title: RPS3A_rep2_IP

city: La Jolla

first: Yue

last: Qin

address: 9500 Gilman Drive

institute: University of California San Diego

description: IP sample from biological replicate 2 of HEK293T with C-terminally FLAG-HA-tagged RPS3A

data_processing:
After sequencing, raw reads were aligned to GRCh38 and analyzed following the detailed instructions in ENCODE eCLIP-seq Processing Pipeline v2.2 (https://www.encodeproject.org/pipelines/ENCPL357ADL/).
Consistent with the ENCODE standard, reads aligning to artifact-enriched or repetitive genomic regions were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed file contains reproducible and significant peaks of aligned reads at IDR cutoff of 0.01, P ≤ 0.001, and fold enrichment ≥ 8. All peaks have annotated genic region based on overlap with GENCODE v26 transcripts.

source_name: Embryonic kidney cells

growth_protocol: HEK293T cells were grown in DMEM media supplemented with 10% fetal bovine serum and 1% penicillin streptomycin at 37°C under 5% CO2.

extract_protocol:
Experiments were performed following a previous published protocol (PMID: 28766298). In brief, >20 million cells were collected for UV crosslink (400 mJoules/cm2, 254 nm), followed by cell lysis, sonication, and RNase I treatment. Anti-HA antibody (BioLegend #901501) was incubated with cell lysates at 4℃ overnight. 2% of samples were saved as paired input before immunoprecipitation (IP) steps. IP samples were washed, followed by RNA dephosphorylation (FastAP, Thermo Fisher; T4 PNK, NEB) and 3’ RNA adaptor ligation (T4 RNA ligase, NEB). IP and input samples were run on a PAGE Bis-Tris protein gel and subsequently transferred to a nitrocellulose membrane, from which regions starting from protein size up to 75 kDa above were excised for proteinase K (NEB) treatment and column purification (Zymo). RNA obtained from input samples was also dephosphorylated and ligated to 3’ RNA adaptors as performed previously to IP samples. Final RNA samples were reverse transcribed, ligated to a 3’ DNA adaptor (T4 RNA ligase, NEB), and PCR amplified to obtain the final library for next generation sequencing.
seCLIP-seq protocol

treatment_protocol: HEK293T cells were transfected using lentivirus harboring a C-terminally FLAG-HA-tagged RPS3A clone from ORFeome v.8.1. Two biological replicates of stable cell lines were created and maintained in 2.5 µg/mL puromycin.

tag: cell line

tag: experimental

value: IP


title: P67_Genomic DNA CART 19

status: Public on Aug 23 2021

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description: Peripheral-blood mononuclear cells were isolated from a fresh leukapheresis product and activated in T-cell medium. On day 2 of culture, activated cells were transduced with the CD19 CAR retrovirus. This construct comprises the variable regions of anti-CD19 monoclonal antibody FMC63 fused to the CD28 costimulatory domain and to the CD3 zeta chain, which were cloned into a mouse stem-cell virus gamma-retroviral backbone. CAR-T-cells were then further expanded in IL-2 containing T- cell medium until day 9–10. High molecular weight DNA was extracted from paired T-cell samples consisting of CART19 untransduced and transduced T-cells before infusion into patients.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting. Briefly, 600 ng of DNA of the studied samples was used to hybridize the BeadChip 850K microarray and scanned using HiScan SQ system (Illumina)

data_processing: Raw signal intensity data were initially QC’d and preprocessed from resulting idat files in R statistical environment (v4.0.3) using minfi Bioconductor package (v1.36.0). A number of quality control steps were applied to minimize errors and remove erratic probe signals, such as failed probes (probes with detection P value > 0.01 in at least 10% of samples were removed. If probe P value > 0.01 in less than 10% of samples, the Beta values of those probes in the failed samples were marked as NAs and later imputed using the median), cross-reacting probes, and probes that overlapped SNPs within ±1 bp of CpG sites, followed by background correction and dye-based normalization using ssNoob algorithm (single-sample normal-exponential out-of-band). All analyses were performed under R statistical environment (v4.0.3)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: High molecular weight DNA extracted from CART 19 transduced T-cells before infusion into patients

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: patient id

tag: matching transduced untransduced samples

value: Yes

tag: transduction status

value: Transduced

tag: gender

value: M

tag: age

tag: disease

value: ALL


title: RPS3A_rep2_Input

type: SRA

state: CA

country: USA

description: Input sample from biological replicate 2 of HEK293T with C-terminally FLAG-HA-tagged RPS3A

library_source: transcriptomic

molecule: total RNA

value: input


title: P66_Genomic DNA CART 19

value: NHL


title: Yami3

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress 24 v1.1 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2.0 with GT module 2.0.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Yami

tag: region

value: East Asia


title: WD1

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

data_processing:
Bulk RNA-seq reads were aligned with STAR v2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M21). Uniquely mapped reads were quantified using HTSeq v0.9.1 suite using protein coding genes by gene.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Input tables are included as tab separated files.
ChIP-seq
ChIP-seq reads were aligned with BWA v0.7.16a to the reference sequence (mm10 from UCSC). Reads were filtered for MAPQ >10 and duplicated reads were removed using samtools. MACS2 v2.1.1 was used to identify peaks. Bedtools v2.25.0 was used to integrate dark/light ChIP-seq data. HOMER v4.9.1 was used for motif analysis.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: bed-files including coordinates of the detected peaks from ChIP-Seq.
Single-nuclei RNA-seq
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1. UMI-tools were used to match barcode and reads. Single-nuclei RNA-seq reads were aligned with STAR v2.5.2b to the reference sequence (mm10 from UCSC). Human reference was used for gene annotation and counting (gencode M17). Gene level expression was calculated using featureCounts v1.6.2. Downstream analysis was performed using Seurat v3.0
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Rdata containing count and meta data tab separated tables

organism: Mus musculus

source_name: Superchiasmatic Nuclei

extract_protocol:
mRNA was extracted from SCN tissue using a Dynabead mRNA DIRECT Micro Kit (Ambion) according to the manufacturer’s instructions. All mRNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer (Agilent).
Samples were randomized for library preparation and sequencing. Libraries were constructed following Truseq protocols (Illumina) and sequencing was performed at the McDermott Sequencing Core at UTSW.

tag: experiment

tag: genotype

value: WT

tag: condition

value: Dark

tag: tissue

value: Superchiasmatic Nuclei

value: 11-12 weeks

tag: Sex

value: male

tag: batch

tag: protocol

value: Protocol 1


title: Yami49


title: RPS3A_rep1_IP

description: IP sample from biological replicate 1 of HEK293T with C-terminally FLAG-HA-tagged RPS3A

tag: cell line


title: Yami16


title: P65_Genomic DNA CART 19

value: F


title: KL3

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

value: KO

value: Light


title: P64_Genomic DNA CART 19

value: Yes


title: RPS3A_rep1_Input

description: Input sample from biological replicate 1 of HEK293T with C-terminally FLAG-HA-tagged RPS3A

tag: experimental


title: KL2

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt


title: P63_Genomic DNA CART 19

tag: patient id

value: Transduced


title: KL1

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt


title: PriGO8A-PREX1_KO_C4_2

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Sequencing data was pseudoaligned to the human GRCh38 reference transcriptome and transcript counts were quantified using Kallisto.
Differential expression between conditions was performed using Sleuth.
Genome_build: GRCh38
Supplementary_files_format_and_content: Differential expression results: Statistics from differential expresison testing along with gene-level TPM quantifications for each sample

source_name: Glioblastoma

growth_protocol: Cells were grown as monolayers on tissue culture plates coated with laminin (Sigma-Aldrich, Oakville ON, Canada) using neurobasal A medium with B27 and N2 supplements and EGF and FGF2 (all from Thermo Fisher Scientific Inc., Waltham MA, USA). Cells were incubated in 5% O2 and 5% CO2 at 37˚C

extract_protocol:
Total RNA was isolated using the GE Illustra RNA Spin Kit (Thermo Fisher Scientific, Ottawa, ON, Canada) according to kit protocol including DNase treatment
RNA-seq libraries were generated from 250ng of total RNA. The NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs) and cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra directional RNA Second Strand Synthesis Modules (New England BioLabs). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

treatment_protocol: Glioblastoma PREX1 knockout cells were generated by electroporation of preformed crRNA/tracrRNA/Cas9 complexes. For the crRNA:tracrRNA duplex, a crRNA sequence targeting exon 2 of PREX1.

tag: cell type

value: glioblastoma

value: PREX1 KO


title: Yami50


title: PriGO8A-PREX1_KO_C4_1


title: AmiA47B

value: Ami


title: AmiA48


title: KD3

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt


title: P62_Genomic DNA CART 19

tag: matching transduced untransduced samples

tag: transduction status

value: M

value: NHL


title: KD2

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

tag: age


title: PriGO8A_2


title: PriGO8A_1


title: P60_Genomic DNA CART 19

tag: gender

tag: disease

value: ALL


title: Skin, T.HS_14

city: Cologne

first: Manolis

last: Pasparakis

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

description:
raw_readcounts.csv
CPM_readcounts.csv

data_processing:
Adapters were trimmed with cutadapt v2.10: cutadapt --minimum-length=35 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -a AGATCGGAAGAGCACACGTCTGAAC -a TGGAATTCTCGGGTGCCAAGG -a AGATCGGAAGAGCACACGTCT -a CTGTCTCTTATACACATCT -a AGATGTGTATAAGAGACAG
Trimmed reads were processed with a custom R script based on the workflow described here: https://rstudio-pubs-static.s3.amazonaws.com/171024_bd9c5ea013a4465cbceb9d435033eadd.html .  (12bp from 5’ end trimmed; bases from 3’ end trimmed if Q<= 29 for >= 6 positions;  trim trailing A-runs; cut 5’ of internal A-runs of length >=  10; discard reads with length < 36bp after processing)
Trimmed and processed reads were aligned to the mouse mm10 genome build (ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.chromosome.*.fa.gz) plus the ERCC92 spike-in sequences (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) using subread-align v2.0.1 : subread-align  -t 0 --multiMapping -B 5. ftp://ftp.ensembl.org/pub/release-100/gtf/mus_musculus/Mus_musculus.GRCm38.100.chr.gtf.gz,augmented by records for the ERCC92 sequences, was provided as annotation file.
Before counting, subread-align matches with mapping quality <30 and secondary matches were removed using samtools 1.7-2-gc6125d0.
Reads per gene were counted from the filtered subread-align output using featureCounts v2.0.1 :  featureCounts -F "GTF" -t "exon" -g "gene_id" --minOverlap 20 -M --primary --fraction -O -J . ftp://ftp.ensembl.org/ plus the ERCC92 spike-in sequences were provided as annotation. Raw reads were converted to cpm values using function cpm() of R package edgeR v3.30.3 (Bioconductor version 3.11).
Genome_build: mm10 (chromosome sequences from ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.chromosome.*.fa.gz, annotation from ftp://ftp.ensembl.org/pub/release-100/gtf/mus_musculus/Mus_musculus.GRCm38.100.chr.gtf.gz)
Supplementary_files_format_and_content: A comma-separated values (csv) file is a delimited text file that uses a comma to separate values. Each line of the file is a data record. Each record consists of one or more fields, separated by commas (definition from https://en.wikipedia.org/wiki/). Here, each record except the first one corresponds to a gene. The first record is a header containing names for the comma-separated fields (=columns). The first comma separated field in each record holds the Ensembl ID of the corresponding gene, and the second field holds the gene symbol. All subsequent fields are numerical and hold read counts per gene in the samples indicated by the column names. The counts are the direct output of featureCounts  in “raw_readcounts.csv”, and have been normalized to Counts Per Million in “CPM_readcounts.csv”.

source_name: skin sample

extract_protocol:
Total RNA was extracted with Trizol Reagent (Life Technologies) and RNeasy Columns (Quiagen)
Lexogen 3' QuantSeq Kit (FWD protocol)

value: skin sample

tag: strain

value: OTULIN-KO

tag: tissue appearance

value: lesional


title: KD1

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

tag: experiment

tag: genotype

value: Dark

value: Superchiasmatic Nuclei

value: 11-12 weeks


title: WL1

description:
Raw_Counts_NPAS4.txt
Rpkm_NPAS4.txt

value: WT

tag: condition

tag: tissue

value: male

value: Protocol 1


title: P59_Genomic DNA CART 19

value: Yes


title: Min30_2s

description:
Raw_Counts_LightPulse.txt
Rpkm_LightPulse.txt

value: Light-Pulse

value: Light

tag: Sex

tag: batch

value: batch 2


title: P61_Genomic DNA CART 19

value: Transduced


title: P58_Genomic DNA CART 19

value: F


title: Skin, T.HS_11

description:
raw_readcounts.csv
CPM_readcounts.csv


title: Min30_2

value: batch 1

tag: protocol


title: P57_Genomic DNA CART 19

value: NHL


title: Min30_1s


title: Skin, T.HS_8

description:
raw_readcounts.csv
CPM_readcounts.csv

value: skin sample


title: Skin, T.HS_5

description:
raw_readcounts.csv
CPM_readcounts.csv

value: OTULIN-KO


title: P56_Genomic DNA CART 19


title: Min30_1


title: AmiA19

tag: population

value: Ami

tag: region

value: East Asia


title: P54_Genomic DNA CART 19

tag: patient id

value: M


title: Skin, C.HS_15

description:
raw_readcounts.csv
CPM_readcounts.csv

value: non-lesional


title: AmiA46


title: AmiA22


title: Hour6_2

value: WT

value: Superchiasmatic Nuclei

value: 11-12 weeks


title: Hour6_1

value: male

value: Protocol 1


title: P55_Genomic DNA CART 19

tag: matching transduced untransduced samples

value: Yes


title: Skin, C.HS_12

description:
raw_readcounts.csv
CPM_readcounts.csv


title: P53_Genomic DNA CART 19

tag: transduction status

value: ALL


title: Hour3_2

value: Light-Pulse

value: Light

tag: age

value: batch 2


title: P52_Genomic DNA CART 19

value: Transduced

tag: gender

value: NHL


title: Ami144


title: WCm_mycHP2

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

library_source: genomic

data_processing:
Library strategy: ChIP-exo
The quality of the sequence reads obtained from ChIP-exo was checked by FastQC.
The sequence reads were aligned to the reference genome using bowtie (version 1.2.2).
Signal-to-noise ratio of each CRP binding site was calculated according to previous studies (Seo, S.W. et al. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun 5, 4910 (2014) & Seo, S.W., Kim, D., O'Brien, E.J., Szubin, R. & Palsson, B.O. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun 6, 7970 (2015)).
Difference of CRP binding signals between wild-type CRP and CRP(T168P) was compared.
Genome_build: CP002185.1, CP002186.1, CP002187.1
Supplementary_files_format_and_content: gff, raw counts of sequencing reads

organism: Escherichia coli

source_name: ATCC 9637

growth_protocol: Overnight cultured E. coli cells were inoculated into 50 mL medium in a 300-mL flask with initial 0.05 OD, and incubated with shaking at 220 rpm at 37 °C. When approximately 0.9 OD was reached, cells were induced for 6 h.

extract_protocol:
The cross-linked cells were sonicated using a Q800R Sonicator (Qsonica). From these lysates, the DNA bound to CRP protein was isolated by ChIP with anti-myc antibody and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) with washings.
The sheared DNA of chromatin beads was end-repaired, dA-tailed, and ligated with the first adapter using the KAPA HyperPrep Kit (KAPA Biosystems). Adapter ligated DNA samples were then nick-repaired and exonuclease-treated. The DNA samples were eluted from the beads by reversing protein-DNA crosslinking at 65 °C. Primer extension and second adapter ligation were performed in sequence. Finally, the DNA samples were enriched by PCR, using KAPA HotStart ReadMix in HyperPrep Kit (KAPA Biosystems). DNA after each reaction were purified and size-selected using either AMPure XP beads (Beckman Coulter, Brea, CA, USA) or Zymo DNA Clean & Concentrator (Zymo, Irvine, CA, USA).

treatment_protocol: Cultured cells were cross-linked by formaldehyde for 25min.

value: W

tag: epitope

value: 8X myc

tag: chip antibody

value: anti-Myc 9E10 (Santa Cruz Biotechnology, Dallas, TX, USA)


title: Hour3_1


title: Skin, T.HS_2

description:
raw_readcounts.csv
CPM_readcounts.csv

value: skin sample

tag: strain

value: OTULIN-KO

tag: tissue appearance

value: lesional


title: Skin, C.HS_9

description:
raw_readcounts.csv
CPM_readcounts.csv

tag: genotype

value: non-lesional


title: WCm_mycHP1


title: AmiA20

value: Ami

value: East Asia


title: Skin, C.HS_6

description:
raw_readcounts.csv
CPM_readcounts.csv


title: AmiA30


title: P51_Genomic DNA CART 19

value: M

tag: disease


title: AmiA10


title: Hour1_2

tag: experiment

value: WT

tag: condition

tag: tissue

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: male

value: Protocol 1


title: WC_mycHP2


title: AmiA43


title: P50_Genomic DNA CART 19

value: Yes

value: Transduced

value: F


title: Skin, C.HS_3

description:
raw_readcounts.csv
CPM_readcounts.csv


title: AmiA21


title: Skin, WT.HS_13

description:
raw_readcounts.csv
CPM_readcounts.csv


title: Ami136


title: CT23_2

value: Light-Pulse

value: Dark

tag: Sex

tag: batch

value: batch 2

tag: protocol


title: ECW_control

value: W

value: anti-Myc 9E10 (Santa Cruz Biotechnology, Dallas, TX, USA)


title: Hour1_1

value: Light


title: P49_Genomic DNA CART 19

tag: patient id

value: NHL


title: P48_Genomic DNA CART 19

tag: matching transduced untransduced samples


title: Ami140

tag: population

value: Ami

tag: region

value: East Asia


title: CT23_1

value: WT

tag: age

value: batch 1


title: P47_Genomic DNA CART 19

tag: transduction status

tag: gender


title: Skin, WT.HS_10

description:
raw_readcounts.csv
CPM_readcounts.csv

value: skin sample

tag: strain

value: non-lesional


title: Skin, WT.HS_7

description:
raw_readcounts.csv
CPM_readcounts.csv

tag: tissue appearance


title: CT17_2s

tag: genotype

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: male

value: Protocol 1


title: AmiA7


title: P46_Genomic DNA CART 19

value: Yes

value: Transduced

value: F

tag: disease


title: Skin, WT.HS_1

description:
raw_readcounts.csv
CPM_readcounts.csv


title: runx1:mCherry+ at 52 hpf #1

city: Bronx

first: Teresa

last: Bowman

state: New York

address: 1300 Morris Park Avenue

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

data_processing:
Illumina BCL output files were generated to FASTQ files using cellranger mkfastq
Custom reference used for alignment was generated using cellranger mkref (10X genomics) on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences.
cellranger count was used on FASTQ files to perform alignment, filtering, barcode counting, and unique molecular identifier counting.
Filtered outputs from cell ranger (features, barcodes, and matrix) were analyzed using Seurat V4 (Hao et al., 2020) and Monocle 3 (Trapnell et al., 2014; Cao et al., 2019)
Loom files were generated using cellranger output and velocyto pipelines (Gioele La Manno et al., 2018). scVelo (Bergen et al., 2020) was used for downstream loom file analysis.
Genome_build: GRCz11/danRer11
Supplementary_files_format_and_content: tab-separated value text files were generated using cell ranger and loom files were generate using velocyto (RNA velocities)

molecule: polyA RNA

organism: Danio rerio

source_name: hematopoietic cells

extract_protocol:
draculin:mCherry+;gata1:GFP- or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria.
Sorted Cell populations were loaded on a Chromium Single Cell Controller (10X Genomics) to generate single-cell gel beads in emulsion (GEMs) by using  Single Cell 3' Reagents Kits v3.1 (10X Genomics). Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). ScRNA-Seq libraries were prepared using Single Cell 3' library Gel Bead Kit v3.1 (10X Genomics) following the manufacture's instructions.

value: 52 hours post fertilization


title: runx1:mCherry+ at 52 hpf #2 (replicate)


title: Ami134


title: Skin, WT.HS_4

description:
raw_readcounts.csv
CPM_readcounts.csv


title: P45_Genomic DNA CART 19

description: T cells were selected by CliniMACs Prodigy ® system (Miltenyi Biotec) from apheresis products and culture in IL-7 and IL-15 containing media. 24 hours upon activation cells were transduced with a lentivirus expressing the anti-hCD19 A3B1 monoclonal antibody conjugated with the costimulatory regions 4-1BB and CD3zeta chain. After expansion during 7-10 days, cells were cryopreserved prior to infusion.

value: No

value: M

value: ALL


title: draculin:mCherry+;gata1:GFP- at 52 hpf #2 (replicate)


title: draculin:mCherry+;gata1:GFP- at 52 hpf #1


title: CT17_2

tag: experiment

value: Light-Pulse

value: Dark


title: Ami127

value: Ami

value: East Asia


title: CT17_1s

value: WT

tag: condition

value: batch 2


title: draculin:mCherry+;gata1:GFP- at 30 hpf #2 (replicate)

value: 30 hours post fertilization


title: P44_Genomic DNA CART 19


title: P43_Genomic DNA CART 19


title: CT17_1

tag: tissue

value: Superchiasmatic Nuclei

value: 11-12 weeks

value: batch 1


title: RNAseq2_BMDM_Dex_dBRD9_IFNg_LPS_rep1 [L_g_D_d1]

city: SCOTTSDALE

first: Zong

last: Wei

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N  sequences and reads with low quality from raw data.
At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the  clean data with high quality. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 and fold change >1.5 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: XLS

growth_protocol: BMDMs were isolated similarly as described before. Briefly, bone marrow from 6-12 weeks old male animals. After lysis with AKC lysis buffer, cells were plated in petri dishes, cultured with media containing RPMI, 20% FBS, 30% L-929 conditional medium, and 1% penicillin/streptomycin or anti-anti. Macrophages were digested with versine and plated with macrophage serum free medium.

extract_protocol: libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For activation of macrophages, cells were treated with vehicle, Dex (1uM), iBRD9 (3 or 10uM), dBRD9 (250nM) or combination for overnight, followed by stimulation of LPS (100ng/ml, Sigma) for 3 hours, before harvested for RNA-seq.

tag: cell type

value: bone marrow-derived macrophage (BMDM)

tag: treatment


title: P42_Genomic DNA CART 19

value: Transduced


title: draculin:mCherry+;gata1:GFP- at 30 hpf #1


title: RNAseq2_BMDM_dBRD9_IFNg_LPS_rep2 [L_g_d9_2]


title: Ami133


title: RNAseq2_BMDM_dBRD9_IFNg_LPS_rep1 [L_g_d9_1]


title: P41_Genomic DNA CART 19


title: Midbrain from Zebrafish Pool 3

city: San Francisco

first: Leah

last: Dorman

address: 499 Illinois St

department: Data Science

institute: CZBiohub

data_processing:
QC with FASTQC (all samples passed)
Alignment in STAR version 2.5.4b
Reads counted with HTSeq (version 0.9.0)
Reads normalization and DEGs calculation using DESeq2 version 1.24.0
Genome_build: GRCz11.98
Supplementary_files_format_and_content: Normalized counts for each sample

source_name: Midbrain

extract_protocol:
Zebrafish brains from mpeg:GFP fish were homogenized and sorted to isolate all mpeg:GFP+ cells
QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: 28 days post-fertilization

tag: biological replicate

value: Mpeg+ myeloid cells


title: WC_mycHP1

value: W

tag: epitope

value: 8X myc

tag: chip antibody

value: anti-Myc 9E10 (Santa Cruz Biotechnology, Dallas, TX, USA)


title: Midbrain from Zebrafish Pool 2


title: P40_Genomic DNA CART 19

tag: patient id

tag: matching transduced untransduced samples

value: No

value: F

value: NHL


title: RNAseq2_BMDM_Dex_IFNg_LPS_rep2 [L_g_D_2]


title: P39_Genomic DNA CART 19

value: M

tag: age

value: ALL


title: RNAseq2_BMDM_Dex_IFNg_LPS_rep1 [L_g_D_1]


title: Ami132

tag: population

value: Ami

tag: region

value: East Asia


title: Optic Tectum Zebrafish Pool 3

source_name: Optic Tectum


title: Midbrain from Zebrafish Pool 1


title: Ami131


title: P38_Genomic DNA CART 19

tag: transduction status

tag: gender


title: Optic Tectum Zebrafish Pool 2


title: 1020_KO_rpl_3

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from heart of SIRT1 KO E18.5 mouse embryos

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: E18.5 SIRT1 KO Heart

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Mice were maintained on normal chow diet

extract_protocol: TRIzol reagent, followed by RNA clean up using the Qiagen RNA easy mini kit with on-column DNAseI treatment

treatment_protocol: No special treatment

value: heart

tag: strain

tag: genotype/variation

value: SIRT1 KO

tag: diet

value: chow diet


title: RNAseq2_BMDM_IFNg_LPS_rep2 [L_g_2]

value: bone marrow-derived macrophage (BMDM)


title: 1020_KO_rpl_2


title: P37_Genomic DNA CART 19

value: Transduced

tag: disease


title: P36_Genomic DNA CART 19


title: RNAseq2_BMDM_vehicle_rep2 [Veh_2]

value: vehicle


title: Ami126


title: RNAseq2_BMDM_IFNg_LPS_rep1 [L_g_1]


title: RNAseq2_BMDM_Dex_dBRD9_IFNg_LPS_rep2 [L_g_D_d2]


title: Hindbrain from Zebrafish Pool 3

source_name: Hindbrain

value: 28 days post-fertilization

value: Mpeg+ myeloid cells


title: Ami104


title: Optic Tectum from Zebrafish Pool 1


title: P35_Genomic DNA CART 19


title: Ami102


title: Ami125


title: 1020_KO_rpl_1

tag: tissue


title: 1020_KO_rpl_4


title: 1020_WT_rpl_3

description: Gene expression from heart of WT E18.5 mouse embryos

source_name: E18.5 WT Heart

value: wild type


title: HNW_PR5316_N_base_org_S72_L004

first: Hanbing

last: Song

address: 513 Parnassus Ave

institute: UCSF

data_processing:
Demultiplexed pair-end FASTQ files were aligned to mm8 whole genome using dropseq_workflow pipeline on Terra
Genome_build: hg19
Supplementary_files_format_and_content: txt format matrix table with raw gene counts for every gene and every cell barcode

source_name: Organoid

extract_protocol:
Tissue samples were minced with surgical scissors and washed with RP-10 (RPMI + 10% FBS). Each sample was centrifuged at 1200 rpm for 5 minutes, resuspended in 10 mL digestive media (HBSS + 1% HEPES) with Liberase TM (Roche, Cat: 5401119001) or 1000 U/mL collagenase type IV (Worthington, Cat: LS004188), and rotated for 30 minutes at 37 °C. Samples were triturated by pipetting ten times after every 10 minutes during the incubation or by pipetting 15 times at the end of the incubation. Each sample was filtered through a 70 µm filter (Falcon, Cat: 352350), washed with RP-10, centrifuged at 1200 rpm for 5 minutes, washed again with RP-10, and resuspended in RP-10. A hemocytometer was used to count the cells.
Libraries were prepared for each pool, using 800-1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides. Library products were purified using SPRI beads, first at 0.6x and then at a 1x volumetric ratio. Libraries were then run on an HSD1000 tape (Agilent, Cat: 50675584) to determine the concentration between 100-1000 bp. For each library, 3 nM dilutions were prepared.

tag: patient

value: Patient 13 Organoid

value: prostate


title: RNAseq1_BMDM_Dex_dBRD9LPS_rep3 [ZW_27]

tag: cell type

tag: treatment


title: Hindbrain from Zebrafish Pool 2

tag: biological replicate


title: RNAseq2_BMDM_vehicle_rep1 [Veh_1]


title: P33_Genomic DNA CART 19

value: No


title: 1020_WT_rpl_4


title: Ami123


title: RmiA_HA_miltefosine_2

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Cafe

country: Brazil

institute: Sao Paulo University

description: cultured colonies

data_processing:
Raw data was aligned to A. fumigatus reference genome using Bowtie2 v2.3.5 tool. Initial 8bp of reads were clipped during mapping step using argument "bowtie2  --trim5 8 --local  "
Normalized the reads depth to 1 million mapped reads using "macs2 bdgopt " command from MACS2 v2.1.1
Converted bedGraph files to bigWig files using UCSC Kent Utils v369 tool "bedGraphToBigWig"
Genome_build: Aspergillus fumigatus Af293 reference genome from AspGD. Version s03-m05-r06
Supplementary_files_format_and_content: bigwig files were generated using UCSC Kent Utils v369; Scores represent normalized read depth to 1 million reads

organism: Aspergillus fumigatus

source_name: RmiA ChIPseq with miltefosine treatment

growth_protocol: Conidia were grown into liquid medium for 16 h at 37oC under shaking conditions

extract_protocol:
Chromatin preparation was performed as described by Suzuki et al., 2012
Library preparation was carried out using NEBNext® Ultra II Library Prep kit (Illumina, cat. no. E7645L) according to manufacturer’s protocol

treatment_protocol: Addition of 12.5ug/ml of miltefosine for 30min

tag: ip tag

value: HA

tag: chip antibody

value: anti-HA (sigma-aldrich)

value: miltefosine


title: PR5274_T_V2_org_S66_L004

value: Patient 12 Organoid


title: RNAseq1_BMDM_Dex_dBRD9LPS_rep2 [ZW_26]


title: Hindbrain from Zebrafish Pool 1


title: P34_Genomic DNA CART 19

tag: patient id

tag: matching transduced untransduced samples

value: F

value: ALL


title: 1020_WT_rpl_1

tag: age

value: heart


title: RNAseq1_BMDM_Dex_dBRD9LPS_rep1 [ZW_25]


title: RmiA_HA_miltefosine_1

description: cultured colonies


title: PR5274_T_V1_org_S63_L004


title: P31_Genomic DNA CART 19


title: RNAseq1_BMDM_Dex_iBRD9LPS_rep3 [ZW_24]


title: PR5269_T_org_S60_L004

value: Patient 11 Organoid


title: PR5316_T_base_org_S36_L003


title: Ami106

tag: population

value: Ami

tag: region

value: East Asia


title: RmiA_HA_2

description: cultured colonies

source_name: RmiA ChIPseq

value: untreated


title: RmiA_HA_1

description: cultured colonies


title: RNAseq1_BMDM_Dex_iBRD9LPS_rep2 [ZW_23]

value: bone marrow-derived macrophage (BMDM)


title: NEM316 Wild type replicate C

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
Experiment 1 - Replicate 3
Total RNA (after ribodepletion)
NEM316_WT_C_
processed data file: BM110-NEM316.core.complete.xls, NEM316.complete.xls

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome (BM110 or NEM136 from NCBI)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g Name -s 2).
Count data were analyzed using R  R (v3.6.1) and the Bioconductor package DESeq2 (v1.26.0). Normalization and dispersion were estimated and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model including the replicate effect as blocking factor was set in order to test for the differential expression between the mutant and the WT strains. For each comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg procedure and genes with an adjusted p-value lower than 0.005 were considered differentially expressed.
Genome_build: Streptococcus agalactiae NEM316 (from NCBI id=165229)
Genome_build: Streptococcus agalactiae BM110 (from NCBI id=318722)
Supplementary_files_format_and_content: DESeq 2 output matrix

organism: Streptococcus agalactiae

source_name: NEM316 Wild type

growth_protocol: 10 ml of fresh THY culture supplemented with 50 mM HEPES was inoculated at 37°C with 1/50 of overnight culture up to mid-exponential phase (OD600 = 0.5-0.6).

extract_protocol:
Total RNA (FastRNA ProBlue, MP Biomedicals) was extracted  and residual DNA removed with the TURBO DNase (Ambion).
DNAse treated RNA molecules were treated for library preparation using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, California) according to manufacturer’s instructions. The ribosomal RNA depletion was realized using the Ribo-Zero rRNA removal kit (bacteria, # MRZB12424, Illlumina). The obtained oriented libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified by spectrofluorimetry (Quant-iT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen).  Sequencing was performed on the Illumina Hiseq2500 platform to generate single-end 65 bp reads bearing strand specificity.

treatment_protocol: 5 min treatment at RT with two volumes of RNAprotect bacteria reagent (Quiagen) for RNA stabilization, centrifugation (4°C, 5 min), cold PBS washing (centrifugation 1 min, 4°C), pellets flash freezed in a bath of  EtOH/dry ice, pellets stored at -80°C

tag: genotypes

value: wild-type

tag: growth condition/phase

value: THY medium + 50 mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)


title: Ami101


title: RNAseq1_BMDM_Dex_iBRD9LPS_rep1 [ZW_22]

tag: strain


title: P29_Genomic DNA CART 19

tag: transduction status

value: Transduced

tag: gender


title: RNAseq1_BMDM_dBRD9LPS_rep3 [ZW_18]


title: PR5261_T_V1_org_S55_L004

value: Patient 10 Organoid

tag: tissue

value: prostate


title: HNW_PR5261_N_V2_org_S37_L003

tag: patient


title: P32_Genomic DNA CART 19

value: No

value: M

tag: disease

value: NHL


title: NEM316 Wild type replicate B

description:
Experiment 1 - Replicate 2
Total RNA (after ribodepletion)
NEM316_WT_B
processed data file: BM110-NEM316.core.complete.xls, NEM316.complete.xls


title: PR5261_T_V2_org_S58_L004


title: RNAseq1_BMDM_dBRD9LPS_rep2 [ZW_17]

tag: cell type

tag: treatment


title: NEM316 Wild type replicate A

description:
Experiment 1 - Replicate 1
Total RNA (after ribodepletion)
NEM316_WT_A
processed data file: BM110-NEM316.core.complete.xls, NEM316.complete.xls


title: PR5261_N_V1_org_S69_L004


title: Ami108


title: PR5254_N_org_pool2_pool3_S65_L004

value: Patient 9 Organoid


title: RNAseq1_BMDM_dBRD9LPS_rep1 [ZW_16]


title: P26_Genomic DNA CART 19

value: F


title: RNAseq1_BMDM_iBRD9LPS_rep3 [ZW_15]


title: P27_Genomic DNA CART 19

value: ALL


title: NEM316 covR D53A replicate C

description:
Experiment 1 - Replicate 3
Total RNA (after ribodepletion)
NEM316_D53A_C
processed data file: BM110-NEM316.core.complete.xls, NEM316.complete.xls

source_name: NEM316 covR D53A

value: CovR D53A


title: P25_Genomic DNA CART 19

source_name: High molecular weight DNA extracted from CART 19 transduced T-cells before infusion into patients


title: P30_Genomic DNA CART 19


title: RNAseq1_BMDM_iBRD9LPS_rep2 [ZW_14]


title: NEM316 covR D53A replicate B

description:
Experiment 1 - Replicate 2
Total RNA (after ribodepletion)
NEM316_D53A_B
processed data file: BM110-NEM316.core.complete.xls, NEM316.complete.xls


title: HNW_PR5254_T_org_S38_L003


title: P24_Genomic DNA CART 19


title: P28_Genomic DNA CART 19


title: HNW_PR5254_N_org_pool1_S39_L003


title: NEM316 covR D53A replicate A

description:
Experiment 1 - Replicate 1
Total RNA (after ribodepletion)
NEM316_D53A_A
processed data file: BM110-NEM316.core.complete.xls, NEM316.complete.xls


title: P23_Genomic DNA CART 19


title: BM110 CovR D53A replicate C

description:
Experiment 1 - Replicate 3
Total RNA (after ribodepletion)
BM110_D53A_C
processed data file: BM110-NEM316.core.complete.xls, BM110.complete.xls

source_name: BM110 CovR D53A


title: RNAseq1_BMDM_iBRD9LPS_rep1 [ZW_13]


title: PR5251_T_org_pool3_S62_L004

value: Patient 8 Organoid


title: HNW_PR5251_T_org_pool1_pool2_S40_L003


title: P22_Genomic DNA CART 19


title: BM110 CovR D53A replicate B

description:
Experiment 1 - Replicate 2
Total RNA (after ribodepletion)
BM110_D53A_B
processed data file: BM110-NEM316.core.complete.xls, BM110.complete.xls


title: RNAseq1_BMDM_DexLPS_rep3 [ZW_9]

value: DexLPS


title: RNAseq1_BMDM_DexLPS_rep2 [ZW_8]


title: P20_Genomic DNA CART 19


title: HNW_PR5251_N_org_pool2_S41_L003


title: BM110 CovR D53A replicate A

description:
Experiment 1 - Replicate 1
Total RNA (after ribodepletion)
BM110_D53A_A
processed data file: BM110-NEM316.core.complete.xls, BM110.complete.xls


title: P21_Genomic DNA CART 19


title: HNW_PR5251_N_org_pool1_S35_L002


title: BM110 Wild type replicate C

description:
Experiment 1 - Replicate 3
Total RNA (after ribodepletion)
BM110_C
processed data file: BM110-NEM316.core.complete.xls, BM110.complete.xls

source_name: BM110 Wild type


title: RNAseq1_BMDM_DexLPS_rep1 [ZW_7]


title: BM110 Wild type replicate B

description:
Experiment 1 - Replicate 2
Total RNA (after ribodepletion)
BM110_B
processed data file: BM110-NEM316.core.complete.xls, BM110.complete.xls


title: PR5249_N_org_pool3_S57_L004

value: Patient 7 Organoid


title: RNAseq1_BMDM_LPS_rep1 [ZW_4]

value: LPS


title: P19_Genomic DNA CART 19


title: P18_Genomic DNA CART 19


title: BM110 Wild type replicate A

description:
Experiment 1 - Replicate 1
Total RNA (after ribodepletion)
BM110_A
processed data file: BM110-NEM316.core.complete.xls, BM110.complete.xls


title: RNAseq1_BMDM_LPS_rep2 [ZW_5]

value: bone marrow-derived macrophage (BMDM)


title: PA_PR5269_4_S28_L002

source_name: Radical Prostatectomy Tumor

value: Patient 11


title: P17_Genomic DNA CART 19


title: HNW_PR5249_N_org_pool1_pool2_S42_L003


title: BM110 Wild type replicate 3

description:
Experiment 2 - Replicate 3
Total RNA (after ribodepletion)
bmWT3
processed data file: BM110.CovRvsWT.complete.xls

value: wild-type

value: THY medium + 50 mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)


title: RNAseq1_BMDM_vehicle_rep3 [ZW_3]

value: vehicle


title: P15_Genomic DNA CART 19

value: Transduced


title: PA_PR5269_2_S26_L002

value: prostate


title: BM110 Wild type replicate 2

description:
Experiment 2 - Replicate 2
Total RNA (after ribodepletion)
bmWT2
processed data file: BM110.CovRvsWT.complete.xls


title: RNAseq1_BMDM_vehicle_rep2 [ZW_2]


title: PA_PR5269_3_S27_L002


title: RNAseq1_BMDM_LPS_rep3 [ZW_6]


title: P16_Genomic DNA CART 19

description: T cells were selected by CliniMACs Prodigy ® system (Miltenyi Biotec) from apheresis products and culture in IL-7 and IL-15 containing media. 24 hours upon activation cells were transduced with a lentivirus expressing the anti-hCD19 A3B1 monoclonal antibody conjugated with the costimulatory regions 4-1BB and CD3zeta chain. After expansion during 7-10 days, cells were cryopreserved prior to infusion.

value: No

value: M


title: P14_Genomic DNA CART 19


title: RNAseq1_BMDM_vehicle_rep1 [ZW_1]


title: PA_PR5269_1_S25_L002


title: CUT&RUN_Raw264.7_dBRD9DexLPS_BRD9

data_processing:
library strategy: CUT&RUN
Paired-end reads were trimmed and quality-filtered using cutadapt (V2.8). Trimmed qualified reads were aligned to mouse reference genome GRCm38 using bowtie2 (v2.3.3.1) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Only reads that were uniquely mapped were retained for further analysis. PCR duplicated reads were removed using “MarkDuplicates.jar” from Picard tools v.2.17.0. RPKM-normalized bigWig files were generated with bamCoverage from deepTools v3.3.2. Heatmaps were generated using computeMatrix and plotHeatmap from deepTools v3.3.2.
CUT&RUN peaks were called using findPeaks within HOMER using default parameters for TF (-style factor). The identified peaks for BRD9 were further screened against ‘mouse blacklisted’ genomic regions, mitochondrial DNA, and pseudo-chromosomes. Known motif finding on identified peaks was done by Homer findMotifsGenome.pl using parameter ‘-size given’.
Genome_build: GRCm38
Supplementary_files_format_and_content: BigWig files

source_name: macrophages

extract_protocol:
The experimental procedure for CUN&RUN was previously described(38).
libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells were pre-treated with vehicle, Dex (1uM), or Dex+dBRD9 (250nM) for overnight and then treated with LPS (100ng/mL) for 3 hours. 0.1 million cells were used for each CUT&RUN.

value: BALB/c

tag: cell line

value: macrophages

value: Dex+dBRD9 (250nM)


title: P13_Genomic DNA CART 19

value: ALL


title: CUT&RUN_Raw264.7_DexLPS_BRD9

value: vehicle, Dex (1uM)


title: BM110 Delta CovR replicate 3

description:
Experiment 2 - Replicate 3
Total RNA (after ribodepletion)
bmCovR3
processed data file: BM110.CovRvsWT.complete.xls

source_name: BM110 Delta CovR

value: {deleta}covR


title: BM110 Delta CovR replicate 2

description:
Experiment 2 - Replicate 2
Total RNA (after ribodepletion)
bmCovR2
processed data file: BM110.CovRvsWT.complete.xls


title: P11_Genomic DNA CART 19


title: ChIPseq_Raw264.7_DexLPS_dBRD9_GR

data_processing:
Sequencing was performed using Illumina technology to generate paired-end reads for each sample.
Sequence data quality was determined using FastQC software. Bowtie2(v2.3.3.1) (--very-sensitive) was used to map ChIP-seq reads to the mouse reference genome GRCm38. Duplicate reads were filtered out using the MarkDuplicate function from Picard tools v.2.17.0 (http://broadinstitute.github.io/picard/).
RPKM-normalized bigWig files were generated with bamCoverage from deepTools v3.3.2. ChIP-Seq peaks were called using findPeaks within HOMER using default parameters for TF (-style factor). De novo and known motif analyses were carried out using the findMotifsGenome.pl module of the HOMER package with the “‐size given” option.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files

extract_protocol:
20 million cells were then harvested for each ChIP assay. The experimental procedure for ChIP was as previously described (Barish et al., 2010). Briefly, after fixation, nuclei from were isolated, lysed, and sheared with a Covaris Ultrasonicator ME220 to yield DNA fragment sizes of 200–1,000 bp followed by immunoprecipitation.
libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells were pre-treated with vehicle, Dex (1uM), or Dex+dBRD9 (250nM) for overnight and then treated with LPS (100ng/mL) for 3 hours.


title: PA_PR5261_N2_S22_L002

source_name: Radical Prostatectomy Paired Normal

value: Patient 10


title: 1020_WT_rpl_2

description: Gene expression from heart of WT E18.5 mouse embryos

value: heart

tag: genotype/variation

value: wild type

tag: diet

value: chow diet


title: BM110 Wild type replicate 1

description:
Experiment 2 - Replicate 1
Total RNA (after ribodepletion)
bmWT1
processed data file: BM110.CovRvsWT.complete.xls

value: wild-type


title: ChIPseq_Raw264.7_DexLPS_GR


title: minus_N_rep3

city: Nagoya

first: Hitoshi

last: Sakakibara

address: Chikusa

country: Japan

institute: Nagoya University

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system  control and base calling through an integrated primary analysis software called RTA (Real Time  Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.  Adapters are not trimmed away from the reads.
The sequencing reads were mapped to the O. longistaminata genome obtained from the Oryza longistaminata Information Resource (http://olinfres.nig.ac.jp/)(Reuscher et al., 2018, Commun Biol 1: 162) using HISAT2 (Kim et al., 2019, Nat Biotechnol 37: 907–915), followed by featureCounts (Liao et al., 2014, Bioinformatics 30: 923–930) for counting reads and edgeR (Robinson et al., 2009, Bioinformatics 26: 139–140) for differential expression analysis.
Low expression genes were removed using filterByExpr function of edgeR with the default setting.
Supplementary_files_format_and_content: Tab-delimited text files include logCPM values for each sample (plus_N_rep1, plus_N_rep2, plus_N_rep3, plus_N_split_rep1, plus_N_split_rep2, plus_N_split_rep3, minus_N_split_rep1, minus_N_split_rep2, minus_N_split_rep3, minus_N_rep1, minus_N_rep2, minus_N_rep3).
Supplementary_files_format_and_content: Matrix table (Raw_gene_counts_matrix.csv) with raw gene counts for every gene and every sample

organism: Oryza longistaminata

growth_protocol: O. longistaminata was hydroponically grown under natural light conditions in a greenhouse with a nutrient solution containing 1 mM NH4Cl as the sole nitrogen source and was renewed once every 3 or 4 days. Pairs of young ramets grown on the proximal nodes of rhizomes were excised and used in experiments. The growth stage of all ramet pairs was similar; each ramet had two to three fully developed leaves.

extract_protocol:
Total RNA was extracted from frozen and ground tissues using the RNeasy Plant Mini Kit (Qiagen) with the RNase-Free-DNase Set (Qiagen) according to the supplier’s protocols.
Libraries were prepared with the TruSeq Standard mRNA Library Prep Kit (Illumina) using 1 µg of total RNA with the standard protocol.

treatment_protocol: The roots of O. longistaminata ramet pair, connected by rhizomes, were incubated in two separate pots for 24 h. One of the roots was treated with the nutrient solution containing 2.5 mM NH4Cl (plus N split), and the other was treated with 0 mM NH4Cl (minus N split). For comparison, both roots were treated with 2.5 mM NH4Cl (plus N) or 0 mM NH4Cl (minus N).

value: root

tag: growth stage

value: each ramet has two to three fully developed leaves.

value: Both romet pair roots were treated with 0 mM NH4Cl for 24 h.


title: P10_Genomic DNA CART 19

tag: patient id

tag: matching transduced untransduced samples

value: Transduced

value: F

tag: age


title: P8_Genomic DNA CART 19

value: No

value: M


title: minus_N_rep2


title: PA_PR5254_N2_S14_L001

value: Patient 9

value: prostate


title: AR-/Y 4

city: Heverlee

first: Sarah

last: El Kharraz

address: Herestraat 49

country: Belgium

institute: KU Leuven

description:
LBD_male_vs_ARKO_KO.absolute_counts.csv
ARKO_KO_vs_WT_male.absolute_counts.csv
RNASeq data with FPKM norm_samplecode.txt

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7
Adapters were filtered with ea-utils fastq-mcf v1.05 Erik Aronesty (2011), ea-utils: “Command-line tools for processing biological sequencing data”; https://github.com/ExpressionAnalysis/ea-utils)
Splice-aware alignment was performed with HiSAT2 against the mouse reference genome mm10. Reads mapping to multiple loci in the reference genome were discarded.
Resulting BAM files were handled with Samtools v1.5 (Li et al, Bioinformatics,2009). Quantification of reads per gene was performed with HT-seq Count v2.7.14.
Count-based differential expression analysis was done with R-based Bioconductor package DESeq2 (Love MI, Huber W, Anders S (2014), “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550).  Reported p-values were adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Testis

extract_protocol:
Testes were removed and snap-freezed in liquid nitrogen. RNA was extracted via Nucleospin Triprep column purification.
Libraries were generated with the Illumina TruSeq Stranded mRNA Sample Preparation Kit 381 and subsequently sequenced on the Illumina HiSeq4000.

value: Testis

tag: genotype

value: AR-/Y


title: PA_PR5261_T2_S24_L002

source_name: Radical Prostatectomy Paired Tumor


title: BM110 Delta CovR replicate 1

description:
Experiment 2 - Replicate 1
Total RNA (after ribodepletion)
bmCovR1
processed data file: BM110.CovRvsWT.complete.xls

tag: genotypes

value: {deleta}covR

tag: growth condition/phase

value: THY medium + 50 mM HEPES, mid-exponential phase (OD600 = 0,5-0,6)


title: minus_N_rep1

tag: strain

value: One ramet root was exposed to 2.5 mM NH4Cl (plus N split), and the other was exposed to 0 mM NH4Cl (minus N split) for 24 h.


title: P12_Genomic DNA CART 19

data_processing: Raw signal intensity data were initially QC’d and preprocessed from resulting idat files in R statistical environment (v4.0.3) using minfi Bioconductor package (v1.36.0). A number of quality control steps were applied to minimize errors and remove erratic probe signals, such as failed probes (probes with detection P value > 0.01 in at least 10% of samples were removed. If probe P value > 0.01 in less than 10% of samples, the Beta values of those probes in the failed samples were marked as NAs and later imputed using the median), cross-reacting probes, and probes that overlapped SNPs within ±1 bp of CpG sites, followed by background correction and dye-based normalization using ssNoob algorithm (single-sample normal-exponential out-of-band). All analyses were performed under R statistical environment (v4.0.3)

extract_protocol: Total DNA was isolated by standard procedures

tag: transduction status

tag: gender

value: ALL


title: PA_PR5261_N1_S21_L002

tag: patient

value: Patient 10

tag: tissue


title: AR-/Y 5


title: P9_Genomic DNA CART 19

tag: disease


title: P7_Genomic DNA CART 19


title: PA_PR5254_N1_S13_L001


title: AR-/Y 2


title: PA_PR5261_T1_S23_L002


title: minus_N_split_rep3

tag: treatment


title: PA_PR5254_T1_S15_L001


title: minus_N_split_rep2


title: P5_Genomic DNA CART 19

value: NHL


title: P6_Genomic DNA CART 19


title: PA_PR5251_T2_S8_L001

value: Patient 8


title: PA_PR5251_T1_S7_L001


title: AR-/Y 1


title: ARLmon/Y 5

description:
LBD_male_vs_WT_male.absolute_counts.csv
LBD_male_vs_ARKO_KO.absolute_counts.csv
RNASeq data with FPKM norm_samplecode.txt

value: ARLmon/Y


title: P4_Genomic DNA CART 19


title: ARLmon/Y 4


title: PA_PR5251_N2_S6_L001


title: plus_N_split_rep2

value: root

value: each ramet has two to three fully developed leaves.


title: plus_N_split_rep3


title: minus_N_split_rep1


title: ARLmon/Y 2


title: PA_PR5249_T2_S4_L001

value: Patient 7


title: AR-/Y 3


title: ARLmon/Y 3


title: P2_Genomic DNA CART 19

value: No

value: Transduced


title: plus_N_rep1

value: Both romet pair roots were treated with 2.5 mM NH4Cl for 24 h.


title: plus_N_rep3


title: P1_Genomic DNA CART 19

value: M


title: PA_PR5251_N1_S5_L001

value: prostate


title: BM110-tet-Tap-pos

description:
TAP treated
RNA after rRNA depletion

data_processing:
Trimming of adapters and reads shorter than 18 nucleotides using cutadapt;
Mapping by  Bowtie 1.1.2 (options -n 2 -l 20 -k 1 -m 4 -p 3) on BM110 genome sequence ( Accession: LT714196.1)
Identification of the position of the 5'ends of reads on the genome by using SAMtools
Statistical assignment of TSS positions by using EdgeR version 3.16.5) as follows: for each TAP+/TAP- pair, a common dispersion was estimated after normalization for the size of the TAP+ and TAP- libraries, assuming that the TSS positions represented only a small fraction of the total positions. This common dispersion value was used with the exact test to generate a list of positions for which reads were statistically more abundant in the TAP+ library. p-values after multiple testing adjustment procedure (Benjamini Hochberg) were calculated but found to be generally too stringent, eliminating many potential TSSs, that were elsewhere characterized in another S. agalactiae strain NEM316 (Rosinski-Chupin et al. https://doi.org/10.1186/s12864-019-5613-5)
Genome_build: Streptococcus agalactiae isolate BM110  from NCBI  (Accession: LT714196.1)
Supplementary_files_format_and_content: list of TSS  with the raw number of counts in TAP+ and TAP- conditions in the 3 experiments, the logFC of TAP+ vs TAP- counts after normalization (EdgeR) and the pvalue as calculated by using edgerR. FDR estimated for these experiments as too stringent and not reported; Sheets M1 counts, M2 counts, M3 counts: details of the counts corresponding to the 5' end position for each position of the genome under TAP+ and TAP- conditions for each experiment:  start of the read, raw number of counts under TAP- condition; raw number of counts under TAP+ condition; orientation of reads; log2FC: log2 of TAP+ vs TAP- counts after normalization (EdgeR); log2CPM: log2 of the mean value of TAP+ and TAP- counts after normalization (EdgeR); pvalue (EdgeR)

source_name: bacteria pellet

extract_protocol:
15-40 ml of bacterial culture were rapidly centrifuged, the pellet was frozen in dry ice/ethanol and stored at -80 degree centigrade. Bacterial pellets were resuspended in 400 µl 10% glucose, 60 mM EDTA, 12.5 mM Tris pH 7.6. Bacteria cell walls were broken by using two cycles in FastPrep (FastPrep FP120 homogenizer- speed: 6, time:30 s) at 4 \"C, separated by 1 min., in the presence of 0.4 g of 200-300 µM glass beads and 500 µl acid phenol pH 4.5. After centrifugation the aquaeous phase was extracted once with 1 ml trizol and 100µl phenol:chloroform:isoamyl alcohol (25:24:1 volume ratio) and once with 200 μl chloroform:isoamyl alcohol and RNA was precipitated by isopropanol. Traces of DNA were removed by using the Turbo DNA-free kit(Life Technologies) according to manufacturer’s instructionq. RNA quality was controled on Agilent 2100 Bioanalyzer with RNA 6000 nanochip and only RNA with RNA Integrity Number (RIN) higher than 9 was used.8 µg total RNA from each RNA sample was depleted in rRNA by using the MICROBExpress bacterial mRNA enrichment kit and rRNA depletion was controled on Agilent Bioanalyzer.
ssRNA-seq performed as follows : depleted RNAs from each of the 6 samples were mixed. Depleted RNA samples were divided into two subsamples (hereby TAP+ and TAP-) containing the equivalent of 7.5 μ g of total RNA. The TAP+ subsample was pretreated with 10 U of Tobacco Acid Phosphatase (Tebu-Bio), the other steps being strictly run in parallel for the two subsamples. TAP treatment was followed by ligation with an excess of 5′ adapter (Illumina TruSeq Small RNA kit) and by reverse transcription using a random primer (RPO primer: 5′ CCTTGGCACCCGAGAATTCCANNNNNN- 3′ ). The first strand cDNA/RNA hybrids were then run on a 2% Low Range Agarose (Biorad). cDNAs ranging from 120 to 250 bp were extracted from a gel slice by using the Qiaquick gel extraction kit (Qiagen) and PCR amplified for 14 cycles using the Illumina primer RP1, and one of the indexed primers (Illumina TruSeq Small RNA kit). The resulting PCR products were purified were purified twice with 1.3 volumes of AMPure beads (Agencourt), DNA concentration was measured using Qubit quantification and size of the PCR products was estimated on DNA 1000 Bioanalyzer chip (Agilent) before sequencing on Illumina GAIIX or HiSeq 2000

tag: strain background

value: wild-type

value: late-exponential phase in TH+Tetracycline 10 mg/l


title: PA_PR5249_N1_S1_L001


title: plus_N_rep2


title: PA_PR5249_N2_S2_L001


title: BM110-TC-Tap-neg

description:
Not treated by TAP
RNA after rRNA depletion

value: Transconjugant


title: P3_Genomic DNA CART 19

value: F


title: WT 3

description:
LBD_male_vs_WT_male.absolute_counts.csv
ARKO_KO_vs_WT_male.absolute_counts.csv
RNASeq data with FPKM norm_samplecode.txt

value: Testis

value: Wild type


title: BM110-TC-Tap-pos

description:
TAP treated
RNA after rRNA depletion


title: T_6h_124

city: Southampton

first: Jodie

last: Ackland

state: Hampshire

address: Mail Point 810, Level F, South Block Southampton General Hospital, Tremona Road

department: Clinical and Experimental Sciences, Faculty of Medicine

country: United Kingdom

institute: University of Southampton

description: Infected (T, treated) sample at 6h (6h) for sample ID 124 (124)

data_processing:
The Spliced Transcripts Alignment to a Reference (STAR) software (version 2.5) was used to map reads to the human genome (hg38) and Bowtie (version 2.2.3) was used to map reads to the NTHi ST14 genome
Aligned reads were quantified using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample for MDM or NTHi data

organism:
Haemophilus influenzae
Homo sapiens

extract_protocol:
miRNeasy kit
ribosomal RNA (rRNA) was removed from all samples using Ribo-Zero™ Magnetic Kit and libraries were generated using the NEBNext®Ultra™ Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Samples from five biological replicates (indicated as numbers at end of sample names; 005, 016, 082, 104, 124) were either infected with NTHi (T, treated) or left uninfected (C, control) for 6h, with RNA extracted after a 90 min gentamicin wash (6h) or after a prolonged incubation until 24h (24)

tag: cell type

value: Monocyte-derived macrophage

tag: treatment/time point

value: Infected (T, treated) sample at 6h (6h)


title: WT 4


title: T_24_104

description: Infected (T, treated) sample at 24h (24) for sample ID 104 (104)


title: PA_PR5199-640K_Pool_1_3_S108_L004

value: Patient 6


title: ARLmon/Y 1

value: ARLmon/Y


title: T_24_124

description: Infected (T, treated) sample at 24h (24) for sample ID 124 (124)


title: plus_N_split_rep1

value: root

tag: growth stage

value: each ramet has two to three fully developed leaves.

value: One ramet root was exposed to 2.5 mM NH4Cl (+N split), and the other was exposed to 0 mM NH4Cl (-N split) for 24 h.


title: PA_PR5199-640K_Pool_2_S56_L002


title: T_6h_104

description: Infected (T, treated) sample at 6h (6h) for sample ID 104 (104)


title: PA_PR5199-193K_Pool_1_2_3_S55_L002


title: BM110-tet-Tap-neg


title: WT 2


title: BM110poolTAPP

description:
TAP treated
RNA after rRNA depletion

value: pool of  RNA prepared under mid-exponential (O.D600= 0.4) and early stationary phase (O.D600= 1.2) in a rich growth medium (TH) and under stationary phase (O.D600= 0.35) in a poor culture medium


title: PA_PR5196-1_Pool_1_2_3_S53_L002

value: Patient 5


title: PA_PR5249_T1_S3_L001

value: Patient 7


title: T_24_082

description: Infected (T, treated) sample at 24h (24) for sample ID 082 (082)


title: PA_PR5196-2_Pool_1_2_3_S54_L002

value: prostate


title: Lmon_Vehicle 5

description:
lmon_testosterone_vs_lmon_vehicle.absolute_counts.csv
wt_vehicle_vs_lmon_vehicle.absolute_counts
RNA-seq Expression Data_sample_code.txt

source_name: Kidney

extract_protocol:
Kidneys were removed after 4 days of replacement therapy and snap-freezed in liquid nitrogen. RNA was extracted via Nucleospin Triprep column purification.
Libraries were generated with the Illumina TruSeq Stranded mRNA Sample Preparation Kit 381 and subsequently sequenced on the Illumina HiSeq4000.

value: Kidney

value: vehicle


title: Lmon_Vehicle 4


title: T_6h_082

description: Infected (T, treated) sample at 6h (6h) for sample ID 082 (082)


title: BM110poolTAPM

value: wild-type

value: pool of RNA prepared under mid-exponential (O.D600= 0.4) and early stationary phase (O.D600= 1.2) in a rich growth medium (TH) and under stationary phase (O.D600= 0.35) in a poor culture medium


title: BON-1: CAFs (10:6)-rep2 [BC26-2]

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in NCBI were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
BOB-1 cells were isolated from the co-culture system by flow cytometry. Then BON-1cells were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using polyA selection RNA-seq protocols

tag: cell line


title: T_24_016

description: Infected (T, treated) sample at 24h (24) for sample ID 016 (016)


title: WT 5

value: Testis


title: WT 1

value: Wild type


title: PA_PR5186_Pool_1_2_3_S27_L001

value: Patient 4


title: T_6h_016

description: Infected (T, treated) sample at 6h (6h) for sample ID 016 (016)

value: Monocyte-derived macrophage

value: Infected (T, treated) sample at 6h (6h)


title: T_24_005

description: Infected (T, treated) sample at 24h (24) for sample ID 005 (005)


title: Lmon_Vehicle 1

value: ARLmon/Y


title: Lmon_Vehicle 3


title: BON-1: CAFs (10:6)-rep3 [BC26-3]


title: PA_PB2B_Pool_2_S26_L001

source_name: Prostate Biopsy

value: Patient 3


title: Lmon_Testosterone 5

description:
lmon_testosterone_vs_lmon_vehicle.absolute_counts.csv
wt_testosterone_vs_lmon_testosterone.absolute_counts.csv
wt_vehicle_vs_lmon_testosterone.absolute_counts.csv
RNA-seq Expression Data_sample_code.txt

value: testosterone


title: Lmon_Testosterone 4


title: Lmon_Testosterone 2


title: PA_PB1B_Pool_3_S51_L002


title: BON-1: CAFs (10:6)-rep1 [BC26-1]


title: BON-1: CAFs (10:2)-rep2 [BC22-2]


title: KO

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

data_processing:
library strategy: CUT&TAG
Data were filtered using the Trimgalore with default model
CUT&TAG reads were aligned to the mm10 genome assembly using Bowtie2 with  end to end ,very sensitive , no mixed, no discordant, -I 10 ,-X 700 model
Replication reads were discarded using picard with default model
peaks were called using HOMER findPeaks with default model.
bigwig files were product using deeptools using ignoreDuplicates model
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, peak files

source_name: Treg cells

extract_protocol:
Lysates were clarified using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech Co., Ltd)  TD901-TD902 and histone-DNA complexes were isolated with antibody
Libraries were prepared according to TruePrep® Index Kit V2 for Illumina®

tag: genotype/variation

value: Nsd2 Treg conditional knock out

value: spleen

value: Treg cells


title: Lmon_Testosterone 1


title: PA_PB2A_Pool_1_3_S25_L001


title: BON-1-rep3 [BC21-3]


title: PA_PB1A_Pool_1_3_S50_L002

value: Patient 2


title: BON-1: CAFs (10:2)-rep3 [BC22-3]


title: Lmon_Testosterone 3


title: BON-1: CAFs (10:4)-rep2 [BC24-2]


title: BON-1: CAFs (10:4)-rep1 [BC24-1]


title: BON-1: CAFs (10:2)-rep1 [BC22-1]


title: PA_AUG_PB_1B_S2

value: Patient 1

value: prostate


title: PA_PB1A_Pool_2_S107_L004


title: PA_PB2B_Pool_1_3_S52_L002


title: PA_AUG_PB_1A_S1


title: WT_Testosterone 5

description:
wt_vehicle_vs_wt_testosterone.absolute_counts
wt_testosterone_vs_lmon_testosterone.absolute_counts.csv
RNA-seq Expression Data_sample_code.txt

value: Kidney


title: WT

value: wild type (WT)


title: PA_PB1B_Pool_2_S24_L001


title: RICU201105-1_002A

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

data_processing:
Sequence reads were mapped to the human reference genome GRCh38 by HISAT2 (version 2.2.0).
Read counts were calculated by featureCounts (Version 2.0.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts for each sample.

source_name: PBMC

extract_protocol:
PAXgene Blood miRNA Kit.
Universal Plus mRNA-Seq library preparation kit with NuQuant.

value: PBMC

tag: time

value: Immunocompetent


title: Rat_epiWAT_P3_rep1

city: Strasbourg

first: Fabrice

last: Bertile

address: 25 rue Becquerel

department: Analytical Sciences

institute: CNRS, IPHC

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 1.0 ST Arrays (Affymetrix) and scanned within the IGBMC microarray and sequencing platform (Strasbourg, France).

scan_protocol: Array scanning using a Affymetrix GeneChip Scanner 3000 7G was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA expression value derived from Expression Console software; extended-gene analysis
Raw data were processed with the GeneChip Operating v1.4 (GCOS) and Expression Console v1.1 softwares (Affymetrix) for  background correction, normalization and quantification. Data analysis and statistical evaluations were performed with customized R codes (version 3.0.2, http://www.r-project.org/). Analysis was performed on the extended set of probesets. Reference genes were eliminated. Levels of expression were considered differential on the basis of ANOVA and post-hoc Tukey tests results. Hierarchical clustering was performed using the Cluster v3.0 software. Dendrograms were generated and vizualized using the Treeview v1.1.3 program.

label: biotin

organism: Rattus norvegicus

source_name: Male rat, epiWAT, Fasted (P3)

label_protocol: cRNA were synthesiszed from total RNA depletd in rRNA. Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix). All assays were performed as per Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev. 2) (http://www.affymetrix.com/support/technical/byproduct.affx?product=raexon-st).

growth_protocol: Male rats were nutritionnaly manipulated to create three different metabolic status, i.e. the fed and two fasted states (phase 2 and phase 3).

extract_protocol: RNA was isolated from homogenized liver samples using the Trizol Reagent, following the manufacturer’s instructions (ThermoFisher Scientific).

treatment_protocol: Epididymal white adipose tissue  samples were quickly collected from freshly sacrificed rats, and pieces were immediately frozen in liquid nitrogen, and then stored at -80°C until analysis. White adipose tissue samples homogenization was obtained using a laboratory ball mill.

value: epididymal white adipose tissue (epiWAT) extracts

tag: nutritional state

value: Phase 3 of fasting

value: Sprague-Dawley

value: male


title: WT_Testosterone 2

tag: genotype

value: Wild type


title: bron-2 mutant rep 2

city: Ames

first: Natalie

middle: M

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

data_processing:
Adapters trimmed using ea-utils
Reads mapped to TAIR10 using Tuxedo and Cufflinks
FPKM obtained from Cufflinks
Genome_build: TAIR10
Supplementary_files_format_and_content: comma separated value (csv) file of FPKM values for each sample

organism: Arabidopsis thaliana

source_name: root tissue

growth_protocol: Seedlings were grown on mesh on plates containing 1xMS, 1% sucrose for five days in long day conditions (16hr light, 8hr dark)

extract_protocol:
Total RNA was isolated from approximately 2 mm of five-day-old root tips using the RNeasy Micro Kit.
cDNA synthesis and amplification were performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina

value: bron-2 mutant


title: Lmon_Vehicle 2

value: ARLmon/Y

value: vehicle


title: BON-1: CAFs (10:4)-rep3 [BC24-3]


title: T_6h_005

description: Infected (T, treated) sample at 6h (6h) for sample ID 005 (005)

value: Monocyte-derived macrophage

value: Infected (T, treated) sample at 6h (6h)


title: RICU201020-2_002A


title: PA_PB1B_Pool_1_2_S74_L003

value: Patient 3


title: bron-2 mutant rep 1


title: Rat_epiWAT_P3_rep4


title: Rat_epiWAT_P3_rep3


title: RICU201015-2_002A


title: Rat_epiWAT_P3_rep2


title: BON-1-rep2 [BC21-2]


title: Rat_epiWAT_P2_rep3

source_name: Male rat, epiWAT, Fasted (P2)

value: Phase 2 of fasting


title: WT_Testosterone 3

value: testosterone


title: WT_Vehicle 4

description:
wt_vehicle_vs_wt_testosterone.absolute_counts
wt_vehicle_vs_lmon_vehicle.absolute_counts
wt_vehicle_vs_lmon_testosterone.absolute_counts.csv
RNA-seq Expression Data_sample_code.txt

value: Kidney


title: Rat_epiWAT_P2_rep1


title: WT control rep 2

value: wild type


title: RICU201022-1_002A

value: PBMC


title: Rat_epiWAT_P2_rep4


title: WT_Vehicle 3


title: WT control rep 1


title: WT_Vehicle 2


title: bron-2 mutant rep 3


title: RICU200623-1_002A

value: Immunocompetent


title: WT_Testosterone 4


title: Adult A

data_processing:
Cell Ranger 3.1.0 (STAR) alignment with Danio rerio (zebrafish) transcriptome z11
Quality control to select cells with <10% mitochondrial RNA, 500-3,000 unique genes, and 1,200-15,000 unique mRNA counts
[scaledata only] Log normalization (Seurat v3.2) with scale factor 10,000
[scaledata only] most variable genes scaled with "vst" algorithm and #genes/cell regressed out (Seurat v3.2)
Genome_build: z11
Supplementary_files_format_and_content: Counts: unnormalized count data for all cells included in the manuscript
Supplementary_files_format_and_content: Metadata: file containing age, individual, and cluster assignment for each cell
Supplementary_files_format_and_content: sc_dr_Silva2021Counts.txt: All cells in paper
Supplementary_files_format_and_content: sc_dr_Silva2021_metadata.csv: All cells in paper
Supplementary_files_format_and_content: sc_dr_Silva2021_JMscaledata.txt: Juvenile Mpeg+ cells
Supplementary_files_format_and_content: sc_dr_Silva2021_Jscaledata.txt: All Juvenile cells
Supplementary_files_format_and_content: sc_dr_Silva2021_Ascaledata.txt: Adult and Juvenile Mpeg+ cells

source_name: Brain and Spinal Cord Mpeg+ and CD45+

extract_protocol:
Zebrafish brains from mpeg:GFP; CD45:DsRed fish were homogenized and sorted to isolate single (CD45:DsRed+) and double (mpeg:GFP+/CD45:DsRed+) positive cells
10x Genomics v3.1 3' Single Index (Chip Kit B) was used to make a single cell suspension in gel beads, and the v3 3' Library Kit was used to prepare cDNA

tag: age

value: 6 months post-fertilization

tag: replicate

value: Adult A

value: Mpeg+ myeloid cells and CD45+ immune cells


title: Rat_epiWAT_P2_rep2

value: epididymal white adipose tissue (epiWAT) extracts

tag: strain

value: Sprague-Dawley

value: male


title: RICU200527-3_002A


title: WT_Vehicle 5

value: Wild type


title: Juvenile B

value: 28 days post-fertilization

value: Juvenile B


title: RICU200915-2_002A


title: 3023_Poly_IC_wt

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
3023_Poly_IC_wt
3023

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment and quatification with Kallisto l using the default parameters
reads mapped to each transcript against the RefSeq mm38 annotation download on March 2018
Normalization using DeSeq2
Genome_build: mm38
Supplementary_files_format_and_content: comma separated files include DeSeq2 normalized counts for each Sample.
Supplementary_files_format_and_content: comma separated files log ttransformed counts corrected for the experimental day for each Sample.

source_name: microglia

extract_protocol:
miRNeasy micro Kit (Qiagen)  according to the manufacturers' recommendations. Total RNA was eluted in RNAse free water.
Samples with more than 100 ng total RNA were converted into NGS libraries using the TruSeq RNA Library Prep Kit v2 (Illumina) at 100 ng input according to manufacturer’s recommendations. The size-distribution of the libraries was determined using the Agilent D1000 assay on a Tapestation 2200 system (Agilent). Libraries were quantified using a Qubit HS dsDNA assay. 75 bp single-end sequencing was performed on a HiSeq1500 system using Rapid v2 chemistry. Base calling from base call files and demultiplexing was performed with CASAVA v1.8 (Illumina). Low input Samples were converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the SMART-Seq2 protocol. Shortly, mRNA was primed for SMART reverse transcription from 5 ng of total RNA using poly-T oligos. cDNA was pre-amplified by SMART ISPCR. Fragmentation was performed using the Illumina Nextera XT kit, followed by PCR amplification and indexing. Size-selection and purification of library fragments preferentially 300-400 bp in length was performed using SPRIBeads (Beckman-Coulter). The size-distribution of cDNA libraries was measured using the Agilent high sensitivity D5000 assay on a Tapestation 4200 system (Agilent). cDNA libraries were quantified using a Qubit high sensitivity dsDNA assay. 75 bp single-end sequencing was performed on a NextSeq500 system using High Output v2.5 chemistry. Base calling from base call files and file conversion to fastq files were achieved by Illumina standard pipeline scripts (bcl2fastq2 v.2.20).

treatment_protocol:
Briefly, after decapitation, extracted brains were collected in ice-cold PBS. Cortices of both hemispheres were collected after removal of meninges and triturated until a single-cell suspension was achieved. Isolated cells were cultivated as mixed glia culture until they reached confluency after approximately 14 days. Cells were cultivated in DMEM high glucose (Gibco, Darmstadt, Germany) containing 10 % fetal calf serum (FCS) (PAA, Freiburg, Germany), 1 % penicillin/streptomycin (Gibco). The medium was changed twice weekly. Microglia cells were harvested by shaking for 1 h at 200 rpm and re-seeded in 24-well plates for stimulation experiments at a density of 1.5 x 105 cells/ml. After re-seeding, cells were rested for 24 h.
For stimulation experiments, cells were treated for 30 min or 16 h with E. coli LPS serotype 0127:B8 (100 ng/ml) (Sigma-Aldrich, Taufkirchen, Germany) and IFNγ (20 ng/ml) (R&D Systems, Wiesbaden, Germany), CpG (1 nmol/mL), or PolyI:C (50g/mL).

value: brain

tag: developmental stage

value: neonatal

value: WT

tag: agent


title: 3021_Poly_IC_wt

description:
3021_Poly_IC_wt
3021

tag: tissue


title: BON-1-rep1 [BC21-1]


title: WT control rep 3


title: 3020_CpG_wt

description:
3020_CpG_wt
3020

value: CpG


title: 3019_CpG_wt

description:
3019_CpG_wt
3019


title: RICU200109-1_002A

tag: patient


title: 3018_CpG_wt

description:
3018_CpG_wt
3018


title: 3022_Poly_IC_wt

description:
3022_Poly_IC_wt
3022


title: bri TRIPLE

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

institute: VIB

description: Root tips of 6-d-old-seedlings Arabidopsis thaliana bri TRIPLE

data_processing:
Demultiplexing; Cell Ranger mkfastq; version 3.0.2
Read alignment + counting; Cell Ranger count; version 3.0.2
Genome_build: TAIR 10; Ensembl Plants, release 40
Supplementary_files_format_and_content: h5 file containing filtered count matrix  (output Cell Ranger count)

source_name: root tip

growth_protocol: All seeds were surface sterilized, sown on solid 1⁄2 MS plates without sucrose, and stratified for 24h at 4°C two days before they were grown at 22°C in continuous light conditions.

extract_protocol:
Root tips of 6-d-old seedlings were cut and incubated in protoplasting Solution B [1.5% (wt/vol) cellulysin and 0.1% (wt/vol) pectolyase in Solution A (600 mM mannitol, 2 mMMgCl2, 0.1% [wt/vol] BSA, 2 mMCaCl2, 2 mMMes, 10mMKCl, pH 5.5)] for approximately 1 h at room temperature. Cells were filtered through a 70 μm cell strainer and spun down at 200 × g for 6 min; resuspended in Solution A, filtered through a 40 μm cell strainer and stained for live/dead using 4′,6- diamidino-2-phenylindole (DAPI) at 14 μM final concentration. Cells were sorted on a BD Aria II, and protoplasts not containing the DAPI signal were selected for further analysis.
Sorted cells were centrifuged at 4°C at 400g and resuspended in solution A to yield an estimated concentration of 1000 cells/μl. Cellular suspensions were loaded on a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit (V3 chemistry, 10X Genomics) according to the manufacturer’s instructions.

tag: ecotype

value: bri TRIPLE

value: root tip


title: WT_8hr_4

description:
BR147
QuantSeq_all_TMM.csv

data_processing:
Raw reads were trimmed and aligned to the genome using the QuantSeq pipeline provided by Lexogen on BlueBee
Adapters trimmed using bbtools
Reads aligned using STAR Aligner. BL_15min_1, WT_15min_3, and BL_8hr_4 had low number of reads aligned and were discarded at this step.
Counts obtained using HTSeq
TMM normalization performed using edgeR
Differential expression performed using PoissonSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: .csv file of  TMM expression in all samples except those discarded after the alignment step

source_name: 7-day old seedling tissue

growth_protocol: Arabidopsis seeds were grown on media plates containing 1uM BRZ on top of nylon mesh for 7 days

extract_protocol:
RNA was extracted using Qiagen RNEasy Mini prep kid
Library was constructed using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina
Sequencing was performed on a HiSeq4000 with 50bp single end reads. All libraries were run twice, and reads were merged prior to data processing.

treatment_protocol: At 7 days, seedlings were transferred to liquid media containing 1uL brassinolide (BL) or 0uL brassinolide (Mock) for 15 min, 30 min, 1 hr, 2 hr, 4hr, or 8 hr. Three or four biological replicates were collected for each time+treatment combination

tag: treatment

value: Mock

value: 8 hr

value: 7-day old seedling tissue


title: WT_Vehicle 1

value: Kidney

value: vehicle


title: RICU191021-1_002A

tag: cell type

value: PBMC

value: Immunocompetent


title: 3017_LPS_IFNg_wt

description:
3017_LPS_IFNg_wt
3017


title: RICU200909-1_002A


title: 3015_LPS_IFNg_wt

description:
3015_LPS_IFNg_wt
3015


title: RICU200130-2_002A


title: Rat_epiWAT_Fed_rep3

source_name: Male rat, epiWAT, Fed

value: epididymal white adipose tissue (epiWAT) extracts

value: Feeding

value: Sprague-Dawley

tag: gender

value: male


title: Juvenile A

value: 28 days post-fertilization

value: Juvenile A

value: Mpeg+ myeloid cells and CD45+ immune cells


title: Rat_epiWAT_Fed_rep4


title: RICU200318-3_002A


title: RICU191224-2_002A


title: RICU190903-1_002A


title: WT_8hr_3

description:
BR146
QuantSeq_all_TMM.csv


title: Rat_epiWAT_Fed_rep2


title: 3013_Unstim_wt

description:
3013_Unstim_wt
3013

value: brain

value: neonatal

value: WT


title: RICU200527-2_002A


title: bri T-RESCUE

value: bri T-RESCUE

value: root tip


title: RICU201029-1_001A


title: RICU201015-1_001A


title: Rat_epiWAT_Fed_rep1


title: RICU201012-1_001A


title: BL_8hr_1

description:
BR140
QuantSeq_all_TMM.csv

value: BL

value: 8 hr

value: 7-day old seedling tissue


title: 3016_LPS_IFNg_wt

description:
3016_LPS_IFNg_wt
3016


title: WT_8hr_2

description:
BR145
QuantSeq_all_TMM.csv

value: Mock


title: RICU200122-1_002A

value: PBMC

value: Immunocompetent


title: RICU200908-2_001A


title: RICU191224-1_002A


title: 3014_Unstim_wt

description:
3014_Unstim_wt
3014


title: Sample_2696_R1_inf

first: Branko

last: Cirovic

address: Carl-Troll Str 31

institute: LIMES

data_processing:
raw data was converted and multiplexed using bcl2fastq2 (v2.20).
reads were aligned to human mm10 index with bowtie1 (v1.1.1).
duplicates were filtered by applying the Picard (v1.134) tool.
removal of adapter offset and creation of bam files was done with samtools.
open chromatin peaks were called using MACS2  (v2.1.0.20140616).
blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were excluded.
peaks were annotated using HOMER (v4.10, applying annotatePeaks.pl). Downstream analysis was performed within the DESeq2 (v1.20.0) package environment.
Genome_build: mm10
Supplementary_files_format_and_content: normalised peak count table derived from DESeq2 analysis containing all samples

source_name: bone marrow, F1T

extract_protocol:
Samples for ATAC-seq analysis were prepared from FACS-enriched GMPs from bone marrow. 50,000 cells were washed in cold PBS and resuspended in cold lysis buffer (10 mM NaCL, 3 mM MgCl2, 0.1 % IGEPAL, 10mM Tris-HCl pH7.4).
After centrifugation, pellets were incubated in primer-loaded transposase Tn5 in reaction buffer (10 mM TAPS-NaOH (pH 8.5) at 25°C, 5 mM MgCl2, 10% DMF) for 30 min at 37ºC. Samples were subsequently immediately purified using the MinElute kit (Qiagen GmbH) according to the manufacturer’s guidelines, eluted in 10 µl H2O and stored at -20 ºC until further processing.

value: bone marrow

tag: condition

value: infected fathers

value: GMP


title: RICU191008-2_002A


title: RICU200616-1_001A


title: BL_8hr_3

description:
BR142
QuantSeq_all_TMM.csv


title: WT_8hr_1

description:
BR144
QuantSeq_all_TMM.csv


title: RICU200520-1_001A


title: BL_8hr_2

description:
BR141
QuantSeq_all_TMM.csv


title: BL_8hr_4

description:
BR143
Discarded due to low read number


title: BL_4hr_2

description:
BR133
QuantSeq_all_TMM.csv

value: 4 hr


title: WT_4hr_3

description:
BR138
QuantSeq_all_TMM.csv


title: Sample_2701_R1_inf


title: 3012_Unstim_wt

description:
3012_Unstim_wt
3012


title: Sample_2700_R1_inf


title: Sample_2703_R1_inf


title: WT_4hr_2

description:
BR137
QuantSeq_all_TMM.csv


title: RICU200121-1_001A


title: Sample_2697_R1_inf


title: RICU201008-1_001A


title: Sample_2691_R1_inf


title: RICU200902-1_001A


title: WT_2hr_4

description:
BR131
QuantSeq_all_TMM.csv

value: 2 hr


title: WT_4hr_1

description:
BR136
QuantSeq_all_TMM.csv


title: WT_4hr_4

description:
BR139
QuantSeq_all_TMM.csv


title: BL_4hr_4

description:
BR135
QuantSeq_all_TMM.csv


title: RICU200102-1_001A


title: Sample_2695_R1_inf


title: RICU191217-2_001A


title: Sample_2688_R1_inf


title: BL_4hr_3

description:
BR134
QuantSeq_all_TMM.csv


title: RICU191217-1_001A


title: RICU200520-2_001A


title: Sample_2699_R1_inf


title: Sample_2694_R1_inf


title: RICU191014-1_001A


title: WT_Testosterone 1

value: Kidney

value: Wild type

value: testosterone


title: Sample_2684_R1_ctrl

source_name: bone marrow, F1R

value: control fathers


title: RICU200311-4_001A


title: BL_2hr_1

description:
BR124
QuantSeq_all_TMM.csv


title: Sample_2692_R1_inf


title: Sample_2693_R1_inf


title: RICU201005-1_002A

value: Immunocompromised

tag: diagnosis

value: Sepsis


title: BL_4hr_1

description:
BR132
QuantSeq_all_TMM.csv

value: BL


title: WT_1hr_3

description:
BR122
QuantSeq_all_TMM.csv

value: 1 hr


title: Sample_2681_R1_ctrl


title: Sample_2680_R1_ctrl


title: RICU200116-1_001A


title: WT_2hr_1

description:
BR128
QuantSeq_all_TMM.csv

value: 7-day old seedling tissue


title: WT_2hr_3

description:
BR130
QuantSeq_all_TMM.csv

value: Mock


title: WT_1hr_1

description:
BR120
QuantSeq_all_TMM.csv


title: Sample_2689_R1_inf


title: Sample_2686_R1_ctrl


title: WT_2hr_2

description:
BR129
QuantSeq_all_TMM.csv


title: RICU200221-2_002A

value: PBMC


title: Sample_2687_R1_ctrl


title: BL_2hr_4

description:
BR127
QuantSeq_all_TMM.csv


title: BL_2hr_3

description:
BR126
QuantSeq_all_TMM.csv


title: RICU190827-1_001A

value: Immunocompetent


title: BL_2hr_2

description:
BR125
QuantSeq_all_TMM.csv


title: RICU200221-1_002A


title: Sample_2685_R1_ctrl

value: bone marrow


title: RICU191001-1_001A


title: RICU201028-1_002A


title: RICU200206-2_002A


title: Sample_2683_R1_ctrl


title: WT_1hr_4

description:
BR123
QuantSeq_all_TMM.csv


title: Sample_2682_R1_ctrl


title: WT_1hr_2

description:
BR121
QuantSeq_all_TMM.csv


title: RICU200727-1_002A


title: Sample_2672_R1_ctrl


title: RICU200417-1_002A


title: RICU191230-1_002A


title: BL_1hr_4

description:
BR119
QuantSeq_all_TMM.csv


title: Sample_2679_R1_ctrl


title: BL_1hr_3

description:
BR118
QuantSeq_all_TMM.csv


title: Donor C (F/45y), NRX/DC

city: Edmonton

first: Adetola

middle: B

last: Adesida

state: Alberta

address: 3.002E Li Ka Shing Centre for Health Research Innovation

department: Surgery

institute: University of Alberta

description: NDC_C (Normoxia dynamic compression C) -> F/45y, NRX, DC)

data_processing:
Partek Flow: Trim bases: Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Partek Flow: Alignment (STAR 2.7.3a): Default settings from Partek Flow
Partek Flow: Quantify to annotation model (Partek E/M): Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Partek Flow: Filter features: Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts
Partek Flow: Normalize counts: Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
Partek Flow: ANOVA for DEGs: Factors: Oxygen Tension + Mechanical Loading + Donor (Random) + Oxygen Tension*Mechanical Loading. Shrinkage of error term variance: Limma-trend

source_name: human engineered meniscus

growth_protocol: Meniscus cells (meniscus fibrochondrocytes) were isolated from partial meniscectomy tissue samples. They were expanded in normoxia (standard 5% CO2, 95% air incubator) to passage 2 (~7 population doublings) with supplementation of TGF-beta1 and FGF-2. They were then seeded onto cylindrical type I collagen scaffolds (6 mm diameter, 3.5 mm height) at a density of 5x10^6 million/cm^3 and cultured for 3 weeks in normoxia in a standard chondrogenic medium containing TGF-beta3 to form engineered meniscus tissues before treatment.

extract_protocol:
RNA was extracted using LunaNano PureSPIN columns with a DNAse digestion step. RNA concentrations were measured using a NanoDrop One. Equal masses of RNA from 4 replicate tissues from each donor in each condition were then pooled together to reduce inter-replicate variability (12 pools in total). These samples were then shipped to the UBC Biomedical Research Center for RNA sequencing.
Illumina NextSeq 500: PolyA selection, 20million paired reads

treatment_protocol: Tissues were randomly allocated into treatments in hypoxia (3% O2, 5% CO2) or normoxia (20% O2, 5% CO2). The loading treatments were then applied: 1. Static: tissues were placed in bioreactor but with no compression, or 2. Dynamic Compression: tissues were compressed to 30% strain and then cycled between 30-40% strain for 60 minutes, alternating between 0.25/1 Hz, for five consecutive days. On the last day, tissues were allowed 30 minutes to rest and then were put into TRIzol reagent and frozen to preserve RNA level changes.

value: human engineered meniscus

tag: donor identifier

tag: oxygen tension

value: NRX (normoxia, 20% O2)

tag: loading group

value: DC (dynamic compression)


title: Sample_2677_R1_ctrl

value: GMP


title: C-DM-W3 RNA-seq

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

data_processing:
Sequenced read quality was checked with FastQC.
After quality control, the fragments were 5’, 3’-adaptor trimmed and fltered <= 20 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with Hisat2 software.
The expression level (FPKM value) of known genes was calculated using ballgown through the transcript abundances estimated with StringTie.
Diﬀerentially expressed gene analysis was performed with R package ballgown.
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression_Gene.xlsx

source_name: regenerative corneal epithelium

extract_protocol:
The regenerative corneal epithelium was disrupted in TRIzol reagent (Invitrogen, USA) immediately and stored at -80°C until further experiments could be performed. The RNA obtained was run on agarose gels to measure degradation and contamination. RNA quantity and quality were also estimated using the NanoDrop ND-1000 system.
Complementary DNA (cDNA) libraries were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina, USA) for mRNA.Then, the quality of the amplified libraries was verified with a 2100 Bioanalyzer (Agilent, USA). Sequencing of high-quality  mRNA was carried out using the Illumina NovaSeq 6000 (Illumina, USA)

value: C57BL/6 + STZ

value: post treatment 16 weeks


title: RICU200206-1_002A

tag: time


title: RICU191230-2_002A


title: Sample_2674_R1_ctrl


title: C-DM-W1 RNA-seq


title: Donor B (M/22y), HYP/Stat

description: HS_B (Hypoxia static B) -> M/22y, HYP, Stat)

value: HYP (hypoxia, 3% O2)

value: Stat (static control)


title: BL_1hr_1

description:
BR116
QuantSeq_all_TMM.csv


title: RICU191125-1_002A

value: Immunocompromised


title: WT_30min_1

description:
BR112
QuantSeq_all_TMM.csv

value: 30 min


title: Donor C (F/45y), NRX/Stat

description: NS_C (Normoxia static C) -> F/45y, NRX, Stat)


title: RICU191217-3_002A

value: Sepsis


title: BL_1hr_2

description:
BR117
QuantSeq_all_TMM.csv

value: BL

value: 1 hr


title: Donor C (F/45y), HYP/DC

description: HDC_C (Hypoxia dynamic compression C) -> F/45y, HYP, DC)


title: WT_30min_3

description:
BR114
QuantSeq_all_TMM.csv

value: Mock

value: 7-day old seedling tissue


title: WT_30min_4

description:
BR115
QuantSeq_all_TMM.csv


title: Donor B (M/22y), HYP/DC

description: HDC_B (Hypoxia dynamic compression B) -> M/22y, HYP, DC)


title: RICU191114-1_002A

value: PBMC


title: Sample_2673_R1_ctrl

value: bone marrow

value: control fathers


title: RICU190911-1_002A


title: WT_30min_2

description:
BR113
QuantSeq_all_TMM.csv


title: C-Ctrl-W3 RNA-seq

value: counterpart


title: C-Ctrl-W1 RNA-seq


title: BL_30min_2

description:
BR109
QuantSeq_all_TMM.csv


title: C-DM-W2 RNA-seq


title: Donor C (F/45y), HYP/Stat

description: HS_C (Hypoxia static C) -> F/45y, HYP, Stat)

value: human engineered meniscus


title: RICU190509-1_002A


title: BL_30min_4

description:
BR111
QuantSeq_all_TMM.csv


title: Donor B (M/22y), NRX/DC

description: NDC_B (Normoxia dynamic compression B) -> M/22y, NRX, DC)

value: NRX (normoxia, 20% O2)

value: DC (dynamic compression)


title: TCR_CtrlDay12 [TCR_N1]

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

data_processing:
Cellranger 10X demultiplexing (mkfastq)
Cellranger 10X quantification (counts)
Genome_build: refdata-cellranger-mm10-3.1.0
Supplementary_files_format_and_content: sparse matrix (mtx)

source_name: T cells

extract_protocol:
BM cells were sorted for viability (Annexin V) and split in B cell and non-B cells: one gate to collect CD19+ OFP+/- cells and one gate to collect CD45+CD19- cells. After sorting cells were washed and counted
Chromium(TM) Single Cell 5' Library & Gel Bead Kit and ChromiumTM Single Cell V(D)J Enrichment Kit, Mouse T Cell (10xGENOMICS) according to manufacturer’s instructions.

treatment_protocol: lineage negative transduced cells transplant

value: untreated

tag: timepoint

tag: celltype

value: T cells


title: Donor B (M/22y), NRX/Stat

description: NS_B (Normoxia static B) -> M/22y, NRX, Stat)

value: Stat (static control)


title: WT_15min_4

description:
BR107
QuantSeq_all_TMM.csv

value: 15 min

tag: replicate


title: Donor A (M/21y), NRX/Stat

description: NS_A (Normoxia static A) -> M/21y, NRX, Stat)


title: TCR_IFNgDay17 [TCR_03]


title: Donor A (M/21y), NRX/DC

description: NDC_A (Normoxia dynamic compression A) -> M/21y, NRX, DC)


title: RICU201021-1_001A

value: Immunocompromised


title: BL_30min_3

description:
BR110
QuantSeq_all_TMM.csv

value: 30 min


title: WT_15min_2

description:
BR105
QuantSeq_all_TMM.csv


title: WT_15min_3

description:
BR106
Discarded due to low read number


title: HaCat cells, siRNA Agrin rep 3

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

data_processing:
Raw reads from fastq files were aligned to the hg38 genome using STAR 2.6.1d (using options --sjdbGTFfile gencode.v29.annotation.gtf --sjdbOverhang 75 --outSAMtype BAM   Unsorted --outSAMstrandField intronMotif  --twopassMode Basic).
Bam files were sorted with samtools sort and indexed with samtools index.
The number of reads mapping to each gene was quantified with htseq-count (using options --format=bam --order=pos --stranded=reverse  --idattr=gene_name --nonunique=all) on features from the gtf file gencode.v29.annotation.gtf.
The raw counts of reads were then imported into EdgeR in R to perform the differential expression analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per million (CPM) from EgdeR in excel format

source_name: Cell line (HaCat)

growth_protocol: HaCat cells were cultured in RPMI (Roswell Park Memorial Institute) media supplemented with 10% (v/v) FBS. All cells were grown at 37°C in an atmosphere of 5% CO2.

extract_protocol:
RNA was isolated from the cells after compound treatment using Quick-RNA Miniprep kit (Zymo Research)
Total RNA, 2.5μg, was used for RNASequencing library preparation with the TruSeq Stranded mRNA Library Prep kit (Illumina) largely according to manufacturer’s instructions.

treatment_protocol: HaCat were treated with siRNA knockdown against Agrin.

tag: cell line

value: human keratinocytes cell line HaCat

tag: genotype

value: Agrin knockdown


title: Donor A (M/21y), HYP/Stat

description: HS_A (Hypoxia static A) -> M/21y, HYP, Stat)

tag: tissue

value: HYP (hypoxia, 3% O2)


title: RICU200928-1_001A

tag: patient

value: Sepsis


title: HaCat cells, siRNA Agrin rep 2


title: RICU181218-1_002B

value: PBMC


title: C-Ctrl-W2 RNA-seq

tag: strain


title: WT_15min_1

description:
BR104
QuantSeq_all_TMM.csv

tag: treatment

value: Mock

value: 7-day old seedling tissue


title: BL_30min_1

description:
BR108
QuantSeq_all_TMM.csv

value: BL


title: HaCat cells, siRNA Agrin rep 1


title: TCR_IFNgDay17 [TCR_04]


title: Donor A (M/21y), HYP/DC

description: HDC_A (Hypoxia dynamic compression A) -> M/21y, HYP, DC)

value: human engineered meniscus


title: TCR_IFNgDay12 [TCR_02]


title: BL_15min_4

description:
BR103
QuantSeq_all_TMM.csv


title: RICU190114-2_002A

tag: cell type


title: RICU190909-1_002A


title: RICU200410-1_001A


title: GEX_CtrlDay17 [GEX_N2]

source_name: BM

value: BM


title: GEX_CtrlDay12_1 [GEX_N1]


title: HaCat cells, siRNA control rep 3

value: control


title: TCR_IFNgDay12 [TCR_01]


title: BL_15min_2

description:
BR101
QuantSeq_all_TMM.csv


title: RICU200213-1_001A


title: HaCat cells, siRNA control rep 1


title: BL_15min_1

description:
BR100
Discarded due to low read number