title: PBMC_53

source_name: Peripheral blood mononuclear cells extracted from a myelofibrosis patient UPN#585953

value: human CD45


title: 1 spleen GFP- Treg

status: Public on Sep 09 2021

type: SRA

city: Hannover

first: Christoph

last: Binz

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Immunologie

country: Germany

institute: Medizinische Hochschule Hannover

library_source: transcriptomic

data_processing:
Fastq files were obtained after demultiplexing, basecalling and quality filtering during the sequencing run on a MiSeq machine.
Data were aligned to the IMGT database from 22.05.2018 using MiXCR (Bolotin, D. A., S. Poslavsky, I. Mitrophanov, M. Shugay, I. Z. Mamedov, E. V. Putintseva, and D. M. Chudakov. 2015. MiXCR: software for comprehensive adaptive immunity profiling. Nature methods 12: 380-381.)
Afterwards the samples were downsampled (Thymus samples to 20000 and spleen samples to 30000) using VDJTOOLS (Shugay, M., D. V. Bagaev, M. A. Turchaninova, D. A. Bolotin, O. V. Britanova, E. V. Putintseva, M. V. Pogorelyy, V. I. Nazarov, I. V. Zvyagin, V. I. Kirgizova, K. I. Kirgizov, E. V. Skorobogatova, and D. M. Chudakov. 2015. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput. Biol. 11: e1004503.).
Supplementary_files_format_and_content: VDJTOOLS.txt files were generated using MiXCR.

molecule: total RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
The desired populations were sorted and the RNA was isolated employing the "RNeasy Plus Micro kit" from Qiagen (Hilden, Germany).
The cDNA was generated by employing ingredients from the TAKARA cDNA Synthesis Kit (TAKARA Bio Europe, France) according to an in-house modified protocol based on the manufacturer’s protocol. The DNA-amplicons for the Illumina sequencing were generated by using Advantage 2 PCR Kit (TAKARA Bio Europe, France). The DNA was then purified using Qiaquick Gel Extraction Kit (Qiagen Hilden, Germany). The purified product of each sample was indexed by an indexing-PCR with Nextera-Primers. Finally a pool of the samples was sequenced employing Illumina MiSeq v2 Reagent Kit (Illumina Inc, San Diego, CA, USA).

tag: strain

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)

tag: population

value: CD4SP RAGGFP-CD25+Foxp3hCD2+

tag: treatment

value: PBS


title: adherent_#1

city: Tokyo

first: Takahiko

last: Murayama

address: 4-6-1 Shirokanedai Minato-ku

country: Japan

institute: University of Tokyo

data_processing:
Sequenced reads were mapped to hg19 whole genome using Tophat version 2.0.10
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a Cufflinks version 2.1.1 following the protocol from Trapnell et al.,Nature Protocols, 2012.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

organism: Homo sapiens

source_name: clinical breast cancer

growth_protocol: Spheres were grown in sphere culture medium (SCM) which consisted of serum-free Dulbecco’s modified Eagle’s Medium: Nutrient Mixture F-12 (DMEM/F-12) medium (GIBCO) supplemented with 20 ng/mL EGF (Millipore), 20 ng/mL bFGF (PeproTech), B27 (GIBCO) and heparin (Stem Cell Technologies). For adherent culture, we used STEMCELL Epicult-B medium (Cat#ST-05601)

extract_protocol:
RNA was collected and amplified using Takara Nucleospin RNA XS Kit (Cat#740902) and Clontech SMARTER Ultra low RNA for Illumina Kit (Cat#634822). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth method

value: adherent

tag: tissue

value: breast cancer

tag: cancer subtype

value: triple negative


title: ADH_2; Sample_6C

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

data_processing:
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on the ENSEMBL reference genomes specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes GRCh38 and GRCm38 respectively using the splice aware short read aligner STAR (v2.5.1b) using PE read input with default options and –sjdbGTFfile pointing to the ENSEMBL .gtf annotation file corresponding to the reference genome file and –outFilterMultimapNmax set to 1.
Species specific read pairs were assigned to known features and counted using featurecounts from the Subread package (v1.5.2). Annotated genes were obtained from the Ensembl ftp repository (Homo_sapiens.GRCh38.87.gtf and Mus_musculus.GRCm38.87.gtf).
Data was later interrogated for differentially expressed genes using the Bioconductor package EdgeR (v3.22.5).
Genome_build: GRCh38.87 and GRCm38.87 were downloaded from the ENSEMBL ftp repository
Supplementary_files_format_and_content: GRCh38_featurecounts_count_table.csv: RAW read count table per feature for all samples with human content after species-based separation of reads of human origin and alignment to GRCh38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.
Supplementary_files_format_and_content: GRCm38_featurecounts_count_table.csv: RAW read count table per feature for all samples with mouse content after species-based separation of reads of murine origin and alignment to GRCm38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: MS-5, Rec-1 (adherent fraction)

growth_protocol: MS-5 cells and Rec-1 cells mono- or co-cultured in αMEM-glutamax (Gibco) supplemented with 10% H.I. FBS (Gibco), 2mM sodium pyruvate, 100U/mL penicillin and 100µg/mL streptomycin (Gibco). All cells were cultivated in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) with QIAshredders following the protocol supplied by the manufacturer.
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

treatment_protocol: 5x10^5 MS-5 stromal cells were seeded 24h in advance to 10cm dishes and 5x10^6 Rec-1 cells were subsequently added. RNA was extracted following 24h of incubation at 37 degrees 5% CO2.

tag: cultivation

value: co-culture of two cell lines

tag: cell type

value: mouse bone marrow derived stromal and human mantle cell lymphoma cell line

tag: cell line

value: MS-5, Rec-1 (adherent fraction)


title: KELLY, BPS2 3

city: Parkville

first: Jack

middle: Aatto Laasonen

last: Cooper

state: Victoria

address: 49 College Crescent

country: Australia

institute: University of Melbourne

data_processing:
fastq files were quality checked using FastQC (0.11.7)
fastq files were quantified against an Ensembl GRCh38 reference genome using salmon (0.8.2)
Salmon quants were aggregated into read counts and imported into R with tximport (1.4.0)
Read counts were normalized using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: "normalized_counts.csv" contains the read counts for each of the 12 samples, normalized in DESeq2.

source_name: KELLY BPS2

growth_protocol: KELLY cell lines were plated, suspended in 10% fetal bovine serum (FBS) and 100 U/mL penicillin streptomycin RPMI containing media, into 6-well plates for 24 hours.

extract_protocol:
Each 6-well was treated with 500 µL of Nucleozol, and left at room temperature (RT) for 10 minutes. Samples were transferred to 1.5 mL tubes, then heated and vortexed at the same time, at 65ºC and 1000 rpm for 10 minutes. Each sample was treated with 200 µL RNase-free water, then again heated and vortexed at the same time, at 65ºC and 1000 rpm for 10 minutes. Samples were left to incubate at RT for  10 minutes, and then centrifuged at 14,000 x g for 15 minutes. Then, 500 µL supernatant of each sample was transferred to a new tube, and treated with isopropanol. After inverting 4-6 times, samples were left at RT for 10 minutes, then centrifuged (14,000 x g) for 10 minutes. A resulting RNA pellet was then washed twice with 70% ethanol (600 uL each time, 8,000 x g for 1.5 minutes) and re-suspended in 30 uL RNase-free water.
RNA extractions were conducted as per manufacturer's instructions, with an incorporated heating and vortexing step.  Samples were sent to the Australian Genome Research Facility (AGRF, Perth and Melbourne, Australia) for whole transcriptome library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) and ribosomal RNA depletion with the Ribo-Zero-Gold kit (Illumina, CA, USA).
Sequencing as performed using an Illumina HiSeq 2500 (Illumina, CA, USA) to generate 100 base pair single end reads, resulting in an average 25 million reads per sample. Raw sequencing files were quality checked using FastQC (0.11.7), with all files passing

treatment_protocol: Media was replaced to 4% FBS-RPMI media, and forward transfection of 50 nM oligonucleotide:leash lipoplexes were conducted. After 48 hours of incubation at 37ºC and 5% carbon dioxide levels, cells were lysed using the Nucleozol reagent from Machery-Nagel ™.

value: KELLY

value: Immortalized neuroblastoma cells

value: BPS2 oligonucleotide


title: WT_Rep3

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

department: UMR 7622 LBD

country: France

institute: Sorbonne Université

description: RNA-seq

data_processing:
trimming using trim_galore with options “--paired --length 35”
mapping to the TAIR10 genome using STAR with options “--alignIntronMin 20 --alignIntronMax 100000 --outFilterMultimapNmax 20 --outMultimapperOrder Random --outFilterMismatchNmax 8 --outSAMtype BAM SortedByCoordinate --outSAMmultNmax 1 --alignMatesGapMax 10000”.
Browser tracks were generated using deeptools function bamCoverage with options “--binSize 10 --normalizeUsing RPKM”.
Read counts were retrieved using htseq-count with options "-s reverse --nonunique all -f bam -i ID -r pos -t locus -a 0"
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

organism: Arabidopsis thaliana

source_name: 7-day-old Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were sterilized with a solution of 75% sodium hypochlorite and 0.1% Tween-20 and stratified at 4°C during 3 days in darkness.  Seedlings were grown in Murashige and Skoog (MS) medium.

extract_protocol:
RNA extraction was performed with FastPrep Plant Total RNA-purification kit, with DNAse treament
DNBseq

treatment_protocol: Light: white light (100 umol m-2 s-1) in a 16-h light/8-h dark period. Dark: continuous darkness.

tag: plant line

value: WT

value: light

tag: sucrose


title: sphere_#1

value: sphere


title: KELLY, BPS2 4


title: ADH_3; Sample_7C


title: ADH_1; Sample_5C


title: BE2C, total

data_processing:
fastq files were quality checked using FastQC (0.11.7)
fastq files were aligned to an ensembl GRCh38 genome using HISAT2 (2.1.0)
sam files were converted to bam files using samtools (1.4.1)
bam files were uploaded to Galaxy and converted to bigwig files using bamCoverage (3.1.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: "bigwig" files contain coverage data for the respective cell lines.

growth_protocol: KELLY cell lines were plated, suspended in 10% foteal bovine serum (FBS) and 100 U/mL penicillin streptomycin RPMI containing media, into 6-well plates for 48 hours. BE2C and SK-N-AS cell lines were plated, suspended in 10% foteal bovine serum (FBS) and 100 U/mL penicillin streptomycin DMEM containing media, into 6-well plates for 48 hours.

extract_protocol:
Each 6-well was treated with 500 µL of Nucleozol, and left at room temperature (RT) for 10 minutes. Samples were transferred to 1.5 mL tubes. Each sample was treated with 200 µL RNase-free water, then shaken by hand for 15 seconds. Samples were left to incubate at RT for  10 minutes, and then centrifuged at 14,000 x g for 15 minutes. Then, 500 µL supernatant of each sample was transferred to a new tube, and treated with isopropanol. After inverting 4-6 times, samples were left at RT for 10 minutes, then centrifuged (14,000 x g) for 10 minutes. A resulting RNA pellet was then washed twice with 70% ethanol (600 uL each time, 8,000 x g for 1.5 minutes) and re-suspended in 30 uL RNase-free water.
RNA samples were sent to the Australian Genome Research Facility (AGRF, Perth and Melbourne, Australia) for whole transcriptome library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) and ribosomal RNA depletion with the Ribo-Zero-Gold kit (Illumina, CA, USA).
Sequencing as performed using an Illumina HiSeq 2500 (Illumina, CA, USA) to generate 50 base pair single end reads, resulting in an average 20 million reads per sample. Raw sequencing files were quality checked using FastQC (0.11.7), with all files passing

treatment_protocol: After 48 hours of incubation at 37ºC and 5% carbon dioxide levels, cells were lysed using the Nucleozol reagent from Machery-Nagel ™.

tag: phenotype

value: MYCN amplified/high-risk


title: WT_PL1

city: qingdao

first: RUIQI

last: SUN

state: China

address: No.72 Binhai Road,

country: China

institute: shandong university

description: WT lateral leaflet

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Genome_build: TAIR10.1
Supplementary_files_format_and_content: The_expression_of_gene_in_Arachis_hypogaea.xls (Gene IDs searchable at https://www.peanutbase.org)

organism: Arachis hypogaea

source_name: Arachis hypogaea wild type

growth_protocol: The plants grew in soil with a photoperiod of 16-h-day/8-h-night, temperature of 22°C and relative humidity of 70% in a growth chamber

extract_protocol:
Total RNA was isolated using TRIzol-RT reagent (Molecular Research Center)
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: age

value: lateral leaflet

tag: genotype

value: wild type


title: SUSP_1; Sample_5D

source_name: MS-5, Rec-1 (suspension fraction)

value: MS-5, Rec-1 (suspension fraction)


title: Monkey-Brain -Mock Rep2

city: Jerusalem

first: Sebastian

last: Kadener

address: SIlberman Institute of Life Sciences, Edmund J. Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
alignemnets to the genomes were done with STAR_2.6.1a_08-27
back spliced and linear reads was done using SRCP
Genome_build: hg38
Genome_build: mm10
Genome_build: rheMac10
Genome_build: rn5
Genome_build: dm6
Supplementary_files_format_and_content: Tables with  back-spliced reads and linear spliced reads.

organism: Macaca mulatta

source_name: Monkey(Rh) Brain (R1534035-50) Biochain

extract_protocol:
RNA purchase/extraction:  Human Adult Normal Brain Total RNA (R1234035-50), Human Adult Normal Cerebellum Total RNA (R1234039-50), Rat Brain Total RNA (R1434035-50), Monkey(Rh) Brain (R1534035-50) Total RNA was obtained by BioChain. Human Blood Total RNA (HR-705) was obtained from Zyagen.One C57BL/6 male and one female were sacrificed at p21, different brain regions were harvested (cerebellum, cortex, olfactory bulb, brain stem and, thalamus) by the Nelson’s lab at Brandeis University. The RNA was extracted with TRI reagent (Sigma, Aldrich) , followed by Zymo RNA cleaning and concentrator -25 Kit (Zymo), according to the manufactures’ instruction. We collected and dissected 10 days old D. melanogaster (Canton-S) heads and brains. Total RNA was  extracted with TRI reagent (Sigma, Aldrich), followed by DNase (DnaseI, NEB) treatment.
Recovered RNA was used to prepare a total RNA library, adapting the protocol from Shishkin et al. , Nature 2015. Specifically, we prepared one library for the RNAseR treated samples and one for the Mock ones. Briefly, RNA was fragmented for 3 min at 92°C in FAstAP 2X buffer (ThermoFisher). Subsequently, samples were dephosphorylated with FastAP enzyme (ThermoFisher), the first linker was ligated, and samples belonging to the same library were pulled together. Retro-transcription was performed using Affinity Script (Agilent). After second ligation, we performed PCR to add the external barcode. For Human Blood RNA samples and D. melanogaster samples, libraries were prepared using the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 by PerkinElmer, following the manufacturer’s instructions.
RnaseR vs Mock ribodepleted total RNA library
The samples were sequenced by Novogene Corporation Inc.(8801 Folsom BLVD, Suite 290, Sacramento, CA 95826)- HiSeq 1% PhiX with HiSeq-4000sequencer

treatment_protocol:
ribodepletion:  For mammalian RNA, ribodepletion was performed on 5ug of Total RNA with Ribo-Zero Gold rRNA Removal Kit according to the manufacturer’s instruction. Degradation of rRNA was checked by TapeStation. For Drosophila RNA, ribodepletion was performed with an homemade protocol. Briefly, rRNA was hybridized with specific DNA probes and degraded with RNasH , followed by DNase treatment for removing the DNA probes from the sample.
RNaseR:  From the collected ribodepleted RNA, 2/5 of the volume was treated with 6Units of RNAseR (Lucigen) or with buffer only (Mock) for 15 min at 37°C. The RNA was immediately extracted with TRI reagent (Sigma, Aldrich) according to the manufacture’s instruction.

tag: Sex

value: Female

tag: treatments

value: ribodepletion, mock


title: WT_DL3

description: WT terminal leaflet

value: terminal leaflet


title: mutant_SAM3

description: mutant shoot apical

source_name: Arachis hypogaea mutant with pentafoliate defects

value: shoot apical

value: mutant with pentafoliate defects


title: MCF-7_co-MDA_3

city: Seoul

first: Seo Young

last: Kang

address: Magokdong-ro 2-gil, Gangseo-gu

country: South Korea

institute: Ewha Womans University College of Medicine

data_processing:
A quality control of raw sequencing data was performed using FastQC.
Adapter and low quality reads (<Q20) were removed using FASTX_Trimmer and BBMap.
Then the trimmed reads were mapped to the reference genome using TopHat.
Gene expression levels were estimated using FPKM (Fragments Per kb per Million reads) values by Cufflinks.
The FPKM values were normalized based on Quantile normalization method using EdgeR within R.
Genome_build: hg19(UCSC)
Supplementary_files_format_and_content: normalized abundance measurements

source_name: breast cancer cells

growth_protocol: MCF7 and MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing10% fetal bovine serum (FBS), 10 U/ml penicillin, and 10 μg/ml streptomycin under humidified 5% CO2 atmospheric conditions and at a temperature of 37 °C.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK). The isolation of mRNA was performed using the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for the cDNA synthesis and shearing, following manufacture’s instruction. Indexing was performed using the Illumina indexes 1-12. The enrichment step was carried out using of PCR. Subsequently, libraries were checked using the Agilent 2100 bioanalyzer (DNA High Sensitivity Kit) to evaluate the mean fragment size. Quantification was performed using the library quantification kit using a StepOne Real-Time PCR System (Life Technologies, Inc., USA). High-throughput sequencing was performed as paired-end 100 sequencing using HiSeq X10 (Illumina, Inc., USA).

treatment_protocol: For co-culture of two cell lines, transwell inserts with a PET membrane of 0.4-μm pore size were used. MDA-MB-231 cells (0.8 × 105 cells per well) were plated on the lower wells and MCF7 (1 × 104 cells) were seeded into the top chamber (24-well insert) and then co-cultured for 24 h (Fig. 1A-B). EV-free FBS, in which EVs have been removed by ultracentrifugation, has been used.

value: co-culture with MDA-MB-235 cells


title: WT_PL2

description: WT lateral leaflet


title: MCF-7_control_1

value: untreated


title: MCF-7_control_2


title: MCF-7_control_3


title: mutant_SAM2

description: mutant shoot apical


title: KELLY, BPS1 4

source_name: KELLY BPS1

value: KELLY

value: BPS1 oligonucleotide


title: Monkey-Brain-RNaseR

description: Female, 4.5 yo

data_processing:
Alignments to the genomes were done with STAR_2.6.1a_08-27.
Back spliced and linear reads was done using SRCP.
Genome_build: Human hg38 (GRCh38)
Genome_build: Mouse mm10 (GRCm38)
Genome_build: Rhesus rheMac10 (Mmul_10)
Genome_build: Rat rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *.txt: Tables with back-spliced reads and linear spliced reads.

extract_protocol:
RNA purchase/extraction: Human Adult Normal Brain Total RNA (R1234035-50), Human Adult Normal Cerebellum Total RNA (R1234039-50), Rat Brain Total RNA (R1434035-50), Monkey(Rh) Brain (R1534035-50) Total RNA was obtained by BioChain. Human Blood Total RNA (HR-705) was obtained from Zyagen. One C57BL/6 male and one female mouse were sacrificed at p21, different brain regions were harvested (cerebellum, cortex, olfactory bulb, brain stem and thalamus) by the Nelson’s lab at Brandeis University. The RNA was extracted with TRI reagent (Sigma, Aldrich), followed by Zymo RNA cleaning and concentrator -25 Kit (Zymo), according to the manufacturers’ instruction.
Recovered RNA was used to prepare a total RNA library, adapting the protocol from Shishkin et al., Nature 2015. Specifically, we prepared one library for the RNaseR treated samples and one for the Mock ones. Briefly, RNA was fragmented for 3 min at 92°C in FAstAP 2X buffer (ThermoFisher). Subsequently, samples were dephosphorylated with FastAP enzyme (ThermoFisher), the first linker was ligated, and samples belonging to the same library were pulled together. Retro-transcription was performed using Affinity Script (Agilent). After second ligation, we performed PCR to add the external barcode.
RNaseR vs. Mock ribodepleted total RNA library.
The samples were sequenced by Novogene Corporation Inc. (8801 Folsom BLVD, Suite 290, Sacramento, CA 95826) - HiSeq 1% PhiX.

treatment_protocol:
Ribodepletion: Ribodepletion was performed on 5ug of Total RNA with Ribo-Zero Gold rRNA Removal Kit according to the manufacturer’s instruction. Degradation of rRNA was checked by TapeStation.
RNaseR: From the collected ribodepleted RNA, 2/5 of the volume was treated with 6 Units of RNAseR (Lucigen) or with buffer only (Mock) for 15 min at 37°C. The RNA was immediately extracted with TRI reagent (Sigma, Aldrich) according to the manufacturer's instruction.

value: Brain

value: Ribodepletion, RNaseR


title: mutant_SAM1

description: mutant shoot apical


title: Monkey-Brain-Mock

description: Female, 4.5 yo

value: Ribodepletion, mock


title: MCF-7_co-MDA_2

value: co-culture with MDA-MB-233 cells


title: MCF-7_co-MDA_1

value: co-culture with MDA-MB-231 cells


title: KELLY, BPS2 2

value: Immortalized neuroblastoma cells

value: BPS2 oligonucleotide


title: KELLY, BPS2 1


title: B73_seedling_leaf_rep_6

city: Brisbane

first: Peter

middle: A

last: Crisp

state: QLD

address: John Hines Building (62), The University of Queensland

department: School of Agriculture and Food Science

institute: The University of Queensland

library_source: genomic

data_processing:
Sequencing reads were trimmed and quality checked using Trim galore! version 0.4.3, powered by cutadapt v1.8.1 (63) and fastqc v0.11.5. For swift libraries, 20bp were trimmed from the 5’ ends both R1 and R2 reads as per the manufacturer’s suggestion.
Reads were aligned with bsmap v2.74 (64) to the respective genomes with the following parameters -v 5 to allow 5 mismatches, -r 0 to report only unique mapping pairs, -p 1, -q 20 to allow quality trimming to q20; Z. mays genome and gene annotation AGPv4 (65) downloaded from MaizeGDB gramene version 36
Output SAM files were parsed with SAMtools (67) fixsam, sorted and indexed. Picard MarkDuplicates was used to remove duplicates, BamTools filter to remove improperly paired reads and bamUtils clipOverlap to trim overlapping reads so as to only count cytosines once per sequenced molecule in a pair for PE reads. The methylratio.py script from bsmap v2.74 was used to extract per site methylation data summaries for each context (CH/CHG/CHH) and reads were summarised into non-overlapping 100bp windows tiling the genome. bedtools and the script bedGraphToBigWig (68) were used to prepare files for viewing in IGV (69).
Genome_build: Z. mays genome and gene annotation AGPv4

molecule: genomic DNA

organism: Zea mays

source_name: seedling

growth_protocol: Leaves of two week old V2 glasshouse grown maize B73 plants

extract_protocol:
DNA was extracted from leaves of two week old V2 glasshouse grown maize B73 plants using the DNeasy Plant Mini kit (Qiagen).
1ug of DNA in 50ug of water was sheared using an Ultrasonicator (Covaris) to approximately 200-350 bp fragments. 20ul of sheared DNA was then bisulfite converted using the EZ DNA Methylation-Lightning Kit (Zymo Research) as per the manufacturer's instructions and eluted in a final volume of 15ul. Then 7.5ul of the fragmented, bisulfite-converted sample was used as input for library preparation using the ACCEL-NGS Methyl-Seq DNA Library Kit (SWIFT Biosciences). Library preparation was performed as per the manufacturer’s instructions except each reaction was scaled by a half. The indexing PCR was performed for 5 cycles. Libraries were then pooled and sequenced on a HiSeq 2500 in high output mode 125bp paired end reads over multiple lanes at the University of Minnesota Genomics Centre.

tag: developmental stage

value: two week old V2


title: THP-1_IgG_Rb_ChIP

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Peaks were called with Homer software for ChIP-seq.
Genome_build: Ensembl GRCh38.p5
Supplementary_files_format_and_content: peaks bed file for ChIP-seq

source_name: THP-1 cell line

extract_protocol:
THP-1 cell lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with indicated antibody.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7600S).

tag: chip antibody

value: Normal Rabbit IgG (Millipore, 12-370, lot 3202364)


title: B73_seedling_leaf_rep_5


title: KELLY, BPS1 1


title: SL376698

city: Nashville

first: Marcela

last: Brissova

state: TN

address: 1211 Medical Center Dr

country: USA

institute: Vanderbilt University Medical Center

data_processing:
CellRanger(v2.1) "mkfastq" ,a 10x-aware convenience wrapper for bcl2fastq, was used for demultiplexing. Alignment to reference transcriptome (CellRanger pre-built refdata-cellranger-GRCh38-1.2.0; gene annotation provided by 10x Genomics) and unique molecular identifier (UMI)-based gene expression quantification was obtained following the Cell Ranger analysis pipeline (v2.1). The “Aggr” function was used to aggregate transcript counts and normalize read depth across 5 islet preparations and their technical replicates, producing one single gene-cell (feature-barcode) matrix.In Figure 2G-I, the CellRanger “Aggr” function was applied to 2 islet preparations(Islet prep 1-14y and Islet prep 2-39y), including the samples that were FACS-sorted. Further data preprocessing and clustering was performed using Seurat version 3.1 (51).Cells with 200-4,000 detected genes and <10% mitochondrial gene expression were retained, and only genes expressed in ≥3 cells were considered for further analysis. Gene expression was normalized for each cell by library size and log-transformed using a size factor of 10,000 molecules per cell. For feature selection, 2,000 highly variable genes were selected using function “FindVariableFeatures.” The data was further centered and scaled to zero mean and unit variance implemented in the “ScaleData” function using parameter “vars.to.regress” to regress out mitochondrial gene expression. Cells co-expressing the insulin (INS) and glucagon (GCG) genes above log expression of 6.5 and 5 respectively, as well as cells expressing INS or GCG in addition to any other cell type gene marker, were removed as doublets (see Table S2 for cell type markers used). Transcript counts from lysed cells (ambient mRNA/background RNA) were estimated and genes identified from empty droplets (droplets without cells) using DropletUtils package (65). Using the raw gene-barcode matrix (Cell Ranger v3.1), UMI threshold of 100 and below were considered ambient transcripts. About ~200 genes were identified as ambient genes and their expression level was noted to remove from the original gene barcode matrix in order to account for transcript stemming from lysed cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file included: 1.  raw expression values for each cell and gene 2. normalized expression values (natural log) for each cell and gene 3. Metadata of each cell ID 4. log2 transcript per million( TPM) values of FACS sorted bulk RNA Alpha and Beta cells

source_name: bulk-RNAseq-FACS sorted Beta cells

extract_protocol:
For single cell RNA-seq: Handpicked pancreatic islets were dispersed by manual pipetting using 0.025% HyClone trypsin (Cytiva/GE Healthcare #SH30042.01) and subsequently quenched with RPMI media containing 20% FBS (Millipore #TMS-013-B). Cells were washed in the same media twice followed by one wash with 0.04% BSA (Thermo Scientific # AM2616) in 1X PBS without calcium and magnesium (Corning Cellgro #21-040-CV). Washed cells were immediately counted in a Trypan blue stain-based Cell Countess II Automated Cell Counter (Thermo Scientific #AMQAX1000). Viability obtained from the cell preparations ranged from 70-85%. Cells were resuspended in 0.04% BSA/1X PBS at a density of 630-1,200 cells/μl in preparation for single cell RNA sequencing. Next, Sorted or dispersed islet cell samples were loaded in triplicate with each technical replicate per channel (approximately 10,000 cells/replicate) of 10x Chromium chips (PN# 1000009). Purification of α and β cell by FACS: Human islets from preparations #1 and 2 (Table S1) were dispersed and sorted for α and β cells following protocol described previously (17, 49, 60). Briefly, 0.025% trypsin was used to disperse islet cells by manual pipetting and subsequently quenched with RPMI containing 10% FBS. Previously characterized primary and secondary antibodies (25, 27, 61) are listed in Table S3 and gating strategy is shown in Figure S2A. Collected α and β cells for scRNA-seq were washed in 1X PBS with 0.04% BSA and immediately loaded into the 10x Chromium Controller at 1,200 cells/μl based on FACS counts, with single cell libraries prepared as described below. In parallel, 10,000 α and β cells from islet preparation #2 were stored in RNA extraction buffer to be processed for bulk RNA-seq as described below. For bulk RNA-seq data: RNA was extracted from sorted α and β cells using the Invitrogen RNAqueous-Micro Total RNA Isolation kit (Thermo Fisher #AM1931). TURBO DNA-free (Ambion) was used to treat any trace DNA contamination. RNA was quantified by Qubit Fluorometer 2.0 and RNA integrity was confirmed (RIN >7) by 2100 Bioanalyzer (Agilent).RNA was amplified using NuGen Ovation RNA amplification kit and sheared to an average size of 200 bp, then libraries were prepared using the NEBNext DNA library prep kit (New England Biolabs). Final libraries were sequenced on a Novaseq platform (Illumina), using paired-end reads (50 bp) targeting 50 million reads per sample. Raw reads were aligned to human reference genome hg38 using STAR v2.6 (62). Strand NGS 3.4 commercial software was used to import aligned files (.bam) and subsequently check alignment quality, filter reads based on read quality, quantify transcripts, and normalize counts to transcript per million (TPM).
Gel Bead in Emulsion (GEM) generation and barcoding were performed on the 10x Chromium Controller according to the manufacturer’s instructions(v2 Chemistry). Immediately after GEMs were generated, samples were transferred to a 0.2ml TempAssure PCR 8-tube strip (USA Scientific #14024700), capped, and placed into a thermocycler (Bio-Rad T100TM Thermal Cycler) for reverse transcription. After incubation, the GEMs were broken, and pooled cDNA proceeded to cleanup using Silane magnetic beads (10x Genomics #2000048) to remove leftover reagents. cDNA was then amplified through 10 cycles of PCR and cleaned using SPRIselect beads (Beckman Coulter # B23318). Resulting cDNA (average 45 ng/replicate) was checked for quality by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific #Q32854) and Agilent Bioanalyzer High Sensitivity Kit (Agilent #5067-4626). Final libraries were constructed according to manufacturer’s instruction and underwent 14 cycles of PCR amplification after sample index addition, yielding ~953ng and average library size of 486bp. Final libraries were sequenced with a Novaseq sequencer (Illumina) using paired-end reads (100 bp) to average depth of ~146,000 reads per cell.
single cell RNAseq, 10x Genomics library construction for Single cell 3'gene expression (v2 chemistry)

value: isolated pancreatic islet cells

value: Beta cells

tag: disease state

value: Non-diabetic


title: SL376697

source_name: bulk-RNAseq-FACS sorted Alpha cells

value: Alpha cells


title: 4752-SL-0037

description: FACS_raw_gene_cell_counts.txt.gz, FACS_normalized_gene_cell_counts.txt.gz,FACS_scRNAseq_metadata.txt.gz

tag: technical replicates

value: Islet prep 1(14y)-FACS sorted-Beta cells-rep2


title: MDA-MB-231_Day35

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

description:
Genome wide CRISPR KO screen
MDA-MB-231.counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
CRISPR library and data were analyzed by MAGeCK and MAGeCK-VISPR
Genome_build: hg19
Supplementary_files_format_and_content: csv file of sgRNA counts table

growth_protocol: The following cell lines were purchased from ATCC: CAL-120,  MCF7, MDA-MB-231, and MCF10A.  All cell lines were cultured in growth medium as specified by the manufacturer, and maintained at 37°C with 5% CO2. The cells were stored in liquid nitrogen at early passages and were cultured within 20 doublings.All cell lines have been authenticated by STR profiling at the Dana-Farber Cancer Institute.

extract_protocol:
Genomic DNA was extracted using the Blood & Cell Culture DNA Midi Kit (Qiagen),
3 rounds of PCR for library preparation. Each library was sequenced to generate 20~40 million reads, to achieve an average CRISPR library coverage of 200~300 ×.

treatment_protocol: CAL-120 cells were treated with DMSO or  300nM infigratinib for 35day

tag: treatment


title: B73_seedling_leaf_rep_3


title: KELLY, Control 3

source_name: KELLY Control

value: control oligonucleotide


title: KELLY, BPS1 3

value: KELLY


title: MDA-MB-231_Day0


title: 4752-SL-0036

tag: tissue

value: Islet prep 1(14y)-FACS sorted-Beta cells-rep1


title: B73_seedling_leaf_rep_2


title: shSETD1A_2_rep2

data_processing:
data type:ChIP-seq; data processing: For overall ChIP-seq datasets, reads were aligned to the Homo sapiens genome (Ensembl GRCh38.p5) using Bowtie2 PE mode with default parameters. Only reads with mapping quality score >30 were retained for further analysis by SAMtools. Two biological replicates were merged to create ‘Tag Directory’ file by ‘makeTagDirectory’. Peak finding and downstream data analysis were performed using HOMER software by ‘findPeaks’ with factor mode.
data type:RNA-seq; data processing: RNA-seq reads were aligned to Homo sapiens genome (Ensembl GRCh38.p5) using Tophat2 PE mode with the default parameters, and uniquely mapped reads were retained for further analysis filter by SAMtools. HTSeq-counts were used for calculating gene counts, and then normalized for transcript per million (TPM) using in-house scripts.
data type:eCLIP-seq; data processing: Peaks were called with clipper software for eCLIP-seq.
Genome_build: Ensembl GRCh38.p5
Supplementary_files_format_and_content: peaks bed file for ChIP-seq; expression matix for RNA-seq; peaks bed file for eCLIP-seq

extract_protocol:
THP-1 cells were treated with QKI5 shRNA (shQKI5-1/shQKI5-2) or shCtrl.
The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: clip antibody

value: SETD1A knock down


title: KELLY, Control 4


title: KELLY, Control 2


title: KELLY, BPS1 2

value: BPS1 oligonucleotide


title: 4752-SL-0034

value: Islet prep 1(14y)-FACS sorted-Alpha cells-rep1


title: B73_seedling_leaf_rep_1


title: B73_seedling_leaf_rep_4


title: 4752-SL-0035

value: Islet prep 1(14y)-FACS sorted-Alpha cells-rep2


title: 4752-SL-0033

value: Islet prep 2(39y)-FACS sorted-Beta cells-rep3


title: sphere_#3

tag: growth method

value: sphere

value: breast cancer

tag: cancer subtype

value: luminal B


title: shPTBP3_2_rep2

value: PTBP3 knock down


title: KELLY, Control 1

tag: cell line

tag: cell type

value: Immortalized neuroblastoma cells


title: MCF10A_RNA-Seq

city: Montpellier

first: Lucile

last: Broseus

address: 141, rue de la Cardonille

institute: CNRS

data_processing:
Base-calling for Nanopore Sequencing: Oxford Nanopore basecaller, Albacore v2.3.3
Hybrid Long Read Correction was performed using TALC (version 1.0)
Long Reads were aligned using Minimap2 (version 2.11-r797) and quantified using featureCount
Short Reads were aligned using Hisat2 (version 2.1.0) and quantified using featureCount
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing read counts per gene were generated from featureCount. Genes are those annotated in Ensembl 94.

source_name: MCF10a-Snail-ER cells

growth_protocol: Human mammary epithelial MCF10a-Snail-ER cells, which stably express the epithelial repressor Snaill fused to the estrogen receptor, were cultured as previously described (Reference: Javaid S et al. Dynamic chromatin modification sustains epithelial-mesenchymal transition following inducible expression of Snail-1. Cell Reports 5, 1679–1689 (2013). ) Briefly, the cells were grown in DMEM/F-12 (Sigma) supplemented with 5% horse serum (Thermofisher), 20 ng/ml EGF (Sigma), 0.5 µg/ml hydrocortisone (Sigma), 100 ng/ml cholera toxin (Sigma), 10 µg/ml insulin (Sigma), 2mM L-Glutamine (Thermofisher) and 1x Pen./Strep. (Sigma)

extract_protocol:
TruSeq stranded mRNA from Illumina
After resuspending cell pellets in Trizol (Life technologies), total RNA was extracted by addition of chloroform and isopropanol precipitation, followed by RNA clean-up using the GeneJET RNA purification kit (Thermofisher).

treatment_protocol: To induce epithelial-to-mesenchymal transition initiation, MCF10-Snail-ER cells were treated with 100 nM tamoxifen (Sigma) for 1 day. Importantly, parental MCF10a cells did not show any differences in cell morphology or transcriptional and splicing patterns upon the same treatment. All cell lines were regularly tested for mycoplasma presence.


title: shSETD1A_1_rep2


title: shPTBP3_1_rep2


title: 4752-SL-0029

value: isolated pancreatic islet cells

value: Islet prep 2(39y)-FACS sorted-Alpha cells-rep2


title: adherent_#3

value: adherent


title: 4752-SL-0031

value: Beta cells

value: Non-diabetic

value: Islet prep 2(39y)-FACS sorted-Beta cells-rep1


title: adherent_#2


title: shSETD1A_1_rep1


title: shPTBP3_1_rep1


title: Bi-N7-AD4-3     HMAP+L #2

city: Cold Spring Harbor

first: Aybuke

last: Alici

state: NY

address: 1 Bungtown Rd.

institute: Cold Spring Harbor Laboratory

description:
HMAP+L #2
Bi-N7-AD4-3
AP+L.txt

data_processing:
RNA-seq data were processed and interpreted with the Genialis visual informatics platform (www.genialis.com).
RNA-seq reads were implemented to trimming (BBDuk), mapping (STAR), and expression quantification (featureCounts), respectively.
Reads were mapped to Homo sapiens GRCh38 (Ensembl, version 92, ERCC)
Differential gene expression analyses were performed using DESeq2 ref. Lowly-expressed genes were filtered out from the differential expression analysis input matrix.
The expression level (TPM, transcripts per kilobase per million) was determined by Cufflinks.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited version of raw counts of sequencing reads for all samples

source_name: Trophoblast-like cells

growth_protocol: iPSCs were maintained routinely on MEFs with hES media (20% KOSR, 1% L-glutamine, 1% non-essential amino acids, 0.055 mM beta-mercaptoethanol, 10 ng/ml bFGF in DMEM/F12)

extract_protocol:
Total RNA was extracted using Trizol.
Library preparation was performed using Truseq stranded mRNA LT Sample Prep Kit (Illumina).

treatment_protocol: iPSCs were exposed to FGF (0.1µM) and ACTIVIN/NODAL inhibitors(0.1µM) (AP) together with either BMP4 (BAP) (10 ng/mL) or BMP inhibitor (AP+L) (100nM).

tag: time(days)


title: Chronic restraint stress 2 h for 14 days and then chronic short-term restraint stress for 5 min for 14 days rep 2

type: RNA

first: Eun-Hwa

last: Lee

address: Science building B214, 52 Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

description:
replicate 2
TEST+B4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: Prelimbic cortex

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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

tag: gender

value: male

tag: strain

value: brain

value: 3 months

tag: condition


title: 4752-SL-0032

value: Islet prep 2(39y)-FACS sorted-Beta cells-rep2


title: shNUDT21_2_rep2

value: NUDT21 knock down


title: Chronic restraint stress 2 h for 14 days and then chronic short-term restraint stress for 5 min for 14 days rep 1

description:
replicate 1
TEST+B3

tag: age


title: Chronic restraint stress 2 h for 14 days rep2

description:
replicate 2
TEST4


title: sphere_#2

data_processing:
Sequenced reads were mapped to hg19 whole genome using Tophat version 2.0.10
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a Cufflinks version 2.1.1 following the protocol from Trapnell et al.,Nature Protocols, 2012.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: clinical breast cancer

extract_protocol:
RNA was collected and amplified using Takara Nucleospin RNA XS Kit (Cat#740902) and Clontech SMARTER Ultra low RNA for Illumina Kit (Cat#634822). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: WT_PL3

description: WT lateral leaflet

value: lateral leaflet

tag: genotype

value: wild type


title: shSETD1A_2_rep1

value: SETD1A knock down


title: 4752-SL-0028

value: Alpha cells

value: Islet prep 2(39y)-FACS sorted-Alpha cells-rep1


title: shPTBP3_2_rep1

value: PTBP3 knock down


title: Naïve control rep1

description:
replicate 1
CON3

value: Naïve control


title: 4752-SL-0030

value: isolated pancreatic islet cells

value: Islet prep 2(39y)-FACS sorted-Alpha cells-rep3


title: Chronic restraint stress 2 h for 14 days rep1

description:
replicate 1
TEST3


title: Bi-N7-AD4-2     HMAP+L #1

description:
HMAP+L #1
Bi-N7-AD4-2
AP+L.txt


title: 4752-SL-0025

description: raw_gene_cell_counts.txt.gz,normalized_gene_counts.txt.gz,scRNAseq_metadata.txt.gz

source_name: Islet prep 1(14y)

value: whole islets

value: Islet prep 1(14y)-rep1


title: 4752-SL-0027

value: Non-diabetic

value: Islet prep 1(14y)-rep3


title: Bi-WT-AD4-3     WTAP+L #2

description:
WTAP+L #2
Bi-WT-AD4-3
AP+L.txt

value: WT


title: Naïve control rep2

description:
replicate 2
CON4

value: male

value: brain

value: 3 months


title: shNUDT21_1_rep2

value: NUDT21 knock down


title: shNUDT21_1_rep1


title: 4752-SL-0026

value: Islet prep 1(14y)-rep2


title: 4752-SL-0023

source_name: Islet prep 2(39y)

value: Islet prep 2(39y)-rep2


title: Bi-WT-AD4-2     WTAP+L #1

description:
WTAP+L #1
Bi-WT-AD4-2
AP+L.txt


title: N7-D4-AP-3     HMAP #2

description:
HMAP #2
N7-D4-AP-3
AP.txt


title: shELAVL1_2_rep2

value: ELAVL1 knock down


title: N7-D4-BAP-3     HMBAP #2

description:
HMBAP #2
N7-D4-BAP-3
BAP.txt


title: 4752-SL-0024

value: Islet prep 2(39y)-rep3


title: Input 14 days3 KA 14

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using the rmaPLM function from the affy R package

label: Biotin

source_name: Input 14 days3 KA 14

label_protocol: 5 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2). Amplification was performed for 22 cycles. 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Animal housing and maintenance protocols followed the guidelines of the Council of the European Convention ETS123 and were performed in accordance with the principals of the European Union adopted Directive (2010/63/EU). All procedures were performed in accordance with the principals of the European Communities Council Directive (86/609/EEC) and National Institute of Health’s Guide for the Care and Use of Laboratory Animals. All were approved by the Research Ethics Committee of the Royal College of Surgeons in Ireland (REC 1322).

extract_protocol: The ipsilateral hippocampi were quickly dissected, homogenized and total RNA was extracted using the Maxwell® 16 LEV simplyRNA Tissue Kit (Promega). Quantification and quality of RNA was analyzed using RNA Qubit Assay ( Qubit Fluorimeter ) and Agilent RNA Nano and Pico Assay (Agilent 2100 Bioanalyzer ).

treatment_protocol: KA into the amygdala (0.3 μg in 0.2 μl vehicle; phosphate-buffered saline (PBS), pH adjusted to 7.4 was injected. Non-seizure control mice received 0.2 μl intra-amygdala vehicle. Lorazepam (6 mg/kg, intraperitoneal) was administered 40 min after KA.

tag: time

value: 14 days

value: KA


title: N7-D4-BAP-2     HMBAP #1

description:
HMBAP #1
N7-D4-BAP-2
BAP.txt


title: 4752-SL-0010

source_name: Islets prep 5(66y)

value: isolated pancreatic islet cells

value: Islets prep 5(66y)-rep1


title: shELAVL1_1_rep1

tag: chip antibody


title: Input 14 days1 KA 14

source_name: Input 14 days1 KA 14


title: N7-D2-BAP-3     HMBAP #2

description:
HMBAP #2
N7-D2-BAP-3
BAP.txt


title: Input 14 days2 KA 14

source_name: Input 14 days2 KA 14


title: N7-D4-AP-2     HMAP #1

description:
HMAP #1
N7-D4-AP-2
AP.txt


title: 4752-SL-0022

value: whole islets

tag: disease state

value: Islet prep 2(39y)-rep1


title: shELAVL1_2_rep1


title: 4752-SL-0011

value: Non-diabetic

tag: technical replicates

value: Islets prep 5(66y)-rep2


title: shCtrl3_rep2

tag: treatment

value: empty vetor


title: N7-D2-BAP-2     HMBAP #1

description:
HMBAP #1
N7-D2-BAP-2
BAP.txt


title: 4752-SL-0012

tag: tissue

value: Islets prep 5(66y)-rep3


title: shELAVL1_1_rep2

tag: clip antibody


title: Input 14 days3 CTR 14

source_name: Input 14 days3 CTR 14

value: ctrl


title: N7-D2-AP-2     HMAP #1

description:
HMAP #1
N7-D2-AP-2
AP.txt


title: 4752-SL-0009

source_name: Islets prep 4(59y)

value: Islets prep 4(59y)-rep3


title: Input 14 days1 CTR 14

source_name: Input 14 days1 CTR 14


title: 4752-SL-0008

value: Islets prep 4(59y)-rep2


title: SUSP_2; Sample_6D

data_processing:
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on the ENSEMBL reference genomes specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes GRCh38 and GRCm38 respectively using the splice aware short read aligner STAR (v2.5.1b) using PE read input with default options and –sjdbGTFfile pointing to the ENSEMBL .gtf annotation file corresponding to the reference genome file and –outFilterMultimapNmax set to 1.
Species specific read pairs were assigned to known features and counted using featurecounts from the Subread package (v1.5.2). Annotated genes were obtained from the Ensembl ftp repository (Homo_sapiens.GRCh38.87.gtf and Mus_musculus.GRCm38.87.gtf).
Data was later interrogated for differentially expressed genes using the Bioconductor package EdgeR (v3.22.5).
Genome_build: GRCh38.87 and GRCm38.87 were downloaded from the ENSEMBL ftp repository
Supplementary_files_format_and_content: GRCh38_featurecounts_count_table.csv: RAW read count table per feature for all samples with human content after species-based separation of reads of human origin and alignment to GRCh38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.
Supplementary_files_format_and_content: GRCm38_featurecounts_count_table.csv: RAW read count table per feature for all samples with mouse content after species-based separation of reads of murine origin and alignment to GRCm38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.

source_name: MS-5, Rec-1 (suspension fraction)

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) with QIAshredders following the protocol supplied by the manufacturer.
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

tag: cultivation

value: co-culture of two cell lines

value: mouse bone marrow derived stromal and human mantle cell lymphoma cell line

value: MS-5, Rec-1 (suspension fraction)


title: Input 8 hours2 KA 8

source_name: Input 8 hours2 KA 8

value: 12 hrs


title: N7-D2-AP-3     HMAP #2

description:
HMAP #2
N7-D2-AP-3
AP.txt


title: Input 8 hours3 KA 8

source_name: Input 8 hours3 KA 8

value: 13 hrs


title: shCtrl1_rep2

source_name: THP-1 cell line


title: Input 8 hours3 CTR 8

source_name: Input 8 hours3 CTR 8

value: 10 hrs


title: 4752-SL-0007

value: isolated pancreatic islet cells

value: Islets prep 4(59y)-rep1


title: Input 8 hours1 KA 8

source_name: Input 8 hours1 KA 8

value: 11 hrs

value: KA


title: Input 14 days2 CTR 14

source_name: Input 14 days2 CTR 14

value: 14 days


title: N7-3IPSC-3     HMiPSC #2

description:
HMiPSC #2
N7-3IPSC-3
IPSC.txt

source_name: iPSCs


title: NO-WT-D4-BAP-3     WTBAP #2

description:
WTBAP #2
NO-WT-D4-BAP-3
BAP.txt

source_name: Trophoblast-like cells

value: WT


title: shCtrl3_rep1

value: empty vetor


title: shNUDT21_2_rep1

value: NUDT21 knock down


title: shADAR_2_rep2

value: ADAR knock down


title: 4752-SL-0004

source_name: Islets prep 3(50y)

value: whole islets

value: Non-diabetic

value: Islets prep 3(50y)-rep1


title: 4752-SL-0005

value: Islets prep 3(50y)-rep2


title: NO-WT-D4-AP-3     WTAP #2

description:
WTAP #2
NO-WT-D4-AP-3
AP.txt


title: NO-WT-D4-BAP-2     WTBAP #1

description:
WTBAP #1
NO-WT-D4-BAP-2
BAP.txt


title: HCI-002 PDOs treated

city: Taipei City

first: Kelvin

middle: Kun-Chih

last: Tsai

address: 7F, 250 Wuxing St, Xinyi Dist

department: Graduate Institute of Clinical Medicine, College of Medicine

country: Taiwan

institute: Taipei Medical University

data_processing:
RNA-seq was performed by Illumina NovaSeq 6000 platform for paired-end sequencing
150-bp read length, for about 20 million raw reads per sample.
RNA sequencing FASTQ files were processed with HISAT2 aligner in default mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89). Differential gene expression analysis was performed using DESeq2 software. Enrichment analysis was performed using ClusterProfiler software.
Genome_build: HG38
Supplementary_files_format_and_content: excek files include FPKM and TPM values for each Sample

source_name: treatment-sensitive HCI-002 PDOs, treated

growth_protocol: HCI-001 or HCI-002 PDOs were grown in DMEM/F-12 medium containing 5% FBS, and supplemented with hEGF (15 ng/ml), Y-27632 (10 μM), Glutamax (1% v/v), HEPES (10 mM), Hydrocortisone (0.5 ug/ml), and Gentamycin (50 ug/ml).

extract_protocol:
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 10 cycles of PCR. Sequencing was performed using 100pM hybridization to a 2x150 paired end flow cell.
Libraries were prepared from 1μg of RNA per sample using Illumina Stranded mRNA Prep (illumina).

treatment_protocol: All PDOs were incubated at 37°C in 5% CO2 and grown to 80-90% confluence follow the 3D culture protocol. PDOs were pretreated with Ac-YVAD-CHO (Caspase-1 inhibitor) 5 uM for 1 hr and treat with Paclitaxel 20 uM for 48 hr before collecting total RNA.

value: Patient-derived organoids

tag: cell source

value: 1° breast tumor

value: Paclitaxel at 20 uM for 48 hr


title: NO-WT-D4-AP-2     WTAP #1

description:
WTAP #1
NO-WT-D4-AP-2
AP.txt


title: shADAR_2_rep1


title: HCI-002 PDOs untreated

source_name: treatment-sensitive HCI-002 PDOs, untreated

tag: cell line

value: Vehicle-treated


title: N7-3IPSC-2     HMiPSC #1

description:
HMiPSC #1
N7-3IPSC-2
IPSC.txt


title: HCI-001 PDOs treated

source_name: treatment-resistant HCI-001 PDOs, treated

tag: cell type


title: SETD1A_ChIP_rep2

extract_protocol:
THP-1 cells were crosslinked by formaldehyde followed by sonication and the lysates were clarified and protein-DNA complexes were isolated with indicated antibody. Then the DNA was purified for subsquential processes.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7335S).

value: SETD1A(ab70378, abcam)


title: HCI-001 PDOs untreated

source_name: treatment-resistant HCI-001 PDOs, untreated


title: NO-WT-D2-BAP-2     WTBAP #1

description:
WTBAP #1
NO-WT-D2-BAP-2
BAP.txt

tag: time(days)


title: NO-WT-D2-BAP-3     WTBAP #2

description:
WTBAP #2
NO-WT-D2-BAP-3
BAP.txt


title: 100nM retinyl proprionate 4

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

description: Gene expression data from hTERT-keratinocytes treated with 100nM retinyl proprionate

hyb_protocol: Biotinylated cRNA was fragmented by limited alkaline hydrolysis and then hybridized overnight to Affymetrix GeneTitan U219 microarray plates using the Affymetrix GeneTitan instrument

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The PLIER algorithm, quantile normalization, was performed in GeneSpring (Agilent) as the processing protocol to normalize the data for subsequent analysis.

source_name: hTERT-keratinocytes

label_protocol: Biotinylated cRNA were prepared  using the Affymetrix HT 3’ IVT Express kit (Cat. #901253) on a Beckman Biomek FXp Laboratory Automation Workstation (Beckman Cat. #A31842).

growth_protocol: hTERT-immortalized keratinocytes were maintained in KBM-Gold Keratinocyte Growth Medium BulletKitTM (Lonza, Cat# 00192060) in the absence of hydrocortisone.

extract_protocol: RNA was extracted from skin cells using an RNeasy Mini Kit (Qiagen, UK)

treatment_protocol: untreated, 100nM retinyl proprionate (Sigma, Cat #87809), 100nM retinol (Sigma, Cat #95144)

tag: agent

value: 100nM retinyl proprionate

tag: time point

value: 24 hours


title: SETD1A_ChIP_rep1


title: NO-WT-D2-AP-3     WTAP #2

description:
WTAP #2
NO-WT-D2-AP-3
AP.txt


title: shADAR_1_rep2


title: Input 8 hours2 CTR 8

source_name: Input 8 hours2 CTR 8

value: 9 hrs

tag: condition

value: ctrl


title: 100nM retinol 4

description: Gene expression data from hTERT-keratinocytes treated with 100nM retinol

value: 100nM retinol


title: 100nM retinyl proprionate 2


title: QKI5_ChIP_rep2

value: QKI5(AB9904, Merck Millipore)


title: Input 8 hours 1 CTR 8

source_name: Input 8 hours 1 CTR 8

value: 8 hrs


title: shADAR_1_rep1

value: ADAR knock down


title: 100nM retinyl proprionate 3


title: 100nM retinyl proprionate 1


title: CA3_infigratinib_rep1

description: PDX treated with infigratinib

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina Bcl2fastq v2.18.
Reads were aligned to hg19 using STAR.
For fpkm calculation cufflinks was used.
Genome_build: hg19
Supplementary_files_format_and_content: Cuff_Gene_Counts_FPKM.csv: FPKM table

source_name: breast cancer cells

growth_protocol: Protocols for all animal experiments were approved by the Animal Care and Use Committee for the Dana-Farber Cancer Institute. PDX tumor fragments were cut into pieces (2 mm in diameter) and were implanted subcutaneously into the right flanks of 8-week-old nude mice. Tumors were grown in mice for 28 days.

extract_protocol:
RNA was extracted from cells with the RNeasy Mini Kit (Qiagen).
The Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 500 ng of purified total RNA, using RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit (NEB #E7760). according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; pooled uniquely indexed RNA-seq libraries in equimolar ratios, and sequenced these to a target depth of 40M reads on an Illumina NovaSeq 6000 run with single-end 75bp reads.

treatment_protocol: When the tumor had grown to the volume of 100-300 mm3in size, mice were randomized to 2 arms for dosing. Infigratinib was formulated in a solution of 10% captisol and 90% water and dosed at 12.5mg/kg.

tag: tumor type

value: Patient-derived xenografts tumors

value: infigratinib


title: CA3_infigratinib_rep2

description: PDX treated with infigratinib


title: 100nM retinol 3


title: QKI5_ChIP_rep1


title: PTBP3_ChIP_rep2

value: PTBP3(PA5-98125, Thermo Fisher Scientific)


title: NO-WT-D2-AP-2     WTAP #1

description:
WTAP #1
NO-WT-D2-AP-2
AP.txt

tag: genotype

value: WT


title: NO-WT-2IPSC-3     WTiPSC #2

description:
WTiPSC #2
NO-WT-2IPSC-3
IPSC.txt


title: CA3_rep1

description: control PDX

value: vehicle


title: CA3_rep2

description: control PDX


title: PTBP3_ChIP_rep1


title: Infigratinib_rep2

description: PDX treated with infigratinib


title: NO-WT-2IPSC-2     WTiPSC #1

description:
WTiPSC #1
NO-WT-2IPSC-2
IPSC.txt


title: PMA_48hr_rep2

extract_protocol:
THP-1 cells were treated with PMA for 48hr or with Ctrl/QKI5/QKI5 M1 over-expression.
The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: PMA induction


title: 100nM retinol 1


title: SEP_4; Sample_8B

value: mono-cultured cell line

value: mantle cell lymphoma cell line


title: Peyer's patch BCR repertoire of WT mice

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

data_processing:
Library strategy: 5' V(D)J scRNAseq
Reads were first demultiplexed with cellranger mkfastq (version 3.0.0)
Single cell BCR repertoires were then assembled with cellranger vdj (version 3.0.0) using the cellranger vdj-GRCm38-alt-ensembl-2.2.0 reference.
Genome_build: GRCm38 vdj 2.2.0
Supplementary_files_format_and_content: 3 files are provided for each sample. One file (clonotypes.txt) indicates each unique clonotype and their frequency. The other 2 files (filtered_contig_annotations.csv and filtered_contig.fasta) can be used as in put to the change-o R package and provide contigs and annotations for each cell barcode.

source_name: Peyer's patch CD45+ cells

extract_protocol:
MACS encriched CD45+ cells from each genotype were pooled and loaded onto the Chromium Controller (10x Genomics). RNA was extracted according to the 10x Genomics 5' Expression library kit.
Libraries were prepared according to the 10x Genomics 5' V(D)J Kit.

value: Peyer's patch

value: H2-Ab1 fl/fl; Villin:Cre-

tag: Sex

value: female


title: Peyer's patch BCR repertoire of mice lacking H2-Ab1 on intestinal epithelial cells

value: H2-Ab1 fl/fl; Villin:Cre+


title: PMA_48hr_rep1

tag: chip antibody


title: SEP_3; Sample_7B

first: Gustav

last: Arvidsson

address: Husargatan 3

institute: Uppsala Universitet


title: vehicle_rep2

description: control PDX

source_name: breast cancer


title: SEP_2; Sample_6B


title: vehicle_rep1

description: control PDX


title: 15342X4, Peyer's patch CD45+ cells WT

description:
PP_5Prime_WT
5' scRNAseq expression

data_processing:
Reads were first demultiplexed with cellranger mkfastq (version 3.0.0)
Count matrices were then created with cellranger count
Genome_build: mm10
Supplementary_files_format_and_content: 3 files are provided for each sample, in one archive. The cell barcodes, the gene identifiers and the matrix of counts.

extract_protocol:
MACS encriched CD45+ cells from each genotype were pooled and loaded onto the Chromium Controller (10x Genomics). RNA was extracted according to the 10x Genomics 5' Expression library kit.
Libraries were prepared according to the 10x Genomics 5' Expression kit.


title: no treatment 4

description: Gene expression data from untreated hTERT-keratinocytes

value: no treatment

value: 24 hours


title: OE_QKI5_rep1

source_name: THP-1 cell line

value: QKI5 overexpression


title: Infigratinib_rep1

description: PDX treated with infigratinib


title: OE_QKI5_rep2


title: SEP_1; Sample_5B

value: human mantle cell lymphoma cell line


title: no treatment 1


title: no treatment 2


title: 100nM retinol 2

value: 100nM retinol


title: platelets, THR-428

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

department: School of Medicine

institute: New York University

data_processing:
Fastq qualtiy assessed via FastQC 0.11.7
Sample contamination assessed via fastqscreen v0.13.0
Fastq files trimmed via Trimmomatic v0.36
Fastq files aligned to the HG38 human genome via STAR v2.7.3a
Reads counted via featurecounts v1.6.3
Genome_build: hg38
Supplementary_files_format_and_content: Raw count table as a .txt file

source_name: platelet

extract_protocol:
Direct-zol RNA microspin columns
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA) as per the manufacturer's instruction

tag: cohort

value: Control

value: Female


title: no treatment 3


title: OE_QKI5_M1_rep2

value: QKI5 M1 overexpression


title: 15342X3, Ileal lamina propria CD45+ cells WT

description:
siLP_5Prime_WT
5' scRNAseq expression

source_name: Ileum lamina propria CD45+ cells

value: Ileum


title: mrg1mrg2_R3

city: Pozuelo de Alarcón

first: Manuel

last: Pineiro

state: Madrid

address: Autopista M-40, Km 38

institute: Centro de Biotecnologia y Genomica de Plantas (CBGP)

data_processing:
FastQ files were mapped to Arabidopsis TAIR10 reference genome using for annotation ensembl release 41.
Mapped reads were quantified using SeqMonk software
Differential expression analysis was performed using DESeq2 module on SeqMonk software
Differential Expressed Genes (DEGs) when FDR≤0.05 and fold change (FC) was either FC≤0.5 (downregulated genes) or FC≥1.5 (Upregulated genes)
Genome_build: TAIR10 (annotation ensembl release 41)
Supplementary_files_format_and_content: An .xls file providing gene ID, fold change and FDR for each DEG as calculated using DESeq2 analysis. In addition, gene raw counts for each sample are also provided

source_name: Aerial part from 12d-old seedling

growth_protocol: Seeds were sown on a soil:vermiculite mix (3:1), stratified at 4ºC for 3 days and grown for 12 days under long day photoperiod at 22ºC.

extract_protocol:
Total RNA was isolated using EZNA Plant RNA kit (Omega) following the manufacturer’s protocol. RNA samples were treated with DNase I (Roche) to remove genomic DNA contamination.
Total RNA was assayed for quality control using an Agilent Bioanalyzer 2100. Libraries were prepared using TrueSeq Stranded total RNA with Ribo-Zero Plant kit following manufacturer protocols. Then, libraries were sequenced on an Illumina HiSeq2000 sequencer generating a minimum of 40 million 50bp single-end reads.

treatment_protocol: Samples were taken at zeitgeber 8 (ZT8) from 12d-old seedlings  growing in control conditions (22ºC, long day photoperiod (16h light:8h dark), light intensity 100 umol m-2 s-1).

tag: ecotype

value: Leaves and stem

tag: developmental stage

value: 12-day-old seedling

value: mrg1 mrg2 Mutant


title: mrg1mrg2_R2

tag: tissue


title: platelets, THR-417

value: Male


title: OE_QKI5_M1_rep1

tag: clip antibody

tag: treatment


title: OE_Ctrl_rep2

value: empty vetor


title: 15342X1, Ileal lamina propria CD45+ cells dIEC

description:
siLP_5Prime_dIEC
5' scRNAseq expression


title: mrg1mrg2_R1


title: platelets, THR-415


title: platelets, THR-399


title: platelets, THR-432


title: NUDT21_ChIP_rep2

value: NUDT21(ab183660, abcam)


title: 15342X3, Peyer's patch CD45+ cells dIEC

description:
PP_5Prime_dIEC
5' scRNAseq expression

value: Peyer's patch

value: female


title: Col-0_R2

value: Wild-type


title: platelets, THR-369


title: NUDT21_ChIP_rep1


title: OE_Ctrl_rep1


title: KHSRP_ChIP_rep2

value: KHSRP(ab264265, abcam)


title: platelets, THR-337


title: Col-0_R1


title: MCA205_Tissue_KO1_SIX1

city: Suzhou

first: Wancheng

last: Liu

state: jiangsu

address: 100 Chongwen Road, Industrial Park

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: On day 8 after incubation

data_processing:
Fastqc software used for quality control.
Sequenced reads were trimmed by trim_galore software for adaptor sequence with parameters -q 25 --phred33 --length 36 -e 0.1 --stringency 5 --paired, then mapped to mm10 whole genome using bowtie2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse fibrosarcoma MCA205 cells

extract_protocol:
MCA205 tumor tissue were harvested on day  8 post-implanted, and MCA205 WT and SIX1-/- cells were were collected, flash frozen on dry ice. Total RNA was extracted using RNeasy Mini Kit (QIAGEN, cat#74104). ProtoScript II Reverse Transcriptase (New England BioLabs, cat#E7420L) was used with 0.6 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCA205 wild type (WT) and SIX1-/- cells (2x10^6 cells in 100ul PBS per mouse) were subcutaneously implanted.

tag: strain

tag: type

value: tumor tissue


title: MCA205_Tissue_KO2_SIX1

description: On day 8 after incubation


title: MCA205_Tissue_KO3_SIX1

description: On day 8 after incubation


title: MCA205_Tissue_WT2

description: On day 8 after incubation

value: wild type


title: platelets, THR-303


title: platelets, THR-313


title: BCR sequencing of naïve and memory B cells 1

city: New York

first: Ryan

last: Smolkin

address: 408 E 69th St

institute: MSKCC

data_processing:
Illumina Casava software was used for base calling
Sequencing files were put through the cellranger 4.0.0 pipeline to align to the mm10 genome and generate feature barcode matrices. The two experimental repliactes were combined using Seurat v3.2.2 in R v4.0.2.
Standard QC and preprocessing filtered out genes expressed in fewer than 3 cells and cells with either 1) greater than 7% alignment to mitochondrial genes, 2) feature counts of fewer than 800 or 3) unique feature counts outside (400,2500). 7033 cells remained
BCR sequencing files were processed through cellranger 4.0.0 vdj pipeline to align to mm10 and combined into a single aggregate matrix using Immcantation toolbox v4.0.0 V)D)J alignment tool, using the IMGT and IgBlast databases. Filtering out nonproductive rearrangements yielded 7006 cells, of which 1061 and 4936 were mapped to memory B cells and naive B cells, respectively, for further processing.
Supplementary_files_format_and_content: mm10

source_name: Primary murine B cells

extract_protocol:
Hemagglutinin-specific (HA+) memory B cells (MBCs) and naïve B cells were sorted from combined mediastinal lymph nodes at d109 post-infection. For each experiment, 50,000-60,000 sorted naïve B cells were mixed with 15,000-16,000 sorted HA+ MBCs, and resuspended at a final concentration of approximately 1,000 cells per mL. 5mL of this mixture was taken and analyzed using flow cytometry as the ‘post-sort’ fraction, and the remaining cells were used for Chromium Single Cell 5’ library construction and V(D)J enrichment (10X Genomics).
Single cell RNA sequencing data were generated using standard 10X and Illumina techniques. Namely, Gel Bead-In-EMulsions were formed using the Chromium Single Cell A Chip Kit (PN-120236) and barcoded with the Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006). Libraries were generated with the Chromium Single Cell 5' Library Construction Kit (PN-1000020), with B cell receptor codes enriched using the Chromium Single Cell V(D)J Enrichment Kit for Mouse B Cells (PN-1000072). Combinatorial libraries were annotated using the Chromium i7 Multiplex Kit (PN-120262) and Chromium i7 Multiplex Kit N, Set A, (PN-1000084) prior to standard Illumina sequencing using a Novaseq (Illumina).

treatment_protocol: In two independent experiments, 30-32 12 week-old mice were infected intranasally with 50 TCID50 influeza A virus (PR8).

value: Lymph Node


title: MCA205_Tissue_WT1

description: On day 8 after incubation


title: Col-0_R3


title: BCR sequencing of naïve and memory B cells 2


title: KHSRP_ChIP_rep1


title: MCA205_cell_KO2_SIX1

value: cell line


title: ELAVL1_ChIP_rep1

value: ELAVL1(ab136542, abcam)


title: platelets, THR-238

value: Control


title: 10X  sequencing of naïve and memory B cells 2

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz


title: ELAVL1_ChIP_rep2


title: 10X  sequencing of naïve and memory B cells 1


title: platelets, COV-10-1

value: COVID

value: Female

value: Dead


title: CLIP_QKI5_rep2

extract_protocol:
THP-1 cells were UV-crosslinked and lysed then proetin-RNA complexes were isolated with indicated antibodies. Then the RNA was purified for subsquential processes.
Libraries were  prepared as described in "Van Nostrand, E. L. et al. Nat Methods, 2016, 13, 508-514"and sequenced by using Illumina Hiseq 1000 with pair end 150bp read length.

value: QKI5(AB9904, Merck Millipore)


title: MCA205_cell_KO1_SIX1


title: Base.2 [6s_rna_t2]

city: Cleveland

first: Thaddeus

last: Stappnbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Cleveland Clinic, Lerner Research Institute

description: run_2927_s_8_withindex_sequence.txt_ACTGTCG

data_processing:
RNA-seq reads aligned to the Shigella flexneri 2a str. 2457T genome (Ensembl bacteria, release 45), top-level assembly to STAR version 2.0.4b
Gene counts derived with subread:feature Count (version 1.4.5)
To identify differentially expressed genes, TMM normalization factors were calculated using EdgeR to adjust for differences in sample read numbers. Differential gene expression analysis was performed in Limma with voom.
Genome_build: Shigella flexneri 2a str. 2457T genome (Ensembl bacteria, release 45)
Supplementary_files_format_and_content: Raw counts per sample

organism: Shigella flexneri

source_name: Bacterial Culture

growth_protocol: Shigella were grown in 96-well plates at 37C, 24h, stationary, and with various treatment conditions.

extract_protocol: Cells lysed witth RiboPure RNA Purification kit (Invitrogen), RNA purified with Rneasy Mini Kit (Qiagen), and DNA removed with TURBO DNA-free kit (Invitrogen)

treatment_protocol: Growth in (i) TSB [control] vs. (ii) TSB + 0.05% sodium deoxycholate (NaDCA) [biofilm] vs (iii) TSB + 0.05% sodium deoxycholate + 20 mM sodium hydroxide (NaOH) [Biofilm with base]

tag: serotype

value: TSB + NADCA + NaOH


title: platelets, COV-8-1

value: Male


title: MCA205_Tissue_WT3

description: On day 8 after incubation


title: CLIP_QKI5_rep1

data_processing:
data type:ChIP-seq; data processing: For overall ChIP-seq datasets, reads were aligned to the Homo sapiens genome (Ensembl GRCh38.p5) using Bowtie2 PE mode with default parameters. Only reads with mapping quality score >30 were retained for further analysis by SAMtools. Two biological replicates were merged to create ‘Tag Directory’ file by ‘makeTagDirectory’. Peak finding and downstream data analysis were performed using HOMER software by ‘findPeaks’ with factor mode.
data type:RNA-seq; data processing: RNA-seq reads were aligned to Homo sapiens genome (Ensembl GRCh38.p5) using Tophat2 PE mode with the default parameters, and uniquely mapped reads were retained for further analysis filter by SAMtools. HTSeq-counts were used for calculating gene counts, and then normalized for transcript per million (TPM) using in-house scripts.
data type:eCLIP-seq; data processing: Peaks were called with clipper software for eCLIP-seq.
Genome_build: Ensembl GRCh38.p5
Supplementary_files_format_and_content: peaks bed file for ChIP-seq; expression matix for RNA-seq; peaks bed file for eCLIP-seq


title: Biofilm.2 [3b_rna_t2]

description: run_2927_s_8_withindex_sequence.txt_CACCTCC

value: TSB + NaDCA


title: CLIP_PTBP3_rep2

value: PTBP3(PA5-98125, Thermo Fisher Scientific)


title: platelets, COV-5-1

value: Alive


title: platelets, COV-7-1


title: Control.2 [1s_rna_t2]

description: run_2927_s_8_withindex_sequence.txt_TGATTAC

value: TSB


title: MCA205_cell_WT1


title: CLIP_PTBP3_rep1


title: Base.1 [6s_rna_t1]

description: run_2927_s_8_withindex_sequence.txt_GCCGTTT


title: M5_WAT_S42

city: Rochester

first: Yang

last: Zhao

address: 60 Crittenden Blvd, Apt1240

department: Biology

institute: University of Rochester

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
cleaned reads were mapped to the genome by  STAR_2.5.2b
gene expression (TPM and reads counts) were calculated by salmon 1.4.0
regions of differential methylation were called by edgeR package in 100 window resolution (R version 3.3.2)
Genome_build: Mouse (Mus musculus): mm10
Genome_build: Blind mole rat (Spalax ehrenbergi):GCF_000622305.1_S.galili_v1.0

source_name: White adipose tissue

growth_protocol: Fibroblasts were maintained at 37 °C incubator in an atmosphere of 5% CO2 and 3% O2 on treated polystyrene culture dishes (Corning) in EMEM media (ATCC) with 15% (vol/vol) fetal bovine serum (FBS).

extract_protocol:
For RNAseq, was extracted using a Quick-RNA MiniPrep Kit (Zymo), with a DNase I on column digestion to remove genomic DNA contamination; For MeDIP, genomic DNA was extracted using a Zymo Quick-DNA Miniprep Plus Kit.
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.

treatment_protocol: No treatment

value: Wild-caught

value: White adipose tissue


title: platelets, COV-3-1


title: platelets, COV-4-1


title: M5_Spleen_S22

source_name: Spleen

value: Spleen


title: CLIP_KHSRP_rep1

first: Yue

last: Huo

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

value: KHSRP(ab264265, abcam)


title: Biofilm.1 [3b_rna_pre]

description: run_2927_s_8_withindex_sequence.txt_TTGCCCC


title: CLIP_KHSRP_rep2


title: Control.1 [1s_rna_t1]

description: run_2927_s_8_withindex_sequence.txt_CGGTGGC


title: platelets, COV-2-1


title: M5_Muscle_S32

source_name: Muscle

value: Muscle


title: M5_Skin_S17

source_name: Skin

value: Skin


title: MCA205_cell_WT2

value: cell line

value: wild type


title: CLIP_input_QKI5_rep1


title: endothelial cells, COV016

source_name: endothelial

treatment_protocol: Human cardiac microvascular endothelial cells exposed to platelet releasate originating from patients with COVID-19 or controls.

value: CONTROL

value: Female


title: M5_Lung_S27

source_name: Lung

value: Lung


title: platelets, COV-1-1

value: COVID


title: exp031020 P8 rep 2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
phaffi_plus_transgenes_031020.fa.gz
dalvie031020_intCt.txt.gz
dalvie031020_l2cpm.txt.gz

data_processing:
MiSeq sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative per unique molecular identifier using a custom script. Gene expression was quantified using salmon (version 1.3.0, Patro et al., 2017) using the indicated Komagataella transcriptomes plus transgenes as selective alignment targets.  The resulting counts were summarized to the gene level using tximport (version 1.12.3) and counts per million (cpm) were calculated using utilities implement in edgeR (version 3.26.8, Chen et al., 2014). The cpm values with a +1 offset were transformed to log2 space for visualization.
Genome_build: Komagataella phaffi WT (PRJNA304977) with indicated transcriptomes
Supplementary_files_format_and_content: phaffi_plus_transgenes_020821.fa.gz is a fasta transcriptome file used for the indicated samples
Supplementary_files_format_and_content: phaffi_plus_transgenes_031020.fa.gz is a fasta transcriptome file used for the indicated samples
Supplementary_files_format_and_content: dalvie020821_intCt.txt.gz is tab delimited integer count data prepared using the phaffi_plus_transgenes_020821.fa.gz target
Supplementary_files_format_and_content: dalvie020821_l2cpm.txt.gz is tab delimited counts per million with a plus 1 offset prepared using the phaffi_plus_transgenes_020821.fa.gz target
Supplementary_files_format_and_content: dalvie031020_intCt.txt.gz is tab delimited integer count data prepared using the phaffi_plus_transgenes_031020.fa.gz target
Supplementary_files_format_and_content: dalvie031020_l2cpm.txt.gz is tab delimited counts per million with a plus 1 offset prepared using the phaffi_plus_transgenes_031020.fa.gz target

organism: Komagataella phaffii

source_name: bulk yeast cell culture

growth_protocol: Cell were harvested after 18 h of production at 3 mL plate scale. Cells were cultivated in complex media (potassium phosphate buffer pH 6.5, 1.34% nitrogen base w/o amino acids, 1% yeast extract, 2% peptone).

extract_protocol:
RNA was extracted and purified according to the Qiagen RNeasy kit (cat #74104) and RNA quality was analyzed to ensure RNA Quality Number >6.5.
3'DGE Nextera

treatment_protocol: Cells were inoculated at 0.1 OD600, outgrown for 24 h with 4% glycerol feed, pelleted, and resuspended in fresh media with 3% methanol to induce recombinant gene expression.

tag: transgene

value: P8 control


title: endothelial cells, COV015


title: CLIP_input_PTBP3_rep2


title: exp031020 P8 rep 1


title: exp031020 RBD rep 13

value: SARS-Cov2 receptor binding domain


title: M5_Liver_S7

source_name: Liver

value: Liver


title: M5_Kidney_S12

source_name: Kidney

value: Kidney


title: endothelial cells, COV014

value: Male


title: CLIP_input_PTBP3_rep1


title: M5_Intestine_S37

source_name: Intestine

value: Wild-caught

value: Intestine


title: shCtrl1_rep1

source_name: THP-1 cell line

extract_protocol:
THP-1 cells were treated with QKI5 shRNA (shQKI5-1/shQKI5-2) or shCtrl.
The cells were collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: empty vetor


title: CLIP_ELAVL1_rep2

value: ELAVL1(ab136542, abcam)


title: exp031020 RBD rep 11


title: CLIP_ELAVL1_rep1


title: endothelial cells, COV012


title: M4_Spleen_S21

value: Spleen


title: exp031020 RBD rep 10


title: endothelial cells, COV011


title: exp031020 P8 rep 3


title: CLIP_ADAR_rep1

value: ADAR(ab168809, abcam)


title: CLIP_ADAR_rep2


title: endothelial cells, COV013


title: M4_Skin_S16

value: Skin


title: exp031020 RBD rep 9


title: endothelial cells, COV010

value: Dead


title: ChIP_input_rep3


title: exp031020 RBD rep 8


title: M4_Muscle_S31

value: Muscle


title: exp031020 RBD rep 12


title: ChIP_input_rep2


title: M4_WAT_S41

value: White adipose tissue


title: exp031020 RBD rep 7


title: endothelial cells, COV007

value: Alive


title: ChIP_input_rep1


title: M4_Liver_S6


title: endothelial cells, COV006

value: CONTROL


title: M4_Lung_S26

value: Lung


title: M4_Kidney_S11


title: ADAR_ChIP_rep2


title: ADAR_ChIP_rep1


title: exp031020 RBD rep 5

value: SARS-Cov2 receptor binding domain


title: endothelial cells, COV003

value: COVID


title: exp031020 RBD rep 3


title: M4_Intestine_S36


title: exp031020 RBD rep 6


title: endothelial cells, COV008


title: endothelial cells, COV002


title: exp031020 RBD rep 2


title: M3_Spleen_S20


title: M3_Skin_S15


title: M3_Muscle_S30


title: exp031020 RBD rep 1


title: CLIP_input_QKI5_rep2


title: exp020821 RBD rep 4

description:
phaffi_plus_transgenes_020821.fa.gz
dalvie020821_intCt.txt.gz
dalvie020821_l2cpm.txt.gz


title: scATAC_vehicle

first: Xintao

last: Qiu

institute: Dana Faber Cancer Institute

description: control PDX

data_processing:
Illumina Bcl2fastq v2.18
fastq processed by using the 10x genomics Cell Ranger atac
Genome_build: hg19
Supplementary_files_format_and_content: cell peak barcode matrix in HD5 format

source_name: breast cancer

growth_protocol: Protocols for all animal experiments were approved by the Animal Care and Use Committee for the Dana-Farber Cancer Institute. PDX tumor fragments were cut into pieces (2 mm in diameter) and were implanted subcutaneously into the right flanks of 8-week-old nude mice. Tumors were grown in mice for 28 days

extract_protocol:
Cell preparation for scATAC-seq was performed according to the manufacturer’s protocol (10X Genomics) targeting 5000 cells from single-cell suspensions of freshly processed prostate lobes.
single-cell ATAC-seq

treatment_protocol: When the tumor had grown to the volume of 100-300 mm3in size, mice were randomized to 2 arms for dosing. infigratinib was formulated in a solution of 10% captisol and 90% water and dosed at 12.5mg/kg.

value: Patient-derived xenograft tumors

value: vehicle


title: endothelial cells, COV005

value: Male


title: M3_WAT_S40

value: Wild-caught


title: ATAC_CAL-120_DMSO_2

description: CAL-120 cells treated with DMSO

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: breast cancer cells

growth_protocol: CAL-120 cells were cultured in DMEM plus 10% FBS

extract_protocol:
Cells were then lysed with 1% SDS lysis buffer (1% SDS, 10mM EDTA (pH=8), 50mM Tris-HCl (pH=8)) containing protease and deacetylase inhibitors, and sonicated for 5 min with settings of PIP 140, DF 5%, cpb 200 on a Covaris E220 (Covaris Inc., Woburn, MA) to obtain 200-600bp chromatin fragments.
libraries were constructed from 2 ng of DNA, using the ThruPLEX DNA-seq kit (#R400427, Rubicon Genomics), according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; ChIP-seq libraries were uniquely indexed in equimolar ratios, and sequenced to a target depth of 40M reads on an Illumina NextSeq500 run, with single-end 75bp reads.

treatment_protocol: CAL-120 cells were treated with DMSO or  300nM infigratinib, or gene knockout

value: DMSO

tag: cell line


title: endothelial cells, COV004

value: Female


title: exp031020 RBD rep 4


title: exp020821 RBD rep 3


title: M3_Lung_S25


title: ATAC_CAL-120_DMSO_1

description: CAL-120 cells treated with DMSO


title: M3_Liver_S5

value: Liver


title: exp020821 RBD rep 2


title: ATAC_CAL-120_Infigratinib_4h_2

description: CAL-120 cells treated with infigratinib for 4h


title: exp020821 RBD rep 1


title: ami no suc, biological rep. 3

city: Umea

first: Johannes

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

institute: Umeå Plant Science Centre

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
ami no suc3

data_processing: Data were analyzed statistically using the R language environment for statistical computing version 3.0 and Bioconductor release 2.12 (Gentleman et al., 2004). Data were normalized using the Robust Multichip Average (RMA) expression measure in the Affy package (Gautier etal., 2004). Differentially expressed genes were identified using the LIMMA package (Smyth, 2004)

source_name: 10 day old seedlings

growth_protocol: 10 day old seedling growth phenotypes were monitored on half strength MS medium with 50 μM estradiol ± 30 mM sucrose (16-h light, 120 µE m-2 s-1).

extract_protocol: Total RNA was isolated and purified using the RNeasy kit (Qiagen) and quantified by NanoDrop. The microarray experiments were performed by ServiceXS (www.servicexs.com) using AffymetrixATH1 GeneChips.

value: whole seedlings

value: ami


title: scATAC_infigratinib

description: PDX treated with infigratinib

value: infigratinib


title: M3_Intestine_S35

value: Intestine


title: ami no suc, biological rep. 2

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
ami no suc2


title: ATAC_CAL-120_Infigratinib_4h_1


title: exp020821 engRBD rep 3

value: engineered SARS-Cov2 receptor binding domain


title: Wt no suc, biological rep. 1

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
Wt no suc 1

value: WT


title: ami no suc, biological rep. 1

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
ami no suc1


title: M2_WAT_S39

value: White adipose tissue


title: ATAC_CAL-120_Infigratinib_2d_2

description: CAL-120 cells treated with infigratinib for 48h


title: Wt no suc, biological rep. 3

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
Wt no suc 3


title: exp020821 engRBD rep 4


title: exp020821 engRBD rep 2


title: Wt no suc, biological rep. 2

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
Wt no suc 2


title: M2_Spleen_S19

value: Spleen


title: M3_Kidney_S10

value: Kidney


title: M2_Skin_S14

value: Skin


title: ATAC_CAL-120_Infigratinib_12d_2

description: CAL-120 cells treated with infigratinib for 12d


title: ami suc, biological rep. 3

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
ami suc3


title: ATAC_CAL-120_Infigratinib_2d_1


title: ami suc, biological rep. 2

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
ami suc2


title: exp020821 engRBD rep 1


title: exp020821 P8 rep 4

value: P8 control


title: M2_Muscle_S29

value: Muscle


title: ATAC_CAL-120_Infigratinib_12d_1


title: exp020821 P8 rep 3


title: BRG_KO1_REP3

description: CAL-120 knocked out with BRG1

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina Bcl2fastq v2.18
Reads were aligned to mm10 using STAR
For fpkm calculation cufflinks was used.
Genome_build: hg19
Supplementary_files_format_and_content: csv file of FPKM table

extract_protocol:
RNA was extracted from cells with the RNeasy Mini Kit (Qiagen).
The Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 500 ng of purified total RNA, using RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit (NEB #E7760).  according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; pooled uniquely indexed RNA-seq libraries in equimolar ratios, and sequenced these to a target depth of 40M reads on an Illumina NextSeq500 run with single-end 75bp reads.

treatment_protocol: CAL-120 cells were treated with DMSO or  300nM infigratinib, gene knockouts

value: knocked out with BRG1


title: M2_Lung_S24

value: Wild-caught

value: Lung


title: Chimera Silibinin

city: Verona

first: Stefano

last: Ugel

address: Piazzale L.A. Scuro, 10

department: Medicine

country: Italy

institute: University and Hospital Trust of Verona

data_processing:
Alignment, barcode processing and UMI counting for each sample was performed using 10x Cell Ranger software v.3.1.0 (cellranger count pipeline) with parameter --expect-cells=4000
Genome_build: mm10
Supplementary_files_format_and_content: Feature-barcode matrix for each sample in the format returned by 10x cellranger count pipeline

source_name: Lung immune cells

extract_protocol: Mice were euthanized by CO2 inhalation and lungs were immediately perfused with 20 mL ice-cold PBS. Lungs were cut in small pieces with scissors, enzymatically digested at 37°C for 45 minutes with a solution containing collagenase IV (1mg/ml), hyaluronidase (0.1mg/ml) and DNase (4.5mg/ml) (Sigma-Aldrich). Cells were then collected, filtered and red blood cells were lysed at RT for 5 minutes with ACK Lysing Buffer (Lonza). Cells were then collected, filtered and pooled as follows: 3 WT mice, 3 untreated-chimera, 3 silibinin-treated, 3 baricitinib-treated and 3 vFLIP-tg mice. The cells were washed with PBS 1x, re-suspended in RPMI 1640 medium supplemented with 5% bovine serum albumin and counted. Cell viability was determined by Trypan blue exclusion. For each sample, cells were resuspended in RPMI supplemented with 5% FBS to a final concentration of 106 /ml for single cell analysis. Cell suspension were processed using the 10x Genomics Chromium Controller and the Chromium NextGEM Single Cell 3′ GEM, Library& Gel Bead kit v3.1 (Pleasanton, California, United States) following the standard manufacturer’s instructions. In brief, 10,000 live cells were loaded into the Chromium controller to recover 4,000 single cell GEMs per inlet uniquely barcoded. After synthesis of cDNA, sequencing libraries were generated. Final 10X library quality was assessed using the Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) and then sequenced on the Illumina NextSeq500 (Illumina, San Diego CA, USA).

value: Rosa26.vFLIPTg LysM-CRE; CD45.1

tag: cell type

value: Lung immune cells

value: Treated with silibinin


title: Wt suc, biological rep. 3

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
Wt suc 3

value: whole seedlings


title: Chimera Baricitinib

value: Treated with baricitinib


title: Wt suc, biological rep. 2

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
Wt suc 2


title: Wt suc, biological rep. 1

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
Wt suc 1


title: exp020821 P8 rep 2


title: ami suc, biological rep. 1

description:
Affymetrix Arabidopsis ATH1 GeneChips (Affymetrix) were performed according to Affymetrix OneCycle Lab protocols (Affymetrix, Santa Clara, CA, USA).
ami suc1

value: ami


title: M2_Kidney_S9


title: BRG_KO1_REP2

description: CAL-120 knocked out with BRG1


title: vFLIP rep2

value: Rosa26.vFLIPTg LysM-CRE

value: Transgenic


title: Chimera UT

value: Untreated


title: anti-GFP-YFP-PIF3-Light-Rep2

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

institute: Sorbonne Université

description: ChIP DNA

data_processing:
trimming using trim_galore with options “--phred33 --paired -q 20 --stringency 1 --length 35”
mapping to the TAIR10 genome using bowtie2 with options “--very-sensitive -I 150 -X 2000 -p 20 --no-mixed”.
filtering using samtools  with options “view -hb -F 1804 –L selected_TAIR10_genome_Chr.bed”, which corresponds to the TAIR10 genome after filtering out genomic regions with aberrant coverage or low sequence complexity (retrieved from Quadrana et al. eLife (2016))
Browser tracks were generated using deeptools function bamCoverage with options “--binSize 20 --normalizeUsingRPKM --extendReads --centerReads --ignoreForNormalization ChrC ChrM”.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: 5-day-old Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were sterilized with a solution of 75% sodium hypochlorite and 0.1% Tween-20 and stratified at 4°C during 3 days in darkness.  Seedlings were grown in Murashige and Skoog (MS) medium.

extract_protocol:
ChIP experiments were performed as in Fiorucci, Bourbousse et al., Genome Biology (2019)
NEBNext Ultra II DNA Library Prep Kit was used, PE 150bp reads were produced

treatment_protocol: Light: white light (100 umol m-2 s-1) in a 16-h light/8-h dark period. Dark: continuous darkness.

value: light

tag: agent

tag: antibody

value: anti-GFP (Life Technologies #11122)


title: vFLIP rep1


title: AAVS1_REP2

city: Boston

address: 440 brookline ave

description: CAL-120 knocked out with AAVS1

value: knocked out with AAVS1


title: M2_Intestine_S34

value: Intestine


title: M1_WAT_S38

value: White adipose tissue


title: anti-GFP-YFP-PIF3-Light-Rep1

description: ChIP DNA

tag: genotype


title: anti-GFP-YFP-PIF3-Dark-Rep2

description: ChIP DNA

value: dark