title: D40NP: NP of patient D40

city: Pok Fu Lam

first: Peikai

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: The sample was then hybridized onto the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array

scan_protocol: The array was probed and stained with biotinylated anti-streptavidin antibody and streptavidin phycoerythrin, respectively. It was scanned by a 7G scanner

data_processing: The array image, CEL file and other related files were generated using Affymetrix GeneChip Command Console. The experiment was conducted as a service at the Centre for PanorOmic Sciences of the University of Hong Kong. CEL and other files were loaded into GeneSpring GX 10 (Agilent) software. The RMA algorithm was used for probe summation. Data were normalized with baseline transformed to median of all samples. Data quality was assessed by correlation and pair-wise comparison of log2 gene expression ratios for all the arrays. A loose filtering based on the raw intensity values was then applied to remove background noise.

source_name: NP of patient D40

label_protocol: Briefly, first cycle cDNA was synthesized from sample RNA using T7-oligo(dT) primer. In vitro transcription on the first cycle cDNA generated antisense RNA (cRNA). In the second cycle, first strand cDNA was synthesized from cRNA using random primers, followed by synthesis of second strand cDNA using T7-oligo(dT) primer. A final cleanup step purified the double-stranded cDNA. In vitro transcription was performed to produce biotin-labled cRNA

growth_protocol: AF and NP tissues were cut into approximately 0.5 cm3 pieces, and put into the Dulbecco's modified Eagle's medium (DMEM) (Gibco) supplemented with 20 mM HEPES (USB), 1% penicillin-streptomycin (Gibco) and 0.4% fungizone (Gibco).

extract_protocol: RNA was extracted from the isolated disc cells using Absolutely RNA Nanoprep Kit (Stratagene), following manufacturer’s protocol. Briefly, a mixture of lysis buffer and 0.1 M β-mercaptoethanol was prepared fresh, and 100 µl of the lysis mixture was added to each sample. An equal volume of RNase-free 70% ethanol was then added to the cell lysate and mixed thoroughly. The mixture was transferred to an RNA-binding nano-spin cup and centrifuged at 12,000 g for 60 sec, followed by washing with 300 µl low-salt wash buffer. DNase I (20 U) was then added and incubated at 37°C for 15 min to remove any contaminating DNA. The sample was washed once with high-salt wash buffer and twice with low-salt wash buffer, each using a 300 µl volume. 10 µl elution buffer which was pre-heated at 60°C was added to the sample and incubated at room temperature for 2 min. RNA was eluted by centrifuging at 12,000 g for 5 min, and stored at -80°C until further processing.

treatment_protocol: The tissues were digested with 0.2% pronase (Roche) for 1 hour, and centrifuged at 200 g for 5 min to remove supernatant. AF and NP were then digested by 0.1% type II collagenase (Worthington Biochemical) for 14 hours and 0.05% type II collagenase for 8 hours, respectively. Cell suspension was filtered through a 70 µm cell strainer (BD Falcon) and centrifuged at 200 g for 5 min. The cell pellet was washed with phosphate buffered saline (PBS) and centrifuged again to remove supernatant.

tag: age

tag: gender

value: female

tag: organ

value: intervertebral disc

value: nucleus pulposus

tag: tissue type

value: degenerated


title: Hepatocytes, ParaDMSO 14hr Rep4

status: Public on Jun 30 2020

type: SRA

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

country: USA

institute: SBP medical discovery institute

library_source: transcriptomic

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were demulitplexed using the bcl2fastq tool, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Reads were then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Hepatocytes

extract_protocol:
[Tissue harvesting] Mice were sacrificed by CO2 inhalation, then liver tissue was harvested and stored at -80 degrees celcius before use.
Poly-A mRNA was extracted using a Qiagen RNeasy Mini kit with on-column Dnase1 digestion, according to the manufacturer’s protocol.
mRNA libraries were prepared using the TruSeq Stranded LT kit according to the manufacturer’s protocol (Illumina)

treatment_protocol: [Mouse treatment protocol]  Nine-week-old C57BL/6 mice were given either 0.5 mg/kg Trichostatin A (TSA) or 10% DMSO (vehicle) via intraperitoneal injection, one day prior to paracetamol administration, for 4 days. Paracetamol was delivered at 350mg/kg where appropriate by single IP injection after a 10 hr fast.

tag: strain

tag: time point

tag: drug treatment

value: DMSO/Paracetamol

tag: cell type

value: Hepatocytes


title: D45NP: NP of patient D45

type: RNA

last: Chen

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NP of patient D45

value: male

tag: tissue


title: C88NP: NP of patient C88

source_name: NP of patient C88

value: non-degenerated


title: Hepatocytes, ParaDMSO 14hr Rep1


title: D45AF: AF of patient D45

source_name: AF of patient D45

value: annulus fibrosus


title: D40AF: AF of patient D40

source_name: AF of patient D40


title: C88AF: AF of patient C88

source_name: AF of patient C88


title: C74NP: NP of patient C74

source_name: NP of patient C74


title: Hepatocytes, TSA 0hr Rep4

value: TSA


title: Hepatocytes, ParaTSA 14hr Rep3

value: TSA/Paracetamol


title: Hepatocytes, TSA 0hr Rep2


title: Hepatocytes, TSA 0hr Rep1


title: Hepatocytes, ParaTSA 14hr Rep1


title: Hepatocytes, DMSO 0hr Rep3

value: DMSO


title: Hepatocytes, DMSO 0hr Rep2


title: Hepatocytes, DMSO 0hr Rep1


title: 14.5cdpp_rep2

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were performed varianse stabilizating tranform and quantile normalization by the lumi package in R

source_name: Testes, 7.5 dpp, 7 days culture

label_protocol: Biotinylated cRNA were prepared with the Illumina RNA Amplification kit (Ambion) for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with FastPure RNA kit (Takara) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: developmental stage

value: 7.5 dpp

tag: tissue derived

value: testis


title: 14.5cdpp_rep1

description: Replicate 1


title: Hippocampal cells_K2-M

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

country: Canada

institute: Western University

data_processing:
Raw reads were pre-processed with the sequence-grooming tool cutadapt40 version 0.4.1 with the following quality trimming and filtering parameters (`--phred33 -- length36 -q 5 --stringency 1 -e 0.1`).
Each set of paired-end reads was mapped against the Mus Musculus GRCm38.p6 primary assembly downloaded from Ensembl41 release 94(https://useast.ensembl.org/Mus_musculus/Info/Annotation) using HISAT2 version 2.0.4.
Bam files from the same sample were then merged.
The read alignments and Mus Musculus GRCm38 genome annotation were provided as input into StringTie  v1.3.342 which returned gene and transcript abundances for each sample.
Genome_build: GRCm38.94
Supplementary_files_format_and_content: Tab-delimited transcript abundances files

source_name: hippocampal cells

extract_protocol:
Hippocampal total RNA was isolated using the miRVANA RNA isolation kit (ThermoFisher)
RNA was quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA) and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) with the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Libraries were prepared, including rRNA reduction, using the ScriptSeq Complete Gold Kit (H/M/R) (Illumina Inc., San Diego, CA).

tag: Sex

tag: genotype

value: Atrx-cKO

value: hippocampal cells


title: Hippocampal cells_K3-M


title: 14.5cdpp_rep3

description: Replicate 3


title: 13.5cdpp_rep3

description: Replicate 3

source_name: Testes, 7.5 dpp, 6 days culture


title: 16.5cdpp_rep1

description: Replicate 1

source_name: Testes, 7.5 dpp, 9 days culture


title: Hepatocytes, TSA 0hr Rep3


title: Hepatocytes, DMSO 0hr Rep4


title: 16.5cdpp_rep3

description: Replicate 3


title: Hippocampal cells_K2-F


title: C74AF: AF of patient C74

source_name: AF of patient C74


title: Hippocampal cells_K1-M


title: 13.5cdpp_rep2

description: Replicate 2


title: 13.5cdpp_rep1

description: Replicate 1


title: 11.5cdpp_rep2

description: Replicate 2

source_name: Testes, 7.5 dpp, 4 days culture


title: 11.5cdpp_rep1

description: Replicate 1


title: 9.5cdpp_rep3

description: Replicate 3

source_name: Testes, 7.5 dpp, 2 days culture


title: 9.5cdpp_rep2

description: Replicate 2


title: 9.5cdpp_rep1

description: Replicate 1


title: 16.5cdpp_rep2

description: Replicate 2


title: Hippocampal cells_K1-F


title: RNA-seq of LNCaP/MYC KD 627 Rep 4

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

data_processing:
Libraries were sequenced with 150 cycles paired-end. FASTQ files were aligned with STAR to grch37-ercc.
FASTQ files were trimmed using TrimGalore and aligned with STAR to grch37-ercc.
Gene level counts were determined using FeatureCounts.
Genome_build: grch37 and ERCC
Supplementary_files_format_and_content: semicolon separated values for gene level counts

source_name: prostate cancer

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Mini Plus kit
1 microgram of RNA was extracted from cells, combined with ERCC spike-in control, and assembled into PolyA selected libraries using the Illumina TruSeq Stranded Total RNA Kit. Libraries were sequenced with 150 cycles paired-end. FASTQ files were aligned with STAR to grch37-ercc.

tag: cell line

value: LNCaP

tag: condition

value: MYC Knockdown Construct 627

tag: replicate


title: Hippocampal cells_C3-M

value: control


title: 16.5dpp_rep3

description: Replicate 3

source_name: Testes, 16.5 dpp, in vivo


title: day 7 immobile isolated nuclei

city: Ann Arbor

first: Amanda

middle: Katherine

last: Huber

state: MI

address: 1000 Wall Street

department: Computational Medicine and Bioinformatics

institute: University of Michigan

library_source: genomic

data_processing:
Cell Ranger Single Cell Software Suite 1.3 was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core
A total of ~200 million reads were generated from the 10X Genomics sequencing analysis for each of the replicates. The sequencing data was first pre-processed using the 10X Genomics software Cell Ranger (10x Genomics Inc., Pleasanton, CA, USA) and aligned to mm10 genome. For quality control, genes expressed in fewer than 10 cells, and cells expressing fewer than 500 genes per cell, or more than 20% mitochondrial UMI content, or UMI content >60,000 were filtered out. Replicates from the same group (condition) were pooled together for downstream analysis. The case group consisted of 7718 cells and 14466 genes (before quality control, 7718 cells and 19333 genes), while the control group consisted of 2760 cells and 12636 genes (before quality control, 3520 cells and 17730 genes). Downstream analysis steps were performed using Seurat pipeline. The downstream analysis steps for each sample type include normalization, scaling, dimensionality reduction (PCA, and t-SNE), unsupervised clustering, cluster consolidation via centroid rank correlation analysis, discovery of differentially expressed cluster specific markers, and marker enrichment.
Genome_build: mm10

molecule: genomic DNA

extract_protocol:
Burn and tenotomy was performed as previously described (PMID 26274052) in Hoxa11CreERt2 +/- TdTom/tom mice. Mice were allowed to ambulate normally or had their injured hindlimb immilized.Tenotomy injury site was harvested from Day 0 (no injury baseline), Day 7 mobile (normal ambulation), Day 7 immobile, and Day 42 mobile mice. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40μm sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website).
3' Samples:
3' V3.1 Chemistry with NextGEM Chip G
NovaSeq 6000 S4 flowcell 300 cycle kit - this was loaded to target 500M reads/sample (5000 cells, 100K reads/cell), at 300pM (these were shared flowcells)
Read lengths: 150 x 8 x 150
ATAC:
ATAC V1.1 Chemistry with NextGEM Chip H
NovaSeq 6000 SP flowcell 100 cycle kit (This was the full flowcell just for you)
Read lengths: 50 x 8 x 16 x 49

treatment_protocol: Mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. The left leg and groin were de-epilated using Nair ointment and cleansed. 10ul of cardiotoxin (3mg/mL) were injected from proximal to distal along the length of the left tibialis anterior muscle. An incision was made at the groin crease and groin fat pad retracted to exposed the femoral vessels. Superficial femoral artery and vein were isolated from the nerve just distal to the profunda femoris takeoff and occluded with an Ackland clamp. The incision was closed temporarily and mice were kept in a warmed anesthetic chamber for 3 hours at which point clamps were removed and incisions formally closed.

tag: treatment

value: burn tenotomy immobilized

value: tenotomy injury site:tendon insertion at the gastrocnemius to the tendon insertion into the calcaneal enthesis

tag: time of harvest

value: Day 7


title: day 42 isolated nuclei from day42_2

value: burn tenotomy

value: Day 42


title: Hippocampal cells_C2-F

value: female


title: Hippocampal cells_C3-F


title: Hippocampal cells_C2-M

value: male


title: Hippocampal cells_C1-M


title: day 7 mobile isolated nuclei

value: burn tenotomy normal ambulation


title: day 0 control isolated nuclei

value: naïve

value: Day 0


title: day 42_2 injury site


title: Hippocampal cells_C1-F


title: day 7 immobile injury site


title: 16.5dpp_rep2

description: Replicate 2

tag: gender


title: day 42_1 injury site


title: 13.5dpp_rep2

description: Replicate 2

source_name: Testes, 13.5 dpp, in vivo


title: 13.5dpp_rep3

description: Replicate 3


title: 13.5dpp_rep1

description: Replicate 1


title: 11.5dpp_rep3

description: Replicate 3

source_name: Testes, 11.5 dpp, in vivo


title: day 7 mobile injury site


title: 16.5dpp_rep1

description: Replicate 1


title: day 0 control injury site

value: Naïve


title: 11.5dpp_rep2

description: Replicate 2

value: testis


title: 9.5dpp_rep3

description: Replicate 3

source_name: Testes, 9.5 dpp, in vivo

value: 9.5 dpp


title: 11.5cdpp_rep3

description: Replicate 3

value: 7.5 dpp


title: IWATKI-HFD-3

city: Los Angeles

first: Celine

last: Riera

address: 8700 Beverly Blvd

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

data_processing:
Quaity check was done by FastQc
Genome Index and mapping was done using STAR
Count tables were generated using htseq
DESeq2 was used for differential expression analysis
Genome_build: GRCm38.p5 Release M21
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Inguinal Adipose Tissue

extract_protocol:
RNA was extracted using Trizol, and cleaned by Qiagen columns
RNA libraries were prepared for sequencing using standard Illumina protocols. Single end, Poly A tail enrichment, Non Stranded

value: Inguinal Adipose Tissue

value: Adv-CGRPalpha+/-


title: 11.5dpp_rep1

description: Replicate 1


title: IWAT- WT-NC-3

value: WT


title: 9.5dpp_rep1

description: Replicate 1


title: IWATKI-HFD-2


title: IWATKI-HFD-1


title: IWAT- WT-NC-2


title: IWAT- WT-NC-1


title: Primary Neurons, Control, Repeat #3

city: Rehovot

first: Orly

last: Reiner

address: 234, Herzl Street,

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
cortical.neurons.P0.WT5
Barcodes used: TCTTCGA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38/mm10 whole genome using Cutadapt  -a $adapter -q 20 fastqf  ($adapter= sequence of adapter Fastqf= fastqfile), STAR and HTSeq (union mode).
Raw counts were processed, and normalized reads were obtained by DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include read values for each sample.

source_name: Brain-cerebral cortex

extract_protocol:
Total RNA was extracted from samples using RNEASY mini-kit (Qiagen)
RNA libraries were prepared for sequencing using bulk MARS-seq protocol [Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–9 (2014).]

value: Post natal Day 0

value: Wild Type

value: Neurons


title: BAT KI-HFD-2

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: Primary Neurons, Control, Repeat #2

description:
cortical.neurons.P0.WT4a
Barcodes used: ACACGTG


title: Primary Neurons, Control, Repeat #1

description:
cortical.neurons.P0.WT3
Barcodes used: ACTCAGG


title: BAT KI-HFD-1


title: BAT WT-NC-3


title: Primary Neurons, MeCP2 Y/-, Repeat #3

description:
cortical.neurons.P0.MeCP2.KO.5
Barcodes used: CGTAACT

value: MeCP2 Y/-


title: 21.5cdpp_rep3

description: Replicate 3

source_name: Testes, 7.5 dpp, 14 days culture


title: 21.5dpp_rep3

description: Replicate 3

source_name: Testes, 21.5 dpp, in vivo


title: 21.5dpp_rep2

description: Replicate 2


title: 14.5dpp_rep3

description: Replicate 3

source_name: Testes, 14.5 dpp, in vivo


title: 21.5cdpp_rep1

description: Replicate 1


title: 7.5dpp_rep3

description: Replicate 3

source_name: Testes, 7.5 dpp, in vivo


title: BAT WT-NC-2


title: 21.5dpp_rep1

description: Replicate 1


title: 14.5dpp_rep1

description: Replicate 1


title: 7.5dpp_rep2

description: Replicate 2


title: 14.5dpp_rep2

description: Replicate 2


title: Primary Neurons, MeCP2 Y/-, Repeat #2

description:
cortical.neurons.P0.MeCP2.KO.10
Barcodes used: ATAACCG


title: BAT WT-NC-1


title: Primary Neurons, MeCP2 Y/-, Repeat #1

description:
cortical.neurons.P0.MeCP2.KO.1
Barcodes used: TGCACAA


title: Primary Neurons, Lis1+/-, Repeat #3

description:
cortical.neurons.P0.LIS1.het.2
Barcodes used: AGCACTG


title: Primary Neurons, Lis1+/-, Repeat #2

description:
cortical.neurons.P0.LIS1.het.10
Barcodes used: ATCTGTC


title: Primary Neurons, Double mutant, Repeat #3

description:
cortical.neurons.P0.Double.KO8
Barcodes used: GCAGTAG

value: Lis1+/-, MeCP2 Y/-


title: BAT KI-HFD-3


title: Primary Neurons, Lis1+/-, Repeat #1

description:
cortical.neurons.P0.LIS1.3
Barcodes used: AGTGCGT


title: 21.5cdpp_rep2

description: Replicate 2

value: male


title: 9.5dpp_rep2

description: Replicate 2


title: Hypoxic kidney, replicate 3

city: Bern

first: Stefan

last: Rudloff

state: BE

address: Freiburgstrasse 15

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern and University Hospital

description:
Gene expression data from fetal kidneys subject to chronic hypoxia
Hy3_eF4

hyb_protocol: 2.3µg biotinylated fragments were hybridized to Affymetrix Mouse Gene 1.0 ST arrays at 45°C for 16h, washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

scan_protocol: The arrays were scanned with Affymetrix GeneChip® Scanner 3000 7G and raw data was extracted from the scanned images and analysed with the Affymetrix Power Tools software package.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files by the Robust Multi-array Average algorithm (RMA). Differential hybridized features were identified using the R Bioconductor package “limma” that implements linear models for microarray data

source_name: Kidney of fetus subject to chronic hypoxia (E14.5-18.5)

label_protocol: 100ng total RNA samples were processed with the Ambion® WT Expression Kit (4411973, life technologies) kit. 5.5µg of the cDNA was fragmented and labelled with GeneChip® WT Terminal Labeling kit (901525, Affymetrix)

extract_protocol: Total RNA from male hypoxic, normoxic and caloric control group E18.5 kidneys was isolated using the RNeasy Mini Kit (Qiagen, 74104)

treatment_protocol: To model chronic fetal hypoxia, timed-mated pregnant mice were exposed to 10% oxygen from E14.5 to E18.5. In the Cc group, normoxic dams were fed with an amount of food matching the amount of food consumed by the hypoxic dams.

value: fetus

value: chronic hypoxia (E14.5-18.5)

value: Kidney E18.5

tag: mother of fetus

value: eF4 (mother F)


title: 7.5dpp_rep1

description: Replicate 1

value: testis


title: Primary Neurons, Double mutant, Repeat #2

description:
cortical.neurons.P0.Double.KO5
Barcodes used: ATCTGCA


title: Hippocampal cells_K3-F

source_name: hippocampal cells

value: female

value: Atrx-cKO

value: hippocampal cells


title: Primary Neurons, Double mutant, Repeat #1

description:
cortical.neurons.P0.Double.KO2
Barcodes used: GTATGCG


title: Hypoxic kidney, replicate 2

description:
Gene expression data from fetal kidneys subject to chronic hypoxia
Hy2_eE6

value: eE6 (mother E)


title: Epithelial cells, Sin3a-LOF_6wk

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
follow default Cellranger v2.2.0
Genome_build: custom mm10/GRCm38 with eGFP reporter sequence added
Supplementary_files_format_and_content: demultiplexed count matrix file

source_name: mouse lung

extract_protocol:
follow standard 10x single cell 3 prime v2 kit manuscript
10x chromium single cell RNAseq

value: tamoxifen treated lungs

tag: time

value: lung

value: epithelial cells


title: Normoxic kidney, replicate 3

description:
Gene expression data from fetal kidneys (normal control)
No3_eC6

source_name: Kidney of fetus (control)

value: none (control)

value: eC6 (mother C)


title: Epithelial cells, control_6wk

tag: strain

value: control


title: Epithelial cells, control_4wk


title: 20nM_GlcNAc_GccF_2

city: Palmerston North

first: Sean

middle: William

last: Bisset

state: Manawatu

address: Tennent Drive

department: School of Fundamental Sciences

country: New Zealand

institute: Massey University

data_processing:
Base calling done using Sanger / Illumina 1.9
Reads were trimmed using BBDuk, using the following parameters: kmer length of 23, hdist of 1, -tbo flag selected.
Trimmed reads were aligned to reference sequence using Bowtie2 version 2.2.9, using the default settings. Samples from strain JH2-2 were aligned to the reference genome for JH2-2, while samples from strain VI01 were aligned to the reference genome V583.
Aligned reads were processed using HTSeq version 0.6.0 to generate lists of counts for each gene.
Genome_build: GCA_000479105.1 (JH2-2), GCA_000007785.1 (V583)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts for each gene/ open reading frame

organism: Enterococcus faecalis

source_name: Bacterial cell

extract_protocol:
Cells were pelleted, and lysed by bead-milling with 0.1 mm diameter glass beads. RNA was isolated using Trizol with a Zymo Direct-zol RNA purification kit.
Library construction was carried out using Illumina TruSeq Stranded RNA Sample Preparation kit with RiboZero bacteria depletion.

value: Cells pre-treated with 1 mM GlcNAc and treated with 20 nM GccF, harvested at 30 minutes


title: VI01_Control_3


title: VI01_Control_2


title: VI01_Control_1


title: VI01_GccF_1

value: Sigma factor 54 knockout cells treated with 100 nM GccF, harvested at 30 minutes


title: Normoxic kidney, replicate 1

description:
Gene expression data from fetal kidneys (normal control)
No1_eA9

value: fetus

value: eA9 (mother A)


title: VI01_GccF_2


title: Normoxic kidney, replicate 2

description:
Gene expression data from fetal kidneys (normal control)
No2_eB2

value: Kidney E18.5

value: eB2 (mother B)


title: 20nM_GlcNAc_GccF_3


title: Caloric control kidney, replicate 3

description:
Gene expression data from fetal kidneys subject to caloric restriction
Cc3_eI5

source_name: Kidney of fetus subject to caloric restriction (E14.5-18.5)

value: caloric restriction (E14.5-18.5)

value: eI5 (mother I)


title: Hypoxic kidney, replicate 1

description:
Gene expression data from fetal kidneys subject to chronic hypoxia
Hy1_eD9

value: chronic hypoxia (E14.5-18.5)

value: eD9 (mother D)


title: 20nM_GlcNAc_Control_2


title: Caloric control kidney, replicate 1

description:
Gene expression data from fetal kidneys subject to caloric restriction
Cc1_eG1

value: eG1 (mother G)


title: 20nM_GlcNAc_Control_1


title: Caloric control kidney, replicate 2

description:
Gene expression data from fetal kidneys subject to caloric restriction
Cc2_eH4

value: eH4 (mother H)


title: 20nM_GccF_3

value: Cells treated with 20 nM GccF, harvested at 30 minutes


title: 20nM_Control_3


title: 20nM_Control_2


title: Epithelial cells, Sin3a-LOF_4wk

value: tamoxifen treated lungs

value: lung

value: epithelial cells


title: 20nM_Control_1

value: control


title: VI01_GccF_3


title: 30_GccF_3

value: Cells treated with 250 nM GccF, harvested at 30 minutes


title: 30_GccF_2


title: 30_GccF_1


title: 30_Control_2


title: 20nM_GlcNAc_GccF_1

value: Cells pre-treated with 1 mM GlcNAc and treated with 20 nM GccF, harvested at 30 minutes


title: 20nM_GlcNAc_Control_3


title: 10_GccF_2

value: Cells treated with 250 nM GccF, harvested at 10 minutes


title: 10_GlcNAc_2

value: Cells treated with 1 mM GlcNAc, harvested at 10 minutes


title: 10_GlcNAc_3


title: 10_GccF_3


title: 10_GlcNAc_1


title: 30_Control_1


title: 10_Control_3


title: 20nM_GccF_2


title: 20nM_GccF_1


title: 10_GccF_1


title: 0_Control_3


title: 0_Control_2


title: 0_GccF_1

value: Cells treated with 250 nM GccF, harvested at 0 minutes


title: 0_GccF_3


title: 0_Control_1


title: 0_GccF_2


title: Fig6_CD44hi_CD69hi_CD103low_rep2

city: Yachiyo-City

first: Kota

last: Kokubo

state: Chiba

address: Yachiyodai-minami 1-10-12

department: Department of Immunology

institute: Chiba University

description: with 7w resting phase

data_processing:
For RNA-Seq, read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
For ATAC-Seq, read sequences (50 bp) were aligned to the mm9 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8).
Bigwig files for each peaks were created by using samtools (version 1.3) and deeptools (version 3.2.0).
Genome_build: mm10 for RNA-Seq. mm9 for ATAC-Seq.
Supplementary_files_format_and_content: CSV files include FPKM values for each sample of RNA-Seq. And processed data of ATAC-Seq show in bigWig files.

source_name: CD44hi CD69hi CD103low T cells in lung treated with Aspergillus antigen

growth_protocol: mice were intranasally treated with Aspergillus antigen 7weeks and rested as indicated in the 'description' field

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen). And total cellular DNA was extracted in accordance with Omni-ATAC protocol(Nature Methods volume 14, pages 959–962 (2017)).
For RNA-Seq, TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol. For ATAC-Seq, library construction was done in accordance with Omni-ATAC protocol(Nature Methods volume 14, pages 959–962 (2017)).

tag: strain background

value: BALB/c

tag: genotype/variation

value: Wild type

value: Aspergillus antigen

value: CD44hi CD69hi CD103low T cells


title: 30_Control_3


title: Fig6_CD44hi_CD69low_rep2

description: with 7w resting phase

source_name: CD44hi CD69low T cells in lung treated with Aspergillus antigen

tag: cell type

value: CD44hi CD69low T cells


title: 10_Control_2


title: PMN-MDSC-URPL-rep1

city: Shanghai

first: Congcong

last: Li

state: Shanghai

address: 160 Pujian Road

department: OB & GYN

country: China

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

description: Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer’s instructions.  Cy5-labeled aRNA was hybridized with Phalanx OneArray and scanned on a G2508C Agilent Microarray Scanner (Agilent Technologies, USA).

hyb_protocol: Cy5-labeled a RNA was hybridized with Phalanx OneArray

scan_protocol: OneArray was scanned on a G2505C Agilent Microarray Scanner (Agilent Technologies, USA) with Agilent 0.1 XDR software.

data_processing: Data were analyzed using Rosetta Resolver System (Rosetta Biosoftware).

source_name: decidua PMN-MDSC from unexplained recurrent pregnancy loss patient

label_protocol: aRNA was labeled with Cy5 dye.

tag: tissue

value: decidua

tag: age

value: 26 years

tag: gestation age

value: 66 days


title: PMN-MDSC-URPL-rep2

description: Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer’s instructions.  Cy5-labeled aRNA was hybridized with Phalanx OneArray and scanned on a G2509C Agilent Microarray Scanner (Agilent Technologies, USA).

value: 22 years

value: 70 days


title: Fig6_CD44low_rep1

description: with 7w resting phase

source_name: CD44low T cells in lung treated with Aspergillus antigen

value: CD44low T cells


title: Fig6_CD44hi_CD69hi_CD103low_rep1

description: with 7w resting phase


title: Fig6_CD44hi_CD69low_rep1

description: with 7w resting phase


title: 10_Control_1

value: control


title: Fig6_CD44low_rep2

description: with 7w resting phase


title: RNA-seq of LNCaP/MYC KD 637 Rep 2

data_processing:
Libraries were sequenced with 125 cycles paired-end. FASTQ files were aligned with RUM to hg19 and sorted with PICARD.
FASTQ files were aligned with RUM to hg19 and sorted with PICARD.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values for gene-level FPKM

source_name: prostate cancer

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Mini Plus kit
1 microgram of RNA was extracted from cells and assembled into PolyA-selected libraries using the Illumina TruSeq Stranded Total RNA Kit.

value: LNCaP

value: MYC Knockdown Construct 637


title: Fig6_CD44hi_CD69hi_CD103hi_rep1

description: with 7w resting phase

source_name: CD44hi CD69hi CD103hi T cells in lung treated with Aspergillus antigen

value: CD44hi CD69hi CD103hi T cells


title: PMN-MDSC-NP-rep3

description: Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer’s instructions.  Cy5-labeled aRNA was hybridized with Phalanx OneArray and scanned on a G2507C Agilent Microarray Scanner (Agilent Technologies, USA).

source_name: decidua PMN-MDSC from normal early pregnancy

value: 30 years

value: 55 days


title: RNA-seq of LNCaP/MYC KD 627 Rep 2

value: MYC Knockdown Construct 627


title: RNA-seq of RWPE/MYC 1 Rep 2

value: MYC Overexpression


title: RNA-seq of LNCaP/Control Rep 2

value: Control


title: RNA-seq of RWPE/MYC 3 Rep 2


title: RNA-seq of RWPE/MYC 2 Rep 2


title: RNA-seq of RWPE/Control 1 Rep 2


title: PMN-MDSC-NP-rep2

description: Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer’s instructions.  Cy5-labeled aRNA was hybridized with Phalanx OneArray and scanned on a G2506C Agilent Microarray Scanner (Agilent Technologies, USA).

value: 25 years

value: 63 days


title: RNA-seq of RWPE/Control 2 Rep 2


title: RNA-seq of LNCaP/MYC KD 637 Rep 1


title: Fig6_CD44hi_CD69hi_CD103hi_rep2

description: with 7w resting phase

value: BALB/c

value: Wild type

value: Aspergillus antigen


title: PMN-MDSC-NP-rep1

description: Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer’s instructions.  Cy5-labeled aRNA was hybridized with Phalanx OneArray and scanned on a G2505C Agilent Microarray Scanner (Agilent Technologies, USA).

value: decidua

value: 34 years

value: 52 days


title: PMN-MDSC-URPL-rep3

description: Total RNA was extracted using Trizol Reagent (Invitrogen, USA) according to the manufacturer’s instructions.  Cy5-labeled aRNA was hybridized with Phalanx OneArray and scanned on a G2510C Agilent Microarray Scanner (Agilent Technologies, USA).

value: 31 years

value: 56 days


title: P01

city: Shenzhen

first: Li

last: Xiaoting

address: 9th Floor, Dabaihui Center, Yantian District, Shenzhen

institute: YuceBio Technology Co., Ltd.

data_processing:
Read quality was checked for each sample using FastQC v0.11.3.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome using START (2.5.3a) with parameters "--quantMode TranscriptomeSAM --outFilterType BySJout --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.04 --alignSJoverhangMin 8 --alignSJDBoverhangMin 5 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --sjdbScore 2 --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --twopassMode Basic --chimSegmentMin 20 --chimJunctionOverhangMin 20 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5"
Aligned RNA reads were then analyzed by using RSEM (v1.3.0) to calculate gene expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genes and corresponding reads raw counts for sample.
Supplementary_files_format_and_content: tab-delimited text files include genes and corresponding TPM values for sample.

source_name: FFPE tumor tissue

extract_protocol:
RNA was extracted using the RNeasy FFPE Kit (QIAGEN) according to the manufacturer’s protocol. Total RNA integrity was checked using the Bioptic Qsep100 (BIOptic) and quantified using a Synergy H1 (BioTek).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: EGFR mutant

value: lung tumor tissue

value: treated with anti-PD-1


title: RNA-seq of LNCaP/Control Rep 1

value: LNCaP


title: RNA-seq of LNCaP/MYC KD 627 Rep 1

value: MYC Knockdown Construct 627


title: RNA-seq of RWPE/MYC 3 Rep 1

value: MYC Overexpression


title: RNA-seq of RWPE/MYC 1 Rep 1


title: RNA-seq of RWPE/MYC 2 Rep 1


title: RNA-seq of RWPE/Control 2 Rep 1

value: Control


title: RNA-seq of RWPE/Control 1 Rep1

data_processing:
Libraries were sequenced with 125 cycles paired-end.
FASTQ files were aligned with RUM to hg19 and sorted with PICARD.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values for gene-level FPKM


title: Col_bleomycin_R3

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

data_processing:
Illumina CASAVA software used for basecalling.
Single-end reads were trimmed for adaptor sequences and aligned to the Araport11 exome using Salmon v0.7.2.
Transcript quantification was also performed by Salmon v0.7.2.
Genome_build: Araport11 exome
Supplementary_files_format_and_content: tab-delimited text files generated from Salmon quantification, contain length of transcript in nucleotides, computed effective length, transcripts per million (TPM) and number of reads.

organism: Arabidopsis thaliana

source_name: Col-0 root tips_bleomycin

growth_protocol: For each sample, approximately 200 Col-0 seeds were sown on top of a nylon mesh on squared plates holding 1/2 MS medium and 1% agar.

extract_protocol:
0.2cm root tips were isolated and frozen in liquid nitrogen. RNA was extracted using QIAGEN Rneasy Mini kit.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Stranded mRNA Sample Prep Kit.

treatment_protocol: Seven days after sowing, the nylon mesh was transferred to either control 1/2 MS medium (control samples) or to 1/2 MS medium containing 0.5 ug/ml Bleomycin (bleomycin samples).

tag: ecotype/line

value: root tips

value: 24h 0.5ug/ml bleomycin


title: Col_bleomycin_R2


title: Col_bleomycin_R1


title: Col_control_R1

source_name: Col-0 root tips_control

value: control


title: Col_control_R3


title: STG_subject00988_NPC_rep1 [X988.C]

type: genomic

city: Pittsburgh

first: Brandon

middle: Chad

last: McKinney

state: PA

address: 3811 O'Hara Street

department: Psychiatry

institute: University of Pittsburgh

hyb_protocol: Following manufacturer's protocol

scan_protocol: Following manufacturer's protocol

data_processing:
Data analyses of raw image array files were performed using the R software environment (www.r-project.org). Color adjustment and background correction were performed using the bgAdjust2C method. Before filtering, normalization was performed using the preprocessQuantile method. In data quality control analysis, probe data for each sample demonstrated mean detection p-values<0.05, so no data was exluded due to failed detection for any sample. At the filtering stage, data from any probes that failed detection in any sample at p>=0.01 (N=12,350) were removed from the dataset. Data from probes on sex chromosomes (N=18,628) and from probes with known SNPs (N=27,395) in any sample were removed from the dataset. Probes that cross-react with multiple genomic regions (N=39,269) were also removed. The remaining data presented here reflects signals at 768,268 probes.
The 'processed_data.txt' contains the normalized (preprocessQuantile method) and Averaged Beta (for 8 subject samples replicated) values.

source_name: postmortem STG of NPC subject 988

label_protocol: Following manufacturer's protocol

extract_protocol: DNA (~10 micrograms) was isolated from STG grey matter (~20 micrograms) using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Bisulfite conversion of 10 micrograms genomic DNA was performed with the EZ DNA methylation kit (Zymo Research).

tag: Sex

value: Male

tag: race

value: White

tag: age (years)

tag: postmortem interval (hours)

tag: mechanism of death

value: Accidental

tag: illness duration (years)

value: postmortem superior temporal gyrus (STG)

tag: molecule subtype

value: bisulfite-treated genomic DNA


title: STG_subject00917_SZ_rep1 [X917.S]

source_name: postmortem STG of SZ subject 917

value: Schizophrenia

value: Female

value: Natural


title: STG_subject00933_SZ_rep1 [X933.S]

source_name: postmortem STG of SZ subject 933


title: STG_subject00904_SZ_rep1 [X904.S]

source_name: postmortem STG of SZ subject 904


title: STG_subject00930_SZ_rep1 [X930.S]

source_name: postmortem STG of SZ subject 930


title: STG_subject00871_NPC_rep1 [X871.C]

source_name: postmortem STG of NPC subject 871


title: STG_subject00878_SZ_rep1 [X878.S]

source_name: postmortem STG of SZ subject 878


title: tcx5/6;cmt3_Rep2_BS-seq

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Bisulfite treated sequenced reads were map to TAIR10 genome assembly using Bismark v 0.19.0  bismark with parameters -N 1 -q --bowtie2 --sam -p 20
Context-dependent (CpG/CHG/CHH/CX) methylation were extracted using bismark_methylation_extractor with parameters --paired-end --no_overlap --report --bedGraph --buffer_size 20G --cytosine_report --CX --comprehensive
Genome_build: TAIR10
Supplementary_files_format_and_content: Bw format files for each chromosome for each cytosine context (CG, CHG, CHH or CX) with following tab-separated information: Chromosome, start coordinate, stop coordinate,and methylation level (methylated cytosines sequenced/total cytosines sequenced).

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS medium plates with a 16 h light/8 h dark photoperiod at 22ºC

extract_protocol:
Genomic DNA was extracted from 12-day old seedlings by CTAB and purified by phenol: chloroform: isoamyl Alcohol 25: 24: 1
DNA libraries were prepared for sequencing using standard Illumina protocols

value: seedlings

tag: genotype


title: STG_subject00852_NPC_rep1 [X852.C]

source_name: postmortem STG of NPC subject 852


title: STG_subject00818_NPC_rep1 [X818.C]

source_name: postmortem STG of NPC subject 818


title: STG_subject00829_SZ_rep1 [X829.S]

source_name: postmortem STG of SZ subject 829

value: Suicide


title: STG_subject00822_NPC_rep1 [X822.C]

source_name: postmortem STG of NPC subject 822

value: Black


title: STG_subject00806_NPC_rep1 [X806.C]

source_name: postmortem STG of NPC subject 806


title: J-DKO 1 PE

city: Boston

first: Kristen

middle: Elaine

last: Pauken

state: MA

address: 77 Avenue Louis Pasteur NRB rm 837

department: Immunology

institute: Harvard Medical School

hyb_protocol: RNA was hybridized to Affymetrix Mouse430_2 microarrays at the Broad Institute of MIT and Harvard Microarray Facility

scan_protocol: Arrays were scanned following manufacturers instructions by the Broad Institute of MIT and Harvard Microarray Facility

data_processing: Microarray CEL files were imported and normalized using rma function from the bioconductor package oligo

source_name: Lung CD8 T cell

label_protocol: cDNA was fragmented and biotinylated using the Nugen FL Ovation cDNA kit according to manufacturer's instructions.

growth_protocol: C57BL/6J mice were infected with 1.6x10^5 TCID50 X31-GP33 (H2N3) influenza intranasally. On day 8 post-infection, mouse lungs were removed for CD8+ T cell isolation

extract_protocol: RNA was extracted using RNAdvance tissue isolation kit (Agencourt) and amplified using the WT-Ovation One Direct System (NuGEN).

treatment_protocol: On day 8 post-infection, mouse lungs were removed and mechanically disrupted in a GentleMACS tissue dissociator (Miltenyi Biotech) and incubated with 2 mg/ml collagenase D (Worthington Biochemical Corp.) and 3 micrograms/ml DNase I (Sigma) at 37oC for 30 minutes. Red blood cells were lysed using ACK lysis buffer (Lonza). The resulting single cell suspensions were filtered through a 70 micron cell strainer (BD Falcon) and labeled with anti-CD8, ant-CD44, and tetramers against the immunodominant epitope of influenza (PE conjugated H-2Db NP366-374) and subdominant epitopes (APC conjugated H-2Db GP33-41 and H2Db PA224-233). Cells were sorted as CD8+ CD44+ H-2Db NP366-374+ for immunodominant samples, and CD8+ CD44+ H-2Db GP33-41+ or H2Db PA224-233+ for subdominant samples.

value: Lung CD8 T cell

value: PD-L1/L2 DKO

tag: cell subtype

value: NP-tetramer


title: N-DKO 2 APC


title: cmt3_Rep2_BS-seq


title: O-WT 2 PE

value: Wildtype


title: STG_subject00857_NPC_rep1 [X857.C]

source_name: postmortem STG of NPC subject 857

value: Control


title: I-WT 2 APC


title: cmt3_Rep1_BS-seq


title: D-DKO 2 PE


title: STG_subject00802_SZ_rep1&2 [X802.S]

description: This represents 2 replicate samples. The beta-values are averaged. IDAT files for each replicate are available

source_name: postmortem STG of SZ subject 802


title: G-WT 4 APC


title: K-DKO 4 APC


title: B-WT 3 PE


title: A-WT 4 PE


title: P-DKO 3 PE


title: STG_subject00722_SZ_rep1 [X722.S]

source_name: postmortem STG of SZ subject 722


title: STG_subject00686_NPC_rep1 [X686.C]

source_name: postmortem STG of NPC subject 686


title: STG_subject00739_NPC_rep1 [X739.C]

source_name: postmortem STG of NPC subject 739


title: L-DKO 1 APC


title: STG_subject00700_NPC_rep1&2 [X700.C]

source_name: postmortem STG of NPC subject 700


title: M-WT 1 APC


title: Col_control_R2

source_name: Col-0 root tips_control

value: root tips

tag: treatment

value: control


title: tcx5/6;cmt3_Rep1_BS-seq


title: tcx5/6-leaf_Rep2_BS-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Bisulfite treated sequenced reads were map to TAIR10 genome assembly using Bismark v 0.22.3  bismark with parameters -N 1 -q --bowtie2 --sam -p 20
Context-dependent (CpG/CHG/CHH/CX) methylation were extracted using bismark_methylation_extractor with parameters --paired-end --no_overlap --report --bedGraph --buffer_size 20G --cytosine_report --ignore_r2 2 --CX --comprehensive
Genome_build: TAIR10
Supplementary_files_format_and_content: Bw format files for each chromosome for each cytosine context (CG, CHG, CHH or CX) with following tab-separated information: Chromosome, start coordinate, stop coordinate,and methylation level (methylated cytosines sequenced/total cytosines sequenced).

extract_protocol:
Genomic DNA was extracted from 12-day old seedlings, 30-days leaf and SAM (shoot apical meristem) by CTAB and purified by phenol: chloroform: isoamyl Alcohol 25: 24: 1
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bisulfite treatment

value: Arabidopsis seedlings


title: tcx5/6-leaf_Rep1_BS-seq


title: WT-leaf_Rep2_BS-seq

value: wild type


title: WT-leaf_Rep1_BS-seq


title: STG_subject00659_NPC_rep1 [X659.C]

source_name: postmortem STG of NPC subject 659

value: Male

value: Other (Asian/Indian)

value: Accidental

value: postmortem superior temporal gyrus (STG)


title: STG_subject00681_NPC_rep1 [X681.C]

source_name: postmortem STG of NPC subject 681

value: White

value: Natural

value: bisulfite-treated genomic DNA


title: STG_subject00727_NPC_rep1 [X727.C]

source_name: postmortem STG of NPC subject 727

value: Black


title: STG_subject00665_SZ_rep1 [X665.S]

source_name: postmortem STG of SZ subject 665

value: Schizophrenia


title: STG_subject00630_NPC_rep1 [X630.C]

source_name: postmortem STG of NPC subject 630


title: tcx5/6-SAM_Rep2_BS-seq

source_name: Arabidopsis seedlings


title: STG_subject00625_SZ_rep1 [X625.S]

source_name: postmortem STG of SZ subject 625


title: STG_subject00587_SZ_rep1 [X587.S]

source_name: postmortem STG of SZ subject 587

value: Female


title: STG_subject00546_NPC_rep1 [X546.C]

source_name: postmortem STG of NPC subject 546


title: STG_subject00566_SZ_rep1 [X566.S]

source_name: postmortem STG of SZ subject 566


title: STG_subject00787_SZ_rep1 [X787.S]

source_name: postmortem STG of SZ subject 787

value: Suicide


title: tcx5/6_Rep1_BS-seq


title: STG_subject00621_SZ_rep1 [X621.S]

source_name: postmortem STG of SZ subject 621


title: WT_Rep2_BS-seq


title: WT-SAM_Rep1_BS-seq


title: tcx5/6_Rep2_BS-seq


title: STG_subject00685_NPC_rep1 [X685.C]

source_name: postmortem STG of NPC subject 685


title: STG_subject01686_SZ_rep1 [X1686.S]

source_name: postmortem STG of SZ subject 1686


title: STG_subject01581_SZ_rep1&2 [X1581.S]

source_name: postmortem STG of SZ subject 1518


title: STG_subject01579_SZ_rep1 [X1579.S]

source_name: postmortem STG of SZ subject 1579


title: WT_Rep1_BS-seq


title: STG_subject01555_NPC_rep1 [X1555.C]

source_name: postmortem STG of NPC subject 1555


title: STG_subject01542_SZ_rep1 [X1542.S]

source_name: postmortem STG of SZ subject 1542

value: Undetermined


title: STG_subject01524_NPC_rep1 [X1524.C]

source_name: postmortem STG of NPC subject 1524

value: Control


title: STG_subject01506_SZ_rep1 [X1506.S]

source_name: postmortem STG of SZ subject 1506


title: STG_subject01488_NPC_rep1 [X1488.C]

source_name: postmortem STG of NPC subject 1488


title: STG_subject01480_NPC_rep1&2 [X1480.C]

source_name: postmortem STG of NPC subject 1480


title: STG_subject00567_NPC_rep1 [X567.C]

source_name: postmortem STG of NPC subject 567


title: WT-SAM_Rep2_BS-seq

source_name: Arabidopsis seedlings


title: TCX5-FLAG Rep1

description: tcx5-/- with ectopic expression of FLAG-TCX5

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.2.6 with parameters -k 1 -N 1 -p 40 --local -q
peaks were called using macs2 version 2.1.1.20160309 with the following setting: macs2 callpeak -f BAM -p 1e-3 -g 1.2e8  --bdg --nolambda --nomodel
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

extract_protocol:
Anti-FLAG M2 Magnetic Beads (M8823; Sigma-Aldrich) were used for the IP of TCX5–3xFlag.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: seedlings

value: tcx5-/- ; FLAG-TCX5

tag: antibody


title: STG_subject01466_NPC_rep1 [X1466.C]

source_name: postmortem STG of NPC subject 1466


title: WT Rep2

value: Anti-FLAG M2 Magnetic Beads (M8823; Sigma-Aldrich)


title: STG_subject01455_SZ_rep1 [X1455.S]

source_name: postmortem STG of SZ subject 1455


title: STG_subject00537_SZ_rep1 [X537.S]

source_name: postmortem STG of SZ subject 537


title: WT Rep1

value: wild type


title: STG_subject01649_SZ_rep1 [X1649.S]

source_name: postmortem STG of SZ subject 1649

value: Male


title: STG_subject01420_SZ_rep1 [X1420.S]

source_name: postmortem STG of SZ subject 1420


title: tcx5/6-SAM_Rep1_BS-seq

value: Arabidopsis seedlings


title: Bisulfite-seq_tcx5/6;ddm1_rep1

extract_protocol:
Genomic DNA was extracted form 12-day old seedlings by CTAB and purified by phenol: chloroform: isoamyl Alcohol 25: 24: 1
DNA libraries were prepared for sequencing using standard Illumina protocols


title: STG_subject01453_SZ_rep1 [X1453.S]

source_name: postmortem STG of SZ subject 1453

value: Accidental


title: fer-4 rep2

first: Chao

address: 500 dongchuan Road

institute: East China Normal University

data_processing:
CASAVA
data filtering:  1) removing reads containing adapter;  2) removing reads containing ploy-N (i.e., unrecognized bases), reads with a ratio greater than 5%;  3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire  read);
RNAseq data were aligned to A. thaliana reference genome TAIR10 using Hisat2 v2.0.5 with default settings
Transcript discovery and quantification was done using Stringtie v1.3.3 with default settings
Genome_build: TAIR10
Supplementary_files_format_and_content: Discovered transcripts and their abudance were presented in FPKM (fragments per kilobase per million mapped reads ) values.

source_name: seedling

growth_protocol: Arabidopsis seedlings were grown vertically on ½ MS plates for 7 days under 16 hour light/8 hour dark conditions.

extract_protocol:
Total RNA was extracted using an RNAprep Pure Plant Kit (Tiangen).
The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library  Prep Kit for Illumina® (Vazyme, NR601) following manufacturer’s recommendations.

treatment_protocol: no treatment

tag: ecotype

value: FERONIA-/-


title: Bisulfite-seq_tcx5/6;ddm1_rep2


title: STG_subject01374_NPC_rep1 [X1374.C]

source_name: postmortem STG of NPC subject 1374

value: White

value: postmortem superior temporal gyrus (STG)


title: WT rep2


title: STG_subject01361_SZ_rep1&2 [X1361.S]

source_name: postmortem STG of SZ subject 1361

value: Natural

value: bisulfite-treated genomic DNA


title: STG_subject01372_NPC_rep1 [X1372.C]

source_name: postmortem STG of NPC subject 1372


title: fer-4 rep1


title: WT rep1


title: TCX5-FLAG Rep2


title: STG_subject01326_NPC_rep1 [X1326.C]

source_name: postmortem STG of NPC subject 1326


title: STG_subject01317_NPC_rep1 [X1317.C]

source_name: postmortem STG of NPC subject 1317


title: STG_subject01307_NPC_rep1 [X1307.C]

source_name: postmortem STG of NPC subject 1307

value: Black


title: STG_subject01296_SZ_rep1 [X1296.S]

source_name: postmortem STG of SZ subject 1296

value: Schizophrenia


title: Bisulfite-seq_ddm1_rep2


title: STG_subject01386_NPC_rep1 [X1386.C]

source_name: postmortem STG of NPC subject 1386


title: STG_subject01284_NPC_rep1 [X1284.C]

source_name: postmortem STG of NPC subject 1284


title: STG_subject01270_NPC_rep1 [X1270.C]

source_name: postmortem STG of NPC subject 1270

value: Female


title: STG_subject01268_NPC_rep1 [X1268.C]

source_name: postmortem STG of NPC subject 1268


title: Bisulfite-seq_ddm1_rep1

source_name: Arabidopsis seedlings


title: STG_subject01391_NPC_rep1 [X1391.C]

source_name: postmortem STG of NPC subject 1391


title: STG_subject01256_SZ_rep1 [X1256.S]

source_name: postmortem STG of SZ subject 1256

value: Suicide


title: STG_subject01255_NPC_rep1 [X1255.C]

source_name: postmortem STG of NPC subject 1255

value: Control


title: STG_subject01247_NPC_rep1 [X1247.C]

source_name: postmortem STG of NPC subject 1247


title: STG_subject01240_SZ_rep1 [X1240.S]

source_name: postmortem STG of SZ subject 1240


title: STG_subject01230_SZ_rep1 [X1230.S]

source_name: postmortem STG of SZ subject 1230


title: STG_subject01341_SZ_rep1 [X1341.S]

source_name: postmortem STG of SZ subject 1341


title: STG_subject01263_SZ_rep1 [X1263.S]

source_name: postmortem STG of SZ subject 1263


title: K562 OR21 treated

city: Saga

first: Shinya

last: Kimura

address: 5-1-1 Nabeshima

department: Drug Discovery and Biomedical Sciences, Faculty of Medicine

institute: Saga University

description: SAMPLE 10

hyb_protocol: According to the manufacturer’s instructions.

data_processing:
Using GeneSpring GX (Agilent Technologies, Inc., CA).
Normalized to expression of housekeeping gene controls using GeneSpring GX (Agilent Technologies, Inc., CA). Gene expression levels between two samples (control or OR21-treated) were compared and expressed as -fold changes.

label: Biotin

source_name: Chronic Myeloid Leukemia

growth_protocol: MDS-L cells were maintained in RPMI-1640 medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% foetal bovine serum (FBS, Sigma-Aldrich, St. Louis, MO, USA), 50 μM 2-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA) and 100 U/mL IL-3 (Peprotech, Rocky Hill, NJ, USA). SKM1, THP-1 and Kasumi-1 cells were maintained in RPMI-1640 medium supplemented with 10% FBS. HL60 (HL60R) and KG1a cells were maintained in Iscove’s Modified Dulbecco’s Medium (Sigma, St. Louis, MO, USA) supplemented with 20% FBS.

extract_protocol: Total RNA was isolated using a Direct-zol RNA MiniPrep kit (Zymo Research, Orange, CA).

treatment_protocol: MDS-L, SKM1 were treated with 100 nM of OR21 and HL60 and K562 were treated with 500 nM of OR21 (96hr).

tag: cell line

tag: cell type

value: Chronic Myeloid Leukemia

value: OR21 Treated

tag: treatment time period

value: 96hrs treatement


title: SKM1 OR21 treated

description: SAMPLE 8

scan_protocol: According to the manufacturer’s instructions.

source_name: Myelodysplastic Syndrome

value: Myelodysplastic Syndrome (MDS) cell line


title: K562 Control

description: SAMPLE 9

label_protocol: According to the manufacturer’s instructions.


title: STG_subject01222_SZ_rep1 [X1222.S]

source_name: postmortem STG of SZ subject 1222

value: Male

tag: tissue


title: STG_subject01211_SZ_rep1 [X1211.S]

source_name: postmortem STG of SZ subject 1211


title: MDSL OR21 treated

description: SAMPLE 6

value: MDSL


title: SKM1 Control

description: SAMPLE 7


title: HL60 OR21 resistant

description: SAMPLE 4

source_name: Acute Myeloid Leukemia

value: Acute Myeloid Leukemia (AML) cell line

tag: cell phenotype/genotype

value: OR21 resistant


title: MDSL Control

description: SAMPLE 5


title: STG_subject01201_NPC_rep1 [X1201.C]

source_name: postmortem STG of NPC subject 1201

tag: Sex

value: White


title: HL60 AZA resistant

description: SAMPLE 3

value: AZA resistant


title: STG_subject01196_NPC_rep1 [X1196.C]

source_name: postmortem STG of NPC subject 1196

tag: race

value: Accidental

value: postmortem superior temporal gyrus (STG)


title: HL60 OR21 treated

description: SAMPLE 2

value: parental


title: T2D 10

first: yihan

last: liu

address: No.10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT v2.0.5 with parameters --rna-strandness RF--dta –t –p 4.
Read Count for each gene in each sample is counted by HTSeq, and FPKM (Fragments Per Kilobase Millon Mapped Reads) were then calculated to represent the expression level of genes in each sample.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: peripheral blood leukocyte

extract_protocol:
Leukocyte were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEB Next Ultra Directional RNA LibraryPrep Kit for Illumina (NEB, Ispawich, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease

value: Type 2 Diabetes Mellitus

value: leukocyte


title: T2D 11


title: HL60 Control

description: SAMPLE 1


title: STG_subject01189_SZ_rep1 [X1189.S]

source_name: postmortem STG of SZ subject 1189

value: Schizophrenia

value: Female

tag: age (years)

tag: postmortem interval (hours)

value: Suicide

value: bisulfite-treated genomic DNA


title: 9CRO_593_3

city: Legnaro

first: Diana

last: Giannuzzi

state: Padova

address: viale dell'Università, 16

department: Dept. of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Biological replicate 12

hyb_protocol: Oligo aCGH analysis was performed following the manufacturer’s recommendations, using  Oligo aCGH/ChIP-on-chip Hybridization Kit

scan_protocol: Arrays were scanned at 3 µm resolution using an Agilent G2565CA scanner, and image data were processed using Feature Extraction version 11.5

data_processing:
Genomic Workbench version 7.0.4 was employed for data analysis, raw data were normalized using the centralization algorithm with a threshold of eight
Aberration Filter:  ( Minimum Number of Probes for Amplification >= 3 AND Minimum Size (Kb) of Region for Amplification >= 0.0 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25 ) OR ( Minimum Number of Probes for Deletion >= 3 AND Minimum Size (Kb) of Region for Deletion >= 0.0 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25 )

organism: Canis lupus familiaris

source_name: MZL

label_protocol: Tumor and reference DNA samples were labelled independently with cyanine 5-deoxyuridine triphosphate (dUTP) and cyanine 3-dUTP, respectively, using SureTag Complete DNA Labeling Kit.

extract_protocol: Genomic DNA was extracted from lymph nodes and skin punches using the DNeasy Blood & Tissue Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instructions.

value: tumor

value: marginal zone lymphoma

source_name: normal

value: skin biopsy


title: 7DEM_602_1

description: Biological replicate 10


title: STG_subject01188_SZ_rep1 [X1188.S]

source_name: postmortem STG of SZ subject 1188

value: Male

tag: mechanism of death

value: Natural

tag: illness duration (years)


title: 8ROS_596_1

description: Biological replicate 11


title: T2D 8


title: T2D 9


title: 54CIO_593_2

description: Biological replicate 9


title: 14VOL_592_3

description: Biological replicate 8


title: T2D 7


title: 62LAR_605_4

description: Biological replicate 7

source_name: FL

value: follicular lymphoma


title: STG_subject01173_SZ_rep1 [X1173.S]

source_name: postmortem STG of SZ subject 1173

value: White

tag: molecule subtype


title: 51PEZ_599_3

description: Biological replicate 6


title: T2D 5

value: Type 3 Diabetes Mellitus with family history


title: STG_subject01159_NPC_rep1 [X1159.C]

source_name: postmortem STG of NPC subject 1159

value: Control


title: STG_subject01099_NPC_rep1 [X1099.C]

source_name: postmortem STG of NPC subject 1099

value: postmortem superior temporal gyrus (STG)


title: STG_subject01119_NPC_rep1 [X1119.C]

source_name: postmortem STG of NPC subject 1119


title: STG_subject01105_SZ_rep1 [X1105.S]

source_name: postmortem STG of SZ subject 1105


title: T2D 2

value: Type 1 Diabetes Mellitus with family history


title: T2D 4

value: Type 2 Diabetes Mellitus with family history


title: T2D 3

value: leukocyte


title: STG_subject01092_NPC_rep1 [X1092.C]

source_name: postmortem STG of NPC subject 1092

value: Black


title: 22AGO_590_3

description: Biological replicate 3


title: 31DON_601_2

description: Biological replicate 5


title: 25BEV_596_3

description: Biological replicate 4


title: T2D 1


title: STG_subject01088_SZ_rep1 [X1088.S]

source_name: postmortem STG of SZ subject 1088

value: Schizophrenia

value: Accidental


title: STG_subject01086_NPC_rep1 [X1086.C]

source_name: postmortem STG of NPC subject 1086

value: bisulfite-treated genomic DNA


title: T2D 6

value: Type 4 Diabetes Mellitus with family history


title: 5Y_MZF1-AS1

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of MZF1-AS1

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 poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: SH-SY5Y stably transfected with MZF1-AS1

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The MZF1-AS1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of neomycin.

value: neuroblastoma

tag: passages


title: 5Y_empty_vector

description: Gene expression after stable transfection of empty vector

source_name: SH-SY5Y stably transfected with empty vector


title: STG_subject01047_NPC_rep1 [X1047.C]

source_name: postmortem STG of NPC subject 1047


title: High Quality eggs from wild female 5

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.1.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Sander lucioperca

source_name: High Quality eggs from wild female

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Domesticated pikeperch broodstock was reared for 6 years in recirculating aquaculture system (RAS) under fully controlled environmental conditions (oxygen level always >80% of saturation, ammonia in the range 0.2–1.1 mg l−1 and nitrite from 0.05–0.70 mg l−1). Water temperature was maintained automatically within the range 8-23°C (±0.5°C). Before the collection of the samples the fish were already successfully reproduced 3 times. The fish were exposed to annual fluctuations of photo-thermal conditions described in our previous studies (Żarski et al. 2019, Aquaculture 503; 527–536). The fish throughout the year were fed with compound feed (50% protein, 11% fat, 10% moisture, 1.55% crude fibre, 1.35% phosphorus, 9.5% ash and 17.9% nitrogen-free extract; Le Gouessant, France) at a rate between 0.2 and 1% of biomass daily, depending on the temperature and appearance of satiation. Wild pikeperch were collected during the spawning season from Vistula Lagoon (North of Poland) with fyke nets, when the average daily water temperature in the lagoon reached for the first time (after wintering) about 10°C.

extract_protocol: The total RNA from eggs was extracted using Total RNA Mini kit (Cat. No. 031-25, A&A Biotechnology, Gdynia, Poland) according to the producer’s protocol. For extraction approximately 50 mg of samples were taken. A NanoDrop® 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) was used to determine the concentration of the RNA samples. The quality of the RNA samples was checked using a 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, USA) and only samples exhibiting RIN value higher than 8.0 were taken for analysis. Genomic DNA was removed from the samples using DNA-free™ DNA Removal Kit (AM1906, Life Technologies, Carlsbad, CA, USA).

treatment_protocol: Controlled reproduction of the fish was performed with the methods described by Żarski et al. (2019, Aquaculture 503; 527–536), where hormonal stimulation of ovulation and spermiation with human chorionic gonadotropin (hCG; Chorulon, Intervet, France) at a dose of 500 and 250 IU kg-1 for males and females, respectively, was applied. At the time of injection the water temperature was 12°C and was kept constant until ovulation. Photoperiod following the induction of ovulation was 14 h of photo-phase. Eggs, for RNA extraction, from each female separately were snap frozen in liquid nitrogen right after collection.

tag: environment

value: Wild

value: female

value: eggs


title: STG_subject01026_NPC_rep1&2 [X1026.C]

source_name: postmortem STG of NPC subject 1026

value: Male

value: Natural


title: High Quality eggs from wild female 7


title: 15GIO_590_1

description: Biological replicate 1

value: tumor

value: follicular lymphoma

value: skin biopsy


title: 20MAG_596_2

description: Biological replicate 2


title: STG_subject01010_SZ_rep1&2 [X1010.S]

source_name: postmortem STG of SZ subject 1010

value: Female

value: postmortem superior temporal gyrus (STG)


title: STG_subject10025_SZ_rep1&2 [X10025.S]

source_name: postmortem STG of SZ subject 10025


title: High Quality eggs from wild female 4


title: STG_subject10026_SZ_rep1 [X10026.S]

source_name: postmortem STG of SZ subject 10026

value: White

value: Suicide


title: High Quality eggs from wild female 6


title: STG_subject10024_SZ_rep1 [X10024.S]

source_name: postmortem STG of SZ subject 10024

value: Schizophrenia

value: Black


title: STG_subject10020_SZ_rep1 [X10020.S]

source_name: postmortem STG of SZ subject 10020

value: bisulfite-treated genomic DNA


title: High Quality eggs from wild female 3


title: High Quality eggs from wild female 2


title: High Quality eggs from wild female 1


title: High Quality eggs from domesticated female 8

value: Domesticated


title: High Quality eggs from domesticated female 6


title: High Quality eggs from domesticated female 7


title: STG_subject10023_SZ_rep1 [X10023.S]

source_name: postmortem STG of SZ subject 10023


title: lon-MM-ChIPseq-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

institute: City University of Hong Kong

data_processing:
ChIP-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using Bowtie (Version 1.2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. Binding peaks (q < 0.05) were identified using MACS software (version 2.1.0).
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR, only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas sringae 1448A
Supplementary_files_format_and_content: txt file containing raw counts of genes in WT and lon mutant, and Lon-HA vs WT narrowPeaks

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

source_name: liquid culture in KB (King's B)  medium

growth_protocol: grow until mid-log phase in KB, then transfer into MM

extract_protocol:
An empty  pHM2 plasmid was transformed into the wild-type strain, and then cultured in KB medium until it reached OD600 of 0.6 before transferring to MM liquid medium for 6 h. The strains were treated with 1% formaldehyde for 10 min at 28°C. Cross-linking was stopped by the addition of 125 mM glycine. The cell cultures were centrifuged, and the pellets were washed twice with Tris-buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl) and then resuspended in 500 μL immunoprecipitation (IP) buffer (50 mM HEPES-KOH [pH 7.5], 1 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail). Next, the DNA was subjected to sonication to produce 100- to 300-bp DNA fragments. The insoluble cellular debris was removed by centrifugation at 4°C, and the supernatant was saved as the input sample in the IP experiments. Both the control and IP samples were washed with protein A beads (General Electric) and mixed with 50 μL agarose-conjugated anti-hemagglutinin (anti-HA) antibodies (Sigma) in IP buffer. The following washing, cross-link reversal, and purification of ChIP-DNA steps were conducted as previously described. DNA fragments (150 to 250 bp) were selected for library construction, and libraries were constructed by using the NEXTflex ChIP-seq kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). All experiments had two repeats.
TruSeq DNA sample prep kit protocol (Illumina)

treatment_protocol: grow until mid-log phase

tag: genotype

value: WT

tag: transformed with

value: empty pHM2 plasmid

tag: growth protocol

value: KB, then MM

tag: chip antibody


title: lon-MM-ChIPseq-2

extract_protocol:
An pHM2-lon-HA plasmid was transformed into the wild-type strain, and then cultured in KB medium until it reached OD600 of 0.6 before transferring to MM liquid medium for 6 h. The strains were treated with 1% formaldehyde for 10 min at 28°C. Cross-linking was stopped by the addition of 125 mM glycine. The cell cultures were centrifuged, and the pellets were washed twice with Tris-buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl) and then resuspended in 500 μL immunoprecipitation (IP) buffer (50 mM HEPES-KOH [pH 7.5], 1 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail). Next, the DNA was subjected to sonication to produce 100- to 300-bp DNA fragments. The insoluble cellular debris was removed by centrifugation at 4°C, and the supernatant was saved as the input sample in the IP experiments. Both the control and IP samples were washed with protein A beads (General Electric) and mixed with 50 μL agarose-conjugated anti-hemagglutinin (anti-HA) antibodies (Sigma) in IP buffer. The following washing, cross-link reversal, and purification of ChIP-DNA steps were conducted as previously described. DNA fragments (150 to 250 bp) were selected for library construction, and libraries were constructed by using the NEXTflex ChIP-seq kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). All experiments had two repeats.
TruSeq DNA sample prep kit protocol (Illumina)

value: pHM2-lon-HA plasmid


title: lon-KB-ChIPseq-1

growth_protocol: grow until mid-log phase in KB

extract_protocol:
An empty pHM2 plasmid was transformed into the wild-type strain, and then cultured in KB medium until it reached OD600 of 0.6 before transferring to MM liquid medium for 6 h. The strains were treated with 1% formaldehyde for 10 min at 28°C. Cross-linking was stopped by the addition of 125 mM glycine. The cell cultures were centrifuged, and the pellets were washed twice with Tris-buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl) and then resuspended in 500 μL immunoprecipitation (IP) buffer (50 mM HEPES-KOH [pH 7.5], 1 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail). Next, the DNA was subjected to sonication to produce 100- to 300-bp DNA fragments. The insoluble cellular debris was removed by centrifugation at 4°C, and the supernatant was saved as the input sample in the IP experiments. Both the control and IP samples were washed with protein A beads (General Electric) and mixed with 50 μL agarose-conjugated anti-hemagglutinin (anti-HA) antibodies (Sigma) in IP buffer. The following washing, cross-link reversal, and purification of ChIP-DNA steps were conducted as previously described. DNA fragments (150 to 250 bp) were selected for library construction, and libraries were constructed by using the NEXTflex ChIP-seq kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). All experiments had two repeats.
TruSeq DNA sample prep kit protocol (Illumina)

value: KB


title: lon-2-KB-RNAseq

extract_protocol:
To examine the effect of Lon on the transcriptome, 2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PS and ∆lon strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

value: lon mutant


title: WT-2-KB-RNAseq


title: High Quality eggs from domesticated female 5

value: female

value: eggs


title: lon-KB-ChIPseq-2

value: anti-hemagglutinin (anti-HA) antibodies (Sigma)


title: WT-1-KB-RNAseq


title: lon-1-KB-RNAseq


title: lon-1-MM-RNAseq


title: WT-2-MM-RNAseq


title: BTXA5

first: Mao

last: Qianying

address: No. 22 Zhong Guan Cun South Street, Haidian District,

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

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: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: gilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

organism: Rattus norvegicus

source_name: submandibular gland

label_protocol: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Healthy Adult male Sprague-Dawley rats(230-250g) were purchased from the Laboratory Animal Service Center, Peking University Health Science Center.We used standard rat chow and water to feed rats. They were placed in polycarbonate micro-isolator cages separately in a controlled environment with a temperature of 20-26 ° c, a relative humidity of 40-70%, and a light-dark cycle of 12 hours bright /12 hours dark.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Eight rats were evenly divided into control and the BTXA group. All the rats were anesthetized by intramuscular injection of ketamine (100 mg/kg body weight) and xylazine (5 mg/kg body weight). A median cervical incision exposed the left submandibular glands. For the control groups, the left gland was injected with 0.1 mL physiological saline, whereas the left gland was injected with 6U BTXA (Lanzhou Biochemical Co, Gansu, China) reconstituted in 0.1 mL physiological saline for the BTXA group. After the operation for 2 weeks, all the left glands were excised and stored at -80°c immediately.

value: submandibular gland

tag: gender

value: male

tag: age

value: 8 week old

tag: group

value: BTXA


title: High Quality eggs from domesticated female 1

tag: Sex

tag: tissue


title: lon-2-MM-RNAseq


title: Ctrl3

value: control


title: WT-1-MM-RNAseq


title: BTXA2


title: BTXA1


title: BTXA3


title: SATxSSA milkripe seeds (10 DAF) rep3

city: Madison

first: Sarah

middle: J

last: Whitcomb

state: WI

address: 502 Walnut St

department: Cereal Crops Research Unit

institute: USDA-ARS

data_processing:
Raw data were mapped against the rice genome using STAR  version 2.7.1a with the parameters --quantMode TranscriptomeSAM GeneCounts, --outSAMtype BAM Unsorted, and --outReadsUnmapped Fastx.
Genome_build: Ensembl version 43 (IRGSP 1.0) genome reference in FASTA format (ftp://ftp.ensemblgenomes.org/pub/release-43/plants/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz) and Ensembl version 43 cDNA Annotation in GTF format (ftp://ftp.ensemblgenomes.org/pub/release-43/plants/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.43.gtf.gz) were used for genome indexing (--sjdbOverhang 149 --genomeSAindexNbases 13)
Supplementary_files_format_and_content: Default STAR output files (ASCII format, tab delimited): Gene identifier, Read count (unstranded RNA-seq), Read count (counts for the 1st read strand aligned with RNA), Read count (counts for the 2nd read strand aligned with RNA)

organism: Oryza sativa Japonica Group

source_name: milkripe seeds (10 DAF)

growth_protocol: Seeds were allowed to germinate at 28°C in the dark on tap water-soaked paper towels. After 10 days, seedlings were transferred to a growth chamber with the following conditions: 12 h day length with a photon flux density of 600 μE m-2 s-1 (Lamps: Iwasaki Eye MT 400 DL/BH E40, DHL Licht, Wülfrath, Germany); 26 °C in the light and 22 °C in the dark; relative humidity of 75 % in the light and 70% in the dark. Single seedlings were transplanted into individual pots (18 cm deep, 10 cm diameter) of waterlogged soil after 7 days of acclimation to the growth chamber. Soil was a mixture of 2 parts potting soil (70 % white moss peat, 30 % clay) and one-part sand. 1 g of slow-release fertilizer (Plantacote Depot 4 M; Lanxess, Langenfeld, Germany) and 0.1 g Fetrilon Combi (Compo, Münster, Germany) was mixed into the soil in each pot. Pots were kept partially submerged in water. Milkripe seed samples were harvested 10 days after flowering on an individual panicle basis.

extract_protocol:
Total RNA was prepared from approximately 100 mg of frozen, finely ground tissue with RibospinTM Seed/Fruit kit (GeneAll Biotechnology, Korea) followed by two rounds of DNase treatment (first round with RiboclearTM plus! from GeneAll, second round with TURBO DNA-free Kit from Invitrogen) and PCR was performed to assess possible remaining genomic DNA contamination. Only those total RNA samples with RIN quality scores greater than 7.3 by Bioanalyzer were submitted for RNA sequencing
Library preparation and sequencing were performed at the Max Planck Genome Center, Cologne, Germany (https://mpgc.mpipz.mpg.de/home). rRNA depletion was performed on 1000 ng total RNA samples with the Ribo-Zero™ rRNA Removal Kit (seed/root) from Illumina. Subsequent library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer's instructions. Quality and quantity were assessed at all steps via capillary electrophoresis (TapeStation, Agilent Technologies) and fluorometry (Qubit, Thermo Fisher Scientific).

tag: line

value: SATxSSA

tag: replicate


title: Ctrl1


title: Mixed_sample_all_conditions

city: Heidelberg

first: Staffan Andreas

last: Johansson

address: Meyerhofstraße 1

country: Germany

institute: EMBL Heidelberg

description: non-demultiplexed raw data

data_processing:
See Matsumura et al. 2011. High-Throughput SuperSAGE. Methods Mol Biol. for detailed instructions for the data processing.
Genome_build: SRA023642
Supplementary_files_format_and_content: Tab-delimited file with counts for each sample

organism: Dunaliella tertiolecta

source_name: Whole cell

growth_protocol: Cultures of Dunaliella tertiolecta were grown under sterile conditions in liquid f/2 - Si media as well as on f/2 - Si agar plates.

extract_protocol:
RNA was extracted using the cetyltrimethylammonium bromide (CTAB) method (Pearson et al. 2006. Simple and rapid RNA extraction from freeze-dried tissue of brown algae and seagrasses. Eur J Phycol.) using 35 mL of samples from cultures of wild type, lca1 and lca2 grown under low, medium and high light. The cells were disrupted on a Tissue Lyser II bead beater (Qiagen, Valencia, CA, USA) using 250 mL of beads at 20 RPM for 5 min with 1.5 mL of CTAB added per sample. The extracted RNA was transcribed into cDNA using the ImProm-II Reverse Transcription System (Promega Corporation, Madison, WI, USA) according to the manufacturer’s instructions.
SAGE libraries were prepared and sequenced at Iwate Biotechnology Research Centre, Kitakami, Iwate, Japan, following the SuperSAGE method (Matsumura et al. 2006. SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Methods.) using a more recent protocol (HT-SuperSAGE) as described in (Matsumura et al. 2011. High-Throughput SuperSAGE. Methods Mol Biol.). The cDNA was digested using the NLAIII restriction enzyme, ligated with adapter sequences and further cleaved using EcoP15I linked to a second set of adapter sequences, including 4-bp index sequences.

treatment_protocol: Growth under low, medium and high light (20, 100, 1200 µmol photons m-2 s-1).

value: Wild type

value: Whole cell


title: Ctrl4


title: Ctrl2


title: High Quality eggs from domesticated female 2

value: Domesticated


title: CGS milkripe seeds (10 DAF) rep4

value: CGS


title: CGS milkripe seeds (10 DAF) rep5


title: SATxSSA milkripe seeds (10 DAF) rep1


title: SAT milkripe seeds (10 DAF) rep3

value: SAT


title: SAT milkripe seeds (10 DAF) rep2


title: SSA milkripe seeds (10 DAF) rep2

value: SSA


title: SAT milkripe seeds (10 DAF) rep1


title: CGS milkripe seeds (10 DAF) rep2


title: SATxSSA milkripe seeds (10 DAF) rep2


title: SSA milkripe seeds (10 DAF) rep3


title: CGS milkripe seeds (10 DAF) rep3


title: epithelial cells, IPF3

first: Changfu

last: Yao

address: 8700 Beverly Blvd. AHSP Room A9401

institute: cedars-sinai medical center

data_processing:
follow default Cellranger v2.2.0
Genome_build: GRCh38
Supplementary_files_format_and_content: demultiplexed count matrix file

source_name: human IPF lung

extract_protocol:
follow standard 10x single cell 3 prime v2 kit manuscript
10x chromium single cell RNAseq

value: IPF

value: lung

tag: cell type

value: epithelial cells


title: CGSxSSA milkripe seeds (10 DAF) rep3

value: CGSxSSA


title: SSA milkripe seeds (10 DAF) rep1


title: CGSxSSA milkripe seeds (10 DAF) rep2


title: CGS milkripe seeds (10 DAF) rep1


title: epithelial cells, IPF2


title: epithelial cells, IPF1


title: Taipei milkripe seeds (10 DAF) rep3

value: Taipei


title: epithelial cells, CON3

source_name: human donor control lung


title: Taipei milkripe seeds (10 DAF) rep2


title: Taipei milkripe seeds (10 DAF) rep1


title: epithelial cells, CON2


title: CGSxSSA milkripe seeds (10 DAF) rep1


title: epithelial cells, CON1


title: High Quality eggs from domesticated female 4

value: female

value: eggs


title: CD8+PBMC_16

status: Public on Jun 29 2020

first: Caroline

last: Wasen

state: Massachusetts

address: 60 Fenwood road

department: Ann Romney Center for Neurological Disease

institute: Brigham and Women's Hospital

hyb_protocol: 2.2 μl of each sample was  mixed with miRNA spike (Cat No TRT-XR304, Toray) and further labeled, hybridized and washed according to the instruction manual from Toray (H-M-R miRNA protocol 4-Plex V3 using Toray miRNA Labeling kit (Cat No TRT-XE211) and Human miRNA Oligo chip 4plex (2), based on miRBase 21 (Cat No TRT- XR520, Toray).

scan_protocol: The intensity of each miRNA was analyzed with the 3D-Gene Scanner 3000 (Toray) with auto gain, auto focus and auto analysis settings, all per manufacturer’s instructions.

data_processing:
The top 125 miRs with the highest average expression from the microarray analysis were log2 transformed and normalized through cyclic loess normalization using R, R studio and the LIMMA (Linear models for microarray data) package. Samples 9 and 10 were excluded due to low number of miRs exceeding the background intensity.
normalized data file includes R computed normalized signal intensity

label: 3D-Gene® miRNA labeling kit

source_name: CD8+ PBMC

growth_protocol: Isolated CD8+ T cells were cultured at a density of 400 000 – 1000 000 cells/ml in 24-well cell culture plates in in RPMI medium including 10% foetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA), 4 mM Glutamax (Gibco), 50 mM b-mercaptoethanol (Gibco) and 50 mg/mL gentamycin (Sanofi-Aventis, Paris, France), a temperature of 37 °C and an atmosphere of 5% CO2.

extract_protocol: RNA was prepared from cell lysates with the microRNA Purification Kit (Norgen Biotec Corp, Canada) according to manufacturer's protocol.

treatment_protocol: Cells were stimulated with phorbol 12-myristate 13-acetate/ionomycin (PMA/IM, 30nM and 500 nM) for 2 h.

value: CD8+ T cells

value: Female

tag: smoker?

value: No

tag: rheumatoid arthritis?

value: Yes


title: CD8+PBMC_15

label_protocol: 2.2 μl of each sample was  mixed with miRNA spike (Cat No TRT-XR304, Toray) and further labeled, hybridized and washed according to the instruction manual from Toray (H-M-R miRNA protocol 4-Plex V3 using Toray miRNA Labeling kit (Cat No TRT-XE211) and Human miRNA Oligo chip 4plex (2), based on miRBase 21 (Cat No TRT- XR520, Toray).


title: CD8+PBMC_14


title: CD8+PBMC_9

description: sample excluded due to low number of miRs exceeding the background intensity


title: CD8+PBMC_7


title: CD8+PBMC_8


title: CD8+PBMC_10


title: CD8+PBMC_13


title: CD8+PBMC_11


title: CD8+PBMC_4


title: CD8+PBMC_6


title: CD8+PBMC_3


title: CD8+PBMC_1


title: CGSxSSA milkripe seeds (10 DAF) rep4


title: CD8+PBMC_2


title: errbs_WT_NB2

city: Farmington

first: Sheng

last: Li

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Adaptor sequences were removed using FAR software.
Preprocessed reads were then aligned to human genome reference using the bismark alignment software.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files contain methylated cytosines positions.

source_name: Naïve B-cells

growth_protocol: Cells were isolated from mouse spleens

extract_protocol:
DNA was extracted using Qiagen Gentra Puregene kit
ERRBS

treatment_protocol: Not applicable

value: Naive B-cells

value: spleen

value: TET2 Wild-Type

tag: strain


title: errbs_KO_NB2

value: TET2 Knock-Out


title: errbs_WT_NB1


title: errbs_KO_NB3


title: TT2 ES ssDNA-seq

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

description: Peak files include ChIP and input island read counts.

data_processing:
Library strategy: ssDNA-seq
Basecalling and adapter sequence trimming was performed using the standard Illumina workflow.
Reads were aligned to the mm9 genome using Bowtie2 v2.3.1 with default parameters.
Non-uniquely mapped reads were filtered out using MapQ > 10 for the "unique-mapping" peak file.
PCR and optical duplicates were removed with Picard v2.9.0.
Peaks were called using SICER v1.1 using an FDR cutoff of 0.01 and input DNA as control with window 200 bp (w200) and gap 600 bp (g600), or alternatively w100 g200.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with 8 tab delimited columns: chrom, start, end, ChIP island read count, CONTROL (input) island read count, p value, fold change, FDR threshold

source_name: ES cell

growth_protocol: ES cells were maintained on feeder cells in DMEM supplemented with 15% fetal bovine serum, 1% non-essential amino acids, 2 mM l-glutamine, 1,000 units of mLIF, 0.1 mM β-mercaptoethanol, and antibiotics. In addition, Cdx2 ES cell media was supplemented with 2 µg/ml doxycycline.

extract_protocol:
Briefly, live cells were treated with 100 mM KMnO4 then lysed. Each subsequent treatment was followed by phenol:chloroform extraction. Lysates were first treated with proteinase and Rnase, then free 3' ends blocked by cordycepin-5’-triphosphate addition wtih TdT. ssDNA was digested with S1 nuclease then free 3' ends biotinylated. Samples were sonicated with Covaris S220 to generate DNA fragments between 200 and 700 bp and biotinylated fragments pulled down using streptavidin-coated beads. Fragments were released by incubating with S1 nuclease and purified with MinElute PCR Purification Kit (Qiagen)
Libraries were prepared using the NEBNext Ultra II DNA Library Prep kit according to the manufacturer’s instructions without size selection.

value: Wild-type

tag: cell line


title: Cdx2 ES ssDNA-seq


title: errbs_KO_NB1


title: CD8+PBMC_12


title: Line 17 WT H3K27me3 rep2

city: Sacramento

first: Paul

last: Knoepfler

state: CA

address: 2425 Stockton Blvd, Room 633

department: Cell Biology and Human Anatomy

institute: University of California Davis

description: Line 17 WT H3K27me3 rep2

data_processing:
Reads were called with illumina bclfastq
Reads were aligned to the hg19 genome with BWA (version 0.7.13-r1126 )
Peaks were called with MACS2 (version 2.1.0.20151222)
Differential peak occupancy analysis was performed with DiffBind (R version 3.5.2)
Downstream analysis was performed on the Galaxy webserver
Genome_build: hg19
Supplementary_files_format_and_content: bed files of peaks

source_name: Line XVII DIPG

growth_protocol: All DIPG cells were cultured in Tumor Stem Medium (Nagaraja et al, 2017), which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies to H3K27me3 (Cell Signaling C36B11) or H3.3  (Millipore #09-838).
Libraries were prepared with the Nextera library prep kit
Libraries were sequenced on the NovaSeq machine with 150 base paired-end sequencing

treatment_protocol: Single-stranded donor oligonucleotide (ssODN) templates were designed with the desired mutations to facilitate homology directed repair (HDR) after cleavage of H3F3A by Cas9n. cells were co-transfected with a combination of pSpCas9n(BB)-2A-GFP-guideA (0.5μg/well), pSpCas9n(BB)-2A-Puro-guideB (0.5μg/well), and ssODN HDR (1μg/well) template using XtremeGene-HP (Sigma).

tag: histone h3.3 status

value: WT

tag: antibody


title: Line 17 H3K27me3 rep1

description: Line 17 H3K27me3 rep1

value: mutant (K27M)


title: Line 17 H3K27me3 rep2

description: Line 17 H3K27me3 rep2


title: Line 17 WT H3K27me3 rep1

description: Line 17 WT H3K27me3 rep1


title: CD8+PBMC_5


title: Line 13 WT H3K27me3 rep1

description: Line 13 WT H3K27me3 rep1

source_name: Line XIII DIPG


title: Line 13 H3K27me3 rep2

description: Line 13 H3K27me3 rep2


title: Line 13 H3K27me3 rep1

description: Line 13 H3K27me3 rep1


title: errbs_WT_NB3

tag: genotype


title: Line 17 WT H3.3 rep2

description: Line 17 WT H3.3 rep2


title: Line 17 WT H3.3 rep1

description: Line 17 WT H3.3 rep1


title: Line 17 H3.3 rep2

description: Line 17 H3.3 rep2


title: Line 17 H3.3 rep1

description: Line 17 H3.3 rep1


title: Line 13 H3.3 rep1

description: Line 13 H3.3 rep1


title: Line 13 WT H3.3 rep1

description: Line 13 WT H3.3 rep1


title: Line 13 H3.3 rep2

description: Line 13 H3.3 rep2


title: Mixed S. cerevisiae and S. Bayanus cells

status: Public on Jun 26 2020

city: West Haven

first: Guste

last: Urbonaite

address: 300 Heffernan Drive, ISTC, Rm 117

department: Molecular and Cellular Biology

institute: Yale University

data_processing:
Paired end reads were combined after trimming of adapters on R1 and subjected to fastq quality control and trimming
Cell barcodes were extracted from reads and attached to read name. This was done using the DropSeq alignment protocol
Reads were aligned to S. cerevisiae genome for MPA experiments, or aligned to the cerevisiae and bayanus genomes for the species mixing experiments
Aligned reads had gene and exon information added to produce digital gene expression data
MPA experiment data was integrated and analyzed using the seurat standard integration protocol
Genome_build: S. cerevisiae genome (R64-1-1), or S. bayanus genome (unassembled CBS 7001)
Supplementary_files_format_and_content: .dge files are in txt format and contain digital gene expression data of individual genes per cell

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

source_name: S. cerevisiae and S. bayanus

growth_protocol: Cells were grown for 18 hrs in CSM 2% glucose in MPA, Guanine, DMSO, or Guanine+MPA for MPA experiments. Cells were grown in CSM 2% glucose for species mixing S. bayanus and S. cerevisiae

extract_protocol:
DropSeq
Nextera XT standard illumina primers
Single cell RNA seq

treatment_protocol: Treated with 10 uM DMSO, MPA, Guanine, of Guanine and MPA. Species mixing experiment cells were not treated

tag: growth period

value: 18 hrs