title: dermis_buttocks

status: Public on Apr 13 2025

type: genomic

city: Nagoya

first: Ryosuke

last: Okuno

state: Aichi

address: 2-7, Torimi-cho, Nishi-ku

country: Japan

institute: Nippon Menard Cosmetic Co., Ltd.

hyb_protocol: Genomic DNA bisulfite-treated using the Zymo Research EZ DNA Methylation Kit (Zymo research), following the protocol for the Illumina Infinium® Methylation Assay, was amplified, fragmented, and hybridized to the Infinium MethylationEPIC V2.0 BeadChip (Illumina).

scan_protocol: Data acquisition was performed using the iScan System (Illumina) with the Methylation NXT settings, following the manufacturer's instructions.

data_processing:
The R package ChAMP (version 2.29.1) was used for data processing.
Normalized Beta

label: Cy3 and Cy5

source_name: dermis

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from cultured cells using NucleoSpin® Tissue (Takara Bio).

value: dermis

value: NHDF

value: fibroblast


title: P35_merfish_CD1-2

type: RNA

city: San Francisco

first: Yajun

last: Xie

state: CA

address: 35 medical center way

country: USA

institute: UCSF

hyb_protocol: The samples were processed according to Vizgen MERSCOPE protocol

scan_protocol: MERSCOPE protocol

data_processing:
Cells with a volume greater than 2000 µm^3, those with fewer than 100 transcripts, and those with DAPI scores less than 500 were excluded from the analysis.
Processed data file: h5ad

label: Gene targeting probes

molecule: total RNA

organism: Mus musculus

source_name: Septum

label_protocol: Vizgen protocol

extract_protocol: 10 µm tissue sections were obtained from along the rostro-caudal axis and adhered to the MERSCOPE Slide. The samples were permeabilized in 70% ethanol overnight, followed by cell boundary staining.

tag: tissue

value: Septum

tag: age


title: dermis_face

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: dermis_abdomen


title: old4

type: SRA

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

library_source: transcriptomic

data_processing:
We performed the pre-processing step according to our pipeline miRMaster 2.0 with standard parameter settings (https://doi.org/10.1093/nar/gkab268).
Assembly: mmu10
Supplementary files format and content: miRNA_expression_raw_microglia.tsv: Tab-separated file of raw feature counts per sample.

source_name: microglia

extract_protocol:
Microglia from young and aged mice (3 and 21 months, C57BL/6, males) were isolated via FACS-sorting following the below described protocol. In brief, mice were anaesthetized with Avertin and perfused with 20 mL ice cold DPBS. Brains were dissected, hemispheres separated, and olfactory bulb and cerebellum removed. Single-cell solutions were created for each hemisphere via mincing and douncing the tissue, the solution was filtered (70µm cell strainers, Falcon 352350) and finally centrifuged (400 x g, 10 mins, 4°C). After resuspension in MACS buffer and addition of myelin removal beads (Miltenyi Biotech, 130-096-433), solutions for each hemisphere were loaded on LD columns (Miltenyi Biotech, 130-042-901) to remove myelin. Columns were washed twice with MACS buffer. Cells were pelleted via centrifugation (400 x g, 5 mins, 4°C) and resuspended in FACS buffer. FC blocking antibody was added and incubated for 5 mins. Primary antibodies (CD11b-FITC (Biolegend 101206); CD-45-BUV396 (Biolegend 50-162-785) and CD206-APC (Biolegend 141707)) were added and incubated for 30 mins on ice. After another centrifugation, samples were resuspended in 0.5 mL FACS buffer and Sytox Blue (Thermo, S34857) was added for live cell labelling. Cells were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology) and selected by gating for live single cells (FSC-A/SSC-A). Further, cells were gated for CD11b+; CD45low; CD206- and sorted directly into 1.5mL tubes containing 50µl FACS buffer. As CD11b+/CD45+ brain cells are mainly infiltrating macrophages (PMID: 32381088) we exclude these macrophages with our sorting strategy. FACS-isolated CD11b+/CD45low/CD206- brain myeloid cells are referred to as microglia in this manuscript. Between 10,000 and 40,000 cells per sample were collected. For aged mouse sample 4, two mice were pooled together to reach the threshold of minimal 10,000 cells as input for RNA isolation. After collection was completed 1 mL QIAzol was added instantly. After vortexing, samples were stored at -80°C until RNA isolation. Since cell sorting provides little input material for RNA isolation, the standard miRNeasy microKit (QIAGEN, cat. no. 217084) was used with standard protocol for elution of separated fractions for RNAs above and below 200 nt, to concentrate the miRNA input for library preparation. Library preparation of microglia miRNAs was optimized and performed as described below, except for the RT-primer input, which was altered to a 1:5 dilution and amplification PCR was 25 cycles long.
The MGIEasy Small RNA Library Prep Kit (Item 940-000196-00) was used for library preparation on the high-throughput MGI SP-960 sample prep system according to the manufacturer's protocol. In principle this library preparation method works by ligating 3’- and 5’-adapters to all RNAs in each sample. During reverse transcription (RT), specific RT primers that bind to the adapters are used to generate cDNA and introduce sample specific barcodes. Amplification of this cDNA is performed via a 21-cycled PCR. Size-selection of this PCR product is performed via magnetic beads (AMPure Beads XP, Beckman Coulter). To focus on the small RNAs a size of around 110 bp was selected, this was checked using an Agilent DNA 1000 Kit (Agilent Technologies). The concentration of each sample was measured by a QuBit 1x dsDNA High Sensitivity Assay (Thermo Fisher Scientific). All samples were pooled in one library after concentration measurement in an equimolar fashion to reach a concentration of 4.56 ng µl-1 for each sample in each pooled library. After circularization the pooled libraries were sent for sequencing.

tag: Sex

value: male

value: microglia

tag: strain


title: old3


title: old2


title: old1


title: young3


title: young4


title: vis_19_Male_80

data_processing:
We performed the pre-processing step according to our pipeline miRMaster 2.0 with standard parameter settings (https://doi.org/10.1093/nar/gkab268).
Assembly: mm10
Supplementary files format and content: miRNA_expression_raw_aging.tsv: Tab-separated file of raw miRNA counts per sample from the aging data set.
Supplementary files format and content: miRNA_expression_raw_young_mouse_plasma.tsv: Tab-separated file of raw miRNA counts per sample from the diet restriction experiment data set.
Supplementary files format and content: miRNA_expression_raw_diet_restriction.tsv: Tab-separated file of raw miRNA counts per sample from the injection experiment data set.
Supplementary files format and content: isomiR_expression_raw_aging.tsv: Tab-separated file of raw isomiR counts per sample from the aging data set.
Supplementary files format and content: isomiR_expression_raw_young_mouse_plasma.tsv: Tab-separated file of raw isomiR counts per sample from the diet restriction experiment data set.
Supplementary files format and content: isomiR_expression_raw_diet_restriction.tsv: Tab-separated file of raw isomiR counts per sample from the injection experiment data set.
Supplementary files format and content: lncRNA_expression_raw_aging.tsv: Tab-separated file of raw lncRNA counts per sample from the aging data set.
Supplementary files format and content: piRNA_expression_raw_aging.tsv: Tab-separated file of raw piRNA counts per sample from the aging data set.
Supplementary files format and content: rRNA_expression_raw_aging.tsv: Tab-separated file of raw rRNA counts per sample from the aging data set.
Supplementary files format and content: scaRNA_expression_raw_aging.tsv: Tab-separated file of raw scaRNA counts per sample from the aging data set.
Supplementary files format and content: snoRNA_expression_raw_aging.tsv: Tab-separated file of raw snoRNA counts per sample from the aging data set.
Supplementary files format and content: snRNA_expression_raw_aging.tsv: Tab-separated file of raw snRNA counts per sample from the aging data set.
Supplementary files format and content: tRNA_expression_raw_aging.tsv: Tab-separated file of raw tRNA counts per sample from the aging data set.

growth_protocol: Male and female C57BL/6JN mice from the National Institute of Aging colony (Charles River) were shipped to the Stanford ChEM-H animal facility (Palo Alto), where they were housed at least one month before euthanasia. For each age group of 3, 12, 15, 18 and 21 months 5 female mice and 5-6 male mice were used; age groups 26 and 28 months consisted only of 5 and 3 male mice respectively. Animals were housed in cages of 2-3 mice, with a 12/12 light/dark cycle, at 19.4 – 22.8 °C and provided with food and water ad libitum. The cohort of mice treated with YMP or PBS were housed at the Palo Alto VA animal facility under a 12 h/12 h light/dark cycle at 68–73 °F under 40–60% humidity.

extract_protocol:
RNA was isolated using the RNeasy 96 kit (Qiagen, 74181) and a TissueLyser II (Qiagen, 85300), according to RNeasy 96 Handbook protocol “Purification of Total RNA from Animal Tissues using Spin Technology” without the optional on-plate DNase digestion.
The MGIEasy Small RNA Library Prep Kit (Item 940-000196-00) was used for library preparation on the high-throughput MGI SP-960 sample prep system according to the manufacturer's protocol. In principle this library preparation method works by ligating 3’- and 5’-adapters to all RNAs in each sample. During reverse transcription (RT), specific RT primers that bind to the adapters are used to generate cDNA and introduce sample specific barcodes. Amplification of this cDNA is performed via a 21-cycled PCR. Size-selection of this PCR product is performed via magnetic beads (AMPure Beads XP, Beckman Coulter). To focus on the small RNAs a size of around 110 bp was selected, this was checked using an Agilent DNA 1000 Kit (Agilent Technologies). The concentration of each sample was measured by a QuBit 1x dsDNA High Sensitivity Assay (Thermo Fisher Scientific). Each library in this dietstudy consisted of 16 samples, barcoded with the following barcodes: 1–4, 13–16 and 25–32. All samples of one library were pooled after concentration measurement in an equimolar fashion to reach a concentration of 4.56 ng µl-1 for each sample in each pooled library. After circularization the pooled libraries were sent for sequencing.
Samples were pooled in libraries at random to avoid technical bias.

treatment_protocol: For diet restriction mice: For the aDR study with C57BL/6JN mice, 18-months-old mice were randomly assigned to AL or aDR. aDR treatment was initiated by transferring mice from AL to 10% aDR for 7 days. After that, aDR was increased to 25%. aDR animals were fed once per day between 3-5 p.m., and all animals were checked daily for their well-being and any deaths. For the first 16 days, weights were checked daily. Mice were euthanized at the ages of 19 months. All mice were euthanized in the morning within a period of 6 hours prior to the regular feeding time of the DR mice. The aDR study with C3B6F1 mice was performed in accordance with the recommendations and guidelines of the Federation of the European Laboratory Animal Science Association (FELASA), with all protocols approved by the Landesamt für Natur, Umwelt und Verbraucherschutz, Nordrhein-Westfalen, Germany (84-02.04.2015.A437). Female F1 hybrid mice (C3B6F1) were generated in-house by crossing C3H/HeOuJ females with C57BL/6NCrl males (strain codes 626 and 027, respectively, Charles River Laboratories). Five female animals were housed as a group in individually ventilated cages under specific-pathogen-free conditions with constant temperature (21 °C), 50–60% humidity and a 12 h/12 h light/dark cycle. For environmental enrichment, mice had constant access to nesting material and chew sticks. All mice received commercially available rodent chow (ssniff R/M-Low phytoestrogen, ssniff Spezialdiäten, Germany) and were provided with filtered water ad libitum. aDR animals received 60% of the food amount consumed by AL animals. aDR treatment was initiated at 20 months of age by directly transferring mice from AL to 40% DR. aDR animals were fed once per day, and all animals were checked daily for their well-being and any deaths. Mice were euthanized at the ages of 24 months. All mice were euthanized in the morning within a period of 3 hours prior to the regular feeding time of the DR mice. Mice were euthanized by cervical dislocation, and tissues were rapidly collected and snap-frozen in liquid nitrogen. For mice of the young mouse plasma cohort: Young Mouse Plasma (YMP) was collected following the protocol described by Villeda et al. Briefly, C57Bl/6J male mice aged 2 months were anesthetized with 2.5% v/v Avertin after being group-housed. Around 700 μl of blood was drawn via cardiac puncture prior to transcardial perfusion. 15 μl of 250 mM EDTA (Thermo Fisher Scientific, 15575020) were used to collect blood. The mixture was centrifuged at 4°C for 15 minutes at 1,000g to obtain plasma. The plasma from 20-25 mice was pooled together and dialyzed in 1X PBS using cassettes (Slide-A-Lyzer Dialysis Cassettes, 3.5 kDa molecular weight cut-off, 3-12 ml) before being frozen at -80°C. For plasma transfer experiments, 18 months old male C57BL/6JN mice were injected retro-orbitally with 150 μl of YMP per injection. Prior to injection, mice were habituated by being placed on the procedure table in their cage. Injections were administered every 3-4 days, alternating between the left and right eye to allow for recovery. Mice were rested for four days before tissue collection.

tag: brain region

value: vis

tag: brain region_long

value: Visual Cortex

value: Male

tag: cohort

tag: experiment

value: young mouse plasma

tag: treatment

value: PBS

tag: injection type

value: retro-orbital

tag: mouse id


title: young1


title: vis_19_Male_76


title: vis_19_Male_84


title: vis_19_Male_73

value: old mice with young plasma


title: young2


title: vis_19_Male_77


title: vis_19_Female_69

value: Female

value: diet restriction

value: control


title: vis_19_Female_68


title: vis_19_Male_81


title: w1118_ovaries_pA_rep2

status: Public on Apr 14 2025

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
Library name: w1118_ovaries_pA_rep2
polyA selected RNA sequencing from w1118 ovaries replicate 2

data_processing:
We used both R1 and R2 reads from the 150bp Novaseq paired-end sequencing runs. Reads were trimmed of the adapters 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' and 'AGATCGGAAGAGCGTCGTGTAGGGAAAGA' at the 3' ends of R1 and R2 reads, respectively, using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting. Trimmed reads were mapped against the dm6 r6.31 transcriptome combined by a collection of D.melanogaster transposon consensus sequences (Senti et al., 2015 EMBO J, PMID: 26302790) using salmon/1.10.0 using options of --validateMappings --incompatPrior 0.0 --seqBias --gcBias. The output files of salmon (quant.sf) were used for the differential expression analysis of transposon and the host mRNAs. The processed quant.sf files contain the counts of r6.31 transcriptome and transposons (marked by TE:<transposon name>.
Assembly: dmel r6.31
Supplementary files format and content: *_quant.sf: mRNA counts produced after the mapping by salmon; <transcript Name> <transcript Length> <Effective Length of the transcript> <transcript counts per one million transcripts (TPM)> <Number of mapped Reads>

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were kept at standard conditions at room temperature.

extract_protocol:
RNA sequencing was performed on Drosophila ovaries. About 10 pairs of ovaries from 2 to 7 days old females have been dissected per genotype, and total RNA was extracted by TRIZOL (Thermo Fisher) and the genomic DNA was removed by DNase I (Thermo Fisher).
The RNA-seq library was made from polyA+ RNA using NEB Ultra II Directional RNA library prep kit (NEB). We used the Kapa LongRange DNA polymerase (Sigma) with TruSeq compatible primers to amplify the libraries.

value: ovaries

value: female

value: Oregon R

tag: genotype

tag: ages

value: 2 -7 days old


title: vis_19_Female_66


title: P35_merfish_CD1-1

value: Septum


title: vis_19_Female_67

value: treatment


title: vis_19_Female_64


title: vis_19_Female_63


title: vis_19_Female_62


title: vis_19_Female_61


title: th_19_Male_84

value: th

value: Thalamus


title: th_19_Male_81


title: th_19_Male_80


title: th_19_Male_77


title: th_19_Male_76


title: th_19_Male_73


title: th_19_Female_69


title: th_19_Female_67


title: th_19_Female_62


title: th_19_Female_66


title: th_19_Female_65


title: th_19_Female_64


title: svz_19_Female_69

value: svz

value: Subventricular zone


title: th_19_Female_63


title: th_19_Female_61


title: svz_19_Female_67


title: svz_19_Female_68


title: svz_19_Female_65


title: svz_19_Female_62


title: svz_19_Female_63


title: svz_19_Female_66


title: vis_19_Female_65

value: vis

value: Visual Cortex


title: svz_19_Female_61


title: pon_19_Female_69

value: pon

value: Pons


title: pon_19_Male_84

value: Male

value: young mouse plasma

value: PBS

value: retro-orbital


title: pon_19_Male_76


title: pon_19_Female_66

value: Female

value: diet restriction

value: control


title: pon_19_Male_80


title: pon_19_Female_63


title: pon_19_Male_81

value: old mice with young plasma


title: pon_19_Female_62

value: treatment


title: pon_19_Female_67


title: pon_19_Female_65


title: pon_19_Female_61


title: plx_19_Male_84

value: plx

value: Choroid Plexus


title: plx_19_Male_80


title: plx_19_Male_76


title: plx_19_Male_73


title: plx_19_Female_69


title: plx_19_Male_72


title: plx_19_Female_66


title: plx_19_Female_67


title: plx_19_Female_68


title: plx_19_Female_65


title: plx_19_Female_63


title: pon_19_Male_77


title: plx_19_Female_61


title: pon_19_Female_68


title: olf_19_Male_81

value: olf

value: Olfactory bulb


title: olf_19_Male_84


title: olf_19_Male_77


title: olf_19_Female_69


title: olf_19_Male_73


title: olf_19_Male_72


title: olf_19_Female_64


title: olf_19_Female_65


title: olf_19_Female_66


title: olf_19_Female_67


title: plx_19_Male_81


title: olf_19_Male_76


title: olf_19_Female_68


title: med_19_Male_81

value: med

value: Medulla


title: med_19_Male_84


title: olf_19_Female_61


title: olf_19_Female_63


title: med_19_Male_80


title: med_19_Male_73


title: med_19_Male_77


title: med_19_Female_68


title: med_19_Male_72


title: med_19_Male_76


title: med_19_Female_69


title: med_19_Female_66


title: med_19_Female_65


title: med_19_Female_67


title: th_19_Male_72

value: th

value: Thalamus


title: pon_19_Male_73

value: pon

value: Pons

value: Male


title: med_19_Female_64


title: olf_19_Male_80

value: young mouse plasma

value: PBS

value: retro-orbital


title: med_19_Female_63

value: Female

value: diet restriction

value: control


title: med_19_Female_62

value: treatment


title: hy_19_Female_67

value: hy

value: Hypothalamus


title: hy_19_Female_68


title: hy_19_Female_69


title: hy_19_Female_66


title: hy_19_Female_63


title: hy_19_Female_65


title: med_19_Female_61


title: olf_19_Female_62

value: olf

value: Olfactory bulb


title: hy_19_Female_62


title: hi_19_Male_81

value: hi

value: Hippocampus (anterior)

value: old mice with young plasma


title: hy_19_Female_61


title: hi_19_Male_76


title: hi_19_Male_80


title: hi_19_Male_72


title: hi_19_Male_77


title: hi_19_Female_69


title: hi_19_Female_68


title: hi_19_Female_67


title: hi_19_Male_73


title: hi_19_Female_66


title: hi_19_Female_64


title: hi_19_Female_63


title: hi_19_Female_61


title: hi2_19_Female_69

value: Hippocampus (posterior)


title: hi_19_Female_65


title: hi2_19_Female_68


title: hi_19_Female_62


title: hi2_19_Female_66


title: hi2_19_Female_67


title: hi2_19_Female_63


title: hi2_19_Female_64


title: ent_19_Female_64

value: ent

value: Entorhinal cortex


title: ent_19_Female_66


title: ent_19_Female_69


title: hi2_19_Female_65


title: ent_19_Female_62


title: cp_19_Male_84

value: cp

value: Caudate putamen

value: Male

value: young mouse plasma


title: ent_19_Female_63

value: Female

value: diet restriction


title: hi2_19_Female_62

value: treatment


title: cp_19_Male_77

value: retro-orbital


title: cp_19_Male_81


title: ent_19_Female_61


title: cp_19_Female_69

value: control


title: cp_19_Female_68


title: cp_19_Male_76

value: PBS


title: cp_19_Female_67


title: cp_19_Female_66


title: cp_19_Male_72


title: cp_19_Female_65


title: cp_19_Female_63


title: cor_19_Male_84

value: cor

value: Motor cortex


title: cp_19_Female_61


title: cor_19_Male_81


title: hi2_19_Female_61


title: ent_19_Female_67


title: cor_19_Male_77


title: cor_19_Male_76


title: cor_19_Male_72


title: cor_19_Female_69


title: cor_19_Female_68


title: cor_19_Female_66


title: cor_19_Female_65


title: cor_19_Female_63


title: cer_19_Male_84

value: cer

value: Cerebellum


title: cp_19_Female_62


title: cor_19_Female_61


title: cer_19_Female_66


title: cer_19_Male_73

value: old mice with young plasma


title: cer_19_Female_69


title: cer_19_Male_80


title: cer_19_Female_68


title: cer_19_Male_81


title: cer_19_Male_77


title: cer_19_Female_62


title: cer_19_Female_64


title: cer_19_Female_61


title: cer_19_Female_63


title: cc_19_Male_84

value: cc

value: Corpus callosum


title: cc_19_Male_81


title: cor_19_Male_80


title: cc_19_Male_80


title: cc_19_Male_73


title: cc_19_Male_76


title: med_28_Male_59

value: med

value: Medulla

value: aging


title: cc_19_Male_72

value: Male

value: young mouse plasma


title: med_28_Male_58


title: med_15_Female_54

value: Female


title: med_21_Female_56


title: cer_19_Male_72


title: cer_19_Female_67

value: diet restriction

value: treatment


title: med_21_Female_52


title: med_18_Female_51


title: med_15_Female_50


title: med_21_Female_48


title: med_15_Female_46


title: med_3_Female_49


title: med_3_Female_45


title: med_18_Female_43


title: med_18_Female_39


title: med_15_Female_42


title: med_15_Female_38


title: med_21_Female_40


title: med_18_Female_47


title: med_28_Male_57


title: med_3_Female_37


title: med_3_Male_33


title: med_21_Male_36


title: med_18_Female_55


title: med_18_Male_35


title: med_21_Male_32


title: med_18_Male_31


title: med_3_Female_53


title: med_3_Male_29


title: med_21_Male_28


title: med_18_Male_27


title: med_15_Male_26


title: med_3_Male_25


title: med_21_Male_24


title: med_3_Female_41


title: med_21_Female_44


title: med_18_Male_23


title: med_12_Male_15


title: med_21_Male_16


title: med_12_Female_13


title: med_3_Male_21


title: med_15_Male_22


title: med_3_Male_17


title: med_18_Male_19


title: med_26_Male_14


title: med_12_Male_12


title: med_15_Male_18


title: med_26_Male_8


title: med_12_Male_9


title: med_12_Male_6


title: med_12_Female_7


title: med_26_Male_5


title: cer_15_Female_54


title: med_15_Male_30


title: med_12_Female_10


title: cer_3_Female_53


title: cer_18_Female_51


title: med_21_Male_20


title: cer_21_Female_48


title: cer_21_Female_52


title: cer_18_Female_47


title: cer_15_Female_50


title: med_26_Male_2


title: cer_28_Male_59


title: med_26_Male_11


title: cer_21_Female_56


title: cer_28_Male_58


title: cer_15_Female_46


title: med_12_Male_3


title: cer_21_Female_40


title: cer_3_Female_41


title: cer_18_Female_39


title: cer_21_Female_44


title: cer_18_Female_55


title: cer_3_Female_45


title: cer_18_Male_27


title: cer_15_Male_30


title: cer_15_Male_26


title: cer_21_Male_28


title: cer_3_Female_49


title: cer_18_Male_23


title: cer_3_Male_25


title: pon_21_Female_40

value: pon

value: Pons


title: pon_18_Female_39


title: med_12_Female_1


title: pon_15_Female_38


title: cer_28_Male_57


title: cer_18_Female_43


title: pon_3_Female_37


title: cer_21_Male_20


title: cer_3_Male_21


title: cer_15_Male_18


title: cer_12_Male_15


title: cer_12_Male_12


title: pon_21_Male_32


title: cer_3_Male_17


title: pon_3_Male_33


title: pon_18_Male_31


title: pon_3_Female_41


title: cer_12_Female_13


title: cer_12_Female_10


title: cer_21_Male_16


title: pon_21_Male_28


title: cer_26_Male_11


title: cer_12_Male_9


title: cer_26_Male_8


title: pon_21_Male_36


title: cer_12_Female_7


title: pon_3_Male_25


title: pon_21_Male_24


title: cer_15_Female_42


title: pon_18_Male_23


title: cer_18_Male_19


title: cer_26_Male_14


title: pon_3_Male_21


title: pon_15_Male_22


title: pon_21_Male_20


title: pon_18_Male_19


title: pon_3_Male_29


title: pon_15_Male_30


title: pon_15_Male_18


title: cer_12_Male_6


title: cer_26_Male_5


title: cer_12_Male_3


title: pon_3_Male_17


title: cer_12_Female_1


title: pon_28_Male_58


title: pon_28_Male_59


title: pon_21_Male_16


title: pon_12_Male_15


title: pon_26_Male_14


title: pon_12_Female_13


title: med_15_Male_34


title: pon_12_Male_12


title: pon_12_Female_10


title: pon_26_Male_8


title: pon_12_Male_6


title: pon_12_Male_9


title: pon_12_Male_3


title: pon_26_Male_5


title: pon_12_Female_7


title: pon_26_Male_2


title: hy_15_Male_30

value: hy

value: Hypothalamus


title: hy_3_Male_29


title: hy_21_Male_28


title: hy_18_Male_27


title: hy_3_Male_25


title: hy_15_Male_26


title: hy_21_Male_24


title: hy_18_Male_23


title: hy_15_Male_22


title: hy_21_Male_20


title: hy_15_Male_18


title: hy_18_Male_19


title: hy_3_Male_17


title: hy_21_Male_16


title: cer_26_Male_2

value: cer


title: ent_15_Female_54

value: ent

value: Entorhinal cortex


title: ent_18_Female_55


title: hy_12_Male_15


title: ent_21_Female_52


title: ent_3_Female_53


title: ent_18_Female_51


title: ent_3_Female_49


title: ent_15_Female_46


title: ent_18_Female_47


title: ent_28_Male_57


title: ent_21_Female_48


title: ent_3_Female_45


title: ent_21_Female_44


title: ent_18_Female_43


title: pon_12_Female_1


title: ent_15_Female_42


title: ent_21_Female_40


title: hy_3_Male_21


title: ent_18_Female_39


title: ent_3_Female_37


title: ent_18_Male_35


title: ent_21_Male_36


title: ent_15_Male_34


title: ent_3_Male_33


title: ent_15_Male_30


title: ent_21_Male_32


title: ent_3_Male_29


title: ent_15_Female_50


title: ent_21_Male_28


title: ent_15_Male_26


title: ent_21_Male_24


title: ent_18_Male_23


title: ent_18_Male_27


title: ent_3_Male_21


title: ent_21_Male_20


title: ent_15_Male_18


title: vis_28_Male_57

value: vis

value: Visual Cortex


title: ent_21_Male_16


title: vis_28_Male_58


title: ent_3_Male_17


title: ent_18_Male_19


title: ent_15_Female_38


title: ent_15_Male_22


title: ent_3_Female_41


title: vis_18_Female_55


title: vis_21_Female_56


title: vis_15_Female_54


title: ent_12_Male_12


title: ent_12_Female_13


title: ent_26_Male_14


title: ent_26_Male_11


title: ent_3_Male_25


title: ent_12_Female_10


title: ent_12_Male_9


title: vis_18_Male_23


title: vis_15_Male_26


title: vis_3_Female_53


title: vis_18_Female_51


title: vis_3_Male_25


title: vis_21_Male_24


title: ent_12_Male_15


title: vis_3_Male_21


title: vis_15_Male_22


title: vis_18_Male_19


title: ent_12_Female_1


title: ent_12_Female_7


title: vis_21_Male_16


title: ent_12_Male_3


title: ent_26_Male_5


title: vis_3_Male_17


title: vis_21_Male_20


title: ent_12_Male_6


title: vis_28_Male_59


title: vis_15_Male_18


title: vis_21_Female_52


title: vis_12_Male_15


title: vis_26_Male_14


title: vis_15_Female_50


title: vis_12_Female_13


title: vis_26_Male_11


title: vis_21_Female_48


title: vis_3_Female_45


title: vis_18_Female_43


title: vis_12_Female_10


title: vis_21_Female_44


title: vis_12_Female_7


title: vis_15_Female_46


title: vis_26_Male_5


title: vis_26_Male_8


title: vis_12_Male_6


title: vis_21_Female_40


title: vis_3_Female_41


title: vis_15_Female_42


title: vis_3_Female_37


title: hi2_12_Male_3

value: Hippocampus (posterior)


title: vis_12_Female_1


title: vis_18_Female_39


title: vis_18_Male_35


title: vis_15_Female_38


title: vis_26_Male_2


title: vis_21_Male_36


title: hi2_28_Male_59


title: hi2_28_Male_58


title: hi2_21_Female_56


title: hi2_18_Female_55


title: hi2_15_Female_54


title: vis_15_Male_34


title: hi2_28_Male_57


title: vis_18_Female_47


title: vis_18_Male_31


title: vis_3_Male_29


title: vis_21_Male_28


title: vis_15_Male_30


title: hi2_21_Female_52


title: vis_18_Male_27


title: vis_3_Male_33


title: hi2_15_Female_50


title: vis_3_Female_49


title: hi2_15_Female_46


title: hi2_3_Female_49


title: hi2_21_Female_48


title: hi2_18_Female_47


title: hi2_3_Female_45


title: hi2_15_Female_42


title: hi2_18_Female_51


title: hi2_21_Female_40


title: hi2_3_Female_41


title: hi2_21_Female_44


title: hi2_18_Female_39


title: plx_18_Female_55

value: plx

value: Choroid Plexus


title: plx_15_Female_54

value: aging


title: hi2_18_Female_43


title: vis_21_Male_32

value: Male


title: plx_21_Female_52

value: Female


title: hi2_3_Female_53


title: plx_15_Female_50


title: plx_18_Female_51


title: hi2_3_Female_37


title: hi2_18_Male_35


title: hi2_21_Male_36


title: hi2_15_Male_34


title: plx_3_Female_49


title: hi2_15_Female_38


title: hi2_21_Male_32


title: hi2_15_Male_30


title: hi2_18_Male_31


title: plx_21_Female_48


title: plx_21_Female_56


title: plx_15_Female_46


title: plx_15_Female_42


title: plx_18_Female_43


title: plx_21_Female_44


title: plx_3_Female_45


title: hi2_21_Male_28


title: hi2_3_Male_29


title: plx_18_Female_47


title: plx_3_Female_53


title: plx_3_Female_41


title: hi2_15_Male_26


title: hi2_18_Male_27


title: hi2_21_Male_24


title: hi2_3_Male_25


title: hi2_18_Male_23


title: plx_21_Female_40


title: hi2_3_Male_33


title: plx_18_Female_39


title: plx_15_Female_38


title: plx_18_Male_35


title: plx_3_Female_37


title: plx_21_Male_36


title: plx_3_Male_33


title: hi2_3_Male_21


title: hi2_18_Male_19


title: hi2_15_Male_18


title: hi2_21_Male_20


title: hi2_12_Male_15


title: hi2_21_Male_16


title: hi2_3_Male_17


title: plx_15_Male_30


title: plx_21_Male_28


title: hi2_26_Male_14


title: plx_18_Male_31


title: plx_15_Male_26


title: plx_3_Male_29


title: plx_18_Male_27


title: plx_3_Male_25


title: hi2_12_Female_13


title: hi2_15_Male_22


title: hi2_12_Male_12


title: hi2_12_Female_10


title: hi2_26_Male_11


title: hi2_12_Male_9


title: hi2_26_Male_8


title: plx_15_Male_34


title: hi2_12_Female_7


title: plx_18_Male_23


title: plx_21_Male_32


title: plx_3_Male_21


title: plx_21_Male_20


title: plx_15_Male_18


title: plx_3_Male_17


title: plx_18_Male_19


title: hi2_26_Male_5


title: vis_12_Male_3


title: plx_12_Female_4


title: hi2_26_Male_2


title: plx_28_Male_59


title: plx_28_Male_57


title: plx_21_Male_16


title: plx_28_Male_58


title: plx_12_Male_15


title: plx_26_Male_14


title: plx_12_Male_12


title: plx_12_Female_10


title: plx_21_Male_24


title: plx_12_Female_13


title: plx_15_Male_22


title: plx_12_Male_9


title: hi2_12_Male_6


title: hi_28_Male_59

value: hi

value: Hippocampus (anterior)


title: hi_28_Male_57


title: hi_18_Female_55


title: hi_15_Female_54


title: ent_26_Male_8


title: hi_3_Female_53


title: hi_18_Female_51


title: hi_21_Female_52


title: hi_15_Female_50


title: hi_3_Female_49


title: hi_21_Female_48


title: hi_18_Female_47


title: hi_3_Female_45


title: plx_26_Male_5


title: hi2_12_Female_4


title: plx_26_Male_11


title: plx_12_Male_3


title: plx_26_Male_2


title: plx_12_Female_7


title: plx_12_Female_1


title: hi_15_Female_42


title: hi_3_Female_41


title: hi_21_Female_56


title: hi_15_Female_38


title: hi_21_Female_40


title: hi_3_Female_37


title: hi2_12_Female_1


title: hi_15_Female_46


title: hi_21_Male_36


title: hi_18_Female_39


title: hi_3_Male_33


title: hi_18_Male_31


title: hi_15_Male_34


title: hi_21_Male_32


title: plx_12_Male_6


title: plx_26_Male_8


title: hi_21_Male_28


title: hi_12_Female_1


title: hi_3_Male_29


title: hy_21_Female_56


title: hy_18_Female_55


title: hy_28_Male_57


title: hi_15_Male_26


title: hy_28_Male_59


title: hi_3_Male_25


title: hi_18_Male_23


title: hi_21_Male_24


title: hi_21_Male_20


title: hi_15_Male_22


title: hy_26_Male_2


title: hi_15_Male_30


title: hy_3_Female_53


title: hy_21_Female_52


title: hy_18_Female_51


title: hy_18_Female_47


title: hy_21_Female_48


title: hy_15_Female_50


title: hy_28_Male_58


title: hi_12_Male_15


title: hi_18_Male_19


title: hi_18_Male_27


title: hi_26_Male_14


title: hi_12_Male_12


title: hi_12_Female_13


title: hi_15_Male_18


title: hi_21_Male_16


title: hi_3_Male_17


title: hy_18_Female_43


title: hy_15_Female_42


title: hy_3_Female_45


title: hy_21_Female_44


title: hi_3_Male_21


title: hy_3_Female_41


title: hy_21_Female_40


title: hy_18_Female_39


title: hy_15_Female_54


title: hi_26_Male_11


title: hi_26_Male_8


title: hi_12_Male_9


title: hi_12_Female_10


title: hi_12_Female_4


title: hi_12_Female_7


title: hi_12_Male_6


title: hy_15_Female_38


title: hi_26_Male_5


title: hy_3_Male_33


title: hy_15_Female_46


title: hy_18_Male_35


title: hy_21_Male_32


title: hy_26_Male_14


title: hy_21_Male_36


title: hy_18_Male_31


title: hy_12_Female_13


title: hy_15_Male_34


title: th_28_Male_57

value: th

value: Thalamus


title: hy_12_Male_12

value: hy


title: hy_26_Male_11

value: Hypothalamus


title: th_21_Female_56


title: th_3_Female_53


title: th_15_Female_54


title: th_21_Female_52


title: th_18_Female_55


title: th_18_Female_51


title: th_15_Female_50


title: hy_3_Female_37


title: th_21_Female_44


title: th_3_Female_45


title: th_15_Female_46


title: th_3_Female_49


title: th_18_Female_47


title: th_3_Female_41


title: th_21_Female_48


title: th_21_Female_40


title: th_15_Female_38


title: th_18_Female_39


title: th_15_Female_42


title: hy_12_Female_10


title: th_18_Male_35


title: th_15_Male_34


title: th_3_Male_33


title: th_21_Male_32


title: th_18_Male_31


title: th_3_Male_29


title: th_21_Male_36


title: th_15_Male_30


title: th_21_Male_28


title: hy_3_Female_49


title: th_18_Male_27


title: th_15_Male_26


title: th_3_Male_25


title: th_21_Male_24


title: th_18_Male_23


title: th_18_Female_43


title: th_3_Male_21


title: th_21_Male_20


title: th_15_Male_22


title: th_15_Male_18


title: th_18_Male_19


title: hy_26_Male_5


title: th_3_Female_37


title: hy_12_Male_6


title: hy_12_Female_4


title: th_26_Male_2


title: hy_12_Male_3


title: th_28_Male_59


title: hy_12_Female_1


title: th_28_Male_58


title: th_12_Male_15


title: th_21_Male_16


title: th_26_Male_14


title: th_26_Male_11


title: th_12_Female_13


title: th_12_Male_12


title: th_26_Male_8


title: th_12_Female_10


title: th_12_Female_7


title: th_12_Male_9


title: th_26_Male_5


title: th_12_Male_6


title: th_12_Female_4


title: th_12_Male_3


title: hi_26_Male_2


title: cc_28_Male_59

value: cc

value: Corpus callosum


title: cc_28_Male_57


title: cc_28_Male_58


title: th_3_Male_17


title: cc_18_Female_55


title: cc_15_Female_54


title: cc_21_Female_56


title: cc_3_Female_53


title: cc_18_Female_51


title: cc_21_Female_52


title: cc_15_Female_50


title: cc_18_Female_47


title: cc_21_Female_48


title: cc_3_Female_45


title: cc_18_Female_43


title: cc_3_Female_41


title: cc_21_Female_40


title: cc_15_Female_42


title: cc_15_Female_46


title: cc_18_Female_39


title: cc_21_Female_44


title: cc_15_Female_38


title: cc_15_Male_34


title: th_12_Female_1


title: cc_18_Male_35


title: cc_3_Male_33


title: cc_3_Female_37


title: cc_18_Male_31


title: cc_21_Male_36


title: cc_15_Male_30


title: cc_21_Male_28


title: cc_21_Male_32


title: cc_15_Male_26


title: cc_3_Male_29


title: cc_18_Male_27


title: cc_3_Female_49


title: cc_21_Male_24


title: cc_3_Male_25


title: cc_18_Male_23


title: cc_15_Male_22


title: cc_21_Male_20


title: cc_18_Male_19


title: cc_15_Male_18


title: cc_12_Female_13


title: cc_26_Male_14


title: hi_18_Female_43


title: cc_21_Male_16


title: cc_3_Male_17


title: cc_26_Male_11


title: cc_12_Male_15


title: cc_12_Male_12


title: cc_26_Male_8


title: cc_12_Female_7


title: cc_12_Male_9


title: cc_12_Female_4


title: cc_12_Male_6


title: cc_12_Male_3


title: cc_26_Male_5


title: svz_28_Male_57

value: svz

value: Subventricular zone


title: cc_12_Female_10


title: svz_18_Female_55


title: svz_28_Male_58


title: svz_28_Male_59


title: svz_15_Female_54


title: svz_21_Female_56


title: cc_3_Male_21


title: svz_18_Female_51


title: svz_15_Female_50


title: svz_3_Female_49


title: svz_21_Female_48


title: svz_15_Female_46


title: svz_18_Female_47


title: svz_21_Female_44


title: svz_21_Female_40


title: svz_15_Female_42


title: svz_18_Female_39


title: svz_15_Female_38


title: svz_21_Male_36


title: svz_18_Male_35


title: svz_3_Female_37


title: svz_15_Male_34


title: svz_18_Male_31


title: svz_3_Female_53


title: svz_15_Male_30


title: svz_21_Female_52


title: svz_21_Male_32


title: svz_3_Male_33


title: svz_18_Male_27


title: svz_21_Male_28


title: svz_3_Male_29


title: svz_3_Male_25


title: svz_15_Male_26


title: svz_21_Male_24


title: svz_18_Male_23


title: svz_3_Female_45


title: svz_18_Female_43


title: svz_3_Male_21


title: svz_15_Male_22


title: svz_21_Male_20


title: svz_3_Female_41


title: svz_15_Male_18


title: svz_3_Male_17


title: svz_26_Male_14


title: svz_21_Male_16


title: svz_12_Female_13


title: svz_12_Male_12


title: svz_12_Male_15


title: svz_12_Male_9


title: svz_26_Male_11


title: svz_12_Female_1


title: svz_26_Male_2


title: svz_12_Female_7


title: svz_18_Male_19


title: cp_28_Male_59

value: cp

value: Caudate putamen


title: svz_12_Male_3


title: svz_26_Male_5


title: svz_12_Male_6


title: cp_21_Female_52


title: cp_28_Male_58


title: cp_28_Male_57


title: cp_3_Female_53


title: cp_15_Female_50


title: cp_21_Female_56


title: svz_12_Female_10


title: cp_21_Female_48


title: cp_18_Female_55


title: cp_15_Female_54


title: cp_15_Female_46


title: cp_18_Female_51


title: cp_3_Female_45


title: cp_21_Female_44


title: cp_15_Female_42


title: cp_21_Female_40


title: cp_15_Female_38


title: cp_21_Male_36


title: cp_18_Female_39


title: cp_18_Male_35


title: cp_18_Male_31


title: cp_3_Female_49


title: cp_21_Male_32


title: cp_15_Male_30


title: cp_21_Male_28


title: cp_18_Male_27


title: cp_3_Male_29


title: cp_3_Male_33


title: cp_15_Male_22


title: cp_15_Male_26


title: cp_18_Male_23


title: cp_21_Male_24


title: cp_3_Male_21


title: cp_3_Female_41


title: svz_12_Female_4


title: cp_18_Female_43


title: cp_21_Male_20


title: cp_18_Female_47


title: cp_26_Male_14


title: cp_15_Male_18


title: cp_12_Male_15


title: cp_21_Male_16


title: cp_3_Male_17


title: cp_3_Female_37


title: cp_12_Male_12


title: cp_26_Male_8


title: cp_12_Female_7


title: cp_12_Female_10


title: cp_26_Male_5


title: cp_26_Male_11


title: cp_12_Male_9


title: cp_12_Male_3


title: cp_12_Female_4


title: cp_26_Male_2


title: cp_12_Female_1


title: cor_28_Male_59

value: cor

value: Motor cortex


title: cor_28_Male_57

value: aging


title: cor_21_Female_56


title: cor_15_Female_54


title: cor_3_Female_53


title: cor_28_Male_58

value: Male


title: cor_18_Female_55

value: Female


title: cor_18_Female_51


title: cp_18_Male_19


title: cor_21_Female_52


title: cp_12_Female_13


title: cor_15_Female_46


title: cp_12_Male_6


title: cor_21_Female_44


title: cor_21_Female_48


title: cor_3_Female_49


title: cor_18_Female_43


title: cor_18_Female_39


title: IPAstro_FGF10_3

description: NextSeq 2000 P3

data_processing:
Sequenced reads were aligned to reference genome assembly and gene counts were quantified using the STAR tool
Differential gene expression testing was performed by DESeq2
Significant genes were identified using a threshold: adjust P<0.01, log2FoldChange >1.
Assembly: GRCm38
Supplementary files format and content: matrix.tsv

source_name: Whole brain (no olfactory bulbs, cerebellum)

extract_protocol:
In vitro astrocyte RNA was purified with an RNeasy Mini Kit (Qiagen). The concentration and quality of the purified RNA were assessed with a BioAnalyzer (Agilent).
The RNA was then reverse-transcribed into cDNA and purified using the Lexogen QuantSeq 3' mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices. Before the library amplification step, the PCR cycle number was determined using the PCR Add-on Reamplification kit V2 (Lexogen). Abundant BC1 transcripts, commonly found in mouse brain samples, were removed using Lexogen's BC1 Module during the RNA removal step. The library pools were quantified using a Qubit fluorometer, and Agilent TapeStation 2200. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on a NextSeq 2000 P3 (1.1 billion clusters) with Index 1 and Index 2 lengths of 12 bp each. On average, 59.41 million input reads were obtained per sample, with an average of 44.76 million uniquely mapped reads.
bulk RNA-seq according to Lexogen  QuanSeq 3'mRNA-Seq v2 Library Prep Kit

treatment_protocol: Drug treatment: SAG (diluted in DMSO to a concentration of 500 ng/ml, Tocris: 4366) and DMSO (control group) were added to 3-day in vitro (DIV) astrocyte cultures for three days. Fgf2 (Peprotech, 450-33) and Fgf10 (R&D, 345-FG-025), both at a working concentration of 50 ng/ml (diluted in PBS), along with PBS as the control group, were added to in vitro astrocyte cultures (DIV2) for seven days.

value: Astrocyte


title: cor_21_Male_20


title: cor_3_Female_41


title: cor_3_Male_21


title: cor_15_Female_42


title: IPAstro_FGF10_2

description: NextSeq 2000 P3

value: Whole brain (no olfactory bulbs, cerebellum)


title: cor_15_Female_50


title: cor_3_Male_17


title: IPAstro_FGF2_3

description: NextSeq 2000 P3


title: cor_18_Female_47


title: cor_21_Male_16


title: cor_3_Female_45


title: IPAstro_FGF2_1

description: NextSeq 2000 P3


title: cor_26_Male_14


title: IPAstro_PBS_4

description: NextSeq 2000 P3

value: PBS


title: IPAstro_FGF2_2

description: NextSeq 2000 P3


title: olf_18_Male_31

value: olf

value: Olfactory bulb


title: IPAstro_PBS_3

description: NextSeq 2000 P3


title: IPAstro_FGF2_4

description: NextSeq 2000 P3


title: cor_15_Male_18


title: IPAstro_PBS_2

description: NextSeq 2000 P3


title: IPAstro_FGF10_1

description: NextSeq 2000 P3


title: cor_15_Female_38


title: IPAstro_PBS_1

description: NextSeq 2000 P3


title: olf_15_Male_30


title: cor_21_Female_40


title: cor_12_Male_15


title: olf_3_Male_29


title: IPAstro_SAG_3

description: NextSeq 2000 P3

value: SAG


title: cor_18_Male_19


title: olf_15_Male_26


title: IPAstro_SAG_2

description: NextSeq 2000 P3


title: IPAstro_SAG_1

description: NextSeq 2000 P3


title: olf_18_Male_27


title: 28_gi-2_3

city: Seoul

first: Hong

middle: Gil

last: Lee

address: Gwanak-ro, Gwanak-gu

country: South Korea

institute: seoul national univesity

data_processing:
RNA-seq data were analyzed using Partek Flow (Partek).
Paired-end reads were mapped to TAIR10 genome using STAR 2.7.10a (Dobin et al., 2013) with ‘pOverlapNbasesMin 12, peOverlapMMp 0.1, twopassMode Basic’ parameters.
Transcript abundance was quantified using RSEM 1.3.1.
Assembly: TAIR10
Supplementary files format and content: Transcription quantificaiton results by RSEM

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
MiniBEST plant RNA extraction kit (Takara)
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used to construct the library, and sequencing was performed on the Illumina Novaseq 6000 platform.

value: seedlings

value: 28°C, short-day, ZT8


title: IPAstro_DMSO_3

description: NextSeq 2000 P3

value: DMSO


title: olf_3_Male_25


title: cor_12_Female_13


title: cor_12_Male_12


title: olf_21_Male_32


title: IPAstro_DMSO_2

description: NextSeq 2000 P3


title: 28_gi-2_2


title: 28_gi-2_1


title: cor_26_Male_11


title: cor_12_Male_9


title: 28_fkf1-t_3


title: WT3F-TN-014

city: Calgary

first: Jonathan

last: Epp

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

description: FFPE tissue processed using Nanostring GeoMX Mouse WTA

data_processing:
FASTQ files were converted to DCC (digital count conversion) files using the GeoMx NGS Pipeline (v3.1.1.5)
Assembly: N/A (reads in FASTQ are barcodes)
Supplementary files format and content: DCC (digital count conversion) comprised the number barcodes for each probe
Library strategy: GeoMX DSP

source_name: brain

extract_protocol:
Mice were perfused with 0.1M phosphate buffered saline followed by 4% formaldehyde. Tissue was post-fixed for 24 hours, embedded in paraffim, and sectioned at 5μm. Tissue was stained using 1:100 Alexa Fluor 488 conjugated anti-NeuN (Sigma-Aldrich; ABN78A4), 1:100 Alexa Fluor 594 (Abcam; ab269822) conjugated in-house to an anti-PV antibody, and 1:100 Alexa Fluor 647 conjugated anti-amyloid (Biolegend; 803020). Transcripts were recovered from PV+ nuclei, NeuN+ nuclei, amyloid+ nuclei, and then a triple negative (TN).
As per manufacturer's instructions (NanoString GeoMX)

treatment_protocol: Mice were aged to 6 months under standard laboratory housing conditions

value: brain

tag: stain

value: TN

value: WT


title: cor_12_Female_10

value: cor


title: cor_12_Female_7

value: Motor cortex


title: WT3F-PV-014

value: PV


title: cor_12_Male_6

value: Male

value: aging


title: 28_fkf1-t_1


title: olf_21_Male_16


title: IPAstro_DMSO_1

description: NextSeq 2000 P3

value: Astrocyte


title: WT3F-NeuN-014

value: NeuN

value: Female


title: olf_26_Male_14

value: olf


title: 28_fkf1-t_2


title: olf_12_Male_15

value: Olfactory bulb


title: olf_12_Female_13


title: TG1F-TN-013


title: olf_12_Female_10


title: olf_26_Male_11


title: 28_fkf1gi_3


title: TG1F-Amyloid-013

value: Amyloid


title: 28_fkf1gi_2

value: seedlings


title: olf_12_Male_9


title: cor_12_Female_4


title: TG1F-NeuN-013


title: cor_26_Male_8


title: cor_26_Male_5


title: 28_Col-0_3

value: Col-0 (wild-type)

value: 28°C, short-day, ZT8


title: olf_28_Male_59


title: TG1F-PV-013

value: brain


title: cor_12_Female_1


title: TG1F-TN-012

value: TN


title: 28_Col-0_2


title: TG1F-Amyloid-012


title: olf_21_Female_56


title: TG1F-NeuN-012


title: 22_svp-32_2

value: 22°C, short-day, ZT8


title: olf_18_Female_55


title: olf_28_Male_58


title: 22_svp-32_3


title: olf_28_Male_57


title: 22_svp-32_1


title: olf_21_Female_52


title: olf_3_Female_53


title: olf_21_Male_28


title: olf_18_Female_51


title: TG2F-TN-011


title: TG1F-PV-012


title: 22_fkf1-t_3


title: cor_12_Male_3

value: cor


title: TG2F-Amyloid-011


title: 22_fkf1-t_2


title: olf_3_Female_49


title: olf_15_Female_50


title: 28_Col-0_1


title: TG2F-NeuN-011


title: olf_18_Female_47


title: olf_15_Female_46


title: 22_fkf1-t_1


title: olf_3_Female_45


title: 22_fkf1gi_3


title: olf_21_Female_44


title: olf_18_Female_43


title: TG2F-PV-011


title: TG2F-TN-010


title: olf_3_Female_41


title: olf_15_Female_54


title: 22_fkf1gi_1


title: TG2F-NeuN-010


title: olf_21_Female_40


title: olf_15_Female_42


title: TG2F-PV-010


title: olf_18_Female_39


title: 22_fkf1gi_2


title: 22_Col-0_3


title: TG3F-TN-009


title: olf_15_Female_38


title: olf_3_Female_37


title: 22_Col-0_2


title: olf_21_Male_36


title: TG3F-Amyloid-009


title: olf_21_Female_48


title: olf_18_Male_35


title: olf_3_Male_33


title: olf_15_Male_34


title: 22_Col-0_1


title: TG3F-PV-009


title: cor_26_Male_2

value: Motor cortex


title: SU-DHL-8 T2-R

city: huaian

first: Liang

last: Yu

address: 1 Huanghe West Road, Huai 'an City, Jiangsu Province

country: China

institute: The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University

description: Library name: SU-DHL-8 T2-R

library_source: genomic

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adapter contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads that passed quality control were mapped to reference genome using Bismark. After alignment, reads were further deduplicated using samtool.
For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated) using per scripts in house and MethPipe.
Differentially methylated regions (DMRs) were calculated by R package-MethylKit with default parameters (1000 bp slide windows, 500 bp overlap, p value<0.05).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lymph node

extract_protocol:
Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany) following the manufacturer's procedure. The quantity of DNA was measured by reading A260/280 ratios by spectrophotometer. When A260/280 ratios located range 1.8 to 2.0, DNA was available.
The fragmented DNA samples by using MspI (NEB, USA, for RRBS) were subjected to bisulfite conversion. The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments. Briefly, as protocol shown below, the Adaptase step is a highly efficient, proprietary reaction that simultaneously performs end repair, tailing of 3’ ends, and ligation of the first truncated adapter complement to 3’ ends. The Extension step is used to incorporate truncated adapter 1 by a primer extension reaction. The Ligation step is used to add the second truncated adapter to the bottom strand only. The Indexing PCR step increases yield and incorporates full length adapters. Bead-based SPRI clean-ups are used to remove both oligonucleotides and small fragments, as well as to change enzymatic buffer composition. Finally, we performed the pair-end 2×150bp sequencing on an illumina Hiseq 4000 platform housed in the LC Sciences.

value: lymph node

value: DLBCL

value: DNMT1 wild type


title: cor_3_Female_37

value: aging


title: SU-DHL-8 T3-R

description: Library name: SU-DHL-8 T3-R


title: TG3F-TN-008


title: cor_18_Male_35

value: Male


title: SU-DHL-8 T1-R

description: Library name: SU-DHL-8 T1-R


title: SU-DHL-8 C3-R

description: Library name: SU-DHL-8 C3-R

value: DMSO


title: cor_21_Male_36


title: TG3F-NeuN-008

value: NeuN

value: Female


title: cor_15_Male_34


title: SU-DHL-8 C2-R

description: Library name: SU-DHL-8 C2-R


title: cor_3_Male_33


title: TG4F-NeuN-007


title: SU-DHL-8 C1-R

description: Library name: SU-DHL-8 C1-R


title: TG4F-TN-007


title: cor_21_Male_32


title: TG3F-NeuN-009


title: TG4F-PV-007

value: PV


title: cor_18_Male_31


title: H1963 FOXA2OE sample2

city: NEW YORK

first: Kenta

last: Kawasaki

state: NEW YORK

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Fastq files were mapped to the human genome (hg38) and read counts per gene were quantified using STAR with default parameters and genecode (v28) annotation file
Differentially expressed genes (DEGs) were identified with DESeq2, with a fold change cutoff of 1.5 and FDR <= 0.01
Assembly: Human GRCh38
Supplementary files format and content: Each column represents a sample and the genes are represented in each raw.
Supplementary files format and content: The table contains the normalized counts from DESeq2's median of ratios method

source_name: cell line

growth_protocol: H1836 was cultured with DMEM/F12 HITES media, H1963, SHP-77 with RPMI+10% fetal bovine serum (FBS).

extract_protocol:
FFPE were initially evaluated for tumor contact by a thoracic pathologist. Ten to 20 unstained sections at 10 μm were then processed for RNA extraction. FFPE sections were deparaffinized in mineral oil. In brief, 800 μL mineral oil (Fisher Scientific, Cat #:AC415080010) and 180 μL Buffer PKD were mixed with the sections, proteinase K was added for tissue digestion, and the sample was incubated at 56°C for 15 minutes. Phase separation was encouraged with centrifugation, and the aqueous phase was chilled 3 minutes to precipitate RNA. After centrifugation for 15 minutes at 20,000 × g, RNA-containing supernatant was removed for extraction. Nucleic acids were isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat #:80204) according to the manufacturer's instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer ATE.
Approximately 500 ng of FFPE RNA was used for RNA library construction using the KAPA RNA Hyper library prep kit (Roche) per the manufacturer's instructions with minor modifications. Customized adapters with unique molecular indexes (UMI; Integrated DNA Technologies) and sample-specific dual-index primers (Integrated DNA Technologies) were added to each library. The quantity of libraries was measured with Qubit (ThermoFisher Scientific), and quality assessed by the TapStation Genomic DNA Assay (Agilent Technologies). Equal amounts of each RNA library were pooled for hybridization capture with IDT Whole-Exome Panel V2 (Integrated DNA Technologies) using a customized capture protocol modified from the NimbleGen SeqCap Target Enrichment system (Roche). The captured DNA libraries were then sequenced on an Illumina HiSeq4000 with paired end reads (2Å ∼ 100 bp), at 50 million reads/sample.

treatment_protocol: RNA-extracted from doxycycline-induced cell line were treated for 5 days at 1 μg/mL

value: cell line


title: H1963 FOXA2OE sample3


title: TG3F-PV-008


title: TG4F-TN-006


title: H1963 FOXA2OE sample1


title: cor_15_Male_30


title: TG4F-NeuN-006


title: olf_21_Male_24

value: olf

value: Olfactory bulb


title: H1963 control sample3


title: TG4F-PV-006

value: brain


title: olf_18_Male_23


title: H1963 control sample2


title: WT1F-TN-005

value: TN

value: WT


title: H1963 control sample1


title: 28_fkf1gi_1

value: seedlings

value: 28°C, short-day, ZT8


title: skin_inflammatory_9

city: Dallas

first: Henry

middle: W

last: Chen

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

hyb_protocol: Biotin labeled cRNA are hybridized with IlluminaHuman-HT-12_V4_0_R2 BeadChips using Illumina standard protocol.

scan_protocol: The BeadChips are scanned using Illumina HiScan scanner.

data_processing: The data is analyzed using Illumina GenomeStudio software.

label: biotin

source_name: skin

label_protocol: The RNA samples are labeled with Biotin using Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (Qiagen) according to manufacturer's protocol.

value: Skin

tag: sample site

value: Inflammatory border

tag: clinical subtype

value: Linear

tag: race

value: White

tag: mlossi

tag: losdi

tag: pga-a

tag: pga-d


title: skin_sclerotic_14

tag: tissue

value: Lesional sclerotic

value: Generalized

tag: age


title: WT1F-NeuN-005

value: NeuN

tag: Sex


title: skin_unaffected_11

value: Unaffected


title: skin_unaffected_9


title: olf_3_Male_21

tag: brain region

tag: brain region_long

value: Male

tag: cohort

tag: experiment

value: aging

tag: strain


title: SHP77, shFOXA2-2 sample3

value: cell line

tag: cell line


title: skin_inflammatory_10


title: skin_sclerotic_15


title: skin_unaffected_8


title: skin_unaffected_10


title: WT1F-PV-005

tag: stain

value: PV

tag: genotype

value: Female


title: SHP77, shFOXA2-2 sample2


title: skin_sclerotic_12

tag: sample site

tag: clinical subtype


title: skin_sclerotic_13

tag: race

tag: mlossi


title: WT1F-TN-004

value: brain

value: TN


title: olf_18_Male_19

value: olf

value: Olfactory bulb

tag: mouse id


title: skin_inflammatory_7

value: Skin

tag: losdi

tag: pga-a

tag: pga-d


title: SHP77, shFOXA2-2 sample1

tag: tissue


title: WT1F-NeuN-004

value: WT

tag: Sex


title: olf_15_Male_18

tag: brain region

tag: brain region_long

tag: age


title: olf_15_Male_22

tag: cohort

tag: experiment

tag: strain


title: skin_inflammatory_8

value: Inflammatory border


title: SHP77, shFOXA2-1 sample3

tag: cell line


title: olf_3_Male_17


title: skin_sclerotic_11

tag: sample site

value: Plaque

value: White


title: WT1F-PV-004

tag: stain

tag: genotype


title: WT2F-TN-003


title: olf_21_Male_20


title: SHP77, shFOXA2-1 sample1


title: SHP77, shFOXA2-1 sample2


title: cor_3_Male_29

value: cor

value: Motor cortex


title: SHP77 control sample3


title: cor_21_Male_28


title: WT2F-PV-003


title: skin_sclerotic_10

value: Lesional sclerotic

tag: clinical subtype

value: Generalized

tag: race

value: African American

tag: mlossi


title: WT2F-NeuN-003

value: NeuN


title: SHP77 control sample2

value: cell line


title: cor_15_Male_26

value: Male

value: aging

tag: mouse id


title: skin_unaffected_7

value: Unaffected

tag: losdi

tag: pga-a

tag: pga-d


title: cor_18_Male_27

tag: brain region

tag: Sex


title: SHP77 control sample1

tag: tissue


title: WT2F-NeuN-002

value: brain

value: Female


title: skin_sclerotic_9

value: Skin

tag: age


title: cor_3_Male_25

tag: brain region_long

tag: cohort

tag: experiment


title: skin_sclerotic_8

tag: sample site


title: skin_unaffected_6


title: WT2F-PV-002

tag: stain

value: PV

value: WT


title: H1836, shFOXA2-2 sample3

tag: cell line


title: WT3F-TN-001

value: TN

tag: genotype


title: cor_18_Male_23

tag: strain


title: WT3F-NeuN-001


title: skin_sclerotic_7

tag: clinical subtype

value: Linear

tag: race

value: White

tag: mlossi


title: skin_inflammatory_6

value: Inflammatory border

tag: losdi

tag: pga-a


title: H1836, shFOXA2-2 sample2


title: skin_inflammatory_5

tag: pga-d


title: cor_15_Male_22

tag: brain region

value: cor

value: Motor cortex

tag: Sex

tag: mouse id


title: olf_26_Male_8

value: olf

tag: brain region_long

value: Olfactory bulb

tag: age


title: H1836, shFOXA2-1 sample2

tag: tissue

value: cell line


title: H1836, shFOXA2-1 sample1


title: WT2F-TN-002


title: cor_21_Male_24

value: Male

tag: cohort

tag: experiment


title: olf_12_Male_6

value: aging


title: WT1M-NeuN-014

tag: stain

value: Neu


title: skin_unaffected_5

tag: sample site

value: Unaffected


title: olf_26_Male_5

tag: strain


title: H1836, control sample3

tag: cell line


title: H1836, shFOXA2-2 sample1


title: WT1M-PV-014

value: brain

tag: genotype


title: H1836, control sample2


title: olf_12_Female_4

value: Female


title: H1836, shFOXA2-1 sample3


title: WT3F-PV-001

value: PV


title: WT2M-TN-013

value: WT


title: H1836, control sample1


title: olf_12_Female_7


title: skin_sclerotic_6

value: Skin

value: Lesional sclerotic

tag: clinical subtype

value: Generalized

tag: race

tag: mlossi


title: olf_12_Male_3


title: WT2M-PV-013


title: skin_sclerotic_5

value: Asian

tag: losdi

tag: pga-a

tag: pga-d


title: Metastatsis, sample24

source_name: Metastasis

value: Metastasis

value: Small cell lung cancer


title: olf_26_Male_2

tag: brain region

value: olf

tag: Sex

tag: mouse id


title: skin_unaffected_4

tag: tissue

tag: age

value: White


title: skin_sclerotic_4


title: Metastatsis, sample25


title: skin_inflammatory_3

value: Inflammatory border


title: skin_unaffected_3


title: olf_12_Female_1

tag: brain region_long

value: Olfactory bulb

tag: cohort

tag: experiment


title: WT3M-NeuN-012

tag: stain

value: Male


title: 6-8h plasmid-transfection, 24h DMSO-treated, rep3

city: Beijing

first: Zhan

address: 38 Xueyuan Rd, Haidian District, Beijing, China

institute: Peking University Health Science Center

data_processing:
FastQC (v0.11.9)
trim_galore (v0.6.7)
STAR (v2.7.9a)
featureCounts (v2.0.1)
Assembly: mm10; hg38

extract_protocol:
Total RNA was purified using TransZol Up Plus RNA Kit (ER501-01-V2, TransGene) with genome DNA removed.
Libraries were constructed by the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (12301, Yeasen).

tag: treatment

value: DMSO

tag: time

value: 24h post DMSO


title: Metastatsis, sample23

tag: cell line


title: WT3M-TN-012

value: brain

value: TN

tag: genotype


title: skin_inflammatory_4

tag: sample site

tag: clinical subtype

value: Linear

tag: race

tag: mlossi


title: Metastatsis, sample22


title: 6-8h plasmid-transfection, 24h DMSO-treated, rep2


title: WT2M-NeuN-013

value: Neu

value: WT


title: Metastatsis, sample21


title: TG3M-TN-011


title: WT3M-PV-012

value: PV


title: skin_sclerotic_3

value: Skin

value: Lesional sclerotic

value: Generalized

tag: losdi

tag: pga-a

tag: pga-d


title: 6-8h plasmid-transfection, 24h DMSO-treated, rep1

tag: tissue


title: Metastatsis, sample19

value: Metastasis

value: Small cell lung cancer


title: TG3M-Amyloid-011

value: amyloid

tag: Sex


title: 6-8h plasmid-transfection, 24h risdiplam-treated, rep3

value: 1uM risdiplam

value: 24h post risdiplam


title: 6-8h plasmid-transfection, 24h risdiplam-treated, rep2


title: TG3M-NeuN-011

value: Male


title: Metastatsis, sample18


title: skin_inflammatory_2

value: Inflammatory border

tag: age

value: White


title: TG3M-PV-011

value: brain


title: 6-8h plasmid-transfection, 24h risdiplam-treated, rep1


title: TG1M-TN-010

value: TN


title: Metastatsis, sample16


title: U937_TMQ0153 20 uM_24 h_Replicate3

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

institute: Seoul National University

description:
Library name: Sample 18
Column name in raw_counts_All_Samples.csv: U937TMQ48h-3

data_processing:
Sequence reads were trimmed for adaptor sequences and low-quality bases using Trim Galore v0.6.10.
Trimmed reads were mapped to the hg38 reference genome using HISAT2 v2.2.1.
Mapped SAM files were converted to BAM format and sorted using Samtools v1.21.
Read quantification: Gene-level read counts were obtained using featureCounts v1.5.3 with the GENCODE v38 annotation
Assembly: hg38
Supplementary files format and content: csv file include raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Pleural effusion

growth_protocol: MV4-11 cells were cultured in RPMI 1640 medium (Lonza, Walkersville, MD, USA) supplemented with 10% (v/v) fetal bovine serum (FBS; Opti-Gold, GenDEPOT, Katy, TX, USA) and 1% penicillin-streptomycin (Lonza, Basel, Belgium) at 37°C with 5% CO₂. U937 cells were grown in RPMI 1640 medium (Lonza) with 10% (v/v) FBS (Biowest, Riverside, MO, USA) and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted using the QIAzol® Lysis Reagent (Qiagen, #79306) and purified with the RNeasy Mini Kit (Qiagen). 1.3 µg of total RNA was used for library construction.
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer’s protocol.

value: Pleural effusion

tag: cell type

value: Monocyte


title: U937_TMQ0153 20 uM_24 h_Replicate2

description:
Library name: Sample 17
Column name in raw_counts_All_Samples.csv: U937TMQ48h-2


title: U937_TMQ0153 20 uM_1 h_Replicate3

description:
Library name: Sample 15
Column name in raw_counts_All_Samples.csv: U937TMQ1h-3


title: skin_sclerotic_2

value: Hispanic


title: skin_unaffected_1

value: Unaffected


title: skin_unaffected_2

value: Skin


title: skin_inflammatory_1


title: skin_sclerotic_1

value: Lesional sclerotic

value: Linear


title: CR-E13-5K-FLAG-1

city: Madison

first: Deneen

middle: Marie

last: Wellik

state: WI

address: 1111 Highland Avenue 4448 WIMR II

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description: Library name: CR-E13-5K-FLAG-1

data_processing:
CUT&Tag and CUT&RUN analysis was conducted using a previously published pipeline (https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-e6nvw93x7gmk/v1) as described in (Ye Zheng, 2020).
Sequencing data quality was assessed using MultiQC.
Trimming was performed with Trimmomatic using the following parameters: ILLUMINACLIP (2:30:10), LEADING (3), TRAILING (3), SLIDINGWINDOW (4:15), and MINLEN (36).
Trimmed reads were aligned to the mouse reference genome (mm39) using Bowtie2 with the parameters: --local, --very-sensitive, --no-mixed, --no-discordant, -I 10, -X 700. For the IgG control sample, duplicates were handled using Picard tools. SAM files were sorted by coordinate with SortSam, and duplicates were marked and removed using MarkDuplicates.
Peak calling for FLAG, was performed with SEACR which calls enriched regions in target data using IgG control track with stringent threshold. Peak annotation was performed with HOMER v4.11.1. To assess peak reproducibility, Irreproducible Discovery Rate (IDR) analysis was performed on FLAG replicates from CUT&Tag. Stringent peaks from FLAG-1 and FLAG-2 replicates were analyzed using IDR v2.0.4 with a threshold of 0.01, ranking peaks by signal intensity to identify high-confidence, reproducible peaks.
Assembly: mm39
Supplementary files format and content: bedgraph
Library strategy: CUT&Run

source_name: Kidney

extract_protocol:
Briefly, E13.5 Hoxa11FL/FL;Hoxd11FL/FL or Hoxa11FL/+;Hoxd11FL/FL kidneys were micro-dissected from embryos and pooled to utilize 200,000 cells/reaction. To obtain a single cell solution, kidneys were dissociated with Liberase (100ug/mL, Roche 05401119001) in PBS at 37C for 5 min, followed by gentle pipetting to disrupt the remaining tissue. CUT&Tag experiments were performed as previously described in (Li et al. 2021). CUT&RUN experiments were performed with EpiCypher’s CUT&RUN kit (SKU: 14-1048) according to manufacturer’s protocol.
CUT& Tag libraries were generated with NEB Next High Fidelity 2x PCR Master Mix and different i5 and i7 primers as previously described by (Li et al. 2021 and Kaya-Okur et al., 2019). Library quality control and fragment size was assessed with a Bioanalyzer system (Agilent), and samples were sequenced on an NovaSeq6000 (Illumina) sequencing system using a paired-end 100bp sequencing run at a sequencing depth of 10 million reads/sample. CUT&RUN libraries were generated using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645S0 and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs, New England Biolabs, E6440S) following the manufacturer’s instructions with 14 cycles of amplification and a 1:25 dilution for the adapter. Libraries were cleaned-up to remove adapters using AMPure XP beads (Beckman Coulter, a63880). Library quality control and fragment size was assessed in a 4200 Tapestation system (Agilent). Samples were sequenced on an NovaSeq6000 (Illumina) sequencing system using a paired-end 150bp sequencing run at a sequencing depth of 5 million reads/sample.

value: Kidney

tag: developmmental stage

tag: antibody

value: anti M2 FLAG (Sigma F3165)


title: Metastatsis, sample15

value: Metastasis

value: Small cell lung cancer


title: Metastatsis, sample20


title: U937_TMQ0153 20 uM_24 h_Replicate1

description:
Library name: Sample 16
Column name in raw_counts_All_Samples.csv: U937TMQ48h-1


title: CR-E13-5K-IgG-1

description: Library name: CR-E13-5K-IgG-1

value: IgG (EpiCypher, 13-0042k)


title: U937_TMQ0153 20 uM_1 h_Replicate2

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.csv: U937TMQ1h-2


title: TG1M-Amyloid-010

tag: stain

value: amyloid

value: Male


title: Metastatsis, sample17


title: CT-E13-5K-FLAG-2

description: Library name: CT-E13-5K-FLAG-2

data_processing:
CUT&Tag and CUT&RUN analysis was conducted using a previously published pipeline (https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-e6nvw93x7gmk/v1) as described in (Ye Zheng, 2020).
Sequencing data quality was assessed using MultiQC.
Trimming was performed with Trimmomatic using the following parameters: ILLUMINACLIP (2:30:10), LEADING (3), TRAILING (3), SLIDINGWINDOW (4:15), and MINLEN (36).
Trimmed reads were aligned to the mouse reference genome (mm39) using Bowtie2 with the parameters: --local, --very-sensitive, --no-mixed, --no-discordant, -I 10, -X 700. For the IgG control sample, duplicates were handled using Picard tools. SAM files were sorted by coordinate with SortSam, and duplicates were marked and removed using MarkDuplicates.
Peak calling for FLAG, was performed with SEACR which calls enriched regions in target data using IgG control track with stringent threshold. Peak annotation was performed with HOMER v4.11.1. To assess peak reproducibility, Irreproducible Discovery Rate (IDR) analysis was performed on FLAG replicates from CUT&Tag. Stringent peaks from FLAG-1 and FLAG-2 replicates were analyzed using IDR v2.0.4 with a threshold of 0.01, ranking peaks by signal intensity to identify high-confidence, reproducible peaks.
Assembly: mm39
Supplementary files format and content: bedgraph
Library strategy: CUT&Tag


title: TG1M-NeuN-010

value: Neu


title: CT-E13-5K-FLAG-1

description: Library name: CT-E13-5K-FLAG-1


title: Metastatsis, sample13


title: TG1M-PV-010

value: brain

value: PV


title: TG1M-TN-009

value: TN


title: U937_Control_Replicate3

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.csv: U937-Con-3

value: Pleural effusion

value: Monocyte


title: CT-E13-5K-IgG-2

description: Library name: CT-E13-5K-IgG-2

value: IgG (Diagenode, #C15410206


title: Metastatsis, sample14


title: Metastatsis, sample12


title: U937_Control_Replicate2

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.csv: U937-Con-2


title: Metastatsis, sample11


title: CT-E13-5K-IgG-1

description: Library name: CT-E13-5K-IgG-1


title: U937_Control_Replicate1

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.csv: U937-Con-1


title: Nkx_septum_P21_neg-4

library_source: transcriptomic single cell

data_processing:
Sequence reads were processed and aligned to the mouse genome GRC38 using 10X Genomics Cell Ranger 6.0.0.
Nuclei expressing fewer than 200 genes, total RNA counts fewer than 1000, and/or a percentage of mitochondrial reads greater than 5% were excluded from the analysis (for astrocyte cluster analysis, mitochondrial reads greater than 2% of total reads were excluded from the analysis).
For snRNA-seq analysis at different ages, a total of 166,418 nuclei (P0: 35,066 nuclei; P3: 36,692 nuclei; P7: 29,034 nuclei; P14: 19,926 nuclei; P21: 45,700 nuclei; GFP+: 72,573 nuclei; GFP-: 93,845 nuclei) were used for downstream analysis.
Low read counts were normalized, and dimensional reduction was performed by PCA (n = 50), followed by regressing out percent mitochondrial reads and number of genes per nucleus
Data from different developmental stages was integrated using the Seurat 4 anchor-based integration pipeline with reciprocal PCA, as recommended by the authors when integrating samples with potentially non-overlapping populations.
Assembly: mm10
Supplementary files format and content: R objects

extract_protocol:
The septum was dissected out from Nkx2.1Cre; Sun1GFP mice. Nuclei were isolated from septal tissue.
The library was prepared according to 10X Genomics platform (Chromium next GEM single cell 3’reagent kits v3.1(dual index))

value: Septum

value: all cell types

tag: postnatal stage

tag: sorted fraction

value: neg


title: Metastatsis, sample10

tag: cell line


title: TG1M-PV-009

tag: genotype


title: Nkx_septum_P21_pos-4

value: pos


title: MV4-11_TMQ0153 20 uM_6 h_Replicate3

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.csv: MV4-11-6h-3

source_name: Peripheral blood

value: Peripheral blood

value: Macrophage


title: MV4-11_TMQ0153 20 uM_6 h_Replicate2

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.csv: MV4-11-6h-2


title: WT1M-TN-008

value: WT


title: Metastatsis, sample8

value: Metastasis

value: Small cell lung cancer


title: MV4-11_TMQ0153 20 uM_6 h_Replicate1

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.csv: MV4-11-6h-1


title: Nkx_septum_P21_pos-3


title: U937_TMQ0153 20 uM_1 h_Replicate1

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.csv: U937TMQ1h-1


title: Metastatsis, sample7


title: Metastatsis, sample9


title: Nkx_septum_P21_neg-2


title: Metastatsis, sample6


title: WT1M-PV-008

value: Male


title: MV4-11_TMQ0153 20 uM_1 h_Replicate2

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.csv: MV4-11-1h-2


title: WT2M-TN-007


title: MV4-11_TMQ0153 20 uM_1 h_Replicate3

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.csv: MV4-11-1h-3


title: TG1M-Amyloid-009

value: amyloid


title: Metastatsis, sample5


title: MV4-11_TMQ0153 20 uM_1 h_Replicate1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.csv: MV4-11-1h-1


title: Nkx_septum_P21_pos-2


title: WT2M-NeuN-007

value: brain

value: Neu


title: TG1M-NeuN-009


title: Nkx_septum_P21_neg-1


title: Metastatsis, sample4


title: MV4-11_Control_Replicate3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.csv: MV4-11-0h-3


title: Nkx_septum_P21_neg-3


title: Nkx_septum_P21_pos-1


title: WT2M-PV-007

description: FFPE tissue processed using Nanostring GeoMX Mouse WTA

value: PV


title: Metastatsis, sample3


title: TG2M-TN-006

value: TN


title: Nkx_septum_P14_neg-2


title: WT1M-NeuN-008


title: Metastatsis, sample2


title: MV4-11_Control_Replicate1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.csv: MV4-11-0h-1


title: Metastatsis, sample1


title: TG2M-Amyloid-006


title: SU-DHL-8 T3

description: Library name: SU-DHL-8 T3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: FPKM, count values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (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 was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were 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 were 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 librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: lymph node

value: DLBCL

value: DNMT1 wild type

tag: treatment


title: Nkx_septum_P14_pos-2

value: Septum

value: all cell types


title: Nkx_septum_P14_neg-1

value: neg


title: TG2M-NeuN-006


title: Met-associated primary tumor , sample5

source_name: primary lung

value: primary lung


title: SU-DHL-8 T2

description: Library name: SU-DHL-8 T2


title: Met-associated primary tumor , sample4


title: TG2M-PV-006


title: SU-DHL-8 T1

description: Library name: SU-DHL-8 T1


title: TG2M-TN-005


title: SU-DHL-8 C3

description: Library name: SU-DHL-8 C3

value: DMSO


title: Met-associated primary tumor , sample3


title: Nkx_septum_P7_neg-2


title: Met-associated primary tumor , sample2


title: TG2M-Amyloid-005


title: Nkx_septum_P7_pos-2

value: pos


title: MV4-11_Control_Replicate2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.csv: MV4-11-0h-2

value: Peripheral blood

value: Macrophage


title: Nkx_septum_P7_neg-1


title: Met-associated primary tumor , sample1

value: Small cell lung cancer


title: TG2M-NeuN-005

value: Male


title: SU-DHL-8 C2

description: Library name: SU-DHL-8 C2


title: SU-DHL-8 C1

description: Library name: SU-DHL-8 C1


title: dermis_buttocks

data_processing:
The raw paired-end sequence reads were quality-controlled using FastQC (Version 0.11.7), followed by trimming with Trimmomatic (Version 0.38).
The trimmed sequence reads were mapped to the reference genome using HISAT2 (Version 2.1.0).
Read counts were estimated with featureCounts (Version 1.6.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each Samples

extract_protocol:
Total RNA was extracted from cultured cells using NucleoSpin® RNA Plus (Takara Bio, Shiga, Japan), and was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) following manufacturer's protocols.

value: dermis

value: NHDF

value: fibroblast

value: WT


title: Never-met primary tumor, sample7


title: Nkx_septum_P7_pos-1


title: TG2M-PV-005

value: brain

value: PV


title: Nkx_septum_P3_neg-2


title: Never-met primary tumor, sample6


title: WT3M-TN-004

value: TN


title: dermis_abdomen


title: Nkx_septum_P14_pos-1

value: Septum


title: Nkx_septum_P3_pos-2

value: all cell types


title: Never-met primary tumor, sample5


title: WT3M-NeuN-004

value: Neu


title: WT3M-PV-004


title: Nkx_septum_P3_neg-1

value: neg


title: Never-met primary tumor, sample4

value: primary lung


title: WT4M-TN-003


title: Nkx_septum_P3_pos-1

value: pos


title: scRNA-seq from small cell lung cancer patient Ru1303B

data_processing:
All analyses were done in Python using Scanpy  (v1.10) unless otherwise specified. Raw FASTQ sequencing files were aligned to the reference genome version GRCh38, barcodes were filtered, and unique molecular identifiers (UMI) were identified using 10x Cell Ranger software (v6.0.1). Cell by gene matrices were loaded as anndata objects. Cells with less than 200 genes or more than 40% mitochondrial content were removed. Doublet cells were removed using scrublet. Highly variable genes were selected using the highly_variable_genes function with the flavor option set to seurat_v3. The raw counts were then normalized by library size and log-transformed with a pseudo-count of 1. Principal component analysis (PCA) was performed retaining the top 50 PCs. Harmonypy (v0.0.9) was used to perform batch correction. The batch corrected embeddings were used for leiden clustering and creating the UMAP [McInnes] projection for visualization.
The major cell components were defined using reference-based mapping in Seurat (v5.0). Briefly, cells were exported to Seurat objects and mapped to the human lung cell atlas using the RunAzimuth() function. This yielded multi-level annotations. Level 1 annotation was used to denote the major compartment for each cell. The above procedure was checked against the following procedure, which gave highly concordant results: the major cell compartments were defined using the markers for each component. Each cell was scored for each of the main compartments using the function score_genes. Then each cell was assigned to the cell compartment with the highest score.
To identify malignant cells in the epithelial compartment, single-cell copy number signal was computed per sample using InferCNV (v1.14) ,utilizing a reference set of cells from all other samples (five cells per sample across major cell compartments: epithelial, stromal (fibroblast), immune and endothelial). Copy number signal was then re-binned to 10Mb sized bins, prior to performing PCA to 50 dimensions and louvain clustering over a nearest neighbor graph with cosine distance. Clusters were manually inspected for each patient to assign malignant cell clusters, which were based near total enrichment of epithelial cells harboring distinct copy number profiles in clusters.
Assembly: Human GRCh38
Supplementary files format and content: The file is in csv format, and each row shows the expression of a gene in all cells
Supplementary files format and content: csv file

molecule: nuclear RNA

source_name: Lymph Node

extract_protocol:
Clinical sample preparation for single-cell RNA-sequencing were prepared as previously described. Clinical samples were mechanically/enzymatically dissociated using the tumor dissociation kit (Miltenyi, Cat #:130-095-929,) and the Gentle MACS Octo Dissociator with Heaters (Miltenyi, Cat#:130-096-427). The samples were processed for dissociation and filtered with MACS Smart Strainers (70 mm) (Miltenyi, Cat#: 130-098-462). The materials were FACS-sorted with DAPI (ThermoFischer Scientific, Cat#:D1306) and processed for scRNA-seq analysis.
After PicoGreen quantification and quality control by Agilent TapeStation, libraries were pooled and run on a NovaSeq 6000 in a PE26/91, PE28/91, PE28/92, PE28/98, or PE30/90 run, using the NovaSeq 6000 S2 or S4 Reagent Kit (100 or 200 Cycles) (Illumina). The loading concentration was 0.8-2.25nM and a 1-2% spike-in of PhiX was added to the run to increase diversity and for quality control purposes. The runs yielded on average 201M reads per sample.

value: Lymph Node

tag: gender


title: Nkx_septum_P0_neg-2


title: WT4M-NeuN-003


title: Never-met primary tumor, sample3


title: Never-met primary tumor, sample2


title: scRNA-seq from small cell lung cancer patient Ru1195A


title: Nkx_septum_P0_pos-2


title: Never-met primary tumor, sample1


title: WT4M-PV-003


title: Nkx_septum_P0_neg-1


title: m15-A2058

city: Shenzhen

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

library_source: other

data_processing:
Raw sequencing data was preprocessed using Ktrim software to remove adapters and low quality cycles; PCR duplicates were removed using in-house programs; the clean reads were subsequently aligned to the mixed human and mouse reference genome (NCBI GRCh38 and GRCm38) using bowtie2 software
The percentage of human DNA is the reads alignned to human genome divided by the total unique reads
Assembly: NCBI GRCh38 and GRCm38
Supplementary files format and content: Fraction of human DNA per cfDNA sample
Library strategy: cfDNA-seq

molecule: other

source_name: Plasma cfDNA

extract_protocol:
Blood was collected from mouse with the cardiac puncture and centrifuged to isolate plasma. CfDNA was extracted from mouse plasma with MagPure Circulating DNA LQ Kit (Magen) and quantified by Qubit dsDNA HS Assay Kit (Invitrogen) in Qubit 3 Fluorometer.
A total of 6 ng cfDNA was used to construct libraries using VAHTS Universal DNA Library Prep Kit for MGI (Vazyme). The concentration of library was detected with Qubit dsDNA HS Assay Kit (Invitrogen) and size was detected using Agilent High Sensitivity D1000 ScreenTape System.

value: Plasma cfDNA

value: luciferase-eGFP expressing human A2066


title: TG3M-TN-002

value: Male


title: TG3M-Amyloid-002

value: amyloid


title: m14-A2058


title: dermis_face

source_name: dermis

value: dermis

value: NHDF


title: Nkx_septum_P0_pos-1

source_name: Septum


title: TG3M-NeuN-002


title: scRNA-seq from small cell lung cancer patient Ru1124A

value: Small cell lung cancer

value: Female


title: m13-A2058


title: scRNA-seq from small cell lung cancer patient Ru737D

source_name: Adrenal glands

value: Adrenal glands


title: WT1M-TN-014

value: brain

value: TN

value: WT


title: scRNA-seq from small cell lung cancer patient Ru1152


title: R848- and IL-4+R848 treated BXD2 B cells - Set 3

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description: 10x Genomics

data_processing:
Cell ranger(v6.0.1) count pipeline was used to analyze sequencing data with feature barcode reference
Seurat (v.4.1.3), implemented using the R package was applied to exclude low-quality cells, identify clusters and differently expression genes.
Assembly: mm10
Supplementary files format and content: feature counts for each sample
Supplementary files format and content: tab-delimited text files include feature counts for all samples

source_name: Spleen

extract_protocol:
Single cells were captured into Gel Bead-in-EMulsions using a 10x chromium controller.
Single-cell 5’ biased transcriptome libraries were prepared using a 5’ Library & Gel Bead Kit (PN-1000014) according to the 10x Genomics manual

treatment_protocol: Female BXD2 mice received intraperitoneal (i.p.) administration of a long acting IL-4/anti-IL-4 stabilized cytokine complex containing 5 µg of recombinant mouse IL-4  + 25 µg of anti-IL-4 antibody (clone: BVD4–1D11) or control (25 µg of anti-IL-4 antibody per mouse).  Two hrs after the injection, all mice received R848 (IP-injection, 40 µg of R848 per 20 g of mouse).  The same treatment was repeated 2 days later.  All mice were sacrificed 2 days later.  B cells  were isolated from the spleen using a negatative selection approach.  Cells were then stained with hashing antibodies and feature-barcoding antibodies for scRNA-seq sample preparation.

value: Spleen

value: primary

value: B cells

value: wild-type BXD2 mice

value: mixed samples(IL4treated, untreated)


title: scRNA-seq from small cell lung cancer patient Ru1181b

value: Lymph Node


title: scRNA-seq from small cell lung cancer patient Ru1334

value: primary lung


title: TG3M-PV-002

value: PV

value: Male


title: m12-A427

value: Plasma cfDNA

value: luciferase-eGFP expressing human A427


title: TG4M-TN-001


title: scRNA-seq from small cell lung cancer patient Ru1305A

source_name: Liver

value: Liver

value: Small cell lung cancer


title: m11-A427


title: scRNA-seq from small cell lung cancer patient Ru426B

value: Female


title: G6-tumor-8h-3-1

city: Shanghai

first: Hui

last: Cui

address: JinKe road

institute: Insilico Medicine

data_processing:
Reads quality control was conducted with FastQC, and raw reads were filtered and mapped to the  mm10 reference genome using DRAGEN RNA Pipeline (Illumina)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include counts for each sample

source_name: Tumor tissue

extract_protocol:
Total RNA was isolated from cell pellets using the Magnetic Tissue/Cell/Blood Total RNA Kit (TIANGEN, DP761) on Kingfisher flex instrument.
RNA samples were quantitated by using Quant-IT RNA kit (Invitrogen, R11490),

value: Tumor tissue


title: TG4M-Amyloid-001

source_name: brain

value: brain

value: amyloid


title: m10-A427


title: TG4M-NeuN-001

value: Neu


title: G6-tumor-8h-2-1


title: TG4M-PV-001


title: m9-A427


title: scRNA-seq from small cell lung cancer patient Ru1449A


title: scRNA-seq from small cell lung cancer patient Ru1441a


title: scRNA-seq from small cell lung cancer patient Ru1338E

source_name: Bone

value: Bone


title: G6-tumor-8h-1-1


title: m4-HCC1937

value: luciferase-eGFP expressing human HCC1937


title: G3-tumor-8h-2-1


title: m3-HCC1937


title: scRNA-seq from small cell lung cancer patient Ru1408a


title: G3-tumor-8h-3-1


title: scRNA-seq from small cell lung cancer patient Ru1144b


title: R848- and IL-4+R848 treated BXD2 B cells - Set 2

description: 10x Genomics

value: Spleen

value: primary

value: B cells

value: wild-type BXD2 mice


title: G3-tumor-8h-1-1


title: SLE-3 w and w/o IL-4_18 hrs [trans]

description: 10x Genomics

data_processing:
Cell ranger(v3.1.0) count pipeline was used to analyze sequencing data with feature barcode reference
The hash coding for the data is as follows: hash1 (control), hash2 (IL4), hash3 (IL4_IL2), hash4 (IL4_IL2_antiFNAR), and hash5 (IL4_IL2_IFN).
Cell ranger(v3.1.0) vdj pipeline was used to analyze V(D)J seq data
Seurat (v.4.1.3), implemented using the R package was applied to exclude low-quality cells, identify clusters and differently expression genes.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files contain feature counts for each sample.
Supplementary files format and content: The annotation file for each sample, "filtered_contig_annotations.csv," is an output from the Cell Ranger VDJ pipeline.
Supplementary files format and content: cell ranger feature reference file: IL4tr_human_feature_ref.csv

source_name: peripheral blood mononuclear cells

extract_protocol:
Single cells were captured into Gel Bead-in-EMulsions using a 10x chromium controller.
Single-cell 5’ biased transcriptome libraries were prepared using a 5’ Library & Gel Bead Kit (PN-1000014) according to the 10x Genomics manual
Single-cell mRNA was reverse transcribed into cDNA, which was then captured by a gel bead carrying barcoding DNA oligos that include a cell barcode and unique molecular identifier (UMI) attached to the VDJ region of the cDNA. The cDNA was subsequently amplified, fragmented, and constructed into a 5’ biased library for RNA sequencing.

treatment_protocol: B cells were stimulated in RPMI with 10% FBS supplemented with or without 20 ng/ml IL-4 for 1 h. Cells were then stimulated with 2 μg/ml CL264, a TLR7 ligand, 2 μg/ml goat F(ab′)2 anti-human Ig, 20 ng/ml IL-21, 20 ng/ml IFNɣ, and 20 ng/ml BAFF.  Cells were harvested at 4 and 18 hrs, followed by hash-tag antibody labeling and scRNA-seq analysis.

value: peripheral blood mononuclear cells

value: mixed samples(control,IL4tr,IL4_IL2tr,IL4_IL2_antiFNAR, and IL4_IL2_IFN)


title: SLE-2 w and w/o IL-4_18 hrs [trans]

description: 10x Genomics


title: SLE-3 w and w/o IL-4_4 hrs [trans]

description: 10x Genomics


title: m1-HCC1937

value: Plasma cfDNA


title: scRNA-seq from small cell lung cancer patient Ru1408e

value: Male


title: R848- and IL-4+R848 treated BXD2 B cells - Set 1

description: 10x Genomics

value: mixed samples(IL4treated, untreated)


title: G2-tumor-8h-6-1

value: Cisplation


title: c4-Control

value: wild-type


title: SLE-1 w and w/o IL-4_4 hrs [trans]

description: 10x Genomics


title: scRNA-seq from small cell lung cancer patient Ru1080C

value: Kidney

value: Small cell lung cancer

value: Female


title: G2-tumor-8h-5-1

value: Tumor tissue


title: c3-Control


title: scRNA-seq from small cell lung cancer patient Ru1108a

value: primary lung


title: m5-HCC1937

value: luciferase-eGFP expressing human HCC1937


title: SLE-2 w and w/o IL-4_18 hrs [HASH]

description: 10x Genomics


title: G2-tumor-8h-4-1


title: c2-Control


title: scRNA-seq from small cell lung cancer patient Ru1473a

value: Liver


title: G1-tumor-8h-6-1

value: Vehicle


title: AAV-injection, risdiplam, 30 day post risdiplam, rep4

source_name: heart apex

value: heart apex

value: 10 mg/kg risdiplam

tag: time

value: P40, 30 day post risdiplam


title: G1-tumor-8h-5-1


title: SLE-2 w and w/o IL-4_4 hrs [HASH]

description: 10x Genomics

value: peripheral blood mononuclear cells

value: B cells

value: mixed samples(control,IL4tr,IL4_IL2tr,IL4_IL2_antiFNAR, and IL4_IL2_IFN)


title: SLE-3 w and w/o IL-4_4 hrs [HASH]

description: 10x Genomics


title: SLE-1 w and w/o IL-4_4 hrs [HASH]

description: 10x Genomics


title: SHP77, input

data_processing:
Raw sequencing reads were trimmed with Trim Galore (v0.4.4). Reads were aligned to human assembly hg38 using bowtie2 v2.3.4 with the default settings
Enriched binding regions were called against the input using MACS2 with p value less than 0.001. The bigwig format for each sample was created using the BEDTools suite (https://bedtools.readthedocs.io) with the normalization factor 10 million
Assembly: Human GRCh38
Supplementary files format and content: bigwiz file is uploaded as processed data
Supplementary files format and content: bigWig

growth_protocol: H1836 was cultured with DMEM/F12 HITES media, SHP-77 with RPMI+10% fetal bovine serum (FBS).

extract_protocol:
ChIP-seq on cell lines (H1836, SHP-77)  were performed using 1x107 cells. Samples were crosslinked at room temperature for 10 min by swirling with 1% formaldehyde (Sigma Aldrich) followed by addition of 125 mM glycine to quench the reaction. After washing the cells with PBS, cells were resuspended with ChIP lysis buffer supplemented with protease inhibitors (Roche cOmplete mini EDTA-free protease inhibitor tablets, Cat #: 11836170001) and phosphatase inhibitors (Thermo Scientific, Halt Phosphatase Inhibitor Cocktail, Cat #: 78427, 1:1000). Cell lysates in 1 mL ChIP lysis buffer were sonicated to shear chromatin to 200-500 bp. Supernatants were incubated with the antibodies (IgG: Cell Signaling Technology, Cat #: 2729S and ASCL1: Cell Signaling Technology, Cat #: 43666S) at 4ºC overnight on a rotator. Dynabeads™ Protein G were blocked with 2.5 mg/mL UltraPure™ BSA (Thermo Scientific, Cat #: AM2616) at 4ºC overnight. The beads were washed three times with ChIP buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100) and incubated with the chromatin-antibody samples. These samples were washed with high salt ChIP buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% of Triton X-100, 0.1% of SDS) followed by washings with Tris-EDTA (TE) buffer. Chromatin complexes were eluted in TE with 1% ultrapure SDS (ThermoFisher Scientific) at 65ºC for 15 min, and reverse-crosslinked with RNAse A (ThermoFisher Scientific, Cat #: EN0531), followed by incubation with Proteinase K solution (ThermoFisher Scientific, Cat #: EO0491). DNA was purified using QIAquick PCR Purification Kit (Qiagen).
Sequencing libraries were sent to the MSK Integrated Genomics Operation core facility for sequencing on a NovaSeq 6000.

tag: chip antibody


title: G1-tumor-8h-4-1


title: WT, solvent, 1 day post solvent, rep5

description:
WTS5
RISH10.markdup.bam
WT_Adult_risdiplam.txt

data_processing:
FastQC (v0.11.9)
trim_galore (v0.6.7)
STAR (v2.7.9a)
featureCounts (v2.0.1)
Assembly: mm10; hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

value: solvent

value: 8 weeks, 1 day post solvent


title: SLE-2 w and w/o IL-4_4 hrs [trans]

description: 10x Genomics


title: AAV-injection, solvent, 30 day post solvent, rep4

value: P40, 30 day post solvent


title: SHP77, IgG1, ChIP, rep2

value: IgG (CST, 2729S)


title: SLE-3 w and w/o IL-4_18 hrs [BCR]

description: 10x Genomics


title: SHP77, IgG1, ChIP, rep1

value: Small cell lung cancer


title: WT, solvent, 1 day post solvent, rep4

description:
WTS4
RISH9.markdup.bam
WT_Adult_risdiplam.txt


title: AAV-injection, risdiplam, 30 day post risdiplam, rep3


title: SLE-2 w and w/o IL-4_18 hrs [BCR]

description: 10x Genomics


title: SHP77, ASCL1, ChIP, rep2


title: AAV-injection, solvent, 30 day post solvent, rep3


title: SLE-3 w and w/o IL-4_18 hrs [HASH]

description: 10x Genomics


title: AAV-injection, solvent, 30 day post solvent, rep2


title: WT, solvent, 1 day post solvent, rep3

description:
WTS3
RISH8.markdup.bam
WT_Adult_risdiplam.txt


title: SLE-3 w and w/o IL-4_4 hrs [BCR]

description: 10x Genomics


title: scRNA-seq from small cell lung cancer patient Ru1308g

value: Female


title: WT, solvent, 1 day post solvent, rep2

description:
WTS2
RISH7.markdup.bam
WT_Adult_risdiplam.txt


title: c1-Control

value: Plasma cfDNA

value: wild-type


title: SHP77, ASCL1, ChIP, rep1


title: AAV-injection, risdiplam, 30 day post risdiplam, rep2


title: SLE-2 w and w/o IL-4_4 hrs [BCR]

description: 10x Genomics


title: H1836, Input


title: WT, solvent, 1 day post solvent, rep1

description:
WTS1
RISH6.markdup.bam
WT_Adult_risdiplam.txt


title: AAV-injection, solvent, 30 day post solvent, rep1


title: H1836, IgG1, ChIP, rep2


title: AAV-injection, risdiplam,11 days post risdiplam,  rep3

description:
OFFR3
H18Aligned.sortedByCoord.out.bam
OFF_counts_CLEAN.txt

value: P20, 11 days post risdiplam


title: WT, risdiplam, 1 day post risdiplam, rep5

description:
WTR5
RISH5.markdup.bam
WT_Adult_risdiplam.txt

value: 8 weeks, 1 day post risdiplam


title: WT, risdiplam, 1 day post risdiplam, rep4

description:
WTR4
RISH4.markdup.bam
WT_Adult_risdiplam.txt


title: H1836, IgG1, ChIP, rep1