title: Donor 11 CD8 T cells CMV.E HELIOS NEG NS


title: AG04441 late passage replicate 2

status: Public on Nov 27 2023

type: SRA

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

country: USA

institute: NIH

library_source: genomic

data_processing:
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For nascent strand peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: T2T
Supplementary files format and content: Bed file format of replication origin peaks
Supplementary files format and content: BigWig file format of replication origin locations
Library strategy: NS-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Skin

growth_protocol: Fibroblasts were grown in MEM medium, 15% FBS

extract_protocol:
DNA from cell cultures was isolated, size fractionated and subject to exonuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of NS samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S).

treatment_protocol: Fibroblast cells were immortalized by human Telomerase Reverse Transcriptase protein (hTERT). Cells were then cultured on a cover glass and treated with and without EX527 (1uM for 48hr). The SIRT1 gene was deleted from the cancer cell lines using CRISPR-Cas9 targeting exon1.

tag: tissue

value: Skin

tag: cell line

tag: cell type

value: Human skin fibroblast

tag: treatment

value: late passage


title: Eif4enif1+/-_arrested_1cell_1

city: Beijing

first: Yuxi

last: Ding

address: D110, Medical Building, 30 Shuangqing Road

country: China

institute: Tsinghua University

description:
ar4
embryo_RNA_count_matrix

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters -q 20 --phred33 --stringency 3 -j 32 --length 50 -e 0.1.
Reads were mapped to  mm10 whole genome using Hisat2 (v2.1.0) with default parameters.
Gene count was calculated using Featurecounts (v1.6.5) with parameters -T 32 -O -t exon -M --extraAttributes gene_name
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: arrested 1-cell embryo

extract_protocol:
For T&T seq transcriptome and RNA-seq data,mRNA was extracted by lysing oocytes or embryos in lysis buffer for direct reverse transcription  Vazyme Single Cell Full Length mRNA-Amplification Kit. For T&T-seq translatome data, ribosome-bound mRNAs were extracted using RiboLace Module 1 Kit following manufacturer's  guidelines and purified using VAHT RNA clean beads. The purified mRNAs were then reverse transcribed with Vazyme Single Cell Full Length mRNA-Amplification Kit. cDNAs were purified using VAHT DNA clean beads.
DNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's instructions.

value: arrested 1-cell embryo

tag: genotype

value: in vitro cultured for 24 hours


title: Donor 11 CD8 T cells CMVA2.B7 HELIOS NEG OKT3

city: Woluwé-Saint-Lambert

first: Damien

last: Neyens

state: Bruxelles

address: Avenue Hippocrate 74

country: Belgium

institute: De Duve Institute

data_processing:
Quality control
Files were trimmed with trimmomatic
alignet to GRCh38 human genome with HISAT2
Read counts were determined with featuresCount
Normalization of read counts and analysis of differentially expressed genes were performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: Count_Helios_normalized.csv (CSF format with normalized read count of each sample included in the  experiment)
Supplementary files format and content: Count_Subpop_Helios_normalized.csv (CSF format with normalized read count of each sample included in the  experiment)
Supplementary files format and content: Count_Tetramer_Helios_normalized.csv (CSF format with normalized read count of each sample included in the  experiment)

source_name: Blood

extract_protocol:
RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (ref AM1975 Thermo Fisher Scientific)
SMART-Seq (Nextera XT DNA Library Preparation Kit (96 samples)  FC-131-1096, Illumina)

treatment_protocol: 5h coated anti-CD3 (clone OKT3 1ug/ml) activation

value: Blood

value: CD8 T cells

tag: marker

value: HELIOS NEG

tag: stimulation

tag: tetramer


title: Donor 11 CD8 T cells CMVA2.B7 HELIOS NEG NS

value: NS


title: AG12851 with hTERT and ex527 replicate 1

value: AG12851 with hTERT and ex527


title: Eif4enif1+/-_2cell_3

description:
HT10
embryo_RNA_count_matrix

source_name: 2-cell embryo

value: 2-cell embryo


title: AG04446 with hTERT and ex527 replicate 1

value: with hTERT and ex527


title: AG04446 with hTERT replicate 2

value: with hTERT


title: O_iPSC_SOX2_17_1

city: Boston

first: Sergiy

last: Velychko

state: MA

address: 77 Avenue Louis Pasteur, Room 232

department: Genetics

institute: Harvard Medical School

data_processing:
NEBNExt ultra Directional RNA Kit with polyA enrichment was used for library preparation. Reads were aligned to the reference genome using CLC Genomics Workbench 12.0
Supplementary files format and content: TPM

source_name: iPSC

extract_protocol: RNA-seq and RRBS were performed for human iPSC at passage 10-12, human ESCs (H6 and H9) at passage 35-36 grown in StemFlex media on Matrigel.

value: iPSC

tag: sox variant

tag: Sex

value: male


title: O_iPSC_AV_5


title: Eif4enif1+/-_2cell_2

description:
HT11
embryo_RNA_count_matrix


title: Donor 11 CD8 T cells CMV.E HELIOS POS NS

value: HELIOS POS


title: AG04446 with hTERT replicate 1


title: O_iPSC_AV_4


title: AG04446 early passage with ex527 replicate 2

value: early passage with ex527


title: O_iPSC_AV_3


title: WT_2cell_3

description:
WT16
embryo_RNA_count_matrix

value: WT


title: Donor 10 CD8 T cells CMV.E HELIOS NEG OKT3


title: AG04446 early passage with ex527 replicate 1

value: Skin

value: Human skin fibroblast


title: O_iPSC_AV_2


title: Donor 10 CD8 T cells CMV.E HELIOS NEG NS


title: WT_2cell_2

description:
WT14
embryo_RNA_count_matrix


title: O_iPSC_SOX2_17_2


title: O_iPSC_AV_1


title: AG04446 late passage replicate 2

value: late passage


title: WT_2cell_1

description:
WT13
embryo_RNA_count_matrix

value: in vitro cultured for 24 hours


title: Donor 10 CD8 T cells CMVA2.B7 HELIOS NEG OKT3

value: Blood


title: AG04446 late passage replicate 1


title: WT_1cell_3

description:
c882
embryo_RNA_count_matrix

source_name: 1-cell embryo

value: 1-cell embryo


title: Donor 10 CD8 T cells CMV.E HELIOS POS OKT3

value: CD8 T cells


title: O_iPSC_WT_5


title: AG04446 early passage replicate 2

value: early passage


title: WT_1cell_2

description:
c881
embryo_RNA_count_matrix


title: AG04446 early passage replicate 1


title: O_iPSC_WT_3


title: Eif4enif1+/-_2cell_1

description:
HT19
embryo_RNA_count_matrix


title: Donor 10 CD8 T cells CMV.E HELIOS POS NS

value: NS


title: Donor 9 CD8 T cells CD161 POS HELIOS NEG OKT3

value: CD161 POS HELIOS POS


title: AG04441 late passage replicate 1


title: WT_1cell_1

description:
c64
embryo_RNA_count_matrix


title: O_iPSC_WT_2


title: Donor 10 CD8 T cells CMVA2.B7 HELIOS NEG NS

value: HELIOS NEG


title: Donor 9 CD8 T cells TBET high HELIOS POS OKT3

value: TBET high HELIOS POS


title: Eif4enif1+/-_1cell_3

description:
c66
embryo_RNA_count_matrix


title: Donor 9 CD8 T cells CD161 POS HELIOS NEG NS


title: O_Fibs

data_processing:
For RRBS analysis Fastq files were trimmed with Trim Galore (bioinformatics.babraham.ac.uk/projects/trim_galore/) flagging the options --RRBS. The trimmed fastq files were aligned to GRCh38 using bwameth (github.com/brentp/bwa-meth) and methylation metrics were extracted using MethylDackel (https://github.com/dpryan79/ MethylDackel), flagging the options --minDepth 10. The genomic coordinates of known imprinted DMRs were converted to GRCh38 using the LiftOver tool from UCSC and the methylation levels of CpGs within these regions were extracted with bedtools intersect (bedtools.readthedocs.io/en/latest/content/tools/intersect.html). Finally, the mean methylation level for all CpGs of a given DMR was calculated. The several DMRs corresponding to SNRPN were collapsed as well. Only DMRs which were represented by all samples were taken into consideration for the comparative LOI analysis. A DMR was considered to lose imprinting if it showed less than 30% mean methylation levels.
Supplementary files format and content: bed

source_name: 56yo Male Dermal fibroblast

extract_protocol:
RNA-seq and RRBS were performed for human iPSC at passage 10-12, human ESCs (H6 1and H9) at passage 35-36 grown in StemFlex media on Matrigel.
Zymo-Seq RRBS Library Kit (Zymo Research, D5461)

value: 56yo Male Dermal fibroblast


title: O_iPSC_WT_1

value: iPSC

value: male


title: Eif4enif1+/-_1cell_2

description:
c65
embryo_RNA_count_matrix


title: Eif4enif1+/-_1cell_1

description:
c62
embryo_RNA_count_matrix


title: Y_Fibs

source_name: Newborn Foreskin fibroblast

value: Newborn Foreskin fibroblast


title: purified plasma cells from the myeloma patient RP1 cultured and treated with vehicle

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
scRNA-seq libraries were sequenced using a NextSeq 500 150-cycle flow cell (Illumina).
Rraw reads were aligned to the  human genomes (hg38), and the digital expression matrix was generated using cellranger count. Individual samples were merged to generate the digital expression matrix using cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: raw count expression matrix in h5 format.

source_name: BM

extract_protocol: For scRNA-seq, sample preparation and sequencing were performed at MD Anderson Cancer Center’s Advanced Technology Genomics Core. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10X Genomics, Pleasanton, CA), and single cells were lysed and barcoded for reverse transcription.

treatment_protocol: JJN3 cells were treated with 1 µM NT or ILF2 ASOs for 3 weeks. In parallel experiments JJN3 cells exposed to 1 µM NT or ILF2 ASOs for 3 weeks were treated with vehicle or 1 µM NSC for 48 hours. Primary PCs were treated with 2 µM NSC for 48 hours. Live cells were sorted by flow cytometry and subjected to scRNA-seq analysis.

value: primary myeloma plasma cells

value: cells treated with Vehicle


title: Donor 9 CD8 T cells TBET high HELIOS POS NS


title: hESC_H9

source_name: ESC

value: ESC

value: female


title: O_iPSC_WT_4


title: WT_2_transcription

description:
105-Z
GV_T&T_count_matrix

source_name: GV oocyte

value: GV oocyte

value: WT


title: Donor 9 CD8 T cells TBET high HELIOS NEG NS

value: Blood

value: TBET high HELIOS NEG


title: purified plasma cells from the myeloma patient RD192 cultured and treated with vehicle

value: normal karyotype and 1q21 amplification


title: WT_2_translation

description:
105-F
GV_T&T_count_matrix


title: Donor 9 CD8 T cells TBET intlow HELIOS POS OKT3

value: CD8 T cells

value: TBET intlow HELIOS POS


title: WT_1_transcription

description:
104-Z
GV_T&T_count_matrix


title: purified plasma cells from the myeloma patient RP1 cultured and treated with NSC

value: cells treated with NSC


title: purified plasma cells from the myeloma patient RD192 cultured and treated with NSC


title: Donor 9 CD8 T cells TBET intlow HELIOS POS NS

value: NS


title: hESC_H6


title: O_iPSC_SS_4


title: Donor 9 CD8 T cells TBET intlow HELIOS NEG OKT3

value: TBET intlow HELIOS NEG


title: WT_1_translation

description:
104-F
GV_T&T_count_matrix


title: O_iPSC_SS_3

value: iPSC


title: Eif4enif1+/-_2_transcription

description:
57-Z
GV_T&T_count_matrix


title: Donor 9 CD8 T cells TBET intlow HELIOS NEG NS


title: purified plasma cells from the myeloma patient RD177 cultured and treated with NSC


title: Donor 9 CD8 T cells TBET high HELIOS NEG OKT3


title: Eif4enif1+/-_2_translation

description:
57-F
GV_T&T_count_matrix


title: JJN3 cells treated with NT ASOs replicate 2

value: myeloma cell line

value: cells treated with NTASOs


title: Donor 3 CD8 T cells CD161 POS HELIOS NEG OKT3

value: CD161 POS HELIOS POS


title: O_iPSC_SS_1

value: male


title: Donor 3 CD8 T cells CD161 POS HELIOS NEG NS


title: JJN3 cells treated with NT ASOs replicate 1


title: O_iPSC_AV_5


title: O_iPSC_SS_5


title: Eif4enif1+/-_1_translation

description:
55-F
GV_T&T_count_matrix


title: JJN3 cells treated with NT ASOs and vehicle

value: cells treated with NT ASOs and vehicle


title: Donor 3 CD8 T cells TBET high HELIOS POS NS

value: TBET high HELIOS POS


title: O_iPSC_AV_3


title: purified plasma cells from the myeloma patient RD177 cultured and treated with vehicle

value: primary myeloma plasma cells

value: cells treated with Vehicle


title: O_iPSC_AV_4


title: JJN3 cells treated with ILF2 ASOs replicate 1

value: cells treated with ILF2 ASOs


title: Donor 3 CD8 T cells TBET high HELIOS POS OKT3

value: Blood


title: O_iPSC_SS_2


title: Donor 3 CD8 T cells TBET high HELIOS NEG OKT3

value: TBET high HELIOS NEG


title: JJN3 cells treated with NT ASOs and NSC

value: cells treated with NT ASOs and NSC


title: Donor 3 CD8 T cells TBET high HELIOS NEG NS

value: CD8 T cells


title: O_iPSC_AV_2


title: O_iPSC_AV_1


title: O_iPSC_WT_5


title: O_iPSC_SOX2_17_3


title: JJN3 cells treated with ILF2 ASOs and NSC

value: cells treated with ILF2 ASOs and NSC


title: JJN3 cells treated with ILF2 ASOs and vehicle


title: JJN3 cells treated with ILF2 ASOs replicate 2


title: O_iPSC_WT_4


title: Donor 3 CD8 T cells TBET intlow HELIOS NEG OKT3


title: Donor 3 CD8 T cells TBET intlow HELIOS POS NS

value: TBET intlow HELIOS POS

value: NS


title: IVT11-5-17585

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description: RNA-seq

data_processing:
RNA-sequencing reads were aligned with Hisat2 version 2.0.4 to the provided and pre-indexed hg38 transcript assembly from UCSC, with alignment tailoring for transcript assemblersenabled. Samtools was used to filter reads with a quality score lower than 20, and PCRduplicates were removed with Picard. Reads per gene were counted with the htseq-countscript from the Hisat2 software suite using the GTF file corresponding to the transcriptassembly, with reverse strandness enabled and identification attribute set to gene_id.Differential gene expression analysis was performed with the DESeq2 package version1.18.1. Genes with no reads mapped in any of the samples were filtered prior to differentialexpression analysis. The ‘rlogTransformation’ function in DESeq2 was used to normalize,transform and noise-stabilize the expression data for visualization purposes.
ChIP sequencing data was aligned to human genome hg19 with BWA. Samtools was usedto filter reads with a quality score lower than 20, and PCR duplicates were removed with Picard. Peaks were identified with MACS 2.2.6 in paired-end mode and ‘call-summits’enabled at a false discovery rate of 0.01. A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in each sample. Read counts wereanalyzed with DESeq2 to identify significant dynamics, as described for the RNA-seq analysis.
Genome_build: RNA-seq: hg38, ChIP-seq: hg19
Supplementary_files_format_and_content: RNA-seq: read counts per transcript, ChIP-seq: bigwig files

molecule: total RNA

source_name: monocytes from healthy donor

growth_protocol: PBMCs were isolated by differential centrifugation over Ficoll-Paque (Lymphoprep, Stemcell Technologies). Cells were washed three times in PBS. PBMCs and monocytes were resuspended in RPMI culture medium supplemented with 2mM glutamax, 1mM pyruvate and penicillin/streptomycin (all from Thermo Fisher Scientific) and counted on a Casy counter. Monocytes were isolated using negative MACS isolation with the Pan monocyte isolation kit (Miltenyi Biotech). Briefly, stimulated PBMCs were washed with PBS and incubated with versene solution (0.48mM EDTA, Sigma Aldrich) for 30 minutes at 37 °C. Cells were scraped from the plates, counted, spun down and resuspended in MACS isolation buffer (PBS with 0.5% BSA and 2mM EDTA).

extract_protocol:
For RNA isolation 1*106 isolated monocytes were resuspended in 350 μl of RNA later Buffer (Qiagen). RNA was isolated using RNeasy kit (Qiagen) including DNAseI (Qiagen) digestions. For ChIP-seq, isolated monocytes were resuspended in RPMI culture medium and fixed using formaldehyde (1% final concentration, Sigma Aldrich) for 10 minutes at room temperature. Unreacted formaldehyde was quenched with 125 mM glycine and incubated for 5 minutes at room temperature. Cells were washed twice in PBS containing protease inhibitor cocktail (Roche) and 1 mM PMSF (Roche), and subsequently snap frozen in liquid nitrogen. Cell pellets were stored at -80 °C for further use. Cells were sonicated at a concentration of 15 million cells/ml using a Bioruptor pico sonicator (Diagenode; 10 cycles, 30s on, 30s off, at 4 °C). Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore) according to manufacturer’s instruction. In short, 500,000 cells were incubated overnight with 1 μg H3K4me3 or H3K27Ac antibody (Diagenode) and protein A magnetic beads at 4 °C. Beads and chromatin/antibody mixture were washed four times for 5 minutes at 4 °C. After washing chromatin was eluted and proteins were degraded using proteinase K. DNA was purified using spin columns and eluted in millliQ.
Total RNA isolated from monocytes was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems). In short, oligo hybridization and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94⁰ C for 6 min. First strand synthesis, second strand synthesis and A-tailing was performed according to protocol. For the adapter ligation, a 1.5 μM stock was used (NextFlex DNA barcodes, Bioo Scientific). First and second post-ligation cleanup was performed according protocol. A total of 11 PCR cycles were performed for library amplification. The library amplification cleanup was done using a 0.8x followed by a 1.0x beadbased cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer kit, and the library concentration was measured using the dsDNA High Sensitivity Assay  17 (Denovix). Paired-end sequencing reads of 50 bp were generated using an Illumina NextSeq 500.   ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications. 2.5 μL of the NEXTflex adapter stock (600 nM, Bioo Scientific) was used for adapter ligation of each sample. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up was used to ensure proper removal of adapters. Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced to a read length of 50 bp on an Illumina NextSeq500.

treatment_protocol: Human PBMCs were trained as described before. In short, 500.000 PBMCs were added into 96-well flat bottom plates. Cells were allowed to adhere for 1h at 37°C. Cells were washed three times with PBS prior to stimulations. After washing cells were incubated with culture medium only as negative control (1), untreated (2),  treated with Rapamycin (3) or Ceranib (4) for 1 hour at 37°C. Subsequently cells were incubated with HKCA for 24 hours together with the respective treatment (untreated, Ceranib or Rapamycin)for 24 hours at 37°C. Subsequently, cells were washed and cells were rested for five days in RPMI culture medium containing 10% FBS.

value: monocytes

value: HKCA+Ceranib

tag: chip antibody


title: O_iPSC_WT_2

value: iPSC


title: Donor 3 CD8 T cells TBET intlow HELIOS NEG NS

value: TBET intlow HELIOS NEG


title: Eif4enif1+/-_1_transcription

description:
55-Z
GV_T&T_count_matrix

value: GV oocyte


title: IVT10-5-17586

description: RNA-seq


title: Donor 8 CD8 T cells CD161 POS HELIOS NEG OKT3

value: CD161 POS HELIOS POS


title: IVT13-4-17587

description: RNA-seq

value: HKCA+Rapamycin


title: O_iPSC_WT_1

value: male


title: Donor 8 CD8 T cells CD161 POS HELIOS NEG NS


title: IVT11-4-17588

description: RNA-seq


title: Y_iPSC_SS_5


title: Donor 3 CD8 T cells TBET intlow HELIOS POS OKT3


title: Conditioned Media (CM3)

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

data_processing:
Illumina CASAVA performed base-calling of Illumina NovaSeq 6000, 150-base paired-end data producing FASTQ files
Data processed using standard Novogene mRNA-seq Service protocol.
Perform alignments with HISAT2 v2.0.5 to the reference.
Assembly: mm10
Supplementary files format and content: Linear normalized FPKM matrix, contains zero values

source_name: Tppp3+ cells

growth_protocol: Lumbar DRGs from three 12-wk-old male C57BL/6J mice were isolated and kept in cold αMEM with 10% FBS and 1x penicillin/streptomycin33.  DRGs were then digested with 1 mg/ml type I collagenase (Thermo Fisher Scientific) and 5 mg/ml dispase II (Thermo Fisher Scientific) in αMEM at 37°C for 70 min, and dissociated into single cells by trituration with a 1-ml pipette tip.  The dissociated cells were filtered with a 70-μm cell strainer and centrifuged at 500 rcf for 5 min.  Cells were immediately mixed with pre-warmed αMEM with 5% FBS, 1x penicillin/streptomycin, 1x Glutamax (Thermo Fisher Scientific), and anti-mitotic reagents (20 μM 5-fluoro-2-deoxyuridine and 20 μM uridine, Sigma-Aldrich) and 10.000 cells were seeded into 12-well plates pre-coated with 100 μg/ml poly-D-lysine (Sigma-Aldrich) and 10 μg/ml laminin (Thermo Fisher Scientific).  Next, to generate conditioned media, DRGs were allowed to grow for 4-5 d to expend their axonal network. The media was then changed to aMEM, 1%FBS, 1%PS.  Neural conditioned medium was harvested every day, filtered (0.22 µm) and frozen at -80 °C until use. Achilles tendons from three 12-wk-old male Tppp3ECE/+;R26RtdT-CreERT2;Scx-GFP  mice were dissected and dissociated in 3 mg/ml collagenase I (Worthington), 4 mg/ml dispase II (Roche) in PBS for 1.5 h at 180 r.p.m. at 37 °C36.  Samples were then lightly triturated with sterilized Pasteur pipettes (VWR), run through a 40 μm filter (VWR) and rinsed with 3 ml αMEM (Gibco) with 20% FBS, 1%PS.  Cells were centrifuged at 300g for 30 min at 4 °C.  The cell pellet was washed twice with 1 ml PBS and spun for 10 min at 300g at 4 °C.  Cells were resuspended in FACS buffer (1% BSA, 1 mM EDTA in PBS).  Cell concentration and viability (by Trypan blue exclusion) were confirmed using a Countess II Automated Cell Counter (Thermo Fisher Scientific) and hemocytometer (VWR).  Cells were distinguished by forward and side scatter, and sorting was gated using FITC-A (GFP) and PE-A (tdT) filters.  tdT sorted cells were cultured in αMEM, 2 mM GlutaMax, 10% FBS and 100 U ml-1 penicillin–streptomycin (Gibco) until they reached 75% confluence the  treated with neural conditioned medium or unconditioned medium. After 24h, we proceeded with an MTS assay.  For total RNA sequencing, Tppp3+ cells were treated with neural conditioned medium or unconditioned medium for 24 h, and RNA isolated with the GenElute™ Single Cell RNA Purification Kit (Sigma).  After purification, total RNA was sequenced with the Illumina NextSeq 500 Mid 1x75bp platform (Illumina, CA,USA).  Data were analyzed using software packages including Partek Genomics Suite (RRID: SCR_011860), Spotfire Decision Site with Functional Genomics (RRID: SCR_008858).  Three technical replicates were used for each group.

extract_protocol:
RNA extraction was performed using GenElute™ Single Cell RNA Purification Kit
Novagen protocol. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Tppp3+ cells were treated with 1% FBS or DRG CM -for 24 h

value: Tppp3+ cells

value: Dorsal Root Ganglion (DRG) CM


title: Donor 8 CD8 T cells TBET high HELIOS POS OKT3

value: Blood

value: TBET high HELIOS POS


title: Conditioned Media (CM2)


title: Donor 8 CD8 T cells TBET high HELIOS POS NS


title: Y_iPSC_SS_3


title: IVT13-5-17584

description: RNA-seq


title: Conditioned Media (CM1)


title: Y_iPSC_SS_4


title: Donor 8 CD8 T cells TBET high HELIOS NEG OKT3

value: TBET high HELIOS NEG


title: O_iPSC_WT_3


title: IVT13-2-17593

description: RNA-seq

value: HKCA


title: Control 3


title: Donor 8 CD8 T cells TBET high HELIOS NEG NS

value: CD8 T cells


title: IVT11-2-17594

description: RNA-seq


title: Y_iPSC_SS_1


title: IVT10-4-17589

description: RNA-seq


title: Y_iPSC_AV_5


title: Control 1


title: IVT13-1-17596

description: RNA-seq

value: untreated


title: Donor 8 CD8 T cells TBET intlow HELIOS POS OKT3

value: TBET intlow HELIOS POS


title: Donor 8 CD8 T cells TBET intlow HELIOS POS NS

value: NS


title: C980-WT

city: San Antonio

first: QIANJIN

last: GUO

email: guoq1@uthscsa.edu, dahia@uthscsa.edu

state: TX

address: 7703 Floyd Curl Dr

institute: UTHSCSA

description: 10x Genomics

library_source: transcriptomic single cell

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

source_name: adrenal glands

extract_protocol:
The ‘tween with salts and tris’ (TST) method (Drokhlyansky et al., 2019; Slyper et al., 2020) was used to isolate nuclei.  A pair of mouse whole adrenals were placed into a well of a 6-well plate on ice with 1 ml of TST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 21 mM MgCl2, 1 mM CaCl2, 0.03% Tween-20, 0.01% BSA in nuclease-free water). Tissue was then chopped using scissors for 10 min. The homogenized solution was then filtered through a 70 µm Falcon cell strainer, and additional 1 ml TST buffer was used to wash the cell strainer. Additional TST buffer was added to bring the total volume up to 5 ml. Sample was transferred into a 15 ml conical tube and centrifuged at 500g for 5 min at 4 °C in a swinging bucket centrifuge, and the pellet was suspended in ST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 21 mM MgCl2, 1 mM CaCl2 in nuclease-free water). The nuclei solution was filtered through a 35 µm Falcon cell strainer twice, stained with 4′9,6-diamidino-2-phenylindole (DAPI) and directly sorted using Flow Activated Nuclei/Cell Sorting with a FACSAriaII instrument.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: KO

value: Female

value: adrenal glands

tag: strain

value: C57BL/6 J

tag: age

value: 10-11 months old


title: Y_iPSC_SS_2

value: iPSC


title: IVT11-1-17597

description: RNA-seq

value: monocytes


title: IVT10-1-17598

description: RNA-seq


title: C973-WT

description: 10x Genomics

value: WT


title: C916-KO

description: 10x Genomics


title: Y_iPSC_AV_1

value: male


title: C979-WT

description: 10x Genomics


title: Donor 7 CD8 T cells CD161 POS HELIOS NEG OKT3

value: Blood

value: CD161 POS HELIOS POS


title: CP-IVT13-5-K4-ChIP-18182

description: H3K4me3 ChIP-seq

value: HKCA+Ceranib


title: Donor 7 CD8 T cells CD161 POS HELIOS NEG NS


title: Y_iPSC_WT_5


title: CP-IVT13-5-K27-ChIP-18177

description: H3K27ac ChIP-seq


title: C935-WT

description: 10x Genomics


title: IVT10-2-17595

description: RNA-seq

value: HKCA


title: Y_iPSC_AV_2


title: CP-IVT13-4-K27-ChIP-18178

description: H3K27ac ChIP-seq

value: HKCA+Rapamycin


title: Donor 7 CD8 T cells TBET high HELIOS POS OKT3

value: CD8 T cells

value: TBET high HELIOS POS


title: Y_iPSC_WT_4


title: Y_iPSC_AV_4


title: C934-KO

description: 10x Genomics


title: Donor 8 CD8 T cells TBET intlow HELIOS NEG OKT3

value: TBET intlow HELIOS NEG


title: CP-IVT13-4-K4-ChIP-18183

description: H3K4me3 ChIP-seq


title: Donor 8 CD8 T cells TBET intlow HELIOS NEG NS

value: NS


title: Donor 7 CD8 T cells TBET high HELIOS POS NS


title: Control 2

value: Tppp3+ cells


title: Y_iPSC_WT_3


title: CP-IVT13-2-K27-ChIP-18180

description: H3K27ac ChIP-seq


title: Cdx1 mutant organoid line 1: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen

city: San Francisco

first: Rachel

middle: Klapper

last: Zwick

address: 513 Parnassus Ave.

institute: University of California, San Francisco

data_processing:
kallisto v. 0.46.0 with standard parameters in paired-end mode was used to obtain abundance measurements from the fastq files
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include transcript length and effective length as well as estimated counts and TPM values for each sample.

source_name: Primary murine organoids from distal small intestine

growth_protocol: Single intestinal epithelial cells were FACs sorted into matrigel-coated plates, and cultured into organoids as described in Sato et al. Nature 2009.  Organoids were propagated  for several passages prior to collection.

extract_protocol:
Organoids were washed with PBS and resuspended in TRI reagent containing 1% 2-Mercaptoethanol. RNA was extracted using Direct-zol RNA Miniprep Plus (Zymo Research).
Prepared by Novogene
Illumina, PE150, 20M Paired Reads

value: Intestinal epithelial cells

value: Lgr5creERT2; Rosa26 LSL-Cas9-eGFP/+; ROSA26tdTomato

tag: time

value: long-term organoid culture seeded with adult intestinal stem cells

tag: organoid type

value: Cdx1 mutant organoid line 1


title: Dual guide RNA targeting Cdx1 infected, untreated, control organoids

value: Primary murine organoids from distal small intestine

value: control organoids


title: CP-IVT13-2-K4-ChIP-18185

description: H3K4me3 ChIP-seq

value: monocytes


title: Y_iPSC_WT_2

value: iPSC

value: male


title: Ppard mutant organoid line 1: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen, 2

value: Ppard mutant organoid line 1


title: Donor 7 CD8 T cells TBET high HELIOS NEG OKT3

value: Blood

value: TBET high HELIOS NEG


title: CP-IVT13-1-K27-ChIP-18181

description: H3K27ac ChIP-seq

value: untreated


title: Y_iPSC_AV_3


title: Y_iPSC_WT_1


title: SCA1_10

city: New Haven

first: Changwoo

last: Lee

state: CT

address: 295 Congress

department: Neuroscience

institute: Yale University

description:
10x Genomics
CNGA-0061

data_processing:
CellRanger (mouse, v6.1.2; human, v7.0.0)
Preprocessing quality control including doublet detection using Scrublet
Normalization and square root transformation
BBKNN batch correction
Cell type annotation
Assembly: mm10 or GRCh38
Supplementary files format and content: h5ad files

molecule: nuclear RNA

source_name: Cerebellar cortex

extract_protocol:
Nuclei were isolated from frozen tissue as previously described.10 For mouse snRNA-seq, hemicerebella of three animals per genotype (WT and SCA1 KI) per timepoint (5, 12, 18, 24, and 30 weeks) were used, for a total of 30 animals. For human post-mortem samples, pieces of cerebellar cortex were harvested from frozen tissue of ten unique individuals per diagnosis (CTRL and SCA1), for a total of 20 human samples. Briefly, frozen mouse or human tissue was gently dounce homogenized in 2mL of ice-cold Nuclei EZ Prep buffer (Sigma; NUC101-1KT) with large clearance pestle “A” and then a small clearance pestle “B” for 25 strokes each, then incubated on ice for five minutes with an additional 2mL of cold EZ Prep buffer. Nuclei were centrifuged at 500xg for five minutes at 4°C. Pelleted nuclei were then washed in 4mL of cold EZ Prep buffer, incubated on ice at five minutes, and centrifuged again at 500xg for five minutes at 4°C. Pelleted nuclei were then washed in 4mL of Nuclei Suspension Buffer (NSB) containing 1x phosphate buffered saline (PBS), 0.01% BSA, and 0.1% RNase inhibitor (Clontech/Takara; 2313B) and centrifuged at 500xg for five minutes at 4°C. Finally, nuclei were resuspended in 1mL of NSB, filtered through a 40mm cell strainer (Fisher Scientific; 22-363-547), and counted using a Countess II FL Cell Counter (Applied Biosystems; A27978). Single-nucleus suspensions were diluted to approximately 1000 nuclei per ml in NSB.
Libraries were prepared from diluted single-nucleus suspensions using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v.3 (mouse dataset) or v.3.1 (human dataset) through the Yale Center for Genome Analysis (YCGA). Briefly, 10,000 cells per sample were added to RT Master Mix, loaded on the Single Cell A Chip, and portioned with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing the following: an Illumina R1 sequence (read 1 sequencing primer), a 16-nucleotide barcode, a 12-nucleotide unique molecular identifier (UMI), and a 30-nucleotide poly-dT primer sequence. Upon dissolution of the Gel Beads in a GEM, the primers were released and mixed with the cell lysate and Master Mix. Incubation of the GEMs then produced barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were then used to remove leftover biochemical reagents from the post-GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction, and enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via end repair, A-tailing, adaptor ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. Libraries were sequenced using the NovaSeq6000 at the YCGA. Sample concentrations were normalized to 1.2nM and loaded onto an Illumina NovaSeq S4 flow cell at a concentration that yielded 20k-50k passing filter clusters per cell per sample. Samples were sequenced using paired-end sequencing on an Illumina NovaSeq6000 instrument according to Illumina protocols using 10x sequencing specifications. The 8bp index was read during an additional sequencing read that automatically followed the completion of read 1. Data generated during sequencing runs were simultaneously transferred to the YCGA high-performance computing cluster. A positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3% to monitor quality in real time. Signal intensities were converted to individual base calls during a run using the system’s Real Time Analysis (RTA) software. Base calls were transferred from the machine’s dedicated personal computer to the Yale high-performance computing cluster via a 1 Gigabit network mount for downstream analysis.
snRNA-seq

value: Cerebellar cortex

value: 66 years


title: Dual guide RNA targeting Ppard infected, untreated, control organoids, 2


title: Donor 7 CD8 T cells TBET intlow HELIOS POS OKT3

value: CD8 T cells

value: TBET intlow HELIOS POS


title: Donor 7 CD8 T cells TBET high HELIOS NEG NS

value: NS


title: Donor 7 CD8 T cells TBET intlow HELIOS POS NS


title: Dual guide RNA targeting Ppard infected, untreated, control organoids, 1

value: Intestinal epithelial cells

value: Lgr5creERT2; Rosa26 LSL-Cas9-eGFP/+; ROSA26tdTomato


title: Ppard mutant organoid line 1: transduced with Ppard-targetting dual guide RNAs, treated with 4-hydroxytamoxifen, 1

value: long-term organoid culture seeded with adult intestinal stem cells


title: CP-IVT11-5-K27-ChIP-18187

description: H3K27ac ChIP-seq

value: HKCA+Ceranib


title: SCA1_9

description:
10x Genomics
CNGA-0047

value: 46 years


title: CP-IVT11-5-K4-ChIP-18192

description: H3K4me3 ChIP-seq

value: monocytes


title: Uninfected, 4-hydroxytamoxifen treated, control organoids

value: Primary murine organoids from distal small intestine

value: Uninfected, 4-hydroxytamoxifen treated

value: control organoids


title: SCA1_8

description:
10x Genomics
CNGA-0064

value: 31 years


title: Donor 7 CD8 T cells TBET intlow HELIOS NEG NS

value: Blood

value: TBET intlow HELIOS NEG


title: SCA1_7

description:
10x Genomics
UMB1354

value: Cerebellar cortex

value: 37 years


title: Donor 6 CD8 T cells HELIOS POS anti-CD3

value: CD8 T cells

value: HELIOS POS


title: Uninfected, untreated, control organoids

value: Uninfected, untreated


title: CP-IVT11-4-K27-ChIP-18188

description: H3K27ac ChIP-seq

value: HKCA+Rapamycin


title: CP-IVT11-4-K4-ChIP-18193

description: H3K4me3 ChIP-seq


title: Intestinal progenitor cell sample (Mouse_scRNA-seq)

description: 10x Chromium single cell data

data_processing:
10x Genomics cellranger count used to produce the filtered gene count matrix files from fastq files
deMULTIplex v 1.0.2 was used to align MULTIseq barcodes and demultiplex the datasets from the "BAR" fastq files
Assembly: mouse mm10-3.0.0 reference (10x Genomics)
Supplementary files format and content: Matrix, barcodes, and features tables with raw gene counts for every gene and every sample

source_name: small intestine

extract_protocol:
The intestine was washed, cut into 30 pieces of equal length, and incubated with media supplemented with 5mM EDTA and 10mM DTT at 37°C with 5% CO2. Cells were triturated, strained, washed, and labelled with barcodes unique to each segment using the MULTIseq method. The target population was FACS sorted.
10x libraries were prepared for sequencing using standard 10x genomics protocols adaoted for MULTIseq as described in McGinnis et al. Nat Methods 2019.
Chromium Single Cell 3'

value: FACS sorted intestinal epithelial progenitor cells (CD45-, EpCAM+, CD44+, Lgr5-DTR+)

value: small intestine

tag: developmental stage

value: adult


title: Donor 6 CD8 T cells HELIOS POS NS

value: NS


title: SCA1_6

description:
10x Genomics
CT


title: CP-IVT13-1-K4-ChIP-18186

description: H3K4me3 ChIP-seq

value: monocytes

value: untreated


title: CP-IVT11-2-K27-ChIP-18190

description: H3K27ac ChIP-seq

value: HKCA


title: Donor 6 CD8 T cells HELIOS NEG anti-CD3

value: HELIOS NEG


title: CP-IVT11-2-K4-ChIP-18195

description: H3K4me3 ChIP-seq


title: Total intestinal epithelial cell sample (Mouse_scRNA-seq)

description: 10x Chromium single cell data

value: FACS sorted intestinal epitheilal cells (CD45-, EpCAM+)


title: Donor 5 CD8 T cells HELIOS POS anti-CD3

value: Blood


title: SCA1_4

description:
10x Genomics
CB


title: CP-IVT11-1-K27-ChIP-18191

description: H3K27ac ChIP-seq


title: mLN_Naive_Memory_4 [MV_024]

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

description:
Antibody-derived oligonucleotide library
TAG_list.csv

library_source: other

data_processing:
Samples were demultiplexed and aligned using Cell Ranger 6.1 (10X Genomics) to genome build mm10 to obtain a raw read count matrix of barcodes corresponding to cells and features corresponding to detected genes.
For ADT libraries, samples were demultiplexed and then processed with CITE-seq-Count v. 1.4.5 (Roelli, P et al. 2019). Later merged and harmonized to remove biological replicate associated effects using harmony.
Assembly: mm10
Supplementary files format and content: Processed data are matrices with raw counts for features in sequenced cells. A list of cell barcodes and detected genes is also included for each sample.
Supplementary files format and content: A list of antibodies used and their Oligo tags is included.

molecule: protein

source_name: mesenteric Lymph node

extract_protocol:
TotalSeqTM-A Custom Mouse panel including 198 antibodies was obtained from Biolegend (#99833). The staining procedure was performed immediately after cell sorting and strictly following manufacturer instructions. Specifically, 25 μl of TotalSeqTM-A antibody cocktail were used to label 25 μl of cell suspension containing 5x105 cells. 4 groups of samples have been prepared for TotalSeqTM-A antibody staining and the following single cell RNA sequencing (scRNAseq), in biological triplicate. After staining with TotalSeqTM-A antibodies, suspensions were used for single cell RNA sequencing (scRNAseq).
CITE-seq: Following the protocol CG000204 RevD from 10X Genomics, we aimed at analyzing 1,000 cells of group 1 (mLN TN and TCM), 5,000 cells of group 2 (mLN TEM), 10,000 cells of group 3 (LP CD8) and 5000 cells of group 4 (IEL CD8). At step 2.2, we followed Biolegend instructions to add ADT additive primers. Step 2.3 (and only this step) was performed following the protocol CG000185 RevD from 10X Genomics. 3' gene expression libraries were further processed following the protocol CG000204 RevD from 10X Genomics, whereas ADT libraries (cell surface protein libraries) were processed following instructions from Biolegend.

value: mesenteric Lymph node

value: Naive and memory CD8 T cell

tag: library type

value: ADT

tag: antibodies


title: Donor 6 CD8 T cells HELIOS NEG NS

tag: tissue

tag: cell line

value: CD8 T cells


title: SCA1_3_replicate_2

description:
10x Genomics
13_2

value: Cerebellar cortex

value: 46 years


title: LP_3 [MV_022]

source_name: Small intestine lamina propria

value: Small intestine lamina propria

tag: cell type


title: Donor 5 CD8 T cells HELIOS POS NS

source_name: Blood

value: HELIOS POS


title: CP-IVT11-1-K4-ChIP-18196

description: H3K4me3 ChIP-seq

tag: treatment


title: IEL_3 [MV_023]

source_name: Small instestine

value: Small instestine

value: Intraepithelial lymphocytes CD8 T cells


title: Donor 5 CD8 T cells HELIOS NEG anti-CD3

tag: marker


title: mLN_Teff_3 [MV_021]

value: Effector CD8 T cells


title: Donor 7 CD8 T cells TBET intlow HELIOS NEG OKT3

value: TBET intlow HELIOS NEG

tag: stimulation


title: CP-IVT10-5-K27-ChIP-18197

description: H3K27ac ChIP-seq

value: monocytes

value: HKCA+Ceranib


title: SCA1_2_replicate_2

description:
10x Genomics
12_2

tag: genotype

value: 80 years


title: Donor 5 CD8 T cells HELIOS NEG NS

value: HELIOS NEG

value: NS

tag: tetramer


title: SCA1_5

description:
10x Genomics
RT


title: SCA1_2_replicate_1

description:
10x Genomics
12


title: mLN_Naive_Memory_3 [MV_020]

value: mesenteric Lymph node


title: Donor 4 CD8 T cells HELIOS POS anti-CD3

value: Blood


title: IEL_2 [MV_019]

value: ADT


title: CP-IVT10-4-K4-ChIP-18203

description: H3K27ac ChIP-seq

value: HKCA+Rapamycin


title: CP-IVT10-2-K27-ChIP-18200

description: H3K4me3 ChIP-seq

value: HKCA


title: SCA1_3_replicate_1

description:
10x Genomics
13

value: Cerebellar cortex

value: 46 years


title: SCA1_1

description:
10x Genomics
11

value: 42 years


title: Donor 4 CD8 T cells HELIOS POS NS

value: CD8 T cells

value: HELIOS POS


title: Donor 4 CD8 T cells HELIOS NEG anti-CD3


title: Control_10

description:
10x Genomics
T1952

value: Control

value: 81 years


title: Donor 4 CD8 T cells HELIOS NEG NS


title: mLN_Teff_2 [MV_017]

value: Effector CD8 T cells


title: LP_2 [MV_018]

value: Small intestine lamina propria


title: Control_9

description:
10x Genomics
T551

value: 77 years


title: IEL_1 [MV_016]

value: Small instestine

value: Intraepithelial lymphocytes CD8 T cells


title: CP-IVT10-4-K27-ChIP-18198

description: H3K4me3 ChIP-seq

value: monocytes


title: Control_8

description:
10x Genomics
T136

value: 64 years


title: CP-IVT10-2-K4-ChIP-18205

description: H3K27ac ChIP-seq


title: CP-IVT10-1-K27-ChIP-18201

description: H3K4me3 ChIP-seq

value: untreated


title: Control_7

description:
10x Genomics
T99

value: 44 years


title: Control_6

description:
10x Genomics
1532

value: 43 years


title: Donor 3 CD8 T cells HELIOS POS anti-CD3

value: Blood


title: mLN_Teff_1 [MV_014]

value: mesenteric Lymph node

value: ADT


title: CP-IVT10-1-K4-ChIP-18206

description: H3K27ac ChIP-seq


title: LP_1 [MV_015]

value: CD8 T cells


title: Donor 3 CD8 T cells HELIOS POS NS

value: HELIOS POS

value: NS


title: Wild type_13w

city: Nagoya

first: Madoka

last: Iida

state: Aichi

address: 65 Tsurumai-cho Showa-ku

department: Neurology department

country: Japan

institute: Nagoya University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spinal cord

extract_protocol:
Mice were deeply anesthetized, and the entire spinal cord were dissected and snap-frozen in powdered CO2 in liquid nitrogen. Spinal cords from 4 mice for each condition were pooled for homogenization and nuclear isolation. Fresh frozen murine spinal cord was placed in a Dounce homogenizer (Kimble Chase 2 ml Tissue Grinder) containing ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal and 0.2 U/μl RNase inhibitor). After homogenizing, the lysate was diluted with 1.4 mL of lysis buffer and incubated for 5 minutes. The homogenate was passed over a 70 μm strainer (Fisher Scientific). The filtered lysate was centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the pellet was resuspended in 1.5 ml lysis buffer and incubated for 3 minutes on ice. Then, the pellet was centrifuged at 500 × g for 5 minutes and resuspended in 1500 µl of wash buffer (1× PBS with 1% BSA and RNase Inhibitor). The nuclei were washed and centrifuged at 500 × g for 5 minutes three times and filtered through a 40 µm cell strainer. The cell suspensions were processed according to the debris removal solution (Milteni Biotec) protocol. Cells were resuspended in cold PBS with 0.04% BSA and stained with DAPI. The nuclei were sorted with a FACS Aria instrument (Becton Dickson) with a 100 nm nozzle and 405 nm excitation laser. These nuclei were centrifuged, inspected for appearance, and concentrated for the next step.
The nuclei per sample were run on the 10 × Chromium Single cell 3’ gene expression v3.1 platform. Sequencing libraries were constructed according to the manufacturer’s instructions, and cDNA samples were run on an Agilent Bioanalyzer using the High Sensitivity DNA Chip as quality control and determination of cDNA concentrations. The samples were run on an Illumina HiSeq X Ten  at Read 1 = 28 bp and Read 2 = 90 bp, with a minimum depth of 20,000 reads per nucleus. For alignment, introns and exons were included in the reference genome (mm10) using the CellRanger v5.0.1 pipeline (10X Genomics). Sequencing data were analyzed using the R package Seurat Version 4.1.3. The gene barcode matrices for each sample were imported into R using the Read10X function.

treatment_protocol: The spinal cord samples were obtained from AR-97Q mice and wild-type mice at four stages: pre-pubertal (3 weeks of age), pre-onset (6 weeks of age), early symptomatic (9 weeks of age) and advanced (13 weeks of age).

value: spinal cord

tag: condition

value: Advanced

value: 13 weeks

value: Wild-type


title: Wild type_9w

value: Early symptomatic

value: 9 weeks


title: Control_5

description:
10x Genomics
1432

value: Cerebellar cortex

value: Control

value: 83 years


title: mLN_Naive_Memory_4 [MV_012]

description:
3' mRNA Library
TAG_list.csv

value: Naive and memory CD8 T cell

value: mRNA


title: Donor 3 CD8 T cells HELIOS NEG NS

value: Blood

value: HELIOS NEG


title: mLN_Naive_Memory_1 [MV_013]

value: mesenteric Lymph node

value: ADT


title: Control_3_replicate_2

description:
10x Genomics
1516_2

value: 30 years


title: Wild type_3w

value: Pre-pubertal

value: 3 weeks


title: Donor 3 CD8 T cells HELIOS NEG anti-CD3

value: CD8 T cells


title: Control_3_replicate_1

description:
10x Genomics
1516


title: Donor 2 CD8 T cells HELIOS POS anti-CD3

value: HELIOS POS


title: Control_4

description:
10x Genomics
729

value: 59 years


title: Control_2_replicate_2

description:
10x Genomics
409_2

value: 48 years


title: IEL_3 [MV_011]

description:
3' mRNA Library
TAG_list.csv

value: Small instestine

value: Intraepithelial lymphocytes CD8 T cells


title: mLN_Teff_3 [MV_009]

description:
3' mRNA Library
TAG_list.csv

value: Effector CD8 T cells


title: Control_2_replicate_1

description:
10x Genomics
409

value: Cerebellar cortex

value: Control


title: Control_1

description:
10x Genomics
14

value: 65 years


title: Donor 2 CD8 T cells HELIOS NEG NS

value: Blood

value: NS


title: Donor 2 CD8 T cells HELIOS NEG anti-CD3

value: HELIOS NEG


title: AR97Q_3w

value: spinal cord


title: AR97Q_13w

value: Advanced

value: 13 weeks


title: Wild type_6w

value: Pre-onset

value: 6 weeks

value: Wild-type


title: Donor 1 CD8 T cells HELIOS POS anti-CD3

value: CD8 T cells

value: HELIOS POS


title: Donor 2 CD8 T cells HELIOS POS NS


title: AR97Q_9w

value: Early symptomatic

value: 9 weeks


title: LP_3 [MV_010]

description:
3' mRNA Library
TAG_list.csv

value: Small intestine lamina propria

value: mRNA


title: Donor 1 CD8 T cells HELIOS POS NS


title: mLN_Naive_Memory_3 [MV_008]

description:
3' mRNA Library
TAG_list.csv

value: mesenteric Lymph node

value: Naive and memory CD8 T cell


title: LP_2 [MV_006]

description:
3' mRNA Library
TAG_list.csv


title: Astrocytes, PGC-1a4 adenovirus infected, rep3

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments  --outFilterMismatchNmax 33 --alignEndsType Local --alignSJoverhangMin 8 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --seedSearchStartLmax 12
Reads aligning to gene exons were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level.
Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package, genes with total raw counts less then 10 across all samples were excluded from analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text file includes differetial gene expression analysis output from DESeq2

source_name: mouse primary astrocyte cells

growth_protocol: Primary cultures of mouse astrocytes were prepared from 1 to 3-day-old CD-1 pups. Cells were maintained at 37°C in a humidified atmosphere of 5% CO2. The medium was firstly changed after 7 days, and then every 3 days, until cultures were confluent at 10 to 13 days in vitro (DIV).

extract_protocol:
Cells were lysed and RNA was extracted using Trizol reagent
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq mRNA.

treatment_protocol: Cells were transduced with adenovirus expressing GFP, used as control, or each different PGC-1α isoform at a multiplicity of infection (MOI) of 100, for 24 h.

value: mouse primary astrocyte cells

value: astrocytes

value: wild-type

value: Adenovirus infection


title: Astrocytes, PGC-1a4 adenovirus infected, rep1


title: Astrocytes, PGC-1a4 adenovirus infected, rep2


title: IEL_2 [MV_007]

description:
3' mRNA Library
TAG_list.csv

value: Small instestine

value: Intraepithelial lymphocytes CD8 T cells


title: IEL_1 [MV_004]

description:
3' mRNA Library
TAG_list.csv


title: Donor 1 CD8 T cells HELIOS NEG anti-CD3

value: Blood

value: HELIOS NEG


title: mLN_Teff_2 [MV_005]

description:
3' mRNA Library
TAG_list.csv

value: Effector CD8 T cells


title: Donor 1 CD8 T cells HELIOS NEG NS

value: CD8 T cells

value: NS


title: Experiment #3, a person with HIV, Donor 9

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

description: 10x Genomics

data_processing:
Raw sequencing .fastq files were used as input into the read mapping and counting software, CellRanger v4.0 or v7.0.1, developed by 10X Genomics, Inc. (Pleasanton, CA, USA). The output filtered_feature_bc_matrix folder, which contains the barcodes after cell-calling filtration, was used for downstream analyses.
The library Seurat in Bioconductor R and custom code were used for all analyses. In experiment #1, data were pre-processed by removing control cells (hashed with TotalSeq™-B0255 antibody) that were not needed for these analyses. The data-driven thresholds for identifying cells positive for a hashing antibody were identified using the mixture model rule. In all experiments, bad quality cells were removed based on a large percentage of reads mapping to mitochondria genes. The data-driven thresholds for removal of these cells were identified using the interquartile rule or the mixture model rule depending on the data distribution. In experiment #1, cell hashing enabled us to identify droplets containing more than one cell, which were removed from the analysis. Cells that did not have any hashes were excluded from the analysis of differential gene expression.
Differentially expressed genes between cells that were negative or positive for HIV RNA were identified using the FindMarker function in the library Seurat. This analysis was conducted for each experiment and each model independently. Furthermore, for the 14-day model, cells that divided many times (CFSElow and hashed with TotalSeq™-B0252); cells that divided a few times (CFSEmed and hashed with TotalSeq™-B0253), and non-dividing cells (CFSEhigh and hashed with TotalSeq™-B0254) were also analyzed separately. The identified differentially expressed genes were then compared across conditions. To define cells as latently infected, two approaches were used. Two populations of HIV-positive cells were detected in both the in vitro models: cells with low levels of HIV RNA (the major peak) and cells with high levels of HIV RNA (the minor peak). The threshold for these populations was identified using the mixture model rule. In the first approach, cells with high levels of HIV RNA were excluded from the analysis. In the second approach, HIV transcript distribution across the HIV genome was assessed in samples from people with HIV, and only the cells with similar profiles in vitro were considered to be latently infected.
Assembly: The Genome Reference Consortium Human Reference 38 combined with HIV genome reference.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
For the 14-day model, cells were stained with Aqua live/dead stain (Thermo Fisher, Inc., Waltham, MA, USA), and live cells were sorted using FACS Aria or the Sony MA900 Multi-Application cell sorter to separate live cells with robust (CFSElow), moderate (CFSEmed) and no response (CFSEhigh) to the T cell receptor stimulus. CFSElow, CFSEmed and CFSEhigh cells were hashed with TotalSeq™-B0252, TotalSeq™-B0253 and TotalSeq™-B0254 antibodies (Biolegend, Inc., San Diego, CA, USA), respectively. CFSEhigh population was stained for cell maturation markers CD45RA (TotalSeq™-B0063) and CD62L (TotalSeq™-B0147) and an early activation marker CD69 (TotalSeq™-B0146). For 2 of the 3 biological replicates (cells donors 2 and 3), an aliquot of CFSEmed cells was hashed with TotalSeq™-B0255 antibody and stained with isotype controls, TotalSeq™-B0090 and TotalSeq™-B0092. Cell hashing antibodies were diluted 1:8; other antibodies were used undiluted. Antibody staining was performed per Biolegend’s protocols. After antibody staining, the cells were mixed back together, 10,000 from each population: CFSElow, CFSEmed, and CFSEhigh, and 500 cells stained with isotype controls, and 12,000 total cells were loaded into the Chromium Controller, aiming to achieve the targeted recovery of 10,000 cells in the scRNA-Seq experiment. For the 10-day model comparing gene expression to the 14-day model, cells were viably frozen and thawed  4 days later, to facilitate occurance of the scRNA-seq experiment on the same day. Cells were stained using Aqua live/dead stain (Thermo Fisher, Inc.) in the end of culture, and live cells were sorted using flow cytometry. Live cells were incubated with antibodies to differentiate cell maturation subsets (CD45RA and CD62L) and activation state (CD69). Additionally, an aliquot of cells from the second biological replicate (donor 2) was hashed at the end of culture with TotalSeq™-B0255 antibody and stained with isotype controls, TotalSeq™-B0090 and TotalSeq™-B0092. The third replicate experiment (donor 2) was conducted in parallel with a mock-infected control, incubated in the same conditions as the latency model, but without the exposure to the virus. This mock-infected control was hashed at the end of culture with TotalSeq™-B0255 antibody and stained with isotype controls, TotalSeq™-B0090 and TotalSeq™-B0092. Cells hashed with isotype controls in replicate experiments 2 and 3 were pooled with the main experimental cells at the ratio of 1:20 before loading into the Chromium Controller. For the 10-day model established using CXCR4- and CCR5-tropic viruses (donors 4-6), fresh CD4+ T cells were used. Biobanked CD4+ T cells from people with HIV (donors 7-9) were viably thawed, stained with Aqua live/dead staining (Thermo Fisher, Inc.) and sorted for live cells. For one of the donors (donor 7), two sequencing reactions were prepared (technical replicate). In all experiments, 12,000 total cells were loaded into the Chromium Controller, aiming to achieve the targeted recovery of 10,000 cells in each scRNA-seq experiment.
Reverse transcription to generate cDNA and library preparation for scRNA-Seq were conducted per the manufacturer’s instructions (10X Genomics, Inc., Pleasanton, CA, USA). For library preparation, 3’ gene expression and 3’ feature barcoding library kits (v3 or v3.1) were used. Briefly, CD4+ T cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reversed transcribed to cDNA, which contains an Illumina 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 appropriate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Sequencing files generated from the gene expression libraries were named with an abbreviation GEX; sequencing files generated from the feature barcoding libraries were named with an abbreviation FBC.

value: Primary CD4+ T cells

tag: cells frozen

value: yes

value: Peripheral blood

tag: library kit

tag: cellranger version


title: Experiment #3, a person with HIV, Donor 7_2

description: 10x Genomics


title: Astrocytes, PGC-1a3 adenovirus infected, rep3

tag: strain


title: Astrocytes, PGC-1a3 adenovirus infected, rep2


title: LP_1 [MV_003]

description:
3' mRNA Library
TAG_list.csv

value: Small intestine lamina propria

value: mRNA


title: mLN_Teff_1 [MV_002]

description:
3' mRNA Library
TAG_list.csv

value: mesenteric Lymph node


title: Experiment #3, a person with HIV, Donor 7_1

description: 10x Genomics


title: WT 24h vehicle rep3

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.7.1a with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 2.0.3 keeping only unambiguous reads
Assembly: GRCh38.104
Supplementary files format and content: Raw counts measurements

source_name: ReNcell VM

growth_protocol: ReNcell VM were cultured in Neurobasal medium supplemented with B-27, MEM Non-essential amino-acids, 1% Penicillin Streptomycin, Glutamax, 1mM Sodium pyruvate, 20ng/ml EGF and 20ng/ml bFGF  on Matrigel coated cells. ReNcell VM were differentiated by removing EGF and FGF in culture medium for 5 days.

extract_protocol:
RNA was extracted using RNAeasy Mini kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 5 days of differentiation, ReNcell were treated with vehicle (saline) or recombinant human  BDNF (100 ng/mL) for 0, 3 and 24 hours

value: neural progenitors

value: WT

value: Non


title: Experiment #2, the 10-day model, CCR5-tropic, Donor 6

description: 10x Genomics

value: no


title: WT 24h vehicle rep4


title: Experiment #3, a person with HIV, Donor 8

description: 10x Genomics


title: Astrocytes, PGC-1a3 adenovirus infected, rep1

value: mouse primary astrocyte cells

value: astrocytes

value: wild-type

value: Adenovirus infection


title: WT 24h vehicle rep2


title: AR97Q_6w

value: spinal cord

value: Pre-onset

tag: age

value: 6 weeks


title: mLN_Naive_Memory_1 [MV_001]

description:
3' mRNA Library
TAG_list.csv

value: Naive and memory CD8 T cell


title: Experiment #2, the 10-day model, CCR5-tropic, Donor 5

description: 10x Genomics

value: Primary CD4+ T cells


title: Experiment #2, the 10-day model, CCR5-tropic, Donor 4

description: 10x Genomics

value: Peripheral blood


title: Astrocytes, PGC-1a2 adenovirus infected, rep3


title: WT 24h vehicle rep1


title: CD8_mLN_Resident_2

description: Low input RNA libraries

data_processing:
Sequenced libraries were processed with deepTools, using STAR , for trimming and mapping, and featureCounts to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2.
Assembly: mm10
Supplementary files format and content: matrix of raw gene counts per sample

source_name: mesenteric lymph node

extract_protocol:
RNA was extracted using RNAqueousTM Total RNA isolation kit (Ambion) according to manufacturer instructions and quantified using Qubit 2.0 (Thermo Fisher Scientific) following manufacturer instructions.
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina and sequenced with a NovaSeq 6000 instrument by the Deep-sequencing Facility at the Max Planck Institute for Immunobiology and Epigenetics.

value: mesenteric lymph node

value: Resident memory CD8 T cells


title: Experiment #2, the 10-day model, CXCR4-tropic, Donor 6

description: 10x Genomics


title: Astrocytes, PGC-1a2 adenovirus infected, rep2


title: WT 24h bdnf rep4

value: BDNF


title: WT 24h bdnf rep3

value: neural progenitors


title: CD8_mLN_Resident_1

description: Low input RNA libraries


title: Experiment #2, the 10-day model, CXCR4-tropic, Donor 5

description: 10x Genomics


title: WT 24h bdnf rep1

value: WT


title: CD8_mLN_Naive_1

description: Low input RNA libraries

value: Naive CD8 T cell


title: Experiment #2, the 10-day model, CXCR4-tropic, Donor 4

description: 10x Genomics

value: no


title: WT 3h vehicle rep4

value: Non


title: Astrocytes, GFP adenovirus infected, rep3

value: mouse primary astrocyte cells

value: astrocytes


title: Astrocytes, PGC-1a1 adenovirus infected, rep1

value: wild-type

value: Adenovirus infection


title: Experiment #1, the 10-day model, donor 1

description: 10x Genomics

value: yes


title: WT 3h vehicle rep3


title: CD8_mLN_Resident_3

description: Low input RNA libraries


title: CD8_mLN_Naive_3

description: Low input RNA libraries


title: WT 24h bdnf rep2


title: Experiment #1, the 14-day model, donor 2

description: 10x Genomics


title: Astrocytes, PGC-1a2 adenovirus infected, rep1


title: Experiment #1, the 10-day model, donor 3

description: 10x Genomics


title: CD8_mLN_Effector_1

description: Low input RNA libraries

value: Effector memory CD8 T cells


title: Astrocytes, PGC-1a1 adenovirus infected, rep2


title: CD8_mLN_Naive_2

description: Low input RNA libraries


title: CD8_mLN_Central_3

description: Low input RNA libraries

value: Central memory CD8 T cells


title: Astrocytes, PGC-1a1 adenovirus infected, rep3


title: Runx1- IAHC

city: Edinburgh

first: Mihaela

last: Crisan

address: 5 Little France Drive

country: United Kingdom

institute: The University of Edinburgh

description: Sample 4. I18-1129-07-HPSCn.fastq.gz

data_processing:
Reads were aligned against the GRCm38/mm10 reference using HiSat2 (version 2.0.4).
Read counts on GENCODE annotation version MM19 were computed using the union mode from the Bioconductor Genomic Alignments package (v1.18.1) and transformed to TPMs.
Assembly: mm10
Supplementary files format and content: Ensemble Gene Id, annotation and TPM values

source_name: E11 AGM Runx1-GFP

extract_protocol:
E11 embryos were obtained from Runx1-GFP/+ males and females time pregnancy and AGM cells stained with NG2 Cy3 (1:100, Millipore), PDGFRβ APC (1:100, Biolegend), CD31 PECy7 (1:4000, eBioscience), CD45 PerCypCy5.5 (1:400, BD Pharmingen), ckit BV421 (1:500, BD Horizon) and CD45 PerCpCy5.5 (1:400, BD Pharmingen) for 30 min at 4oC, washed, centrifuged, then resuspended in PBS/FCS/PS for analysis and cell sorting. Cells were purified using BD FACS ARIA Fusion cell sorter (BD Bioscience) and Sytox AAD was used to select viable cells. Sorted cells were sorted and collected directly into 20μl of lysis buffer containing Nuclease-free water (Ambion AM9930) 0.2% Triton and 1/20 RNAse inhibitor (Thermoscientific 10777019).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: developmental stage

value: FACS sorted


title: Experiment #1, the 14-day model, donor 3

description: 10x Genomics

value: Primary CD4+ T cells

value: Peripheral blood


title: Experiment #1, the 10-day model, donor 2

description: 10x Genomics


title: CD8_mLN_Effector_3

description: Low input RNA libraries

value: mesenteric lymph node


title: Experiment #1, the 14-day model, donor 1

description: 10x Genomics


title: WT 3h bdnf rep4

value: BDNF


title: Astrocytes, GFP adenovirus infected, rep2


title: CD8_mLN_Effector_2

description: Low input RNA libraries


title: CD8_mLN_Central_2

description: Low input RNA libraries


title: WT 3h bdnf rep3

value: neural progenitors


title: RELA_rep4

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: RELA overexpressing cells, sorted for high levels of MGT#4 activation

data_processing:
Illumina index demultiplexing was performed using the bcl2fastq conversion software (v2.20.0).
The oligo-dT barcode sequences from Read 1 were extracted using cutadapt (v2.1) for subsequent internal demultiplexing of reads using BRBseqTools-1.6.jar (http://github.com/DeplanckeLab/BRB-seqTools).
The BRBseqTools demultiplexed data was aligned to a custom genome (MGT#4-containing GRCh38) using STAR (v2.7.8a).
HTSeq (v2.0.2) was used to generate the count matrices.
Assembly: GRCh38.107 + MGT#4
Supplementary files format and content: Tab-delimited text file including raw counts for each sample.

source_name: Brain

growth_protocol: The IDH-wt-hGICs-MGT#4-dEGFP dCas9-VPR were propagated in RHB-A medium (Takara), supplemented with EGF (20 ng/ml; R&D), bFGF (20 ng/ml; R&D), heparin (1 μg/ml; Sigma), PDGF-aa (20 ng/ml; R&D), 1% penicillin and streptomycin. Cells were cultured at 37°C in a 5% CO2, 3% O2 and 95% humidity incubator.

extract_protocol:
Total RNA extraction from IDH-wt-hGICs-MGT#4-dEGFP dCas9-VPR cells was performed using the TRIzol Reagent (Invitrogen, 15596026), followed by isopropanol precipitation and subsequent AMPure XP beads (Beckman Coulter, #A63881) purification.
Multiplexed 3'-cDNA libraries were constructed starting from 60 ng of total RNA per sample as input, utilizing barcoded oligo-dT primers (Datlinger et al., 2021) in an adapted version of Bulk RNA barcoding and sequencing (BRB-seq) protocol (Alpern et al., 2019).

value: Brain

value: IDH-wt-hGICs-MGT#4-dEGFP dCas9-VPR

value: Transformed neural progenitor cells from the subventricular zone

value: RELA overexpressing


title: WT 3h vehicle rep2

value: WT

value: Non


title: WT 3h vehicle rep1


title: Astrocytes, GFP adenovirus infected, rep1

value: mouse primary astrocyte cells

value: astrocytes

value: wild-type


title: EC

description: Sample 1. I18-1129-05-ECs.fastq.gz


title: WT 3h bdnf rep2


title: Runx1+ IAHC

description: Sample 3. I18-1129-08-HPSCp.fastq.gz


title: RELA_rep2


title: RELA_rep1


title: D6 NGFP2 N+/- (EV)_rep2

city: Jerusalem

first: Yosef

last: Buganim

address: Hadassah Medical School

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

data_processing:
Raw reads (fastq files) were inspected for quality issues with FastQC (v0.11.2,http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). According to the FastQC report, reads were then trimmed to a length of 50 bases with fastx_trimmer of the FASTX package (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/), and quality-trimmed at both ends, using in-house perl scripts, with a quality threshold of 32. In short, the scripts use a sliding window of 5 base pairs from the read's end and trim one base at a time until the average quality of the window passes the given threshold. Following quality-trimming, adapter sequences were removed by Trim Galore (version 0.3.7, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), using the command “trim_galore -a $adseq –length 15” where $adseq is the appropriate adapter sequence. The remaining reads were further filtered to remove very low quality reads, using the fastq_quality_filter program of the FASTX package, with a quality threshold of 20 at 90 percent or more of the read's positions
The cleaned fastq files were mapped to the mouse transcriptome and genome, Ensembl version GRCm38 from Illumina's iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html), using TopHat (v2.0.11), allowing up to 3 mismatches and a total edit distance of 8 (full command: tophat -G Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf -N 3 --read-gap-length 5 --readedit-dist 8 --segment-length 18 --read-realign-edit-dist 5 --b2-i S,1,0.75 --b2-mp 3,1 --b2-score-min L,-0.5,-0.5 Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/genome clean.fastq).
Quantification and normalization were done with the Cufflinks package (v2.2.1). Quantification was done with cuffquant, using the genome bias correction (-b parameter), multi-mapped reads assignment algorithm (-u parameter) and masking for genes of type IG, TR, pseudo, rRNA, tRNA, miRNA, snRNA and snoRNA (-M parameter). Normalization was done with cuffnorm (using output format of Cuffdiff).
Processed data file contains a re-analysis of two Samples from GSE64684, ESCs and MEFs.
Genome_build: GRCm38
Supplementary_files_format_and_content: Xls count and fpkm quantifications

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were grown on gelatine and cultured with S/Lif and Dox for 6 days

extract_protocol:
Total RNA was isolated using the Macherey-Nagel RNA NucleoSpin kit (Ornat)
mRNA libraries were prepared using the SENSE mRNA-seq library prep kit V2 (Lexogen)

value: Double heterozygous mouse embryonic fibroblasts


title: RAC1_rep4

description: RAC1 overexpressing cells, sorted for high levels of MGT#4 activation

value: RAC1 overexpressing


title: CD8_mLN_Central_1

description: Low input RNA libraries

value: Central memory CD8 T cells


title: WT 0h rep4


title: CD8_Lamina_Resident_1

description: Low input RNA libraries

value: Small intestine lamina propria

value: Resident memory CD8 T cells


title: CD8_Lamina_Resident_2

description: Low input RNA libraries


title: WT 3h bdnf rep1


title: WT 0h rep3


title: CD8_Lamina_Effector_3

description: Low input RNA libraries

value: Effector memory CD8 T cells


title: D6 NGFP2 N+/- (EV)_rep1


title: WT 0h rep2


title: RELA_rep3


title: RAC1_rep2


title: D6 NGFP2 N+/-_rep1


title: RAC1_rep3


title: HEC

description: Sample 2. I18-1129-06-HECs.fastq.gz

value: FACS sorted


title: RAC1_rep1


title: CD8_Lamina_Effector_2

description: Low input RNA libraries


title: CD8_Lamina_Resident_3

description: Low input RNA libraries


title: D6 NGFP2 N+/-;E+/-_rep2


title: NTRK2ko vehicle 24h rep4

value: neural progenitors

value: NTRK2 KO


title: MGT4_VPR_rep3

description: Parental bulk control

value: Brain

value: IDH-wt-hGICs-MGT#4-dEGFP dCas9-VPR

value: Parental bulk control


title: WT 0h rep1

value: WT


title: CD8_IEL_Resident_3

description: Low input RNA libraries

source_name: Small intestine intraepithelium

value: Small intestine intraepithelium


title: CD8_Lamina_Effector_1

description: Low input RNA libraries


title: NTRK2ko vehicle 24h rep3

value: Non


title: D6 NGFP2 N+/-;E+/-_rep1


title: MGT4_VPR_rep2

description: Parental bulk control

value: Transformed neural progenitor cells from the subventricular zone


title: D6 NGFP2 N+/-;U+/-_rep2

value: Single heterozygote mouse embryonic fibroblasts


title: CD8_IEL_Resident_2

description: Low input RNA libraries


title: NTRK2ko vehicle 24h rep2


title: D6 NGFP2 N+/-;S+/-_rep2


title: NTRK2ko vehicle 24h rep1


title: D6 NGFP2 N+/-;U+/-_rep1


title: CD8_IEL_Resident_1

description: Low input RNA libraries


title: FOSL1_rep4

description: FOSL1 overexpressing cells, sorted for high levels of MGT#4 activation

value: FOSL1 overexpressing


title: D6 NGFP2 N+/-_rep2

value: Double heterozygous mouse embryonic fibroblasts


title: D6 NGFP2 N+/-;S+/-_rep1


title: E11 AGM cells - NG2-Cre; Runx1 fl/fl (cKO)

data_processing:
Alignment of scRNA-seq data and barcode counting using 10X Genomics Cell Ranger (v3.1.0) with reference dataset mm10/GRCm38-3.0.0.
Filtering of empty and/or low quality cells using EmptyDrops and Scater (v1.14.6) Bioconductor packages
Differential expression computed using the Scran (v1.14.6) Bioconductor package
Enrichment analysis of differential expression results and additional data mining of Gene Ontology terms with the Panther classification system and AmiGO (v2.5.13)
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain tab separated feature and barcode sequences corresponding to matrix row and column indices respectively, as output by 10X Cell Ranger
Supplementary_files_format_and_content: mtx files contain market exchange formatted matrices of UMI counts associated with a feature (row) and barcode (column), as output by 10X Cell Ranger

source_name: aorta-gonads-mesonephros region

extract_protocol:
Hematopoietic organs were dissected and dissociated into single cells with collagenase type I (Sigma, C0130, 0.12% v/v)
AGMs from NG2 +/+; Runx1 fl/fl and NG2-Cre; Runx1 fl/fl embryos were dissected, dissociated, washed, counted and assessed for viability using a Bio-Rad TC20. Cells were then loaded at a concentration for the recovery of 7,000 cells and processed through the 10x Chromium Controller. Single cell libraries were obtained according to manufacturer protocol. RNA concentration was obtained using Quibit RNA HS (Thermo-Fisher) and the quality of the libraries was verified using the LabChip GX24 (Perkin Elmer).

value: NG2-Cre; Runx1 fl/fl (cKO)

value: aorta-gonads-mesonephros region


title: FOSL1_rep2


title: NTRK2ko bdnf 24h rep4

value: BDNF


title: NTRK2ko bdnf 24h rep2


title: NTRK2ko bdnf 24h rep3


title: SGFP1 S2+/-;S4+/-_rep3

data_processing:
Raw reads were quality-trimmed and adapters removed using trim galore (v0.4.5).
Bismark (v 0.22.1) was used to align the paired-end reads to the mouse genome (GRCm38)
The methylation ratio of CpGs with sequencing depth of at least 10 reads were computed based on 100bp tiles.
Differential analysis was done using the R package Methylkit  (version 1.18.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab limitied methylation coverage

growth_protocol: MEFs were grown on gelatine and cultured with 10% serum.

extract_protocol:
DNA was isolated from cultured MEFs  and incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. RRBS libraries were prepared as described (Boyle et al., 2012) and run on Hiseq 2500 (Illumina).
RRBS


title: SGFP1 S2+/-;S4+/-_rep2


title: FOSL1_rep1


title: d2_MEF_O6KS2AV_input

data_processing: fastqc Reads were aligned to mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive –end-to-end. Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read was retained. Samtools was used to discard reads with mapping quality < 10 Peaks were called using MACS2 with options --call-summits --to-large -p 0.0001 –bdg options. For each binding location, the read coverage for all libraries was calculated using the bedtools multicov function. Genome_build: mm10 Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed followed by bedGraphToBigWig.

extract_protocol: As described by Malik et al., Nature Comm., 2019. Reprogramming sample grown in fibroblast media were collected at day 2 after Dox induction by trypsinization and washed twice with PBS. Cells were resuspended in PBS at a density of 5 x 105/mL and then chemically crosslinked by the addition of 1% PFA for 10 min at room temperature with gentle rotation. Crosslinking was stopped by the addition of glycine to a final concentration of 125 mM for 5 min at room temperature.

tag: chip antibody

value: MEF


title: d2_MEF_O6KS2_input


title: NTRK2ko bdnf 24h rep1


title: MGT4_VPR_rep1

description: Parental bulk control


title: SGFP1 S2+/-;S4+/-_rep1


title: d2_MEF_O4KS2AV_input


title: HSPC Excess Leucine rep

city: Mohali

first: Lolitika

last: Mandal

state: Punjab

address: Sector 81, SAS Nagar

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Mohali

description:
Treatment 2
S3_HSPC_Rep.

data_processing:
FastQC/Trimmomatic was used for trimming adaptors and low quality sequences to obtain only High quality reads
TopHat v 2.1.1 was used to read mapping from Homo sapiens GRCh38.dna.toplevel.fa
Cufflinks v2.2.1 program assembles transcriptomes from RNA-Seq data and quantifies their expression.
Cuffmerge to merge the individual assemblies
FPKM values were used to calculate the log fold change as log2(FPKM_Experimental/FPKM_Control).
tab-delimited text files include  Log2 Fold Change (log2FC) values greater than zero were considered up-regulated whereas less than zero were down-regulated along with P-value threshold of 0.05 for statistically significant results.
Supplementary files format and content: count

source_name: BM derived HSPCs

growth_protocol: Bone Marrow derived CD34+ve cells were maintained in DMEM-Leucine -Methionine (Invitrogen) supplemented with 0.8 mM methionine and 0.8 mM leucine 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
after 6Hrs of treatment without leucine and excess leucine, the RNA of  Control, Treatment 1 and Treatment 2 replicates were isolated using Trizol RNA samples were processed for purification using RNAClean XP beads to remove  RNA samples were processed for purification using RNAClean XP beads
RNA libraries for RNA-seq were prepared using TruSeq mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: HSPC for treatment 1 were maintained in DMEM (-LM) with no Leucine added, for Treatment 2 additional leucine was added to a final contration of 2mM

value: BM derived HSPCs

value: CD34 +ve Cd10 -ve HSPCs

value: Excess Leucine


title: d2_MEF_O4KS2_input


title: NTRK2ko vehicle 3h rep4

value: neural progenitors

value: NTRK2 KO


title: HSPC Excess Leucine

description:
Treatment 2
S3_HSPC.


title: FOSL1_rep3

value: Brain

value: IDH-wt-hGICs-MGT#4-dEGFP dCas9-VPR


title: SGFP1 S2+/-_rep3


title: HSPC No leucine rep

description:
Treatment 1
S2_HSPC_Rep.

value: Leucine Deprivation


title: d2_MEF_KS2AV_input


title: HSPC No leucine

description:
Treatment 1
S2_HSPC.


title: E11 AGM cells - NG2 +/+; Runx1 fl/fl (WT)

value: NG2 +/+; Runx1 fl/fl (WT)


title: SGFP1 S2+/-_rep1


title: SGFP1 S2+/-_rep2


title: NTRK2ko vehicle 3h rep1

value: Non


title: HSPC control rep

description:
Untreated Control
S1_HSPC_Rep.

value: Control


title: d2_MEF_KS2_input


title: d2_MEF_O6KS2AV_ChIP_Oct6


title: NTRK2ko bdnf 3h rep4


title: NTRK2ko bdnf 3h rep3


title: Splenic CD19+ Ig transcript library, Mtv8KO C57BL/6J sample 3

city: Chicago

first: Helen

middle: A

last: Beilinson

state: IL

address: 924 E 57TH ST

department: Microbiology

institute: University of Chicago

description:
Immunoglobulin libraries were generated from 1 mg of CD19+ splenocyte RNA using the NEBNext Immune Sequencing Kit, specifically enriching for B cell receptor chains during the first PCR step
Mtv8_Ig_Repertoire_Summary.xlsx

data_processing:
Preprocessing of BCR sequences was performed using the open-source workflow pRESTO NEBNext Immune Sequencing Kit Workflow (v3.2.0) on Galaxy
Reads with a Phred quality score <20 were removed for quality control. Reads that did not match to the constant region primer (maximum error rate 0.2) were removed. Reads that did not match to the template switch sequence (maximum error rate 0.5) were removed. The first 17 bp following the template switch site were a unique molecular identifier (UMI) on each read. Sequences with identical UMIs were collapsed into consensus sequences with sequences found in less than 60% of reads removed. Positions with more than 50% gap sequences were removed. Mate-pairs were assembled with a minimum of 8 bp overlap (maximum error rate of 0.3). Assembled reads were assigned isotype-constant region identities based on local alignment of the 3’ ends of the reads (maximum error rate of 0.3).
V, (D), and J gene segments were assigned using MiGMAP mapper (Galaxy Version 1.0.3+galaxy2).
Subsequent analyses were done using R Studio. Statistically significance was calculated using unpaired Welch’s t test with Bonferroni correction.
Assembly: mm10
Supplementary files format and content: Final Ig repertoire summary and raw counts: Mtv8_Ig_Repertoire_Summary.xlsx

source_name: Spleen

extract_protocol:
CD19+ splenocytes were isolated 10.5-week-old 3 WT and 3 Mtv8KO C57BL/6J female mice. Red blood cell lysed splenocytes were labeled with microbeads conjugated to monoclonal anti-mouse CD19 antibodies (isotype: rat IgG2a) (Miltenyi Biotec, Bergisch Gladbach, Germany) and positively sorted as detailed by the manufacturer. RNA was isolated from isolated CD19+ splenocytes using guanidine thiocyanate extraction and CsCl gradient centrifugation.
Immunoglobulin libraries were generated from 1 mg of CD19+ splenocyte RNA using the NEBNext Immune Sequencing Kit (New England Biolabs, Ipswich, Massachusetts, USA) according to manufacturer’s instructions, specifically enriching for B cell receptor chains during the first PCR step.
Six libraries were pooled in equimolar amounts and were sequenced by paired-end 300 bp sequencing on an Illumina MiSeq by The University of Chicago Genomics Facility.

value: Spleen

tag: strain background

tag: Sex

value: Female

value: 10.5 weeks


title: Splenic CD19+ Ig transcript library, Mtv8KO C57BL/6J sample 2

tag: tissue


title: NTRK2ko vehicle 3h rep3


title: Bisulfite-seq_cultured_ductal_methyl_4

first: Pei

last: Wang

department: Cell Systems & Anatomy

institute: University of Texas Health San Antonio

data_processing:
Genomic alignment and CpG calling was performed with Bismark 0.19.1.
Detected sites among all samples were collated, and only those withat least 10 read coverage (methylated + unmethylated) for all samples were retained for analysis.
Assembly: hg38
Supplementary files format and content: bismark.cov are tab delimited tables of all detected DNA methylation sites with beta value, methylated reads, and unmethylated reads for each site
Supplementary files format and content: DNA_methylation_beta_tab.txt.gz is a tab delimited table with beta value for all samples for all retained DNA methylation sites (2349323 sites)

source_name: exocrine pancreas

extract_protocol:
Genomic DNA was extracted  with Zymo Quick-DNA miniprep kit.
Reduced-representation bisulfite converted DNA methylation libraries were contructed from genomic DNA with Illumina Truseq methyl capture kit, as per manufacturer instruction.

treatment_protocol: "KPTS" genotype cells have enforced expression of oncogenic KRAS-G12V and CRISPR/Cas9 knockout of P16, P53, and SMAD4 .

value: exocrine pancreas

tag: cell type

value: ductal

value: KPTS

value: monolayer culture


title: NTRK2ko vehicle 3h rep2


title: Splenic CD19+ Ig transcript library, Mtv8KO C57BL/6J sample 1


title: Splenic CD19+ Ig transcript library, WT C57BL/6J sample 3

value: WT


title: NTRK2ko bdnf 3h rep2

value: BDNF


title: NTRK2ko bdnf 3h rep1

value: neural progenitors


title: Bisulfite-seq_cultured_ductal_methyl_3


title: d2_MEF_O6KS2AV_ChIP_Sox2

first: Sergiy

last: Velychko

address: 77 Avenue Louis Pasteur, Room 232

institute: Harvard Medical School

tag: cell line

value: MEF

tag: treatment


title: Splenic CD19+ Ig transcript library, WT C57BL/6J sample 2


title: NTRK2ko 0h rep4

value: NTRK2 KO

tag: stimulation


title: Splenic CD19+ Ig transcript library, WT C57BL/6J sample 1

tag: genotype


title: HSPC control

description:
Untreated Control
S1_HSPC.

value: BM derived HSPCs

value: CD34 +ve Cd10 -ve HSPCs


title: d2_MEF_O6KS2_ChIP_Sox2


title: NTRK2ko 0h rep3


title: Bisulfite-seq_cultured_ductal_methyl_1


title: Bisulfite-seq_cultured_acinar_methyl_5

value: acinar

value: organoid culture


title: d2_MEF_O6KS2_ChIP_Oct6


title: Bisulfite-seq_cultured_acinar_methyl_4


title: d2_MEF_O4KS2AV_ChIP_Sox2


title: d2_MEF_O4KS2AV_ChIP_Oct4


title: Bisulfite-seq_cultured_acinar_methyl_3


title: d2_MEF_O4KS2_ChIP_Sox2


title: d2_MEF_KS2AV_ChIP_Sox2


title: Bisulfite-seq_cultured_acinar_methyl_2


title: S9_S22

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
Read trimming and filtering were performed with Trimmomatic (version 0.39).
Fastq file was converted to fasta file.
Reads were mapped to the sequence of three genotypes of HIV-1 (CH185 wild-type, the CH185_dPTAP1 mutant, and the CH185_dPTAP2) using BLASTn (version 2.6.0).
Reads were assigned to the top hit genotype. If tie, the read was discarded.
Reads assigned to each genotype were counted.
Genome_build: CH185_WT; AGGGAAAATCTGGCCTTCCAACaaggggaggccagggaatttccttCAGAACAGAGCAGAGCCAACAGCCCCACCAGCAGAGAGCTTCCCTCAGAGCAGACCAGAGCCAACAGCTCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Genome_build: CH185_dPTAP1; AGGGAAAATCTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCCTCAGAGCAGACCAGAGCCAACAGCTCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Genome_build: CH185_dPTAP2; AGGGAAAATCTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCTTCAGAACAGAGCAGAGCCAACAGCCCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Supplementary_files_format_and_content: blast output

organism: Human immunodeficiency virus 1

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 355F1

growth_protocol: Three different HIV-1, CH185 wild-type, the CH185 deltaP1 mutant, and the CH185 deltaP2 mutant were co-inoculated into nine humanized mice.

extract_protocol:
for plasma samples, QIAamp viral RNA mini kit (Qiagen); for speen samples, QIAamp RNA blood mini kit (Qiagen)
DNA library preparation kit (NEB)
OTHER: RT-PCR amplicon sequencing

tag: model

value: HIV1-infected humanized mouse


title: d2_MEF_O4KS2_ChIP_Oct4

city: Boston


title: NTRK2ko 0h rep1

value: Non


title: d2_MEF_KS2_ChIP_Sox2


title: Bisulfite-seq_cultured_ductal_methyl_2

tag: condition


title: Bisulfite-seq_cultured_acinar_methyl_1


title: scRNA,SD48h

city: Beijing

first: Erquan

last: Zhang

address: 7 Science Park Road, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
adaptor and low-quality sequencing data were removed by trimmomatic(v0.39)
Filtered reads were processed with the standard Cellranger v4.0.0 pipeline, and then mapped to the prebuilt mouse reference dataset GRCm38/mm10.
The barcode-feature matrixes generated by Cellranger were further analyzed with Seurat v3.0 pipeline in R v4.0.2.
Assembly: GRCm38/mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Each mouse was anesthetized with pentobarbital (i.p. 80 mg/kg) and taken 500 μL blood retro-orbitally which was collected in an EDTA anticoagulant tube (BD Biosciences). The blood sample was transferred into 5-fold volume of Ammonium-Chloride-Potassium (ACK) lysis buffer (150 mM NH4Cl, 10mM KHCO3, Na2·EDTA 0.1nM), and incubated on ice (gently turn upside down 2 times during incubation) for 10 min. After 500×g centrifugation at 4℃ for 10 min, the supernatant was completely discarded. The cell pellet was washed with 2-fold volume of ACK lysis buffer, and 500×g centrifuged at 4℃ for 10 min.
The leukocyte pellets of 3 mice in the same group were resuspended in equal amount with DPBS (containing 0.04% BSA), and adjusted the cell concentration to 500-1,200 cells/μL. Each library was designed to contain around 7,000 cells, and sequencing depth was about 50,000 reads per cell. All libraries for single-cell RNA sequencing were prepared by
Chromium Single Cell 3’ Reagent Kits (v3 Chemistry) (10x Genomics) according to the manufacturer’s instructions. Qualitative analysis of each DNA library was performed using an Agilent 2100 Bioanalyzer. The concentration of each DNA library was measured using a Qubit fluorometer (Invitrogen).

value: Blood

value: Leukocyte

tag: time


title: Hap1_Baz2B_KO_2

type: RNA

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

description: Human near-haploid cell line derived from the chronic myelogenous leukemia (CML) cell line KBM-7

hyb_protocol: 3.8 µg of fragmented and labeled ssDNA were hybridized to Affymetrix Human Gene 2.0 ST arrays for 16h at 45°C in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software

data_processing: Microarray analysis was conducted using the oligo package. Briefly, probe intensities were normalized using the RMA function and only probes exhibiting intensities greater than 3.5 in at least two samples, were kept for further analysis.

label: biotin

source_name: Hap1 cell line Baz2B-KO

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, InC., Santa Clara, CA, USA). In brief, 200 ng of total RNA were used to generate double-stranded sDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endunuclease 1 (APE1) followed by a terminal labeling with biotin.

growth_protocol: The cells were cultured in IMDM (from Gibco, serum free medium) supplemented with L-glutamine, phenol red indicator and 10% FCS. Typically, cells were maintained at 40-90% confluency and pasagged every 2-3 days. Both cell lines were treated separately.

extract_protocol: To extract total RNA, the Machery-Nagel NucleoSpin RNA kit (Bioanalytik) was used. RNA concentration was measured with NanoDrop.

treatment_protocol: The cells were trypsinized

value: Hap1 Baz2B-KO


title: S7_S20

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 352M6


title: S8_S21

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 353M2


title: Bisulfite-seq_fresh_ductal_methyl_5

address: 7703 Floyd Curl Dr

value: exocrine pancreas

value: ductal

value: freshly sorted


title: scRNA,SD24h

source_name: Blood


title: Bisulfite-seq_fresh_ductal_methyl_4

value: WT


title: S6_S19

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 352M4


title: Hap1_Baz2B_KO_1


title: NTRK2ko 0h rep2


title: Hap1_ctrl_1

source_name: Hap1 cell line

value: Hap1 parental control


title: iWAT aKO_4

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

description: Gene expression profiles of iWAT obtained from Senp2-aKO mouse

hyb_protocol: Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent. Then, it was hybridized on microarrays for 40h at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: The array was scanned using a SureScan Microarray Scanner (Agilent).

data_processing: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software (version 11.5.1) (Agilent). The log2-intensities of the probes from the arrays were normalized using the quantile normalization method.

source_name: inguinal white adipose tissue

label_protocol: Cy3 labeled cRNA was prepared from 0.5 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: All animals were housed at 22-24°C, with a 12:12-h light-dark cycle and ad libitum access to diet and water.

extract_protocol: Total RNAs were isolated using TRIzol (Invitrogen, MA, USA) according to the manufacturer’s instruction.

treatment_protocol: Eight week-old mice were fed a high-fat diet, (HFD; 58 kcal% fat w/sucrose, D12331; Research Diets, New Brunswick, NJ, USA) for 12 weeks.

value: inguinal white adipose tissue

value: Senp2flox/flox ; Adipoq Cre


title: S5_S18

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 352F1


title: Hap1_ctrl_2


title: Bisulfite-seq_fresh_ductal_methyl_3

city: San Antonio


title: SASD,120h

data_processing:
adaptor and low-quality sequencing data were removed by trimmomatic(v0.39)
each sample were mapped to the mouse genome (mm10) via STAR (v2.7.9a)
Uniquely mapped reads were assigned to genes based on the annotation file using FeatureCounts (v2.0.3) from Subread package
Assembly: mm10
Supplementary files format and content: tab-delimited text files include feature count values for each Sample

extract_protocol:
For blood sampling, each mouse was anesthetized with pentobarbital (i.p. 80 mg/kg) and taken 500 μL blood retro-orbitally which was collected in an EDTA anticoagulant tube (BD Biosciences). Total RNA was extracted from the blood samples of 3 mice in the same group with QIAamp RNA Blood Mini Kit (52304, Qiagen) following the manufacturer’s instructions.
The sequencing libraries were prepared with Illumina Truseq Library Prep Kits v2 (Illumina) according to the manufacturer’s instructions. All libraries were guaranteed quality with quality check


title: S4_S17

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 353F3


title: SASD,24h


title: S3_S16

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 353F1


title: Bisulfite-seq_fresh_acinar_methyl_5


title: Bisulfite-seq_fresh_acinar_methyl_4


title: Bisulfite-seq_fresh_ductal_methyl_1


title: SASD,12h


title: scRNA,Con


title: SASD,6h


title: Bisulfite-seq_fresh_acinar_methyl_3


title: P9_S13

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 355F1


title: SD,48h


title: iWAT aKO_1


title: iWAT cont_3

description: Gene expression profiles of iWAT obtained from control mouse


title: iWAT aKO_3


title: S2_S15

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 344F2