title: Recruited airway macrophages, engulfing, rep2

description: Library name: CD11b_6_plus


title: AP218192E23

status: Public on May 01 2026

type: protein

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

country: USA

institute: Eli Lilly and Company

description: title describes sample ID used in raw data (NPX.csv)

data_processing:
A set of internal controls (incubation, extension and amplification) was used to assess overall assay quality.  Internal plate controls were used to normalize the data and to calculate the limit of detection (LOD) for each assay.
Protein expression levels are given as normalized protein expression (NPX) values, which are arbitrary units used on a log2 scale that were normalized to the plate controls.

molecule: protein

organism: Homo sapiens

source_name: Whole blood

extract_protocol: Baseline SLE serum samples were collected according to the clinical trial protocols. Blood was collected using a tube containing a clotting agent (BD SST 5ml tube). Circulating proteins were assayed using the Olink Explore 3072 panel, a proteomics platform that combines an antibody-based immunoassay with a proximity oligonucleotide extension assay and signal detection with next-generation sequencing on the NovaSeq6000 instrument (Ilumina Inc.).

tag: Sex

value: F

tag: disease

value: SLE


title: AP250345E23


title: AP340622D23


title: AP920987D23


title: 49407

type: SRA

description: Library name: Sample 303

library_source: transcriptomic

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

molecule: polyA RNA

source_name: whole blood

extract_protocol:
Whole blood RNA was extracted from PAXgene blood RNA tubes. Briefly, frozen tubes were thawed at room temperature and centrifuged according to the manufacturer’s protocol. The resulting pellet was then washed with nuclease free water, resuspended in sterile PBS, and split in half. RNA was extracted from one half of the suspension using the QIAsymphony PAXgene Blood RNA Kit (Qiagen). The other half of the suspension was used for DNA extraction. RNA concentration and integrity were assessed using the Ribogreen Assay (Thermo) and a Fragment Analyzer (Agilent), respectively.
Polyadenylated RNA was enriched using NEBNext Magnetic Oligo(dT)25 Beads and prepared into RNA-seq libraries using the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs, Ipswich, MA, USA). Unique dual-index barcodes were incorporated as specified per manufacturer’s protocol. Library concentration was measured using the Quant-iT PicoGreen dsDNA Reagent (Thermo), and library size distribution and quality were checked using a DNA chip on Caliper Gx Touch (Revity). Library quantification was further refined by qPCR using the KAPA Library Quantificaiton Kit (Roche). Paired-end sequencing (2 x 100 bp, 100 million reads per sample) was carried out on an Illumina NovaSeq 6000 platform (Illumina) following manufacturer’s recommended protocols.

tag: tissue

value: whole blood

tag: genotype


title: Recruited airway macrophages, non-engulfing, rep4

city: Denver

first: Alexandra

last: McCubbrey

state: CO

address: 1400 Jackson St

institute: National Jewish Health

description: Library name: CD11b_8_minus

data_processing:
FASTQ files were generated from BCL files using Illumina bcl2fastq converter without adapter trimming.
Nf-core RNA-seq pipeline (version v3.9) run with Nextflow version 20.04.1
Assembly: GRCm38
Supplementary files format and content: raw_gene_counts.tsv: Gene-level counts; genes are rows and columns are library names

organism: Mus musculus

source_name: Recruited airway macrophages

extract_protocol:
RNA was isolated using the RNeasy Plus Micro isolation kit (QIAGEN) per the manufacturer’s instructions with addition of β-mercaptoethanol to RLT Plus buffer. RT-PCR was performed using the SensiFast Hi-ROX One-Step Kit (Meridian Bioscience) per the manufacturer’s instructions.
Libraries were built using the standard Kapa Biosystems library preperation kit.

tag: cell type

value: Recruited airway macrophages

tag: engulfment

value: non-engulfing

tag: replicate


title: AP340623D23


title: 49408

description: Library name: Sample 304


title: 49406

description: Library name: Sample 302


title: Recruited airway macrophages, engulfing, rep1

description: Library name: CD11b_5_plus

value: engulfing


title: AP554776D23


title: Recruited airway macrophages, non-engulfing, rep3

description: Library name: CD11b_7_minus


title: AP092616D23


title: Recruited airway macrophages, non-engulfing, rep2

description: Library name: CD11b_6_minus


title: AP920988D23


title: AP922093D23


title: 49306

description: Library name: Sample 299


title: AP554774D23


title: AP693899D23


title: Recruited airway macrophages, non-engulfing, rep1

description: Library name: CD11b_5_minus


title: 49404

description: Library name: Sample 300


title: 49405

description: Library name: Sample 301


title: 49205

description: Library name: Sample 298


title: AP306507D24


title: AP306506D23


title: PUER cells, GCSF, OHT, 168h, Rep2

city: Grand Forks

first: Manu

last: Manu

state: ND

address: 10 Cornell Street, Stop 9019

department: Biology

institute: University of North Dakota

description:
Library name: m17_121_211
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 168h after the addition of OHT.

data_processing:
We used Salmon to map the reads to the GRCm38 reference genome with the selective alignment strategy and to determine transcript abundances. The median-of-ratios method of DESeq2, which computes the ratio of each transcript's abundance in each sample to the geometric mean of the expression across samples and then determines a size factor for each sample as the median of these ratios, was used to normalize gene expression to library size.
Assembly: mm10
Supplementary files format and content: CSV file containing read counts for each transcript in each sample

source_name: PUER

growth_protocol: PUER cells were routinely maintained in complete Iscove’s Modified Dulbecco’s Glutamax medium (IMDM; Gibco, 12440061) supplemented with 10% FBS, 50μM β-mercaptoethanol, 5ng/ml IL3 (Peprotech, 213-13).

extract_protocol:
Total RNA was extracted on a Bio-Mek FXP liquid handling workstation (Beckman Coulter) using the RNAdvance Tissue total RNA isolation kit (Beckman Coulter, A32649) from 3 replicates in a 96-well format following the manufacturer's protocol. Genomic DNA contamination was assessed by reverse transcribing the RNA with and without reverse-transcriptase and detecting GAPDH using qPCR. The number of additional cycles required to reach a threshold (ΔCt) was utilized to assess the fraction of genomic DNA (2- ΔCt) and only samples with less than 1% genomic DNA were utilized for library preparation. The quality of the RNA was assessed by capillary gel electrophoresis on the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano kit (Agilent, 5067-1511). Only samples with RNA integrity numbers (RIN) greater than or equal to 9.5 were utilized, although there was only one sample with a RIN of 9.5 and the median RIN was 9.9. The concentration of RNA was determined using the Qubit fluorometer and the Qubit RNA High Sensitivity kit (Invitrogen, Q32855). With the exception of 8 samples with lower RNA yield, the samples were standardized to a mass of 1,875 ng in a 25µl volume. The samples with lower yield were standardized to a mass of 1,437.5 ng in a 25µl volume. 3.75µl or 2.88µl of a 1:100 dilution of the External RNA Control Consortium (ERCC) ExFold RNA Spike-In mix (Invitrogen, 4456739) was added to the high- and low-yielding samples respectively.
Illumina libraries were prepared by Novogene Corporation Inc. (Chula Vista, CA) using the NEB Ultra II RNA Library Prep Kit for Illumina according to manufacturer protocols. The libraries were sequenced on an Illumina Novaseq 6000 S2 2 X 150 bp flow cell to an average depth of 29.24 X 106 raw reads per sample for a total of 4.82 X 109 reads. The sequencing provider filtered the reads to remove ones containing Illumina adaptors, or more than 10% indeterminate bases (“N”s), or having more than half bases with a phred score below 5. The remaining “clean” reads, representing 95.52% of raw reads, were used for processing.

treatment_protocol: PUER cells were expanded in T-75 flasks prior to the initiation of differentiation. GCSF pre-treatment was initiated by washing the cells 3 times with PBS and then seeding in 48-well plates at a concentration of 5X10^5 cells/ml in PUER cell culture medium in which IL3 had been replaced by 10ng/mL Granulocyte Colony Stimulating Factor (GCSF; Peprotech, 300-23). At the same time, the PUER cells destined for the macrophage differentiation were seeded in 48-well plates at a concentration of 5X10^5 cells/ml in IL3 PUER cell culture medium. After 48 hours of GCSF pre-treatment, the neutrophil differentiation was commenced by the addition of 100nM 4-hydroxy-tamoxifen (OHT; Sigma, H7904-5MG) to the GCSF-conditioned media. The macrophage differentiation was initiated at the same time by the addition of 200nM OHT. We regard time zero (0h) of differentiation as occurring just before the addition of OHT. With this starting point, the initiation of GCSF pre-treatment occurs immediately after -48h while cells pre-treated with GCSF for 48h but not yet induced by OHT are at 0h.  Since both treatments start with uninduced PUER cells, the data for the -48h time point of the neutrophil differentiation and 0h time point of the macrophage differentiation are derived from the same samples and are identical. OHT rapidly converts from the Z isomer to the E isomer, having 100-fold lower activity, in cell culture media. Half the medium was replaced and fresh OHT was added at 40h, 88h, and 136h in order to maintain differentiation pressure.

tag: cell line

value: PUER

value: bone marrow-derived progenitors

tag: treatment

value: IL3 replaced with GCSF at -48h. Tamoxifen (OHT) added at 0h

tag: time


title: PUER cells, GCSF, OHT, 168h, Rep3

description:
Library name: m17_121_212
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 168h after the addition of OHT.


title: 49202

description: Library name: Sample 297


title: AP306504D23


title: AP306503D23


title: AP693900D23


title: AP092864D23


title: 49115

description: Library name: Sample 296


title: PUER cells, IL3, OHT, 168h, Rep3

description:
Library name: m17_121_215
RNA-seq of PUER cells 168h after the addition of OHT.

value: Tamoxifen (OHT) added at 0h


title: 49106

description: Library name: Sample 294


title: 49112

description: Library name: Sample 295


title: AP350228D23


title: PUER cells, GCSF, OHT, 168h, Rep1

description:
Library name: m17_121_209
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 168h after the addition of OHT.


title: PUER cells, IL3, OHT, 168h, Rep2

description:
Library name: m17_121_214
RNA-seq of PUER cells 168h after the addition of OHT.


title: 49105

description: Library name: Sample 293


title: AP092904D23

value: M


title: AP706086D23


title: AP706084D23


title: AP032273E23


title: PUER cells, GCSF, OHT, 160h, Rep3

description:
Library name: m17_121_204
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 160h after the addition of OHT.


title: AP636908D23


title: AP032272E23


title: AP693902D23


title: PUER cells, IL3, OHT, 168h, Rep1

description:
Library name: m17_121_216
RNA-seq of PUER cells 168h after the addition of OHT.


title: 49103

description: Library name: Sample 291


title: 49101

description: Library name: Sample 290


title: AP636907D23


title: AP626457E22


title: 49104

description: Library name: Sample 292


title: PUER cells, GCSF, OHT, 160h, Rep1

description:
Library name: m17_121_203
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 160h after the addition of OHT.


title: PUER cells, GCSF, OHT, 160h, Rep2

description:
Library name: m17_121_201
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 160h after the addition of OHT.


title: 44903

description: Library name: Sample 289


title: AP780639D23


title: AP251960D23


title: AP651817D23


title: PUER cells, IL3, OHT, 160h, Rep3

description:
Library name: m17_121_205
RNA-seq of PUER cells 160h after the addition of OHT.


title: AP350201D23


title: AP651816D23


title: 44506

description: Library name: Sample 287


title: PUER cells, IL3, OHT, 160h, Rep2

description:
Library name: m17_121_206
RNA-seq of PUER cells 160h after the addition of OHT.


title: PUER cells, IL3, OHT, 160h, Rep1

description:
Library name: m17_121_208
RNA-seq of PUER cells 160h after the addition of OHT.


title: AP589635D23


title: 44503

description: Library name: Sample 286


title: AP503651E24


title: PUER cells, GCSF, OHT, 152h, Rep2

description:
Library name: m17_121_195
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 152h after the addition of OHT.


title: AP350200D23


title: AP858095C23


title: 44103

description: Library name: Sample 285


title: AP858096C23


title: PUER cells, GCSF, OHT, 152h, Rep1

description:
Library name: m17_121_196
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 152h after the addition of OHT.


title: 44601

description: Library name: Sample 288


title: 44004

description: Library name: Sample 284


title: AP243836D23


title: AP243833D23


title: AP374943D23


title: 44001

description: Library name: Sample 283


title: AP374942D23


title: PUER cells, IL3, OHT, 152h, Rep3

description:
Library name: m17_121_200
RNA-seq of PUER cells 152h after the addition of OHT.


title: AP271494D23


title: PUER cells, IL3, OHT, 152h, Rep1

description:
Library name: m17_121_197
RNA-seq of PUER cells 152h after the addition of OHT.


title: AP271496D23

description: title describes sample ID used in raw data (NPX.csv)


title: 43917

description: Library name: Sample 282


title: AP809634D23


title: PUER cells, IL3, OHT, 152h, Rep2

description:
Library name: m17_121_198
RNA-seq of PUER cells 152h after the addition of OHT.


title: AP809637D23


title: AP809633D23


title: 43913

description: Library name: Sample 280


title: AP368506E30


title: PUER cells, GCSF, OHT, 144h, Rep1

description:
Library name: m17_121_177
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 144h after the addition of OHT.


title: 43914

description: Library name: Sample 281


title: LP641108A22


title: LP539674A30


title: PUER cells, GCSF, OHT, 144h, Rep3

description:
Library name: m17_121_179
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 144h after the addition of OHT.


title: AP271456D23


title: 43907

description: Library name: Sample 279


title: LP539625A23


title: AP809632D23


title: 43906

description: Library name: Sample 278


title: PUER cells, IL3, OHT, 144h, Rep2

description:
Library name: m17_121_181
RNA-seq of PUER cells 144h after the addition of OHT.


title: LP539626A23


title: 43811

description: Library name: Sample 277


title: LP539630A23


title: 43801

description: Library name: Sample 275


title: LP498766A23


title: PUER cells, GCSF, OHT, 144h, Rep2

description:
Library name: m17_121_180
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 144h after the addition of OHT.


title: LP498765A23


title: LP656728A22


title: PUER cells, GCSF, OHT, 136h, Rep3

description:
Library name: m17_121_186
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 136h after the addition of OHT.


title: PUER cells, IL3, OHT, 144h, Rep1

description:
Library name: m17_121_183
RNA-seq of PUER cells 144h after the addition of OHT.


title: 43809

description: Library name: Sample 276


title: 43710

description: Library name: Sample 274


title: LP539333A23


title: LP539332A23


title: PUER cells, GCSF, OHT, 136h, Rep2

description:
Library name: m17_121_185
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 136h after the addition of OHT.


title: PUER cells, GCSF, OHT, 136h, Rep1

description:
Library name: m17_121_187
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 136h after the addition of OHT.


title: LP494159A23


title: PUER cells, IL3, OHT, 136h, Rep3

description:
Library name: m17_121_191
RNA-seq of PUER cells 136h after the addition of OHT.


title: LP513724A23


title: LP439217A23


title: 43601

description: Library name: Sample 273


title: LP439220A23


title: PUER cells, IL3, OHT, 136h, Rep2

description:
Library name: m17_121_192
RNA-seq of PUER cells 136h after the addition of OHT.


title: 42102

description: Library name: Sample 270


title: LP494157A23


title: PUER cells, IL3, OHT, 136h, Rep1

description:
Library name: m17_121_189
RNA-seq of PUER cells 136h after the addition of OHT.


title: LP439218A23


title: LP539329A23


title: 43413

description: Library name: Sample 272


title: LP391196A23


title: PUER cells, GCSF, OHT, 128h, Rep3

description:
Library name: m17_121_169
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 128h after the addition of OHT.


title: LP439221A23


title: LP391197A23


title: 40701

description: Library name: Sample 269


title: 40602

description: Library name: Sample 268


title: LP439225A23


title: 42402

description: Library name: Sample 271


title: PUER cells, GCSF, OHT, 128h, Rep2

description:
Library name: m17_121_171
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 128h after the addition of OHT.


title: PUER cells, IL3, OHT, 144h, Rep3

description:
Library name: m17_121_184
RNA-seq of PUER cells 144h after the addition of OHT.


title: LP494404A23


title: LP494161A23


title: LP494405A23


title: LP454647A23


title: 40406

description: Library name: Sample 267


title: LP454649A23


title: PUER cells, IL3, OHT, 128h, Rep3

description:
Library name: m17_121_175
RNA-seq of PUER cells 128h after the addition of OHT.


title: LP454648A23

description: title describes sample ID used in raw data (NPX.csv)


title: 40404

description: Library name: Sample 266


title: 40309

description: Library name: Sample 265


title: LP513329A23


title: PUER cells, IL3, OHT, 128h, Rep2

description:
Library name: m17_121_173
RNA-seq of PUER cells 128h after the addition of OHT.


title: LP513326A23


title: 40304

description: Library name: Sample 264


title: LP513325A23


title: LP434307A23


title: LP498568A24


title: LP513416A24


title: PUER cells, IL3, OHT, 128h, Rep1

description:
Library name: m17_121_174
RNA-seq of PUER cells 128h after the addition of OHT.


title: LP498566A23


title: LP498565A24


title: PUER cells, GCSF, OHT, 120h, Rep3

description:
Library name: m17_114_002
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 120h after the addition of OHT.


title: 40243

description: Library name: Sample 262


title: PUER cells, GCSF, OHT, 120h, Rep1

description:
Library name: m17_114_004
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 120h after the addition of OHT.


title: 40232

description: Library name: Sample 261


title: PUER cells, GCSF, OHT, 120h, Rep2

description:
Library name: m17_114_003
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 120h after the addition of OHT.


title: 40227

description: Library name: Sample 260


title: LP623468A22


title: 40301

description: Library name: Sample 263


title: LP692205A22


title: LP601330A23


title: LP512686A23


title: LP512688A23


title: PUER cells, IL3, OHT, 120h, Rep2

description:
Library name: m17_114_007
RNA-seq of PUER cells 120h after the addition of OHT.


title: 40205

description: Library name: Sample 258


title: PUER cells, IL3, OHT, 120h, Rep1

description:
Library name: m17_114_006
RNA-seq of PUER cells 120h after the addition of OHT.


title: LP512689A23


title: 40212

description: Library name: Sample 259


title: PUER cells, GCSF, OHT, 128h, Rep1

description:
Library name: m17_121_172
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 128h after the addition of OHT.


title: LP512685A23


title: LP443430A24


title: PUER cells, GCSF, OHT, 112h, Rep1

description:
Library name: m17_121_164
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 112h after the addition of OHT.


title: LP452584A23


title: PUER cells, IL3, OHT, 112h, Rep3

description:
Library name: m17_121_168
RNA-seq of PUER cells 112h after the addition of OHT.


title: 40113

description: Library name: Sample 257


title: LP391872A24


title: LP391871A23


title: PUER cells, IL3, OHT, 112h, Rep2

description:
Library name: m17_121_167
RNA-seq of PUER cells 112h after the addition of OHT.


title: LP452592A23


title: PUER cells, GCSF, OHT, 112h, Rep2

description:
Library name: m17_121_163
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 112h after the addition of OHT.


title: 40107

description: Library name: Sample 256


title: LP452585A23


title: 40104

description: Library name: Sample 255


title: 40101

description: Library name: Sample 253


title: 40103

description: Library name: Sample 254


title: LP459889A24


title: LP440735A23


title: LP391870A23


title: PUER cells, IL3, OHT, 112h, Rep1

description:
Library name: m17_121_165
RNA-seq of PUER cells 112h after the addition of OHT.


title: PUER cells, GCSF, OHT, 104h, Rep3

description:
Library name: m17_121_153
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 104h after the addition of OHT.


title: 36308

description: Library name: Sample 252


title: EP182414E23


title: EP825218E22


title: LP452588A23


title: PUER cells, GCSF, OHT, 104h, Rep2

description:
Library name: m17_121_154
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 104h after the addition of OHT.


title: EP140148E23


title: 36307

description: Library name: Sample 251


title: EP181469E23


title: 36304

description: Library name: Sample 250


title: EP812487E23


title: EP194150E23


title: PUER cells, GCSF, OHT, 104h, Rep1

description:
Library name: m17_121_155
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 104h after the addition of OHT.


title: 36303

description: Library name: Sample 249


title: EP748465D23

description: title describes sample ID used in raw data (NPX.csv)


title: EP672622D23


title: 36302

description: Library name: Sample 248


title: PUER cells, IL3, OHT, 104h, Rep3

description:
Library name: m17_121_159
RNA-seq of PUER cells 104h after the addition of OHT.


title: 36209

description: Library name: Sample 247


title: EP672621D23


title: PUER cells, IL3, OHT, 104h, Rep1

description:
Library name: m17_121_157
RNA-seq of PUER cells 104h after the addition of OHT.


title: EP754787E23


title: 36207

description: Library name: Sample 246


title: PUER cells, IL3, OHT, 104h, Rep2

description:
Library name: m17_121_158
RNA-seq of PUER cells 104h after the addition of OHT.


title: EP457670D23


title: PUER cells, GCSF, OHT, 96h, Rep1

description:
Library name: m17_121_145
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 96h after the addition of OHT.


title: 36206

description: Library name: Sample 245


title: EP903536D23


title: PUER cells, GCSF, OHT, 96h, Rep2

description:
Library name: m17_121_147
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 96h after the addition of OHT.


title: EP457671D23


title: 36204

description: Library name: Sample 244


title: EP995087E22


title: PUER cells, IL3, OHT, 96h, Rep3

description:
Library name: m17_121_150
RNA-seq of PUER cells 96h after the addition of OHT.


title: EP320193E23


title: EP338524D23


title: EP473311D23


title: 36203

description: Library name: Sample 243


title: EP320195E23


title: PUER cells, IL3, OHT, 96h, Rep2

description:
Library name: m17_121_152
RNA-seq of PUER cells 96h after the addition of OHT.


title: 36201

description: Library name: Sample 242


title: EP420677D23


title: 36107

description: Library name: Sample 241


title: PUER cells, IL3, OHT, 96h, Rep1

description:
Library name: m17_121_149
RNA-seq of PUER cells 96h after the addition of OHT.


title: EP473312D23


title: PUER cells, GCSF, OHT, 88h, Rep3

description:
Library name: m17_121_139
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 88h after the addition of OHT.


title: EP636677D23


title: EP636676D23


title: PUER cells, GCSF, OHT, 88h, Rep2

description:
Library name: m17_121_138
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 88h after the addition of OHT.


title: EP081186E23


title: EP326427D23


title: EP636678D23


title: PUER cells, GCSF, OHT, 88h, Rep1

description:
Library name: m17_121_137
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 88h after the addition of OHT.


title: 36102

description: Library name: Sample 239


title: EP583330E23


title: 36104

description: Library name: Sample 240


title: 36015

description: Library name: Sample 238


title: EP995086E22


title: EP583331E23


title: EP166328E23


title: 36014

description: Library name: Sample 237


title: PUER cells, IL3, OHT, 88h, Rep2

description:
Library name: m17_121_142
RNA-seq of PUER cells 88h after the addition of OHT.


title: EP204600E23


title: PUER cells, IL3, OHT, 88h, Rep1

description:
Library name: m17_121_141
RNA-seq of PUER cells 88h after the addition of OHT.


title: EP184140F22


title: LP512687A23


title: EP212174E23


title: PUER cells, IL3, OHT, 88h, Rep3

description:
Library name: m17_121_144
RNA-seq of PUER cells 88h after the addition of OHT.


title: 36006

description: Library name: Sample 236


title: 36005

description: Library name: Sample 235


title: EP825280E22


title: PUER cells, GCSF, OHT, 80h, Rep3

description:
Library name: m17_121_131
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 80h after the addition of OHT.


title: EP290839E23


title: 36001

description: Library name: Sample 234


title: EP170035E23


title: EP907228E22


title: EP169836F22


title: 35903

description: Library name: Sample 233


title: 35901

description: Library name: Sample 232


title: PUER cells, GCSF, OHT, 80h, Rep2

description:
Library name: m17_121_130
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 80h after the addition of OHT.


title: EP192795E23

description: title describes sample ID used in raw data (NPX.csv)


title: EP496245D23


title: LP440737A23


title: PUER cells, GCSF, OHT, 80h, Rep1

description:
Library name: m17_121_129
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 80h after the addition of OHT.


title: EP784149E23


title: EP708737E23


title: EP266945F22


title: PUER cells, IL3, OHT, 80h, Rep3

description:
Library name: m17_121_135
RNA-seq of PUER cells 80h after the addition of OHT.


title: PUER cells, IL3, OHT, 80h, Rep2

description:
Library name: m17_121_136
RNA-seq of PUER cells 80h after the addition of OHT.


title: EP420436E23


title: EP650468E23


title: 35804

description: Library name: Sample 231


title: AP633439E22


title: EP382439E23


title: PUER cells, IL3, OHT, 80h, Rep1

description:
Library name: m17_121_133
RNA-seq of PUER cells 80h after the addition of OHT.


title: 35802

description: Library name: Sample 230


title: 35709

description: Library name: Sample 229


title: PUER cells, GCSF, OHT, 72h, Rep3

description:
Library name: m17_121_121
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 72h after the addition of OHT.


title: EP140147E23


title: AP634880E22


title: PUER cells, GCSF, OHT, 72h, Rep2

description:
Library name: m17_121_123
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 72h after the addition of OHT.


title: PUER cells, GCSF, OHT, 72h, Rep1

description:
Library name: m17_121_122
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 72h after the addition of OHT.


title: 35702

description: Library name: Sample 227


title: AP634906E22


title: 35708

description: Library name: Sample 228


title: AP592710E22


title: PUER cells, IL3, OHT, 72h, Rep3

description:
Library name: m17_121_125
RNA-seq of PUER cells 72h after the addition of OHT.


title: AP509702E22


title: AP698570E22


title: 35617

description: Library name: Sample 226


title: AP709412E22


title: AP634272E22


title: AP509701E22


title: 35612

description: Library name: Sample 224


title: AP707019E22


title: PUER cells, IL3, OHT, 72h, Rep2

description:
Library name: m17_121_126
RNA-seq of PUER cells 72h after the addition of OHT.


title: AP490644E22


title: PUER cells, IL3, OHT, 72h, Rep1

description:
Library name: m17_121_127
RNA-seq of PUER cells 72h after the addition of OHT.


title: 35614

description: Library name: Sample 225


title: AP528573E22


title: AP545250E22


title: PUER cells, GCSF, OHT, 64h, Rep2

description:
Library name: m17_121_116
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 64h after the addition of OHT.


title: PUER cells, GCSF, OHT, 64h, Rep3

description:
Library name: m17_121_115
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 64h after the addition of OHT.


title: AP528571E22


title: 35609

description: Library name: Sample 222


title: 35611

description: Library name: Sample 223


title: 35607

description: Library name: Sample 221


title: PUER cells, GCSF, OHT, 64h, Rep1

description:
Library name: m17_121_114
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 64h after the addition of OHT.


title: AP634742E22


title: AP827005D24


title: AP205986E23


title: AP528566E22


title: 35605

description: Library name: Sample 220


title: AP528567E22


title: PUER cells, IL3, OHT, 64h, Rep2

description:
Library name: m17_121_117
RNA-seq of PUER cells 64h after the addition of OHT.


title: 35601

description: Library name: Sample 218


title: AP278268E23


title: PUER cells, IL3, OHT, 64h, Rep1

description:
Library name: m17_121_120
RNA-seq of PUER cells 64h after the addition of OHT.


title: AP278269E23


title: AP479260E22


title: 35604

description: Library name: Sample 219


title: AP912850D23


title: 35513

description: Library name: Sample 217


title: 35511

description: Library name: Sample 216


title: AP640891D23


title: AP912847D23


title: AP841265D24


title: PUER cells, GCSF, OHT, 56h, Rep3

description:
Library name: m17_121_108
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 56h after the addition of OHT.


title: PUER cells, IL3, OHT, 64h, Rep3

description:
Library name: m17_121_118
RNA-seq of PUER cells 64h after the addition of OHT.


title: AP602912D23

description: title describes sample ID used in raw data (NPX.csv)


title: PUER cells, GCSF, OHT, 56h, Rep1

description:
Library name: m17_121_105
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 56h after the addition of OHT.


title: PUER cells, GCSF, OHT, 56h, Rep2

description:
Library name: m17_121_106
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 56h after the addition of OHT.


title: PUER cells, IL3, OHT, 120h, Rep3

description:
Library name: m17_114_005
RNA-seq of PUER cells 120h after the addition of OHT.


title: AP995860D23


title: AP602911D23


title: 35510

description: Library name: Sample 215


title: 35508

description: Library name: Sample 214


title: AP718294D23


title: AP492334D23


title: PUER cells, IL3, OHT, 56h, Rep2

description:
Library name: m17_121_111
RNA-seq of PUER cells 56h after the addition of OHT.


title: AP705195D23


title: 35507

description: Library name: Sample 213


title: AP776353D23


title: AP998906D23


title: PUER cells, IL3, OHT, 56h, Rep3

description:
Library name: m17_121_112
RNA-seq of PUER cells 56h after the addition of OHT.


title: 35413

description: Library name: Sample 211


title: 35501

description: Library name: Sample 212


title: AP463506E22


title: AP297292E22


title: AP430538D23


title: PUER cells, GCSF, OHT, 48h, Rep2

description:
Library name: m17_121_099
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 48h after the addition of OHT.


title: PUER cells, IL3, OHT, 56h, Rep1

description:
Library name: m17_121_109
RNA-seq of PUER cells 56h after the addition of OHT.


title: AP244803D23


title: AP448672D23


title: 35406

description: Library name: Sample 209


title: PUER cells, GCSF, OHT, 48h, Rep1

description:
Library name: m17_121_097
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 48h after the addition of OHT.


title: 35410

description: Library name: Sample 210


title: PUER cells, GCSF, OHT, 48h, Rep3

description:
Library name: m17_121_100
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 48h after the addition of OHT.


title: AP037112E23


title: AP448673D23


title: AP292627C23


title: AP690130D23


title: AP826940D23


title: AP338876D30


title: 35404

description: Library name: Sample 208


title: PUER cells, IL3, OHT, 48h, Rep3

description:
Library name: m17_121_102
RNA-seq of PUER cells 48h after the addition of OHT.


title: PUER cells, IL3, OHT, 48h, Rep1

description:
Library name: m17_121_101
RNA-seq of PUER cells 48h after the addition of OHT.


title: AP512668E22


title: 35316

description: Library name: Sample 207


title: AP338850D23


title: PUER cells, IL3, OHT, 48h, Rep2

description:
Library name: m17_121_103
RNA-seq of PUER cells 48h after the addition of OHT.


title: AP292672C23


title: AP512667E22


title: PUER cells, GCSF, OHT, 40h, Rep3

description:
Library name: m17_121_089
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 40h after the addition of OHT.


title: 35311

description: Library name: Sample 205


title: 35313

description: Library name: Sample 206


title: AP993215C23


title: AP993214C23


title: 35308

description: Library name: Sample 203


title: AP993212C23


title: AP993213C23


title: 35309

description: Library name: Sample 204


title: PUER cells, GCSF, OHT, 40h, Rep1

description:
Library name: m17_121_091
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 40h after the addition of OHT.


title: PUER cells, IL3, OHT, 40h, Rep3

description:
Library name: m17_121_095
RNA-seq of PUER cells 40h after the addition of OHT.


title: AP667588C23


title: 35212

description: Library name: Sample 202


title: PUER cells, GCSF, OHT, 40h, Rep2

description:
Library name: m17_121_090
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 40h after the addition of OHT.


title: PUER cells, IL3, OHT, 40h, Rep2

description:
Library name: m17_121_094
RNA-seq of PUER cells 40h after the addition of OHT.


title: AP239124E24

description: title describes sample ID used in raw data (NPX.csv)


title: 35209

description: Library name: Sample 201


title: 35208

description: Library name: Sample 200


title: AP527700C23


title: AP293435C23


title: AP547937D24


title: 35206

description: Library name: Sample 199


title: PUER cells, GCSF, OHT, 32h, Rep3

description:
Library name: m17_121_084
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 32h after the addition of OHT.


title: AP473509C23


title: PUER cells, IL3, OHT, 40h, Rep1

description:
Library name: m17_121_093
RNA-seq of PUER cells 40h after the addition of OHT.


title: AP450981D23


title: 35204

description: Library name: Sample 198


title: AP741361C23


title: AP547938D24


title: AP802490D23


title: 35202

description: Library name: Sample 197


title: AP660542E22


title: 35110

description: Library name: Sample 195


title: 35111

description: Library name: Sample 196


title: PUER cells, GCSF, OHT, 32h, Rep2

description:
Library name: m17_121_082
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 32h after the addition of OHT.


title: AP258069D23


title: PUER cells, GCSF, OHT, 32h, Rep1

description:
Library name: m17_121_083
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 32h after the addition of OHT.


title: 35103

description: Library name: Sample 194


title: AP802488D23


title: AP802489D24


title: 35101

description: Library name: Sample 193


title: PUER cells, IL3, OHT, 32h, Rep1

description:
Library name: m17_121_085
RNA-seq of PUER cells 32h after the addition of OHT.


title: AP714174C23


title: PUER cells, IL3, OHT, 32h, Rep3

description:
Library name: m17_121_087
RNA-seq of PUER cells 32h after the addition of OHT.


title: AP736676C23


title: AP802486D23


title: PUER cells, IL3, OHT, 32h, Rep2

description:
Library name: m17_121_086
RNA-seq of PUER cells 32h after the addition of OHT.


title: 35011

description: Library name: Sample 192


title: AP576105C23


title: AP714171C23


title: AP736678C23


title: AP714173C23


title: PUER cells, GCSF, OHT, 24h, Rep2

description:
Library name: m17_121_074
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 24h after the addition of OHT.


title: AP648132E22


title: AP576104C23


title: 35009

description: Library name: Sample 191


title: PUER cells, GCSF, OHT, 24h, Rep1

description:
Library name: m17_121_073
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 24h after the addition of OHT.


title: AP057943D23


title: 35006

description: Library name: Sample 190


title: PUER cells, IL3, OHT, 24h, Rep3

description:
Library name: m17_121_078
RNA-seq of PUER cells 24h after the addition of OHT.


title: AP418447C23


title: AP057941D23


title: PUER cells, IL3, OHT, 24h, Rep2

description:
Library name: m17_121_079
RNA-seq of PUER cells 24h after the addition of OHT.


title: AP705332D23


title: AP057940D24


title: 35004

description: Library name: Sample 189


title: AP057939D23


title: 35003

description: Library name: Sample 188


title: AP815886D23


title: AP815885D23


title: 35002

description: Library name: Sample 187


title: PUER cells, GCSF, OHT, 20h, Rep3

description:
Library name: m17_121_068
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 20h after the addition of OHT.


title: AP292606C23


title: 30918

description: Library name: Sample 186


title: PUER cells, GCSF, OHT, 20h, Rep1

description:
Library name: m17_121_067
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 20h after the addition of OHT.


title: 30916

description: Library name: Sample 185


title: PUER cells, IL3, OHT, 20h, Rep3

description:
Library name: m17_121_071
RNA-seq of PUER cells 20h after the addition of OHT.


title: 30914

description: Library name: Sample 184


title: AP342306D23


title: mApple_Young 4

type: genomic

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description:
207363410118_R01C01
Infinium Mouse Methylation BeadChip

hyb_protocol: 500 ng of DNA was bisulfite converted using the Zymo EZ DNA Methylation Kit. Bisulfite converted DNA was then amplified, fragmented, and hybridized to the BeadChip. Following a wash step to remove unhybridized DNA, primer extention and staining was performed.

scan_protocol: BeadChips were imaged with an Illumina iScan.

data_processing:
Analysis was conducted with SeSAMe v1.18.4.
[processed value definition] SeSAMe v1.18.4 computed beta values

label: Cy3, Cy5

molecule: genomic DNA

source_name: Liver

label_protocol: Samples were processed for methylation analysis on the Illumina Infinium Mouse Methylation BeadChip following the manufacturer’s protocol (Infinium HD Methylation Assay manual workflow).

extract_protocol: DNA was derived from whole mouse livers using the Zymo quick-DNA miniprep kit (Zymo D3024).

value: Liver

value: WT

tag: age

value: Young

value: Male

tag: strain


title: mApple_Old 4

description:
207363410118_R02C02
Infinium Mouse Methylation BeadChip

value: Old


title: Myc_Old 2

description:
207363410118_R03C01
Infinium Mouse Methylation BeadChip


title: PUER cells, IL3, OHT, 24h, Rep1

description:
Library name: m17_121_077
RNA-seq of PUER cells 24h after the addition of OHT.


title: Myc_Old 3

description:
207363410118_R04C01
Infinium Mouse Methylation BeadChip


title: Myc_Young 4

description:
207363410118_R05C01
Infinium Mouse Methylation BeadChip


title: Myc_Old 4

description:
207363410118_R06C01
Infinium Mouse Methylation BeadChip


title: mApple_Old 3

description:
207363410118_R02C01
Infinium Mouse Methylation BeadChip


title: PUER cells, IL3, OHT, 20h, Rep2

description:
Library name: m17_121_072
RNA-seq of PUER cells 20h after the addition of OHT.


title: mApple_Young 3

description:
207363410057_R06C02
Infinium Mouse Methylation BeadChip


title: PUER cells, GCSF, OHT, 20h, Rep2

description:
Library name: m17_121_065
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 20h after the addition of OHT.


title: PUER cells, GCSF, OHT, 16h, Rep3

description:
Library name: m17_121_059
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 16h after the addition of OHT.


title: Myc_Old 1

description:
207363410057_R06C01
Infinium Mouse Methylation BeadChip


title: mApple_Old 2

description:
207363410057_R05C02
Infinium Mouse Methylation BeadChip


title: mApple_Old 1

description:
207363410057_R05C01
Infinium Mouse Methylation BeadChip


title: 30901

description: Library name: Sample 180


title: Myc_Young 3

description:
207363410118_R01C02
Infinium Mouse Methylation BeadChip


title: 30911

description: Library name: Sample 182


title: PUER cells, GCSF, OHT, 16h, Rep2

description:
Library name: m17_121_060
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 16h after the addition of OHT.


title: Myc_Young 2

description:
207363410057_R04C02
Infinium Mouse Methylation BeadChip


title: 30835

description: Library name: Sample 179


title: PUER cells, IL3, OHT, 20h, Rep1

description:
Library name: m17_121_069
RNA-seq of PUER cells 20h after the addition of OHT.


title: Myc_Young 1

description:
207363410057_R03C02
Infinium Mouse Methylation BeadChip


title: PUER cells, GCSF, OHT, 16h, Rep1

description:
Library name: m17_121_057
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 16h after the addition of OHT.


title: 30902

description: Library name: Sample 181


title: young replicate 3, batch 1 (mixed line), 204375590039_R06C01

description:
204375590039_R06C01
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip

source_name: Isolated Hepatocytes

extract_protocol: Hepatocytes were isolated from young and old mice using 2-step perfusion. Hepatocytes were snap frozen and DNA was derived for analysis using the Zymo quick-DNA miniprep kit (Zymo D3024).

value: Isolated Hepatocytes

tag: batch


title: old replicate 1, batch 1 (mixed line), 204375590039_R06C02

description:
204375590039_R06C02
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: young replicate 2, batch 1 (mixed line), 204375590039_R05C02

description:
204375590039_R05C02
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: mApple_Young 2

description:
207363410057_R02C02
Infinium Mouse Methylation BeadChip


title: 30832

description: Library name: Sample 177


title: PUER cells, IL3, OHT, 16h, Rep1

description:
Library name: m17_121_061
RNA-seq of PUER cells 16h after the addition of OHT.


title: young replicate 1, batch 1 (mixed line), 204375590039_R05C01

description:
204375590039_R05C01
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: 30834

description: Library name: Sample 178


title: PUER cells, IL3, OHT, 16h, Rep3

description:
Library name: m17_121_064
RNA-seq of PUER cells 16h after the addition of OHT.


title: PUER cells, IL3, OHT, 16h, Rep2

description:
Library name: m17_121_063
RNA-seq of PUER cells 16h after the addition of OHT.


title: mApple_Young 1

description:
207363410057_R01C02
Infinium Mouse Methylation BeadChip


title: old replicate 3, batch 1 (mixed line), 204375590039_R04C01

description:
204375590039_R04C01
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: old replicate 4, batch 1 (mixed line), 204375590039_R04C02

description:
204375590039_R04C02
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: old replicate 2, batch 1 (mixed line), 204375590039_R03C01

description:
204375590039_R03C01
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: 30828

description: Library name: Sample 176


title: 30825

description: Library name: Sample 175


title: young replicate 5, batch 1 (mixed line), 204375590039_R03C02

description:
204375590039_R03C02
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: 30822

description: Library name: Sample 174


title: old replicate 1, batch 1 (mixed line), 204375590039_R02C02

description:
204375590039_R02C02
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: PUER cells, GCSF, OHT, 12h, Rep3

description:
Library name: m17_121_049
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 12h after the addition of OHT.


title: PUER cells, GCSF, OHT, 12h, Rep2

description:
Library name: m17_121_050
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 12h after the addition of OHT.


title: young replicate 3, batch 1 (mixed line), 204375590039_R02C01

description:
204375590039_R02C01
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: 30819

description: Library name: Sample 173


title: 30818

description: Library name: Sample 172


title: young replicate 2, batch 1 (mixed line), 204375590039_R01C02

description:
204375590039_R01C02
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: young replicate 1, batch 1 (mixed line), 204375590039_R01C01

description:
204375590039_R01C01
Beta_Matrix_Original.tsv
Infinium Mouse Methylation BeadChip


title: old replicate 3, batch 2 (single line), 207097260059_R05C02

description:
207097260059_R05C02
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip


title: PUER cells, IL3, OHT, 12h, Rep3

description:
Library name: m17_121_054
RNA-seq of PUER cells 12h after the addition of OHT.


title: old replicate 4, batch 2 (single line), 207097260059_R06C02

description:
207097260059_R06C02
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip


title: old replicate 1, batch 2 (single line), 207097260059_R02C02

description:
207097260059_R02C02
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip


title: PUER cells, IL3, OHT, 12h, Rep2

description:
Library name: m17_121_056
RNA-seq of PUER cells 12h after the addition of OHT.


title: old replicate 2, batch 2 (single line), 207097260059_R03C02

description:
207097260059_R03C02
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip


title: young replicate 5, batch 2 (single line), 207097260059_R04C02

description:
207097260059_R04C02
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip


title: 30810

description: Library name: Sample 171


title: 30809

description: Library name: Sample 170


title: 30806

description: Library name: Sample 168


title: PUER cells, GCSF, OHT, 8h, Rep3

description:
Library name: m17_121_043
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 8h after the addition of OHT.


title: PUER cells, GCSF, OHT, 8h, Rep2

description:
Library name: m17_121_041
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 8h after the addition of OHT.


title: PUER cells, IL3, OHT, 12h, Rep1

description:
Library name: m17_121_055
RNA-seq of PUER cells 12h after the addition of OHT.


title: 30808

description: Library name: Sample 169


title: young replicate 3, batch 2 (single line), 207097260059_R01C02

description:
207097260059_R01C02
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip


title: PUER cells, GCSF, OHT, 8h, Rep1

description:
Library name: m17_121_044
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 8h after the addition of OHT.


title: young replicate 2, batch 2 (single line), 207097260060_R01C01

description:
207097260060_R01C01
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip


title: 30804

description: Library name: Sample 166


title: 30805

description: Library name: Sample 167


title: hog1_24h_2_1

city: kunming

first: Si

last: Chen

address: Yunnan university 2th hubei road,wuhuaqu

country: China

institute: yunnan university

description: Library name: Sample 17

data_processing:
The data from high-throughput sequencing were analyzed using the Omicsmart tools, a free online platform for data analysis (www.omicsmart.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: .xlsx

molecule: total RNA

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The WT and ΔAohog1 mutant strains were incubated on PDA plates with cellophane at 28°C for 3 days. Equal amounts of nematodes were added to the induction traps, and three independent biological replicates for each mycelial sample were collected at 0, 12, and 24 h.

value: Fungal hyphae

value: Fungal hyphae cells

value: Aohog1 knockdown

value: Trap induction with nematode


title: hog1_24h_3_1

description: Library name: Sample 18


title: hog1_12h_3_1

description: Library name: Sample 15


title: hog1_24h_1_1

description: Library name: Sample 16


title: hog1_12h_2_1

description: Library name: Sample 14


title: PUER cells, IL3, OHT, 8h, Rep3

description:
Library name: m17_121_047
RNA-seq of PUER cells 8h after the addition of OHT.


title: hog1_0h_3_1

description: Library name: Sample 12

value: no treatment


title: PUER cells, IL3, OHT, 8h, Rep2

description:
Library name: m17_121_045
RNA-seq of PUER cells 8h after the addition of OHT.


title: PUER cells, IL3, OHT, 8h, Rep1

description:
Library name: m17_121_046
RNA-seq of PUER cells 8h after the addition of OHT.


title: hog1_12h_1_1

description: Library name: Sample 13


title: 30709

description: Library name: Sample 164

value: whole blood

value: SLE


title: 30705

description: Library name: Sample 162


title: 30708

description: Library name: Sample 163


title: WT_24h_1_1

description: Library name: Sample 7

value: wild type


title: PUER cells, GCSF, OHT, 4h, Rep2

description:
Library name: m17_121_034
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 4h after the addition of OHT.

value: PUER

value: bone marrow-derived progenitors

value: IL3 replaced with GCSF at -48h. Tamoxifen (OHT) added at 0h


title: WT_24h_3_1

description: Library name: Sample 9


title: 30703

description: Library name: Sample 161


title: WT_12h_2_1

description: Library name: Sample 5


title: 30913

description: Library name: Sample 183


title: 30803

description: Library name: Sample 165


title: PUER cells, GCSF, OHT, 4h, Rep1

description:
Library name: m17_121_035
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 4h after the addition of OHT.


title: 30701

description: Library name: Sample 160


title: PUER cells, IL3, OHT, 4h, Rep3

description:
Library name: m17_121_039
RNA-seq of PUER cells 4h after the addition of OHT.

value: Tamoxifen (OHT) added at 0h


title: WT_12h_1_1

description: Library name: Sample 4


title: WT_0h_2_1

description: Library name: Sample 2


title: 30608

description: Library name: Sample 159


title: WT_0h_1_1

description: Library name: Sample 1


title: 30606

description: Library name: Sample 158


title: 30605

description: Library name: Sample 157


title: Sample_72_High_Repeat_FC

city: Fontenay-aux-Roses

first: Imène

last: GARALI

address: 31 Av. de la Division Leclerc

country: France

institute: ASNR

description: Library name: Sample 72

data_processing:
Sequencing was performed at Genewiz Azenta Life Sciences (Leipzig, Germany) on a NovaSeq 6000 machine (Illumina) to generate at least 20 million reads. In this study, the sequencing coverage was limited to 20,000,000 reads per sample due to budgetary constraints, a compromise that, although cost-effective, posed challenges in achieving sufficient data coverage and accurate detection of low expression levels.
Quality control was performed on the raw FASTQ files using FastQC.
Trimming was carried out with the Trimmomatic tool.
Alignment was performed using TopHat2
Counting and normalization were conducted with StringTie (Coverage).
Assembly: The Rattus norvegicus reference genome mRatBN7.2 was used.
Supplementary files format and content: The tsv file includes coverage values for each sample.

organism: Rattus norvegicus

source_name: frontal cortex (FC)

extract_protocol:
Total RNA was extracted from cell lines of the frontal cortex using an RNAEasy Kit (Qiagen), and isolation of polyadenylated RNA (mRNA) from total RNA samples was performed with the same kit.
RNA-Sequence libraries were prepared with the TruSeq Stranded mRNA Prep Kit (Illumina, San Diego, CA, USA)

value: frontal cortex (FC)

value: Exposure to tungsten particles via inhalation

tag: concentration


title: hog1_0h_1_1

description: Library name: Sample 10


title: hog1_0h_2_1

description: Library name: Sample 11


title: v8609 Pairname L27 Pair time6wk_pair

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

description:
Library name: v8609
tpm_all_samples.csv

data_processing:
Data was mapped to the vole genome  (Microtus_ochrogaster.MicOch1.0.dna.toplevel.fa, Microtus_ochrogaster.MicOch1.0.115.gtf) and reads were counted per gene via the nfcores RNA-seq nextflow pipeline (version 3.17.0). Microtus_ochrogaster.MicOch1.0.dna.toplevel.fa, Microtus_ochrogaster.MicOch1.0.115.gtf
The dds created by the nfcores RNA-seq pipeline was read into R, and expression was normalized via both tpm and deseq2. The normlaized counts from deseq where used to look at correlation of gene expression between paired voles and previously paired voles.
Assembly: Microtus_ochrogaster.MicOch1.0.dna.toplevel.fa
Supplementary files format and content: tpm caulcated from the raw data
Supplementary files format and content: deseq2 normliazed counts for the data used in the publication

organism: Microtus ochrogaster

source_name: BRAIN nucleus accumbens

growth_protocol: Voles were bred in the University of Colorado animal facilities under standardized husbandry protocols.

extract_protocol:
Brain tissue was frozen at -80C and later the nucleus accumbens was dissected from each brain separately.
RNA purity, quantity and integrity was determined with NanoDrop (ThermoFisher Scientific) and TapeStation 4200 (Agilent) analysis prior to RNA-seq library preparation.  The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries.  Paired-end sequencing reads of 150bp was generated on NovaSeq X (Illumina) sequencer at a target depth of 80 million paired-end reads per sample.  Raw sequencing reads were de-multiplexed using bcl2fastq.

treatment_protocol: Voles were mated to a partner. Some of the voles were then separated at 2 weeks from there partner and then sacrificed. Other voles were kept with there partner for 2 weeks or 6 weeks.

value: BRAIN nucleus accumbens

tag: pair

tag: gender

value: female

tag: cohort batch


title: PUER cells, IL3, OHT, 4h, Rep1

description:
Library name: m17_121_037
RNA-seq of PUER cells 4h after the addition of OHT.


title: PUER cells, IL3, OHT, 4h, Rep2

description:
Library name: m17_121_038
RNA-seq of PUER cells 4h after the addition of OHT.


title: Sample_70_High_Repeat_FC

description: Library name: Sample 70


title: WT_24h_2_1

description: Library name: Sample 8


title: PUER cells, GCSF, OHT, 3h, Rep3

description:
Library name: m17_121_026
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 3h after the addition of OHT.


title: PUER cells, GCSF, OHT, 4h, Rep3

description:
Library name: m17_121_036
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 4h after the addition of OHT.


title: 30604

description: Library name: Sample 156


title: PUER cells, GCSF, OHT, 3h, Rep2

description:
Library name: m17_121_027
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 3h after the addition of OHT.


title: v8605 Pairname L25 Pair time4wk_sep

description:
Library name: v8605
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 30504

description: Library name: Sample 155


title: PUER cells, GCSF, OHT, 3h, Rep1

description:
Library name: m17_121_025
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 3h after the addition of OHT.


title: Sample_69_High_Repeat_FC

description: Library name: Sample 69


title: 30410

description: Library name: Sample 154


title: PUER cells, IL3, OHT, 3h, Rep3

description:
Library name: m17_121_031
RNA-seq of PUER cells 3h after the addition of OHT.


title: Sample_68_High_Repeat_FC

description: Library name: Sample 68


title: Sample_67_High_Repeat_FC

description: Library name: Sample 67


title: 30409

description: Library name: Sample 153


title: PUER cells, GCSF, OHT, 12h, Rep1

description:
Library name: m17_121_051
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 12h after the addition of OHT.


title: 30405

description: Library name: Sample 152


title: PUER cells, IL3, OHT, 3h, Rep2

description:
Library name: m17_121_030
RNA-seq of PUER cells 3h after the addition of OHT.


title: Sample_66_High_Repeat_FC

description: Library name: Sample 66


title: v8595 Pairname L20 Pair time4wk_sep

description:
Library name: v8595
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: male


title: v8593 Pairname L19 Pair time4wk_sep

description:
Library name: v8593
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: Sample_65_High_Repeat_FC

description: Library name: Sample 65


title: PUER cells, IL3, OHT, 3h, Rep1

description:
Library name: m17_121_029
RNA-seq of PUER cells 3h after the addition of OHT.


title: v8594 Pairname L22 Pair time6wk_pair

description:
Library name: v8594
tpm_all_samples.csv


title: Sample_64_Low_Repeat_FC

description: Library name: Sample 64

value: 5 mg/m3


title: 30324

description: Library name: Sample 150


title: PUER cells, GCSF, OHT, 2h, Rep2

description:
Library name: m17_121_018
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 2h after the addition of OHT.


title: PUER cells, GCSF, OHT, 2h, Rep3

description:
Library name: m17_121_020
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 2h after the addition of OHT.


title: 30403

description: Library name: Sample 151


title: v8592 Pairname L18 Pair time6wk_pair

description:
Library name: v8592
tpm_all_samples.csv


title: 30323

description: Library name: Sample 149


title: Sample_63_Low_Repeat_FC

description: Library name: Sample 63


title: v8591 Pairname L17 Pair time4wk_sep

description:
Library name: v8591
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: PUER cells, GCSF, OHT, 2h, Rep1

description:
Library name: m17_121_019
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 2h after the addition of OHT.


title: Sample_62_Low_Repeat_FC

description: Library name: Sample 62


title: 30322

description: Library name: Sample 148


title: v8590 Pairname L21 Pair time4wk_sep

description:
Library name: v8590
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 30319

description: Library name: Sample 147


title: young replicate 1, batch 2 (single line), 207097260030_R06C02

description:
207097260030_R06C02
Beta_Matrix.tsv
Infinium Mouse Methylation BeadChip

value: Isolated Hepatocytes

value: WT

tag: Sex

value: Male


title: PUER cells, IL3, OHT, 2h, Rep3

description:
Library name: m17_121_024
RNA-seq of PUER cells 2h after the addition of OHT.


title: v8588 Pairname L32 Pair time4wk_sep

description:
Library name: v8588
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 30318

description: Library name: Sample 146


title: PUER cells, IL3, OHT, 2h, Rep2

description:
Library name: m17_121_023
RNA-seq of PUER cells 2h after the addition of OHT.


title: Sample_61_Low_Repeat_FC

description: Library name: Sample 61


title: PUER cells, GCSF, OHT, 24h, Rep3

description:
Library name: m17_121_076
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 24h after the addition of OHT.


title: Sample_60_Low_Repeat_FC

description: Library name: Sample 60


title: PUER cells, IL3, OHT, 2h, Rep1

description:
Library name: m17_121_022
RNA-seq of PUER cells 2h after the addition of OHT.


title: Sample_59_Low_Repeat_FC

description: Library name: Sample 59


title: 30316

description: Library name: Sample 144


title: PUER cells, GCSF, OHT, 1h, Rep3

description:
Library name: m17_121_009
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 1h after the addition of OHT.


title: v8587 Pairname L31 Pair time4wk_sep

description:
Library name: v8587
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: v8585 Pairname L30 Pair time4wk_sep

description:
Library name: v8585
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: v8584 Pairname L24 Pair time4wk_sep

description:
Library name: v8584
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: Sample_58_Low_Repeat_FC

description: Library name: Sample 58


title: PUER cells, GCSF, OHT, 1h, Rep2

description:
Library name: m17_121_011
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 1h after the addition of OHT.


title: 30317

description: Library name: Sample 145


title: v8583 Pairname L23 Pair time4wk_sep

description:
Library name: v8583
tpm_all_samples.csv


title: Sample_57_Low_Repeat_FC

description: Library name: Sample 57


title: v8598 Pairname L28 Pair time4wk_sep

description:
Library name: v8598
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: PUER cells, GCSF, OHT, 1h, Rep1

description:
Library name: m17_121_012
RNA-seq of PUER cells 48h after replacing IL3 with GCSF and 1h after the addition of OHT.


title: PUER cells, IL3, OHT, 1h, Rep3

description:
Library name: m17_121_013
RNA-seq of PUER cells 1h after the addition of OHT.


title: Sample_56_Control_Repeat_FC

description: Library name: Sample 56

value: 0 mg/m3


title: 30311

description: Library name: Sample 142

value: whole blood


title: 30310

description: Library name: Sample 141

value: SLE


title: 30315

description: Library name: Sample 143


title: v8581 Pairname L22 Pair time6wk_pair

description:
Library name: v8581
tpm_all_samples.csv


title: v8582 Pairname L31 Pair time4wk_sep

description:
Library name: v8582
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: PUER cells, IL3, OHT, 1h, Rep2

description:
Library name: m17_121_014
RNA-seq of PUER cells 1h after the addition of OHT.


title: 30306

description: Library name: Sample 140


title: Sample_54_Control_Repeat_FC

description: Library name: Sample 54


title: v8580 Pairname L30 Pair time4wk_sep

description:
Library name: v8580
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 30305

description: Library name: Sample 139


title: PUER cells, IL3, OHT, 1h, Rep1

description:
Library name: m17_121_015
RNA-seq of PUER cells 1h after the addition of OHT.


title: Sample_53_Control_Repeat_FC

description: Library name: Sample 53


title: PUER cells, GCSF, OHT, 0h, Rep3

description:
Library name: m17_121_005
RNA-seq of PUER cells 48h after replacing IL3 with GCSF.

value: IL3 replaced with GCSF at -48h


title: v8579 Pairname L21 Pair time4wk_sep

description:
Library name: v8579
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 30304

description: Library name: Sample 138


title: Sample_52_Control_Repeat_FC

description: Library name: Sample 52


title: Sample_55_Control_Repeat_FC

description: Library name: Sample 55


title: 30303

description: Library name: Sample 137


title: v8576 Pairname L24 Pair time4wk_sep

description:
Library name: v8576
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: PUER cells, GCSF, OHT, 0h, Rep2

description:
Library name: m17_121_008
RNA-seq of PUER cells 48h after replacing IL3 with GCSF.

value: PUER


title: Sample_51_Control_Repeat_FC

description: Library name: Sample 51


title: v8575 Pairname L32 Pair time4wk_sep

description:
Library name: v8575
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 30302

description: Library name: Sample 136


title: PUER cells, IL3, no OHT, 0h, Rep3

description:
Library name: m17_121_003
RNA-seq of undifferentiated PUER cells.

value: bone marrow-derived progenitors


title: Sample_50_Control_Repeat_FC

description: Library name: Sample 50


title: 30105

description: Library name: Sample 135


title: Sample_49_Control_Repeat_FC

description: Library name: Sample 49


title: v8572 Pairname L27 Pair time6wk_pair

description:
Library name: v8572
tpm_all_samples.csv


title: PUER cells, GCSF, OHT, 0h, Rep1

description:
Library name: m17_121_007
RNA-seq of PUER cells 48h after replacing IL3 with GCSF.


title: v8571 Pairname L26 Pair time4wk_sep

description:
Library name: v8571
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: PUER cells, IL3, no OHT, 0h, Rep2

description:
Library name: m17_121_002
RNA-seq of undifferentiated PUER cells.


title: v8569 Pairname L25 Pair time4wk_sep

description:
Library name: v8569
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 30103

description: Library name: Sample 134


title: SCN9A_2544 treated L6-DRG Rep5

city: Yes

first: Wimalanathan

last: Kokulapalan

state: Massachusetts

address: 51 SLEEPER ST FL 7

department: Neuroscience Biology

institute: Atalanta Therapeutics

description: Library name: SCN9A_2544-Rep5

data_processing:
The RNA-seq data generated by Azenta was processed using the nf-core/rnaseq pipeline (v3.9).  The nf-core/rnaseq pipeline used STAR (v2.7.10a) to align RNA-seq reads to the mRatBN7.2 genome downloaded from Ensembl.  The mRatBN7.2.109 gene annotation file downloaded from Ensembl was used to count uniquely mapped reads aligned to rat transcript exons and summarized for each rat gene.  All samples passed quality control and were used for downstream differential gene expression analysis using in-house R scripts.  The scripts utilized DESeq2 (v1.44.0) package to normalize read counts and compare gene expression between PBS treated and SCN9A_2544 treated samples.  Genes with FDR adjusted p-value < 0.05 and absolute log2(fold change) > 1 were called as differentially expressed genes (DEGs).
Assembly: mRatBN7.2
Supplementary files format and content: Tab delimited file with gene_id, gene_name and raw counts for each sample in additional columns

source_name: L6 dorsal root ganglia

extract_protocol:
RNA was isolated via phenol chloroform separation followed by purification of the aqueous/ethanol fraction using an RNeasy 96 plate (Qiagen) according to standard kit protocol, using a vacuum manifold.
Library preparation was performed using the NEBNext® Ultra™ II RNA Library Prep Kit using poly(A) enrichment.  Samples were barcoded and multiplexed, and paired end 150 bp (2 x 150bp) sequencing was executed with an Illumina NovaSeq machine.

treatment_protocol: Animals were pair housed and acclimatized for 1 week prior to surgical implantation of a sterile intrathecal catheter (PE-10 tubing, Braintree Scientific) into the lumbar spinal cord (IT-L) under isoflurane anesthesia. The catheter was inserted between the L6 and S1 vertebrae and advanced rostrally 1.5 cm to approximately the level of the L4/L5 vertebrae before being secured with sutures, sealed, and buried subcutaneously to prevent damage.  Animals were given meloxicam SR (sustained release) for post-operative analgesia.  At the time of treatment, 5 days post-surgery, rats were randomly allocated to groups, dosed via the implanted IT-L catheter under brief isoflurane anesthesia, and given meloxicam SR for post-operative analgesia.  The test articles were vortexed and drawn up in a Hamilton syringe.  The catheter was accessed, opened, flushed with a small volume of saline (~10 uL) to ensure patency, and then 30-45 uL of test article was administered, followed by flushing with a small volume of additional saline (~10 uL) to account for the dead volume of the catheter, and the catheter was resealed and reburied subcutaneously.

value: L6 dorsal root ganglia

tag: timepoint

value: 14 days

value: 7-8 weeks

value: Sprague Dawley

tag: dose


title: PUER cells, IL3, no OHT, 0h, Rep1

description:
Library name: m17_121_001
RNA-seq of undifferentiated PUER cells.

tag: genotype


title: v8565 Pairname L29 Pair time4wk_sep

description:
Library name: v8565
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

tag: tissue

value: BRAIN nucleus accumbens


title: SCN9A_2544 treated L6-DRG Rep4

description: Library name: SCN9A_2544-Rep4


title: 30102

description: Library name: Sample 133


title: 29401

description: Library name: Sample 131


title: SCN9A_2544 treated L6-DRG Rep3

description: Library name: SCN9A_2544-Rep3


title: Liver, vehicle2, HFHC,16 wks

city: Nanjing

first: Mingyu

last: Sun

address: Chunhua Subdistrict,Jiangning District

institute: China Pharmaceutical University

description:
Library name: HFHC_2
Wild type, vehicle treatment

data_processing:
CLC Genomics Workbench V11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: LIVER

growth_protocol: 6-week-old wild type mice were fed with a 16-week HFHC diet, with vehicle or DDK administered during the final 4 weeks.

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1.3μg total RNA was used for the construction of suquencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufaturer's protocols.

treatment_protocol: Liver rapidly frozen in liquid nitrogen, were stored at -80°C for subsequent RNA extraction

value: LIVER

value: wild type

value: Vehicle


title: Liver, vehicle1, HFHC,16 wks

description:
Library name: HFHC_1
Wild type, vehicle treatment


title: 29302

description: Library name: Sample 130


title: SCN9A_2544 treated L6-DRG Rep2

description: Library name: SCN9A_2544-Rep2


title: v8563 Pairname L19 Pair time4wk_sep

description:
Library name: v8563
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: female


title: Liver, vehicle3, HFHC,16 wks

description:
Library name: HFHC_3
Wild type, vehicle treatment


title: v8562 Pairname L18 Pair time6wk_pair

description:
Library name: v8562
tpm_all_samples.csv


title: 29003

description: Library name: Sample 129


title: WT_12h_3_1

description: Library name: Sample 6

value: Fungal hyphae

tag: cell type

value: Fungal hyphae cells

value: Trap induction with nematode


title: Liver, DDK3, HFHC, 16 wks

description:
Library name: DDK_3
Wild type, DDK treatment

value: DDK


title: SCN9A_2544 treated L6-DRG Rep1

description: Library name: SCN9A_2544-Rep1


title: v8564 Pairname L20 Pair time4wk_sep

description:
Library name: v8564
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 29403

description: Library name: Sample 132

value: whole blood

value: SLE


title: PBS treated L6-DRG Rep5

description: Library name: PBS-Rep5

value: PBS


title: PBS treated L6-DRG Rep4

description: Library name: PBS-Rep4


title: 29002

description: Library name: Sample 128


title: v8561 Pairname L28 Pair time4wk_sep

description:
Library name: v8561
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: male


title: v8560 Pairname L17 Pair time4wk_sep

description:
Library name: v8560
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: Liver, DDK2, HFHC, 16 wks

description:
Library name: DDK_2
Wild type, DDK treatment


title: Liver, DDK1, HFHC, 16 wks

description:
Library name: DDK_1
Wild type, DDK treatment


title: PBS treated L6-DRG Rep3

description: Library name: PBS-Rep3

value: L6 dorsal root ganglia


title: v8190 Pairname L11 Pair time2wk_pair

description:
Library name: v8190
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 27218

description: Library name: Sample 127


title: 26003

description: Library name: Sample 126


title: PBS treated L6-DRG Rep1

description: Library name: PBS-Rep1

value: 14 days


title: v8188 Pairname L10 Pair time2wk_pair

description:
Library name: v8188
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: v8186 Pairname L9 Pair time2wk_pair

description:
Library name: v8186
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: v8185 Pairname L16 Pair time2wk_pair

description:
Library name: v8185
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 25406

description: Library name: Sample 124


title: PBS treated L6-DRG Rep2

description: Library name: PBS-Rep2

value: 7-8 weeks


title: v8184 Pairname L15 Pair time2wk_pair

description:
Library name: v8184
tpm_all_samples.csv


title: 25408

description: Library name: Sample 125


title: 25309

description: Library name: Sample 123


title: engulfing, rep3

description: Library name: plus_3

data_processing:
FASTQ files were generated from BCL files using Illumina bcl2fastq converter without adapter trimming.
Nf-core RNA-seq pipeline (version v1.4.2) run with Nextflow version 20.04.1
Assembly: GRCm38
Supplementary files format and content: genecounts_all.tsv: Gene-level counts; genes are rows and columns are library names

source_name: Peritoneal macrophages

extract_protocol:
RNA was isolated using the RNeasy Plus Micro isolation kit (QIAGEN) per the manufacturer’s instructions with addition of β-mercaptoethanol to RLT Plus buffer. RT-PCR was performed using the SensiFast Hi-ROX One-Step Kit (Meridian Bioscience) per the manufacturer’s instructions.
Libraries were built using the standard Kapa Biosystems library preparation kit.

value: Peritoneal macrophages

tag: group

value: engulfing


title: engulfing, rep1

description: Library name: plus_1


title: control, rep2

description: Library name: zero_2

value: control


title: v8182 Pairname L14 Pair time2wk_pair

description:
Library name: v8182
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: BRAIN nucleus accumbens


title: engulfing, rep2

description: Library name: plus_2


title: 25205

description: Library name: Sample 122


title: control, rep3

description: Library name: zero_3


title: control, rep1

description: Library name: zero_1


title: 25203

description: Library name: Sample 121


title: control_33

city: Chengdu

first: feipeng

last: jiang

address: #37 Guoxue Alley, Wuhou District, Chengdu, Sichuan Province, P.R.China

institute: west china hospital

description: Library name: sample 3

data_processing:
The reads were filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
Assembly: mRatBN7.2
Supplementary files format and content: excel file containing raw counts for each sample
Supplementary files format and content: excel file containing fpkm values for each sample

source_name: retina

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
After total RNA was extracted, 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.

treatment_protocol: The BN rats were anesthetized, and the pupils were dilated as described above. Proparacaine hydrochloride eye drops were administered for local anesthesia before further processing. A puncture on the sclera near the limbus at the medial canthus was made via a 34G microneedle under a stereomicroscope. Two microliters of DMP (10 mg/mL in H2O) or saline were then delivered into the vitreous by a Hamilton microliter syringe through the puncture. The syringe was held for 20 s before it was removed to minimize leakage. The eyes were treated with levofloxacin eye gel after all the procedures were performed to prevent infection.

value: retina

value: WT

value: Intravitreal Injection of saline


title: DMP_30

description: Library name: sample 4

value: Intravitreal Injection of DMP


title: DMP_31

description: Library name: sample 5


title: DMP_33

description: Library name: sample 6


title: v8181 Pairname L16 Pair time2wk_pair

description:
Library name: v8181
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: female


title: control_31

description: Library name: sample 2


title: non-engulfing, rep3

description: Library name: minus_3

value: non-engulfing


title: v8180 Pairname L13 Pair time2wk_pair

description:
Library name: v8180
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 25202

description: Library name: Sample 120

value: whole blood


title: non-engulfing, rep2

description: Library name: minus_2


title: 25201

description: Library name: Sample 119

value: SLE


title: control_30

description: Library name: sample 1


title: v8179 Pairname L12 Pair time2wk_pair

description:
Library name: v8179
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: non-engulfing, rep1

description: Library name: minus_1


title: v8178 Pairname L15 Pair time2wk_pair

description:
Library name: v8178
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: rMSC cultured in wave-forming nanotextured disc for 3 days under osteogenic condition

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

country: South Korea

institute: Dankook University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mRatBN7.2 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: rat bone marrow-derived stem cells (rBMSC)

growth_protocol: rat MSCs were maintained in alpha MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Ribostpin II (Geneall). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Osteogenic differentiation was induced in the cells 1 or 3 days after seeding them for 24 hours.

value: Osteogenic differentiation

tag: culture condition

value: wave-forming nanotextured titanium disc for 3 day


title: rMSC cultured in flat titanium disc for 3 days under osteogenic condition

value: rat bone marrow-derived stem cells (rBMSC)

tag: treatment

value: flat titanium disc for 3 day


title: 25102

description: Library name: Sample 118


title: rMSC cultured in wave-forming nanotextured disc for 1 day under osteogenic condition

value: wave-forming nanotextured titanium disc for 1 day


title: v8174 Pairname L9 Pair time2wk_pair

description:
Library name: v8174
tpm_all_samples.csv


title: 25026

description: Library name: Sample 116


title: v8171 Pairname L13 Pair time2wk_pair

description:
Library name: v8171
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 3dpMI-WT

city: 任何人

first: canbiao

last: wang

state: State

address: wenlan ,nanjing jiangsu

institute: nanjing normal university

description:
Library name: Sample1
10× Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: Mouse mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: heart

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: heart

tag: cell line

value: Mononuclear macrophages


title: 25025

description: Library name: Sample 115


title: rMSC cultured in flat titanium disc for 1 day under osteogenic condition

value: flat titanium disc for 1 day


title: v8173 Pairname L8 Pair time2wk_pair

description:
Library name: v8173
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: BRAIN nucleus accumbens

value: male


title: 25024

description: Library name: Sample 114


title: 25030

description: Library name: Sample 117


title: 3dpMI-CD40-KO

description:
Library name: Sample2
10× Genomics


title: sc V(D)J-seq of TCR in mouse30_liver

city: xiamen

first: Lianghua

last: Lin

state: Fujian

address: Xiang An Nan Lu 4221

institute: 生命科学学院

description: Library name: mouse30_liver_TCR

data_processing:
SeekSoul Tools was used to process raw sequencing data. Reads were aligned to the mouse reference genome (GRCm38/mm10) and gene expression matrices were generated. Cells were filtered using default cell calling algorithms to obtain the final filtered feature-barcode matrices.
Raw sequencing data were processed using the SeekSoul® Tools vdj (v1.2.1) to assemble full-length V(D)J sequences and identify CDR3 regions. Using barcode and raw clonotype ID information, productive clonotypes were filtered. Processed FASTA sequences were further annotated using IMGT database.
Assembly: mm10
Supplementary files format and content: Filtered gene-barcode matrix in MEX format, provided as three separate files per sample: barcodes.tsv.gz (cell barcodes passing filtering), features.tsv.gz (gene identifiers and names), and matrix.mtx.gz (sparse UMI count matrix). The matrix contains only cells that passed the default cell calling filters from the SeekSoul pipeline.
Supplementary files format and content: filtered_contig_annotations.csv contains high-confidence V(D)J contig annotations for each cell barcode. This file includes information such as chain type (IGH, IGK, IGL for BCR), V/D/J gene calls, CDR3 nucleotide and amino acid sequences, and productive status.
Library strategy: TCR-Seq

source_name: white nodules in liver

growth_protocol: Mice were euthanized for analysis upon observation of poor condition or obvious visible enlargement.

extract_protocol:
The harvested white nodules were preserved in tissue storage solution and sent to SeekGene for tissue dissociation. The nodules were washed in ice-cold PBS, and dissociated using SeekMate Tissue Dissociation Reagent Kit A Pro or SeekMate Tissue Dissociation Kit C from SeekGene following the manufacturer’s instructions. Samples were treated with DNase I and analyzed by Fluorescence Cell Analyzer or SeekMate Tinitan Fluorescence Cell Counter with AO/PI reagent after lysis of erythrocytes to measure cell counts and viability. Dead cells and debris were removed using Dead Cell Removal Kit. Cells were then washed twice with RPMI1640 and resuspended in RPMI1640 with 2% FBS at 1×106 cells per mL for further sorting or single cell sequencing library construction.
Single-cell V(D)J-seq libraries were constructed using SeekOne® DD Single Cell 5’ library preparation kit and SeekOne® DD Single Cell V(D)J Enrichment Kit (human TCR&BCR, SeekGene, Catalog No. K00601&K00701) or (mouse TCR&BCR, SeekGene, Catalog No. K01101&K01201) following the manufacturer’s instructions. The indexed sequencing libraries were cleaned up with VAHTS DNA Clean Beads (Vazyme, N411-01) and analyzed by Qubit (Thermo Fisher Scientific, Q33226) and Bio-Fragment Analyzer (Bioptic, Qsep400).

value: white nodules in liver

value: total cells in white nodules

value: The nodules were preserved in tissue storage solution and sent to SeekGene for tissue dissociation and then dead cell removal

tag: age

value: 14 months


title: sc V(D)J-seq of TCR in mouse32_spleen

description: Library name: mouse32_spleen_TCR

source_name: white nodules in spleen

value: white nodules in spleen

value: 12 months


title: 25017

description: Library name: Sample 113

value: whole blood

value: SLE


title: scRNA-seq of mouse30_liver

description: Library name: mouse30_liver

data_processing:
SeekSoul Tools was used to process raw sequencing data. Reads were aligned to the mouse reference genome (GRCm38/mm10) and gene expression matrices were generated. Cells were filtered using default cell calling algorithms to obtain the final filtered feature-barcode matrices.
Raw sequencing data were processed using the SeekSoul® Tools vdj (v1.2.1) to assemble full-length V(D)J sequences and identify CDR3 regions. Using barcode and raw clonotype ID information, productive clonotypes were filtered. Processed FASTA sequences were further annotated using IMGT database.
Assembly: mm10
Supplementary files format and content: Filtered gene-barcode matrix in MEX format, provided as three separate files per sample: barcodes.tsv.gz (cell barcodes passing filtering), features.tsv.gz (gene identifiers and names), and matrix.mtx.gz (sparse UMI count matrix). The matrix contains only cells that passed the default cell calling filters from the SeekSoul pipeline.
Supplementary files format and content: filtered_contig_annotations.csv contains high-confidence V(D)J contig annotations for each cell barcode. This file includes information such as chain type (IGH, IGK, IGL for BCR), V/D/J gene calls, CDR3 nucleotide and amino acid sequences, and productive status.


title: scRNA-seq of mouse32_spleen

description: Library name: mouse32_spleen


title: v8157 Pairname L11 Pair time2wk_pair

description:
Library name: v8157
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: female


title: v8168 Pairname L12 Pair time2wk_pair

description:
Library name: v8168
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: Ad5-HA-VLP_1_D7

city: Wuhan

first: YUAN

last: ZHANG

state: Hubei

address: Shizishan Street, Hongshan District, Wuhan City, Hubei Province

institute: Huazhong Agricultural University

description:
Library name: Ad5-HA-VLP-1
10× Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Lung

treatment_protocol: Following intranasal immunization with Ad5-HAPR8 or Ad5-HAPR8-VLP, lungs were harvested at 7 dpi. Lung tissues were mechanically dissociated using the gentleMACS™ Octo Dissociator (Lung_01_02 program; Miltenyi Biotec), followed by enzymatic digestion with a Lung Dissociation Kit for mice (Cat. No. 130-095-927, Miltenyi Biotec) for 30 min at 37°C. Tissues were further dissociated (gentleMACS™ Lung_02_01 program), filtered through a 40-μm nylon strainer, and subjected to red blood cell (RBC) lysis using ACK lysis buffer (Cat. No. BL503B, Biosharp). Single-cell suspensions were resuspended in ice-cold MACS® buffer (PBS + 0.5% BSA + 2 mM EDTA) and incubated with CD45 MicroBeads (Cat. No. 130-110-618, Miltenyi Biotec) for 15 min at 4°C. After washing with 2 mL MACS® buffer and centrifugation (300 ×g, 5 min), cells were filtered through a 30-μm pre-separation filter and magnetically sorted using a pre-wetted MS column on a MACS® Separator (Miltenyi Biotec). Purified cells were resuspended in 1 mL RPMI 1640 medium (Cat. No. 10-040-CVR, Corning) supplemented with 0.04% (w/v) BSA. Single-cell concentration and viability (>85% viability threshold) were quantified using the LUNA-FL™ automated cell counter (Logos Biosystems, South Korea).

value: Lung

value: immune cell


title: Sample_71_High_Repeat_FC

description: Library name: Sample 71

value: frontal cortex (FC)

value: Exposure to tungsten particles via inhalation


title: Ad5-HA-VLP_3_D7

description:
Library name: Ad5-HA-VLP-3
10× Genomics


title: sc V(D)J-seq of BCR in mouse34_LungThy

description: Library name: mouse34_LungThy_BCR

data_processing:
SeekSoul Tools was used to process raw sequencing data. Reads were aligned to the mouse reference genome (GRCm38/mm10) and gene expression matrices were generated. Cells were filtered using default cell calling algorithms to obtain the final filtered feature-barcode matrices.
Raw sequencing data were processed using the SeekSoul® Tools vdj (v1.2.1) to assemble full-length V(D)J sequences and identify CDR3 regions. Using barcode and raw clonotype ID information, productive clonotypes were filtered. Processed FASTA sequences were further annotated using IMGT database.
Assembly: mm10
Supplementary files format and content: Filtered gene-barcode matrix in MEX format, provided as three separate files per sample: barcodes.tsv.gz (cell barcodes passing filtering), features.tsv.gz (gene identifiers and names), and matrix.mtx.gz (sparse UMI count matrix). The matrix contains only cells that passed the default cell calling filters from the SeekSoul pipeline.
Supplementary files format and content: filtered_contig_annotations.csv contains high-confidence V(D)J contig annotations for each cell barcode. This file includes information such as chain type (IGH, IGK, IGL for BCR), V/D/J gene calls, CDR3 nucleotide and amino acid sequences, and productive status.
Library strategy: BCR-Seq

source_name: white nodules in lung&thymus

value: white nodules in lung&thymus

value: 9 months


title: v8156 Pairname L10 Pair time2wk_pair

description:
Library name: v8156
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: BRAIN nucleus accumbens


title: v8607 Pairname L26 Pair time4wk_sep

description:
Library name: v8607
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 25009

description: Library name: Sample 112

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

source_name: whole blood


title: WT_0h_3_1

description: Library name: Sample 3

value: Fungal hyphae

value: Fungal hyphae cells

value: wild type

value: no treatment


title: 25005

description: Library name: Sample 111


title: v8155 Pairname L2 Pair time2wk_pair

description:
Library name: v8155
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: male


title: v8153 Pairname L14 Pair time2wk_pair

description:
Library name: v8153
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: 25003

description: Library name: Sample 109


title: scRNA-seq of mouse34_LungThy

description: Library name: mouse34_LungThy

value: total cells in white nodules

value: The nodules were preserved in tissue storage solution and sent to SeekGene for tissue dissociation and then dead cell removal


title: sc V(D)J-seq of BCR in mouse27_liver

description: Library name: mouse27_liver_BCR

value: white nodules in liver

value: 12 months


title: v8148 Pairname L8 Pair time2wk_pair

description:
Library name: v8148
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

value: female


title: 25004

description: Library name: Sample 110

value: whole blood

value: SLE


title: Ad5-HA_2_D7

description:
Library name: Ad5-HA-2
10× Genomics

value: Lung

value: immune cell


title: 25002

description: Library name: Sample 108


title: v8142 Pairname L2 Pair time2wk_pair

description:
Library name: v8142
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv


title: Ad5-HA_1_D7

description:
Library name: Ad5-HA-1
10× Genomics


title: Naive_2_D0

description:
Library name: Naive-2
10× Genomics


title: sc V(D)J-seq of BCR in mouse33_thymus

description: Library name: mouse33_thymus_BCR

source_name: white nodules in thymus

value: white nodules in thymus

value: 16 months


title: scRNA-seq of mouse33_thymus

description: Library name: mouse33_thymus


city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 120 South Road

institute: University of North Carolina

description:
Library name: B4+veh
Wild-type callus line B4 treated with vehicle control

data_processing:
For transcript quantification, raw sequencing reads were pseudo-aligned to the Oryza sativa Japonica reference transcriptome (IRGSP-1.0, ENA Assembly GCA_001433935.1) using Kallisto v0.46.1. Transcript-level abundance estimates (TPM and estimated counts) were generated using default parameters.
Assembly: IRGSP-1.0 (GCA_001433935.1)
Supplementary files format and content: Each processed data file is a tab-delimited text file with five columns: target_id (transcript identifier), length (transcript length in nucleotides), eff_length (effective transcript length used in abundance estimation), est_counts (estimated number of reads assigned to each transcript), and tpm (transcripts per million, a normalized expression estimate).

organism: Oryza sativa

source_name: callus

growth_protocol: Callus was cultured from seeds. Seeds were dehusked, rinsed in 70% ethanol for 1 minute, rinsed with sterile deionized water, and  sterilized for 30 minutes in 50% bleach. After five rinses with sterile deionized water, seeds were placed on plates containing Initiation medium and incubated at 29°C under a 16 h light / 8 h dark cycle. Callus was cut from the seeds and sub-cultured onto fresh Initiation medium every 2-3 weeks.

extract_protocol:
Tissue was flash frozen in liquid nitrogen and then ground with a mortar and pestle. RNA was extracted from the ground tissue with RNAzol (Sigma, R4533). RNA quantity and quality was assessed using the Agilent 4200 Tapestation System (Agilent, G2991BA).
RNA-seq library preparation was performed by Innomics (Sunnyvale, CA, USA). Total RNA was enriched for mRNA using oligo(dT) beads, followed by fragmentation and first and second strand cDNA synthesis. Second strand synthesis incorporated dUTP to enable strand specificity. After end-repair and 3′ adenylation, adaptors were ligated, and libraries were PCR-amplified. Libraries were quality checked, circularized, and amplified into DNA nanoballs (DNBs) for sequencing. Sequencing was performed on a DNBSEQ-T7 platform (MGI Technology).

treatment_protocol: Tissue was incubated in Kimura B nutrient solution supplemented with either 5 μM BA or vehicle control for 1 hour, shaking.

tag: cultivar

value: Kitaake

value: callus

value: wild-type

value: vehicle control


title: scRNA-seq of mouse27_liver

description: Library name: mouse27_liver


title: Naive_1_D0

description:
Library name: Naive-1
10× Genomics


title: 24101

description: Library name: Sample 106


description:
Library name: B4+BA
Wild-type callus line B4 treated with BA

value: 5 μM BA


title: 24204

description: Library name: Sample 107


title: 24011

description: Library name: Sample 104


title: 24014

description: Library name: Sample 105


title: Naive_3_D0

description:
Library name: Naive-3
10× Genomics


description:
Library name: B1+BA
Wild-type callus line B1 treated with BA


title: sc V(D)J-seq of BCR in mouse31_spleen

description: Library name: mouse31_spleen_BCR

value: white nodules in spleen

value: 13 months


title: scRNA-seq of mouse31_spleen

description: Library name: mouse31_spleen

value: total cells in white nodules

value: The nodules were preserved in tissue storage solution and sent to SeekGene for tissue dissociation and then dead cell removal