title: Adult_gut_sox10:cre;Cherry_negative_4

status: Public on Sep 14 2020

first: Vassilis

last: Pachnis

state: London

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

molecule: nuclear RNA

organism: Danio rerio

extract_protocol:
Nuclear RNA was isolated using PureLink RNA Micro Kit (Invitrogen #12183016) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies, Inc.). cDNA was quantified on a Qubit 3.0 fluorometer (Thermo Fisher Scientific, Inc.), and then fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris, Inc.) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies, Inc.). A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies, Inc.). The libraries were then normalized to 4 nM, pooled and loaded onto a HiSeq4000 (Illumina, Inc.) to generate 100 bp paired-end reads.

treatment_protocol: Nuclei were purified by FACS (fluorescent-activated cell sorting), representing both the Cherry+ (entire ENS) and Cherry- (non-ENS) muscularis externa cell populations of Tg(sox10:Cre;Cherry) zebrafish gut

value: adult gut

value: non-ENS

tag: rna fraction

value: Nuclear mRNA


title: Adult_gut_sox10:cre;Cherry_negative_3

type: SRA

city: London

address: 1 Midland Road

country: United Kingdom

library_source: transcriptomic

tag: tissue

tag: cell type


title: Macrophage_tg_4

status: Public on Sep 15 2020

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Retinoid- CD146- CD11b+ F4/80+

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: tumor bearing liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Macrophages were isolated by a collagenase digest, a gradient centrifugation and magnetic labeling. Magnetically enriched macrophages were further FACS purified using CD11b, F4/80, CD146 and live/dead cell discrimination. RNA was immediately extracted once the cell sorting procedure was complete.

extract_protocol: PicoPuro extraction kit (Life technologies) according to the manufacturer's instructions.

value: tumor bearing liver

value: macrophage

tag: genotype


title: Adult_gut_sox10:cre;Cherry_positive_4

value: ENS


title: Hep_tg_1

description:
primary isolated hepatocytes
HYP

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

growth_protocol: Primary hepatocytes were isolated through a perfusion with EGTA and collagenase buffer. Primary hepatocytes were cultivated for 4 hours. Medium change was performed to remove non-adherent cells. Cells were cultivated for another 20 hours and after this RNA extraction performed. Only samples with a RIN higher than 7 were used for expression profiling analysis.

extract_protocol: RNA was extracted using the Nucleo Spin RNA II kit (Macherey Nagel) according to the manufacturer's instructions.

value: liver


title: fetal cord tissue, S0001

type: genomic

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition]  chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: cord tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Prior to purification, 250 mg crushed cord tissue was enzymatically digested with hyaluronidase (~2.7U in 250 µl PBS) for 30 minutes at 37 C, mixed with 250 µl TNES lysis buffer, transferred to gentleMACS M Tubes (Miltenyi 130-093-236) for 1-minute homogenization followed by overnight treatment with 200 µg Proteinase K at 55 C. QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

value: fetal cord tissue

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)

tag: pre-pregnancy bmi (kg/m^2)


title: Adult_gut_sox10:cre;Cherry_negative_5


title: Adult_gut_sox10:cre;Cherry_positive_3


title: Hep_tg_2

description:
primary isolated hepatocytes
HYP


title: Adult_gut_sox10:cre;Cherry_negative_2


title: Hep_tg_3

description:
primary isolated hepatocytes
HYP


title: Adult_gut_sox10:cre;Cherry_positive_2


title: Hep_wt_3

description:
primary isolated hepatocytes
WT

value: WT


title: Adult_gut_sox10:cre;Cherry_positive_5


title: Epidermis_DKO_6mo_rep1

city: Hong Kong

first: Jing

last: Zhang

address: 11 Yuk Choi Rd, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.

country: Hong Kong

institute: The Hong Kong Polytechnic University

data_processing:
SOAPnuke version1.5.2 was used for the filtering of the raw sequencing data.
HISAT2 version2.1.0 was used for the alignment of clean sequencing data to the reference genome.
RSEM version1.2.8 was used for the quantification of gene expression.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: csv format, gene expression matrix.

extract_protocol:
After euthanization, dorsal skin samples of 2cm2 were collected. The dermal side of skin was then placed in a sterile culture dish in 60ºC water bath for 1 minute. Sterile forceps and scalpels were used to separate the dermis from the epidermis. The epidermis was collected and homogenized in TRIzol reagent (Invitrogen), and enriched by removing rRNA with RNaseH. The purified mRNA was fragmented into short fragments. The cDNA was generated using random hexamer-primed reverse transcription, and assessed using Agilent 2100 BioAnalyzer (Thermo Fisher Scientific).
The cDNA libraries were sequenced on the BGISEQ-500 platform (BGI-Shenzhen) with 50 single-end read.

tag: strain background

value: VDR fl/fl, Med1 fl/fl, K14 Cre+/-

tag: age

value: post natal 6 months

value: Epidermis


title: Epidermis_DKO_6mo_rep3


title: Adult_gut_sox10:cre;Cherry_negative_1


title: Epidermis_DKO_6mo_rep2


title: Hep_wt_1

description:
primary isolated hepatocytes
WT


title: Epidermis_CON_6mo_rep1

value: VDR fl/fl, Med1 fl/fl, K14 Cre-/-


title: Epidermis_CON_6mo_rep3


title: Epidermis_CON_P36_rep1

value: post natal day 36


title: Epidermis_CON_6mo_rep2


title: Adult_gut_sox10:cre;Cherry_positive_1


title: Epidermis_DKO_P36_rep3


title: Epidermis_DKO_P36_rep2


title: Epidermis_DKO_P36_rep1


title: Epidermis_CON_P36_rep3


title: 546CFA14

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

country: USA

institute: UVa School of Medicine

data_processing:
Demultiplexed FASTQ files were processed with the Dada2 v1.12.1 function "filterAndTrim": truncLen = c(300,250), maxN = 0, maxEE = c(10,10), truncQ = 2, rm.phix = TRUE, compress = TRUE, multithread = TRUE
Error learning with Dada2 v1.12.1 "learnErrors" for R1 and R2 reads: multithread = TRUE, Dereplication with "derepFastq": verbose = TRUE
Amplicon Sequence Variant Identification with  Dada2 v1.12.1 "dada" from learned error rates and dereplicated FASTQ reads: multithread = TRUE
Read pair merging with  Dada2 v1.12.1 "mergePairs": verbose = TRUE
Chimera identification and removal with  Dada2 v1.12.1 "removeBimeraDenovo": nethod = "consensus", multithread = TRUE, verbose = TRUE
Taxonomy assignment with  Dada2 v1.12.1 "assignTaxonomy": multithread = TRUE
Genome_build: Taxonomy was assigned manually with input from the following 16S reference databases: Silva v132, Greengenes v13_8_set_97, GTDB bac-arc_ssu_r86, and RefSeq RDB16S v2_May2018
Supplementary_files_format_and_content: comma separated files (.csv) containing: 1. ASV abundances per sample, 2. Taxonomy of each ASV, and 3. Sample parameter data and Identification

source_name: CFA_14d_mouse fecal matter

growth_protocol: Female C57BL/6 mice were maintained on a 12 hours light/dark cycle with lights on at 7am and provided with standard food and water ad libitum. Mice were housed at 2-3 per cage and experimental treatment was assigned randomly to each cage.

extract_protocol:
Fecal samples were collected from live mice restrained with a tail scruff. DNA for 16S amplification was extracted with a phenol-chloroform method: Fecal pellets were placed in 2 mL tubes containing 200 μL silica-zirconia beads (0.1 mm). The tubes were filled with 750 μL extraction buffer, 200 μL 20% SDS and 750 μL phenol-chloroform-isoamyl alcohol (25:24:1). After disruption, the aqueous phase was separated by centrifugation and cleaned up with two washes of chloroform-isoamyl alcohol (24:1). The DNA was precipitated and resuspended in 10 mM Tris solution.
The V3-V4 region of the 16S rRNA gene was amplified for 25 cycles using specific primers with adapter overhangs as per the Illumina library preparation guide (Forward Primer: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, Reverse Primer: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC). Following purification of the PCR products, individual indexes were added to the amplicons by PCR. The amplicons were purified, pooled in equal quantities, and then sequenced on the Illumina MiSeq platform.
V3-V4 16S-seq

treatment_protocol: Each group recieved different treatments: naïve mice recieved no treatment, EAE (MOG+CFA) mice were immunized subcutaneously with 50 μg of myelin oligodendrocyte glycoprotein peptide 35–55 (MOG35–55) (CSBIO #CS0681) emulsified at a 1:1 ratio in Complete Freud’s Adjuvant (Sigma Aldrich #F5881). On days 0 and 2, 250 ng of pertussis toxin (List Biologicals #180) was administered intraperitoneally. CFA imce recieved only the equivalent dose of Complete Freud’s Adjuvant.

tag: strain

tag: body weight (grams)

tag: eae clinical score

tag: immunization

value: CFA

tag: day (relative to immunization)

tag: molecule subtype

value: 16S Amplicon


title: Macrophage_tg_1

description: Retinoid- CD146- CD11b+ F4/80+


title: Epidermis_CON_P36_rep2


title: P. syringae B728a broth rep 3

city: Central Point

first: Monica

middle: Nicole

last: Hernandez

state: OR

address: 569 Hanley Road

institute: Oregon State University

data_processing:
Reads were uploaded to Galaxy and cleaned using Trimmomatic.
Reads were aligned to the Pseudomonas syringae B728a genome using Salmon Transcript Quantification  in Galaxy.
The program edgeR in R was then used to assess the statistical significance of differential gene expression. Gene expression levels were normalized using a weighted trimmed mean of M values (TMM; where M is the log expression ratio per gene between treatments).
Supplementary_files_format_and_content: Raw gene counts for every gene and sample

organism: Pseudomonas syringae pv. syringae B728a

source_name: P. syringae B728a cells

growth_protocol: Bacterial cells were grown with shaking in King's medium B broth at 28°C until cultures reached a cell density of 5x10^8 cells/ml. Three replicate cultures were used. 300 µl of each culture was then applied to a 0.4 µm Isopore® membrane filter and excess liquid was removed by exposing the filter to a vacuum source for 5 seconds. Filters were then immediately placed onto King's medium B plates to incubate at 28°C for two hours while broth cultures were returned to a shaker and incubated at 28°C for two more hours.

extract_protocol:
Cells in broth cultures were harvested by pipetting 1 ml of suspension into a 15 mL conical tube containing 125 µl ice-cold EtOH/Phenol stop solution (5% water-saturated phenol (pH<7.0) in ethanol). Filters were immersed in the EtOH/Phenol stop solution and cells were harvested by sonication for 30 seconds followed by vortexing for 20 seconds to ensure complete cell detachment from the filters. Cells were then collected by centrifugation at 12,000 rpm (13,800 x g) for five minutes at 4°C. Supernatant was decanted and the cells were frozen in liquid nitrogen and stored at -80℃ until RNA isolation. RNA isolation was performed using a Direct-zol™ RNA Kit (Zymo Research). RNA was stored frozen at -80°C.
1 µl of each sample was diluted into 4 µl of RNase free water and submitted to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley where Ribo-Zero was used for rRNA removal. RNA abundance and purity were determined using a 2100 Bioanalyzer (Agilent Technologies) and quantified using Qubit (Invitrogen). After reverse transcription, shearing of cDNA, size fractionation, and Illumina library production, the Vincent J. Coates Genomics Sequencing Laboratory samples were sequenced using an Illumina HiSeq4000 platform with 50 base pair, single-end reads. Three biological replicates were sequenced per treatment.

value: wild-type

value: bacterial


title: P. syringae B728a broth rep 1


title: P. syringae B728a broth rep 2


title: CEMBA190625_10E_3_CEMBA190625_10E_4_G12_ad001

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male


title: CEMBA190625_10E_3_CEMBA190625_10E_4_H3_ad007


title: P. syringae B728a filter rep 3

tag: cell type


title: P. syringae B728a filter rep 2

tag: genotype


title: P. syringae B728a filter rep 1


title: CEMBA190625_10E_3_CEMBA190625_10E_4_G7_ad004


title: CEMBA190625_10E_3_CEMBA190625_10E_4_F4_ad012


title: CEMBA190625_10E_3_CEMBA190625_10E_4_F5_ad001


title: CEMBA190625_10E_3_CEMBA190625_10E_4_F8_ad012


title: CEMBA190625_10E_3_CEMBA190625_10E_4_B6_ad012


title: CEMBA190625_10E_3_CEMBA190625_10E_4_E8_ad007


title: CEMBA190625_10E_3_CEMBA190625_10E_4_G11_ad008


title: CEMBA190625_10E_3_CEMBA190625_10E_4_E6_ad012


title: CEMBA190625_10E_3_CEMBA190625_10E_4_A9_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H9_ad007


title: CEMBA190625_10E_3_CEMBA190625_10E_4_A10_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H9_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H9_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H9_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H8_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H8_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H9_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H9_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H8_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H9_ad006


title: CEMBA190625_10E_3_CEMBA190625_10E_4_G2_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H8_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H8_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H8_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H7_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H7_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H6_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H6_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H5_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H7_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H5_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H6_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H4_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H6_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H4_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H4_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H5_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H5_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H4_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H7_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H3_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H2_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H3_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H2_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H3_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H3_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H6_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H11_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H2_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H5_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H12_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H11_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G9_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G9_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H11_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H11_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H2_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H11_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G9_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G9_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H1_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G9_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H1_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G8_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G9_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H1_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G9_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H11_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G8_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G8_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G8_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H1_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G8_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G6_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G5_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G6_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G5_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G6_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G6_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G7_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G4_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_H10_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G5_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G5_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G8_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G3_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G3_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G3_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G5_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G4_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G4_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G3_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G2_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G2_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G2_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G2_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G6_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G2_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G2_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G5_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G2_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G12_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G12_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G12_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G12_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G11_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G11_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G12_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G12_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G4_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G11_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G11_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G11_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G11_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G1_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F9_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F9_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F9_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G12_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G1_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F9_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G1_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F9_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G1_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G11_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_G10_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F9_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F8_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F8_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F8_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F8_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F8_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F8_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F7_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F7_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F7_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F6_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F6_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F7_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F6_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F6_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F6_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F5_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F5_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F5_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F5_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F4_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F5_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F4_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F4_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F4_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F8_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F3_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F3_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F2_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F2_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F11_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F11_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F11_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F11_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F11_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F11_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F11_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F3_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F1_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F1_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F3_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F12_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E9_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E9_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E9_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E9_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E9_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E9_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E9_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_F10_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E7_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E7_ad006


title: CD94posILC donor D121

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

description: CD94posILC donor: D121

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: R/Bioconductor, limma rma

source_name: CD94+ ILC

label_protocol: Obtained (depleted) cell suspensions were stained for 30 min at 4°C with fluorochrome-conjugated antibodies (Lin: CD1a, CD3, CD4, CD14, CD34, CD19, FcRεR1a, BDCA2, CD123, TCRαβ, TCRγδ, CRTH2 all in FITC. CD3 in AF700, CD45 in APC-Cy7, CD127 in PECY7, CD161 in BV510, CD94 in PE, CD56 in PETX, NKp44 in APC, CD117 in PEcy5.5). The cells were purified by flow cytometry using a FACSAria IIU (BD Biosciences).

extract_protocol: Human pediatric tonsils were obtained from pediatric tonsillectomies performing within the Amsterdam UMC or Onze Lieve Vrouwe Gasthuis hospital (Amsterdam, The Netherlands).   Tonsils were processed to obtain cell suspensions as described before (Krabbendam&Nagasawa et al 2018). For ILC enrichment tonsil cell suspensions were depleted for CD3 and CD19 by MACS depletion and peripheral blood cell suspensions were depleted for CD3, CD14 and CD19 using Mojosort magnetic cell separation system (BioLegend, San Diego, CA, USA).

tag: donor id

tag: tissue

value: Tonsil

value: Freshly isolated CD94+ ILC3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E7_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E6_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E5_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E5_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E6_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E8_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E5_ad002


title: FG1924_05

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

country: Austria

institute: University of Innsbruck

description:
Illumina files raw files of FG1924_05 were accidentially named FG1922_05_xx
FG1922_05_47980-B04_TATCGCACCTTAGTGT_L001_R1_001_HF2YWDRXX
processed data file: IL-14-12_vs_FG1924.xlsx

data_processing:
Illumina NovaSeq6000 RTA3 software used for basecalling: version 3.4.4
For comparison between FG1924 and FG1817, all forward reads were trimmed to a final size of 50 nt using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.13) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 1.9) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9) (Anders et al., 2015)
Differentially expressed genes were identified using DESeq version 1.34.1 (run in R version 3.5.2) (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj; sample x; Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component

organism: Anguilla anguilla

source_name: exercised eels_EF

growth_protocol: European eels were caught by local fishermen and kept in freshwater for a few days.

extract_protocol:
Total RNA was isolated from gas gland tissue using the Qiagen miRNeasy kit. Quality and integrity of the RNA waere checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip.
Illumina RNASeq libraries were prepared from 0.5 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2.

treatment_protocol: Two weeks prior to the experiments, the salinity was increased to 35 PSU. Eels were transferred to the swim tunnel and acclimatized to the new environment at a pressure of 1 bar and a flow rate of 0.1 m s-1 for 2 h at a temperature of 14°C. Over a period of 16 h, eels were acclimatized to higher flow rates of up to 0.5 bl s-1, which corresponds to the estimated swimming speed of the spawning migration. Pressure was elevated at a rate of 1 bar min-1 which corresponds to the natural diving speed of 0.15 m s-1 to finally 8 bar. The 24 h experiment was terminated by 8 h of exercise at a velocity of 0.5 bl s-1 and a pressure of 8 bar (= 0.8 MPa). At the end of the experiment, pressure was reduced to atmospheric pressure at a rate of 1 bar min-1 and water velocity was reduced to 0.1 m s-1. Eels were removed from the tunnel, immediately anesthetized with 2-phenoxyethanol (1 ml l-1), and subsequently decerebrated and spinally pithed. The swimbladder was dissected and the epithelium, consisting of gas gland cells, was carefully freed from connective tissue. The epithelium was transferred into RNAlater™ solution and stored at -80oC until further use.

tag: swimming exercise

value: exercised

tag: swimbladder functional/non-functional

value: healthy, functional swimbladders (EF)

value: gas gland tissue

value: swimbladder gas gland cells


title: FG1924_06

description:
Illumina files raw files of FG1924_06 were accidentially named FG1922_06_xx
FG1922_06_47980-B05_CGCTATGTTCCGACAC_L001_R1_001_HF2YWDRXX
processed data file: IL-14-12_vs_FG1924.xlsx


title: FG1924_04

description:
FG1924_04_47980-B03_TCTGTTGGTCGAATGG_L001_R1_001_HF2YWDRXX
processed data file: IL-14-12_vs_FG1924.xlsx


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E7_ad002


title: ILC3 donor D121

description: ILC3 donor: D121

value: Freshly isolated ILC3


title: ILC3 donor D120

description: ILC3 donor: D120


title: NK donor D121

description: NK donor: D121

source_name: NK

value: Freshly isolated NK cells


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E5_ad001


title: FG1924_03

description:
FG1924_03_47980-B02_CTCACCAACTAGGCAA_L001_R1_001_HF2YWDRXX
processed data file: IL-14-12_vs_FG1924.xlsx


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E4_ad006


title: NK donor D120

description: NK donor: D120


title: CD94posILC donor D119

description: CD94posILC donor: D119


title: ILC3 donor D119

description: ILC3 donor: D119


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E4_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E4_ad012


title: FG1924_01

description:
FG1924_01_47980-A12_AGGTTATACAGTTCCG_L001_R1_001_HF2YWDRXX
processed data file: IL-14-12_vs_FG1924.xlsx


title: FG1924_02

description:
FG1924_02_47980-B01_GAACCGCGTGACCTTA_L001_R1_001_HF2YWDRXX
processed data file: IL-14-12_vs_FG1924.xlsx


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E6_ad006


title: CD94posILC donor D120

description: CD94posILC donor: D120


title: NK donor D119

description: NK donor: D119


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E4_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E3_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E3_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E3_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E3_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E2_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E2_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E2_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E4_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad007


title: erythroid cell obtained from CD34 culture  - 48h - vehicle vehicle_t1.CEL

city: Paris

first: Ismael

last: Boussaid

address: 22 Rue Mechain

country: France

institute: Inserm

description:
erythroid cell obtained from CD34 culture  - 48h - vehicle
erythroid cell obtained from CD34 culture

hyb_protocol: cDNA was hybridized to HTA2.0 affymetrix microarrays following standard

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA)

label_protocol: Briefly, linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labelling System (NuGEN, San Carlos, CA).

growth_protocol: Human CD34+ progenitors were purified from cord blood units on MidiMacs system (Miltenyi Biotech, Bergisch Gladbach, Germany). Murine Extensively Self-Renewing Erythroblasts (ESREs) were derived from fetal livers. Cell differentiation was followed by cytological examination and by flow cytometry (see supplemental material).

extract_protocol: RNA was extracted using the Kit QIAamp® RNA Blood MiniKit. RNA from ribosomal fractions was purified using Trizol (Invitrogen).

treatment_protocol: CX-5461 or vehicle were used on erythroid cell obtained from CD34 culture

tag: time


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad006


title: erythroid cell obtained from CD34 culture  - 48h - CX-5461 cx50_t1.CEL

description:
erythroid cell obtained from CD34 culture  - 48h - CX-5461
erythroid cell obtained from CD34 culture

scan_protocol: affymetrix microarrays following standard


title: erythroid cell obtained from CD34 culture  - 48h - Rapamycine rapa_t1.CEL

description:
erythroid cell obtained from CD34 culture  - 48h - Rapamycine
erythroid cell obtained from CD34 culture


title: erythroid cell obtained from CD34 culture  - 96h - DMSO DMSO_t2.CEL

description:
erythroid cell obtained from CD34 culture  - 96h - DMSO
erythroid cell obtained from CD34 culture


title: erythroid cell obtained from CD34 culture  - 96h - vehicle vehicle_t2.CEL

description:
erythroid cell obtained from CD34 culture  - 96h - vehicle
erythroid cell obtained from CD34 culture


title: erythroid cell obtained from CD34 culture  - 48h - vehicle 5_vehicle


title: erythroid cell obtained from CD34 culture  - 48h - CX-5461 6_CX50


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad002


title: erythroid cell obtained from CD34 culture  - 48h - DMSO DMSO_t1.CEL

description:
erythroid cell obtained from CD34 culture  - 48h - DMSO
erythroid cell obtained from CD34 culture


title: erythroid cell obtained from CD34 culture  - 96h - Rapamycine rapa_t2.CEL

description:
erythroid cell obtained from CD34 culture  - 96h - Rapamycine
erythroid cell obtained from CD34 culture


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E2_ad001


title: erythroid cell obtained from CD34 culture  - 48h - Rapamycine 2_Rapa_J10


title: erythroid cell obtained from CD34 culture  - 96h - CX-5461 cx50_t2.CEL

description:
erythroid cell obtained from CD34 culture  - 96h - CX-5461
erythroid cell obtained from CD34 culture


title: erythroid cell obtained from CD34 culture  - 96h - Rapamycine 4_Rapa_J12


title: erythroid cell obtained from CD34 culture  - 48h - CX-5461 06_CO35-CX


title: erythroid cell obtained from CD34 culture  - 96h - DMSO 3_DMSO_J12


title: erythroid cell obtained from CD34 culture  - 48h - CX-5461 8_CX50


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad008


title: erythroid cell obtained from CD34 culture  - 48h - DMSO 1_DMSO_J10


title: erythroid cell obtained from CD34 culture  - 48h - vehicle 05_CO35-CTL


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E11_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E11_ad010


title: erythroid cell obtained from CD34 culture  - 48h - vehicle 7_vehicle


title: erythroid cell obtained from CD34 culture  - 48h - CX-5461 04_CO26-CX


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E11_ad007


title: erythroid cell obtained from CD34 culture  - 48h - CX-5461 02_CO6-CX


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E12_ad004


title: Cappable _sRNA-seq.expon.r2

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

institute: University College London

data_processing:
In order to remove poly(A)-tails and adaptors, we trimmed the reads using the program Cutadapt in two rounds with the following settings to prevent trimming of naturally occurring A-rich RNAs due to the low GC-content of the S. solfataricus genome: (i) -a “A{15}” -e 0 -m 15 to remove all poly(A) stretches of at least 15 nt length plus downstream regions and (ii) -a “A{15}”X -e 0 -O 5 to terminal shorter  poly(A) stretches of minimum 5 nt length.
Trimmed and untrimmed reads were split into separate fastq files using awk.
Both fastq files were aligned to the S. solfataricus genome using bowtie v1.2.2 61 (parameters -v 1 -m 1 –-best –-strata -S) with untrimmed 75 nt reads shortened to 71 nt (-3 4)
The bam file output was merged, sorted and indexed using SAMtools
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bam files with trimmed reads for two biological replicates.

organism: Saccharolobus solfataricus P2

source_name: exponential phase, 0.1% tryptone, 0.2% glucose

growth_protocol: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% glucose, 0.1% tryptone to mid-exponential growth phase

extract_protocol:
15 ml cell culture was rapidly mixed with 30 ml pre-cooled RNAprotect Bacteria Reagent (Qiagen) placed in an ice bath. Cells were harvested by centrifugation (5 min at 4000 x g at 4 ºC). Pellets were immediately subjected to RNA isolation using the mirVana miRNA isolation kit (Ambion) with an initial resuspension buffer volume of 200 µl following the protocol for small RNAs (20-200 nt length).
Library preparation and deep sequencing was conducted at Vertis Biotechnologie (Germany). In brief, 5’-triphosporylated RNA was capped with 3’-desthiobiotin-TEG-GTP (NEB)) using the Vaccinia virus Capping enzyme (NEB) and biotinylated RNA species were subsequently enriched by affinity purification using streptavidin beads yielding 0.6 to 1.3% of the sRNA preparation. The eluted RNA was poly-adenylated using E. coli Poly(A) polymerase and 5’-ends were converted to mono-phosphates by incubation with RNA 5’ Pyrophosphohydrolase (NEB). Subsequently, an RNA adapter was ligated to the newly formed 5'-monophosphate structures. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M- MLV reverse transcriptase at 42 ºC. The resulting cDNA was finally PCR-amplified (12 cycles) with TruSeq Dual Index sequencing primers (Illumina).

tag: growth


title: erythroid cell obtained from CD34 culture  - 48h - vehicle 03_CO26-CTL


title: Cappable _sRNA-seq.expon.r1

value: exponential phase, 0.1% tryptone, 0.2% glucose


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E11_ad006

tag: age


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E11_ad004

tag: strain


title: 4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG) hearts at 7 dpa rep2

city: Shanghai

first: Peilu

last: She

address: 500 Dongchuan Road

department: School of Life Sciences

country: China

institute: East China Normal University

description:
gene_expression_oe_vs_ctl.xlsx
E1

data_processing:
Illumina HiSeq X Ten software used for base-calling.
Sequencing raw reads were preprocessed using Seqtk to filter out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads to get clean reads for data analysis.
Hisat2 (version 2.0.4) was used to map the clean reads to the zebrafish GRCz10 reference genome. After genome mapping, the mapped reads of genes were converted to FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Stringtie (version 1.3.0) (Pertea et al., 2016; Pertea et al., 2015) for standardization of gene expression.
Genes with differential expression levels between samples were analyzed using edgeR.
Genome_build: GRCz10
Supplementary_files_format_and_content: The microsoft excel files include gene ID, gene name, description and RPKM values for each Sample.

source_name: heart

growth_protocol: Tg(cmlc2:creER;cmlc2:nRSGG), Tg(cmlc2:nRSGG), grl5nt-/- and wild-type zebrafish were raised at a density of 3 fish/L and conducted experiments at 5 months of age.

extract_protocol:
4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG), 4-HT-treated Tg(cmlc2:nRSGG), grl5nt-/- and wild-type ventricles at 7 dpa were collected. Total RNAs of the ventricles were isolated using TRIzol Reagents and quality controlled using the Agilent 2100 Bioanalyzer system.
Libraries were constructed according to the TruSeq RNA Sample Preparation Kit Protocol followed by quality check with Qubit 2.0 Fluorometer and the Agilent 2100 Bioanalyzer system.

treatment_protocol: Tg(cmlc2:creER;cmlc2:nRSGG) fish and Tg(cmlc2:nRSGG) control fish at 5 months of age were incubated with 5 μM 4-HT for bath treatment for 2 days. Then, we performed ventricular resection surgeries 3 days later and collected hearts at 7 dpa. grl5nt-/- and wild-type zebrafish at 5 months of age were conducted ventricular resection surgeries and collected hearts at 7 dpa.

value: AB

value: heart

value: 5 months

tag: genotype/variation

tag: treatment

value: 4-HT-treated Tg


title: erythroid cell obtained from CD34 culture  - 48h - vehicle 01_CO6-CTL


title: 4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG) hearts at 7 dpa rep1

description:
gene_expression_oe_vs_ctl.xlsx
X3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad010


title: 4-HT-treated Tg(cmlc2:creER;cmlc2:nRSGG) hearts at 7 dpa rep3

description:
gene_expression_oe_vs_ctl.xlsx
E2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E11_ad002


title: 4-HT-treated Tg(cmlc2:nRSGG) control hearts at 7 dpa rep2

description:
gene_expression_oe_vs_ctl.xlsx
W1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad006


title: 4-HT-treated Tg(cmlc2:nRSGG) control hearts at 7 dpa rep1

description:
gene_expression_oe_vs_ctl.xlsx
X1


title: grl5nt-/- hearts at 7 dpa rep2

description:
gene_expression.xls
D

value: untreated


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad007


title: 4-HT-treated Tg(cmlc2:nRSGG) control hearts at 7 dpa rep3

description:
gene_expression_oe_vs_ctl.xlsx
W2


title: grl5nt-/- hearts at 7 dpa rep1

description:
gene_expression.xls
B


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E10_ad001


title: wild-type hearts at 7 dpa rep3

description:
gene_expression.xls
E

value: wild type


title: wild-type hearts at 7 dpa rep2

description:
gene_expression.xls
C


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E1_ad006

value: CA


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E1_ad002

value: male


title: cd34-8d

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: 8days after the addition of differentiation media

data_processing:
RNA-Seq reads were mapped to the hg19 revision of the human reference genome using tophat  with -G set to a GTF containing RefSeq transcript locations.  Expression values for RefSeq transcripts were determined using RPKM_count.py from the RSeQC package .
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq_analyzed_RPKM.xlsx

extract_protocol:
25ng/ml hrBMP4 for 2hrs prior to collection
RNA from one million cells was isolated with Trizol according to the manufacturer’s instructions. The RNA was DNAse treated using the RNase free DNase set from Qiagen (79254) according to the instructions. The whole amount of RNA was treated with the Ribo-Zero Gold kit (Human/Mouse/Rat, Epicentre) according to the manufacturer’s instructions.
Ribo-zero treated RNA was used to create multiplexed RNA-seq libraries using the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer’s instructions.

treatment_protocol: Human CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were used.Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with StemSpan CC100 cytokine mix (Stem Cell Technologies Inc.)For studying differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 mM dexamethasone, and 1 mM b-estradiol).

value: mobilized peripheral blood CD34+ cells

value: day 8 of differentiation

value: 25ng/ml hrBMP4 for 2hrs before collection


title: wild-type hearts at 7 dpa rep1

description:
gene_expression.xls
A


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E1_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_E1_ad004


title: cd34-6d

description: 6days after the addition of differentiation media

value: day 6 of differentiation


title: cd34-5d

description: 5days after the addition of differentiation media

value: day 5 of differentiation


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D9_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D9_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D9_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D9_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D9_ad001


title: cd34-2d

description: 2 days after the addition of differentiation media

value: day 2 of differentiation


title: grl5nt-/- hearts at 7 dpa rep3

description:
gene_expression.xls
F


title: cd34-4d

description: 4days  after the addition of differentiation media

value: day 4 of differentiation


title: cd34-3d

description: 3 days after the addition of differentiation media

value: day 3 of differentiation


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D8_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D8_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D8_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D8_ad010


title: cd34-6hrs

description: 6hrs after the addition of differentiation media

value: hour 6 of differentiation


title: cd34-pro

description: progenitor cells before differentiation

value: hour 0 of differentiation


title: cd34-1d

description: 1 day after the addition of differentiation media

value: day 1 of differentiation


title: cd34-7d

description: 7days after the addition of differentiation media

value: day 7 of differentiation


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D8_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D8_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D7_ad008


title: Day5 SmaD1

description: D5 Smad1

data_processing:
Aligned using bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Erythrocyte precursors

growth_protocol: Human CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were used.Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with StemSpan CC100 cytokine mix (Stem Cell Technologies Inc.). For studying differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 mM dexamethasone, and 1 mM b-estradiol).

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with antibody
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: 25ng/ml hrBMP4 for 2hrs prior to collection

tag: purification target

tag: chip antibody

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog id


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D7_ad004

tag: brain region

tag: Sex


title: Day5 Input:Gata2, H3K27ac

description: D5 Input:Gata2, H3K27ac

tag: cell type


title: Day5 Input: SmaD1, Gata1

description: D5 Input: Smad1, Gata1


title: Day5 H3K27ac

description: D5 H3K27ac

value: Abcam


title: Day5 Gata2

description: D5 Gata2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D7_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D6_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D6_ad004


title: Day4 Input: Gata2, H3K27ac

description: D4 Input: Gata2, H3K27ac


title: Day5 Gata1

description: D5 Gata1


title: Day4 H3K27ac

description: D4 H3K27ac


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D5_ad004


title: Day4 Gata2

description: D4 Gata2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D5_ad006


title: cd34-2hrs

description: 2hrs after the addition of differentiation media

value: hour 2 of differentiation


title: Day0 Gata2

description: D0 Gata2

source_name: Hemoatopoietic stem and progenitor cells

value: day 0 of differentiation


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D5_ad001

value: CA

value: male


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D4_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D4_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D4_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D4_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D3_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D3_ad004


title: Day0 SmaD1

description: D0 Smad1

value: mobilized peripheral blood CD34+ cells


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D3_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D7_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D6_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D2_ad006


title: Day0 Input

description: D0 Input

value: 25ng/ml hrBMP4 for 2hrs before collection


title: Homozygous (Ubc9+/+) intestinal cells from mouse 5

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

institute: CRCT

hyb_protocol: 5.5 μg of fragmented and labeled ss-cDNA was hybridized for 16 hr at 45C on GeneChip™ Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using the limma software standard pipeline (R package). The data were normalized using Robust Multichip Average (RMA) algorithm, collpased using a Fred’s Softwares microarray algorithm, and finally normalized using the surrogate variable analysis (SVA) package to remove sources of unwanted variation and consider batch effects.

source_name: FACS-purified Lgr5-EGFP+ CBC cells from Ubc9+/- mouse

label_protocol: Biotinylated cRNA was prepared from 50 ng total RNA, according to the standard Affymetrix protocol (Manual Target Prepartion for GeneChip Whole Transcription Expression Array, 20013, Affymetrix).

growth_protocol: Mice were bred in SPF conditions.

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

treatment_protocol: Intestines were obtained, washed with PBS and opened longitudinaly. Villi cells were scrapped-off using glass slides and crypts were liberated by incubation (2X) with EDTA 10 mM. Crypts were later on disgregated with Dispase solution containing DNAseI and ROCK-inhibitor and stained with antibodies against EpCam and CD24, and PI. Lgr5-EGFPhigh, CD24middle, EpCampositive and PInegative intestinal stem cells were sorted into RNA later solution and kept at -80ºC until further processing

value: Intestine

value: FACS-purified Lgr5-EGFPhigh cells

tag: genotype

value: Homozygous (Ubc9+/+)


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D2_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D2_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D2_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D12_ad012


title: Heterozygous (Ubc9+/-) intestinal cells from mouse 4

source_name: FACS-purified Lgr5-EGFP+ CBC cells from Ubc9+/+ mouse

tag: tissue

value: Heterozygous (Ubc9+/-)


title: Homozygous (Ubc9+/+) intestinal cells from mouse 2


title: Heterozygous (Ubc9+/-) intestinal cells from mouse 5


title: Homozygous (Ubc9+/+) intestinal cells from mouse 3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D12_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D12_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D12_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D3_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D12_ad006


title: Homozygous (Ubc9+/+) intestinal cells from mouse 1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D12_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D12_ad001


title: Homozygous (Ubc9+/+) intestinal cells from mouse 4


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D10_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D10_ad010


title: Homozygous (Ubc9+/+) mouse 3, normal tissue 1

data_processing: The data were analyzed using the limma software standard pipeline (R package) and normalized using Robust Multichip Average (RMA) algorithm.

source_name: Normal tissue (1) from Homozygous (Ubc9+/+) mouse 3

label_protocol: Biotinylated cRNA was prepared from 100 ng total RNA, according to the standard Affymetrix protocol (Manual Target Prepartion for GeneChip Whole Transcription Expression Array, 20013, Affymetrix).

treatment_protocol: Intestines were obtained, washed with PBS and openned longitudinaly and were scored for polyps under the stereoscope. Polyps and normal tissues of about 1 mm (on average) were harvested, frozen in liquid nitrogen and kept at -80ºC until further processing

tag: tissue orirgin

tag: tissue type

value: Normal


title: Heterozygous (Ubc9+/-) intestinal cells from mouse 1


title: Homozygous (Ubc9+/+) mouse 3, polyp 1

source_name: Polyp (1) from Homozygous (Ubc9+/+) mouse 3

value: Polyp


title: Homozygous (Ubc9+/+) mouse 3, normal tissue 2

source_name: Normal tissue (2) from Homozygous (Ubc9+/+) mouse 3


title: Homozygous (Ubc9+/+) mouse 2, polyp 1

source_name: Polyp (1) from Homozygous (Ubc9+/+) mouse 2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D10_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D10_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D10_ad002


title: Homozygous (Ubc9+/+) mouse 2, normal tissue 1

source_name: Normal tissue (1) from Homozygous (Ubc9+/+) mouse 2


title: Homozygous (Ubc9+/+) mouse 3, polyp 2

source_name: Polyp (2) from Homozygous (Ubc9+/+) mouse 3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D10_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D10_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D1_ad006


title: Homozygous (Ubc9+/+) mouse 2, polyp 2

source_name: Polyp (2) from Homozygous (Ubc9+/+) mouse 2


title: Homozygous (Ubc9+/+) mouse 2, normal tissue 2

source_name: Normal tissue (2) from Homozygous (Ubc9+/+) mouse 2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D1_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: Homozygous (Ubc9+/+) mouse 1, normal tissue 1

source_name: Normal tissue (1) from Homozygous (Ubc9+/+) mouse 1


title: Heterozygous (Ubc9+/-) mouse 3, polyp 1

source_name: Polyp (1) from Heterozygous (Ubc9+/-) mouse 3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D1_ad001


title: Heterozygous (Ubc9+/-) intestinal cells from mouse 3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C9_ad010


title: Heterozygous (Ubc9+/-) mouse 3, polyp 2

source_name: Polyp (2) from Heterozygous (Ubc9+/-) mouse 3


title: Heterozygous (Ubc9+/-) intestinal cells from mouse 2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C9_ad004


title: Heterozygous (Ubc9+/-) mouse 2, polyp 1

source_name: Polyp (1) from Heterozygous (Ubc9+/-) mouse 2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C9_ad002


title: Heterozygous (Ubc9+/-) mouse 3, normal tissue 1

source_name: Normal tissue (1) from Heterozygous (Ubc9+/-) mouse 3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C8_ad008


title: Heterozygous (Ubc9+/-) mouse 2, polyp 2

source_name: Polyp (2) from Heterozygous (Ubc9+/-) mouse 2


title: WT_fract_10_2

city: Cambridge

first: Anne

last: Bertolotti

address: Francis Crick Avenue

department: Neurobiology

institute: MRC Laboratory of Molecular Biology

description:
SLX-15542.gene_exp.diff
SLX-15542.genes.count_tracking
SLX-15542.genes.fpkm_tracking
SLX-15542.genes.read_group_tracking

data_processing:
Reads were aligned with TopHat v2.0.13 (--no-coverage-search, --library-type fr-firststrand)
Transcript abundances and differentially expressed genes were identified with Cufflinks v2.2.1 (--library-type fr-firststrand, --frag-bias-correct, --multi- read-correct)
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_exp.diff = gene-level differential expression; genes.count_tracking = gene-level counts; genes.fpkm_tracking = gene-level FPKMs; genes.read_group_tracking = per-replicate, gene-level counts/FPKMs

source_name: liver

growth_protocol: Experimental mice were kept in specific pathogen free ventilated cages (Tecniplast GM500, Techniplast) on Lignocel FS14 spruce bedding (IPS, Ltd.) and Enviro-Dri nesting material (LBS) at 19-23°C with 12 hours light dark cycle with light from 7.00 am to 7.00 pm. Animals were fed with Dietex CRM pellets (Special Diet Services) with free access on food and water. For the tunicamycin (Tm) experiment, 15 C57BL/6 (The Jackson Laboratory) 5-week- old males were used. Males were weaned at 3-4 weeks of ages and 2 to 3 animals were caged together.

extract_protocol:
Total RNAs were isolated from 0.01 g of liver using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. For the isolation of the polysomal RNAs, the ‘heavy’ polysomal fractions (more than 3 ribosomes) were pooled and RNAs were precipitated in three volumes of 100% ethanol overnight at -20°C. The following day, RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. To allow quantification of RNAs from polysomal fractions, 200 ng of Luciferase RNA was spiked in to every fraction prior to precipitation when indicated (Luciferase control RNA, Promega).
2 μg and 0.5 μg of total and polysomal RNAs, respectively, were used to prepare sequencing libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Mice were injected intraperitoneally (IP) with 0.1 mg/kg Tm (Sigma-Aldrich) at 8 am. The day before injection, animals were weighted, and average weight was used to calculate the volume of Tm injected. Mice were culled at 10 am (2 hours), noon (4 hours), and 6 pm (10 hours) hours by cervical dislocation, respectively, and livers were collected. The control mice (0 hours) were culled at 9 am.

value: liver

value: tunicamycin

tag: timepoint

tag: rna fraction

value: heavy polysomal

tag: library pool


title: WT_fract_10_3

tag: strain


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C8_ad006

tag: age


title: WT_fract_10_1

tag: treatment


title: Heterozygous (Ubc9+/-) mouse 1, polyp 2

source_name: Polyp (2) from Heterozygous (Ubc9+/-) mouse 1


title: Heterozygous (Ubc9+/-) mouse 2, normal tissue 1

source_name: Normal tissue (1) from Heterozygous (Ubc9+/-) mouse 2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C8_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C8_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C8_ad001


title: Homozygous (Ubc9+/+) mouse 1, polyp 2

source_name: Polyp (2) from Homozygous (Ubc9+/+) mouse 1


title: Homozygous (Ubc9+/+) mouse 1, polyp 1

source_name: Polyp (1) from Homozygous (Ubc9+/+) mouse 1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C8_ad012


title: Tm4_polyH_3

description:
SLX-10469.gene_exp.diff
SLX-10469.genes.count_tracking
SLX-10469.genes.fpkm_tracking
SLX-10469.genes.read_group_tracking


title: WT_tot_10_3

value: total


title: CEMBA190625_10E_1_CEMBA190625_10E_2_D1_ad004


title: WT_tot_10_2


title: Heterozygous (Ubc9+/-) mouse 2, normal tissue 2

source_name: Normal tissue (2) from Heterozygous (Ubc9+/-) mouse 2


title: WT_tot_10_1


title: Heterozygous (Ubc9+/-) mouse 1, polyp 1

source_name: Polyp (1) from Heterozygous (Ubc9+/-) mouse 1


title: Heterozygous (Ubc9+/-) mouse 1, normal tissue 1

source_name: Normal tissue (1) from Heterozygous (Ubc9+/-) mouse 1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C7_ad006


title: Homozygous (Ubc9+/+) mouse 1, normal tissue 2

source_name: Normal tissue (2) from Homozygous (Ubc9+/+) mouse 1


title: Heterozygous (Ubc9+/-) mouse 1, normal tissue 2

source_name: Normal tissue (2) from Heterozygous (Ubc9+/-) mouse 1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C7_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: Tm4_2


title: Tm4_polyH_1


title: Heterozygous (Ubc9+/-) mouse 3, normal tissue 2

source_name: Normal tissue (2) from Heterozygous (Ubc9+/-) mouse 3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C6_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C7_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C6_ad006


title: Tm2_polyH_1


title: Tm2_polyH_2


title: Tm4_1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C6_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C6_ad001


title: Tm2_3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C5_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C4_ad006


title: Tm0_polyH_1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C5_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C7_ad004


title: Tm2_1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C5_ad006


title: Tm0_polyH_2


title: Tm0_3


title: Tm2_2


title: Tm0_1


title: PPARA_KO liver_Wy-14,643_Pool3_G134_M24

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: poly-A selected, stranded library

data_processing:
Data were analyzed using a custom RNA-seq analysis pipeline (PMID: 28323953, Connerney, 2017) as described elsewhere (PMID: 28903501, Lodato, 2017). Briefly, Paired  sequence reads were analzyed using FastQC (Andrews, 2016) for quality control and were mapped to the mouse genome (release mm9) using TopHat2 (v2.1.1) (Kim et al, PMID: 23618408). Reads were counted for each gene in each sample, and were converted to RPKM. Reads were counted for each RefSeq or LncRNA gene in each sample, and were converted to RPKM. LncRNA genes werre based on a set of 15,558 liver-expressed lncRNA genes whose gene and isoform structures are described in Melia et al, 2019 (PMID: 30840070).
QUANTIFICATION: FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq and long noncoding RNA (lncRNA) genes. Transcripts were quantified by counting sequence reads that map to a the gene body of a gene. Reads were counted for each RefSeq or LncRNA gene in each sample, and were converted to RPKM. LncRNA genes are based on a set of 15,558 liver-expressed lncRNA genes whose gene and isoform structures are described in Melia et al, 2019 (PMID: 30840070).
DIFFERENTIAL EXPRESSION: Differential expression analysis for RefSeq genes and long noncoding genes was conducted using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel workbook containing gene expression data and results of differential expression analysis for 24,197 mouse RefSeq  genes and for 15,558 liver-expressed lncRNA genes, with the latter gene set and ther annotations described in Melia et al, 2019 (PMID: 30840070) and in Lodato et al, 2017 (PMID: 28903501).

source_name: liver tissue

growth_protocol: Mice were housed in light and temperature-controlled rooms and were provided with water and pelleted chow ad libitum.Mice were provided a grain-based control diet or matched diet containing 0.1% Wy-14643 for 48 hours.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA) was used to extract total RNA from livers from four different treatment and control groups: wild-type mice and Ppara-/- mice fed either control diet or fed a diet containing 0.1% WY-14643 for 48 hours and euthanized between 1 and 3 PM. RNAs were extracted from individual livers, followed by quality assessment of RNA by TapeStation 4200 (Agilent, Santa Clara, CA, USA), to identify high quality RNA samples (RIN>9.0) for pooling.
Stranded RNA-seq libraries were prepared from polyA-selected total liver RNA using an Illumina stranded TruSeq mRNA Prep Kit (Illumina, San Diego, CA, USA). Three independent RNA pools were prepared for each of the 4 treatment groups, with each pool comprised of n = 3, 4 or 5 individual liver RNA samples.
RNA-seq libraries were subjected to 126 cycle paired-end sequencing using an Illumina HiSeq 2500 instrument (Illumina) at a depth of 30-42 million read pairs for each of the 12 RNA-seq libraries.

treatment_protocol: Wy-14643 was dissolved in 1% carboxymethyl cellulose (CMC) solution and orally administered (50 mg/kg in 200 μl) for indicated time points

value: 12 weeks old

tag: genotype/variation

tag: diet


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C5_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C3_ad006


title: PPARA_KO liver_Wy-14,643_Pool2_G134_M23

description: poly-A selected, stranded library


title: PPARA_KO liver_Control diet_Pool3_G134_M21

description: poly-A selected, stranded library

value: Control diet


title: PPARA_KO liver_Wy-14,643_Pool1_G134_M22

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C3_ad001


title: PPARA_KO liver_Control diet_Pool2_G134_M20

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C2_ad006


title: Tm4_3


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C9_ad006


title: PPARA_KO liver_Control diet_Pool1_G134_M19

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C2_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C2_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C4_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C4_ad004


title: Tm0_2


title: Wild-type liver_Control diet_Pool3_G134_M3

description: poly-A selected, stranded library

value: Wild-type


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C4_ad002

value: CA


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C3_ad004

value: male


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C3_ad002


title: Wild-type liver_Wy-14,643_diet_Pool1_G134_M4

description: poly-A selected, stranded library


title: Wild-type liver_Wy-14,643_diet_Pool3_G134_M6

description: poly-A selected, stranded library


title: Wild-type liver_Wy-14,643_diet_Pool2_G134_M5

description: poly-A selected, stranded library


title: Gm15441-LSL liver_WY-14,643 diet_Pool1_G167_M10

description: poly-A selected, stranded library

data_processing:
Data were analyzed using a custom RNA-seq analysis pipeline (PMID: 28323953, Connerney, 2017) as described elsewhere (PMID: 28903501, Lodato, 2017). Briefly, Paired  sequence reads were analzyed using FastQC (Andrews, 2016) for quality control and were mapped to the mouse genome (release mm9) using TopHat2 (v2.1.1) (Kim et al, PMID: 23618408). Reads were counted for each RefSeq or LncRNA gene in each sample, and were converted to RPKM. LncRNA genes are based on a set of 15,558 liver-expressed lncRNA genes whose gene and isoform structures are described in Melia et al, 2019 (PMID: 30840070).
QUANTIFICATION: FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq and long noncoding genes (Lodato et al 2017). Transcripts were quantified by counting sequence reads that map to a the gene body of a gene.
DIFFERENTIAL EXPRESSION: Differential expression analysis for RefSeq genes and long noncoding genes was conducted using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel workbook containing gene expression data and results of differential expression analysis for 24,197 mouse RefSeq  genes and for 15,558 liver-expressed lncRNA genes, with the latter gene set and ther annotations described in Melia et al, 2019 (PMID: 30840070) and in Lodato et al, 2017 (PMID: 28903501).

growth_protocol: Gm15441-knockout mice (Gm15441-LSL) were developed using CRISPR/Cas gene targeting technologies. The targeting strategy results in the insertion of a floxed cassette containing a transcriptional stop repeat within the first intron of Gm15441 (NR_040409.1). The presence of the Lox-Stop-Lox (LSL) cassesste after exon 1 prevents Gm15441 expression.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA) was used to extract total RNA from livers from four different treatment and control groups: wild-type mice and Gm15441-LSL mice fed either control diet or fed a diet containing 0.1% WY-14643 for 24 hours and euthanized between 1 and 3 PM. RNAs were extracted from individual livers, followed by quality assessment of RNA by TapeStation 4200 (Agilent, Santa Clara, CA, USA), to identify high quality RNA samples (RIN>9.0) for pooling.
Stranded RNA-seq libraries were prepared from polyA-selected total liver RNA using an Illumina stranded TruSeq mRNA Prep Kit (Illumina, San Diego, CA, USA). Three independent RNA pools were prepared for each of the 4 treatment groups, with each pool comprised of n = 2-3 individual liver RNA samples.
RNA-seq libraries were subjected to 150 cycle paired-end sequencing using an Illumina HiSeq 2500 instrument (Illumina) at a depth of 13-21 million read pairs for each of the 12 RNA-seq libraries.

treatment_protocol: Mice were housed in light and temperature-controlled rooms and were provided with water and pelleted chow ad libitum. Mice were provided a grain-based control diet or matched diet containing 0.1% Wy-14643 for 24 hours.


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C11_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C11_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C12_ad010


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C11_ad004


title: Wild-type liver_Control diet_Pool2_G134_M2

description: poly-A selected, stranded library


title: Wild-type liver_WY-14,643 diet_Pool1_G167_M7

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C12_ad008


title: Gm15441-LSL liver_Control diet_Pool3_G167_M6

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C12_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C12_ad004


title: Wild-type liver_Control diet_Pool1_G134_M1

description: poly-A selected, stranded library


title: Gm15441-LSL liver_WY-14,643 diet_Pool3_G167_M12

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C11_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C12_ad002


title: Gm15441-LSL liver_WY-14,643 diet_Pool2_G167_M11

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C12_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C10_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C12_ad001


title: Wild-type liver_WY-14,643 diet_Pool3_G167_M9

description: poly-A selected, stranded library


title: Wild-type liver_WY-14,643 diet_Pool2_G167_M8

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C10_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C11_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C11_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C1_ad004


title: NPC_1mln_rep1_MTS

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

institute: University of Edinburgh

description: nascent-RNA profiling with fastGRO was performed in NPC differentiated cells

data_processing:
Image analysis:: Firecrest (Illumina pipeline 1.9, default parameters)
base calling:: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (RNAseq, chromatin RNA-seq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg19:
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization):

source_name: NPC differentiated cells

growth_protocol: NPC differentated cells were mainted in 50% Neurobasal Medium/50% advanced DMEM with 1x Neural Induction Supplement

extract_protocol: NEBNext ChIP-Seq ULTRAII RNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: NPC differentated cells were treated with PSC Neural Induction Medium for 7 days and then expanding using Neural Expansion Medium for 6 days

tag: cell line

value: NPC

tag: agent

tag: experiment

value: fastGRO


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C1_ad002

tag: brain region

tag: Sex


title: Wild-type liver_Control diet_Pool1_G167_M1

description: poly-A selected, stranded library


title: NPC_5mln_rep1_MTS


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C1_ad006


title: Gm15441-LSL liver_Control diet_Pool1_G167_M4

description: poly-A selected, stranded library


title: THP1_30minLPS

description: nascent-RNA profiling with fastGRO was performed in 30 minutes LPS treated THP1 cells after flavaporidol treatment

source_name: THP1 cell line

growth_protocol: THP1 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) of FBS and 2 mM of L-glutamine.

treatment_protocol: THP1 cells were treated with 2uM flavopiridol for 2 hours and then after washout 5 µg/ml of LPS for 30 minutes


title: Gm15441-LSL liver_Control diet_Pool2_G167_M5

description: poly-A selected, stranded library


title: Wild-type liver_Control diet_Pool3_G167_M3

description: poly-A selected, stranded library


title: THP1_15minLPS

description: nascent-RNA profiling with fastGRO was performed in 15 minutes LPS treated THP1 cells after flavaporidol treatment

treatment_protocol: THP1 cells were treated with 2uM flavopiridol for 2 hours and then after washout 5 µg/ml of LPS for 15 minutes


title: THP1_5minLPS

description: nascent-RNA profiling with fastGRO was performed in 5 minutes LPS treated THP1 cells after flavaporidol treatment

treatment_protocol: THP1 cells were treated with 2uM flavopiridol for 2 hours and then after washout 5 µg/ml of LPS for 5 minutes


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C10_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B9_ad002


title: Wild-type liver_Control diet_Pool2_G167_M2

description: poly-A selected, stranded library


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B9_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B8_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C10_ad002


title: HeLa_100mln

description: nascent-RNA profiling with fastGRO was performed in HeLa cells

source_name: HeLa cell line

growth_protocol: HeLa cells were maintained in DMEM medium supplemented with 10% (v/v) of SCS and 2 mM of L-glutamine.

value: HeLa


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C10_ad001


title: Ig_Treated_CX

data_processing:
Sequence reads were mapped using Bowtie (v2.3.4.3) against the human genome hg19 assembly (Genome Reference Consortium Human Build 37) downloaded from the UCSC Genome Browser (http://genome.ucsc.edu).
Alignment files were converted into bam files using Samtools (v1.9). Mapped reads (sequences) were transformed into a genome-wide read density (coverage) by bamCoverage (v3.3.0) from deepTools suite using the parameter –normalize Using RPKM to normalize the number of reads per bin to reads per kilobase per million mapped reads.
Peak calling was performed using Homer (v4.10,5-16-2018) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: Erythroblasts were collected at day 11

growth_protocol: Human CD34+ progenitors were purified from cytapheresis or cord blood units on MidiMacs system (Miltenyi Biotech, Bergisch Gladbach, Germany) and cultured in Iscove’s modified Dulbecco medium (IMDM; Life Technologies, Grand Island, NY) supplemented with 15% serum substitute (StemCell Technologies, Vancouver, Canada), 100ng/mL SCF, 10ng/mL interleukin (IL)-6 and 1 UI/mL IL-3 for 6 days. Dexamethasone (1 µM) was added on day 1. From day 7, the cells were maintained in SCF and EPO until day 11

extract_protocol:
Lysates were clarified from sonicated nuclei and p53-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's standard instructions

treatment_protocol: Erythroblasts were collected at day 11 and these immature erythroblasts were compared with mature erythroblasts enriched by a 2-day treatment by CX-5461 at day 9 and 10.

tag: cell type

value: erythroid cells

tag: chip antibody

value: rabbit IgG (sc-2027 Santa Cruz)

value: treated CX5461


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C1_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B8_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B8_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B7_ad004


title: P53_Treated_CX

value: rabbit anti-p53 polyclonal antibody (sc-6243, Santa Cruz)


title: NPC_20mln_HPDP


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B7_ad001


title: TFEbeta.stat.chip-seq.r1

data_processing:
paired-end reads were trimmed to 50 bp and aligned with bowtie to the Saccharolobus solfataricus P2 genome using the following settings: -v 2 -m 1 --fr
we sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 120 bp, sd 18 bp) using a custom R script(www.github.com/fblombach)
Coverage was calculated using bamCoverage from the deeptools package
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width)
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with score representing either raw coverage after sampling ("Coverage") or coverage normalised to input after sampling ("normRatio")

organism: Saccharolobus solfataricus

growth_protocol: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% glucose, 0.1% tryptone to late stationary growth phase

extract_protocol:
Cells were lysed in lysis buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100) and DNA was sheared by sonication. Lysates were cleared by centrifugation. Chromatin-immunoprecipitation was carried out with protein-A-purified polyclonal antibodies (custom made). Immunoprecipitated DNA was recovered by QIAquick PCR purification
NEBnext Ultra II DNA library preparation

treatment_protocol: Cells were crosslinked with 0.4% formaldehyde for 1 min before quenching by addition of 100 mM TRIS/Cl pH 8.0, cells were washed in PBS buffer 3x

tag: growth

value: stationary phase, 0.1% tryptone, 0.2% glucose

value: polyclonal antibodies against TFEbeta


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B6_ad006


title: TFEalpha.stat.chip-seq.r1

value: polyclonal antibodies against TFEalpha


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B6_ad002


title: THP1_2hoursflavopiridol

description: nascent-RNA profiling with fastGRO was performed in flavopiridol treated THP1 cells

treatment_protocol: THP1 cells were treated with 2uM flavopiridol for 2 hours


title: NPC_5mln_rep2_MTS


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B8_ad004


title: Ig_NoTreat_CTRL

value: untreated


title: TFB.H2O2.permanganate.ChIP-seq.r1

data_processing:
reads were aligned with bowtie to the Saccharolobus solfataricus P2 genome using the following settings: -v2 -m1 --best --strata -S -t
Bam files were converted to strand-specific 5’-end coverage data using MACE v1.2 pre-processor function with default settings normalised to 1x genome coverage
The 5'-end position was corrected by -1 nt  corresponding to the position of the nucleotide modified by permanganate treatment and consequently eliminated by piperidine cleavage.
Data were filtered retaining only  genomic positions of thymidines to account for the nucleotide bias of permanganate treatment
Background signal was calculated as from four neighbouring non-T positions for each T (the two closest non-T residues on either side). The median background signal was subtracted and the resulting T-specific signal was normalised to 1x genome coverage of Ts for both strands.
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with 1x genome coverage of 5'-ends strand-specific for two biological replicates, filtered for T positions, corrected for non-T background.

growth_protocol: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% tryptone to mid-exponential growth phase and treated with 30 µM hydrogen peroxide for 105 min

extract_protocol:
Cells were lysed in lysis buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100) and DNA was sheared by sonication. Lysates were cleared by centrifugation. Chromatin-immunoprecipitation was carried out with protein-A-purified polyclonal antibodies.
Immunoprecipitated complexes were treated ChIP-exo protocol using the ChIP-exo kit from Active Motif based on the protocol published by Serandour et al. (Genome Biology 14:R147 (2013) with the following modifications to adapt the protocol for permanganate ChIP-seq: lambda and RecJF exonuclease digestion steps were ommitted. Purified DNA was instead treated with 10% piperidine at 90 ºC for 30 min before 1-butanol and chloroform extractions. Second strand synthesis and all following steps were carried out according to the chip-exo protocol.
Permanganate ChIP-seq

treatment_protocol: Cells were crosslinked with 0.4% formaldehyde for 1 min before quenching by addition of 100 mM TRIS/Cl pH 8.0, cells were washed in PBS buffer 1x, treated with 10 mM potassium permanganate in PBS buffer for 1 min at room temperature. The permanganate treatment was stopped by adding 1 vol PBS, 0.8M 2-mercaptoethanol, 40 mM EDTA

value: 30 µM hydrogenperoxide treated cells, 0.2% tryptone medium

value: polyclonal antibodies against TFB1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B9_ad004

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B4_ad002


title: Tm4_polyH_2

source_name: liver

tag: tissue

value: liver

value: tunicamycin

value: heavy polysomal


title: P53_NoTreat_CTRL


title: input.stat.chip-seq.r1

value: none (input)


title: TFB.expon.permanganate.ChIP-seq.r1

description: 15691X3_181219_D00550_0537_ACCV9FANXX_S100_L008

value: exponential phase, 0.1% tryptone, 0.2% glucose


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B3_ad006

value: CA

value: male


title: TFB.stat.chip-seq.r1

value: polyclonal antibodies against TFB


title: RNA-seq.stat.r3

data_processing:
Alignment of reads to the Sso P2 genome, read counting, normalization, and differential expression analysis was performed using the Rockhopper 2 software package (Tjaden, 2015, GENOME BIOLOGY 16:1)
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with raw coverage for three biological replicates.

source_name: cells during stationary phase

extract_protocol:
Total RNA was isolated using the Trizol method (Thermo Fisher). Genomic DNA was removed using the TURBO DNA-free kit (Thermo Fisher)
TruSeq® Stranded Total RNA Library Prep kit (Illumina) including partial ribosomal RNA depletion with the Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina)
RNA-seq dUTP method

tag: growth phase

value: stationary phase (grown in  0.1% tryptone, 0.2% glucose)


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B6_ad004

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: Spt45.stat.chip-seq.r1

value: polyclonal antibodies against Spt4/5


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B7_ad006


title: TFB.H2O2.permanganate.ChIP-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B5_ad006


title: Rpo47.expon.permanganate.ChIP-seq.r2

description: 15691X6_181219_D00550_0537_ACCV9FANXX_S94_L008

value: polyclonal antibodies against RNA polymerase subunits 4/7


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B3_ad002


title: RNA-seq.stat.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B3_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B5_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_C8_ad002


title: Rpo47.H2O2.permanganate.ChIP-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B5_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B2_ad006


title: Rpo47.H2O2.permanganate.ChIP-seq.r1


title: TFB.expon.permanganate.ChIP-seq.r2

description: 15691X5_181219_D00550_0537_ACCV9FANXX_S96_L008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B3_ad004


title: Rpo47.stat.chip-seq.r1

value: stationary phase, 0.1% tryptone, 0.2% glucose


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B2_ad001


title: input.stat.chip-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B2_ad002


title: TFEbeta.expon.chip-exo.r3

data_processing:
reads were aligned with bowtie to the Saccharolobus solfataricus P2 genome using the following settings: -v2 -m1 --best --strata -S -t
Bam files were converted to strand-specific 5’-end coverage data using MACE v1.2 pre-processor function with default settings normalised to 1x genome coverage
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with 1x genome coverage of 5'-ends strand-specific for three biological replciates. The file labelled "GM" shows the geometric mean of three biological replicates scaled to 1x coverage (available on series record).

extract_protocol:
Cells were lysed in lysis buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100) and DNA was sheared by sonication. Lysates were cleared by centrifugation. Chromatin-immunoprecipitation was carried out with protein-A-purified polyclonal antibodies.
Immunoprecipitated complexes were treated ChIP-exo protocol using the ChIP-exo kit from Active Motif based on the protocol published by Serandour et al. (Genome Biology 14:R147 (2013)

value: polyclonal antibodies against TFEbeta

tag: protocol

value: ChIP-exo


title: TFEbeta.expon.chip-exo.r2


title: TFEbeta.stat.chip-seq.r2


title: TFEbeta.expon.chip-exo.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B5_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B12_ad006


title: Rpo47.expon.permanganate.ChIP-seq.r1

description: 15691X4_181219_D00550_0537_ACCV9FANXX_S98_L008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B12_ad004


title: TFB.expon.chip-exo.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B12_ad001


title: RNA-seq.stat.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B2_ad004


title: Spt45.stat.chip-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B11_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B12_ad007


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B12_ad010


title: TFEalpha.stat.chip-seq.r2

value: polyclonal antibodies against TFEalpha


title: Rpo47.expon.chip-exo.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B12_ad008


title: TFB.expon.chip-exo.r3


title: RNA-seq.expon.r1

data_processing:
Alignment of reads to the Sso P2 genome, read counting, normalisation, and differential expression analysis was performed using the Rockhopper 2 software package (Tjaden, 2015, GENOME BIOLOGY 16:1)
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with raw coverage for two biological replicates.


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B12_ad002


title: Rpo47.expon.chip-exo.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B4_ad006


title: TFB.stat.chip-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B11_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B10_ad012


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B10_ad007


title: Rpo47.stat.chip-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B11_ad007


title: TFB.H2O2.chip-exo.r2

data_processing:
reads were aligned with bowtie to the Saccharolobus solfataricus P2 genome using the following settings: -v2 -m1 --best --strata -S -t
Bam files were converted to strand-specific 5’-end coverage data using MACE v1.2 pre-processor function with default settings normalised to 1x genome coverage
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with 1x genome coverage of 5'-ends strand-specific for three biological replciates. The file labelled "GM" shows the geometric mean of three biological replicates scaled to 1x coverage (available on the series record).

value: 30 µM hydrogenperoxide treated cells, 0.2% tryptone


title: TFB.expon.chip-exo.r1

value: polyclonal antibodies against TFB1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B11_ad006


title: Rpo47.expon.chip-exo.r3


title: RNA-seq.expon.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B11_ad004


title: TFB.H2O2.chip-exo.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B1_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B11_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B1_ad001


title: TFB.H2O2.chip-exo.r3


title: Rpo47.H2O2.chip-exo.r3


title: Rpo47.expon.chip-seq.r2

extract_protocol:
Cells were lysed in lysis buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100) and DNA was sheared by sonication. Lysates were cleared by centrifugation. Chromatin-immunoprecipitation was carried out with protein-A-purified polyclonal antibodies. Immunoprecipitated DNA was recovered by QIAquick PCR purification
NEBnext Ultra II DNA library preparation


title: RNA-seq.mock.r1

description: 180209_K00166_0338_BHNVKKBBXX_8_11182WF0018L01

value: mock-treated with H2O, 0.2% tryptone medium


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A9_ad004


title: RNA-seq.mock.r2

description: 180209_K00166_0338_BHNVKKBBXX_8_11182WF0009L01


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B10_ad006


title: Rpo47.H2O2.chip-exo.r2


title: Rpo47.expon.chip-seq.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B1_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A9_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B10_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A9_ad006


title: Rpo47.H2O2.chip-exo.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A9_ad001


title: RNA-seq.H2O2.r2

description: 180209_K00166_0338_BHNVKKBBXX_8_11182WF0008L01

value: 30 µM hydrogenperoxide treated cells, 0.2% tryptone medium


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B1_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A8_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B11_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_B10_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A8_ad006


title: Day0 SmaD2

description:
mobilised peripheral blood CD34+ cells
10ng/ml hrBMP4 for 2hrs before collection

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph pileup from MACS 2.0 output

source_name: Hemoatopoietic stem and progenitor cells

treatment_protocol: 10ng/ml hrTGFb for 2hrs prior to collection

tag: antibody

tag: antibody vendor

value: Cell Signaling Technology, 5339S


title: Day0 SmaD2 Input

description: mobilised peripheral blood CD34+ cells

value: Hemoatopoietic stem and progenitor cells


title: input.mock.chip-seq.r2

growth_protocol: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% tryptone to mid-exponential growth phase and mock treated with water, as control for 30 µM hydrogen peroxide treatment (GSE141033)

tag: strain

value: mock treated cells, 0.2% tryptone

value: none (input)


title: RNA-seq.H2O2.r1

description: 180209_K00166_0338_BHNVKKBBXX_8_11182WF0015L01

tag: treatment


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A8_ad002

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

value: CA

value: male

tag: age


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A8_ad001


title: input.mock.chip-seq.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A7_ad006