title: Era- pre-osteoclast progenitors 3

source_name: Era- pre-osteoclast progenitors

value: ERalphaf/f;LysM-Cre

value: bone marrow

value: pre-osteoclast progenitors


title: 12M_KB13

status: Public on Feb 14 2020

type: SRA

city: Brisbane

first: Kyle

middle: R

last: Upton

state: Qld

address: Cooper Road

department: SCMB

country: Australia

institute: University of Queensland

library_source: transcriptomic

data_processing:
To confirm all libraries had high quality reads, all fastq files were first checked using FastQC
Trimmomatic was used to remove adapter sequences from reads.
Sequencing reads were aligned to GRCh38.p12 using HISAT2 with default options.
HTSeq was used to generate tag count files with default options
EdgeR with a standard generalised linear model was used to identify differentially expressed genes from the read count files. Reported results are from virus infected vs mock infected for normoglycemic (7M) and hyperglycemic (12M) samples separately.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tabular files with raw read counts. CSV files with Edge-R output

molecule: total RNA

organism: Homo sapiens

source_name: HPMEC

growth_protocol: Human epithelial NCl-H441 cells were obtained from the American Type Culture Collection and cultured in Roswell Park Memorial Institute medium (RPMI) with 10% fetal bovine serum and 1% penicillin-streptomycin. NC1-H441 cells were used at passages 3-8. Primary human pulmonary microvascular endothelial cells (HPMEC) were obtained from Sciencell (Carlsbad, CA, USA) and cultured in endothelial cell growth medium (Sciencell) in fibronectin coated tissue culture flasks (2μg/cm2, Sigma). HPMEC cells were used at passages 3-7. In vitro co-culture and mono-culture models of the pulmonary epithelial-endothelial barrier were established as described in Short et al. (European Respiratory Journal 2016; 47(3): 954). Once the NCI-H441 cells reached confluency, the media in both upper and lower compartments was refreshed every 12 hours. The medium of the upper compartment was refreshed with RPMI (5% FBS, 1μM dexamethasone and 7mM of glucose) (Gibco), while the lower compartment was refreshed with RPMI (5% FBS and either 7mM glucose or 12mM glucose) until a trans-barrier electrical resistance (TER) of greater than 800Ω was observed. Influenza virus strain A/Solomon Islands/03/2006 (Solomon Islands/f06; H1N1) was used to model IAV infection. Virus stocks were prepared in embryonated chicken eggs. Titres of IAV were determined by plaque assays on MDCK cells.

extract_protocol:
Qiagen RNeasy plus mini kit (manufacturers recommended protocol was used)
Stranded

treatment_protocol: One hour prior to infection, the medium of the transwell plate was refreshed with RPMI (2% FBS). Cells were infected or mock infected by adding A/Solomon Islands/03/2006 (Solomon Islands/06; H1N1) at multiplicity of infection (MOI) OF 0.5 or PBS respectively to the upper compartment of the transwell system. Virus was not removed after infection and cells were monitored for a duration of 24 hr post-infection.

tag: tissue

value: Human epithelial cells and human pulmonary microvascular endothelial cells

tag: treatment

value: high glucose

value: Mock Infection


title: Yerong, waterlogged 72h, replicate 4

city: Brandon

first: Ana

last: Badea

state: Manitoba

address: 2701 Grand Valley Rd

country: Canada

institute: Agriculture and Agri-Food Canada

description:
fpkm.xls
readcount.xls

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly (publicly available Morex genome assembly (International Barley Genome Sequencing Consortium, 2012) was accessed through Ensembl Plants (release 40)). Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: GCA_901482405.1, Ensembl 40
Supplementary_files_format_and_content: Data is provided in .xls file containing fragments per kilobase of transcript per million mapped reads (FPKM) values for each gene and sample.

organism: Hordeum vulgare

source_name: Roots

growth_protocol: Seeds of Yerong and Deder2 barley genotypes were placed in cone-tainer cells with a dimension of 4 × 14 cm (top diameter × height) in growth chamber conditions (20 ± 2°C, 16 h photoperiod) at Brandon Research and Development Centre (BDRC), Brandon, Manitoba, Canada. Cones were filled with the soil collected from a field where water is prone to accumulate creating excess moisture problems. The experiment consisted of four replications for both the control and treatments for each of the two genotypes tested. Plants were watered on demand from germination.

extract_protocol:
Root tissue was pulverized in liquid nitrogen using a mortar and pestle, and total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen, Canada) following the manufacturer’s protocol. Four biological replicates of Yerong at 0 and 72 h, and of Deder2 at 0, 72, and 120 h time-points, were subjected to RNA-seq analysis. The RNA quality and concentration were verified using a NanoDrop 1000 spectrophotometer (ThermoFisher Scientific, Canada) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Canada) prior to sequencing.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase （RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Two-week-old Yerong and Deder2 seedlings were submitted to waterlogging treatment, which involved keeping the water level above soil level for the duration of the treatment. Root tissue samples were collected at the time-points 0 and 72 h of treatment for Yerong from both treated and control plants, and at the points 0, 72, and 120 h of treatment for Deder2 from both treated and control plants. All samples collected were immediately submerged in liquid nitrogen and stored at -80 °C until further processing.

value: Roots

tag: genotype

value: Yerong

value: Waterlogging

tag: time point


title: 7V_KB12

value: standard glucose

value: Virus Infection


title: Era- pre-osteoclast progenitors 2

type: RNA

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

country: USA

institute: University of Arkansas for Medical Sciences

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: The data were normalised using quantile normalisation with IlluminaGUI in R

data_processing: quantile normalized

label: biotin

organism: Mus musculus

label_protocol: Standard Illumina hybridization protocol

growth_protocol: Cells were plated in α-MEM complete media (10% fetal bovine serum, 100 U ml-1 penicillin, and 100 µg ml-1 streptomycin). Twenty-four hours later, non-adherent cells were re-plated in Petri dishes with 30 ng ml-1 M-CSF for 4 days to obtain macrophages. To generate pre-osteoclasts and mature osteoclasts, macrophages were cultured in α-MEM complete media with 30 ng ml-1 M-CSF and 30 ng ml-1 RANKL (R&D Systems) for 2 and 4 days, respectively

extract_protocol: A RNA extraction kit

treatment_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

tag: strain background

tag: genotype/variation

tag: cell type


title: ein5-1 dcl4-2 aerial part_rep4 (smRNA)

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

description:
SmallRNA_processed_data
ed4_smRNA_rep4

data_processing:
Sequence reads were filtered and then mapped to TAIR10 genome using Bowtie-1.2.2 with following parameters: -v  0  -a  -M  3  --best  --strata
22-nt small RNA read were selected using samtools v1.9
Tags Per Million (TPM) were calculated and differential 22-nt siRNA production genes were called out using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include TPM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons

organism: Arabidopsis thaliana

source_name: ein5-1 dcl4-2 aerial part

growth_protocol: plants were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old were collected for small RNA extraction.

extract_protocol:
miRNeasy mini kit(Qiagen)
NEBNext® Small RNA Library Prep Set for Illumina

treatment_protocol: No treatment

value: aerial part

tag: age

value: 20-day-old plant

value: ein5-1 dcl4-2


title: Era- osteoclast progenitors 3

source_name: Era- osteoclast progenitors

value: osteoclast progenitors


title: Yerong, waterlogged 72h, replicate 1

description:
fpkm.xls
readcount.xls


title: Yerong, waterlogged 72h, replicate 2

description:
fpkm.xls
readcount.xls


title: Era- pre-osteoclast progenitors 1


title: 7V_KB19


title: 7V_KB4


title: Deder2, waterlogged 72h, replicate 4

description:
fpkm.xls
readcount.xls


title: Deder2, waterlogged 72h, replicate 2

description:
fpkm.xls
readcount.xls


title: ein5-1 dcl4-2 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
ed4_smRNA_rep1


title: Control mature-osteoclast progenitors 2

source_name: Control mature-osteoclast progenitors

value: ERalphaf/f control

value: mature-osteoclast progenitors


title: Control mature-osteoclast progenitors 3


title: ein5-1 dcl2-1 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
ed2_smRNA_rep1

source_name: ein5-1 dcl2-1 aerial part

value: ein5-1 dcl2-1


title: 7M_KB10


title: 12M_KB22


title: 7V_KB3


title: ein5-1 dcl4-2 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
ed4_smRNA_rep3


title: Control mature-osteoclast progenitors 1

value: bone marrow


title: Deder2, waterlogged 72h, replicate 3

description:
fpkm.xls
readcount.xls


title: Era- osteoclast progenitors 1

value: ERalphaf/f;LysM-Cre


title: ein5-1 dcl4-2 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
ed4_smRNA_rep2


title: 7M_KB2

value: Human epithelial cells and human pulmonary microvascular endothelial cells


title: Yerong, control 72h, replicate 4

description:
fpkm.xls
readcount.xls

value: Control


title: 7M_KB17

value: Mock Infection


title: Yerong, control 72h, replicate 3

description:
fpkm.xls
readcount.xls

value: Roots


title: Yerong, waterlogged 72h, replicate 3

description:
fpkm.xls
readcount.xls

value: Yerong


title: Deder2, waterlogged 72h, replicate 1

description:
fpkm.xls
readcount.xls

value: Waterlogging


title: Control pre-osteoclast progenitors 2

source_name: Control pre-osteoclast progenitors

value: pre-osteoclast progenitors


title: ski2-2 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
ski2_smRNA_rep3

source_name: ski2-2 aerial part


title: ski2-2 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
ski2_smRNA_rep1


title: ski2-2 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
ski2_smRNA_rep4


title: ein5-1 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
ein5_smRNA_rep4

source_name: ein5-1 aerial part


title: Control pre-osteoclast progenitors 3


title: 7M_KB1

value: standard glucose


title: ski2-2 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
ski2_smRNA_rep2

value: aerial part


title: Control pre-osteoclast progenitors 1


title: ein5-1 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
ein5_smRNA_rep2

value: 20-day-old plant


title: Control osteoclast progenitors 1

source_name: Control osteoclast progenitors


title: Yerong, control 72h, replicate 1

description:
fpkm.xls
readcount.xls


title: Deder2, control 72h, replicate 2

description:
fpkm.xls
readcount.xls


title: Control osteoclast progenitors 3


title: MCF7_plusDOX_E2_RNAseq

city: HOUSTON

first: Eric

middle: C.

last: Chang

state: TX

address: ONE BAYLOR PLZ

department: BREAST CENTER

institute: BAYLOR COLLEGE OF MEDICINE

data_processing:
RNA-seq:  Reads were aligned to hg19 (GRCh37) reference genome using RSEM v1.2.31 and Bowtie 2
RNA-seq:  Differential gene expression was performed using EBseq (FDR < 0.2)
RNA-seq:  Differentially expression genes were used in Gene Set Enrichment Analysis (GSEA) for "Hallmark Pathways" in the Molecular Signatures Database (MSigDB)
RNA-seq:  Heatmaps were created using RSEM generated log2TPM values
Genome_build: hg19
Supplementary_files_format_and_content: RSEM tab-delimited output files for RNAseq data include gene id, transcript id, gene length, expected read counts used for differential gene analysis, TPM, and FPKM

growth_protocol: MCF7 cells were maintained in high glucose DMEM supplemented with 10% FBS.

extract_protocol:
Cells were grown in hormone-deprived media for 48 hrs before treatment for 24 hrs. Dox was added when seeding. RNA was isolated using Qiagen Rneasy kit and eluted in water.
Illumina TruSeq Stranded mRNA-Seq Sample Prep kit was used for library preparation

treatment_protocol: DOX-inducible NF1 knock-down MCF-7 cells were seeded in phenol-red-free RPMI1640 and 10% charcoal-stripped FBS (hormone-deprived media) for 48 hrs before treatment for 24h. Dox was added when seeding. CRISPR knock-in MCF-7 cells were grown in phenol-red-free RPMI1640 and 10% charcoal-stripped FBS (hormone-deprived media) for 72 hrs.

value: Luminal breast carcinoma epithelial MCF-7 cells

tag: cell subtype

value: Doxycycline inducible NF1 knockdown model

tag: cell line

tag: condition

value: Hormone-deprived media + E2


title: MCF7_plusDOX_Veh_RNAseq

value: Hormone-deprived media


title: MCF7_plusDOX_4OHT_RNAseq

value: Hormone-deprived media + 4OHT


title: MCF7_minusDOX_E2_RNAseq

extract_protocol:
Cells were grown in hormone-deprived media for 48 hrs before treatment for 24 hrs.  RNA was isolated using Qiagen Rneasy kit and eluted in water.
Illumina TruSeq Stranded mRNA-Seq Sample Prep kit was used for library preparation


title: Control osteoclast progenitors 2

value: ERalphaf/f control

value: bone marrow

value: osteoclast progenitors


title: ein5-1 dcl2-1 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
ed2_smRNA_rep2

value: ein5-1 dcl2-1


title: ein5-1 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
ein5_smRNA_rep1


title: Control

city: Shihez

first: xiaoni

last: zhang

address: Shihezi, China

institute: Medical College of Shihezi University

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix® GeneChip® Command Console® Software.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human umbilical vein endothelial cells(HUVECs)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA .

growth_protocol: Microarray analysis was undertaken using RNA samples from HCMV-infected HUVECs, HUVECs treated with high glucose (HG; 4500 mg/L), and oxidized low-density lipoprotein (ox-LDL; 100 mg/L) for 48 h, as well as HCMV-infected HUVECs treated with HG and ox-LDL; uninfected cells were processed in parallel as a control.

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

treatment_protocol: The dish was rinsed with PBS, then placed in Trizol solution and placed on ice.


title: Deder2, control 72h, replicate 1

description:
fpkm.xls
readcount.xls

value: Control


title: Deder2, control 72h, replicate 4

description:
fpkm.xls
readcount.xls

value: Roots


title: MCF7_minusDOX_Veh_RNAseq


title: ein5-1 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
ein5_smRNA_rep3


title: MCF7_minusDOX_4OHT_RNAseq


title: Deder2, control 72h, replicate 3

description:
fpkm.xls
readcount.xls


title: dcl4-2 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
dcl4_smRNA_rep4

source_name: dcl4-2 aerial part


title: Yerong, control 72h, replicate 2

description:
fpkm.xls
readcount.xls

value: Yerong


title: Yerong, control 0h, replicate 4

description:
fpkm.xls
readcount.xls

value: 0 h


title: ski2-2 dcl2-1 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
sd2_smRNA_rep3

source_name: ski2-2 dcl2-1 aerial part

value: ski2-2 dcl2-1


title: dcl4-2 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
dcl4_smRNA_rep2


title: Yerong, control 0h, replicate 3

description:
fpkm.xls
readcount.xls


title: dcl4-2 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
dcl4_smRNA_rep3


title: MCF7_NF1-I417M_RNAseq

extract_protocol:
Cells were grown in hormone-deprived media for 72 hrs before RNA was isolated using Qiagen Rneasy kit and eluted in water.
Illumina TruSeq Stranded mRNA-Seq Sample Prep kit was used for library preparation

value: NF1 I417M mutated by CRISPR knock-in


title: LSK cells, 14936X1 control shRNA

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 2.1.1 to create I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to  refdata-cellranger-mm10-2.1.0 from 10x Genomics
Barcodes and UMIs were counted using cellranger count version 2.1.1 with expected-cells=3500
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count

molecule: polyA RNA

source_name: LSK cells transduced with control shRNA

growth_protocol: LSK cells grown in DMEM media with 20% fetal bovine serum supplemented with 10ng/ml GM-CSF and 10ng/ml SCF.

extract_protocol: Cell suspensions were partitioned into an emulsion of nanoliter-sized droplets using a 10X Genomics Chromium Single Cell Controller and RNA sequencing libraries were constructed using the Chromium Single Cell 3’ Reagent Kit v2 (10X Genomics Cat#PN-120237). Briefly, droplets contained individual cells, reverse transcription reagents and a gel bead loaded with poly(dT) primers that include a 16 base cell barcode and a 10 base unique molecular index. Lysis of the cells and gel bead enables priming and reverse transcription of poly-A RNA to generate barcoded cDNA molecules. Libraries were constructed by End Repair, A-Tailing, Adapter Ligation and PCR amplification of the cDNA molecules. Purified cDNA libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (Agilent Cat#5067-5582 and Cat#5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (Kapa Biosystems Cat#KK4824). HiSeq 125 Cycle Paired-End Sequencing v4: Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003).

treatment_protocol: LSK cells in the third day of growth in myeloid differentiation culture were collected and without any freezing or fixation steps, the single cell populations were immediately processed.

tag: strain

value: Bone marrow

value: LSK cells (Bone marrow cells in culture)

tag: isolation

value: LSK cells in the third day of myeloid differentiation culture

value: control


title: HCMV+HG+ox-LDL

source_name: HCMV-infected HUVECs treated with high glucose and oxidized low-density lipoprotein

value: Human umbilical vein endothelial cells(HUVECs)


title: DSS.AZ.5

city: wuhan

first: xiaomeng

last: wang

address: Donghu Road 115

institute: Wuhan University

description:
otu_table.c28.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls

library_source: genomic

data_processing:
Library strategy: 16s rRNA seq
Illumina NovaSeq software used for basecalling.
Paired-end reads were merged using FLASH (V1.2.7）
Sequences analysis were performed by Uparse software (Uparse v7.0.1001）
Shannon indice was calculated with QIIME(Version 1.7.0) and displayed with R software(Version 2.15.3).
PCoA analysis was displayed by WGCNA package, stat packages and ggplot2 package in R software(Version 2.15.3).
Genome_build: mm9
Supplementary_files_format_and_content: xls files include otu/shannon/pcoa value of each sample

molecule: genomic DNA

source_name: Feces

extract_protocol:
Total genome DNA from samples was extracted using CTAB/SDS method.
Sequencing libraries were generated usingTruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA). The library quality was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific) and AgilentBioanalyzer 2100 system. At last, the library was sequenced on an Illumina NovaSeq platform and 250 bp paired-end reads were generated.

value: wild type

value: DDS and AZ1


title: dcl4-2 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
dcl4_smRNA_rep1

value: aerial part

value: 20-day-old plant


title: MCF7_NF1-WT_RNAseq

value: Luminal breast carcinoma epithelial MCF-7 cells

value: wild-type NF1

value: Hormone-deprived media


title: Yerong, control 0h, replicate 2

description:
fpkm.xls
readcount.xls

value: Roots

value: Control


title: HG+ox-LDL

source_name: HUVECs treated with high glucose and oxidized low-density lipoprotein


title: DSS.AZ.4

description:
otu_table.c27.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls


title: Yerong, control 0h, replicate 1

description:
fpkm.xls
readcount.xls

value: Yerong

value: 0 h


title: HCMV

source_name: HCMV-infected HUVECs


title: KBN_N3AB

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

data_processing:
FASTQs extracted with Cell Ranger v3.0.2 mkfastq.
UMI count matrices with Cell Ranger v3.0.2 count.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrices

source_name: Dissociated synovial cells

extract_protocol:
Synovial dissociation followed protocol from Donlin, L. T. et al. Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue. Arthritis Res. Ther. 20, 139 (2018).
For scRNAseq experiments, viable cells in single cell suspension were resuspended in 0.4% BSA in PBS at a concentration of 1,000 cells per ul. 7,000 cells were loaded onto a single lane (Chromium chip, 10X Genomics) followed by encapsulation in lipid droplet (Single Cell 3’ kit, 10X Genomics).
cDNA and library generation per manufacturer protocol.

value: Dissociated synovial cells

tag: disease state

value: Arthritis

value: antiNotch3 mAB


title: DSS.AZ.3

description:
otu_table.c26.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls


title: KBN_ISO

value: Isotype control


title: dcl2-1 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
dcl2_smRNA_rep4

source_name: dcl2-1 aerial part


title: dcl2-1 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
dcl2_smRNA_rep3


title: LSK cells, 14936X2 knockdown Cxxc5

source_name: LSK cells transduced with shRNA targeting Cxxc5

value: Bone marrow

value: LSK cells (Bone marrow cells in culture)

value: LSK cells in the third day of myeloid differentiation culture

value: Cxxc5 knockdown


title: Deder2, control 0h, replicate 2

description:
fpkm.xls
readcount.xls

source_name: Roots


title: KBN_KO

value: Notch3-/- knockout


title: MCF7_NF1-R1362Q_RNAseq

value: NF1 R1362Q mutated by CRISPR knock-in


title: Deder2, control 0h, replicate 3

description:
fpkm.xls
readcount.xls


title: DSS.AZ.1

description:
otu_table.c24.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls

value: wild type

value: DDS and AZ1


title: KBN_WT

value: Wild Type


title: dcl2-1 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
dcl2_smRNA_rep1

value: aerial part

value: 20-day-old plant


title: DSS.AZ.2

description:
otu_table.c25.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls


title: Ctrl_KO

value: Healthy


title: Deder2, control 0h, replicate 1

description:
fpkm.xls
readcount.xls

value: Roots

value: Control

value: 0 h


title: DSS.PBS.4

description:
otu_table.c22.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls

value: DDS and PBS


title: Deder2, control 0h, replicate 4

description:
fpkm.xls
readcount.xls


title: dcl2-1 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
dcl2_smRNA_rep2


title: DSS.PBS.5

description:
otu_table.c23.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls


title: Col-0 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
Col_smRNA_rep4

source_name: Col-0 aerial part


title: Ctrl_WT

value: Dissociated synovial cells


title: DSS.PBS.2

description:
otu_table.c20.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls


title: Brainstem, Mutant 5

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

institute: Princess Margaret Cancer Centre, University Health Network

data_processing:
The 75-basepair paired-end reads from the sequencer were quality-checked using FASTQC v0.11.5 and MultiQC v0.8 (Ewels et al., 2016) software packages, and aligned to the Mus musculus genome assembly version GRCm38 (mm10) from the Genome Reference Consortium using the STAR aligner v2.5.2b. The aligned transcripts were quantified using RSEM v1.3.0, and a gene-by-sample expression matrix was generated using in-house R scripts. The matrix of raw RSEM expected counts was input into the DESeq2 R package v1.20.0 for differential expression analysis. Since the samples were processed and sequenced in two batches, the batch information was included as a feature variable in the linear modeling design formula to account for any batch effects. For statistical analyses, only genes with FPKM>10 were considered. The baseMean (mean of normalized counts across samples), log2FoldChange, and the adjusted p-values obtained using the Benjamini-Hochberg procedure, were used to arrive at the set of top differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RSEM expected count, TPM, and FPKM values for each sample

source_name: Brainstem

extract_protocol:
Brainstem tissues were dissected, snap-frozen on dry ice, and stored at -80C. RNA was extracted using the NucleoSpin RNA Plus kit (Macherey-Nagel #740984). Samples were first homogenized in LPB buffer from the NucleoSpin RNA Plus kit using a Buller Blender Gold apparatus (Next Advance) and 0.5 mm zirconium oxide beads. RNA was then extracted following the kit's instructions.
Library preparation was performed using the TruSeq Stranded Total RNA kit (Illumina), following the manufacturer’s instructions.

value: Mixed 129P2/OlaHsd-C57Bl/6J

value: Brainstem

value: Postnatal day 7

tag: sequencing batch

value: Batch 2


title: Col-0 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
Col_smRNA_rep2


title: Brainstem, Mutant 3

value: Batch 1


title: Brainstem, Mutant 2


title: DSS.PBS.3

description:
otu_table.c21.relative.tran.xls
pcoa_weighted_unifrac_dss_otu_table.xls
alpha_otu_table_shannon.xls


title: Patient 4 Pp07p

city: Foshan

first: Huishan

last: Zhang

address: No.11 Reminxi Road, Foshan, Guangdong,  China

institute: Foshan Institute of Fetal Medicine, Southern Medical University Afliated Maternal & Child Health Hospital of Foshan

description: gene expression in invasive placenta tissues.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (part number G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization, at least 5 out of 10 samples of LncRNAs and mRNAs have flags in Present or Marginal (“All Targets Value”), they were chosen for further data analysis. Differentially expressed LncRNAs and differentially expressed mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Dysregulated lncRNAs and mRNAs between the two groups were identified through a Fold Change >1.5.

source_name: placenta accreta spectrum disorders

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, p/n, 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from frozen samples using TRIzol (Invitrogen, USA), according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 (Thermo Fisher, USA). RNA integrity was assessed by standard denaturing agarose gel electrophoresis and Agilent 2100 Bioanalyzer (Agilent, USA).

value: placenta

tag: histology grade

value: increte

tag: gestational age

tag: intraoperative bleeding of patients


title: AZ.4

description:
otu_table.c18.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls

value: wild type

tag: treatment


title: Patient 5 Pp11p

tag: tissue

value: accrete


title: Brainstem, Mutant 4

tag: genotype


title: Col-0 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
Col_smRNA_rep1

value: aerial part


title: AZ.3

description:
otu_table.c17.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls


title: s07_nrpb2-Y732F_RNAseq_biorep1

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

description: RNA-Seq of mutant seedlings with accelerated transcription speed (replicate 1)

data_processing:
Illumina Casava v1.7 software was used for basecalling.
PlaNET-Seq: 1) Trim 4bp UMI barcodes from 5' ends of both R1 and R2 reads (UMI-Tools extract v0.5.3); 2) Align R2 reads to TAIR10 (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1 --clip3pAdapterSeq GATCGTCGGACT); 3) Sort BAM files (Samtools v1.3.1); 4) Remove PCR duplicates (UMI-Tools dedup); 5) Remove reads aligned to rRNA, tRNA, snRNA or snoRNA loci from Araport11 (BEDTools v2.17.0); 6) Remove reads with MAPQ < 10 (Samtools v1.3.1); 7) Import BAM files into R environment v3.5.1 (GenomicAlignments_1.18.1, GenomicRanges_1.34.0); 8) Flip the strand orientation; 9) Skip all split reads; 10) Skip reads with 3' end overlapping known splice sites (combined from TxDb.Athaliana.BioMart.plantsmart28_3.2.2 and Araport11); 11) Convert reads to genomic coverage (separately for + and - strands); 12) Export as BigWig files (rtracklayer_1.42.2). RNA-Seq: 1) Trim adapters using Trim Galore v0.4.3 (--paired --illumina); 2) Align to TAIR10 using STAR v2.5.2b (--outSAMmultNmax 1 --alignEndsType Local --outSAMtype BAM Unsorted); 3) Sort BAM files and remove reads with MAPQ < 10 using Samtools v1.3.1; 4) Convert BAM files to Bedgraph using BEDtools genomecov v2.26.0 (-bg -split); 5) Convert Bedgraph files to BigWig using kentUtils bedGraphToBigWig v4.
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files show sequencing coverage with single base resolution (no signal smoothing, transformation or normalization were applied). PlaNET-Seq BigWigs are strand-specific, RNA-Seq BigWigs are unstranded.

source_name: Whole seedlings

growth_protocol: Arabidopsis seedlings were grown on plates (1/2 Murashige and Skoog medium, 1% sucrose) with a 16h light/8h dark cycle at 22°C/18°C. Light intensity during day hours was approximately 100 µE m-2 s-1.

extract_protocol:
PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit.
PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2.

value: Whole seedlings

tag: ecotype

value: Columbia (Col-0)

value: 14 day


title: s05_WT_RNAseq_biorep1

description: RNA-Seq of wild type seedlings (replicate 1)

value: Wild type


title: Brainstem, Mutant 1


title: Col-0 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
Col_smRNA_rep3

value: 20-day-old plant


title: s06_WT_RNAseq_biorep2

description: RNA-Seq of wild type seedlings (replicate 2)


title: AZ.2

description:
otu_table.c16.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls


title: Deder2, waterlogged 120h, replicate 1

description:
fpkm.xls
readcount.xls

value: Roots

value: Waterlogging

tag: time point


title: Brainstem, Control 4

value: Mixed 129P2/OlaHsd-C57Bl/6J


title: Patient 1 Pp03p

value: percrete


title: Brainstem, Control 5

value: Brainstem

value: Postnatal day 7


title: AZ.5

description:
otu_table.c19.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls


title: s04_nrpb2-Y732F_plaNETseq_biorep2

description:
library strategy: PlaNET-Seq
Nascent RNA
PlaNET-Seq of mutant seedlings with accelerated transcription speed (replicate 2)

value: 10 day


title: Brainstem, Control 3

value: Batch 1


title: AZ.1

description:
otu_table.c15.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls


title: Brainstem, Control 2


title: Patient 4 Pc07p

description: gene expression in adherent normal placenta tissues.

value: placenta

value: normal


title: s02_WT_plaNETseq_biorep2

description:
library strategy: PlaNET-Seq
Nascent RNA
PlaNET-Seq of wild type seedlings (replicate 2)


title: s03_nrpb2-Y732F_plaNETseq_biorep1

description:
library strategy: PlaNET-Seq
Nascent RNA
PlaNET-Seq of mutant seedlings with accelerated transcription speed (replicate 1)


title: Patient 5 Pc11p


title: s08_nrpb2-Y732F_RNAseq_biorep2

description: RNA-Seq of mutant seedlings with accelerated transcription speed (replicate 2)


title: Patient 2 Pp04p

value: increte


title: Patient 3 Pc05p


title: PBS.4

description:
otu_table.c13.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls

value: wild type

value: PBS


title: Brainstem, Control 1


title: PBS.3

description:
otu_table.c12.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls


title: Era- osteoclast progenitors 2

source_name: Era- osteoclast progenitors

tag: strain background

tag: genotype/variation

value: ERalphaf/f;LysM-Cre

value: bone marrow

tag: cell type

value: osteoclast progenitors


title: Patient 3 Pp05p

tag: age


title: PBS.5

description:
otu_table.c14.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls


title: Male LCWE + Anakinra 4

city: Los Angeles

first: Rebecca

middle: Amelia

last: Porritt

state: CA

address: 8700 Beverly Blvd

department: Pediatrics

institute: Cedars Sinai

data_processing:
Raw sequencing data were demultiplexed and converted to FASTQ format by using bcl2fastq v2.20
Raw reads were uploaded to Bluebee® Genomics Platform for quality control, alignment, and expression quantification using QuantSeq FWD-UMI Data Analysis Pipeline
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³2-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: Mouse reference genome GRCm38
Supplementary_files_format_and_content: tab delimited file includes raw counts for each gene transcript

source_name: Male LCWE + Anakinra

growth_protocol: Abdomial Aorta was harvested from male or female C57BL/6J mice

extract_protocol:
RNA was isolated using the miRNeasy Min Kit (Qiagen) and processed as per manufacturer’s instructions.
Library construction was performed using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: 5 wk. old male and female mice were treated with PBS, LCWE or LCWE + Anakinra for 14 days

tag: background strain

value: wild-type

value: LCWE + Anakinra

value: Abdominal Aorta Tissue

tag: Sex

value: Male


title: Male LCWE + Anakinra 5


title: ein5 dcl4 dcl2 AGO1 IP aerial part_rep2 (AGO1-associated small RNAs)

description:
Only Read1 were used for analysis
AGO1_IP_processed_data
edd_IP_rep2

data_processing:
Read1 were filtered and then mapped to TAIR10 genome using using Bowtie-1.2.2 with following parameters: -v  0  -a  -M  3  --best  --strata
21-nt and 22-nt small RNA read were selected using samtools v1.9
Tags Per Million (TPM) were calculated were called out using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel file includes TPM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons

source_name: ein5 dcl4 dcl2 AGO1 IP

growth_protocol: Plants were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old plant were collected at 15:00.

extract_protocol:
AGO1-associated small RNAs were isolated with AGO1 antibody.
NEBNext® Small RNA Library Prep Set for Illumina

value: aerial part

value: 20-day-old plant

value: ein5 dcl4 dcl2

tag: rip antibody

value: AGO1 antibody (Agrisera, Catalog #AS09527)


title: Patient 2 Pc04p


title: ein5 dcl4 dcl2 AGO1 IP aerial part_rep1 (AGO1-associated small RNAs)

description:
Only Read1 were used for analysis
AGO1_IP_processed_data
edd_IP_rep1


title: s01_WT_plaNETseq_biorep1

description:
library strategy: PlaNET-Seq
Nascent RNA
PlaNET-Seq of wild type seedlings (replicate 1)

value: Whole seedlings

value: Columbia (Col-0)

value: Wild type

value: 10 day


title: PBS.1

description:
otu_table.c10.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls

tag: strain

value: wild type


title: Male LCWE + Anakinra 3


title: Model3 [MX2_3]

city: Beijing

first: Ying

last: Bai

state: Beijing

address: No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing

institute: Beijing University of Chinese Medicine

data_processing:
Real Time Analysis (RTA) v2.3.9 software used for basecalling.
Data filtering used cutadapt1.9 to remove low-quality reads, reads containing polyA/polyT and reads whose length are not 15-34nt.
Data quality assessment was accomplished by FastQC0.10.1
Read alignment software used blast2.2.28+ and Bowtie2.2.4.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPM values for each sample.

extract_protocol:
livers were removed, flash frozen on dry ice, and RNA was harvested using TRIzol reagent (Invitrogen/Life Technologies).
Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol.

treatment_protocol: All mice were fed high-fat diet from beginning, then after 12 weeks,  mice JXTK1, JTXK2, JTXK3 received 8 weeks' treatment with JTXK granule by gavage, while Model1, Model2, Model3 received sterile water.

value: ICR

value: 30 week

value: sterile water

value: liver


title: Model2 [MX2_2]


title: Male LCWE + Anakinra 2

value: wild-type


title: Male LCWE + Anakinra 1

value: LCWE + Anakinra


title: Male LCWE 5

source_name: Male LCWE

value: LCWE

value: Abdominal Aorta Tissue


title: Col-0 AGO1 IP aerial part_rep2 (AGO1-associated small RNAs)

description:
Only Read1 were used for analysis
AGO1_IP_processed_data
Col_IP_rep2

source_name: Col-0 AGO1 IP

value: aerial part


title: Col-0 AGO1 IP aerial part_rep1 (AGO1-associated small RNAs)

description:
Only Read1 were used for analysis
AGO1_IP_processed_data
Col_IP_rep1

value: 20-day-old plant


title: ski2-2 dcl4-2 dcl2-1 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
sdd_mRNA_rep3

data_processing:
Sequence reads were filtered and then mapped to TAIR10 genome using TopHat V2.1.1 with default parameters
Differential expressed genes and Fragment Per Kilobase Per Million (FPKM) were called using cuffdiff program
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons

source_name: ski2-2 dcl4-2 dcl2-1 aerial part

growth_protocol: Plants were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old plant were collected at 15:00 for total RNA extraction.

extract_protocol:
RNAeasy plant mini Kit (Qiagen)
stander Illumina mRNA-seq protocol

value: ski2-2 dcl4-2 dcl2-1


title: Male LCWE 3

value: Male


title: Male LCWE 4


title: Model1 [MX1_3]


title: JTXK2 [GJ2_4]

value: JTXK granule by gavage


title: ein5 dcl4 AGO1 IP aerial part_rep2 (AGO1-associated small RNAs)

description:
Only Read1 were used for analysis
AGO1_IP_processed_data
ed_IP_rep2

source_name: ein5 dcl4 AGO1 IP

value: ein5 dcl4

value: AGO1 antibody (Agrisera, Catalog #AS09527)


title: JTXK1 [GJ2_2]


title: ski2-2 dcl4-2 dcl2-1 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
sdd_mRNA_rep1


title: ski2-2 dcl4-2 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
sd4_mRNA_rep3

source_name: ski2-2 dcl4-2 aerial part

value: ski2-2 dcl4-2


title: Patient 1 Pc03p

value: placenta

value: normal


title: JTXK3 [GJ2_5]

value: ICR

value: 30 week

value: wild type


title: ein5 dcl4 AGO1 IP aerial part_rep1 (AGO1-associated small RNAs)

description:
Only Read1 were used for analysis
AGO1_IP_processed_data
ed_IP_rep1


title: Male PBS 5

source_name: Male PBS

value: wild-type

value: PBS


title: PBS.2

description:
otu_table.c11.relative.tran.xls
pcoa_weighted_unifrac_QUE_otu_table.xls
alpha_otu_table_shannon.xls

source_name: Feces


title: ski2-2 dcl4-2 dcl2-1 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
sdd_mRNA_rep2


title: Male LCWE 2

value: LCWE


title: ski2-2 dcl4-2 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
sd4_mRNA_rep1


title: Male PBS 2

value: Abdominal Aorta Tissue


title: blood, sepsis10

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs. Followed fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the microarray. After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix).

scan_protocol: Scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately.

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs, followed by fragmentation and biotin labeling.

growth_protocol: Mononuclear cells (MNCs) were isolated, and then stored at -80 ℃ before RNA extraction.

extract_protocol: Total RNA was extracted using RNAiso (TaKaRa, Dalian, China).

tag: disease state

value: sepsis

value: blood


title: Male PBS 3


title: blood, sepsis09


title: ski2-2 dcl2-1 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
sd2_mRNA_rep1

source_name: ski2-2 dcl2-1 aerial part

value: aerial part

value: 20-day-old plant

value: ski2-2 dcl2-1


title: ski2-2 dcl2-1 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
sd2_mRNA_rep3


title: Male PBS 4

value: Male


title: Male LCWE 1


title: blood, sepsis07


title: blood, sepsis08


title: blood, sepsis06


title: blood, sepsis05


title: Female LCWE + Anakinra 5

source_name: Female LCWE + Anakinra

value: LCWE + Anakinra

value: Female


title: ski2-2 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
s2_mRNA_rep2

source_name: ski2-2 aerial part


title: Female LCWE + Anakinra 4


title: Female LCWE + Anakinra 3


title: ski2-2 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
s2_mRNA_rep3


title: ski2-2 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
s2_mRNA_rep1


title: ski2-2 dcl2-1 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
sd2_mRNA_rep2


title: 201501980036_R08C01

type: genomic

first: Olivia

last: Okereke

state: MASSACHUSETTS

address: One bowdoin square, room no. 745

institute: Massachusetts General Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadArray technology (Methyl850K chip) using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN Reader using standard recommended Illumina scanner setting

data_processing: Minfi bioconductor package :  ‘noob’ function was used for the background correction using negative control probe signal intensities.

label: Cy5 and Cy3

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood leukocytes (buffy-coat cryotubes had been stored in the vapor phase of liquid nitrogen freezers at ≤−130°C for later use) using the QIAamp® DNA Blood Mini Kit (Qiagen Inc., Valencia, CA), and PicoGreen DNA quantitation was performed using a Molecular Devices 96-well spectrophotometer.

value: peripheral blood leucocytes

tag: gender

tag: disease status

value: psychiatric case

tag: race /ethnicity

value: White


title: Female LCWE + Anakinra 2

tag: treatment


title: 201501980036_R06C01

tag: tissue


title: ein5-1 dcl4-2 dcl2-1 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
edd_mRNA_rep3

source_name: ein5-1 dcl4-2 dcl2-1 aerial part

tag: genotype

value: ein5-1 dcl4-2 dcl2-1


title: 201501980036_R07C01


title: blood, sepsis02


title: Male PBS 1


title: blood, sepsis03


title: Female LCWE + Anakinra 1


title: ski2-2 dcl4-2 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
sd4_mRNA_rep2

value: ski2-2 dcl4-2


title: ein5-1 dcl4-2 dcl2-1 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
edd_mRNA_rep2


title: 201501980023_R06C01

value: healthy control


title: 201501970005_R08C01


title: blood, control12

value: control


title: 201501990024_R05C01

value: Black


title: Female LCWE 3

source_name: Female LCWE

value: wild-type

value: LCWE

value: Abdominal Aorta Tissue


title: blood, sepsis01

value: sepsis

value: blood


title: 201501980036_R05C01


title: Female LCWE 4


title: 201501970005_R06C01


title: ein5-1 dcl2-1 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
ed2_mRNA_rep2

source_name: ein5-1 dcl2-1 aerial part

value: aerial part

value: 20-day-old plant

value: ein5-1 dcl2-1


title: 201501980023_R04C01

value: Female


title: 201501970005_R04C01

value: peripheral blood leucocytes


title: blood, control09


title: Female LCWE 1


title: Female LCWE 2


title: ein5-1 dcl2-1 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
ed2_mRNA_rep3


title: ein5-1 dcl2-1 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
ed2_mRNA_rep1


title: DRG_CCD_7d_rep3

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from Wistar rat with CCD surgery

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on  [Clariom_S_Rat] Affymetrix Clariom S Assay, Rat. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

organism: Rattus norvegicus

source_name: Wistar rat with CCD surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: All rats were housed in a room at least 1 wk  with pathogen-free air at 20 ± 2℃, with two rats to a cage, at a 12-h light/dark cycle. Water and food were available ad libitum.

extract_protocol: Total RNA of rat DRG was extracted and purified with a RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction. The quality and amount of RNA were measured using NanoDrop 2000 (Thermo, USA). mRNA expression profiling was performed using Affymetrix Clariom D Rat array (Affymetrix; Thermo Fisher Scientific, Inc), which contains 46,800 gene-level probe sets.

treatment_protocol: All rats were randomly undertaken sham surgery or CCD surgery. DRG were harvested on the 7th day post-surgery for further analysis.

value: Wistar

value: Male

value: L4 and L5 DRG


title: Female PBS 4

source_name: Female PBS

value: PBS


title: blood, control10


title: DRG_CCD_7d_rep4


title: ein5-1 dcl4-2 dcl2-1 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
edd_mRNA_rep1

value: ein5-1 dcl4-2 dcl2-1


title: blood, sepsis04


title: DRG_CCD_7d_rep2


title: Female PBS 3


title: ein5-1 dcl4-2 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
ed4_mRNA_rep3

source_name: ein5-1 dcl4-2 aerial part

value: ein5-1 dcl4-2


title: 201501980036_R04C01

value: psychiatric case

value: White


title: ein5-1 dcl4-2 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
ed4_mRNA_rep2


title: Female PBS 2

value: wild-type


title: 201501970005_R03C01


title: 201501970005_R05C01

value: healthy control


title: 201501980023_R07C01

value: Black


title: 201501980023_R05C01


title: ein5-1 dcl4-2 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
ed4_mRNA_rep1


title: 201501980036_R03C01


title: Female PBS 1

value: Abdominal Aorta Tissue


title: 201501970005_R02C01


title: blood, control08

value: control

value: blood


title: blood, control11


title: ein5-1 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
e5_mRNA_rep3

source_name: ein5-1 aerial part

value: aerial part

value: 20-day-old plant


title: DRG_sham_7d_rep5

description: Gene expression data from Wistar rat with sham surgery

source_name: Wistar rat with sham surgery


title: blood, control05


title: 201501980023_R03C01

value: peripheral blood leucocytes

value: Female


title: blood, control04


title: ein5-1 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
e5_mRNA_rep1


title: dcl2-1 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
dcl2_mRNA_rep3

source_name: dcl2-1 aerial part


title: ein5-1 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
e5_mRNA_rep2


title: DRG_sham_7d_rep3

value: Wistar

value: Male


title: dcl2-1 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
dcl2_mRNA_rep2


title: NNV infection alive rep3

city: xiamen

first: hui

last: Ge

state: fujian

address: No.361012, haishan road no.7, huli district

institute: Fisheries Research Institute of Fujian

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then use Trinity for assembly  with default parameters
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using RSEM software with  with default parameters .
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Epinephelus coioides

source_name: eye

extract_protocol:
All samples were immediately kept in RNAlater (Ambion, USA) and stored at -80 °C for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: eye

value: post natal day 20

tag: infection

value: NNV infection alive


title: 201501980036_R02C01


title: DRG_sham_7d_rep1

value: L4 and L5 DRG


title: DRG_CCD_7d_rep1


title: Muscle_depleted

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: gastrocnemius, Pdgfra-CreER:R26-DTA

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

extract_protocol: RNA samples were extracted from cells using miRNeasy mini kit (Qiagen).

treatment_protocol: Tamoxifen was injected intraperitoneally at 9 wks of age for 5 consecutive days. Two days after last tamoxifen injection, mice were sacrificed and muscles were rapidly frozen.

value: Gastrocnemius


title: blood, control07


title: blood, control03


title: 201501980023_R02C01

value: White


title: blood, control02


title: NNV infection alive rep1


title: DRG_sham_7d_rep2


title: NNV infection alive rep2


title: dcl4-2 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
dcl4_mRNA_rep3

source_name: dcl4-2 aerial part


title: NNV infection moribund rep3

value: NNV infection moribund


title: N4

city: Qingdao

first: Zhi

last: Ma

address: No.308 Ningxia Rd

institute: Qingdao University

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: The circRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a T-test p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: normal control_cumulus cells

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: indications for ivf-et/icsi

value: Bilateral Salpingectomy

value: cumulus cells


title: dcl2-1 aerial part_rep1 (mRNA)

first: Bosheng

last: Li

address: SUStech Huiyuan #1 406

institute: SUSTC (current, may different with previous institution )

description:
mRNA_processed_data
dcl2_mRNA_rep1


title: dcl4-2 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
dcl4_mRNA_rep2


title: Muscle_control

source_name: gastrocnemius, wild type:R26-DTA

value: Wild type:R26-DTA


title: 201501970005_R01C01

value: healthy control


title: 201501980036_R01C01

value: psychiatric case

value: Black


title: Aged CD31+ or CD45+ cells

description: A 31.45

source_name: CD31+ or CD45+ cells from aged hind limb, freshly sorted

extract_protocol: RNA samples were extracted from cells using RNeasy micro kit (Qiagen).

tag: strain/background

value: CD31+ or CD45+ cells


title: 201501980023_R01C01

value: peripheral blood leucocytes

value: Female


title: DRG_sham_7d_rep4

value: Wistar

value: Male


title: NNV infection moribund rep2

value: eye

value: post natal day 20


title: N6


title: blood, control01

value: control

value: blood


title: N5


title: blood, control06


title: dcl4-2 aerial part_rep1 (mRNA)

description:
mRNA_processed_data
dcl4_mRNA_rep1

value: aerial part

value: 20-day-old plant


title: Control rep3

value: Control


title: Col-0 aerial part_rep3 (mRNA)

description:
mRNA_processed_data
Col_mRNA_rep3

source_name: Col-0 aerial part

value: wild type


title: NNV infection moribund rep1

value: NNV infection moribund


title: N2

value: Male factor

value: cumulus cells


title: Control rep2


title: Col-0 aerial part _rep1 (mRNA)

description:
mRNA_processed_data
Col_mRNA_rep1


title: Control rep1


title: N1

value: Bilateral Salpingectomy


title: Aged PDGFRa+ mesenchymal progenitors

description: A Pα

source_name: PDGFRa+ cells from aged hind limb, freshly sorted

value: PDGFRa+ mesenchymal progenitors


title: Young satellite cells

description: Y SC

source_name: Satellite cells from young hind limb, freshly sorted

value: Young (8-10 wk)

value: Satellite cells


title: Young CD31+ or CD45+ cells

description: Y 31.45

source_name: CD31+ or CD45+ cells from young hind limb, freshly sorted

value: CD31+ or CD45+ cells


title: P6

source_name: PCOS patient_cumulus cells

value: PCOS


title: Young PDGFRa+ mesenchymal progenitors

description: Y Pα

source_name: PDGFRa+ cells from young hind limb, freshly sorted


title: RNA-Seq CD8T IL21 rep2

status: Public on Feb 13 2020

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: pre-activated, IL-21

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.2.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes among different conditions.
Genome_build: mm10

source_name: pre-activated, IL-21

growth_protocol: CD8+ T lymphocytes were isolated using the EasySep Mouse CD8+ T cell isolation kit (STEMCELL #19853) and cultured in RPMI 1640 medium (Thermo 11875093) containing 10% fetal bovine serum (FBS), 1 x Glutamax (Life Technologies #35050-061), 1 mM sodium pyruvate, 0.1% β-mercaptoethanol, and penicillin/streptomycin.

extract_protocol: For RNA-seq, RNA was extracted using the Zymo RNA miniprep kit (Zymo Research), and 500 ng RNA was used for library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were recovered and purified with Zymoclean Gel DNA Recovery Kit (Zymo Research).  After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq3000 system.

treatment_protocol: Cells were plated in 24-well tissue culture plates precoated with mouse anti-CD3 (2 µg/ml) and cultured with soluble mouse anti-CD28 (2 µg/ml) for 48 h. After incubation, cells were pooled, washed twice in media, and re-plated at 1 x 106 cells/ml. Cells were stimulated without cytokine or with 100 IU/ml human IL-2 or 100 ng/ml mouse IL-21. Unless otherwise specified, cells were stimulated for 48 h before being harvested. Where noted, cells were treated (1 µM) with a novel, pyrazole-based LDH inhibitor (NCI-737, herein denoted as LDHi) that was developed under the auspices of the NCI Experimental Therapeutics Program. LDHi was added at the time of anti-CD3 + anti-CD28 treatment and replenished after cells were washed and replated in either IL-2 or IL-21, as indicated.

value: spleen

value: CD8+ T cells


title: RNA-Seq CD8T IL2+LDHi rep2

description: pre-activated, IL-2 + LDHi

source_name: pre-activated, IL-2 + LDHi


title: RNA-Seq CD8T NC rep2

description: pre-activated, no cytokine

source_name: pre-activated, no cytokine


title: RNA-Seq CD8T IL2 rep2

description: pre-activated, IL-2

source_name: pre-activated, IL-2


title: RNA-Seq CD8T IL2+LDHi rep1

description: pre-activated, IL-2 + LDHi


title: RNA-Seq CD8T IL21+LDHi rep1

description: pre-activated, IL-21 + LDHi

source_name: pre-activated, IL-21 + LDHi


title: Col-0 aerial part_rep2 (mRNA)

description:
mRNA_processed_data
Col_mRNA_rep2


title: N3


title: RNA-Seq CD8T IL21 rep1

description: pre-activated, IL-21


title: P5


title: RNA-Seq CD8T NC rep1

description: pre-activated, no cytokine


title: RNA-Seq CD8T IL2 rep1

description: pre-activated, IL-2


title: P4


title: P3


title: LTHSC-TET2-30d_scRRBS_Pool4

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Single cell RRBS (from scRRBs + RNA protocol)

data_processing:
Single cell RNA sequencing data generated with Chromium 10x v2 was processed using Cell Ranger (v2.1.0) with default parameters, and data generated with Chromium v3 was processed using the updated version of Cell Ranger (v3.1). For both chemistry versions, samples were sequenced at an average of 50,000 reads per cell. Raw sequencing data was de-multiplexed and post-processed following the custom pipelines provided by 10x Genomics. Briefly, raw base calls were de-multiplexed into fastq files using the cellranger mkfastq command, followed by alignment to the selected reference mm10 genome for mouse samples or hg19 genome for the human subject data, respectively. Barcode and UMI counting was performed using the cellranger count command with default parameters. Cell barcodes with UMI < 1,000 or mitochondrial gene percentage > 20% were filtered out.
For Drop-seq data, samples were prepared for sequencing using the Illumina Nextera XT kit, and sequenced on a NextSeq 500 (Illumina, San Diego, CA) at an average of 70,000 reads per cell. Libraries with large numbers of cells were divided into technical replicates, which were processed independently. Raw reads were processed and aligned (STAR aligner106) using the standard Drop-seq pipeline, and according to the ‘Drop-seq Alignment Cookbook’, both found at http://mccarrolllab.com/dropseq/.Reads were aligned to the mm10 transcriptome. For each read, a single optimal mapping position was retained. Unique transcripts mapping to alternative splice variants were combined for subsequent analysis. Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). Cells with UMI < 200 or mitochondrial gene percentage > 20% were filtered out.
For the dual protocol experiments, each pool of 96 cells was first demultiplexed by Illumina i7 barcodes, resulting in four pools of 24 cells. Each pool of 24 cells was further demultiplexed by unique cell barcodes. Reads were assigned to a given cell if they matched 80% of the template adapters. Adapters and adapter reverse complements (6 bp) were trimmed from the raw sequence reads. After adapter removal, reads were trimmed from their 3’ end for read quality by applying a 4 bp sliding window and removing bases until the mean base quality of the window had a Phred quality score greater than 15. We aligned trimmed reads in single-end mode to the mm10 mouse genome assembly using Bismark (v.0.14.5; parameters: -multicore 4 -X 1000 --un –ambiguous) running on bowtie2-2.2.8 aligner. Bismark methylation extractor (--bedgraph --comprehensive) was used to determine the methylation state of each individual CpG. For the single cell RNA, the sequenced paired-end read fragments were mapped against the mm10 mouse genome assembly using the 2pass default mode of STAR (version 2.5.2a) with the annotation of GENCODE (version 19). The number of read counts overlapping with annotated genes was quantified applying the ‘GeneCounts’ option in the STAR alignment.
ATAC-Bseq data was aligned to mm10 genome and methylation calling was performed through Bismark (version 0.14.4; parameters: --q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --maxins 500 Option '--directional' specified) running on bowtie2-2.2.8 aligner112. Accessibility peaks for each individual replicate were defined using MACS2 (v2.1.1.2); parameters: -f BAMPE --broad --broad-cutoff 0.1 -m 2 100).
Genome_build: mm10 for Mus musculus samples,  hg19 for Homo sapiens sample.
Supplementary_files_format_and_content: csv; Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). UMItabs contain the UMI count for each specified gene (rows) for each cell (columns). Cell barcodes are provided in the ".CellBarcodes" file for each sample.

source_name: Long-term hematopoietic stem cells from bone marrow

extract_protocol: Bone marrow (BM) cells were isolated into cold phosphate-buffered saline (PBS), without Ca2+ and Mg2+, and supplemented with 2% bovine serum albumin (BSA) to generate single cell suspensions. Red blood cells (RBCs) were removed using ammonium chloride-potassium bicarbonate (ACK) lysis buffer, resuspended in PBS/2% BSA, and filtered through a 40μm cell strainer. Cells were sorted and inmediately underwent the indicated protocol.

treatment_protocol: Recombination was induced by 3 doses of polyinosinic:polycytidylic acid (pIpC; 12mg/kg/day; GE Healthcare) every other day via intra-peritoneal injection.

tag: weeks after recombination

tag: sorting strategy

tag: genotype/variation

value: Mx1-Cre Tet2 fl/fl


title: LTHSC-TET2-30a_scRRBS_Pool1

value: Long-term hematopoietic stem cells from bone marrow


title: LTHSC-TET2-30c_scRRBS_Pool3


title: LTHSC-TET2-30b_scRRBS_Pool2


title: LTHSC_TET2_30_cDN_H8_S92

description: Single cell RNA-seq from Smart-seq (from scRRBs + RNA protocol)


title: LTHSC_TET2_30_cDNA_H7_S91


title: LTHSC_TET2_30_cDNA_H6_S90


title: LTHSC_TET2_30_cDNA_H2_S86


title: LTHSC_TET2_30_cDNA_H3_S87


title: LTHSC_TET2_30_cDNA_H4_S88


title: LTHSC_TET2_30_cDNA_H12_S96


title: LTHSC_TET2_30_cDNA_H11_S95


title: LTHSC_TET2_30_cDNA_H10_S94


title: LTHSC_TET2_30_cDNA_G8_S80


title: LTHSC_TET2_30_cDNA_H9_S93


title: LTHSC_TET2_30_cDNA_G6_S78


title: LTHSC_TET2_30_cDNA_G7_S79


title: LTHSC_TET2_30_cDNA_G3_S75


title: LTHSC_TET2_30_cDNA_G4_S76


title: LTHSC_TET2_30_cDNA_G11_S83


title: LTHSC_TET2_30_cDNA_G5_S77


title: LTHSC_TET2_30_cDNA_G2_S74


title: LTHSC_TET2_30_cDNA_G10_S82


title: LTHSC_TET2_30_cDNA_F9_S69


title: LTHSC_TET2_30_cDNA_F7_S67


title: LTHSC_TET2_30_cDNA_F6_S66


title: Aged satellite cells

description: A SC

source_name: Satellite cells from aged hind limb, freshly sorted

tag: age

tag: cell type


title: LTHSC_TET2_30_cDNA_F8_S68


title: LTHSC_TET2_30_cDNA_F5_S65


title: LTHSC_TET2_30_cDNA_F3_S63


title: LTHSC_TET2_30_cDNA_H1_S85


title: LTHSC_TET2_30_cDNA_G1_S73


title: P1


title: LTHSC_TET2_30_cDNA_F1_S61


title: LTHSC_TET2_30_cDNA_F11_S71


title: LTHSC_TET2_30_cDNA_F12_S72


title: LTHSC_TET2_30_cDNA_E8_S56


title: LTHSC_TET2_30_cDNA_E7_S55


title: LTHSC_TET2_30_cDNA_E6_S54


title: LTHSC_TET2_30_cDNA_E9_S57


title: LTHSC_TET2_30_cDNA_F2_S62


title: LTHSC_TET2_30_cDNA_E5_S53


title: LTHSC_TET2_30_cDNA_E1_S49


title: LTHSC_TET2_30_cDNA_E3_S51


title: LTHSC_TET2_30_cDNA_E2_S50


title: LTHSC_TET2_30_cDNA_E4_S52


title: LTHSC_TET2_30_cDNA_F10_S70


title: LTHSC_TET2_30_cDNA_E12_S60


title: LTHSC_TET2_30_cDNA_E10_S58


title: LTHSC_TET2_30_cDNA_D8_S44


title: LTHSC_TET2_30_cDNA_D9_S45


title: LTHSC_TET2_30_cDNA_F4_S64


title: LTHSC_TET2_30_cDNA_D4_S40


title: LTHSC_TET2_30_cDNA_D6_S42


title: LTHSC_TET2_30_cDNA_D3_S39


title: LTHSC_TET2_30_cDNA_E11_S59


title: LTHSC_TET2_30_cDNA_D1_S37


title: LTHSC_TET2_30_cDNA_D11_S47


title: LTHSC_TET2_30_cDNA_D5_S41


title: LTHSC_TET2_30_cDNA_D2_S38


title: LTHSC_TET2_30_cDNA_C9_S33


title: LTHSC_TET2_30_cDNA_C5_S29


title: UCH7_Methylation

city: London

first: Adrienne

middle: M

last: Flanagan

state: Middlesex

address: Huntley Street

country: United Kingdom

institute: University College London

description: Chordoma cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC using standard Illumina protocol

scan_protocol: Arrays were imaged using NextSeq 550 using standard recommended Illumina scanner setting

data_processing: BeadStudio software

source_name: Chordoma cell line

growth_protocol: Cells were grown according to ATCC protocol.

extract_protocol: Genomic DNA was extracted and purified from cell lines using Qiagen DNeasy Kit according to standard instructions

tag: tumour anatomical location

value: Sacrum

value: Chordoma cell line

tag: cell line


title: LTHSC_TET2_30_cDNA_C8_S32


title: MUG_Methylation

description: Chordoma cell line

value: MUG


title: UMChor_Methylation

description: Chordoma cell line

value: Clivus

value: UMChor


title: U2OS_Methylation

description: Osteosarcoma cell line

source_name: Osteosarcoma cell line

value: Tibia

value: Osteosarcoma cell line


title: LTHSC_TET2_30_cDNA_C4_S28


title: LTHSC_TET2_30_cDNA_D12_S48


title: LTHSC_TET2_30_cDNA_C6_S30


title: LTHSC_TET2_30_cDNA_D7_S43


title: UCH1_Methylation

description: Chordoma cell line


title: LTHSC_TET2_30_cDNA_C2_S26


title: LTHSC_TET2_30_cDNA_C7_S31


title: LTHSC_TET2_30_cDNA_D10_S46


title: LTHSC_TET2_30_cDNA_C3_S27


title: LTHSC_TET2_30_cDNA_C11_S35


title: LTHSC_TET2_30_cDNA_C12_S36


title: LTHSC_TET2_30_cDNA_C10_S34


title: LTHSC_TET2_30_cDNA_B8_S20


title: LTHSC_TET2_30_cDNA_B9_S21


title: LTHSC_TET2_30_cDNA_B5_S17


title: LTHSC_TET2_30_cDNA_B2_S14


title: LTHSC_TET2_30_cDNA_B3_S15


title: LTHSC_TET2_30_cDNA_B11_S23


title: LTHSC_TET2_30_cDNA_A9_S9


title: LTHSC_TET2_30_cDNA_B6_S18


title: LTHSC_TET2_30_cDNA_B4_S16


title: LTHSC_TET2_30_cDNA_A8_S8


title: LTHSC_TET2_30_cDNA_B10_S22


title: LTHSC_TET2_30_cDNA_B12_S24


title: LTHSC_TET2_30_cDNA_B1_S13


title: LTHSC_TET2_30_cDNA_A7_S7


title: LTHSC_TET2_30_cDNA_A2_S2


title: LTHSC_TET2_30_cDNA_G12_S84


title: LTHSC_TET2_30_cDNA_A3_S3


title: LTHSC_TET2_30_cDNA_A5_S5


title: LTHSC_TET2_30_cDNA_A6_S6


title: LTHSC_TET2_30_cDNA_A4_S4


title: LTHSC_TET2_30_cDNA_A1_S1


title: LTHSC_TET2_30_cDNA_G9_S81


title: LTHSC_TET2_30_cDNA_B7_S19


title: RNA-Seq CD8T IL21+LDHi rep2

description: pre-activated, IL-21 + LDHi

tag: strain


title: LTHSC_TET2_30_cDNA_C1_S25


title: LTHSC_TET2_30_cDNA_A12_S12


title: LTHSC-WT-846-scRRBS_Pool4_S4


title: LTHSC_TET2_30_cDNA_A10_S10


title: LTHSC-WT-846-scRRBS_Pool3_S3


title: LTHSC-WT-846-scRRBS_Pool2_S2


title: LTHSC-WT-846-scRRBS_Pool1_S1


title: P2

value: cumulus cells


title: LTHSC_WT_846_cDNA_H7_S91


title: LTHSC_WT_846_cDNA_H6_S90


title: LTHSC_WT_846_cDNA_H3_S87


title: LTHSC_WT_846_cDNA_H5_S89


title: LTHSC_WT_846_cDNA_H9_S93


title: LTHSC_TET2_30_cDNA_H5_S89


title: LTHSC_WT_846_cDNA_H4_S88


title: LTHSC_WT_846_cDNA_H2_S86


title: LTHSC_WT_846_cDNA_H8_S92


title: LTHSC_WT_846_cDNA_H1_S85


title: LTHSC_WT_846_cDNA_H12_S96


title: LTHSC_WT_846_cDNA_H10_S94


title: LTHSC_WT_846_cDNA_H11_S95


title: LTHSC_WT_846_cDNA_G6_S78


title: LTHSC_WT_846_cDNA_G8_S80


title: LTHSC_WT_846_cDNA_G9_S81


title: LTHSC_WT_846_cDNA_G7_S79


title: LTHSC_WT_846_cDNA_G5_S77


title: LTHSC_WT_846_cDNA_G4_S76


title: LTHSC_WT_846_cDNA_G2_S74


title: LTHSC_WT_846_cDNA_G12_S84


title: LTHSC_WT_846_cDNA_G3_S75


title: LTHSC_WT_846_cDNA_G1_S73


title: LTHSC_WT_846_cDNA_G10_S82


title: LTHSC_WT_846_cDNA_F8_S68


title: LTHSC_WT_846_cDNA_F7_S67


title: LTHSC_WT_846_cDNA_F9_S69


title: LTHSC_WT_846_cDNA_F5_S65


title: LTHSC_WT_846_cDNA_F1_S61


title: LTHSC_WT_846_cDNA_F6_S66


title: LTHSC_WT_846_cDNA_F12_S72


title: LTHSC_WT_846_cDNA_F2_S62


title: LTHSC_WT_846_cDNA_F10_S70


title: LTHSC_WT_846_cDNA_F3_S63


title: LTHSC_WT_846_cDNA_F4_S64


title: LTHSC_WT_846_cDNA_E8_S56


title: LTHSC_WT_846_cDNA_E2_S50


title: LTHSC_WT_846_cDNA_E4_S52


title: LTHSC_WT_846_cDNA_E1_S49


title: LTHSC_WT_846_cDNA_E5_S53


title: LTHSC_WT_846_cDNA_F11_S71


title: LTHSC_WT_846_cDNA_E9_S57


title: LTHSC_WT_846_cDNA_E3_S51


title: LTHSC_WT_846_cDNA_E12_S60


title: LTHSC_WT_846_cDNA_E7_S55


title: LTHSC_WT_846_cDNA_E11_S59


title: LTHSC_WT_846_cDNA_E6_S54


title: LTHSC_WT_846_cDNA_D9_S45


title: LTHSC_WT_846_cDNA_D8_S44


title: LTHSC_WT_846_cDNA_D7_S43


title: LTHSC_WT_846_cDNA_D6_S42


title: LTHSC_WT_846_cDNA_G11_S83


title: LTHSC_WT_846_cDNA_E10_S58


title: LTHSC_TET2_30_cDNA_A11_S11


title: LTHSC_WT_846_cDNA_D4_S40


title: LTHSC_WT_846_cDNA_D3_S39


title: LTHSC_WT_846_cDNA_D2_S38


title: LTHSC_WT_846_cDNA_D1_S37


title: LTHSC_WT_846_cDNA_D12_S48


title: LTHSC_WT_846_cDNA_D11_S47


title: LTHSC_WT_846_cDNA_D10_S46


title: LTHSC_WT_846_cDNA_C7_S31


title: LTHSC_WT_846_cDNA_C5_S29


title: LTHSC_WT_846_cDNA_C4_S28


title: LTHSC_WT_846_cDNA_C8_S32


title: LTHSC_WT_846_cDNA_C2_S26


title: LTHSC_WT_846_cDNA_C1_S25


title: LTHSC_WT_846_cDNA_C12_S36


title: LTHSC_WT_846_cDNA_C11_S35


title: LTHSC_WT_846_cDNA_B9_S21


title: LTHSC_WT_846_cDNA_B7_S19


title: LTHSC_WT_846_cDNA_C10_S34


title: LTHSC_WT_846_cDNA_C6_S30


title: LTHSC_WT_846_cDNA_B8_S20


title: LTHSC_WT_846_cDNA_B1_S13


title: LTHSC_WT_846_cDNA_B5_S17


title: LTHSC_WT_846_cDNA_B4_S16


title: LTHSC_WT_846_cDNA_D5_S41


title: LTHSC_WT_846_cDNA_B3_S15


title: LTHSC_WT_846_cDNA_B12_S24


title: LTHSC_WT_846_cDNA_B10_S22


title: LTHSC_WT_846_cDNA_C9_S33


title: LTHSC_WT_846_cDNA_A9_S9


title: LTHSC_WT_846_cDNA_A7_S7


title: LTHSC_WT_846_cDNA_A5_S5


title: LTHSC_WT_846_cDNA_A6_S6


title: LTHSC_WT_846_cDNA_C3_S27


title: LTHSC_WT_846_cDNA_B2_S14


title: LTHSC_WT_846_cDNA_A4_S4


title: LTHSC_WT_846_cDNA_A3_S3


title: LTHSC_WT_846_cDNA_A12_S12


title: LTHSC_WT_846_cDNA_A11_S11


title: LTHSC_WT_846_cDNA_B6_S18


title: LTHSC_WT_846_cDNA_A2_S2


title: LTHSC_WT_846_cDNA_A10_S10


title: LTHSC-DNMT3A_675_scRRBS_Pool3

value: Mx1-Cre Dnmt3a fl/fl


title: LTHSC-DNMT3A_675_scRRBS_Pool2


title: LTHSC-DNMT3A_675_scRRBS_Pool1


title: LTHSC-DNMT3A_675_H7_S91


title: LTHSC-DNMT3A_675_H9_S93


title: LTHSC-DNMT3A_675_H6_S90


title: LTHSC-DNMT3A_675_H4_S88


title: LTHSC-DNMT3A_675_H5_S89


title: LTHSC-DNMT3A_675_H3_S87


title: LTHSC_WT_846_cDNA_A8_S8


title: LTHSC-DNMT3A_675_H2_S86


title: LTHSC-DNMT3A_675_H1_S85


title: LTHSC-DNMT3A_675_H12_S96


title: LTHSC-DNMT3A_675_H11_S95


title: LTHSC-DNMT3A_675_H10_S94


title: LTHSC_WT_846_cDNA_A1_S1


title: LTHSC-DNMT3A_675_G7_S79


title: LTHSC-DNMT3A_675_G9_S81


title: LTHSC-DNMT3A_675_G8_S80


title: LTHSC-DNMT3A_675_scRRBS_Pool4


title: LTHSC-DNMT3A_675_G6_S78


title: LTHSC-DNMT3A_675_G5_S77


title: LTHSC-DNMT3A_675_G2_S74


title: LTHSC-DNMT3A_675_G1_S73


title: LTHSC-DNMT3A_675_G4_S76


title: LTHSC-DNMT3A_675_H8_S92


title: LTHSC-DNMT3A_675_G11_S83


title: LTHSC-DNMT3A_675_G10_S82


title: LTHSC-DNMT3A_675_F9_S69


title: LTHSC-DNMT3A_675_G3_S75


title: LTHSC-DNMT3A_675_G12_S84


title: LTHSC-DNMT3A_675_F8_S68


title: LTHSC-DNMT3A_675_F7_S67


title: LTHSC-DNMT3A_675_F4_S64


title: LTHSC-DNMT3A_675_F5_S65


title: LTHSC-DNMT3A_675_F1_S61


title: LTHSC-DNMT3A_675_F3_S63


title: LTHSC-DNMT3A_675_F12_S72


title: LTHSC-DNMT3A_675_F11_S71


title: LTHSC-DNMT3A_675_E9_S57


title: LTHSC-DNMT3A_675_F10_S70


title: LTHSC-DNMT3A_675_E7_S55


title: LTHSC-DNMT3A_675_E2_S50


title: LTHSC-DNMT3A_675_E12_S60


title: LTHSC-DNMT3A_675_E4_S52


title: LTHSC-DNMT3A_675_E6_S54


title: LTHSC-DNMT3A_675_E11_S59


title: LTHSC-DNMT3A_675_E10_S58


title: LTHSC-DNMT3A_675_F6_S66


title: LTHSC-DNMT3A_675_E3_S51


title: LTHSC-DNMT3A_675_E1_S49


title: LTHSC-DNMT3A_675_D5_S41


title: LTHSC-DNMT3A_675_D9_S45


title: LTHSC-DNMT3A_675_D6_S42


title: LTHSC-DNMT3A_675_D3_S39


title: LTHSC-DNMT3A_675_D7_S43


title: LTHSC-DNMT3A_675_D8_S44


title: LTHSC-DNMT3A_675_D1_S37


title: LTHSC-DNMT3A_675_D4_S40


title: LTHSC-DNMT3A_675_D12_S48


title: LTHSC-DNMT3A_675_F2_S62


title: LTHSC-DNMT3A_675_C9_S33


title: LTHSC-DNMT3A_675_D10_S46


title: LTHSC-DNMT3A_675_E8_S56


title: LTHSC-DNMT3A_675_C8_S32


title: LTHSC-DNMT3A_675_D11_S47


title: LTHSC-DNMT3A_675_C7_S31


title: LTHSC-DNMT3A_675_C6_S30


title: LTHSC-DNMT3A_675_E5_S53


title: LTHSC-DNMT3A_675_C5_S29


title: LTHSC-DNMT3A_675_C4_S28


title: LTHSC-DNMT3A_675_C12_S36


title: LTHSC-DNMT3A_675_C1_S25


title: LTHSC-DNMT3A_675_C2_S26


title: LTHSC-DNMT3A_675_C11_S35


title: LTHSC-DNMT3A_675_C3_S27


title: LTHSC-DNMT3A_675_C10_S34


title: LTHSC-DNMT3A_675_B9_S21


title: LTHSC-DNMT3A_675_D2_S38


title: LTHSC-DNMT3A_675_B6_S18


title: LTHSC-DNMT3A_675_B2_S14


title: LTHSC-DNMT3A_675_B5_S17


title: LTHSC-DNMT3A_675_B4_S16


title: LTHSC-DNMT3A_675_B8_S20


title: LTHSC-DNMT3A_675_B1_S13


title: LTHSC-DNMT3A_675_B11_S23


title: LTHSC-DNMT3A_675_B3_S15


title: LTHSC-DNMT3A_675_B7_S19


title: LTHSC-DNMT3A_675_B12_S24


title: LTHSC-DNMT3A_675_B10_S22


title: LTHSC_WT_846_cDNA_B11_S23


title: LTHSC-DNMT3A_675_A8_S8


title: LTHSC-DNMT3A_675_A7_S7


title: LTHSC-DNMT3A_675_A5_S5


title: LTHSC-DNMT3A_675_A6_S6


title: LTHSC-DNMT3A_675_A2_S2


title: LTHSC-DNMT3A_675_A3_S3


title: LTHSC-DNMT3A_675_A1_S1


title: LTHSC-DNMT3A_675_A12_S12


title: LTHSC_TET272_scRRBS_Pool3


title: LTHSC-DNMT3A_675_A11_S11


title: LTHSC-DNMT3A_675_A10_S10


title: LTHSC_TET272_scRRBS_Pool2


title: LTHSC_TET272_scRRBS_Pool1


title: LTHSC_TET2_272_H9_S93


title: LTHSC_TET2_272_H8_S92


title: LTHSC-DNMT3A_675_A9_S9


title: LTHSC-DNMT3A_675_A4_S4


title: LTHSC_TET2_272_H5_S89


title: LTHSC_TET2_272_H2_S86


title: LTHSC_TET2_272_H1_S85


title: LTHSC_TET2_272_H7_S91


title: LTHSC_TET2_272_H3_S87


title: LTHSC_TET2_272_H12_S96


title: LTHSC_TET2_272_H11_S95


title: LTHSC_TET2_272_G7_S79


title: LTHSC_TET2_272_G6_S78


title: LTHSC_TET2_272_G9_S81


title: LTHSC_TET2_272_G4_S76


title: LTHSC_TET2_272_G5_S77


title: LTHSC_TET2_272_G3_S75


title: LTHSC_TET2_272_G2_S74


title: LTHSC_TET272_scRRBS_Pool4


title: LTHSC_TET2_272_G10_S82


title: LTHSC_TET2_272_G12_S84


title: LTHSC_TET2_272_G1_S73


title: LTHSC_TET2_272_G11_S83


title: LTHSC_TET2_272_H4_S88


title: LTHSC_TET2_272_H6_S90


title: LTHSC_TET2_272_H10_S94


title: LTHSC_TET2_272_F6_S66


title: LTHSC_TET2_272_F5_S65


title: LTHSC_TET2_272_F9_S69


title: LTHSC_TET2_272_F7_S67


title: LTHSC_TET2_272_F4_S64


title: LTHSC_TET2_272_G8_S80


title: LTHSC_TET2_272_F3_S63


title: LTHSC_TET2_272_F2_S62


title: LTHSC_TET2_272_F10_S70


title: LTHSC_TET2_272_F11_S71


title: LTHSC_TET2_272_E8_S56


title: LTHSC_TET2_272_F12_S72


title: LTHSC_TET2_272_F1_S61


title: LTHSC_TET2_272_E7_S55


title: LTHSC_TET2_272_E5_S53


title: LTHSC_TET2_272_E6_S54


title: LTHSC_TET2_272_F8_S68


title: LTHSC_TET2_272_E4_S52


title: LTHSC_TET2_272_E3_S51


title: LTHSC_TET2_272_E2_S50


title: LTHSC_TET2_272_E1_S49


title: LTHSC_TET2_272_E9_S57


title: LTHSC_TET2_272_E11_S59


title: LTHSC_TET2_272_E12_S60


title: LTHSC_TET2_272_E10_S58


title: LTHSC_TET2_272_D7_S43


title: LTHSC_TET2_272_D9_S45


title: LTHSC_TET2_272_D8_S44


title: LTHSC_TET2_272_D6_S42


title: Blastocyst embryos Library 1

city: Utrecht

first: Maya

last: Sen

address: 8 Uppsalalaan

country: Netherlands

institute: Hubrecht Institute

data_processing:
Library strategy: scMspJ1-seq
Fastq files are parsed for library barcodes. Read 1 was mapped to the mm10 or hg19 build using the Bowtie2, filtered for unique mapping full-length reads and demultiplexed. 5mCG positions are obtained from the sequencing data using custom scripts in R and Perl identifying CG dinucleotides in the mm10 or hg19 genome at the expected distance from the mapped read position. Finally, all PCR duplicates are removed. Computer codes will be made available upon request.
Hairpin bisulfite sequencing was performed on bulk mouse embryos samples ( 2-cell to 64 cell stage). The bulk embryos were treated with protease treatment (1 uL of 25 ug/uL Qiagen Protease, 1 uL of 10X NEB Buffer 4, and 8 uL of nuclease free water). Then, 0.5 ng of genomic DNA was digested with 20 mL of MspI master mix (1 uL of MspI R0104L, 2 mL 10X NEB Cutsmart buffer in a total volume of 20 uL) and incubated at 37 C for an hour. After digestion, the digested genomic DNA was ligated with 1 uL of 10 uM phosphorylated hairpin oligo and ligation master mix (1 mL of NEB T4 ligase M0202M, 1 uL of 10X NEB T4 Ligase buffer, 2 uL of 10mM ATP, 5 uL of nuclease free water) and incubated overnight at 16 C. For purification of the ligation mixture, we used Dynabeads? M-280 Streptavidin and followed the recommended protocol with the following exceptions: the bead-ligation mixture was incubated for at least an hour at RT on a rotator and cold 10 mM Tris-HCl wash step was included. Subsequently, we performed BS-seq on the sample using the protocol Clark, et al. 2017. After sequencing the libraries on a Miseq 300x300 or NextSeq 75x75 pair-end kit, we used HBS-tools (Sun, MA et al. 2015) and custom perl scripts were used to analyze the methylated CpG dyads. Hairpin oligo (G/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/GG/iMe-dC/AAG/iBiodT/GAAG/iMe-dC/iMe-dC/G/iMe-dC/iMe-dC/GG/iMe-dC/G) was resuspended in 100 uM of Low-TE. The hairpin oligo was phosphorylated (1 uL of 100 uM hairpin oligo, 3 uL of 10X T4 Ligase Buffer, 1 uL T4 PNK and 5 uL of nuclease free water) and incubated at 37 C for an hour. Subsequently the phosphorylated oligo heated at 94 C and placed in ice water to generate the loop.
Published scNMT libraries (GSE109262) analyzed for the bisulfite results were processed as described previously. The first nine bases of the raw reads were trimmed using Trim Galore (v0.5.0) and mapped using Bismark to the mouse genome (mm10) with the 129/CAST background. SNPs specific to 129/CAST mouse genome were prepared using SNPsplit (v0.3.2) and a list of known variant call files from the Mouse Genomes Project (http://www.sanger.ac.uk/resources/mouse/genomes/). After mapping with Bismark, duplicate sequences were removed and CpG methylation calls were extracted with strand-specific information. Further data analysis and visualization of the methylation calls used custom scripts that will be made available upon request.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: mText files with 4 columns: Single Cell ID, chromosome, coordinate, strand, CNNR motif and strain [mouse only])

source_name: Embryos

growth_protocol: Cast/B6 mouse embryos were obtained from four 3-month-old superovulated B6 mothers (injected with pregnant mare serum gonadotropin (PMSG) and human chorionic gonadotropin (HCG) 22 h later) and incubated in M16 medium at 37°C and 5% CO2.

extract_protocol:
Cells were isolated using hyaluronic acid (Sigma) and trypsin (Life Technologies) and manually deposited into 384-well 10 plates containing lysis buffer and Vapor-lock.
Single cells were incubated at 50C for 15 hours, 75C for 20 minutes and 80C for 5 minutes. Glucosylation of 5hmC sites followed by dispensing 0.1 L of T4-BGT (NEB), 0.1 L of UDP-Glucose (NEB), 0.05 L of 10X NEB Buffer 4 and 0.25 L of nuclease-free water (final vol 0.5mL). After incubation at 37C for 16 hours, 0.5 L of the following reaction mixture is added: 0.1L of 25g/L Qiagen Protease, 0.05L of 10X NEB Buffer 4 and 0.35 L of nuclease-free water. The plate is then incubated at 50 o C for 5 hours, 75 o C for 20 minutes and 80 o C for 5 minutes. Thereafter, gDNA is digested by the restriction enzyme MspJI by the addition of 0.5 L of the following reaction mixture: 0.02 L of MspJI (NEB), 0.12 L of 30X enzyme activator solution (NEB), 0.05 L of 10X NEB Buffer 4 and 0.31 L of nuclease-free water. The digestion is performed at 37 o C for 5 hours followed by heat inactivation of MspJI at 65 o C for 20 minutes. Next, 0.2 L of cell-specific double-stranded adaptors are added to individual wells and these adapters are ligated to the fragmented gDNA molecules by adding 0.8 L of the following reaction mixture: 0.07 L of T4 DNA ligase (NEB), 0.1 L of T4 DNA ligase buffer (NEB), 0.3 L of 10 mM ATP (NEB) and 0.33 L of nuclease-free water. The ligation is performed at 16 o C for 16 hours. Next, wells containing unique cell-specific adapters are pooled using a multichannel pipette and incubated with 0.8X Agencourt Ampure (Beckman Coulter) beads for 30 minutes, washed twice with 80% ethanol and resuspended in 6.4 L of nuclease-free water. In vitro transcription and Illumina library preparation is performed as described previously in the scAba-seq protocol.

tag: developmental stage

value: Blastocyst embryos


title: Blastocyst embryos Library 3

extract_protocol:
Embryos were picked manually and deposited into a 0.5 mL eppendorf with lysis buffer and Vapor-lock.
Single cells were incubated at 50C for 15 hours, 75C for 20 minutes and 80C for 5 minutes. Glucosylation of 5hmC sites followed by dispensing 0.1 L of T4-BGT (NEB), 0.1 L of UDP-Glucose (NEB), 0.05 L of 10X NEB Buffer 4 and 0.25 L of nuclease-free water (final vol 0.5mL). After incubation at 37C for 16 hours, 0.5 L of the following reaction mixture is added: 0.1L of 25g/L Qiagen Protease, 0.05L of 10X NEB Buffer 4 and 0.35 L of nuclease-free water. The plate is then incubated at 50 o C for 5 hours, 75 o C for 20 minutes and 80 o C for 5 minutes. Thereafter, gDNA is digested by the restriction enzyme MspJI by the addition of 0.5 L of the following reaction mixture: 0.02 L of MspJI (NEB), 0.12 L of 30X enzyme activator solution (NEB), 0.05 L of 10X NEB Buffer 4 and 0.31 L of nuclease-free water. The digestion is performed at 37 o C for 5 hours followed by heat inactivation of MspJI at 65 o C for 20 minutes. Next, 0.2 L of cell-specific double-stranded adaptors are added to individual wells and these adapters are ligated to the fragmented gDNA molecules by adding 0.8 L of the following reaction mixture: 0.07 L of T4 DNA ligase (NEB), 0.1 L of T4 DNA ligase buffer (NEB), 0.3 L of 10 mM ATP (NEB) and 0.33 L of nuclease-free water. The ligation is performed at 16 o C for 16 hours. Next, wells containing unique cell-specific adapters are pooled using a multichannel pipette and incubated with 0.8X Agencourt Ampure (Beckman Coulter) beads for 30 minutes, washed twice with 80% ethanol and resuspended in 6.4 L of nuclease-free water. In vitro transcription and Illumina library preparation is performed as described previously in the scAba-seq protocol.


title: LTHSC_TET2_272_D5_S41


title: LTHSC_TET2_272_D3_S39


title: Colorectal cancer lymph node no3

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

hyb_protocol: cRNA hybridized on Sentrix HumanRef-8_V2streptavidin-Cy3

scan_protocol: Illumina Beadstation GX

data_processing: Illumina Beadstudio software version 3.3

source_name: Lymph node

label_protocol: Illumina Totalprep RNA Amplification Kit

extract_protocol: Acid guanidine-phenol-cholorform method according to Chomczynski P and Sacchi N (Nat Protoc. 2006: 1, 581–585).

tag: disease state

value: stage III


title: LTHSC_TET2_272_D4_S40


title: Normal colon no2

source_name: Normal colon

value: normal colon


title: Colorectal cancer primary tumor no2

source_name: Primary tumor


title: Control lymph node no4

value: Crohn's disease


title: Normal colon no1


title: Colorectal cancer primary tumor no1


title: Control lymph node no3

value: ulcerative colitis


title: Normal colon no3


title: Colorectal cancer primary tumor no3


title: Control lymph node no2_2

value: lipoma


title: LTHSC_TET2_272_D2_S38

value: Mx1-Cre Tet2 fl/fl


title: Colorectal cancer lymph node no4


title: Blastocyst embryos Library 2


title: Morula and blastocyst embryos - Library 1

value: Morula and blastocyst embyos


title: Morula and blastocyst embryos - Library 2


title: Control lymph node no2


title: Control lymph node no1 UC


title: Colorectal cancer lymph node no2


title: LTHSC_TET2_272_D1_S37

value: Long-term hematopoietic stem cells from bone marrow


title: LTHSC_TET2_272_D11_S47


title: LTHSC_TET2_272_D10_S46


title: 16-cell and morula embryos - Library 1

value: 16-cell and morula embryos


title: 4-cell embryos - Library 2

value: 4-cell embryos


title: LTHSC_TET2_272_C9_S33


title: Colorectal cancer lymph node no1_2


title: LTHSC_TET2_272_C7_S31


title: LTHSC_TET2_272_C8_S32


title: LTHSC_TET2_272_C6_S30


title: 24h UCB_sEV treatment_A [4_EV_1]

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description:
4_EV_1.FCC66DFACXX_L3_R*_IGATCAG
CD34+ Hematopoietic stem and progenitor cells from donor A at t=24hr with addition of sEV

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: CD34+ UC-HSPCs_24hs_EV treatment

growth_protocol: UCB was collected in Erasmus University Medical Center using Stemcare®/CB collection blood bag system (Fresenius Kabi Norge AS. Halden. Norway). Within 48 hours after collection, mononuclear cells were isolated using ficoll (Lymphoprep™, Fresenius Kabi Norge AS). CD34+ cells and viable DAPI-Lin-CD34+CD38lowCD45RAlowCD90+ cells were isolated. CD34+ cells and CD34+CD90+ cells were cultured in either serum-free Cellgenix GMP SCGM (Cellgenix, Freiburg, Germany) or Glycostem Basic Growth Medium (Glycostem, Oss, the Netherlands) supplemented with SCF (50 ng/ mL, Cellgenix) and Flt3L (50 ng/ mL, Cellgenix) at 37°C in a humidified atmosphere of 5% CO2. Cells were refreshed every 2-3 days.

extract_protocol:
RNA from CD34+ UC-HSPCs was isolated using NucleoSpin RNA XS kit (Macherey-Nagel, Duren, Germany)
mRNA version 2 library prep kit (Illumina)

treatment_protocol: UCB were treatemed with or without EVs isolated from 20 mL conditioned medium (from svHFOs) by low speed centrifugation (1500 rpm, 5 minutes; 4500 rpm, 10 minutes) followed by ultracentrifugation (20,000g, 30 minutes; 100,000g, 1 hour at 4°C) of the supernatant using the SW32Ti rotor (Beckman Coulter, Fullerton, CA, USA).

value: Umbillical cord blood (UCB)

value: extracellular vesicles (EVs)

value: CD34+ Hematopoietic stem and progenitor cells (CD34+ UC-HSPCs)


title: 24h UCB_Control_B [5_Control_2]

description:
5_Control_2.FCC66DFACXX_L3_R*_ITAGCTT
CD34+ Hematopoietic stem and progenitor cells from donor B at t=24hr without addition of sEV

source_name: CD34+ UC-HSPCs_24h Control


title: 24h UCB_sEV treatment_B [6_EV_2]

description:
6_EV_2.FCC66DFACXX_L3_R*_IGGCTAC
CD34+ Hematopoietic stem and progenitor cells from donor B at t=24hr with addition of sEV


title: 4-cell embryos - Library 1


title: 2-cell embryos - Library 1

value: 2-cell embryos


title: LTHSC_TET2_272_C2_S26


title: LTHSC_TET2_272_D12_S48


title: LTHSC_TET2_272_C5_S29


title: LTHSC_TET2_272_C4_S28


title: LTHSC_TET2_272_C3_S27


title: LTHSC_TET2_272_C12_S36


title: 0h UCB_B [2_0h_1B]

description:
2_0h_1B.FCC66DFACXX_L3_R*_ITTAGGC
CD34+ Hematopoietic stem and progenitor cells from donor B at t=0

source_name: CD34+ UC-HSPCs_0h


title: LTHSC_TET2_272_C1_S25