title: StsR_microaerobic_exp_rep1

description: Biologoical replicate 1

value: chromosomal deletion of StsR encoding gene


title: rne_phototrophic_72h_rep3

status: Public on Sep 13 2024

type: SRA

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description: Biologoical replicate 3

library_source: transcriptomic

data_processing:
The software Curare v0.6 Blumenkamp et al., 2024)  was used for the differential gene expression analysis. The raw sequencing data was adapter trimmed and quality filtered (phred score < 20 filtered out) with fastp v0.23.4 (Chen et al., 2018 ). Afterward, the reads were aligned to the reference genome of R. sphaeroides (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2 and NC_009008.1) using bowtie2 v2.5.2 (Langmead and Salzberg)  and saved as binary alignment maps (BAM) with Samtools v1.18 (Danecek et al., 2021 ).
The differential gene expression analysis used subreads featureCounts v2.0.6 (Yang et al., 2014)  for counting and DESeq2 v1.40.2 (Love et al., 2014)  for the statistical analyses. Counting was done in featureCounts with "-s 1 -M --fraction" options on the "gene" level, and the NCBI GFF file for assembly GCF_000012905.2 was used as an annotation.
The alignments were summarized as bedgraph files using deeptools' v3.5.4 bamCoverage function [Ramirez et  al., 2016). The coverage data (bedgraph files) was normalized by dividing each data point/base position by the total read number in each sample. For the screenshots, the replicates of each condition were averaged by the arithmetic mean.
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: count tabl/gene expression matrixe created with featureCounts in tab-separated format

molecule: total RNA

organism: Cereibacter sphaeroides 2.4.1

source_name: rne(ts) strain (substitution of native rne gene with thermosensitive rne gene from E. coli)

growth_protocol: Independent biological triplicates of each strain were grown in malate minimal medium under microaerobic (~25 µM dissolved oxygen) or phototrophic (anaerobic and illuminated with 60 W per square meter) growth conditions to exponential or late stationary growth phase (72 hours).

extract_protocol:
Total RNA was isolated as published (Grützner et al., 2021, Nucelic Acids Res. 49(6), doi: 10.1093/nar/gkab146)
RNA was processed as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146); NEBnext Multiplex Small RNA Library Prep Set

treatment_protocol: Cells were grown under microaerobic or phototrophic conditions and harvested during exponential or late stationary growth phase.

tag: cell line

tag: treatment

value: phototrophic growth to late stationary phase


title: Control Choroidal explant Sample 1

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

data_processing:
Fastq files obtained from the sequencing facility were trimmed using Trimmomatic v0.39 using the NexteraPE-PE adapter file. The paired reads were then aligned using STAR (v2.7.9a) against the mouse reference genome from Ensembl v106 (generated 2022/06/21), with option “--quantMode GeneCounts” to extract the raw counts for each gene, then all count files were concatenated into a single file.
A sample file was created with the sample data including the conditions (CTL, DOPA) and the replicate numbers. The count file and the sample file were loaded in our in-house R Shiny application EYE DV seq.
We added 1 to all counts in the count file to avoid any 0 read count errors. We then removed the genes having a total count < 10 across all samples. Finally the DESeq2 (v1.40.2) analysis was performed comparing the groups defined in the ‘condition’ column, with ‘CTL’ as control group and ‘DOPA’ as condition.
The results were then filtered for significant genes using the p-values (< 0,05). An enrichment analysis was performed to study the implicated pathways, using the Reactome database (using the Bioconductor package ‘ReactomePA’ (v1.44.0) and the GO database (using the Bioconductor packages ‘org.Mm.eg.db’ (3,10,0) and ‘clusterProfiler’ (v 4.8.1)).
Assembly: GRCm38 Ensembl release 106
Supplementary files format and content: Comma-separated file including raw counts for all Samples
Supplementary files format and content: Comma-separated file containing all Samples metadata

organism: Mus musculus

source_name: Choroidal explants

growth_protocol: Choroidal explants dissected from 2 week-old mice were embeded in matrigel and kept in culture in supplemented EGM2  (CC-3156 & CC-4176) for 3 days to allow vascular sprounting.

extract_protocol:
On day 4, choroidal explants were dissociated with collagenase, and CD31+CD11b- cells were sorted on a BD FACS melody cell sorter. Cells were immediatly flash frozen in in 96 well plates until library construction
Libraries were made from 500  sorted endothelial cells using smartseq V4 (Takara)

treatment_protocol: On day 3, choroidal explants were stimulated with 1 µM Dopamine

tag: tissue

value: Choroidal explants

tag: genotype

value: wt

value: Control


title: 154469 WT 24M H3K27me3

city: Hobart

first: Phillippa

middle: Claire

last: Taberlay

state: Tasmania

address: 17 Liverpool St

department: College of Health and Medicine

country: Australia

institute: University of Tasmania

library_source: genomic

data_processing:
Sequenced using HiSeq 2500 - mean read depth 13.9M H3K4me3, 16.2M H3K27ac.
Removed library tags.
Pseudoreplicates generated.
Mapped to MM10 using bowtie2.
bigwigs generated.
Assembly: MM10
Supplementary files format and content: Bigwigs

molecule: genomic DNA

source_name: brain

extract_protocol:
Mice aged and samples collected at 3, 12, 24m, purified neurons extracted with FACS
Nugen Ovation Ultralow V2 library preparation - amplification for 17 cycles (H3K27ac), or 18 cycles (H3K4me3) 0347 V2 1-96/0344 V2 1-16.

value: brain

tag: cell type

value: neurons

value: WT


title: rne_phototrophic_72h_rep2

description: Biologoical replicate 2

value: rne(ts) strain (substitution of native rne gene with thermosensitive rne gene from E. coli)


title: WT_D4_rep2

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Sequenced reads were mapped to the Synechococcus elongates PCC7942 reference genome sequences using Rockhopper
The normalization and differentially expressed genes test were implemented by DESeq2.
Assembly: GCF_000012525.1_ASM1252v1
Supplementary files format and content: Excel file with all normalized counts for each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: bacterial cell

extract_protocol:
Total RNA was extracted as previously described Simkovsky, R., et al. Front Microbiol, 2022. 13: p. 899150.
rRNA-depleted RNA (1 µg) was used for library construction using KAPA mRNA HYPER-PREP (KK8581) according to manufacturer's protocol, with a 7 cycles PCR (Kapa, Roche).

value: bacterial cell

value: wild-type


title: WT_D1_rep3


title: 156509 WT 12M H3K27me3


title: 154468 WT 24M H3K27me3


title: rne_microaerobic_72h_rep3

description: Biologoical replicate 3

value: microaerobic growth to late stationary phase


title: rne_microaerobic_72h_rep2

description: Biologoical replicate 2


title: Control Choroidal explant Sample 2


title: rne_microaerobic_72h_rep1

description: Biologoical replicate 1


title: WT_D4_rep1


title: 155688 WT 12M H3K27me3


title: rnc_phototrophic_72h_rep3

description: Biologoical replicate 3

source_name: rnc- strain (inactivation of catalytic function)


title: WT_D1_rep1


title: 155668 WT 12M H3K27me3


title: 156508 WT 12M H3K27me3


title: rnc_phototrophic_72h_rep2

description: Biologoical replicate 2

value: rnc- strain (inactivation of catalytic function)


title: SIGF2_D4_rep4


title: 517 WT 3M H3K27me3


title: SIGF2_D1_rep4


title: rnc_phototrophic_72h_rep1

description: Biologoical replicate 1


title: 513 WT 3M H3K27me3


title: rnc_microaerobic_72h_rep3

description: Biologoical replicate 3


title: J365_p20_1

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: Gene expression of myeloid and melanoma cells

hyb_protocol: Agilent-074809 Whole Mouse Genome Microarray 4x44K v2 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: 1 million of B16F1-GFP-M, B16F1-GFP-D, B16F1-GFP-DB#1,  B16F1-GFP-DB#2 and B16F1-GFP-DB#3 melanoma cells were cultured in DMEM 10% FBS medium.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: The cells were rinsed twice with sterile PBS. Total RNA extraction was performed following the manufacturer's protocol (RNeasy Kit, Qiagen, Courtaboeuf, France) with optional DNase treatment.

value: myeloid cells


title: SIGF2_D1_rep3


title: 512 WT 3M H3K27me3


title: M0_p20_3


title: rnc_microaerobic_72h_rep2

description: Biologoical replicate 2


title: 368 WT 3M H3K27me3


title: rnc_microaerobic_72h_rep1

description: Biologoical replicate 1


title: J365_p20_3


title: SigF2_D4_rep2


title: M0_p20_2


title: M0_p20_1


title: SigF2_D1_rep2


title: SigF2_D4_rep1


title: wt_phototrophic_72h_rep3

description: Biologoical replicate 3

source_name: wild type

value: wild type


title: wt_phototrophic_72h_rep2

description: Biologoical replicate 2


title: M0_p20


title: SIGF2_D4_rep3


title: J365_p20


title: B16F1-GFP-DB#3_5

value: melanoma cells


title: SigF2_D1_rep1


title: Young,Uterus,rep3 [Y31_H3K9me3]

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

description:
ChIP-seq of uterine stromal cells from young female, replicate 5
Y31_H3K9me3

data_processing:
Indexed libraries were pooled and sequenced on an Illumina HiSeq2500 sequencer, using a 50bp paired-end protocol. Read depth per sample was between 7.7M and 20.4M reads.
Raw fastq data were mapped to the Mus musculus GRCm38 genome assembly with Bowtie2
Peaks were called using the MACS peak caller in SeqMonk. Differential enrichment was determined using the DESeq2 package or LIMMA statistics in SeqMonk.
Bigwig files were generated from the bam files using bamCoverage from deeptools with options --normalizeUsing CPM --minMappingQuality 20
Bedgraph files were exported from Seqmonk and Bigwig files were generated from the bam files using bamCoverage from deeptools with options --normalizeUsing CPM --minMappingQuality 20
Assembly: GRCm38
Supplementary files format and content: Bigwig and Bedgraph files are provided for each chip relative to input

source_name: Uterus

growth_protocol: Uterine stromal cells were isolated as described previously (Woods et al., 2017). In brief, uteri from E3.5 mice were slit longitudinally and disaggregated with 2.5% pancreatin and 0.5% trypsin (type III) in Hank’s basic salt solution-calcium/magnesium free for 1.5 hour on ice. The digested tissue was vortexed and the medium was removed and the remaining tissue washed twice in HBSS (discarding luminal epithelial cells) and incubated 30 min at 37oC in HBSS containing 0.007% collagenase, 0.02% DNase, 0.008% protease with vortexing every 5 min. Dissociated tissues were then triturated, filtered through a 70μm cell strainer (BD Biosciences) and spun at 3000 rpm for 5min at 4ºC. Cell pellets were resuspended in standard growth medium and plated.

extract_protocol:
Histone ChIP was performed on pellets of 200,00 uterine stromal cells. Chromatin was digested with micrococcal nuclease and ChIP performed with antibodies against H3K4me3 (Abcam ab8580) and H3K9me3 (Abcam ab8898). 10% of chromatin was kept back and sequenced as Input. Following the chromatin immunoprecipitation procedure, DNA was isolated using proteinase K digestion followed by clean-up using the QiaQuick PCR purification kit (Qiagen 28104).
Input and ChIP DNA was used for library build with the NEBNext Ultra II DNA library prep kit (Illumina E7645)

treatment_protocol: Cells were isolated from uteri of young and aged females.

value: Uterus

value: Uterine stromal Cells

value: Wild-type

value: Young


title: B16F1-GFP-DB#3_4


title: Young,Uterus,rep3 [Y31_H3K4me3]

description:
ChIP-seq of uterine stromal cells from young female, replicate 4
Y31_H3K4me3


title: B16F1-GFP-DB#2_3


title: B16F1-GFP-DB#3_3


title: SIGF1_D4_rep4


title: Young,Uterus,rep3 [Y31_input]

description:
ChIP-seq of uterine stromal cells from young female, replicate 3
Y31_input


title: wt_phototrophic_72h_rep1

description: Biologoical replicate 1

value: phototrophic growth to late stationary phase


title: 363 WT 3M H3K27me3


title: wt_microaerobic_72h_rep3

description: Biologoical replicate 3


title: Young,Uterus,rep2 [Y30_H3K9me3]

description:
ChIP-seq of uterine stromal cells from young female, replicate 2
Y30_H3K9me3


title: SIGF1_D1_rep4


title: wt_microaerobic_72h_rep2

description: Biologoical replicate 2


title: SIGF1_D4_rep3


title: Young,Uterus,rep2 [Y30_H3K4me3]

description:
ChIP-seq of uterine stromal cells from young female, replicate 5
Y30_H3K4me3


title: B16F1-GFP-DB#1_4


title: wt_microaerobic_72h_rep1

description: Biologoical replicate 1


title: B16F1-GFP-DB#2_2


title: B16F1-GFP-DB#2_1


title: M. abscessus_untreated_biol_rep_3

city: London

first: Gerald

middle: J

last: Larrouy-Maumus

address: South Kensington Campus

country: United Kingdom

institute: Imperial College London

data_processing:
https://imperial-genomics-facility.github.io/igf-pipeline-help/alignment_qc.html#qc-of-transcriptomic-data:~:text=Go%20to%20Top-,QC%20of%20transcriptomic%20data,-Sequencing%20data%20for
Assembly: Mycobacterium abscessus ATCC 19977 (GenBank: CU458896)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mycobacteroides abscessus

source_name: Cell culture

extract_protocol:
Bacteria were harvested by 10-minute centrifugation at 4,000 x g, 4°C and washed twice with cold sterile PBS. Total RNA was extracted using a FastRNA Pro Blue kit (MP) according to the manufacturer’s instructions.
The samples were treated with RNase-free Dnase (Promega) for 1 hour at 37°C to remove contamination of genomic DNA. The samples were purified with RNAeasy columns (Qiagen) according to the manufacturer’s instructions. The quantity and quality of RNA were assessed using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer with an RNA 6000 Nano LabChip kit (Agilent). RNA sequencing was performed using an Illumina HiSeq4000 sequencer in the Imperial BRC Genomics Facility at Imperial College London.

value: Cell culture

value: Mycobacterium abscessus ATCC19977

value: bacterial cells

value: wildtype

value: untreated


title: Young,Uterus,rep1 [Y20_H3K9me3]

description:
ChIP-seq of uterine stromal cells from young female, replicate 3
Y20_H3K9me3


title: SigF1_D1_rep2

value: bacterial cell


title: Young,Uterus,rep2 [Y30_input]

description:
ChIP-seq of uterine stromal cells from young female, replicate 4
Y30_input


title: SigF1_D4_rep2


title: M. abscessus_untreated_biol_rep_2


title: Young,Uterus,rep1 [Y20_H3K4me3]

description:
ChIP-seq of uterine stromal cells from young female, replicate 2
Y20_H3K4me3


title: B16F1-GFP-DB#1_2


title: B16F1-GFP-DB#1_1


title: B16F1-GFP-DB#1_3


title: M. abscessus_nickel_biol_rep_3

value: 2.5 mM Ni2+, 2-hour incubation


title: B16F1-GFP-D_4


title: SigF1_D1_rep1


title: SIGF1_D1_rep3


title: SigF1_D4_rep1


title: Young,Uterus,rep1 [Y20_input]

description:
ChIP-seq of uterine stromal cells from young female, replicate 1
Y20_input


title: B16F1-GFP-D_3


title: M. abscessus_untreated_biol_rep_1


title: PilB_D1_rep4

value: pilB-mutant


title: B16F1-GFP-D_2


title: Aged,Uteris,rep3 [A29_input]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 3
A29_input

value: Aged


title: M. abscessus_nickel_biol_rep_2


title: Aged,Uteris,rep3 [A29_H3K9me3]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 5
A29_H3K9_me3


title: B16F1-GFP-M_3


title: PilB_D4_rep4


title: Aged,Uteris,rep3 [A29_H3K4me3]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 4
A29_H3K4_me3


title: Aged,Uterus,rep2 [A16_H3K9me3]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 4
A16_H3K9me3


title: M. abscessus_nickel_biol_rep_1


title: M. abscessus_copper_biol_rep_2

value: 0.156 mM Cu2+, 2-hour incubation


title: PilB_D4_rep3


title: L_CD74_H

city: 武汉

first: ZHEN

last: TANG

state: 湖北

address: 医学研究院

country: China

institute: 武汉大学

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36) (parameter- ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co., Ltd.）
The de-duplicated consensus sequences were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung

growth_protocol: Neutrophils were sorted from lung tumors of KPIL8 mice that were intranasally injected with Ad-Cre (2x106 pfu per mouse)

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）.  Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

value: lung

value: Neutrophils

value: 10 weeks after intranasal injection of Ad-Cre


title: PilB_D1_rep3


title: H_CD74_L


title: M. abscessus_copper_biol_rep_1


title: Aged,Uterus,rep2 [A16_H3K4me3]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 3
A16_H3K4me3

value: Uterus

value: Uterine stromal Cells


title: Aged,Uterus,rep1 [A24 H3K9me3]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 3
A24_H3K9me3

value: Wild-type


title: Aged,Uterus,rep2 [A16_input]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 2
A16_input


title: M. abscessus_cobalt_biol_rep_2

value: 0.625 mM Co2+, 2-hour incubation


title: L_CD74_L


title: B16F1-GFP-M_1

description: Gene expression of myeloid and melanoma cells

value: melanoma cells


title: B16F1-GFP-D_1


title: PilB_D4_rep1


title: PilB_D1_rep2


title: dunnart face P0 rep3

city: Berkeley

first: Laura

middle: E

last: Cook

state: California

address: 1 Cyclotron Road

department: Biosciences

country: USA

institute: Lawrence Berkeley National Laboratory

data_processing:
The raw reads were first trimmed using trimmomatic v0.39 (Bolger et al., 2014) [ILLUMINACLIP:2:30:10 SLIDINGWINDOW:5:15 MINLEN:50 AVGQUAL:20]. Reads were mapped with hisat2 v2.21 (Zhang et al., 2021) [--fr --no-mixed --no-discordant] and alignments were filtered using samtools view (Li et al., 2009) [-f 1 -F 2316]. Finally the count table was generated using featureCounts from the Subread package v2.0.1 (Liao et al., 2013) [-s 2 -p -t exon --minOverlap 10].
Assembly: Scras_dunnart_assem1.0_pb-ont-illsr_flyeassem_red-rd-scfitr2_pil2xwgs2_60chr.fasta
Supplementary files format and content: featureCounts

organism: Sminthopsis crassicaudata

source_name: face

extract_protocol:
The reads for three replicates were generated from facial prominences of P0 dunnart pouch young. Each replicate is a pool of two pouch young
Libraries were prepared using the Illumina stranded mRNA kit and were sequenced to a depth >=50M read pairs (i.e. 25M F + 25M R) in 2x100bp format.

value: face


title: PilB_D1_rep1


title: Aged,Uterus,rep1 [A24 H3K4me3]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 2
A24_H3K4me3


title: M. abscessus_copper_biol_rep_3

value: Cell culture

value: Mycobacterium abscessus ATCC19977

value: bacterial cells


title: B16F1-GFP-M_2


title: dunnart face P0 rep2


title: M. abscessus_cobalt_biol_rep_1

value: wildtype


title: PilB_D4_rep2

value: bacterial cell


title: Aged,Uterus,rep1 [A24 input]

description:
ChIP-seq of uterine stromal cells from aged female, replicate 1
A24_input


title: 2026 RVA AA/AG

status: Public on Sep 12 2024

city: Tucson

first: Eugene

last: Chang

state: Arizona

address: 1501 N Campbell Ave, PO Box 245074

department: Otolaryngology

institute: University of Arizona

description: Total RNA was collected at baseline (Control) or 48 hours post RV infection. RNA integrity was determined using a fragement analyzer and Qubit high sensitivity assay. Purified RNA was hybridized at 65⁰ C overnight (17h). The ncounter Human Host Response Panel consisted of 785 well annoated immune response genes, in addition to housekeeping genes used to normalize probe counts.

hyb_protocol: Samples were run targeting between 100 ng - 225 ng depending on individual QC and hybridized for 17 hours at 65⁰C.

scan_protocol: Scanning was perfomed on the nCounter Digital Analyzer

data_processing: Data was upper-quantile normalized and the log counts per million were calcuated. Technical variation was removed using removeBatchEffect from limma using the RUVg results as covariates and the RV-stimulation & genotype were used for the design.

organism: Homo sapiens

source_name: Sinonasal Epithelial Cells

label_protocol: RNA was analyzed and labeling was performed according to the manufacturer's instruction of the Nanostring nCounter system. 2 sets of Nanostring assays were run (nCounter Human Host Response Panel and Custom Panel PLUS)

growth_protocol: Primary nasal epithelial cells (NECs) were obtained from nasal brushings collected from individuals in our studies as well as from our biorepository of nasal cells from adults with CRS. The cells were initially expanded on collagen-coated flasks and cryopreserved at passages 0 and 1. For differentiation, cells were plated on collagen-coated transwell inserts at a density of 3x10^5 cells/cm2 and maintained at the air-liquid interface for 21 days or longer until fully differentiated.

extract_protocol: Total RNA was extracted from control or RV-infected cells using the RNeasy Mini kit (Qiagen) 48 hours after infection.

treatment_protocol: Differentiated ALI cultures were infected with RV-A16 and RV-C15 for 48 hours.

value: Sinonasal Epithelial Cells

tag: cdhr3 genotype

value: AA/AG

tag: gender

value: Male

tag: asthma status

value: No

tag: presence of polyps

tag: allergic rhinitis status


title: 2024 RVC AA/AG

value: Yes


title: 2026 Ctl AA/AG


title: dunnart face P0 rep1


title: M. abscessus_cobalt_biol_rep_3


title: 1943 RVC AA/AG

value: Female


title: 2024 Ctl AA/AG


title: 1662 RVA AA/AG


title: 2024 RVA AA/AG


title: 1885 RVC AA/AG


title: 1662 RVC AA/AG


title: 1906 Ctl AA/AG


title: 1885 RVA AA/AG


title: 1893 RVA AA/AG


title: 1893 RVC AA/AG


title: 1906 RVC AA/AG


title: 2026 RVC AA/AG


title: 1885 Ctl AA/AG


title: 1906 RVA AA/AG


title: 1893 Ctl AA/AG


title: 1876 RVC AA/AG


title: 1639 RVC AA/AG


title: 1639 RVA AA/AG


title: 1876 Ctl AA/AG


title: 1876 RVA AA/AG


title: 1662 Ctl AA/AG


title: 1639 Ctl AA/AG


title: 1943 Ctl AA/AG


title: 1408 Ctl AA/AG


title: 1943 RVA AA/AG


title: 1724 Ctl AA/AG


title: 1408 RVC AA/AG


title: 1724 RVC AA/AG


title: 1601 RVA AA/AG


title: 1599 RVA AA/AG


title: 1601 RVC AA/AG


title: 1724 RVA AA/AG


title: 1457 RVC AA/AG


title: 1457 Ctl AA/AG


title: 1457 RVA AA/AG


title: 1443 RVC AA/AG


title: 1981 Ctl GG

value: GG


title: 1981 RVA GG


title: 1949 RVC GG


title: 1949 Ctl GG


title: 1599 RVC AA/AG


title: 1599 Ctl AA/AG


title: 1443 Ctl AA/AG


title: 1949 RVA GG


title: 1408 RVA AA/AG


title: 1601 Ctl AA/AG


title: 1921 RVC GG


title: 1921 RVA GG


title: 1443 RVA AA/AG


title: 1921 Ctl GG


title: 1981 RVC GG


title: 1347.2 RVC GG


title: 1903 Ctl GG


title: 1903 RVA GG


title: 1644 RVC GG


title: 1347.2 RVA GG


title: 1903 RVC GG


title: 1347.2 Ctl GG


title: 1644 Ctl GG


title: 1580 RVA GG


title: 1284 RVA GG


title: 1902 RVC GG


title: 1595 Ctl GG


title: 1644 RVA GG


title: 1902 Ctl GG


title: 1487 Ctl GG


title: 1580 RVC GG


title: 1284 Ctl GG


title: 1403 RVC GG


title: 1487 RVA GG


title: 1595 RVC GG


title: 1284 RVC GG


title: 1595 RVA GG


title: 1340 RVC GG


title: 1403 RVA GG


title: 1403 Ctl GG


title: 1902 RVA GG


title: 1470 RVC GG


title: 1242 Ctl GG


title: 1470 RVA GG


title: 1580 Ctl GG


title: Blood, collected from mice across the injection of the LNP_nsRNA treatment on day 4, REP2

city: changsha

first: yujie

last: Liao

address: tongzipo

institute: central south university

description: D4_LNP_nsRNA 2

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/mus musculus c57bl6nj/dna/) to map reads to the reference genome of mus musculus Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mus musculus Ensembl_v107
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

molecule: polyA RNA

source_name: blood

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: blood

value: Injection of LNP

value: Injection of LNP_nsRNA


title: Blood, collected from mice across the injection of the LNP_nsRNA treatment on day 4, REP1

description: D4_LNP_nsRNA 1


title: 1340 RVA GG


title: 1340 Ctl GG


title: Blood, collected from mice across the injection of the LNP_nsRNA treatment on day 1, REP3

description: D1_LNP_nsRNA 3


title: Blood, collected from mice across the injection of the PBS treatment on day 1, REP2

description: D1_PBS 2

value: WT

value: Injection of PBS


title: Blood, collected from mice across the injection of the PBS treatment on day 1, REP1

description: D1_PBS 1


title: Blood, collected from mice across the injection of the LNP_nsRNA treatment on day 1, REP1

description: D1_LNP_nsRNA 1


title: 1242 RVC GG


title: Blood, collected from mice across the injection of the LNP_siUSP33 treatment on day 1, REP3

description: D1_LNP_siUSP33 3

value: Injection of LNP and knockdown of USP33

value: Injection of LNP_siUSP33


title: Blood, collected from mice across the injection of the PBS treatment on day 4, REP3

description: D4_PBS 3


title: 1487 RVC GG


title: Blood, collected from mice across the injection of the PBS treatment on day 4, REP1

description: D4_PBS 1


title: Blood, collected from mice across the injection of the LNP_nsRNA treatment on day 4, REP3

description: D4_LNP_nsRNA 3


title: Blood, collected from mice across the injection of the LNP_siUSP33 treatment on day 4, REP1

description: D4_LNP_siUSP33 1


title: 1242 RVA GG


title: 1470 Ctl GG


title: Blood, collected from mice across the injection of the LNP_siUSP33 treatment on day 4, REP2

description: D4_LNP_siUSP33 2


title: Blood, collected from mice across the injection of the LNP_siUSP33 treatment on day 4, REP3

description: D4_LNP_siUSP33 3


title: Blood, collected from mice across the injection of the PBS treatment on day 1, REP3

description: D1_PBS 3


title: J774 cells, SLC12A9 sgRNA 15, replicate 1

city: Stanford

first: Roni

last: Levin-Konigsberg

state: CA

address: 240 Pasteur Dr

department: Genetics

institute: Stanford Univeristy

data_processing:
STAR, HT-seq
Assembly: mm10
Supplementary files format and content: tsv. gene level counts

growth_protocol: J774 macrophages were cultured in glutamine-free DMEM supplemented with 10% fetal bovine serum, L-glutamine and penicillin and streptomycin

extract_protocol:
RNA was harvested using Rneasy mini plus kit from Qiagen
PolyA-enriched, rRNA depleted, RNA fragmentation, cDNA reverse transcription

treatment_protocol: J774 macrophages were incubated in serum-free and glutamine-free DMEM supplemented with Penicilin and Streptomycin for 6 h before total RNA extraction

value: Macrophages

value: SLC12A9 knockdown

value: serum-free


title: J774 cells, SLC12A9 sgRNA 15, replicate 2


title: J774 cells, SLC12A9 sgRNA 11, replicate 1


title: Blood, collected from mice across the injection of the PBS treatment on day 4, REP2

description: D4_PBS 2


title: J774 cells, Safe sgRNA, replicate 2


title: J774 cells, Safe sgRNA, replicate 1


title: Blood, collected from mice across the injection of the LNP_nsRNA treatment on day 1, REP2

description: D1_LNP_nsRNA 2


title: Blood, collected from mice across the injection of the LNP_siUSP33 treatment on day 1, REP2

description: D1_LNP_siUSP33 2


title: Blood, collected from mice across the injection of the LNP_siUSP33 treatment on day 1, REP1

description: D1_LNP_siUSP33 1


title: D68 [502-0152-5]

type: genomic

city: Chicago

first: Abhimanyu

state: Illinois

address: 920 E 58th Street

institute: University of Chicago

description: Infinium Methylation EPIC

hyb_protocol: Illumina Infinum BeadArray protocol

scan_protocol: iScan Illumina

data_processing: Minfi package in R

source_name: Peripheral Blood Mononuclear cell

label_protocol: As instructed by Illumina

growth_protocol: PBMCs from venous Blood

extract_protocol: DNA extarcted using QIAGEN DNA kit

tag: disease state

value: tuberculosis (TB)

value: Peripheral Blood Mononuclear cell

value: STD treatment


title: J774 cells, SLC12A9 sgRNA 11, replicate 2


title: J774 cells, SLC12A9 sgRNA 11, replicate 3


title: J774 cells, Safe sgRNA, replicate 3


title: D63 [502-0088-3]

description: Infinium Methylation EPIC


title: OTI Thy1.1+ CD8+ T in CD11c-GSK3b-/- mice 4 days post adoptively transfer, scRNAseq

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

institute: Henry Ford Health

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger-6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
For isolation of adoptively transferred Pmel-1 Thy1.1+ CD8+ T cells, spleen cells from immunized mice were first enriched with anti-Thy1.1 magnetic microbeads and sorted using BD FACSAira II
scRNA-seq libraries were generated using the 10X Genomics Chromium Single Cell 3′ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller as described in the manufacturer's  instructions. Briefly, FACS-sorted cells were loaded into each reaction for gel bead-in-emulsion (GEM) generation and cell barcoding. Reverse transcription of the GEM (GEM-RT) was performed using a Veriti™ 96-Well Fast Thermal Cycler (Applied Biosystems) at 53 °C for 45 min, 85 °C for 5 min, and a 4 °C hold. cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) using the same thermocycler (98 °C for 3 min, 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1 min, followed by a 12 cycle repeat at 72 °C for 1 min and a 4 °C hold). Amplified cDNA was cleaned up with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA) that was followed by a library construction procedure, including fragmentation, end repair, adapter ligation, and library amplification. An Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using a paired-end flow cell: Read 1, 26 cycles; i7 index, 8 cycles; Read 2, 98 cycles.

value: spleen

value: CD8 T cells

value: CD11c- GSK3b-/-  mice

value: injected intravenously (i.v.) with 10 mg of anti-DEC-205-OVA, with CpG (100 mg) as adjuvant


title: OTI Thy1.1+ CD8+ T in CD11c-GSK3b WT mice 10 days post adoptively transfer, scRNAseq

description: 10X Genomics

value: CD11c- GSK3b WT mice


title: DCs in CD11c-GSK3b-/- mice, scRNAseq

description: 10X Genomics

value: DCs


title: D61 [551-0039-3]

description: Infinium Methylation EPIC


title: OTI Thy1.1+ CD8+ T in CD11c-GSK3b WT mice 4 days post adoptively transfer, scRNAseq

description: 10X Genomics


title: OTI Thy1.1+ CD8+ T in CD11c-GSK3b-/- mice 10 days post adoptively transfer, scRNAseq

description: 10X Genomics


title: DCs in CD11c-GSK3b  WT mice as control, scRNAseq

description: 10X Genomics


title: CR, GEX, islets, rep2

city: Nashville

first: Rafael

last: Arrojo e Drigo

state: TN

address: 2201 West End Ave, Molecular Physiology and Biophysics, LH718

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

description: GEX (3' mRNA library): read1 file contains the cell barcode and UMI and read2 contains the transcript

data_processing:
Raw sequencing reads were analyzed using Cell Ranger ARC Count v2.0.1 via 10x Genomics Cloud Analysis using default parameters and the mm10 2020-A-2.0.0 reference genome. Frag-ment and alignment files were input into AMULET (v1.1)  to detect multiplet droplets with mm10 repetitive elements from the UCSC genome browser. SoupX (v1.6.0)  was used to remove ambient RNA signal detected in empty droplets from nuclei-containing droplets. The contamination fraction of ambient RNA was estimated using the autoEstCont function. Seurat V4  objects containing assays for gene expression and chromatin accessibility were created for each sample and filtered for multiplets detected by AMULET.
DoubletFinder (v2.0)  was used to detect heterotypic droplet doublets based on gene expres-sion results. Peak calling was performed using the MACS (v2.2.7.1)  peak caller.
Futher processing if the gene expression data was performed using Seurat(v4) and ATAC data using Signac(v1.9.0). Independent biological replicates were integrated by first merging Seurat V4 objects and then performing batch correction using Harmony (v0.1). Batch correction was also performed for the ATAC peaks using reciprocal latent semantic index-ing (rLSI) in Signac.
Transcription factor (TF) motifs were identified based on the JASPAR2020 database using the AddMotifs function in Signac.
Assembly: mm10
Supplementary files format and content: CellRanger output files
Library strategy: Single Cell Multiome ATAC + RNA

molecule: nuclear RNA

source_name: Pancreatic islets

growth_protocol: Male and female FVB/NJ and C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) and then were housed in cages of five mice and maintained on a 12-hour light/dark cycle with controlled temperature (21C) and humidity. The mice had ad-libitum access to chow food (Rodent Diet 20 5053, PicoLab) and water. At 2 months of age, the mice were random-ized to ad-libitum diet (AL), 20% caloric restriction (CR) or 60% high-fat diet (HF) for 2 or 12 months. Both diets were purchased from Lab Diet (CR and AL: Rodent Diet 5053, 4.11 Kcal/g; HF: Rodent Diet 58Y1, 5.10 Kcal/g; St. Louis, MO). For the CR protocol, mice were fed with 80% of the daily consumption of the AL group, which corresponds to a moderate caloric re-striction of 20% of the control intake (REF). CR mice were fed once a day between 4:00 – 5:00 pm. A gradual reduction in food intake was performed (by 10% to 20% per week) to avoid an abrupt decline in body weight and maladaptation. In vivo or ex-vivo experiments were performed after 2 or 12 months on diet, and the mice were euthanized by inhaled isoflurane and immediate-ly beheaded after cessation of their reflexes. The experiments were performed in several sets of mice to confirm the phenotype and verify the robustness of the data replication

extract_protocol:
Single nuclei were isolated from snap-frozen isolated islet pellets from AL, CR, and HFD mice after 2 months on diet. Nuclei were isolated using the 10x Genomics protocol for nuclei isolation from embryonic mouse brain. Briefly, the islet pellet was lysed and homogenized in 0.1x Lysis Buffer solution (Tris-HCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.01%, IGEPAL CA-630 0.01%, Digitonin 0.01%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/ul). Then, the lysate was incubated on ice for 5 min, pipette mixed and incubated on ice for additional 10 min. Next, chilled wash buffer (Tris-HCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Tween-20 0.1%, BSA 1%, DTT 1 mM, RNase inhibitor 1 U/ul) was added to the sample, pipette mixed, and the sample was filtered through a Flowmi Cell Strainer. Then, the pellet was washed with chilled wash buffer and the nuclei concentration was deter-mined using Trypan Blue Stain (0.4%) and hemocytometer. The final nuclei concentration (1000 nuclei/ul) was resuspended in chilled Diluted Nuclei Buffer (10x Genomics).
Isolated nuclei were processed for transposition, barcoding, library construction and sequencing according to 10x Genomics Guidelines for Single Cell Multiome ATAC + Gene Expression.

treatment_protocol: Pancreatic islets were isolated from mice after 2-or-12 months on diet by collagenase digestion method (ref). Briefly, a collagenase solution (0.6 mg/ml) was injected into the pancreatic duct and the isolated pancreas was digested at 37°C for 10 min. Cold Hank’s Solution (HBSS) with 10% fetal bovine serum (FBS) was added to stop the enzyme activity. After centrifugation the pellet was washed with HBSS 10% FVB and then the islets were purified with a Histopaque gra-dient. After a new set of washing and centrifugation the islets were hand-picked. The fresh islets were used for perfusion assay or immediately snap freeze for RNA/DNA extraction.

value: Pancreatic islets

value: CR


title: D66 [550-0069-5]

description: Infinium Methylation EPIC


title: D67 [550-0070-7]

description: Infinium Methylation EPIC


title: D65 [550-0064-0]

description: Infinium Methylation EPIC


title: HF, GEX, islets, rep2

value: HF


title: D64 [502-0121-1]

description: Infinium Methylation EPIC


title: D60 [551-0041-6]

description: Infinium Methylation EPIC


title: HF, ATAC, islets, rep2

description: ATAC: read 1 and read2 contains transposed DNA


title: DCs in CD11c-b-catenin active mice, scRNAseq

description: 10X Genomics

value: CD11c-b-catenin active mice


title: AL, ATAC, islets, rep2

value: AL


title: CR, ATAC, islets, rep2


title: CR, GEX, islets, rep1


title: D59 [550-0029-1]

description: Infinium Methylation EPIC


title: D58 [502-0036-6]

description: Infinium Methylation EPIC


title: AL, GEX, islets, rep1


title: DCs in CD11c-b-catenin WT mice as control, scRNAseq

description: 10X Genomics

value: CD11c-b-catenin WT mice


title: D57 [551-0014-6]

description: Infinium Methylation EPIC


title: D55 [502-0163-7]

description: Infinium Methylation EPIC


title: D56 [550-0009-9]

description: Infinium Methylation EPIC


title: CR, ATAC, islets, rep1


title: D53 [502-0118-7]

description: Infinium Methylation EPIC

value: Everolimus


title: AL, GEX, islets, rep2


title: J774 cells, SLC12A9 sgRNA 15, replicate 3

value: Macrophages

value: SLC12A9 knockdown

value: serum-free


title: D62 [502-0082-7]

description: Infinium Methylation EPIC

value: tuberculosis (TB)

value: Peripheral Blood Mononuclear cell

value: STD treatment


title: AL, ATAC, islets, rep1


title: HF, GEX, islets, rep1


title: D51 [502-0059-1]

description: Infinium Methylation EPIC


title: D47 [551-0090-0]

description: Infinium Methylation EPIC


title: NP_25_L

city: Santa Cruz

first: Paloma

last: Medina

address: 1156 High St.

institute: University of California Santa Cruz

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome (GRCm39/mm39) and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat281 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts82 v1.5.0-p3 was used to count the reads numbers mapped to each gene. Gene expression was then converted to transcripts per million (TPM) by normalizing for gene length, then sequencing depth. TPM was chosen as a normalization method as it allows for the more accurate comparison across samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Mammary epithelial cells

extract_protocol:
L2-5 and R2-5 mammary glands were harvested, minced, and chemically digested overnight in Advanced DMEM F/12 with 1% PSA, gentle collagenase/hyaluronidase, and DNAse I at 37C, 5% CO2, and added humidity. Partially digested glands were then mechanically digested by pipetting with a serological pipette until no tissue pieces were visible. Digested glands were washed with staining buffer (Hank’s Balanced Salt Solution, 2% Bovine Calf Serum, 1% PSA) and centrifuged (1500RPM) at 4C for 5 minutes. Red blood cells were lysed with 5mL of ACK Lysis buffer for 5 minutes, and cells were washed with 15mL of staining buffer. Cells were treated with 0.25% Trypsin with EDTA and gently pipetted continuously for 2-3 minutes to digest the basement membrane. Cells were then treated with DNAse I and Dispase and pipetted continuously for 2-3 minutes to prevent clumping. The single-cell suspension was then filtered through a 40um mesh strainer and pelleted via centrifugation (1500RPM, 4C, 5 minutes).
RNA was isolated according to manufacturers instructions (Qiagen RNEasy Plus Micro Kit No. 74034). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library80. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Mammary epithelial cells

value: C57Bl/6 WT

tag: time


title: NP_24_L


title: D54 [550-0058-3]

description: Infinium Methylation EPIC


title: P_24_L


title: D49 [551-0117-0]

description: Infinium Methylation EPIC


title: D50 [551-0001-2]

description: Infinium Methylation EPIC


title: D48 [551-0096-6]

description: Infinium Methylation EPIC


title: M3_24_L


title: M3_25_L


title: P_23_L


title: NP_23_L


title: D44 [551-0060-7]

description: Infinium Methylation EPIC


title: P_25_B


title: D43 [551-0049-4]

description: Infinium Methylation EPIC


title: M3_25_B


title: D46 [551-0078-6]

description: Infinium Methylation EPIC


title: P_25_L


title: HF, ATAC, islets, rep1


title: NP_25_B


title: P_24_B


title: M3_23_L


title: D41 [550-0089-7]

description: Infinium Methylation EPIC


title: D42 [551-0004-5]

description: Infinium Methylation EPIC


title: D40 [550-0088-6]

description: Infinium Methylation EPIC


title: D52 [551-0029-2]

description: Infinium Methylation EPIC


title: D39 [550-0083-1]

description: Infinium Methylation EPIC


title: D38 [550-0067-3]

description: Infinium Methylation EPIC


title: P_23_B


title: NP_24_B


title: D45 [551-0061-8]

description: Infinium Methylation EPIC


title: D37 [550-0066-2]

description: Infinium Methylation EPIC


title: M3_24_B


title: D36 [550-0048-2]

description: Infinium Methylation EPIC


title: D31 [550-0027-9]

description: Infinium Methylation EPIC


title: NP_23_B


title: D35 [550-0045-9]

description: Infinium Methylation EPIC


title: D34 [550-0043-7]

description: Infinium Methylation EPIC


title: D30 [550-0019-0]

description: Infinium Methylation EPIC


title: M3_23_B


title: D32 [550-0031-4]

description: Infinium Methylation EPIC


title: D29 [550-0007-7]

description: Infinium Methylation EPIC


title: D33 [550-0039-2]

description: Infinium Methylation EPIC


title: C4_Saline_145

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the 10X Genomics Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: Raw count matrices in H5 format

source_name: left atrial tissue

extract_protocol:
Left atrial tissues from vehicle- and anti-Trem2-siSpp1-treated HOMER mice were microdissected using a dissection microscope and subsequently snap-frozen in liquid nitrogen. Nuclei were then isolated using the 10X Chromium Nuclei Isolation kit according to the manufacturer’s protocol. In detail, frozen samples were homogenized using a pestle and lysis buffer and passed through a column. Next, debris was removed via centrifugation in debris removal buffer. The nuclei were then washed, resuspended and visualized under a microscope to determine nuclei concentration and quality. The isolated nuclei were immediately loaded on a 10X Genomics Chromium Single Cell G chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent kit v3.1 user guide. As nuclei have a lower RNA content than whole cells, the cDNA amplification cycles were increased by 1-2 cycles, as recommended by 10X Genomics.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent kit v3.1 user guide with appropriate modifications to the PCR cycles based on the cDNA concentration. Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR and subsequently sequenced on an Illumina NovaSeq 6000 system as recommended by 10X Genomics.
snRNA-seq

value: left atrial tissue

value: nuclei

value: vehicle


title: C9_Saline_151

description: 10x Genomics


title: T3_ARC_144

description: 10x Genomics


title: D25 [502-0217-7]

description: Infinium Methylation EPIC


title: C7_Saline_149

description: 10x Genomics


title: D27 [502-0228-9]

description: Infinium Methylation EPIC


title: D24 [502-0212-2]

description: Infinium Methylation EPIC


title: D26 [502-0225-6]

description: Infinium Methylation EPIC


title: D28 [502-0229-0]

description: Infinium Methylation EPIC


title: T8_ARC_150

description: 10x Genomics


title: T1_ARC_142

description: 10x Genomics


title: D21 [502-0192-9]

description: Infinium Methylation EPIC


title: D20 [502-0154-7]

description: Infinium Methylation EPIC


title: LP, G < GL, replicate 1

city: Houston

first: Humam

last: Kadara

state: Texas

address: 1515 Holcombe Blvd Unit 2951

department: Translational Molecular Pathology

institute: The University of Texas MD Anderson Cancer Center

description: Chromium Next GEM Single Cell 5′ Kit v2 (10X Genomics)

data_processing:
Raw sequencing reads were demultiplexed, and initial quality control was performed using the Cell Ranger software suite (10X Genomics, version 3.1). Read counts were aligned to the mouse reference genome (GRCm38) and quantified to generate feature-barcode matrices. The Seurat R package (v3.1.5) was utilized for the preliminary analysis, which included filtering of barcodes based on UMI counts to identify and retain genuine single-cell transcriptomes.
A stringent quality control pipeline was implemented to ensure high data fidelity in the same manner as our previous reports. To remove damaged or dying cells, those with low gene counts (under 200 genes per cell) and high mitochondrial content (over 15% of total reads) were excluded from downstream analysis. Library size normalization was applied to the remaining dataset using the NormalizeData function in Seurat, followed by the identification and regression of unwanted sources of variation such as cell cycle effects.
DoubletFinder (version 3.0) was used alongside Seurat to predict and exclude doublets from the dataset. Parameters for doublet identification were determined by assessing the distribution of read counts and the co-expression of genes typically not co-expressed in the same cell. This iterative process involved refining the parameters and reassessing the dataset until the removal of probable doublets was maximized.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Colonic lamina propria

extract_protocol:
Tumor tissues freshly collected from syngeneic mice were dissociated into single-cell suspensions using the Tumor Dissociation Kit (Catalog No. 130-096-730, Miltenyi Biotec). Colon tissues were dissected, promptly immersed in ice-cold PBS, and kept on ice for subsequent processing. The colon sections were carefully opened, and any feces present were removed. Colonic tissues were then cut into pieces measuring 1–2 cm in length. Lamina propria cells were isolated using the Miltenyi Biotec Lamina Propria Dissociation Kit (Catalog No. 130-097-410), following the guidelines provided by the manufacturer.  Tissues were processed in a gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec), operating under the program settings recommended by the manufacturer for optimal tissue dissociation while preserving cell viability. The resulting cell suspensions were filtered through a 70 μm cell strainer to remove debris and aggregates. Subsequently, red blood cells were lysed using ACK Lysis Buffer (Thermo Fisher Scientific, Catalog No. A1049201) for 5 minutes at room temperature. Lysed suspensions were then neutralized and washed, and cells were resuspended in ice-cold Fetal Bovine Serum (FBS, Catalog No. 16140071, Thermo Fisher Scientific) to protect cell integrity. Cell suspensions were then passed through a 40 μm FlowMi cell strainer (Millipore, Catalog No. BAH136800040) to ensure homogeneity for downstream processing.
Single-cell suspensions were freshly processed and labeled with Sytox Green (Thermo Fisher Scientific, Catalog No. S7020) to stain dead cells for exclusion. Live cells were sorted using a FACS Aria I flow cytometer (BD Biosciences), collecting only Sytox Green-negative cells. Sorted cells were then washed with PBS containing 2% FBS (Catalog No. 10270106, Thermo Fisher Scientific) to remove any extracellular RNA. Cell viability and number were assessed via Trypan Blue (Catalog No. T8154, Sigma-Aldrich) exclusion using a hemocytometer. Viable cells were encapsulated into Gel beads-in-emulsion (GEMs) using the Chromium Next GEM Single Cell 5′ Kit v2 (10X Genomics, Catalog No. PN-1000263) and Chromium Next GEM Chip G Single Cell Kit (10X Genomics, Catalog No. PN-1000120), following the manufacturer's protocol. Barcoding, reverse transcription, and cDNA amplification were conducted as per standard procedures. Amplified cDNA was subjected to a quality check using the Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent, Catalog No. 5067-4626). The cDNA libraries were then fragmented, size-selected, and underwent end-repair, A-tailing, adapter ligation, and PCR amplification with unique indexing. The final library was validated for quality and quantified using a Qubit 4 Fluorometer with the dsDNA HS Assay Kit (Thermo Fisher Scientific, Catalog No. Q32851). The libraries were normalized based on molarity, pooled, and sequenced on an Illumina NovaSeq 6000 system (Illumina, Catalog No. 20012866) following the manufacturer's instructions for high-throughput sequencing.

value: Colonic lamina propria

tag: Sex

value: Male

value: Live cells

value: FMT from Gprc5a-/-, Lcn2-/- donor


title: D22 [502-0193-0]

description: Infinium Methylation EPIC


title: Tumor, G < GL, replicate 2

source_name: Subcutaneous tumor tissue

value: Subcutaneous tumor tissue

value: Female


title: Tumor, G < G, replicate 2

value: FMT from Gprc5a-/- donor


title: Tumor, G < GL, replicate 1


title: LP, G < G, replicate 2


title: Tumor, G < G, replicate 1


title: D19 [502-0148-0]

description: Infinium Methylation EPIC

value: Everolimus


title: D18 [502-0143-5]

description: Infinium Methylation EPIC


title: Female_Aged_3_Section3_2_interaction

city: New York

first: Abdulraouf

last: Abdulraouf

state: NY

address: 1230 York Ave

institute: Rockefeller University

library_source: other

data_processing:
cDNA data processing:
Initial Data Preparation: After the sequencing process, the data is obtained in the form of two sets of FASTQ files: R1 and R2. R1 FASTQ files contain the barcode sequences for receiver bead along with their associated Unique Molecular Identifiers (UMIs). R2 FASTQ files contain the tagmented cDNA sequences.
Barcode Mapping and Tagging: The barcode sequences from R1 are mapped to a whitelist of bead barcodes with a tolerance of 1 base pair error. The identified bead barcode is then added as an identifier (ID) for the corresponding sequences in R2.
Read2 File Generation and PolyA Trimming: New Read2 files are generated where the name of each sequence in R2 contains the corresponding Read1 barcode. Additionally, any PolyA tails present at the end of the sequences are trimmed to ensure accurate mapping and analysis.
Read Mapping to Genome: The filtered and trimmed reads are then mapped to the reference genome using a tool such as STAR(25) (Spliced Transcripts Alignment to a Reference). This step involves aligning the sequences from R2 to the genomic sequences to identify their locations and potential splice sites.
Duplicate Removal: After mapping, duplicate reads are identified and removed to eliminate redundant data and ensure accuracy in downstream analysis. This process generates new SAM (Sequence Alignment/Map) files containing the mapped reads with duplicates removed.
Gene Count Matrices Generation: From the processed SAM files, gene count matrices are generated for each associated receiver bead. This involves counting the number of reads aligned to each gene for every receiver bead, providing quantitative information about gene expression levels.
Beads Connections processing
Initial Data Preparation: Following the sequencing process, data from two beads, namely receiver bead and sending beads, are obtained. Each bead connection includes unique molecular identifiers (UMIs) which help in identifying and quantifying individual connection molecules. Additionally, there are two types of reads: R1, which contains the barcode for receiver beads, and R2, which contains the barcodes for receiver beads. The reads are mapped to a whitelist of barcodes with 1 base pair error, including the UMI sequence. Duplicated reads are then filtered, and a csv file is generated with receiver bead, UMI, and sending bead barcode, where each line represents a unique molecular connection between receiver and sending beads.
Assembly: STAR_hg19_mm10_RNAseq
Supplementary files format and content: Please check below. Annotation column has content description as well.
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Mouse Brain

extract_protocol:
10 um thick mouse brains were cryosectioned, and RNA was hybridized to a barcoded hydrogel bead based array
Barcoded beads have a PCR handle, and Template Switching Oligo was utilized to amplify bound nucleic acid molecules.

value: Mouse Brain


title: LP, G < G, replicate 1


title: LP, G < GL, replicate 2


title: Female_Aged_3_Section2_interaction


title: D17 [502-0122-2]

description: Infinium Methylation EPIC

value: tuberculosis (TB)


title: Female_Aged_3_Section3_1_interaction


title: D16 [502-0111-0]

description: Infinium Methylation EPIC

value: Peripheral Blood Mononuclear cell


title: Female_Aged_2_Section3_1_interaction


title: Female_Aged_2_Section3_2_interaction


title: D23 [502-0202-1]

description: Infinium Methylation EPIC

value: STD treatment


title: D14 [502-0104-2]

description: Infinium Methylation EPIC


title: D12 [502-0093-9]

description: Infinium Methylation EPIC


title: Female_Aged_2_Section2_interaction


title: D11 [502-0086-1]

description: Infinium Methylation EPIC


title: D10 [502-0085-0]

description: Infinium Methylation EPIC


title: Female_Aged_2_Section1_interaction


title: D9 [502-0078-2]

description: Infinium Methylation EPIC


title: Female_Aged_1_Section1_interaction


title: D8 [502-0071-5]

description: Infinium Methylation EPIC


title: Female_Aged_1_Section2_interaction


title: D7 [502-0056-8]

description: Infinium Methylation EPIC


title: D6 [502-0055-7]

description: Infinium Methylation EPIC


title: Female_Young_3_Section3_1_interaction


title: Female_Aged_1_Section3_1_interaction


title: Female_Young_3_Section3_2_interaction


title: D15 [502-0110-9]

description: Infinium Methylation EPIC


title: Female_Aged_3_Section1_interaction


title: D5 [502-0050-2]

description: Infinium Methylation EPIC


title: Female_Young_3_Section2_interaction


title: D13 [502-0094-0]

description: Infinium Methylation EPIC


title: D3 [502-0039-9]

description: Infinium Methylation EPIC


title: Female_Young_2_Section3_2_interaction


title: D2 [502-0035-5]

description: Infinium Methylation EPIC


title: Female_Young_3_Section1_interaction


title: D1 [502-0005-2]

description: Infinium Methylation EPIC


title: Female_Young_2_Section1_interaction


title: Female_Young_2_Section2_interaction


title: Female_Young_2_Section3_1_interaction


title: Female_Aged_3_Section3_1_cDNA

data_processing:
cDNA data processing:
Initial Data Preparation: After the sequencing process, the data is obtained in the form of two sets of FASTQ files: R1 and R2. R1 FASTQ files contain the barcode sequences for receiver bead along with their associated Unique Molecular Identifiers (UMIs). R2 FASTQ files contain the tagmented cDNA sequences.
Barcode Mapping and Tagging: The barcode sequences from R1 are mapped to a whitelist of bead barcodes with a tolerance of 1 base pair error. The identified bead barcode is then added as an identifier (ID) for the corresponding sequences in R2.
Read2 File Generation and PolyA Trimming: New Read2 files are generated where the name of each sequence in R2 contains the corresponding Read1 barcode. Additionally, any PolyA tails present at the end of the sequences are trimmed to ensure accurate mapping and analysis.
Read Mapping to Genome: The filtered and trimmed reads are then mapped to the reference genome using a tool such as STAR(25) (Spliced Transcripts Alignment to a Reference). This step involves aligning the sequences from R2 to the genomic sequences to identify their locations and potential splice sites.
Duplicate Removal: After mapping, duplicate reads are identified and removed to eliminate redundant data and ensure accuracy in downstream analysis. This process generates new SAM (Sequence Alignment/Map) files containing the mapped reads with duplicates removed.
Gene Count Matrices Generation: From the processed SAM files, gene count matrices are generated for each associated receiver bead. This involves counting the number of reads aligned to each gene for every receiver bead, providing quantitative information about gene expression levels.
Beads Connections processing
Initial Data Preparation: Following the sequencing process, data from two beads, namely receiver bead and sending beads, are obtained. Each bead connection includes unique molecular identifiers (UMIs) which help in identifying and quantifying individual connection molecules. Additionally, there are two types of reads: R1, which contains the barcode for receiver beads, and R2, which contains the barcodes for receiver beads. The reads are mapped to a whitelist of barcodes with 1 base pair error, including the UMI sequence. Duplicated reads are then filtered, and a csv file is generated with receiver bead, UMI, and sending bead barcode, where each line represents a unique molecular connection between receiver and sending beads.
Assembly: STAR_hg19_mm10_RNAseq
Supplementary files format and content: Please check below. Annotation column has content description as well.


title: Female_Aged_3_Section3_2_cDNA


title: D5_LPS_24h

description:
SAMPLE 28
Infinium Methylation EPIC

data_processing:
Minfi package in R
Average Beta

source_name: Monocyte-Macrophages

growth_protocol: Plastic Adhesion derived MDMs grown in RPMI+ 10% Human AB-serum + L-gluatmine+ penicillin and streprtomycin (1%)

treatment_protocol: Treated with LPS alone or in Combination with TCA inhbitors

value: Monocyte-Macrophages


title: D6_ITA_LPS

description:
SAMPLE 26
Infinium Methylation EPIC

value: Itaconic Acid_LPS


title: D3_ITA_LPS

description:
SAMPLE 25
Infinium Methylation EPIC


title: D6_LPS_24h

description:
SAMPLE 29
Infinium Methylation EPIC


title: D1_LPS_24h

description:
SAMPLE 27
Infinium Methylation EPIC


title: D4 [502-0040-1]

description: Infinium Methylation EPIC


title: Female_Aged_2_Section3_1_cDNA


title: D3_SUC_LPS

description:
SAMPLE 22
Infinium Methylation EPIC


title: D5_SUC_LPS

description:
SAMPLE 21
Infinium Methylation EPIC


title: D4_LL_GLYNAC

description:
SAMPLE 20
Infinium Methylation EPIC

value: LPS + GLYCINE_N-acetyl Cytsteine


title: Female_Aged_3_Section2_cDNA


title: Female_Aged_2_Section3_2_cDNA


title: D5_ITA_LPS

description:
SAMPLE 24
Infinium Methylation EPIC


title: D6_SUC_LPS

description:
SAMPLE 23
Infinium Methylation EPIC


title: Female_Aged_3_Section1_cDNA


title: D4_LPS_LPS

description:
SAMPLE 17
Infinium Methylation EPIC

value: LPS


title: D4_LL_MET

description:
SAMPLE 19
Infinium Methylation EPIC

value: LPS+METFORMIN


title: D4_LL_EVERO

description:
SAMPLE 18
Infinium Methylation EPIC

value: LPS+EVEROLIMUS


title: Female_Aged_2_Section1_cDNA


title: Female_Aged_2_Section2_cDNA


title: Female_Aged_1_Section3_1_cDNA


title: Female_Aged_1_Section1_cDNA


title: Female_Aged_1_Section2_cDNA


title: D4_NIL-NIL

description:
SAMPLE 16
Infinium Methylation EPIC


title: D3_LL_GLYNAC

description:
SAMPLE 15
Infinium Methylation EPIC


title: D3_LL_MET

description:
SAMPLE 14
Infinium Methylation EPIC


title: Female_Young_3_Section2_cDNA


title: Female_Young_2_Section3_2_cDNA


title: Female_Young_3_Section3_1_cDNA


title: Female_Young_3_Section1_cDNA


title: D3_LPS_LPS

description:
SAMPLE 12
Infinium Methylation EPIC


title: D3_LL_EVERO

description:
SAMPLE 13
Infinium Methylation EPIC


title: D3_NIL-NIL

description:
SAMPLE 11
Infinium Methylation EPIC


title: Female_Young_2_Section3_1_cDNA


title: Female_Young_2_Section1_cDNA


title: Female_Young_2_Section2_cDNA


title: D2_LL_MET

description:
SAMPLE 9
Infinium Methylation EPIC


title: Wild Type

city: Hefei

first: Zhenya

last: Tan

address: 81th Meishan Road

institute: Anhui Medical University

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. Cell Ranger (vision 5.0.0) pipeline was used for sample demultiplexing, barcode processing and gene counting. For dimensional reduction, clustering and downstream analysis, Cell Ranger output was loaded to Seurat (version 3.1.1) after genome aligning.
Assembly: mm10
Supplementary files format and content: qualified 8,818 and 10,177 cells from Ptpn11 +/+ and Ptpn11 E76K/+ groups, respectively for further bioinformatics analyses

source_name: bone marrow cells

extract_protocol:
Fresh  bone marrow cells from 3 mice per group were collected mixed together, The Erythrocytes were lysed, followed by the execution of the recommended protocol for the scRNA-seq 10x Genomics platform using v3 chemistry
scRNA-seq raw reads were obtained following the standard protocol for Chromium Single Cell 3ʹ Reagent Kits v3.
CellRanger 1 software from 10x Genomics was employed to identify cell-discriminating barcode sequence markers and unique molecular identifier (UMI) markers for different mRNA molecules within each cell

value: bone marrow cells


title: Mutant


title: D2_LL_EVERO

description:
SAMPLE 8
Infinium Methylation EPIC


title: EAE-chronic-Brain CD45-, scRNAseq

city: Xi'an

first: Zhe

last: Feng

address: No.620 West Chang'an Street

institute: Shaanxi Normal University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Brain tissue was minced and centrifuged at 300g for 5 min at 4°C. The supernatant was discarded. Add enzyme I mixture, resuspend and then add enzyme II mixture, incubate at 37°C, 90 rpm, 3 times for 10 min each time, filter through a 70 μm filter. Then centrifuge and discard the supernatant, add pre-cooled D-PBS and resuspend, and afterwards add debris remover, mix well and slowly add pre-cooled D-PBS, thoroughly remove the upper two layers, add pre-cooled D-PBS, resuspended and centrifuge for 10 min. Centrifuge for 10 min, completely remove the upper two layers, add pre-cooled D-PBS and resuspend, centrifuge and discard the supernatant, and resuspend the cells in PBS containing 0.1% BSA and pass through a 30 μm sterile cell strainer.
Library was performd accordiing to the manufacter's instructions（10×Genomics Chromium Single Cell 3’ Reagent Guidelines v3 Chemistry; https://support.10×genomics.com/single-cell-gene-expression）.Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion（GEM）.The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular Identifier（UMI）and the 10× Barcode. The pooled barcode cDNA was then cleaned up with Silane DynaBeads, amplifiled by PCR and the apropiated sized fragments were selected for subsequent library construction. Read 2 is used for downstream analysis in Cell ranger, which is added during library construction by end repair, adenine tailing, junction ligation and PCR.

value: brain cells

value: brain

tag: strain

tag: age


title: D2_LPS_LPS

description:
SAMPLE 7
Infinium Methylation EPIC


title: EAE-chronic-Brain CD45+, scRNAseq

description: 10x Genomics


title: D2_NIL-NIL

description:
SAMPLE 6
Infinium Methylation EPIC


title: D1_LL_GLYNAC

description:
SAMPLE 5
Infinium Methylation EPIC


title: EAE-peak-Brain CD45-, scRNAseq

description: 10x Genomics


title: D1_LPS_LPS

description:
SAMPLE 2
Infinium Methylation EPIC


title: unstimulated, vimentin positive, biorep3

city: Aurora

first: Tonya

last: Brunetti

state: CO

address: 12800 East 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina universal adapters were removed, bases were trimmed if the Phred Score was less than 24, and any reads after trimming that were fewer than 20 base pairs in length were discarded using Cutadapt v4.4 under Python version 3.10.
Reads were aligned and quantified to the mm10 reference genome using STAR v2.7.10b
Differential gene expression was performed using two R packages: RUVseq v1.20.0 and DESeq2 v1.26.0
Assembly: mm10
Supplementary files format and content: The four csv files with the suffix *results_deseq2_regress_surrogate_RUV_vars.csv contain the DESeq2 differential expression results for the comparisons listed
Supplementary files format and content: The .Rdat file is an R data object that contains the pre-filtered raw counts for all genes for samples used in the analysis; can be loaded into R using the load() function

source_name: Bone Marrow

extract_protocol:
RNA was extracted using RNeasy micro kit (Qiagen, 74004) and DNase treatment occurred using Turbo DNA-free DNAse (Qiagen, AM2238).
polyA selected RNA and preparation using Universal Plus mRNA-Seq library preparation kit with NuQuant

value: Bone Marrow

value: neutrophils

value: WT

value: unstimulated


title: D1_LL_MET

description:
SAMPLE 4
Infinium Methylation EPIC


title: unstimulated, vimentin positive, biorep1


title: D1_LL_EVERO

description:
SAMPLE 3
Infinium Methylation EPIC


title: EAE-peak-Brain CD45+, scRNAseq

description: 10x Genomics


title: Normal brain, scRNAseq

description: 10x Genomics


title: D1_NIL-NIL

description:
SAMPLE 1
Infinium Methylation EPIC


title: unstimulated, vimentin negative, biorep3

value: Vimentin KD


title: D2_LL_GLYNAC

description:
SAMPLE 10
Infinium Methylation EPIC


title: unstimulated, vimentin negative, biorep2


title: 250_5

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

data_processing:
BGI’s process included filtration and removal of reads with high levels of unknown base N, adaptor sequences and low-quality reads from raw reads.
Reads were mapped to the EMBL human genome 38, patch release 13 using the splice-aware aligner STAR v2.7.10a (parameters: --twopassMode Basic , --outFilterIntronMotifs RemoveNoncanonical , --outSAMstrandField intronMotif , --outSAMtype BAM Unsorted , --alignSoftClipAtReferenceEnds No , --outFilterMatchNmin 100 , --outSAMattrIHstart 0 , --alignEndsType EndToEnd)
BAM files were sorted and indexed using SAMtools v1.9
StringTie v2.1.7 was used to extract the gene and transcript abundances of each gene (parameters: -rf , -e)
Assembly: hg38.p13
Supplementary files format and content: gene_count_matrix.csv is a csv file of the raw counts for each gene
Supplementary files format and content: transcript_count_matrix.csv is a csv file of the raw counts of each transcript for each gene generated by StringTie

source_name: Cortical Brain organoids

growth_protocol: Cerebral organoids were derived from hiPSC using the STEMdiff™ Cerebral Organoid Kit following the manufacturer´s instructions (StemCell Technologies, #08570, #08571)

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Plus kit by Macherey and Nagel following the manufacturer’s guidelines
Library construction was performed at the Beijing Genomics Institute (BGI, Shenzhen/Hong Kong, China https://en.genomics.cn) using the DNBseq platform on a strand-specific cDNA library generating 100 bp paired-end reads. The library preparation included a mRNAs enrichment step using oligo(dT)-attached magnetic beads.
ssRNA-seq (stranded RNA-seq)

treatment_protocol: Cortical organoids were treated once with 50 nM T3 at either day 24, 44 or 59 and collected for sequencing 48h later

value: Cortical Brain organoids

tag: # pooled_organoids

tag: hipsc line

tag: study day

value: 50 nM T3


title: stimulated w/LPS, vimentin positive, biorep3

tag: treatment

value: stimulated w/LPS


title: unstimulated, vimentin negative, biorep1

tag: tissue


title: 250_35

tag: # of_cells_(milion)


title: 043_4

tag: cell type


title: stimulated w/LPS, vimentin positive, biorep1

tag: genotype


title: stimulated w/LPS, vimentin negative, biorep3


title: 043_34


title: 043_15


title: stimulated w/LPS, vimentin negative, biorep1


title: stimulated w/LPS, vimentin negative, biorep2


title: 01B_14


title: GDMSON_8, Myrf fl/fl Sox10 CreERT WT/WT, snRNAseq

city: Portland

first: Ben

last: Emery

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Neurology

institute: Oregon Health & Science University

description: 10x Genomics

data_processing:
Fastq files were prepared using bcl2fastq (Illumina) and then aligned to a reference genome using Cellranger v. 7.0.0 (10x Genomics). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Ambient RNA contamination was estimated and removed using SoupX v. 1.6.2
Mitochondrial features were manually removed by excluding all features starting with mt-
The normalized count matrix integration, batch effect correcting, and cell clustering were performed using Seurat v. 4.3.0
Nuclei were filtered based on 1,000 < nFeature_RNA < 4,000 as well as 1,250 < nCount_RNA < 10,000
Assembly: mm10
Supplementary files format and content: Raw feature-barcode matrices from each replicate
Supplementary files format and content: Filtered feature-barcode matrices from each replicate
Library strategy: snRNA-seq

source_name: Optic Nerve

extract_protocol:
Blood was removed from deeply anesthetized mice (360mg/kg ketamine, 48mg/kg xylazine) via intracardiac perfusion with 10mL 1x PBS. Optic nerves were dissected out and immediately snap-frozen on dry ice. Frozen tissue was stored at -80°C for up to six months, until subsequent tissue processing. The nuclei isolation buffer (NIB, includes 146 mM NaCl, 5 mM Tris-HCl, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, 0.01% BSA, 1 µg/mL actinomycin D, pH 7.5) was prepared with 1 tablet of protein inhibitor cocktail (cOMPLETE Mini lacking EDTA, Sigma) along with 15uL of RNAsin (40U/µL) per 10 mL NIB. When optic nerves were removed from the freezer, they were immediately placed in 2mL NIB solution in a 7mL Dounce grinder and ground 20 times with a loose pestle (A). Then, the homogenate was passed through a 200 µm strainer. The homogenate was ground 10 times with a tight pestle (B), then 2 mL NIB was added and the homogenate was passed through a 40 µm strainer. The homogenate was ground 5 times with a tight pestle (B), then passed through a 20 µm filter. The sample was then centrifuged at 500 x g for 5 minutes at 4°C, the supernatant discarded, and the sample placed on ice. The pellet was resuspended in 1.5 mL of NIB, then centrifuged at 500 x g for 5 min at 4°C, the supernatant discarded, and the pellet resuspended in 0.5 mL Resuspension Buffer (NIB + 50uL SuperaseIN [20U / µL] + 1% BSA). The nuclei suspension was mixed 1:200 with RedDot (2.5uL). The samples were then isolated from debris by fluorescence-activated nuclei sorting (FANS). Two main gates were used: a 561+683 emission for the RedDot stain and a low trigger pulse width as singlet discriminator. 100,000 nuclei were aimed to be sorted. Following sorting, samples were centrifuged at 300 x g for 1 min at 4°C, held on ice for 1 minute then spun for 1 minute at 300 x g at 4°C. The top supernatant was carefully removed and loaded onto the 10x microfluidics chromium chips.
snRNAseq was performed using a Chromium Next GEN Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Single nuclei were partitioned in droplets with single Gel Beads, which contained primers with cell-tagging indexes. Single nucleus suspensions with concentration of at least ~3000/µl were loaded targeting 10,000 nuclei per sample. The resulting cDNA was profiled on a Bioanalyzer NanoChip (Agilent), then used as a template for library preparation according to the reagent kit protocol. (https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry).

value: Optic Nerve

value: Male

tag: age (weeks)

tag: agent

value: tamoxifen

value: 10 weeks


title: GDMSON_7, Myrf fl/fl Sox10 CreERT WT/WT, snRNAseq

description: 10x Genomics

value: Female


title: 250_4

value: control


title: 250_34


title: GDMPON_6, Myrf fl/fl PLP CreERT WT/WT, snRNAseq

description: 10x Genomics


title: 043_33


title: GDMSON_4, Myrf fl/fl Sox10 CreERT Cre/WT, snRNAseq

description: 10x Genomics

value: Myrf iCKO


title: 043_3


title: 250_14


title: GDMSON_3, Myrf fl/fl Sox10 CreERT Cre/WT, snRNAseq

description: 10x Genomics


title: 043_14


title: GDMPON_5, Myrf fl/fl PLP CreERT Cre/WT, snRNAseq

description: 10x Genomics


title: 01B_13


title: A24_thyroid

data_processing:
BGI’s process included filtration and removal of reads with high levels of unknown base N, adaptor sequences and low-quality reads from raw reads.
Reads were mapped to the EMBL human genome 38, patch release 13 using the splice-aware aligner STAR v2.7.10a (parameters: --twopassMode Basic , --outFilterIntronMotifs RemoveNoncanonical , --outSAMstrandField intronMotif , --outSAMtype BAM Unsorted , --alignSoftClipAtReferenceEnds No , --outFilterMatchNmin 100 , --outSAMattrIHstart 0 , --alignEndsType EndToEnd)
BAM files were sorted and indexed using SAMtools v1.9
StringTie v2.1.7 was used to extract the gene and transcript abundances of each gene (parameters: -rf , -e)
Assembly: hg38.p13
Supplementary files format and content: gene_count_matrix.csv is a csv file of the raw counts for each gene
Supplementary files format and content: transcript_count_matrix.csv is a csv file of the raw counts of each transcript for each gene

source_name: Thyroid

extract_protocol:
Total RNA was isolated by a modified guanidinium thiocyanate method by TaKaRa Bio, Inc. (https://www.takarabio.com/)
Library construction was performed at the Beijing Genomics Institute (BGI, Shenzhen/Hong Kong, China https://en.genomics.cn) using the DNBseq platform on a strand-specific cDNA library generating 100 bp paired-end reads. The library preparation included a mRNAs enrichment step using oligo(dT)-attached magnetic beads.
ssRNA-seq (stranded RNA-seq)

value: Thyroid

tag: reported takara_lot_number


title: A23_smooth_muscle

source_name: Smooth Muscle

value: Smooth Muscle


title: GDMPON_1, Myrf fl/fl PLP CreERT Cre/WT, snRNAseq

description: 10x Genomics


title: RNA-3.3S31A-inject

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

data_processing:
For RNA-seq analysis of embryos, FastQC was performed for Illumina reads. We used Fastp software to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases. Next, we downloaded the mouse reference genome (genome assembly: mm10) from the UCSC database and used bowtie2 software for read alignment. The gene-level quantification approach was used to aggregate raw counts of mapped reads using the featureCounts tool. Gene expression was quantified by calculating the normalized fragments per kilobase of transcript per million mapped reads (FPKM) value. Next, we used the R package DESeq2 for differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: count.txt

source_name: zygote

extract_protocol:
Embryos were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Phusion Hot Start II High-Fidelity PCR Master Mix (Thermo Fisher).
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

tag: cell line

value: zygote


title: A22_skeletal_muscle

source_name: Skeletal Muscle

value: Skeletal Muscle


title: RNA-3.3S31A-con


title: 01B_34


title: A21_pancreas

source_name: Pancreas

value: Pancreas


title: A20_lung

source_name: Lung

value: Lung


title: k27ac-3.3S31A-con [Cut&Tag]

data_processing:
library strategy: Cut&Tag
We aligned paired-end CUT&Tag reads of H3K18lac to the mm10 reference genome using Bowtie2 v2.4.4 software. Unmapped and non-uniquely mapped reads were removed by picard & samtools. Next, we pooled the biological replicates and performed downstream analysis.  CUT&Tag peaks were called on merged replicates and normalized to input using MACS2 v2.2.7.1 software. Peak annotation was performed using the R package ChIPseeker with the default parameters. For quantitative analysis, we normalized the read counts by computing the number of reads using merged replicate BAM files with the bamCoverage tool in deepTools software.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used.
CUT&Tag was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech). Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries under the following conditions: 72°C for 3 min, 98°C for 30 s, 17 cycles of 98°C for 10 s and 60°C for 5 s, and a final extension at 72°C for 1 min with a hold at 4°C. For single-cell CUT&Tag of human embryos, CUT&Tag was performed in well of a microplate. After tagmentation, single human embryos were transferred to 200µl tubes containing 5% Proteinase K. After embryos lysis, PCR buffer and adaptors were directly added to tubes, normal PCR cycle was performed. Post-PCR clean-up was performed by adding a 1.5× volume of DNA Clean Beads (Vazyme Biotech).


title: A18_kidney

source_name: Kidney

value: Kidney


title: A17_adrenal_gland

source_name: Adrenal Gland

value: Adrenal Gland


title: 3.3-zygote-MO [Cut&Tag]


title: GDMPON_2, Myrf fl/fl PLP CreERT WT/WT, snRNAseq

description: 10x Genomics

value: WT


title: HB16 hepatoblastoma tumoroid

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HB16 tumoroid

extract_protocol:
Fresh tumor specimens were obtained from patients and processed for primary tumoroid culture (Wu and Nusse, Methods Mol Biol 2022). Tumoroids grown in Matrigel were harvested at P1 or P2 for single cell RNA sequencing. Briefly, dispase was added for 30 minutes at 37C with intermittent mechanical disruption of Matrigel drops. Tumoroids released from Matrigel were spun down at 50g for 5 minutes and washed twice with liver perfusion media/5% FBS. Tryple Express was added for 10-15 minutes at 37C to digest tumoroids to single cells. Liver perfusion media/5% FBS was added at the end of the digestion and cells were collected by centrifugation at 300g x 5 minutes. Cells were resuspended in William's media/10% FBS, counted, and resuspended in the appropriate volume to target 5000 cells for 10x scRNA sequencing.
Libraries were constructed according to the manufacturer's specifications (10x Genomics 3' v2 for sample HB1 and v3 for all other samples)

value: HB16 tumoroid

value: hepatoblastoma


title: 3.3-zygote-con [Cut&Tag]


title: HB17 hepatoblastoma tumoroid

description: 10x Genomics

source_name: HB17 tumoroid

value: HB17 tumoroid


title: androgenetic_24h_input

data_processing:
We aligned reads of to the mm10 reference genome using Bowtie2 v2.4.4 software. Unmapped and non-uniquely mapped reads were removed by picard & samtools. Next, we pooled the biological replicates for each stage and performed downstream analysis. For quantitative analysis, we normalized the read counts by computing the number of reads using merged replicate BAM files with the bamCompare tool in deepTools software. Peaks were screened on merged replicates by the normalized RPKM in 10000bp bins. Peak annotation was performed using the R package ChIPseeker with the default parameters.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: 24h Embryo

extract_protocol:
embryos were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA Hyper Prep Kit for illumina platform (kk8504)

value: 24h Embryo


title: HB14 hepatoblastoma tumoroid

description: 10x Genomics

source_name: HB14 tumoroid

value: HB14 tumoroid


title: A14_small_intestine

source_name: Small Intestine

value: Small Intestine


title: androgenetic_24h


title: RNA-3.3-MO-con


title: 01B_33

value: Cortical Brain organoids

value: control


title: A13_colon

source_name: Colon

value: Colon


title: HB13 hepatoblastoma tumoroid

description: 10x Genomics

source_name: HB13 tumoroid

value: HB13 tumoroid


title: 250_15

source_name: Cortical Brain organoids

value: 50 nM T3


title: HB12 hepatoblastoma tumoroid

description: 10x Genomics

source_name: HB12 tumoroid

value: HB12 tumoroid


title: k27ac-3.3S31A-inject [Cut&Tag]

value: zygote


title: NSC shPHF2 2

city: Barcelona

first: Samuel

last: Aguirre Infantes

state: Barcelona

address: Baldiri Reixac 15-21

department: Department of Structural and Molecular Biology

country: Spain

institute: IBMB-CSIC

data_processing:
Paired-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.3.5.1) and specifying the "--very-sensitive-local" mode.
SAMtools (v1.9) was used to filter out the low-quality reads with the flag 1796, remove reads mapped in the mitochondrial chromosome, and discard those with a MAPQ score below 20.
The resulting BAM files were sorted and deepTools was used to generate counts per million (CPM) normalized signal tracks (bamCoverage --samFlagInclude 64 --normalizeUsing CPM) in bigWig format.
The peak calling was performed with MACS2 (v.2.1.2) by specifying the -BAMPEmode.
Assembly: mm10
Supplementary files format and content: processed data files are input-substracted bigWig. bigWig files include normalized ATAC-Seq signal

source_name: forebrain E12.5

growth_protocol: Neural Stem Cells were extracted from E12.5 mice forebrain and disgregated. Then cultured in DMEM+Neurobasal media with supplements and growth factors to maintain the stem status.

extract_protocol:
Cells were scrapped and resuspended in RBS buffer and then Igepal CA-630 0.1% was added to achieve cell lysis. Transposition reaction with Transposes enzyme and buffer kits (Illumina, FC-121-1030) and immediately following transposition, DNA was purified.
Nextera DNA Library Prep Kit (FC-121-1030), along with unique dual index barcodes for each sample and NEBNext High-Fidelity 2x PCR Master Mix (New England Lab, M0541) were used.
Ampure XP beads (Beckman Coulter, A63880) were prepared for size selection. Libraries were then pair-end sequenced using NextSeq2000 and approximately 50M reads per sample were obtained.

treatment_protocol: Cells were infected with lentiviral shRNA either scramble (control) or against PHF2 (shPHF2)

value: forebrain E12.5

value: Neural Stem Cell

value: infected with shPHF2


title: androgenetic_12h_input

source_name: 12h Embryo

value: 12h Embryo


title: A19_liver

source_name: Liver

value: Liver


title: NSC shPHF2 1


title: A12_spleen

source_name: Spleen

value: Spleen


title: K27-zygote-3.3con [Cut&Tag]

source_name: zygote


title: A16_adipose_tissue

source_name: Adipose Tissue

value: Adipose Tissue


title: NSC shCT

value: infected with shControl

value: shCT


title: A15_stomach

source_name: Stomach

value: Stomach


title: HB15 hepatoblastoma tumoroid

description: 10x Genomics

source_name: HB15 tumoroid

value: HB15 tumoroid

value: hepatoblastoma


title: 3D_PUUV_C

city: Rotterdam

first: Barry

last: Rockx

address: Wytemaweg 80

department: Viroscience

country: Netherlands

institute: Erasmus MC

data_processing:
Demultiplexing: Illumina DRAGEN BCLConvert version 3.8.4
Adapter Trimming: AdapterTrimmer [https://github.com/erasmus-center-for-biomics/AdapterTrimmer]
alignment: HiSat2 version 2.2.1
expression level counting: htseq-count version 0.12.4
gene filtering: keep only genes with count >=5 in at least 6 samples
Assembly: GRCh38
Supplementary files format and content: .tsv file: tab-separated text file of raw counts, genes in rows and samples in columns.

source_name: primary pooled human umbilical vein endothelial cells

growth_protocol: Primary pooled human umbilical vein endothelial cells (PromoCell) were cultured in endothelial cell growth medium MV2 (PromoCell) supplemented with 100 IU/ml penicillin and 100 µg/ml streptomycin (Lonza) at 37 degrees Celcius in a humidfied CO2 incubator. Medium was refreshed 2-3 times per week. Endothelial cells were either cultured as three-dimensional (3D) vessels-on-chip or static 2D, i.e. in 96-wells plates (Greiner) lacking flow.

extract_protocol:
High pure RNA isolation kit (Roche)
Illumina TruSeq Stranded mRNA

treatment_protocol: Puumala orthohantavirus strain Cg 18-20 (European Virus Archive Global #007v-00809, P+3) infection with MOI of 1.0 or mock infection with equal amounts of Dulbecco's Modified Eagle Medium (Lonza) supplemented with 5% fetal calf serum, HEPES, sodium bicarbonate, 100 IU/ml penicillin and 100 µg/ml streptomycin (Lonza) for two hours. Two hours post-infection, cells were washed three times with PBS and refreshed with endothelial cell medium. Medium was refreshed every two days. As additional conditions, endothelial cells were stimulated with 100 ng/ml tumor necrosis factor alpha (TNFα) for 24 hours. Samples were harvested at 4 days post-infection.

tag: condition

value: Vessel-on-chip

value: PUUV


title: 3D_PUUV_B

value: primary pooled human umbilical vein endothelial cells


title: A11_heart

source_name: Heart

value: Heart


title: 3D_PUUV_A


title: androgenetic_5h_input

source_name: 5h Embryo

value: 5h Embryo


title: A10_spinal_cord_total

source_name: Spinal Cord

value: Spinal Cord


title: 3D_TNFa_C

value: TNFa


title: A09_dorsal_root_ganglion

source_name: Dorsal Root Ganglion

value: Dorsal Root Ganglion


title: androgenetic_5h


title: 3D_TNFa_A


title: A08_brain_temporal_lobe

source_name: Brain, Temporal Lobe

value: Brain, Temporal Lobe


title: 3D_Mock_C

value: Mock


title: androgenetic_3h_input

source_name: 3h Embryo

value: 3h Embryo


title: androgenetic_3h


title: 3D_Mock_A


title: 3D_TNFa_B


title: 3D_Mock_B


title: mablast_input

source_name: Blastocyst

value: Blastocyst


title: A07_brain_postcentral_gyrus

source_name: Brain, Postcentral Gyrus

value: Brain, Postcentral Gyrus


title: 2D_PUUV_C

value: Static 2D


title: androgenetic_12h

value: 12h Embryo


title: 2D_PUUV_B


title: 2D_PUUV_A


title: 2D_TNFa_C


title: mablast_HA


title: A05_brain_occipital_pole

source_name: Brain, Occipital Pole

value: Brain, Occipital Pole


title: 2D_TNFa_B


title: 2D_TNFa_A


title: 2D_Mock_C


title: 2D_Mock_B


title: maMO_HA

source_name: morula Embryo

value: morula Embryo


title: A04_brain_insula

source_name: Brain, Insula

value: Brain, Insula


title: 2D_Mock_A


title: ma8cell_input

source_name: 8cell Embryo

value: 8cell Embryo


title: ma8cell_HA


title: 08_MDAMB468_CE_Acetalax_treated_S8

city: Bethesda

first: Anjali

last: Dhall

state: MD

address: 37 Convent Drive

department: DTB

institute: NCI

data_processing:
STAR  2.7.11b aligner used to generate BAM files (Alignment files)
Raw read count were extracted using --quantMode GeneCounts mode of STAR alinger
Assembly: hg19
Supplementary files format and content: comma seprated text file of raw counts for each Sample

source_name: breast

growth_protocol: Cells were cultured in RPMI medium containing 10% fetal bovine serum and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted as per protocol using PureLink® RNA Mini Kit (Cat:12183018A. Invitrogen)
800 ng of total RNA samples to generate the library (PolyA selected). The kits used for the library prep were NEBNext PolyA mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB, E6440).

treatment_protocol: Treated group cells were treated with Acetalax 1 μM for 6 hours

value: breast

value: MDAMB468 with chronic exposure

value: TNBC cells


title: 07_BT549_CE_Acetalax_treated_S7

value: BT549 with chronic exposure


title: A01_brain_total

source_name: Brain Total

value: Brain Total


title: 06_MDAMB468_Acetalax_treated_S6


title: A06_brain_parietal_lobe

source_name: Brain, Parietal Lobe

value: Brain, Parietal Lobe


title: 05_BT549_Acetalax_treated_S5


title: ma4cell_input

source_name: 4cell Embryo

value: 4cell Embryo


title: 03_BT549_CE_control_S3

value: Control


title: 02_MDAMB468_control_S2


title: 04_MDAMB468_CE_control_S4


title: 01_BT549_control_S1