title: C2

city: jinan

first: shigang

last: zhao

address: No.44, Wenhua Xi Road

department: center for reproductive medicine

institute: shandong university

data_processing:
The software of fastqc was used for the quality control analysis of the reads.
Using Tophat2, the reads were aligned to Ensembl_GRCh38.
the software of RseQC was used to do the quality control for the alignment data.
According to the reads alignment results, reads were assigned to specific transcripts to count the transcript reads.
TPM (Transcripts per Million) was adopted and used for standardization.Reads were aligned to mRNA sequences by the bowtie software and the mRNA quantitative analyses were done using Express software. Differential Expression Analysis of mRNA was performed by DESeq software.
Genome_build: Ensembl_GRCh38.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: cultured by IVM without growth hormone

growth_protocol: human GV-stage oocytes donated by patients

extract_protocol:
Each oocyte was collected and transferred into a 0.2 ml RNase-free microcentrifuge tube containing 2ul lysis buffer, which was composed of 0.2% Triton X-100 and 2 U/µl of RNase inhibitor . Then the cDNA was obtained by the Smart-Seq 2 method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: these GV-stage oocytes were cultured in vitro for 24h with the IVM medium containing growth hormone or not

value: human oocyte


title: G3

status: Public on Jun 29 2019

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: cultured by IVM with growth hormone

tag: tissue


title: C3


title: G2


title: NONLESIONAL.DAY1 [patient: 6]

type: RNA

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from skin biopsy

hyb_protocol: Affymetrix Human U133Plus 2.0 gene arrays were used. Total RNA (50 ng) was reverse transcribed and amplified with Ovation Whole Blood Solution from NuGen (San Carlos, CA). The labeled target was fragmented and hybridized to probe gene arrays, using Encore Biotin Module from NuGen (San Carlos, CA). The chips were washed, stained with streptavidin-phycoerythrin, and scanned (HP GeneArray Scanner; Hewlett-Packard Company, Palo Alto, CA). On each chip, the human housekeeping genes β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) served as controls. Suite 5.0 software normalized the expression level values using these controls.

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing: Quality control of Affymetrix chips was done using standard QC metrics and R packages. Expression measures were obtained using GC Robust Multi-array Average (GCRMA) algorithm. Batch effects corresponding to the hybridization date were detected by principal component analyses and adjusted using ComBat algorithm from R’s sva package. Probe sets with expression >3 in at least 15 samples were used for further analyses. Gene expression changes were modeled using mixed-effect models, with treatment, time and tissue type as a fixed interaction term, and a random effect for each patient. Fold changes (FCHs) for the comparisons of interest were estimated, and hypothesis testing was conducted with contrasts under the general framework of linear models in the R limma package. P-values were adjusted for multiple hypotheses using the Benjamini-Hochberg procedure, which controls the false discovery rate (FDR).

label: biotin

source_name: Skin biopsy

label_protocol: Ovation WB Reagent (Nugen)

extract_protocol: Skin biopsies were stored in RNAlater® (Invitrogen) until further processing. RNA was extracted (Covance Genomics Lab).

value: NONLESIONAL

tag: week

tag: treatment


title: G1


title: NONLESIONAL.DAY1 [patient: 5]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 5]

description: Gene expression data from skin biopsy

value: LESIONAL

value: Vehicle


title: Crisaborole.DAY8 [patient: 5]

description: Gene expression data from skin biopsy

value: Crisaborole


title: Crisaborole.DAY8 [patient: 7]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 6]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 7]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 6]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 7]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 6]

description: Gene expression data from skin biopsy


title: C1


title: Crisaborole.DAY15 [patient: 6]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 5]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 25]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 5]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 5]

description: Gene expression data from skin biopsy


title: Primary MEFs, NM1 KO 03

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
All the analysis was performed using the NYU Abu Dhabi High Performance Computational (HPC) cluster called “Dalma” running SLURM. All of the analysis, including quality trimming and subsequent analysis, was executed using the BioSAILs  workflow execution system. The raw reads were quality trimmed using Trimmomatic  version 0.36 to trim low quality bases, systematic base calling errors, as well sequencing adapter contamination, specifically, the parameters used were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15MINLEN:36”. FastQC  was used to assess the quality of the sequenced reads pre/post quality trimming. Only the reads that passed quality trimming in pairs were retained for further downstream analysis.
The quality trimmed RNAseq reads were aligned to the Mus Musculus GRCm38 (mm10) genome using HISAT2  version 2.0.4. The resulting SAM alignment files for each sequenced sample were then converted to BAM format and sorted by coordinate using SAMtools  version 0.1.19. These alignment files were then processed using STRINGTIE  version 1.3.0 together with the corresponding GTF annotation file of the reference genome, to produce a GTF file per sample. The resulting GTF files were then combined using STRINGTIE –merge to produced a “merged” GTF file for all the samples, before running STRINGTIE again on a per sample basis (using the merged GTF file produced earlier). The BAM alignment files were also processed using HTseq-count  using the reference annotation file to produce raw counts for each sample. The raw counts were then analyzed using the online analysis portal NASQAR  in order to merge, normalize and identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

organism: Mus musculus

source_name: primary MEFs

growth_protocol: Full DMEM medium with 10%FBS and Pen/Strep

extract_protocol:
E14 embryos were isolated without head and red organs, minced with razor and incubated 15 min with 0.05% Trypsin and 100 Kunitz units of Dnase I. Cells were centrifuged and plated on petri dishes coated with 0.2% gelatine. Cells used for RNA seq analysis were coming prom passage 3. RNAzol was used to isolate total RNA.
Total RNA was extracted from three replicates of NM1 WT and NM1 KO primary MEFs with TRI Reagent (Millipore-Sigma) according to the manufacturer protocol. The RNA seq library was prepared by using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced with the HiSEq 2500 sequencing platform

treatment_protocol: no treatment

tag: age

tag: cell type

value: mouse embryonic fibroblasts

tag: passages

tag: strain

tag: genotype

value: NM1 knock out


title: Primary MEFs, NM1 KO 02


title: Primary MEFs, NM1 KO 01


title: Primary MEFs, NM1 WT 03

value: NM1 wild type


title: Primary MEFs, NM1 WT 02


title: Primary MEFs, NM1 WT 01


title: Vehicle.DAY15 [patient: 4]

description: Gene expression data from skin biopsy


title: Vehicle.DAY8 [patient: 3]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 3]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 4]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 4]

description: Gene expression data from skin biopsy


title: melanocytes_KO_ctrl_1

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187

label: Biotin

source_name: Autophagy deficient mouse melanocytes (Atg7 f/f Tyr::Cre)

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: Autophagy deficient and competent mouse melanocytes were grown in MGM-2 medium for 22 days

extract_protocol: RNA was extracted with TriFast Reagent (VWR Peqlab) and subsequent RNA cleanup and concentration was performed using the Rneasy MinElure Cleanup Kit (Qiagen)

treatment_protocol: Melanocytes were isloated from 1- to 5-day-old pups and kept in culture für 22 days. Cells were treated with 20J/cm² UVA-1 or sham treated. RNA was isolated 6h post treatment.

tag: gender

value: female


title: melanocytes_WT_UVA_2

source_name: mouse melanocytes (Atg7 f/f) treated with UVA-1, 6h


title: melanocytes_KO_ctrl_2


title: NONLESIONAL.DAY1 [patient: 3]

description: Gene expression data from skin biopsy


title: Vehicle.DAY1 [patient: 4]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 1]

description: Gene expression data from skin biopsy


title: Vehicle.DAY15 [patient: 3]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 3]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 1]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY1 [patient: 3]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY15 [patient: 1]

description: Gene expression data from skin biopsy


title: Crisaborole.DAY8 [patient: 1]

description: Gene expression data from skin biopsy


title: melanocytes_KO_UVA_2

source_name: Autophagy deficient mouse melanocytes (Atg7 f/f Tyr::Cre) treated with UVA-1, 6h


title: melanocytes_WT_ctrl_1

source_name: mouse melanocytes (Atg7 f/f)


title: melanocytes_KO_UVA_1


title: Crisaborole.DAY15 [patient: 3]

description: Gene expression data from skin biopsy


title: melanocytes_WT_UVA_1


title: Vehicle.DAY8 [patient: 1]

description: Gene expression data from skin biopsy


title: 23 cKit-neg_IL-1B  IL-23

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Total RNA was isolated and analyzed on Affymetrix Clariom S Human arrayto generate expression profiles

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Clariom S Assay HT arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the rma_sketch  algorithm (target signal = 100) using APT (Affymetrix powertools),

source_name: PBMC

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: PBMC-derived ILC2s were cultured in Yssels medium containing 1% human serum at 37°C

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

treatment_protocol: PBMC-derived ILC2 subsets were stimulated with indicated cytokine(s)

value: c-kit‒ ILC2s

tag: stimulation

value: IL-1β and IL-23


title: melanocytes_WT_ctrl_2


title: Vehicle.DAY15 [patient: 1]

description: Gene expression data from skin biopsy


title: NONLESIONAL.DAY1 [patient: 4]

description: Gene expression data from skin biopsy


title: 24 cKit-neg_IL-1B  IL-23  TGF-B

value: IL-1β, IL-23 and TGF-β


title: 21 cKit-neg_IL-1B


title: Heart, Sham-2

city: Wallingford

first: Venkata

middle: Naga Srikanth

last: Garikipati

state: Pennsylvania

address: 3500 N, Broad St, 908B MERB

institute: Temple University

description: total RNA from Sham mouse hearts

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

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 4 samples have flags in P or M (All Targets Value) were retained for further analyses.

source_name: Mouse heart

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer™ protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000.

extract_protocol: total RNA was isolated using miReasy RNA isolation kit from Qiagen# 217004

value: sham

tag: time

value: 3 days


title: Heart, MI-1

description: total RNA from Myocardial infarction mouse hearts

value: MI

value: 3 days after myocardial infarction


title: Heart, MI-2


title: Heart, Sham-1

description: total RNA from Sham mouse hearts


title: 17 cKit-pos_IL-1B

value: c-Kit+ ILC2s


title: 16 cKit-neg_IL-1B  IL-23  TGF-B


title: 19 cKit-pos_IL-1B  IL-23


title: 15 cKit-neg_IL-1B  IL-23


title: 20 cKit-pos_IL-1B  IL-23  TGF-B


title: 09 cKit-pos_IL-1B


title: 12 cKit-pos_IL-1B  IL-23  TGF-B


title: 11 cKit-pos_IL-1B  IL-23


title: T3_IFNg_96h_D3: OPC cells treated with T3 and IFNg for 96hr, Donor3

city: Baltimore

first: Peter

middle: Arthur

last: Calabresi

state: MD

address: 600 N. Wolfe St

department: Neurology

institute: Johns Hopkins Univbersity

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: Data was proprocessed and normalized using RMA method, and group comparison was performed using the Limma package

organism: Rattus norvegicus

source_name: oligodendrocyte precursor cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PDGF vs withdrawal and T3

extract_protocol: RNA was obtained using QIAGEN Rneasy mini kit, following manufacturer protocol, cells were lysated then cDNA was removed through purification columns, ending with total RNA.

treatment_protocol: IFNg

value: oligodendrocyte precursor cells

value: T3 and IFNg

tag: donor


title: Vehicle.DAY1 [patient: 1]

description: Gene expression data from skin biopsy

value: LESIONAL


title: 07 cKit-neg_IL-1B  IL-23


title: T3_IFNg_24h_D3: OPC cells treated with T3 and IFNg for 24hr, Donor3


title: T3_IFNg_48h_D3: OPC cells treated with T3 and IFNg for 48hr, Donor3


title: PDGF_0_D3: OPC cells treated with PDGF, Donor3

description: OPC cells treated with PDGF, Donor3

value: PDGF


title: T3_96h_D2: OPC cells treated with T3 for 96hr, Donor2


title: T3_24h_D3: OPC cells treated with T3 for 24hr, Donor3


title: T3_IFNg_8h_D3: OPC cells treated with T3 and IFNg for 8hr, Donor3


title: T3_8h_D3: OPC cells treated with T3 for 8hr, Donor3


title: 08 cKit-neg_IL-1B  IL-23  TGF-B


title: T3_IFNg_96h_D2: OPC cells treated with T3 and IFNg for 96hr, Donor2


title: T3_96h_D3: OPC cells treated with T3 for 96hr, Donor3


title: T3_48h_D3: OPC cells treated with T3 for 48hr, Donor3


title: T3_IFNg_48h_D2: OPC cells treated with T3 and IFNg for 48hr, Donor2


title: 13 cKit-neg_IL-1B


title: 05 cKit-neg_IL-1B


title: 04 cKit-pos_IL-1B  IL-23  TGF-B


title: T3_IFNg_24h_D2: OPC cells treated with T3 and IFNg for 24hr, Donor2


title: T3_48h_D2: OPC cells treated with T3 for 48hr, Donor2


title: T3_IFNg_8h_D2: OPC cells treated with T3 and IFNg for 8hr, Donor2


title: PDGF_0_D2: OPC cells treated with PDGF, Donor2

description: OPC cells treated with PDGF, Donor2


title: T3_IFNg_96h_D1: OPC cells treated with T3 and IFNg for 96hr, Donor1


title: 01 cKit-pos_IL-1B


title: T3_24h_D2: OPC cells treated with T3 for 24hr, Donor2


title: T3_IFNg_24h_D1: OPC cells treated with T3 and IFNg for 24hr, Donor1


title: Dorsal Spinal Cord Sample 3

city: Middleton

first: Robert

last: Bradley

state: WI

address: 8460 Market Street Apt 412

department: Waisman Center

institute: University of Wisconsin - Madison

data_processing:
Reads were mapped back to the genome using the short read aligner Bowtie (Langmead et al., 2009), followed by RSEM (Li et al., 2011) to estimate gene expression. Each sample was sequenced over lanes (L004/L005 or L006/L007); and we combine reads across lanes.
Given estimates of gene expression provided by RSEM, we generate the estimated gene expression matrix for later analysis
All analyses were carried out in R (R Development Core Team, 2012), a publicly available statistical analysis environment. Specific software packages were obtained from Bioconductor, an on-line suite of tools for the analysis of genomic data (Gentleman et al. 2004), unless otherwise noted.
EBSeq (Leng et al., 2013) was applied to identify differentially expressed genes
Supplementary_files_format_and_content: File contains gene expression data in transcripts per million (TPM)

source_name: Astrocyte

growth_protocol: Astrocyte progenitors were grown in media containing BMP4 and CNTF (10ng/mL) for 7 days prior to RNA purification

extract_protocol:
Total RNA was extracted using Qiagen RNEasy RNA purification kit following manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hPSC-derived astrocytes

tag: hpsc line

value: Dorsal Spinal Cord


title: Ventral Spinal Cord Sample 2

value: Ventral Spinal Cord


title: Dorsal Spinal Cord Sample 2


title: Ventral Spinal Cord Sample 3


title: PDGF_0_D1: OPC cells treated with PDGF, Donor1

description: OPC cells treated with PDGF, Donor1


title: T3_96h_D1: OPC cells treated with T3 for 96hr, Donor1


title: 03 cKit-pos_IL-1B  IL-23


title: Ventral Spinal Cord Sample 1


title: T3_8h_D2: OPC cells treated with T3 for 8hr, Donor2


title: T3_48h_D1: OPC cells treated with T3 for 48hr, Donor1


title: T3_24h_D1: OPC cells treated with T3 for 24hr, Donor1


title: T3_IFNg_8h_D1: OPC cells treated with T3 and IFNg for 8hr, Donor1


title: T3_IFNg_48h_D1: OPC cells treated with T3 and IFNg for 48hr, Donor1


title: Sorbitol_treatment_2h_bioRep3

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Alternaria brassicicola

label_protocol: 400 ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred either to a second PDA medium supplemented with 1.2 M sorbitol for 2h.

extract_protocol: Total RNA was extracted by using a modified cetyltrimethylammonium bromide method (Verdier et al., 2008)

tag: tissus

value: germlings

tag: genetic background

value: Wild-type

value: sorbitol 2 h

value: 1 day


title: Sorbitol_control_2h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 2 h.

value: control sorbitol 2 h


title: Dorsal Spinal Cord Sample 1


title: T3_8h_D1: OPC cells treated with T3 for 8hr, Donor1


title: Sorbitol_treatment_2h_bioRep1


title: Sorbitol_control_2h_bioRep3


title: Sorbitol_treatment_2h_bioRep2


title: Sorbitol_control_2h_bioRep1


title: Desiccation_treatment_4h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred in sealed boxes containing silica gel beads for 4h.

value: desiccation 4h:RH decrease with silica gel beads


title: Ventral Forebrain Sample 2

value: Ventral Forebrain


title: Ventral Forebrain Sample 3


title: Desiccation_treatment_4h_bioRep3


title: Dorsal Forebrain Sample 1

value: Dorsal Forebrain


title: Dorsal Forebrain Sample 2


title: Ventral Forebrain Sample 1


title: Desiccation_treatment_4h_bioRep1


title: Vehicle.DAY1 [patient: 5]

description: Gene expression data from skin biopsy

value: Vehicle


title: HNS3_rep3

city: Beijing

first: Yanting

last: Chang

address: Futongdong Rd, Wang Jing, Chaoyang District

department: State Forestry Administration, Institute of Horticultural Flower and Landscape

institute: International Centre for Bamboo and Rattan

data_processing:
The raw RNA-seq reads from Illumina were filtered using ng_QC (-t 4 -L 20 -N 0.001)
The clean reads was mapped to our IOS-seq transcript sequence using bowtie2 with parameters end-to-end、sensitive
expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Li Bet al., BMC bioinformatics, 2011.
Genome_build: de novo
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Paeonia lutea x Paeonia suffruticosa

extract_protocol:
RNA was harvested using RNeasy Plant Mini kit (Qiangen, 74904)
The mRNA was enriched by Oligo dT beads and followed by fragmentation in fragmentation buffer. Then first-strand cDNA and second-strand cDNA was synthesized with random hexamers and dNTPs, respectively. The cDNA was subjected to purification by AMPure XP beads, end pairing, the addition of a single “A” bases, and ligation with an Illumina adapter. The ligation products were size fractioned by AMPure XP beads, and fragments were excised for PCR amplification.

value: floral bud

tag: cultivar

value: High Noon


title: HNS3_rep2


title: ∆BbbrlA [brlA_R2]

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

description: Replicate 2 of library ∆BbbrlA

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with DESeq software.
Screening of differentially expressed genes in paired library of WT/disruption mutant. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files, including Gene ID, annotation, reads data, FPKM values, log2(fold change), FDR-value and  regulation trends for the paired sample.

organism: Beauveria bassiana

source_name: ∆BbbrlA

growth_protocol: Conidia suspension (100 ul,5X106 conidia ml-1) of WT and mutant strains of Beauveria bassiana were inoculated on the SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar), respectively, and incubated at 25 °C for 84 hours.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates.

value: ARSEF 2860

tag: genotype/variation

value: {delta}BbbrlA

tag: incubation time

value: 84 hours

value: mycelia


title: ∆BbbrlA [brlA_R1]

description: Replicate 1 of library ∆BbbrlA

tag: tissue


title: ∆BbabaA [abaA_R2]

description: Replicate 2 of library ∆BbabaA

source_name: ∆BbabaA

value: {delta}BbabaA


title: Desiccation_control_4h_bioRep1

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred in sealed boxes without silica gel beads for 4h.

tag: treatment

value: control desiccation 4h


title: Sorbitol_control_30min_bioRep3

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred to a second PDA medium for 0.5 h.

value: germlings

value: control sorbitol 0.5 h

tag: age


title: Sorbitol_treatment_30min_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred either to a second PDA medium supplemented with 1.2 M sorbitol for 0.5 h.

value: Wild-type

value: sorbitol 0.5 h


title: ∆BbabaA [abaA_R1]

description: Replicate 1 of library ∆BbabaA


title: HNS3_rep1


title: HNS2_rep2


title: HNS2_rep3


title: HNS2_rep1


title: Desiccation_control_4h_bioRep3

value: 1 day


title: Sorbitol_treatment_30min_bioRep1


title: Desiccation_control_1h_bioRep2

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred in sealed boxes without silica gel beads for 1 h.

value: control desiccation 1h


title: Sorbitol_control_30min_bioRep2


title: HNS1_rep3


title: Sorbitol_control_30min_bioRep1


title: Desiccation_control_4h_bioRep2


title: Desiccation_treatment_1h_bioRep3

growth_protocol: Conidia were first incubated for 24 h on cellophane disks overlaid on solid PDA medium. Germlings and the underlying cellophanes were then taken off from the agar plate and transferred in sealed boxes with silica gel beads for 1 h.

value: desiccation 1h:RH decrease with silica gel beads


title: Desiccation_treatment_1h_bioRep2


title: WT [WT_R1]

description: Replicate 1 of library WT

source_name: WT

value: WT


title: Sorbitol_treatment_30min_bioRep3


title: HNS1_rep2


title: Desiccation_control_1h_bioRep3


title: Desiccation_treatment_1h_bioRep1


title: HNS1_rep1


title: 3-Col-0

status: Public on Jun 28 2019

city: Shanghai

first: fei

last: huang

address: No. 3888 Chenhua Road, Shanghai 201602, P. R. China

institute: Chinese Academy of Sciences (CAS)

data_processing:
the low quality (Q < 17) sequences of raw reads were removed using SolexaQA (verison 2.2)
the adapter sequences were trimmed by Cutadapt (version 1.4)
after trimming, the short reads (length < 25bp) were discarded by SolexaQA (verison 2.2)
paired-end reads were mapped to the genome of Arabidopsis thaliana (TAIR 10) using Tophat
the mapped reads on each gene were counted by htseq-count
the differentially expressed genes (DEGs) were identified using the R package edgeR (FDR < 0.05, log2FoldChange > 1)
the Gene Ontology enrichment analysis of DEGs was performed by R package topGO
Genome_build: TAIR 10
Supplementary_files_format_and_content: xlsx files for up- and down-regulated genes and pdf file for pca, htseq-count results txt

organism: Arabidopsis thaliana

source_name: Arabidopsis

growth_protocol: Plants were grown under LD (16-h light/8-h dark) under cool white fluorescent at around 22 ℃.

extract_protocol:
Total RNAs were extracted from the aerial parts of 11-day-old seedlings by Rneasy Plus mini kit (Qiagen) flowering the manufacturer's instructions.
Total RNAs (1.0μg) form each sample were used for library preparation with NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England BioLabs, E7420L) flowering the manufacturer's instructions. Prepared libraries were assessed for quality using NGS High-Seneitivity kit on a fragment analyzer (AATI) and quantified using a Qubit 2.0 fluorometer(Thermo Fisher Scientific).

tag: ecotype

value: Aerial parts of seedlings

tag: development stage

value: wild type


title: 1-Col-0


title: 3-snl12345

value: snl1/2/3/4/5 quintuple mutant


title: 2-Col-0


title: 1-snl12345


title: Hela, ATailing_RNaseR_LiCl_Rep2

city: Philadelphia

first: Jeremy

middle: E.

last: Wilusz

state: PA

address: 363 Clinical Research Building, 415 Curie Boulevard

department: Department of Biochemistry & Biophysics

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
Raw reads were mapped to GRCh38 by tophat2 (version 2.0.14) with default parameters
Circular RNAs were predicted by using both CIRI2 (version 2.0.6) and CIRCexplorer2 (version 2.3.3)
Gene expression levels were calculated by cufflinks (version 2.2.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Txt files contain the raw output of the RPKM value from cufflinks
Supplementary_files_format_and_content: bedGraph files contain the bedGraph data for Genome Browser visualization

source_name: HeLa cell

growth_protocol: HeLa cells were grown at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing high glucose (Thermo Fisher Scientific 25030081), supplemented with 10% fetal bovine serum and 1% (v/v) penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using Trizol (Thermo Fisher Scientific 15596018) as per the manufacturer's instructions.
TruSeq RNA Library Preparation Kit v2
RNA-seq with Ribo Zero

treatment_protocol: Samples 1 to 4: 10 mg of HeLa total RNA from two biological replicates was incubated at 37°C for 15 min in 20 mL reactions containing 10 U RNase R (Lucigen RNR07250) or KCl-containing buffer alone.  Samples 5 to 10: 10 mg of HeLa total RNA was subjected to poly(A) tailing in a 50 mL reaction using the Poly(A) Tailing Kit (Thermo Fisher Scientific AM1350) following the manufacturer's instructions except that reactions were incubated at 37°C for 10 min and 40 U RNase Inhibitor (Thermo Fisher Scientific N8080119) was added to each reaction. Control reactions were set up similarly except that E. coli Poly(A) Polymerase I was omitted. After incubation, RNAs were acid-phenol chloroform extracted, chloroform extracted, ethanol precipitated, and dissolved in nuclease-free water. The RNAs were then incubated at 37°C for the indicated amounts of time in 20 mL reactions that contained 2 mL 10x RNase R Buffer (0.2 M Tris-HCl (pH 8.0), 1 mM MgCl2, and 1 M KCl, NaCl, or LiCl) and 0.5 mL (10 U) RNase R. Control reactions were similarly performed but water was added in place of the RNase R enzyme. Reactions were purified with RNA Clean & Concentrator-25 (Zymo Research R1018) according to the manufacturer's instructions and the RNA was eluted in 25 mL nuclease-free water.

tag: cell line

value: HeLa

value: Treated with E-PAP for 10 min, followed by RNA purification, folllowed by treatment with RNase R in LiCl containing buffer for 90 min


title: Hela, ATailing_RNaseR_LiCl_Rep1


title: Hela, Control_LiCl_Rep3

value: Treated with A-tailing buffer for 10 min, followed by RNA purification, folllowed by treatment with LiCl containing buffer for 90 min


title: Hela, Control_LiCl_Rep1


title: Hela, Control_LiCl_Rep2


title: Hela, ATailing_RNaseR_LiCl_Rep3


title: Hela, RNaseR_KCl_Rep2

value: Treated with RNase R in KCl containing buffer for 15 min


title: Desiccation_control_1h_bioRep1

tag: genotype


title: Hela, RNaseR_KCl_Rep1


title: Hela, Control_KCl_Rep2

value: Treated with KCl containing buffer for 15 min


title: -dox_4d_Ser5P_rep2_ChIPSeq

first: Liming

last: H ou

institute: NYU Langone Health

library_source: genomic

data_processing:
[RNA-seq]  For RNA-seq analysis, paired-end reads were aligned using STAR aligner. Reads that were not properly paired, non-uniquely aligned, or potential PCR duplicates were removed, and the remaining reads were used for subsequent analysis. DESeq2 (1.10.1) was used to identify differentially expressed mRNA. Only genes that had both a DESeq2 adjusted p value < 0.05 and a log2 (FPKM) of at least 1 (fold change = 2) in either direction were considered as differentially expressed genes.
[ChIP-seq and MNase-seq analysis]   Reads were aligned using Bowtie2. Only reads that were properly paired and uniquely aligned were used for subsequent processing. Potential PCR duplicates were removed using Picard Suite. Reads for ChIP-seq and Proseq data were normalized per kilobase per million for data visualization in IGV.
[ATACseq]  For ATAC-seq analysis, raw reads were aligned to the mm9 reference genome using Bowtie2. PCR duplicates were removed with Picard. Mitochondrial reads were removed prior to downstream analysis, and the remaining reads were corrected to account for the 9 bp insert introduced by the Tn5 transposase by offsetting the 5' ends by either +4 (for plus strand) or -5 (for minus strand).
[Pro-seq ]   Reads were aligned using Bowtie2. Only reads that were properly paired and uniquely aligned were used for subsequent processing. Potential PCR duplicates were removed using Picard Suite. Reads for ChIP-seq and Proseq data were normalized per kilobase per million for data visualization in IGV.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: mouse C2C12 myoblast cells

growth_protocol: [growth protocol]  C2C12 myoblasts (ATCC, Cat# CRL-1772) were grown in DMEM (Corning, Cat #15-013-CV) supplemented with 100 IU penicillin, 100 μg/ml streptomycin, 2 mM L-Glutamine (Thermo Fisher, Cat#25030081), and 10 % fetal bovine serum (Thermo Fisher, Cat# MT35011CV). All cells were cultured at 37°C under 5% (vol/vol) CO2. Paf1 inducible KO clones were maintained in 1 mg/ml doxycycline (Dox).

extract_protocol:
[ATAC-seq extract and library construction protocol]   ATAC-seq was performed as described previously (1). Briefly, 500,000 cells were harvested and washed with 500 μl cold PBS and resuspended in 500 μl cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40), and nuclei were pelleted with low speed centrifugation (500g, 4°C, 10 min). Nuclei from 50,000 cells were resuspended in 25 μl TD Buffer (10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 10% dimethlyformamide), and 2.5 μl Tn5 Transposase (Illumina, Cat #FC-121-130) and incubated at 37°C for 30 min. Fragmented DNA was purified using a MinElute kit (Qiagen, Cat#28206), and libraries were generated by PCR using NEB Next High-Fidelity 2x PCR Master Mix (NEB, Cat#M0541). An appropriate number of PCR cycles was determined by qPCR as described (2). Tagmentation was confirmed via Tapestation. Libraries were sequenced on HiSeq 2500 with paired-end reads (51bp).
[ssRNA-seq extract and library construction protocol]  TRIzol (Thermo Fisher, Cat# 15596018) was used to isolate total RNA according to the manufacturer’s instructions. For RNA-seq, genomic DNA was removed from total RNA using the TURBO DNA-free™ Kit (Thermo Fisher, Cat#AM1907), the quality of RNA was assessed using Agilent High Sensitivity RNA ScreenTape (Agilent, Cat#5067-5579), 2 μg of total RNA (with RIN® > 8) was depleted of ribosomal RNA using a Ribo-Zero Gold rRNA Removal Kit (H/M/R) (Illumina, Cat# MRZG126) according to manufacturer's instructions, and RNA was purified using RNA Clean & Concentrator-5 kit (Zymo Research, Cat#R1015). Purified mRNA was fragmented using NEBNext® Magnesium RNA Fragmentation Module (NEB, Cat#E6150S1) at 94°C for 5 min followed by purification and elution into 17.5 μl H2O. Dephosphorylation of the 3’phosphate group was performed with shrimp alkaline phosphatase (SAP) (Worthington, Cat#M0371S), followed by inactivation of phosphatase. Phosphorylation of RNA was performed with T4 Kinase (NEB, Cat# M0201S). Strand-specific cDNA libraries were prepared using NEBNext® Multiplex Small RNA Library Prep kit for Illumina (NEB, Cat#E7300S) according to manufacturer’s instructions. Libraries were quantified using Qubit dsDNA HS assay kit (Thermo Fisher, Cat#Q32854), and the quality and average size of the libraries were assessed using Agilent D1000 ScreenTape (Agilent, Cat#5067-5582) on the Agilent 2200 Tapestation. Paired-end sequencing was performed using NextSeq 500/550 High Output v2 kit (75 cycles) (Illumina, Cat# FC-404-2005) on NextSeq 550 System.
[ChIP-seq extract and library construction protocol]  ChIP and ChIP-seq libraries were prepared as described (Asp, P., Blum, R., Vethantham, V., Parisi, F., Micsinai, M., Cheng, J., . . . Dynlacht, B. D. (2011). Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A, 108(22), E149-158. doi:10.1073/pnas.1102223108) and sequenced (51 bp, single-end reads) using an Illumina HiSeq2500 machine or (37bp, paired end) using an Illumina NextSeq 500 machine
[MNase-seq extract and library construction protocol]  MNase-seq libraries were prepared as described (Asp, P., Blum, R., Vethantham, V., Parisi, F., Micsinai, M., Cheng, J., . . . Dynlacht, B. D. (2011). Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A, 108(22), E149-158. doi:10.1073/pnas.1102223108) and sequenced (51 bp, single-end reads) using an Illumina HiSeq2500 machine or (37bp, paired end) using an Illumina NextSeq 500 machine
[extract nuclei for Pro-seq ]  Nuclei were isolated from C2C12 cell as described (Core et al., 2008) with some modifications. Briefly, 3-4 15 cm2 plates of C2C12 cells (20 x106 cells) were washed twice with ice cold PBS and collected into 50 ml centrifuge tubes using a plastic cell scraper in cold room. Cells were resuspended in 5 ml of ice cold swelling buffer (20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 1:10000 dilution of 20 U/μL SUPERase• In™ RNase Inhibitor) and allowed to swell on ice for 5 min. Cells were pelleted at 4 °C for 10 min (2000 rpm), cells were resuspended in 5 ml of lysis buffer tNuclei were isolated from C2C12 cell as described (5) with some modifications. Briefly, 3-4 15 cm2 plates of C2C12 cells (~ 20 x106 cells) were washed twice with ice cold PBS and collected using a cell scraper. Cells were resuspended in 5 ml of ice cold swelling buffer (20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 1:10000 dilution of 20 U/μL SUPERase In™ RNase Inhibitor) and allowed to swell on ice for 5 min. Cells were pelleted at 4 °C for 10 min (2000 rpm) and resuspended in 5 ml of lysis buffer twice (swelling buffer + 0.5 % NP40, + 10 % glycerol + 1:10000 dilution of 20 U/μL SUPERase  In™ RNase Inhibitor) and gently pipetted up and down 20 times using a p1000 tip with the end cut off to reduce shearing, the nuclei were pelleted and resuspended in 1ml Freezing buffer (50 mM Tris-HCl pH 8.3, 40 % glycerol, 5 mM MgCl2, 0.1 mM EDTA), and transferred to a 1.5 ml centrifuge tube. Nuclei were spun down and resuspended in Freezing Buffer (5x106 nuclei per 100 μl). wice (swelling buffer + 0.5 % NP40, + 10 % glycerol + 1:10000 dilution of 20 U/μL SUPERase• In™ RNase Inhibitor) and gently pipetted up and down 20 times using a p1000 tip with the end cut off to reduce shearing, the nuclei were pelleted and resuspended in 1ml Freezing buffer (50 mM Tris-HCl pH 8.3, 40 % glycerol, 5 mM MgCl2, 0.1 mM EDTA), and transferred to a 1.5 ml centrifuge tube. Nuclei were spun down and resuspended in Freezing Buffer (5x106 nuclei per 100 μl).
[Pro-seq library construction protocol]  Proseq was based on a published Proseq protocol (6) with some modifications. Nuclear run-on reactions were performed by adding 100 μl of nuclei (5x106) to 100 μl of preheated (37°C) 2x nuclear run-on (NRO) master mix (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 300 mM KCl , 1 mM DTT, 250 mM ATP, 250 mM GTP, 50 mM biotin-11-CTP, 50 mM biotin-11-UTP, and 1% Sarkosyl), pipetting the mixture 15 times, and incubating reactions at 37°C for 5 min. Reactions were stopped with Trizol LS, and RNA was extracted once with chloroform and precipitated with ethanol (vol/vol), and the pellet was washed in 75% ethanol once and re-dissolved in DEPC-H2O. Next, RNA fragmentation was performed using base hydrolysis, biotin RNA enrichment was performed using pre-washed streptavidin beads once at room temperature for 30 min, and the beads were washed twice in ice-cold high-salt wash buffer (50 mM Tris-HCl pH 7.4, 2 M NaCl and 0.5 % (vol/vol) Triton X-100 in DEPC H2O), twice in binding buffer (10 mM Tris-HCl pH 7.4, 300 mM NaCl and 0.1 % Triton X-100), and once in low-salt wash buffer (5 mM Tris-HCl pH 7.4 and 0.1 % Triton X-100). RNA was extracted from beads using Trizol, ethanol precipitated, and dissolved in H2O. The 5' cap of RNA was removed from unhydrolyzed short nascent RNA using 5U RNA 5' pyrophosphohydrolase (RppH), and the 5' OH generated by base hydrolysis was then converted to 5' phosphate by treatment with 25U T4 polynucleotide kinase (PNK). RNA was extracted with Trizol and dissolved in H2O, and libraries were prepared using NEB Next Multiple Small RNA library Prep set for Illumina (NEB, Cat#E7300S), following manufacturer's indications. Libraries were sequenced on the Illumina NextSeq 550.

treatment_protocol:
[DRB treatment protocol ]   For Proseq experiments, DRB (Sigma, Cat# D1916) in DMSO was added to the media at a final concentration of 100 mM for indicated times (5 min, 15 min, and 30 min), and the cells were quickly washed twice with cold PBS and collected.
[siRNA KD treatment protocol ]   All siRNAs were synthesized by Dharmacon or Qiagen. Six hours before transfection, 1x105 C2C12 cells were seeded in 6-well plates and siRNAs were transfected into cells using Lipofectamine RNAiMAX (Invitrogen), at a final concentration of 50 nM. Cells were harvested 48 h post transfection.

value: conditional Paf1_KO

tag: treatment condition

tag: chip antibody

value: Rabbit Anti-RNA polymerase II CTD (phospho S5) (Abcam,ab5131)


title: -dox_4d_input DNA_ChIPSeq (Spt6,Ser2P-rep2,Ser5P-rep2)


title: -dox_4d_Spt16_ChIPSeq

value: Rabbit monoclonal anti-SPT16 (Cell Signaling Technology,12191S)


title: +dox_input DNA_ChIPSeq (Spt6,Ser2P-rep2,Ser5P-rep2)

value: +dox (1 ug/ml Dox)


title: +dox_Ser2P_rep2_ChIPSeq

value: Rabbit Anti-RNA polymerase II CTD (phospho S2) (Abcam,ab5095)


title: +dox_Spt6_ChIPSeq

value: Rabbit polyclonal anti-Spt6 (Novus,NB100-2582)


title: -dox_4d_Spt6_ChIPSeq


title: -dox_4d_Ser2P_rep2_ChIPSeq


title: -dox_4d_Ser5P_rep1_ChIPSeq


title: WT [WT_R2]

description: Replicate 2 of library WT

tag: strain

value: ARSEF 2860

value: 84 hours

value: mycelia


title: +dox_Ser5P_rep1_ChIPSeq


title: +dox_Ser2P_rep1_ChIPSeq


title: -dox_4d_Spt5_ChIPSeq

value: Rabbit polyclonal anti-SUPT5H (Bethyl,A300-868A)


title: -dox_4d_Ser2P_rep1_ChIPSeq


title: -dox_4d_input DNA_ChIPSeq (Spt5,Spt16,Ser2P-rep1,Ser5P-rep1)


title: Hela, Control_KCl_Rep1


title: +dox_input DNA_ChIPSeq (Spt5,Spt16,Ser2P-rep1,Ser5P-rep1)


title: +dox_Ser5P_rep2_ChIPSeq


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP18-p6-002-p6-B1]

city: Utrecht

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

institute: Single Cell Discoveries

data_processing:
CEL-seq were mapped with bwa using custom scripts as previously described (Grün et al., Nature Methods, 2014)
Genome_build: mouse: mm10
Supplementary_files_format_and_content: *.txt Tab separated txt file for all processed libaries together. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. Column names indicate the cell name.
Supplementary_files_format_and_content:.R: scripts for both the full dataset (Seurat) and the pancreatic cell types subset (Seurat and Monocle).
Supplementary_files_format_and_content:.Rdata: R workspaces for the full dataset (Seurat) and the pancreatic cell types subset (Seurat and Monocle).

source_name: developing mouse embryonic pancreas

growth_protocol: Embryo’s were isolated from pregnant mip-gfp expressing female mice between embryonic ages E12.5 and E18.5. Individual embryos were dissected, and the embryonic pancreas was isolated by visual observation. Tissues were dispersed using trypLE for 8-10 minutes at 37C, after which they were washed in PBS containing 10% FBS and filtered using a 70um mesh. Immediately before FACS sorting, DAPI or PE was added for live-death staining. Cells were seleted based on size and complexity, then live cells were selected by negative selection for the viability dye. Live cells were picked from the viable cell population. GFP positive cells were gated based on GFP intensity as measured by FACS. Single cells were sorted into 384 wells plates containing...

extract_protocol:
Cells were sorted into 5µl Vapor-Lock (Qiagen) or mineral oil (Sigma) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by the SORT-seq protocol (Muraro et al. Cell Sys. 2016) Libraries were sequenced on a Illumina NextSeq500 using 75bp paired end sequencing.

tag: enrichment

value: MIP-GFP cells

tag: developmental stage


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP18-p6-002-p6-A1]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP18-p6-002-p6-B2]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP18-p6-002-p6-A2]


title: Embryonic pancreas day E12.5, live population (Dapi -) [EP18-p4-001-B2]

value: live cells


title: Embryonic pancreas day E12.5, live population (Dapi -) [EP18-p4-001-A1]


title: Embryonic pancreas day E12.5, live population (Dapi -) [EP18-p4-001-B1]


title: +dox_Spt16_ChIPSeq


title: +dox_Spt5_ChIPSeq


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP17p6001A1]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP17p6001B1]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP17p4002B2]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP17p4002A1]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP17p4002B1]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP16P6-001-4]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP17p6001B2]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP16P6-001-3]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP17p4002A2]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP16P6-001-2]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP16P6-001-1]


title: Embryonic pancreas day E18.5, live population (Dapi -) [EP16P4-001-4]


title: Embryonic pancreas day E18.5, live population (Dapi -) [EP16P6-002-mosquito]


title: Embryonic pancreas day E18.5, live population (Dapi -) [EP16P4-001-1]


title: Embryonic pancreas day E18.5, live population (Dapi -) [EP16P4-001-2]


title: Embryonic pancreas day E18.5, live population (Dapi -) [EP16P4-001-3]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP14-P6-4]


title: Embryonic pancreas day E12.5, live population (Dapi -) [EP18-p4-001-A2]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP14-P6-2]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP14-P6-1]


title: Embryonic pancreas day E14.5, MIP-GFP population  [EP14-P6-3]


title: Embryonic pancreas day E14.5, live population (Dapi -) [EP14-P4-4]


title: Embryonic pancreas day E14.5, live population (Dapi -) [EP14-P4-1]


title: Embryonic pancreas day E13.5, MIP-GFP population  [EP12-P6-4]


title: Embryonic pancreas day E13.5, MIP-GFP population  [EP12-P6-2]


title: Embryonic pancreas day E14.5, live population (Dapi -) [EP14-P4-3]


title: Embryonic pancreas day E13.5, MIP-GFP population  [EP12-P6-3]


title: Embryonic pancreas day E13.5, MIP-GFP population  [EP12-P6-1]


title: Embryonic pancreas day E13.5, live population (Dapi -) [EP12-P4-1]


title: Embryonic pancreas day E13.5, live population (Dapi -) [EP12-P4-2]


title: Embryonic pancreas day E13.5, live population (Dapi -) [EP12-P4-3]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP11P6-2]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP11P6-4]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP11P6-3]


title: Embryonic pancreas day E12.5, live population (Dapi -) [EP11P4-4]


title: Embryonic pancreas day E12.5, live population (Dapi -) [EP11P4-2]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP10P6-3]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP10P6-1]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP10P6-4]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP11P6-1]


title: Embryonic pancreas day E12.5, live population (Dapi -) [EP11P4-3]


title: Embryonic pancreas day E15.5, MIP-GFP population  [EP10P6-2]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP10P4-4]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP10P4-2]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP10P4-3]


title: Embryonic pancreas day E15.5, live population (Dapi -) [EP10P4-1]


title: Embryonic pancreas day E15.5, MIP-GFP population


title: Embryonic pancreas day E15.5, live population (Dapi -)


title: Embryonic pancreas day E12.5, live population (Dapi -)

data_processing:
CEL-seq were mapped with bwa using custom scripts as previously described (Grün et al., Nature Methods, 2014)
Genome_build: mouse: mm10
Supplementary_files_format_and_content: *.txt Tab separated txt file for all processed libaries together. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. Column names indicate the cell name.
Supplementary_files_format_and_content:.R: scripts for both the full dataset (Seurat) and the pancreatic cell types subset (Seurat and Monocle).
Supplementary_files_format_and_content:.Rdata: R workspaces for the full dataset (Seurat) and the pancreatic cell types subset (Seurat and Monocle).
Supplementary_files_format_and_content:.R: scripts for both the full dataset (Seurat) and the pancreatic cell types subset (Seurat and Monocle).
Supplementary_files_format_and_content:.Rdata: R workspaces for the full dataset (Seurat) and the pancreatic cell types subset (Seurat and Monocle).


title: Dorsal Forebrain Sample 3

tag: cell type

value: hPSC-derived astrocytes

tag: hpsc line

value: Dorsal Forebrain


title: Embryonic pancreas day E12.5, MIP-GFP population


title: Embryonic pancreas day E13.5, live population (Dapi -) [EP12-P4-4]


title: -dox_H2Bub_ChIPSeq

value: C2C12 cells

value: anti-Ubiquityl-Histone H2B (Lys120) (CST,5546S)


title: -dox_ssRNA-seq_rep1

description:
rRNA depleted total RNA
-dox_ssRNA-seq_rep1


title: +dox_ssRNA-seq_rep2

description:
rRNA depleted total RNA
+dox_ssRNA-seq_rep2


title: F0C

city: ShenYang

first: Li

last: Hailong

state: Liaoning

address: NO. 3-11, Wenhua Road, Heping District

institute: Northeastern University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2.
Genome_build: Mus_musculus.GRCm38
Genome_build: GCF_000364345.1_Macaca_fascicularis_5.0
Genome_build: Cryptococcus neoformans var. grubii H99
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include NCBI Gene IDs and reads values (raw counts) for each Sample.

source_name: Lung RNA-seq sample, extracted from uninfected mouse, replicate 1

extract_protocol:
For the transcriptome analysis, mice and monkey were sacrificed at 7-day post infection. Lung and brain tissue were isolated and resuspended in RNAlater. Monkey lung tissues were removed from the chest, and cut into 0.5 cm X 0.5 cm X 0.5 cm cubes. Tissues were then processed for RNA-seq analysis. PBS treated mice and monkeys were used as RNA-seq analysis reference samples. Total RNA was isolated with Trizol. RNA library construction and sequencing were generated by using the TruSeq RNA Sample Preparation Kit based on the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: gender

value: female

value: 6-8 weeks

value: Lung

value: uninfected


title: N0A

source_name: Brain RNA-seq sample, extracted from uninfected mouse, replicate 1

value: Brain


title: F0F

source_name: Lung RNA-seq sample, extracted from uninfected mouse, replicate 3


title: N0C

source_name: Brain RNA-seq sample, extracted from uninfected mouse, replicate 2


title: rescue_Mnase-seq_rep1

tag: genotype/variation

value: conditional Paf1_KO

value: -dox_4d&+dox_4d (1 ug/ml Dox)


title: +dox_MNase-seq_rep2

value: +dox (1 ug/ml Dox)


title: F0E

source_name: Lung RNA-seq sample, extracted from uninfected mouse, replicate 2

tag: tissue


title: -dox_MNase-seq_rep1


title: rescue_Mnase-seq_rep2


title: N0D

source_name: Brain RNA-seq sample, extracted from uninfected mouse, replicate 3

tag: treatment


title: -dox_DRB_30min_Pro-seq_rep2

description:
biotin labelled nascent RNA
-dox_DRB_30min_Pro-seq_rep2

value: -dox_4d (treat with 100uM DRB for 30min)


title: +dox_MNase-seq_rep1


title: +dox_H2Bub_ChIPSeq


title: -dox_DRB_15min_Pro-seq_rep2

description:
biotin labelled nascent RNA
-dox_DRB_15min_Pro-seq_rep2

value: -dox_4d (treat with 100uM DRB for 15min)


title: +dox_DRB_15min_Pro-seq_rep2

description:
biotin labelled nascent RNA
+dox_DRB_15min_Pro-seq_rep2

value: +dox (treat with 100uM DRB for 15min)  (1 ug/ml Dox)


title: -dox_DRB_5min_Pro-seq_rep2

description:
biotin labelled nascent RNA
-dox_DRB_5min_Pro-seq_rep2

value: -dox_4d (treat with 100uM DRB for 5min)


title: +dox_input DNA_H2Bub_ChIPSeq

description: +dox_input DNA_H2Bub_ChIPSeq


title: +dox_DRB_5min_Pro-seq_rep2

description:
biotin labelled nascent RNA
+dox_DRB_5min_Pro-seq_rep2

value: +dox (treat with 100uM DRB for 5min)  (1 ug/ml Dox)


title: -dox_DRB_30min_Pro-seq_rep1

description:
biotin labelled nascent RNA
-dox_DRB_30min_Pro-seq_rep1


title: +dox_DRB_30min_Pro-seq_rep2

description:
biotin labelled nascent RNA
+dox_DRB_30min_Pro-seq_rep2

value: +dox (treat with 100uM DRB for 30min)  (1 ug/ml Dox)


title: -dox_Pro-seq_rep2

description:
biotin labelled nascent RNA
-dox_Pro-seq_rep2

value: -dox_4d (no DRB treatment)


title: -dox_MNase-seq_rep2

value: C2C12 cells


title: -dox_input DNA_H2Bub_ChIPSeq

description: -dox_input DNA_H2Bub_ChIPSeq


title: +dox_Pro-seq_rep2

description:
biotin labelled nascent RNA
+dox_Pro-seq_rep2

value: +dox (no DRB treatment)  (1 ug/ml Dox)


title: -dox_ssRNA-seq_rep2

description:
rRNA depleted total RNA
-dox_ssRNA-seq_rep2


title: +dox_DRB_15min_Pro-seq_rep1

description:
biotin labelled nascent RNA
+dox_DRB_15min_Pro-seq_rep1

value: +dox (treat with 100uM DRB for 15min) (1 ug/ml Dox)


title: +dox_DRB_30min_Pro-seq_rep1

description:
biotin labelled nascent RNA
+dox_DRB_30min_Pro-seq_rep1


title: -dox_Pro-seq_rep1

description:
biotin labelled nascent RNA
-dox_Pro-seq_rep1


title: IUGR16

city: London

first: Victor

last: Han

state: Ontario

address: 1151 Richmond Street

department: Biochemistry

country: Canada

institute: Western University

description:
PE16-05
MasterCount_IUGRONLY.txt

data_processing:
FastQC was used to determine if adaptors need to be cut
Sequence reads were aligned to human transcriptome index (genome_build 37) using bowtie2
Sam files were used to create .txt containing abundance count of each feature per sample
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Placenta

extract_protocol:
Total RNA was isolated from 50-100mg of tissue from the two central and two peripheral regions of each placenta, using the mirVana® RNA isolation kit (Life Technologies™, Burlington, Ontario)
The Truseq RNA kit provided by Ilumina, used as per manufacturer's protocol

value: Placenta

tag: disease group

value: Intrauterine Growth Restriction only


title: -dox_Pol2_ChIPSeq

value: anti-RNA Polymerase II RPB1 Antibody (8WG16) (BioLegend,664906)


title: -dox_DRB_5min_Pro-seq_rep1

description:
biotin labelled nascent RNA
-dox_DRB_5min_Pro-seq_rep1


title: IUGR13

description:
PE15-24
MasterCount_IUGRONLY.txt


title: IUGR14

description:
PE 15-25
MasterCount_IUGRONLY.txt


title: IUGR11

description:
IUGR 14-11
MasterCount_IUGRONLY.txt


title: +dox_DRB_5min_Pro-seq_rep1

description:
biotin labelled nascent RNA
+dox_DRB_5min_Pro-seq_rep1

value: +dox (treat with 100uM DRB for 5min) (1 ug/ml Dox)


title: IUGR18

description:
PE16-21
MasterCount_IUGRONLY.txt


title: IUGR10

description:
IUGR14-10
MasterCount_IUGRONLY.txt


title: +dox_Pro-seq_rep1

description:
biotin labelled nascent RNA
+dox_Pro-seq_rep1

value: conditional Paf1_KO

value: +dox (no DRB treatment) (1 ug/ml Dox)


title: -dox_input DNA_ChIPSeq (Pol2)

description: -dox_input DNA_ChIPSeq (Pol2)


title: +dox_Pol2_ChIPSeq

value: +dox (1 ug/ml Dox)


title: IUGR9

description:
27033
MasterCount_IUGRONLY.txt


title: +dox_input DNA_ChIPSeq (Pol2)

description: +dox_input DNA_ChIPSeq (Pol2)


title: IUGR17

description:
PE16-06
MasterCount_IUGRONLY.txt


title: IUGR8

description:
26714
MasterCount_IUGRONLY.txt


title: +dox_ssRNA-seq_rep1

description:
rRNA depleted total RNA
+dox_ssRNA-seq_rep1


title: IUGR15

description:
PE15-32
MasterCount_IUGRONLY.txt


title: IUGR12

description:
IUGR15-06
MasterCount_IUGRONLY.txt


title: IUGR6

description:
26571
MasterCount_IUGRONLY.txt


title: 2-snl12345

tag: ecotype

value: Aerial parts of seedlings

value: snl1/2/3/4/5 quintuple mutant


title: IUGR5

description:
78
MasterCount_IUGRONLY.txt


title: IUGR4

description:
42
MasterCount_IUGRONLY.txt


title: IUGR3

description:
36
MasterCount_IUGRONLY.txt


title: IUGR2

description:
33b
MasterCount_IUGRONLY.txt


title: IUGR1

description:
17
MasterCount_IUGRONLY.txt


title: -dox_DRB_15min_Pro-seq_rep1

description:
biotin labelled nascent RNA
-dox_DRB_15min_Pro-seq_rep1

value: -dox_4d (treat with 100uM DRB for 15min)


title: PEIUGR19

description:
PE15-30
MasterCount_PEIUGR.txt

value: Preeclampsia and Intrauterine Growth Restriction


title: PEIUGR18

description:
PE15-08
MasterCount_PEIUGR.txt


title: PEIUGR16

description:
PE 14-20
MasterCount_PEIUGR.txt


title: PEIUGR15

description:
PE 14-08
MasterCount_PEIUGR.txt


title: PEIUGR17

description:
PE 14-32
MasterCount_PEIUGR.txt


title: PEIUGR14

description:
PE 13-22
MasterCount_PEIUGR.txt


title: IUGR7

description:
26572
MasterCount_IUGRONLY.txt


title: PEIUGR12

description:
IUGR 15-08
MasterCount_PEIUGR.txt


title: PEIUGR9

description:
396-10_a
MasterCount_PEIUGR.txt


title: PEIUGR8

description:
364-09
MasterCount_PEIUGR.txt


title: PEIUGR7

description:
314-07
MasterCount_PEIUGR.txt


title: PEIUGR4

description:
27
MasterCount_PEIUGR.txt


title: PEIUGR10

description:
9177
MasterCount_PEIUGR.txt


title: PEIUGR3

description:
24
MasterCount_PEIUGR.txt


title: PEIUGR6

description:
287-06
MasterCount_PEIUGR.txt


title: PEIUGR1

description:
1
MasterCount_PEIUGR.txt


title: PEIUGR2

description:
2
MasterCount_PEIUGR.txt


title: PEIUGR20

description:
PE16-08
MasterCount_PEIUGR.txt


title: PE20

description:
PE 14-09
MasterCount_PEONLY.txt

value: Preeclampsia only


title: PEIUGR11

description:
IUGR 15-01
MasterCount_PEIUGR.txt


title: PE18

description:
PE15-33
MasterCount_PEONLY.txt


title: PE19

description:
PE16-03
MasterCount_PEONLY.txt


title: PE16

description:
PE 14-21
MasterCount_PEONLY.txt


title: PE15

description:
PE 14-11
MasterCount_PEONLY.txt


title: PE14

description:
PE 14-10
MasterCount_PEONLY.txt


title: PEIUGR13

description:
PE 12-06
MasterCount_PEIUGR.txt


title: PEIUGR5

description:
270-06
MasterCount_PEIUGR.txt


title: PE17

description:
PE15-19
MasterCount_PEONLY.txt


title: PE13

description:
PE 14-03
MasterCount_PEONLY.txt


title: PE12

description:
PE 13-35
MasterCount_PEONLY.txt


title: PE9

description:
PE 13-29
MasterCount_PEONLY.txt


title: PE7

description:
PE 13-19
MasterCount_PEONLY.txt


title: PE8

description:
PE 13-24
MasterCount_PEONLY.txt


title: PE11

description:
PE 13-33
MasterCount_PEONLY.txt


title: PE10

description:
PE 13-30
MasterCount_PEONLY.txt


title: Control19

description:
PE 14-22
MasterCount_ControlONLY.txt

value: Control


title: PE5

description:
336-08
MasterCount_PEONLY.txt


title: PE2

description:
255-05
MasterCount_PEONLY.txt


title: Control20

description:
PE 14-33
MasterCount_ControlONLY.txt


title: PE1

description:
239-05
MasterCount_PEONLY.txt


title: PE4

description:
283-06
MasterCount_PEONLY.txt


title: Control21

description:
PE15-26
MasterCount_ControlONLY.txt


title: Control13

description:
PE 12-08
MasterCount_ControlONLY.txt


title: Control12

description:
PE 12 -03
MasterCount_ControlONLY.txt


title: PE3

description:
257-05
MasterCount_PEONLY.txt


title: Control14

description:
PE 13-16
MasterCount_ControlONLY.txt


title: Control9

description:
401-10
MasterCount_ControlONLY.txt


title: Control10

description:
403-10
MasterCount_ControlONLY.txt


title: Control8

description:
400-10
MasterCount_ControlONLY.txt


title: Control18

description:
PE 14-19
MasterCount_ControlONLY.txt


title: Control16

description:
PE 13-27
MasterCount_ControlONLY.txt


title: Control5

description:
338-08
MasterCount_ControlONLY.txt


title: Control6

description:
383-10
MasterCount_ControlONLY.txt


title: Control4

description:
328-08
MasterCount_ControlONLY.txt


title: Control7

description:
399-10
MasterCount_ControlONLY.txt


title: PE6

description:
9409
MasterCount_PEONLY.txt


title: Control3

description:
293-06
MasterCount_ControlONLY.txt


title: Control2

description:
279-06
MasterCount_ControlONLY.txt


title: PE16-05

data_processing:
FastQC was used to determine if adaptors need to be cut
To cut adaptor sequnce we used "cutadapt" function in terminal
Sequence reads were aligned to mature miRNA human index (miRbase v.21, genome_build 38)
Sam files were used to create .txt containing abundance count of each feature per sample
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

extract_protocol:
Total RNA was isolated from 50-100mg of tissue from the two central and two peripheral regions of each placenta, using the mirVana® RNA isolation kit (Life Technologies™, Burlington, Ontario)
The Truseq smRNA kit provided by Ilumina, used as per manufacturer's protocol


title: PE16-06


title: Control17

description:
PE 13-31
MasterCount_ControlONLY.txt


title: Control11

description:
550
MasterCount_ControlONLY.txt


title: IUGR 14-11


title: IUGR15-06


title: PE15-24


title: PE 15-25


title: PE15-32


title: 78


title: 9230


title: 9232


title: 9310


title: 33


title: 42


title: 17


title: PE16-08


title: Control1

description:
267-05
MasterCount_ControlONLY.txt


title: PE15-08


title: PE15-30


title: PE 14-32


title: PE 14-08


title: 36


title: PE16-21


title: PE 14-20


title: 9609


title: IUGR14-10


title: IUGR 15-01


title: IUGR 15-08


title: PE 13-22


title: 396-10_a


title: 9177


title: 364-09


title: 314-07


title: 287-06


title: 270-06


title: 27


title: 2


title: PE16-03


title: PE15-19


title: PE 14-21


title: Control15

description:
PE 13-20
MasterCount_ControlONLY.txt


title: PE 14-11


title: PE 14-10


title: PE 14-03


title: PE 13-33


title: 283-06


title: 257-05


title: PE 13-24


title: PE 13-29


title: 9409


title: 336-08


title: PE 13-19


title: PE 12-06


title: 239-05


title: 1


title: 24


title: PE15-26


title: PE 14-19


title: 255-05


title: PE15-33


title: PE 13-31


title: PE 13-20


title: PE 12-08


title: PE 13-35


title: PE 16-22


title: PE 13-30


title: 550


title: 400-10


title: 401-10


title: PE 12 -03


title: 403-10


title: PE 13-27


title: 399-10


title: 293-06


title: 279-06


title: 328-08


title: PE 14-33


title: PE 14-22


title: AA6241

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

institute: Cancer Research Center of Toulouse

data_processing:
Low-quality 5' and 3' ends were trimmed using Sickle (Phred score <20). Overlapping reads were merged using SeqPrep and split in half with a Awk routine. Paired-ends with one read shorter than 30 bp were discarded.
Transcriptomic (coding RefSeq genes from Hg19 UCSC Table Browser fixed on 2014/01) alignments were performed by TopHat2. Once aligned, paired-end reads that mapped at multiple locations on transcriptome, low-quality (score <20) and discordant paired-end reads were discarded using SAMtools. MarkDuplicates removed PCR duplicates.
Cufflinks estimated gene abundance.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited expression matrix (units are log2[FPKM+1])

molecule: polyA RNA

source_name: Leiomyosarcoma

extract_protocol:
Standard TRIzol (Life Technologies) / chloroform extraction followed by 100% ethanol precipitation and RNA purification using the RNeasy Mini Kit (Qiagen) with a DNase treatment (RNase-Free DNase Set, Qiagen). RNA were quantified using a Nanodrop 1000 spectrophotometer (Thermo Scientific) and were qualified with the Agilent 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano Kit (Agilent) according to the manufacturer’s instructions. An ERCC RNA Spike-In Mix (Life technologies) was added to each RNA as recommended by the manufacturer.
RNA-seq libraries were prepared with a TruSeq stranded mRNA library prep kit. Library were sequenced using a HiSeq 2000 (Illumina). Image analysis, base calling and base quality scoring of the run were processed by integrated primary analysis software - Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA (v1.8).

tag: Sex

value: Male

tag: age

value: Trunk wall

tag: tissue type

value: Leiomyosarcoma

tag: fnclcc grade


title: 383-10


title: AA6238

value: Female


title: AA6240

source_name: Angiosarcoma

value: Angiosarcoma


title: AA6239

source_name: Pleomorphic rhabdomyosarcoma

value: Pleomorphic rhabdomyosarcoma


title: AA6234


title: AA6236


title: AA6235

source_name: Undifferentiated spindle cell sarcoma

value: Undifferentiated spindle cell sarcoma


title: AA6233

source_name: Extraskeletal osteosarcoma

value: Upper limb

value: Extraskeletal osteosarcoma


title: AA6237


title: AA6232


title: PE 13-16

value: Placenta


title: AA6230

source_name: Intimal sarcoma

value: Intimal sarcoma


title: AA6231

source_name: Dedifferentiated liposarcoma

value: Dedifferentiated liposarcoma


title: AA6229

source_name: Undifferentiated pleomorphic sarcoma

value: Undifferentiated pleomorphic sarcoma


title: AA6226

value: Head and neck


title: AA6228

source_name: Malignant mesenchymoma

value: Malignant mesenchymoma


title: AA6224


title: AA6225


title: AA6227

value: Unknown


title: AA6223


title: AA6221


title: 267-05

value: Control


title: AA6220

value: Male


title: AA6222

source_name: Myxofibrosarcoma

value: Trunk wall

value: Myxofibrosarcoma


title: AA6217

value: Female


title: AA6218

value: Leiomyosarcoma


title: AA6216

value: Gyneacological area


title: 338-08


title: AA6214


title: AA6215


title: AA6213

value: Angiosarcoma


title: AA6212


title: AA6208


title: AA6210

value: Lower limb


title: AA6209


title: AA6206

value: Upper limb


title: AA6207


title: AA6204


title: AA6205


title: AA6211


title: AA6202


title: AA6203


title: AA6201


title: AA6200


title: AA6198


title: AA6197


title: AA6196


title: AA6219


title: AA6193


title: AA6192


title: AA6191


title: AA6188


title: AA6190


title: AA6187

value: Extraskeletal osteosarcoma


title: AA6189


title: AA6186


title: AA6185


title: AA6184


title: AA6182

value: Undifferentiated spindle cell sarcoma


title: AA6183

source_name: Osteosarcoma

value: Osteosarcoma


title: AA6180


title: AA6178


title: AA6181

value: Undifferentiated pleomorphic sarcoma


title: AA6177


title: AA6176


title: AA6195


title: AA6173


title: AA6174


title: AA6172


title: AA6171


title: AA6169


title: AA6168

value: Head and neck


title: AA6167


title: AA6194


title: AA6175


title: AA6199

source_name: Malignant peripheral nerve sheath tumour


title: AA6166


title: AA6165


title: AA6170


title: AA6179


title: miR142F/F_Foxp3Cre_Rep2

first: Graham

last: Lord

address: 5th Floor Tower Wing, Guy's Hospital

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King's College London

description: CD4+ CD25+ YFP+ cells from the lymph nodes and spleens of FoxP3YFP-Cre x Mir142fl/fl mice

hyb_protocol: Per King’s College London Genomics Centre facility

data_processing: RMA normalized through oligo package in Bioconductor

source_name: Thymically-derived Treg cells from miR-142-defcient mice

label_protocol: Ovation Pico WTA kit (NuGEN)

growth_protocol: Magnetic positive selection of CD4+ cells followed by flow-cytometric sorting of CD4+ CD25+ YFP+ cells to >95% purity.

extract_protocol: TRIsure (Bioline) extraction of total RNA

treatment_protocol: Ex vivo isolated

tag: genotype

value: FoxP3YFP-Cre x Mir142fl/fl

value: Thymically-derived regulatory T cells

tag: phenotype markers

value: :CD4+ CD25+ YFP+

value: Spleen, lymph node


title: miR142WT/WT_Foxp3Cre_Rep1

description: CD4+ CD25+ YFP+ cells from the lymph nodes and spleens of FoxP3YFP-Cre x Mir142+/+ mice

scan_protocol: Per King’s College London Genomics Centre facility

source_name: Thymically-derived Treg cells from wild-type mice

tag: strain

value: FoxP3YFP-Cre x Mir142+/+


title: CULA

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

description: C57BL/6 Urethane induced Lung Adenocarcinoma (CULA)

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: FULA and CULA mouse lung adenocarcinoma cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

extract_protocol: Trizol followed by RNAeasy spin columns

treatment_protocol: Not applicable

tag: cell line

value: CULA


title: FVB Lungs Urethane 2

description: FVB Lungs, one week after urethane intraperitoneal injection

growth_protocol: Not applicable, all cells were submitted directly to RNA extraction

value: FVB

value: lungs


title: FVB Lungs Urethane 1

source_name: FVB Lungs, one week after urethane intraperitoneal injection


title: FULA 3

description: FVB Urethane induced Lung Adenocarcinoma 3 (FULA 3)

value: FULA


title: miR142WT/WT_Foxp3Cre_Rep2

tag: cell type


title: Mouse macrophages

description: Mouse bone marrow derived macrophages cultured with unconditioned media

source_name: Mouse bone marrow derived macrophages

growth_protocol: Cancer cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

value: unconditioned media


title: Mast cells_IL3/KITL

description: Mouse mast cells derived from bone marrow and matured with IL-3 and KITL

tag: media

value: non-conditioned


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep4

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

data_processing:
Data analysis of DamID samples: First, the constant DamID adapter was trimmed from the 65 bp single-end reads (with cutadapt 1.11 and custom scripts). The remaining gDNA starting with GATC was mapped to hg19 with bowtie2 2.2.6. Uniquely mapped reads (filtered for bowtie’s XS-tag) were counted to GATC fragments.
Genome_build: hg19 for homo sapiens samples, mm10 for mus musculus samples

source_name: DamID, Dam-LMNB1, F121-9, PASins Cobl

growth_protocol: Cells were cultured according to 4DNucleome SOP, https://www.4dnucleome.org/cell-lines.html

extract_protocol:
DamID-seq was performed as described in (Brueckner et al. 2016) with slight modifications. Instead of plasmid transfections, Dam-LMNB1 or Dam were added by Lentiviral transduction. Three days after infection, cells were collected for gDNA isolation. gDNA was pre-treated with SAP (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 1 h followed by heat inactivation at 65°C for 20 min to remove signal from apoptotic fragments. gDNA was digested with DpnI (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 8 h followed by heat inactivation at 80 °C for 20 min. Fragments were ligated to 12.5 pmol DamID adapters using T4 ligase (2.5 U, New England Biolabs) in T4 ligase buffer in a total volume of 20 µl incubated at 16 °C for 16 h. The reaction was heat inactivated for 10 min at 65 °C. Products were then digested with DpnII to remove partially methylated fragments. DpnII buffer and DpnII (10 U, New England Biolabs) were added in a total volume of 50 µl and incubated at 37 °C for 1 h. 8 µl of DpnII-digested products was amplified by PCR with MyTaq Red Mix (Bioline) and 2.5 µM primers Adr-PCR-Rand1 in a total volume of 40 µl. PCR settings were 8 min at 72 °C (1×) followed by 20 s at 94 °C, 30 s at 58 °C, 20 s at 72 °C (24× for Dam, 28x for DamLMNB1 samples) and 2 min at 72 °C (1×). Remaining steps were performed as previously described.
DamID-seq was performed as described in (Brueckner et al. 2016) with slight modifications. Instead of plasmid transfections, Dam-LMNB1 or Dam were added by Lentiviral transduction. Three days after infection, cells were collected for gDNA isolation. gDNA was pre-treated with SAP (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 1 h followed by heat inactivation at 65°C for 20 min to remove signal from apoptotic fragments. gDNA was digested with DpnI (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 8 h followed by heat inactivation at 80 °C for 20 min. Fragments were ligated to 12.5 pmol DamID adapters using T4 ligase (2.5 U, New England Biolabs) in T4 ligase buffer in a total volume of 20 µl incubated at 16 °C for 16 h. The reaction was heat inactivated for 10 min at 65 °C. Products were then digested with DpnII to remove partially methylated fragments. DpnII buffer and DpnII (10 U, New England Biolabs) were added in a total volume of 50 µl and incubated at 37 °C for 1 h. 8 µl of DpnII-digested products was amplified by PCR with MyTaq Red Mix (Bioline) and 2.5 µM primers Adr-PCR-Rand1 in a total volume of 40 µl. PCR settings were 8 min at 72 °C (1×) followed by 20 s at 94 °C, 30 s at 58 °C, 20 s at 72 °C (24× for Dam, 28x for DamLMNB1 samples) and 2 min at 72 °C (1×). Remaining steps were performed as previously described.

treatment_protocol: RPE-1 cells: sgRNAs were cloned into Lentiguide-Puro vector (Addgene #52963) using restriction enzyme BsmBI, and Lentivirus was prepared. RPE-1 cells stably expressing SunTag-CRISPRa were infected with LentiGuide virus and selected with 10 µg/µl Puromycin for one week to obtain stable polyclonal cell pools.

tag: genotype/cell type

value: F121-9 mESC with heterozygous Blast-PAS integration in 129Sv allele


title: Mouse macrophages exposed to B16F10 melanoma cells

description: Mouse bone marrow derived macrophages cultured with B16F10 mouse melanoma cells conditioned media


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep8


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep5


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep3


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep6


title: FULA 1 #1

description: FVB Urethane induced Lung Adenocarcinoma 1 (FULA 1)


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep7


title: FVB mTECs 1

description: FVB mouse tracheal epithelial cells

source_name: FVB mouse tracheal epithelial cells

value: tracheal epithelial cells


title: Mast cells exposed to B16F10 melanoma-conditioned medium_IL3

description: Mouse mast cells exposed to B16F10 mouse  melanoma-conditioned medium. Bone marrow derived mast cells matured with IL3

value: IL-3 only

value: melanoma-conditioned


title: FVB Lungs Saline 1

description: FVB Lungs, one week after saline intraperitoneal injection


title: FVB mTECs 2

description: FVB mouse tracheal epithelial cells


title: FVB Lungs Saline 2

source_name: FVB Lungs, one week after saline intraperitoneal injection


title: Mast cells exposed to B16F10 melanoma-conditioned medium_IL3/KITL

description: Mouse mast cells exposed to B16F10 melanoma-conditioned medium. Bone marrow derived mast cells matured with IL3/KITL


title: FULA 4

description: FVB Urethane induced Lung Adenocarcinoma 4 (FULA 4)


title: miR142F/F_Foxp3Cre_Rep1


source_name: mT/MG;Lyz2.Cre bone marrow derived macrophages. Tomato macrophages


title: Mast cells_IL3

description: Mouse mast cells derived from bone marrow and matured with IL-3


title: FULA 1 #2

source_name: FVB Urethane induced Lung Adenocarcinoma 1 (FULA 1)


title: FULA 1 #3


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep1


source_name: IKKbetaf/f;Lyz2.Cre bone marrow derived macrophages. Macrophages lacking IKKbeta gene


title: DamID, Dam-LMNB1, F121-9, PASins Cobl, rep2


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep4

description: 5056_26_B11_DL_r2_LBR2_sgRNA_timepoint2_serie_2_AGCAGGAA_S34

value: F121-9 mESC with heterozygous promoter deletions of Morc, Morc1 and Dppa2 in 129Sv allele


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep1


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep3

description: 5056_25_B11_DL_r1_LBR2_sgRNA_timepoint24_serie_2_AGATCGCA_S33


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep4

description: 5056_24_A12_DL_r2_LBR2_sgRNA_timepoint24_serie_1_AGAGTCAA_S32


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep1

value: F121-9 mESC with heterozygous promoter deletion of Morc  in 129Sv allele


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep2


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep2


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep4

description: 5056_28_E2_DL_r2_LBR2_sgRNA_timepoint4_serie_2_ATCCTGTA_S29


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneE2, rep3

description: 5056_27_E2_DL_r1_LBR2_sgRNA_timepoint3_serie_2_AGTCACTA_S35


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep1


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep1


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep3

description: 5056_21_A6_DL_r1_LBR2_sgRNA_timepoint21_serie_1_ACGCTCGA_S22


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep2


title: DamID, Dam-LMNB1, F121-9, TALE-VP64, Sox6, rep1

description: 4591_7_F121-9_Sox6_DamLAM_r1_CAGATCTG_S12

value: F121-9 mESC


title: DamID, Dam-LMNB1, F121-9, TALE-VP64, Nrp1, rep2

description: 4591_4_F121-9_Nrp1_DamLAM_r2_ACCACTGT_S8


title: DamID, Dam-LMNB1, F121-9, TALE-VP64, Sox6, rep2

description: 4591_8_F121-9_Sox6_DamLAM_r2_ATGCCTAA_S14


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneA12, rep3

description: 5056_23_A12_DL_r1_LBR2_sgRNA_timepoint23_serie_1_ACTATGCA_S31


title: DamID, Dam-LMNB1, F121-9 clone CM1420, rep1

description: 4524_11_exp1_CM1420_137_DamLAM_r1_AACAACCA_S6

source_name: DamID, Dam-LMNB1, F121-9 clone CM1420

value: F121-9 mESC with hPGK-EGFP integrations


title: DamID, Dam-LMNB1, F121-9 clone CM1420, rep2

description: 4524_12_exp1_CM1420_137_DamLAM_r2_AACCGAGA_S12


title: DamID, Dam-LMNB1, F121-9 clone CM1417, rep4

description: 4524_8_exp2_CM1417_137_DamLAM_r2_AGTACAAG_S11

source_name: DamID, Dam-LMNB1, F121-9 clone CM1417


title: DamID, Dam-LMNB1, F121-9 clone CM1420, rep4

description: 4524_16_exp2_CM1420_137_DamLAM_r2_ACACAGAA_S16


title: DamID, Dam-LMNB1, F121-9, Morc1 Cdel, cloneA6, rep4

description: 5056_22_A6_DL_r2_LBR2_sgRNA_timepoint22_serie_1_ACGTATCA_S30


title: DamID, Dam-LMNB1, F121-9 clone CM1417, rep3

description: 4524_7_exp2_CM1417_137_DamLAM_r1_CTGTAGCC_S10


title: DamID, Dam-LMNB1, F121-9 clone CM1417, rep2

description: 4524_4_exp1_CM1417_137_DamLAM_r2_CGCTGATC_S8


title: DamID, Dam-LMNB1, F121-9, TALE-VP64, Nrp1, rep1

description: 4591_3_F121-9_Nrp1_DamLAM_r1_ACATTGGC_S4


title: DamID, Dam-LMNB1, F121-9 clone CM1417, rep1

description: 4524_3_exp1_CM1417_137_DamLAM_r1_AACGTGAT_S4


title: DamID, Dam-LMNB1, F121-9, Morc1 ABCdel, cloneB11, rep2


title: DamID, Dam-LMNB1, F121-9 clone CM1420, rep3

description: 4524_15_exp2_CM1420_137_DamLAM_r1_AAGGTACA_S15


title: DamID, Dam, F121-9, PASins Cobl, rep6

source_name: DamID, Dam, F121-9, PASins Cobl


title: DamID, Dam, F121-9, PASins Cobl, rep7


title: DamID, Dam, F121-9, PASins Cobl, rep5


title: DamID, Dam, F121-9, PASins Cobl, rep4


title: DamID, Dam, F121-9, PASins Cobl, rep3


title: DamID, Dam, F121-9, PASins Cobl, rep2


title: DamID, Dam, F121-9, PASins Cobl, rep1


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep3

description: 5056_9_A12_D_r1_LBR2_sgRNA_timepoint9_serie_1_CTGTAGCC_S14


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep4

description: 5056_10_A12_D_r2_LBR2_sgRNA_timepoint10_serie_1_AGTACAAG_S11


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep3

description: 5056_11_B11_D_r1_LBR2_sgRNA_timepoint11_serie_1_CATCAAGT_S17


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep1


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep2


title: DamID, Dam, F121-9, PASins Cobl, rep8


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep2


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneB11, rep4

description: 5056_12_B11_D_r2_LBR2_sgRNA_timepoint12_serie_1_AGTGGTCA_S18


title: DamID, Dam, F121-9, Morc1 ABCdel, cloneA12, rep1


title: DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep4

description: 5056_14_E2_D_r2_LBR2_sgRNA_timepoint14_serie_1_AACCGAGA_S20

source_name: DamID, Dam, F121-9, Morc1 Cdel, cloneE2


title: DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep2


title: DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep4

description: 5056_8_A6_D_r2_LBR2_sgRNA_timepoint8_serie_1_ATGCCTAA_S13

source_name: DamID, Dam, F121-9, Morc1 Cdel, cloneA6


title: DamID, Dam, F121-9, TALE-VP64, Sox6, rep1

source_name: DamID, Dam, F121-9, TALE-VP64, Sox6


title: DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep1


title: DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep1


title: DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep3

description: 5056_7_A6_D_r1_LBR2_sgRNA_timepoint7_serie_1_CAGATCTG_S12


title: DamID, Dam, F121-9, TALE-VP64, Nrp1, rep2

source_name: DamID, Dam, F121-9, TALE-VP64, Nrp1


title: DamID, Dam, F121-9, Morc1 Cdel, cloneA6, rep2


title: DamID, Dam, F121-9, TALE-VP64, Nrp1, rep1


title: DamID, Dam, F121-9 clone CM1420, rep4

description: 4524_14_exp2_CM1420_137_Dam_r2_AAGACGGA_S14

source_name: DamID, Dam, F121-9 clone CM1420


title: DamID, Dam, F121-9 clone CM1420, rep1

description: 4524_9_exp1_CM1420_137_Dam_r1_CATCAAGT_S1


title: DamID, Dam, F121-9 clone CM1420, rep2

description: 4524_10_exp1_CM1420_137_Dam_r2_AGTGGTCA_S3


title: DamID, Dam, F121-9 clone CM1420, rep3

description: 4524_13_exp2_CM1420_137_Dam_r1_AACGCTTA_S13


title: DamID, Dam, F121-9 clone CM1417, rep2

description: 4524_2_exp1_CM1417_137_Dam_r2_ACATTGGC_S5

source_name: DamID, Dam, F121-9 clone CM1417


title: DamID, Dam, F121-9, Morc1 Cdel, cloneE2, rep3

description: 5056_13_E2_D_r1_LBR2_sgRNA_timepoint13_serie_1_AACAACCA_S19


title: DamID, Dam, F121-9 clone CM1417, rep1

description: 4524_1_exp1_CM1417_137_Dam_r1_AAACATCG_S2


title: Citro SI-3

first: Gavin

last: Kelly

state: London

address: 1 Midland Road

institute: Francis Crick institute

data_processing:
Quality trimming with cutadapt 1.9.1 to a quality threshold of 10 and a minimum length of 25bp
Read counts quantified with RSEM 1.2.31 and Bowtie2 2.2.9
Counts normalised with DESeq2 1.16.1
Genome_build: GRCm38
Supplementary_files_format_and_content: *.genes.results.txt files are the qunatified read counts from RSEM; the rds files contain DESeq2 objects of class DESeqDataSet

source_name: C. rodentium-infected_Small intestine

extract_protocol:
Th17 cells were FACS-sorted from intestinal single cell suspensions. RNA was isolated with miRNeasy Micro kit (Quiagen) and amplified cDNA was prepared using the SMART-Seq V4 ultra low input RNA kit (Takara).
Sequencing libraries were generated using the Ovation Ultralow V2 kit (NuGEN).

treatment_protocol: Mice were colonised with segmented filamentous bacteria (SFB) or C. rodentium and used for the experiment 2 weeks post-colonisation.

value: wild type

value: C. rodentium-infected

value: Small intestine

value: Sorted Th17 cells


title: Citro SI-1


title: SFB SI-3

source_name: SFB-colonised_Small intestine

value: SFB-colonised


title: Citro colon-1

source_name: C. rodentium-infected_Colon

value: Colon


title: Citro colon-2


title: SFB colon-5


title: SFB SI-1


title: Citro SI-2


title: SFB colon-3


title: Citro colon-3


title: SFB colon-4


title: KPK siRNA Fbxo22 (siFbxo22)_3

city: New York

first: Shaowen

last: Jiang

address: 227 East 30th

department: Department of Pathology

institute: NYU Langone

data_processing:
Sequencing reads were mapped to the mouse reference genome (GRCm38.85/mm10) using the STAR aligner (v2.5.0c)
Alignments were guided by a Gene Transfer Format file (Ensembl GTF version GRCh38.85)
The mean read insert sizes and their standard deviations were calculated using Picard tools (v1.126)
Genome_build: mm10
Supplementary_files_format_and_content: The raw read count table were generated using HTSeq(v0.6.0)
Supplementary_files_format_and_content: The normalized based on their library size factors using DEseq2

source_name: KPK siRNA Fbxo22 (siFbxo22)_lung

extract_protocol:
Qiagen RNeasy Mini Kit
RNA libraries were prepared with the Illumina truseq ribozero gold library kit. Input was 1 microgram for all samples, per cycles x10. Libraries were normalized, pool, and run on 3 lanes of paired end 50 hiseq 4000.

tag: strain background

value: lung adenocarcinoma


title: MMR knockdown Virus C

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
The reads were mapped to the human transcriptome (hg19) using STAR and the influenza genome using Bowtie and samples were run on Basespace (Illumina).
Mapped reads were normalized and averaged; fold change then calculated by comparing the virus-infected samples to mock-infected samples.

source_name: NCI-H441 human club cell line

growth_protocol: H441 cells maintained throughout in complete growth media.

extract_protocol:
At 24 hpi, cells were lysed and total RNA collected using the Monarch Total RNA Miniprep Kit (NEB).
mRNA was prepped for sequencing using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II RNA Library Prep Kit (NEB #E7770), and NEBNext Multiplex Oligos for Illumina (NEB #E7335, #E7500).

treatment_protocol: Cells were transfected with siRNA, incubated for 48 h, then infected with mock or A/Puerto Rico/8/1934 influenza virus for 1 h before replacing the media with complete media and incubating another 24 h.

tag: infection

value: A/Puerto Rico/8/1934 influenza virus

tag: sirna transfection


title: MMR knockdown Virus A


title: KPK siRNA Fbxo22 (siFbxo22)_1

tag: genotype/variation

tag: tissue


title: MMR knockdown Virus B


title: SFB colon-2

tag: treatment


title: KPK siRNA control (siCtrl)_2

source_name: KPK siRNA control (siCtrl)_lung


title: KPK siRNA control (siCtrl)_3


title: DamID, Dam, F121-9 clone CM1417, rep3

description: 4524_5_exp2_CM1417_137_Dam_r1_CAGATCTG_S9


title: MMR knockdown Mock B

value: Mock


title: DamID, Dam, F121-9 clone CM1417, rep4

description: 4524_6_exp2_CM1417_137_Dam_r2_ATGCCTAA_S7


title: KPK siRNA Fbxo22 (siFbxo22)_2


title: MMR knockdown Mock C


title: SFB colon-1


title: KPK siRNA control (siCtrl)_1


title: MMR knockdown Mock A


title: SFB SI-2


title: KP siRNA Fbxo22 (siFbxo22)_3

source_name: KP siRNA Fbxo22 (siFbxo22)_lung


title: Non-targeting Virus C

value: Non-targeting


title: KP siRNA Fbxo22 (siFbxo22)_2


title: Non-targeting Virus A


title: KP siRNA control (siCtrl)_3

source_name: KP siRNA control (siCtrl)_lung


title: DamID, Dam, F121-9, TALE-VP64, Sox6, rep2


title: KP siRNA Fbxo22 (siFbxo22)_1


title: KP siRNA control (siCtrl)_2


title: Non-targeting Mock C


title: Non-targeting Mock B


title: Non-targeting Virus B


title: Non-targeting Mock A


title: KP siRNA control (siCtrl)_1


title: s2

city: Milan

first: Francesco

last: Cianflone

address: via Olgettina 60

department: Department of Urology

country: Italy

institute: IRCCS Ospedale San Raffaele

description: processed data file: counts.txt

data_processing:
Data was allineated with STAR, version2.5.3a.
Genome_build: hg38, Gencode version 25
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file contains RNA counts.

source_name: ccRCC primary tumor

extract_protocol:
RNA was extracted from tumor tissue with TRIzol reagent (Invitrogen).
Lexogen QuantSeq 3’UTR.

value: ccRCC primary tumor

tag: tumor stage

tag: tumor grading


title: s1

description: processed data file: counts.txt

tag: age


title: s5

description: processed data file: counts.txt


title: s4

description: processed data file: counts.txt


title: s3

description: processed data file: counts.txt


title: s6

description: processed data file: counts.txt


title: PC3-FLAG-MED25 FLAG ChIPseq rep2

city: Salt Lake City

first: Kathleen

last: Clark

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Reads aligned to genome version hg19 using Bowtie 1.0.1
Peak caliing performed with ChIPseq app from Useq package 8.8.5 to generate bedfile, comparing each ChIP experiment to the input and incorporating replicates .
Shared regions between ETV4 and MED25 enriched regions were defined using IntersectRegion in Useq package with no gap
Sorted BAM files were generated from the Bowtie output SAM files using Samtools v. 1.5
Bigwig files were generated from the sorted BAM files using DeepTools
Heatmaps of shared regions were generated with DeepTools [84] using a bedfile corresponding to coordinates from the MED25-ETV4 shared regions from MED25 dataset, and bigwig files generated from the aligned ETV4, MED25 and input ChIPseq reads for one replicate.
Genome_build: HG 19
Supplementary_files_format_and_content: Bigwig

extract_protocol:
RIPA lysis with sonication; ChIP isolation of DNA
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina.

treatment_protocol: Early passage PC3 cells were infected with retrovirus expressing FLAG-MED25 and selected with hygromycin for 2 weeks. Cells were expanded in multiple 150 mm dishes and harvested for ChIPseq

value: retrovirally-infected PC3 cells

tag: chip antibody

value: anti-FLAG (Sigma Life Sciences, F1804)


title: shRNA-MED25B KD RNAseq rep3

data_processing:
Reads aligned to genome version hg19 using using Novoalign v.3.08.02
Differentially expressed transcripts determined with drds analysis package in Useq  8.8.5. Expression changes of an absolute log 2 fold change > 0.585 and FDR <1%, relative to control shRNA, were counted as significant
Genome_build: hg19
Supplementary_files_format_and_content: txt; table of differentially expressed transcripts from drds package. The lenti-control KD was used for the MED25* KD and retro-control KD used for the ETV4* KD.

extract_protocol:
Qiagen Rneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Early passage PC3 cells were infected with lentivirus expressing MED25 shRNA (sequence B)and harvested 7 days post-infection.

value: Lentiviral-infected PC3 cells

tag: genotype


title: lenti-control KD RNAseq rep 3

source_name: lenti-cont-shRNA

treatment_protocol: Early passage PC3 cells were infected with lentivirus expressing luciferase shRNA and harvested 7 days post-infection.

value: lenti-cont-shRNA


title: PC3-FLAG_MED25 ETV4 ChIPSeq rep1

value: anti-ETV4 (Aviva Systems Biology, ARP32262)


title: shRNA-ETV4A KD RNAseq rep1

treatment_protocol: Early passage PC3 cells were infected with retroivirus expressing ETV4 shRNA (sequence A) and harvested 7 days post-infection.

value: Retrovirally-infected PC3 cells


title: shRNA-ETV4B KD RNAseq rep1

treatment_protocol: Early passage PC3 cells were infected with retroivirus expressing ETV4 shRNA (sequence B) and harvested 7 days post-infection.


title: lenti-control KD RNAseq rep 1


title: shRNA-ETV4B KD RNAseq rep2


title: retro-control KD RNAseq rep 1

source_name: retro-cont-shRNA

treatment_protocol: Early passage PC3 cells were infected with retroivirus expressing retrovirally driven control shRNA and harvested 7 days post-infection.

value: retro-cont-shRNA


title: shRNA-MED25A KD RNAseq rep3

treatment_protocol: Early passage PC3 cells were infected with lentivirus expressing MED25 shRNA (sequence A) and harvested 7 days post-infection.


title: shRNA-MED25A KD RNAseq rep2


title: PC3-FLAG_MED25_input

extract_protocol:
RIPA lysis with sonication
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina.


title: PC3-FLAG-MED25 FLAG ChIPseq rep1


title: lenti-control KD RNAseq rep 2


title: shRNA-ETV4A KD RNAseq rep2


title: shRNA-MED25A KD RNAseq rep1


title: shRNA-MED25B KD RNAseq rep1


title: retro-control KD RNAseq rep 2


title: RNA-seq, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep1 [4861_11_plb184_3_GTCCGCA]

city: Amsterdam

data_processing:
Reads were aligned to hg19  using TopHat version 2.1, with Ensembl genome build 75.
Genome_build: GRCh37.75

extract_protocol: total RNA was extracted using TRIsure and selected for polyadenylated fraction

treatment_protocol: sgRNAs were cloned into Lentiguide-Puro vector (Addgene #52963) using restriction enzyme BsmBI, and Lentivirus was prepared. RPE-1 cells stably expressing SunTag-CRISPRa were infected with LentiGuide virus and selected with 10 µg/µl Puromycin for one week to obtain stable polyclonal cell pools.

value: stably expressing SunTag-CRISPRa

tag: transfected protein


title: shRNA-ETV4B KD RNAseq rep3


title: shRNA-ETV4A KD RNAseq rep3


title: shRNA-MED25B KD RNAseq rep2


title: RNA-seq, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep2 [4862_11_plb184_3_ACTGATA]


title: RNA-seq, RPE, CRISPRa, SOX6, rep2 [4862_4_plb163_GATCAGA]


title: PC3-FLAG_MED25 ETV4 ChIPSeq rep2


title: RNA-seq, RPE, CRISPRa, SOX6, rep1 [4861_4_plb163_GCCAATA]