title: Mettl3_OE-3

city: 上海

first: xiang

middle: chen

last: xi

address: siping road 1239

institute: tongji university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

source_name: reprogramming cells day 3

growth_protocol: The reprogrammable MEFs were cultured in DMEM supplemented with 10% fetal bovine serum and Glutamine. The reprogramming cells were induced with doxycycline (Dox) (1ug/ml) for 3 ，6，9，12，15days in ES medium consisted of DMEM supplemented with 15% fetal bovine serum,  nonessential amino acids, Glutamine, Nucleosides, 2-mercaptoethanol, LIF.

extract_protocol:
For RNA-seq, the cells were lysed using RLT buffer supplemented with β-mercaptoethanol and processed using the RNeasy mini kit (Cat. 74104). Glycine was added to stop the cross-linking at final concentration of 0.125 M and the cells were rinsed in PBS. Then the cells were re-suspended in lysis buffer containing protease inhibitors and chromatin was sonicated to 100-400 bp with Covaris M220 system.
KAPA Stranded mRNA-Seq Kit (KK8420)

treatment_protocol: The reprogrammable MEFs (0 day and 3，6，9，12，15 days post-Dox induction with or without Mettl14,mettl3’s overexpression) were digested to single cell and harvested to performed RNA-seq

tag: timepoint

tag: condition


title: Mettl3_OE-2

status: Public on Aug 24 2022

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus


title: Rb19 - Primary Retinoblastoma - RNA-Seq

city: Miami

first: Matthew

last: Field

state: FL

address: 900 NW 17th St

country: USA

institute: University of Miami

data_processing:
Reads were aligned and gene counts were made using STAR (2.5.2a) with parameters --runThreadN 16 --genomeSAindexNbases 12 --genomeSAsparseD 2 --twopassMode Basic --twopass1readsN -1 --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignMatesGapMax 200000 --alignIntronMax 200000 --alignSJDBoverhangMin 10 --quantMode GeneCounts
Gene expression was normalized and batch corrected using EdgeR (3.32.1) according to tutorial recommendations
For knockdown experiments, batch correction was utilized for cell line and adjusted using estimateDisp()
assembly: hg19
tab-delimited text files for RNA-Seq data with STAR gene counts for all RNA-Seq samples
normalized abundance measurements using EdgeR for RNA-Seq data with p-values calculated for knockdown experiments (shESRRG compared to shGFP)

molecule: total RNA

organism: Homo sapiens

source_name: Primary Retinoblastoma

extract_protocol:
RNA was extracted using TriZol and the RNeasy Mini RNA isolation kit
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA prep kit with Ribo-Zero Gold to remove cytoplasmic and mitochondrial rRNA according to the manufacturer's recommendation (Illumina, San Diego, CA). Total RNA-seq libraries were run on an Illumina NextSeq 500 sequencing instrument according to the manufacturer’s protocol.

tag: tissue

value: primary retinoblastoma

tag: iirc tumor class

value: Class E

tag: familial

value: No


title: Subject_38_PolyIC_Cord

city: Perth

first: James

last: Read

state: WA

address: 15 Hospital Ave.

country: Australia

institute: Telethon Kids Institute

data_processing:
Data was generated with the Illumia NovaSeq 6000 platform and the bcl2fastq pipeline was used to convert base calls (BCL) to fastq files.
Read libraries were mapped to the human genome (hg38) using HISAT2. Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps, and Pre- and post-alignment QC was assessed with FastQC and SAMStat, respectively.
(For corrected gene counts) Raw transcripts were removed if they had no counts in any sample, lacked annotation, or had 0.5 counts per million in ≤ 25 samples. Size factors were estimated using the median ratio method with the 'estimateSizeFactors' function (DESeq2 R package) and variance stabilizing transformation (VST) was applied to the count data (DESeq2). Unwanted variation was identified with the 'RUVg' function from the RUVSeq R package. RUVg trends which related to technical variation and culture batch were removed as covariates with a linear model ('removeBatchEffect' function from the limma R package).
Genome_build: hg38
Supplementary_files_format_and_content: CBMC_genecounts.txt file contain a matrix of raw gene counts (unfiltered and un-normalised data), with transcripts as rows and samples as columns. Transcript information (e.g. EnsembleID, gene symbol) are supplied in the final columns. CBMC_corrected_counts.txt contains a matrix of VST transformed and batch/RUV corrected gene counts, formatted as the raw gene count file.

source_name: CBMC

extract_protocol:
Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (QIAGEN). Total RNA libraries were prepared using NEBNext Ultra II Kits (New England BioLabs). Sequencing was performed by the Australian Genome Research Facility (Illumina NovaSeq 6000, 100bp paired-end reads).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cryopreserved cord blood mononuclear cells were thawed and stimulated with LPS, Imiquimod or Poly(I:C), of left untreated, and cultured at 37oC (5% CO2) for 18 hrs.

tag: stimuli

value: PolyIC

value: Cord

tag: Sex

value: Female

value: Yes


title: Control 5

city: Scottsdale

first: Alfred

last: Doyle

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using FastQC
The RNA paired end reads were aligned using the STAR aligner 2.6.1c
Gene counts were generated using subread featuerCounts
Assembly: mm10
Supplementary files format and content: tab-delimited files with RNA-Seq gene expression

source_name: esophagus

extract_protocol:
Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit (Qiagen).
Library Preparation with PolyA selection and Illumina Sequencing. RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using  manufacturer’s instructions.

treatment_protocol: To investigate the effects of the common household detergent Sodium Dodecyl Sulfate (SDS) on the esophagus we provided mice with 0.5% SDS in their drinking water for 14 days and assessed the effects by various methods including RNA-Seq of whole esophagus homogenates.

value: esophagus

tag: cell type

value: WT

tag: treatment

tag: time

value: Day 14


title: Control 4


title: Mettl14_OE-3


title: AFP-negative 3 [839NT]

city: Suita

first: Yuki

last: Makino

state: Osaka

address: 2-2, Yamadaoka

country: Japan

institute: Osaka University Graduate School of Medicine

data_processing:
Tag count and normalization was performed using cuffdiff: v2.2.1 (4237)
Assembly: NOT PROVIDED
Supplementary files format and content: NOT PROVIDED

source_name: liver

extract_protocol:
Total RNA was extracted from formalin-fixed, paraffin-embedded liver tissues at 4 months of age by laser microdissection.
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
The libraries were sequenced by NovaSeq 6000 sequencing instrument (101 bp, paired-end)

value: liver

tag: age

value: 4 months

value: AFP-negative

tag: genotype

value: LiKM (KrasG12D mutation and Mdm2 loss in the liver)


title: Mettl14_OE-2


title: AFP-positive 3 [839T]

value: AFP-positive


title: Subject_39_LPS_Cord

value: LPS


title: Control 2


title: AFP-positive 2 [262T]


title: Control 3


title: MEF-3

source_name: reprogramming cells day 0

value: MEF


title: AFP-negative 2 [262NT]


title: Subject_37_PolyIC_Cord


title: Sertoli1_MSUS

city: Zurich

first: Kristina

middle: Maria

last: Thumfart

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH

data_processing:
Fastq files were trimmed with Trimgalore (v 0.6.5)
pseudo-mapped with Salmon (v 1.1.0)
Assembly: GENCODE annotation of transcripts (vM23)
Supplementary files format and content: csv-file includes raw counts for each sample obtained from Salmon

source_name: testis

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
Libraries for RNA sequencing were prepared from 5 ng RNA per sample using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara)

treatment_protocol: pups in the MSUS group were separated from their mother for 3 h per day at unpredictable times from postnatal day (PND) 1 to 14. During separation, the mothers underwent an acute swim in cold water (18°C for 5 min) or 20-min restraint in a tube.

value: testis

value: Sertoli cell

value: Bl6 wt

value: MSUS


title: Mettl3_OE-1


title: Subject_38_CTRL_Cord

value: CTRL

value: Cord


title: AFP-negative 1 [50NT]


title: Subject_37_LPS_Cord

value: Female

value: Yes


title: Subject_38_IMIQ_Cord

value: IMIQ


title: Subject_37_CTRL_Cord


title: MEF-1


title: Subject_37_IMIQ_Cord


title: Control-3

value: OSKM+Vector


title: MEF-2


title: WT, S2, E17.5

city: Shanghai

first: Yaqiong

last: Wang

address: 399 Wanyuan Rd

institute: Children's hospital of Fudan University

description: 2X150 paired-end sequence reads

data_processing:
RNA-seq data were processed through the Nextflow nf-core/rnaseq pipeline (v3.4) with default parameters
Adapter and quality trimming by Trim Galore
sequence reads were aligned to the mouse genome (GRCm39 and GENCODE vM27) using STAR (v2.6)
gene counts were quantified using Salmon (v1.5)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes read counts values for each sample

source_name: cerebral cortex

growth_protocol: All C57BL/6J mice were experimental model and were fed in a specific pathogen-free room with automatically controlled temperature (16℃), humidity (40%), ventilation and light conditions (light, 6:00 to 18:00; dark, 18:00 to 6:00)

extract_protocol:
Total RNA was isolated with Trizol according to the manufacturer’s instructions.
Total mRNA concentration was determined with Agilent 2100 and RNA-seq libraries were prepared according to the manufacturer’s instruction followed by sequencing on Illumina, which was performed by Personalbio

treatment_protocol: Satb2 knock out model was generated through CRISPR-Cas9 technology by Biocytogen Pharmaceuticals (Beijing) Co., Ltd

value: cerebral cortex

tag: strain

value: WT


title: Subject_38_LPS_Cord


title: WT, S2.2, E17.5

description: 2X150 paired-end sequence reads


title: Mut, S52.5, E17.5

description: 2X150 paired-end sequence reads

value: Satb2 KO


title: Lin-Kit+ hematopoietic stem and progenitor cells - heparan sulfate low

city: Bronx

first: Emily

last: Schwenger

state: NY

address: 1300 Morris Park Ave.

department: Cell Biology

institute: Albert Einstein College of Medicine

library_source: transcriptomic single cell

data_processing:
alevin
Assembly: mm10
Supplementary files format and content: Tab-deliminited matrix with raw gene counts for every gene and every sample

source_name: Bone marrow hematopoietic stem and progenitor cells (HSPCs)

extract_protocol:
FACS-purified HSPCs (Lin-c-kit+) sorted on HS scFv binding were used to prepare scRNA-seq libraries using the 10x Genomics Chromium 3’ v3 kit according to manufacturer protocol (10x Genomics).
Single cells were isolated using the Gemcode technology platform using barcoded droplets and paired-end reads of 150 bp.
10x Genomics Chromium 3' v3 kit. Libraries were submitted for sequencing to Novogene using an Illumina Hi-Seq platform with a target of 10,000 cells per condition.

tag: heparan sulfate binding

value: Low


title: Control-2


title: MEP - low HS3A8 - rep3

data_processing:
Reads were mapped to the mm10 transcriptome using STAR aligner v2.5.
 HTSeq v0.6.1 was used to count the read numbers mapped of each gene
Assembly: mm10
Supplementary files format and content: Tab-deliminited matrix with raw gene counts for every gene and every sample

source_name: Bone marrow MEP

extract_protocol:
25,000 FACS-purified MEPs (Lin-ckit+CD34-FcγRII/IIIlo) sorted on HS scFv binding were used to prepare bulk RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: scfv binding

value: MEP (Lin-ckit+CD34-FcgammaRII/IIIlo)


title: Subject_36_PolyIC_Cord

value: PolyIC

value: Male

value: No


title: Lin-Kit+ hematopoietic stem and progenitor cells - heparan sulfate high

value: High


title: MEP - high HS3A8 - rep3


title: Control 1

value: esophagus

value: Day 14


title: Mut, S1, E17.5

description: 2X150 paired-end sequence reads


title: Mettl14_OE-1


title: Day9_Mettl3-OE-2

source_name: reprogramming cells day 9


title: Lin-Kit+ hematopoietic stem and progenitor cells - control

value: Control


title: Control-1


title: LiKM mice 3 [KM2451]

data_processing:
The libraries were sequenced by NovaSeq 6000 sequencing instrument (100 bp, paired-end)
FastQC software v0.11.7 was used to assess the read quality.
We used featureCounts (featureCounts, RRID:SCR_012919) v1.4.6 to count the read numbers mapped to each gene.
Supplementary files format and content: text files include count data for each Sample

extract_protocol:
Total RNA was extracted from the liver at 6 weeks of age.
TruSeq stranded mRNA Kit

value: liver

value: LiKM


title: AFP-positive 1 [50T]

value: 4 months

value: AFP-positive

value: LiKM (KrasG12D mutation and Mdm2 loss in the liver)


title: Subject_36_IMIQ_Cord

value: IMIQ

value: Cord


title: Day9_Mettl3-OE-3


title: Subject_35_PolyIC_Cord

value: Female

value: Yes


title: MEP - low HS3A8 - rep2

value: Low

value: MEP (Lin-ckit+CD34-FcgammaRII/IIIlo)


title: MEP - low HS3A8 - rep1


title: MEP - control - rep3


title: Subject_36_LPS_Cord

value: LPS

value: Male


title: Mut, S52.4, E17.5

description: 2X150 paired-end sequence reads

value: cerebral cortex

value: Satb2 KO


title: LiK mice 3 [KM2477]

value: LiK


title: MEP - high HS3A8 - rep1

value: High


title: Day9_Mettl14-OE-2


title: Day9_Mettl3-OE-1


title: LiK mice 2 [KM2292]

value: liver


title: MEP - control - rep1

value: Control


title: Subject_35_CTRL_Cord

value: CTRL


title: MEP - high HS3A8 - rep2


title: Subject_36_CTRL_Cord

value: No


title: Day9_Mettl14-OE-3


title: Subject_35_LPS_Cord


title: Day9_Control-2

value: OSKM+Vector


title: Day9_Mettl14-OE-1


title: MEP - control - rep2


title: Subject_35_IMIQ_Cord

value: IMIQ


title: LiK mice 1 [KM2282]


title: Day9_Control-3


title: ST8

city: Columbus

first: Steve

last: Oghumu

address: 1841 Neil Ave

institute: Ohio State University

data_processing:
Illumina sequencing
pair end 150 base pairs
CASAVA base calling
STAR software mapping
expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: HNSCC Tumor

extract_protocol:
RNA was extracted using QIAGEN total RNA isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/C

value: Stat1 knock out mouse

tag: injected cell line

value: Tumor


title: Subject_34_PolyIC_Cord

value: PolyIC

value: Cord


title: LiKM mice 2 [KM2445]

value: LiKM


title: Subject_34_IMIQ_Cord

value: Male


title: ST6


title: Subject_34_CTRL_Cord


title: LiKM mice 1 [KM2429]


title: Subject_34_LPS_Cord

value: LPS


title: LiKM mice fed ACR diet 3

data_processing:
The libraries were sequenced by NovaSeq6000 (Illumina) in 101 bp single-end mode, generating 10 million reads per sample
The raw counts were calculated using featureCounts ver 2.0.0
Assembly: mm10
Supplementary files format and content: raw counts

source_name: non-tumorous liver tissue

extract_protocol:
Total RNA was extracted from non-tumorous liver tissues.
TruSeq Stranded mRNA kit

treatment_protocol: LiK and LiKM mice were fed a normal diet or a diet containing 0.06% ACR from 5 weeks of age until sacrifice at 4 months of age.

value: non-tumorous liver tissue

value: 4 months

tag: gender

value: male

tag: diet

value: ACR diet


title: ST7

value: WT mouse


title: Subject_33_PolyIC_Cord

value: Female

value: Yes


title: ST5


title: Day9_Control-1

tag: timepoint

tag: condition

value: OSKM+Vector


title: Subject_33_IMIQ_Cord

value: IMIQ

value: No


title: ST4

value: BALB/C

value: Stat1 knock out mouse

tag: tissue


title: LiKM mice fed normal diet 3

value: normal diet


title: Day6_Mettl3-OE-3

source_name: reprogramming cells day 6


title: LiK mice fed normal diet 2

value: LiK


title: LiKM mice fed normal diet 2

value: LiKM


title: 3LL_MRTX_28h_3

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Genome_build: GRCm38 Ensembl release 89
Supplementary_files_format_and_content: normalized counts per gene per sample

source_name: 3LL cells

extract_protocol:
RNA was extracted via a column-based method
mRNA KAPA Hyper Prep

treatment_protocol: Cells and tumours were treated with vehicle or MRTX1257 for different time points

tag: cell line

value: 3LL DNRAS #86

tag: replicate

value: replicate 3


title: Subject_33_CTRL_Cord

tag: stimuli

value: CTRL

value: Cord

tag: Sex


title: LiKM mice fed normal diet 1

value: non-tumorous liver tissue

value: 4 months

value: male


title: Day6_Control-3


title: 3LL_MRTX_8h_3

tag: treatment

value: MRTX1257 8h


title: ST3

value: WT mouse

value: Tumor


title: LiKM mice fed ACR diet 2

value: ACR diet


title: Day6_Control-2

value: OSKM+Vector


title: LiK mice fed normal diet 3


title: ST2

value: BALB/C


title: Subject_33_LPS_Cord

value: LPS

value: Female

value: Yes

value: No


title: Day6_Mettl3-OE-1


title: LiK mice fed normal diet 1

value: LiK

value: normal diet


title: Subject_32_IMIQ_Cord

value: IMIQ

value: Male


title: Day6_Mettl14-OE-3


title: Day6_Mettl14-OE-2


title: LiK mice fed ACR diet 3

value: non-tumorous liver tissue


title: Day6_Mettl14-OE-1


title: Day12_Mettl3-OE-3

source_name: reprogramming cells day 12


title: LiKM mice fed ACR diet 1

value: 4 months

value: LiKM


title: Subject_31_IMIQ_Cord

value: Cord


title: Subject_32_LPS_Cord


title: Day12_Mettl3-OE-2


title: Subject_32_PolyIC_Cord

value: PolyIC


title: 3LL_Vehicle_3

value: 3LL DNRAS #86

value: replicate 3

value: DMSO control


title: KO3: P14 Ednrb-KO small intestine ENS cells – scRNAseq

city: Boston

first: Allan

middle: M

last: Goldstein

state: MA

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

description: Individual mouse P14

data_processing:
Sequencing performed using Illumina NextSeq or NovaSeq platforms
Genome alignment and counts matrices generated using 10X Genomics Cell Ranger pipeline
Assembly: mm10

source_name: Small intestine

extract_protocol: 10X Genomics Single cells (scRNAseq)

tag: cell type

value: tdTomato-positive enteric nervous system (ENS) cells

value: Ednrb-KO

tag: disease model

value: Hirschsprung disease


title: Day6_Control-1

value: OSKM+Vector


title: Subject_32_CTRL_Cord

value: CTRL

value: Yes

value: No


title: LiK mice fed ACR diet 1

tag: age

value: LiK

value: male

value: ACR diet


title: ST1

tag: strain

value: BALB/C

tag: genotype

value: WT mouse

value: Tumor


title: LiK mice fed ACR diet 2

value: non-tumorous liver tissue

value: 4 months


title: Day12_Mettl3-OE-1


title: Subject_31_PolyIC_Cord

value: PolyIC

value: Cord

value: Female


title: Day6_Mettl3-OE-2


title: 3LL_MRTX_8h_2

value: 3LL DNRAS #86

value: replicate 2

value: MRTX1257 8h


title: 3LL_MRTX_28h_2


title: Day12_Mettl14-OE-2


title: 3LL_Vehicle_1

value: replicate 1

value: DMSO control


title: MRTX 6day mouse3 tumour5

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Assembly: GRCm38 Ensembl release 89
Supplementary files format and content: tab separated text files with counts per gene per sample

source_name: KPAR1.3-G12C lung tumour

treatment_protocol: Cells and tumours were treated with vehicle or MRTX849 for different time points

value: F-replicate 9

value: MRTX849 6 days


title: Subject_31_LPS_Cord

value: LPS

value: No

value: Yes


title: 3LL_Vehicle_2


title: KO2: P14 Ednrb-KO small intestine ENS cells – scRNAseq

description: Individual mouse P14

value: tdTomato-positive enteric nervous system (ENS) cells

value: Ednrb-KO

value: Hirschsprung disease


title: MRTX_8day_mouse3_tumour4

source_name: 3LL lung tumour

value: replicate 6

value: MRTX1257 8 days


title: 3LL_MRTX_28h_1


title: Day12_Mettl14-OE-3


title: Subject_31_CTRL_Cord

source_name: CBMC

value: CTRL

value: Cord


title: Subject_30_CTRL_Cord

value: Female


title: Subject_30_PolyIC_Cord

value: PolyIC


title: Vehicle Mouse3 tumour4

value: D-replicate 9

value: Vehicle control


title: KO1: P14 Ednrb-KO small intestine ENS cells – scRNAseq

description: Individual mouse P14


title: Subject_30_IMIQ_Cord

value: IMIQ


title: 3LL_MRTX_8h_1

value: 3LL DNRAS #86

value: replicate 1

value: MRTX1257 8h


title: MRTX_8day_mouse2_tumour1

value: replicate 3


title: Day12_Mettl14-OE-1


title: Subject_30_LPS_Cord

value: LPS

value: No


title: Day12_Control-2

value: OSKM+Vector


title: Day12_Control-3


title: Subject_29_IMIQ_Cord

value: Male


title: MRTX_8day_mouse2_tumour2

value: replicate 4


title: MRTX 6day mouse2 tumour3

value: F-replicate 6

value: MRTX849 6 days


title: MRTX 6day mouse3 tumour1

value: F-replicate 7


title: Subject_29_PolyIC_Cord

value: Cord


title: Day12_Control-1


title: MRTX 6day mouse3 tumour2

value: F-replicate 8


title: MRTX_8day_mouse1_tumour5

value: replicate 2

value: MRTX1257 8 days


title: MRTX_8day_mouse3_tumour3

value: replicate 5


title: Vehicle Mouse2 tumour4

value: D-replicate 8

value: Vehicle control


title: Day15_Mettl3-OE-3

source_name: reprogramming cells day 15


title: Subject_29_CTRL_Cord

value: CTRL


title: Day15_Mettl3-OE-1


title: Day15_Mettl14-OE-3


title: MRTX_8day_mouse1_tumour2

value: 3LL DNRAS #86

value: replicate 1


title: MRTX 6day mouse2 tumour2

value: F-replicate 5


title: Day15_Mettl3-OE-2


title: MRTX 6day mouse1 tumour3

value: F-replicate 3


title: MRTX 6day mouse2 tumour1

value: F-replicate 4


title: Subject_29_LPS_Cord

value: LPS

value: Male

value: No


title: Subject_28_PolyIC_Cord

value: PolyIC

value: Female


title: Subject_28_LPS_Cord

value: Cord


title: Subject_28_IMIQ_Cord

value: IMIQ


title: Day15_Control-3

value: OSKM+Vector


title: MRTX_2day_mouse2_tumour4.1

value: replicate 5

value: MRTX1257 2 days


title: MRTX_2day_mouse2_tumour4

value: replicate 3


title: MRTX_2day_mouse1_tumour3

value: replicate 2


title: Day15_Mettl14-OE-2


title: Day15_Mettl14-OE-1


title: MRTX_2day_mouse2_tumour1

value: 3LL DNRAS #86

value: replicate 4


title: MRTX_2day_mouse1_tumour1

value: replicate 1


title: MRTX_2day_mouse2_tumour5

value: replicate 6


title: MRTX 6day mouse1 tumour2

value: F-replicate 2

value: MRTX849 6 days


title: Day15_Control-1


title: MRTX 6day mouse1 tumour1

value: F-replicate 1


title: MRTX 2day mouse3 tumour1

value: E-replicate 7

value: MRTX849 2 days


title: Subject_27_LPS_Cord

value: LPS

value: Male

value: Yes


title: Vehicle_Mouse3_tumour2

value: Vehicle control


title: MRTX 2day mouse2 tumour3

value: E-replicate 6


title: Subject_27_CTRL_Cord

value: CTRL

value: Cord


title: MRTX 2day mouse2 tumour2

value: E-replicate 5


title: Subject_26_PolyIC_Cord

value: PolyIC

value: No


title: Vehicle_Mouse2_tumour3

value: 3LL DNRAS #86

value: replicate 4


title: Subject_26_IMIQ_Cord

value: IMIQ


title: MRTX 2day mouse1 tumour3

value: E-replicate 3


title: RNA-Seq Glutamatergic neurons, WT, rep2

city: Atlanta

first: Yulin

last: Jin

state: GA

address: 615 Micheal Street

department: Human Genetics

institute: Emory University

data_processing:
For all WGBS libraries, 15 bp was trimmed off the 5'- end of R2 and the 3' end of R1 to remove bases derived from the adaptor tag introduced in the library preparation procedure using Cutadapt v2.10. The processed reads were aligned to the mouse genome (mm9), deduplicated, examined for coverage, and extracted to CG and CH count matrix using Bismark v0.19.0. Briefly, reference sequences were converted to map both cytosine and thymine. The mapping of WGBS libraries was performed with the bismark module followed by duplication removal using deduplicate_bismark. Methylation calling was processed using a module called Methylation Extractor, which classified methylation sites as CG and CH (CHH and CHG contexts). The modules of bismark2bedGraph and coverage2cytosine were used to extract non-CpG sites and estimate their methylation levels.
RNA-seq reads were aligned to mm9 mouse genome using TopHat v2.1.1. The number of reads aligned to each gene was tabulated using FeatureCount v1.5.3. All reads mapped to gene bodies were used for differential gene expression analysis by using R packages edgeR v3.32.1 and DEseq2 v1.30.1.  Genes displaying low expression due to a substantially low number of mapped reads and whose edgeR CPM values satisfied the condition 'rowSums(cpm(data_y)) < 2' were filtered out from differential gene expression analyses. For each comparison, the results from both edgeR and DESeq2 analyses were merged into a final nonredundant and Padj-controlled list of genes to avoid method-specific biases.
Differential methylation regions (DMRs) were called by utilizing the package DSS (Dispersion Shrinkage for Sequencing). First, DMLtest function was used to perform statistical tests for all CpG sites with smoothing. Second, the qualified CpG sites were subjected for calling differential methylated loci (DML) using callDML function. The difference of mean methylation level between the MeCP2 KO and WT was compared with the global methylation difference using a Wald test at each CpG site. DMLs are those CpG sites with FDR-corrected P-value less than 0.05. Finally, callDMR function was used to call DMRs with following settings: each DMR has minimum length of 50 bp, has at least 4 DMLs, a minimum length of 50 bp, an absolute difference of methylation level greater than 0.2 relative to the global methylation difference in the comparison, and a detected P value less than 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: DNA methylation coverage files were generated by Bismark. The six columns represent chromosome, start, end, methylation ratio, methylated counts, unmethylated counts for each genomic site in CG context
Supplementary_files_format_and_content: RNA-Seq.read.counts (Gene reads counts for each RNA-Seq sample are summarized in this file)

source_name: Glutamatergic neurons WT

extract_protocol:
The brain tissues were rapidly dissected in ice-cold homogenization buffer and the INTACT procedure was applied to affinity purify GFP+ nuclei. For brain tissue of each mouse, half of the isolated nuclei were resuspended in 600 μl Lysis buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl) for DNA purification, 25 μl Proteinase K (Thermo Fisher, cat# EO0491) treatment at 55°C for overnight using an end-to-end rotator. The second day, the samples were incubated at 85°C for 45 minutes to inactive Proteinase K followed by the treatment of 5 μl RNase A for 1 hour at room temperature. The entire solution was then transferred to a pre-spun “Phase Lock Gel (PLG) 2 ml Heavy” tube. Equal volume of Phenol:Chloroform:Isoamyl Alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppendorf tube and precipitated with 600 μL isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion). Another half of the beads-bonded nuclei were directly resuspended in TRIzol Reagent for RNA extraction following the standard protocol.
For each cell type and genotype, two biological replicates were subjected to WGBS and RNA-Seq. The EZ DNA Methylation Gold kit was used for sodium bisulfite conversion prior to library preparation. All WGBS libraries were prepared from 100 ng nuclei DNA. Accel-NGS Methyl-Seq (Swift BioSciences) kit was used for library preparation according to the manufacturer's protocols.
For each replicate, 4 μg of total RNA was used for RNA-seq library construction following instructions of Illumina mRNA sample prep kit. Briefly, total RNA was depleted of ribosomal RNAs, subjected to 5 min of heat fragmentation, and converted to strand-specific cDNA libraries using the TruSeq Total RNA library prep kit with RiboZero depletion (Illumina). Libraries were submitted for 150 paired-end sequencing on the Illumina HiSeq 2500 platform.

value: Camk2a-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cortex

value: Glutamatergic neurons

tag: developmental stage

value: 6-7 weeks


title: Vehicle_Mouse1_tumour2

value: replicate 2


title: Subject_26_LPS_Cord

value: LPS

value: Male


title: MRTX 2day mouse1 tumour2

value: E-replicate 2

value: MRTX849 2 days


title: Vehicle_Mouse1_tumour1

value: replicate 1

value: Vehicle control


title: Subject_27_IMIQ_Cord

value: Cord

value: Yes


title: Subject_27_PolyIC_Cord

value: PolyIC


title: MRTX 2day mouse3 tumour2

value: E-replicate 8


title: Day15_Control-2

value: OSKM+Vector


title: MRTX 2day mouse2 tumour1

value: E-replicate 4


title: Subject_25_IMIQ_Cord

value: IMIQ


title: RNA-Seq GABAergic neurons, WT, rep1

source_name: GABAergic neurons WT

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cortex

value: GABAergic neurons

value: 5-6 weeks


title: RNA-Seq Purkinje neurons, WT, rep1

source_name: Purkinje neurons WT

value: Pcp2-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cerebellum

value: Purkinje neurons

value: 6-7 weeks


title: Subject_28_CTRL_Cord

value: CTRL

value: Female

value: No


title: Subject_26_CTRL_Cord

value: Cord

value: Male


title: Vehicle_Mouse2_tumour2

value: 3LL DNRAS #86

value: replicate 3

value: Vehicle control


title: Vehicle Mouse2 tumour2

value: D-replicate 5


title: Vehicle Mouse3 tumour1

value: D-replicate 6


title: MRTX 2day mouse3 tumour3

value: E-replicate 9

value: MRTX849 2 days


title: RNA-Seq Glutamatergic neurons, MeCP2 KO, rep2

source_name: Glutamatergic neurons MeCP2 KO

value: cortex

value: Glutamatergic neurons


title: RNA-Seq Glutamatergic neurons, MeCP2 KO, rep1


title: XEN_hyp_d2_RNA_rep2

city: Berlin

first: Natalia

last: Lopez-Anguita

state: Berlin

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Raw reads were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --overlap 20 --minimum-length 25 --adapter "A[100]" --adapter "T[100]").
Reads were aligned to the mouse reference genome (mm10) using STAR (version 2.7.5a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts) and transcripts were assembled using StringTie (version 2.0.6; parameters: -e) with GENCODE annotation (VM19).
Table of read counts was generated using featureCounts function of the Rsubread package (version 1.32.4).
Transcripts Per Kilobase Million (TPM) was used to generate normalized expression values using EdgeR package (version 3.26.8).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text table containing TPM values per gene and sample for merged biological replicates

source_name: Extraembryonic stem cells

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74004). 500ng RNA was used as input for library preparacion.
Library preparation was performed using KAPA RNA HyperPrep Kit (Kapa Biosystems, KR1350) following manufacturer's instructions.

value: hypoxia d2

value: Extraembryonic stem cells


title: RNA-Seq GABAergic neurons, MeCP2 KO, rep1

source_name: GABAergic neurons MeCP2 KO

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc; MeCP2 -/Y

value: GABAergic neurons

value: 6-7 weeks


title: Subject_25_PolyIC_Cord

value: PolyIC

value: Yes


title: RNA-Seq Glutamatergic neurons, WT, rep1

value: Camk2a-cre; R26-LSL-CAG-Sun1-GFP-myc


title: MRTX 2day mouse1 tumour1

value: E-replicate 1


title: Subject_24_PolyIC_Cord

value: Cord

value: Male


title: RNA-Seq Purkinje neurons, WT, rep2

value: Pcp2-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cerebellum

value: Purkinje neurons


title: Subject_25_LPS_Cord

value: LPS


title: Vehicle Mouse3 tumour2

value: D-replicate 7

value: Vehicle control


title: XEN_hyp_d7_RNA_rep2

value: hypoxia d7


title: RNA-Seq GABAergic neurons, WT, rep2

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cortex


title: Subject_24_IMIQ_Cord

value: IMIQ


title: RNA-Seq GABAergic neurons, MeCP2 KO, rep2

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc; MeCP2 -/Y

value: GABAergic neurons

value: 5-6 weeks


title: XEN_norm_RNA_rep1

value: normoxia

value: Extraembryonic stem cells


title: Vehicle Mouse2 tumour1

value: D-replicate 4


title: Vehicle_Mouse3_tumour3

value: 3LL DNRAS #86

value: replicate 6


title: XEN_hyp_d2_RNA_rep1

value: hypoxia d2


title: XEN_hyp_d7_RNA_rep1


title: Subject_25_CTRL_Cord

value: CTRL

value: Cord

value: Male

value: Yes


title: TS_norm_RNA_rep2


title: KPAR MRTX 24h 2

source_name: KPAR1.3-G12C cells

value: C-replicate 2

value: MRTX849 24h


title: TS_hyp_d7_RNA_rep2

value: hypoxia d7


title: WGBS Purkinje neurons, WT, rep2

library_source: genomic

molecule: genomic DNA

value: Pcp2-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cerebellum

value: Purkinje neurons

value: 6-7 weeks


title: Vehicle Mouse1 tumour2

value: D-replicate 2

value: Vehicle control


title: WGBS Purkinje neurons, WT, rep1


title: Vehicle Mouse1 tumour3

value: D-replicate 3


title: Subject_23_LPS_Cord

value: LPS

value: No


title: E14_ES_hyp_d7_RNA_rep2

source_name: Embryonic stem cells

value: Embryonic stem cells


title: KPAR Vehicle 2

value: A-replicate 2

value: DMSO control


title: WGBS Glutamatergic neurons, WT, rep1

value: Camk2a-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cortex

value: Glutamatergic neurons


title: TS_hyp_d7_RNA_rep1

value: Extraembryonic stem cells


title: TS_hyp_d2_RNA_rep2

value: hypoxia d2


title: Subject_23_PolyIC_Cord

value: PolyIC

value: Cord

value: Male


title: Subject_23_CTRL_Cord

value: CTRL


title: E14_ES_hyp_d7_RNA_rep1

value: hypoxia d7


title: Subject_24_CTRL_Cord

value: Yes


title: Subject_24_LPS_Cord


title: WGBS GABAergic neurons, MeCP2 KO, rep1

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc; MeCP2 -/Y

value: GABAergic neurons

value: 6-7 weeks


title: KPAR Vehicle 3

value: A-replicate 3


title: XEN_norm_RNA_rep2

value: normoxia


title: Subject_23_IMIQ_Cord

value: IMIQ

value: No


title: KPAR MRTX 24h 3

value: C-replicate 3

value: MRTX849 24h


title: Subject_22_LPS_Cord

value: LPS

value: Female


title: Vehicle Mouse1 tumour1

value: D-replicate 1

value: Vehicle control


title: WGBS Glutamatergic neurons, MeCP2 KO, rep2

value: cortex

value: Glutamatergic neurons


title: WGBS Glutamatergic neurons, WT, rep2

value: Camk2a-cre; R26-LSL-CAG-Sun1-GFP-myc


title: Subject_22_CTRL_Cord

value: CTRL

value: Cord

value: Yes


title: E14_ES_hyp_d2_RNA_rep1

value: hypoxia d2

value: Embryonic stem cells


title: WGBS GABAergic neurons, WT, rep2

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc

value: GABAergic neurons

value: 6-7 weeks


title: KPAR MRTX 8h 3

value: B-replicate 3

value: MRTX849 8h


title: WGBS Glutamatergic neurons, MeCP2 KO, rep1


title: KPAR Vehicle 1

value: A-replicate 1

value: DMSO control


title: TS_hyp_d2_RNA_rep1

value: Extraembryonic stem cells


title: E14_ES_norm_RNA_rep2

value: normoxia


title: TS_norm_RNA_rep1


title: Sample 6-1-4

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

description:
Skin_6_1_4
Skin tissue from 6-8 week old BALB/c mice

data_processing:
Illumina Pipeline Software 1.82 to generate raw fastq files
Raw fastq files processed with RNASik v1.4.7 , alignment with STAR v2.5.2
FeatureCounts used to quantify read counts to annotated genes of the reference genome
Differential expression analysis using Degust v4.1.5
GO analysis using EnhancedVolcano version 1.10.0, alluvial version 0.1-2 and gplots version 3.1.1. GO enrichment analysis was performed using GOrilla (Gene Ontology enRIchment anaLysis and visuaLizAtion tool)
Genome_build: GRCm38
Supplementary_files_format_and_content: counts table of genes and samples in this experiement

source_name: skin

extract_protocol:
Baseline or lesional skin tissue was excised and snap-frozen. Total RNA was extracted using a TRIzol/chloroform method followed by  purification and concentration  using RNeasy Microkit (Qiagen).  Extracted RNA was subjected to fragment analyzer to assess the quantity and integrity of RNA before samples were further processed using the Illumina TruSeq RNA RNA preparation kit (Illumina).
Illumina TruSeq RNA Sample Preparation Kit as per manufacturer's instructions

treatment_protocol: Mice received sodium butyrate (SCFA) in the drinking water at a final concentration of 400 mM for 2 weeks prior to epicutaneous house dust mite allergens (4 x 15ug over 2 weeks) exposure and throughout the experiment. For baseline skin experiments, mice were administered SCFA as mentioned above but not exposed to allergen epicutaneously. For such experiments, skin of baseline subjects was collected at the end of the SCFA treatment.

value: Vehicle

tag: disease state

value: Atopic dermatitis

value: 6-8 week old

value: BALB/c


title: KPAR MRTX 8h 2

value: B-replicate 2


title: Subject_21_IMIQ_Cord

value: IMIQ

value: Cord

value: Female

value: No

value: Yes


title: input_br1

data_processing:
Raw reads of treatment and input samples were subjected to adapter and quality trimming with cutadapt (Martin, 2011) (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC).
Reads were aligned to the mouse genome (mm10) using BWA with the ‘mem’ command (version 0.7.17, default parameters).
A sorted BAM file was obtained and indexed using samtools with the ‘sort’ and ‘index’ commands (version 1.10). Duplicate reads were identified and removed using GATK (version 4.1.4.1) with the ‘MarkDuplicates’ command and default parameters.
Peaks were called with reads aligning to the mouse genome only using MACS2 ‘callpeak’ (version 2.1.2; parameters --bdg --SPMR) using the input samples as control samples. For identification of consistent peaks, only those that were identified in both replicates were used for downstream analyses. Peaks were annotated using ChIPseeker package (version 1.20.0) using default parameters (TSS region ±3-Kb).
For downstream analyses, after validation of reproducibility, replicates were pooled using samtools ‘merge’. Genome-wide coverage tracks (signal files) for merged replicates normalized by library size were computed using samtools bamCoverage (version 3.4.3) (parameters: --normalizeUsing CPM --extendReads).
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing narrow peaks for each biological replicate
Supplementary_files_format_and_content: bigwig files of genome-wide coverage tracks for merged replicates and normalized by library size (CPM).

extract_protocol:
Chromatin extracts were prepared as described in (Brookes et al., 2012). Briefly, cells were fixed with 1% formaldehyde (Thermo, 28906) in PBS at RT for 10 minutes. Then, 0.125M glycine (Sigma, 50046) was added to quench formaldehyde at RT for 5 minutes. Cells were washed twice with ice-cold PBS. To lyse, fixed cells were treated with swelling buffer (25mM HEPES pH 7.9, 1.5mM MgCl2, 10mM KCl (Invitrogen, AM9640G), 0.1% Igepal 630, 1x protease inhibitor cocktail, 1mM PMSF, 2mM NaVO3, 5mM NaF) at 4°C for 10 minutes. Cells were scraped on ice and passed thought 18G needles before centrifugation at 3000g, 4°C for 5 minutes. Cell pellet, corresponding to nuclei was carefully resuspended in sonication buffer (50mM HEPES pH 7.9, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium-deoxycholade (Thermo, 89904), 0.1% SDS (Invitrogen, AM9822), 1mM PMSF, 2mM NaVO3, 5mM NaF) and incubated on ice for 10 minutes before sonication. Chromatin was sheared to an average size of 200-300bp with E220 Evolution Covaris sonicator for 6 cycles, 1 minute each. Shearing efficiency was checked by agarose gel
Library preparation was performed using KAPA Hyper Prep Kit (Kapa Biosystems, KR0961) (input amount 10ng DNA, adapter concentration 1.5 µM and size selection of 200-700-bp after PCR with cycle number = 15) and following manufacturer's instructions.

tag: chip antibody


title: KPAR MRTX 8h 1

value: B-replicate 1


title: Subject_21_LPS_Cord

data_processing:
Data was generated with the Illumia NovaSeq 6000 platform and the bcl2fastq pipeline was used to convert base calls (BCL) to fastq files.
Read libraries were mapped to the human genome (hg38) using HISAT2. Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps, and Pre- and post-alignment QC was assessed with FastQC and SAMStat, respectively.
(For corrected gene counts) Raw transcripts were removed if they had no counts in any sample, lacked annotation, or had 0.5 counts per million in ≤ 25 samples. Size factors were estimated using the median ratio method with the 'estimateSizeFactors' function (DESeq2 R package) and variance stabilizing transformation (VST) was applied to the count data (DESeq2). Unwanted variation was identified with the 'RUVg' function from the RUVSeq R package. RUVg trends which related to technical variation and culture batch were removed as covariates with a linear model ('removeBatchEffect' function from the limma R package).
Genome_build: hg38
Supplementary_files_format_and_content: CBMC_genecounts.txt file contain a matrix of raw gene counts (unfiltered and un-normalised data), with transcripts as rows and samples as columns. Transcript information (e.g. EnsembleID, gene symbol) are supplied in the final columns. CBMC_corrected_counts.txt contains a matrix of VST transformed and batch/RUV corrected gene counts, formatted as the raw gene count file.

value: LPS


title: Subject_22_PolyIC_Cord

value: PolyIC


title: Subject_21_CTRL_Cord

value: CTRL


title: Sample 6-1-5

description:
Skin_6_1_5
Skin tissue from 6-8 week old BALB/c mice


title: Sample 5-3-1

description:
Skin_5_3_1
Skin tissue from 6-8 week old BALB/c mice

value: SCFA

value: Baseline


title: Brainstem Recovery Sleep

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

description: scRNA-Seq

data_processing:
FASTQ files containing sequence reads were mapped to the mouse reference genome using Cell Ranger Version 2.2.0
The output of the Cell Ranger pipeline (filtered counts) was parsed into R version 3.5.3 to perform downstream analysis with the various R packages.
Genome_build: GRCm38

source_name: Brainstem

growth_protocol: Mice were selected such that, at the time of experiments, they were aged between 9-11 weeks. Before sleep deprivation, mice were singly housed in automated sleep fragmentation chambers for habituation with ad libitum access to food and water under standard humidity and temperature (21±10C) on a 12-h light:12-h dark cycle.

extract_protocol:
The single cell suspensions preparation procedure for all the three brain regions was adapted from Holt and colleagues. Briefly, tissues were dissociated with Papain in the manufacturer supplied medium followed by manual trituration using a fire polished silanized Pasteur pipette and filtration through 70µm cell strainer. Cells were pelleted at 300 x g, 10 min, the supernatant was discarded, and cells resuspended in a minimal volume of PBS with 0.5% of BSA. To reduce the debris, we incubated the cell suspensions with myelin removal beads and passed it through an LS Column with 70µm pre-separation filter. Flow-through containing single cell suspension were collected and estimated the yield and viability.
Single cell suspension were diluted in PBS with 0.5% of BSA to obtain ~ 350 cells/ µl and followed the 10X Genomics Chromium Single Cell Kit Version 2 manual for the capture, cDNA synthesis, library preparation, and sequencing.

treatment_protocol: To assess how 12-h of sleep deprivation affected the sleep/wake behaviours, 3 days baseline EEG/EMG were recorded after mice were acclimatized for a week. Mice were recorded from for next 3-4 days (which encompassed sleep deprivation and recovery phases). Sleep deprivation was initiated at lights on [Zeitgeber Time 0 (ZT0)] by switching on the motors, choosing the continuous sweeping mode. Post sleep deprivation, animals were allowed to recover for 24-h. Baseline recording 1-day before sleep deprivation was used as the control condition (normal sleep). Following sacrifice by cervical dislocation, whole brains were isolated at ZT12 (i.e. lights off) for ad libitum Normal Sleep (NS, ZT0-12), Sleep Deprivation (SD, ZT0-12) and 12-h sleep deprivation followed by 12-h of Recovery Sleep (RS, ZT12-12) groups. Brainstem, cortex and hypothalamus were quickly dissected and tissue collected for preparation of single cell suspensions.

value: Brainstem

value: 9 to 11 weeks


title: Brainstem Normal Sleep

description: scRNA-Seq


title: Subject_22_IMIQ_Cord

extract_protocol:
Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (QIAGEN). Total RNA libraries were prepared using NEBNext Ultra II Kits (New England BioLabs). Sequencing was performed by the Australian Genome Research Facility (Illumina NovaSeq 6000, 100bp paired-end reads).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: WGBS GABAergic neurons, WT, rep1

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc

value: cortex

value: GABAergic neurons

value: 5-6 weeks


title: Subject_20_PolyIC_Cord

value: Male


title: WGBS GABAergic neurons, MeCP2 KO, rep2

value: Cad2-cre; R26-LSL-CAG-Sun1-GFP-myc; MeCP2 -/Y


title: Sample 6-3-4

description:
Skin_6_3_4
Skin tissue from 6-8 week old BALB/c mice

value: Atopic dermatitis

value: 6-8 week old

value: BALB/c


title: E14_ES_hyp_d2_RNA_rep2

value: hypoxia d2

value: Embryonic stem cells


title: hif1a_hyp_d6_br2

value: hypoxia d6

value: Hif1a (Cell Signalling Technologies 36169, lot:2


title: hif1a_hyp_d6_br1


title: E14_ES_norm_RNA_rep1

value: normoxia


title: input_br2


title: hif1a_hyp_d2_br2


title: hif1a_hyp_d2_br1


title: Sample 5-3-3

description:
Skin_5_3_3
Skin tissue from 6-8 week old BALB/c mice

value: SCFA

value: Baseline


title: LentiGuide_EPIKOL

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

description: contains Epigenome-wide knockout library (EPIKOL) in LentiGUIDE lentiviral backbone

data_processing:
Library strategy: CRISPR Amplicon Sequencing
Base calling was performed with Illumina HiSeq platforms (Genewiz, USA)
sgRNA counting, gene summarization and comparative analyses between samples were performed using MAGeCK version 0.5.8 (Li, W., et al., 2014) using median normalization and the RRA method. R1 fastq files were used in counting.
Genome_build: sgRNA counted by matching to custom CRISPR Screen library; Epigenetic Knock-out Library (EPIKOL)
Supplementary_files_format_and_content: txt files containing MAGeCK outputs; normalized counts, gene summary and sgRNA summary

molecule: other

organism: synthetic construct

source_name: plasmid pool

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum and %1 Penicillin/Streptomycin. SUM159 and SUM149 cell lines were cultured with Ham’s F12 nutrient mix supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone and 10 mM HEPES. Immortalized human breast epithelial cells (HMLE) were cultured in MEGM medium. Briefly, MEGM Bullet Kit (Lonza,Swiss) (by excluding gentamicin/amphotericin-B) was used and supplemented with the same volume of DMEM:F12 (1:1), 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF, and %1 Penicillin/Streptomycin. All prostate cell lines except RWPE-1 were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. RWPE-1 cells were cultured in Keratinocyte SFM media supplemented with 0.05 mg/mL bovine pituitary extract and 5 ng/mL human recombinant epidermal growth factor.

extract_protocol:
Genomic DNA (gDNA) was isolated by NucleoSpin Tissue kit (Macherey-Nagel, Germany) for TNBC cell lines and by PureLink Genomic DNA mini kit (ThermoFischer K-1820) for PCa cell lines according to manufacturer’s instructions
Library was constructed with Illumina-compatible adapters. sgRNA cassettes were amplified from genomic DNA using pLentiGuide specific forward and reverse primers in the first PCR. For second PCR, %1-2.5 of the first PCR product was amplified with forward stagger and reverse index primers (specific to sample). Final library fragments of ~350 bp were agarose gel purified. Fragments were quality checked with fragment analyzer and sequenced with Illumina Hiseq (Genewiz, USA)

treatment_protocol: Cells were transduced with EPIKOL at low MOI (0.3-0.4) with 1000x coverage for TNBC and 500x coverage for PCa in the presence of 8 μg/ml protamine sulphate. Following three days of puromycin selection, initial reference point pellets were collected as 8 million cells for TNBC and 4 million cells for PCa. Later, cells were maintained with the indicated coverage for each line. After 15-16 population doublings, screens were ended and cell pellets were collected.

value: plasmid pool


title: Sample 6-3-3

description:
Skin_6_3_3
Skin tissue from 6-8 week old BALB/c mice


title: KPAR MRTX 24h 1

value: C-replicate 1

value: MRTX849 24h


title: Subject_19_IMIQ_Cord

value: IMIQ

value: Cord

value: Female

value: No


title: Cortex Sleep Deprived

description: scRNA-Seq

source_name: Cortex

value: Cortex

value: 9 to 11 weeks


title: Brainstem Sleep Deprived

description: scRNA-Seq

value: Brainstem


title: MOS3

city: Zhengzhou

first: Jiaqing

last: Zhang

address: No. 116 Huayuan Road

department: Institute of Animal Husbandry and Veterinary Science

institute: Henan Academy of Agricultural Sciences

data_processing:
The raw reads were subjected to ACGT101-miR (LC Sciences , USA)
BLAST was used to map unique 18 to 26 nucleotide long sequences to specific precursors in miRBase 21.0 to detect the known miRNAs and novel 3p-derived and 5p-derived miRNAs
The alignment parameters allowed length variations at both the 5’ and 3’ ends as well as one sequence mismatch
The known miRNAs were classified as the unique sequences that mapped to specific species mature miRNAs in hairpin arms
BLAST was used to map the remaining sequences to other species precursors
Assembly: Susscrofa 10.2
Supplementary files format and content: excel,expression profiles

organism: Sus scrofa

source_name: ovary

growth_protocol: Porcine primary granulosa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
The TRIzol reagent was used to isolate total RNA following the specified protocol
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program,

treatment_protocol: The cells were teated with medium containing 5% FBS and 100 or 300 μM H2O2 for 12h

value: ovary

tag: breed

value: LandracexYorkshire crossbred sows

value: granulosa cell

value: 300uM H2O2 for12h


title: hif1a_norm_br1

value: normoxia

value: Hif1a (Cell Signalling Technologies 36169, lot:2


title: DDC1w_STAT3KO_hep_rep3

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ). Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
The sequencing reads were mapped to the mm10 using STAR algorithm.
Htseq-count algorithm was used to count reads mapped to each gene uniquely.
DESeq2 R package was used to detect differentially expressed genes (DEGs) between groups.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver hepatocyte

extract_protocol:
Liver was perfused using three-steps methods. Cells in liver were sorted by BD FACSAriaIII. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice was fed with normal and DDC diet for 1 week for isolation of immune cells. And, for discovering IL-6/STAT3 signaling in hepatocyte, mice was treated with DDC diet or IL-6 via HTVi of IL6 plasmids in physiological saline (5ug/mL). To deplete STAT3 in hepatocyte, mice was tail-vein injected AAV-TBG-Cre with the titer of 2.5x10^11, while control mice was injected AAV-TBG-GFP.

value: AAV-TBG-Cre for 2 weeks, DDC diet for 1 week

value: liver

value: hepatocyte


title: Subject_20_IMIQ_Cord

value: Male


title: Sample 5-1-2

description:
Skin_5_1_2
Skin tissue from 6-8 week old BALB/c mice

value: Vehicle

value: Baseline

value: 6-8 week old

value: BALB/c


title: MOS2


title: DDC1w_STAT3KO_hep_rep2


title: Sample 5-1-1

description:
Skin_5_1_1
Skin tissue from 6-8 week old BALB/c mice


title: Hypothalamus Normal Sleep

description: scRNA-Seq

source_name: Hypothalamus

value: Hypothalamus


title: Hypothalamus Sleep Deprived

description: scRNA-Seq

value: 9 to 11 weeks


title: MOS1


title: Hypothalamus Recovery Sleep

description: scRNA-Seq


title: Subject_18_PolyIC_Cord

source_name: CBMC

value: PolyIC

value: Cord

value: Female

value: Yes

value: No


title: Subject_20_LPS_Cord

value: LPS


title: pLentiCRISPR_EPIKOL_rep1

description: contains Epigenome-wide knockout library (EPIKOL) in pLentiCRISPR lentiviral backbone

value: plasmid pool


title: RNA-seq_fio1-1 rep2

city: Frederiksberg C

first: Bin

last: Sun

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: Copenhagen Plant Science Centre – University of Copenhagen

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 using trim-galore 0.6.3 on Galaxy.
Trimmed reads mapped to Arabidopsis thaliana whole genome using HISAT2 2.1.0+galaxy5 on Galaxy.
Reads counted using htseq-count 0.9.1 on Galaxy.
Differentially expressed genes were calculated using limma_voom/3.38.3+galaxy3 on Galaxy.
Genome_build: Arabidopsis thaliana TAIR10. 45
Supplementary_files_format_and_content: tabular include reads count and differentially expressed genes

organism: Arabidopsis thaliana

source_name: 14 days old seedlings

growth_protocol: Seeds were stratified 48h at 4°C, and grown on soil in a plant growth chamber under long day light conditions (16h light /8h dark) at (22°C day /18°C night).

extract_protocol:
14 days old seedling were quick freeze in liquid nitrogen, then grind with mortar. RNA were harvested using Sigma Spectrum™ Plant Total RNA Kit (STRN50).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: seedlings

value: 14 days old


title: Subject_19_PolyIC_Cord

first: James

last: Read

address: 15 Hospital Ave.

institute: Telethon Kids Institute


title: LOS2

value: ovary

value: LandracexYorkshire crossbred sows

value: granulosa cell

value: 100uM H2O2 for12h


title: DDC1w_hep_rep1

value: AAV-TBG-GFP for 2 weeks, DDC diet for 1 week

value: liver

value: hepatocyte


title: Gastruloid

data_processing:
Illumina files were demultiplexed into FASTQ files using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 1.3.1, default parameters).
FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("count pipeline", version 1.3.1, default parameters The genomic reference "refdata-cellranger-mm10-1.2.0", prepared by 10x Genomic was used to alignment.
To de-multiplex samples within our single scRNAseq dataset, we used the deMULTIplex R package (version 1.0.2).
The initial quality control was performed with Seurat. Cells with less than 3 cells, less than 200 or more than 2,500 unique feature counts and a mitochondrial fraction above 5% were removed from the analysis. Quality control features were checked for each individual sample.
Genome_build: mm10

growth_protocol: Male F1G4 mouse ES cells (George et al., 2007) were cultured on 6cm plates (Corning 430166) gelatinized with 0.1% gelatin (Sigma G1393) and coated with mitotically inactive primary mouse embryo fibroblasts (3-4x104 cells/cm²) with standard ES medium containing 15% FCS and 1000 U/ml leukemia inhibitory factor (LIF, Chemicon ESG1107) at 37°C and 5% CO2. ES cells were split every second day with a 1:10 dilution. For splitting, media was aspirated and cells were washed once with PBS and trypsinized (Trypsin-EDTA (0.05%) (Gibco 25300054)) for 5-10 minutes at 37°C. Trypsin was neutralized by 3 ml ES media and cells centrifuged for 5 minutes at 1000 rpm, after which the pellet was resuspended in ES media. ES cells were cultured in normoxia or hypoxia for 7 days. Gastruloids were then generated as described previously (Veenvliet et al., 2020) with some minor modifications. Briefly, ES cells were first depleted of feeders, then washed once in 5ml pre-heated (37°C) PBS containing MgCl2 and CaCl2 (Sigma D8662) and once in 5ml NDiff227 medium (Takara Y40002) pre-conditioned in normoxia or hypoxia. ES cells were then pelleted by centrifugation for 5 minutes at 1000rpm and resuspended in 250µl of NDiff227. 10µl of the cell suspension was mixed with 10µl of Trypanblue (Bio-Rad 1450021) for automated cell counting with Luna Automated Cell Counter. 400 live cells were plated in a volume of 35µl NDiff227 into each well of a 96-well round bottom, low attachment plate (Costar 7007 ultra-low attachment 96 well plate (7007)). Cells were then allowed to aggregate for 48 h under normoxic or hypoxic conditions. After 48h, the aggregates were treated with 3µM CHIR99021 (CHIR, Merck Millipore) in 150µl NDiff227 for 24h to induce robust gastruloid formation. For “-Chi” aggregates, 150µl NDiff227 without CHIR was added. Between 72 and 120h, medium was refreshed every 24h by removing 150µl of the old media and adding the same volume of new, pre-conditioned NDiff227.

extract_protocol:
Gastruloids from NN+CHI, NH+CHI and NH-CHI conditions were generated as described above. From each condition, 28 structures were selected based on the occurrence of a symmetry breaking event and pooled for the single-cell experiment.. Gastruloids were picked with a p200 with the pipette tip cut-off at the 50µl mark, and pooled in a 1,5ml tube filled with ice cold PBS. The three pools were washed twice with ice cold PBS. Next, structures were dissociated in 50µl TrypLE Express (Gibco) for 20 minutes at 37ºC, with pipetting after 10 minutes.
A 10x lipid-modified oligonucleotides (LMOs) – Barcode (BC) oligo solution was prepared (1:1; 2µM each) in PBS for each of the three samples on ice. From here on, every step has been performed on ice. After cell dissociation, LMOs – BC solutions were added to each sample separately (final concentration 200nM), and samples were incubated for 5min on ice. In the meantime a 10x co-anchor solution was prepared (2µM) in PBS. Following the 5 min incubation, co-anchor solution was added to each sample (final concentration 200nM), and samples were further incubated for 5min on ice. The reactions was then quenched by adding 1ml PBS+1% BSA to each tube. Cells were then washed twice with 1ml PBS+1% BSA with centrifugation steps performed for 5 minutes at 300g at 4°C in low DNAbind Eppendorf tubes. Next, cell pellets were resuspended in 100ul PBS+0,4% BSA and pooled together in one new tube. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40µm. Cells where then centrifuged for 5 minutes at 300g at 4°C, and resuspended in 45ul PBS+0,4% BSA and The cell concentration was determined using a hemocytometer. Cells were then subjected to single-cell RNA sequencing (10x Genomics, Chromium™ Single Cell 3’ v3; one reaction). Single-cell libraries were generated according to the manual, with one modification: MultiSeq additive primer (5’-CTTGGCACCCGAGAATTCC-3’) was added at the cDNA amplification step (see McGinnis, Patterson et al 2019 for detailed protocol). During amplified cDNA cleanup, the MultiSeq BCs fraction was isolated and a separate library was performed as described in McGinnis, Patterson et al 2019. cDNA library was sequenced with a minimum of 400 million fragments according to parameters described in the manual and MultiSeq BCs library was sequenced with a minimum of 50 million fragments.
Single-cell transcriptome profiling using MultiSeq

value: 28x pool of three different conditions

tag: gastruloid conditions

value: NN +Chi, NH+Chi, NH-Chi


title: hif1a_norm_br2

tag: condition

value: normoxia

value: Hif1a (Cell Signalling Technologies 36169, lot:2


title: pLentiCRISPR_EPIKOL_rep2

tag: tissue


title: RNA-seq_fio1-1 rep1


title: Subject_18_LPS_Cord

value: Cord

value: Female

value: Yes


title: Subject_20_CTRL_Cord

value: CTRL

value: Male

value: No


title: Subject_19_LPS_Cord

value: LPS


title: IL6_STAT3KO_hep_rep3

value: AAV-TBG-Cre for 2 weeks, HTVi of IL6 plasmids for 1 week


title: Cortex Recovery Sleep

description: scRNA-Seq

value: Cortex

value: 9 to 11 weeks


title: Subject_21_PolyIC_Cord

value: PolyIC


title: IL6_STAT3KO_hep_rep2

value: liver


title: RNA-seq_fio1-2 rep2

value: seedlings

value: 14 days old


title: DDC1w_STAT3KO_hep_rep1

value: AAV-TBG-Cre for 2 weeks, DDC diet for 1 week

value: hepatocyte


title: Subject_17_PolyIC_Cord


title: LOS1

value: ovary

value: LandracexYorkshire crossbred sows

value: granulosa cell

value: 100uM H2O2 for12h


title: IL6_STAT3KO_hep_rep1


title: Subject_19_CTRL_Cord

value: CTRL

value: Cord

value: Female


title: pSTAT3_ChIP_rep4

data_processing:
Basecalls performed using CASAVA version 1.4
aligned signals in raw (bam) files were filtered to remove reads that aligned to multiple locations,Duplicate reads were removed using DeepTools v2.1.0
Peaks were identified using MACS v1.4 with the p-value cut-off 10-5 and peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to chrX, chrY, chrM.
Raw signals from individual samples were converted to signal files (bigWig) using DeepTools v2.1.0
signals were quantile-normalized using Haystack, with 25-bp windows
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Liver were perfused and hepatocytes were isolated and lysed. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified ChIP DNA was used to prepare sequencing libraries via NEBNext Ultra DNA Library Prep Kit for the Illumina (E7370).

value: WT

value: normal diet feeding with HTVi of IL6 plasmids

value: pSTAT3 (CST, 9145S)


title: Cortex Normal Sleep

description: scRNA-Seq

value: Cortex

value: 9 to 11 weeks


title: shp53-AZA biol rep3

city: Rome

first: panatta

last: emanuele

state: RM

address: Via Montpellier, 1

country: Italy

institute: University of Rome "Tor Vergata"

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing NextSeq 500 are mapped to the mouse genome (mm10) using the BWA algorithm with default settings
Sequence reads were analyzed with the STAR alignment; the number of fragments overlapping predefined genomic features of interest and only read pairs that have both ends aligned, are counted.
The gene annotations come from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene.
DESeq2 was used for differential analyses to identify statistically significant differential genes. The DESeq2 model internally corrects for library size using their median-of-ratios method.
After a differential test, the p-value of each gene is calculated and adjusted to control the number of false positives among all discoveries at a proper level (multiple testing adjustment).
All genes with average normalized counts below a filtering threshold from multiple testing adjustment are omitted. Differential genes are detected by DESeq2 at 0.1 (or 10%) FDR.
Assembly: mm10
Supplementary files format and content: An Excel file containing DESeq2-normalized gene counts and the results of the performed differential analyses

extract_protocol:
RNeasy mini kit QIAGEN  following manufacture's instruction
Illumina’s TruSeq Stranded mRNA Library kit following manufacture's instruction

tag: cell line

value: PDAC derived


title: Subject_17_CTRL_Cord

city: Perth

value: Yes


title: LOS3


title: RNA-seq_Col-0 rep2

value: wild type

value: seedlings

value: 14 days old


title: pSTAT3_ChIP_rep3

value: liver

value: hepatocyte


title: Subject_17_IMIQ_Cord

value: IMIQ


title: CON2

value: ovary

value: LandracexYorkshire crossbred sows

value: granulosa cell

value: 0uM H2O2 for12h


title: RNA-seq_fio1-2 rep1


title: Capture Area 658 - Y4 and A4

city: Lone Tree

first: Mary

middle: E

last: Haywood

state: CO

address: 10290 RidgeGate Circle

institute: CCRM

description: Capture area contains one young sample (3-4 months, left specimen) and one aged sample (15-16 months, right specimen)

data_processing:
Reads were aligned to the mouse reference mm10 (GENCODE vM23/Ensembl 98) version 2020-A and processed using the spaceranger-1.2.1 pipeline.
Spots corresponding to less than approximately 25% tissue or to unidentifiable tissue residue were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Per 10x Genomics, the processed files contain the following: Filtered feature matrix files contain per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries, features (genes), and barcode lists used for the analysis. Scalefactors json files contain the folloiwng fields: tissue_hires_scalef - a scaling factor that converts pixel positions in the original, full-resolution image to pixel positions in tissue_hires_image.png. tissue_lowres_scalef - a scaling factor that converts pixel positions in the original, full-resolution image to pixel positions in tissue_lowres_image.png. fiducial_diameter_fullres - the number of pixels that span the diameter of a fiducial spot in the original, full-resolution image. spot_diameter_fullres - the number of pixels that span the diameter of a tissue spot in the original, full-resolution image. Tissue positions list files contain a table with rows that correspond to spots. There are 4,992 rows, which is the number of spots in the spatial array. Columns correspond to the following fields: barcode - the sequence of the barcode associated to the spot. in_tissue - a binary, indicating if the spot falls inside (1) or outside (0) of tissue. array_row - the row coordinate of the spot in the array from 0 to 77. The array has 78 rows. array_col - the column coordinate of the spot in the array. In order to express the orange crate arrangement of the spots, this column index uses even numbers from 0 to 126 for even rows, and odd numbers from 1 to 127 for odd rows. Notice then that each row (even or odd) has 64 spots. pxl_row_in_fullres - the row pixel coordinate of the center of the spot in the full resolution image. pxl_col_in_fullres: The column pixel coordinate of the center of the spot in the full resolution image.

source_name: Ovary

growth_protocol: All animal experiments were conducted according to the Guide for the Care and Use of Laboratory Animals (8th edition) and approved by the Fertility Laboratories of Colorado Ethics in Research Committee. Outbred CD-1 female mice were obtained from Charles River Laboratories (Wilmington, MA, USA) at 3-4 weeks of age. Mice were housed at a controlled photoperiod (14h light, 10h dark), temperature (20◦C-26◦C), and humidity (30%-40%), with food and water available ad libitum. Females were naturally aged to represent young (Young; 3-4 months old) and AMA (Aged; 15-16 months old) populations. All animals were sacrificed via cervical dislocation.

extract_protocol:
Ovaries were retrieved from Young and Aged females (n=4 per age group) for spatial transcriptomic analysis. Ovaries were rinsed in cold PBS, cryo-preserved in TissueTek Optimal Cutting Temperature (OCT) compound (VWR International), and stored at -80°C in an airtight container, as recommended by the manufacturer protocol (10x Genomics, Visium Spatial, CG000240 Rev C). Before proceeding with the full spatial transcriptomics protocol, a tissue optimization experiment was performed to identify the optimal length of permeabilization time for maximum RNA capture (10x Genomics, Visium Spatial, CG000238 Rev A). Briefly, ovaries were sectioned in a pre-cooled cryostat at 10uM thickness onto seven 8mm x 8mm capture areas on a Visium Tissue Optimization Slide (10x Genomics) containing oligonucleotides for mRNA capture.  Tissue was permeabilized for various amounts of time before captured RNA underwent a reverse transcription (RT) reaction in the presence of fluorescently labeled nucleotides. Fluorescent cDNA footprints were generated and analyzed using the Nikon Ti-E Fluorescent Microscope with an Andor Zyla 4.2 camera to reveal 18 minutes as the optimum permeabilization time for mouse ovaries (Supplementary Figure 1).  Young and Aged ovary sections were then processed for complete spatial transcriptomic analysis as per the manufacturer’s instruction (10x Genomics, Visium Spatial, CG000239 Rev D).  Tissue sections were cut, as previously described, onto a Visium Gene Expression slide with four 6.5mm x 6.5mm capture areas each consisting of 5,000 oligo-barcoded spots. One Young and one Aged ovary section were mounted adjacent to each other within each capture area, effectively increasing the number of biological replicates on each Gene Expression slide (n=4 per age group). The slide underwent methanol fixation and hematoxylin and eosin (H&E) staining with immediate imaging at 40x magnification on the Aperio AT2 (Leica Biosystems) (Supplementary Figure 2).
Tissue was the subjected to permeabilization with proprietary enzyme (18 minutes), reverse transcription and second strand synthesis, all performed on the slide. Amplification of cDNA was executed by quantitative-PCR (qPCR) using the KAPA SYBR FAST-qPCR kit (KAPA Biosystems) and analyzed on the Veriti Thermal Cycler (Applied Biosystems). Amplified cDNA was quantified using a Bioanalyzer High Sensitivity Chip (Agilent).  Following library construction, as per manufacturer’s instructions, libraries were quantified using the KAPA-Illumina PCR quantification kit (KAPA Biosystems) and pooled at 4nM concentration with a sample ratio corresponding to the slide surface area of tissue coverage obtained from the H&E imaging. Pooled, paired-end libraries were sequenced on a NextSeq 550 (Illumina) at the Massachusetts Institute of Technology using a 75nt NextSeq kit (Illumina) loaded at a concentration of 1.8pM. A total of four capture areas and eight tissue sections were sequenced on one Visium Gene Expression Slide.

value: 3-4 months and 15-16 months


title: Subject_16_LPS_Cord

value: LPS

value: Cord

value: Male

value: No


title: DDC1w_hep_rep2

value: AAV-TBG-GFP for 2 weeks, DDC diet for 1 week


title: Subject_18_IMIQ_Cord

value: Female

value: Yes


title: shp53-AZA biol rep2

value: PDAC derived


title: meRIP_fio1-2

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 using trim-galore 0.6.3 on Galaxy.
Trimmed reads mapped to Arabidopsis thaliana whole genome using HISAT2 2.1.0+galaxy5 on Galaxy.
Peaks were called by MACS on Galaxy.
Count reads form each sample by bedtools MultiCovBed on Galaxy
Peak annotation by ChIPseeker
Genome_build: Arabidopsis thaliana TAIR10. 45
Supplementary_files_format_and_content: tabular include reads count and differentially expressed genes

extract_protocol:
14 days old seedling were quick freeze in liquid nitrogen, then grind with mortar. RNA were harvested using Sigma Spectrum™ Plant Total RNA Kit (STRN50).
RNA libraries were prepared for sequencing according Dominissini, Dan, et al. Nature protocols 8.1 (2013): 176-189.

value: seedlings

value: 14 days old

tag: rip antibody

value: anti-methylated RNA antibody (Synaptic Systems, catalog number 202003)


title: meRIP_fio1-1


title: Capture Area 656 - Y2 and A2


title: Subject_17_LPS_Cord

tag: stimuli


title: CON1


title: CON3


title: Subject_16_PolyIC_Cord

value: PolyIC

tag: Sex


title: meRIP_Col-0

value: wild type


title: pSTAT3_ChIP_rep2

value: WT

tag: treatment

value: normal diet feeding with HTVi of IL6 plasmids

value: pSTAT3 (CST, 9145S)

value: liver

value: hepatocyte


title: Subject_15_PolyIC_Cord

value: Cord


title: shCTR-AZA biol rep2

tag: cell type


title: shCTR-NT biol rep3

value: not tretaed


title: Capture Area 657 - Y3 and A3

value: 3-4 months and 15-16 months


title: shp53-NT biol rep3


title: shCTR-AZA biol rep3


title: Negative_control_input_rep1

city: Jinan

first: liangran

last: zhang

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

institute: Shandong University

data_processing:
The raw reads were filtered based on the quality value (q20 and q30) using FASTX Toolkit (Version 0.0.14)
The filtered reads were aligned to the Saccharomyces cerevisiae reference genome (SacCer2, 2008) using BOWTIE2 (Version 2.4.2; Langmead et al., 2009)
The ChIP and input data were normalized to reads per kilobase per million (RPKM) by using DEEPTOOLS (Version 3.3.2; Zhang et al., 2008)
Fold enrichment for each sample was determined by comparing the signal ratio between normalized ChIP and input for every bin (bin=50bp) across the whole genome using DEEPTOOLS (Version 3.3.2; Ramírez et al., 2016)
For peak calling, paired-end BAM was set as input file format, the effective genome size was set to 1.21x107bp, and MACS2 (Version 2.1.1; Zhang et al., 208) was used with the following parameters: Nomodel mode, 200bp extension size, the cutoff of FDR (q-value) at 0.05, and without broad region for peaks.
Assembly: Sacer2(2008)
Supplementary files format and content: bedgraph, enrichment

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: Synchronized cells were grown  in SPM at 30℃

extract_protocol:
Cells were lysed in 1ml of lysis buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) by Tissue Lyser . Crosslinked chromatin was sheared to 200-500bp by 12 × 10s pulses using a Biorupter sonicator. Genomic DNA was purified after being treated with 100μg/ml RNase A and 100μg/ml proteinase K. 5% purified DNA was treated as input DNA for subsequent experiments. 5μg purified DNA was incubated with 30µl Dynabeads MyOne streptavidin overnight at 4°C. The ChIP–DNA was eluted from the beads with 250µl elution buffer (95% formamide, 10mM EDTA) at 90 °C for 20 min and purified with Qiagen PCR clean up kit.
ChIP and input DNA was end-repaired and efficiently ligated to Illumina adapters with different indexes. Adapter ligation products were purified with the magic bead and amplified by PCR with 12 cycles. Amplified DNA was incubated with the magic bead to select fragments between 200 to 500bp. After selection, DNA was washed with 80% ethanol and eluted with 30µl TE buffer.

treatment_protocol: Cells were treated with 0.1% Sodium azide for 30min at 30°C and permeabilized with 0.1% digitonin for 30min at 30 °C. Collected cells were incubated with bTMP (200µg per 109 cells) in the dark for 30min and cross-linked by 365 nm UV light to form covalent linkage between DNA and bTMP.

tag: time in_spm_medium(h)


title: IL6_hep_rep3

value: HTVi of IL6 plasmids for 1 week


title: Negative_control_input_rep2


title: PND5_scSEQ

city: Providence

first: Kathryn

middle: J

last: Grive

state: RI

address: 200 Chestnut Street, Kilguss Research Institute, Rm 108, Grive Lab

department: OB-GYN

institute: Women & Infants Hospital of RI

data_processing:
10X Genomics cellranger(v2.1.0) mkfastq was used to generate demultiplexed fastq files
10X Genomics cellranger(v2.1.0) count was used to map reads to the reference genome and generate a gene-BC matrix.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz are TSV files containing barcodes present in dataset; features.tsv.gz files are TSV files containing IDs of quantified genes; matrix.mtx.gz files are matrix files containing a matrix of count values (with gene IDs and cellular barcodes)

growth_protocol: mice were raised in standard lab housing

extract_protocol:
Ovaries were collected from animals at designated ages, dissociated by gentle trypsin and Dnase digestion, and passed through a 40uM filter. Final single-celll suspension was made in 1x DPBS + 10% serum.
10X Genomics Single Cell 3' RNAseq v2

tag: cell suspension

value: single cell suspension

value: enzymatic digestion only

tag: protocol


title: shCTR-NT biol rep2

value: PDAC derived

tag: genotype


title: Subject_16_IMIQ_Cord

value: IMIQ

value: Male

value: Yes

value: No


title: RNA-seq_Col-0 rep1

value: wild type

value: seedlings

tag: developmental stage

value: 14 days old


title: P21 auditory nerve Mef2c heterozygote-8

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Fastq files were imported into the Partek Flow system
Alignment to Mouse mm10 was done with STAR
Aligned reads were quantified to annotation model (Partek E/M) using mm10 with settings: a) strict paired-end compatibility, b) require junction reads to match introns, c) min read overlap with feature 100% of read length, d) min reads 10
Gene counts were analyzed by DESeq2 to determine normalized counts and statistical measures between samples types
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of normalized counts and comparison measures

source_name: Auditory nerve cells

extract_protocol:
Microdissections were performed to isolate the auditory nerves from mouse cochleas. Two cochleas from each mouse were pooled for individual samples. Total RNA was purified from each sample using the RNeasy Micro Kit (Qiagen) per manufacturer’s instructions. Quality of each total RNA isolation was assessed by TapeStation and samples with low-quality (RIN<7)  were excluded.
Libraries were prepared from polyA preps made using 50ng input total RNA and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module.

value: Isolated auditory nerves

tag: age


title: pSTAT3_ChIP_rep1

city: Shanghai

tag: strain

value: WT

value: normal diet feeding with HTVi of IL6 plasmids

tag: chip antibody

value: pSTAT3 (CST, 9145S)

value: liver


title: Negative_control_IP_rep2

value: bTMP(cat#29986, Thermo Fisher Scientific)


title: Subject_16_CTRL_Cord

value: CTRL

value: Cord


title: Subject_15_CTRL_Cord


title: PND3_scSEQ

value: single cell suspension

value: enzymatic digestion only


title: Subject_15_LPS_Cord

value: LPS


title: shp53-NT biol rep2

value: PDAC derived

value: not tretaed


title: Subject_15_IMIQ_Cord

value: IMIQ

value: Male

value: Yes

value: No


title: PND1_scSEQ


title: shp53-NT biol rep1


title: P21 auditory nerve Mef2c heterozygote-7

value: Isolated auditory nerves


title: shCTR-AZA biol rep1


title: Subject_14_PolyIC_Cord

value: PolyIC

value: Female


title: shp53-AZA biol rep1


title: Subject_18_CTRL_Cord


title: shCTR-NT biol rep1


title: Capture Area 655 - Y1 and A1

description: Capture area contains one young sample (3-4 months, bottom specimen) and one aged sample (15-16 months, top specimen)

value: 3-4 months and 15-16 months


title: Negative_control_IP_rep1

value: WT


title: Subject_14_LPS_Cord


title: E18.5_scSEQ


title: P21 auditory nerve WT-4

value: wildtype


title: top2-L475A_input_rep1


title: pCLB2-TOP2_input_rep2


title: spo11-Y135F_input_rep2


title: Subject_14_CTRL_Cord

value: CTRL


title: top2-L475A_input_rep2


title: P21 auditory nerve Mef2c heterozygote-6


title: shCTR-AZA 3

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing NextSeq 500 are mapped to the mouse genome (mm10) using the BWA algorithm with default settings
Reads were aligned using the BWA algorithm (mem mode; default settings); duplicate reads were removed.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome; the resulting histograms were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Assembly: mm10
Supplementary files format and content: an Excel file lists all Merged Regions (genomic  regions containing 1 or multiple overlapping Intervals; formerly called “Active Regions”)
Supplementary files format and content: bigWig. Files with extension *.bw. Binary files that can be opened in or uploaded to genome  browsers and show the fragment density for 32-nt bins along the genome (“signal map”)

extract_protocol:
cells were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Illumina's Nextera Library Prep Kit following manufacture's instruction


title: P21 auditory nerve WT-1


title: pCLB2-TOP2_input_rep1


title: Non-SMC#2_rep3

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

data_processing:
RNA-seq reads were mapped to the mouse reference genome mm10 with STAR v2.6.1b
Differential expression analysis of genes was performed with DESeq2

source_name: small cell lung cancer cells

growth_protocol: All cell lines were incubated at 37℃ in 5% CO2 with RPMI1640 plus 10% FBS, and 10% Penicillin-Streptomycin

extract_protocol:
Total RNAs from SMC or Non-SMC were extracted by TRIzol reagent (Life Technologies) according to the manufacturer’s instruction.
Libraries were prepared according to Illumina's instructions

value: mixed genetic background (C57Bl/6, Balb-c, and S129)

value: lung

value: untreated


title: P21 auditory nerve WT-3


title: shp53-NT 3


title: shp53-NT 2


title: Subject_14_IMIQ_Cord

value: Cord


title: Subject_13_PolyIC_Cord


title: spo11-Y135F_input_rep1


title: Subject_12_PolyIC_Cord


title: shCTR-AZA 2

value: PDAC derived


title: P21 auditory nerve WT-2


title: top2-L475A_5h_IP_rep2

value: bTMP(cat#29986, Thermo Fisher Scientific)


title: P21 auditory nerve Mef2c heterozygote-5


title: shCTR-NT 3

value: not tretaed


title: shp53-AZA 3


title: Non-SMC#2_rep1


title: SMC#2_rep3


title: WT_input_rep2


title: Subject_12_LPS_Cord

value: LPS


title: WT_input_rep1


title: Non-SMC#2_rep2


title: Subject_12_IMIQ_Cord

value: IMIQ

value: Yes


title: Murine Podocyte Celsl (Mundel) 2

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

data_processing:
RNA-seq data analysis pipeline
Sequence reads were trimmed for adaptor sequence and remove low-quality sequence/reads using Trimmomatic (v0.39)
Trimmed sequence reads were mapped to GENCODE GRCm38 release M24 Mouse reference genome by using STAR aligner (v2.7.3a)
Reads mapped to genes were summarized by the featureCounts program (57) in subread v1.6.4
Genes were filtered by CPM ≥ 1 in at least 2 samples, and data were normalized to effective library size by edgeR
Assembly: GENCODE GRCm38 release M24 Mouse reference genome
Supplementary files format and content: tab-delimited text files include normalized log2CPM values for each Sample

source_name: Kidney

extract_protocol:
RNA was extracted using RNeasy Plus Mini kit (Qiagen). 100ng total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Library Prep (Illumina) following manufacturer's protocols.

value: Kidney

value: Murine Podocyte Cell (Mundel)

value: Murine Podocyte Cell


title: top2-L475A_4h_IP_rep2


title: top2-L475A_5h_IP_rep1


title: Subject_11_IMIQ_Cord

data_processing:
Data was generated with the Illumia NovaSeq 6000 platform and the bcl2fastq pipeline was used to convert base calls (BCL) to fastq files.
Read libraries were mapped to the human genome (hg38) using HISAT2. Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps, and Pre- and post-alignment QC was assessed with FastQC and SAMStat, respectively.
(For corrected gene counts) Raw transcripts were removed if they had no counts in any sample, lacked annotation, or had 0.5 counts per million in ≤ 25 samples. Size factors were estimated using the median ratio method with the 'estimateSizeFactors' function (DESeq2 R package) and variance stabilizing transformation (VST) was applied to the count data (DESeq2). Unwanted variation was identified with the 'RUVg' function from the RUVSeq R package. RUVg trends which related to technical variation and culture batch were removed as covariates with a linear model ('removeBatchEffect' function from the limma R package).
Genome_build: hg38
Supplementary_files_format_and_content: CBMC_genecounts.txt file contain a matrix of raw gene counts (unfiltered and un-normalised data), with transcripts as rows and samples as columns. Transcript information (e.g. EnsembleID, gene symbol) are supplied in the final columns. CBMC_corrected_counts.txt contains a matrix of VST transformed and batch/RUV corrected gene counts, formatted as the raw gene count file.

value: Female

value: No


title: Subject_13_LPS_Cord

value: Male


title: shp53-AZA 2


title: Subject_13_IMIQ_Cord


title: Subject_11_PolyIC_Cord

value: PolyIC


title: Podocyte Derived Myosin 1e KO 3

value: Podocyte Derived Myosin 1e KO

value: Podocyte Derived Cell

value: Myosin 1e KO


title: shCTR-NT 2


title: Murine Podocyte Cells (Mundel) 3

value: WT


title: top2-L475A_3h_IP_rep1


title: Subject_13_CTRL_Cord

value: CTRL

value: Cord


title: pCLB2-TOP2_5h_IP_rep2

value: bTMP(cat#29986, Thermo Fisher Scientific)


title: Non-SMC#1_rep1

value: mixed genetic background (C57Bl/6, Balb-c, and S129)

value: lung

value: untreated


title: SMC#2_rep1


title: Podocyte Derived Myosin 1e KO 1

value: Kidney


title: Non-SMC#1_rep3


title: top2-L475A_3h_IP_rep2


title: SMC#1_rep3


title: pCLB2-TOP2_4h_IP_rep2


title: Podocyte Derived Myosin 1e KO 2


title: Murine Podocyte Cells (Mundel) 1

value: Murine Podocyte Cell (Mundel)


title: Non-SMC#1_rep2


title: Subject_12_CTRL_Cord

value: Yes


title: top2-L475A_4h_IP_rep1


title: OE 3

city: Newcastle-Upon-Tyne

first: Ella

middle: Patricia

last: Dennis

address: Inst. of Genetic Medicine, Int’l Centre for Life, Central Parkway

institute: Newcastle University

description: Overexpressing CRELD2 pcDNA3.1+

data_processing:
HISAT2 was used for pseudo-alignment and quantification, against the mouse GRCh38 mm10 transcriptome.
Mapped transcripts were converted to a gene level using the Galaxy annotateMyIDs.
limma-voom was used to calculate P-values and log2 fold-changes (logFC).
Assembly: Mouse GRCh38 (mm10)
Supplementary files format and content: *.txt: Tab-delimited text files include abundance measurements.

growth_protocol: Cells were cultured in Alpha MEM.

extract_protocol:
RNA was extracted from cells using the Promega ReliaPrep Cell Miniprep System following the manufacturer’s protocol.
The sequencing library was prepared using the Illumina TruSeq Stranded mRNA sample preparation kit following the manufacturer’s protocol.

treatment_protocol: 100 ng/mL recombinant RANKL was added to cells and cells were harvested 48 hours after stimulation.

value: CRELD2 overexpression

value: RANKL


title: OE 2

description: Overexpressing CRELD2 pcDNA3.1+


title: SMC#2_rep2


title: Subject_11_CTRL_Cord

extract_protocol:
Total RNA was extracted with TRIzol (Ambion) followed by RNAeasy (QIAGEN). Total RNA libraries were prepared using NEBNext Ultra II Kits (New England BioLabs). Sequencing was performed by the Australian Genome Research Facility (Illumina NovaSeq 6000, 100bp paired-end reads).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Female

value: No


title: OE 1

description: Overexpressing CRELD2 pcDNA3.1+


title: SMC#1_rep2


title: pCLB2-TOP2_4h_IP_rep1


title: CON 3

description: Empty pcDNA3.1+ Vector Control

value: Control


title: Subject_11_LPS_Cord

value: LPS


title: Subject_10_LPS_Cord


title: SMC_TAZ4SA_2

data_processing:
RNA-seq reads were aligned to the mouse reference genome mm10 using STAR version 2.6 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: read count text files

extract_protocol:
Total RNAs from SMC with or without TAZ4SA ectopic expression were extracted by TRIzol reagent (Life Technologies) according to the manufacturer’s instruction.
Libraries were prepared according to Illumina's instructions

value: SMC

tag: overexpression


title: Subject_09_PolyIC_Cord

value: PolyIC

value: Male


title: Subject_10_PolyIC_Cord

value: Cord


title: SMC#1_rep1


title: spo11-Y135F_5h_IP_rep2

value: bTMP(cat#29986, Thermo Fisher Scientific)


title: pCLB2-TOP2_5h_IP_rep1


title: Subject_10_IMIQ_Cord

value: IMIQ


title: CON 2

description: Empty pcDNA3.1+ Vector Control


title: SMC_TAZ4SA_3

value: mixed genetic background (C57Bl/6, Balb-c, and S129)

value: lung


title: pCLB2-TOP2_3h_IP_rep2


title: Subject_10_CTRL_Cord

value: CTRL


title: Subject_09_IMIQ_Cord


title: pCLB2-TOP2_3h_IP_rep1


title: CON 1

description: Empty pcDNA3.1+ Vector Control


title: SMC_Ctrl_3

value: untreated

value: control


title: spo11-Y135F_4h_IP_rep2


title: Subject_09_LPS_Cord

value: Yes


title: spo11-Y135F_3h_IP_rep2


title: SMC_TAZ4SA_1


title: SMC_Ctrl_2


title: Subject_09_CTRL_Cord


title: Carm1_knockout, biological rep3

city: Ottawa

first: Goutham

last: Vasam

state: ON

address: 451 Smyth Rd

department: Faculty of Health Sciences

country: Canada

institute: University of Ottawa

data_processing:
RTA 2.0 software used for basecalling.
Sequenced reads were mapped to Mus musculus (UCSC mm10) whole genome using RNA-Seq Alignment (BaseSpace Workflow, Illumina) v1.1.0 with STAR (Aligner) vSTAR_2.5.0b
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) calculation, followed by differential expression analysis were performed using Cufflinks Assembly & DE (Basespace Workflow, Illumina) v2.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: tibialis anterior muscle

extract_protocol:
Trizol extraction of total RNA was performed for each sample from flash frozen muscle. Total RNA samples were quantified using Qubit HS RNA assay (Thermo) and fragment size was evaluated using the Fragment Analyzer HS NGS assay (AATI)Library construction was performed using Truseq RNA v2 (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tibialis anterior muscle

value: Carm1 skm-/-


title: Carm1_knockout, biological rep4


title: SMC_Ctrl_1


title: Subject_08_PolyIC_Cord


title: spo11-Y135F_4h_IP_rep1


title: Carm1_knockout, biological rep2


title: spo11-Y135F_5h_IP_rep1


title: spo11-Y135F_3h_IP_rep1


title: Carm1_wildtype, biological rep4

value: Carm1 skm+/+


title: 9509 input for ChIP-seq

city: Athens

first: Robert

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: ChIP

data_processing:
For MethylC-seq, single-end short read libraries (150 bp) were aligned and methylation levels assessed using the methylpy pipeline (https://github.com/yupenghe/methylpy)
Raw ChIP reads were trimmed for adapters and low-quality bases using Trimmomatic with the following options: reads were trimmed for TruSeq version 3 single-end adapters with a maximum of two seed mismatches, palindrome clip threshold of 30, and simple clip threshold of 10. Trimmed reads were mapped to the genome using bowtie1 with “-v 2 --best --strata -m 1”. Mapped reads were sorted using SAMtools (Li and Durbin 2009) and then clonal duplicates were removed using picard (http://broadinstitute.github.io/picard/). Remaining reads were converted to BED format with Bedtools. H3K9me2 enriched regions were identified with MACS2 with parameter “--keep-dup all --broad”
Genome_build: Spirodela polyrhiza line 9509: https://genomevolution.org/coge/OrganismView.pl?gid=51364. Spirodela polyrhiza line 7498: https://genomevolution.org/coge/GenomeInfo.pl?gid=37349

organism: Spirodela polyrhiza

source_name: whole plant

growth_protocol: Plants were grown in liquid Hoaglands No. 2 Basal Salt Mixture powder.

extract_protocol:
Bisulfite-Seq: 1ug of DNA was used to prepare libraries as previously described (Urich et al. 2015).
ChIP Seq:1 g of fresh duckweed plantlets were crosslinked in 1% formaldehyde for 10 min. Nuclei were then isolated and sonicated for 15 min, twice. Histone-DNA complexes were pulled down with anti-H3K9me2 (Cell Signaling Technology antibody #9753s). DNA was isolated and used to prepare ChIP-seq libraries with the TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1012), including a gDNA input control. Sequencing was performed on an Illumina NextSeq500 in Georgia Genomics and Bioinformatics Core (GGBC) in the University of Georgia


title: 9509 MethylC-seq

description: Methylation


title: 9509 H3K9me2 ChIP-seq

description: ChIP


title: Subject_08_CTRL_Cord


title: 7498 MethylC-seq

description: Methylation


title: Carm1_knockout, biological rep1


title: Carm1_wildtype, biological rep3


title: WT_5h_IP_rep2

value: WT


title: Subject_08_IMIQ_Cord


title: Subject_08_LPS_Cord

value: LPS


title: Subject_07_PolyIC_Cord

value: No


title: WT_3h_IP_rep2


title: EGFRviii.Tumor

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Cell Ranger (10X Genomics) was used for align reads, generate gene-cell matrices and perform clustering and gene expression analysis
Samples were aligned using the mouse genome 10-3.0.0 (Mm10, 10X genomics)
Assembly: Mm10
Supplementary files format and content: Feature, barcode, matrix

source_name: Glioma infiltrated leukocyte

growth_protocol: Mice were housed in specific pathogen free (SPF) facility or KAIST, Korea.

extract_protocol:
Mice were transcardially perfused with 50 ml cold DPBS to remove the blood before isolating tissues. The right hemisphere of the brain was minced into small pieces by blade and digested with 2 mg/ml collagenase IV (Worthington) and 30 μg/ml DNase I (Rhoche) at 37℃ for 30 min. Tissues were passed through a 70 μm strainer. To remove non-immune cells from tumor samples, cells were resuspended in 4 ml of 30% percoll (GE Healthcare) containing DMEM CM and loaded onto 3 ml of 70% percoll containing DPBS supplemented with 1% BCS. Immune cells and myelin were separated by centrifugation. Cells were treated with ACK lysis buffer for 5 min at RT to remove residual red blood cells. Cells were stained with anti-mouse CD45.2-APC or CD45-APC and propidium iodide. PI-negative and CD45.2/CD45-positive live immune cells were sorted with FACS Aria.
library were constructed with Single Cell 3' Reagent Kit v3 (10x genomics) following manufacturer's instruction.

treatment_protocol: LSL-EGFRviii homo mice were injected with plasmid containing Cas9 gene with small guide RNA for PTEN and TP53 into brain ventricle, and subjected to electroporation

value: FVB

value: Brain

value: CD45 immune cell


title: Carm1_wildtype, biological rep1


title: WT_4h_IP_rep2

value: bTMP(cat#29986, Thermo Fisher Scientific)


title: Subject_07_IMIQ_Cord

value: IMIQ

value: Cord

value: Male


title: Carm1_wildtype, biological rep2


title: WT_4h_IP_rep1


title: WT_5h_IP_rep1


title: Subject_07_LPS_Cord


title: EGFRviii.Normal

source_name: Brain leukocyte (no glioma)