequencing reads from each sample were processed, and converted to digital gene expression matrices after mapping to the reference genome (GRCh38-2020-A) using the Cell Ranger Single Cell Software Suite (v5.0.0) provided on 10x genomics website. Individual datasets were aggregated using the CellRanger aggr command without subsampling normalization.
Assembly: Human reference, GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Gingiva

extract_protocol:
For v_i group, the gingival tissues from interdental space of periodontitis affected site were harvested during guided tissue regeneration procedure. For h_h and v_h group, gingival tissues from interdental space along the extended crevicular incision were harvested during open flap surgery of adjacent affected teeth.Gingival samples were minced into small pieces of less than 1 mm3 by surgical scissors and dissociated into single cells in dissociation solution (2 mg/ml Ⅳ collagenase , 2 units/ml Dispase Ⅱ in Ca2+- and Mg2+-free HBSS) at 37°C for 60 min; 0.1 mg/mL DNase I was added in the last 10 min. Cell suspension was filtered by 70μm cell strainers. Cells were subjected to red blood cell lysis for 10 min and centrifuged and re-suspended (500 g, 10min) twice. After resuspension in defined volumes of PBS + 0.04% BSA, cells were stained with 0.4% Trypan blue, and cell viability was evaluated under microscope. When the viability of cells was higher than 80%, the experiment of library construction was performed.
The single-cell library was constructed using the ChromiumTM Controller and ChromiumTM Single Cell 3’ Reagent Version 3 Kit (10x Genomics, Pleasanton, CA). Briefly, single cells, reagents and Gel Beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized GEMs (Gel Bead in emulsion) using the GemCode Technology. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM. The post RT-GEMs were cleaned up by silane magnetic beads, and cDNA were amplified by PCR. cDNA was fragmented and fragments end were repaired, as well A-tailing was added to the 3’ end. Solid Phase Reversible Immobilization (SPRI) beads were used to remove large and small fragments. Another double sided SPRI selection was carried out after sample index PCR. The final library quantification was performed by checking the distribution of the fragments size using the Agilent 2100 bioanalyzer, and by using real-time quantitative PCR (QPCR) (TaqMan Probe). The final products were sequenced using the Illumina Hiseq 4000 (BGI-Shenzhen, China).

treatment_protocol: Scaling and root planning with ultrasonic device was performed. Two months after treatment, the periodontal status was re-evaluated.

value: Gingiva

tag: disease stage

value: Periodontitis(stage III , generalized type, grade C)

tag: type of_alveolar_bone_loss

value: Vertical bone loss

tag: healing outcome

value: poor


title: Gingiva_vh

description: 10x Genomics

tag: tissue

value: good


title: P2120_N706-S508

first: Pere

tag: strain

value: NOD

tag: treatment


title: P2120_N706-S517

tag: cell type


title: Pt15Dx_U2AF1.S34F_XVseq

description: XV-seq

value: Bone marrow

value: Male

tag: age


title: Pt15Dx_ASXL1.V807fs_XVseq

description: XV-seq

value: Diagnosis

value: Yes


title: P2120_N706-S507

value: T cell


title: s_B16_R1_IC_2

description:
Proj_09317_D
s_B16_R1_IC_2.bam

value: LeptoM

value: mouse melanoma


title: Pt15Dx_TET2.R1516_XVseq

description: XV-seq


title: Gingiva_hh

description: 10x Genomics

value: Horizontal bone loss


title: A39000 cells grown for 4h at 37ºC [cdc28.13.4h.d226031]

value: yeast


title: A40439 cells grown for 2h at 37ºC [WT.BCY1.2h.d226027]

growth_protocol: Growth at 37ºC for 2 hours in YEPD + 0.0138% glacial acetic acid, kept between OD600 = 0.2 and OD600 = 0.8

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: Pt14Dx_IDH2.R140Q_XVseq

description: XV-seq


title: P2120_N706-S506

value: pMHCII-NPs


title: P2120_N706-S505


title: A2587 cells grown for 4h at 37ºC [WT.4h.d226025]

value: Nasmyth Lab


title: A40501 cells grown for 6h at 37ºC [d113024.cdc15.2.BCY.6]

value: Amon Lab

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, cdc15-2, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: Pt14Dx_EZH2.P132L_XVseq

description: XV-seq


title: P2120_N706-S504


title: P2120_N706-S503


title: Pt12Rel_TET2.Q1537_XVseq

description: XV-seq

value: Relapse


title: A2587 cells grown for 6h at 37ºC [WT.6h.d226026]


title: Pt14Dx_ETV6.R369W_XVseq

description: XV-seq


title: Pt12Rel_NOTCH1.3pUTR_XVseq

description: XV-seq


title: A2596 cells grown for 4h at 37ºC [d113020.cdc15.2.4]

value: MATa, cdc15-2, leu2-3, ura3, trp1-1, omns, ade1


title: Pt12Rel_NFIC.3pUTR_XVseq

description: XV-seq


title: P2120_N706-S502

value: NOD


title: A2596 cells grown for 2h at 37ºC [d113019.cdc15.2.2]


title: P2120_N705-S517


title: Pt12Rel_MALAT1.n.G3541A_XVseq

description: XV-seq

value: Bone marrow


title: A40499 cells grown for 6h at 37ºC [d113018.cdc20.1.BCY.6]

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, cdc20-1, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: P2120_N705-S508


title: A40501 cells grown for 4h at 37ºC [d113023.cdc15.2.BCY.4]


title: P2120_N705-S507


title: A40501 cells grown for 2h at 37ºC [d113022.cdc15.2.BCY.2]


title: A40499 cells grown for 4h at 37ºC [d113017.cdc20.1.BCY.4]


title: Pt12Dx_TET2.Q1537_XVseq

description: XV-seq

value: Male

value: Diagnosis

value: No


title: P2120_N705-S506

value: T cell


title: Sup skin PBS-treated rep1

first: Liangling

last: Shen

address: 389 Xincun Road

institute: Tongji Hospital, Tongji University

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.

hyb_protocol: 2.5 μg of the Cy3- and Cy5-labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μl 10× blocking agent and 1 μl of 25× fragmentation buffer, heating at 60°C for 30 min and combining with 25 μl 2× hybridization buffer. Next, 50 μl hybridization solution was dispensed into the gasket slide and assembled to the m6A epitranscriptomic microarray slide. The slides were incubated at 65°C for 17 h in an Agilent hybridization oven (Agilent, CA, USA). Finally, the hybridized arrays were washed and fixed.

scan_protocol: The array images were analyzed using Agilent Feature Extraction software.

data_processing:
The raw intensities of IP and Sup were normalized with an average of log2-scaled spike-in RNA intensities. Following normalization, probe signals with Present or Marginal QC flags in at least four out of eight samples were retained for further m6A methylation level, m6A quantity and expression level analyses. For determining the m6A methylation level, the percentage modification was calculated based on the normalized intensities of IP and Sup. For determining the m6A quantity, the m6A methylation amount was calculated based on normalized intensities of IP. The expression level was calculated based on the total normalized intensities of IP and Sup. An additional quantile normalization method in the limma package was used to normalize the RNA expression level between arrays before probe flag screening.
Filtering with fold change ≥1.5 and p < 0.05 (unadjusted p-values) was used to identify differentially m6A-methylated RNAs between the two comparison groups.

source_name: skin

label_protocol: An equal amount of calibration spike-in control RNA was added to the immunoprecipitated RNA (IP) and supernatant RNA (Sup), following which they were amplified and labeled with Cy3 (for Sup) and Cy5 (for IP) using Arraystar Super RNA Labeling Kit (Arraystar). The synthesized cRNAs were purified using RNeasy Mini Kit (Sigma Aldrich). The cRNA concentration and specific activity were measured using NanoDrop™ ND-1000

growth_protocol: Female Balb/c mice aged 6–8 weeks were acquired from Charles River Laboratories (Shanghai, China). Sixteen mice were randomly divided into two groups: the control and a BLM-treated (BLM) group. In the BLM group, 100 μl BLM (1 mg/ml; Thermo Fisher Scientific, MA, USA) was injected subcutaneously into the back of the mice daily for 28 consecutive days. Similarly, mice in the control group were injected with 100 μl phosphate-buffered saline daily for 28 days. In the BLM group, a circular depilation area with a diameter of 0.1 cm was observed at the injection site, along with scar formation.

extract_protocol: Skin tissue was cut into small pieces and homogenized in TRIzol reagent to isolate total RNA.

tag: gender

value: female

value: Balb/c

value: 100 ul phosphate-buffered saline

tag: antibody


title: Pt12Dx_NFIC.3pUTR_XVseq

description: XV-seq


title: A40499 cells grown for 2h at 37ºC [d113016.cdc20.1.BCY.2]

value: yeast

tag: strain source

tag: strain genotype


title: Sup skin Bleomycin-treated rep3

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.

value: 100 ul BLM


title: Sup skin PBS-treated rep3


title: Sup skin PBS-treated rep2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Sup skin PBS-treated rep4

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Sup skin Bleomycin-treated rep2


title: Sup skin Bleomycin-treated rep1


title: P2120_N705-S505

last: Santamaria

address: C/Rosselló 149-153

institute: IDIBAPS

value: pMHCII-NPs


title: Pt12Dx_MALAT1.n.G3541A_XVseq

description: XV-seq


title: A937 cells grown for 6h at 37ºC [d113015.cdc20.1.6]

value: Nasmyth Lab

value: MATalpha, cdc20-1, ura3, trp1, leu2,  his3 , ade2, can1

tag: temperature


title: A937 cells grown for 4h at 37ºC [d113014.cdc20.1.4]


title: A2596 cells grown for 6h at 37ºC [d113021.cdc15.2.6]


title: Pt12Dx_NOTCH1.3pUTR_XVseq

description: XV-seq


title: Pt10Rel_CDKN2a.hom.deletion5_XVseq

description: XV-seq

value: Relapse

value: Yes


title: A937 cells grown for 2h at 37ºC [d113013.cdc20.1.2]


title: A40444 cells grown for 6h at 37ºC [d113012.cdc28.13.BCY.6]

value: Amon Lab

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, cdc28-13::URA, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: P2120_N705-S503

value: NOD


title: P2120_N705-S502


title: Pt10Rel_CDKN2a.hom.deletion3_XVseq

description: XV-seq

value: Bone marrow

value: Male


title: P2120_N705-S504


title: A40444 cells grown for 4h at 37ºC [d113011.cdc28.13.BCY.4]


title: IP skin Bleomycin-treated rep4


title: Pt10Rel_CDKN2a.hom.deletion2_XVseq

description: XV-seq


title: IP skin PBS-treated rep2


title: Pt10Rel_CDKN2a.hom.deletion1_XVseq

description: XV-seq


title: A40444 cells grown for 2h at 37ºC [d113010.cdc28.13.BCY.2]


title: P2120_N704-S507


title: IP skin Bleomycin-treated rep3


title: IP skin PBS-treated rep4


title: Pt10Rel_CDKN2a.hom.deletion4_XVseq

description: XV-seq


title: A39000 cells grown for 6h at 37ºC [d113009.cdc28.13.6]


title: Sup skin Bleomycin-treated rep4


title: IP skin PBS-treated rep1


title: P2120_N704-S517


title: IP skin PBS-treated rep3


title: A39000 cells grown for 2h at 37ºC [d113007.cdc28.13.2]


title: P2120_N704-S506


title: P2120_N704-S505


title: Pt10Rel_TET2.R1216_XVseq

description: XV-seq


title: Pt10Rel_TET2.S792_XVseq

description: XV-seq


title: A39000 cells grown for 4h at 37ºC [d113008.cdc28.13.4]


title: RNA-seq data of lug replicate3

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
ATAC-seq read adaptors were removed with trim_galore and then mapped to the Arabidopsis thaliana reference genome TAIR10 using Bowtie (-X 2000 -m 1).
Reads aligned to chloroplast and mitochondrial DNA were filtered out and duplicated reads were removed using SAMtools.
RNA-seq analysis: Cleaned short reads were aligned to reference genome tair10 by Bowtie2 (v2.1.0), and expression abundance was calculated by RSEM with default parameters68. Heatmaps were visualized with the R package pheatmap. To reduce false positive of differential expression, transcripts with less than 5 reads of all replicates in total were regarded as lowly expressed genes and have been removed in subsequent analysis. Differential expression analysis was conducted using edgeR. A threshold of p value < 0.05 and Fold Change > 2 were used to decide whether significant expression difference exists between samples.
ChIP-seq analysis: ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie (v1.1.2)70, allowing only uniquely mapping reads with 0 mismatches. Duplicated reads were removed by Samtools. ChIP-seq peaks were called by MACS2 (v2.1.1) and annotated with ChIPseeker71. Differential peaks were called by bdgdiff function in MACS2. ChIP-seq data metaplots were plotted by deeptools (v2.5.1)72. For Pol II 5’ occupancy analysis, Pol II occupancy was calculated based normalized reads count (RPKM) on a TSS +/- 200 bp region and a TSS +500 bp to TTS gene body region by bedtools.
Assembly: tair10

organism: Arabidopsis thaliana

source_name: RNA-seq data of lug

growth_protocol:
Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants
All Arabidopsis plants used in this study are in Columbia (Col-0) ecotype and were grown at 22°C in LD (16 hours light, 8 hours dark) conditions.

extract_protocol:
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).
ATAC-seq: Nuclei were subjected to transposition reaction with Tn5 (Illumina, cat. no. FC-121-1030). For transposition reaction, 25 µl of 2x DMF (66mM Tris-acetate (pH=7.8), 132 mM K-Acetate, 20mM Mg-Acetate, 32 % DMF) was mixed with 2.5 µl Tn5 and 22.5 µl nuclei suspension at 37 °C for 30 min. Transposed DNA fragments were purified with ChIP DNA Clean & Concentrator Kit (Zymo, cat. no. D5205). Libraries were preparated with Phusion High-Fidelity DNA Polymerase (NEB, cat. no. M0530S) (12.5µl 2x Phusion, 1.25µl 10 mM Ad1 primer, 1.25µl 10 mM Ad2 primer, 4 µl ddH2O and 6µl purified transposed DNA fragments).
Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
RNA-seq library preparation: Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
ChIP-seq library preparation: 10 grams of inflorescence and meristem tissues were used for Flag, HA, Pol II, H3, and H3K36me2/3 ChIP-seq. ChIP were performed as described previously60 with anti-FLAG M2 (Sigma), anti-HA (Roche), anti-Pol II (Ab26721, Abcam), anti-H3 (Ab1791, Abcam), anti-H3K36me2 (Ab9049, Abcam), and anti-H3K36me3 (Ab9050, Abcam) antibodies.

value: floral tissue

tag: developmental stage

value: 5-6 weeks

tag: cultviar

value: Ler


title: P2120_N704-S508

source_name: Tetramer+ CD4+ T cells

value: T cell


title: Pt10Rel_TET2.Q1034_XVseq

description: XV-seq

tag: Sex

tag: disease state


title: A40439 cells grown for 6h at 37ºC [d113006.WT.BCY.6]

value: MATa, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+, KanMX:pRFA1:9Myc-AID*-BCY1, leu2::pTEF1-osTIR::LEU2


title: P2120_N704-S504


title: RNA-seq data of lug replicate1


title: RNA-seq data of lug replicate2


title: P2120_N704-S503


title: Pt10Rel_TET2.H1380Y_XVseq

description: XV-seq

tag: bone marrow_involvement


title: IP skin Bleomycin-treated rep1

value: female

value: Balb/c


title: A40439 cells grown for 2h at 37ºC [d113004.WT.BCY.2]

value: yeast


title: Pt10Rel_RAB9A.3pUTR_XVseq

description: XV-seq


title: RNA-seq data of ler replicate3

source_name: RNA-seq data of ler


title: P2120_N704-S502

value: pMHCII-NPs


title: IP skin Bleomycin-treated rep2

value: 100 ul BLM


title: A40439 cells grown for 4h at 37ºC [d113005.WT.BCY.4]


title: RNA-seq data of ler replicate2


title: P2120_N703-S517


title: A2587 cells grown for 6h at 37ºC [d113003.WT.6]

value: Nasmyth Lab


title: Pt10Rel_CWF19L2.K221R_XVseq

description: XV-seq

value: Relapse

value: Yes


title: RNA-seq data of ler replicate1


title: P2120_N703-S507


title: RNA seq data of heat treatment hex T48 replicate2

source_name: RNA seq data of heat treatment hex 48 hours

value: heat


title: RNA seq data of heat treatment WT T48 replicate3

source_name: RNA seq data of heat treatment WT 48 hours


title: A2587 cells grown for 2h at 37ºC [d113001.WT.2]


title: A2587 cells grown for 4h at 37ºC [d113002.WT.4]


title: RNA seq data of heat treatment hex T48 replicate3


title: A33728 cells treated with rapamycin for 5h at 30ºC rep 2 [d139047.D_5h_2]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5nM rapamycin for 5 hours

value: Fink Lab

value: MATa/alpha, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+


title: Pt10Rel_DOLPP1.R227S_XVseq

description: XV-seq

value: Bone marrow

value: Male


title: P2120_N703-S508

value: NOD


title: Pt10Rel_HNRNPUL1.F559F_XVseq

description: XV-seq


title: A33728 cells treated with rapamycin for 5h at 30ºC rep 1 [d139046.D_5h]


title: RNA seq data of heat treatment WT T48 replicate2

value: floral tissue

value: 5-6 weeks


title: P2120_N703-S505

value: T cell


title: Pt10Rel_ASXL1.G642fs_XVseq

description: XV-seq


title: P2120_N703-S504


title: Pt10Rel_ACAP2.L97L_XVseq

description: XV-seq


title: A2587 cells treated with rapamycin for 5h at 30ºC rep 2 [d139045.H_5h_2]


title: P2120_N703-S503


title: RNA seq data of heat treatment hex T0.5 replicate2

source_name: RNA seq data of heat treatment hex 0.5 hours


title: A2587 cells treated with rapamycin for 5h at 30ºC rep 1 [d139044.H_5h]

source_name: yeast


title: Pt10Dx_CDKN2a.hom.deletion5_Xvseq

description: XV-seq

value: Diagnosis

value: No


title: Pt10Dx_CDKN2a.hom.deletion4_Xvseq

description: XV-seq


title: P2120_N703-S502


title: RNA seq data of heat treatment hex T0.5 replicate1


title: A33728 cells treated with rapamycin for 4h at 30ºC rep 2 [d139043.D_4h_2]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5nM rapamycin for 4 hours

value: yeast


title: A33728 cells treated with rapamycin for 4h at 30ºC rep 1 [d139042.D_4h]


title: RNA seq data of heat treatment WT T0.5 replicate3

source_name: RNA seq data of heat treatment WT 0.5 hours


title: P2120_N702-S517

value: pMHCII-NPs


title: Pt10Dx_CDKN2a.hom.deletion3_Xvseq

description: XV-seq


title: RNA seq data of heat treatment WT T0.5 replicate2


title: Pt10Dx_CDKN2a.hom.deletion1_Xvseq

description: XV-seq


title: A2587 cells treated with rapamycin for 4h at 30ºC rep 1 [d139040.H_4h]


title: P2120_N702-S507


title: P2120_N702-S506


title: RNA seq data of heat treatment WT T0.5 replicate1


title: RNA seq data of heat treatment hex T0 replicate3

source_name: RNA seq data of heat treatment hex 0 hours


title: A2587 cells treated with rapamycin for 4h at 30ºC rep 2 [d139041.H_4h_2]


title: P2120_N702-S508


title: RNA seq data of heat treatment WT T48 replicate1


title: A33728 cells treated with rapamycin for 3h at 30ºC rep 2 [d139039.D_3h_2]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5nM rapamycin for 3 hours


title: Pt10Dx_TET2.S792_XVseq

description: XV-seq


title: RNA seq data of heat treatment hex T0 replicate2


title: P2120_N702-S505


title: Pt10Dx_TET2.R1216_XVseq

description: XV-seq


title: A33728 cells treated with rapamycin for 3h at 30ºC rep 1 [d139038.D_3h]


title: RNA seq data of heat treatment hex T0 replicate1


title: P2120_N702-S504


title: A2587 cells treated with rapamycin for 3h at 30ºC rep 2 [d139037.H_3h_2]


title: Pt10Dx_TET2.H1380Y_XVseq

description: XV-seq


title: P2120_N702-S503


title: RNA seq data of heat treatment WT T0 replicate3

source_name: RNA seq data of heat treatment WT 0 hours


title: Pt10Dx_CDKN2a.hom.deletion2_Xvseq

description: XV-seq


title: A2587 cells treated with rapamycin for 3h at 30ºC rep 1 [d139036.H_3h]


title: Pt10Dx_TET2.Q1034_XVseq

description: XV-seq


title: P2120_N702-S502


title: RNA seq data of heat treatment WT T0 replicate1


title: P2120_N701-S517


title: Pt10Dx_RPS24.I25T_XVseq

description: XV-seq


title: A33728 cells treated with rapamycin for 2h at 30ºC rep 1 [d139034.D_2h]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5nM rapamycin for 2 hours


title: ChIP seq data of WT rep2

source_name: ChIP seq data of WT

value: Anti-flag (Abcam)

tag: target protein

value: Flag


title: Pt10Dx_RAB9A.3pUTR_XVseq

description: XV-seq


title: ChIP seq data of WT rep1


title: P2120_N701-S507


title: A2587 cells treated with rapamycin for 2h at 30ºC rep 1 [d139032.H_2h]

value: Nasmyth Lab


title: ChIP seq data of LUG in morchex

source_name: ChIP seq data of LUG in morchex


title: Pt10Dx_MAP4K5.P667S_XVseq

description: XV-seq


title: Pt10Rel_MAP4K5.P667S_XVseq

description: XV-seq

value: Relapse

value: Yes


title: A33728 cells treated with rapamycin for 1h at 30ºC rep 2 [d139031.D_1h_2]

growth_protocol: Log-phase culture grown at 30ºC in YEPD, treated with 5nM rapamycin for 1 hour

value: Fink Lab


title: P2120_N701-S506


title: ChIP seq data of LUG in WT

source_name: ChIP seq data of LUG in WT


title: Pt10Dx_SMARCD1.L456F_XVseq

description: XV-seq

source_name: Bone marrow


title: A33728 cells treated with rapamycin for 1h at 30ºC rep 1 [d139030.D_1h]

value: MATa/alpha, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+


title: Pt10Dx_HNRNPUL1.F559F_XVseq

description: XV-seq

value: Bone marrow


title: A33728 cells treated with rapamycin for 2h at 30ºC rep 2 [d139035.D_2h_2]


title: Pt10Dx_DOLPP1.R227S_XVseq

description: XV-seq

value: Male


title: P2120_N701-S505

value: NOD


title: RNA seq data of heat treatment WT T0 replicate2

value: floral tissue

value: heat


title: P2120_N701-S504

value: T cell


title: A2587 cells treated with rapamycin for 1h at 30ºC rep 2 [d139029.H_1h_2]


title: P2120_N703-S506


title: ChIP seq data of TPL in WT

source_name: ChIP seq data of TPL in WT

value: 5-6 weeks


title: Pt10Dx_CWF19L2.K221R_XVseq

description: XV-seq

value: Diagnosis

value: No


title: A2587 cells treated with rapamycin for 2h at 30ºC rep 2 [d139033.H_2h_2]

value: yeast


title: P2120_N701-S503

value: pMHCII-NPs


title: P2120_N701-S508


title: ATAC seq data of morchex replicate3

source_name: ATAC seq data of morchex


title: Pt10Dx_PRKDC.D3353N_XVseq

description: XV-seq


title: A2587 cells treated with rapamycin for 1h at 30ºC rep 1 [d139028.H_1h]


title: Pt10Dx_ASXL1.G642fs_XVseq

description: XV-seq


title: P2120_N701-S502


title: A33728 cells treated with rapamycin for 0h at 30ºC rep 2 [d139027.D_0h_2]

growth_protocol: Log-phase culture grown at 30ºC in YEPD


title: ATAC seq data of morchex replicate2


title: A33728 cells treated with rapamycin for 0h at 30ºC rep 1 [d139026.D_0h]


title: TF_Stim_rep3

description:
aCD3/CD28-stimulated Tetramer- T follicular (CXCR5+/PD-1+) CD4+ T cells from pMHCII-NP-treated NOD mice
Tet_TF_Basal_Stim_Raw_counts.xlsx

data_processing:
Contaminant rRNA filtering with Bowtie2 (2.2.5)
Mouse samples: Alignment with STAR 2.5.3a to the GENCODE  release 16 of the Mus musculus genome (mm10 assembly)
Human samples: Alignment with STAR 2.5.3a to the GENCODE  release 29 of the Homo sapiens genome (hg38 assembly)
Raw count of reads per gene was obtained with Partek “Quantify to annotation model (Partek E/M)” tool
Counts were normalized by CPM
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheets (xlsx) containing raw counts

source_name: Stimulated Tetramer- TF CD4+ T cells

extract_protocol:
RNA purification using Rneasy Mini kit (QIAGEN)
TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer's protocol (Illumina, San Diego, CA)

treatment_protocol: Samples are obtained from mice that have received intravenously 10 doses of pMHCII-NPs.  Stimulated cells have been cultured with aCD3/CD28 beads previous to RNA extraction.

value: pMHCII-NPs + Ex vivo a-CD3/CD28 stimulation


title: Pt10Dx_ACAP2.L97L_XVseq

description: XV-seq


title: Pt5Dx_ZRSR2.Y175_XVseq

description: XV-seq


title: TF_Stim_rep2


title: ChIP seq data of TPL in morchex

source_name: ChIP seq data of TPL in morchex

value: Anti-flag (Abcam)

value: Flag


title: A2587 cells treated with rapamycin for 0h at 30ºC rep 2 [d139025.H_0h_2]

value: Nasmyth Lab


title: ATAC seq data of morchex replicate1


title: Pt5Dx_TET2.N281fs_XVseq

description: XV-seq


title: TF_Stim_rep1


title: TF_Basal_rep3

description:
Unstimulated Tetramer- T follicular (CXCR5+/PD-1+) CD4+ T cells from pMHCII-NP-treated NOD mice
Tet_TF_Basal_Stim_Raw_counts.xlsx

source_name: Unstimulated Tetramer- TF CD4+ T cells


title: A33728 cells grown for 24h at 30ºC rep 2 [d139023.D_24h_2]

growth_protocol: 24 hours growth at 30ºC in YEPD

value: Fink Lab


title: ATAC seq data of morc6 replicate3

source_name: ATAC seq data of morc6


title: A2587 cells treated with rapamycin for 0h at 30ºC rep 1 [d139024.H_0h]


title: ATAC seq data of morc6 replicate2


title: Pt5Dx_TET2.V1395fs_XVseq

description: XV-seq


title: TF_Basal_rep2


title: Pt1Rem_TET2.Q960_XVseq

description: XV-seq

value: Remission


title: A33728 cells grown for 24h at 30ºC rep 1 [d139022.D_24h]

value: MATa/alpha, ade2-1, leu2-3, ura3, trp1-1, his3-11,15, can1-100, GAL, psi+


title: ATAC seq data of morc6 replicate1


title: TF_Basal_rep1


title: ATAC seq data of morc47 replicate3

source_name: ATAC seq data of morc47


title: Pt1Rem_SMARCC1.3pUTR_XVseq

description: XV-seq

value: Bone marrow

value: Male


title: A2587 cells grown for 24h at 30ºC rep 2 [d139021.H_24h_2]


title: ATAC seq data of morc47 replicate2

value: floral tissue


title: Tet_Stim_rep3

description:
aCD3/CD28-stimulated Tetramer+ CD4+ T cells from pMHCII-NP-treated NOD mice
Tet_TF_Basal_Stim_Raw_counts.xlsx

source_name: Stimulated Tetramer+ CD4+ T cells

value: NOD


title: Pt1Rem_SETX.3pUTR_XVseq

description: XV-seq


title: A2587 cells grown for 24h at 30ºC rep 1 [d139020.H_24h]


title: Pt1Rem_FAM98C.G228S_XVseq

description: XV-seq


title: Tet_Stim_rep2

value: T cell


title: A33728 cells grown for 10h at 30ºC rep 2 [d139019.D_10h_2]

growth_protocol: 10 hours growth at 30ºC in YEPD


title: ATAC seq data of col replicate2

source_name: ATAC seq data of col

value: 5-6 weeks


title: Pt1Rem_ASXL1.L697fs_XVseq

description: XV-seq


title: ATAC seq data of morc47 replicate1


title: Tet_Stim_rep1


title: A33728 cells grown for 10h at 30ºC rep 1 [d139018.D_10h]

source_name: yeast


title: Tet_Basal_rep3

description:
Unstimulated Tetramer+ CD4+ T cells from pMHCII-NP-treated NOD mice
Tet_TF_Basal_Stim_Raw_counts.xlsx

source_name: Unstimulated Tetramer+ CD4+ T cells


title: ATAC seq data of col replicate1


title: Tet_Basal_rep2


title: A2587 cells grown for 10h at 30ºC rep 1 [d139016.H_10h]


title: Pt1Dx_SETX.3pUTR_XVseq

description: XV-seq

value: Diagnosis

value: Yes


title: Pt1Dx_SMARCC1.3pUTR_XVseq

description: XV-seq