title: Retina, Fbxl11-CKO1, P1, H3K36me2

value: abcam, ab9049


title: Retina, WT2, P1, H3K36me3

status: Public on Oct 13 2022

type: SRA

city: Tokyo

first: Toshiro

last: Iwagawa

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
library strategy: CUT&Tag
The sequenced reads were mapped to mouse (GENCODE GRCm38.p6) and Escherichia coli (GenBank: CP053595.1) genomes with Bowtie2 to the genomes of mouse (GENCODE GRCm38.p6) and E. coli (GenBank: CP053595.1). The mapping results were converted to BAM and BED formats using SAMtools and scaled by the number of E. coli-derived reads using bedtools. Peak calling and peak annotation were performed using SEACR and ChIPseeker, respectively.
Assembly: GRCm38
Supplementary files format and content: bedgraph files. Reads were mappend on mouse genome, and then scaled with the number of reads mapped on E. coli genome.

molecule: genomic DNA

organism: Mus musculus

source_name: retina

extract_protocol:
Control or Fbxl11-CKO retinal cells at P1 (1 x 105 cells/sample) were mixed with human colorectal cancer cell line SW480 (1 x 104 cells/sample), and resuspended in buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Nacalai Tesque), 1x Protease Inhibitor Cocktail) at 1 x 105 cells/100 μl. Concanavalin A magnetic beads (Bangs Laboratories, USA) were mixed with the cells in binding buffer  (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and rotated for 20 minutes at room temperature. Then, the cells were resuspended in 100 μl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Nacalai Tesque), 1x Protease Inhibitor Cocktail, 0.05% Digitonin (Millipore), 2 mM EDTA, and 0.1% bovine serum albumin) containing antibodies listed below at 10 μg/mL and rotated overnight at 4℃. The cells were washed and resuspended in 100 μl Dig-wash Buffer containing 10 μg/ml anti-rabbit IgG antibody (Rockland Immunochemicals, USA, 611-201-122), rotated for 1 hr at room temperature, and resuspended in Dig-300 Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 1x Protease Inhibitor Cocktail) containing 0.8 μl pAG-Tn5 adapter complex and rotated for 1 hr at room temperature. The cells were washed with Dig-300 Buffer three times, resuspended in 100 μl Tagmentation Buffer (Dig-300 Buffer containing 10 mM MgCl2), and incubated for 1 hr at 37℃. Then 2 μl of 10 mg/mL Proteinase K was added and further incubated at 37℃ for 30 min. DNA was purified by Phenol-Chloroform protocol and dissolved in 25 μl water.
The DNA was subjected to PCR (72℃ (5 mins) x 1, 98℃ (30 sec) x 1, 98℃ (10 sec)/ 63℃ (15 sec) x 17, 72℃ (1 min) x 1) using i5 and i7 primers and Q5 High-Fidelity 2x Master Mix (New England Biolabs, USA). The library was sequenced with Novaseq6000.

tag: tissue

value: retina

tag: time

tag: antibody

value: abcam, ab9050

tag: genotype

value: WT


title: HS360-Day20-rep2 [sc2d20-ctrl scRNA-seq]

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

library_source: transcriptomic

data_processing:
mkfastq was perfomed using standard settings. cellRanger-count was used to remove and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
cellranger-3.1.0 -count was used to generate single cell feature counts for a single library,  cellranger count  run was performed with the following arguments --expect-cells for each timepoint
cellRanger-count was used to remove and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
run cellranger aggr to aggregate multiple GEM wells from a single experiment that were analyzed by cellranger count and down stream analysis was perfomed using  R programming languages and its package  Seurat version 4
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: Cell ranger count output: filtered count matrix, barcodes and features.

molecule: total RNA

organism: Homo sapiens

source_name: HS360, day 20, past stage III maturation

growth_protocol: Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.

extract_protocol:
Cells were harvested using Accutase, counted and processed on the 10x Chromium controller (10x Genomics). Approximately 2,300 cells were loaded per channel on the Chromium Chip B (10x Genomics) to give an estimated recovery of 1,400 cells.
The Chromium Single Cell 3´ Library & Gel Bead Kit v3 (10x Genomics) and Chromium i7 Multiplex Kit (10x Genomics) were used to generate scRNA-seq libraries.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. At Day 13, cells were collected for passaging into the maturation phase, counted and seeded on precoated PO+F+Geltrex 12 well dishes and Stage III Neural maturation medium (NMM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 0.5% B27, 10 ng/ml FGF2, 10 ng/ml EGF) was changed daily till Day 20, where cells were collected.

tag: source cell line/type

value: Human embryonic stem cells HS360

tag: time point

value: Day 20

tag: gender

value: male

tag: tissue/cell type

value: maturated NPCs


title: 1_Exp1_1_Veh+Veh

city: Corvallis

first: Andrey

last: Morgun

state: Oregon

address: Pharmacy Building, 1601 SW Jefferson Way

department: College of Pharmacy

country: USA

institute: Oregon State University

data_processing:
RNA libraries were prepared with the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System and sequenced using Illumina NextSeq.
The sequences were processed to remove the adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/) using bbduk parameters of k=13, ktrim=r, forcetrimleft=12, useshortkmers=t, mink=5, qtrim=r, trimq=15, minlength=20.
The reads were aligned to the human genome and transcriptome (Gencode v40) using STAR v2.5.3a.
The number of reads per million for cells were counted using HTSeq (v 0.6.0)
Assembly: The human genome and transcriptome (Gencode v40) were used for assembly
Supplementary files format and content: text file of relativized per million reads

source_name: LX2 cell line

growth_protocol: LX2 cells were obtained from SL Friedman (Mount Sani Medical School) (46). LX2 cells are activated human hepatic stellate cells; they were maintained in DMEM with 10% FCS containing penicillin and streptomycin. Cells were plated onto 100 mm plastic petri dishes ∼100,000 cells/plate and treated with fatty acids (at 50 μM) in endotoxin-free BSA (at 20 μM) during the growth phase. Fatty acids [oleic acid (18:1 ω9) and DHA (22:6, ω3); Nu-Chek Prep] were used at 50 μM for 2- 48-hour cycle treatments.

extract_protocol:
RNA was extracted from cell lysates using the RNeasy Mini Kit and subjected to a DNase treatment according to manufacturer's protocols (Qiagen) then stored at -80 ºC until further use.
mRNA libraries were prepared for sequencing with the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) HT for Illumina Sequencing platforms (Kit#k15.384) and sequenced on the Illumina NextSeq at Oregon State University.

treatment_protocol: After this pre-treatment, cells were trypsinized, washed in PBS, counted and plated at 3000 cells/well in a 96-well plate. Cells were fed DMEM with 1 % FCS without or with betacellulin (human recombinant betacellulin (BTC), R&D Systems) and with or without fatty acids at 50 After this pre-treatment, cells were trypsinized, washed in PBS, counted and plated at 3000 cells/well in a 96-well plate. Cells were fed DMEM with 1 % FCS without or with betacellulin (human recombinant betacellulin (BTC), R&D Systems) at 50 μM for 72 hrs. Cells were then seeded onto 6-well plates at 40,000 cells/well; and cells were treated with fatty acids for 96 hrsAfterward, media was removed, and cells were  treated without and with BTC at 20 ng/ml for 72 hrs.

tag: cell line

tag: group

value: Veh+Veh

tag: sample number

tag: cohort

tag: treatment

value: DMEM and 1% FCS


title: 2_Exp1_2_Veh+BTC

value: Veh+BTC

value: DMEM and 1% FCS and 20 ng/ML BTC for 72 hours


title: P1290LO

type: genomic

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

hyb_protocol: DNA extraction and Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Molecular Genomics Core of Norris Cancer Center at University of Southern California.

data_processing: For all analyses, probes were removed in minfi if: they had a detection P-value<0.01; were cross-reactive; contained a SNP at the single base extension or CpG interrogation site at any MAF; were not present in a CpG context; were present on either sex chromosome. Given the cancer-related nature of some of the datasets analyzed, we also assessed probes in SeSAMe. Probes that failed under default parameters were also removed prior to analysis. For all analyses, DMRs were generated using DMRcate on beta values. A comparison of DMRs across conditions was then carried out by setting lambda=1000 and minimum CpGs=7.

label: Cy3, Cy5

source_name: Colon Organoid

label_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

growth_protocol: Normal 3D colon organoids included in the study were developed from biopsies of distal colon using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol: Genomic DNA was extracted using the Qiagen UCP DNA kit (Catalog No: 56204; Qiagen; Hilden, Germany) with few exceptions. For elution, a 5 minute final incubation of Buffer AUE was preferred to increase yield. Further, the elution step was carried out twice using two volumes of 25μl. DNA quality was assessed using gel electrophoresis to ensure that DNA was not heavily fragmented.

tag: Sex

value: M

tag: age

tag: smoking

value: Current

tag: phenotype

value: CTL


title: HS360-Day20-rep1 [sc1d20-ctrl scRNA-seq]


title: Retina, WT2, P1, IgG

tag: tissue

value: Cell Signaling, 2729S


title: IgMposX7posX12pos rep5

city: Bellinzona

first: Mathilde

last: Foglierini

address: Via Vincenzo Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Raw sequences reads were trimmed to remove adapter contamination and poor-quality base calls using Trim Galore v0.6.4.
Transcript abundance was quantified using Salmon v1.2.1 and  the Ensembl human transcriptome build GRCh38 v97 was used as reference.
For further analysis Salmon output was imported into R (version 4.0.2) using the Bioconductor R package tximport.
Differential expression calling was performed with the package DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts (by DESeq2) for every gene and every sample

source_name: lymphoma B cells

growth_protocol: VAL and DOHH2 cells were stained with Ab anti IgM and anti-ACKR3 anti-human Ab at 4°C for 15 min. Cells were washed 2x in MACS Buffer and sorted for IgM+ ACKR3+ and IgM- ACKR3- (only ACKR3 marker for DOHH2 cells. Cells were kept in culture for 2 days in RPMI Complete Medium.

extract_protocol:
RNA was extracted with Zymo column RNA Isolation kit (Cat. R1050)
NEB (NewEnglandBiolab)E7765L NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads and E7490L NEBNext® Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: At day 3, cells were stimulated with 300 nM of chimera chemokine CXCL11_12 (APC) for 4 hours or CXCL12 (647) and sorted for 647 positivity or negativity.

value: VAL

tag: clone

value: positive

tag: igm

tag: cell type

value: lymphoma


title: HS360-Day13-rep2 [sc2d13-ctrl scRNA-seq]

source_name: HS360, day 13, past stage II self-patterning

tag: source cell line/type

value: Day 13

value: self-patterning NPCs


title: HS360-Day7-rep5 [5-d7-ctr-1 methylation array]

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip v-1-0_B3 using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan System using standard recommended Illumina scanner settings

data_processing:
R software, Minfi package v 1.36.0m Background correction was performed using NOOB method and β values were normalized using functional normalization. Probes with detection p values >0.01 (n = 12538) and cross-reactive probes (n = 42844) were removed, resulting in a final data set consisting of 810477
meth_unmeth_detP.txt: Unmethylated and methylated signal intensities
rgSet_Neurodiff.Rdata: Minfi object with all data except control probes, removed due to data sensitivity.

label: cy3, cy5

source_name: HS360, day 7, past stage I neural induction

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from cultured cells using Norgen RNA/DNA purification kit according to the manufacturer's instructions

value: Human embryonic stem cells HS360

tag: time point

value: Day 7

value: neural rosettes, neural induction


title: HS360-Day7-rep6 [6-d7-ctr-2 methylation array]

tag: gender

value: male


title: IgMposX7posX12pos rep4

tag: genotype


title: Retina, WT1, P1, IgG

value: retina

tag: time

tag: antibody

value: WT


title: HS360-Day13-rep1 [sc1d13-ctrl scRNA-seq]

tag: tissue/cell type


title: Retina, WT1, P1, H3K36me2

value: abcam, ab9049


title: IgMposX7posX12pos rep3

tag: cell line


title: IgMposX7posX12pos rep2


title: KO_1

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description:
RNA libraries
MSC_PDGFRa_KO_74

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

molecule: polyA RNA

source_name: Mesenteric adipose tissue

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

value: Mesenteric adipose tissue

value: Stromal cell

tag: library type

value: mRNA


title: KO_2

description:
RNA libraries
MSC_PDGFRa_KO_80


title: HS360-Day7-rep1 [sc1d7-ctrl scRNA-seq]


title: WT_3

description:
RNA libraries
MSC_PDGFRa_WT_76


title: IgMposX7posX12pos rep1


title: HS360-Day0-rep2 [sc2d0-ctrl scRNA-seq]

source_name: HS360, day 0, hESCs undifferentiated

value: Day 0

value: hESCs


title: HS360-Day7-rep2 [sc2d7-ctrl scRNA-seq]


title: IgMposX7posX11-12pos rep4

value: VAL


title: HS360-Day0-rep1 [sc1d0-ctrl scRNA-seq]


title: WT_2

description:
RNA libraries
MSC_PDGFRa_WT_75


title: HS360-Day0-rep5 [1-d0-1 methylation array]


title: WT_1

description:
RNA libraries
MSC_PDGFRa_WT_73


title: HS360-Day0-rep6 [2-d0-2 methylation array]


title: IgMposX7posX11-12pos rep3

value: positive


title: IgMposX7posX11-12pos rep2

value: lymphoma


title: HS360-Day20-rep4 [29-sc2-D20-ctrl-B]

data_processing:
BBDuk (BBMap v. 34.56) was used to reomve and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
Reads were mapped to the human genome/transcriptome ENSEMBL GRCh38.p5 release 83 using hisat2 v2.1.0
FeatureCounts v.1.4.6-p1 was used to count the reads mapping to the features using default configurations
Downstream normalisation and differential expression analysis was performed using R software DEseq2 package v 1.30.1.
Genome_build: ENSEMBL GRCh38.p5 release 83 (genome-build-accession NCBI:GCA_000001405.20)
Supplementary_files_format_and_content: Count files with data matrix with unnormalized counts for each sample. Additionaly, "normcounts.control.csv" contains a normalized count matrix for all samples.

extract_protocol:
Total RNA was extracted from cultured cells using Norgen RNA/DNA purification kit or Qiagen RNeasy kit and treated with DNase according to manufacturer´s instructions.
Illumina TruSeq Stranded mRNA Library Prep kit was used to contruct the sequencing library according to manufacturer´s instructions. Libraries were sequenced on an Illumina Novaseq 6000 S1 flow cell with 100bp pair end reads.

value: Day 20

value: maturated NPCs


title: Trp/Trp renal F4/80+, biol rep 3 [Trp_Trp_3]

city: Nashville

last: Alexander

state: TN

address: 1211 Medical Center Drive

institute: Vanderbilt University Medical Center

data_processing:
Read alignment was performed with the mouse mm10 genome using a STAR based aligner and the Illumina DRAGEN RNA pipeline.
Assembly: mm10
Supplementary files format and content: tab-delimited files after analysis from DeSeq2

source_name: renal F4/80+ macrophages

extract_protocol:
Kidneys isolated from mice after 4 weeks of Ang II infusion were stored in RNALater and homogenized in Trizol (Invitrogen) reagent using a rotor homogenizer. Separate kidneys underwent Percoll gradient ultracentrifugation followed by isolation of F4/80+ cells using anti-F4/80 microbeads (Miltenyi). Cell pellets were lysed and stored in Trizol. RNA isolation was performed using chloroform and isopropyl alcohol according to the Trizol manufacturer’s instructions.
cDNA library preparation was performed using a polyA-selected library preparation kit (New England Biolabs).

value: renal F4/80+ macrophages

value: Trp/Trp


title: Trp/Trp renal F4/80+, biol rep 2 [Trp_Trp_2]


title: IgMposX7posX11-12pos rep1


title: HS360-Day20-rep5 [186-D20-Ctr-A methylation array]

value: Human embryonic stem cells HS360


title: HS360-Day20-rep6 [187-D20-Ctr-B methylation array]

value: male


title: HS360-Day20-rep3 [28-sc1-D20-ctrl-B]


title: Trp/Trp renal F4/80+, biol rep 1 [Trp_Trp_1]


title: IgMposX7pos rep5


title: IgMposX7posX11-12pos rep5


title: HS360-Day20-rep2 [13-sc2-D20-ctrl-A]


title: Arg/Arg renal F4/80+, biol rep 3 [Arg_Arg_3]

value: Arg/Arg


title: HS360-Day20-rep1 [12-sc1-D20-ctrl-A]


title: Arg/Arg renal F4/80+, biol rep 2 [Arg_Arg_2]


title: 8_Exp2_2_Veh+BTC

tag: group

value: Veh+BTC

tag: sample number

tag: cohort

tag: treatment

value: DMEM and 1% FCS and 20 ng/ML BTC for 72 hours


title: HS360-Day13-rep4 [26-sc2-D13-ctrl-B]

value: Day 13

value: self-patterning NPCs


title: Arg/Arg renal F4/80+, biol rep 1 [Arg_Arg_1]


title: IgMposX7pos rep3

tag: phenotype


title: HS360-Day13-rep3 [25-sc1-D13-ctrl-B]


title: IgMposX7pos rep2

tag: clone


title: Trp/Trp kidney, biol rep 3 [TT_3]

source_name: Kidney

tag: tissue

value: Kidney


title: Trp/Trp kidney, biol rep 2 [TT_2]


title: HLOs, 72_3, GCKR:CC, day 25, biol rep2 [KIM52_1]

city: Cincinnati

first: Kentaro

last: Iwasawa

state: OH

address: 3333 BURNET AVENUE

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Samples were sequenced with 150bp pair-end sequencing at a depth of 20M reads per sample by Novogene. Inc.
Clean data were generated from the raw data that was filtered by data-processing steps, including removal of adapter sequences, reads with more than 10% N, and low-quality sequences (the percentage of low-quality bases of quality value ≤ 5 is greater than 50% in a read)
Trimmed sequence reads were mapped hg19 using Computational Suite for Bioinformaticians and Biologists version 3.0 (CSBB-v3.0, https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists) to obtain raw transcript counts.
The trimmed mean of M-values (TMM) normalized Log2 Counts-per-Million (CPM) values were obtained and analyzed for differential expression with the interactive Gene Expression Analysis Kit (Choi and Ratner, 2019)
Assembly: GRCh37/hg19
Supplementary files format and content: comma-separated values files include CPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Over 1.7 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

tag: cell type

value: Human Liver Organoids

value: No treatment

value: Day 25


title: HS360-Day20-rep4 [29-sc2-D20-ctrl-B methylation array]

tag: source cell line/type


title: HS360-Day20-rep3 [28-sc1-D20-ctrl-B methylation array]

tag: time point


title: HS360-Day13-rep1 [10-sc1-D13-ctrl-A]

tag: gender


title: IgMmin-X7neg rep5

value: VAL

tag: genotype

value: negative

tag: igm


title: Trp/Trp kidney, biol rep 1 [TT_1]


title: HS360-Day20-rep2 [13-sc2-D20-ctrl-A methylation array]

value: Day 20


title: IgMmin-X7neg rep4

value: lymphoma


title: HS360-Day20-rep1 [12-sc1-D20-ctrl-A methylation array]

value: maturated NPCs


title: HLOs, 285, GCKR:CC, day 25, biol rep2 [KIM42_1]

tag: time


title: HLOs, 72_3, GCKR:CC, day 25, biol rep1 [KIM51_1]


title: HS360-Day7-rep6 [151-D7-ctrl-B]

value: Day 7

tag: tissue/cell type

value: neural rosettes, neural induction


title: HS360-Day7-rep5 [150-D7-ctrl-A]

value: Human embryonic stem cells HS360

value: male


title: HS360-Day13-rep2 [11-sc2-D13-ctrl-A]


title: Arg/Arg kidney, biol rep 2 [AA_2]

value: Arg/Arg


title: HS360-Day13-rep1 [10-sc1-D13-ctrl-A methylation array]


title: IgMmin-X7neg rep3

tag: cell line


title: IgMposX7pos rep1

value: positive


title: Arg/Arg kidney, biol rep 3 [AA_3]


title: HS360-Day7-rep4 [248-D7-CTRL]


title: HLOs, 285, GCKR:CC, day 25, biol rep1 [KIM41_1]


title: HLOs, HPSI0314, GCKR:CC, day 25, biol rep2 [KIM32_1]


title: IgMmin-X7neg rep1


title: Arg/Arg kidney, biol rep 1 [AA_1]


title: HLOs, HPSI0314, GCKR:CC, day 25, biol rep1 [KIM31_1]


title: HS360-Day7-rep3 [20-sc1-D7-ctrl-B]


title: Single-cell training high-fat diet rep4 [TH4.SM]

city: Boston

first: Jiekun

last: Yang

address: 32 Vassar Street

institute: MIT

data_processing:
Gene count matrices for each single-cell sample were generated by aligning reads to the mm10 genome (refdata-gex-mm10-2020-A) using 10X Genomics Cell Ranger software v4.0.0.
For each sample, we removed ambient RNA contamination using SoupX with a fixed contamination fraction of 20%.
We then excluded low-quality cells using four quality control (QC) metrics: (i) number of genes with non-zero expression fewer than 500; (ii) number of UMIs fewer than 200 or more than 6000; (iii) percentage of reads mapping to mitochondrial genes more than 10; and (iv) number of reads mapped to Mki67 more than 0.
We removed potential cell doublets using DoubletFinder with default parameters and 3.1% homotypic doublet proportion estimation based on statistics published by 10X Genomics.
Next we integrated all the 41 samples across three tissues together for an atlas, and samples belonging to a single tissue together for tissue-specific maps. Integration was done without any batch correction using Seurat v3.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object saved in R qs format for all the 204,883 cells included in the atlas

source_name: skeletal muscle (triceps)

extract_protocol:
Fresh tissues were enzymatically digested and dissociated according to tissue dissociation kit protocols (adipose tissue Cat No 130-105-808, skeletal muscle Cat No 130-098-305 by Miltenyi) using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS and immediately processed for the generation of single-cell RNA (scRNA) libraries using the droplet-based RNA sequencing technology.
Briefly, 5000-6000 cells were profiled per sample using the Chromium Single Cell 3’ RNA reagent kit v3 according to the 10X Genomics protocol.

treatment_protocol: Mice were separated into standard vs. high-fat diet groups (10% vs. 60% Kcal fat ad libitum, weeks 0-6) and each group was further separated into sedentary and training by voluntary wheel running (weeks 3-6). Tissue collection was done following a 6-hour fast and a 24-hour exercise wash-out done by locking of the wheels.

tag: strain

value: skeletal muscle (triceps)

tag: age

value: 12-week old

value: 6-week high-fat-diet and 3-week training interventions


title: IgMmin-X7neg rep2


title: HLOs, CR12, GCKR:TT, day 25, biol rep2 [KIM22_1]

value: Human Liver Organoids


title: HS360-Day7-rep4 [248-D7-CTRL methylation array]


title: DOHH2-X7pos rep5


title: HS360-Day7-rep2 [5-sc2-D7-ctrl-A]


title: Single-cell training high-fat diet rep3 [TH3.SM]


title: DOHH2-X7pos rep4


title: HLOs, CR12, GCKR:TT, day 25, biol rep1 [KIM21_1]

value: No treatment


title: Single-cell training high-fat diet rep2 [TH2.SM]


title: DOHH2-X7pos rep3


title: HS360-Day7-rep1 [4-sc1-D7-ctrl-A]


title: HS360-Day0-rep5 [19-sc2-D0-ctrl-B]

value: Day 0

value: hESCs


title: HS360-Day0-rep3 [3-sc2-D0-ctrl-A methylation array]


title: HS360-Day7-rep2 [5-sc2-D7-ctrl-A methylation array]


title: HS360-Day0-rep4 [18-sc1-D0-ctrl-C]


title: HS360-Day0-rep1 [1-sc1-D0-ctrl-A methylation array]


title: HLOs, 1383D6, GCKR:TT, day 25, biol rep2 [KIM12_1]

value: Day 25


title: HS360-Day0-rep3 [3-sc2-D0-ctrl-A]


title: DOHH2-X7pos rep2

value: negative


title: HS360-Day7-rep3 [20-sc1-D7-ctrl-B methylation array]


title: DOHH2-X7neg rep5

value: lymphoma


title: DOHH2-X7pos rep1


title: HS360-Day0-rep2 [2-sc1-D0-ctrl-B]


title: Single-cell sedentary high-fat diet rep2 [SH2.SM]

value: 6-week high-fat-diet and 3-week sedentary interventions


title: HLOs, 1383D6, GCKR:TT, day 25, biol rep1 [KIM11_1]


title: Single-cell training high-fat diet rep1 [TH1.SM]


title: Single-cell sedentary high-fat diet rep1 [SH1.SM]


title: DOHH2-X7neg rep3


title: Colon Organoid, P1291

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d) and RSEM (v1.3.1).
Briefly, 100bp paired-end reads were trimmed and aligned to the GENCODE reference transcriptome using STAR and reads were quantified using HT-Seq. Gene counts were generated for each sample and collated into a singular matrix for fixed-effects regression model in DESeq2.
Assembly: GrCh38, GENCODE release 29
Supplementary files format and content: "Pheno.csv" contains sample metadata, "counts.csv" contains raw counts, "SummaryStats.csv" contains the number and percentages of reads mapped for each sample

growth_protocol: Normal 3D colon organoids included in the study were developed from distal colon biopsies of either distal using a modification of the method described by Sato et al. After isolation, colon crypts were embedded in Matrigel, and cell lines were established in growth media that included: advanced DMEM/F-12, 100U/ml penicillin, 100μg/ml streptomycin, 10mM Hepes, 1x N2, 1x B27, 2mM GlutaMAX, 1mM N-acetyl-cysteine, 10mM gastrin, 50% L-WRN conditioned media, 500nM A83-01, 10uM SB202190, 10mM nicotinamide, 50ng/ml EGF, 10μM Y27632. Colon organoids were grown and passaged as needed in 48-well culture plates.

extract_protocol:
For RNA isolation, media was gently removed and 300μl RNA lysis Solution RA1 + 6μl TCEP (Machery-Nagel; Cat No: 740902.50) was added to each well. The lysate was collected in a 1.5ml Eppendorf tube. Each tube was vortexed vigorously and placed on ice. Further steps were carried out according to manufacturer’s protocol of the Machel-Nagel RNA XS kit. RNA was checked for quality using the Agilent 4200 Tapestation. Samples with RIN > =8.5 were considered for library preparation and sequencing using the Illumina NovoSeq
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II). Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.
Libraries were multiplexed and sequenced on Illumina Novaseq6000 to generate 100bp PE reads.

value: Colon Organoid

tag: Sex

value: FAP

value: Left colon

tag: smoking

value: Never


title: DOHH2-X7neg rep4


title: Single-cell training standard (chow) diet rep3 [TC3.SM]

tag: treatment

value: 6-week chow-diet and 3-week training interventions


title: HS360-Day13-rep2 [11-sc2-D13-ctrl-A methylation array]

value: Human embryonic stem cells HS360

value: Day 13

value: male

value: self-patterning NPCs


title: HS360-Day13-rep4 [26-sc2-D13-ctrl-B methylation array]


title: Pomc Cre IP 4

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

country: Germany

institute: Max Planck Institute for Metabolism Research

description:
pomc_ip_4
3 mice pooled
pomc_deseq.csv
pomc_counts.csv

data_processing:
After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System), transcriptome libraries were pooled. The pool was quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on an Illumina HiSeq 4000 sequencing instrument with a 2 × 100-bp paired-end read length protocol.
We applied the community-curated nfcore rnaseq analysis pipeline (version 1.4) (https://nf-co.re/ rnaseq).
The gene-level quantification was carried out using Salmon (version 0.14.1) using the reference genome GRCm38
Differential analysis between ribosomal pulldown (IP) and the hypothalamic background (Input) using differential gene expression analysis with the DESeq2 R package 1.26.0
Assembly: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary files format and content: DESeq2 contrasts IP vs Input for Glp1r, Pomc and Agrp
Supplementary files format and content: Salmon counts

source_name: Hypothalamic cells expressing Pomc

extract_protocol:
Affinity purification of translating ribosomes was performed as described by Heiman et al. (https://doi.org/10.1038/nprot.2014.085) with minor modifications. The hypothalamus was rapidly dissected using a stainless steel brain matrix (World Precision Instruments) and immediately snap frozen in liquid nitrogen until translating ribosome affinity purification (TRAP). Protein A Dynabeads (375µl per IP; Invitrogen) were washed three times and subsequently resuspended in 275µl 0.15 M KCl wash buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 150 mM KCl, 1% NP40, 0.5 mM DTT and 100µg/ml cycloheximide). Next, 50µg of two anti-GFP antibodies (HtzGFP-19F7 and Htz-GFP-19C8, Memorial Sloan Kettering Monoclonal Antibody Facility) were added to the beads respectively and incubated with slow end-over-end mixing at 4◦C overnight. Then, Protein A Dynabeads were washed three times and resuspended in 200µl wash buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 150 mM KCl, 1% NP40, 0.5 mM DTT and 200µg/ml cycloheximide). Pooled hypothalamic tissue (4 mice pooled for each Glp1rCre ROSA26lSlEGFPL10a replicate, 4 replicates; 3 mice pooled for each POMCCre ROSA26lSlEGFPL10a replicate, 4 replicates; 3 mice pooled for each AGRPCre ROSA26lSlEGFPL10a replicate, 3 replicates) was homogenized in lysis buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 150 mM KCl, 0.5 mM DTT, 40 U/ml RNasin, 100µg/ml cycloheximide, protease inhibitor cocktails [1 tablet of cOmplete mini EDTA-free protease inhibitor cocktail/10 mL]) 2 times at 250 rpm, and 9 times at 750 rpm on a rotating glass/teflon potter homogenizer (Potter S, Braun) at 4◦C. Homogenates were transferred to low binding microcentrifuge tubes (Nonstick, RNase-free microfuge tubes, 1.5 ml, Ambion, Invitrogen) and centrifuged at 2,000xg for 10 min at 4◦C. The supernatant was transferred to a new microcentrifuge tube on ice and NP-40 (Applichem) and 1,2-diheptanoyl-sn-glycero3-phosphocholine (DHPC; Avanti Polar Lipids) were added to the supernatant at a final concentration of 1% and 30 mM, respectively. After incubation on ice for 5 min, the clarified lysate was centrifuged at 17,000xg for 10 min at 4◦C. The supernatant was transferred to a new tube on ice and a 30µl aliquot was snap frozen in liquid nitrogen until RNA extraction as input sample. Then, 200µl of anti-GFP antibody-coated Protein A magnetic beads were added to the supernatant and incubated at 4◦C with end-over-end rotation for 1h. Next, beads were collected with a magnet and subsequently washed four times with 0.35 M KCl wash buffer (20 mM HEPES [pH 7.4], 5 mM MgCl2, 350 mM KCl, 1% NP40, 0.5 mM DTT, 100µg/ml cycloheximide). After the final wash the beads were collected with a magnet and the supernatant was removed. Input and IP beads were resuspended and incubated in RLT buffer (RNeasy Micro Kit, QIAGEN) for 5 mins at RT. RNA was purified subsequently using the RNeasy Micro Kit (QIAGEN). RNA integrity was assessed using an Agilent 2100 bioanalyzer.
Pre-amplification was performed using the Ovation RNA-seq system (V2). Total RNA was used for first-strand cDNA synthesis, using both poly(T) and random primers, followed by second-strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input.

treatment_protocol: 10 weeks old male Glp1rCre ROSA26lSlEGFPL10a mice, 12 weeks old POMCCre ROSA26lSlEGFPL10a and 12 weeks old AGRPCre ROSA26lSlEGFPL10a were sacrificed in a random-fed state. The ROSA26lSlEGFPL10a (ROSA26-CAGS-lox-STOP-lox-EGFPL10a-WPRE) mouse line was generated by breeding ROSA26lSlrSrEGFPL10a (ROSA26-CAGS-lox-STOP-lox-roxSTOP-rox-EGFPL10a-WPRE) 7 with a ubiquitously expressed CAGGS-Dre deleter line. Glp1rCre ROSA26lSlEGFPL10a mice were generated via mating homozygous Glp1r-ires-Cre mice to homozygous ROSA26fl/fl mice of the EGFPL10a construct. A similar breeding strategy was used for the POMCCre and AgrpCre ROSA26lSlEGFPL10a mice. Resulting double transgenic Cre+/- ROSA26fl/wt mice were used as experimental animals.

value: Hypothalamic cells expressing Pomc

value: PomcCre+/- ROSA26lSlrSrEGFPL10a+/-

value: random-fed state

value: 12 weeks


title: HS360-Day13-rep3 [25-sc1-D13-ctrl-B methylation array]


title: DOHH2-X7neg rep2

tag: phenotype


title: Single-cell training standard (chow) diet rep2 [TC2.SM]

value: skeletal muscle (triceps)

value: 12-week old


title: Colon Organoid, P1284

value: female


title: Colon Organoid, P1261


title: Single-cell training standard (chow) diet rep1 [TC1.SM]


title: DOHH2-X7neg rep1

tag: clone

value: negative

value: lymphoma


title: HS360-Day0-rep2 [2-sc1-D0-ctrl-B methylation array]

value: Day 0

value: hESCs


title: Colon Organoid, P1229

value: Colon Organoid

value: Healthy

tag: tissue

value: Left colon

value: Never


title: Pomc Cre IP 3

description:
pomc_ip_3
3 mice pooled
pomc_deseq.csv
pomc_counts.csv

tag: cell type


title: HS360-Day0-rep1 [1-sc1-D0-ctrl-A]

tag: source cell line/type

value: Human embryonic stem cells HS360

value: male


title: Pomc Cre IP 1

description:
pomc_ip_1
3 mice pooled
pomc_deseq.csv
pomc_counts.csv

value: Hypothalamic cells expressing Pomc


title: Pomc Cre IP 2

description:
pomc_ip_2
3 mice pooled
pomc_deseq.csv
pomc_counts.csv

value: PomcCre+/- ROSA26lSlrSrEGFPL10a+/-


title: D02-X7pos rep4

value: VAL

value: IgMmut

value: positive


title: D02-X7pos rep5


title: Pomc Cre Input 4

description:
pomc_input_4
3 mice pooled
pomc_deseq.csv
pomc_counts.csv

source_name: Hypothalamus

value: Hypothalamus

value: Hypothalamic cells

value: random-fed state

value: 12 weeks


title: Single-cell training standard (chow) diet rep4 [TC4.SM]

value: skeletal muscle (triceps)

value: 12-week old

value: 6-week chow-diet and 3-week training interventions


title: HS360-Day7-rep1 [4-sc1-D7-ctrl-A methylation array]

tag: time point

value: Day 7

value: neural rosettes, neural induction


title: HS360-Day0-rep4 [18-sc1-D0-ctrl-C methylation array]

value: Day 0

tag: gender

value: hESCs


title: Single-cell sedentary standard (chow) diet rep2 [SC2.SM]

value: 6-week chow-diet and 3-week sedentary interventions


title: Colon Organoid, P1228

value: Colon Organoid

value: female

value: FAP

value: Left colon

value: Never


title: Colon Organoid, P1236

value: male

value: Healthy


title: Single-cell sedentary high-fat diet rep3 [SH3.SM]

value: 6-week high-fat-diet and 3-week sedentary interventions


title: Single-cell sedentary standard (chow) diet rep3 [SC3.SM]


title: Single-cell sedentary standard (chow) diet rep1 [SC1.SM]


title: D02-X7pos rep2

value: VAL

tag: genotype

value: IgMmut

value: positive

value: lymphoma


title: Single-cell training high-fat diet rep4 [TH4.vWAT]

source_name: visceral white adipose tissue

value: visceral white adipose tissue

value: 12-week old

value: 6-week high-fat-diet and 3-week training interventions


title: Colon Organoid, P1210


title: D02-X7pos rep1

tag: igm


title: Pomc Cre Input 2

description:
pomc_input_2
3 mice pooled
pomc_deseq.csv
pomc_counts.csv

value: Hypothalamus

value: Hypothalamic cells

value: PomcCre+/- ROSA26lSlrSrEGFPL10a+/-

value: random-fed state

value: 12 weeks


title: Colon Organoid, P1179

value: Colon Organoid

value: female

value: Left colon

value: Current


title: IgMposX7pos rep4


title: Single-cell training high-fat diet rep3 [TH3.vWAT]


title: Colon Organoid, P1169

value: male

value: FAP

value: Never


title: Pomc Cre Input 1

description:
pomc_input_1
3 mice pooled
pomc_deseq.csv
pomc_counts.csv


title: D02-X7neg rep5

value: VAL

value: IgMmut

value: negative


title: D02-X7neg rep4

value: lymphoma


title: Colon Organoid, P1164


title: Single-cell training high-fat diet rep2 [TH2.vWAT]

value: visceral white adipose tissue

value: 12-week old

value: 6-week high-fat-diet and 3-week training interventions


title: Glp1r Cre IP 4

description:
glp1r_ip_4
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv

source_name: Hypothalamic cells expressing Glp1r

value: Hypothalamic cells expressing Glp1r

value: Glp1rCre+/- ROSA26lSlrSrEGFPL10a+/-

value: 10 weeks


title: Single-cell training high-fat diet rep1 [TH1.vWAT]


title: Glp1r Cre IP 3

description:
glp1r_ip_3
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv

value: random-fed state


title: D02-X7neg rep3


title: Colon Organoid, P1112

value: Colon Organoid

value: female

value: Healthy


title: Glp1r Cre IP 2

description:
glp1r_ip_2
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv


title: Pomc Cre Input 3

description:
pomc_input_3
3 mice pooled
pomc_deseq.csv
pomc_counts.csv

value: Hypothalamus

value: Hypothalamic cells

value: PomcCre+/- ROSA26lSlrSrEGFPL10a+/-

value: 12 weeks


title: Single-cell sedentary high-fat diet rep2 [SH2.vWAT]

value: 6-week high-fat-diet and 3-week sedentary interventions


title: Colon Organoid, P1074

value: male

value: Left colon

value: Former


title: Single-cell sedentary high-fat diet rep3 [SH3.vWAT]

value: visceral white adipose tissue

value: 12-week old


title: Glp1r Cre IP 1

description:
glp1r_ip_1
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv

value: Hypothalamic cells expressing Glp1r


title: D02-X7neg rep1

value: VAL

value: IgMmut

value: negative

value: lymphoma


title: D02-X7neg rep2


title: Glp1r Cre Input 4

description:
glp1r_input_4
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv

value: Glp1rCre+/- ROSA26lSlrSrEGFPL10a+/-

value: random-fed state

value: 10 weeks


title: D02-X7pos rep3

value: positive


title: Colon Organoid, P1055

value: Colon Organoid

value: female

value: Healthy

value: Never


title: surgically resected tumor 928_2

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

data_processing:
10x Space Ranger v5.1.0
R Seurat processing - normalization, integration, clustering
Genome_build: GRCh38
Supplementary_files_format_and_content: gene counts matrix
Supplementary_files_format_and_content: cell-level metadata

source_name: surgically resected tumor

extract_protocol:
Tumor resected as part of standard clinical care
10x Visium Fresh Frozen

value: surgically resected tumor

tag: diagnosis

value: ependymoma PFA subgroup

tag: age at time of surgery (years)


title: Single-cell sedentary high-fat diet rep1 [SH1.vWAT]

value: visceral white adipose tissue

value: 6-week high-fat-diet and 3-week sedentary interventions


title: C2-B1-X7pos rep4

tag: cell line


title: Single-cell training standard (chow) diet rep4 [TC4.vWAT ]

tag: strain

value: 12-week old

value: 6-week chow-diet and 3-week training interventions


title: surgically resected tumor 1513


title: Single-cell training standard (chow) diet rep2 [TC2.vWAT]

tag: age


title: Glp1r Cre Input 3

description:
glp1r_input_3
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv

value: Hypothalamus

value: Hypothalamic cells


title: surgically resected tumor 1239


title: C2-B1-X7pos rep2

value: VAL

value: IgMmut

value: lymphoma


title: surgically resected tumor 928


title: C2-B1-X7pos rep3


title: C2-B1-X7pos rep1


title: Single-cell training standard (chow) diet rep1 [TC1.vWAT]


title: surgically resected tumor 1269


title: Agrp Cre IP 4

description:
agrp_ip_4
3 mice pooled
agrp_deseq.csv
agrp_counts.csv

source_name: Hypothalamic cells expressing Agrp

value: Hypothalamic cells expressing Agrp

value: AgrpCre+/- ROSA26lSlrSrEGFPL10a+/-

value: random-fed state

value: 12 weeks


title: Glp1r Cre Input 1

description:
glp1r_input_1
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv

value: Glp1rCre+/- ROSA26lSlrSrEGFPL10a+/-

value: 10 weeks


title: C2-B1-X7neg rep5

value: negative


title: Single-cell sedentary standard (chow) diet rep3 [SC3.vWAT]

value: 6-week chow-diet and 3-week sedentary interventions


title: Agrp Cre IP 3

description:
agrp_ip_3
3 mice pooled
agrp_deseq.csv
agrp_counts.csv


title: surgically resected tumor 1101

value: surgically resected tumor

value: ependymoma PFA subgroup


title: Single-cell sedentary standard (chow) diet rep2 [SC2.vWAT]

value: visceral white adipose tissue

value: 12-week old


title: C2-B1-X7pos rep5

value: positive


title: Agrp Cre IP 2

description:
agrp_ip_2
3 mice pooled
agrp_deseq.csv
agrp_counts.csv


title: Agrp Cre IP 1

description:
agrp_ip_1
3 mice pooled
agrp_deseq.csv
agrp_counts.csv


title: C2-B1-X7neg rep4


title: C2-B1-X7neg rep3


title: surgically resected tumor 821


title: Agrp Cre Input 4

description:
agrp_input_4
3 mice pooled
agrp_deseq.csv
agrp_counts.csv

value: Hypothalamus

value: Hypothalamic cells


title: Glp1r Cre Input 2

description:
glp1r_input_2
4 mice pooled
glp1r_deseq.csv
glp1r_counts.csv


title: C2-B1-X7neg rep2

value: VAL

value: IgMmut


title: Single-cell training high-fat diet rep4 [TH4.scWAT]

source_name: subcutaneous white adipose tissue

value: subcutaneous white adipose tissue

value: 6-week high-fat-diet and 3-week training interventions


title: Single-cell sedentary standard (chow) diet rep1 [SC1.vWAT]


title: surgically resected tumor 723_2


title: Single-cell training standard (chow) diet rep3 [TC3.vWAT]

value: 6-week chow-diet and 3-week training interventions


title: Single-cell training high-fat diet rep3 [TH3.scWAT]


title: C2-B1-X7neg rep1

value: lymphoma


title: Agrp Cre Input 3

description:
agrp_input_3
3 mice pooled
agrp_deseq.csv
agrp_counts.csv

value: AgrpCre+/- ROSA26lSlrSrEGFPL10a+/-

value: random-fed state

value: 12 weeks


title: Single-cell training high-fat diet rep2 [TH2.scWAT]


title: C2-A1-X7pos rep5


title: Agrp Cre Input 1

description:
agrp_input_1
3 mice pooled
agrp_deseq.csv
agrp_counts.csv


title: Single-cell training high-fat diet rep1 [TH1.scWAT]


title: Agrp Cre Input 2

description:
agrp_input_2
3 mice pooled
agrp_deseq.csv
agrp_counts.csv


title: surgically resected tumor 812


title: C2-A1-X7pos rep4


title: Single-cell sedentary high-fat diet rep3 [SH3.scWAT]

value: 6-week high-fat-diet and 3-week sedentary interventions


title: surgically resected tumor 848

value: surgically resected tumor


title: surgically resected tumor 727

value: ependymoma PFA subgroup


title: surgically resected tumor 723


title: Single-cell sedentary high-fat diet rep2 [SH2.scWAT]


title: C2-A1-X7pos rep3


title: GFP_Leftovers-2

city: Los Angeles

first: Xia

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1
Assembly: Rnor_6.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Cultured olfactory ensheathing cells

growth_protocol: Olfactory bulbs were collected from 8-10 weeks old GFP-labeled Sprague-Dawley rats. The first two layers of the olfactory bulb were dissected, isolated, and then washed in Hank’s Balanced Salt Solution (HBSS, Gibco, Rockville, MD) prior to tissue centrifugation at 365 g for 5 min. The tissue pellet was resuspended in 0.1% trypsin and HBSS without Ca2+/Mg2+ (Gibco, Rockville, MD), then placed in a 37°C water bath, and mixed intermittently for 10 min. A mixture of 1:1 DMEM and Ham’s F12 (D/F medium, Gibco) supplemented with 10-15% Fetal Bovine Serum (FBS, Hyclone, Logan, UT) and 1% Penicillin/Streptomycin (P/S, Gibco; D/F-FBS-P/S medium) was used to inactivate trypsin prior to centrifugation. Dissociated cells were rinsed, centrifuged 3 times, and plated into 12.5 cm2 culture flasks pre-coated with 0.05mg/ml poly-L-lysine (PLL, Sigma, St. Louis, MO). Cells were maintained at 37°C for 5-8 days and D/F-FBS-P/S medium was changed every 2 days.

extract_protocol:
Flasks with purified OECs and leftover cells were rinsed with HBSS and dissociated with trypsin-EDTA as above. Cells were washed in D/F-FBS-P/S medium and further resuspended with silconized pipettes. Media and cells were washed and centrifuged at 365 g for 10 min, and resuspended. After the final wash, cells for sequencing were resuspended in PBS+BSA in volumes of 1200 cells/µL. 4 flasks of cells (2 purified OECs and 2 ‘leftovers’) were generated on each of 2 different culture dates for scRNA-seq, yielding 8 samples in total (4 purified OECs and 4 ‘leftovers’). Extra cells from the same preparation were plated on PLL-coated coverslips in 24-well plates with 500µL D/F-FBS-P/S medium changed after 2 days. Cells were cultured for 3 days, fixed in cold 4% paraformaldehyde for 20 min, washed 3X with PB and stored in PB with 0.06% sodium azide.
scRNA-seq was performed using the 10X Genomics Chromium scRNA-seq system which incorporates microfluidic capture-based encapsulation, barcoding, and library preparation (10X Genomics, Pleasanton, CA). About 10,000 cells per OEC or leftover preparation were loaded into a Chromium Chip B along with partitioning oil, reverse transcription reagents, and a mix of hydrogel beads containing 3,500,000 unique 10X barcodes.

treatment_protocol: Immunopurification was carried out using hydrophobic petri dishes coated overnight with Biotin-SP-conjugated AffiniPure goat anti-rabbit IgG (1:1000; Jackson ImmunoResearch, West Grove, PA) in 50 mM Tris buffer at 4°C followed by another overnight incubation at 4°C with either mouse anti-nerve growth factor receptorp75 for rat OECs (anti-NGFRp75, 1:5, clone 192, Chandler et al., 1984)  in 25mM PBS. Dishes were rinsed 3 times with 25mM PBS and treated with a mixture of PBS and 0.5% BSA for 1 h at room temperature. Prior to the addition of cells, antibody-treated dishes were washed with PBS and DMEM. Two pairs of adult rat olfactory bulbs were dissociated with 0.25% trypsin-EDTA at 37°C for 3 mins and D/F-FBS-P/S medium was added to inactivate trypsin. Following a medium rinse and centrifugation, resuspended cells were seeded onto pre-treated mouse or rabbit anti-p75-NGFR petri dishes and incubated at 37°C for 10 mins. Unbound rat cells were removed with medium and saved as ‘leftover’ control cells for the single cell sequencing. A cell scraper was used to recover bound cells that were then subjected to a second round of immunopanning in which purified cells from 2 rats were combined yielding 2 samples of each condition, i.e. purified p75-NGFR-positive rat OECs and ‘leftover” control cells. All cells for sequencing were replated into PLL-coated flasks. Immunopurified p75-NGFR-positive mouse OECs were plated on PLL-coated 4-chamber polystrene-vessel culture slides (BD Falcon, San Jose, CA). Purified OECs and ‘leftover’ controls were incubated at 37°C with 5% CO2 for 7-8 days in D/F-FBS-P/S medium supplemented with pituitary extract (20 μg/ml, Gibco) and forskolin (2 μM, Sigma). Media was changed every 2 days and mitogens were withdrawn 2 days prior to use.

value: Sprague-Dawley

value: Cultured olfactory ensheathing cells

value: female


title: C2-A1-X7pos rep2

value: positive


title: surgically resected tumor 459


title: GFP_Leftovers-1

description: 10x Genomics


title: C2-A1-X7pos rep1


title: Primary liver cancer single-cell S035

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

data_processing:
Basecalling perormed by RTA.
Demultiplexing performed by Bcl2fastq.
Alignment, tagging, gene and transcript counting performed CellRanger.
Aggregation performed by CellRanger.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1) cell barcodes (barcodes.tsv) 2) genes (genes.tsv), 3) count matrix (matrix.mtx), and 4) cell information (Info.txt)

source_name: Primary liver cancer single-cell

extract_protocol: Cryopreserved samples were thawed and prepared according to the Single Cell 5' Reagent Kits User Guide. Specifically, the samples were washed and re-suspended in PBS + 0.04% BSA. Cell viability was determined. The cDNAs was obtained after the GEM generation and barcoding, followed by GEM RT reaction. Purified cDNA was amplified for 14 cycles. A clean up using SPRIselect beads was performed. cDNA libraries were prepared with 10x Genomics Single Cell 5’ library & gel bead kit v1.1. cDNA concentration was determined by Bioanalyzer.

tag: cancer type

value: Hepatocellular carcinoma

tag: tissue type

value: Tumor core


title: Single-cell sedentary high-fat diet rep1 [SH1.scWAT]

value: 12-week old

tag: treatment


title: GFP_OEC-1

description: 10x Genomics


title: GFP_OEC-2

description: 10x Genomics


title: Single-cell training standard (chow) diet rep4 [TC4.scWAT]

value: subcutaneous white adipose tissue


title: C2-A1-X7neg rep5

source_name: lymphoma B cells

tag: phenotype

value: VAL

value: IgMmut

value: negative


title: surgically resected tumor 459_2


title: C2-A1-X7neg rep4

tag: clone

value: lymphoma


title: Single-cell training standard (chow) diet rep3 [TC3.scWAT]

tag: tissue

value: 6-week chow-diet and 3-week training interventions


title: Leftovers-2

description: 10x Genomics

tag: cell type


title: Leftovers-1

description: 10x Genomics


title: Primary liver cancer single-cell S034


title: Primary liver cancer single-cell S032

value: Intrahepatic cholangiocarcinoma

value: Adjacent non-tumor tissue


title: Single-cell training standard (chow) diet rep2 [TC2.scWAT]


title: Single-cell training standard (chow) diet rep1 [TC1.scWAT]


title: C2-A1-X7neg rep3


title: C2-A1-X7neg rep2


title: OEC-2

description: 10x Genomics


title: Primary liver cancer single-cell S031

value: Tumor border


title: Single-cell sedentary standard (chow) diet rep3 [SC3.scWAT]

value: 6-week chow-diet and 3-week sedentary interventions


title: Primary liver cancer single-cell S030


title: OEC-1

description: 10x Genomics

value: Sprague-Dawley


title: C2-A1-X7neg rep1


title: Feijin4

city: Changsha

first: Kailin

state: Hunan

address: Xueshi Road No. 300

country: China

institute: Hunan University of Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as  differentially expressed.

source_name: Brain tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
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, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Brain tissue

value: Sprague-Dawley rats

value: MCAO/R model + Bundled and electroacupuncture at Tianfu acupoint, Chize acupoint, Kongzui acupoint and Taiyuan acupoint


title: Primary liver cancer single-cell S029

value: Hepatocellular carcinoma


title: ACKR3-WT rep5

value: wt


title: Single-cell sedentary standard (chow) diet rep2 [SC2.scWAT]

value: 12-week old


title: Primary liver cancer single-cell S028

value: Tumor core


title: Primary liver cancer single-cell S027


title: Single-cell sedentary standard (chow) diet rep1 [SC1.scWAT]

value: subcutaneous white adipose tissue


title: ACKR3-WT rep4

value: VAL


title: Feijin3


title: ACKR3-WT rep3


title: Primary liver cancer single-cell S026


title: 6090-RB-0032

city: Birmingham

first: Ravi

last: Bhatia

state: AL

address: 2555A North Pavilion, 1802 6th Avenue South

department: Division of hematology and oncology

institute: The university of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.20 was used for basecalling
Raw sequence FASTQ reads were trimmed using Trim Galore! version 0.6.5 using parameters --paried --trim1
Trimmed sequence FASTQ reads were aligned using STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from alignments using HTSeq-count version 0.11.2 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
Raw read counts were normalized followed by differential expression using DESeq2 version 1.26.0 using the default parameters in their vignette
Genome_build: Gencode GRCm38 p6 Release M24
Supplementary_files_format_and_content: tab delimited Excel file of raw counts for each gene in each sample

source_name: Bone marrow cells

extract_protocol:
RNA was extracted from BM LSK and GMP cells using RNeasy Plus Micro kit (Qiagen, Valencia, CA) with four biological replicates per group
Libraries were prepared using SMARTer Ultra Low Input RNA Kits for Sequencing (v4, TaKaRa Clontech) and Nextera XT DNA Library Preparation Kit (Illumina). Sequencing was performed by HudsonAlpha Discovery Biosciences using the Novaseq 6000 Sequencing System, S4 flow cell, using paired end sequencing with 150bp reads

value: FACS sorted LSK

value: Combination


title: ACKR3-WT rep2

value: lymphoma


title: Feijin1


title: 6090-RB-0031


title: Primary liver cancer single-cell S025


title: ACKR3-WT rep1


title: Model4

value: MCAO/R model + Bundled with the same degree and duration during the intervention, without electroacupuncture intervention


title: Model3


title: ACKR3-KO rep5


title: 6090-RB-0029


title: Primary liver cancer single-cell S023


title: Primary liver cancer single-cell S022


title: ACKR3-KO rep4


title: Primary liver cancer single-cell S021

value: Adjacent non-tumor tissue


title: ACKR3-KO rep3


title: Control4

value: Bundled with the same degree and duration during the intervention, without electroacupuncture intervention


title: 6090-RB-0028


title: 6090-RB-0027


title: Feijin2


title: 6090-RB-0026


title: ACKR3-KO rep2


title: 6090-RB-0025


title: Primary liver cancer single-cell S020

value: Tumor border


title: Control3


title: Primary liver cancer single-cell S019


title: 6090-RB-0030


title: Control2


title: Control1


title: Primary liver cancer single-cell S018


title: 6090-RB-0024


title: ACKR3-KO rep1


title: Model2


title: Primary liver cancer single-cell S024


title: 6090-RB-0023


title: Primary liver cancer single-cell S017


title: Model1


title: Primary liver cancer single-cell S016


title: 6090-RB-0021


title: SCZ-16p11.2 duplication 3, 7WIV iEN, Sample B

city: Chicago

first: Peter

last: Penzes

state: IL

address: 303 E. Chicago ave

department: Neuroscience

institute: Northwestern University

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC. Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered. The reads were also filtered if they aligned to rat (rn6).
The cleaned reads were aligned to the human (hg38) genome using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file (Ensembl).
Normalization and differential expression were determined using DESeq2
Assembly: Human (hg38)
Supplementary files format and content: Processed files = Total compiled read counts with control vs duplication statistics (Isogenic_WT_vs_DUP_Differential_Expression.xlsx, Patient_WT_vs_DUP_Differential_Expression.xlsx)
Supplementary files format and content: Deseq normalized counts (Patient_deseq_norm_counts_annotated.csv, Isogenic_deseq_norm_counts_annotated.csv)

source_name: SCZ  with 16p11.2 Duplication Patient 3

growth_protocol: iEN induction was performed as previously reported (PMID: 23764284). using lentivirus generated with rtTA (Addgene #20342) and Ngn2 constructs (FUW-TetO-Ngn2-P2A-puromycin, Addgene #52047). 1 day following plating, medium was changed to Neurobasal “complete” (Neurobasal medium (Gibco, #21103049), supplemented with GlutaMAX™ Supplement (1X, Gibco, #35050061), B27 (1X, Gibco, #17504044), N-2 (1X, Gibco, #17502048), MEM Non-Essential Amino Acids Solution (1X, Gibco, #11140050), BDNF, GDNF and NT3 (10 ug/ml) and Doxycycline (3 μg/mL, Stemgent, #04-2016). DIV2-3 medium contained puromycin (2 µg/mL, Gibco, #A11138-03). Cells were cryopreserved at DIV4. PDL pre-coated coverslips (Neuvitro Corporation, GG-18-15-PDL) were coated with laminin (ThermoFisher #23017015, 1 μg/mL) for one hour. Astrocytes were seeded at 75k cells per well (24 well) or 150k (12 well) and grown to confluency for 1-2 days. Induced neurons were seeded at 60,000 per cm2 area of coverslip. Cells were fed 3x weekly by a half medium change for 2 weeks before doxycycline retraction.

extract_protocol:
Total RNA extraction was performed as per manufacturer’s instructions using the mirVANA miRNA isolation kit (Thermofisher, #AM1560)
The Illumina TruSeq Stranded Total RNA Library Preparation Kit was used to prepare sequencing libraries from 100 ng of total RNA samples
RNA-SEQ (lllumina HiSeq 4000 Sequencer was used to sequence the libraries with the production of single-end, 50 bp reads at the sequencing depth of at least 20-25 million reads per sample).

treatment_protocol: Neuronal differentiation (all samples)

value: iPSC

value: 16p11.2 Duplication

value: Directed differentiation into cortical excitatory neurons


title: SCZ-16p11.2 duplication 2, 7WIV iEN, Sample B

source_name: SCZ  with 16p11.2 Duplication Patient 2


title: Primary liver cancer single-cell S015


title: SCZ-16p11.2 duplication 2, 7WIV iEN, Sample A


title: 6090-RB-0019

value: Vehicle


title: Primary liver cancer single-cell S013

value: Hepatocellular carcinoma


title: 6090-RB-0018


title: Primary liver cancer single-cell S012


title: Primary liver cancer single-cell S011

value: Intrahepatic cholangiocarcinoma


title: SCZ-16p11.2 duplication 1, 7WIV iEN, Sample B

source_name: SCZ  with 16p11.2 Duplication Patient 1


title: 6090-RB-0022


title: 6090-RB-0016

value: FACS sorted GMP


title: SCZ-16p11.2 duplication 1, 7WIV iEN, Sample A


title: SCZ-16p11.2 duplication 3, 7WIV iEN, Sample A


title: Healthy individual control 3, 7WIV iEN, Sample B

source_name: Healthy Individual 3

value: Control


title: Primary liver cancer single-cell S010

value: Tumor core


title: Primary liver cancer single-cell S014


title: 6090-RB-0020


title: Healthy individual control 3, 7WIV iEN, Sample A


title: 6090-RB-0014


title: HF73 cells_IHSF115 and HS_ replicate 4

type: RNA

city: Madrid

first: Nuria

last: Vilaboa

state: Madrid

address: Edificio IdiPAZ segunda planta, Hospital Universitario La Paz, Paseo de la Castellana 261

country: Spain

institute: Fundación para la Investigación Hospital La Paz, G83727057

hyb_protocol: Biotinylated cRNA was hybridized with GeneChip Human Gene 2.0 ST Array (Applied Biosystems), following the manufacturer´s instructions.

scan_protocol: Arrays were scanned with a GeneChip scanner 3000 7G (Applied Biosystems).

data_processing: Raw data were normalized and gene levels analyzed using the RMA algorithm (Transcriptome Analysis Console Software; Applied Biosystems).

label: biotin

source_name: HF73 cells incubated at 37C for 2h with 25mM IHSF115, then heat treated at 43C for 30min and  further incubated at 37C for 1h

label_protocol: Total RNA was processed using the GeneChip WT PLUS Reagent kit (Applied Biosystems, Waltham, MA).

growth_protocol: Cells were maintained in a humidified 5% CO2 atmosphere at 37ºC. Hela cells were cultured in Dulbecco’s modified Eagle’s medium (Lonza, Basel, Switzerland) supplemented with 10%(v/v) fetal bovine serum, 10U/ml penicillin and 0.01mg/ml streptomycin. HSF2-deficient cell line HF73 was prepared by transfection of HeLa cells with equal amounts of the three plasmids of the human HSF2 sgRNA CRISPR/Cas9 All-in-One Lentivector set of Applied Biological Materials.Transfections employed Lipofectamine reagent (Invitrogen). Cell line HF73 was isolated after selection with 1.3mg/ml puromycin. HF73 cells were cultured in  Dulbecco’s modified Eagle’s medium supplemented with 10%(v/v) fetal bovine serum, 10U/ml penicillin, 0.01mg/ml streptomycin and 1.3mg/ml puromycin.

extract_protocol: Total RNA prepared using the RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Samples C1,2,3-HeLa and C1,2,3,4,5-HF73  were prepared from cells incubated at 37ºC for 3.5h with 0.25% DMSO. Samples H1,2,3-HeLa and  H1,2,3,4,5-HF73  were prepared from cells incubated at 37ºC for 2 h with 0.25% DMSO, then heat treated at 43ºC for 30min in a water bath and further incubated at 37ºC for 1h.  Samples HT1,2,3-HeLa and  HT1,2,3,4,5-HF73  were prepared from cells incubated at 37ºC for 2 h with 25 mM IHSF115, then heat treated at 43ºC for 30min in a waterbath and further incubated at 37ºC for 1h.

value: HF73 cells


title: Healthy individual control 2, 7WIV iEN, Sample B

source_name: Healthy Individual 2


title: HF73 cells_IHSF115 and HS_ replicate 3


title: HF73 cells_IHSF115 and HS_ replicate 1


title: 6090-RB-0017

value: FACS sorted LSK


title: Primary liver cancer single-cell S008


title: HF73 cells_DMSO and HS_ replicate 2

source_name: HF73 cells incubated at 37C for 2h with 0.25% DMSO, then heat treated at 43C for 30min and  further incubated at 37C for 1h


title: Healthy individual control 2, 7WIV iEN, Sample A


title: 6090-RB-0013

value: Combination


title: HF73 cells_IHSF115 and HS_ replicate 5


title: Primary liver cancer single-cell S009


title: HF73 cells_IHSF115 and HS_ replicate 2


title: Primary liver cancer single-cell S007


title: Healthy individual control 1, 7WIV iEN, Sample A

source_name: Healthy Individual 1


title: HF73 cells_DMSO and HS_ replicate 4


title: Primary liver cancer single-cell S006


title: Healthy individual control 1, 7WIV iEN, Sample B


title: 6090-RB-0015


title: HF73 cells_DMSO_ replicate 5

source_name: HF73 cells incubated at 37C for 3.5h with 0.25% DMSO


title: HF73 cells_DMSO and HS_ replicate 3


title: 6090-RB-0011


title: HF73 cells_DMSO and HS_ replicate 1


title: HF73 cells_DMSO and HS_ replicate 5


title: HF73 cells_DMSO_ replicate 4


title: Primary liver cancer single-cell S005


title: Primary liver cancer single-cell S003


title: Primary liver cancer single-cell S004


title: HF73 cells_DMSO_ replicate 3


title: Isogenic 16p11.2 duplication, 7WIV iEN, clone 2, Sample B

source_name: Isogenic 16p11.2 duplication Clone 2


title: Isogenic 16p11.2 duplication, 7WIV iEN, clone 2, Sample A


title: 6090-RB-0008


title: 6090-RB-0012


title: 6090-RB-0009


title: 6090-RB-0007


title: Primary liver cancer single-cell S002


title: HF73 cells_DMSO_ replicate 2


title: Isogenic 16p11.2 duplication, 7WIV iEN, clone 1, Sample B

source_name: Isogenic 16p11.2 duplication Clone 1


title: HF73 cells_DMSO_ replicate 1


title: 6090-RB-0006


title: Primary liver cancer single-cell S001


title: Hela cells_IHSF115 and HS_ replicate 2

source_name: HeLa cells incubated at 37C for 2h with 25mM IHSF115, then heat treated at 43C for 30min and  further incubated at 37C for 1h

value: HeLa cells (ATCC CCL-2)


title: Isogenic 16p11.2 duplication, 7WIV iEN, clone 1 , Sample A


title: Hela cells_IHSF115 and HS_ replicate 3


title: 6090-RB-0010


title: P-limited T. erythraeum under acidified condition - rep2

city: Eilat

first: Futing

last: Zhang

address: Interuniversity Institute for Marine Sciences, Eilat, P.O.B 469

country: Israel

description:
treated with 750 µatm pCO2 (acidified)
LP_800B

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were filtered by removing low quality reads and reads containing adapter and ploy-N, and calculated Q20, Q30 and GC content, and then mapped to whole genome using bowtie v2-2.2.3.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM), were calculated using a protocol from (Trapnell, Cole, et al., 2010).
Genome_build: NC_008312.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Trichodesmium erythraeum IMS101

source_name: Trichodesmium cells

growth_protocol: T. erythraeum cells were grown in Aquil-tricho medium at 27 ℃ and ~80 μmol photons m-2 s-1 (14 h:10 h light-dark cycle) in algae chamber. The cells were first semi-continuously cultured at low phosphorus under two pCO2 levels (400 µatm and 750  µatm) for more than one year, and then were grown in continuous chemostat cultures under steady-state phosphate-limited conditions for at least five generations prior to sampling for RNA-Seq.

extract_protocol:
Total RNA was extracted using TRIzol Reagent. Genomic DNA was removed thoroughly by treating with RNAase-free DNase I. Ribosomal RNA was removed from a total amount of 3 µg RNA using Ribo-zero kit (Illumina). Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit.
Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations.

treatment_protocol: Three replicates were treated with low phosphorus and 400 µatm pCO2 (LP_400); three replicates were treated with low phosphorus and 750 µatm pCO2 (LP_800)

value: acidified


title: P-limited T. erythraeum under acidified condition - rep3

institute: Interuniversity Institute for Marine Sciences

description:
treated with 750 µatm pCO2 (acidified)
LP_800C


title: Isogenic control, 7WIV iEN, clone 2, Sample B

source_name: Isogenic Control Clone 2


title: 6090-RB-0005


title: Isogenic control, 7WIV iEN, clone 2, Sample C


title: 6090-RB-0004


title: Isogenic 16p11.2 duplication, 7WIV iEN, clone 1, Sample C


title: Isogenic control, 7WIV iEN, clone 2, Sample A


title: P-limited T. erythraeum under acidified condition - rep1

description:
treated with 750 µatm pCO2 (acidified)
LP_800A


title: P-limited T. erythraeum under ambient condition - rep3

description:
treated with 400 µatm pCO2 (ambient)
LP_400C

value: ambient


title: 6090-RB-0003


title: P-limited T. erythraeum under ambient condition - rep2

description:
treated with 400 µatm pCO2 (ambient)
LP_400B


title: Isogenic control, 7WIV iEN, clone 1, Sample C

source_name: Isogenic Control Clone 1


title: Isogenic control, 7WIV iEN, clone 1, Sample B


title: 6090-RB-0001


title: P-limited T. erythraeum under ambient condition - rep1

description:
treated with 400 µatm pCO2 (ambient)
LP_400A


title: Hela cells_DMSO and HS_ replicate 3

source_name: HeLa cells incubated at 37C for 2h with 0.25% DMSO, then heat treated at 43C for 30min and  further incubated at 37C for 1h


title: Hela cells_DMSO and HS_ replicate 2


title: DKD_100

status: Public on Oct 12 2022

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

data_processing:
Import the CEL files into Axiom Analysis Suite, using Best Practices Workflow from the recommendations of the Axiom Genotyping Solution-Data Analysis Guide. Annotation and library downloaded from Taiwan Biobank (https://www.biobank.org.tw/fd.php)
processed data file includes: SNP ID: dbSNP_RS_ID and affy_snp_id; SNP Call: AA, AB, BB, and NoCall; SNP Annotation: Allele_A, Allele_B, Ref_Allele and Alt_Allele; SNP Quality: CR(Call Rate), ConversionType; SNP frequency: n_AA, n_AB, n_BB, n_NC and MinorAlleleFrequency.

source_name: peripheral white blood cells

label_protocol: Type 2 diabetes mellitus (DM) was defined as a fasting glucose larger than 126 mg/dL, a glycosylated hemoglobin larger than 6.5, or the use of hypoglycemic medications. CKD was defined using the National Kidney Foundation: Kidney Disease Outcomes Quality Initiative classification with a persistent proteinuria or an eGFR of less than 60 mL/min/1.73 m2, as determined by the abbreviated Modification of Diet in Renal Disease equation. DKD was diagnosed if subjects fulfilled both DM criteria and CKD criteria at the same time.

growth_protocol: Peripheral venous blood was obtained after an overnight fast.

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

value: peripheral white blood cells

value: DKD

tag: Sex

value: male


title: Isogenic control, 7WIV iEN, clone 1, Sample A

value: iPSC


title: DKD_95

scan_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

value: female


title: DKD_93


title: DKD_97


title: DKD_96


title: DKD_98


title: DKD_99


title: DKD_94


title: Hela cells_DMSO and HS_ replicate 1


title: Hela cells_IHSF115 and HS_ replicate 1


title: Hela cells_DMSO_ replicate 2

source_name: HeLa cells incubated at 37C for 3.5h with 0.25% DMSO


title: DKD_92


title: DKD_88


title: DKD_90


title: DKD_91


title: DKD_89


title: DKD_86


title: DKD_87


title: Hela cells_DMSO_ replicate 1


title: DKD_84


title: DKD_81


title: DKD_82


title: DKD_83


title: Hela cells_DMSO_ replicate 3


title: DKD_79


title: DKD_78


title: DKD_76


title: DKD_77


title: DKD_75


title: DKD_72


title: DKD_74


title: DKD_73


title: DKD_67


title: DKD_69


title: DKD_66


title: DKD_71


title: DKD_68


title: DKD_63


title: DKD_64


title: DKD_70


title: DKD_65


title: DKD_59


title: DKD_85


title: DKD_61


title: DKD_58


title: DKD_62


title: DKD_80


title: DKD_57


title: DKD_53


title: DKD_55


title: DKD_54


title: DKD_56


title: DKD_52


title: DKD_51


title: DKD_49


title: DKD_50


title: DKD_47


title: DKD_44


title: DKD_60


title: DKD_45


title: DKD_42


title: DKD_41


title: DKD_46


title: DKD_43


title: 6090-RB-0002

source_name: Bone marrow cells

value: Vehicle


title: DKD_36


title: DKD_37


title: DKD_35


title: DKD_39


title: DKD_34


title: DKD_33


title: DKD_30


title: DKD_31


title: DKD_29


title: DKD_28


title: DKD_26


title: DKD_27


title: DKD_25


title: DKD_24


title: DKD_21


title: DKD_22


title: DKD_48


title: DKD_20


title: DKD_16


title: DKD_19


title: DKD_13


title: DKD_18


title: DKD_17


title: DKD_38


title: DKD_11


title: DKD_12


title: DKD_8


title: DKD_23


title: DKD_10


title: DKD_32


title: DKD_14


title: DKD_7


title: DKD_6


title: DKD_3


title: DKD_4


title: DKD_2


title: DKD_40


title: CKD_73

value: CKD


title: DKD_1


title: CKD_71


title: CKD_72


title: CKD_69


title: DKD_15


title: CKD_68


title: CKD_70


title: DKD_9


title: CKD_62


title: CKD_64


title: CKD_65


title: CKD_66


title: CKD_59


title: CKD_67


title: CKD_63


title: CKD_61


title: CKD_60


title: CKD_58


title: CKD_54


title: CKD_57


title: CKD_53


title: CKD_55


title: CKD_48


title: CKD_52


title: CKD_49


title: CKD_45


title: DKD_5


title: CKD_46


title: CKD_47


title: CKD_43


title: CKD_41


title: CKD_40


title: CKD_44


title: CKD_56


title: CKD_42


title: CKD_39


title: CKD_37


title: CKD_35


title: CKD_36


title: CKD_34


title: CKD_38


title: CKD_32


title: CKD_33


title: CKD_31


title: CKD_27


title: CKD_50


title: CKD_29


title: CKD_26


title: CKD_25


title: CKD_30


title: CKD_28


title: CKD_24


title: CKD_23


title: CKD_20


title: CKD_19


title: CKD_21


title: CKD_51


title: CKD_15


title: CKD_16


title: CKD_18


title: CKD_14


title: CKD_13


title: CKD_10


title: CKD_11


title: CKD_12


title: CKD_7


title: CKD_9


title: CKD_6


title: CKD_5


title: CKD_8


title: CKD_3


title: CKD_4


title: CKD_2


title: CKD_1


title: DM_105

value: DM


title: DM_106


title: DM_104


title: DM_102


title: DM_103


title: DM_101


title: CKD_22


title: DM_100


title: DM_99


title: CKD_17


title: DM_97


title: DM_94


title: DM_96


title: DM_95


title: DM_92


title: DM_89


title: DM_90


title: DM_86


title: DM_84


title: DM_85


title: DM_88


title: DM_83


title: DM_87


title: DM_81


title: DM_82


title: DM_78


title: DM_80


title: DM_79


title: DM_98


title: DM_76


title: DM_73


title: DM_72


title: DM_74


title: DM_71


title: DM_75


title: DM_70


title: DM_93


title: DM_68


title: DM_67


title: DM_66


title: DM_64


title: DM_63


title: DM_62


title: DM_58


title: DM_57


title: DM_56


title: DM_54


title: DM_59


title: DM_77


title: DM_60


title: DM_55


title: DM_53


title: DM_49


title: DM_69


title: DM_51


title: DM_44


title: DM_45


title: DM_46


title: DM_47


title: DM_48


title: DM_65


title: DM_43


title: DM_42


title: DM_39


title: DM_40


title: DM_50


title: DM_61


title: DM_37


title: DM_52


title: DM_35


title: DM_32


title: DM_33


title: DM_29


title: DM_34


title: DM_28


title: DM_30


title: DM_27


title: DM_25


title: DM_26


title: DM_24


title: DM_16


title: DM_22


title: DM_19


title: DM_18


title: DM_20


title: DM_41


title: DM_36


title: DM_38


title: DM_17


title: DM_91


title: DM_13


title: DM_12


title: DM_14


title: DM_9


title: DM_11


title: DM_31


title: DM_7


title: DM_10


title: DM_6


title: DM_21


title: DM_5


title: DM_8


title: DM_3


title: DM_23


title: DM_2


title: DM_15


title: control_337

value: control


title: DM_1


title: control_335


title: control_331


title: control_336


title: control_332


title: control_330


title: control_328


title: control_329


title: control_327


title: control_326


title: control_324


title: control_325


title: control_323


title: DM_4


title: control_321


title: control_322


title: control_319


title: control_317


title: control_320


title: control_318


title: control_316


title: control_313


title: control_314


title: control_334


title: control_310


title: control_333


title: control_312


title: control_311


title: control_309


title: control_308


title: control_307


title: control_306


title: control_304


title: control_305


title: control_302


title: control_303


title: control_301


title: control_299


title: control_295


title: control_293


title: control_297


title: control_298


title: control_300


title: control_296


title: control_291


title: control_315


title: control_294


title: control_290


title: control_289


title: control_286


title: control_285


title: control_288


title: control_287


title: control_282


title: control_279


title: control_292


title: control_284


title: control_283


title: control_278


title: control_280


title: control_276


title: control_275


title: control_277


title: control_274


title: control_272


title: control_281


title: control_271


title: control_273


title: control_270


title: control_269


title: control_267


title: control_266


title: control_268


title: control_265


title: control_263


title: control_262


title: control_261


title: control_259


title: control_260


title: control_264


title: control_256


title: control_258


title: control_257


title: control_255


title: control_254


title: control_252


title: control_253


title: control_249


title: control_251


title: control_250


title: control_247


title: control_248


title: control_246


title: control_245


title: control_244


title: control_238


title: control_243


title: control_234


title: control_233


title: control_237


title: control_240


title: control_241


title: control_226


title: control_227


title: control_230


title: control_242


title: control_235


title: control_229


title: control_231


title: control_239


title: control_219


title: control_223


title: control_213


title: control_224


title: control_236


title: control_214


title: control_228


title: control_225


title: control_215


title: control_211


title: control_210


title: Astro TKO 3

city: Indianapolis

first: Cristian

last: Lasagna-Reeves

state: IN

address: 320 West 15th Street

department: Anatomy & Cell Biology

institute: Indiana University School of Medicine

hyb_protocol: 100 ng of total mRNA were loaded on a nCounter Mouse Glial Profiling Panel (Nanostring) 770 specific probes contained in the nCounter Mouse Glial Profiling Panel (Nanostring). Hybridization for 16 h at 65 ℃.

scan_protocol: nCounter analysis system

data_processing:
NanoString nCounter Advanced Analysis Report software. Counts for target genes were normalized to the best fitting housekeeping genes as determined by nSolver software to account for variation in RNA content. The background signal was calculated as the mean value of the negative hybridization control probes. The expression data were excluded when the background signals were lower than the average negative control background signal, and probes with <100 reads for 6 or more samples were removed from the analysis
Dynamic normalization provided by software

source_name: TKO astrocyte primary culture

growth_protocol: Astrocytes derived from cortexes of WT or TauKO newborn pups, seeded and grown for 11 days. At DIV 11, total mRNA was extracted and purified.

extract_protocol: The RNeasy Mini Kit (Qiagen) was used to extract total mRNA following the manufacturer's instructions.

treatment_protocol: No treatment was used in these experiments

tag: developmental stage

value: newborn pup

value: cortex

value: astrocyte

value: TKO

tag: div

value: 11 DIV

tag: amount loaded


title: control_222


title: control_207


title: Astro WT 1

source_name: WT astrocyte primary culture

tag: genotype

value: WT


title: control_232

tag: diagnosis


title: control_221


title: control_205


title: placenta_obese_16

first: Perrie

last: O'Tierney-Ginn

state: MA

address: 800 Washington Street

department: Mother Infant Research Institute

institute: Tufts Medical Center

hyb_protocol: Assays used 140ng of RNA and 24 h hybridization at 67C. https://nanostring.com/wp-content/uploads/MAN-10086-01_nCounter_Elements_XT_RUO_User_Manual_USA_Replaces_LBL-C0266.pdf

scan_protocol: Data generated using the nCounter (NanoString Technologies, WA, USA) system as per manufacturer's instructions (https://nanostring.com/wp-content/uploads/MAN-10086-01_nCounter_Elements_XT_RUO_User_Manual_USA_Replaces_LBL-C0266.pdf)

data_processing: Data were analyzed using the proprietary nSolver software (NanoString Technologies, WA, USA) and normalized to internal controls and housekeeping genes to correct for major sources of error including pipetting errors, instrument scan resolution, batch variations, and sample input variability. Five samples in total (n=2, lean; n=3, obese) were excluded from further analysis due to differential clustering as outliers in PCA plot data. All raw data included, but values for 5 outliers not included in normalized matrix table.

source_name: placenta

growth_protocol: Following collection at time of procedure, tissue was snap frozen in liquid nitrogen and stored at -80C until extracted.

extract_protocol: Total RNA was extracted from frozen placenta tissue using TRIZOL reagent following manufacturer's protocol. RNA integrity was assessed for each sample by visualizing ribosomal RNA via gel electrophoresis and quantified and assessed for purity using a Nanodrop OneC (ThermoScientific) spectrophotometer.

tag: gestational age (weeks)

tag: smoking

value: No

tag: body mass index (kg/m2)


title: control_217


title: control_220


title: control_204


title: control_218


title: control_201


title: control_203


title: control_216


title: control_200


title: placenta_obese_13

tag: age


title: placenta_obese_9

value: yes


title: control_209

value: peripheral white blood cells


title: control_199


title: control_208


title: control_198


title: Astro WT 2


title: Astro TKO 2


title: Astro TKO 1


title: placenta_obese_7


title: control_206


title: Astro WT 3


title: control_212


title: placenta_obese_6

value: no


title: placenta_obese_14


title: control_202


title: placenta_obese_11


title: placenta_obese_15


title: control_191

value: male


title: placenta_obese_10


title: placenta_obese_12


title: placenta_obese_8


title: placenta_lean_15

value: Yes


title: placenta_lean_14


title: control_195

value: female


title: control_197


title: placenta_obese_5


title: placenta_obese_4


title: placenta_obese_3


title: control_194


title: control_192


title: placenta_obese_2


title: placenta_lean_10


title: control_188


title: control_186


title: control_193


title: control_189


title: control_185


title: control_190


title: placenta_lean_16


title: control_183


title: control_187


title: placenta_lean_6


title: placenta_lean_11


title: control_184


title: placenta_lean_12


title: control_180


title: placenta_lean_13


title: control_196


title: control_182


title: placenta_lean_7


title: control_179


title: control_181


title: placenta_lean_9


title: placenta_lean_8


title: placenta_obese_1


title: control_178


title: control_177


title: placenta_lean_3


title: control_176


title: control_175


title: placenta_lean_2


title: placenta_lean_4


title: control_174


title: placenta_lean_5


title: control_172


title: control_173


title: RNA-seq of adult Amphiouxus lanceolatum epidermis [Bla_Epidermis_c]

city: Barcelona

first: Federica

last: Mantica

address: Dr. Aiguader 88

institute: CRG

description: Pooled epidermis from adult individuals

data_processing:
Estimated counts and TPMs were computed by Kallisto (v0.44.0)
Supplementary files format and content: Tab-delimited file with length, effective length, estimated counts and transcript per million (TPM) for all species protein coding genes in the relative GTF

organism: Branchiostoma lanceolatum

source_name: Adult epidermis

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epidermis

tag: genome build

tag: gtf


title: placenta_lean_1


title: control_170


title: control_169


title: control_167


title: control_166


title: control_165


title: Parental line 0 Gray Replicate 2

city: Antwerpen

first: Bart

last: Cuypers

state: Antwerp

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: Adrem Data Lab

data_processing:
Alignment and read count table generation with STAR v2.7.3a
Differential expression analysis with DESEQ2
Circular RNA detection with CIRCexplorer2 and CIRI2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: count table txt files generated with STAR for linear mRNAs, and CIRCexplorer2 and CIRI2 for the circular RNAs
Supplementary_files_format_and_content: diffential expression anysis CSV files with fold changes and p-values generated with DESEQ2

source_name: MCF7 cell culture

extract_protocol:
Three independent replicates each of exponentially growing PAR, AMC and FIR20 cells were seeded in 25 cm flasks and incubated for 48 h followed by RNA extraction. Cell pellets were collected by trypsinization, snap frozen and stored at -80oC until further use. Total RNA was extracted from the cell pellets using RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) as described by the manufacturer. During the extraction procedure, genomic DNA was removed using a genomic DNA eliminator spin column (Qiagen). Sample RNA concentrations were measured and assessed for the presence of contaminants using a NanoDrop ND-2000 spectrophotometer (Thermo Scientific, USA) and the DropSense™ 16 spectrometer (Trinean, Ghent, Belgium). RNA integrity was subsequently assessed using Agilent 2100 bioanalyzer (Agilent Technologies, Inc Palo Alto, CA, USA).
Total RNA was depleted of ribosomal RNA (rRNA) using the Ribo-Zero HMR kit (Illumina, USA) according to manufacturer instructions. The rRNA-depleted RNA was then purified using 2x RNAClean XP beads (Beckman Coulter) followed by first and second-strand synthesis using NEBNext, New England Biolabs reagents. The generated cDNA was purified with 1.8x SPRIselect Beads (Beckman Coulter). Endprep reaction was performed following the manufacturer’s protocol for NEBNext Ultra II End Prep Reaction for the rest of the procedure. Adaptor ligation was then performed using NEBNext Ultra II Ligation protocols (New England Biolabs) and the ligated product was purified by SPRIselect Beads (Beckman Coulter) followed by elution in nuclease-free water. PCR was carried out using NEBNext Ultra II Q5 Master Mix, and primers and the final library was subsequently purified with SPRIselect Beads

tag: sample type

value: Parental line

tag: replicate

value: Replicate 2


title: control_164

value: control


title: control_163


title: Parental line 0 Gray Replicate 1

value: Replicate 1


title: Fractionally Irradiated to 20 Gray Replicate 3

value: Fractionally Irradiated

value: Replicate 3


title: Splenic sample (control) rep4

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Gene expression data from spleen

hyb_protocol: Clariom S arrays (Affymetrix) under standard conditions

scan_protocol: Standard Affymetrix protocol

data_processing: Upon microarray hybridization, the raw data was normalized with RMA using R (v.3.6.3).

source_name: Spleen (control animals)

label_protocol: Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 mg/sample) to generated labeled cRNA probes according to the manufacturer's instructions (Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

value: control (Trp53KI/KI)

value: Spleen


title: control_171

tag: tissue


title: Splenic sample from lymphoma-bearing animals rep3

description: Gene expression data from spleen

source_name: Spleen (lymphoma-bearing animals)


title: Splenic sample from lymphoma-bearing animals rep4

description: Gene expression data from spleen


title: Splenic sample from lymphoma-bearing animals rep2

description: Gene expression data from spleen


title: Splenic sample from lymphoma-bearing animals rep1

description: Gene expression data from spleen


title: Splenic sample (control) rep1

description: Gene expression data from spleen


title: Splenic sample (control) rep3

description: Gene expression data from spleen


title: control_168


title: Splenic sample (control) rep2

description: Gene expression data from spleen


title: control_161


title: control_162


title: Age-matched control 0 Gray Replicate 3

value: Age-matched control


title: Fractionally Irradiated to 20 Gray Replicate 1


title: Age-matched control 0 Gray Replicate 2


title: Fractionally Irradiated to 20 Gray Replicate 2


title: RNA-seq of adult Amphiouxus lanceolatum muscle [Bla_Muscle_c]

description: Muscle from an adult individual

source_name: Adult muscle

value: Muscle


title: Age-matched control 0 Gray Replicate 1


title: control_156


title: control_160


title: control_159


title: control_155


title: control_154


title: Parental line 0 Gray Replicate 3


title: control_153


title: control_151


title: control_150


title: control_152


title: control_158


title: control_149


title: control_157