title: uvr8-6_wl3


title: KO_TA_2

status: Public on Feb 05 2020

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.
They were mapped to the mouse GRCm38 genome assembly using Hisat2 2.1.0 (no soft clipping)
BAM files were imported into Seqmonk v1.43.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 annotated list of differentially expressed genes

molecule: total RNA

organism: Mus musculus

source_name: small intestinal crypt

extract_protocol:
1-80 thousand ISC, 1-135 thousand TA, 100 thousand AE and 75-100 thousand colon epithelial cells (CO) were sorted per sample into RLT buffer for subsequent RNA-isolation with the RNeasy Micro kit (Qiagen 74004) with on-column DNA digestion.
Libraries were generated from 10 ng total RNA according to NEB Ultra II Directional RNA Library Preparation Kit for Illumina (E7760), Poly(A) mRNA magnetic isolation module (E7490) and multiplex oligos (E7335, 7500) manuals with the following modifications: RNA was fragmented for 20 min. Adaptor stock was diluted 150x.  15 PCR-amplification cycles were performed. SPRI select beads were substituted with Seramag Speedbeads (Thermo scientific 65152105050250) for size selection steps. Seramag beads were washed with TE buffer and resuspended in 50 volumes of PEG 8000 (Sigma 1546605) with 2.5M NaCl, 10mM Tris-Cl pH 8.0, 1mM EDTA, 0.05% Tween 20. PEG 8000 amounts used were corresponding to 10 and 12 % final PEG concentrations on sample addition. Size selection steps were performed at room temperature, adding the sample topped up to 100 µl with nuclease free water to 80 µl of bead suspension, followed by resuspension by pipetting, incubation for 10 min and precipitation on a magnetic rack. After removal of supernatant (SN), the beads were washed twice with 80% ethanol and moderately dried before elution with TE buffer. The size selection after second strand DNA-synthesis was performed with 12% PEG concentration, the remaining size selections with 10 % PEG. After PCR-amplification the size selection was performed twice (10 % PEG).  Libraries were sequenced on an Illumina HiSeq2500 as HiSeq 50 bp Single End reads.

treatment_protocol:
cell isolation protocol: Small intestines were dissected as described by Kazakevych et al., Nucleic Acids Res. 2017. Colons were dissected by the same protocol with extended PBS-EDTA incubation (30 min) and crypt shaking extraction (5 min).  Single cell material was derived from intestinal crypts by digestion with Dispase II (Sigma D4693, 0.05 mg/ml final concentration), DNase (Qiagen 79254, 20 Kunitz U/ml final concentration) and Collagenase (Sigma C7657, 0.15 mg/ml final concentration), while villus single cells were derived without digestion, by vigorous pipetting only.
flow-sorting protocol: Cell suspensions for RNA-seq were stained and flow-sorted: Small intestinal villus- and colon crypt-derived cells were stained in 2 % fetal bovine serum (FBS)/PBS with 1:200 APC-conjugated Epcam antibody (CD326, eBioscience 17-5791-82), 1:1000 AF488-conjugated CD45 antibody (Biolegend 103122) and 1:1000 AF488-conjugated CD31 antibody (Biolegend 102414) for 15 minutes at room temperature, washed 3 times and resuspended in 2 % FBS/PBS with 3.2 µg/ml ROCK-inhibitor (Y-27632, Sigma). All cell preparations were stained with 4’,6-diamidino-2-phenylindole (DAPI) prior to sorting. Epcam-high CD31- CD45- DAPI- cells were sorted on BD Aria III SORP cell sorter with a 100 µM nozzle. RNA from ISC (GFP-high DAPI-) and transit amplifying cells (TA, GFP-medium DAPI-) was isolated from single cell crypt suspensions of Lgr5-GFP+ mice and processed as above except the antibody staining step.

tag: genotype/variation

value: Vil-Cre mediated KO

tag: strain

value: C57BL/6 Lgr5-GFP

tag: cell type

value: TA

tag: isolation type


title: SMGX75-15

city: Swords

first: Shannon

last: Nelson

state: Dublin

address: Glasnevin

department: NICB

country: Ireland

institute: DCU

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

data_processing:
Raw sequencing files were merged for each sample to generate a single fastq file per sample. Cutadapt was used to remove adapter sequences.
Trimmed reads were aligned against the Homo sapiens Ch37 genome (hg19) with hisat2 with the following paramaters hisat2 --no-mixed --summary-file hg19/Align_stats -p 8 -x /home/Indexes/hg19/ -1 reads1List -2 reads2List --no-unal | samtools view -Sb | samtools sort -o
The resulting sam file was piped into samtools for bam conversion and sorting. The resulting featureCounts object can easily be manipulated to generate a counts matrix for DESeq2. This counts generation is written to counts.tsv for further analysis.
Up/down regulated genes: differential expression genes (p < 0.001 and |log2 fold-change| ≧ 2) are detected using DESeq2 after filtering out reads count less than 10. Compare CLOs with CLs; compare PT127 PDX, CLO with CL; compare PT291 organoids, CLO with CL. The correlation of paired groups - for each sample, reads count is normalised to TPM. Median is applied if there is more than one sample in a group. Linear regression was performed to identify the relationship of paired groups: PT291 ORG and PT127 PDX; PT127 PDX and PT127 CLO; PT291 ORG and PT291 CLO, (p < 0.05).
Genome_build: Homo sapiens Ch37 genome (hg19)
Supplementary_files_format_and_content: Excel spreadsheet, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj

organism: Homo sapiens

source_name: PT127 Cell Line Organoid Rep 3

growth_protocol:
Cell lines - PDX tumours were dissociated to single cells, and infiltrating mouse cells were removed using a Mouse Cell Removal Kit (Miltenyi Biotec). Cells were seeded in 1mg/mL matrigel until cells attached to plate. Cells were scaled up, and were grown in a T75 tissue culture flask, cells were maintained with Gibco DMEM-High glucose Glutamax media with 10% FBS, and placed in a 5% CO2 37 °C incubator for until they reached 80% confluency.
Organoids –PDX tumours were dissociated to single cells, and infiltrating mouse cells were removed using a Mouse Cell Removal Kit (Miltenyi Biotec). Cell were seeded in 8-12 mg/mL ECM Gel from Engelbreth-Holm-Swarm murine sarcoma, and maintained using media containing 50% L-WRN conditioned media 50% DMEM-high glucose Glutamax, and A83-01, hFGF10, Gastrin I, N-acetylcysteine, Nicotinammide, B-27 Supplement. Cells were also supplemented with Y-27632 when dissociated to single cells. Cells were grown for a 14 days before RNA extraction.
Cell line organoids - a cell lines were trypsinised, and cells were seeded at 5x10^4 cells/well in 8-12 mg/mL ECM Gel from Engelbreth-Holm-Swarm murine sarcoma, and maintained using media containing 50% L-WRN conditioned media 50% DMEM-high glucose Glutamax, and A83-01, hFGF10, Gastrin I, N-acetylcysteine, Nicotinammide, B-27 Supplement. Cells were also supplemented with Y-27632 when dissociated to single cells. Cells were grown for a 14 days before passaging. Fourteen days after passaging, RNA was extracted.

extract_protocol:
TRI-reagent® (Sigma) was used to lyse cells, and RNA isolation was performed using Direct-zol RNA Miniprep Plus Kit (Zymo Research, R2072).
RNA samples were quality controlled with an RNA Screen Tape (Agilent) and quantified with Qubit RNA HS Assay kit. Sequencing libraries were prepared with 200 ng of total RNA for all samples. The Nugen Universal Plus mRNA protocol was followed as recommended by the manufacturer. Libraries were amplified by 15 cycles of PCR. Libraries were sequenced in one NextSeq 550 run with the NextSeq 500/550 High Output Kit v2.5 (300 cycles), sequencing was done with Paired End 150 nt reads and 8 nt indexes. Libraries were loaded at 1.4 pM, 5% PhiX control was used.

tag: model type

value: Pancreatic cancer

tag: culture method

value: Cell Line Organoid

tag: source

value: PDX tumour


title: WT_wCO_colitis_2

description:
RNA-seq_DESeq2_FDR_005 wCO colitisVScontrol WT
RNA-seq_DESeq2_FDR_005 wCO KOvsWT colitis

data_processing:
Libraries were sequenced on the BGISEQ500 platform by BGI Hong Kong.
low-quality, N-rich or adaptor-polluted reads prefiltered according to BGI Hong Kong standard procedure
Reads were mapped to the mouse GRCm38 genome assembly using Hisat2 2.1.0 (no soft clipping, --no-mixed --no-dicscordant)
BAM files were imported into Seqmonk v1.42.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
rRNA reads were removed using the attached custom rRNA annotation track (downloaded from the UCSC table browser)
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 annotated list of differentially expressed genes

source_name: colon

extract_protocol:
The colon was cut open longitudionally, washed in PBS to remove faeces and snap frozen in liquid nitrogen.
25-100 mg frozen tissue was ground to powder with dry ice in a precooled mortar. After addition of 1ml Trizol, the sample was collected and incubated 5 min at RT. 200 µl Chloroform were added prior vigorous vortexing and centrifugation 20 min at 16,000 g, 4 °C. The upper phase was transferred to 500 µl isopropanol, vortexed and incubated 15 min at RT before centrifuging 10 min at 16,000g, 4°C. To deplete DSS, after discarding the supernatant, LiCl-precipitation was performed at 4 °C by dissolving the pellet in 120 µl H2O and addition of 80 µl 2M LiCl and 2h incubation prior to centrifugation for 30 min at 14,000 g. LiCl-precipitation was repeated once more and the pellet dissolved in 200 µl H2O. Next, the RNA was precipitated substituting LiCl with 20 µl 3M NaAc pH 5.2 and 400 µl 100% EtOH for 30 min incubation at -20 °C. After centrifugation, the pellet was washed once in 70% EtOH and dried on ice before resuspending in ice cold H2O.
Libraries were generated from total RNA by BGI Hong Kong. Libraries were sequenced on the BGISEQ500 platform as 100bp Single End reads.

treatment_protocol:
microbiome enrichment: Enriched microbiota was provided starting 2 weeks before colitis induction by bedding transfer and co-ventilation with the donor C57BL/6 females obtained from an SPF facility in York.
DSS-induced colitis: 1% DSS (Dextran sulphate sodium salt, Sigma Aldrich 42867) was continuously administered with drinking water and exchanged every 3 days.Tissue was harvested after 15 days DSS-administraton.

value: wild type

value: whole tissue

value: whole tissue, DSS depletion


title: WT_wCO_colitis_1


title: gastrocnemius_anti210lna_non-diabetic_rep7

type: RNA

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: LNA oligonucleotides against miR-210

hyb_protocol: The obtained cRNAs were hybridized on a MouseWG-6 v2 BeadChip Array according to the Standard Illumina hybridization protocol.

scan_protocol: Hybridized chips were then scanned and intensities were generated by GenomeStudio Software, according to the standard Illumina scanning protocol.

data_processing: GenomStudio’s bead summary probe level data, not normalized and not background corrected, were analyzed using Bioconductor. Quality was assessed by plotting the intensities of regular and control probes and the correct clustering of biological replicates was checked by PCA (Principal Component Analysis). Sample intensities were quantile normalized and filtered for expression and probe quality using the beadarray R package: only probes with Detection P-value<0.05 in at least one condition and whose quality categories was defined “Perfect” or “Good” were kept.

label: biotin

source_name: gastrocnemius muscle

label_protocol: Biotinylated cRNA was generated starting from 200ng total RNA per sample using the Ambion Illumina RNA amplification kit.

growth_protocol: C57BL/6N male mice (8-12 weeks old, Charles River laboratories) underwent hind limb ischemia and then they were randomized in two groups.

extract_protocol: RNA samples were extracted from gastrocnemius muscles (n= 11/group), using TRIzol (Invitrogen) and the TissueLyser system (Qiagen), according to the manufacturer's instructions. Following extraction, RNA integrity was checked with Agilent RNA Nano Kit and all samples had a RIN (RNA Integrity Number) >7.

treatment_protocol: After 5 days of ischemia, intraperitoneal injection of LNA oligonucleotides (In vivo LNAmicroRNA Inhibitors; Exiqon) against miR-210 (ANTI-210) or a scrambled control sequence (SCR) was carried out.

tag: experiment group

value: ANTI-210 LNA


title: uvr8-6_wl1

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description:
processed data file: rawcounts.txt
processed data file: normcounts.txt

data_processing:
Illumina Casava2.2 software used for basecalling.
Quality control was performed with FastQC v.0.11.5.
Reads were mapped to Arabidopsis TAIR-10 genome using STAR v2.5.3a software.
Biological quality control was done with the PicardTools v2.9.0.
The gene features were counted with HTSeq v.0.9.1 (htseq-count).
Normalization and differential expression analysis were performed with the statistical analysis R/Bioconductor package edgeR v.3.22.3 for the genes annotated in TAIR10.
Genome_build: TAIR10
Supplementary_files_format_and_content: rawcounts.txt: Tab-delimited text file includes raw count values for each Sample.
Supplementary_files_format_and_content: normcounts.txt: Tab-delimited text file includes normalized expression values (cpm = count per millions) for each Sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seeds were surface sterilized with sodium hypochlorite and sown on half-strength Murashige and Skoog basal salt medium (MS; Duchefa) containing 1% (wt/vol) agar (Applichem) and 1% (wt/vol) sucrose. Seeds were germinated aseptically at 22°C in a white light field under continuous irradiation provided by Osram L18W/30 tubes (3.6 μmol m−2 s−1; measured with an LI-250 Light Meter). UV-B was supplemented for the indicated times with Philips TL20W/01RS narrowband UV-B tubes (0.06 mW cm−2 s-1; measured with a VLX-3W Ultraviolet Light Meter equipped with a CX-312 sensor, Vilber Lourmat). The UV-B range was modulated by the use of 3-mm transmission cut-off filters of the WG series (Schott Glaswerke) with half-maximal transmission at the indicated wavelength (WG304 for UV-B-treated and WG368 for non-UV-B-treated controls).

extract_protocol:
Whole seedlings material of 30 seedlings per sample were collected in 1.5ml eppendorf tubes. Plant materials were ground using silamat and RNA was isolated with Plant RNeasy kit (Qiagen) and treated with DNaseI according to the manufacturer’s instructions. DNase was heat inactivated in the presence of 2 mM EDTA. The libraries were prepared with 400 ng of total RNA as starting material and processed with the TruSeqUD Stranded mRNA (Illumina), and sequencing on an Illumina HiSeq 4000 System using 100 bp single-end reads protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: On day 4, half plates remained in white light (3.6 μmol m−2 s−1) and the other half transferred to white light supplemented with narrowband UV-B (0.06 mW cm−2 s-1) under WG304 filters.

tag: ecotype/background

tag: tissue

value: Whole seedlings

tag: age

value: 4 days

tag: light treatment

value: low white light


title: gastrocnemius_anti210lna_non-diabetic_rep6

description: LNA oligonucleotides against miR-210


title: SMGX75-14

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT127 Cell Line Organoid Rep 2


title: Col_6h3

value: Wild type

value: 6h acclimation-level UV-B


title: SMGX75-13

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT127 Cell Line Organoid Rep 1


title: RNA-seq D2

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
RNA-seq: Raw data (raw reads) of fastq format were filtered by CUTADAPT
RNA-seq: Files were then processed by FASTQC
RNA-seq: Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR
RNA-seq: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene
RNA-seq: Differential expression analysis was performed using the DESeq2 R package. Genes with an adjusted P-value≤0.05 and │FoldChange│> 1.2 found by DESeq were assigned as differentially expressed
Genome_build: Sparassis latifolia (assembly ASM260774v1)

organism: Sparassis latifolia

source_name: mycelia

growth_protocol: Samples of fungi in three different groups (mycelia, light induced mycelia，and primordia) were harvested in the cultivation bags used in industry.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

tag: treatment

value: mycelia under dark

tag: time

value: SP-C


title: SMGX75-12

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Cell Line Organoid Rep 3


title: gastrocnemius_anti210lna_non-diabetic_rep4

description: LNA oligonucleotides against miR-210


title: KO_wCO_control_3

description:
RNA-seq_DESeq2_FDR_005 wCO colitisVScontrol KO
RNA-seq_DESeq2_FDR_005 wCO KOvsWT control

value: Vil-Cre mediated KO


title: KO_wCO_control_2


title: uvr8-6_wl2


title: Col_6h1


title: WT_wCO_control_3

description:
RNA-seq_DESeq2_FDR_005 wCO colitisVScontrol WT
RNA-seq_DESeq2_FDR_005 wCO KOvsWT control


title: Col_6h2


title: SMGX75-10

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Cell Line Organoid Rep 1


title: WT_wCO_control_2


title: KO_wCO_control_1


title: SMGX75-11

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Cell Line Organoid Rep 2


title: SMGX75-9

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Organoid Rep 3

value: Organoid


title: gastrocnemius_anti210lna_non-diabetic_rep3

description: LNA oligonucleotides against miR-210


title: Col_WL3


title: gastrocnemius_anti210lna_non-diabetic_rep1

description: LNA oligonucleotides against miR-210


title: gastrocnemius_anti210lna_non-diabetic_rep2

description: LNA oligonucleotides against miR-210


title: gastrocnemius_anti210lna_non-diabetic_rep11

description: LNA oligonucleotides against miR-210


title: WT_wCO_control_1


title: SMGX75-8

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Organoid Rep 2


title: Col_WL1


title: vts1∆_rep2

city: Stanford

first: Anupam

middle: K.

last: Chakravarty

state: CA

address: 269 Campus Dr, CCSR3120

department: Chemical & Systems Biology

country: USA

institute: Stanford University

description:
Ribo-Zero rRNA removal
1304B

data_processing:
fastq files were pseudo-aligned to version (S288C_reference_genome_R64-2-1_2015011) of budding yeast reference genome using kallisto package and default settings.
Genome_build: S288C_reference_genome_R64-2-1_20150113
Supplementary_files_format_and_content: tab-delimited text files include counts and transcripts per million (tPM) values for each gene in each Sample

organism: Saccharomyces cerevisiae

growth_protocol: 50 ml of cells were grown to midexponential phase (OD600 of ~0.6) before harvesting.

extract_protocol:
RNA extraction was performed using standard kits.
Library construction was performed using standard kits (Ribo-Zero rRNA removal was conducted).

treatment_protocol: A transient overexpression of Vts1 gene was carried out for 48 h using a plasmid and then eliminated and passaged for several generations. Details in Chakrabortee, Byers et al (https://doi.org/10.1016/j.cell.2016.09.017).

tag: strain background

tag: genotype

value: vts1 deletion

value: untreated

tag: growth phase

value: mid-exponential culture


title: SMGX75-7

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Organoid Rep 1

value: Pancreatic cancer

value: PDX tumour


title: uvr8-6_6h2

tag: genotype/variation


title: BW-cic1

city: Busan

first: Kwang-sun

last: Kim

address: 63 beon-gil 2, Jangjeon-dng, Geumjeong-gu

department: Chemistry

country: South Korea

institute: Pusan National University

description: Growth in the presence of 12.5 ug/mL ciclopirox (Replicate 1)

data_processing:
CLRNASeq V.1.00 (From ChunLab, Inc.)
Trimmed Mean of M-value of library size were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Elimination of <100 reads with or without treatment of ciclopirox
Supplementary_files_format_and_content: excel files include RLE (Relative Log Expression) normalized values for each sample.

organism: Escherichia coli K-12

source_name: growth in the presence of 12.5 ug/mL ciclopirox (Replicate 1)

growth_protocol: Growth in LB media to OD600=1.0 in the absence or presence of ciclopirox at 37C

extract_protocol:
RNA was extracted from OD600=1.0 using RNA Protect Bacteria (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ciclopirox (0 or 12.5 ug/mL) in LB media was prepared and the bacterial cells were grown in this media with vigorous shaking

tag: strain

value: wild type


title: gastrocnemius_anti210lna_non-diabetic_rep5

description: LNA oligonucleotides against miR-210


title: vts1∆_rep1

description:
Ribo-Zero rRNA removal
1304A


title: gastrocnemius_scramble_non-diabetic_rep11

description: scrambled control sequence

value: SCR


title: gastrocnemius_scramble_non-diabetic_rep8

description: scrambled control sequence


title: gastrocnemius_scramble_non-diabetic_rep9

description: scrambled control sequence


title: ATAC-seq P2

library_source: genomic

data_processing:
ATAC-seq: Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using Cutadapt
ATAC-seq: Quality filtered reads were then mapped to S. latifolia strain SP-C reference genome  using BWA(0.7.10)
ATAC-seq: Sam files were converted to Bam format using Samtools and used for peak calling.
ATAC-seq: The consensus map was created by merging the ATAC-seq peaks from all samples using the BEDTools  merge command.
ATAC-seq: MACS2 (2.1.1)   was used to call peaks and an initial threshold defined as │log2FC｜> 0.26, with p <0.05
Genome_build: Sparassis latifolia (assembly ASM260774v1)

molecule: genomic DNA

source_name: primordia

extract_protocol:
ATAC-seq: Harvest and count cells. Cells should be intact and in a homogenous, single-cell suspension. Centrifuge 50,000 cells 5 min at 500 × g, 4°C. The number of cells at this step is crucial, as the transposase-to-cell ratio determines the distribution of DNA fragments generated. See Critical Parameters. Remove and discard supernatant. Wash cells once with 50 μl of cold PBS buffer. Centrifuge 5 min at 500 × g, 4°C. Remove and discard supernatant. Gently pipet up and down to resuspend the cell pellet in 50 μl of cold lysis buffer. Centrifuge immediately for 10 min at 500 × g, 4°C. Discard the supernatant, and immediately continue to transposition reaction.
follow the protocol: ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide

value: primordia


title: SMGX75-6

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Cell Line Rep 3

value: Cell Line


title: ATAC-seq P1


title: naive_rep1

description:
Ribo-Zero rRNA removal
128A

source_name: naive

value: wild-type


title: SMGX75-4

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Cell Line Rep 1


title: naive_rep2

description:
Ribo-Zero rRNA removal
128B


title: Col_WL2

value: Whole seedlings

value: 4 days

value: low white light


title: MPS1_32°C_IP

city: Montpellier

first: Giorgia

last: Benzi

address: 1919 route de mende

country: France

institute: CRBM-CNRS

data_processing:
DROMPA software (Nakato and Shirahige, 2018).
Genome_build: Saccer3
Supplementary_files_format_and_content: bedGraph

source_name: yeast

growth_protocol: cells grown at 25°C in YEPD, synchronised with alpha factor and then released either at 32°C or 34°C (as indicated in the sample section) in presence of Nocodazole . Samples taken at 90min from release in Nocodazole

extract_protocol:
100 mL of cells (concentration 107cells/mL) were fixed in 1% formaldehyde for 30’ at RT with shaking and then transferred ON at 4°C. Cells were then spun down 3min at 3000 rpm at 4°C and washed three times with TBS. Cells were resuspended in 0.4 mL of 50mM Hepes-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton-X100, 0.1% Na-deoxicholate containing a cocktail of protease inhibitors (Complete EDTA-free Roche) and 1mM PMSF, followed by cell breakage through a Multi-beads shaker (Yasui-Kikai) at 0°C. Lysates were eluted in 15mL Falcon tubes (centrifuged twice at 3000 rpm for 1 min at 4°C), transferred in 1.5 Eppendorf tube, centrifuged at 5000 rpm 1 min at 4°C and sonicated through a Sonifyer Branson 2508 (5-7 cycles of 15sec, tune 1.5 with centrifugation of 5000 rpm for 1 min between each cycle). Sonicated lysates were then centrifuged for 5 min at 15000 rpm at 4°C. Supernatants were recovered. 10 µL of lysates were withdrawn at this stage (=Inputs). For immunoprecipitations (IPs), 60 µL of Protein G-dynabeads pre-washed twice with PBS containing 5 mg/mL BSA and pre-adsorbed with 3 µg Babco 16B12 anti-HA antibody were added to each lysate and incubated ON at 4°C on a nutator. IPs were then washed twice with ice-cold 50mM Hepes-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton-X100, 0.1% Na-deoxicholate, twice with ice-cold 50mM Hepes-KOH pH7.5, 500mM NaCl, 1mM EDTA, 1% Triton-X100, 0.1% Na-deoxicholate, twice with ice-cold 10mM Tris-Cl pH8, 250mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1mM EDTA and once with ice-cold TE (50mM Tris-Cl pH8, 1mM EDTA pH8). IPs were eluted at 65°C for 15min with 50µL of 50mM Tris-Cl pH8, 10mM EDTA, 1% SDS, resuspended in 50 µL of TE/1% SDS and incubated overnight at 65°C to reverse crosslinking. IPs were then incubated at 37°C for 1 hour with 100 µL of TE containing 10 µg of RNAseA and 2 hours at 37°C with 2 µL of ProteinaseK 50 mg/mL. DNA was then purified with the Qiagen PCR purification kit
Libraries for Illumina sequencing have been prepared following the NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: Nocodazole 15ug/mL was used for 90 minutes at the reported temperatures

tag: antibodies

value: Babco 16B12 anti-HA


title: gastrocnemius_scramble_non-diabetic_rep10

description: scrambled control sequence

source_name: gastrocnemius muscle


title: gastrocnemius_scramble_non-diabetic_rep7

description: scrambled control sequence


title: [SMAUG+]_inductant2_rep2

description:
Ribo-Zero rRNA removal
121B

value: transient overexpression of VTS1 gene


title: ATAC-seq L1

value: light induced mycelia

value: SP-C


title: SMGX75-2

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT127 Cell Line Rep 2


title: SMGX75-3

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT127 Cell Line Rep 3


title: [SMAUG+]_inductant2_rep1

description:
Ribo-Zero rRNA removal
121A


title: gastrocnemius_scramble_non-diabetic_rep6

description: scrambled control sequence


title: SMGX75-5

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT291 Cell Line Rep 2


title: gastrocnemius_scramble_non-diabetic_rep4

description: scrambled control sequence


title: gastrocnemius_scramble_non-diabetic_rep3

description: scrambled control sequence


title: gastrocnemius_scramble_non-diabetic_rep5

description: scrambled control sequence


title: ATAC-seq D2

source_name: mycelia

value: mycelia under dark


title: ATAC-seq L2


title: SMGX75-1

description: PT291_PT127 ORG_CLO_PDX_vs_CL.xlsx

source_name: PT127 Cell Line Rep 1


title: [SMAUG+]_inductant1_rep2

description:
Ribo-Zero rRNA removal
120B


title: ATAC-seq D1


title: [SMAUG+]_inductant1_rep1

description:
Ribo-Zero rRNA removal
120A


title: gastrocnemius_scramble_non-diabetic_rep2

description: scrambled control sequence


title: Skin, EV3

status: Public on Feb 04 2020

city: Amsterdam

first: Victoria

last: Iglesias

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
The 65 bp single end reads were mapped to the mouse reference genome (GRCm38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: Skin

extract_protocol:
Whole skin (30-35 mg)  from the vaccinated area was isolated and immediately frozen in dry ice
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: E7SH/EV vaccination

tag: time (skin isolation post-treatment)

value: day 4


title: Skin, EV1


title: Skin, ΔGG2

value: E7SH/ISG15-ΔGG vaccination


title: HFD_cns_ND_3_17

city: Basel

first: Marc

last: Donath

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University of Basel

description: Mice fed normal diet (chow)

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequences using Trimmomatic  v0.36, then mapped to mm10 mouse genome using STAR v2.5.1a allowing for maximum 5% mismatching bases per read (parameters: --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05). BAM files were indexed by SAM tools v.1.4
Reads per gene were counted with the featureCounts function of the Rsubread package (v1.30.4) using gencode version M13 gtf gene annotation file. Reads mapping to multiple sequences were not counted. (parameters:  GTF.featureType="exon", GTF.attrType="gene_id", strandSpecific=0, countMultiMappingReads=FALSE)
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing not normalized counts per gene. Separate files for samples from FARE and HFD experiments

molecule: polyA RNA

source_name: microglia

extract_protocol:
RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, Thermo Fisher Scientific, USA), followed by DNase I treatment
Smart-seq2 protocol (Picelli et al., 2014)

treatment_protocol: Mice were treated with protocols specified in the description column of the sample table. Cells were isolated with protocols specific for each macrophage subtype and purified using FACS with macrophage subtype specific antibodies

value: microglia

tag: cohort

tag: starting number of cells

tag: experiment

value: HFD

tag: sample name in counts table


title: HFD_cns_ND_3_18

description: Mice fed normal diet (chow)


title: gastrocnemius_scramble_non-diabetic_rep1

description: scrambled control sequence

tag: experiment group

value: SCR


title: Skin, EV2

tag: tissue


title: Skin, ΔGG1


title: HFD_cns_HFD_3_16

description: Mice fed high fat diet for 8 weeks


title: Skin, ΔGG3


title: HFD_cns_HFD_STZ_3_15

description: Mice fed high fat diet for 8 weeks and treated with Streptozotocin at week 4


title: HFD_cns_ND_1_6

description: Mice fed normal diet (chow)


title: HFD_cns_HFD_3_14

description: Mice fed high fat diet for 8 weeks


title: HFD_cns_HFD_1_2

description: Mice fed high fat diet for 8 weeks


title: HFD_cns_ND_1_5

description: Mice fed normal diet (chow)


title: HFD_peri_HFD_STZ_5_15

value: peritoneal macrophages


title: HFD_cns_HFD_STZ_2_9


title: HFD_peri_HFD_5_14

description: Mice fed high fat diet for 8 weeks


title: HFD_peri_HFD_STZ_4_12


title: HFD_cns_HFD_STZ_1_4


title: HFD_peri_ND_5_13

description: Mice fed normal diet (chow)


title: HFD_peri_HFD_2_5

description: Mice fed high fat diet for 8 weeks


title: HFD_peri_ND_4_10

description: Mice fed normal diet (chow)


title: HFD_peri_ND_3_7

description: Mice fed normal diet (chow)


title: HFD_peri_HFD_STZ_2_6


title: HFD_cns_HFD_STZ_3_13


title: HFD_cns_HFD_1_3

description: Mice fed high fat diet for 8 weeks


title: HFD_peri_HFD_STZ_1_3


title: HFD_peri_ND_2_4

description: Mice fed normal diet (chow)


title: HFD_islets_HFD_STZ_5_15

value: islet macrophages


title: HFD_peri_ND_1_1

description: Mice fed normal diet (chow)


title: HFD_islets_HFD_1_2

description: Mice fed high fat diet for 8 weeks


title: HFD_peri_HFD_1_2

description: Mice fed high fat diet for 8 weeks


title: HFD_islets_HFD_3_8

description: Mice fed high fat diet for 8 weeks


title: HFD_islets_HFD_STZ_4_12


title: HFD_islets_ND_4_10

description: Mice fed normal diet (chow)


title: HFD_islets_HFD_5_14

description: Mice fed high fat diet for 8 weeks


title: HFD_peri_HFD_4_11

description: Mice fed high fat diet for 8 weeks


title: HFD_islets_ND_5_13

description: Mice fed normal diet (chow)


title: HFD_islets_ND_1_1

description: Mice fed normal diet (chow)


title: HFD_islets_HFD_STZ_3_9


title: HFD_islets_ND_3_7

description: Mice fed normal diet (chow)


title: HFD_islets_HFD_4_11

description: Mice fed high fat diet for 8 weeks


title: HFD_peri_HFD_STZ_3_9


title: FARE_peri_RE_9_115

description: Mice fasted for 12h and refed with chow food for 2h

value: refed

value: FARE


title: FARE_peri_RE_8_108


title: FARE_peri_RE_6_80


title: FARE_peri_FA_8_94

description: Mice fasted for 12h

value: fasted


title: FARE_peri_RE_2_24


title: FARE_peri_RE_1_17


title: FARE_peri_FA_7_87

description: Mice fasted for 12h


title: FARE_peri_FA_5_59

description: Mice fasted for 12h


title: FARE_peri_FA_6_66

description: Mice fasted for 12h


title: FARE_peri_FA_4_38

description: Mice fasted for 12h


title: FARE_peri_FA_2_10

description: Mice fasted for 12h


title: FARE_peri_FA_3_31

description: Mice fasted for 12h


title: FARE_liver_RE_7_105

value: Kupffer cells


title: FARE_liver_RE_9_119


title: FARE_liver_RE_8_112


title: FARE_liver_RE_1_21

description: Mice fasted for 12h


title: FARE_peri_FA_1_3

description: Mice fasted for 12h


title: FARE_liver_RE_4_56


title: FARE_liver_FA_3_35

description: Mice fasted for 12h


title: FARE_liver_FA_1_7

description: Mice fasted for 12h


title: FARE_liver_RE_3_49


title: FARE_liver_FA_7_91

description: Mice fasted for 12h


title: FARE_liver_RE_2_28

description: Mice fasted for 12h


title: FARE_peri_RE_7_101


title: FARE_islet_RE_9_118


title: FARE_liver_FA_2_14

description: Mice fasted for 12h


title: FARE_liver_FA_4_42

description: Mice fasted for 12h


title: FARE_islet_RE_7_104


title: FARE_peri_RE_4_52


title: FARE_peri_RE_5_73


title: FARE_islet_RE_8_111


title: FARE_islet_RE_5_6_76


title: FARE_islet_RE_3_48

description: Mice fasted for 12h


title: FARE_islet_RE_4_55


title: FARE_islet_RE_1_2_20

description: Mice fasted for 12h


title: FARE_islet_FA_7_90

description: Mice fasted for 12h


title: FARE_islet_FA_4_41

description: Mice fasted for 12h


title: FARE_islet_FA_8_97

description: Mice fasted for 12h


title: FARE_islet_FA_5_6_62

description: Mice fasted for 12h


title: FARE_islet_FA_1_2_6

description: Mice fasted for 12h


title: FARE_islet_FA_3_34

description: Mice fasted for 12h


title: FARE_intest_RE_9_114

value: colonic macrophages


title: FARE_intest_RE_8_107


title: FARE_intest_RE_6_79


title: FARE_intest_FA_8_93

description: Mice fasted for 12h


title: FARE_intest_RE_4_51


title: FARE_intest_RE_1_16


title: FARE_intest_FA_6_65

description: Mice fasted for 12h


title: FARE_intest_FA_4_37

description: Mice fasted for 12h


title: FARE_intest_RE_3_44


title: FARE_intest_FA_1_2

description: Mice fasted for 12h


title: FARE_intest_FA_3_30

description: Mice fasted for 12h


title: FARE_intest_RE_7_100


title: FARE_cns_RE_9_113


title: FARE_intest_FA_5_58

description: Mice fasted for 12h


title: FARE_intest_FA_2_9

description: Mice fasted for 12h


title: FARE_cns_RE_6_78


title: FARE_cns_RE_5_71


title: FARE_cns_FA_8_92

description: Mice fasted for 12h


title: FARE_cns_RE_3_43


title: FARE_cns_RE_4_50


title: FARE_cns_RE_7_99


title: FARE_intest_RE_5_72


title: FARE_cns_RE_2_22


title: FARE_intest_RE_2_23


title: FARE_cns_FA_7_85

description: Mice fasted for 12h


title: FARE_cns_RE_1_15


title: FARE_cns_FA_6_64

description: Mice fasted for 12h


title: FARE_cns_FA_3_29

description: Mice fasted for 12h


title: FARE_cns_FA_2_8

description: Mice fasted for 12h


title: FARE_cns_FA_1_1

description: Mice fasted for 12h


title: FARE_blood_RE_9_117

source_name: monocytes

value: monocytes


title: FARE_intest_FA_7_86

description: Mice fasted for 12h


title: FARE_cns_RE_8_106


title: FARE_blood_RE_7_103


title: FARE_blood_RE_8_110


title: FARE_blood_RE_6_82


title: FARE_blood_RE_4_54


title: FARE_blood_RE_5_75


title: FARE_blood_RE_3_47


title: FARE_blood_RE_2_26


title: FARE_blood_RE_1_19


title: FARE_blood_FA_8_96

description: Mice fasted for 12h


title: FARE_blood_FA_7_89

description: Mice fasted for 12h


title: FARE_cns_FA_5_57

description: Mice fasted for 12h


title: FARE_blood_FA_6_68

description: Mice fasted for 12h


title: FARE_blood_FA_5_61

description: Mice fasted for 12h


title: FARE_blood_FA_2_12

description: Mice fasted for 12h


title: FARE_blood_FA_3_33

description: Mice fasted for 12h


title: FARE_blood_FA_4_40

description: Mice fasted for 12h


title: FARE_cns_FA_4_36

description: Mice fasted for 12h


title: FARE_adi_RE_9_116

value: adipose tissue macrophages


title: FARE_blood_FA_1_5

description: Mice fasted for 12h


title: FARE_adi_RE_8_109


title: FARE_adi_RE_4_53


title: FARE_adi_RE_6_81


title: FARE_adi_RE_7_102


title: FARE_adi_RE_5_74


title: FARE_adi_RE_3_46


title: FARE_adi_RE_2_25


title: HHDST_2358

city: Boston

first: Alice

middle: H

last: Lichtenstein

state: MA

address: 711 Washington St

department: Jean Mayer USDA Human Nutrition Research Center on Aging

institute: Tufts University

data_processing:
Base-calling was performed using bcl2fastq v2.17.1.14
Alignment 1 (*_NR112918.csv files): RNA-seq reads were trimmed for adapter sequence and quality then aligned to reference (see genome build) using CLC Bio's Genomics Workbench v10.1.2 with parameters: quality limit = 0.01, min length = 100, Length fraction = 0.95, Similarity fraction = 0.95.
Alignment 2 (*_Sscrofa10.2.csv files): RNA-seq reads were trimmed for adapter sequence and quality then aligned to the Sus scrofa 10.2 genome assembly using CLC Bio's Genomics Workbench v9.0.1 with parameters: quality limit = 0.01, min length = 100, Length fraction = 0.95, Similarity fraction = 0.95
Reads that mapped uniquely to exons were used as counts (Unique Exon Reads) for differential expression analysis using the Bioconductor package: edge R. Genes were filtered based on a minimum of at least one count per million across six samples in all groups and normalized using the TMM method. Differentially expressed genes were identified using the Cox-Reid profile-adjusted likelihood method and likelihood ratio test. A Benjamini-Hochberg false discovery rate (FDR) method was used to adjust p-values for multiple comparisons
Genes were considered differentially expressed based on an FDR adjusted p <0.1 and absolute fold change ≥1.5. Fold change for genes identified by the edge R two-factor model were interpreted as diet effect: fold change of WD relative to HHD and statin effect: fold change of atorvastatin relative to no atorvastatin. Differentially expressed genes were only attributed to main effects (diet and statin) if there was no significant diet x statin interaction. A significant diet x stain interaction is indicated by a FDR adjusted p <0.1.
Ingenuity Pathway Analysis (IPA; v 9.0, Mountain View, CA, USA) was used to determine relevant biological pathways and functional annotation of differentially expressed genes. Pathways with an absolute Z score ≥ 2 and an FDR adjusted p-value ≤ 0.05 were considered statistically significant.
Genome_build: Alignment 1: "Assembly 11/29/18" from Porcine Translational Research Database (Dawson, Harry D., et al. "The porcine translational research database: a manually curated, genomics and proteomics-based research resource." BMC genomics 18.1 (2017): 643.)
Genome_build: Alignment 2: Sscrofa10.2
Supplementary_files_format_and_content: comma-separated value files with Unique Exon Read values for each sample

organism: Sus scrofa

source_name: Epicardial Adipose tissue

extract_protocol:
EAT was homogenized and RNA was isolated using RNeasy Universal Midi kit (Qiagen, Valencia, CA). Isolated RNA was treated with Turbo DNase (Ambion, Waltham, MA) to minimize genomic DNA contamination. RNA quality was assessed using the Experion RNA analysis electrophoresis kit (Bio-Rad, Hercules, CA). Only samples with an RNA Quality Indicator (RQI) greater than 7 were sequenced.
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (mRNA purification and fragmentation, cDNA synthesis, end repair, 3’ adenylation, adaptor ligation, and DNA enrichment) per the manufacturer’s instructions. DNA fragment size was determined using Experion DNA 1K chips (Bio-Rad, Hercules, CA) and library quantification was performed using the KAPA Library Quantification kit (KAPA Biosystems, Wilmington, MA).

value: Epicardial Adipose tissue

tag: diet

value: Heart Healthy + Statin

tag: rna id


title: FARE_adi_RE_1_18

tag: treatment


title: FARE_adi_FA_7_88

description: Mice fasted for 12h


title: FARE_adi_FA_8_95

description: Mice fasted for 12h


title: HHDST_2339


title: HHDST_2334


title: HHDST_2329


title: FARE_adi_FA_6_67

description: Mice fasted for 12h


title: FARE_adi_FA_5_60

description: Mice fasted for 12h


title: FARE_adi_FA_4_39

description: Mice fasted for 12h


title: HHD_2343

value: Heart Healthy


title: HHD_2356


title: FARE_adi_FA_2_11

description: Mice fasted for 12h


title: FARE_adi_FA_1_4

description: Mice fasted for 12h


title: Ba_DKO_Blgpos_L2 [A918U18]

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provide

source_name: Mammary cells

growth_protocol: Not applied (fresh tissue)

extract_protocol:
Qiagen micro-columns
RNA libraries were prepared for sequencing using SMARTer v4 protocol

tag: developmental stage

tag: sample obtention

value: Isolated from fresh tissu by FACs


title: HHD_2341


title: HHDST_2366B


title: HHD_2336


title: Ba_DKO_Blgpos_L2 [A918U17]


title: Ba_DKO_Blgpos_L2 [A918U16]


title: HHD_2330


title: ARST_2362

value: Atherogenic + Statin


title: ARST_2352


title: HHD_2325


title: Ba_Ctrl_Blgneg_L2 [A918U15]

value: Ctrl


title: ARST_2349


title: Ba_Ctrl_Blgneg_L2 [A918U14]


title: ARST_2345


title: HHDST_2327


title: ARST_2340


title: Ba_Ctrl_Blgneg_L2 [A918U13]


title: ARST_2333


title: ARST_2332


title: FARE_adi_FA_3_32

description: Mice fasted for 12h


title: Ba_Ctrl_Blgneg_L2 [A918U12]


title: ARST_2326


title: APP_treated_4

city: Epalinges

first: Tatiana

last: Petrova

state: VD

address: 155, Chemin des Boveresses

department: Oncology

institute: University of Lausanne

data_processing:
Target transcript sequences were obtained from ENSEMBLE (GRCm38.p6), and the abundance of transcripts were quantified using kallisto (0.44.0) with sequence based bias correction. All other parameters were set to default.
Kallisto's transcript-level estimates were summarized at the gene-level using tximport (1.8.0) from Bioconductor, and rounded up to the nearest integer.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text file providing gene-by-sample matrix of estimated counts.

source_name: bulk tumor

growth_protocol: Tumors induced in Apcflox/flox;Tp53flox/flox;villin-CreERT2 (AP) or Apcflox/flox;Tp53flox/flox;Prox1flox/flox;villin-CreERT2 (APP) mice for two weeks by intracecal injection of tamoxifen

extract_protocol:
RNA was extracted using QIAGEN RNeasy Plus Mini Kit following the manufacturer's instructions
Illumina TruSeq, 500 ng of total RNA

treatment_protocol: PBS or control IgG or A2V+CD40

tag: genotype

value: APP

tag: Sex

value: m

tag: mouse age in weeks

tag: sample id


title: AR_2363

value: Atherogenic


title: AP_control_6

value: AP


title: AR_2351


title: APP_control_5


title: FARE_liver_FA_8_98

description: Mice fasted for 12h


title: AP_treated_4

value: f


title: AP_treated_3


title: AR_2348


title: AP_control_5


title: AR_2342


title: AR_2337


title: AP_control_4


title: AR_2331


title: APP_control_6


title: APP_control_3


title: AP_control_3


title: AP_control_2


title: APP_control_1


title: Vehicle treated sample 3

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Transcript quantification was performed on the raw demultiplexed FASTQ files using Kallisto against the Ensembl mouse transcriptome GRCm38 release 79, with 30 bootstrap samples and the options bias (sequence based bias correction) and rfstranded (strand specific reads, first read reverse).
The resulting abundance estimates were imported into the DESeq2 R package using the tximport R package generating estimated normalized counts.
Only genes for which reads were detected are included in the counts table.
Genome_build: GRCm38 release 79
Supplementary_files_format_and_content: Tab-separated text giving estimated read counts per transcript (identified by Ensembl transcript ID) for each sample.

source_name: WT Pancreatic islets

growth_protocol: Islets were isolated from 10-12 week old mice and cultured in the conditions specified above.

extract_protocol:
RNA isolation was performed using the  RNeasy Micro and Mini kits (Qiagen)
Following RNA isolation, total RNA integrity was checked using an Agilent 2100 Bioanalyzer. RNA concentrations were measured using the NanoDrop Spectrophotometer (Thermo Fisher Scientific). Preparation of the RNA sample library and sequencing were performed by the Genomics Core Laboratory at Weill Cornell Medicine. Messenger RNA was prepared using a TruSeq Stranded mRNA Sample Library  Preparation kit (Illumina), according to the manufacturer’s instructions

treatment_protocol: Islets were isolated from 10-12 week old mice and treated in the following conditions: 1) vehicle 2) vehicle+C3a 3) palmitate 4) palmitate +C3a

tag: sequencing batch

value: Vehicle


title: Vehicle+C3a treated sample 3

value: Vehicle + C3a


title: Palmitate+C3a treated sample 3

value: Palmitate + C3a


title: Palmitate treated sample 3

value: Palmitate


title: APP_treated_3


title: Vehicle+C3a treated sample 2


title: Palmitate treated sample 2


title: APP_treated_2


title: AP_control_1


title: Vehicle treated sample 2


title: Palmitate+C3a treated sample 1


title: AR_2338


title: Palmitate treated sample 1

description: Pa


title: AP_treated_2


title: AP_treated_1


title: Vehicle treated sample 1

description: Veh


title: Vehicle+C3a treated sample 1


title: APP_control_2


title: Pancreatic islets, db/db AAV Adipsin 3

data_processing:
Raw sequence reads were mapped to the mouse genome mm10/GRCm38 using the STAR aligner
Mapped reads were counted at the gene level using the Rsubread R package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Ensembl gene ID) in each sample

source_name: Pancreatic islets

growth_protocol: Islets were isolated from db/db mice treated with AAV-Adipsin vs AAV-GFP were isolated, maintained in culture for 12 hours before perfoming RNA extraction

treatment_protocol: db/db mice were treated with AAV-GFP vs AAV-Adipsin for 4 weeks before islet extraction and RNA isolation

value: db/db

value: Adipsin

value: Pancreatic islets


title: Lmna WT rep3

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

institute: CNR and Istituto Nazionale Genetica Molecolare

data_processing:
Basecalls performed using Phred33 quality score
Sequenced reads were trimmed for quality and adaptor sequence using Trimmomatic v0.32 with ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50 in paired-end mode
Trimmed reads were mapped to mm10 whole genome using STAR v2.5.2b
Raw counts were quantified using HTSeq v0.6.1 with parameters -s reverse -t exon -i gene_id -m union
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw counts generated with HTSeq

source_name: Muscle stem (satellite) cells_Lmna Δ8-11 +/+

extract_protocol:
cell extraction protocol: Satellite cells were isolated from hind-limb muscle and sorted using FACS
Total RNA from freshly isolated satellite cells from 3 mice for each condition was extracted in TRI-Reagent
Illumina TruSeq Stranded Total RNA with Ribo-Zero GOLD

tag: strain background

tag: genotype/variation

value: Lmna {delta}8-11 +/+

tag: age

value: Post natal day 19

tag: cell type

value: Muscle stem (satellite) cells


title: Lmna WT rep2


title: Palmitate+C3a treated sample 2


title: Pancreatic islets, db/db AAV Adipsin 1

description: Adipsin


title: Pancreatic islets, db/db AAV Adipsin 2


title: Lmna HOM rep3

source_name: Muscle stem (satellite) cells_Lmna Δ8-11 -/-

value: Lmna {delta}8-11 -/-


title: Lmna HOM rep2


title: Pancreatic islets, db/db AAV-GFP 4

value: Control


title: Lmna HOM rep1


title: Beko RBPJ DMSO rep 1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Quality control of FASTQ files was done using FastQC.
Reads were aligned to a pre-compiled index of the mouse mm9  genome using Bowtie2 (default options) 2.2.9
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
For Browser visualization bigwig files with coverage information were generated using deeptools bamCoverage function
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files (of coverage) at 25 bp resolution

source_name: Beko pre-T cell line

growth_protocol: Mouse pre-T (Beko) cells were grown at 37°C with 5% CO2 in IMDM medium (Gibco 21980-065) supplemented with 2% FCS, peptone, insulin, nonessential aminoacids and penicillin/streptomycin.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907)
Lybrary-prep kit: Diagenode MicropPlex Library Preparation kit v2 (C05010012)

treatment_protocol: Mouse pre-T (Beko) cells were treated for 24 hours with 0.01 mg/ml apicidin, 10 mg/ml DAPT (GSI) or with DMSO as control.

tag: cell line

value: Beko pre-T

tag: chip antibody

value: Cell Signaling, #5313

value: 24 hours with DMSO.


title: Pancreatic islets, db/db AAV-GFP 1

description: GFP

tag: tissue


title: Pancreatic islets, db/db AAV-GFP 3


title: Pancreatic islets, db/db AAV-GFP 2


title: Beko Input GSI

value: 24 hours with 10 mg/ml DAPT (GSI).


title: Beko RBPJ DMSO rep 2


title: WT.Ctx_6

city: Baltimore

first: Ali

last: Fatemi

state: MD

address: 707 N Broadway

department: Neurogenetics

institute: Kennedy Krieger Institute

data_processing:
RNA-seq analysis was executed and visualized using an in-house platform, consisting of the following steps. Alignment to the mouse transcriptome was performed with the STAR aligner (Dobin et al, 2013) and quantification of transcript abundances in units of Transcript Per Million (TPM) units was performed with MMSEQ (Turro et al. 2011).  Differential expression analysis between the genotypes was performed with MMDIFF (Turro et al., 2014), producing gene-level effect sizes and posterior probability values for comparison of DARS2-Flox/CamKII-Cre(+) and DARS2-Flox/CamKII-Cre(-) cortices.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance measurements for RNA-seq
Supplementary_files_format_and_content: Differential expression test between WT ahd DARS2 KO animals using MMDiff

source_name: WT

growth_protocol: Cortical samples were collected from DARS2-Flox/CamKII-Cre(+) and DARS2-Flox/CamKII-Cre(-) at 14 weeks of age

extract_protocol:
RNA-seq libraries were prepared using purified RNA isolated from frozen tissue using the RNeasy Mini kit. RNA quality and concentration were assayed using a Fragment Analyzer instrument.
RNA-seq libraries were prepared using purified RNA isolated from frozen tissue using the RNeasy Mini kit.

treatment_protocol: RNA-seq libraries were prepared using purified RNA isolated from frozen tissue using the RNeasy Mini kit. RNA quality and concentration were assayed using a Fragment Analyzer instrument. RNA-seq libraries were prepared using the TruSeq Stranded mRNA PolyA (Unique Dual Index) kit.. Libraries were sequenced on an Illumina HiSeq 4000 instrument.

value: Cortex

value: male

value: WT

tag: replicate


title: WT.Ctx_5


title: Beko Input Apicidin

value: 24 hours with 0.01 mg/ml apicidin.


title: Beko Input DMSO


title: APP_control_4

value: APP

value: f


title: Beko H3K27ac GSI rep 2

value: diagenode, pAb-174-050


title: Lmna WT rep1


title: WT.Ctx_3


title: WT.Ctx_2


title: WT.Ctx_1


title: Beko H3K27ac DMSO rep 2


title: Beko H3K27ac DMSO rep 1


title: Beko H3K27ac Apicidin rep 2


title: Beko H3K27ac Apicidin rep 1


title: KO.Ctx_6

source_name: KO

value: KO


title: KO.Ctx_4


title: KO.Ctx_3


title: serB.wt.rep2

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

institute: University of Regensburg

data_processing:
Base calling was performed using MiSeq Control Software 2.6.2.1.
Adapters were trimmed with SeqPrep v1.3.2-1 (github.com/jstjohn/SeqPrep).
Trimmed reads were mapped using Bowtie2 with default settings to the E. coli K-12 genome (www.ecogene.org).
Samtools v1.3.1 was used to remove optical duplicates.
HTseq-count v0.9.1 was used for counting against an annotation database (www.ecogene.org_Ecoli_annotation_110217-065029).
Differential expression analysis was carried out with R and the Bioconductor package DESeq2 .
Genome_build: E. coli K-12 MG1655 U00096.3
Supplementary_files_format_and_content: Excel file with count table and DESeq2 result tables.

organism: Escherichia coli

growth_protocol: Cells were grown in LB medium to midlog phase. After harvesting, cells were washed three times with 1 % NaCl and used to inoculate minimal M9-glucose medium and shaken at 30° C until the culture reached an optical density of 0.5.

extract_protocol:
Cells were lysed in RNase-free TE buffer (30 mM Tris-HCl, 1 mM EDTA, pH 8.0) containing 1 mg/ml Lysozyme for 30 min at room temperature. Total RNA was prepared using an RNeasy Mini Kit (Qiagen). Genomic DNA was removed by RNase-free DNase (Qiagen). RNA quality was assayed using a NanoDrop and a 4200 TapeStation system (Agilent Technologies Inc.). Ribosomal RNA was depleted using a Ribo-Zero rRNA Removal Kit Bacteria (Illumina) and successful rRNA depletion verified by TapeStation.
Ribosomal RNA was depleted using Ribo-Zero rRNA Removal Kit Bacteria (Illumina). The library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). After quality and quantity assessment on the TapeStation the libraries were pooled equimolar. The resulting library pool was sequenced on a MiSeq sequencer (Illumina) performing a 2x 80 cycles paired-end run.
stranded RNA-Seq with rRNA depletion

treatment_protocol: After the culture reached an optical density of 0.5 cells were mixed with two volumes of RNAprotect Bacteria Reagent (Qiagen), harvested and stored at -80° C

tag: strain

value: strain BW25113

tag: mutation

value: delta(araD-araB)567, delta-lacZ4787(::rrnB-3), gamma-, rph-1, delta(rhaD-rhaB)568, hsdR514

tag: f-factor

value: F-


title: serB.wt.rep1


title: pdxJ.X3p.rep1


title: KO.Ctx_1


title: pdxJ.11p.rep1


title: 3mo_skM_hetX753_2

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: Whole tissue, skeletal muscle (skM)

extract_protocol:
RNA was column-extracted using Rneasy Fibrous Tissue Mini kit (Qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Skeletal muscle (skM, gastrocnemius) from 3-month-old wildtype and two BubR1 MVA allele carriers, BubR1+/L1002P and BubR1+/X753 were collected and harvested from naturally aged mice, euthanized at 3 months of age. RNA was extracted from tissues and was used for RNA sequencing.

value: gastrocnemius muscle

tag: background strain

value: 129Sve/C57BL/6 mix

value: 3 months


title: WT.Ctx_4

tag: genotype


title: pdxJ.X3p.rep2


title: pdxJ.11p.rep2


title: 3mo_skM_hetX753_3


title: 3mo_skM_hetX753_1


title: pdxJ.11m.rep3


title: 3mo_skM_hetL1002P_3


title: pdxJ.11m.rep2


title: Beko H3K27ac GSI rep 1

value: Beko pre-T

tag: treatment


title: 3mo_skM_hetL1002P_2


title: 3mo_skM_hetL1002P_1


title: KO.Ctx_7

tag: Sex


title: nanE.7.rep1


title: nanE.7.rep3


title: 3mo_skM_WT_2


title: pdxJ.11m.rep1


title: KO.Ctx_5


city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
10x Genomics – v1
Sciatic nerve macrophages 5 days after nerve crush

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger 2.0.2 mkfastq
Demultiplexed data was then processed using the Cell Ranger 2.0.2 count pipeline
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output CellRanger Count) for each sample

source_name: Sciatic nerve

extract_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.

tag: number of cells


title: nanE.7.rep2


title: KO.Ctx_2


title: 3mo_skM_WT_1


title: 10mo_fat_HH_4

source_name: Whole tissue, fat (IAT)

extract_protocol:
RNA was column-extracted using Rneasy Fibrous Tissue Mini kit (skM) and Rneasy Lipid Tissue Mini Kit (fat) (Qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Skeletal muscle (skM, gastrocnemius) and fat (IAT) from 8-10-month-old wildtype and progeroid BubR1 MVA mutant mice (BubR1H/L1002P and BubR1H/H) were collected and harvested from naturally aged mice, euthanized at 8-10 months of age. RNA was extracted from tissues and was used for RNA sequencing.

value: fat (IAT)

value: 8-10 months

value: HH


description:
10x Genomics – v1
Sciatic nerve macrophages 1 day after nerve crush

treatment_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.


title: 10mo_fat_HH_3


title: 10mo_fat_HL1002P_4


title: Steady state Sciatic nerve marcrophages

description:
10x Genomics – v1
Steady state Sciatic nerve marcrophages


title: 10mo_fat_HH_1


title: 10mo_fat_HL1002P_3


title: PP2Aa deficient B cells [000008518869_C03]

first: George

middle: C

last: Tsokos

state: Massachusetts

address: CLS-928, 3 Blackfan Circle

department: Rheumatology/BIDMC

institute: Harvard Medical School

data_processing:
base calling by bustard
Alignment using BWA to mouse assembly 9 (UCSC 2009).
The processed data is separated by sample barcode and aligned using Tophat version 2.0.10 (Kim et. al. 2013) with default settings.
Transcripts are quantified using the Cufflinks suite version 2.2.1 (Trapnell et. al. 2012).
Data are processed through CuffNorm if 50% of the reads align and there are at least 100,000 aligned pairs per sample. This filtering is done to ensure the quality of the normalization step.
Genome_build: Mouse assembly 9 (UCSC 2009)
Supplementary_files_format_and_content: txt file with gene count from CuffNorm

source_name: PP2Aa deficient B cells

extract_protocol:
Peritoneal cells were collected by lavage with PBS.  1x10E6 cells were dissolved in RLT buffer (Qiagen).  Total RNA was isolated by Qiagen RNAeasy Micro kit.
Illumina SmartSeq2 low-input RNA-seq

treatment_protocol: Cells were extracted from 8 week-old C57BL/6 or PP2Aa-deficient  mice by peritoneal lavage

value: 8 weeks

value: spleen

value: B-cells


title: PP2Aa deficient B cells [000008518869_C04]


title: 3mo_skM_WT_3

value: WT


title: WT B cells [000008518869_C01]

source_name: WT B cells

value: wild type


title: 10mo_fat_WT_4


title: WT B cells [000008518869_B11]


title: WT B cells [000008518869_B12]


title: PP2Aa deficient B cells [000008518869_C02]


title: splenocytes, RT3

city: Tsukuba

first: Mamiko

last: Sakata-Yanagimoto

state: Ibaraki

address: 1-1-1 Tennodai

department: Hematology

country: Japan

institute: University of Tsukuba

data_processing:
CLC Genomics Workbench version 9.5.1 (Quigen, Hilden, Germany) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome
Reads Per Kilobase of exon per Megabase of library size (RPKM) values were estimated for each gene and filtered by Empericial Analysis of Digital Gene Expression tool.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: spleen

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen, Holden, Germany) with DNase I (BD Biosciences, CA, USA) following the manufacture's protocol.
Libraries were made from 150 ng of total RNA by TrueSeq RNA Sample Preparation v2 LS kit (Illumina, CA, USA) following the manufacture's protocol.

treatment_protocol: Mouse CD4+ splenocytes were sorted by BD FACS Aria II (BD Biosciences, CA, USA)

value: splenocyte

value: RT


title: splenocytes, RT2


title: 10mo_fat_HL1002P_2


title: splenocytes, RT1


title: 10mo_fat_WT_2


title: 10mo_fat_WT_1


title: splenocytes, WT4


title: Adam10_Het_p4_Rep2

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

description: processed data file: p4_Adam10_KO_deseq2.xlsx

data_processing:
Reads were aligned to mm10 using Hisat2 (2.1.0).
Raw reads obtained from bam files using featureCounts and mm10 annotation file from Ensembl (Mus_musculus.GRCm38.94.gtf).
DESeq2 package in R was used to determine differentially expressed genes between samples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_deseq2.xlsx: Differential gene expression analysis

source_name: Post natal day 4 mouse keratinocytes

extract_protocol:
Zymoresearch RNA Extraction Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Primary keratinocytes

tag: marker


title: 10mo_fat_HH_2


title: Adam10_Hom_p4_Rep1


title: Adam10_Het_p4_Rep1


title: Adam10_Hom_p4_Rep2


title: splenocytes, WT3


title: Control_WT_Rep1


title: sgAjuba_p4_Rep2

description: processed data file: p4_sgAjuba_deseq2.xlsx


title: 10mo_skM_HH_3


title: 10mo_fat_HL1002P_1


title: Control_for_Ajuba_p4_Rep2


title: splenocytes, WT2


title: sgAjuba_p4_Rep1


title: 10mo_skM_HH_2


title: sgAdam10_p4_Rep2

description: processed data file: p4_sgAdam10_deseq2.xlsx


title: sgAdam10_p4_Rep1


title: 10mo_skM_HH_1


title: Control_for_Ajuba_p4_Rep1


title: Control_sgLacZ_p4_Rep2


title: 10mo_skM_HL1002P_3


title: splenocytes, WT1


title: Control_WT_Rep2


title: 10mo_skM_HL1002P_4


title: 10mo_skM_HL1002P_2


title: Control_sgLacZ_p4_Rep1


title: Het_V65M_5367

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the standard Ensembl gtf annotation and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and human-Mfn2 cDNA), using tophat v2.1.1.
htseq-count (authored by Simon Anders) was used in union mode to assign tophat-aligned reads to gene entries in the standard Ensembl gtf annotation supplied with the bowtie2 iGenome.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Genome_build: GRCm38 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes htseq-count values for each gene

source_name: heart, left ventricle

extract_protocol:
Hearts were removed and ventricular apexes were dissected into RNAlater, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.
non-strand-specific, single-end RNA-Seq

value: Heterozygote, Kcnj8[V65M] cohort

value: heart, left ventricle

value: Male


title: Het_V65M_5307


title: Het_V65M_5302


title: Het_V65M_5769


title: WT_96h_2

first: Andrew

last: Lane

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
ChiLin pipeline 2.0.0 for QC and preprocessing (Qin et al., 2016).
Burrows-Wheeler Aligner (BWA) for read mapping (Li and Durbin, 2009).
Model-based Analysis of ChIP-seq (MACS) for peak calling (Zhang et al., 2008).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: HoxB8_WT_OE_ATAC_counts.xlsx: Excel matrix containing read count analysis values for each peak.

source_name: myeloid cells

extract_protocol:
Nuclei harvested from 100,000 cells per sample. Each sample of the same genotype/timepoint is a biologically independent replicate (n=3 biological replicates).
Direct library construction by the Omni-ATAC protocol, in which cell nuclei were incubated directly with transposase.

value: Myeloid cells

tag: differentiation time


title: WT_0h_3

tag: genotype/variation


title: Het_V65M_5306

tag: age

value: 3 months


title: WT_96h_3

tag: cell type


title: 10mo_skM_WT_4

value: gastrocnemius muscle

value: 129Sve/C57BL/6 mix


title: WT_0h_2


title: 10mo_skM_HL1002P_1

value: 8-10 months


title: WT_V65M_5768

value: Wild-type littermate, Kcnj8[V65M] cohort


title: WT_V65M_5770


title: WT_0h_1


title: WT_96h_1


title: 10mo_skM_WT_3


title: WT_V65M_5301


title: Hom_A478V_6537

value: Homozygote, Abcc9[A478V] cohort


title: WT_V65M_5305


title: OE_96h_3

value: HMGN1 overexpression


title: OE_96h_2


title: 10mo_fat_WT_3

value: fat (IAT)


title: WT_V65M_5304


title: Hom_A478V_6535


title: Hom_A478V_5354


title: 10mo_skM_WT_1

value: WT


title: Hom_A478V_5346


title: OE_96h_1


title: Hom_A478V_5343


title: OE_0h_3


title: Het_A478V_6557

value: Heterozygote, Abcc9[A478V] cohort


title: Het_A478V_5344


title: Het_A478V_5357


title: OE_0h_2


title: OE_0h_1


title: Het_A478V_5316


title: 10mo_skM_WT_2


title: OE2_96h_H3K27me3_60u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_OE_96h.tdf

data_processing:
Demultiplex Illumina NextSeq sequencing libraries using .bcl2fastq2-2.15.0.4.
Demultiplex reads based on barcode at the start of Read1, trim adapter barcode (the provided fastqs are trimmed).
Alignment of fastqs to mm9 using BWA.
Filter improperly paired and collapse duplicated reads from bam file.
Convert to bed files using BEDTools and call peaks using Homer.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: tdf files for IGV visualization.

growth_protocol: HMGN1 over expressing mouse myeloid cells in vitro.

extract_protocol:
Lysis and chromatin digestion with MNase (15 units or 60 units) as described in the Mint-ChIP3 protocol on https://www.protocols.io/view/mint-chip3-a-low-input-chip-seq-protocol-using-mul-wbefaje
T7 adapter ligation, linear amplification, reverse transcription and PCR as described in the Mint-ChIP3 protocol.

treatment_protocol: Over expression of control (WT) or HMGN1 (OE), and induction of differentiation by E2 depletion (0-36-96h).

value: HMGN1 over expression

tag: mnase units

value: Replicate 2


title: OE2_36h_H3K27me3_60u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_OE_36h.tdf

tag: chip antibody


title: ZAP1_ALL_Kang2020

city: St. Louis

first: Yiming

last: Kang

state: MO

address: 1 Brookings Dr

department: Computer Science and Engineering

institute: Washington University in St. Louis

description: Calling Card Assay for in vivo Transcription Factor Binding: a retrotransposon is directed into the genome at loci bound by a given transcription factor

data_processing:
Library strategy: "Calling Card" Assay
Paired-End sequence reads were filtered for presence of Read1 initial 5bp barcode followed by unique 17-mer sequence (AATTCACTACGTCAACA) and Read2 initial 8bp barcode.
The remaining sequence after the 17-mer sequence of Read1 was mapped to the 2008 S. cerevisiae reference genome (R-61-1-1) sequence using NovoAlign with default parameter settings.
Insertion position and number of reads mapping to each insertion are reported in gnashy file.
Genome_build: S288C-R61
Supplementary_files_format_and_content: gnashy: a table indicating genomic position of the retrotransposon insertion and number of reads aligning to that position

growth_protocol: The indicated yeast strain was co-transformed with a plasmid carrying the indicated transcription factor fused at the C-terminus to Sir4p and a plasmid carrying a barcoded HIS3-carrying Ty5 retrotransposon under the control of the GAL1/10 promoter.  A single clone was then incubated for 3 days on selective media with galactose as the carbon source.  Plates were then sequentially replica-plated to YPD (2 days), followed by SC-HIS with 5'FOA agar plates (3 days).

extract_protocol:
Genomic DNA was extracted from all cells using standard glass bead-beating, phenol chloroform isoamyl alcohol purification, and NH4Ac ethanol protocol.
Genomc DNA was digested in three separate restriction enzyme digests (HinPI1, HpaII, and Taq-alphaI), self-ligated with T4 DNA ligase, and an inverse PCR reaction was performed to amplify genomic DNA downstream of each inserted Ty5 retrotransposon.
"Calling Card" Assay to identify in vivo genomic targets of DNA-binding factors

treatment_protocol: "Calling Card" Assay performed as previously described: 1. "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins." Wang H, Mayhew D, Chen X, Johnston M, Mitra RD.  Genome Research, 2011, May 21(5):748-55. PMID 21471402. 2. "Calling Card Analysis in Budding Yeast." Mayhew D, Mitra RD.  Cold Spring Harbor Protocols, 2016, Feb 1, 2016(2). PMID 26832687.

tag: transcription factor


title: SFP1_ALL_Kang2020


title: WT_A478V_5316

value: Wild-type littermate, Abcc9[A478V] cohort

tag: tissue


title: WT_A478V_5354

tag: strain


title: LEU3_ALL_Kang2020


title: WT_A478V_5355


title: WT_A478V_6555


title: OE2_0h_H3K27me3_60u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_OE_0h.tdf

tag: replicate


title: INO4_ALL_Kang2020


title: Het_A478V_6558


title: OE1_96h_H3K27me3_60u

value: Replicate 1


title: WT_A478V_6556

value: heart, left ventricle


title: OE1_36h_H3K27me3_60u


title: WT2_96h_H3K27me3_60u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_WT_96h.tdf

value: Control


title: OE1_0h_H3K27me3_60u

value: Myeloid cells


title: WT2_0h_H3K27me3_60u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_WT_0h.tdf


title: ScMacs 37 days after nerve crush SnMac_D37_1

description:
ScMacs 37 days after nerve crush
ScMacs 37 days after nerve crush

hyb_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using limma Bioconductor. Normalisation was done by RMA.

source_name: Sciatic Nerve


title: seedling, rpoTmp in dark, biological repl3

city: Hannover

first: Thomas

last: Pflannschmidt

address: Herrenhäuser Straße 2

institute: Leibniz-Universität Hannover

description:
Arabidopsis seedlings day 4 in dark; with proplastids during skotomorphogenesis
rpoTmp dark 3

hyb_protocol: ssDNA were hybridized on an Affymetrix Chip, Arabidopsis Gene 1.0 ST Array as described in the manual (GeneChip® WT Terminal  Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, Rev. 7, Affymetrix).

scan_protocol: Standard Affyemtrix protocol

data_processing: The data were analyzed with RobiNA (1.2.4_build656) using default analysis settings and normalization method RMA with p-value correction after Benjamini-Hochberg method.

source_name: Arabidopsis seedlings day 4 in dark

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Terminal  Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, Rev. 7, Affymetrix).

growth_protocol: Seeds were surface-sterilized (Ethanol) and spread on MS agar plates with 1% sucrose and powdered charcoal (4 ml / 1 l MS-medium).  The plates were kept for 72 h at 4°C in darkness and were exposed to light for 6h to induce germination. Plants grow at 21°C.

extract_protocol: Total RNA from seedlings was isolated using and RNeasy Plant Mini Kit (Qiagen) with on-column DNase I (Qiagen) treatment.

treatment_protocol: Plants grow under continuous light at 150 µmol of photons m-2 s-1 for 5 days and in darkness for 4 days respectively.

value: whole seedling

value: rpoTmp mutant

value: dark

value: 4 days


title: WT2_36h_H3K27me3_60u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_WT_36h.tdf


title: WT1_96h_H3K27me3_60u


title: MHCII low scMacs 10 days after nerve crush SnMac_MHCII_lo_D10_3

description:
MHCII low scMacs 10 days after nerve crush
MHCII low scMacs 10 days after nerve crush

label_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.


title: seedling, rpoTmp in dark, biological repl2

description:
Arabidopsis seedlings day 4 in dark; with proplastids during skotomorphogenesis
rpoTmp dark 2


title: MHCII high scMacs 10 days after nerve crush SnMac_MHCII_hi_D10_1

description:
MHCII high scMacs 10 days after nerve crush
MHCII high scMacs 10 days after nerve crush

growth_protocol: All Methods listed in Ydens et al.  Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.


title: H1299__spautin_24H_rep3

city: Hradec Kralove

first: Lucie

last: Cechakova

address: Trebesska 1575

department: Department of Radiobiology

country: Czech Republic

institute: University of Defense in Brno

hyb_protocol: Hybridization of the labelled samples to microarrays was performed using Gene Expression Hybridization Kit (Agilent). Two samples (each 900 ng), one labelled Cy3-CTP and the other Cy5-CTP, were hybridized to one microarray. Hybridization was carried out for 17 hours at 65 ° C in a rotating hybridization oven (Agilent). The microarray slide washes were performed with the Gene Expression Wash Pack (Agilent) kit on the following day.

scan_protocol: The slides were then scanned using a GenePix 4000B scanner (Molecular Devices) at a resolution of 5 μm.

data_processing: Data were processed in R. Each channel was treated as a separate sample. Data were normalized with quantile normalization and color batch effects were removed. Probes with flags in 15 of 32 slides were removed from the analysis. The experimental groups were compared with limma package with linear regression with Empirical Bayes correction. P values were adjusted for multiple testing with Benjamini-Hochberg method.

source_name: H1299, spautin, 24H

label_protocol: Synthesis of aRNA was performed from a total template RNA (500 ng) using Low Input Quick Amp Labeling Kit (Agilent) with Cy3-CTP and Cy5-CTP (GE Healthcare) fluorescence nucleotides. The labelled aRNA was purified by RNeasy Mini Kit (Qiagen) and measured spectroscopically (NanoDrop OneC, ThermoFisher).

growth_protocol: Non-small cell lung carcinoma cells (H1299) were obtained from the American Type Culture Collections (Manassas, VA, USA). The cells were cultured at 37°C in a humidified incubator under a controlled 5% CO2 atmosphere and maintained in RPMI medium 1640 (Gibco, Paisley, UK) supplemented with 10% fetal bovine serum, 150 UI/ml penicillin and 50 mg/ml streptomycin (all from Sigma-Aldrich, St. Louis, MO, USA). The culture was divided twice per week by dilution to a concentration of 2x105 cells/10ml. The cell line in the maximal range of up to 15 passages was used for this study.

extract_protocol: Total mRNA was extracted from the samples with RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. Quantity of the RNA was measured spectrophotometrically with NanoDrop OneC. Quality of the RNA was evaluated with Agilent Bioanalyzer 2100 (Agilent). The samples had RIN 9.2 or above.

treatment_protocol: The cells were treated by autophagy inhibitors Lys05 (a kind gift from Dr. Amaravadi, Pennsylvania University, Philadelphia, USA) and Spautin-1 (Calbiochem, Ukraine) in various concentrations of 2, 5 and 10 μM and Baf in 15 nM concentration.  Inhibitors were added to the cells 1 hour prior to irradiation. The cells in either flask, tube, or 6-well plate, were irradiated using a 60Co gamma-ray source with a dose-rate of 0.44 Gy.min-1. After irradiation, the cells were transferred back into an incubator and cultivated further for the prescribed time according to the particular experiment.

tag: cell line

value: spautin

tag: time


title: H1299__2Gy_irradiated_Lys05_48H_rep3

source_name: H1299, 2Gy_irradiated_Lys05, 48H


title: ScMacs 37 days after nerve crush SnMac_D37_2


title: seedling, rpoTmp in dark, biological repl1

description:
Arabidopsis seedlings day 4 in dark; with proplastids during skotomorphogenesis
rpoTmp dark 1

tag: genotype


title: H1299__2Gy_irradiated_control_48H_rep2

source_name: H1299, 2Gy_irradiated_control, 48H

tag: treatment


title: MHCII high scMacs 10 days after nerve crush SnMac_MHCII_hi_D10_3


title: MHCII low scMacs 10 days after nerve crush SnMac_MHCII_lo_D10_1


title: H1299__2Gy_irradiated_spautin_48H_rep3

source_name: H1299, 2Gy_irradiated_spautin, 48H


title: MHCII high scMacs 5 days after nerve crush ScMac_MHCII_hi_D5_3

description:
MHCII high scMacs 5 days after nerve crush
MHCII high scMacs 5 days after nerve crush


title: MHCII high scMacs 10 days after nerve crush SnMac_MHCII_hi_D10_4


title: MHCII high scMacs 5 days after nerve crush ScMac_MHCII_hi_D5_2


title: MHCII high scMacs 10 days after nerve crush SnMac_MHCII_hi_D10_2


title: MHCII low scMacs 10 days after nerve crush SnMac_MHCII_lo_D10_2


title: MHCII low scMacs 5 days after nerve crush SnMac_MHCII_lo_D5_3

description:
MHCII low scMacs 5 days after nerve crush
MHCII low scMacs 5 days after nerve crush


title: ScMacs 37 days after nerve crush SnMac_D37_3


title: WT1_0h_H3K27me3_60u


title: H1299__2Gy_irradiated_spautin_48H_rep1


title: OE2_96h_H3K27ac_60u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_OE_96h.tdf


title: MHCII high scMacs 5 days after nerve crush ScMac_MHCII_hi_D5_1


title: OE2_36h_H3K27ac_60u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_OE_36h.tdf


title: MHCII low scMacs 1.5 days after nerve crush SnMac_MHCII_lo_D1.5_3

description:
MHCII low scMacs 1.5 days after nerve crush
MHCII low scMacs 1.5 days after nerve crush


title: H1299__Lys05_48H_rep2


title: H1299__2Gy_irradiated_Lys05_48H_rep1


title: MHCII low scMacs 1.5 days after nerve crush SnMac_MHCII_lo_D1.5_2


title: H1299__control_48H_rep3

source_name: H1299, control, 48H

value: control


title: MHCII low scMacs 1.5 days after nerve crush SnMac_MHCII_lo_D1.5_1


title: MHCII high scMacs 1.5 days after nerve crush SnMac_MHCII_hi_D1.5_2

description:
MHCII high scMacs 1.5 days after nerve crush
MHCII high scMacs 1.5 days after nerve crush


title: MHCII high scMacs 1.5 days after nerve crush SnMac_MHCII_hi_D1.5_3


title: Steady state scMacs SnMac_StSt_3

description:
Steady state scMacs
Steady state scMacs


title: MHCII high scMacs 1.5 days after nerve crush SnMac_MHCII_hi_D1.5_1


title: BAFkd_st_2

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

hyb_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization

data_processing: RMA

source_name: 3T3 fibroblasts with Brg1/Brm knock-down, 1hr after TNF-alpha treatment

growth_protocol: Subconfluent growth in cell culture

extract_protocol: Qiagen RNeasy

treatment_protocol: 5ng/ml mouse TNF-alpha for 1hr

tag: tnfa

value: yes

tag: bafkd


title: OE2_0h_H3K27ac_60u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_OE_0h.tdf


title: OE1_36h_H3K27ac_60u


title: OE1_0h_H3K27ac_60u


title: BAFkd_st_1

scan_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization


title: WT2_96h_H3K27ac_60u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_WT_96h.tdf


title: Steady state scMacs SnMac_StSt_2

description:
Steady state scMacs
Steady state scMacs


title: H1299__spautin_48H_rep1

source_name: H1299, spautin, 48H


title: BAFkd_st_3

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization


title: H1299__2Gy_irradiated_spautin_24H_rep2

source_name: H1299, 2Gy_irradiated_spautin, 24H


title: DPY27 HiChIP long reads

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

description: DPY27 HiChIP long reads

data_processing:
Library strategy: HiChIP
Reads were trimmed and then processed using juicer.
Supplementary_files_format_and_content: .hic containing interactions

organism: Caenorhabditis elegans

source_name: hermaphordite late embryos

growth_protocol: N2 strain was cultured under standard conditions on NG agar plates with E. coli (OP50) as a food source.

extract_protocol:
Embryos were crosslinked with 1.1% formaldehyde. Nuclei were isolate in a dounce and recrosslinked with 1% formaldehyde for 10 minutes.Chromatin was digested by DpnII, filled in with biotin-dCTP, and ligated. DNA was then isolated for Hi-C library prep. For HiChIP, ligated chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-DPY27 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation.
Libraries were constructed using the standard protocol or using a Tn5 library prepartion protocol. Genomic fragments were end repaired, A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). For Tn5 protocol, samples were incubated with Tn5 transposase in the presence of adaptors. Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

tag: developmental stage

value: late embryos

tag: Sex

value: hermaphrodite


title: control_st_1

source_name: 3T3 fibroblasts, 1hr after TNF-alpha treatment

value: no


title: H1299__2Gy_irradiated_control_24H_rep3

source_name: H1299, 2Gy_irradiated_control, 24H


title: WT2_36h_H3K27ac_60u

city: Boston

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_WT_36h.tdf

tag: genotype/variation

tag: differentiation time


title: Steady state scMacs SnMac_StSt_1

description:
Steady state scMacs
Steady state scMacs


title: control_ns_3

source_name: 3T3 fibroblasts


title: H1299__control_48H_rep1


title: H1299__2Gy_irradiated_control_24H_rep1


title: H1299__2Gy_irradiated_Lys05_24H_rep2

source_name: H1299, 2Gy_irradiated_Lys05, 24H


title: control_ns_1


title: WT2_0h_H3K27ac_60u

description:
H3K27ac_ChIP-seq
processed data file: H3K27ac_WT_0h.tdf

tag: cell type


title: control_st_2


title: control_ns_2


title: WT1_96h_H3K27ac_60u

tag: mnase units


title: astrocytes, T05-Quinpirole2

city: Nanjing

first: Yao

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing University of Chinese medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: GRCm38
Supplementary_files_format_and_content: comma seprated gene expression file

source_name: astrocyte seperated from mice brain

extract_protocol:
Astrocytes were seperated from mice brain and RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®UltraTM RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: brain

tag: age

value: 3 month

value: wild type

value: Quinpirole


title: WT1_36h_H3K27ac_60u

source_name: myeloid cells

tag: chip antibody

value: Replicate 1


title: astrocytes, T06-Quinpirole3

tag: tissue


title: MHCII low scMacs 5 days after nerve crush SnMac_MHCII_lo_D5_2

source_name: Sciatic Nerve

tag: strain


title: astrocytes, T04-Quinpirole1


title: H1299__Lys05_24H_rep1


title: H1299__control_24H_rep2

source_name: H1299, control, 24H


title: H1299__Lys05_24H_rep3


title: H1299__2Gy_irradiated_Lys05_1H_rep3

source_name: H1299, 2Gy_irradiated_Lys05, 1H


title: WT1_0h_H3K27ac_60u

value: Control

tag: replicate


title: H1299__2Gy_irradiated_control_1H_rep2

source_name: H1299, 2Gy_irradiated_control, 1H

tag: cell line


title: astrocytes, T03-Mock3

value: Mock


title: H1299__spautin_24H_rep2

source_name: H1299, spautin, 24H

tag: time


title: OE2_96h_H3_60u

description:
H3_ChIP-seq
processed data file: H3_OE_96h.tdf

value: Myeloid cells

value: HMGN1 over expression

value: Replicate 2


title: astrocytes, T02-Mock2

tag: genotype


title: astrocytes, T01-Mock1

tag: treatment


title: fibro_control_st_rep1

data_processing:
alignment to mm9 reference genome (bowtie v 2 -a -m 5 --tryhard)
removal of duplicates (reads that mapped to the exact same genomic location were eliminated if there were significantly more than expected based on the local read density in a range of ±2bp at a p-value of 0.05)
selection of reads mapping to refGene promoters ±10kb (intersectBed)
normalization (read counts in overlapping 60bp windows at 10bp intervals were normalized by the local read density in the surrounding 600bp window)
mapping around promoters (mean normalized signal in 3 adjacent bins was calculated at 10bp intervals surrounding and centred-on refGene promoters ±1kb)
Genome_build: mm9
Supplementary_files_format_and_content: matrix files = gzip-compressed files of comma-separated values, representing normalized nucleosome occupancy at 10bp intervals surrounding refGene promoters, beginning at position -1000bp and ending at position +1000bp relative to the direction of transcription; promoter_data.bed file = list of refGene promoters used in BED+4 format, score indicates ChIP-MNase coverage level, additional fields indicate FPKM expression in DCs & fibroblasts, and log2-fold stimulus-driven activatio of inducible genes n in DCs & fibroblasts; example.r = example R script using matrix files & promoter_data.bed file to analyse nucleosome occupancies at distinct classes of genes.

extract_protocol:
Cells were fixed for 10minutes with 4% formaldehyde and used to prepare chromatin.  Chrromatin was fragmented to approximately 5-10kb fragments and used for ChIP.  ChIP-enriched chromatin was then digested using micrococcal nuclease (MNase) to generate approximately 80% mononucleosomal fragments.
NebNext Ultra II DNA library kit

value: 3T3 fibroblast

value: TNFa 5ng/ml

tag: chip target


title: fibro_control_ns_rep2

tag: bafkd


title: fibro_st_S7P_ChIP-MNase_rep2

value: RNA pol II S7P


title: OE2_36h_H3_60u

description:
H3_ChIP-seq
processed data file: H3_OE_36h.tdf


title: H1299__2Gy_irradiated_spautin_1H_rep3

source_name: H1299, 2Gy_irradiated_spautin, 1H


title: fibro_st_S7P_ChIP-MNase_rep1


title: fibro_BAFkd_st_rep2

value: yes


title: OE2_0h_H3_60u

description:
H3_ChIP-seq
processed data file: H3_OE_0h.tdf


title: fibro_control_ns_rep1


title: fibro_BAFkd_st_rep1


title: fibro_st_reps1+2


title: H1299__Lys05_1H_rep2


title: H1299__2Gy_irradiated_spautin_1H_rep1


title: OE1_96h_H3_60u


title: DC_st_reps1+2

source_name: dendritic cells, 1hr after LPS treatment

value: dendritic cells

value: LPS 100ng/ml


title: WT2_36h_H3_60u

description:
H3_ChIP-seq
processed data file: H3_WT_36h.tdf


title: control_st_3

tag: tnfa

value: no


title: DC_ns_reps1+2

source_name: dendritic cells


title: H1299__control_1H_rep3

source_name: H1299, control, 1H

value: control


title: fibro_BAFkd_ns_rep1

source_name: 3T3 fibroblasts with Brg1/Brm knock-down


title: H1299__2Gy_irradiated_Lys05_1H_rep1


title: EphB2- sorted P6 intestinal IκBa KO cells rep 2

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads. Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using bowtie2 with default parameters
htseq software was used to estimate the raw gene counts
DESeq2 R package was run to infer differentially expressed genes accross samples
Genome_build: mm10
Supplementary_files_format_and_content: txt files are generated from htseq and DESeq2 results using R

growth_protocol: Starting material was freshly isolated intestinal cells, which were trypsinized and filtered to obtain single-cell suspension. Then sorted by their EphB2 expression [APC mouse anti-human EphB2 antibody, BD Pharmingen 564699]

extract_protocol:
Direct RNA isolation with RNeasy Mini Kit [Qiagen Ref. 74004]
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

value: intestine

value: IkBa KO

value: EphB2- sorted cells


title: fibro_BAFkd_ns_rep2


title: H1299__spautin_1H_rep1

source_name: H1299, spautin, 1H

value: spautin


title: WT1_96h_H3_60u

description:
H3_ChIP-seq
processed data file: H3_WT_96h.tdf

value: Control

value: Replicate 1


title: OE1_0h_H3_60u

value: Myeloid cells


title: fibro_control_st_rep2

source_name: 3T3 fibroblasts, 1hr after TNF-alpha treatment


title: H1299__Lys05_48H_rep3


title: EphB2+ sorted P6 intestinal IκBa KO cells rep 2

value: EphB2+ sorted cells


title: WT2_96h_H3_60u

value: Replicate 2


title: fibro_ns_reps1+2

value: 3T3 fibroblast


title: OE1_36h_H3_60u

value: HMGN1 over expression


title: EphB2+ sorted P6 intestinal IκBa KO cells rep 3


title: WT2_0h_H3_60u

description:
H3_ChIP-seq
processed data file: H3_WT_0h.tdf


title: EphB2- sorted P6 intestinal IκBa KO cells rep 1


title: H1299__Lys05_1H_rep3


title: EphB2- sorted P6 intestinal WT cells rep 1

value: wild type


title: EphB2- sorted P6 intestinal WT cells rep 2


title: WT1_36h_H3_60u


title: EphB2+ sorted P6 intestinal WT cells rep1


title: EphB2+ sorted P6 intestinal WT cells rep2


title: Input from P6 WT intestinal cells [INWT]

description: No use of DSP crosslink

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC software was used to summarize the quality of the sequenced reads
Reads were aligned to the mm10 genome assembly using Bowtie2 (see materials and methods main paper)
htseq software was used to estimate the raw gene counts
peaks were called using MACS2 with the following setting: ChIP threshold FDR (0.1)
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph and bigWig files are generated from MACS2 peak calling output using bamtools

source_name: Intestine

extract_protocol:
Cells were crosslinked with 0.5% formaldehyde and lysated. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. DNA purification with GFX Kit [GE Healthcare Life Sciences Ref.28-9034-71]
Samples were digested with 0.1% collagenase and single-cell suspension was stained as described. Different subpopulations were directly sorted in a total volume of 10  ml of reaction buffer and processed for obtaining cDNA following manufacture’s protocol. cDNA amplification was performed by Long Distance PCR (LD-PCR) and the PCR-amplified cDNA purified by immobilization on AMPure XP beads (Agencourt AMPure XP kit). Samples were analyzed with Agilent High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626). Covaris shearing was used for Illumina Low input sample preparation and Double last bead purification was performed to remove fragments below 200 bp. Next, samples were used to generate an Illumina sequencing library by NEBNext Ultra protocol following kit instructions. After PCR amplification of the library, the quality was checked on a Bioanalyzer and total cDNA was sequenced using an Illumina HiSeq 2000 sequencer.

treatment_protocol: Starting material was directly extracted P6 intestines, which were frozen and smashed with liquid nitrogen in ceramic mortar and pestle.

value: Intestine


title: OE2_96h_H3K27me3_15u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_OE_96h.tdf


title: OE2_36h_H3K27me3_15u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_OE_36h.tdf


title: WT1_0h_H3_60u


title: Input from P6 IkBa KO intestinal cells [INKO]

description: No use of DSP crosslink


title: EphB2+ sorted P6 intestinal IκBa KO cells rep 1


title: H3K27me3 ChIP-seq from P6 IkBa KO intestinal cells [K9H3]

description: No use of DSP crosslink

value: H3K27me, Millipore #07-449


title: H3K27me3 ChIP-seq from P6 WT intestinal cells [W2H3]

description: No use of DSP crosslink


title: H1299__2Gy_irradiated_control_48H_rep3

source_name: H1299, 2Gy_irradiated_control, 48H


title: H3K27me3 ChIP-seq from P6 IkBa KO intestinal cells [K8H3]

description: No use of DSP crosslink


title: OE2_0h_H3K27me3_15u

description:
H3K27me3_ChIP-seq
processed data file: H3K27me3_OE_0h.tdf


title: H1299__2Gy_irradiated_spautin_48H_rep2

source_name: H1299, 2Gy_irradiated_spautin, 48H


title: IkBa ChIP-seq from P6 WT intestinal cells [W5DI]

description: Cells treated with DSP crosslink

value: IkappaBalpha, Abcam ab32518


title: IkBa ChIP-seq from P6 WT intestinal cells [W5CI]

description: No use of DSP crosslink


title: H1299__control_1H_rep1


title: OE1_36h_H3K27me3_15u


title: H1299__spautin_48H_rep3

source_name: H1299, spautin, 48H


title: H1299__2Gy_irradiated_control_48H_rep1


title: OE1_96h_H3K27me3_15u

source_name: myeloid cells