title: brain tissue, zika, day 9, rep3

city: Guangzhou

first: zheng

last: wenjiang

state: Guangdong

department: The First Clinical Medical School

institute: Guangzhou University of Chinese Medicine

description:
zika-brain-3
brain count.xlsx
brain FPKM.xlsx

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000.
Filtering of Clean Reads: Reads obtained from the sequencing machines include raw reads containing adapters or low-quality bases which will affect the following assembly and analysis. Thus, to get high-quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low-quality reads containing more than 50% of low-quality (Q-value≤20) bases.
Alignment with Ribosome RNA (rRNA): Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to the ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
Alignment with Reference Genome: An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT (version 2. 2.4) with “-rna-strandness RF” and other parameters set as a default.
Quantification of Gene Abundance: The mapped reads of each sample were assembled by using StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
The FPKM method is able to eliminate the influence of different gene lengths and sequencing data amounts on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference in gene expression among samples.
Differential gene expression analysis was performed using the DESeq2 (2014) R package
Assembly: (GRCm39) http://ftp.ensembl.org/pub/release-104/gtf/mus_musculus/
Supplementary files format and content: Excel files include count values for each sample

source_name: brain

growth_protocol: IFNAR-/- mice on the C57BL/6J background were generated and bred in-house under specific pathogen-free conditions in our laboratory at 21 °C in 55% humidity on a 12:12 h light: dark cycle.

extract_protocol:
Total RNA was extracted from mouse brain and liver tissue using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end-repaired, and A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X). Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq 6000.

treatment_protocol:
Male mice (6-8 weeks old) were challenged intraperitoneally (i.p.) with the zika virus (zika virus infection group, n=3, 1×10^6 PFU) .
Mice injected with an equivalent volume of PBS (mock infection) were used as negative controls (n=3).

value: IFNAR knockdown

value: zika virus i.p.

tag: time

value: day 9

value: brain


title: BTH-treated root, 14 days after transplantation, rep 3

status: Public on Dec 06 2022

type: SRA

city: Ghent

first: Willem

last: Desmedt

address: Valentin Vaerwyckweg 1

department: Plants and Crops

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
Quality assesment using FastQC v0.11.8
Trimming with Trimmomatic v0.38 (Phred > 20, length > 40)
Mapping to rice reference genome (MSU 7.0) using STAR v2.6.1d
Counting reads using R GenomicAlignments package (summarizeOverlaps function)
Normalization and differential expression analysis using the R DeSeq2 package
Genome_build: MSU 70.
Supplementary_files_format_and_content: DeSeq2-output in a csv file
Supplementary_files_format_and_content: count table (normalized using DeSeq2)

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Rice root

growth_protocol: Rice seedlings (cv. Kitaake) were  germinated on wet tissue paper (28°C, dark), transplanted to individual PVC tubes 5 days after germination and placed in a growth chamber (28°C, 12 hours of light)

extract_protocol:
Plants were washed, pooled (4 plants per sample) and root and shoot tissues were ground seperately in liquid nitrogen. RNA was extracted using a Qiagen RNEasy Plant Mini Kit per manufacturer's instructions.
QuantSeq 3′mRNA-Seq Library Prep Kit (Lexogen) as per manufacturer's instruction, starting from 2 µg RNA.

treatment_protocol: Plants were foliarly sprayed with a solution containing 0.1 v/v% Tween 20 and the active compound 13 days post transplantation.

tag: tissue

value: root

tag: cultivar

value: Kitaake

tag: age

value: 14 days post transplantation

tag: treatment time

value: 13 days post transplantation

tag: treatment

value: acibenzolar-S-methyl (250 microM)


title: Quiescent CM+ IgG rep 4

city: South San Francisco

first: David

last: Garfield

state: CA

address: 1 DNA Way

department: OMNI Bx

country: USA

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie v4.2.2
GSNAP v2013-11-01 was used for alignment, through the HTSeqGenie wrapper, against the mouse reference genome (NCBI Build 38).
Read counts were scaled by library size, quantile normalized and precision weights were calculated using the voom R package
Differential expression analysis was performed using the limma package
Assembly: mm10
Supplementary files format and content: TSV count matrices

organism: Mus musculus

source_name: Small intestine, Jejunum

growth_protocol: Mouse intestinal organoids were cultured in Intesticult, which is referred as complete culture media (STEMCELL technologies).

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
cDNA library was generated from 2 ng of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara). 150 pg of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina)

treatment_protocol: Organoids were either cultured in quiescent or senescent conditioned media or Wnt5a containing media with IgG or anti-Ptk7 antibodies.

value: Small intestine, Jejunum

tag: cell type

value: Intestinal organoids

tag: strain

value: Quiescent CM+ IgG


title: brain tissue, zika, day 9, rep2

country: China

description:
zika-brain-2
brain count.xlsx
brain FPKM.xlsx

tag: genotype


title: iPSC 104 ENDO

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: iPSC 104 ENDO

data_processing:
Quality Control: FastQC
Trimming adaptor and low quality seqs: Trimmomatic
Alignment: Star-aligner
Read counting: FeatureCount
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

organism: Homo sapiens

source_name: iPSC

growth_protocol: The iPSC lines were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew XF (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany).
Library preparation was carried out using QuantSeq 3´-mRNA (Lexgon) according to the manufacturer's instructions. Sequencing was done using NovaSeq 6000 sequencer (Ilumina). Library preparation and sequencing was carried out by Life&Brain (Bonn, Germany).

tag: gender

value: female

tag: time (days)

tag: sample group

value: endoderm


title: brain tissue, zika, day 9, rep1

description:
zika-brain-1
brain count.xlsx
brain FPKM.xlsx


title: iPSC 106 MESO

description: iPSC 106 MESO

value: male

value: mesoderm


title: PN21 Cell 43

city: Stanford

first: Christin

middle: S

last: Kuo

address: 240 Pasteur Dr.

institute: Stanford University

data_processing:
Raw sequence reads were demultiplexed using bcl2fastq (v1.8.4, Illumina)
sequences aligned to the mouse reference genome (GRCm38-mm10, UCSC, supplemented with Zsgreen1 sequence) with STAR
number of reads that mapped to each annotated gene (gene counts) determined with HTSEQ (v0.6.1p1, default parameters except Stranded set to false and Mode set to intersection-nonempty)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: postnatal 21 days

value: wild type

tag: group


title: iPSC 104 ECTO

description: iPSC 104 ECTO

value: ectoderm


title: PA1x-treated root, 14 days after transplantation, rep 3

value: Piperonylic acid (300 microM)


title: brain tissue, control, day 9, rep3

description:
control-brain-3
brain count.xlsx
brain FPKM.xlsx

value: IFNAR knockdown

value: PBS i.p.

value: day 9

value: brain


title: BTH-treated root, 14 days after transplantation, rep 1

value: root

value: Kitaake

value: 14 days post transplantation

value: 13 days post transplantation

value: acibenzolar-S-methyl (250 microM)


title: brain tissue, control, day 9, rep2

description:
control-brain-2
brain count.xlsx
brain FPKM.xlsx


title: iPSC 102 undifferentiated

description: iPSC 102 undifferentiated

value: female

value: undifferentiated


title: PA1x-treated root, 14 days after transplantation, rep 2


title: PN21 Cell 42


title: BABA-treated root, 14 days after transplantation, rep 3

value: R,S-BABA (3.5 mM)


title: PN21 Cell 41

value: lung


title: PA1x-treated root, 14 days after transplantation, rep 1


title: iPSC 102 ECTO

description: iPSC 102 ECTO


title: BABA-treated root, 14 days after transplantation, rep 1


title: BABA-treated root, 14 days after transplantation, rep 2


title: liver tissue, zika, day 9, rep3

description:
zika-liver-3
liver count.xlsx
liver FPKM.xlsx

source_name: liver

value: zika virus i.p.

value: liver


title: iPSC 102 ENDO

description: iPSC 102 ENDO

value: endoderm


title: brain tissue, control, day 9, rep1

description:
control-brain-1
brain count.xlsx
brain FPKM.xlsx


title: BTH-treated root, 14 days after transplantation, rep 2


title: PN21 Cell 39

value: postnatal 21 days

value: wild type


title: Mock-treated root, 14 days after transplantation, rep 3

value: Mock


title: PN21 Cell 38


title: liver tissue, zika, day 9, rep1

description:
zika-liver-1
liver count.xlsx
liver FPKM.xlsx

value: IFNAR knockdown

value: day 9


title: PN21 Cell 37


title: liver tissue, control, day 9, rep3

description:
control-liver-3
liver count.xlsx
liver FPKM.xlsx

value: PBS i.p.


title: Mock-treated root, 14 days after transplantation, rep 1

value: root

value: Kitaake


title: Mock-treated root, 14 days after transplantation, rep 2

value: 14 days post transplantation

value: 13 days post transplantation


title: NCS 24 rep 3

city: Minneapolis

first: Eric

last: Batchelor

state: Minnesota

department: Integrative Biology and Physiology

institute: University of Minnesota

data_processing:
aligned reads to the genome using Hisat2 with default settings
Aligned reads were counted using the htseq-count module within Galaxy
Counted reads were then input into DESeq2 to identify differentially expressed genes.  To enable comparisons between both untreated and treated samples, as well as across treatments we used the output of all levels vs all levels.
Additional output from DESeq2 included rLog normalized counts
Genome_build: hg19
Supplementary_files_format_and_content: rLog normalized counts output from DESeq2

source_name: pancreatic cell line

growth_protocol: The immortalized non-transformed pancreatic cell line hTERT-HPNE was obtained from the ATCC (CRL-4023) and were maintained in growth media consisting of 75% DMEM without glucose (ThermoFisher, 11966025) and 25% M3 BaseF media (InCell, M300F).  Media was supplemented with 5% FBS, 1X Amphotericin B/penicillin/streptomycin mix (Fisher Scientific, 50-751-7247) , 5.5 mM D-glucose (VWR, MK491212), and 750 ng/ml puromycin.  10 ng/ml EGF (Peprotech, AF-100-15) was added fresh to media prior to use with cells.

extract_protocol:
RNA was isolated at 0, 4, 8, and 24-hours post-treatment using the RNeasy Plus Minikit (Qiagen, Cat#74134) according to manufacturer specifications.  For each time point and condition we collected 3 biological replicates. RNA integrity was confirmed by Agilent TapeStation
library prepared using TruSeq Stranded mRNA library prep

treatment_protocol: Media was replaced with fresh media and cells were treated with either 400 ng/ml NCS or 300 µM H2O2.

value: 400 ng/ml Neocarzinostatin

tag: cell line

value: hTERT-HPNE

tag: time point


title: NCS 24 rep 2


title: iPSC 102 MESO

description: iPSC 102 MESO

value: female

value: mesoderm


title: liver tissue, control, day 9, rep2

description:
control-liver-2
liver count.xlsx
liver FPKM.xlsx


title: PN21 Cell 36

value: lung


title: NCS 24 rep 1


title: liver tissue, control, day 9, rep1

description:
control-liver-1
liver count.xlsx
liver FPKM.xlsx

value: liver


title: PN21 Cell 40


title: REP3-PA-6h

data_processing:
Quality assesment using FastQC v0.11.8
Trimming with Trimmomatic v0.38 (Phred > 20, length > 40)
Mapping to rice reference genome (MSU 7.0) using STAR v2.6.1d
Counting reads using R GenomicAlignments package (summarizeOverlaps function)
Normalization and differential expression analysis using the R DeSeq2 package
Genome_build: MSU 70.
Supplementary_files_format_and_content: count table (normalized using DeSeq2)

molecule: polyA RNA

source_name: PA-treated root, 6h after second treatment, rep 2

growth_protocol: Rice seedlings (cv. Nipponbare) were  germinated on wet tissue paper (28°C, dark), transplanted to individual PVC tubes 5 days after germination and placed in a growth chamber (28°C, 12 hours of light)

extract_protocol:
Plants were washed, pooled (4 plants per sample) and root and shoot tissues were ground seperately in liquid nitrogen. RNA was extracted using a Zymo Plant RNA kit as per manufacturer's instructions (Zymo Research).
QuantSeq 3′mRNA-Seq Library Prep Kit (Lexogen) as per manufacturer's instruction, starting from 2 µg RNA.

treatment_protocol: Plants were foliarly sprayed with a solution containing 300 µM PA and 0.1 v/v% Tween 20 or a corresponding mock solution 13 days post transplantation.

value: Nipponbare

value: Piperonylic acid (300 uM)


title: PN21 Cell 35

value: postnatal 21 days

value: wild type


title: PN21 Cell 34


title: liver tissue, zika, day 9, rep2

description:
zika-liver-2
liver count.xlsx
liver FPKM.xlsx

value: IFNAR knockdown

value: zika virus i.p.


title: NCS 8 rep 1


title: 29

city: Dallas

first: Zhenyu

last: Zhong

state: Texas

address: 5323 Harry Hines Blvd, NA7.108B

department: Immunology

institute: UT Southwestern Medical Center

data_processing:
Trim the ends of sequences with remaining adapter or quality scores < 25. Remove any sequence less than 35bp after trimming, then generate a file for capturing information about how many sequences were trimmed.
Trimmed Fastq files are aligned to the selected reference genome using HiSAT2 (Kim et al. 2015) or STAR (Dobin et al. 2012)
Marks Duplicates using SAMBAMBA
Features (genes, transcripts and exons) are counted using featureCounts (Liao et al 2014) and StringTie (Pertea et al. 2015) using the Gencode feature table(Harrow et al. 2012)
Basic pairwise differential expression analysis is performed using EdgeR (Robinson et al. 2010) and DESeq
Abundances of transcripts are calculated using ballgown (Frazee et al. 2014)
Identify gene fusions or fused transcripts using STAR-Fusion.
Assembly: mm10
Supplementary files format and content: xls, fpkm value or samples, Sample_description

source_name: Liver macrophages WD

extract_protocol:
Cells were lyzed in Trizol for 10 minutes (min) at room temperater (RT). Then 200μl chloroform were added. Votex to mix well and stand at RT for 15 min. After 10 min centrifuge at 12000rpm and 4oC, upper clear layer (350μl) with RNA inside was collected. Later steps were performed with a QIAprep Spin Miniprep Kit according to the instrucions provided.
After the QC procedures, mRNA was enriched using oligo(dT) beads.  First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamer primers, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

value: Liver macrophages

value: Liver

tag: diet

value: WD


title: REP2-PA-24h

source_name: PA-treated root, 24h after second treatment, rep 2

value: root

value: 14 days post transplantation


title: 25


title: REP2-PA-6h

source_name: PA-treated root, 6h after second treatment, rep 1

value: 13 days post transplantation


title: PN21 Cell 33


title: NCS 4 rep 2

value: 400 ng/ml Neocarzinostatin

value: hTERT-HPNE


title: NCS 4 rep 3


title: REP1-PA-24h

source_name: PA-treated root, 24h after second treatment, rep 1


title: 24


title: PN21 Cell 31


title: PN21 Cell 30


title: NCS 4 rep 1


title: 35

source_name: Liver macrophages  ND

value: ND


title: 21


title: REP3-PA-24h


title: NCS 8 rep 3


title: REP1-PA-6h


title: H2O2 24 rep 3


title: PN21 Cell 32

value: lung


title: PN21 Cell 29


title: NCS 8 rep 2


title: PN21 Cell 28


title: 33


title: H2O2 24 rep 2


title: REP2-CON-24h

source_name: Mock-treated root, 24h after second treatment, rep 2

value: Mock


title: REP3-CON-24h

source_name: Mock-treated root, 24h after second treatment, rep 3

value: Nipponbare


title: 34


title: PN21 Cell 27


title: H2O2 24 rep 1


title: REP2-CON-6h

source_name: Mock-treated root, 6h after second treatment, rep 2


title: 31


title: PN21 Cell 26


title: H2O2 8 rep 3


title: PN21 Cell 25


title: REP1-CON-24h

source_name: Mock-treated root, 24h after second treatment, rep 1


title: Liver macrophages Normal Diet 18 weeks M673

data_processing:
Trim the ends of sequences with remaining adapter or quality scores < 25. Remove any sequence less than 35bp after trimming, then generate a file for capturing information about how many sequences were trimmed.
Trimmed Fastq files are aligned to the selected reference genome using HiSAT2 (Kim et al. 2015) or STAR (Dobin et al. 2012)
Marks Duplicates using SAMBAMBA
Features (genes, transcripts and exons) are counted using featureCounts (Liao et al 2014) and StringTie (Pertea et al. 2015) using the Gencode feature table(Harrow et al. 2012)
Basic pairwise differential expression analysis is performed using EdgeR (Robinson et al. 2010) and DESeq
Abundances of transcripts are calculated using ballgown (Frazee et al. 2014)
Identify gene fusions or fused transcripts using STAR-Fusion.
Genome_build: mm10
Supplementary_files_format_and_content: xls, fpkm value or samples, Sample_description

source_name: Liver macrophages

value: Normal diet 18 weeks


title: H2O2 8 rep 2


title: Liver macrophages Normal Diet 18 weeks M671


title: R3-PA-Mg-96h

description: PA-treated, M. graminicola-inoculated root, 96h after second treatment, rep 3

data_processing:
Quality assesment using FastQC v0.11.8
Trimming with Trimmomatic v0.38 (Phred > 20, length > 40)
Mapping to rice reference genome (MSU 7.0) using STAR v2.6.1d
Counting reads using R GenomicAlignments package (summarizeOverlaps function)
Normalization and differential expression analysis using the R DeSeq2 package
Genome_build: MSU 70.
Supplementary_files_format_and_content: DeSeq2-output in a csv file

source_name: Rice root

treatment_protocol: Plants were foliarly sprayed with a solution containing 300 µM PA and 0.1 v/v% Tween 20 or a corresponding mock solution at two time points: 7 and 14 days post transplantation.

value: 17 days post transplantation

value: 7 and 13 days post transplantation

value: Piperonylic acid (300 uM) + M. graminicola inoculation


title: Liver macrophages Normal Diet 18 weeks M670


title: H2O2 8 rep 1


title: PN21 Cell 24

value: postnatal 21 days

value: wild type


title: H2O2 4 rep 3


title: REP3-CON-6h

source_name: Mock-treated root, 6h after second treatment, rep 3


title: PN21 Cell 23


title: REP1-CON-6h

source_name: Mock-treated root, 6h after second treatment, rep 1


title: Liver macrophages High Fat Diet 18 weeks M646

value: Liver

value: High fat diet 18 weeks


title: R3-PA-Mg-48h

description: PA-treated, M. graminicola-inoculated root, 48h after second treatment, rep 3

value: root

value: 15 days post transplantation


title: PN21 Cell 22

source_name: Lung


title: R2-PA-Mg-96h

description: PA-treated, M. graminicola-inoculated root, 96h after second treatment, rep 2


title: H2O2 4 rep 2


title: Liver macrophages High Fat Diet 18 weeks M639


title: H2O2 4 rep 1


title: Liver macrophages High Fat Diet 18 weeks M640


title: PN21 Cell 21


title: R2-PA-Mg-48h

description: PA-treated, M. graminicola-inoculated root, 48h after second treatment, rep 2


title: H2O2 0 rep 3

value: Untreated


title: PN21 Cell 20


title: R1-PA-Mg-96h

description: PA-treated, M. graminicola-inoculated root, 96h after second treatment, rep 1


title: KOS1P_94

data_processing:
Trim the ends of sequences with remaining adapter or quality scores < 25. Remove any sequence less than 35bp after trimming, then generate a file for capturing information about how many sequences were trimmed.
Trimmed Fastq files are aligned to the selected reference genome using HiSAT2 (Kim et al. 2015) or STAR (Dobin et al. 2012).
Marks Duplicates using SAMBAMBA.
Features (genes, transcripts and exons) are counted using featureCounts (Liao et al. 2014) and StringTie (Pertea et al. 2015) using the Gencode feature table (Harrow et al. 2012).
Basic pairwise differential expression analysis is performed using EdgeR (Robinson et al. 2010) and DESeq.
Abundances of transcripts are calculated using ballgown (Frazee et al. 2014).
Identify gene fusions or fused transcripts using STAR-Fusion.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: fpkm_sample.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Primary bone marrow derived macrophages

growth_protocol: Fresh bone marrow cells from C57BL/6 mice were maintained in condition culture medium derived form L929 cells supplemented with 10% FBS and 1% penicillin and streptomycin for 7 days before further treatments.

extract_protocol:
Cells were lyzed in Trizol for 10 minutes (min) at room temperature (RT). Then 200μl chloroform were added. Vortex to mix well and stand at RT for 15 min. After 10 min centrifuge at 12000rpm and 4oC, upper clear layer (350μl) with RNA inside was collected. Later steps were performed with a QIAprep Spin Miniprep Kit according to the instructions provided.
After the QC procedures, mRNA was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamer primers, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: A number of 2X10^6 differentiated BMDM cells were placed in 6-well plates, which were than incubated with apoptotic cell culture medium or S1P (500nM) for 24 hours before harvest for RNA extraction. (ACM: After 24-hour treatment with 800μM palmitic, AML12 cells were identified as apoptotic. After the apoptotic cells were established, the cells were placed in fresh FBS-free medium for 24 hours for the generation of apoptotic cell culture medium (ACM)).

value: Primary BMDM

value: S1P treated


title: H2O2 0 rep 2

source_name: pancreatic cell line

value: hTERT-HPNE


title: KOS1P_92


title: PN21 Cell 19

value: lung


title: KOS1P_93


title: R1-PA-Mg-48h

description: PA-treated, M. graminicola-inoculated root, 48h after second treatment, rep 1


title: H2O2 0 rep 1


title: PN21 Cell 18


title: KOS1P_91


title: PN21 Cell 17


title: 96_Macro-DNS4-CSF1-IL32_IL32

city: Nantes

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

data_processing:
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq files into a single-end fastq file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Macrophage

growth_protocol: Monocytes were obtained by elutriation and T cells were separated using anti-human CD3 magnetic beads. Monocyte-derived macrophages were differentiated with  CSF1 (5 days).

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)

treatment_protocol: treated with recombinant human (rh)IL32β (100 ng/ml)  for 24 hours

value: treated with recombinant human (rh)IL32β (100 ng/ml)  for 2 days


title: R3-CON-Mg-48h

description: Mock-treated, M. graminicola-inoculated root, 48h after second treatment, rep 3

value: Nipponbare

value: Mock + M. graminicola inoculation


title: 95_Macro-DNS4-CSF1_CT

value: untreated


title: PN21 Cell 16


title: KOACM_88

value: ACM treated


title: KOACM_87


title: R2-CON-Mg-96h

description: Mock-treated, M. graminicola-inoculated root, 96h after second treatment, rep 2

value: 17 days post transplantation

value: 7 and 13 days post transplantation


title: KOACM_86


title: PN21 Cell 14

value: postnatal 21 days

value: wild type


title: 93_Macro-DNS3-CSF1_CT


title: 94_Macro-DNS3-CSF1-IL32_IL32


title: R1-CON-Mg-96h

description: Mock-treated, M. graminicola-inoculated root, 96h after second treatment, rep 1


title: PN21 Cell 12


title: R3-CON-Mg-96h

description: Mock-treated, M. graminicola-inoculated root, 96h after second treatment, rep 3


title: R1-CON-Mg-48h

description: Mock-treated, M. graminicola-inoculated root, 48h after second treatment, rep 1


title: KOACM_85


title: PN21 Cell 13


title: R3-PA-96h

description: PA-treated root, 96h after second treatment, rep 3

value: Piperonylic acid (300 uM)


title: PN21 Cell 11


title: KONC_81

value: Untreated control


title: R3-PA-48h

description: PA-treated root, 48h after second treatment, rep 3

value: root

value: 15 days post transplantation


title: KONC_80

value: Primary BMDM


title: PN21 Cell 15


title: R3-PA-24h

description: PA-treated root, 24h after second treatment, rep 3

value: 14 days post transplantation


title: PN21 Cell 9


title: KONC_79


title: R2-CON-Mg-48h

description: Mock-treated, M. graminicola-inoculated root, 48h after second treatment, rep 2


title: R2-PA-96h

description: PA-treated root, 96h after second treatment, rep 2


title: 92_Macro-CSF1-IL32_IL32


title: 90_Mono-3--IL32-24H_IL32

source_name: Monocyte

value: treated with recombinant human (rh)IL32β (100 ng/ml)  for 24 hours


title: 91_Macro-CSF1_CT


title: 102_MONO-5-Ct_Ct


title: 103_MONO-5-IL32_IL32


title: 89_Mono-3-ct-24H_CT


title: KONC_82


title: PN21 Cell 8

value: lung


title: WTS1P_28

value: WT

value: S1P treated


title: R2-PA-48h

description: PA-treated root, 48h after second treatment, rep 2

value: Nipponbare


title: PN21 Cell 7


title: R2-PA-24h

description: PA-treated root, 24h after second treatment, rep 2


title: WTS1P_27


title: 85_Mono-1-ct-24H_CT

value: untreated


title: R1-PA-96h

description: PA-treated root, 96h after second treatment, rep 1


title: PN21 Cell 10


title: 84_LT-DNS751-IL32-24H_IL32

source_name: T Lymphocyte


title: PN21 Cell 5


title: WTS1P_26


title: WTS1P_25


title: R1-PA-48h

description: PA-treated root, 48h after second treatment, rep 1


title: 83_LT-DNS751-ct-24H_CT


title: R1-PA-24h

description: PA-treated root, 24h after second treatment, rep 1


title: PN21 Cell 4


title: WTACM_22

value: ACM treated


title: 82_LT-DNS561-IL32-24H_IL32


title: PN21 Cell 3


title: WTACM_20


title: WTACM_21


title: R3-CON-48h

description: Mock-treated root, 48h after second treatment, rep 3

value: Mock


title: 81_LT-DNS561-ct-24H_CT


title: PN21 Cell 2


title: R3-CON-96h

description: Mock-treated root, 96h after second treatment, rep 3

value: 17 days post transplantation

value: 7 and 13 days post transplantation


title: R3-CON-24h

description: Mock-treated root, 24h after second treatment, rep 3


title: 80_LT-DNS614-iL32-24H_IL32


title: 79_LT-DNS614-ct-24H_CT


title: PN21 Cell 1

value: postnatal 21 days

value: wild type


title: WTNC_4

value: Untreated control


title: WTACM_19


title: R2-CON-96h

description: Mock-treated root, 96h after second treatment, rep 2

value: root


title: PN21 Cell 6


title: 86_Mono-1--IL32-24H_IL32


title: WTNC_3


title: SNPH KO cells, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: SNPH KO cells, replicate 2

data_processing:
RNA-Seq data analysis was done with RSEM (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: bone marrow neutrophils

extract_protocol:
Neutrophils were isolated using Ly6G beads with purity was >95%
RNA-seq libraries were constructed using Lexogen QuantSeq kit

tag: condition

value: KO

tag: snph

value: knockout

tag: replicate


title: R2-CON-48h

description: Mock-treated root, 48h after second treatment, rep 2

tag: cultivar

tag: tissue

value: 15 days post transplantation


title: SNPH KO cells, replicate 3

description: SNPH KO cells, replicate 3


title: T0519-siCIRBP-replicate3

city: Beijing

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

growth_protocol: T0519 cells were cultured in Prigrow I medium supplemented with 10% fetal bovine serum and 1% antibiotics, at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Immortalized human cardiomyoctes

value: CIRBP knockdown


title: WTNC_2

value: WT

value: Primary BMDM


title: SNPH KO cells, replicate 1

description: SNPH KO cells, replicate 1


title: R2-CON-24h

description: Mock-treated root, 24h after second treatment, rep 2

value: Nipponbare

tag: age

value: 14 days post transplantation

tag: treatment time


title: T0519-siCIRBP-replicate2

tag: cell type

tag: treatment


title: WTNC_1

tag: strain

tag: genotype


title: T0519-NC-replicate3

value: NC


title: SNPH WT cells, replicate 3

description: SNPH WT cells, replicate 3

value: control


title: R1-CON-96h

description: Mock-treated root, 96h after second treatment, rep 1

value: 17 days post transplantation

value: Mock


title: SNPH WT cells, replicate 2

description: SNPH WT cells, replicate 2


title: sample1_GEX

city: Warsaw

first: Pawel

last: Segit

address: Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description: sample1 (hashed 6 samples: female control, male control, female tumor D14, male tumor D14, female tumor D21, male tumor D21); 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v3.0.1 (10x Genomics) and bcl2fastq v2.20.0.422 (Illumina)
Cell Ranger v4.0.0 count was used to align the demultiplexed reads to the reference genome (mm10), perform filtering, barcode counting, UMI (unique molecule identifier) counting and estimate the number of cells.
Data analysis was performed in R using Seurat v3 package.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: brain CD11b+, mRNA-derived cDNA

extract_protocol:
Animals were perfused transcardially with ice-cold phosphate-buffered saline (PBS), in order to remove blood cells from the brain. Next, brains were dissected and tumor-bearing hemispheres or whole brains (controls) were dissociated enzymatically.
Cell encapsulation and library preparation was performed with Chromium Controller (10x Genomics) and Chromium Next GEM Single Cell 3’ Reagent Kit v3 with Feature Barcoding technology for Cell Surface Protein (10x Genomics) according to the producer’s user guide (CG000185 Rev D).

value: Brain

value: 12 weeks

tag: library type

value: mRNA

tag: antibodies/tags


title: T0519-NC-replicate2


title: R1-CON-48h

description: Mock-treated root, 48h after second treatment, rep 1

value: root

value: 7 and 13 days post transplantation


title: sample1_ADT

description: sample1 (hashed 6 samples: female control, male control, female tumor D14, male tumor D14, female tumor D21, male tumor D21); Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein

source_name: brain CD11b+, ADT-derived cDNA

value: ADT

value: (CITE-seq, conjugated in-house) Recombinant Anti-TMEM119 antibody [106-6] - BSA and Azide free; (CITE-seq, conjugated in-house) Purified anti-mouse CD74 (CLIP) Antibody; (CITE-seq, conjugated in-house) Anti-CD52 (CAMPATH-1) (Mouse) mAb; (CITE-seq) TotalSeq™-B0014 Anti-CD11b; (CITE-seq) TotalSeq™-B0096 Anti-CD45; (CITE-seq) TotalSeq™-B0013 Anti-Ly-6C; (CITE-seq) TotalSeq™-B0116 Anti-Gr-1; (CITE-seq) TotalSeq™-B0190 Anti-CD274 (PD-L1); (CITE-seq) TotalSeq™-B0078 Anti- CD49d; (CITE-seq) TotalSeq™-B0117 Anti-I-A/I-E (MHCII); TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody; TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody; TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody; TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody; TotalSeq™-B0305 anti-mouse Hashtag 5 Antibody; TotalSeq™-B0306 anti-mouse Hashtag 6 Antibody


title: T0519-NC-replicate1

value: Immortalized human cardiomyoctes


title: R1-CON-24h

description: Mock-treated root, 24h after second treatment, rep 1


title: ATAC_P30_KO_1 [cone-ATAC-seq]

status: Public on Dec 05 2022

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

library_source: genomic

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq3000 Sequencer at NIDDK Genomics Facility
single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.3a)
Output RNA-seq bam files were analyzed with Genomatix programs with transcripts levels calculated as counts/reads per million mapped reads (CPM). ChAP-seq and ATAC-seq data were analyzed by MACS2 (v2.2.7.1)  for peak calling.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each gene of all samples

molecule: genomic DNA

organism: Mus

source_name: cone-ATAC-seq

extract_protocol:
Pieces from superior or inferior zones of retina were dissected from Trb2Cre:Ai6 mice, then dissassociated into suspension cells after brief papain treatment. Fluorescent cells were identified on a Zeiss Axiovert 200M microscope and collected individually using an Eppendorf micromanipulator and suction pipette. Collected single cone cells were transfer into individual PRC tubes for RNA-seq library construction. For ChAP-seq, retinas from ThrbHAB/HAB;Rosa26BirA/BirA and control Rosa26BirA/BirA E18 embryos were cross-linked and affinity-purified with streptavidin to collect the TRb-bound-DNA. For ATAC-seq, cone nuclei were immunopurified from retinas from control (TRb2Cre-het) and TRb2Cre-KO mice on a Rosa26Sun1Gfp/Sun1Gfp background, these purified cone nuclei were treated with Tagment enzyme (using Tagment DNA kit) before DNA purification.
Single-cell RNA-seq libraries were constructed by using SMART-Seq v4 Ultra Low Input RNA Kit and ThruPLEX DNA-Seq Kit. For ChAP-seq, the enriched-DNA samples were constructed into sequencing library by using ThruPLEX DNA-Seq Kit. For ATAC-seq,  Tagment-enzyme processed DNA samples were constructed into ATAC-seq library by using Tagment DNA kit.

value: purified cones

value: post natal day 30


title: ATAC_P30_Ctrl_1 [cone-ATAC-seq]


title: ChAP_e18_ctrl_1 [retina Trb-ChAP-seq]

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq3000 Sequencer at NIDDK Genomics Facility
single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.3a)
Output RNA-seq bam files were analyzed with Genomatix programs with transcripts levels calculated as counts/reads per million mapped reads (CPM). ChAP-seq and ATAC-seq data were analyzed by MACS2 (v2.2.7.1)  for peak calling.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each gene of all samples
Library strategy: ChAP-seq

source_name: Thrb-HAB-ChAP-seq

value: retina

value: BirA


title: ChAP_e18_TrbHAB_1 [retina Trb-ChAP-seq]


title: ChAP_e18_TrbHAB_2 [retina Trb-ChAP-seq]


title: ATAC_P30_Ctrl_2 [cone-ATAC-seq]


title: ChAP_e18_ctrl_2 [retina Trb-ChAP-seq]


title: 2m_Rod_29 [Single rod cell RNA-seq]

library_source: transcriptomic single cell

source_name: 2month single rod

value: rod

value: 2 month old


title: 2m_Rod_24 [Single rod cell RNA-seq]


title: 2m_Rod_23 [Single rod cell RNA-seq]


title: 2m_Rod_25 [Single rod cell RNA-seq]


title: 2m_Rod_28 [Single rod cell RNA-seq]


title: T0519-siCIRBP-replicate1

value: CIRBP knockdown


title: 2m_Rod_26 [Single rod cell RNA-seq]


title: 2m_Rod_22 [Single rod cell RNA-seq]


title: ATAC_P30_KO_2 [cone-ATAC-seq]


title: 2m_Rod_27 [Single rod cell RNA-seq]


title: SNPH WT cells, replicate 1

description: SNPH WT cells, replicate 1

value: WT

value: control


title: 2m_Rod_19 [Single rod cell RNA-seq]


title: 2m_Rod_18 [Single rod cell RNA-seq]


title: 2m_Rod_20 [Single rod cell RNA-seq]


title: 2m_Rod_16 [Single rod cell RNA-seq]


title: 2m_Rod_15 [Single rod cell RNA-seq]


title: 2m_Rod_14 [Single rod cell RNA-seq]


title: 2m_Rod_13 [Single rod cell RNA-seq]


title: 2m_Rod_11 [Single rod cell RNA-seq]


title: 2m_Rod_09 [Single rod cell RNA-seq]


title: 2m_Rod_10 [Single rod cell RNA-seq]


title: 2m_Rod_08 [Single rod cell RNA-seq]


title: 2m_Rod_07 [Single rod cell RNA-seq]


title: 2m_Rod_04 [Single rod cell RNA-seq]


title: 2m_Rod_21 [Single rod cell RNA-seq]


title: 2m_Rod_06 [Single rod cell RNA-seq]


title: 2m_Rod_02 [Single rod cell RNA-seq]


title: 2m_Rod_05 [Single rod cell RNA-seq]


title: 2m_KO_sup_48 [Single cone cell RNA-seq]

source_name: 2month KO single cone

value: superior-cone


title: 2m_KO_sup_49 [Single cone cell RNA-seq]


title: 2m_Rod_01 [Single rod cell RNA-seq]


title: 2m_KO_sup_43 [Single cone cell RNA-seq]


title: 2m_Rod_03 [Single rod cell RNA-seq]


title: 2m_KO_sup_46 [Single cone cell RNA-seq]


title: 2m_KO_sup_50 [Single cone cell RNA-seq]


title: 2m_KO_sup_47 [Single cone cell RNA-seq]


title: 2m_KO_sup_44 [Single cone cell RNA-seq]


title: 2m_KO_sup_42 [Single cone cell RNA-seq]


title: 2m_Rod_17 [Single rod cell RNA-seq]


title: 2m_KO_sup_40 [Single cone cell RNA-seq]


title: 2m_KO_sup_37 [Single cone cell RNA-seq]


title: 2m_KO_sup_39 [Single cone cell RNA-seq]


title: 2m_Rod_12 [Single rod cell RNA-seq]


title: 2m_KO_sup_38 [Single cone cell RNA-seq]


title: 2m_KO_sup_41 [Single cone cell RNA-seq]


title: 2m_KO_sup_35 [Single cone cell RNA-seq]


title: 2m_KO_sup_34 [Single cone cell RNA-seq]


title: 2m_KO_sup_33 [Single cone cell RNA-seq]


title: 2m_KO_sup_32 [Single cone cell RNA-seq]


title: 2m_KO_sup_28 [Single cone cell RNA-seq]


title: 2m_KO_sup_26 [Single cone cell RNA-seq]


title: 2m_KO_sup_30 [Single cone cell RNA-seq]


title: 2m_KO_sup_29 [Single cone cell RNA-seq]


title: 2m_KO_sup_31 [Single cone cell RNA-seq]


title: 2m_KO_sup_27 [Single cone cell RNA-seq]


title: 2m_KO_sup_25 [Single cone cell RNA-seq]


title: 2m_KO_sup_45 [Single cone cell RNA-seq]


title: 2m_KO_sup_24 [Single cone cell RNA-seq]


title: 2m_KO_sup_20 [Single cone cell RNA-seq]


title: 2m_KO_sup_15 [Single cone cell RNA-seq]


title: 2m_KO_sup_18 [Single cone cell RNA-seq]


title: 2m_KO_sup_21 [Single cone cell RNA-seq]


title: 2m_KO_sup_17 [Single cone cell RNA-seq]


title: 2m_KO_sup_23 [Single cone cell RNA-seq]


title: 2m_KO_sup_22 [Single cone cell RNA-seq]


title: 2m_KO_sup_13 [Single cone cell RNA-seq]


title: 2m_KO_sup_14 [Single cone cell RNA-seq]


title: 2m_KO_sup_11 [Single cone cell RNA-seq]


title: 2m_KO_sup_36 [Single cone cell RNA-seq]


title: 2m_KO_sup_10 [Single cone cell RNA-seq]


title: 2m_KO_sup_12 [Single cone cell RNA-seq]


title: 2m_KO_sup_08 [Single cone cell RNA-seq]


title: 2m_KO_sup_06 [Single cone cell RNA-seq]


title: 2m_KO_sup_09 [Single cone cell RNA-seq]


title: 2m_KO_sup_07 [Single cone cell RNA-seq]


title: 2m_KO_sup_04 [Single cone cell RNA-seq]


title: 2m_KO_sup_05 [Single cone cell RNA-seq]


title: 2m_KO_sup_03 [Single cone cell RNA-seq]


title: 2m_KO_sup_19 [Single cone cell RNA-seq]


title: 2m_KO_sup_02 [Single cone cell RNA-seq]


title: 2m_KO_sup_16 [Single cone cell RNA-seq]


title: 2m_KO_inf_44 [Single cone cell RNA-seq]

value: inferior-cone


title: 2m_KO_inf_48 [Single cone cell RNA-seq]


title: 2m_KO_sup_01 [Single cone cell RNA-seq]


title: 2m_KO_inf_45 [Single cone cell RNA-seq]


title: 2m_KO_inf_47 [Single cone cell RNA-seq]


title: 2m_KO_inf_46 [Single cone cell RNA-seq]


title: 2m_KO_inf_43 [Single cone cell RNA-seq]


title: 2m_KO_inf_37 [Single cone cell RNA-seq]


title: 2m_KO_inf_40 [Single cone cell RNA-seq]


title: 2m_KO_inf_38 [Single cone cell RNA-seq]


title: 2m_KO_inf_39 [Single cone cell RNA-seq]


title: 2m_KO_inf_41 [Single cone cell RNA-seq]


title: 2m_KO_inf_42 [Single cone cell RNA-seq]


title: 2m_KO_inf_31 [Single cone cell RNA-seq]


title: 2m_KO_inf_35 [Single cone cell RNA-seq]


title: 2m_KO_inf_33 [Single cone cell RNA-seq]


title: 2m_KO_inf_32 [Single cone cell RNA-seq]


title: 2m_KO_inf_29 [Single cone cell RNA-seq]


title: 2m_KO_inf_34 [Single cone cell RNA-seq]


title: 2m_KO_inf_27 [Single cone cell RNA-seq]


title: 2m_KO_inf_26 [Single cone cell RNA-seq]


title: 2m_KO_inf_25 [Single cone cell RNA-seq]


title: 2m_KO_inf_23 [Single cone cell RNA-seq]


title: 2m_KO_inf_20 [Single cone cell RNA-seq]


title: 2m_KO_inf_21 [Single cone cell RNA-seq]


title: 2m_KO_inf_22 [Single cone cell RNA-seq]


title: 2m_KO_inf_18 [Single cone cell RNA-seq]


title: 2m_KO_inf_14 [Single cone cell RNA-seq]


title: 2m_KO_inf_17 [Single cone cell RNA-seq]


title: 2m_KO_inf_16 [Single cone cell RNA-seq]


title: 2m_KO_inf_19 [Single cone cell RNA-seq]


title: 2m_KO_inf_15 [Single cone cell RNA-seq]


title: 2m_KO_inf_36 [Single cone cell RNA-seq]


title: 2m_KO_inf_13 [Single cone cell RNA-seq]


title: 2m_KO_inf_30 [Single cone cell RNA-seq]


title: 2m_KO_inf_08 [Single cone cell RNA-seq]


title: 2m_KO_inf_10 [Single cone cell RNA-seq]


title: 2m_KO_inf_12 [Single cone cell RNA-seq]


title: 2m_KO_inf_06 [Single cone cell RNA-seq]


title: 2m_KO_inf_28 [Single cone cell RNA-seq]


title: 2m_KO_inf_24 [Single cone cell RNA-seq]


title: 2m_KO_inf_02 [Single cone cell RNA-seq]


title: 2m_KO_inf_04 [Single cone cell RNA-seq]


title: 2m_KO_inf_03 [Single cone cell RNA-seq]


title: 2m_KO_inf_01 [Single cone cell RNA-seq]


title: 2m_KO_inf_05 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_53 [Single cone cell RNA-seq]

source_name: 2month single cone


title: 2m_ctrl_sup_51 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_52 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_50 [Single cone cell RNA-seq]


title: MICA II 064 RML

type: RNA

city: Southampton

first: Hannah

last: Burke

state: Hampshire

address: Tremona Road

country: United Kingdom

institute: University Hospital Southampton

description: COPD

data_processing: The mean Cq for all the universally expressed “normaliser” miRNA was calculated to give a Geomean Cq. Then, the following formula was used to calculate the normalized Cq values:  Normalized Cq of miRNA of interest (ΔCq) = Geomean Cq – miRNA of interest Cq  A higher value thus indicates that the miRNA is more abundant in the particular sample. Values were then presented as 2ΔCq to represent fold change.

label: FAM

source_name: Bronchoalveolar lavage extracellular vesicles

label_protocol: Reverse transcription was performed in 10µL reactions using the miRCURY LNA RT kit (Qiagen®). Following cDNA synthesis, qPCR was performed in a LightCycler® 480 Real-Time PCR System (Roche®) in 384 well plates. Amplification curves were analysed using the Roche LC software, for both determination of Cq (by the 2nd derivative method) and for melting curve analysis.

extract_protocol: Prior to RNA isolation, EVs (suspended in up to 200 μL of 1X PBS) were lysed using Buffer RPL at room temperature for 3 min. In order to assess the quality of RNA isolation across samples, Qiaseq miRNA Library Quality control (QC) Spike-Ins solution (contents listed in Table 2.3) was added to each of the lysed EV samples. RNA from EVs was then isolated by Qiagen® using the miRNeasy® Serum/Plasma Advanced kit (Qiagen®) following the manufacturer’s instructions.

tag: gender

value: Male


title: 2m_KO_inf_11 [Single cone cell RNA-seq]


title: MICA II 130 LLL

description: Healthy ES


title: MICA II 141 RML

description: Healthy ES

value: Female


title: 2m_KO_inf_07 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_49 [Single cone cell RNA-seq]


title: MICA II 140 RML

description: Healthy ES


title: 2m_KO_inf_09 [Single cone cell RNA-seq]


title: MICA II 133 RML

description: COPD


title: MICA II 046 RUL

description: Healthy ES


title: 2m_ctrl_sup_46 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_45 [Single cone cell RNA-seq]


title: MICA II 093 RML

description: COPD


title: MICA II 069 RML

description: COPD


title: MICA II 128 RLL

description: Healthy ES


title: MICA II 061 RLL

description: Healthy ES


title: 2m_ctrl_sup_43 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_44 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_42 [Single cone cell RNA-seq]


title: MICA II 056 RLL

description: Healthy ES


title: 2m_ctrl_sup_48 [Single cone cell RNA-seq]


title: MICA II 082 LLL

description: COPD


title: MICA II 147 LLL

description: COPD


title: 2m_ctrl_sup_40 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_39 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_47 [Single cone cell RNA-seq]


title: MICA II 135 LLL

description: Healthy ES


title: 2m_ctrl_sup_37 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_36 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_35 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_34 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_38 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_33 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_32 [Single cone cell RNA-seq]


title: MICA II 097 RUL

description: COPD


title: MICA II 144

description: COPD


title: MICA II 098 RML

description: COPD


title: MICA II 081 RML

description: COPD


title: MICA II 073 RLL

description: Healthy ES


title: MICA II 054 RML

description: COPD


title: 2m_ctrl_sup_31 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_41 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_30 [Single cone cell RNA-seq]


title: MICA II 085 RUL

description: COPD


title: MICA II 134 LLL

description: Healthy ES


title: 2m_ctrl_sup_29 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_28 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_27 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_26 [Single cone cell RNA-seq]


title: MICA II 077 RML

description: Healthy ES


title: 2m_ctrl_sup_25 [Single cone cell RNA-seq]


title: MICA II 079 RML

description: COPD


title: MICA II 131 RML

description: Healthy ES


title: MICA II 139 RUL

description: COPD


title: MICA II 105 RML

description: COPD


title: MICA II 132 RML

description: COPD


title: 2m_ctrl_sup_23 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_24 [Single cone cell RNA-seq]


title: MICA II 091 RML

description: COPD


title: 2m_ctrl_sup_22 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_21 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_20 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_18 [Single cone cell RNA-seq]


title: MICA II 034 RML

description: Healthy ES


title: MICA II 150 LLL

description: Healthy ES


title: 2m_ctrl_sup_17 [Single cone cell RNA-seq]


title: MICA II 148 LUL

description: COPD


title: MICA II 065 LLL

description: Healthy ES


title: MICA II 094 LLL

description: COPD


title: 2m_ctrl_sup_19 [Single cone cell RNA-seq]


title: MICA II 104 RML

description: COPD


title: MICA II 078 RML

description: COPD


title: 2m_ctrl_sup_16 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_15 [Single cone cell RNA-seq]


title: MICA II 062 RML

description: Healthy ES


title: MICA II 151 RML

description: COPD


title: 2m_ctrl_sup_14 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_13 [Single cone cell RNA-seq]


title: MICA II 095 LLL

description: Healthy ES


title: Control_Lung 1_IP

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

data_processing:
Removal of adapters and low-quality reads through Trimmomatic
Mapping through HISAT2
MeTDiff was used to find the differentially m6A peaks between the infected and non-infected samples with parameters-WINDOW_WIDTH=50, SLIDING_STEP=50, FRAGMENT_LENGTH=100, PEAK_CUTOFF_FDR=0.05, FOLD_ENRICHMENT=1 and DIFF_PEAK_CUTOFF_FDR=0.05
ChipSeekeer for annotation of differentially m6A peaks
Differential gene expression by edgeR package
Genome_build: ARS1 Goat Genome
Supplementary_files_format_and_content: .Xlsx -Differentially  m6A peaks  and Differenitally expressed genes

organism: Capra hircus

extract_protocol:
RNA isolation was carried out using Trizol
Truseq RNA Sample Preparation Kit-Nonstranded

value: Lung

tag: m6a antibody

value: m6A  antibody (NEB #E1610S)


title: 2m_ctrl_sup_11 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_12 [Single cone cell RNA-seq]


title: MICA II 100 LLL

description: COPD


title: MICA II 109 RML

description: Healthy ES


title: MICA II 076 LUL

description: Healthy ES


title: PPRV_Lung 2_IP


title: 2m_ctrl_sup_09 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_10 [Single cone cell RNA-seq]


title: PPRV_Lung 1_IP


title: 2m_ctrl_sup_08 [Single cone cell RNA-seq]


title: Control_Lung 2_Input


title: 2m_ctrl_sup_06 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_05 [Single cone cell RNA-seq]


title: PPRV_Lung 2_Input


title: MICA II 007 RML

description: Healthy ES


title: Control_Lung 1_Input


title: 2m_ctrl_sup_04 [Single cone cell RNA-seq]


title: DBP6-HTP

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

institute: Université Paris Descartes

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, using Flexbar with a barcode and an adaptor file using --adapter-trim-end RIGHT option.
Alignement was performed using Novoalign and -r Random option.
Aligned reads were analyzed using pyCRAC software.
Assembly: R64 (S.cerevisiae)
Supplementary files format and content: One of the sequence analysis corresponds to the numbert of hits in each genes per 1000000 reads.
Library strategy: CRAC

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast were grown in YMM, -trp + glucose, until final OD=0.6

extract_protocol:
Cell lysis was perfomed using Zirconium beads (5x 1minutes, with 1 minutes intervals on ice). Complex was isolated by two succesive IPs.
Library was constructed by linking to digested RNA illumina compatible 5' Adaptaters and 3' linkers. Then, those modified RNA were extracted and a Reverse Transcription was performed using Superscript III followed by a final moderate PCR enrichement (16 cycles). This was then analyzed on MiSeq plateform from illumina.

treatment_protocol: Protein were cross-linked to RNA using Megatron

value: HTP (His-Tev-ProtA)


title: 2m_ctrl_sup_03 [Single cone cell RNA-seq]


title: BY4742 control_1

value: no Tag


title: PPRV_Lung 1_Input


title: KO Neonate 3 [ATAC-seq]

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

data_processing:
alignment; bowtie2 with default parameters
create common peak set; bedops merge with default parameters
sort; samtools sort with default parameters
remove PCR duplicates; picard MarkDuplicates with REMOVE_DUPLICATES=TRUE
peak calling; macs callpeak with parameters -q 0.05 --keep-dup all
create common peak set; bedops merge with default parameters
generate count matrix; featureCounts
Assembly: mm10
Supplementary files format and content: text file; a count matrix with counts of raw reads overlapping peaks in each sample

extract_protocol:
Transposed DNA extracted with Qiagen MiniElute.
100bp paired-end

value: Alveolar macrophages

value: Postnatal Day 3


title: KO Neonate 2 [ATAC-seq]


title: 2m_ctrl_sup_01 [Single cone cell RNA-seq]


title: 2m_ctrl_sup_02 [Single cone cell RNA-seq]


title: KO Neonate 1 [ATAC-seq]


title: 2m_ctrl_sup_07 [Single cone cell RNA-seq]


title: WT Neonate 2 [ATAC-seq]

value: WT (C57Bl/6J)


title: 2m_ctrl_inf_46 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_49 [Single cone cell RNA-seq]


title: KO Adult 2 [ATAC-seq]

source_name: Broncho-alveolar lavage

value: Broncho-alveolar lavage

value: 6-8 weeks


title: 2m_ctrl_inf_50 [Single cone cell RNA-seq]

value: 2 month old


title: 2m_ctrl_inf_44 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_43 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_48 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_47 [Single cone cell RNA-seq]


title: WT Neonate 1 [ATAC-seq]

source_name: Lung


title: 2m_ctrl_inf_41 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_45 [Single cone cell RNA-seq]


title: KO Adult 3 [ATAC-seq]


title: 2m_ctrl_inf_39 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_38 [Single cone cell RNA-seq]


title: KO Adult 1 [ATAC-seq]


title: 2m_ctrl_inf_37 [Single cone cell RNA-seq]


title: WT Adult 3 [ATAC-seq]


title: Wild-type control mouse 2

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

description:
10x Genomics
P7832

data_processing:
The demultiplexing of samples P7644 and P7643 was done by Cellranger v4.0.0, and the demultiplexing of samples P7830, P7831, P7832 and P7833 was done by Cellranger v 6.0.1
Raw, demultiplexed fastq files were analyzed by CellRanger (v5.0.1) using reference genome mm10 (refdata-gex-mm10-2020-A, with the addition of human ATXN1 gene locus), with the option that allows alignment to un-spliced pre-mRNAs (--include-introns).
The raw UMI count matrix was cleaned via DIEM algorithm (PMID:32620816). In summary, DIEM models cell debris using cells with less than 1000 UMI detected (min_counts = 1000). In case of big input datasets, we increased the threshold to 3000 (for sample P7644 and P7643). Then the debris scores were manually inspected to exclude true debris.
The cleaned gene count table per donor was analyzed with R (v4.1.0) package Seurat (v 4.0.4) for cell type clustering and visualization. Further cell type identification was accomplished with SingleR (v 1.6.1) using DropViz Cerebellum MetaCells reference. We assigned cell types by requiring the same Seurat cluster and the same SingleR annotation.
Assembly: mm10 with human ATXN1 locus
Supplementary files format and content: Comma-separated values files

source_name: Cerebellum

extract_protocol:
Frozen or fresh whole cerebellum was placed into 1.5mL tube with 500uL pre-chilled detergent lysis buffer [low sucrose buffer (LSB) (sucrose 0.32M, 10 mM HEPES, 5mM CaCl2, 3mM MgAc, 0.1mM EDTA, 1mM DTT) with 0.1% Triton-X] and the tissue was homogenized using a mechanical homogenizer. A 40um strainer was placed over a pre-chilled 50mL tube and pre-wetted with 1ml LSB. 1mL of LSB was added to the tube containing the crude nuclei in the lysis buffer and mixed gently by pipetting (2-3 times). Crude nuclei prep was then passed over the 40uM strainer into the pre-chilled 50mL tube, washed with 1 ml LSB and centrifuged at 3200g for 10 minutes at 4C.  The pellet was resuspended in 3mL of LSB while gently swirling to remove the pellet from the wall, facilitating resuspension, and left on ice for 2 min. The suspension was transferred to an Oak Ridge tube and nuclei were homogenized in LSB for 15-30s, all while keeping the sample on ice. Using a serological pipette, 12.5mL of density sucrose buffer (sucrose 1M, 10 mM HEPES, 3mM MgAc, 1mM DTT) was layered underneath the LSB homogenate, taking care not to create a bubble which would disrupt the density layer. Samples were then centrifuged at 3200g for 20 minutes at 4C and pelleted nuclei were resuspended in the resuspension solution (PBS, 0.4 mg/ml BSA, 0.2 U/μl RNAse inhibitor). Nuclei were filtered through a 40um pore-size strainer followed by a 30um and 20um pore-size strainers. A small sample of nuclei was pelleted and added to a slide with VectaShield with DAPI to verify single nuclei isolation under fluorescent microscope.
Library construction and sequencing were done by University of Minnesota Genomic Center according to the manufacter’s instructions (10x Genomics).

value: Individual nuclei

value: Cerebellum

value: 12 weeks old


title: Wild-type control mouse 3

description:
10x Genomics
P7833


title: WT Adult 1 [ATAC-seq]


title: WT Neonate 3 [ATAC-seq]


title: 2m_ctrl_inf_40 [Single cone cell RNA-seq]


title: Wild-type control mouse 1

description:
10x Genomics
P7643


title: WT Adult 2 [ATAC-seq]


title: 2m_ctrl_inf_42 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_36 [Single cone cell RNA-seq]


title: SCA1 mouse 1

description:
10x Genomics
P7644


title: 2m_ctrl_inf_33 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_32 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_31 [Single cone cell RNA-seq]


title: KO [scRNA-seq]

data_processing:
cellranger 3.1.1
Assembly: mm10
Supplementary files format and content: text file; a gene x cell count matrix of scRNAseq reads

extract_protocol:
Single cell suspensions were loaded on a Next GEM Chip G (PN-1000120) together with Next GEM Single Cell 3ʹ GEM Kit v3.1 (PN-1000121) and single cells were captured on a 10X Genomics Chromium controller. cDNAs were generated following the 10X Genomics protocol. cDNAs were size selected using SPRIselect beads from Beckman Coulter (B23318), and their quality was checked with a Bioanalyzer High Sensitivity DNA Kit from Agilent (5067-4626). One quarter of the total cDNA was used to generate libraries using Chromium Next GEM Single Cell Library Kit (PN-1000121) and barcoded using the Single Index Kit Set A (PN-111213) following the 10X Genomics protocol. Libraries were size selected using SPRIselect beads and their quality was checked with the Bioanalyzer High Sensitivity DNA Kit.
read1=28 ; i7=10 ; i5=10 ; read2=90

value: CD45+ cells

value: Postnatal Day 1


title: SCA1 mouse 3

description:
10x Genomics
P7831


title: 2m_ctrl_inf_34 [Single cone cell RNA-seq]

value: inferior-cone


title: 2m_ctrl_inf_30 [Single cone cell RNA-seq]


title: SCA1 mouse 2

description:
10x Genomics
P7830


title: Samhd1_2_DP

city: Boston

first: Catherine

last: Wu

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome using STAR (v2.4.0.1).
Count value was used to measure gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including count values for all samples

source_name: edited B cell fraction from 4 month old spleen of Samhd1-depleted mouse

extract_protocol:
Harvested spleens were mechanically dissociated to form a single cell suspension. Erythrocyte lysis was carried out using ACK buffer and B cells from edited and unedited fractions isolated by cell sorting. Cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit.
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina).

value: spleen

value: Splenic B cell

tag: cell fraction

value: edited B cell fraction


title: Trp53_2_GFP

source_name: unedited B cell fraction from 4 month old spleen of Trp53-depleted mouse

value: unedited B cell fraction


title: Trp53_1_DP

source_name: edited B cell fraction from 4 month old spleen of Trp53-depleted mouse


title: 2m_ctrl_inf_35 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_26 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_25 [Single cone cell RNA-seq]


title: Samhd1_2_GFP

source_name: unedited B cell fraction from 4 month old spleen of Samhd1-depleted mouse


title: WT [scRNA-seq]

value: Lung


title: 2m_ctrl_inf_29 [Single cone cell RNA-seq]


title: Mga_1_DP

source_name: edited B cell fraction from 4 month old spleen of Mga-depleted mouse

value: Mga-depleted


title: Trp53_1_GFP


title: 2m_ctrl_inf_21 [Single cone cell RNA-seq]


title: MICA II 126 RML

description: COPD

value: Male


title: 2m_ctrl_inf_28 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_27 [Single cone cell RNA-seq]


title: Samhd1_1_DP


title: 2m_ctrl_inf_19 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_18 [Single cone cell RNA-seq]


title: Samhd1_1_GFP


title: Chd2_1_DP

source_name: edited B cell fraction from 4 month old spleen of Chd2-depleted mouse


title: 2m_ctrl_inf_16 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_24 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_14 [Single cone cell RNA-seq]


title: Trp53_2_DP


title: Birc3_2_GFP

source_name: unedited B cell fraction from 4 month old spleen of  Birc3-depleted mouse


title: 2m_ctrl_inf_13 [Single cone cell RNA-seq]


title: Mga_2_DP


title: 2m_ctrl_inf_23 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_22 [Single cone cell RNA-seq]


title: Atm_1_DP

source_name: edited B cell fraction from 4 month old spleen of Atm-depleted mouse

value: Atm-depleted


title: Mga_1_GFP

source_name: unedited B cell fraction from 4 month old spleen of Mga-depleted mouse


title: 2m_ctrl_inf_20 [Single cone cell RNA-seq]


title: Chd2_2_DP


title: Birc3_1_DP

source_name: edited B cell fraction from 4 month old spleen of  Birc3-depleted mouse


title: 2m_ctrl_inf_09 [Single cone cell RNA-seq]


title: Chd2_1_GFP

source_name: unedited B cell fraction from 4 month old spleen of Chd2-depleted mouse


title: 2m_ctrl_inf_17 [Single cone cell RNA-seq]

source_name: 2month single cone


title: Chd2_2_GFP


title: Birc3_2_DP


title: 2m_ctrl_inf_05 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_06 [Single cone cell RNA-seq]


title: RNA_MSC_HFD_OVX_2

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

description: RNA-seq, Primary stromal cells from bone marrow of OVX operated mice on high fat diet

data_processing:
RNA-seq reads were aligned to mm10 genome using STAR aligner and default settings.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Group (CTR_SHAM, CTR_OVX, HFD_SHAM, and HFD_OVX) into the design matrix, excluding genes which were not detected in any sample. Log 2 fold changes and FDR values were calculated with respect to CTR_SHAM.
Genome_build: mm10
Supplementary_files_format_and_content: Txt file containing raw counts and DEseq2 derived normalized andrlog transformed counts as well as p values, adjusted p values and logFC in comparison to CTR_SHAM

growth_protocol: Front and hind limbs were collected after 12 weeks of diet intervention, crushed and digested with 5% collagenase (StemCell). After filtration and washing steps with PBS/2%FBS, BMSCs were obtained as negative fraction from triple staining with antibodies against CD45, CD31 and Ter119 (Miltenyi Biotec) and passing through the magnetic columns. BMSCs were cultivated and expanded using standard tissue culture conditions and alpha-MEM supplemented with 20% FBS, 1% Penicilin-Strepotomycin 1% Glutamax, non-essential amino acids (NEAA) and pyruvate sodium (Gibco). At passage 3 cells were used for the subsequent molecular and cellular analyses.

extract_protocol:
RNA was extracted from cultured cells using Trizol combined with the Qiagen Rneasy Mini Kit (Qiagen).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol: Female C57BL/6J mice (Taconic, Rensselaer, NY, USA) at 8 weeks of age were assigned for either ovariectomy (OVX) or sham operation and afterwards fed a R-70 normal-diet (ND) (containing Kcal%: protein 14.5%, carbohydrates 60%, and fat 4.5%) or high-fat diet (HFD) (Research Diet [New Brunswick, NJ, USA] D12492, containing Kcal%: protein 20%, carbohydrates 20%, and fat 60%). Mice were anesthetized before ovariectomy by the dorsal approach using intraperitoneal injection of ketamine (100mg/kg) and xylazine (10mg/kg). Animals were fed ad libitum and housed (4 animals per cage) under standard conditions (21°C, 55% relative humidity) on a 12-hour light/dark cycle for a period of 12 weeks. All experimental procedures were approved by the Danish Animal Ethical committee (2017-15-0201-01210).

value: Primary stromal cells


title: 2m_ctrl_inf_15 [Single cone cell RNA-seq]


title: RNA_MSC_HFD_OVX_1

source_name: Primary stromal cells from bone marrow of OVX operated mice on high fat diet


title: Mga_2_GFP


title: Birc3_1_GFP

source_name: unedited B cell fraction from 4 month old spleen of Birc3-depleted mouse


title: 2m_ctrl_inf_12 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_03 [Single cone cell RNA-seq]


title: Atm_2_DP


title: Atm_2_GFP

source_name: unedited B cell fraction from 4 month old spleen of Atm-depleted mouse


title: 2m_ctrl_inf_11 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_08 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_01 [Single cone cell RNA-seq]


title: Atm_1_GFP


title: RNA_MSC_HFD_OVX_4


title: RNA_MSC_CTR_OVX_4

description: RNA-seq, Primary stromal cells from bone marrow of OVX operated mice on control diet


title: 2m_ctrl_inf_07 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_04 [Single cone cell RNA-seq]


title: RNA_MSC_CTR_OVX_2

source_name: Primary stromal cells from bone marrow of OVX operated mice on control diet


title: RNA_MSC_HFD_OVX_3


title: RNA_MSC_CTR_SHAM_3

description: RNA-seq, Primary stromal cells from bone marrow of sham operated mice on control diet


title: RNA_MSC_HFD_SHAM_4

description: RNA-seq, Primary stromal cells from bone marrow of sham operated mice on high fat diet


title: P60_ctrl_sup_24 [Single cone cell RNA-seq]

source_name: P60 single cone

value: superior-cone

value: post natal day 60


title: P60_ctrl_sup_23 [Single cone cell RNA-seq]


title: RNA_MSC_HFD_SHAM_1

source_name: Primary stromal cells from bone marrow of sham operated mice on high fat diet


title: P60_ctrl_sup_26 [Single cone cell RNA-seq]


title: RNA_MSC_HFD_SHAM_3


title: RNA_MSC_CTR_OVX_3


title: RNA_MSC_CTR_SHAM_1

source_name: Primary stromal cells from bone marrow of sham operated mice on control diet


title: RNA_MSC_HFD_SHAM_2


title: Bone marrow-derived CD19+ cells RAG-/- µ+ HiC E34.KO_1

city: San Diego

first: Edgar

middle: Mauricio

last: Barajas-Mora

address: 9500 Gilman Dr, La Jolla, CA

department: Molecular BIology

institute: UCSD

data_processing:
Samples were demultiplexed using bcl2fastq v1.8.4 Conversion Software (Illumina, San Diego, CA).
Hi-C data analysis pipeline to preprocess the Hi-C data available at https://github.com/ren-lab/hic-pipeline, as described in previous studies (Dixon et al., 2015; Schmitt et al., 2016; Zhang et al., 2019). Briefly, each single end read from the fastq files was mapped to the reference genome mm9 that retained uniquely mapped reads. PCR duplicates were removed. Next, juicer software (Durand et al., 2016) available at https://github.com/aidenlab/juicer was used to convert the mapped reads into the .hic files. Finally, we generated 50Kb bin resolution Hi-C raw contact matrices from the .hic files for the downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: hic matrix containing chromatin interaction frequencies.

growth_protocol: C57BL/6 or E34.KO RAG-/- µ+ pre-B cells were isolated by CD19+ MACS column separation.

extract_protocol:
HiC samples were prepared according to Arima-HiC+ kit (cat# A101020) following the manufacturer instructions.
HiC library was prepared according to Arima-HiC+ kit (cat# A101020) following the manufacturer instructions.

tag: genotype/variation

value: E34.KO RAG-/- u+ mice bearing a rearranged IgM transgene

value: Bone marrow-derived CD19+ cells


title: P60_ctrl_sup_27 [Single cone cell RNA-seq]


title: P60_ctrl_sup_20 [Single cone cell RNA-seq]


title: P60_ctrl_sup_18 [Single cone cell RNA-seq]


title: P60_ctrl_sup_25 [Single cone cell RNA-seq]


title: Bone marrow-derived CD19+ cells RAG-/- µ+ HiC E34.KO_2


title: Bone marrow-derived CD19+ cells RAG-/- µ+ HiC WT_1

value: RAG-/- u+ mice bearing a rearranged IgM transgene


title: P60_ctrl_sup_22 [Single cone cell RNA-seq]


title: 2m_ctrl_inf_10 [Single cone cell RNA-seq]

value: 2 month old


title: 2m_ctrl_inf_02 [Single cone cell RNA-seq]


title: RNA_MSC_CTR_SHAM_2


title: P60_ctrl_sup_21 [Single cone cell RNA-seq]


title: P60_ctrl_sup_19 [Single cone cell RNA-seq]


title: Bone marrow-derived CD19+ cells RAG-/- µ+ HiC WT_2


title: P60_ctrl_sup_17 [Single cone cell RNA-seq]


title: P60_ctrl_sup_14 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- µ+ RNA WT_1

data_processing:
Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).
RNAseq analysis. Fastq files were uploaded to usergalaxy.org. RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.7.8a) was run to obtain Bam files with the default parameters. Bam files were converted with CONVERTER_bam_to_bigwig_0 to bigwig files for visualization in the UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for reads

source_name: Bone marrow-derived pre-B cells RAG-/- µ+

growth_protocol: C57BL/6 or E34.KO RAG-/- µ+ pre-B cell were isolated by FACS after CD19+ colum separation enrichment.

extract_protocol:
RNA was isolated from 1x10^5-2x10^6 cells using QIAshredder (Cat. #79654, Qiagen) and the RNeasyTM Plus Mini Kit (Cat. #74134, Qiagen)
RNA sequencing libraries were generated using the Illumina Ribo-Zero Plus rRNA Depletion Kit with IDT for Illumina RNA UD Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions. Resulting libraries were multiplexed and sequenced with 100 bp Paired End (PE100) to a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000.

value: Bone marrow-derived pre-B cells


title: P60_ctrl_sup_13 [Single cone cell RNA-seq]


title: P60_ctrl_sup_12 [Single cone cell RNA-seq]


title: P60_ctrl_sup_16 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ H3K27me3 E34.KO_2

data_processing:
Library strategy: CUT&RUN
Samples were demultiplexed using bcl2fastq v1.8.4 Conversion Software (Illumina, San Diego, CA).
CUT&RUN analysis. Fastq files were uploaded to usergalaxy.org. These files were aligned to the mouse genome built mm9 using Bowtie2 with the default parameters except the minimum and maximum fragment lengths for valid paired-end alignments were set to 10 and 700 respectively, mate dove tailing was also allowed, and the analysis mode was set to “Very sensitive local”. Next, Samtools merge was used to combine data from the two biological replicas with default parameters. Then, merged Bam files were converted to bigwig files for visualization in the UCSC genome browser using bamCoverage tool set to normalize the samples to reads per kilobase per million (RPKM). Significant peaks were called using MACS2 callpeak on the merged BAM files.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for RPKM and MAC2 peaks called.

growth_protocol: C57BL/6 or E34.KO RAG-/- µ+ pre-B cell were isolated by FACS after CD19+ column separation enrichment.

extract_protocol:
CUT& RUN was from (Hainer and Fazzio, 2019) with some modifications. 33.3 ul of Concanavalin A beads (Bangs Laboratories, cat# BP531) were used per 1x106 cells. 1-3x106 cells were used per sample. Incubation of nuclei-bound beads with antibody was done overnight at 4°C on a rotating platform. All antibodies were used in a 1/100 dilution. DNA purification after fragment release was done using NucleoSpin Gel and PCR Clean‑up kit (Ref#740609.50, Macherey-Nagel) instead of phenol-chloroform-isoamyl solution extraction.
CUT&RUN libraries for illumina sequencing were prepared with KAPA HyperPrep Kit (KK8502) using KAPA Unique Dual-Indexed (UDI) Adapters (KK8727).

tag: cut&run antibody

value: Tri Methyl Histone H3 (Lys27) Rabbit mAb cell signaling cat#(C36B11)


title: pre-B cells RAG-/- u+ H3K27me3 E34.KO_1


title: P60_ctrl_sup_10 [Single cone cell RNA-seq]


title: P60_ctrl_sup_11 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ H3K9me3 E34.KO_2

value: H3K9me3 polyclonal antibody Diagenode cat#C15410193


title: pre-B cells RAG-/- u+ H3K27me3 WT_2


title: pre-B cells RAG-/- u+ H3K27me3 WT_1


title: pre-B cells RAG-/- µ+ E34.KO_2


title: pre-B cells RAG-/- µ+ E34.KO_1


title: P60_ctrl_sup_15 [Single cone cell RNA-seq]


title: P60_ctrl_sup_08 [Single cone cell RNA-seq]


title: P60_ctrl_sup_05 [Single cone cell RNA-seq]


title: P60_ctrl_sup_09 [Single cone cell RNA-seq]


title: P60_ctrl_sup_07 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ H3K9me3 WT_2


title: pre-B cells RAG-/- u+ H3K9me3 E34.KO_1


title: pre-B cells RAG-/- u+ H3K9me3 WT_1


title: pre-B cells RAG-/- µ+ RNA WT_2


title: pre-B cells RAG-/- u+ H3K27ac E34.KO_2

value: H3K27ac Active Motif cat#39034


title: P60_ctrl_sup_04 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ H3K27ac E34.KO_1


title: P60_ctrl_sup_02 [Single cone cell RNA-seq]


title: P60_ctrl_sup_03 [Single cone cell RNA-seq]


title: P60_ctrl_inf_21 [Single cone cell RNA-seq]

value: inferior-cone


title: P60_ctrl_inf_20 [Single cone cell RNA-seq]


title: P60_ctrl_sup_01 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ H3K27ac WT_2


title: P60_ctrl_sup_06 [Single cone cell RNA-seq]


title: P60_ctrl_inf_16 [Single cone cell RNA-seq]


title: P60_ctrl_inf_18 [Single cone cell RNA-seq]


title: P60_ctrl_inf_19 [Single cone cell RNA-seq]


title: P60_ctrl_inf_17 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ H3K27ac WT_1


title: pre-B cells RAG-/- u+ H3K4me1 E34.KO_2

value: Histone H3 (mono methyl K4) antibody - ChIP Grade cat#ab8895


title: P60_ctrl_inf_13 [Single cone cell RNA-seq]


title: P60_ctrl_inf_15 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ H3K4me1 E34.KO_1


title: Biliary epithelial organoids, Knock-out 2

city: New York

first: Allen

middle: Charles

state: NY

address: 200 West 108th Street

institute: Icahn School of Medicine at Mount Sinai

data_processing:
RNA was sequenced in bulk at depth of 25 million reads and length of 2x300 base lengths. The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15 TMM method was used for the normalization of the raw count.
Differentially expressed genes were identified using the edgeR program.
Supplementary files format and content: mm10
Supplementary files format and content: KO_ControlvsWT_Control_all_detectable_genes.csv (RSEM-normalized counts)

source_name: extrahepatic bile duct

growth_protocol: EHBD-derived organoids from wildtype (Prom1WT), Prom1KO, Prom1Cre/+-GFP+/- and Prom1Cre/+-mTmG+/- mice were collected and cultured as previously reported.(2, 3) EHBD tissue from anesthetized mice were dissected and collected en bloc and mechanically dissociated in wash buffer. EHEHBD-derived organoids from wildtype (Prom1WT), Prom1KO, Prom1Cre/+-GFP+/- and Prom1Cre/+-mTmG+/- mice were collected and cultured as previously reported.(2, 3) EHBD tissue from anesthetized mice were dissected and collected en bloc and mechanically dissociated in wash buffer. EHBD tissue was then enzymatically digested with collagenase solution (Miltenyi, Cambridge, MA) @ 37oC for 30 minutes. EHBD tissue was then centrifuged (500g x 5 min), resuspended in Matrigel in 40 μL of Matrigel (Corning, Tewksbury, MA), plated on a 96-well plate, and incubated in a CO2 incubator at 37°C for 30 minutes. After polymerization of the Matrigel, the cells were cultured in organoid culture media (Sup. Table 2). Culture media was then changed every 48-72 hours and passaged after ~1 week of culture. BD tissue was then enzymatically digested with collagenase solution (Miltenyi, Cambridge, MA) @ 37oC for 30 minutes. EHBD tissue was then centrifuged (500g x 5 min), resuspended in Matrigel in 40 μL of Matrigel (Corning, Tewksbury, MA), plated on a 96-well plate, and incubated in a CO2 incubator at 37°C for 30 minutes. After polymerization of the Matrigel, the cells were cultured in organoid culture media (Sup. Table 2).

extract_protocol:
Once organoids reached confluence (~3 days after first passage), the organoids were extracted with Cell Recovery Solution (Corning, Tewksbury, MA). RNA was then extracted utilizing the RNeasy micro kit (Qiagen, Redwood, CA).
Total RNA was isolated by Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. RNA purity was assessed by the 260/280 and 260/230 nm absorbance ratio of 2 or greater. 1 µg of total RNA was used for cDNA synthesis using the Bio-Rad iScript cDNA synthesis kit (Bio-Rad Life Science, Hercules, CA). Analysis of gene expression via Reverse-Transcription Polymerase Chain Reaction (RTPCR) was performed on Bio-Rad C1000 Thermal cycler using Taq PCR Master Mix Kit (Qiagen, Valencia, CA) and intron spanning gene specific primers (Table S2). Quantitative Real-Time PCR (qPCR) was performed using cDNA using Light-Cycler Taqman Master (Roche Applied Science, Indianapolis, IN) and probes from the Universal Probe Library (Roche Applied Science) using intron spanning, gene specific primers. Relative expression levels were calculated by Δ–Δ Ct method. Actin was used to normalize the gene expression.

treatment_protocol: No treatments

value: Prom1 knock-out (Prom1 Cre/Cre)

value: biliary luminal epithelium

value: Biliary epithelial organoids


title: Biliary epithelial organoids, Knock-out 3


title: Biliary epithelial organoids, Wild-type 2

value: Wild-type


title: Biliary epithelial organoids, Wild-type 1


title: Biliary epithelial organoids, Knock-out 1


title: Biliary epithelial organoids, Wild-type 3


title: pre-B cells RAG-/- u+ H3K4me1 WT_2


title: pre-B cells RAG-/- u+ H3K4me1 WT_1


title: pre-B cells RAG-/- u+ CTCF E34.KO_2

value: CTCF  Cell Signaling cat#2899S


title: VPS34in1, rep 2

city: New York City

first: Agata

last: Kurowski

address: 1180 5th Avenue

department: Department of Dermatology

description:
VPS34in1_2
SKS8
150bp read length

data_processing:
The RNA-Seq reads were aligned, indexed and annotated using STAR (Spliced Transcripts Alignment to a Reference) 2.5.2b.
Aligned reads were quantified using featureCounts3 with the Bioconductor package Rsubread.
Assembly: GRCh38/hg38
Supplementary files format and content: mydata.txt: Tab-delimited text file includes raw count values for each sample.

growth_protocol: PANC-1 cells were cultured in DMEM (GIBCO) supplemented with 10% FBS (Crystalgen) and antibiotics/antimycotic at 37℃ in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) and sent to BGI for further library generation and sequencing.
Library was generated by BGI as follows: 1. mRNA isolation: mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads; 2. mRNA fragmentation: mRNA molecules were fragmented into small pieces using fragmentation reagent; 3. cDNA Synthesis: First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis; 4. End Repair, Add A and adaptor ligation: the synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adapters were ligated to the ends of these 3' adenylated cDNA fragments; 5. PCR: cDNA fragments were amplified and the PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution; 6. Circularization: The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were generated as the final library; 7. Sequencing: The library was amplified with phi29 to make DNA nanoball (DNB) and the DNBs were loaded into the patterned nanoarray for PE100 or PE150 sequencing on DNBseq platform.

treatment_protocol: Treatment with 5uM ULK100, 10 uM VPS34-in1 or DMSO for 24h.

tag: cell line

value: pancreatic cancer

value: 5 uM ULK100


title: VPS34in1, rep 3

description:
VPS34in1_3
SKS9
150bp read length


title: P60_ctrl_inf_08 [Single cone cell RNA-seq]

value: post natal day 60


title: P60_ctrl_inf_12 [Single cone cell RNA-seq]


title: P60_ctrl_inf_10 [Single cone cell RNA-seq]


title: P60_ctrl_inf_11 [Single cone cell RNA-seq]


title: P60_ctrl_inf_07 [Single cone cell RNA-seq]


title: P60_ctrl_inf_09 [Single cone cell RNA-seq]


title: VPS34in1, rep 1

description:
VPS34in1_1
SKS7
150bp read length


title: pre-B cells RAG-/- u+ CTCF E34.KO_1

value: E34.KO RAG-/- u+ mice bearing a rearranged IgM transgene


title: P60_ctrl_inf_14 [Single cone cell RNA-seq]


title: ULK100, rep 3

description:
ULK100_3
SKS6
150bp read length

value: 10 uM VPS34-in1


title: P60_ctrl_inf_06 [Single cone cell RNA-seq]


title: P60_ctrl_inf_05 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ CTCF WT_2

value: RAG-/- u+ mice bearing a rearranged IgM transgene


title: ULK100, rep 2

description:
ULK100_2
SKS5
150bp read length


title: P60_ctrl_inf_03 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ CTCF WT_1

value: Bone marrow-derived pre-B cells


title: P60_ctrl_inf_02 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ ATACseq E34.KO_2

data_processing:
Samples were demultiplexed using bcl2fastq v1.8.4 Conversion Software (Illumina, San Diego, CA).
ATACseq analysis. Fastq files were uploaded to usergalaxy.org. These files were aligned to the mouse genome built mm9 using Bowtie2 with the default parameters except the minimum and maximum fragment lengths for valid paired-end alignments were set to 10 and 700 respectively, mate dove tailing was also allowed, and the analysis mode was set to "Very sensitive local". Next, Samtools merge was used to combine data from the two biological replicas with default parameters. Then, merged Bam files were converted to bigwig files for visualization in the UCSC genome browser using bamCoverage tool set to normalize the samples to reads per kilobase per million (RPKM). Significant peaks were called using MACS2 callpeak on the merged BAM files.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for RPKM and MAC2 peaks called.

source_name: Bone marrow-derived pre-B cells RAG-/- u+

growth_protocol: C57BL/6 or E34.KO RAG-/- µ+ pre-B cells were isolated by FACS after CD19+ MACS column separation enrichment.

extract_protocol:
Sorted pre-B cells were frozen and keep at -80°C in RPMI media supplemented with 10% FBS, Fetal Bovine Serum (FBS), 2 mM L-glutamine, 1% Penicillin/Streptomycin, 0.05 mM β-mercaptoethanol and 5% DMSO. Permeabilized nuclei were obtained by resuspending cells in 250µL Nuclear Permeabilization Buffer [0.2% IGEPAL-CA630 (I8896, Sigma), 1mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)], and incubating for 10 min on a rotator at 4°C. Nuclei were then pelleted by centrifugation for 5 min at 500 xg at 4°C. The pellet was resuspended in 25µL ice-cold Tagmentation Buffer [33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg-acetate (M2545, Sigma), 16 % DMF (DX1730, EMD Millipore) in Molecular biology water (46000-CM, Corning). An aliquot was then taken and counted by hemocytometer to determine nuclei concentration. Approximately 50,000 nuclei were resuspended in 20µL ice-cold Tagmentation Buffer, and incubated with 1µL Tagmentation enzyme (FC-121-1030; Illumina) at 37 °C for 30 min with shaking 500 rpm. The tagmentated DNA was purified using MinElute PCR purification kit (28004, Qiagen).
The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 min, denaturation at 98°C for 30 s, followed by 8 cycles of denaturation at 98°C for 10 s, annealing at 63°C for 30 s and extension at 72°C for 60 s. Amplified libraries were then purified using MinElute PCR purification kit (28004, Qiagen), and two size selection steps were performed using SPRIselect bead (B23317, Beckman Coulter) at 0.55X and 1.5X bead-to-sample volume rations, respectively.


title: ULK100, rep 1

description:
ULK100_1
SKS4
150bp read length


title: P60_ctrl_inf_01 [Single cone cell RNA-seq]


title: DMSO, rep 3

description:
DMSO_3
SKS3
150bp read length

value: DMSO


title: pre-B cells RAG-/- u+ ATACseq E34.KO_1


title: P21_ctrl_sup_23 [Single cone cell RNA-seq]

source_name: P21 single cone

value: superior-cone

value: post natal day 21


title: DMSO, rep 2

description:
DMSO_2
SKS2
150bp read length


title: P21_ctrl_sup_24 [Single cone cell RNA-seq]


title: P21_ctrl_sup_21 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ ATACseq WT_2


title: P21_ctrl_sup_15 [Single cone cell RNA-seq]


title: P21_ctrl_sup_16 [Single cone cell RNA-seq]


title: P21_ctrl_sup_20 [Single cone cell RNA-seq]


title: P21_ctrl_sup_14 [Single cone cell RNA-seq]


title: DMSO, rep 1

description:
DMSO_1
SKS1
150bp read length


title: P21_ctrl_sup_18 [Single cone cell RNA-seq]


title: pre-B cells RAG-/- u+ ATAseq WT_1


title: P60_ctrl_inf_04 [Single cone cell RNA-seq]

value: inferior-cone


title: IKZF3mut mouse model transplanted animal

description: recipient animal NSG

data_processing:
demultiplexing of illumina BCL files with cellranger-atac mkfastq version 1.2
alignment of sequencing reads to a modified mm10 reference using cellranger-atac count version 1.2
calling of single cells using the default parameters in cellranger-atac
Genome_build: mm10
Supplementary_files_format_and_content: processed fragment files from cellranger-atac count

source_name: Spleen

extract_protocol:
direct harvest from murine spleens and cryopreservation in FBS + 10% DMSO
droplet-based scATAC-seq optimized for capture of mitochondrial DNA (mtscATAC-seq) as previously described (PMID 32788668, PMID 34112698)

value: spleen

tag: disease state

value: CLL active disease


title: P21_ctrl_sup_19 [Single cone cell RNA-seq]

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq3000 Sequencer at NIDDK Genomics Facility
single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.3a)
Output RNA-seq bam files were analyzed with Genomatix programs with transcripts levels calculated as counts/reads per million mapped reads (CPM). ChAP-seq and ATAC-seq data were analyzed by MACS2 (v2.2.7.1)  for peak calling.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each gene of all samples


title: P21_ctrl_sup_22 [Single cone cell RNA-seq]


title: del(13q) MDR mouse model transplanted animal

description: recipient animal


title: IKZF3mut mouse model parental animal

description: parental animal


title: adult V-SVZ aNSCs biological replicate 3

city: Basel

first: Fiona

last: Doetsch

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Raw data was loaded into the ExpressionSuite program v1.3 (ThermoFischer) and four control RNAs (U6, sno135, sno202 and miR-16-5p) were used to normalize the dataset.
Target gene signals normalized to control RNAs ; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_Control RNAs)]
Fold Change worksheet reports 2^-ΔΔCt, where -ΔΔCt = -[ΔCtpopulation -ΔCtqNSCs]

source_name: V-SVZ FACS-purified cells, male and female mixed cells

label_protocol: miRNAs were pre-amplified and profiled using TaqMan® Array Rodent MicroRNA A Cards v2.0 A as specified by the manufacturer.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen)

value: pooled male and female

value: 2-4 month old mice

value: adult brain

value: microdissected V-SVZ from adult brain

tag: cell population

value: aNSCs


title: adult V-SVZ TACs biological replicate 1

tag: tissue

value: TACs


title: RS CRISPR mouse model parental animal

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome using STAR (v2.4.0.1).
Count value was used to measure gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Counts file.txt for RNA-seq samples; tsv files (scATAC-seq fragments) for scATAC-seq samples

extract_protocol:
Harvested spleens were mechanically dissociated to form a single cell suspension. Erythrocyte lysis was carried out using ACK buffer and B cells were immunomagnetically selected from the resulting cell suspension using the MACS B cell Isolation Kit. Cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit.
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina).  Droplet-based scATAC-seq optimized for capture of mitochondrial DNA (mtscATAC-seq) described in Lareau et al. (PMID 32788668)

tag: condition

value: CLL

value: Malignant B cells

value: Multi-plex LOF


title: P21_ctrl_sup_07 [Single cone cell RNA-seq]

extract_protocol:
Pieces from superior or inferior zones of retina were dissected from Trb2Cre:Ai6 mice, then dissassociated into suspension cells after brief papain treatment. Fluorescent cells were identified on a Zeiss Axiovert 200M microscope and collected individually using an Eppendorf micromanipulator and suction pipette. Collected single cone cells were transfer into individual PRC tubes for RNA-seq library construction. For ChAP-seq, retinas from ThrbHAB/HAB;Rosa26BirA/BirA and control Rosa26BirA/BirA E18 embryos were cross-linked and affinity-purified with streptavidin to collect the TRb-bound-DNA. For ATAC-seq, cone nuclei were immunopurified from retinas from control (TRb2Cre-het) and TRb2Cre-KO mice on a Rosa26Sun1Gfp/Sun1Gfp background, these purified cone nuclei were treated with Tagment enzyme (using Tagment DNA kit) before DNA purification.
Single-cell RNA-seq libraries were constructed by using SMART-Seq v4 Ultra Low Input RNA Kit and ThruPLEX DNA-Seq Kit. For ChAP-seq, the enriched-DNA samples were constructed into sequencing library by using ThruPLEX DNA-Seq Kit. For ATAC-seq,  Tagment-enzyme processed DNA samples were constructed into ATAC-seq library by using Tagment DNA kit.

tag: age


title: P21_ctrl_sup_12 [Single cone cell RNA-seq]


title: RS CRISPR mouse model transplanted animal

description: recipient animal NSG


title: P21_ctrl_sup_11 [Single cone cell RNA-seq]


title: P21_ctrl_sup_08 [Single cone cell RNA-seq]


title: P21_ctrl_sup_17 [Single cone cell RNA-seq]


title: P21_ctrl_sup_13 [Single cone cell RNA-seq]


title: adult V-SVZ aNSCs biological replicate 1

tag: cell type


title: adult V-SVZ qNSCs biological replicate 3

value: qNSCs


title: P21_ctrl_sup_04 [Single cone cell RNA-seq]


title: P21_ctrl_sup_05 [Single cone cell RNA-seq]


title: adult V-SVZ aNSCs biological replicate 2


title: adult V-SVZ TACs biological replicate 2


title: RS6 (RNA-seq)

description: Counts file.txt

source_name: RS

value: RS


title: adult V-SVZ qNSCs biological replicate 2


title: P21_ctrl_sup_10 [Single cone cell RNA-seq]


title: P21_ctrl_sup_09 [Single cone cell RNA-seq]


title: del(13q) MDR mouse model parental animal

source_name: CLL

value: MDR


title: P21_ctrl_sup_03 [Single cone cell RNA-seq]

value: superior-cone


title: P21_ctrl_sup_02 [Single cone cell RNA-seq]

value: post natal day 21


title: P21_ctrl_inf_23 [Single cone cell RNA-seq]

value: inferior-cone


title: adult V-SVZ qNSCs biological replicate 1


title: P21_ctrl_sup_01 [Single cone cell RNA-seq]


title: RS4_T (RNA-seq)

description: Counts file.txt


title: P21_ctrl_inf_24 [Single cone cell RNA-seq]


title: RS5 (RNA-seq)

description: Counts file.txt


title: P21_ctrl_inf_22 [Single cone cell RNA-seq]


title: P21_ctrl_inf_21 [Single cone cell RNA-seq]


title: T cells, control (CON), replicate 3

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38) (default parameters)
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (v2.7.1a) with default parameters
Read count extraction and normalization were performed using DESeq2 (v1.28.1).
Assembly: hg38
Supplementary files format and content: tab-delimited tsv file include FPKM values for all samples

source_name: PBMC

growth_protocol: Human peripheral blood mononuclear cells (PBMC) from healthy donors were cultured in RMPI-1640 medium supplemented with 5% Human Serum AB (Gemini), 1% penicillin-streptomycin, 1% non-essential amino acids, 1% GlutaMAX, 1mM sodium pyruvate, 0.1M HEPES, 50μM β-mercaptoethanol in the presence of human IL-2 (100U/ml, Peprotech).

extract_protocol:
Total RNA was extracted by homogenizing in Trizol (Takara) and freezing in RNase-free tubes with liquid nitrogen
RNA libraries for RNA-seq were prepared using TruSeq RNA sample prep kit (FC-122-1001, Illumina) following manufacturer's protocols.

treatment_protocol: 1. PBMCs were activated individually in 24-well plates by human anti-CD3/CD28 and expanded in completed medium for 11 days, and then cultured in control or lactic acid (10mM) conditions for 24 h. 2. PBMCs were activated individually in 24-well plates by human anti-CD3/CD28 and expanded for 12 days under control or sodium lactate (10mM or 40mM) conditions.

value: PBMC

value: T cells

tag: treatment

value: Control


title: T cells, control (CON), replicate 1


title: RS4 (RNA-seq)

description: Counts file.txt

tag: strain


title: P21_ctrl_sup_06 [Single cone cell RNA-seq]

tag: genotype


title: T cells, 40mM sodium lactate, replicate 3

value: 40mM sodium lactate


title: P21_ctrl_inf_20 [Single cone cell RNA-seq]


title: RS24 (RNA-seq)

description: Counts file.txt


title: RS20 (RNA-seq)

description: Counts file.txt


title: RS8 (RNA-seq)

description: Counts file.txt


title: P21_ctrl_inf_15 [Single cone cell RNA-seq]


title: P21_ctrl_inf_19 [Single cone cell RNA-seq]


title: RS3 (RNA-seq)

description: Counts file.txt


title: T cells, 10mM sodium lactate, replicate 2

value: 10mM sodium lactate


title: P21_ctrl_inf_18 [Single cone cell RNA-seq]


title: RS13 (RNA-seq)

description: Counts file.txt


title: T cells, 10mM sodium lactate, replicate 1


title: T cells, 40mM sodium lactate, replicate 2


title: P21_ctrl_inf_17 [Single cone cell RNA-seq]


title: P21_ctrl_inf_10 [Single cone cell RNA-seq]


title: P21_ctrl_inf_16 [Single cone cell RNA-seq]


title: T cells, 40mM sodium lactate, replicate 1


title: P21_ctrl_inf_14 [Single cone cell RNA-seq]


title: T cells, control (CON), replicate 2


title: P21_ctrl_inf_08 [Single cone cell RNA-seq]


title: P21_ctrl_inf_13 [Single cone cell RNA-seq]


title: P21_ctrl_inf_12 [Single cone cell RNA-seq]