title: single cell RNA-low 78


title: single cell RNA-low 77

status: Public on Dec 31 2020

type: SRA

city: Toronto

first: Alyssa

middle: M

last: Molinaro

state: Ontario

address: 686 Bay Street

department: Molecular Genetics

country: Canada

institute: University of Toronto

library_source: transcriptomic

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Trimmed reads (3' 15 bp) were aligned to the transcriptome associated with NCBI BioProject PRJNA215411 using the program Bowtie2. Raw counts were extracted from resulting SAM files.
For bulk samples, raw counts were normalized to the number of mapped reads to calculate Reads Per Million (RPM) prior to analysis. For single cell samples, raw counts were log2 normalized with a small pseudocount of +1 prior to analysis.
Genome_build: NCBI BioProject 215411, SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: Excel tab delimited. Raw counts.

molecule: total RNA

organism: Schmidtea mediterranea

source_name: planarian whole body

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.

extract_protocol:
Bulk samples were RNA extracted in Trizol reagent.
Bulk samples were library prepped using Illumina's Truseq Library kits. Single cell samples were prepped using the Smart-seq2 protocol.

treatment_protocol: Animals were dissociated by douncing in cold CMF + 1% BSA and cells were stained with Hoechst and pyrnonin Y prior to FACS.

tag: facs gate

value: RNA-low

tag: sample type

value: single cell

tag: treatment

value: Hoechst/pyronin Y stain & FACS

tag: tissue

value: sorted cells

tag: strain

value: Asexual CIW4


title: MDA-MB-231 stably expressing MYOSIN10 shRNA 1

type: RNA

city: Changchun

first: Rangjuan

last: Cao

state: jilin

address: 5268 Renmin Street

department: Institute of Genetics and Cytology

country: China

institute: Northeeast Normal University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain  Kit  (Cat#900720,  Affymetrix,  Santa  Clara,  CA,  US) in  Hybridization  Oven  645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw  data  were  normalized  by  MAS  5.0  algorithm,  Gene  Spring  Software  11.0 (Agilent technologies, Santa Clara, CA, US).
probe group file: HuGene-1_0-st-v1.r4.pgf/HG-U133_Plus_2.pgf
meta-probeset_file: HuGene-1_0-st-v1.r4.mps/HG-U133_Plus_2.mps

label: Biotin

organism: Homo sapiens

source_name: Human brest cancer cell

label_protocol: Total  RNA  were  amplified,  labeled  and  purified  by  using  GeneChip 3’IVT  Express  Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: MDA-MB-231 cells were cultured in Leibovitz’s L-15 medium with 10% FBS at 37 ºC without CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell line

tag: expression

value: MYOSIN10 shRNA


title: single cell RNA-low 76


title: single cell RNA-low 75


title: single cell RNA-low 73


title: Hypoxic Glioblastoma 10 Stem-like cell line, exposed to Normoxia for 48 h

city: Hamburg

first: Katrin

last: Lamszus

address: Martinistrasse 52

country: Germany

institute: UKE

hyb_protocol: Standard Affymetrix protocols

scan_protocol: Standard Affymetrix protocols

data_processing: Background-adjusted, normalized intensities were computed using the gcRMA package. Gene detection was performed using the PANP package (http://bioconductor.org/packages/bioc/vignettes/panp/inst/doc/panp.pdf) for the R program.

label: biotin

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 10, exposed to Normoxia for 48 h

label_protocol: Standard Affymetrix protocols

growth_protocol: Glioblastoma stem-like cell lines (GS lines): neurobasal medium with B27 supplement (20 μl ml−1), Glutamax (10 μl ml−1), fibroblast growth factor-2 (20 ng ml−1), epidermal growth factor (20 ng ml−1) and heparin (32 IE ml−1)

extract_protocol: Total RNA was extracted from cells using the RNeasy Protect Mini Kit (Qiagen). Genomic DNA contamination was removed through an on-column DNase digestion step

treatment_protocol: Cell dissociation and exposure to normoxic or hypoxic conditions for 48 h

tag: cell type

value: exposed to Normoxia for 48 h


title: single cell RNA-low 72


title: Normoxic Glioblastoma 10 Stem-like cell line

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 10


title: single cell RNA-low 71


title: Normoxic Glioblastoma 11 Stem-like cell line

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 11


title: Hypoxic Glioblastoma 10 Stem-like cell line

source_name: Hypoxic Glioblastoma Stem-like cell line derived from tumor 10


title: single cell RNA-low 70


title: Tumor 13

source_name: Glioblastoma Tumor 13

value: Glioblastoma Tumor


title: Tumor 12

source_name: Glioblastoma Tumor 12


title: Tumor 11

source_name: Glioblastoma Tumor 11


title: single cell RNA-low 69


title: single cell RNA-low 68


title: single cell RNA-low 67


title: single cell RNA-low 65


title: single cell RNA-low 66


title: single cell RNA-low 64


title: single cell RNA-low 63


title: single cell RNA-low 62


title: single cell RNA-low 74


title: single cell RNA-low 59


title: single cell RNA-low 61


title: single cell RNA-low 58


title: single cell RNA-low 60


title: single cell RNA-low 55


title: single cell RNA-low 57


title: single cell RNA-low 54


title: single cell RNA-low 53


title: single cell RNA-low 52


title: single cell RNA-low 51


title: single cell RNA-low 50


title: Tumor 10

source_name: Glioblastoma Tumor 10


title: P4_4-NGF_axon_2_TGACCA_L005

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end stranded RNA-seq reads of 150 bp were mapped to the reference rat genome (UCSC, rn5) using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml) allowing up to 20 multi-alignments and 2 read mismatches.
3' UTR isoforms were then re-annotated using the cutom made bioinformatic pipeline accessible in Github repository https://github.com/RLuisier/my3UTRs. The novel 3' UTR annotation can be downloaded at https://github.com/RLuisier/my3UTRs/blob/master/utrid/APA/L2.gtf
Genome_build: rn5
Supplementary_files_format_and_content: Relative 3' UTR isoform abundance obtained by counting the reads mapping to the last 500 nt fragments of each 3' UTR isoform of the file https://github.com/RLuisier/my3UTRs/blob/master/utrid/APA/L2.gtf

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Post-mitotic sympathetic neurons

growth_protocol: Superior cervical ganglia were dissected from post-natal day 1 (P1) Sprague Dawley rats , enzymatically dissociated and plated in compartmentalized chambers, as previously described Andreassi et at doi: 10.1038/nn.2486

extract_protocol:
To ensure that the axons were free of cell bodies, prior to each experiment axon compartments were incubated with Hoechst 33342 (10mg/mL in PBS for 20 min at 37˚C) and observed under an inverted fluorescent microscope. Cultures showing cell nuclei in the axon compartments or leakage of the dye in the central compartment were discarded. Total axonal and cell bodies RNA was purified from the lateral compartments of 52 or 36 chambers and the central compartment of 7 or 6 chambers respectively obtained from 3 or more independent cultures. Total RNA was isolated using PureLink® RNA Micro Scale Kit, according to the manufacturer’s instructions with minor modifications. Briefly, axons and cell bodies were collected from chambers using lysis buffer (300L) containing 10%mercaptoethanol. Total mRNA bound to the columns was washed and eluted twice in elution buffer (12L). Aliquots of each sample was reverse transcribed in a 20L reaction volume containing random hexamer mix and 50U SuperScript III Reverse Transcriptase at 50°C for 1 hr. To check the quality of samples and the absence of cell bodies contamination in axon samples, first-strand cDNAs (5L) were PCR amplified in a 25L PCR reaction containing actin beta or histone H4 specific primers (0.20M), dNTPs (200nM) and Go Taq polymerase (1.25U, Promega).
Libraries were prepared at the Liverpool Centre for Genomic Research using the strand-specific Script-seq protocol (Illumina). Paired-end sequencing (2x 150bp) of four indexed libraries was performed on the Illumina HiSeq2000 platform, generating in excess of 80M mappable reads per sample.

tag: compartment

value: axon

tag: neurotrophic factor

value: NGF

tag: replicates


title: P4_5-NT3_cb_1_ACAGTG_L005

value: cb


title: P4_6-NT3_cb_2_TAGCTT_L005


title: P4_8-NGF_cb_2_CTTGTA_L005


title: P4_3-NGF_axon_1_ACTTGA_L005


title: single cell RNA-low 48


title: P4_7-NGF_cb_1_GGCTAC_L005


title: P4_1-NT3_axon_1_ATCACG_L005


title: P4_2-NT3_axon_2_CGATGT_L005


title: single cell RNA-low 45


title: single cell RNA-low 47


title: P3_8-NGF_cb_2_CTTGTA_L001


title: single cell RNA-low 44


title: single cell RNA-low 56


title: P3_7-NGF_cb_1_GGCTAC_L001


title: single cell RNA-low 42


title: P3_6-NT3_cb_2_TAGCTT_L002


title: single cell RNA-low 43


title: P3_7-NGF_cb_1_GGCTAC_L002


title: single cell RNA-low 40


title: single cell RNA-low 41


title: single cell RNA-low 49


title: P3_5-NT3_cb_1_ACAGTG_L002


title: single cell RNA-low 39


title: single cell RNA-low 38


title: single cell RNA-low 46


title: single cell RNA-low 36


title: P3_3-NGF_axon_1_ACTTGA_L001


title: P3_5-NT3_cb_1_ACAGTG_L001


title: P3_3-NGF_axon_1_ACTTGA_L002


title: single cell RNA-low 35


title: single cell RNA-low 34


title: single cell RNA-low 32


title: single cell RNA-low 33


title: single cell RNA-low 31


title: P3_2-NT3_axon_2_CGATGT_L001


title: P2_8-NGF_cb_2_CTTGTA_L002


title: P2_8-NGF_cb_2_CTTGTA_L001


title: P2_7-NGF_cb_1_GGCTAC_L001


title: single cell RNA-low 29


title: P3_6-NT3_cb_2_TAGCTT_L001


title: single cell RNA-low 28


title: P2_6-NT3_cb_2_TAGCTT_L002


title: P2_7-NGF_cb_1_GGCTAC_L002


title: single cell RNA-low 27


title: P2_6-NT3_cb_2_TAGCTT_L001


title: single cell RNA-low 37


title: P2_5-NT3_cb_1_ACAGTG_L002


title: P3_2-NT3_axon_2_CGATGT_L002


title: single cell RNA-low 26


title: P2_5-NT3_cb_1_ACAGTG_L001


title: single cell RNA-low 24


title: P3_1-NT3_axon_1_ATCACG_L001


title: P2_3-NGF_axon_1_ACTTGA_L002


title: P2_4-NGF_axon_2_TGACCA_L001


title: single cell RNA-low 25


title: single cell RNA-low 22


title: single cell RNA-low 23


title: P2_2-NT3_axon_2_CGATGT_L002


title: P2_3-NGF_axon_1_ACTTGA_L001


title: single cell RNA-low 20


title: single cell RNA-low 21


title: single cell RNA-low 19


title: single cell RNA-low 30


title: P2_1-NT3_axon_1_ATCACG_L002


title: P2_1-NT3_axon_1_ATCACG_L001


title: single cell RNA-low 17


title: single cell RNA-low 14


title: single cell RNA-low 16


title: single cell RNA-low 15


title: single cell RNA-low 13


title: P2_4-NGF_axon_2_TGACCA_L002


title: single cell RNA-low 11


title: single cell RNA-low 10


title: single cell RNA-low 9


title: Drosophila wing disc Sce RNAi Ubx-GAL4>Dam rep3

city: Melbourne

first: Michael

middle: Joseph

last: Murray

state: VIC

address: Parkville

department: School of BioSciences

country: Australia

institute: University of Melbourne

description: DNA amplicon

library_source: genomic

data_processing:
Sequencing was performed on a  HiSeq 2000 using the HiSeq SR Cluster Kit V4 cBot and HiSeq SBS Kit V4 reagents.
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer.
Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Sequencing data was mapped to release 6.03 of the Drosophila genome and Dampol/Dam bedgraph ratio files created using damidseq_pipeline (Marshall and Brand, 2015,Bioinformatics 31:3371).
Genome_build: Drosophila genome annotation release 6.03
Supplementary_files_format_and_content: CTL1_DamPol2.gatc.bedgraph: Dampol2 vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: CTL2_DamPol2.gatc.bedgraph: Dampol2 vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: CTL3_DamPol2.gatc.bedgraph: Dampol2 vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: CTL_DamPol2.scaled.average.gatc.bedgraph: average of three CTL replicates scaled by dividing by standard deviation
Supplementary_files_format_and_content: SceIR1_DamPol2.gatc.bedgraph: Dampol2 vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: SceIR2_DamPol2.gatc.bedgraph: Dampol2 vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: SceIR3_DamPol2.gatc.bedgraph: Dampol2 vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: SceIR_DamPol2.scaled.average.gatc.bedgraph: average of three SceIR replicates scaled by dividing by standard deviation

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: third instar wing imaginal disc

growth_protocol: wing discs dissected out of wandering third instar larvae raised at 29C

extract_protocol:
30 wing discs were dissected in 1xPBS, were frozen at -80˚C, thawed, 40ul of 500mM EDTA, 180ul of ATL buffer, and 20ul Proteinase K added, mixed gently and incubated for 56˚C overnight, cooled to RT and 20ul of RNAase (12.5ul/ul) added and incubated for 2 mins. 400ul of a 1:1 mix of Buffer AL and 100% ethanol was added and mixed gently, before processing through the DNeasy kit spin columns. The genomic DNA was then digested overnight with DpnI, cleaned up with a Qiagen PCR Purification kit, and DamID Adapters blunt ligated with T4 ligase, digested again with DpnII, and then adapter-ligated fragments PCR amplified using DamID primers and Advantage PCR kit DNA polymerase (Clontech). Adapters were then removed with AlwI digestion,
Libraries were prepared using standard Illumina DNA shotgun library preparation with bead size selection protocol

value: UAS-mCherry-Dam

value: third instar wing imaginal disc


title: P2_2-NT3_axon_2_CGATGT_L001


title: Drosophila wing disc Sce RNAi Ubx-GAL4>Dam rep2

description: DNA amplicon


title: Drosophila wing disc Sce RNAi Ubx-GAL4>DamPol2 rep3

description: DNA amplicon

value: UAS-mCherry-Dam-Pol II


title: single cell RNA-low 8


title: single cell RNA-low 12


title: Drosophila wing disc Sce RNAi Ubx-GAL4>DamPol2 rep2

description: DNA amplicon


title: single cell RNA-low 6


title: single cell RNA-low 3


title: single cell RNA-low 4


title: Drosophila wing disc Sce RNAi Ubx-GAL4>DamPol2 rep1

description: DNA amplicon


title: Drosophila wing disc ControlUbx-GAL4>Dam rep3

description: DNA amplicon


title: single cell RNA-low 2


title: single cell RNA-low 1


title: Drosophila wing disc ControlUbx-GAL4>DamPol2 rep2

description: DNA amplicon


title: Drosophila wing disc ControlUbx-GAL4>DamPol2 rep3

description: DNA amplicon


title: Drosophila wing disc Control Ubx-GAL4>DamPol2 rep1

description: DNA amplicon


title: Drosophila wing disc Sce RNAi Ubx-GAL4>Dam rep1

description: DNA amplicon


title: 4T1_TAK_1uM_rep2

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

country: USA

institute: University of Michigan

data_processing:
Quality of the raw reads data for each sample was first evaluated using FastQC (version 0.11.3). RNA-seq data were mapped to the reference genome (hg38 and mm10) using Bowtie/TopHat. The reads were counted with HTSeq, and the differential expression between experimental groups was quantified using DESeq2 (Fold change > 2 and P value < 0.05)
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: .txt and counts

organism: Mus musculus

growth_protocol: 2×10e5 MDA-MB-231 cells were plated in a 6-well plate for 24 h and then treated with ENMD-2076 at 2.5 or 5 µmol/L(or TAK901 at 1 or 2 µmol/L) for 24 h. 1 × 105 4T1 cells were plated in a 6-well plate for 24 h and then treated with ENMD-2076 at 1 or 2 µmol/L(or TAK901 at 1 or 2 µmol/L) for 24 h

extract_protocol:
total RNA was isolated using TRIzol (Invitrogen).
The libraries were constructed by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on HiSeq 2500 sequencing system (Illumina)


title: 4T1_TAK_2uM_rep1


title: 4T1_DMSO_3_2

value: DMSO


title: 4T1_DMSO_1


title: 4T1_DMSO_4_2


title: 4T1_TAK_2uM_rep2


title: single cell RNA-low 5


title: single cell RNA-low 7


title: 4T1_DMSO_2


title: Sample 28: Tumor-bearing PPM1D transgenic mouse

city: Stockholm

first: Per

last: Kogner

address: Tomtebodavägen 18a

department: Dept of Women's and Children's Health

country: Sweden

institute: Karolinska institutet

data_processing:
Samples were aligned to the mm10 reference genome using STAR verson 2.4.2 in 2-pass mode as recommended in the STAR manual. Briefly, a genome index was generated using --runMode genomeGenerate with annotations and the option --sjdbOverhang set to (read length - 1). First-pass alignemt was performed using basic options only. A new index was then generated for each sample using the SJ.out.tab file from the first-pass alignment and --sjdbOverhang set to (read length - 1). Finally, a second alignment was performed.
The number of aligned reads per gene was calculated using htseq-count version 0.9.0 with the --stranded=reverse, --type=exon, and --id=gene_id options.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file consists of an expression matrix with raw counts per gene per sample (generated using htseq-count).

source_name: thymic lymphoma

extract_protocol:
RNA extraction and sequencing was performed by Otogenetics, Atlanta, USA. Total RNA was extracted using the Rneasy Mini Kit (Qiagen). RNA quality was assessed using the Agilent Bioanalyzer platform.
Sequencing libraries were prepared using the TruSeq Stranded cDNA kit. Paired-end reads of length 100-125 bp were generated using the Illumina HiSeq 2500 platform. Sequencing depth was approximately 40 million reads for each sample.

tag: genotype

value: PPM1D transgenic

tag: Sex

value: f

tag: age at irradiation (days)

tag: age at sacrifice (days)


title: 4T1_TAK_1uM_rep1


title: Sample 26: Tumor-bearing PPM1D transgenic mouse

value: m


title: Sample 19: Tumor-bearing PPM1D transgenic mouse


title: Drosophila wing disc ControlUbx-GAL4>Dam rep2

description: DNA amplicon


title: Sample 18: Tumor-bearing PPM1D transgenic mouse


title: Sample 25: Tumor-bearing PPM1D transgenic mouse


title: Sample 27: Tumor-bearing PPM1D transgenic mouse


title: Sample 22: Tumor-bearing PPM1D transgenic mouse


title: Drosophila wing disc ControlUbx-GAL4>Dam rep1

description: DNA amplicon


title: Sample 23: Tumor-bearing PPM1D transgenic mouse


title: Sample 20: Tumor-bearing PPM1D transgenic mouse


title: single cell RNA-low 18

value: RNA-low

value: single cell


title: Sample 17: Tumor-bearing PPM1D transgenic mouse


title: Sample 15: Tumor-bearing PPM1D transgenic mouse


title: Sample 16: Tumor-bearing PPM1D transgenic mouse


title: Macrophage M-CSF replicate 1

city: Madrid

first: Amaya

last: Puig

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital Gregorio Marañón

description: Sample name: M2 d1 -

hyb_protocol: Standard Agilent protocols

scan_protocol: Scanned on an GenePix 4000B scanner

data_processing:
Scanned images and raw data were pre-processed with GeneSpring v12 (Agilent).
Raw signal values (in log base 2) were thresholded to 1 and arrays were normalized using quantiles.

source_name: M-CSF Macrophage

label_protocol: 2 ug of total RNA was used to obtain cRNA. 10 ug of cRNA was labeled with Cy5-Streptavidin. All experimental procedures were performed following manufacturer instructions. Now available in http://appliedmicroarrays.com/pdf/codelink_16-assay.pdf

growth_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FCS containing either GM-CSF or M-CSF, and after an initial exposure (at day 0) to 5 micromolar MTX

extract_protocol: Total RNA from each condition was extracted and purified using the RNasey kit (Qiagen).Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Cells were were treated with GM-CSF (1000 U/ml) or M-CSF (10 ng/ml) every 48 hours

tag: individual

value: Healthy donor d1

value: M-CSF Macrophage

tag: agent

value: control


title: Macrophage M-CSF +MTX replicate 2

description: Sample name: M2 d4 +MTX

source_name: M-CSF +MTX Macrophage

value: Healthy donor d4

value: MTX


title: Macrophage M-CSF replicate 3

description: Sample name: M2 d7 -

value: Healthy donor d7


title: Sample 14: Tumor-bearing PPM1D transgenic mouse


title: single cell RNA-low 84

tag: facs gate

value: Hoechst/pyronin Y stain & FACS

value: sorted cells

value: Asexual CIW4


title: Macrophage GM-CSF replicate 2

description: Sample name: M1 d4 -

source_name: GM-CSF Macrophage

value: GM-CSF Macrophage


title: Macrophage M-CSF replicate 2

description: Sample name: M2 d4 -


title: control_rep3

city: Novosibirsk

first: Elena

middle: V

last: Ubogoeva

address: Lavrentyeva 10

country: Russia

institute: Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences

description:
contains two technical replicates and paired-end reads
GSE_raw_counts_before_filtering.xlsx

data_processing:
Demultiplexing, barcodes removal, and filtering of reads with ambiguous (N) bases was carried out by the sequencing company. Read quality was checked in each sample using FastQC.
Raw reads were mapped to the Arabidopsis thaliana genome (TAIR10) using STAR (v2.5.2b) with default parameters, then technical replicates were merged using samtools merge
Uniquely mapped reads were counted using "summarizeOverlaps" function from GenomicAlignments package (v1.22.1) with the annotation file from TAIR10
Genes in which 0 reads mapped in each sample were excluded from the analysis
DEGs were detected using the Bioconductor package DESeq2 (v1.26.0), the false discovery rate was controlled via Benjamini-Hochberg method
Genome_build: TAIR10
Supplementary_files_format_and_content: xlsx table with raw counts, and xlsx table with differential gene expression statitics (DESeq2 results)

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis Col-0 seeds were surface-sterilized and vernalized for 7 days at 4°C. Seedlings were grown vertically at 22°C and 150 µmol m-2 s-1 under a 16-h light/8-h dark cycle on 1/2 Murashige and Skoog (MS) media (Sigma).

extract_protocol:
Roots were collected in liquid nitrogen. Each replicate contained approximately 100 roots. Total RNA from the roots was extracted using TRIzol® Reagent (Ambion, Cat. Num. 15596-018) and DNaseI (Promega), and total RNA yields were measured using an Invitrogen® Qubit™ fluorometer and Agilent Bioanalyzer 2100 microfluidics (Agilent, Santa Clara, CA).
Total RNA samples with an RNA integrity number (RIN) above 7.9 were sent to Beijing Genomics Institute (BGI), where they were ribodepleted, and RNA libraries were prepared according to Illumina TruSeq protocol. The libraries were sequenced for 100 bps in paired-end mode on the Illumina HiSeq2000 platform.

treatment_protocol: Three days after germination (dag), seedlings were incubated in liquid 1/2 MS (mock) and 1/2 MS supplemented with 1 µM IAA for 1 h.

tag: ecotype

value: wild type

value: root

tag: age

value: 3 days after germination

value: mock


title: IAA_rep1

tag: tissue

tag: treatment

value: 1uM IAA for 1h


title: IAA_rep2


title: Macrophage M-CSF +MTX replicate 1

description: Sample name: M2 d1 +MTX


title: control_rep2


title: Sample 24: Tumor-bearing PPM1D transgenic mouse

value: PPM1D transgenic

value: f


title: Macrophage GM-CSF +MTX replicate 3

description: Sample name: M1 d7 +MTX

source_name: GM-CSF +MTX Macrophage


title: Macrophage M-CSF +MTX replicate 3

description: Sample name: M2 d7 +MTX


title: Macrophage GM-CSF +MTX replicate 2

description: Sample name: M1 d4 +MTX


title: Macrophage GM-CSF replicate 3

description: Sample name: M1 d7 -


title: Normoxic Glioblastoma 10 Stem-like cell line, exposed to Hypoxia for 48 h

source_name: Normoxic Glioblastoma Stem-like cell line derived from tumor 10, exposed to Hypoxia for 48 h

value: exposed to Hypoxia for 48 h


title: Macrophage GM-CSF replicate 1

description: Sample name: M1 d1 -

value: Healthy donor d1


title: IAA_rep3


title: control_rep1


title: Sample 35: PPM1D transgenic mouse, irradiated, replicate1

source_name: control thymus tissue


title: Sample 33: Wildtype mouse, irradiated, replicatSample 33: e 2

value: wt


title: Sample 40: PPM1D transgenic mouse, non-irradiated, replicate 3


title: Sample 32: Wildtype mouse, irradiated, replicate 1


title: Sample 36: PPM1D transgenic mouse, irradiated, replicate 2


title: Sample 39: PPM1D transgenic mouse, non-irradiated, replicate 2


title: Macrophage GM-CSF +MTX replicate 1

description: Sample name: M1 d1 +MTX


title: Sample 38: PPM1D transgenic mouse, non-irradiated, replicate 1


title: Sample 31: Wildtype mouse, non-irradiated, replicate 3


title: cGVHD-Lu-PSGL1hi rep2

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
cGVHD-Lu-PSGL1hi
Sample_24951_LUB8_S50

data_processing:
Reads were trimmed to remove Illumina adapters and poly(A) tails
Trimmed reads were aligned to mm9 genome using Tophat v2.0.8 with default settings
Expression of Refseq genes were summarized by HTseq-count
Genome_build: mm9
Supplementary_files_format_and_content: raw counts in text format

source_name: lung

extract_protocol:
cGVHD and and GVHD-free mice were setup in the BALB/C recipient in receiving B6 derived TCD-BM plus or not splenocytes, and spleen, liver and lung tissues were harvest at 30 days after HCT. Donor derived PSGL1lo and PSGL1hi CD4+ T cells were sorted and total RNA were extracted by Qiagen RNeasy Kit.
Kapa mRNA HyperPrep Kit following manufacturer's instructions

tag: strain

tag: gvhd status

value: cGVHD

value: lung

tag: psgl1 status


title: cGVHD-Lu-PSGL1hi rep1

description:
cGVHD-Lu-PSGL1hi
Sample_24949_LUA8_S48

tag: cell type


title: Sample 29: Wildtype mouse, non-irradiated, replicate 1


title: cGVHD-Lu-PSGL1lo rep1

description:
cGVHD-Lu-PSGL1lo
Sample_24948_LUA7_S47


title: cGVHD-Li-PSGL1hi rep1

description:
cGVHD-Li-PSGL1hi
Sample_24944_LA7_S44

source_name: liver

value: liver


title: cGVHD-Li-PSGL1hi rep2

description:
cGVHD-Li-PSGL1hi
Sample_24945_LB7_S45


title: cGVHD-Li-PSGL1lo rep2

description:
cGVHD-Li-PSGL1lo
Sample_24947_LB8_S46


title: cGVHD-Sp-PSGL1hi rep2

description:
cGVHD-Sp-PSGL1hi
Sample_11260_WT_up2_GTCCGC

source_name: spleen

value: spleen


title: cGVHD-Lu-PSGL1lo rep2

description:
cGVHD-Lu-PSGL1lo
Sample_24950_LUB7_S49


title: cGVHD-Sp-PSGL1hi rep1

description:
cGVHD-Sp-PSGL1hi
Sample_11259_WT_up1_CCGTCC


title: cGVHD-Sp-PSGL1lo rep1

description:
cGVHD-Sp-PSGL1lo
Sample_11257_WT_extra1_AGTTCC


title: cGVHD-Sp-PSGL1lo rep2

description:
cGVHD-Sp-PSGL1lo
Sample_11258_WT_extra2_ATGTCA


title: GVHD-free-Sp-PSGL1lo rep2

description:
GVHD-free-Sp-PSGL1lo
Sample_11256_WTCD_extra2_AGTCAA

value: GVHD-free


title: RNAseq Dnmt3b+/- 3

city: Gainesville

first: Rene

last: Opavsky

state: FL

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

data_processing:
Quality check, trimming, filtering, and alignment of reads to the Mus musculus UCSC mm10 reference genome was performed at the ICBR Bioinformatics Core (UF, Florida). Methylation calling was performed with Methyldackel (v 0.3.0.1) using the mm10-CG index. Only CpG sites with a minimum sequencing depth 5x were included in analysis. Differentially methylated regions (DMRs) were determined by Metilene and defined based on average of minimum three consecutive differentially methylated cytosines (DMCs) with methylation change of ≥30% in the same direction with p values < 0.05 (as determined by MWU test). Maximal base pair cut-off for a distance between consecutive DMCs in DMR was set to 50 bp.
For RNA-seq, trimmed sequencing data were first aligned to mm10 reference genome using STAR aligner. RNA-seq data with minimum mapped quality 50 were quantitated using the RNA-seq quantitation pipeline in SeqMonk software. For differentially expressed genes, only genes with a fold change ≥ 2 and a p-value < 0.05 (by DeSeq2) were considered to be significant.
Genome_build: mm10 - Mus musculus GRCm38 (08/06/2012)
Supplementary_files_format_and_content: Processed data files are bigwig files, they contain methylation value for CpG sites whith coverage ≥ 5x

source_name: peripheral T-cell lymphoma

extract_protocol:
For WGBS, genomic DNA was isolated from two independent Dnmt3b+/- PTCL samples using phenol/chloroform. For RNA-seq, total RNA was isolated by trizol from three independent  Dnmt3b+/- PTCL samples.
The WGBS libraries were prepared and sequenced on an Illumina NovaSeq6000 sequencer using 150 bp long paired-end reads. The RNAseq libraries were generated and sequenced on Illumina HiSeq 2500 platform using paired-end 150 bp runs.

value: lymph node

value: FVB


title: RNAseq Dnmt3b+/- 2


title: RNAseq Dnmt3b+/- 1


title: YAPKO_EV_rep2

city: Singapore

first: Rong

address: 5A Engineering Drive 1

department: Mechanobiology Institute (MBI)

country: Singapore

institute: National University of Singapore

description: Replicate 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads containing adapter, ploy-N and low quality reads were removed from raw data.
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, mismatch=2
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: Human GRCh37, release 82
Supplementary_files_format_and_content: Comma Separated Values (csv) file include FPKM values for all samples

source_name: Gastric cancer cell line

growth_protocol: MKN28 cells were cultured in RPMI-1640 medium, supplemented with 10% (v/v) heat-inactivated FBS and 1% (v/v) penicillin-streptomycin in the incubator at 37oC, 5% CO2.

extract_protocol:
The cells at ~50% confluent in a 100 mm dish were collected and RNA was prepared with miRNeasy Mini Kit (QIAGEN). NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing following manufacturer’s recommendations (NEBNext UltraTM Directional RNA Library Prep Kit for Illumina).

tag: cell line

tag: background

value: YAP Knock out (YAP KO)

tag: manipulation

value: Transduced with empty vector


title: YAPKO_TAZOE_rep1

description: Replicate 1

value: Transduced with active TAZ (TAZ S89A)


title: TAZKO_YAPOE_rep2

description: Replicate 2

value: TAZ Knock out (TAZ KO)

value: Transduced with active YAP (YAP S127A)


title: TAZKO_YAPOE_rep1

description: Replicate 1


title: YAPKO_TAZOE_rep2

description: Replicate 2


title: TAZKO_EV_rep2

description: Replicate 2


title: YAPKO_EV_rep1

description: Replicate 1


title: TAZKO_EV_rep1

description: Replicate 1


title: LVAD1

city: San Diego

first: Oscar

middle: E

last: Echeagaray

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

data_processing:
98 bp Read1, 8 bp i7 Index, and 26 bp Read2
The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 3.0). Reads were aligned to the Homo sapiens GrCh38-3 genome.
Preparations derived from in vitro studies, yielded 4722 barcoded cells for analysis, from which 2943, and 1779 corresponded to LVAD and Neonatal derived, respectively. Cells with less than 200 genes or more than 10% of mitochondrial gene count were filtered out and genes detected less than in three cells were filtered out. Approximately 2,029 variable genes were selected based on their expression and kept for downstream analysis using Seurat R Package (v2.3.4).
Sequenced reads were aligned to the human reference genome GrCh38-3
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode

extract_protocol:
Briefly, heart samples were mechanically minced into 1-mm3 pieces and digested in collagenase II (150 U mg/mL, Worthington, LS004174) followed by brief low-speed (850 rpm for 2 minutes) centrifugation to remove cardiomyocytes and tissue debris. The supernatant was subjected to magnetic-activated cell sorting using c-kit–conjugated microbeads (Miltenyi Biotec, #130-091-332), and c-kit– enriched cells were plated in human c-kit CIC media. Neonatal and LVAD derived cCICs were incubated at 37°C in 5% CO2 to passage 5 and used for single cell RNASEQ (scRNASEQ). Media used in the study are listed in Table S1. Media used in the study contained: 10% ES FBS (16141061, Gibco), 1% Penicillin-Streptomycin-Glutamine (100X, 10378016, Gibco), 5 mU/mL human erythropoietin (H5166, Sigma), 10 ng/mL human recombinant basic FGF (GMP100-18B, Peprotech), 0.2 mMol/L L-Glutathione (10007461, Cayman) in F12 HAM's (1x) (SH30026.01, HyClone).
The Chromium Single Cell 3' Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3' Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V2 User Guide.

tag: cell sorting

value: cKit +

value: LVAD-derived cCICs

tag: passages


title: LVAD2


title: Neonatal

source_name: Neonatal

value: Neonatal-derived cCICs


title: GVHD-free-Sp-PSGL1lo rep1

description:
GVHD-free-Sp-PSGL1lo
Sample_11255_WTCD_extra1_CTTGTA


title: Sample 30: Wildtype mouse, non-irradiated, replicate 2

tag: genotype

tag: Sex

value: f

tag: age at irradiation (days)

tag: age at sacrifice (days)


title: Chicken_HH3_Epiblast_50K_ATACseq

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools 1.2
Reads were mapped to the mouse (mm10) and chicken (galGal6) genome reference assembly using BWA 0.7.7 and PCR dupicates were removed using Picard-Tools 2.5.0
Normalized bedGraph files were generated using DeepTools 2.5.7
Peaks were called using MACS2.1.1.20160309
Genome_build: galGal6, mm10

organism: Gallus gallus

source_name: Epiblast from HH3 chicken embryos

extract_protocol:
Fertilized chicken eggs (white leghorn; Gallus gallus domesticus) were obtained from a local breeder (LSL Rhein-Main) and incubated at 37°C and 80% humidity in a normal poultry egg incubator (Typenreihe Thermo-de-Lux). Following microsurgical procedures, the eggs were re-incubated until the embryos reached the desired developmental stages. The developmental progress was determined according to the staging system of HH (Hamburger and Hamilton, 1992). Mice were housed and bred under standard conditions in the CECAD ivRF. The breedings described were approved by the Landesamt für Natur, Umwelt, und Verbraucherschutz Nordrhein-Westfalen (LANUV), Germany (animal application 84-02.04.2015.A405).
Tissue were extracted and resuspended to single cell level. ATAC-seq was essentially conducted following Buenrostro et al. Nat Methods 2013. In short, single cells were centrifugated at 5000 g for 5 min and supernatant was removed. Cells were then lysed with 100 µl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0,1% IGEPAL CA-630) substituted with 4 µl of protease inhibitor (1 tablet/2 mL conc.) for at least 15 minutes on ice. Immediately after lysis, nuclei were centrifugated at 6000 g for 10 minutes at 4°C. Pellet was resuspended in transposase reaction mix (25µl 2x TD buffer, 10 µl transposase (Illumina), 15 µl nuclease-free H2O) and incubated for 30 min at 37°C. Finally sample was purified using Qiagen MinElute PCR purification kit according to the manufacturer’s protocol.

value: Epiblast from HH3 chicken embryos

value: WT

value: ATAC


title: cHH3_H3K27me3

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools 1.2
Reads were mapped to the mouse (mm10) and chicken (galGal6) genome reference assembly using BWA 0.7.7 and PCR dupicates were removed using Picard-Tools 2.5.0
Normalized bedGraph files were generated using DeepTools 2.5.7
Peaks were called using MACS2.1.1.20160309
Genome_build: mm10, galGal6

growth_protocol: 10cm plates were coated in 0.1% gelatine generally overnight. Cells (E14 WT, EED−/− and RING1a−/−RING1bfl/fl mESC) were thawed and resuspended in 10ml of medium (serum + LIF). Standard serum + LIF medium contained 500 mL Knock-out DMEM (Gibco 10829-018), 95 mL of filtered ES FBS (Gibco 16141-061), 5.9 mL of antibiotics (Hyclone SV30079.01), 5.9 mL Glutamax (Gibco 35050-038), 5.9 mL MEM NEAA (Gibco 11140-035), 4.7 mL titrated LIF (Miltenyi Biotec 130-095-777), and 1.3 mL Beta-mercaptoethanol 55 mM (Gibco 21985-023). Cells were split once (1/3 or 1/4) every two days. When they reached 80-100% confluence protein was extracted using the abcam cell nuclear protein preparation protocol for western blot. RNA was was extracted with 400ul (for 6wp) or 1 mL (for 10cm plates) of Lysis Solution RL (Guanidinium Thiocyanate; analytik jena), stored at -80°C or then purified using the innuPREP DNA/RNA Mini Kit (analytik jena) according to the manufacturer’s instructions, and reverse transcribed with ProtoScript II First Strand cDNA Synthesis Kit (E6560L, NEB). For RING1a−/−RING1bfl/fl mESC cells we added 1000x Tamoxifen (OHT) for 72h right after first passage. Floxed deletion was assessed after ChIP / HiChIP lysis in electrophoresis gel using flanking primers. Deleted protein was assessed via standard Western blot (using plate reader).

extract_protocol:
Fertilized chicken eggs (white leghorn; Gallus gallus domesticus) were obtained from a local breeder (LSL Rhein-Main) and incubated at 37°C and 80% humidity in a normal poultry egg incubator (Typenreihe Thermo-de-Lux). Following microsurgical procedures, the eggs were re-incubated until the embryos reached the desired developmental stages. The developmental progress was determined according to the staging system of HH (Hamburger and Hamilton, 1992). Mice were housed and bred under standard conditions in the CECAD ivRF. The breedings described were approved by the Landesamt für Natur, Umwelt, und Verbraucherschutz Nordrhein-Westfalen (LANUV), Germany (animal application 84-02.04.2015.A405). Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies againts the specific proteins of interest in each case.
Cells were crosslinked in 1% of formaldehyde for 20 minutes (rotating at RT) with subsequent quenching by glycine (0.125M; rotating at RT). Washed twice with PBS and 25x Roche protease inhibitor. Then flash frozen in liquid nitrogen and stored at -80°C. Afterwards cells were thawed for ~30 minutes and lysed for 10 minutes at 4°C rotating in 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% TX-100 together with protease inhibitor (Lysis Buffer 1). After centrifugation for 5 min at 2000rcf at 4°C and discarding the supernatant, pellet was resuspended in 10 mM Tris, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, protease inhibitor (Lysis Buffer 2) and lysed for 10 minutes at 4°C rotating. After centrifugation for 5 min at 2000rcf at 4°C and discarding the supernatant, pellet was resuspended in 10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate and 0.5% N-lauroylsarcosine with protease inhibitor (Lysis Buffer 3). Cells were then sonicated with ActiveMotif Sonicatior (amplitude: 25%, on=20s, off=30s, 20 cycles). Debris was then centrifugated for 10 minutes, 16000rcf at 4°C. Supernatant was resuspended with 10% Triton X-100 and 10% of mixture taken for input sample. 5 ul antibody (1 ng/ul) was added to sonicated chromatin aliquot for each ChIP reaction and inverted to mix. Then rotated vertically at 4°C overnight (12-16 hrs) to bind antibody to chromatin. On the next day, 50ul (for low cell numbers) or 75ul (for higher cell numbers) of magnetic Dynabeads (Protein G) were washed three times (3X) in 1 mL cold Block Solution (0.5% BSA (w/v), 1x PBS). Antibody-bound chromatin was added to beads and inverted to mix. Then rotated vertically at 4°C for at least 4 hrs. Afterwards bound beads were washed 5X in 1 mL cold RIPA buffer (50 mM Hepes, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Then washed once in 1 mL TE + 50 mM NaCl on ice and centrifugated for 3 minutes at 1000rcf at 4°C to remove all remaining TE. 210 uL Elution Buffer was added to beads and DNA was eluted for 15 min at 65°C, 900 RPM, before centrifugating beads 1 min at 16000rcf at RT, adding to magnet and transferring supernatant (~200 uL) to fresh microfuge tube once beads settled. Both sample and input were then reverse crosslinked in appropriate amount of TE wash buffer, 20 mg/mL of RNAse, then Proteinase K, before extracting the DNA by phenol-chlorophorm. DNA content was measured using Qubit and the HS DNA Kit. Enrichment was measured using technical triplicates (input: 1%) by ChIP-qPCR with custom-made primers (Suppl.) on a Light Cycler 480II (Roche). All antibodies used in this study have been previously reported as suitable for ChIP: H3K4me3 (39159, Active Motif), H3K27ac (39133, Active Motif), H3K27me3 (39155, Active Motif).

treatment_protocol: A full E14 WT 10cmp vial was thawed and resuspended in 10 mL of serum + LIF. The next day, cells were washed with PBS and medium was changed and the day after cells were split ¼. We began the differentiation the day after (d0). First, we trypsinized cells with 2mL TrypLE Express (Life technologies). After 5 minutes, Trypsin was quenched using 4 mL of serum + LIF. We then took 400ul for RNA extraction and the residual cells for differentiation. Both vials were centrifugated (750 and 1000 RPM respectively). Supernatant was discarded and cell pellet for RNA extraction was resuspended in Lysis Solution RL. The other vial was heavily resuspended in 5 mL of N2B27 with 0.1% of BSA (Life Technologies) and 0.1% of bFgf (Life Technologies) to get single cells. Cell resuspension and count was assessed using the BioRad TC20. We placed droplets of 15000 cells / cm2 in 10 mL of N2B27 with 0.1% of BSA and 10 ng/mL of bFgf. On d1 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 10 ng/mL bFgf) without PBS washing. On d2 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA, 10 ng/mL bFgf and 5 μM Xav939/Wnt inhibitor) without PBS washing. On d3 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 5 μM Xav939/Wnt inhibitor) without PBS washing. On d4 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 5 μM Xav939/Wnt inhibitor) without PBS washing. On the last day of differentiation (d5), we washed 1-2 with PBS (depending on amount of dead cells), resuspended plate in 5 mL of N2B27, scratched off cells, then extracted RNA and crosslinked these. Differentiation was assessed using RT-qPCR on a Light Cycler 480II comparing AntNPC d5 vs. E14 WT d0 relative gene expression levels (using the 2ΔCt method) with house keeping gene (Eef1a1), pluripotency markers (Pou5f1/Oct4 and Nanog), mesoderm marker (T) and ectoderm markers (Six3 and Lhx5). Standard deviations were calculated from technical triplicate reactions and were represented as error bars. Primers used can be found in the Supplemental Table.

tag: chip antibody

value: H3K27me3 (39155, Active Motif)


title: 231_TAK_2uM_rep1


title: 231_TAK_2uM_rep2


title: m497-4

city: xi'an

first: SI

last: WANG

state: shaanxi

address: no.76 yanta west road

institute: xi'an jiaotong university

data_processing:
Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer
The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) or Ribo-Zero™ rRNA removal Kit
generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®)
The PCR products were cleaned up using AxyPrep Mag PCR Clean-up , validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 2.0 Fluorometer
HiSeq Sequencing using TrySeq Kit v4-HS
Genome_build: dbSNP database version 135

source_name: Synovium of knee joint

growth_protocol: Grow in DMEM/F 12 medium containing 10% FBS, and incubate the culture dish at 37°C and 5% carbon dioxide at a constant temperature

extract_protocol:
Obtain primary cells from patient tissues, transfect the corresponding miRNA mimic and extract RNA with Trizol for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: patients-derived Synovial fibroblasts

tag: developmental stage

value: Primary cells

tag: disease

value: Rheumatoid arthritis

tag: gender

value: F

tag: age (years)

tag: disease duration (years)

tag: rf (iu/ml)

tag: esr (mm/h)

tag: crp (mg/l)

tag: anti-ccp positive ratio


title: m497-2

tag: cell type


title: 231_TAK_1uM_rep2

tag: cell line

tag: treatment


title: Chicken_HH3_input

description: input

tag: tissue

tag: genotype


title: 231_TAK_1uM_rep1


title: m424-4


title: m424-3


title: 231_ENMD_2.5uM_rep2


title: m424-2


title: 231_DMSO_rep2

value: DMSO


title: m424-1


title: 231_ENMD_2.5uM_rep1


title: 231_DMSO_rep1


title: mNC-4


title: MDA-hyb1

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 3000ng of labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

source_name: MDA-MB-231/MSC derived breast cancer hybrids-1

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) using 500ng of total RNA as input and according to the manufacturer’s recommendations, except that reaction volumes were halved.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

tag: sample type


title: MDA-hyb3

source_name: MDA-MB-231/MSC derived breast cancer hybrids-3


title: MDA-MB-231-cherry

source_name: human MDA-MB-231 breast carcinoma cell line


title: MDA-hyb5

source_name: MDA-MB-231/MSC derived breast cancer hybrids-5


title: 231_ENMD_5uM_rep2


title: mNC-3


title: 231_ENMD_5uM_rep1


title: m497-3


title: cGVHD-Li-PSGL1lo rep1

description:
cGVHD-Li-PSGL1lo
Sample_24946_LA8_S18

tag: strain

tag: gvhd status

value: cGVHD

value: liver

tag: psgl1 status


title: IP 6-4PP 100 J/m2 UVC - Replicate B

city: Stanford

first: Brian

last: Perez

state: California

address: Gilbert Biology Building, 371 Serra Mall

institute: Stanford University

description: Barcode: CAAT

data_processing:
Library strategy: CPD-seq
Sequencing quality assess with FastQC and strand correlation analysis.
Data processing was conducted using specifications for the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline (ENCODE Project Consortium et al, 2012). Sequenced reads were mapped to the reference human genome (hg19) using Bowtie2 version 2.2.6 and signal track files were generated using MACS2.0. Sonicated DNA was used as the Input control and was prepared for sequencing. Technical replicates (IP/Input) were averaged together into one file using the mean.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: IP 6-4PP 100 J/m2 UVC, IMR-90

growth_protocol: IMR-90 human embryo lung fibroblasts, obtained from the Coriell Institute, were maintained in DMEM/15% FBS and passaged 1:2 every two days.

extract_protocol:
Cells were lysed immediately after treatment (<5 seconds) with 1% SDS and DNA was subsequently purified by exhaustive ethanol precipitations.
Libraries were prepared for single-end, single-index sequencing on an Illumina HiSeq platform using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (E6240, New England Biolabs), following manufacturer's instructions. Library samples were barcoded and amplified using NEBNext® Multiplex Oligos for Illumina® [Index Primers Set 1] (E7335, New England Biolabs).

treatment_protocol:
100J/m2 UVC treatments of confluent cells were performed at passage number 10 using a UV Stratalinker 1800.
IP was followed by repair of DNA lesions (both CPDs and 6-4 PPs).

value: Lung fibroblast

tag: passages

value: 100J/m2 UVC

tag: ip antibody

value: anti-6-4PP (64M-2 from Cosmo Bio USA)


title: m497-1

tag: developmental stage

tag: disease

tag: gender

tag: age (years)


title: mNC-2

tag: disease duration (years)

tag: rf (iu/ml)

tag: esr (mm/h)

tag: crp (mg/l)


title: mNC-1

tag: cell type

tag: anti-ccp positive ratio


title: 48431_(Retina_5_years): Control Retina

city: La Jolla

first: Debashis

last: Sahoo

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

description:
sailaja-2020-cells-expr.txt
Retina_5_years

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). Transcript level TPM values were added together to generate a gene-level TPM value. A custom perl script was used to organize and normalize data using log2(TPM+1).
Genome_build: Genome assembly: GRCh38.p12, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary_files_format_and_content: tab-delimited text file includes log2(TPM+1) values for each Sample

source_name: Control Retina

growth_protocol: Retinoblastoma cell line NCC-RbC-51 (Riken, Japan) was maintained in Roswell Park Memorial Institute media (RPMI 1640, Gibco, A10491-01).  These were the cells grown in 2 dimensions on normal tissue culture plate.  The cells grown on graphene sponge were considered as invitro 3-dimensional model for cell growth. PLL was added onto the graphene foam surface in 1:10 (v/v) dilution with sterile water and incubated for 3 h prior to NCC-RbC-51 cell seeding followed by washes with PBS and allowed to dry. Prior to cell seeding on to the scaffold the cells were made into cancer cell clusters as single cell suspensions did not attach well on the foams and they went through the pores and attached to the bottom of the cell culture plate. The NCC-RbC-51 cells under normal culture conditions form grape like clusters of 50-100 cells. These clusters were retained during cell seeding by gentle collection of the cells with minimal media volume (~200μl for 1 cm2 foam).  After incubation time, complete media were supplemented. Caution was taken during media supplementation as sudden jerky movements caused dislodging of the cells from the scaffold. The cells were grown for 72h and taken for global transcriptomic studies by RNA sequencing as tissue culture plate grown cells exhibited increased cell death after this time period.

extract_protocol:
RNA extraction for sequencing experiments were performed using RNeasy Mini Kit (Qiagen, Cat# 74104) then quantified using Qubit RNA Assay HS (Invitrogen, Cat# Q32855). RNA was isolated  from NCC-RbC-51 cells grown on tissue culture plate, graphene sponges and xenograft tissue s(N=3).  RNA purity was checked using QIAxpert and RNA integrity was assessed on TapeStation using RNA ScreenTapes (Agilent, Cat# 5067-5576).
NEB Ultra RNA-Seq Library Prep kit protocol (NEB, E7530L) was used to prepare libraries for total RNA sequencing. RNA (200ng) was depleted ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Cop rRNA removal beads. Following purification, the ribodepleted RNA was fragmented using divalent cations under elevated temperatures. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase. Second strand cDNA synthesis was performed, using DNA Polymerase I and RNase H enzyme. The cDNA fragments were then subjected to a series of enzymatic steps which repair the ends, tails the 3’ end with a single ‘A’ base, followed by ligation of the adapters. The adapter ligated products were then purified and enriched using the following thermal conditions: initial denaturation 98°C for 30sec; 13 cycles of - 98°C for 10sec, 65°C for 75sec; final extension of 65°C for 5mins. PCR products are then purified and checked for fragment size distribution on TapeStation using D1000 DNA ScreenTapes (Agilent, Cat# 5067-5582).  The adapter sequences used are presented in Supplementary Table 3. Prepared libraries were quantified using Qubit High Sensitivity Assay (Invitrogen, Cat# Q32854). The obtained libraries were pooled and diluted to final optimal loading concentration before cluster amplification on Illumina flow cell. Once the cluster generation is completed, the cluster flow cell is loaded on Illumina HiSeq 4000 instrument to generate 40M, 100bp paired end reads. The raw reads were filtered using Trimmomatic for Quality scores and adapters. Filtered reads were aligned to human genome using splice aware aligner like HISAT2 to quantify reads mapped to each transcript.

treatment_protocol: Normal retina, retinoblastoma, xenografts, cultured cell lines in standard plate and graphene sponge were used to perform RNA-seq.

tag: tissue

value: Control Retina

tag: age

value: 5 years

tag: condition

value: Primary tissue


title: IP 6-4PP 100 J/m2 UVC - Replicate A

description: Barcode: AGTG

tag: cell line

tag: treatment


title: 48432_(RB_14): Retinoblastoma

description:
sailaja-2020-cells-expr.txt
RB_14

source_name: Retinoblastoma

value: RB

value: 8 months


title: D2i8-PTc1: Pkd2+Ift88 rep3

city: New Haven

first: Stefan

last: Somlo

state: Connecticut

address: 333 Cedar Street

department: Internal Medicine/Nephrology

institute: Yale University

data_processing:
Read alignment: STAR 2.5.0
Gene count quantification: HTSeq 0.6.1
Differential expression analysis: DESeq2

source_name: Kidney

extract_protocol:
At 10 weeks old, all the mice were sacrificed. Kidney total RNA was extraced using Trizol
The library was made using the standard PolyA library protocol from Illumina

treatment_protocol: All the mice were subjected to oral doxycycline (2mg/ml) starting from P28 for two weeks

tag: strain

value: Kidney

value: postnatal day 70

tag: genotype


title: mono-culture NHLF TGFß1  72 h rep3

city: Biberach

first: Karsten

last: Quast

address: Birkendorfer Str. 65

department: Computational Biology

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

description:
mono-culture NHLF TGFß1  72 h
rep3

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.1 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
Genome_build: ensembl70
Supplementary_files_format_and_content: tab-delimited text files contain RPKM values for each sample

source_name: mono-culture

growth_protocol: NHLFs were grown in Fibroblast Growth Medium-2 (GIBCO, CC-3132). Fibroblasts from passages 4-8 were used for all experiments. A549 alveolar epithelial cells were grown in DMEM with 10% fetal calf serum (GIBCO).

extract_protocol:
Total RNA were extracted using Rneasy 96 Kit (QIAGEN, 74181)
Library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) according manufacturer's manual. Sequencing was then performed on an Illumina HiSeq3000 instrument

treatment_protocol: 200 000 A549 were seeded on 24 mm Transwell (Corning, 0.4 µm pore size, PET membrane, 3450). 100 000 Fibroblasts per well (6-well plate, Corning, 3516) were seeded. Cells were starved overnight and medium was replaced by fresh DMEM with 200 µl apical and 2000 µl basolateral before experiment start. The two compartments were then brought together and 1 ng/ml TGFß1 were applied apically.

value: Lung fibroblasts

value: 1 ng/ml TGFbeta1 apical treatment

tag: time of treatment


title: mono-culture NHLF TGFß1  72 h rep2

description:
mono-culture NHLF TGFß1  72 h
rep2


title: 48437_(768_13): Retinoblastoma

description:
sailaja-2020-cells-expr.txt
768_13

value: 6 years


title: D2i8PTc105: Pkd2+Ift88 rep1


title: D2i8PTc116: Pkd2+Ift88 rep2


title: 48429_(67_13): Retinoblastoma

description:
sailaja-2020-cells-expr.txt
67_13

value: 1 year


title: D2PTc86: Pkd2 rep3


title: mono-culture NHLF CTRL 72 h rep3

description:
mono-culture NHLF CTRL 72 h
rep3

value: control


title: D2D2PTc46: Pkd2 rep2


title: D2D2PTc38: Pkd2 rep1


title: mono-culture NHLF CTRL 72 h rep1

description:
mono-culture NHLF CTRL 72 h
rep1


title: 48428_(348_12): Control Retina

description:
sailaja-2020-cells-expr.txt
348_12

value: 12 years


title: 48436_(172_22): Control Retina

description:
sailaja-2020-cells-expr.txt
172_22

value: 22 years


title: 48434_(647_13): Retinoblastoma

description:
sailaja-2020-cells-expr.txt
647_13


title: mono-culture NHLF TGFß1  72 h rep4

description:
mono-culture NHLF TGFß1  72 h
rep4


title: 48430_(1563_15): Retinoblastoma

description:
sailaja-2020-cells-expr.txt
1563_15

value: 3 years


title: mono-culture A549 TGFß1  72 h rep4

description:
mono-culture A549 TGFß1  72 h
rep4

value: Lung epithelial cells


title: DFnPTc46: WT rep3

value: Wild type


title: 48433_(1630_15): Retinoblastoma

description:
sailaja-2020-cells-expr.txt
1630_15


title: mono-culture A549 TGFß1  72 h rep3

description:
mono-culture A549 TGFß1  72 h
rep3


title: 48435_(1548_14): Retinoblastoma

description:
sailaja-2020-cells-expr.txt
1548_14


title: KD2PTc127: WT rep2


title: mono-culture A549 TGFß1  72 h rep2

description:
mono-culture A549 TGFß1  72 h
rep2


title: mono-culture NHLF TGFß1  72 h rep1

description:
mono-culture NHLF TGFß1  72 h
rep1


title: mono-culture NHLF CTRL 72 h rep4

description:
mono-culture NHLF CTRL 72 h
rep4


title: mono-culture A549 TGFß1  72 h rep1

description:
mono-culture A549 TGFß1  72 h
rep1


title: AD 2m-3

city: Seoul

first: Su Woong

last: Jung

address: 892, Dongnam-ro, Gangdong-gu

country: South Korea

institute: Kyung Hee University Hospital at Gangdong

description: processed data file: standard_diet_versus_adenine-enriched_diet_genes.txt

data_processing:
Basecalls performed using bcl2fastq 2.0.
Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20.
Filtered reads were mapped to the reference genome related to the species using the aligner TopHat.
Gene expression level was measured with Cufflinks v2.1.1 using the gene annotation database of the species. To improve the accuracy of the measurement, multi-read-correction and frag-bias-correct options were applied.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: young_versus_old_genes.txt: Tab-delimited text file includes gene-based FPKM.
Supplementary_files_format_and_content: standard_diet_versus_adenine-enriched_diet_genes.txt: Tab-delimited text file includes gene-based FPKM.

source_name: kidneys

extract_protocol:
The total RNA was extracted from whole kidneys using the Nucleospin® RNA Isolation Kit (MACHEREY-NAGEL, Germany).
The libraries were prepared for 100bp paired-end sequencing using TruSeq RNA Sample Prep Kit (Illumina, CA, USA). Total 1μg of RNA molecules were purified and fragmented and synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. After sequential process of end repair, A-tailing and adapter ligation, cDNA libraries were amplified with PCR (Polymerase Chain Reaction). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). They were quantified with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s library quantification protocol. Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×100bp) using Illumina HiSeq2500 (Illumina, CA, USA).

treatment_protocol: Natural aging and adenine-enriched diet.

value: kidneys

value: adenine-enriched diet


title: C42-B_ENZ_1

city: Cleveland

first: Sanjay

last: Gupta

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

description: Derivative subline of human prostate cancer LNCaP-derived C4-2 cells.

data_processing:
Illumina HiSeq 1000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm10 reference genome and the GENCODE transcript annotation vM10
Supplementary_files_format_and_content: FastaQ files were generated

growth_protocol: The C42-B parent cell lines and C42-B-ENZU (resistance) cell lines were cultured in RPMI-1640 media, contained 10%FBS. The cell lines were maintained in a 5% CO2 atmosphere at 37 °C.

extract_protocol:
Total RNA was extracted from C42-B parental and C42-B-ENZU (resistance) cells treated with enzalutamide (10uM), using RNA RNeasy kit (Qiagen).
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
The quality of total RNA integrity (RIN) was assessed using an RNA 6000 nanochip (Agilent technologies, Lexington, MA) on a Bioanalyzer 2100 (Agilent Technologies). Libraries were prepared using the Illumina TruSeq Stranded Total RNA sample preparation kit according to the manufacturer’s protocol. 50 bp single-end sequencing was performed on pooled libraries using an Illumina HiSeq 2500 platform. Sequencing reads generated were assessed for quality using FastQC. The library preps and sequencing were performed in the Genomics Core Facility at Case Western Reserve University. Differential expression was determined using Cufflinks v2.2.1. Differentially expressed genes (DEGs) were identified using a multiple testing corrected q-value < 0.05.

treatment_protocol: C42-B  cells were recurrently exposed to increasing concentrations of enzalutamide (1-20μM) by passage in complete cell culture medium containing enzalutamide. In each concentration of enzalutamide, the cells were grown in RPMI 1640 (GE Healthcare) for a week allowing them to acclimatize and propagate for a minimum of six months. The resistant cells generated from 20 µM enzalutamide were maintained in media containing 5 µM enzalutamide, defined here as  C42BP enzalutamide resistant cells.

value: Human prostate cancer cell line derived from subcutaneous LNCaP xenografts in castrated nude mice

tag: phenotype

value: enzalutamide resistant cells


title: C42-B_ENZ_2


title: mono-culture A549 CTRL 72 h rep4

description:
mono-culture A549 CTRL 72 h
rep4


title: AD 2m-2


title: C42-B_ENZ_0


title: mono-culture A549 CTRL 72 h rep3

description:
mono-culture A549 CTRL 72 h
rep3


title: mono-culture NHLF CTRL 72 h rep2

description:
mono-culture NHLF CTRL 72 h
rep2


title: C42-B_2


title: mono-culture A549 CTRL 72 h rep2

description:
mono-culture A549 CTRL 72 h
rep2


title: standard diet 2m-3

value: standard diet


title: C42-B_1


title: standard diet 2m-1


title: standard diet 2m-2


title: mono-culture A549 CTRL 72 h rep1

description:
mono-culture A549 CTRL 72 h
rep1


title: co-culture NHLF TGFß1  72 h rep4

description:
co-culture NHLF TGFß1  72 h
rep4

source_name: co-culture


title: KD2PTc120: WT rep1

value: Kidney


title: co-culture NHLF TGFß1  72 h rep2

description:
co-culture NHLF TGFß1  72 h
rep2


title: co-culture NHLF TGFß1  72 h rep3

description:
co-culture NHLF TGFß1  72 h
rep3


title: C42-B_0


title: PBMCs, Healthy indivudual_2

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

data_processing:
FastQC
Trimmomatic
HISAT2
Cufflinks
DESeq2
Genome_build: hg 38
Supplementary_files_format_and_content: genecount_ensembl.csv

source_name: PBMCs isolated from Healthy individuals

growth_protocol: Not applicable

extract_protocol:
Whole RNA was isolated using RNeasy Mini Kit (QIAGEN; Cat No./ID: 74104).
rRNA-depleted RNA
TruSeq RNA Library Prep Kit v2 was used as per the manufacture’s instruction

treatment_protocol: PBMCs were isolated using Histopaque-1077 from whole blood.

value: PBMC

tag: disease state


title: PBMCs, Healthy indivudual_3


title: PBMCs, Healthy indivudual_4


title: co-culture NHLF TGFß1  72 h rep1

description:
co-culture NHLF TGFß1  72 h
rep1

value: Lung fibroblasts


title: co-culture NHLF CTRL 72 h rep4

description:
co-culture NHLF CTRL 72 h
rep4


title: PBMCs, Healthy indivudual_1


title: AD 2m-1


title: PBMCs, Tuberculosis patient_5

source_name: PBMCs isolated from naïve active tuberculosis patients

value: tuberculosis


title: PBMCs, Tuberculosis patient_4


title: co-culture NHLF CTRL 72 h rep3

description:
co-culture NHLF CTRL 72 h
rep3


title: PBMCs, Tuberculosis patient_3


title: PBMCs, Tuberculosis patient_1


title: co-culture NHLF CTRL 0 h rep4

description:
co-culture NHLF CTRL 0 h
rep4

value: 0 h


title: co-culture NHLF CTRL 72 h rep2

description:
co-culture NHLF CTRL 72 h
rep2


title: co-culture NHLF CTRL 0 h rep1

description:
co-culture NHLF CTRL 0 h
rep1


title: co-culture NHLF CTRL 0 h rep3

description:
co-culture NHLF CTRL 0 h
rep3


title: co-culture NHLF CTRL 0 h rep2

description:
co-culture NHLF CTRL 0 h
rep2


title: co-culture A549 TGFß1  72 h rep4

description:
co-culture A549 TGFß1  72 h
rep4

value: 1 ng/ml TGFbeta1 apical treatment


title: Mouse diabetic colonic ICC: Lepob/ob;KitcopGFP/+

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 N Virginia St

department: Physiology & Cell Biology

institute: University of Nevada, Reno

description: Kit+ ICC miRNA sequencing analysis; Kit+ ICC miRNA sequencing reads

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase mouse v.20.0
Supplementary_files_format_and_content: excel,expression profiles

source_name: Interstitial Cells of Cajal

extract_protocol:
Whole colonic or jejunal GI tissue was extracted and dispersed for cellular dissociation and prepared for cell sorting. Utilizing Fluoresence Activated Cell Sorting (FACS), cells positive for GFP signal were isolated as these cells represent Kit+ in GI tissue, which are ICC. These isolated KitcopGFP/+ cells were then placed into Lysis/Binding Buffer from the mirVana miRNA isolation kit (Thermo-Fisher) and extracted under manufacturer protocol. Samples from same genotypes (15 each) were pooled together to create the sample ready for processing and sequencing.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: FACS isolated Kit+ ICC

value: Interstitial Cell of Cajal (ICC)

value: 11-20 weeks

value: Lepob/ob;KitcopGFP/+; diabetic


title: co-culture A549 TGFß1  72 h rep2

description:
co-culture A549 TGFß1  72 h
rep2

value: Lung epithelial cells


title: co-culture A549 TGFß1  72 h rep3

description:
co-culture A549 TGFß1  72 h
rep3


title: Mouse healthy colonic ICC: Lepob/+;KitcopGFP/+

value: Lepob/+;KitcopGFP/+; Wild type


title: co-culture A549 TGFß1  72 h rep1

description:
co-culture A549 TGFß1  72 h
rep1


title: N061311-siCTRL-TNFposBud

city: Philadelphia

first: Blanca

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_control_full_DESeq2_results.txt
CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_TNF_full_DESeq2_results.txt

data_processing:
STAR was used to align sequencing reads to the hg38 reference genome.
HTSeq was used to quantify transcript levels corresponding to the hg38 reference genome
DESeq2 was used to perform differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Space-delimited text files include mapped read values per gene for each sample that passed QC (CEBPD_htseq_gene.txt) and transcript-based differential expression results for pairs of samples that passed QC for the siCEBPD Bud vs. control, siCEBPD TNF vs. control, siCEBPD TNFposBud vs. control, siCEBPD TNFposBud vs. TNF, siCTRL Bud vs. control,  siCTRL TNF vs. control, siCTRL TNFposBud vs. control and siCTRL TNFposBud vs. TNF comparisons. (CEBPD_healthy_siCEBPD_Bud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt, CEBPD_healthy_siCEBPD_TNF_vs_healthy_siCEBPD_control_full_DESeq2_results.txt, CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt, CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_TNF_full_DESeq2_results.txt, CEBPD_healthy_siCTRL_Bud_vs_healthy_siCTRL_control_full_DESeq2_results.txt, CEBPD_healthy_siCTRL_TNF_vs_healthy_siCTRL_control_full_DESeq2_results.txt, CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_control_full_DESeq2_results.txt, CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_TNF_full_DESeq2_results.txt)
Supplementary_files_format_and_content: CEBPD_htseq_gene.txt: Estimates of mapped reads to reference genes for each sample.
Supplementary_files_format_and_content: CEBPD_healthy_siCEBPD_Bud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt: Differential expression results for siCEBPD Bud treatment vs. control samples
Supplementary_files_format_and_content: CEBPD_healthy_siCEBPD_TNF_vs_healthy_siCEBPD_control_full_DESeq2_results.txt: Differential expression results for siCEBPD TNF treatment vs. control samples
Supplementary_files_format_and_content: CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt: Differential expression results for siCEBPD TNFposBud treatment vs. control samples
Supplementary_files_format_and_content: CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_TNF_full_DESeq2_results.txt: Differential expression results for siCEBPD TNFposBud treatment vs. TNF samples
Supplementary_files_format_and_content: CEBPD_healthy_siCTRL_Bud_vs_healthy_siCTRL_control_full_DESeq2_results.txt: Differential expression results for siCTRL Bud treatment vs. control samples
Supplementary_files_format_and_content: CEBPD_healthy_siCTRL_TNF_vs_healthy_siCTRL_control_full_DESeq2_results.txt: Differential expression results for siCTRL TNF treatment vs. control samples
Supplementary_files_format_and_content: CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_control_full_DESeq2_results.txt: Differential expression results for siCTRL TNFposBud treatment vs. TNF samples
Supplementary_files_format_and_content: CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_TNF_full_DESeq2_results.txt: Differential expression results for siCTRL TNFposBud treatment vs. control samples

source_name: Airway Smooth Muscle

extract_protocol:
Total RNA was extracted with the miRNAeasy kit (Qiagen Sciences, Inc., Germantown, MD)
Kapa mRNA HyperPrep kit (Kapa Biosystems, Wilmington, MA)

treatment_protocol: Primary human airway smooth muscle (ASM) cells were transfected with 25pmol of siRNA non-targeting control or siCEBPD SMARTpool using RNAiMax (Life technologies). Three days after transfection, cells were treated with 100nM Budesonide, 10ng/ml TNF-alpha, or both for 18 hours.

value: siCTRL-TNFposBud

tag: donor

value: Airway Smooth Muscle


title: Mouse diabetic jejunal ICC: Lepob/ob;KitcopGFP/+


title: co-culture A549 CTRL 72 h rep4

description:
co-culture A549 CTRL 72 h
rep4

value: control


title: Mouse healthy jejunal ICC: Lepob/+;KitcopGFP/+


title: N021612-siCTRL-TNFposBud


title: co-culture A549 CTRL 72 h rep2

description:
co-culture A549 CTRL 72 h
rep2


title: N051911-siCTRL-TNFposBud


title: N061311-siCTRL-TNF

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCTRL_TNF_vs_healthy_siCTRL_control_full_DESeq2_results.txt
CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_TNF_full_DESeq2_results.txt

value: siCTRL-TNF


title: co-culture A549 CTRL 72 h rep3

description:
co-culture A549 CTRL 72 h
rep3


title: PBMCs, Tuberculosis patient_2


title: N010912-siCTRL-TNFposBud


title: co-culture NHLF CTRL 72 h rep1

description:
co-culture NHLF CTRL 72 h
rep1


title: co-culture A549 CTRL 0 h rep4

description:
co-culture A549 CTRL 0 h
rep4


title: co-culture A549 CTRL 0 h rep3

description:
co-culture A549 CTRL 0 h
rep3


title: co-culture A549 CTRL 0 h rep2

description:
co-culture A549 CTRL 0 h
rep2


title: co-culture A549 CTRL 0 h rep1

description:
co-culture A549 CTRL 0 h
rep1


title: N021612-siCTRL-TNF


title: N010912-siCTRL-TNF


title: N051911-siCTRL-TNF


title: N051911-siCTRL-control

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCTRL_Bud_vs_healthy_siCTRL_control_full_DESeq2_results.txt
CEBPD_healthy_siCTRL_TNF_vs_healthy_siCTRL_control_full_DESeq2_results.txt
CEBPD_healthy_siCTRL_TNFposBud_vs_healthy_siCTRL_control_full_DESeq2_results.txt

value: siCTRL-control


title: HidradenitisSuppurativa_9L

city: Collegeville

first: Johannes

last: Freudenberg

state: Pennsylvania

address: 1250 S Collegeville Rd

department: Human Genetics

institute: GlaxoSmithKline

data_processing:
Skewer v0.2.218 was used to trim RNA-seq reads with end quality of less than 20.
We aligned RNA-seq reads to the human reference genome (Genome Reference Consortium Human Build 38 assembly) using “Splice Transcripts Alignment to a Reference” tool (STAR, version 2.5.1b). We then used featurecounts tool from the Subread package v1.4.6-p5 to generate count data with the following parameters “-s 2 --primary -p –C”
Ensembl human gene model (GRCh38.86) was used to generate count data
Genome_build: Genome Reference Consortium Human Build 38 assembly
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
Punch biopsies from lesional and peri-lesional skin areas were transferred to 1.5 ml RNAlater tissue protect tubes (Qiagen, Germantown, MD). Samples were kept at 4 °C for 24 h after which they were transferred and stored at − 80 °C. Biopsy samples were lysed using a mechanical bead-based disruption method. RNA was extracted from the minced tissue using the Qiagen RNeasy Mini Kit following manufacturer’s recommendations for fibrous tissue RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: Lesion

tag: gender

value: F

tag: race

value: W

tag: smoker

value: E

tag: bmi


title: HidradenitisSuppurativa_9N

value: Perilesion


title: N021612-siCTRL-control


title: HidradenitisSuppurativa_8L

value: M

value: Y


title: HidradenitisSuppurativa_7N

value: B


title: N061311-siCTRL-Bud

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCTRL_Bud_vs_healthy_siCTRL_control_full_DESeq2_results.txt

value: siCTRL-Bud


title: HidradenitisSuppurativa_8N


title: N051911-siCTRL-Bud


title: N010912-siCTRL-control


title: HidradenitisSuppurativa_7L


title: co-culture A549 CTRL 72 h rep1

description:
co-culture A549 CTRL 72 h
rep1

tag: cell type

value: Lung epithelial cells


title: N010912-siCTRL-Bud


title: N021612-siCTRL-Bud


title: HidradenitisSuppurativa_6L


title: N061311-siCEBPD-TNFposBud

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt
CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_TNF_full_DESeq2_results.txt

value: siCEBPD-TNFposBud


title: HidradenitisSuppurativa_6N


title: HidradenitisSuppurativa_4N


title: N021612-siCEBPD-TNFposBud


title: HidradenitisSuppurativa_5L

value: N


title: N010912-siCEBPD-TNFposBud

value: Airway Smooth Muscle


title: N061311-siCEBPD-TNF

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCEBPD_TNF_vs_healthy_siCEBPD_control_full_DESeq2_results.txt
CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_TNF_full_DESeq2_results.txt

value: siCEBPD-TNF


title: HidradenitisSuppurativa_2N


title: HidradenitisSuppurativa_4L


title: N051911-siCEBPD-TNFposBud


title: HidradenitisSuppurativa_2L


title: N051911-siCEBPD-TNF


title: N021612-siCEBPD-TNF


title: HidradenitisSuppurativa_22N


title: N061311-siCTRL-control


title: HidradenitisSuppurativa_21N

value: O


title: SHPetoh121

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

data_processing:
RNA-seq reads were aligned to the December 2011 mouse reference genome (GRCm38) using Novoalign short-read alignment software version 1.0A
SAM files were converted to BAM files using the SamTransctiptomeParser application from the USeq software package version 8.8.5
Differentially expressed genes were determined using the DefinedRegionDifferentialSeq application from the USeq software package version 8.8.5
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: FPKM normalized values in Excel spreadsheet

source_name: Liver

extract_protocol:
Zymo Research Direct-zol RNA Miniprep
Illumina TruSeq RNA Library Preparation Kit v2 with poly(A) Selection
RNA-seq, HiSeq 50 cycle single-read sequencing v3

treatment_protocol: 5% ethanol liquid diet

value: Liver

tag: genotype/strain

value: SHP knockout

value: Ethanol

tag: timepoint


title: SHPctrl122

tag: tissue


title: N061311-siCEBPD-control

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCEBPD_Bud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt
CEBPD_healthy_siCEBPD_TNF_vs_healthy_siCEBPD_control_full_DESeq2_results.txt
CEBPD_healthy_siCEBPD_TNFposBud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt

value: siCEBPD-control


title: SHPetoh122


title: SHPctrl121


title: HidradenitisSuppurativa_5N

value: Skin

tag: age

value: F


title: HidradenitisSuppurativa_21L

value: Lesion


title: N010912-siCEBPD-control


title: N021612-siCEBPD-control


title: SHPetoh62


title: HidradenitisSuppurativa_1L


title: N061311-siCEBPD-Bud

description:
CEBPD_htseq_gene.txt
CEBPD_healthy_siCEBPD_Bud_vs_healthy_siCEBPD_control_full_DESeq2_results.txt

value: siCEBPD-Bud


title: SHPetoh61


title: HidradenitisSuppurativa_19N

value: Perilesion

value: W


title: N021612-siCEBPD-Bud


title: HidradenitisSuppurativa_18N

value: Y


title: HidradenitisSuppurativa_19L


title: SHPctrl62


title: Diabetic gastroparesis 2

description:
miRNA sequencing analysis
All_Expressed_miRNA_Human.xlsx

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase human v.22.0
Supplementary_files_format_and_content: excel,expression profiles

source_name: Plasma

extract_protocol:
Frozen serum samples from various patients with various presentations of diabetes and/or gastroparesis with ages ranging from 23-66. Seral miRNAs were extracted through use of mirVana miRNA isolation kit according to manufacturer's protocol and samples were pooled together based on phenotype (Healthy, Idiotpathic Gastroparesis, or Diabetic Gastroparesis) as well as level of insulin present in samples from idiopathic gastroparesis patients.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood


title: SHPetoh60


title: SHPetoh120


title: N051911-siCEBPD-Bud


title: SHPctrl61


title: HidradenitisSuppurativa_18L


title: Diabetic gastroparesis 1


title: HidradenitisSuppurativa_22L

value: E


title: N010912-siCEBPD-TNF


title: SHPctrl60


title: HidradenitisSuppurativa_17L

value: N


title: HidradenitisSuppurativa_1N

value: B


title: SHPctrl120


title: Idiopathic gastroparesis low insulin 1

value: M


title: SHPetoh01

value: Control


title: N051911-siCEBPD-control

value: Airway Smooth Muscle


title: Idiopathic gastroparesis low insulin 2


title: HidradenitisSuppurativa_16N


title: SHPetoh02

value: Liver

value: SHP knockout


title: Idiopathic gastroparesis high insulin 1


title: HidradenitisSuppurativa_16L


title: SHPctrl02


title: HidradenitisSuppurativa_15N


title: Healythy control 2


title: SHPetoh00


title: SHPctrl00


title: Healythy control 1


title: HidradenitisSuppurativa_14N


title: SHPetoh182


title: HidradenitisSuppurativa_17N


title: SHPetoh181


title: HidradenitisSuppurativa_12N


title: SHPctrl182


title: HidradenitisSuppurativa_12L


title: SHPctrl181


title: HidradenitisSuppurativa_13L


title: HidradenitisSuppurativa_13N


title: SHPetoh180


title: HidradenitisSuppurativa_11N


title: WTetoh122

value: Wild-type C57BL/6

value: Ethanol


title: Tet2 wt and KitD816V, Rep2 [Rieu]

city: MARSEILLE

first: erinn

last: soucie

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

description:
Rieu_Tet2_wt_L6_R1_001_V5EKa3UlA2FJ
Sample_Rieu_Tet2_wt

data_processing:
Sequencing quality control was done with FastQC v.0.11.2. Reads were mapped with the TopHat v2.0.13 software to the UCSC  human (GRCh37) reference genome, with on average 20 million aligned reads/sample. Biological quality control and summarization were done with RSeQC v2.6.1, PicardTools v1.8 respectively. The count data, prepared with HTSeq v.0.6.1 (parameters: --mode=union,  --stranded=no ). The raw count data are filtered. We filtered out very lowly expressed genes, keeping genes that are expressed at a reasonable level. Since the group size average is 3, we kept genes that achieved 10 counts in at least 3 samples. 23,710- 14,298 = 9,412 - ~40% (human). The filtered data were normalized by the library size using R/Bioconductor edgeR package v.3.10.5 .
Genome_build: hg19  (GRCh37)
Supplementary_files_format_and_content: tab-delimited text file include raw and normalized counts for all samples

source_name: Tet2 wt and KitD816V

growth_protocol: Fresh or frozen whole bone marrow biopsy material from patients was stained with the following antibody cocktail: anti-humanCD3-ECD, anti-humanCD14-alexa647, anti-humanCD25-PE and anti-humanFcepsilonGR1a-FITC (all from BD Biosciences). Cells were sorted on an FACSAria using DIVATM (Becton-Dickinson) software. Dead cells were excluded using DRAQ7TM, and CD3-CD14-CD25+FcER1A+ cell populations (which represented between 0,2-5% of total live cells gated) were directly lysed and RNA was isolated using the RNAeasyPlus Micro Kit (Qiagen) and sent for sequencing.

extract_protocol:
Sorted cell populations were directly lysed and RNA was isolated using the RNAeasyPlus Micro Kit (Qiagen)
sequencing Libraries were prepared using the Illumina TrueSeq protocol: Smarter+Nextera,6-indexed libraries multiplexed one lane of an Illumuna HiSeq2500, sequencing for 50 single-end reads

tag: subject status

value: systemic mastocytosis patient

tag: genotype/variation

value: Tet2 wt and KitD816V

value: Human mast cells from bone marrow


title: Tet2 wt and KitD816V, Rep3 [Thev]

description:
Thev_Tet2_mutated_L6_R1_001_hmSkrCJKuHNg
Sample_Thev_Tet2_mutated


title: HidradenitisSuppurativa_11L

value: Skin

value: Lesion

value: F


title: Idiopathic gastroparesis high insulin 2

value: Blood


title: HidradenitisSuppurativa_15L


title: Tet2-mut and KitD816V, Rep3 [1968]

description:
1968_Tet2_wt_L6_R1_001_hoiFEGJyIaRR
Sample_1968_Tet2_wt

source_name: Tet2-mut and KitD816V

value: Tet2-mut and KitD816V


title: WTetoh121

tag: treatment


title: SHPctrl180


title: HidradenitisSuppurativa_10N

value: Perilesion

value: W

value: Y


title: WTctrl122


title: Tet2 wt and KitD816V, Rep1 [327]

description:
327_Sorted_Mast_cells_L6_R1_001_uLsXRmVFaMCT
Sample_327_Sorted_Mast_cells


title: WTetoh120


title: HidradenitisSuppurativa_14L

value: N


title: HidradenitisSuppurativa_10L


title: Tet2-mut and KitD816V, Rep1 [1365]

description:
1365_Tet2_wt_L6_R1_001_pZrWJex78uQN
Sample_1365_Tet2_wt


title: WTctrl120


title: SHPctrl01

value: Control


title: WTetoh62

value: Liver


title: WTetoh60


title: PAEC_IL1b_TGFb2_1

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

description: PAEC treated with TGFb2 and IL1b replicate1

data_processing:
Fastq files obtained from Beckman Coulter Genomics
Gene quantification (read count and normalised expression value as FPKM) was obtained using RSEM 1.3.0 (options: -bowtie2 -forward-prob 0 -paired-end), based on GENCODE annotation version 26 (primary assembly).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with FPKM

source_name: Primary Endothelial Cells

growth_protocol: Primary endothelial cells (HUVEC #C2519A, HPAEC #CC-2530) were purchased from Lonza (Basel) and maintained in endothelial cell growth medium (EGM-2 BulletKit™) (Lonza) supplemented with foetal bovine serum (FBS) (10%, Life Technologies) and Penicillin-Streptomycin (100U/ml) (Gibco).

extract_protocol:
Total RNA isolation was performed using the miRNEasy Mini Kit (Qiagen), according to the manufacturer’s instructions, including on-column DNAse digestion.
Ribosomal-depleted stranded libraries were prepared by Beckman Coulter Genomics using the TruSeq Stranded Total RNA kit with Ribo-Zero Gold.

treatment_protocol: Endothelial cells were plated at a density of 5x104 cells/well in collagen coated 6-well culture plates and were treated with TGF-β2 (10 ng/ml, PeproTech) and IL-1β (1ng/ml, PeproTech) in for 7 consecutive day in EGM-2 BulletKit™ supplemented with 10% FBS and refreshed every 24 hours.

value: PAEC

tag: replicates

value: Replicate 1


title: StagT

city: Shanghai

first: Zikai

last: Zhou

state: Shanghai

address: 600 Wan Ping Nan Road

department: Research Center

institute: Shanghai Mental Health Center

data_processing:
Cell Ranger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
read1: contains the 16bp 10X barcode and the 10bp UMI (bases 17-26), Index contains the sample barcode Read2 contains the cDNA information.
Genome_build: mm10
Supplementary_files_format_and_content: xls files include normalized median scaling values for each cell.

source_name: Spleen

extract_protocol:
Splenic CD4+CD25+ Treg cells were purified using EasySep™MouseCD4+CD25+Regulatory Tcell Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Age-matched C57BL/6 mice were i.p. injected with STAg or vehicle PBS.

tag: strain

value: CD4+CD25+ Treg cells

value: 2 months

value: STAg


title: PAEC_IL1b_TGFb2_3

description: PAEC treated with TGFb2 and IL1b replicate3

value: Replicate 3


title: WTetoh61

value: Wild-type C57BL/6

value: Ethanol


title: PAEC_Control_3

description: PAEC Control replicate3

value: No Treatment


title: PBST

value: PBS


title: Tet2-mut and KitD816V, Rep2 [1601]

description:
1601_Tet2_mutated_L6_R1_001_ystgVraIryGl
Sample_1601_Tet2_mutated

value: systemic mastocytosis patient

value: Tet2-mut and KitD816V

value: Human mast cells from bone marrow


title: PAEC_Control_1

description: PAEC Control replicate1


title: HUVEC_IL1b_TGFb2_3

description: HUVEC treated with TGFb2 and IL1b replicate3

value: HUVEC


title: HUVEC_IL1b_TGFb2_2

description: HUVEC treated with TGFb2 and IL1b replicate2

value: Replicate 2


title: WTctrl121


title: PAEC_Control_2

description: PAEC Control replicate2


title: WTctrl60


title: WTetoh01

value: Control


title: WTctrl61

value: Liver


title: HUVEC_TGFb2_3

description: HUVEC treated with TGFb2 replicate3


title: PAEC_IL1b_TGFb2_2

description: PAEC treated with TGFb2 and IL1b replicate2

value: PAEC


title: HUVEC_TGFb2_1

description: HUVEC treated with TGFb2 replicate1

value: Replicate 1


title: HUVEC_IL1b_TGFb2_1

description: HUVEC treated with TGFb2 and IL1b replicate1


title: WTctrl00


title: WTctrl01


title: HUVEC_TGFb2_2

description: HUVEC treated with TGFb2 replicate2


title: WTctrl02


title: HUVEC_IL1b_3

description: HUVEC treated with IL1b replicate3


title: HUVEC_IL1b_2

description: HUVEC treated with IL1b replicate2


title: WTetoh182


title: WTetoh180


title: WTctrl62


title: WTetoh181


title: HUVEC_Control_3

description: HUVEC Control replicate3


title: HUVEC_IL1b_1

description: HUVEC treated with IL1b replicate1


title: HUVEC_Control_2

description: HUVEC Control replicate2


title: HUVEC_Control_1

description: HUVEC Control replicate1


title: WTctrl180


title: WTetoh02