title: PFC DKO-4

city: Charlottesville

first: Michael

middle: Murray

last: Scott

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of virginia

description: Genomic DNA was isolated from FACS-sorted pyramidal neuronal nuclei (SATB2 positive) expressing GFP

data_processing:
Samples were sequenced on Illumina HiSeq3000 platform in 50bp single-end mode. Base calling was performed by Illumina Real Time Analysis ( version 2.7.7) software and the base calls were converted to short reads using Illumina2bam tool. Quality of sequencing reads was checked by Fastqc.
Reads were trimmed for low-quality bases (phred score < 30) and adaptor sequences by Trimmomatic-0.32. Reads shorter than 18 bp were discarded.
Bismark program (version 0.19.1), in combination with Bowtie2, was used to map the reads to mouse genome (mm10) and subsequent methylation calling.
CX-report containing methylation calls for all Cytosine contexts was generated and for downstream analysis CpG and CpH contexts were separated.
methylKit (version 0.99.2) identified the differentially methylated cytosine. replicates were pooled and cytosine loci with at least 10 reads per group were considered for differential methylation analysis. Cytosine loci with 30% difference in methylation between groups along with p value < 0.01 were considered significantly differentially methylated (dmCpGs and dmCpHs). Since RRBS covered regions are mostly focused on promoters and CpG-rich regions, only cytosines in CpG context were analyzed.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing total coverage, methylated and non-methylated reads for CpG and CpH loci as determined by Bismark program. Column header are self explanatory. These are the input files for Methylkit analysis.
Supplementary_files_format_and_content: Supplementary file in the series section is a tab delimited text file containing list of significantly differenitally methylated Cytosine residues along with statistics. A difference in methylation of 30% with q-value less than 0.01 was considered significant. Column header are self explanatory.

source_name: brain cortex

growth_protocol: Mice were group housed (up to 5 mice per cage) under standard climate-controlled conditions on a 12 h light–dark cycle (lights on at 6:00 AM) with standard rodent chow (Harlan Teklad, TD7912) and water available ad libitum. Six-8 weeks-old male mice were used for all experiments.

extract_protocol:
Mice were anaesthetized with 0.12 mL euthanasia solution i.p., immediately followed by cervical dislocation and decapitation. Unfixed PFC tissue was roughly harvested, snap frozen in liquid nitrogen, and stored at -70°C until further processing. Batches of tissue punches were processed for nuclear isolation as described previously (Grindberg et al., 2013). Briefly, individual tissue punches were incubated in a Tris-buffered magnesium and potassium salt solution containing protease inhibitor and dithiothreitol. Tissue was triturated using a 1 ml pipette and was then homogenized using a polytron homogenizer. Triton-X100 was then added and the tissue Dounce homogenized using two pestles of decreasing size. Homogenate was strained through a 70 µm filter and centrifuged at 1000 x g for 8 min at 4°C. Nuclei pellet was resuspended, layered on a 29% Iodixanol gradient and centrifuged at 10,300 x g for 20 min at 4°C. Supernatant was collected, nuclei were counted from an aliquot. Nuclei in supernatant were incubated for 1 h with DAPI and anti-Satb2 antibody (1:100, abcam ab34735) conjugated to R-Phycoerythrin (RPE) using the Lightening-Link® R-Phycoerythrin conjugating kit (703-0010, Innova Biosciences), performed as per manufacturer’s instructions. Triple positive (GFP, RPE and DAPI) nuclei were FACS-sorted and were spun down at 500 x g for 10 min at 4°C, nuclei pellet was snap frozen in liquid nitrogen and stored at -70°C until further processing.
Reduced Representation Bisulfite Sequencing libraries were prepared as described previously (Bock et al., 2010).

treatment_protocol: For neuron-specific double conditional knockouts of DNMT1 and DNMT3a in mPFC (PFC DKO), we used AAV2.1-Syn-Cre-GFP (UNC vector core) to produce the deletion. Wild-type mice (C57BL6J) injected with same vector served control. Virus (200 nL/side) was delivered to the mPFC bilaterally using coordinates +2.05 mm anterior from Bregma, +/- 0.35 mm lateral to midline, and -1.5 mm ventral from dura.

value: DNMT1 and DNMT3a floxed

value: medial prefrontal cortex


title: PFC DKO-3

status: Public on May 24 2021

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: genotype

tag: tissue


title: 107606_Xen_LBst50

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

country: Germany

institute: EMBL Heidelberg

library_source: transcriptomic

data_processing:
Cell Ranger (10x Genomics) was used to align sequencing reads originating from Xenopus samples using default parameters. Reads originating from axolotl libraries were mapped using STARsolo (STAR 2.7.5a, Dobin et al., 2013) with parameters mimicking Cell Ranger’s (10x Genomics) transcript counting strategy.
Cellranger and STARsolo generated transcript count matrix files readable by the R package Seurat.
Seurat (v3.1) was used to normalize and scale raw counts which were used for all analyses.
Genome_build: Xenbase v9.2 (Xenopus laevis) (www.xenbase.org, Karimi et al., 2018)
Genome_build: AmexG (Ambystoma mexicanum) (www.axolotl-omics.org, Nowoshilow and Tanaka, 2020)
Supplementary_files_format_and_content: tab-delimited text files include either cellular barcodes or gene features and matrix files contain raw transcript counts for each gene across all cells

molecule: total RNA

organism: Xenopus laevis

source_name: hindlimb

extract_protocol:
Single-cell suspensions were obtained by chopping the tissues into <1mm cubes and immediately transferring the cubes to a tube of digesting solution (0.13WU/mL Liberase in 0.7x PBS). The enzymatic digestion was placed on a rotating wheel at room temperature for 45 minutes and then the cells were mechanically dissociated by pipetting 10-15 times with a P1000 pipet tip. Enzymatic reactions were stopped by adding high-serum culture medium (HS-AMEM, 125ml MEM, 20ml heat inactivated A1 FCS, 2ml insulin, 2mL glutamine, 2mL Pen/Strep, 50mL ddH2O), and samples were filtered sequentially through 70 μm and 30 μm MACS® SmartStrainers (Miltenyi Biotec, 130-098-458 and 130-098-462). Dissociated cells were pelleted using 300x rcf centrifugation for 5 minutes at room temperature, then washed twice with 0.7x PBS before resuspension in serum-free medium (114.3ml F12:DMEM+Glutmax, 1.5ml Sodium pyruvate, 1.5ml B27 supplement, 1.5ml MEM NEAA, 1.5ml insulin, 1.5ml Pen/Strep, 28.2mL ddH2O) on ice.
Single-cell cDNA and sequencing libraries were generated following the manufacturer recommendations (10X Genomics, 3’ library kit, v3 chemistry). The quality of the cDNA and resulting sequencing libraries were checked by either bioanalyzer or fragment analyzer.

value: limb bud

tag: Stage

value: GFP


title: 131283_Axo_LBst50

organism: Ambystoma mexicanum

value: wt


title: GER043_Axo_BL5dpa

source_name: upper forelimb

value: blastema


title: GER045_Axo_BL5dpa


title: PFC DKO-2


title: GER044_Axo_BL5dpa


title: PFC DKO-1


title: 107606_Xen_LBst52

value: GFP/Venus


title: 107606_Xen_Pool_BL14_20_52dpa

source_name: upper hindlimb

value: TFP/mCherry/Venus


title: Control-4

value: Wild type


title: Control-3


title: Control-1


title: Muscle_HF_1

type: RNA

city: Fujisawa

first: Naho

last: Kitamura

state: Kanagawa

department: Graduate School of Media and Governance

country: Japan

institute: Keio University

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: Gastrocnemius muscle of mice fed a HF diet

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany) was used to extract skeletal muscle total RNA. Total RNA was extracted from the tissue cryopreserved with liquid nitrogen according to the kit’s instructions.

tag: gender

value: male

value: Gastrocnemius

tag: food

tag: age

value: 21 months


title: NLE-Vok-input

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

data_processing:
DATA PROCESSING STEPS TO GENERATE THE *summary.txt FILES:
Raw reads were trimmed using Trimmomatic [11] to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
We used seqtk to randomly select 2.5 million trimmed read pairs from each ChIP sample. The random subsets of reads were converted to fasta format using manual bash scripts.
Repeats in the pre-processed ChIP-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family in each of the read pair files, and to calculate the %count and %length (of total repeats) they constituted
Genome_build: Not applicable
Supplementary_files_format_and_content: Text files summarizing the %count and %length of each repeat, repeat family and repeat class among randomly subsampled reads from each ChIP library.
DATA PROCESSING STEPS TO GENERATE THE *contigs.fa FILES:
We used the K-mer Analysis Toolkit (KAT) to determine the optimal k-mer size and predicted genome coverage for each library.
We used RepARK for de novo assembly of reads from each ChIP-seq library.
Genome_build: not applicable
Supplementary_files_format_and_content: Fasta files representing assembled contigs obtained from each ChIP-seq library.
DATA PROCESSING STEPS TO GENERATE THE CENP_BroadPeaks_sortedbyFE.xlsx FILE:
Raw reads were trimmed using Trimmomatic to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
Trimmed reads were aligned to the gibbon genome (Nleu3.0) using Bowtie2, with "very sensitive" paired-end settings.
Significant (q<0.01) broad peaks were identified using MACS2,while allowing maximum fof two read duplcates. Peaks were sorted based on fold enrichment.
Genome_build: Nleu3.0
Supplementary_files_format_and_content.xlsx spreadsheet containing the coordinates of all broad peaks across CENP libraries. Peaks are sorted from high fold-enrichment (FE) to low FE.

organism: Nomascus leucogenys

source_name: northern white-cheeked gibbon (Nomascus leucogenys)

extract_protocol:
We performed ChIP-seq using the Magnify ChIP kit (Thermo Fisher Scientific) according to manufacturer’s instructions with minor modifications. Briefly, per ChIP assay we fixed 3x105 EBV transformed gibbon LCLs with 1% formaldehyde at room temperature for 10 min. Fixation was quenched with glycine, and cells were washed three times with cold 1XPBS. Cells were lysed for 10 min on ice using the Magnify Lysis buffer, in presence of Proteinase inhibitor cocktail. Lysed cells were then sonicated using the Bioruptor Pico sonicator (Diagenode) for 12 cycles (30 sec on/off) and spun down to remove cell debris. A 1% aliquot was taken from the chromatin as input, and the rest was incubated with the appropriate antibody [CENP-A (ab13939): 2ug, CENP-B (ab25734): 4ug, CENP-C (ab50974): 2ug] at 4℃, with rotation overnight. The next day we incubated samples with Dynabead protein A/G rotating at 4℃ for 2 hours, followed by bead washes, reverse-crosslink and DNA purification according to Magnify ChIP kit protocol.
All sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) for 1-5ng of starting material and without size selection. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

tag: cell line

value: EBV-tranformed lymphocyte cell line

tag: chip antibody


title: NLE-Vok-CENPC


title: Muscle_Control_1

source_name: Gastrocnemius muscle of mice fed a Control diet


title: Liver_HF_1

source_name: Liver of mice fed a HF diet

extract_protocol: RNeasy Mini Kit (Qiagen, Hilden, Germany) was used to extract liver total RNA. Total RNA was extracted from the tissue cryopreserved with liquid nitrogen according to the kit’s instructions.

value: Liver


title: NLE-Vok-CENPB


title: Liver_HF+SFC_1

source_name: Liver of mice fed a HF+SFC diet

value: D12492+0.023% (w/w) sodium ferrous citrate


title: Liver_Control_1

source_name: Liver of mice fed a Control diet


title: 88527_Xen_BL14dpa

value: Venus


title: NLE-Vok-CENPA


title: Control-2


title: 40-IP_db/db-1

status: Public on May 25 2021

city: Beijing

first: wenhao

last: ju

address: chaoyang

country: China

institute: pumc

data_processing:
library strategy: meRIP-seq
FastQC (v0.11.7) was used for quality inspection of raw sequence data
original sequence filtered using Trimmomatic (V0.32)
Filtered high-quality data were compared with the reference genome (HISAT2 v2.1.0) in the Ensembl database
exomePeak (v2.13.2) used to identify peaks in each sample and differentially methylated peaks in compared samples.
Genome_build: mm9
Supplementary_files_format_and_content: excel format

extract_protocol:
Hearts collected in 1.5 ml RNase-free centrifuge tubes, immediately immersed in liquid nitrogen to prevent RNA degradation, and finally stored at -80°C.RNA was harvested using Trizol reagent.Complete mRNA was obtained by purification  using Arraystar Seq-StarTM ploy(A) mRNA Isolation Kit
A KAPA Stranded mRNA-seq Kit (Illumina) was used to construct sequencing libraries of post-enrichment m6A mRNA.

value: db/db

value: heart

tag: antibody

value: Affinity purified anti-m6A rabbit (Synaptic Systems, 202003, 2-108)


title: Muscle_HF+SFC_1

source_name: Gastrocnemius muscle of mice fed a HF+SFC diet


title: NLE-Vok-RNA

data_processing:
DATA PROCESSING STEPS TO GENERATE THE '*_summary.txt' FILES:
Raw reads were trimmed using Trimmomatic to remove adaptor sequences, as well as low quality and short reads (2:30:10:26:true SLIDINGWINDOW:4:20 TRAILING:20 LEADING:20 MINLEN:50).
Trimmed RNA-seq libraries were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Supplementary_files_format_and_content: Text files (*_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

DATA PROCESSING STEPS TO GENERATE THE '*_mapped.fasta.out_summary.txt' FILES:
The Burrow's Wheeler Aligner bwa-mem algorithm was used to map RNA-seq reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data.
Reads that successfully aligned to the de novo assemblies were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Supplementary_files_format_and_content: Text files (*_mapped.fasta.out_summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

DATA PROCESSING STEPS TO GENERATE THE '*-RM-summary.txt' FILES:
RNA-seq library reads were mapped to the Nleu3.0 genome using the Burrows-Wheeler Aligner bwa-mem algorithm.
Unaligned reads, assumed to contain centromere-derived reads, were separated using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Next, we used the Burrow's Wheeler Aligner bwa-mem algorithm to map the unaligned reads to de novo assembled contigs generated from CENP-A, CENP-B, and CENP-C ChIP-sequencing data.
Reads that successfully aligned to the de novo assemblies, assumed to be enriched for centromere-derived reads, were extracted using SAMtools and converted to FASTA format using Bedtools and Seqtk.
Repeats in the subsequent processed FASTA files were annotated using RepeatMasker version 4.0.3. The gibbon (Hylobates sp.) 20150807 Repbase library was used for annotation.
We used a custom script to group repeats in each library based on repeat class and family, and to calculate the %count and %length (of total repeats) they constituted.
Genome_build: Nleu3.0
Supplementary_files_format_and_content: Text files (*-RM-summary.txt) summarizing the %count and %length of each repeat, repeat family and repeat class of the annotated RNA-seq reads.

extract_protocol:
Total RNA was extracted using the mirVana™ Total RNA Isolation kit (ThermoFisher Scientific) following the manufacturer's instructions on each EBV-transformed lymphocyte cell line.
High-quality RNA was subjected to llumina Tru-seq stranded total RNA library preparation, including Ribo-depletion. The Qubit dsDNA High Sensitivity kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 were used to QC the libraries.

value: EBV-transformed lymphocyte cell line


title: Renal MSC sample #3

city: Nashville

first: Jose

middle: A

last: Gomez

state: Tennessee

address: 2220 Pierce Ave, 502 RRB

institute: Vanderbilt University Medical Center

description: Data expression of MSC isolated from adult C57BL6 Ren1c YFP mice

hyb_protocol: Hybridization protocol was preformed as recommended by Affimetrix for the Mosue 430 2.0 microarray chip

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G System

data_processing: Data was processed using dChip

label: Biotin

source_name: Mouse renal MSC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA following Affymetrix recommended protocol.

growth_protocol: Mouse renal MSC groth in DMEM 10% FBS

extract_protocol: Picopure Arcturus RNA isolation

tag: genotype/variation

value: Ren1c YFP

tag: cell type

value: renal MSC


title: JG cells YFP+ sample #2

description: Data expression of Juxtaglomerular cells isolated from adult C57BL6 Ren1c YFP mice

source_name: Mouse juxtaglomerular cells

value: Juxtaglomerular


title: 1712A-CN-209

city: chongqin

first: Yao

last: Yang

state: chongqin

address: Gaotanyan

institute: TMMU

data_processing:
Sequenced reads were trimmed for adaptor sequence by FastQC（v0.10.1）and Cutadapt（version 1.9.1）, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2（V2.0.1)
Raw count were calculated by htseq-count based on gencode V35
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Total RNA from 4 mL peripheral whole blood of each samples were extracted by 12 mL TRIzol reagent according to manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
lncRNA sequencing

value: Whole blood

tag: treatment

value: healthy controls


title: 1712A-CN-207


title: Hippocampus_CRL_rep3

city: Madrid

first: Pau

middle: B.

last: Esparza-Molto

state: Madrid

address: Calle Nicolas Cabrera, 1

country: Spain

institute: Universidad Autonoma de Madrid

description: Gene expression in the hippocampus of CRL mouse

hyb_protocol: The samples were placed on ice and immediately loaded onto arrays, hybridized at 65ºC for 17 h in a hybridization oven and then washed in GE Wash Buffer 1 at room temperature (1 min) and in GE Wash Buffer 2 at 37ºC (1 min). Arrays were dried by centrifugation at 2,000 rpm for 2 minutes. Slides were from Mouse GE 4x44K v2 Microarray Kit (G4846A).

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Background correction and normalization of expression data were performed using LIMMA. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate, p-values were corrected by using the method of Benjamini and Hochberg.

source_name: Hippocampus, CRL, replicate 3

label_protocol: Total RNA (200 ng) was amplified using One Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen). Probe preparation and hybridization was performed as described in One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5 (Agilent Technologies). Briefly, for each hybridization 600 ng of Cy3 probes were mixed and added to 5 μl of 10x Blocking Agent, 1 μl of 25x Fragmentation Buffer and Nuclease free water in a 25 μl reaction, incubated at 60ºC for 30 min to fragment RNA and stopped with 25 μl of 2x Hybridization Buffer.

growth_protocol: Mice were housed in a humidity- and temperature-controlled room on a 12-h light/dark cycle, receiving water and regular chow diet ad libitum.

extract_protocol: RNA was extracted from the hippocampus of IF1-KO, CRL and IF1-TG mice (n = 3 mice per genotype) using Trizol (Invitrogen) and cleaned up with RNeasy columns (Qiagen). Each RNA preparation was tested for degradation using Agilent 2100 Bioanalyzer (Agilent Technologies).

value: 9 months

value: hippocampus

value: control (CRL)


title: 1712A-CN-206

value: fracture only patients


title: JG cells YFP+ sample #3


title: Hippocampus_TG_rep2

description: Gene expression in the hippocampus of IF1-TG mouse

source_name: Hippocampus, TG, replicate 2

value: male

value: IF1-overexpressing transgenic (TG)


title: jLS_16

type: genomic

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
BeadChip idat files were read into GenomeStudio (v2011.1) Methylation Suite (v1.9.0) (Illumina; San Diego, USA). Probe intensity values were normalized to internal, non-CpG control probes. Array background was subtracted from normalized probe intensities using unhybridized in-array control probes. β values were calculated from normalized, background-subtracted probe intensity values and range from 0% to 100% methylation.
value definition: Average Beta

label: Cy5 and Cy3

source_name: PBMC DNA

label_protocol: standard Illumina protocol

extract_protocol: PBMCs were extracted from whole blood samples following density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare Bio-Sciences; Piscataway, NJ, USA) and stored in liquid nitrogen until DNA extraction. PBMCs were thawed and washed with ice-cold PBS. Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen; Germantown, MD, USA). DNA concentration was measured using the Qubit dsDNA Broad Range Assay using a Qubit Fluorometer (ThermoFisher Scientific; Waltham, MA, USA). 300 ng of each sample was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research; Irvine, CA, USA) according to manufacturer's directions. The thermocycler settings recommended for Illumina methylation BeadChip assays were used. DNA methylation was measured using the Infinium MethylationEPIC BeadChip array (Illumina; San Diego, USA). Array sample preparation and BeadChip scanning were performed at the University of Michigan Advanced Genomics Core.

value: PBMC

tag: disease

value: juvenile localized scleroderma

tag: Sex

value: Female

tag: age (years)

tag: ancestry

value: European-American


title: 1712A-CN-203

value: fracture concomitated with TIB patients


title: jSSc _16

value: juvenile systemic sclerosis


title: Hippocampus_CRL_rep1

source_name: Hippocampus, CRL, replicate 1

tag: strain


title: 1712A-CN-208


title: Hippocampus_CRL_rep2

source_name: Hippocampus, CRL, replicate 2

tag: genotype


title: JG cells YFP+ sample #1

value: Ren1c YFP


title: 1712A-CN-205

tag: tissue


title: jSSc _15


title: HC_16

value: healthy control


title: Hippocampus_TG_rep3

source_name: Hippocampus, TG, replicate 3


title: 1712A-CN-204


title: Hippocampus_KO_rep2

description: Gene expression in the hippocampus of IF1-KO mouse

source_name: Hippocampus, IF1-KO, replicate 2


title: Renal MSC sample #2

value: renal MSC


title: Hippocampus_TG_rep1

source_name: Hippocampus, TG, replicate 1


title: 1712A-CN-202

value: Whole blood


title: Hippocampus_KO_rep1

source_name: Hippocampus, IF1-KO, replicate 1


title: Renal MSC sample #1


title: Hippocampus_KO_rep3

source_name: Hippocampus, IF1-KO, replicate 3


title: HC_15


title: 1712A-CN-201


title: T24, Lean_Muscle

city: Tucson

first: Dawn

middle: K

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

institute: UNIVERSITY OF ARIZONA

data_processing:
Data was collected using HiSeq data collection version 1.5.15.1 software, and the bases were called using Illumina’s RTA version 1.13.48.
Briefly, FASTQ were trimmed to remove adaptor sequences, and any reads with less than 15bp were discarded. Trimmed Fastqs were then aligned against the reference genome Hg19 using BSMAP
Samtools was used to get mpileup and custom PERL scripts were used to determine CpG methylation and bisulfite conversion ratios
To determine differences in methylation between groups, the aligned data was imported into the free open source R package, methylSig.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig data files were generated using custom scripts and score represent the methylation level at that loci.

source_name: Vastus lateralis muscle

extract_protocol:
Homogenization of the muscle biopsy was performed in 1X PBS with the Bullet Blender (Integrated Scientific Solutions). DNA was isolated using QIAamp DNA mini kit (Qiagen).
Briefly, DNA was digested with Msp1 (New England Biolabs) and purified using QIAquick Nucleotide Removal Kit (Qiagen).  End-repair A tailing was performed (New England Biolabs) and TruSeq methylated indexed adaptors (Illumina) were ligated with T4 DNA ligase (New England Biolabs). Size selection was performed with Agencourt AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research) as recommended by the manufacturer with the exception that incubation was performed using 55 cycles of 95 ̊C for 30 seconds and 50°C for 15 minutes.  Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo C Hotstart DNA Polymerase (Agilent Technologies). The final libraries from RRBS were prepared for sequencing as per the manufacturer’s instructions in the Illumina cBot and HiSeq Paired end cluster kit version 3. The flow cell was then loaded into the Illumina cBot for generation of cluster densities. After cluster generation, the flow cells were sequenced as 51 x 2 paired end reads using Illumina HiSeq 2000 with TruSeq SBS sequencing kit version 3.

treatment_protocol: Participants underwent euglycemic hyperinsulinemic clamps with muscle biopsies. The biopsies were immediately frozen in liquid nitrogen.

tag: individual id

tag: pre_or_post surgery

value: Control-no surgery

tag: bmi status

value: Lean

value: Vastus lateralis muscle


title: BS07 post, Obese_Muscle

tag: gender

tag: age

value: Post-surgery

value: Obese


title: BS06 pre, Obese_Muscle

value: Pre-surgery


title: BS06 post, Obese_Muscle


title: P01, Lean_Muscle


title: BS04 post, Obese_Muscle


title: jSSc _13


title: jLS_14


title: HC_14


title: BS07 pre, Obese_Muscle


title: BS04 pre, Obese_Muscle


title: jLS_15


title: jLS_13


title: BS03 post, Obese_Muscle


title: BS02 pre, Obese_Muscle


title: SB3_16S

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
Adult flies, 3 to 4 days after eclosion.
16S rRNA
16S_OTU_counts.txt

data_processing:
Library strategy: 16S rRNA sequencing
All raw sequencing data were quality controlled by fastq (version 0.18.0). Adapters, reads with more than 10% unknown nucleotide (N) content, and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data:
The sequencing data after quality control was firstly mapped to ribosome RNA (rRNA) database using Bowtie2 (version 2.2.8) to remove rRNA reads and get the clean sequencing data.
The clean sequencing data were mapped to the Drosophila melanogaster reference genome (dm6) using HISAT2 (version 2.2.4) with "-rna-strandness RF" and other default parameters after index building of the transcriptome.
The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
RNA differential expression analyses among groups were performed by DESeq2 (version 1.30.1), and RNA differential expression analyses between two samples were performed by edgeR (version 3.32.1). The genes/transcripts with a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
For 16S-seq clean data:
Paired-end clean reads were merged as raw tags using FLASH (version 1.2.11) with a minimum overlap of 10 bp and a mismatch error rate of 2%.
Noisy sequences of the raw tags were filtered by QIIME (version 1.9.1) pipeline under specific filtering conditions to obtain the high-quality clean tags.
Clean tags were searched against the reference database (version r20110519, http://drive5.com/uchime/uchime_download.html) to perform reference-based chimera checking using UCHIME algorithm. All chimeric tags were removed to obtain the effective tags for downstream analyses.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Sterile_RNA_counts.txt: Tab-delimited text file includes raw read counts for the RNA-seq data of sterile samples.
Supplementary_files_format_and_content: RNA_counts.txt: Tab-delimited text file includes raw read counts for RNA-seq samples.
Supplementary_files_format_and_content: 16S_OTU_counts.txt: Tab-delimited text file includes raw OTU counts for the 16S rRNA sequencing samples.

organism: insect gut metagenome

source_name: Midgut

growth_protocol: The Drosophila melanogaster w1118 samples were reared on yeast-glucose medium (1L water, 100 g yeast, 100 g glucose, 1.2% agar, and 0.1% potassium sorbate) stocks at 25°C under 12 hours light/12 hours dark cycles in an artificial climate box.

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitated by isopropyl alcohol. Total DNA of 16S-seq samples were extracted from Drosophila midgut using TIANamp genomic DNA kit (Tiangen, DP304) following the manufacturer's protocol.
After total RNAs of each sample were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmentation buffer and reverse transcribed into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Genedenovo Biotechnology Co, Ltd.

treatment_protocol: For treatment group, 100mM sodium butyrate (Sigma) was added to Drosophila medium.

value: Midgut of Drosophila

value: Adult

tag: culture environment

value: Bacteria

value: Sodium butyrate feeding

tag: replicate


title: BS02 post, Obese_Muscle

value: Female


title: T20, Lean_Muscle


title: BS01 post, Obese_Muscle


title: T09, Lean_Muscle


title: jSSc _12

value: PBMC

value: European-American


title: BS01 pre, Obese_Muscle


title: jLS_12

value: juvenile localized scleroderma


title: jSSc _14

value: juvenile systemic sclerosis


title: BS05 post, Obese_Muscle


title: BS05 pre, Obese_Muscle


title: HC_11

value: healthy control


title: jSSc _11


title: BS03 pre, Obese_Muscle


title: jSSc _10


title: Sample_DKO_M_ABC_rep2

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

data_processing:
RNAseq: Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to the mouse genome (mm10) and reads in exons were counted against Gencode v27 with STAR2.6 Aligner. Differential gene expression analysis was performed in R using edgeR3.24.3. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an unadjusted p-value less than 0.01 were considered differentially expressed. Downstream analyses were performed in R using a visualization platform built with Shiny developed by bioinformaticians at the David Z. Rosensweig Genomics Research Center at HSS
ATACseq: Paired-end 50bp sequences were generated from samples with an Illumina HiSeq2500 and, following adapter trimming with FastP, were aligned against mouse genome (mm10) using bowtie2 with –local -q -p options. Peaks were called with MACS2 with --macs2 callpeak -f BAMPE --nomodel --shit -100 --extsize 200 --B --SPMR -g $GENOMESIZE -q 0.01 options. Peak-associated genes were defined based on the closest genes to these genomic regions using RefSeq coordinates of genes. We used the annotatePeaks command from HOMER to calculate ATAC-seq tag densities from different experiments and to create heatmaps of tag densities. Sequencing data were visualized by preparing custom tracks for the UCSC Genome browser. De novo transcription factor motif analysis was performed with motif finder program findMotifsGenome from HOMER package on ATAC-seq peaks. Peak sequences were compared to random genomic fragments of the same size and normalized G+C content to identify motifs enriched in the targeted sequences.
Cut&Run: The data was processed using CUT&RUNTools (Zhu, Q., Liu, N., Orkin, S.H. et al. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol 20, 192 (2019) pipeline. The peaks from IgG isotype controls were excluded in the SECAR peak calling program. A master file of H3K27me3 peaks across all the conditions and replicates was created with bedops (v2.4.35) using bedops --everything option. computeMatrix and plotHeap map functions were used from deepTools package to plot average tag densities and heatmap.
Genome_build: mm10
Supplementary_files_format_and_content: DKO_ABC_FoB_M_F_YAA_out_list_updated_1.42019-10-28.xlsx multi-worksheet xlsx file containing  unprocessed read count matrix, filtered and normalized read count matrices and the results of edgeR differential expression analysis for DKO_ABC_FoB_M_F_YAA experiments
Supplementary_files_format_and_content: DKO_GCB_PC_M_F_YAA_edgeR_DEGs_with_IgG_batch_corrected_2019-09-15.xlsx multi-worksheet xlsx file containing  unprocessed read count matrix, filtered and normalized read count matrices and the results of edgeR differential expression analysis for GCB_OC/PB_M_F_YAA experiments
Supplementary_files_format_and_content: bigWig files contain normalized big wig profiles for ATAC seq and Cut&Run experiments. Public UCSC browser session for ATACseq profile is available at https://genome.ucsc.edu/s/chinenovy%40hss.edu/ATAC_seq_AWS_S3
Supplementary_files_format_and_content: bed files contains chromosomal coordinates of peaks from Cut&Run experiments
Supplementary_files_format_and_content: tsv – Tab-separated files. Cut&Run peaks statistics

source_name: spleen

growth_protocol: Various population B-lymphocytes were obtained by flow sorting single-cell suspensions of spleens from SWAP-70 and DEF6 double knockout (DKO) female or male mice or from DKO male mice containing the Yaa duplication (Yaa-DKO).

extract_protocol:
RNAseq: Total RNA from sorted B -lymphocytes was isolated using the RNeasy Plus Mini kit (Qiagen).
ATACseq: The nuclei of sorted ABCs from female DKO, male DKO, or Yaa-DKO mice were prepared by incubation of cells with nuclear preparation buffer (0.30M sucrose, 10mM Tris pH 7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 0.1% NP40, 0.15mM spermine, 0.5mM spermidine, and 2mM 6AA)
Cut&Run: Sorted cells were immediately incubated overnight with H3K27me3 (anti- Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology #Rabbit mAb #9733) or IgG isotype controls (Guinea Pig anti-Rabbit IgG (H+L) Secondary Antibody (novusbio #NBP1-72763) at 1:50 dilution of antibody binding buffer with a final concentration of 0.05% digitonin. Following incubation and digestion CUTANA™ pAG-MNase from EpiCypher (SKU: 15-1116) the digested DNA fragments were release and purified by QIAquick PCR purification kit (#2810).
RNAseq: Quality of all RNA and library preparations were evaluated with BioAnalyzer 2100 (Agilent). Sequencing libraries were sequenced by the Epigenomics Core Facility at Weill Cornell Medicine using a HiSeq2500, 50-bp paired-end reads at a depth of ~15-50 million reads per sample
ATACseq: sequencing libraries were constructed as described in PMID: 26083756: Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590. Epub 2015 Jun 17.
Cut&Run:The resulting DNA fragments were end-repaired and barcoded libraries were made with the NEB Ultra II DNA Library Prep kit ((E7645S, E7335S & E7500S)). The libraries were sequenced on Illumina NextSeq 500 to a minimum of 15 million reads per sample.

value: Male

value: Age/autoimmune-associated B cells


title: Sample_YaaDKO_M_ABC_rep1

tag: duplication

value: YAA


title: Sample_YaaDKO_M_ABC_rep2

tag: cell type


title: Sample_DKO_F_ABC_rep1


title: Sample_DKO_M_ABC_rep1


title: Sample_DKO_F_ABC_rep2


title: YAA_DKO_CD11c-pos_PC_2

description: DKO_GCB_PC_M_F_YAA_edgeR_DEGs_with_IgG_batch_corrected_2019-09-15.xlsx

molecule: polyA RNA

value: Plasmablasts/plasma cells


title: YAA_DKO_CD11c-pos_PC_3


title: HC_13


title: Memory_T_cell_CITE-seq

city: Boston

first: Aparna

last: Nathan

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School, Brigham and Women's Hospital

data_processing:
We used Cell Ranger (3.1.0) to map mRNA reads to the GRCh38 build of the human genome and surface antibody oligonucleotide tags to a barcode library.
We demultiplexed pooled samples with Demuxlet.
We removed cells with < 500 genes expressed or > 20% mitochondrial UMIs, and cells with non-memory T cell surface or trancriptomic phenotypes.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited matrix of raw read counts for each gene/surface protein in each cell.
Supplementary_files_format_and_content: Tab-delimited matrix of normalized expression for each gene/surface protein in each cell.
Supplementary_files_format_and_content: Tab-delimited table of metadata for each cell.

source_name: Memory T cells

extract_protocol:
To isolate memory T cells, we added anti CD45RA biotin to the Pan T cell negative Isolation magnetic-activated cell sorting (MACS) kit (Miltenyi Biotec). We stained memory T cells with a panel of 31 TotalSeq-A (BioLegend) oligonucleotide-labeled antibodies according to an optimized version of the CITE-seq protocol (Stoeckius, et al. 2018), washed, and sorted up to 10,000 live cells from each sample. Then we pooled cells into batchesof 6 donors.
We prepared libraries with the Chromium Single Cell 3' v3 kit (10x Genomics).

value: Peripheral Blood Mononuclear Cells

value: Memory T cells


title: YAA_DKO_CD11c-pos_PC_1


title: MOLM14, siCTRL, 3

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

hyb_protocol: cRNA products were randomly fragmented and labeled prior hybridization onto Affymetrix GeneChips.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: CEL files were preprocessed into Partek Genomic Suite ® using default option

source_name: MOLM14 transfected with a scrambled siRNA , technical replicate 3

label_protocol: 100 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT PLUS Reagent kit (Affymetrix) according to the manufacturer’s standard protocols (P/N 703174 Rev.2 )

growth_protocol: RPMI glutamax 10% serum

extract_protocol: Trizol

treatment_protocol: The transfection of small interfering RNA (siRNA) into MOLM-14 cells was carried out using the Neon transfection system (Life technologies), according to the manufacturer’s recommendations. Briefly, 70 nM of siRNA was used per condition. RNA interference-mediated gene knockdown was achieved using pre-validated Santa Cruz Biotechnology  siRNAs for ATF4 (sc-35112) and Dharmacon (Chicago, IL, USA) siGENOME Control Pool Non-Targeting #2 (D-001206-14-20).

tag: cell line

tag: sirna

value: siCTRL


title: jSSc _9

tag: disease

tag: Sex

value: African-American


title: jLS_9

tag: age (years)

tag: ancestry


title: YAA_DKO_CD11c-neg_PC_3

tag: genotype

tag: strain


title: YAA_DKO_CD11c-neg_PC_2


title: jLS_11


title: MOLM14, siATF4, 1

source_name: MOLM14 transfected with siRNA against ATF4, technical replicate 1


title: MOLM14, siCTRL, 1

source_name: MOLM14 transfected with a scrambled siRNA , technical replicate 1


title: MOLM14, siATF4, 3

source_name: MOLM14 transfected with siRNA against ATF4, technical replicate 3


title: HC_12


title: YAA_DKO_CD11c-neg_PC_1


title: HC_9


title: MOLM14, siCTRL, 2

source_name: MOLM14 transfected with a scrambled siRNA , technical replicate 2


title: MOLM14, siATF4, 2

source_name: MOLM14 transfected with siRNA against ATF4, technical replicate 2


title: jLS_10

source_name: PBMC DNA


title: F_DKO_CD11c-pos_PC_1


title: F_DKO_CD11c-pos_PC_3


title: F_DKO_CD11c-pos_PC_2


title: jSSc _8


title: F_DKO_CD11c-neg_PC_1


title: F_DKO_CD11c-neg_PC_3


title: jSSc _7


title: jLS_8


title: HC_8


title: YAA_DKO_CD11c-neg_GCB_3

value: Germinal Center B Cells


title: F_DKO_CD11c-pos_GCB_3


title: jLS_7


title: YAA_DKO_CD11c-pos_GCB_3


title: HC_7


title: jSSc _6


title: jLS_6


title: YAA_DKO_CD11c-neg_GCB_2


title: F_DKO_CD11c-pos_GCB_2


title: F_DKO_CD11c-pos_GCB_1


title: HC_6


title: F_DKO_CD11c-neg_GCB_2


title: F_DKO_CD11c-neg_PC_2


title: F_WT_ABC_2

description: DKO_ABC_FoB_M_F_YAA_out_list_updated_1.42019-10-28.xlsx

value: WT


title: YAA_DKO_CD11c-neg_GCB_1


title: F_WT_ABC_1


title: F_DKO_ABC_4


title: jSSc _5


title: F_DKO_CD11c-neg_GCB_1


title: YAA_DKO_CD11c-pos_GCB_1


title: F_WT_FoB_2

value: Folicular B cells


title: F_DKO_ABC_5

value: Female


title: F_WT_FoB_1


title: jLS_5

value: PBMC


title: YAA_DKO_FoB_3


title: YAA_DKO_CD11c-pos_GCB_2


title: YAA_DKO_ABC_3


title: jLS_4

value: European-American


title: HC_4


title: M_DKO_FoB_3


title: F_DKO_CD11c-neg_GCB_3


title: Plasmid-Rep2

city: Stanford

first: Stephen

middle: B

last: Montgomery

state: Califonia

address: 300 Pasteur Drive, Edwards Building R248A

institute: Stanford University

description: barcode sequencing of plasmid DNA

data_processing:
Library strategy: MPRA
Barcodes were clustered using Bartender v1.1 and assigned to their parent designed oligo if perfectly matching. Bracode counts were summed across all barcodes within each oligo to generate the oligo count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: Oligo count text files contain columns for the oligo specification as well as the raw oligo count in each sample. The designed library includes columns for the oligo name and the sequences used for library synthesis.

organism: synthetic construct

source_name: plasmid DNA

growth_protocol: Transient transfection by Neon electoporation followed by 24 hours of recovery in RPMI + 15% FBS

extract_protocol:
Standard trizol extraction followed by GFP mRNA isolation and reverse transcription
PCR amplification of oligo or barcode sequences from plasmid or cDNA samples followed by multiplexing for Illumina sequencing

value: plasmid DNA


title: Oligo-Pool

description: plasmid sequencing of barcoded oligos


title: Plasmid-Rep1

description: barcode sequencing of plasmid DNA


title: Plasmid-Rep3

description: barcode sequencing of plasmid DNA


title: MOLM13-YTHDC1-ADAR-3

city: New York

first: Yuanming

last: Cheng

address: 417 E68 Street

institute: MSKCC

data_processing:
The paired-end RNA-seq reads to human (hg19) genome using STAR aligner (Dobin et al., 2013)
All mutations (SNP) were identified for each RNA-seq library using the GATK (Van der Auwera et al., 2013) workflow for calling variants in RNA-seq
The mutations were then restricted to annotated mRNA transcripts, as well as restricted to A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand.
Data were then filtered using mutations found in the dbSNP database since they are most likely DNA-level mutations.
The filtered sets of RNA editing events from all RNA-seq libraries of the same experiment were combined, and counted the number of reads containing reference (A/T) and alternative (G/C) alleles from each library at each site
Genome_build: hg19
Supplementary_files_format_and_content: "MOLM13_YTHDC1_snp_counts_snp_counts_significance_fpkm.csv" file shows a matrix table including coordinates of the editing sites, strand, entrez id, gene symbol, annotation, reference nucleotide, alternative nucleotide (edited nucleotide).

source_name: Molm13 human leukemia cell line

growth_protocol: MOLM-13 cells (obtained from ATCC) were cultured in RPMI plus 10% FBS and 1%L-Glutamine PenStrep.

extract_protocol:
0.5 million of MOLM13 cells per sample were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.
After PicoGreen quantification and quality control by Agilent BioAnalyzer, 1ug RNA input was used for library preparation (TrueSeq Stranded mRNA LT Sample Prep Kit)

treatment_protocol: Cells were infected with virus expressing YTHDC1-ADAR or controls at 1:1 ratio (v/v) cell: virus at 0.5 million cells per mL (final density). Spinoculation was done with 10ug/mL Polybrene (Millipore #TR-1003-G) at 1500rpm for 1 hour at 32oC. Cells were incubated for 48hrs and then havested for RNA-seq.

value: leukemia cell line

tag: treatment

value: transduced with virus expressing YTHDC1-ADAR


title: M_DKO_ABC_3

value: Male


title: MOLM13-YTHDC1-ADAR-2

description: MOLM13_YTHDC1_snp_counts_snp_counts_significance_fpkm


title: jSSc _3

value: juvenile systemic sclerosis


title: F_DKO_ABC_3

value: Age/autoimmune-associated B cells


title: HC_5

value: healthy control


title: MOLM13-YTHDC1-ADAR-1


title: F_DKO_FoB_3


title: HC_3


title: MOLM13-control-3

value: transduced with virus expressing empty vector


title: jSSc _4


title: YAA_DKO_ABC_2

value: YAA


title: YAA_DKO_FoB_2


title: jSSc _2


title: MOLM13-control-2


title: MOLM13-control-1


title: jLS_2

value: juvenile localized scleroderma


title: HC_2


title: MOLM13-sh2-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR aligner
FPKM was caculated and differential expression analysis was conducted using the DESeq software package.
Genome_build: hg19
Supplementary_files_format_and_content: MOLM13-YTHDC1 knockdown-RNA-seq counts.xlsx to show a Matrix table with raw gene counts for every gene and every sample

extract_protocol:
3 million cells per sample were harvested and frozen in TRIzol reagent. RNA was extracted using Phenol-Chloroform.
After PicoGreen quantification and quality control by Agilent BioAnalyzer, 1ug RNA input was used for library preparation (TrueSeq Stranded mRNA LT Sample Prep Kit)

treatment_protocol: Cells were infected with virus expressing YTHDC1 shRNA1,  or YTHDC1 shRNA2 or control shRNA at 1:1 ratio (v/v) cell: virus at 0.5 million cells per mL (final density). Spinoculation was done with 10ug/mL Polybrene (Millipore #TR-1003-G) at 1500rpm for 1 hour at 32oC. Cells were incubated for 48hrs and then selected by 3ug/ml puromycin for 48hrs.

value: transduced with virus expressing YTHDC1 shRNA-2


title: jSSc _1


title: M_DKO_ABC_2


title: M_DKO_FoB_2


title: MOLM13-sh2-2

description: MOLM13-YTHDC1 knockdown-RNA-seq counts.xlsx


title: jLS_1


title: F_DKO_ABC_2


title: MOLM13-sh1-3

value: transduced with virus expressing YTHDC1 shRNA-1


title: F_DKO_FoB_2


title: jLS_3


title: HC_1


title: YAA_DKO_FoB_4


title: MOLM13-sh2-1


title: YBT7

city: Jerusalem

first: Yonatan

last: Tzur

address: Givat-Ram

country: Israel

institute: Hebrew University of Jerusalem

description: Sample name: D3

data_processing:
Low quality bases, poly-G, adapters, and poly-A sequences were removed with cutadapt, v1.12, with parameters -O 1, -m 15, and --use-reads-wildcards
Low quality reads were filtered out with fastq_quality_filter of the FASTX package, v0.0.14, with parameters -q 20 and -p 90.
Processed reads were aligned with tophat, v2.1.1, 2 mismatches and 5-base gaps and used gene annotations from Ensembl release 36.
Raw counts were obtained with htseq-count, v0.6.0, withusing default parameters
Normalization and differential expression were done with DESeq2, v1.12.4 with at least 3 raw counts using default parameters
Genome_build: WBcel235
Supplementary_files_format_and_content: Excel file with the analysis results include general gene details (A-F), raw counts for each strain (G and H), normalized counts (I and J), the DESeq2 calculated baseMean (K), the DESeq2 calculated lfcMLE (L), and a column for the final decision of differential expression (M).

organism: Caenorhabditis elegans

source_name: YBT7 Wild type Adult worms' gonads

growth_protocol: Solid media

extract_protocol:
Gonads disected. TRIzol  + Zymo Research Direct-zol RNA miniprep plus kit
RT,  second-strand cDNA synthesis, In-vitro transcription, fragmentation, RT, amplification, , ligation of Adapters

value: deg-1(huj32) linc-20(huj2) hujCf1

tag: tissue

value: gonad


title: MOLM13-sh1-2


title: YAA_DKO_ABC_4


title: WT

description: Sample name: WT

source_name: N2 Wild type Adult worms' gonads

value: Wild type


title: M_DKO_FoB_4

value: Folicular B cells


title: MOLM13-shCtrl-3

value: transduced with virus expressing control shRNA


title: AuHH_G_dg

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

description: degradome-seq processed data.xlsx

data_processing:
Library strategy: degradome-Seq
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)

organism: Triticum turgidum subsp. durum

source_name: Developing grain tissue

growth_protocol: Durum wheat variety DBA Aurora plants were grown in controlled glasshouse conditions as previously described (Liu et al., 2019). The standard growing conditions were 22°C/12°C (day/night) with a 12h photoperiod.

extract_protocol:
Total RNA was extracted using the Tri reagent (Sigma-Aldrich) and treated with TURBO DNase (ThermoFisher Scientific). RNA concentration, quality and integrity was assessed by NanoDrop, gel electrophoresis and Bioanalyzer.
The sRNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Kit. The transcriptome libraries were constructed using the Illumina mRNA-Seq sample preparation kit. For degradome-seq, mRNA was enriched using oligo-d(T) magnetic beads. The enriched mRNA was mixed with biotinylated random primers and were ligated to 5' adaptors. First-strand cDNA was reverse-transcribed from ligated mRNA products and then amplified with PCR.

treatment_protocol: The treatment groups are: AuCC (DBA Aurora progeny treated with the control, originated from control group parents), AuCH (DBA Aurora progeny treated with heat stress, originated from control group parents), AuHC (DBA Aurora progeny treated with the control, originated from heat stress group parents), AuHH (DBA Aurora progeny treated with heat stress, originated from heat stress group parents). _L indicates flag leaf library and _G indicates developing grains library. Durum wheat plants were grown in pots (one plant per pot) in the glasshouse under controlled conditions as previously described [1]. Control group plants were grown under the standard growing temperature for the whole crop cycle. For the heat stress group, post-anthesis heat stress was applied at five timepoints [5, 15, 25, 35, and 45 days post anthesis (DPA)]. Plants were placed in a heat stress growth chamber at each timepoint under 37 °C/27 °C day/night temperature for 24h, then they were moved back to the standard growing conditions. All heat stress group plants had undergone five times of heat stress treatment. Flag leaf and developing grains of the main tiller were sampled from four biological replicates per treatment group at 5 DPA.

value: Developing grain tissue

value: DBA Aurora

tag: origin of the parental plants

value: Heat stress group parents

tag: progeny treatment

value: Heat stress group


title: MOLM13-shCtrl-2

value: leukemia cell line


title: MOLM13-shCtrl-1


title: AuHC_G_dg

description: degradome-seq processed data.xlsx

value: Control group


title: AuCH_G_dg

description: degradome-seq processed data.xlsx

value: Control group parents


title: M_DKO_ABC_4

value: Male

value: Age/autoimmune-associated B cells


title: AuCC_G_dg

description: degradome-seq processed data.xlsx


title: DKO-M-FoB-Isotype-Rep2

description:
B-Cell-H3K27me3_peaks.quant.raw_coverages.tsv
B-Cell-H3K27me3_peaks.quant.TPM_normalized_coverages.tsv
B-Cell-H3K27me3_peaks.quant.Library_normalized_coverages.tsv
B-Cell-H3K27me3_peaks.quant.FPKM_normalized_coverages.tsv
B_Cell_Comp_Matrix_H3K27me3.gz
B_Cell_Comp_Matrix_H3K27me3.bed
H3K27me3-Isotype-filtered.stringent.sort.bed

data_processing:
Library strategy: CUT&RUN
RNAseq: Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to the mouse genome (mm10) and reads in exons were counted against Gencode v27 with STAR2.6 Aligner. Differential gene expression analysis was performed in R using edgeR3.24.3. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an unadjusted p-value less than 0.01 were considered differentially expressed. Downstream analyses were performed in R using a visualization platform built with Shiny developed by bioinformaticians at the David Z. Rosensweig Genomics Research Center at HSS
ATACseq: Paired-end 50bp sequences were generated from samples with an Illumina HiSeq2500 and, following adapter trimming with FastP, were aligned against mouse genome (mm10) using bowtie2 with –local -q -p options. Peaks were called with MACS2 with --macs2 callpeak -f BAMPE --nomodel --shit -100 --extsize 200 --B --SPMR -g $GENOMESIZE -q 0.01 options. Peak-associated genes were defined based on the closest genes to these genomic regions using RefSeq coordinates of genes. We used the annotatePeaks command from HOMER to calculate ATAC-seq tag densities from different experiments and to create heatmaps of tag densities. Sequencing data were visualized by preparing custom tracks for the UCSC Genome browser. De novo transcription factor motif analysis was performed with motif finder program findMotifsGenome from HOMER package on ATAC-seq peaks. Peak sequences were compared to random genomic fragments of the same size and normalized G+C content to identify motifs enriched in the targeted sequences.
Cut&Run: The data was processed using CUT&RUNTools (Zhu, Q., Liu, N., Orkin, S.H. et al. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol 20, 192 (2019) pipeline. The peaks from IgG isotype controls were excluded in the SECAR peak calling program. A master file of H3K27me3 peaks across all the conditions and replicates was created with bedops (v2.4.35) using bedops --everything option. computeMatrix and plotHeap map functions were used from deepTools package to plot average tag densities and heatmap.
Genome_build: mm10
Supplementary_files_format_and_content: DKO_ABC_FoB_M_F_YAA_out_list_updated_1.42019-10-28.xlsx multi-worksheet xlsx file containing  unprocessed read count matrix, filtered and normalized read count matrices and the results of edgeR differential expression analysis for DKO_ABC_FoB_M_F_YAA experiments
Supplementary_files_format_and_content: DKO_GCB_PC_M_F_YAA_edgeR_DEGs_with_IgG_batch_corrected_2019-09-15.xlsx multi-worksheet xlsx file containing  unprocessed read count matrix, filtered and normalized read count matrices and the results of edgeR differential expression analysis for GCB_OC/PB_M_F_YAA experiments
Supplementary_files_format_and_content: bigWig files contain normalized big wig profiles for ATAC seq and Cut&Run experiments. Public UCSC browser session for ATACseq profile is available at https://genome.ucsc.edu/s/chinenovy%40hss.edu/ATAC_seq_AWS_S3
Supplementary_files_format_and_content: bed files contains chromosomal coordinates of peaks from Cut&Run experiments
Supplementary_files_format_and_content: tsv – Tab-separated files. Cut&Run peaks statistics

tag: cut&run antibody

value: IgG isotype controls (Guinea Pig anti-Rabbit IgG (H+L) Secondary Antibody (novusbio #NBP1-72763)


title: DKO-M-FoB-Isotype-Rep3


title: AuHC_L_dg

description: degradome-seq processed data.xlsx

source_name: Flag leaf tissue

value: Flag leaf tissue


title: AuHH_L_dg

description: degradome-seq processed data.xlsx


title: DKO-M-FoB-Isotype-Rep1


title: DKO-M-FoB-H3K27me3-Rep3

value: H3K27me3 (anti- Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology #Rabbit mAb #9733)


title: N67CInfected.Rep2.MeRIP

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15)
The Fastq files were aligned to the reference genome using  STAR
The m6A peak calling method was modified from published work.The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform.
For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
Sequence motifs on m6A peaks were identified by HOMER
Genome_build: mm10 and PlasmodiumYoelii
Supplementary_files_format_and_content: txt

source_name: Spleen

growth_protocol: C57BL/6 mice (aged 6-8 weeks) were used in this study according to the Institutional Animal Care and Use Committee (IACUC) at the National Institute of Allergy and Infectious Diseases (NIAID).

extract_protocol:
Spleens were removed, flash frozen on dry ice, and RNAs were harvested using Trizol reagent. Total RNA was purified using PolyATtract® mRNA Isolation System IV followed by RiboMinus transcriptome isolation kit for human/mouse. PolyA-selected and ribodepletion-treated mRNA samples were used for RNA fragmentation followed by immunoprecipitation with EpiMark® N6-Methyladenosine Enrichment Kit. Input RNAs and immunoprecipitated RNAs were used for library preparation using TruSeq Stranded mRNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly thawed N67 and N67C parasites were injected into mice to initiate infection, an inoculum containing 1×106 iRBCs suspended in 100 μl phosphate buffer saline from the donor mice was injected i.v. into experimental mice.

value: Spleen

tag: age

value: 6-8 weeks


title: MOLM13-sh1-1

value: transduced with virus expressing YTHDC1 shRNA-1


title: N67CInfected.Rep2.Input


title: N67CInfected.Rep1.MeRIP


title: N67Infected.Rep2.Input


title: DKO-M-FoB-H3K27me3-Rep2

value: Folicular B cells


title: N67Infected.Rep1.MeRIP


title: N67CInfected.Rep1.Input


title: DKO-M-FoB-H3K27me3-Rep1


title: DKO-M-ABC-Isotype-Rep1


title: AuCH_L_dg

description: degradome-seq processed data.xlsx


title: N67Infected.Rep2.MeRIP


title: AuCC_L_dg

description: degradome-seq processed data.xlsx


title: DKO-M-ABC-H3K27me3-Rep3


title: DKO-M-ABC-Isotype-Rep2


title: BioGRO_xrn1delta

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

institute: Universitat de Valencia

data_processing:
Overall quality control: Overall quality metrics of the sequencing process were evaluated with FastQC.
Adapter trimming and quality filtering: Trimmomatic was used to perform the removal of Illumina adapters, to trim portions of the reads with poor sequencing quality and to drop reads below 20 bases.
Alignment: TopHat 2.1.1 was used to align sequences to the reference genome
Genome_build: sacCer3 - R64
Supplementary_files_format_and_content: Raw read count matrix derived from the featureCounts tool from the R package Subread

organism: Saccharomyces cerevisiae

source_name: Xrn1Δ from Euroscarf collection.

growth_protocol: Growth and harvesting: 100-ml cultures were grown to DO600 = 0.55. Cells were collected by centrifugation and frozen in liquid nitrogen. Frozen pel- lets were transferred immediately to −20◦C. After at least 3 h, cells were thawed on ice and permeabilized with 10 ml of 0.5% sarkosyl solution.

extract_protocol:
RNA extraction: After run-on labelling, cells were kept on ice for 5 min and harvested by centrifugation. RNA extraction was done using the ‘MasterPure Yeast RNA Purification Kit’ (Epicentre) following the manufacturer’s instructions. Once extracted, genomic DNA was removed by digesting with 2 uL of RNase-free DNase I (Roche) for 30 min at 37 ºC. Purified RNA was resuspended in 32 uL of water and was spectrophotometrically quantified.
Biotinilated RNA purification: Labelled RNA was subjected to 1 round of affinity purification with streptavidin paramagnetic beads Dynabeads M-280 Streptavidin (Invitrogen).
Purified labelled RNA was end-repaired with PNK prior to library preparation with the NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible)

treatment_protocol:
RNase treatment    : RNase trimming was achieved by incubating cells with 32 ul of RNase A (10 mg/ml) dissolved in 3.2 ml of 0.5% sarkosyl solution under agitation conditions for 10 min at 30◦C. In order to remove RNase, cells were washed three times with 50 ml of 0.5% sarkosyl and were then transferred to an eppendorf tube.
Run-on reaction: Cells were resuspended in 120 uL of water plus 5 uL of RNase OUT to protect the integrity of nRNAs from any residual RNase. The run-on reaction was performed by incubating the mixture at 30 ºC for 5 min with transcription buffer containing Bio-11-UTP. The reaction was stopped with 1 mL of cold water.

tag: genotype/variation

value: Xrn1 mutant


title: BioGRO_wt

source_name: Yeast strain BY4741

value: wild type


title: MNase Xrn1 mutant rep2

data_processing:
Sequencer Software HiSeq Control Software 2.2.58
AfterQC v0.9.6 was used with default parameters to do the quality control, filtering and trimming of the sequences
reads were mapped to the Saccharomyces cerevisiae reference genome version R64 (SacCer3) using Bowtie2 v2.3.3.1
DANPOS v2.2.2 was used to determine nucleosome positions
Supplementary_files_format_and_content: wig files for merged NAKED, WT and mutant samples generated by DANPOS
Genome_build: sacCer3 - R64

growth_protocol: YPAD medium

extract_protocol:
described in Gutiérrez et al. 2017 doi: 10.1186/s13072-017-0165-x
Standard Illumina 50 paired end HiSeq Sequencing v4 Chemistry

treatment_protocol: MNase digestion protocol was derived from Gutiérrez et al. 2017 doi: 10.1186/s13072-017-0165-x


title: MNase Naked DNA

tag: sample type

value: Naked DNA control


title: Noninfected.Rep2.Input


title: MNase Xrn1 mutant rep1


title: DKO-M-ABC-H3K27me3-Rep2

source_name: spleen

tag: cell type


title: DKO-M-ABC-Isotype-Rep3


title: Noninfected.Rep2.MeRIP


title: Noninfected.Rep1.MeRIP


title: MNase WT rep2


title: DKO-F-FoB-Isotype-Rep3

value: Female


title: Noninfected.Rep1.Input


title: MNase WT rep1


title: DKO-F-FoB-Isotype-Rep2


title: HC_10

value: PBMC

value: healthy control

value: European-American


title: N67Infected.Rep1.Input


title: N6

first: Nadia

last: Dahmane

state: NY

address: 525 East 68 Street, Box 99

institute: Cornell University

data_processing:
FastQC was applied on raw fastq files to examine the sequence quality
Kallisto was applied for pseudoalignment and estimation
Genome_build: mm9
Supplementary_files_format_and_content: Kallisto tpm outputs

source_name: RP58-/- mouse cortices

extract_protocol: Illumina stranded RNA-seq workflow (TruSeq Stranded Total RNA Library Prep Kit) was used followed by sequencing using Illumina HiSeq 4000

value: neuron


title: DKO-F-FoB-Isotype-Rep1


title: DKO-F-FoB-H3K27me3-Rep3


title: N7


title: N5


title: N8

source_name: RP58+/+ mouse cortices


title: DKO-F-FoB-H3K27me3-Rep1


title: DKO-F-ABC-Isotype-Rep3


title: N1


title: DKO-M-ABC-H3K27me3-Rep1

value: Male


title: AuHH_G_mRNA

description: mRNA-seq processed data.xlsx

data_processing:
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)

value: Developing grain tissue

value: DBA Aurora

value: Heat stress group parents

value: Heat stress group


title: DKO-F-ABC-Isotype-Rep2

value: Age/autoimmune-associated B cells

value: IgG isotype controls (Guinea Pig anti-Rabbit IgG (H+L) Secondary Antibody (novusbio #NBP1-72763)


title: AuHC_G_mRNA

description: mRNA-seq processed data.xlsx

value: Control group


title: DKO-F-ABC-Isotype-Rep1


title: AuCH_G_mRNA

description: mRNA-seq processed data.xlsx

value: Control group parents


title: DKO-F-ABC-H3K27me3-Rep3

value: H3K27me3 (anti- Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technology #Rabbit mAb #9733)


title: DKO-F-FoB-H3K27me3-Rep2

value: Folicular B cells


title: AuCC_G_mRNA

description: mRNA-seq processed data.xlsx


title: N9


title: DKO-F-ABC-H3K27me3-Rep2


title: AuHC_L_mRNA

description: mRNA-seq processed data.xlsx

value: Flag leaf tissue


title: DKO-F-ABC-H3K27me3-Rep1

value: Female


title: AuCH_L_mRNA

description: mRNA-seq processed data.xlsx


title: PLZF_ON_rep_3

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

hyb_protocol: Incubeted with rotation at 60 RPM for 16 hours at 45C

scan_protocol: Scanned with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (Affymetrix®)

data_processing: Data summarized and normalized using the RMA routine as implemented in the oligo R library

source_name: expressing a constitutive acetylated form of PLZF

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix manual target preparation for genechip ®  whole transcript expression array.

extract_protocol: Total RNA was extracted from frozen tissue samples using the RNeasy Mini Kit Plus protocol

value: iNKT cells


title: MOVAS cholesterol

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.4.11 running under NextSeq System Suite version 2.2.0.2.
Illumina BCL files were demultiplexed using the mkfastq command from cellranger version 3.0.2 (10x Genomics).
The cellranger count pipeline (version 3.0.2; 10x Genomics) and the mm10 reference package (version 3.0.0; 10x Genomics) were used to process the fastq files, including genome alignment, UMI deduplication, transcript counting, cell barcode attachment and cell calling steps.
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix.txt (Matrix table with raw counts for each cell barcode and gene. Barcodes not called as cells have been excluded.)

source_name: aorta

growth_protocol: Immortalized mouse smooth muscle cell line (MOVAS, purchased from ATCC) was cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin and 200 µg/ml geneticin (Gibco) and incubated at 37°C in 5% CO2 environment.

extract_protocol:
Cells were loaded onto the 10x Genomics Chromium Single Cell B Chip and the resulting emulsion was incubated according to the manufacturer's protocol to release the RNA from cells and perform reverse transcription.
The library was constructed using the 10x Genomics Chromium Single Cell 3' Reagent Kit (v3 Chemistry) following the manufacturer's protocol.

treatment_protocol: Twenty-four hours before cholesterol loading, culture media was replaced with DMEM supplemented with 0.02% BSA. Next, the media was replaced with DMEM supplemented with 0.02% BSA and cholesterol/methyl-β-cyclodextrin (C4951, Sigma Aldrich) and treated for 72 hours, after which the cells were collected for scRNA-Seq. Approximately 2000 cells treated with 0, 25, 50 and 100 µg/ml cholesterol were pooled, yielding a total of approximately 8000 cells for Chromium loading. The Chromium lane was shared with approximately 8000 human cells from another experiment.

tag: cell line

value: MOVAS

value: mixed sample (non-demultiplexed) representing different concentrations of cholesterol


title: AuCC_L_mRNA

description: mRNA-seq processed data.xlsx


title: AuHH_L_mRNA

description: mRNA-seq processed data.xlsx


title: WT_control_rep_1

source_name: control

value: WT


title: HepG2 bortezomib TRIB3 IP, 2 [HepG2-TRIB3-Flag-clone1]

city: Tartu

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.11.3 running under NextSeq Control Software version 4.0.1.41.
ChIP-Seq reads were processed with the nf-core ChIP-Seq pipeline (version 1.2.1) using the hg19 genome and BWA for alignment and MACS2 with the narrow peak profile for calling peaks and peak summits. Input DNA libraries were used as the background control.
From the aligned reads, HOMER (version 4.11) was used to create bedGraph visualization files with depth normalized to 1e7 tags, resolution 1 bp and with no file size reduction.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph format for displaying read coverage in genome browsers

source_name: liver cancer cell line

growth_protocol: HepG2 cells (ATCC) were maintained in Dulbecco’s Modified Eagle Medium (DMEM; 4.5 g/l D-glucose) supplemented with 10% fetal bovine serum and 1× penicillin-streptomycin at 37 °C in a 5% CO2 atmosphere (all medium components from Gibco).

extract_protocol:
Cells were dual-crosslinked with 1.5 mM ethylene glycol bis(succinimidyl succinate) (Thermo Scientific Pierce #21565) for 20 min, after which formaldehyde was added to a final concentration 1.5% and cells were incubated for another 15 min at room temperature. The crosslinking reaction was stopped by adding 0.125 M glycine. Fixed cells were treated with nuclei isolation buffer (10 mM Hepes, pH 7.9, 85 mM KCl, 0.5% NP-40, Roche Complete protease inhibitor cocktail), resuspended in ChIP lysis buffer (50 mM Tris-HCl, pH 8.0, 0.3% SDS, 10 mM EDTA, protease inhibitors) and sonicated with  Bioruptor Plus (Diagenode) for 20 cycles (30 s on, 30 s off) at 4 °C with power set to high. Sonicated chromatin was diluted 3-fold in ChIP dilution buffer (5 mM Tris-HCl, pH 8.0, 250 mM NaCl, 1.1% Triton X-100, protease inhibitors) and immunoprecipitated using mouse anti-Flag M2 monoclonal antibody (Sigma #F3165) or rabbit anti-ATF4 polyclonal antibody (Santa Cruz Biotechnology sc-200) with rotation overnight at 4 °C. Immunocomplexes were isolated by Protein G sepharose beads (Amersham Biosciences) pre-blocked in 0.05% BSA. Subsequently, chromatin crosslinking was reversed and DNA was purified using QIAquick PCR Purification Kit (Qiagen).
ChIP-seq libraries were prepared from 10 ng immunoprecipitated or input DNA using the NuGEN Ovation Ultralow V2 DNA-Seq library preparation kit (NuGEN Technologies). Library DNA was size selected with SPRI beads (Beckman Coulter) to retain 200-500 bp fragments. The libraries were sequenced on an Illumina NextSeq 500 using 76 bp single-end reads.

treatment_protocol: To perform chemical compound treatments, the growth medium was aspirated from the cells and replaced with fresh complete growth medium (described above) supplemented with 50 nM bortezomib or with vehicle (DMSO) as control. The treatment time was 9 h.

value: bortezomib 50nM 9h

tag: chip target


title: SB2_RNA

description:
Adult flies, 3 to 4 days after eclosion.
RNA_counts.txt

data_processing:
All raw sequencing data were quality controlled by fastq (version 0.18.0). Adapters, reads with more than 10% unknown nucleotide (N) content, and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data:
The sequencing data after quality control was firstly mapped to ribosome RNA (rRNA) database using Bowtie2 (version 2.2.8) to remove rRNA reads and get the clean sequencing data.
The clean sequencing data were mapped to the Drosophila melanogaster reference genome (dm6) using HISAT2 (version 2.2.4) with "-rna-strandness RF" and other default parameters after index building of the transcriptome.
The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
RNA differential expression analyses among groups were performed by DESeq2 (version 1.30.1), and RNA differential expression analyses between two samples were performed by edgeR (version 3.32.1). The genes/transcripts with a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
For 16S-seq clean data:
Paired-end clean reads were merged as raw tags using FLASH (version 1.2.11) with a minimum overlap of 10 bp and a mismatch error rate of 2%.
Noisy sequences of the raw tags were filtered by QIIME (version 1.9.1) pipeline under specific filtering conditions to obtain the high-quality clean tags.
Clean tags were searched against the reference database (version r20110519, http://drive5.com/uchime/uchime_download.html) to perform reference-based chimera checking using UCHIME algorithm. All chimeric tags were removed to obtain the effective tags for downstream analyses.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Sterile_RNA_counts.txt: Tab-delimited text file includes raw read counts for the RNA-seq data of sterile samples.
Supplementary_files_format_and_content: RNA_counts.txt: Tab-delimited text file includes raw read counts for RNA-seq samples.
Supplementary_files_format_and_content: 16S_OTU_counts.txt: Tab-delimited text file includes raw OTU counts for the 16S rRNA sequencing samples.

organism: Drosophila melanogaster

source_name: Whole adult

value: Whole body

value: Adult

tag: culture environment

value: Bacteria

value: Sodium butyrate feeding

tag: replicate


title: WT_control_rep_3


title: WT_control_rep_2


title: PLZF_ON_rep_1


title: AuHH_G_sRNA

description: sRNA-seq processed data.xlsx

value: Developing grain tissue

value: DBA Aurora

value: Heat stress group parents

value: Heat stress group


title: PLZF_ON_rep_2


title: AuHC_G_sRNA

description: sRNA-seq processed data.xlsx

value: Control group


title: C2_RNA

value: Untreated


title: SB1_RNA


title: HepG2 bortezomib Input, 2 [HepG2-TRIB3-Flag-clone1]

value: none (Input sample)


title: HepG2 bortezomib ATF4 IP [HepG2-TRIB3-Flag-pool]


title: HepG2 bortezomib TRIB3 IP [HepG2-TRIB3-Flag-pool]


title: C1_RNA


title: AuCH_G_sRNA

description: sRNA-seq processed data.xlsx

value: Control group parents


title: HepG2 bortezomib Input [HepG2-TRIB3-Flag-pool]


title: AuCC_G_sRNA

description: sRNA-seq processed data.xlsx


title: HepG2 untreated TRIB3 IP [HepG2-TRIB3-Flag-clone1]

value: vehicle treated 9h


title: SB3_sterile_RNA

description:
Adult flies, 3 to 4 days after eclosion.
Sterile_RNA_counts.txt

value: Sterile


title: SB2_sterile_RNA


title: AuHH_L_sRNA

description: sRNA-seq processed data.xlsx

value: Flag leaf tissue


title: AuHC_L_sRNA

description: sRNA-seq processed data.xlsx


title: HepG2 untreated Input [HepG2-TRIB3-Flag-clone1]


title: SB1_sterile_RNA


title: AuCH_L_sRNA

description: sRNA-seq processed data.xlsx


title: HepG2 untreated TRIB3 IP [HepG2-TRIB3-Flag-pool]


title: S3_sterile_RNA


title: HepG2 untreated Input [HepG2-TRIB3-Flag-pool]


title: S2_sterile_RNA


title: AuCC_L_sRNA

description: sRNA-seq processed data.xlsx


title: HepG2 bortezomib TRIB3 IP, 1 [HepG2-TRIB3-Flag-clone1]


title: S1_sterile_RNA


title: C3_sterile_RNA


title: HepG2 bortezomib Input, 1 [HepG2-TRIB3-Flag-clone1]


title: SCI.GFP

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the brains of 4 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 4.0.0. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Spinal cord

growth_protocol: not applicable

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

value: 4-5 months

tag: gender

value: female

tag: treatment protocol

value: T9 crush injury with fone forceps


title: SCI.WT


title: C2_sterile_RNA

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitated by isopropyl alcohol. Total DNA of 16S-seq samples were extracted from Drosophila midgut using TIANamp genomic DNA kit (Tiangen, DP304) following the manufacturer's protocol.
After total RNAs of each sample were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmentation buffer and reverse transcribed into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Genedenovo Biotechnology Co, Ltd.

value: Whole body

value: Adult


title: HepG2 bortezomib Input [HepG2-unedited]

value: bortezomib 50nM 9h


title: EAE.WT

description: RNA was isolated from the brains of 3 mice.

value: MOG35-55 immunization


title: 22/04_PDD

city: Singapore

first: Michelle

middle: GK

last: Tan

address: 20 College Road

department: Clinical Translational Research

country: Singapore

institute: Singapore General Hospital

description: PDD

hyb_protocol: Samples were hybridized to Affymetrix GeneChip HTA2.0 arrays at 45°C for 16 hours with rotation at 60rpm, then washed and stained in a Fluidics Station using the FS450_0001 fluidics protocol.

scan_protocol: Gene chips were scanned by an Affymetrix 3000 7G scanner.

data_processing:
CEL files were generated from Affymetrix GeneChip Command Console (AGCC) Software. Data was analyzed with Partek Genomics Suite 7 (http://www.partek.com/partekgs) using the exon array workflow with default conditions (Robust Multi-Chip analysis (RMA) background corrections, quantile normalization, log 2 base transformation and summarization by Median Polish).
probe_group_file: HTA-2_0.r3.pgf
meta-probeset_file: HTA-2_0.r1.Partek.mps

source_name: prefrontal cortex BA9 of PDD patient

label_protocol: 100ng total RNA samples was processed and labeled using GeneChip WT PLUS Reagent Kit according to manufacturer's instructions

extract_protocol: Total RNA was isolated using Trizol reagents (Invitrogen) according to the manufacturer's instructions. Microarray service was conducted by Origen Labs Inc (Singapore).

tag: Sex

value: Male

tag: pmi


title: EAE.GFP

tag: strain


title: HepG2 bortezomib neg control anti-Flag IP [HepG2-unedited]

tag: treatment

value: Flag


title: 80/02_PDD

description: PDD


title: C1_sterile_RNA

tag: tissue

value: Bacteria


title: ST22/02_PDD

description: PDD

value: Female


title: 5GB1_vial_woLa_TR2

city: Seattle

first: Erin

last: Wilson

state: WA

address: 185 E Stevens Way NE

department: The Paul G. Allen School of Computer Science & Engineering

institute: University of Washington

description: vial sample, without lanthanum

data_processing:
BWA version 0.7.12-r1044 was used to align the reads to the 5GB1C genome using the BWA-MEM algorithm and default parameters
Read alignments were converted into sorted BAM files using SAMTools version 1.2-232-g87cdc4a
The htseq-count tool from the “HTSeq” framework version 0.6.1p1 was used to attribute the reads to ORFs using the “intersection-nonempty” mode, providing estimates of raw read counts
Raw counts were then normalized by sample and transcript length to reflect transcripts per million (TPM) for each genome feature.
The locus tags refer to the locus_tag field in the *M. buryatense*  genome file, available here: https://www.ncbi.nlm.nih.gov/nuccore/1678288454?report=genbank
Genome_build: NCBI: NZ_CP035467.1
Supplementary_files_format_and_content: TPM

organism: Methylotuvimicrobium buryatense

source_name: vial culture

extract_protocol:
RNA was extracted as previously described (Chu and Lidstrom, 2016).
RNA sequencing and library construction was performed by GENEWIZ (South Plainfield, NJ, USA) using Illumina HiSeq

value: NoLanthanum


title: ST04/01_PDD

description: PDD


title: SKO2

city: shanghai

first: qiang

last: fang

address: 1239 Siping Road

institute: tongji university

data_processing:
Paired-end reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of control and Mps1 knockout (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
GO and KEGG enrichment analysis of the DEGs was implemented with the clusterProfiler R package
Genome_build: mm10
Supplementary_files_format_and_content: expr_matrix.txt includes the raw counts and FPKM values of genes. Downregulated_GOenrich.txt and Upregulated_KEGGenrich.txt include GO and KEGG analysis of DEGs.

source_name: testis

growth_protocol: For Mps1sKO mouse, we knocked out the Mps1 gene in germ cells at the beginning of meiosis by mating with Stra8-cre mice, which specifically express Cre recombinase at P3 (early spermatogonia) and exhibit increased expression until P7 (preleptotene spermatocytes) in testes.

extract_protocol:
Total RNA was extracted from whole testes at P10.
mRNA-Seq libraries were constructed from 1 μg of RNA using an NEBNext UltraTM RNA Library Prep Kit (NEB, USA) following the manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq platform with 150 bp paired-end reads.

tag: genotype

value: Mps1 Stra8-cre knockout

value: post natal day 10

value: male

value: testis


title: 134/03_PDD

description: PDD


title: 575/10_DLB

description: DLB

source_name: prefrontal cortex BA9 of DLB patient


title: HepG2 bortezomib ATF4 IP [HepG2-TRIB3-Flag-clone1]


title: ST24/03_PDD

description: PDD


title: ST30/04_PDD

description: PDD


title: ST23/03_PDD

description: PDD


title: ST03/01_PDD

description: PDD


title: 5GB1_FM81_t2_TR3

description: Fermentor run 81, low O2, slow growth, extra nitrate

source_name: bioreactor culture


title: 5GB1_vial_wLa_TR3

description: Vial sample, with lanthanum

value: WithLanthanum


title: 85/04_DLB

description: DLB


title: SKO1


title: op470_DLB

description: DLB


title: HepG2_Nelf_20uM_S14_rep2

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.11.3 running under NextSeq Control Software version 4.0.1.41.
RNA-Seq reads were trimmed to remove Illumina adapter, poly(A) and low-quality bases using cutadapt (version 2.8).
The trimmed reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2) with trimming disabled and with STAR selected to align the reads to the hg19 human genome. Read counts in transcripts were determined according to Ensembl GRCh37/hg19 release 87 gene annotations for protein coding, lincRNA and antisense gene biotypes.
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix (genes with zero overall counts have been removed)

extract_protocol:
Total RNA from four biological replicates per condition was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol for cultured cells, including on-column DNase I digestion. RNA yield and purity were measured on a NanoDrop 1000 Spectrophotometer (Thermo Scientific) to verify an A260/A280 nm ratio >1.8 and A260/A230 nm ratio ~2.
Libraries were prepared from 250 ng of total RNA per sample using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (FWD) according to the manufacturer's instructions. Libraries were quantified with the Qubit dsDNA HS assay kit (Life Technologies) and combined in equimolar ratio. The pool of libraries was sequenced at the Estonian Genome Center Core Facility using the Illumina NextSeq500 platform with 80 bp single-end reads.

treatment_protocol: To perform chemical compound treatments, the growth medium was aspirated from the cells and replaced with fresh complete growth medium (described above) supplemented with the indicated chemical compound(s) or with vehicle as control. The chemical concentrations were as follows: bortezomib 50 nM, ISRIB 50 nM and nelfinavir 20 uM. Treatment time was 10 h.

value: liver cancer cell line

value: nelfinavir 20uM for 10h


title: op51_DLB

description: DLB


title: 04/03_PDD

description: PDD


title: ST11/02_PDD

description: PDD


title: 5GB1_FM81_t1_TR3


title: CTRL2

value: control


title: HepG2_Nelf_20uM_S15_rep3


title: ST12/02_PDD

description: PDD


title: HepG2_Nelf_20uM_S16_rep4


title: 105/07_DLB

description: DLB


title: HepG2_ISRIB_50nM_S9_rep4

value: ISRIB 50nM for 10h


title: HepG2_Nelf_20uM_S13_rep1


title: 30/05_DLB

description: DLB


title: 40/05_DLB

description: DLB


title: CTRL1


title: op439_DLB

description: DLB


title: 5GB1_FM69_t4_TR1_UW

description: Fermentor run 69, high O2, slow growth


title: HepG2_ISRIB_50nM_S10_rep1


title: HepG2_ISRIB_50nM_S11_rep2


title: 5GB1_FM80_t4_TR1

description: Fermentor run 80, low O2, slow growth, extra nitrate


title: A231/06_DLB

description: DLB


title: 5GB1_FM80_t2_TR1


title: 07/03_DLB

description: DLB


title: HepG2_ISRIB_50nM_S12_rep3


title: 5GB1_FM69_t3_TR1

description: Fermentor run 69, high O2, slow growth


title: A359/08_CTRL

description: CTRL

source_name: prefrontal cortex BA9 of control patient


title: HepG2_DMSO_S3_rep3

value: DMSO for 10h


title: 5GB1_FM69_t4_TR1

description: Fermentor run 69, high O2, slow growth


title: 5GB1_FM69_t3_TR1_UW

description: Fermentor run 69, high O2, slow growth


title: HepG2_DMSO_S4_rep4


title: 5GB1_FM40_T90m_TR2_QC

description: Fermentor run 40, Cu transition, T90m (after Cu)

value: medCu


title: HepG2_DMSO_S2_rep2


title: A196/09_DLB

description: DLB


title: 5GB1_FM40_T90m_TR2


title: Hippocampal Astrocytes Ketogenic Biological Sample 4

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

source_name: Hippocampal Astrocytes Ketogenic Diet

label_protocol: The NuGEN Pico WTA v2 kit was used as described in the manufacturer's manual.

growth_protocol: Mouse hippocampus dissected from mice expressing a tagged ribosome specifically in astrocytes.

extract_protocol: Actively translating mRNAs were determined using translating ribosomal affinity purification based on established protocols.   Kulicke, R., Fenster, R. J., Greengard, P., Heintz, N. & Heiman, M. Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP). Nature Protocols 9, 1282–1291 (2014).

treatment_protocol: Mice  were subjected to one of three dietary conditions: four weeks of normal chow diet, four weeks of ketogenic diet (high-fat, low-carbohydrate)43, or an 18-hour fast

tag: dietary challenge

value: Ketogenic Diet

value: hippocampus


title: A072/09_DLB

description: DLB

tag: age


title: HepG2_DMSO_S1_rep1


title: Hippocampal Astrocytes fasted Biological Sample 2

source_name: Hippocampal Astrocytes fasted

value: 24hr fasted


title: Hippocampal Astrocytes fasted Biological Sample 3


title: Hippocampal Astrocytes fasted Biological Sample 1


title: Hippocampal Astrocytes Ketogenic Biological Sample 1


title: 5GB1_FM40_T60m_TR1_QC

description: Fermentor run 40, Cu transition, T60m (after Cu)

value: lowCu


title: Hippocampal Astrocytes Ketogenic Biological Sample 2


title: 5GB1_FM40_T60m_TR1


title: A320/94_CTRL

description: CTRL

value: Male


title: Hippocampal Astrocytes Ketogenic Biological Sample 3


title: 5GB1_FM40_T40m_TR1

description: Fermentor run 40, Cu transition, T40m (after Cu)


title: B03_W12

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

description: Single-cell RNA transcriptome analysis

data_processing:
Customized Macaca mulatta reference package was created by the mkref function in Cell Ranger software (version 3.1.0) using the Macaca mulatta reference genome from Ensembl (Mmul_8.0.1, release 97)
Unique molecular identifier (UMI) counts generated by aligning raw FASTQ files to the customized reference tracscriptome using the count function of Cell Ranger (version 3.1.0)
Genome_build: Mmul 8.0.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Macaca mulatta

source_name: Outbred Chinese origin and female

extract_protocol:
The Chromium Single Cell V(D)J Reagent Kit from 10X genomics were used according to the manufacturer’s protocol.  In brief, purified CD8+ T cells were subjected to single cell encapsulation by 10X Chromium Controller, followed by barcoding, reverse transcription for cDNA synthesis, clean up and cDNA amplification and target enrichment from cDNA for subsequent library construction.
Library construction followed the protocol of 10X Chromium Single Cell V(D)J Reagent Kit

value: female

value: Purfied peripherial CD8+ T cells

value: 12 weeks post immunization of pRhPD-1-p27 DNA vaccine