title: Bisulfite-seq_Lens fiber cells_rep3

city: Boca Raton

first: Marc

last: Kantorow

address: 777 Glades Road

institute: Florida Atlantic University

data_processing:
CASAVA base calling and Trimmomatic read trimming and alignment to the galgal6 reference genome using Bismark software [238].
DSS analysis software based on beta-binomial distribution was used for the identification of DMRs as described previously [239,240] with consideration of the spatial correlation, read depth of the sites, and the variance among biological replicates. The parameters were smoothing = TRUE, smoothing.span = 200, delta = 0, p.threshold = 1 × 10−5, minlen = 50, minCG = 3, dis.merge = 100, and pct.sig = 0.5.
Genome_build: galgal6
Supplementary_files_format_and_content: mCG differentially methylated regions (DMR) text files: 7,621 differentially methylated mCG regions were identified between lens epithelial and fiber cells; file contains: bed coordinates, diff.methyl, and genomic loci of DMRs

organism: Gallus gallus

source_name: Lens Fiber cells

extract_protocol:
Lenses were isolated from White Leghorn embryonated chicken eggs (Charles River Laboratories, Storrs, CT) at embryonic developmental stage day 13 (E13). 25 lenses per biological replicate were microdissected into epithelial cells and fiber cells as previously described [217]. Microdissected epithelial and fiber cells from 25 lenses were pooled and stored in CryoStor CS10 cryopreservation media containing 10% DMSO (Stemcell, Vancouver, Canada) and stored at −80 °C as previously described [237].
Tissue in CryoStor media was thawed on ice, centrifuged at 800 x g for 5 mins and the CryStor removed. DNA was isolated using Qiagen Genomic-tip 20/G along with the Qiagen Genomic DNA buffer set according to the manufacturer’s instructions.
Bisulfite-seq was performed by Novogene (Sacramento CA) using an Illumina HiSeqTM2500/MiSeq platform using their standard protocols

tag: cell type

value: Lens Fiber cells

value: Embryonic day 13

value: White leghorn


title: DT0hRep1

status: Public on Mar 31 2022

type: SRA

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

country: USA

institute: Purdue University

library_source: transcriptomic

data_processing:
The libraries were sequenced on Illumina HiSeq 2500 platform with 101 bp paired-end reads.
FASTX-Toolkit was used to perform quality control for RNA-Seq data w8ith at least 30 base quality score and at least 50 bps of read length.
TopHat was used to align the reads to the switchgrass reference genome
FPKM values were calculated using the Cufflinks
Reads counts performed usign HTSeq
Genome_build: Pvirgatum_450_v4.1 (https://phytozome-next.jgi.doe.gov/info/Pvirgatum_v4_1)
Supplementary_files_format_and_content: txt

molecule: total RNA

organism: Panicum virgatum

source_name: leaf tissue

growth_protocol: The ramets of lowland ecotype Alamo, AP13 genotype of switcghrass were transplanted in 3GP nursery pots and later transferred to the green house for optimum conditions at the Samuel Roberts Noble Foundation in Ardmore, Oklahoma.

extract_protocol:
Total RNA was extracted from all  samples, contamination of genomic DNA removed by DNAase treatment, quality of RNA's checked, and 1 µg  of RNA used for cDNA sythnesis.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit following manufacturers protocol.

treatment_protocol: The control and drought treated plants were arranged in one growth chamber and palnts with drought and heat treatment in a separate chamber

tag: developmental stage

tag: tissue

value: leaf

tag: treatment

value: drought

tag: biomaterial provider

value: Robert Nobel Foundation


title: 8_cell_input2

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences
The trimmed reads were align to Bos_taurus_UMD_3.1.1 by Bowtie2
Reads with low map quality were removed by Samtools, and PCR duplicates were removed by Picard
Genome_build: Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: Bigwig files are generated using bamCoverage mode of DeepTools, and the reads counts were normalized to RPKM.

molecule: genomic DNA

organism: Bos taurus

source_name: embryo

extract_protocol:
The embryos were washed 3 times in 0.5% BSA after removal of zona pellucida.  After cell lysis, the chromatin was digested with micrococcal nuclease and histone-DNA complexes were isolated with H3K4me3 antibody.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645)

tag: age

value: 2.5 day post insemination

value: Wild type

tag: chipseq antibody


title: Control1wkRep3

value: untreated


title: Bisulfite-seq_Lens fiber cells_rep1

state: FL

tag: strain


title: Bisulfite-seq_Lens epithelial cells_rep3

source_name: Lens epithelial cells

value: Lens epithelial cells


title: Mo_input1

value: morula

value: 6 day post insemination


title: 8_cell_input1


title: Bisulfite-seq_Lens fiber cells_rep2


title: Bisulfite-seq_Lens epithelial cells_rep1


title: 2_cell_H3K4me3_IP2

value: 1.5 day post insemination


title: Control1wkRep2


title: Col-0/hpEIN2[GU]-13

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

data_processing:
Adapters were removed using cutadapt
Bowtie V1.0 was used to align reads to genome
reads were normalized to reads per million
Custom pearl scripts were used to extract reads mapped to hairpin constructs and gene targets (EIN2, PDS, GUS transgene)
Genome_build: TAIR 10
Supplementary_files_format_and_content: Single excel file with read counts to hairpin transgenes and target genes

organism: Arabidopsis thaliana

source_name: 3 week old whole plant

growth_protocol: Plant seeds were sown either directly into soil, or placed first on MS plate for germination followed by transferring seedlings to soil. Plants were grown in a growth room (16 hours light/8 hours dark) at 22-24 °C.

extract_protocol:
Total RNA was extracted using Trizol
Standard illumina library sRNA-seq library preparation by service provider

tag: ecotype

value: Columbia

tag: genotype

value: hpEIN2[G:U] transgene

value: 3 week old whole plant

tag: target gene


title: 2_cell_input2


title: Col-0/hpEIN2[GU]-12


title: Control1wkRep1


title: Col-0/hpEIN2[WT]-15

value: hpEIN2[WT] transgene


title: ocp11/hpEIN2[GU]-6

value: ocp11 mutant /hpEIN2[WT] transgene


title: Control144Rep3


title: ocp11/hpEIN2[GU]-4


title: ocp11/hpEIN2[WT]-11


title: MII_H3K4me3_IP2

value: oocyte

value: MII


title: nrpd1a/hpEIN2[GU]-18

value: nrpd1a mutant /hpEIN2[G:U] transgene


title: Control144Rep2

value: leaf


title: Control144Rep1

value: Robert Nobel Foundation


title: Bisulfite-seq_Lens epithelial cells_rep2

value: Embryonic day 13

value: White leghorn


title: nrpd1a/hpEIN2[GU]-2


title: MII_H3K4me3_IP1

value: Wild type


title: nrpd1a/hpEIN2[WT]-2

value: nrpd1a mutant /hpEIN2[WT] transgene


title: 2_cell_H3K4me3_IP1


title: Control120Rep2

value: untreated


title: Control120Rep3


title: MII_input2


title: MII_input1


title: GV_H3K4me3_IP2

value: GV


title: Control120Rep1


title: GV_H3K4me3_IP1


title: Control96hRep3


title: plate_530s_M6_S47_L003

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain single cell 628

data_processing:
The sequencing reads were first aligned to the mouse reference genome Gencode M26 genome with STAR software.
Genome_build: Gencode M26
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
We used transgenic mouse reporter line (SM22-Cre;Rosa26-stop-tdTomato). We chosed to focus our efforts to adult mice brain cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: brain

value: adult mice

tag: notch3 genotype

value: WT

tag: celltype

value: Macrophages


title: control morpholino (3 ng)

city: Beijing

first: Shuyan

last: Yang

address: 2# Yabao Road

institute: Children's Hospital of Capital Institute of Pediatrics

data_processing:
Clean-tags were mapped to the reference genome and genes available at the Zebrafish Genome.
For gene expression analysis, the matched reads were calculated and then normalized to RPKM using RESM software
The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2 Ratio ≥1 and FDR ≤ 0.001.
Library construction and sequencing were performed on a BGISEQ-500.
Assembly: Zv11

organism: Danio rerio

source_name: 24 hour post fertilization zebrafish embryos

growth_protocol: Zebrafish embryos were harvested and incubated in holfreter water at d at 28.5℃.

extract_protocol:
30 pooled embryos at 24 hpf from different experiment  were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA of each group was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
Library construction and sequencing were performed on a BGISEQ-500 by CapitalBio Technology (www.capitalbiotech.com, Beijin, China). Clean-tags were mapped to the reference genome and genes available at the Zebrafish Genome.

treatment_protocol: Different doses of hnrnpaba MO reagent (3ng and 6 ng) were  microinjected into each zebrafish embryos at the 1-cell stage. A standard control MO was used as  controls. The injected embryos were raised at 28.5℃ and harvested at 24 hpf for RNA extraction.

value: Tuebingen

value: embryo

tag: development stage

value: 24 hour post fertilization

value: control morpholino (3 ng)


title: Control96hRep2


title: plate_530s_M7_S55_L003

description: Brain single cell 629


title: 2_cell_input1

value: 1.5 day post insemination


title: HNRNPAB morpholino (6ng）

value: HNRNPAB morpholino(6ng)


title: ocp11/hpEIN2[WT]-10

value: Columbia

value: ocp11 mutant /hpEIN2[WT] transgene

value: 3 week old whole plant


title: plate_530s_M5_S39_L003

description: Brain single cell 627


title: nrpd1a/hpEIN2[WT]-3


title: plate_530s_M24_S191_L003

description: Brain single cell 625


title: Control96hRep1

value: leaf

value: Robert Nobel Foundation


title: GV_input2

value: oocyte

value: Wild type


title: HNRNPAB morpholino (3ng）

value: HNRNPAB morpholino(3ng)


title: Control72hRep3

value: untreated


title: plate_530s_M16_S127_L003

description: Brain single cell 621

value: brain

value: adult mice

value: WT


title: plate_530s_M20_S159_L003

description: Brain single cell 623

value: Macrophages


title: plate_530s_M17_S135_L003

description: Brain single cell 622


title: plate_530s_M23_S183_L003

description: Brain single cell 624


title: plate_530s_M13_S103_L003

description: Brain single cell 620


title: Control72hRep1


title: Control72hRep2


title: Control0hRep3


title: Control0hRep2


title: plate_530s_L7_S246_L003

description: Brain single cell 616


title: plate_530s_M1_S7_L003

description: Brain single cell 618


title: Combination2

city: Okayama

first: Yoshihiro

last: Otani

address: 2-5-1, Shikata, Kita-ku

department: Neurological Surgery

country: Japan

institute: Okayama University Hospital

data_processing:
To analyze the RNAseq of co-culture samples, we mapped the sequencing reads to Human and Mouse genome references using STAR mapper (version 2.5.3a) to generate bam files.
XenofilteR (version 1.6) was further used for computational deconvolution of the mouse and human reads.
The raw count of reads for the genomic features was evaluated by htseq-count (version 0.9.1).
Genome_build: Human: Grch38; Mouse: Grch38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

organism:
Homo sapiens
Mus musculus

source_name: U87ΔEGFR and Raw264.7

growth_protocol: Cells were cultured in DMEM/RPMI containing 2% FBS.

extract_protocol:
We isolated total RNA using the RNeasy kit (Qiagen, Germantown, MD) and RNase-free DNase set (Qiagen)
Illumina sequencing and library prep was carried out at Novogene Bioinformatics Technology Co., Ltd., in Beijing, China.

treatment_protocol: U87ΔEGFR cells were infected with 0.5 MOI of rHSVQ in the presence of DMSO or DAPT (25µM) for 1 hour. Media was changed into new media containing DMSO or DAPT and overlaid with Raw264.7 cells at a 1:2 ratio for 12 hours.

value: human glioblastoma cell and murine macrophage cell

value: GSI and oHSV (DAPT 25uM and 0.5MOI of rHSVQ)


title: Combination3


title: Combination1


title: plate_530s_L8_S254_L003

description: Brain single cell 617


title: oHSV4

value: oHSV (0.5MOI of rHSVQ)


title: plate_530s_M4_S31_L003

description: Brain single cell 626

value: Microglia


title: GV_input1

value: GV


title: plate_530s_L5_S230_L003

description: Brain single cell 614


title: Combination4


title: Control0hRep1


title: plate_530s_L4_S222_L003

description: Brain single cell 613


title: plate_530s_L3_S214_L003

description: Brain single cell 612


title: oHSV3


title: plate_530s_L24_S382_L003

description: Brain single cell 611


title: oHSV2


title: plate_530s_M11_S87_L003

description: Brain single cell 619


title: oHSV1


title: plate_530s_L23_S374_L003

description: Brain single cell 610


title: plate_530s_L17_S326_L003

description: Brain single cell 609


title: plate_530s_L6_S238_L003

description: Brain single cell 615


title: pFUS 7-weeks DIO-stz Kidney 11

city: Niskayuna

first: John

last: Graf

state: New York

address: One Research Circle

institute: GE Global Research

data_processing:
Fastq files of the paired end reads were merged into two files for each sample, one for R1 and one for R2 using Unix commands.
Base quality control was checked using Fast QC v0.10.1 from Babraham Bioinformatics.
Sequencing reads were mapped to the annotated rat genome version, Rattus norvegicus Rnor 6.0.91, using STAR_2.5.3a aligner.
Transcript abundance estimates were generated from the sorted BAM files using RSEM.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rsem_genes_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every gene and every sample
Supplementary_files_format_and_content: rsem_isoforms_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every transcript and every sample

organism: Rattus norvegicus

source_name: DIO-stz

extract_protocol:
Tissue were rapidly collected at the terminal time point and and treated with RNAlater tissue storage reagent. RNA extraction from tissues, assessment of RNA quality and RNA sequencing were performed at the Roswell Park Cancer Institute, Genomics Shared Resource, Buffalo, New York.
Sequencing RNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions for the RNA from all tissues except the pancreas and adipose. For these samples, TruSeq Stranded Total RNA Sample Preparation Kit was used.

treatment_protocol: The porta hepatis was targeted for ultrasound stimulation using a 1.1 MHz single-element focused ultrasound system comprised of a signal generator (Model 33120A, Agilent Technologies Inc., Santa Clara, CA), a RF power amplifier (Model 350L, Electronics & Innovation Ltd., Rochester, NY) and a 1.1 MHz focused single-element ultrasound transducer (Model H102, Sonic Concepts Inc., Bothell, WA). The transducer was acoustically coupled to the animal through a 6-cm tall plastic standoff cone filled with degassed water. Prior to treatments, all rats were anesthetized at 2-4% isoflurane at 1 L/min O2. The Target porta hepatis was localized using a custom ultrasound imaging device (Vivid E9; GE Healthcare). Animals either received 3 minutes of ultrasonic stimulus (1.1 MHz, 200mV per pulse, 150 burst cycles, 500 µs burst period) or Sham stimulus where no energy was applied.

tag: model

value: DIO-stz

value: Kidney

tag: gender

value: Female

value: pFUS 7-weeks


title: pFUS 7-weeks DIO-stz Brain 11

value: Brain


title: pFUS 7-weeks DIO-stz Blood 11

value: Blood


title: plate_530s_L11_S278_L003

description: Brain single cell 606


title: plate_530s_K9_S70_L003

description: Brain single cell 605


title: GSI4

value: GSI (DAPT 25uM)


title: plate_530s_L13_S294_L003

description: Brain single cell 607


title: GSI3


title: pFUS 7-weeks DIO-stz Pancreas 11

value: Pancreas


title: plate_530s_K7_S54_L003

description: Brain single cell 603

value: brain


title: plate_530s_K8_S62_L003

description: Brain single cell 604

value: adult mice


title: pFUS 7-weeks DIO-stz Muscle 11

value: Muscle


title: plate_530s_K22_S174_L003

description: Brain single cell 601

value: WT

value: Macrophages


title: plate_530s_K4_S30_L003

description: Brain single cell 602


title: GSI2

value: human glioblastoma cell and murine macrophage cell


title: plate_530s_L14_S302_L003

description: Brain single cell 608


title: GSI1


title: plate_530s_K21_S166_L003

description: Brain single cell 600


title: plate_530s_K20_S158_L003

description: Brain single cell 599


title: pFUS 7-weeks DIO-stz Intestine 10

value: Intestine

value: Male


title: WT1

type: genomic

city: Taipei

first: Chun-Hao

middle: James

last: Hung

state: TAIWAN

address: 128 Academia Road, Section 2, Nankang, Taipei, Taiwan

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica

description: Chip-chip WT fetal liver AEK

hyb_protocol: The hybridization procedure was applied as recommended by the manufacturer. There were 768,217 probes on the NimbleGen 385K ChIP-chip array. These probes were grouped into 21,536 sequence ids each of which contained 5 to 320 probes that ranged from 49 bp to 74 bp in length. The distances between the probes in the same sequence id ranged from 100 bp to 3,700 bp. In general, these sequence ids are located in the promoter regions of genes, roughly from -3.75kb to +0.75 kb relative to the 160 transcription start site (TSS). The sequence id would be assigned a gene name when the gene’s coding sequence overlapped with the region from 10 kb upstream to 10 kb downstream of the sequence id. In this way, 652 sequence ids were found to be located in the intergenic regions and 20,884 sequence ids were near the coding regions of genes.

scan_protocol: The hybridized arrays were scanned on an Axon 4000B microarray scanner.

data_processing: Arrays were processed using Nimblegen's standard protocol for Mouse NimbleGen 385K ChIP-Chip array.

label: Alexa 532

source_name: AEK ChIP DNA from fetal livers

label_protocol: standard protocol

growth_protocol: Primary fetal liver without culture

extract_protocol: ~1x10^7 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. And then followed th standard protocol. DNAs were then purified from the immunoprecipitated chromatin samples by QIAquick PCR purification kit (Qiagen) and amplified by the Sigma GenomePlex WGA kit.

treatment_protocol: Primary E14.5 fetal liver cells  extracted directly

value: liver

tag: chip antibody

value: AEK antibody

label: Alexa 635

source_name: Input DNA from fetal livers


title: WT2

description: Chip-chip WT fetal liver AEK


title: plate_530s_K18_S142_L003

description: Brain single cell 597

value: Microglia


title: pFUS 7-weeks DIO-stz Blood 10

value: DIO-stz


title: plate_530s_K12_S94_L003

description: Brain single cell 596


title: Control2

tag: cell type

value: PBS (DMSO 25uM)


title: plate_530s_K1_S6_L003

description: Brain single cell 593


title: plate_530s_K10_S78_L003

description: Brain single cell 594


title: plate_530s_K11_S86_L003

description: Brain single cell 595


title: pFUS 7-weeks DIO-stz Kidney 10

value: Kidney

value: pFUS 7-weeks


title: pFUS 7-weeks DIO-stz Liver 10

value: Liver


title: pFUS 7-weeks DIO-stz Pancreas 10

value: Pancreas


title: Control1


title: plate_530s_J9_S261_L003

description: Brain single cell 592

value: brain


title: Control4


title: plate_530s_J7_S245_L003

description: Brain single cell 590

value: adult mice


title: pFUS 7-weeks DIO-stz Liver 11

value: Female


title: plate_530s_K19_S150_L003

description: Brain single cell 598

value: WT


title: plate_530s_J8_S253_L003

description: Brain single cell 591

value: Macrophages


title: plate_530s_J6_S237_L003

description: Brain single cell 589


title: plate_530s_J4_S221_L003

description: Brain single cell 588


title: plate_530s_J3_S213_L003

description: Brain single cell 587


title: plate_530s_J22_S365_L003

description: Brain single cell 586


title: pFUS 7-weeks DIO-stz Brain 9

value: Brain


title: Control3

value: human glioblastoma cell and murine macrophage cell


title: plate_530s_J21_S357_L003

description: Brain single cell 585


title: pFUS 7-weeks DIO-stz Intestine 9

value: Intestine

value: Male


title: Treg cells Junbfl/flCd4-Cre2

type: RNA

city: Tokyo

first: Takaharu

last: Katagiri

address: 5-21-16 Omori-Nishi,Ota-ku

department: Biochemistry

institute: Toho University School of Medicine

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent SureScan G4900DA Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: In vitro differentiated Treg cells

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Not applicable

extract_protocol: Total RNAs were extracted from the colon of mice of the indicated genotype using Trizol according to the manufacturer’s instructions

treatment_protocol: Naive CD4+ T cells (CD4+CD62LhighCD44lowCD25– cells) were sorted using FACSAria Ⅲ cell sorter (BD Biosciences), and cultured for 3 days in the presence of plate-bound anti-CD3 (1 μg/ml), anti-CD28 (0.5 μg/ml), anti-IFN-γ (5 μg/ml), nti-IL-4 (5 μg/ml), and recombinant human TGF-Β1 (5 ng/ml).

value: Treg cells


title: Treg cells Junbfl/flCd4-Cre1


title: plate_530s_J20_S349_L003

description: Brain single cell 584


title: pFUS 7-weeks DIO-stz Kidney 9


title: pFUS 7-weeks DIO-stz Muscle 9

value: Muscle


title: plate_530s_J18_S333_L003

description: Brain single cell 581


title: HGOXA-3

city: Kongens Lyngby

first: Xiao

last: Wang

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

data_processing:
Quality control by removing the contaminated reads for adapters (> 5 bp adapter sequences), low quality reads (Phred quality value <= 19 more than 15%) and reads with Ns (Ns > 5%)
Clean reads were aligned to the human reference genome GRCh38.p13 (Genome Reference Consortium Human Build 38)
The fragments per kilobase millon mapped reads (FPKM) was calculated to estimate the expression levels of genes in each sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Homo sapiens

source_name: Kidney

growth_protocol: HK-2 cells were cultured in Dulbeccos modified eagles medium (DMEM) with the low glucose (Sigma-Aldrich Inc, St. Louis, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, USA), 10 units/ml penicillin and 10 mg/ml streptomycin. They were maintained in the continuous culture at 37 °C in a humidified atmosphere (5% CO2) in an incubator. Growth medium was changed every second day, and cells were sub-cultured until further measurements at 80% colony confluency.

extract_protocol: Libraries were prepared according to Illumina's instructions

treatment_protocol: Three replicates of them were exposed 40 mM oxamate (case group), while the other  replicates were still under the same HG condition but 40 mM oxamate expose (control group)

tag: group

value: Case group

value: Human renal proximal tubular epithelial cell line


title: plate_530s_J2_S205_L003

description: Brain single cell 583

tag: tissue


title: HGOXA-2


title: plate_530s_J14_S301_L003

description: Brain single cell 579


title: plate_530s_J13_S293_L003

description: Brain single cell 578

value: Microglia


title: HG-3

value: Control group


title: plate_530s_J16_S317_L003

description: Brain single cell 580


title: plate_530s_J12_S285_L003

description: Brain single cell 577


title: plate_530s_J11_S277_L003

description: Brain single cell 576


title: pFUS 7-weeks DIO-stz Blood 9

value: DIO-stz

value: Blood

tag: treatment

value: pFUS 7-weeks


title: HG-2


title: pFUS 7-weeks DIO-stz Adipose 9

value: Adipose


title: pFUS 7-weeks DIO-stz Liver 9

value: Liver


title: Treg cells Control2

value: Junbfl/fl


title: plate_530s_J1_S197_L003

description: Brain single cell 575

value: brain

value: adult mice

value: WT

value: Macrophages


title: pFUS 7-weeks DIO-stz Intestine 8

value: Intestine

value: Male


title: HG-1


title: plate_530s_I8_S61_L003

description: Brain single cell 573


title: cRBM2_D24_E2F3

city: Houston

first: Yao

last: Yu

state: TX

address: 1155 Pressler

institute: UT MD Anderson Cancer Center

data_processing:
QC: FastQC v0.11.5. Sequenced reads were then trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNAeq Alignment: TopHat v2.1.1 for RNASeq, Bowtie2 for ChIPseq
RNAseq normalization: Cufflinks v2.2.1
RNA-seq (HOS samples): alternative splicing analysis for intron retention: juncBASE
ChIPseq sorting, normalization, and visualization: MACS2
Genome_build: hg19
Supplementary_files_format_and_content: RNASeq: FPKM data in .csv; ChIPSeq: genome browser tracks in .bedGrap

source_name: osteoblast

growth_protocol: fibroblasts are frown in DMEM with 15% FBS,mesenchyma stem cells are grwon in aMEM with 10% FBS,osteoblasts are grown in osteogenic differentiation medium (α-MEM supplemented with 10% FBS, 10 mM β-glycerol phosphate, 200 μM ascorbic acid, and 0.1 μM dexamethasone and osteosarcoma cancer cells are grown in DMEM with 10% FBS.

extract_protocol:
Cells samples were lysed in Trizol reagent (Invitrogen, 10296010).ChIP-seq, cells were fixed, quenched, sonicated to ~250 bp in 1% SDS lysis buffer, and incubated with Protein A/G Dynabeads and 5 µg of the indicated antibody. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. After wash, treatment with RNAse A and Proteinase K, DNA was eluted and purified with Qiagen's PCR purification kit (28106).
For RNASeq, library construction was performed using NEBNext Ultra II RNA Library Prep Kit (E7770) following manufacturer’s instructions. For ChIPSeq, library construction was performed using KAPA Hyper Prep Kit (KK8500)  according to manufacturer's conditions. Libraries were submitted to PE150 high-throughput sequencing.

treatment_protocol: Cells were treated with 1 nM Pladienolide B (TOCRIS, #6070) for 6 hours.

tag: cell

value: osteoblast

tag: time point

value: Corrected RB1 mutation

tag: antibody

value: anti-E2F3, abcan, ab50917


title: plate_530s_I9_S69_L003

description: Brain single cell 574

tag: strain

tag: age

value: Microglia


title: plate_530s_J19_S341_L003

description: Brain single cell 582


title: plate_530s_I7_S53_L003

description: Brain single cell 572


title: plate_530s_I6_S45_L003

description: Brain single cell 571


title: pFUS 7-weeks DIO-stz Liver 8


title: Treg cells Control1

value: Treg cells

tag: genotype


title: plate_530s_I5_S37_L003

description: Brain single cell 570


title: cRBM2_D24_RB1

value: anti-RB1, cell signaling #9309


title: plate_530s_I3_S21_L003

description: Brain single cell 569


title: plate_530s_I23_S181_L003

description: Brain single cell 568


title: plate_530s_I21_S165_L003

description: Brain single cell 567


title: HOS_WT_PB1nM

source_name: osteosarcoma cancer cell

value: osteosarcoma cancer cell

value: Pladienolide B

value: wild type


title: plate_530s_I20_S157_L003

description: Brain single cell 566


title: HOS_RB1KO_PB1nM


title: plate_530s_I2_S13_L003

description: Brain single cell 565


title: pFUS 7-weeks DIO-stz Adipose 8

value: DIO-stz

value: Adipose

value: pFUS 7-weeks


title: HOS_RB1KO_DMSO

value: DMSO


title: pFUS 7-weeks DIO-stz Pancreas 8

value: Pancreas


title: HOS_WT_DMSO


title: plate_530s_I19_S149_L003

description: Brain single cell 564

value: brain

value: adult mice

value: WT

value: Macrophages


title: pFUS 7-weeks DIO-stz Intestine 11

value: Intestine

value: Female


title: plate_530s_I18_S141_L003

description: Brain single cell 563


title: pFUS 7-weeks DIO-stz Liver 7

value: Liver

value: Male


title: plate_530s_I15_S117_L003

description: Brain single cell 560


title: cRBD3_D24

value: osteoblast

value: Corrected RB1 mutation


title: plate_530s_I16_S125_L003

description: Brain single cell 561

value: Microglia


title: pFUS 7-weeks DIO-stz Brain 7

value: Brain


title: plate_530s_I14_S109_L003

description: Brain single cell 559


title: pFUS 7-weeks DIO-stz Pancreas 7

value: DIO-stz


title: pFUS 7-weeks DIO-stz Muscle 8

value: Muscle


title: plate_530s_I10_S77_L003

description: Brain single cell 557


title: cRBD2_D24


title: plate_530s_I12_S93_L003

description: Brain single cell 558


title: pFUS 7-weeks DIO-stz Blood 8

value: Blood

value: pFUS 7-weeks


title: plate_530s_H7_S244_L003

description: Brain single cell 556


title: cRBD1_D24


title: RBD3_D24

value: RB1 mutation


title: plate_530s_H4_S220_L003

description: Brain single cell 555

value: brain


title: pFUS 7-weeks DIO-stz Intestine 7


title: plate_530s_H3_S212_L003

description: Brain single cell 554

value: adult mice


title: pFUS 7-weeks DIO-stz Blood 7


title: plate_530s_I17_S133_L003

description: Brain single cell 562

value: WT


title: plate_530s_H23_S372_L003

description: Brain single cell 553


title: plate_530s_H21_S356_L003

description: Brain single cell 552

value: Macrophages


title: pFUS 7-weeks DIO-stz Adipose 7

value: Adipose


title: plate_530s_H2_S204_L003

description: Brain single cell 550


title: RBD2_D24


title: Control 7-weeks DIO-stz Blood 6

value: Control 7-weeks


title: plate_530s_H13_S292_L003

description: Brain single cell 546


title: plate_530s_H19_S340_L003

description: Brain single cell 549


title: Control 7-weeks DIO-stz Kidney 6

value: Kidney


title: cRBM3_D24


title: Control 7-weeks DIO-stz Pancreas 6

value: Pancreas

value: Male


title: plate_530s_H15_S308_L003

description: Brain single cell 547


title: RBD1_D24

value: osteoblast


title: Control 7-weeks DIO-stz Adipose 6


title: plate_530s_H18_S332_L003

description: Brain single cell 548


title: cRBM1_D24

value: Corrected RB1 mutation


title: plate_530s_H11_S276_L003

description: Brain single cell 545


title: plate_530s_H1_S196_L003

description: Brain single cell 543


title: RBM3_D24


title: cRBM2_D24


title: plate_530s_H10_S268_L003

description: Brain single cell 544


title: Control 7-weeks DIO-stz Intestine 6

value: Intestine


title: plate_530s_G9_S68_L003

description: Brain single cell 542

value: Microglia


title: plate_530s_G8_S60_L003

description: Brain single cell 541


title: RBM2_D24


title: plate_530s_H20_S348_L003

description: Brain single cell 551


title: plate_530s_G5_S36_L003

description: Brain single cell 539


title: plate_530s_G6_S44_L003

description: Brain single cell 540


title: RBM1_D24


title: plate_530s_G23_S180_L003

description: Brain single cell 537


title: WT3_D24

value: wild type


title: Control 7-weeks DIO-stz Muscle 6

value: DIO-stz

value: Muscle


title: Control 7-weeks DIO-stz Brain 6

value: Brain


title: plate_530s_G21_S164_L003

description: Brain single cell 536

value: brain


title: plate_530s_G20_S156_L003

description: Brain single cell 535

value: adult mice


title: plate_530s_G2_S12_L003

description: Brain single cell 534

value: WT


title: Control 7-weeks DIO-stz Pancreas 5


title: WT2_D24


title: WT1_D24


title: Control 7-weeks DIO-stz Muscle 5


title: plate_530s_G16_S124_L003

description: Brain single cell 531

value: Macrophages


title: cRBD3_D15

source_name: pre-osteoblast

value: pre-osteoblast


title: plate_530s_G19_S148_L003

description: Brain single cell 533


title: plate_530s_G13_S100_L003

description: Brain single cell 529


title: plate_530s_G15_S116_L003

description: Brain single cell 530


title: cRBD2_D15


title: Control 7-weeks DIO-stz Liver 5

value: Liver

value: Control 7-weeks


title: plate_530s_G11_S84_L003

description: Brain single cell 528


title: plate_530s_G10_S76_L003

description: Brain single cell 527


title: Control 7-weeks DIO-stz Blood 5

value: Blood


title: plate_530s_G1_S4_L003

description: Brain single cell 526


title: plate_530s_G4_S28_L003

description: Brain single cell 538


title: Control 7-weeks DIO-stz Kidney 5

value: Kidney

value: Male


title: cRBD1_D15

value: Corrected RB1 mutation


title: plate_530s_F4_S219_L003

description: Brain single cell 523


title: RBD3_D15

value: RB1 mutation


title: RBD2_D15


title: plate_530s_F24_S379_L003

description: Brain single cell 522


title: plate_530s_F6_S235_L003

description: Brain single cell 525


title: plate_530s_G17_S132_L003

description: Brain single cell 532


title: Control 7-weeks DIO-stz Adipose 5

value: Adipose


title: plate_530s_F5_S227_L003

description: Brain single cell 524


title: plate_530s_F20_S347_L003

description: Brain single cell 520

value: Microglia


title: Control 7-weeks DIO-stz Intestine 5

value: DIO-stz

value: Intestine


title: RBD1_D15


title: Control 7-weeks DIO-stz Brain 5

value: Brain


title: Control 7-weeks DIO-stz Muscle 4

value: Muscle

value: Female


title: plate_530s_F2_S203_L003

description: Brain single cell 519

value: brain

value: adult mice

value: WT


title: Control 7-weeks DIO-stz Liver 4

value: Liver


title: plate_530s_F19_S339_L003

description: Brain single cell 518


title: cRBM3_D15

value: pre-osteoblast


title: plate_530s_F17_S323_L003

description: Brain single cell 516


title: Control 7-weeks DIO-stz Kidney 4

value: Control 7-weeks


title: cRBM2_D15


title: plate_530s_F16_S315_L003

description: Brain single cell 515

value: Macrophages


title: cRBM1_D15


title: plate_530s_F15_S307_L003

description: Brain single cell 514


title: Control 7-weeks DIO-stz Pancreas 4

value: Pancreas


title: plate_530s_F14_S299_L003

description: Brain single cell 513


title: plate_530s_F13_S291_L003

description: Brain single cell 512


title: RBM3_D15


title: Control 7-weeks DIO-stz Intestine 4


title: plate_530s_F23_S371_L003

description: Brain single cell 521


title: plate_530s_F10_S267_L003

description: Brain single cell 509


title: plate_530s_F12_S283_L003

description: Brain single cell 511


title: plate_530s_F11_S275_L003

description: Brain single cell 510


title: plate_530s_F1_S195_L003

description: Brain single cell 508


title: Control 7-weeks DIO-stz Brain 4


title: RBM1_D15


title: Control 7-weeks DIO-stz Blood 4

value: Blood


title: plate_530s_F18_S331_L003

description: Brain single cell 517


title: WT3_D15

value: wild type


title: plate_530s_E6_S43_L003

description: Brain single cell 506


title: plate_530s_E7_S51_L003

description: Brain single cell 507


title: Control 7-weeks DIO-stz Adipose 4

value: Adipose


title: WT2_D15


title: plate_530s_E3_S19_L003

description: Brain single cell 505


title: WT1_D15


title: plate_530s_E22_S171_L003

description: Brain single cell 502


title: plate_530s_E24_S187_L003

description: Brain single cell 504


title: Control 7-weeks DIO-stz Muscle 3


title: Control 7-weeks DIO-stz Brain 3


title: plate_530s_E21_S163_L003

description: Brain single cell 501


title: cRBD3_D0

source_name: mesenchyma stem cell

value: mesenchyma stem cell

value: Corrected RB1 mutation


title: plate_530s_E20_S155_L003

description: Brain single cell 500


title: plate_530s_E2_S11_L003

description: Brain single cell 499


title: RBM2_D15

value: RB1 mutation


title: Control 7-weeks DIO-stz Liver 3

value: DIO-stz


title: plate_530s_E19_S147_L003

description: Brain single cell 498


title: cRBD2_D0


title: plate_530s_E18_S139_L003

description: Brain single cell 497


title: Control 7-weeks DIO-stz Blood 3


title: Control 7-weeks DIO-stz Kidney 3

value: Kidney


title: plate_530s_E17_S131_L003

description: Brain single cell 496


title: plate_530s_E10_S75_L003

description: Brain single cell 494


title: plate_530s_E23_S179_L003

description: Brain single cell 503

value: Microglia


title: plate_530s_E13_S99_L003

description: Brain single cell 495

value: brain


title: RBD3_D0


title: RBD2_D0


title: plate_530s_D9_S258_L003

description: Brain single cell 492

value: adult mice


title: Control 7-weeks DIO-stz Pancreas 3

value: Female


title: plate_530s_E1_S3_L003

description: Brain single cell 493

value: WT


title: Control 7-weeks DIO-stz Adipose 3


title: RBD1_D0


title: plate_530s_D6_S234_L003

description: Brain single cell 490


title: plate_530s_D22_S362_L003

description: Brain single cell 489


title: plate_530s_D21_S354_L003

description: Brain single cell 488


title: cRBM3_D0


title: pFUS 7-weeks DIO Diet Resistant Pancreas 2

source_name: DIO Diet Resistant

value: DIO Diet Resistant

value: pFUS 7-weeks


title: plate_530s_D20_S346_L003

description: Brain single cell 487

value: Macrophages


title: cRBM2_D0


title: plate_530s_D18_S330_L003

description: Brain single cell 486


title: pFUS 7-weeks DIO Diet Resistant Blood 2


title: plate_530s_D16_S314_L003

description: Brain single cell 485


title: cRBM1_D0


title: cRBD1_D0


title: plate_530s_D13_S290_L003

description: Brain single cell 483


title: plate_530s_D14_S298_L003

description: Brain single cell 484


title: pFUS 7-weeks DIO Diet Resistant Liver 2

value: Liver


title: pFUS 7-weeks DIO Diet Resistant Kidney 2


title: plate_530s_D11_S274_L003

description: Brain single cell 481


title: plate_530s_D7_S242_L003

description: Brain single cell 491


title: RBM2_D0


title: RBM1_D0


title: plate_530s_D1_S194_L003

description: Brain single cell 480


title: pFUS 7-weeks DIO Diet Resistant Intestine 2

value: Intestine


title: plate_530s_C9_S66_L003

description: Brain single cell 479


title: plate_530s_C23_S178_L003

description: Brain single cell 477


title: plate_530s_C8_S58_L003

description: Brain single cell 478


title: pFUS 7-weeks DIO Diet Resistant Pancreas 1

value: Pancreas


title: pFUS 7-weeks DIO Diet Resistant Muscle 2

value: Muscle


title: WT2_D0

value: mesenchyma stem cell

value: wild type


title: WT1_D0


title: pFUS 7-weeks DIO Diet Resistant Muscle 1


title: pFUS 7-weeks DIO Diet Resistant Liver 1


title: plate_530s_C17_S130_L003

description: Brain single cell 474


title: plate_530s_C15_S114_L003

description: Brain single cell 472


title: RBM3_D0

value: RB1 mutation


title: plate_530s_C19_S146_L003

description: Brain single cell 475


title: pFUS 7-weeks DIO Diet Resistant Kidney 1


title: pFUS 7-weeks DIO Diet Resistant Intestine 1


title: plate_530s_D12_S282_L003

description: Brain single cell 482


title: plate_530s_C14_S106_L003

description: Brain single cell 471


title: WT3_D0


title: plate_529s_N9_S263_L002

description: Brain single cell 468

value: Het


title: plate_530s_C12_S90_L003

description: Brain single cell 470


title: fibroblast_daughter

data_processing:
Library strategy: WES
QC: FastQC v0.11.5. Sequenced reads were then trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNAeq Alignment: TopHat v2.1.1 for RNASeq, Bowtie2 for ChIPseq
RNAseq normalization: Cufflinks v2.2.1
RNA-seq (HOS samples): alternative splicing analysis for intron retention: juncBASE
ChIPseq sorting, normalization, and visualization: MACS2
Genome_build: hg19
Supplementary_files_format_and_content: RNASeq: FPKM data in .csv; ChIPSeq: genome browser tracks in .bedGrap

source_name: fibroblast

value: fibroblast


title: plate_530s_C21_S162_L003

description: Brain single cell 476


title: plate_529s_N22_S367_L002

description: Brain single cell 464

value: Microglia


title: plate_530s_C1_S2_L003

description: Brain single cell 469

value: brain


title: pFUS 7-weeks DIO Diet Resistant Blood 1

value: Blood


title: plate_529s_N5_S231_L002

description: Brain single cell 466

value: adult mice


title: plate_529s_N3_S215_L002

description: Brain single cell 465


title: fibroblast_father


title: pFUS 7-weeks DIO Diet Resistant Brain 1

value: Brain

value: Female


title: plate_529s_N6_S239_L002

description: Brain single cell 467


title: plate_530s_C16_S122_L003

description: Brain single cell 473

value: WT


title: plate_529s_N17_S327_L002

description: Brain single cell 461


title: plate_529s_N21_S359_L002

description: Brain single cell 463

value: Macrophages


title: Control 3-days Obese ZDF Muscle 44

source_name: Obese ZDF

value: Obese ZDF

value: Male

value: Control 3-days


title: plate_529s_N11_S279_L002

description: Brain single cell 458


title: Control 3-days Obese ZDF Adipose 44

value: Adipose


title: pFUS 7-weeks DIO Diet Resistant Adipose 1

value: DIO Diet Resistant

value: pFUS 7-weeks


title: Control 3-days Obese ZDF Liver 44

value: Liver


title: SS-5

city: Rome

first: Daniela

last: Palacios

address: Largo Francesco Vito 1

country: Italy

institute: Università Cattolica del Sacro Cuore

data_processing:
Read quality was asserted through FastQC, and quality/adapter trimming was carried out using Cutadapt.
Single end reads were aligned to mouse reference mm10 using STAR aligner. Subsequently, reads were counted for genes using htseq-count (features from Ensemble gtf file, ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/).
Differential expression of genes was conducted using DESeq2 with default options. Genes were considered differentially expressed if the adjusted p-value was less than 0.05.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: brain

extract_protocol:
Brains were excised, flash frozen on dry ice, and punches form ventral tegmental areas were dissected.  RNA was extracted using Norgen minicolumn ( Total RNA purification Kit)  and quality checked via Agilent   2100 bioanalyzer assay
Universal Plus mRNA-Seq kit (Tecan Genomics, Redwood City, CA) was used for library preparation following the manufacturer’s instructions.

treatment_protocol: Social stress in early life was based on previously published paradigm (Lo Iacono et al. Addiction biology 2017), The exposure of pups (30 min) to the threatening adult mouse was repeated for 7 consecutive days from P14-P21.

value: Brain punches - Ventral tegmental area

value: Social Stress

tag: Sex

value: male


title: fibroblast_mother

value: fibroblast

value: wild type


title: SS-4


title: SS-2


title: Control 3-days Obese ZDF Liver 43


title: CTR-3

value: Unhandled Control


title: plate_529s_M24_S191_L002

description: Brain single cell 454

value: brain

value: adult mice

tag: notch3 genotype

value: Het

value: Microglia


title: Control 3-days Obese ZDF Muscle 43

value: Obese ZDF

value: Muscle


title: CTR-5


title: CTR-2


title: SS-3


title: plate_529s_M9_S71_L002

description: Brain single cell 456

tag: celltype


title: plate_529s_M10_S79_L002

description: Brain single cell 451


title: plate_529s_N16_S319_L002

description: Brain single cell 460

value: Macrophages


title: plate_529s_M7_S55_L002

description: Brain single cell 455


title: plate_529s_N20_S351_L002

description: Brain single cell 462


title: plate_529s_M21_S167_L002

description: Brain single cell 453


title: Control 3-days Obese ZDF Muscle 42

value: Male

value: Control 3-days


title: Control 3-days Obese ZDF Adipose 43

value: Adipose


title: CTR-1


title: plate_529s_M18_S143_L002

description: Brain single cell 452


title: plate_529s_N15_S311_L002

description: Brain single cell 459


title: plate_529s_M1_S7_L002

description: Brain single cell 450


title: plate_529s_N1_S199_L002

description: Brain single cell 457


title: plate_529s_L6_S238_L002

description: Brain single cell 449


title: plate_529s_L24_S382_L002

description: Brain single cell 447


title: Control 3-days Obese ZDF Liver 42

value: Liver


title: plate_529s_L3_S214_L002

description: Brain single cell 448


title: Control 3-days Obese ZDF Adipose 42


title: Control

city: Chicago

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

institute: Northwestern University

data_processing:
Alignment (Bowtie Version 1)
Raw reads normalized to total reads for each sample on BigWIg file
Northwestern quest server's "findPeaks" command to call peaks
UCSC Genome Browser ENCODE was used for visualization
Genome_build: mm9

source_name: Bone marrow-derived macrophages

extract_protocol:
Start with two confluent 150 cm2 dishes (1x107- 5x107 cells per dish).  Cross-link proteins to DNA by adding formaldehyde drop-wise directly to the culture media for a final concentration of 1% and rotate gently at room temperature (RT) for 10 min. Add glycine to a final concentration of 125 mM to the media and incubate with rotating for 5 min at RT.
Libraries were  constructed according to TacGen

treatment_protocol: Primary macrophages were collected from C57BL/6J and co-cultured with apoptotic Jurkat cells cells (compared to control no AC cells).

value: Bone marrow-derived macrophages

value: Media


title: plate_529s_L23_S374_L002

description: Brain single cell 446

source_name: Brain


title: plate_529s_L17_S326_L002

description: Brain single cell 445


title: plate_529s_L14_S302_L002

description: Brain single cell 444


title: Control 3-days Obese ZDF Liver 41


title: Control 3-days Obese ZDF Muscle 41


title: differentiating C2C12 cells #2

city: Toyoake

first: Takahiko

last: Sato

state: Aichi

address: 1-98, Dengakugakubo, Kutsukakecho

institute: Fujita Health University

data_processing:
After trimming adaptor sequences and low-quality bases with cutadapt-1.9.1, the sequenced reads were mapped to the mouse reference genome (mm10) with TopHat2 v 2.1.0 , and expression levels were calculated as FPKM using Cuf-flinks  v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: differentiation control2

growth_protocol: C2C12 myogenic cells were cultured in DMEM containing 10% FBS.

extract_protocol:
miRNeasy Micro Kit (QIAGEN)
The 500 ng total RNAs were used as starting materials to generate RNA-seq libraries with the TruSeq Stranded mRNA LT sample prep kit (Illumina).

treatment_protocol: After a few days of cell culture at 70~80% of confluency, these cells were differentiated into myotubes in DMEM supplemented with 2% horse serum or 0.2% FBS with or without additional exosomes derived from FBS.

value: skeletal muscle

tag: cell line


title: plate_529s_K6_S46_L002

description: Brain single cell 440


title: plate_529s_K9_S70_L002

description: Brain single cell 443


title: plate_529s_K8_S62_L002

description: Brain single cell 442


title: differentiating C2C12 cells +exosome #2

source_name: differentiation +exosome

value: 0.2%FBS +exosome


title: differentiating C2C12 cells +exosome #3


title: Control 3-days Obese ZDF Adipose 41

tag: model


title: ACs

value: UV-Irradiated Jurkat co-culture


title: pFUS 3-days AM only x10 Obese ZDF Muscle 40

tag: gender

value: pFUS 3-days AM only x10


title: differentiating C2C12 cells +exosome #1

value: 2%HS +exosome


title: plate_529s_K7_S54_L002

description: Brain single cell 441

value: brain

value: adult mice


title: plate_529s_K4_S30_L002

description: Brain single cell 439

value: Het

value: Microglia


title: growing C2C12 cells

source_name: growth control


title: pFUS 3-days AM only x10 Obese ZDF Liver 40

value: Obese ZDF


title: plate_529s_J8_S253_L002

description: Brain single cell 435


title: pFUS 3-days AM only x10 Obese ZDF Adipose 40


title: plate_529s_J23_S373_L002

description: Brain single cell 434


title: differentiating C2C12 cells #1

source_name: differentiation control


title: plate_529s_J22_S365_L002

description: Brain single cell 433


title: RNAseq_SETDB1sh2_UT_R2

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

description: RNAseq

data_processing:
Reads were quality filtered according to the illumina pipeline
Single-end reads were mapped after adapter trimming to the mouse genome assembly mm10 (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html), and the Refseq transcript annotation (ncbiRefSeqCurated 2017/11/16) using topHat2 (TopHat v2.1.1) (Trapnell et al. 2012) with parameters: --max-multihits 1 --b2-very-sensitive).
Reads mapping to the ENCODE black-list regions (https://github.com/Boyle-Lab/Blacklist) (Amemiya et al. 2019) were removed using standard bedtools operations (bedtools v2.29.2).
Per gene read counts were retrieved using standard R/Bioconductor packages (e.g. GenomicRanges and GenomicAlignment together with the proper GFF Refseq annotation ncbiRefSeqCurated 2017/11/16).
Sample normalization was achieved by selecting invariant genes across samples/conditions (Gualdrini et al. 2016).  Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Differentially regulated genes were selected using DESEq2 (R/Bioconductor package version 1.26.0; R version 3.6.2) after turning off the default normalization DESEq2 applies.
Genome_build: mm10
Supplementary_files_format_and_content: .bw are BigWig normalised files

molecule: polyA RNA

source_name: mouse bone marrow derived macrophages

extract_protocol:
Total RNA was extracted from 105 cells using the Zymo Quick-RNA kit (Zymo Research code R1055). RNA-seq was carried out using the SMART-seq2 protocol (Picelli et al. 2014b) with minor modifications. Briefly, 5 ng of total RNA were reverse transcribed with template-switching using oligo(dT) primers and an LNA-containing template-switching oligo (TSO). The resulting cDNA was pre-amplified, purified and tagmented with Tn5 transposase produced in-house using a described protocol (Picelli et al. 2014a). cDNA fragments generated after tagmentation were gap-repaired, enriched by PCR and purified to create the final cDNA library for Illumina NextSeq500 sequencing.
RNAseq_Smartseq2

value: BMDM


title: plate_529s_J19_S341_L002

description: Brain single cell 432


title: plate_529s_J10_S269_L002

description: Brain single cell 430

value: Macrophages


title: RNAseq_SETDB1sh2_UT_R1

description: RNAseq


title: plate_529s_J13_S293_L002

description: Brain single cell 431


title: RNAseq_SETDB1sh2_LPS_R2

description: RNAseq

value: 2h LPS 10 ng/ml


title: pFUS 3-days AM only x10 Obese ZDF Adipose 39

value: Adipose

value: Male


title: pFUS 3-days AM only x10 Obese ZDF Muscle 39

value: Muscle


title: plate_529s_J1_S197_L002

description: Brain single cell 429


title: plate_529s_K17_S134_L002

description: Brain single cell 437


title: plate_529s_K20_S158_L002

description: Brain single cell 438


title: pFUS 3-days AM only x10 Obese ZDF Liver 39

value: Liver


title: plate_529s_I7_S53_L002

description: Brain single cell 428


title: pFUS 3-days AM only x10 Obese ZDF Muscle 38


title: plate_529s_I5_S37_L002

description: Brain single cell 427


title: plate_529s_I16_S125_L002

description: Brain single cell 424


title: plate_529s_K1_S6_L002

description: Brain single cell 436


title: plate_529s_I14_S109_L002

description: Brain single cell 423


title: RNAseq_SETDB1sh2_LPS_R1

description: RNAseq


title: plate_529s_I3_S21_L002

description: Brain single cell 426


title: pFUS 3-days AM only x10 Obese ZDF Liver 38


title: pFUS 3-days AM only x10 Obese ZDF Adipose 38


title: plate_529s_I11_S85_L002

description: Brain single cell 421


title: plate_529s_I24_S189_L002

description: Brain single cell 425

value: WT


title: RNAseq_SETDB1sh1_LPS_R2

description: RNAseq


title: plate_529s_H12_S284_L002

description: Brain single cell 419


title: RNAseq_SETDB1sh1_UT_R1

description: RNAseq


title: plate_529s_I12_S93_L002

description: Brain single cell 422


title: plate_529s_H7_S244_L002

description: Brain single cell 420


title: RNAseq_SETDB1sh1_LPS_R1

description: RNAseq


title: pFUS 3-days AM only x10 Obese ZDF Liver 37


title: pFUS 3-days AM only x10 Obese ZDF Muscle 37


title: pFUS 3-days AM only x1 Obese ZDF Muscle 36

value: pFUS 3-days AM only x1


title: plate_529s_G5_S36_L002

description: Brain single cell 417


title: RNAseq_NTsh2_UT_R2

description: RNAseq


title: RNAseq_SETDB1sh1_UT_R2

description: RNAseq


title: pFUS 3-days AM only x10 Obese ZDF Adipose 37


title: RNAseq_NTsh2_UT_R1

description: RNAseq


title: plate_529s_G15_S116_L002

description: Brain single cell 414


title: plate_529s_G21_S164_L002

description: Brain single cell 415


title: plate_529s_G23_S180_L002

description: Brain single cell 416


title: RNAseq_NTsh2_LPS_R1

description: RNAseq


title: plate_529s_F7_S243_L002

description: Brain single cell 411


title: plate_529s_G10_S76_L002

description: Brain single cell 412


title: RNAseq_NTsh1_UT_R2

description: RNAseq


title: plate_529s_G11_S84_L002

description: Brain single cell 413


title: RNAseq_NTsh2_LPS_R2

description: RNAseq


title: plate_529s_G9_S68_L002

description: Brain single cell 418


title: plate_529s_F24_S379_L002

description: Brain single cell 410


title: pFUS 3-days AM only x1 Obese ZDF Muscle 35


title: pFUS 3-days AM only x1 Obese ZDF Adipose 36


title: pFUS 3-days AM only x1 Obese ZDF Liver 36


title: plate_529s_F16_S315_L002

description: Brain single cell 408


title: RNAseq_NTsh1_UT_R1

description: RNAseq


title: plate_529s_F10_S267_L002

description: Brain single cell 406


title: plate_529s_F18_S331_L002

description: Brain single cell 409


title: pFUS 3-days AM only x1 Obese ZDF Liver 35


title: plate_529s_F14_S299_L002

description: Brain single cell 407


title: plate_529s_E6_S43_L002

description: Brain single cell 405


title: RNAseq_NTsh1_LPS_R2

description: RNAseq


title: pFUS 3-days AM only x1 Obese ZDF Adipose 35


title: plate_529s_E22_S171_L002

description: Brain single cell 403


title: plate_529s_E21_S163_L002

description: Brain single cell 402


title: RNAseq_NTsh1_LPS_R1

description: RNAseq


title: pFUS 3-days AM only x1 Obese ZDF Muscle 34


title: pFUS 3-days AM only x1 Obese ZDF Adipose 34


title: plate_529s_E14_S107_L002

description: Brain single cell 400


title: pFUS 3-days AM only x1 Obese ZDF Liver 34


title: CTCF_NTsh2_UT

description: ChIPseq

data_processing:
Reads were quality filtered according to the illumina pipeline
Single end reads were mapped to the mouse mm10 genome (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html) by exploiting the mapping steps of ShortStack (Johnson et al. 2016).Briefly, ShortStack exploits bowtie to identify all best-matched alignments for each read. It will compute a probability for each alignment to different loci in the genome. To do so the frequency of uniquely aligned reads mapping within the vicinity of multi-mapping reads is used to redistribute multi-mapping reads accordingly.
Mapped reads were filtered in order to remove randomly placed multi-mappers and unmapped reads using SAMtools standard procedure (version 1.9)(Li et al. 2009).
In order to identify high confidence genome wide site of enrichment per antibody we implemented three strategies accordingly to the type of signal distribution evaluated after visual inspection of bigwig tracks on IGV (Robinson et al. 2011):  (i) For narrow TFs-like peaks such as PU.1 and CTCFs we implemented MACS2 version 2.2.6 (Zhang et al. 2008) with parameters “--keep-dup 'all' --call-summits --nomodel --nolambda --extsize 300”. Each ChIP was compared to the input DNA from bone marrow-derived macrophages. A reference set of peaks per antibody was generated by selecting significant peaks in each samples/replicate (qvalue ≤ 10E-5 for CTCF and qvalue ≤ 10E-15 for PU.1) and being consistent between replicates (overlapping area of at least 50% between replicates).  (ii) For H2K27Ac we used peaks identified in ATAC-seq samples (see below) expanding the ATAC peaks by 1.5 kb on both sides.   (iii) For H3K9me3 we exploited SICER v1.1 (Zang et al. 2009) with parameters “mm10 1 250 300 0.80 1000 .01” against the input DNA from macrophages. To increase the signal-to-noise, given the lower and more dispersed signal of H3K9me3 in euchromatic active compartments, we combined the samples by conditions and selected significant blocks with an FDR ≤0.01.
Read counts per samples at the identified loci were retrieved using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013). Sample normalization was achieved by selecting invariant peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Differentially regulated peaks were selected using DESEq2 (R/Bioconductor package version 1.26.0; R version 3.6.2) (Love et al. 2014) after turning off the default normalization DESEq2 applies.
Genome_build: mm10
Supplementary_files_format_and_content: .bw are BigWig normalised files

extract_protocol:
genomic DNA
ChIP-seq was carried out as previously described (Balestrieri et al. 2018). Briefly, 106 lentiviral-infected BMDM cells (H3K27ac, H3K9m3, PU.1) or 5 x 106 lentiviral-infected BMDM cells (CTCF) were fixed with 1% of formaldehyde (Merck cod. 252549) for 10 min at RT and lysed to prepare nuclear extracts. After chromatin shearing by sonication with a Branson Ultrasonics™ Sonifier™, lysates were incubated overnight at 4°C with protein G Dynabeads (Invitrogen, cod.10009D) previously coupled with 1 μg of anti-histone antibody or 10 μg of anti-TF antibody (all the antibodies are listed in the Suppl. Table 7). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Immunoprecipitated chromatin was eluted and cross-link reverted overnight at 65°C. DNA was purified with QIAquick PCR Purification Kit (QIAGEN) and then quantified with QuantiFluor (Promega). DNA libraries were prepared for NextSeq500 sequencing as described (Austenaa et al. 2021). The purified DNA libraries were quantified with the Quantifluor reagent (Cod.E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the High Sensitivity Assay HD5000 (Agilent cod.5067-5592). Library DNA were diluted to a working concentration of 4 nM and Single Reads (76bp) sequenced on an Illumina NextSeq500 platform.

treatment_protocol: LPS (10 ng/ml) treatment for 2h


title: CTCF_NTsh2_LPS

description: ChIPseq


title: plate_529s_D3_S210_L002

description: Brain single cell 397


title: plate_529s_E20_S155_L002

description: Brain single cell 401


title: pFUS 3-days AM only x1 Obese ZDF Muscle 33


title: plate_529s_D7_S242_L002

description: Brain single cell 398


title: plate_529s_D14_S298_L002

description: Brain single cell 395


title: pFUS 3-days AM only x1 Obese ZDF Liver 33


title: CTCF_SETDBsh2_UT

description: ChIPseq


title: plate_529s_D16_S314_L002

description: Brain single cell 396


title: plate_529s_E23_S179_L002

description: Brain single cell 404


title: CTCF_SETDBsh2_LPS

description: ChIPseq


title: plate_529s_C5_S34_L002

description: Brain single cell 393


title: plate_529s_C14_S106_L002

description: Brain single cell 389


title: plate_529s_D10_S266_L002

description: Brain single cell 394


title: CTCF_SETDBsh1_LPS

description: ChIPseq


title: plate_529s_C19_S146_L002

description: Brain single cell 391


title: plate_529s_C22_S170_L002

description: Brain single cell 392


title: CTCF_SETDBsh1_UT

description: ChIPseq


title: plate_529s_C17_S130_L002

description: Brain single cell 390


title: pFUS 4-weeks AM & PM x10 Obese ZDF Muscle 32

value: pFUS 4-weeks AM & PM x10


title: pFUS 4-weeks AM & PM x10 Obese ZDF Liver 32


title: plate_529s_D8_S250_L002

description: Brain single cell 399


title: plate_529s_B5_S225_L002

description: Brain single cell 387


title: plate_529s_B23_S369_L002

description: Brain single cell 386


title: plate_529s_B7_S241_L002

description: Brain single cell 388


title: plate_529s_B22_S361_L002

description: Brain single cell 385


title: pFUS 4-weeks AM & PM x10 Obese ZDF Adipose 32


title: CTCF_NTsh1_LPS

description: ChIPseq


title: pFUS 3-days AM only x1 Obese ZDF Adipose 33


title: PU.1_NTsh2_UT

description: ChIPseq

value: PU.1_home made


title: PU.1_NTsh2_LPS

description: ChIPseq


title: plate_529s_A18_S137_L002

description: Brain single cell 382


title: plate_529s_A20_S153_L002

description: Brain single cell 383


title: plate_529s_B11_S273_L002

description: Brain single cell 384


title: pFUS 4-weeks AM & PM x10 Obese ZDF Liver 31


title: pFUS 4-weeks AM & PM x10 Obese ZDF Muscle 31


title: pFUS 4-weeks AM & PM x10 Obese ZDF Adipose 31


title: PU.1_SETDBsh2_UT

description: ChIPseq


title: plate_524s_N21_S359_L001

description: Brain single cell 378


title: plate_524s_N23_S375_L001

description: Brain single cell 379


title: plate_524s_M23_S183_L001

description: Brain single cell 377


title: pFUS 4-weeks AM & PM x10 Obese ZDF Muscle 30


title: PU.1_SETDBsh1_UT

description: ChIPseq


title: plate_524s_N7_S247_L001

description: Brain single cell 380


title: plate_529s_A10_S73_L002

description: Brain single cell 381


title: PU.1_SETDBsh2_LPS

description: ChIPseq


title: pFUS 4-weeks AM & PM x10 Obese ZDF Liver 30


title: CTCF_NTsh1_UT

description: ChIPseq


title: plate_524s_M16_S127_L001

description: Brain single cell 375


title: pFUS 4-weeks AM & PM x10 Obese ZDF Adipose 30


title: PU.1_SETDBsh1_LPS

description: ChIPseq


title: plate_524s_M15_S119_L001

description: Brain single cell 374


title: plate_524s_M14_S111_L001

description: Brain single cell 373


title: pFUS 4-weeks AM & PM x10 Obese ZDF Muscle 29


title: plate_524s_L10_S270_L001

description: Brain single cell 369


title: pFUS 4-weeks AM & PM x10 Obese ZDF Adipose 29


title: plate_524s_L5_S230_L001

description: Brain single cell 371


title: plate_524s_L8_S254_L001

description: Brain single cell 372


title: plate_524s_K6_S46_L001

description: Brain single cell 368


title: pFUS 4-weeks AM & PM x10 Obese ZDF Liver 29


title: plate_524s_K4_S30_L001

description: Brain single cell 367


title: plate_524s_L15_S310_L001

description: Brain single cell 370


title: PU.1_NTsh1_LPS

description: ChIPseq


title: H3K9me3_NTsh2_UT

description: ChIPseq


title: H3K9me3_NTsh2_LPS

description: ChIPseq


title: plate_524s_M18_S143_L001

description: Brain single cell 376


title: pFUS 4-weeks AM only x10 Obese ZDF Muscle 28

value: pFUS 4-weeks AM only x10


title: H3K9me3_SETDBsh2_UT

description: ChIPseq


title: plate_524s_K19_S150_L001

description: Brain single cell 364

value: brain


title: pFUS 4-weeks AM only x10 Obese ZDF Liver 28


title: plate_524s_K22_S174_L001

description: Brain single cell 365

value: adult mice


title: plate_524s_K18_S142_L001

description: Brain single cell 363

value: Het


title: plate_524s_K13_S102_L001

description: Brain single cell 362


title: plate_524s_K10_S78_L001

description: Brain single cell 361


title: plate_524s_K24_S190_L001

description: Brain single cell 366

value: Microglia


title: H3K9me3_SETDBsh2_LPS

description: ChIPseq


title: pFUS 4-weeks AM only x10 Obese ZDF Adipose 28

value: Obese ZDF


title: pFUS 4-weeks AM only x10 Obese ZDF Muscle 27


title: plate_524s_J4_S221_L001

description: Brain single cell 360


title: H3K9me3_SETDBsh1_UT

description: ChIPseq

value: BMDM


title: PU.1_NTsh1_UT

description: ChIPseq


title: H3K9me3_SETDBsh1_LPS

description: ChIPseq


title: plate_524s_J14_S301_L001

description: Brain single cell 358


title: plate_524s_J22_S365_L001

description: Brain single cell 359


title: pFUS 4-weeks AM only x10 Obese ZDF Muscle 26


title: plate_524s_I15_S117_L001

description: Brain single cell 355

value: Macrophages


title: pFUS 4-weeks AM only x10 Obese ZDF Adipose 27


title: plate_524s_J10_S269_L001

description: Brain single cell 357


title: plate_524s_I4_S29_L001

description: Brain single cell 356


title: plate_524s_H7_S244_L001

description: Brain single cell 353


title: H3K9me3_NTsh1_UT

description: ChIPseq


title: plate_524s_I1_S5_L001

description: Brain single cell 354


title: H3K9me3_NTsh1_LPS

description: ChIPseq

value: 2h LPS 10 ng/ml


title: plate_524s_H4_S220_L001

description: Brain single cell 352


title: H3K27Ac_NTsh2_LPS

description: ChIPseq


title: pFUS 4-weeks AM only x10 Obese ZDF Liver 26


title: H3K27Ac_NTsh2_UT

description: ChIPseq


title: plate_524s_H23_S372_L001

description: Brain single cell 351


title: pFUS 4-weeks AM only x10 Obese ZDF Muscle 25


title: plate_524s_G20_S156_L001

description: Brain single cell 347


title: plate_524s_G19_S148_L001

description: Brain single cell 346


title: plate_524s_G5_S36_L001

description: Brain single cell 348


title: plate_524s_H12_S284_L001

description: Brain single cell 349


title: plate_524s_H19_S340_L001

description: Brain single cell 350


title: H3K27Ac_SETDBsh2_LPS

description: ChIPseq


title: H3K27Ac_SETDBsh2_UT

description: ChIPseq


title: pFUS 4-weeks AM only x10 Obese ZDF Liver 27


title: plate_524s_E8_S59_L001

description: Brain single cell 344

value: KO


title: plate_524s_E9_S67_L001

description: Brain single cell 345


title: pFUS 4-weeks AM only x10 Obese ZDF Liver 25

value: Male


title: pFUS 4-weeks AM only x10 Obese ZDF Adipose 25

value: Adipose


title: H3K27Ac_SETDBsh1_UT

description: ChIPseq


title: plate_524s_E7_S51_L001

description: Brain single cell 343


title: plate_524s_E4_S27_L001

description: Brain single cell 340


title: plate_524s_E5_S35_L001

description: Brain single cell 341


title: pFUS 4-weeks AM & PM x1 Obese ZDF Liver 24

value: Liver

value: pFUS 4-weeks AM & PM x1


title: plate_524s_E6_S43_L001

description: Brain single cell 342


title: plate_524s_E3_S19_L001

description: Brain single cell 339


title: pFUS 4-weeks AM & PM x1 Obese ZDF Muscle 24

value: Muscle


title: plate_524s_E23_S179_L001

description: Brain single cell 338


title: pFUS 4-weeks AM & PM x1 Obese ZDF Adipose 24


title: H3K27Ac_NTsh1_UT

description: ChIPseq


title: H3K27Ac_SETDBsh1_LPS

description: ChIPseq


title: pFUS 4-weeks AM only x10 Obese ZDF Adipose 26


title: ATAC_SETDB1sh2_UT_R3

data_processing:
Reads were quality filtered according to the illumina pipeline
Following adapter trimming, single end reads were trimmed with trimmomatic (Bolger et al. 2014) (version 0.39 flags: EADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:38).
Resulting reads were mapped with ShortStack (Axtell 2013).
Resulting bam files were then filtered using SAMtools (version 1.9) in order to remove unmapped reads, failing quality or mapping to mitochondrial chromosome.
Reads were then shifted of 4nt on the positive strand and -5nt on the negative strand using basic awk operations (Buenrostro et al. 2013).
Peak calling was performed using MACS2 (version 2.2.6; options --nomodel --extsize 146 --nolambda --keep-dup 'all' --call-summits). A reference set of peaks was created by selecting peaks called in each samples/replicate with qvalue ≤ 0.01 and being consistent between replicates (overlapping area of at least 50% between replicates).
The resulting set of peaks was used to count reads in each sample using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013).
Sample normalization was achieved by selecting invariant ATAC peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Differentially regulated peaks were selected using DESEq2 (R/Bioconductor package version 1.26.0; R version 3.6.2) after turning off the default normalization DESEq2 applies.
Genome_build: mm10
Supplementary_files_format_and_content: .bw are BigWig normalised files

extract_protocol:
genomic DNA
5 × 104 lentiviral-infected BMDM cells were pelleted by centrifugation and resuspended in 50 µl of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM MgCl2, 0.1% Igepal CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation for 10 min at 500g at 4 °C and resuspended in 25 µl of reaction buffer containing 1 µl of Tn5 transposase made in-house using a described protocol (Picelli et al. 2014a), 5 µl of 5x transposase buffer (50 mM Tris-HCl, (pH 8.4) and 25 mM MgCl2), and 19 µl of milliQ water. The tagmentation mix was incubated at 37 °C for 60 min gently shaking, in order to avoid precipitation of nuclei. The reaction was stopped by the addition of 5 µl of cleanup buffer (900 mM NaCl, 30 mM EDTA), 2 µl of 5% SDS and 2 µl of Proteinase K (20 µg /µl) (Merck cod. P2308) and incubation for 30 min at 40 °C. Tagmented DNA was isolated using 2× Agencourt Ampure Xp beads (Beckman cod.A63881) and amplified by PCR with the HotStart Kapa HiFi enzyme (Roche cod. 07958889001). Fragments smaller than 600 bp were isolated by negative size selection (using 0.65× Agencourt Ampure Xp beads) and then purified with 1.8× Agencourt Ampure Xp beads. Libraries were single-end sequenced (76 bp) on an Illumina NextSeq500 platform.


title: plate_524s_E21_S163_L001

description: Brain single cell 336


title: H3K27Ac_NTsh1_LPS

description: ChIPseq


title: pFUS 4-weeks AM & PM x1 Obese ZDF Muscle 23


title: plate_524s_E20_S155_L001

description: Brain single cell 335


title: ATAC_SETDB1sh2_UT_R2


title: plate_524s_E2_S11_L001

description: Brain single cell 334


title: plate_524s_E19_S147_L001

description: Brain single cell 333


title: pFUS 4-weeks AM & PM x1 Obese ZDF Liver 23


title: plate_524s_E18_S139_L001

description: Brain single cell 332


title: plate_524s_E17_S131_L001

description: Brain single cell 331


title: pFUS 4-weeks AM & PM x1 Obese ZDF Adipose 23


title: pFUS 4-weeks AM & PM x1 Obese ZDF Muscle 22


title: plate_524s_E16_S123_L001

description: Brain single cell 330


title: ATAC_SETDB1sh2_LPS_R3


title: plate_524s_E15_S115_L001

description: Brain single cell 329


title: ATAC_SETDB1sh2_LPS_R2


title: plate_524s_E22_S171_L001

description: Brain single cell 337


title: pFUS 4-weeks AM & PM x1 Obese ZDF Liver 22


title: plate_524s_E14_S107_L001

description: Brain single cell 328


title: plate_524s_E13_S99_L001

description: Brain single cell 327


title: ATAC_SETDB1sh2_LPS_R1


title: plate_524s_D8_S250_L001

description: Brain single cell 323


title: plate_524s_E11_S83_L001

description: Brain single cell 325


title: pFUS 4-weeks AM & PM x1 Obese ZDF Adipose 22


title: plate_524s_D9_S258_L001

description: Brain single cell 324


title: pFUS 4-weeks AM & PM x1 Obese ZDF Muscle 21


title: plate_524s_D7_S242_L001

description: Brain single cell 322


title: ATAC_SETDB1sh2_UT_R1


title: pFUS 4-weeks AM & PM x1 Obese ZDF Liver 21


title: plate_524s_D6_S234_L001

description: Brain single cell 321


title: plate_524s_D24_S378_L001

description: Brain single cell 319


title: ATAC_SETDB1sh1_UT_R2


title: plate_524s_D5_S226_L001

description: Brain single cell 320


title: pFUS 4-weeks AM & PM x1 Obese ZDF Adipose 21


title: pFUS 7-weeks Lean Zucker Muscle 19

source_name: Lean Zucker

value: Lean Zucker

value: pFUS 7-weeks


title: plate_524s_D20_S346_L001

description: Brain single cell 316


title: plate_524s_D21_S354_L001

description: Brain single cell 317


title: ATAC_SETDB1sh1_LPS_R3


title: pFUS 7-weeks Lean Zucker Adipose 19


title: ATAC_SETDB1sh1_LPS_R1


title: plate_524s_D19_S338_L001

description: Brain single cell 315


title: plate_524s_E12_S91_L001

description: Brain single cell 326


title: plate_524s_D17_S322_L001

description: Brain single cell 313


title: pFUS 7-weeks Lean Zucker Muscle 18


title: plate_524s_D16_S314_L001

description: Brain single cell 312


title: ATAC_SETDB1sh1_UT_R3


title: plate_524s_D18_S330_L001

description: Brain single cell 314


title: plate_524s_D14_S298_L001

description: Brain single cell 310


title: plate_524s_D15_S306_L001

description: Brain single cell 311


title: plate_524s_D22_S362_L001

description: Brain single cell 318


title: plate_524s_D13_S290_L001

description: Brain single cell 309


title: pFUS 7-weeks Lean Zucker Adipose 18


title: pFUS 7-weeks Lean Zucker Adipose 17


title: pFUS 7-weeks Lean Zucker Muscle 17


title: ATAC_NTsh2_UT_R1


title: ATAC_SETDB1sh1_UT_R1


title: pFUS 7-weeks Lean Zucker Muscle 16


title: ATAC_NTsh2_LPS_R3


title: plate_524s_D11_S274_L001

description: Brain single cell 307


title: pFUS 7-weeks Lean Zucker Adipose 16


title: ATAC_SETDB1sh1_LPS_R2


title: ATAC_NTsh2_LPS_R2


title: plate_524s_D1_S194_L001

description: Brain single cell 305


title: ATAC_NTsh2_UT_R3


title: plate_524s_C23_S178_L001

description: Brain single cell 302


title: ATAC_NTsh2_UT_R2


title: plate_524s_C8_S58_L001

description: Brain single cell 304


title: plate_524s_D12_S282_L001

description: Brain single cell 308


title: ATAC_NTsh2_LPS_R1


title: Control 7-weeks Lean Zucker Muscle 14

value: Control 7-weeks


title: Control 7-weeks Lean Zucker Adipose 14


title: plate_524s_C11_S82_L001

description: Brain single cell 299

value: brain


title: plate_524s_C21_S162_L001

description: Brain single cell 301

value: adult mice


title: plate_524s_C3_S18_L001

description: Brain single cell 303


title: plate_524s_C17_S130_L001

description: Brain single cell 300


title: plate_524s_D10_S266_L001

description: Brain single cell 306


title: Control 7-weeks Lean Zucker Muscle 13


title: plate_524s_B8_S249_L001

description: Brain single cell 298


title: plate_524s_A24_S185_L001

description: Brain single cell 291


title: ATAC_NTsh1_UT_R2


title: plate_524s_B15_S305_L001

description: Brain single cell 294


title: Control 7-weeks Lean Zucker Muscle 12


title: plate_524s_A4_S25_L001

description: Brain single cell 292


title: ATAC_NTsh1_UT_R1


title: Control 7-weeks Lean Zucker Adipose 13


title: ATAC_NTsh1_LPS_R3


title: plate_060s_M9_S71_L006

description: Brain single cell 290


title: plate_060s_M7_S55_L006

description: Brain single cell 289


title: ATAC_NTsh1_LPS_R2


title: ATAC_NTsh1_UT_R3


title: plate_524s_B4_S217_L001

description: Brain single cell 295


title: Control 7-weeks Lean Zucker Muscle 11


title: plate_524s_B6_S233_L001

description: Brain single cell 297


title: plate_524s_B5_S225_L001

description: Brain single cell 296


title: Control 7-weeks Lean Zucker Adipose 11


title: plate_060s_M5_S39_L006

description: Brain single cell 287


title: Control 7-weeks Lean Zucker Adipose 12


title: ATAC_NTsh1_LPS_R1


title: plate_060s_M4_S31_L006

description: Brain single cell 286


title: plate_060s_M6_S47_L006

description: Brain single cell 288


title: M12

city: London

first: Esteban

middle: Alberto

last: Gomez Cifuentes

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

description:
Differential Gene Expression Analysis were made to compare transcriptomic profiles between  different leukocytes population from treatment (mice treated with MCTR3 stimulated monocytes) and control.
MONOUMIrawcounts.txt

data_processing:
Illumina NextSeq 500
10X Genomics cellranger pipeline: fastq files were generated for every sample, followed by barcode processing, trimming, cleaning and aligment to the genome reference.
Filtering: genes were considered to be expressed at a reasonable level if at least two cells contain more than 2 transcript from the gene.
Aggregation: Before differential gene expression analysis, different samples for each group were aggregated (to have a normalized set of cells per group) using “cell ranger aggr” function. and t-SNE analysis were performed for clustering different cell types.
Differential Gene Expression Analysis between treatment (MCTR3 stimulated-monocytes) vs control (vehicle-monocytes):  likelihood ratio test method from the Bioconductor package "edgeR" (adjust p value < 0.05 using BH correction).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene UMI counts for each cell in the treatment (MCTR3) and control (MONO) groups.

source_name: CD45+ cells (Leukocytes)

extract_protocol:
Following paw tissue digestion, live cells were obtained using EasySep Dead cell Removal Kit. Cells were incubated with AF700 CD45 for 30 minutes at 4C. Cells were suspended in FACS buffer and BD FACS Aria II was used to sort for CD45 positive cells, which were collected for single cell sequencing.
Single Cell libraries were created using the Chromium 3' Library & Gel Bead Kit as described in the manufacturers user guide.

value: paw joints

value: Mice were treated with monocytes isolated from arthritic mice that were previously incubated with vehicle

tag: pre-analysis test

value: Raw seq were demultiplexes, cleaned, filtered and align using Cell Ranger pipeline


title: M10


title: plate_524s_B13_S289_L001

description: Brain single cell 293

value: Microglia


title: pFUS 7-weeks Obese ZDF Adipose 10

value: Obese ZDF


title: plate_060s_M3_S23_L006

description: Brain single cell 285

value: Macrophages


title: M9


title: plate_060s_M23_S183_L006

description: Brain single cell 284

value: KO


title: pFUS 7-weeks Obese ZDF Adipose 9

value: Male


title: plate_060s_M21_S167_L006

description: Brain single cell 282


title: plate_060s_M19_S151_L006

description: Brain single cell 280


title: M5

description:
Differential Gene Expression Analysis were made to compare transcriptomic profiles between  different leukocytes population from treatment (mice treated with MCTR3 stimulated monocytes) and control.
MCTR3UMIrawcounts.txt

value: Mice were treated with monocytes isolated from arthritic mice that were previously incubated with 1nM MCTR3


title: pFUS 7-weeks Obese ZDF Adipose 6

value: Adipose


title: M4


title: plate_060s_M10_S79_L006

description: Brain single cell 276


title: M7

value: Mice were treated with monocytes isolated from arthritic mice that were previously incubated with vehicle.


title: Control 7-weeks Obese ZDF Adipose 4


title: plate_060s_M17_S135_L006

description: Brain single cell 279


title: Control 7-weeks Obese ZDF Adipose 5


title: plate_060s_M14_S111_L006

description: Brain single cell 277


title: plate_060s_M16_S127_L006

description: Brain single cell 278


title: M1


title: M3


title: plate_060s_L8_S254_L006

description: Brain single cell 275


title: plate_060s_M2_S15_L006

description: Brain single cell 281


title: Control 7-weeks Obese ZDF Adipose 2


title: plate_060s_L7_S246_L006

description: Brain single cell 274


title: Control 7-weeks Obese ZDF Adipose 1


title: plate_060s_M22_S175_L006

description: Brain single cell 283


title: plate_060s_L21_S358_L006

description: Brain single cell 273


title: plate_060s_L2_S206_L006

description: Brain single cell 272


title: B17924

city: Dallas

first: Sara

last: Hildebrand

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

description:
Rnps1 ub/ub TNF -/-
Dataset S3 Dataset isoform_switches_with_consequence_HSCs
Dataset S7 Dataset_splicing F181I/F181I_vs_F181I/F181I_TNF_KO (HSCs)
Dataset S9 Dataset_splicing F181I/+_TNF_KO_vs_F181I/F181I_TNF_KO (HSCs)

data_processing:
Adapters were trimmed from fastq.gz files using cutadapt v1.9.dev4
Trimmed fastq.gz were aligned to the mm10 reference genome using tophat-2.0.10
BAM files resulting from alignments were run through cuffdiff (cufflinks v2.1.1) for differential expression
BAM files were also run through ASpli v1.8.1 (R v3.5.3) for splicing analysis
Genome_build: mm10
Supplementary_files_format_and_content: excel file include FPKM values for each Sample (Cd8+ T cells)
Supplementary_files_format_and_content: excel files including PIR and PSI metrics for splicing (all samples)

source_name: HSCs

extract_protocol:
Total RNAs from the splenic CD8+ T or HECs cells were extracted using the RNeasy Plus kit with genomic DNA elimination (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared using the KAPA Stranded RNA-Seq kit with RiboErase (HMR) (Kapa Biosystems), according to the manufacturer’s instructions.

tag: cell type

value: HSCs

value: Rnps1 ub/ub TNF -/-

value: no treatment


title: pFUS 7-weeks Lean Zucker Liver 20

value: Lean Zucker

value: Liver

value: pFUS 7-weeks


title: plate_060s_L19_S342_L006

description: Brain single cell 271

data_processing:
The sequencing reads were first aligned to the mouse reference genome Gencode M26 genome with STAR software.
Genome_build: Gencode M26
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

value: brain

value: adult mice


title: B17923

description:
Rnps1 +/ub TNF -/-
Dataset S3 Dataset isoform_switches_with_consequence_HSCs
Dataset S9 Dataset_splicing F181I/+_TNF_KO_vs_F181I/F181I_TNF_KO (HSCs)

value: Rnps1 +/ub TNF -/-


title: pFUS 7-weeks Lean Zucker Brain 20

value: Brain


title: pFUS 7-weeks Obese ZDF Adipose 8

value: Obese ZDF


title: plate_060s_L11_S278_L006

description: Brain single cell 266

value: Macrophages


title: plate_060s_L17_S326_L006

description: Brain single cell 269

value: KO


title: B17922


title: plate_060s_L16_S318_L006

description: Brain single cell 268


title: plate_060s_L18_S334_L006

description: Brain single cell 270


title: B18682

description:
Rnps1 ub/ub TNF +/+
Dataset S3 Dataset isoform_switches_with_consequence_HSCs
Dataset S5 Dataset_splicing F181I/F181I_WT (HSCs)
Dataset S7 Dataset_splicing F181I/F181I_vs_F181I/F181I_TNF_KO (HSCs)

value: Rnps1 ub/ub TNF +/+


title: plate_060s_L13_S294_L006

description: Brain single cell 267

value: Microglia


title: B18681

description:
Rnps1 +/+ TNF +/+
Dataset S3 Dataset isoform_switches_with_consequence_HSCs
Dataset S5 Dataset_splicing F181I/F181I_WT (HSCs)

value: Rnps1 +/+ TNF +/+


title: B18679


title: B18683


title: pFUS 7-weeks Lean Zucker Blood 20

value: Blood

value: Male


title: pFUS 7-weeks Lean Zucker Blood 19


title: plate_060s_K6_S46_L006

description: Brain single cell 264


title: plate_060s_K5_S38_L006

description: Brain single cell 263


title: pFUS 7-weeks Lean Zucker Brain 19


title: Z1204

description:
Rnps1 ub/ub TNF -/-
Dataset S6 Dataset_splicing F181I/F181I_vs_F181I/F181I_TNF_KO (primary CD8+ T cells)
Dataset S8 Dataset_splicing F181I/+_TNF_KO_vs_F181I/F181I_TNF_KO (primary CD8+ T cells)

source_name: Cd8+ T-cells

value: Cd8+ T-cells

value: Rnps1 ub/ub TNF -/-


title: plate_060s_K23_S182_L006

description: Brain single cell 261


title: plate_060s_K22_S174_L006

description: Brain single cell 260


title: plate_060s_K20_S158_L006

description: Brain single cell 259


title: B18680

value: HSCs

value: no treatment


title: plate_060s_K3_S22_L006

description: Brain single cell 262


title: Z1203


title: pFUS 7-weeks Lean Zucker Brain 18

value: Lean Zucker

value: pFUS 7-weeks


title: pFUS 7-weeks Lean Zucker Liver 18

value: Liver


title: plate_060s_K18_S142_L006

description: Brain single cell 257

value: brain

value: adult mice


title: plate_060s_K16_S126_L006

description: Brain single cell 256


title: Z1202


title: pFUS 7-weeks Lean Zucker Blood 18


title: plate_060s_L10_S270_L006

description: Brain single cell 265


title: plate_060s_K14_S110_L006

description: Brain single cell 254


title: plate_060s_K13_S102_L006

description: Brain single cell 253


title: plate_060s_K15_S118_L006

description: Brain single cell 255


title: pFUS 7-weeks Lean Zucker Blood 17


title: pFUS 7-weeks Lean Zucker Liver 17


title: pFUS 7-weeks Lean Zucker Brain 17

value: Brain


title: Z1201

description:
Rnps1 +/ub TNF -/-
Dataset S8 Dataset_splicing F181I/+_TNF_KO_vs_F181I/F181I_TNF_KO (primary CD8+ T cells)

value: Rnps1 +/ub TNF -/-


title: plate_060s_K11_S86_L006

description: Brain single cell 252

value: KO


title: Z1199


title: P3_spot

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

data_processing:
Sequenced reads were trimmed for adaptor sequence, low-quality base calls using Skewer v0.2.2 with parameters -m pe -l 36 -q 15 -Q 15
Reads were mapped to CBS138 whole genome using TopHat v2.1.1 with parameters -p 12 -g 1 --b2-very-sensitive --library-type fr-firststrand
Reads counts per feature (ORF) were obtained with the htseq-count script from HTSeq (v 0.7.1) using parameters -m union -s reverse -t gene -i Name
Genome_build: CBS138
Supplementary_files_format_and_content: Table with read counts for each feature (ORF)

organism: Nakaseomyces glabratus

source_name: Cell culture solid

growth_protocol: Cells were grown in liquid or solid medium and exposed to fluconazole stress for 1h or 24h, respectively, or in absence of fluconazole (control). Cells were collected and frozen at -80ºC until RNA extraction

extract_protocol:
Ambion Ribopure-Yeast RNA kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols


title: P2_spot


title: P1_spot


title: plate_060s_K19_S150_L006

description: Brain single cell 258

extract_protocol:
We used transgenic mouse reporter line (SM22-Cre;Rosa26-stop-tdTomato). We chosed to focus our efforts to adult mice brain cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology


title: pFUS 7-weeks Lean Zucker Liver 19


title: Z1200


title: plate_060s_K1_S6_L006

description: Brain single cell 250


title: plate_060s_J9_S261_L006

description: Brain single cell 249

value: Macrophages


title: P3_liq

source_name: Cell culture liquid


title: Z1198

description:
Rnps1 ub/ub TNF +/+
Dataset S6 Dataset_splicing F181I/F181I_vs_F181I/F181I_TNF_KO (primary CD8+ T cells)

value: Rnps1 ub/ub TNF +/+


title: Z1197


title: plate_060s_K10_S78_L006

description: Brain single cell 251


title: pFUS 7-weeks Lean Zucker Liver 16


title: K3_spot

value: WT


title: P2_liq


title: Control 7-weeks Lean Zucker Liver 15

value: Control 7-weeks


title: plate_060s_J3_S213_L006

description: Brain single cell 246


title: Z1196


title: pFUS 7-weeks Lean Zucker Brain 16

value: Male


title: plate_060s_J8_S253_L006

description: Brain single cell 248


title: RNAseq_tumor_associated_macrophages_Ahr_cKO_rep3

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Alignment: Sequencing reads were aligned against the mouse reference genome sequence mm10 using the STAR aligner. Only uniquely mapped reads were kept.
Read counting: STAR integrated function --quantMode GeneCounts was applied using Ensembl Genes V85 gene annotations. Only reverse-mapping read counts (RF) were utilized for downstream analyses.
Normalization: FPKM normalization was applied using edgeR after intra- and inter-sample normalization (“calcNormFactors” and “estimateTagwiseDisp”).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNAseq_FPKM.tsv: Tab-separated table of FPKM values.

source_name: tumor associated macrophages

growth_protocol: Tumors were implanted orthotopically in the pancreas with 10x10^3 cells of the KPC primary pancreatic adenocarcinoma organoid cell line MT4. 14 days after tumor implantation, tumors were dissociated using Collagenase and DNase 1. CD45+CD11b+F4/80+ Macrophages were enriched by flow cytometry sorting from normal pancreas or PDAC tumors.

extract_protocol:
Extraction of RNA was performed using Norgen Single Cell RNA extraction kit or RNeasy Plus Mini extraction kit.
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech #634894) was used per manufacturer’s instructions for amplification of RNA and subsequent cDNA synthesis. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V1 or V2 Set A (FC-131-1002 or FC-131-2001) followed by manufacturer’s instructions.

value: C57/BL6 Ahr fl/fl Lys M

tag: disease status

value: orthotopic PDAC tumors

value: tumor associated macrophages


title: plate_060s_J22_S365_L006

description: Brain single cell 245

tag: tissue

value: Microglia


title: P1_liq


title: pFUS 7-weeks Lean Zucker Blood 16

data_processing:
Fastq files of the paired end reads were merged into two files for each sample, one for R1 and one for R2 using Unix commands.
Base quality control was checked using Fast QC v0.10.1 from Babraham Bioinformatics.
Sequencing reads were mapped to the annotated rat genome version, Rattus norvegicus Rnor 6.0.91, using STAR_2.5.3a aligner.
Transcript abundance estimates were generated from the sorted BAM files using RSEM.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rsem_genes_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every gene and every sample
Supplementary_files_format_and_content: rsem_isoforms_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every transcript and every sample

value: Lean Zucker

value: Blood

tag: treatment


title: plate_060s_J5_S229_L006

description: Brain single cell 247


title: plate_060s_J20_S349_L006

description: Brain single cell 243


title: Control 7-weeks Lean Zucker Blood 14


title: RNAseq_tumor_associated_macrophages_WT_rep3

value: C57/BL6 Ahr fl/fl


title: plate_060s_J21_S357_L006

description: Brain single cell 244

value: brain


title: K1_spot


title: RNAseq_tumor_associated_macrophages_Ahr_cKO_rep2


title: Control 7-weeks Lean Zucker Brain 14


title: K2_liq


title: K3_liq


title: RNAseq_tumor_associated_macrophages_Ahr_cKO_rep1


title: Control 7-weeks Lean Zucker Blood 15


title: RNAseq_tumor_associated_macrophages_WT_rep2


title: K2_spot


title: plate_060s_J2_S205_L006

description: Brain single cell 242

value: adult mice


title: K1_liq


title: Control 7-weeks Lean Zucker Liver 14

value: Liver


title: plate_060s_J17_S325_L006

description: Brain single cell 241


title: RNAseq_resident_macrophages_rep4

source_name: pancreas resident macrophages

value: C57/BL6 WT

value: healthy control

value: pancreas resident macrophages


title: RNAseq_tumor_associated_macrophages_WT_rep1


title: Control 7-weeks Lean Zucker Brain 13

value: Brain


title: plate_060s_J16_S317_L006

description: Brain single cell 240

value: KO


title: Control 7-weeks Lean Zucker Blood 13

value: Control 7-weeks


title: Control 7-weeks Lean Zucker Liver 13

value: Male


title: RNAseq_resident_macrophages_rep3


title: Control 7-weeks Lean Zucker Brain 15


title: RNAseq_resident_macrophages_rep2


title: Control 7-weeks Lean Zucker Brain 12


title: plate_060s_J11_S277_L006

description: Brain single cell 236


title: nutrient starvation replicate 1

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

description:
rRNA depletion
PBS rep1
directional RNA-Seq

data_processing:
Adapter sequence was trimmed using trim_galore.
The trimmed reads were mapped to the TB genome using bowtie2.
The number of read pairs mapped to each gene were counted using featureCount.
The differential expression was analyzed using DESeq2.
Assembly: Mycobacterium tuberculosis H37Rv assembly ASM19595v2.
Supplementary files format and content: *.deseq.gene.txt: Tab-delimited DESeq2 results.

organism: Mycobacterium tuberculosis H37Rv

source_name: nutrient starvation

growth_protocol: M. tuberculosis was grown shaking at 37°C in Middlebrook 7H9 supplemented with 10% (v/v) OADC enrichment (5% (w/v) bovine albumin fraction V, 2% (w/v) dextrose, 0.003% (w/v) catalase, 0.85% (w/v) sodium chloride in water), 0.2% (v/v) glycerol and 0.05% (v/v) tyloxapol unless otherwise described in treatment protocol.

extract_protocol:
Cultures were spun down, resuspended in TRIzol, lyzed and the supernatants were transferred to Zymo-Spin IICR Columns and processed according to the manufacturer’s Direct-zolTM RNA Miniprep protocol.
RNA libraries were prepared for sequencing using NEB bacteria rRNA depletion kit and Ultra II directional RNAseq kit.

treatment_protocol: For nutrient limitation, actively growing cells were spun down, washed twice in PBS and resuspended in PBS supplemented with 0.05% tyloxapol. The cultures were incubated shaking at 37°C for 14 days. Stationary phase cultures of M. tuberculosis were obtained by incubating M. tuberculosis cultures shaking at 37°C for four weeks. Microaerophilic cultures of M. tuberculosis cultures were obtained by growing the cultures at 37°C in a glove box containing 1% oxygen and 5% CO2 for 14 days. Actively growing M. tuberculosis cultures in media acidified to pH 5.8 were grown shaking at 37°C for 14 days.

value: wild type

tag: growth phase

value: Exponential

tag: condition

value: PBS medium


title: plate_060s_J12_S285_L006

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

description: Brain single cell 237

value: Macrophages


title: acidic replicate 2

description:
rRNA depletion
ph5_rep2
directional RNA-Seq

source_name: acidic

value: pH 5 medium


title: microaerophilic condition replicate 2

description:
rRNA depletion
Oxygen rep2
directional RNA-Seq

source_name: microaerophilic condition

value: microaerophilic condition 1% oxygen


title: Control 7-weeks Lean Zucker Liver 12

extract_protocol:
Tissue were rapidly collected at the terminal time point and and treated with RNAlater tissue storage reagent. RNA extraction from tissues, assessment of RNA quality and RNA sequencing were performed at the Roswell Park Cancer Institute, Genomics Shared Resource, Buffalo, New York.
Sequencing RNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions for the RNA from all tissues except the pancreas and adipose. For these samples, TruSeq Stranded Total RNA Sample Preparation Kit was used.

value: Lean Zucker


title: RNAseq_resident_macrophages_rep1


title: microaerophilic condition replicate 1

description:
rRNA depletion
Oxygen rep1
directional RNA-Seq


title: acidic replicate 1

description:
rRNA depletion
ph5_rep1
directional RNA-Seq


title: Old-6-DistCol_scRNA-seq

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: Single cell RNA sequencing

data_processing:
The fastq files are mapped against mm10.e87 genome following by counting the UMI and removing duplicates for single cells using 'cellranger count' (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count ) with default parameters.
Genome_build: mm10.e87
Supplementary_files_format_and_content: The processed data is the expression matrix (raw counts) with genes in row (first column is the gene names) and cells in columns (firs row is the cell index)

source_name: Distal Colon

growth_protocol: 5 Young (1x 8week, 3x 12week and 1x 20week) and 6 old (2x 90week, 1x 92week ,3x 108week) female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility

extract_protocol:
Crypts from cecum, proximal and distal colon were isolated as described previously(Asad A Ahmad et al., 2014). After centrifugation, the crypts were re-suspended in 3ml of Single-Cell Isolation Solution (TrypLE supplemented with: 1mg/ml DNaseI, 5mM MgCl2, 80μM Y27) and incubated at 37°C for 20min, vortexing for 5 seconds after first 10min. Reaction was quenched by addition of 27ml ice-cold PBS and cells were centrifuged at 1000g for 5minutes at 4°C. Cell pellet was re-suspended in FACS staining medium (FSM - PBS supplemented with 2% Fetal Bovine Serum, 80μM Y27, 3mM EDTA) and treated with CD326 (EpCAM) (G8.8), PE-Cyanine7 coupled rat monoclonal antibody and a TotalSeq Hashtag antibody for 30min on ice in the dark. The cells were then centrifuged at 450g for 5min at 4°C and re-suspended in 500μl fresh FSM. An input of 10000 EpCAM positive FACS sorted single cells per compartment was added to each 10X Chromium Controller channel.
The 10X Single Cell 3’ v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction.

value: Distal Colon


title: plate_060s_J1_S197_L006

description: Brain single cell 235

source_name: Brain

value: brain

value: adult mice

value: Microglia


title: Old-5-DistCol_scRNA-seq

description: Single cell RNA sequencing


title: Control 7-weeks Lean Zucker Blood 12

value: Blood


title: stationary phase (dormancy) replicate 2

description:
rRNA depletion
Stationary rep2
directional RNA-Seq

source_name: stationary phase (dormancy)

value: Stationary

value: standard growth medium


title: Control 7-weeks Lean Zucker Liver 11

value: Liver


title: plate_060s_I7_S53_L006

description: Brain single cell 234

value: KO


title: stationary phase (dormancy) replicate 1

description:
rRNA depletion
Stationary rep1
directional RNA-Seq


title: plate_060s_J15_S309_L006

description: Brain single cell 239


title: Old-4-DistCol_scRNA-seq

description: Single cell RNA sequencing


title: plate_060s_J14_S301_L006

description: Brain single cell 238