title: Co_D19

city: Beijing

first: Jing

last: Zhang

address: 38 Life Science Park Road

institute: Beijing Institute of Lifeomics

data_processing:
Illumina Casava 1.8 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 v2.0.5.Reference genome and gene model annotation files were downloaded from genome website   directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean   reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the   mapping tool for that Hisat2 can generate a database of splice junctions based on the gene   model annotation file and thus a better mapping result than other non-splice mapping tools
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced(FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: gene_count.xls file include readcount values for each Sample

source_name: PBMC

extract_protocol:
RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（NEB #E7530S/L）was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B cell


title: Ctnnb1-ex3-rep1

status: Public on Jul 01 2024

type: SRA

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

library_source: transcriptomic

data_processing:
Transcript abundances were quantified using salmon65 with parameters --gcBias --seqBias –validateMappings. Transcript abundances were imported into DESeq266 using tximport67 to perform differential expression analyses. Fold changes were calculated with DESeq2 with default settings and fold changes and p-values corrected with the bioconductor packages apglm68 and IHW69, respectively. Genes with an absolute log2 fold change >= 1 and FDR < 5% were considered as differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: differential expression
Supplementary_files_format_and_content: salmon quant
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

organism: Mus musculus

source_name: intestinal organoids

growth_protocol: Mouse organoids were obtained from small intestines as previously described61. A detailed description can be found in supplementary information. Wild-type organoids were cultured in presence of recombinant Wnt3a (homemade), R-spondin1 (homemade), 0.1 μg/ml Noggin, 0.05 μg/ml EGF.  Apc-/- and CtnnB1-ex3 organoids were only supplemented with 0.1 μg/ml Noggin and 0.05 μg/ml EGF.

extract_protocol: RNA-seq libraries were prepared using a custom Smart-seq2 procedure that was previously described65. A detailed description of the library preparation procedure is available in supplementary information.

tag: treatment


title: D1S

city: Not Hispanic or Latino

first: Sheng

last: Zhao

address: #87, Dingjiaqiao, Gulouqu

department: Biochemistry and Molecular biology

country: China

institute: Southeast University

description: The focal regions of caudate putamen ischemia were carefully micro-punched under a cryostat based on the location indicated by T2-weighted magnetic resonance images from the mice. Tissue from 6 animals per time point were mixed as single sample for each time point.

data_processing:
Illumina HiSeq 2500 platform to get the raw data
Clean reads were generated from row reads by Trimmomatic (ver. 0.36) using default parameters
The clean reads were mapped to reference genome (Ensembl Mus_musculus GRCm38.90) with Hisat2 (ver. 2.1.0)
Mapped data were assembled by Stringtie (ver. 1.3.4d) with default parameters
Group comparison using GFold (ver. 1.1.4, sc=0.01) was performed to estimate the differential gene expression by the Reads per kilobase per million mapped reads (RPKM)
Genome_build: Ensembl Mus_musculus GRCm38.90
Supplementary_files_format_and_content: Excel file of differential expressed genes (adjusted p value<0.01, RPKM, Gfold score, and the differential expression data.)  RPKM also provided for all genes at all p-values.

molecule: total RNA

source_name: right focal region 1 day after stroke

growth_protocol: Standard animal care

extract_protocol:
Mixed tissue of each group were then performed standard RNA extraction using Trizol
RNA-seq library construction according to the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme Biotech Co.,Ltd, Nanjing, China)

treatment_protocol: After anesthetization with isoflurane gas, the mouse head was fixed using a small animal stereotactic frame. A scalp incision of 1 cm was made in the midline and a small hole was made on the skull above the caudate putamen (0.5 mm anterior to bregma, +/-2.5 mm lateral to midline). An unjacked optical fiber with 125 μm outer diameter and 50 μm core diameter was placed into a 28-gauge straight stainless steel needle. The other end of the optical fiber was connected to a 532 nm laser source (Shanghai Laser & Optics Century Co., Ltd, China). With the guidance of the needle, the optical fiber was stereotactically positioned to the caudate putamen (3 mm ventral to dura mater) in the mouse brain. 100 mg/kg rose bengal were then injected intraperitoneally (Sigma-Aldrich) 5 min before laser irradiation (another 2 min with 30mW output). On the sham side, all procedures were performed the same as above except applying the laser irradiation before rose bengal injection. After the scalp wound was secured, the mice were released from the stereotactic frame and transferred to a recovery chamber.

tag: tissue

value: caudate putamen

tag: disease state

value: photothrombotic internal ischemia stroke

tag: time point

value: 1 day after stroke

tag: strain


title: cut_tag_igg_muscle_WT_0h_rep2

city: Wuhan

first: Xuan

middle: Wen

last: Wang

state: Hubei Province

address: No. 1 Shizishan Street

institute: Huazhong Agriculture University

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to Sscrofa11.1 genome
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the macs2.  narrowPeak files were generated using MACS v2 with default settings.
Assembly: Sscrofa11.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Sus scrofa

source_name: muscle

growth_protocol: C3H cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Permeabilized cells in ice-cold NE1 on ice for 10 min, followed by light crosslinking with formaldehyde to fix nuclei. Then, cells nuclei bound to Concanavalin A-coated Magnetic Bead
Performed chromatin profiling with CUT&Tag according to its latest protocol

treatment_protocol: The cells were treated with 5uM/ml SGC-CBP30 for 48h in the proliferation phase and 60h in the differentiation phase

value: muscle

tag: cell line

tag: cell type

value: muscle satellite cell

tag: genotype

value: cell proliferation

tag: chip antibody


title: WT-rep2

value: WT


title: Ctr

description: The contralateral sham sides (left) of each mouse were also punched and mixed as control group

source_name: left contralateral sham region

value: sham


title: genomic DNA from Patient79_week25

type: genomic

city: Oslo

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Touleimat and Tost, Epigenomics 2012
Average Beta

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using the QIAcube and AllPrep DNA/RNA Mini Kit 350 or 600 for biopsies from the first two or the last time point, respectively (Qiagen) according to the company’s standard protocol.

tag: gender

value: Female

tag: sample type

value: Tumor biopsy

value: Breast cancer

tag: agent

value: Chemotherapy

tag: timepoint


title: ND1

city: Kobe

first: Kazuya

last: Miyagawa

address: 5-7-1 Koji-dai, Nishi

country: Japan

institute: Kobe City Nishi-Kobe Medical Center

data_processing:
Trimmed using FASTQ groomer.
Aligned to the human genome using HISAT2.
Assembly: hg19
Supplementary files format and content: A txt file is generated using DEseq2 on Seqmonk.

source_name: Peripheral blood mononucleor cells

extract_protocol:
Total RNA were extracted using Maxwell® RSC instrument and Maxwell® RSC simply RNA Blood Kit (Promega) according to manufacturer’s instructions
Libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina)

tag: subject status

value: early stage non-severe COVID-19 patient

tag: subject group

value: non-deteriorated, based on the subsequent clinical courses

value: Peripheral blood mononucleor cells


title: Co_D14


title: ND5


title: cut_tag_igg_muscle_WT_0h_rep1


title: genomic DNA from Patient75_week25


title: Co_D12


title: ATAC_muscle_CBP_60h_rep2

extract_protocol:
The reaction system was incubated at 37 °C for 1 h followed immediately by purification with a QIAGEN MinElute PCR Purification Kit (QIAGEN, 28006)
Performed chromatin profiling with ATAC-Seq according to its latest protocol

value: cell differentiation


title: ND3


title: genomic DNA from Patient11_week25


title: Co_D8

value: B cell


title: genomic DNA from Patient83_week25


title: ATAC_muscle_CBP_60h_rep1


title: D0


title: day10.1R

description: right focal region 10 day after stroke

data_processing:
Illumina HiSeq 2500 platform to get the raw data
Clean reads were generated from row reads by Trimmomatic (ver. 0.36) using default parameters
The clean reads were mapped to reference genome (Ensembl Mus_musculus GRCm38.90) with Hisat2 (ver. 2.1.0)
Mapped data were assembled by Stringtie (ver. 1.3.4d) with default parameters
Group comparison using Ballgown (ver. 2.5.3) timecourse comparison (with df=4) was performed to estimate the differential gene expression by the fragment per kilobase per million mapped reads (FPKM)
Genome_build: Ensembl Mus_musculus GRCm38.90
Supplementary_files_format_and_content: Excel file of differential expressed genes (q value<0.05, FPKM and the differential expression data.)

source_name: right focal region 10 day after stroke

extract_protocol:
The focal regions of cerebral ischemia were carefully micro-punched under a cryostat based on the location indicated by T2-weighted magnetic resonance images from the mouse with stroke after 4 hours, 1 day, 3 days, and 10 days (3 animals for sham animal and each time point). Three contralateral sham sides (left) of the mouse with stroke were randomly chosen as a left control group. The brain tissue with similar size at the right side region corresponding to the focal region in stroke mice were also punched from the sham mouse as a right control group. Punched tissue within each group (triplicate in each group) were then performed standard RNA extraction using Trizol.
RNA-seq library construction according to the VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme Biotech Co.,Ltd, Nanjing, China)

treatment_protocol: Mice were anesthetized and injected intraperitoneally with rose bengal (100 mg/kg) 5 min before laser irradiation by optic fiber centered 2 mm to skull right of the bregma. The brains were illuminated for 15 min (40mW output, 532nm from a 2mm diameter laser fiber), and the mice then recovered from anesthesia.

value: cerebral

tag: Sex

value: male

value: photothrombotic cerebral ischemia

value: 10 day after stroke


title: ATAC_muscle_CBP_0h_rep2

value: muscle

value: muscle satellite cell


title: DKO5

city: Mannheim

first: Shu

last: Li

address: Neckarpromenade

country: Germany

institute: ECAS

data_processing:
Raw sequence data with adapter sequences or low-quality sequences was filtered.
Filtered reads were aligned to the Zebrafish reference genome (GRCz11)
Raw counts levels were quantified using FeatureCounts (v2.0.3)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Danio rerio

source_name: larvae

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit(QIAGEN), 3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library.

value: larvae

value: DKO


title: ATAC_muscle_CBP_0h_rep1

value: cell proliferation


title: day3.2R

description: right focal region 3 day after stroke

source_name: right focal region 3 day after stroke

value: 3 day after stroke


title: day3.8R

description: right focal region 3 day after stroke


title: genomic DNA from Patient62_week25

value: Female

value: Tumor biopsy

value: Breast cancer


title: DKO4


title: day10.5R

description: right focal region 10 day after stroke


title: genomic DNA from Patient14_week25

value: Chemotherapy


title: ATAC_muscle_WT_60h_rep2


title: day3.1R

description: right focal region 3 day after stroke


title: day10.2R

description: right focal region 10 day after stroke


title: genomic DNA from Patient96_week25


title: ATAC_muscle_WT_60h_rep1


title: genomic DNA from Patient85_week25


title: DKO3


title: DKO2


title: day1.4R

description: right focal region 1 day after stroke

value: 1 day after stroke


title: genomic DNA from Patient124_week25


title: day1.3R

description: right focal region 1 day after stroke


title: ATAC_muscle_WT_0h_rep2


title: DKO1


title: genomic DNA from Patient1_week25

value: Chemotherapy+bevacizumab


title: day1.1R

description: right focal region 1 day after stroke


title: GLO1KO5


title: genomic DNA from Patient38_week25


title: E60, scRNAseq

first: Songlin

address: No. 4 Tiantanxili, Dongcheng District

institute: Beijing Laboratory of Oral Health, Capital Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mandibular bone and dental tissue

extract_protocol:
The mandibular bone containing one DC and one PC was dissected from E60 miniature pigs . The SDL and the mesenchyme surrounding the PC were separated by microdissection and digested into single-cell suspension.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: mesenchyme and epithelium

value: mandibular bone and dental tissue

value: miniature pig

tag: age

value: embryos at E60


title: hour4.6R

description: right focal region 4 hour after stroke

source_name: right focal region 4 hour after stroke

value: cerebral

value: male

value: photothrombotic cerebral ischemia

value: 4 hours after stroke


title: GLO1KO4

value: larvae


title: E60, Spatial Transcriptomics

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the spaceranger 1.2.0 (https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest)
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

extract_protocol:
We dissected the mandibular bone containing one DC and one PC from E60 miniature pigs. These mandible slice samples were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA, USA) on dry ice and cut at 10-μm thickness using a Leica Cryostat CM1850 (Wetzlar, Germany), after which the frozen sections were transferred to a Visium slide (10x Genomics, Shanghai, China).
Library was performed according to the manufacter’s instructions (Spatial 3' v1 protocol, 10x Genomics). Briefly, a 10-μm thickness fresh frozen slice was placed onto a Capture Area of the gene expression slide. Each Capture Area has thousands of barcoded spots containing millions of capture oligonucleotides with spatial barcodes unique to that spot.The tissue is permeabilized to release mRNA from the cells, which binds to the spatially barcoded oligonucleotides present on the spots. A reverse transcription reaction produces cDNA from the captured mRNA. The barcoded cDNA is then pooled for downstream processing to generate a sequencing-ready library. The next frozen slice was fixed and stained (hematoxylin and eosin) to visualize tissue structures on slides using a brightfield microscope.


title: genomic DNA from Patient87_week25


title: GLO1KO3


title: genomic DNA from Patient44_week25


title: genomic DNA from Patient17_week25


title: PBS11

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
The RNA sequencing data were analyzed using the RASflow pipeline mapping the reads to the transcriptome (Mus_musculus.GRCm39.cdna) using the hisat2 aligner and counting features using featureCounts. For the genome and transcriptome datasets, any missing gene names (using mmusculus_gene_ensembl) are replaced with gene IDs and unnecessary columns like 'gene_id' are dropped. We filtered out sparse genes, which we defined as those with over 50% zero values, to concentrate on genes with meaningful expression levels and to decrease computational complexity. We started with 35453 genes and removed 14981 sparse genes, leaving us with 20472 genes. Following this, we normalized the data with a scaling factor of 10^6. The purpose of this normalization was to make the samples comparable by compensating for variations in library sizes.
Assembly: Mus_musculus.GRCm39.cdna
Supplementary files format and content: Xlsx file includes RPKM values for each Sample

source_name: Colon

growth_protocol: Mice grown under germ-free conditions

extract_protocol:
RNA from frozen colonic tissues was extracted using Qiagen RNeasy Universal kit. Integrity of the isolated RNA was analysed using the Agilent TS HS RNA Kit and TapeStation 4200
1000ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L). RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L). Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: 8 to 14-week-old germ-free mice were treated twice a day for 3 days with 2.5 mg  vancomycin dissolved in 100µl PBS via i.p..

value: Colon

value: WT

tag: treatment

value: PBS


title: PBS10

tag: tissue


title: GLO1KO2


title: hour4.3R

description: right focal region 4 hour after stroke

tag: disease state


title: genomic DNA from Patient67_week25

value: Female

value: Tumor biopsy


title: genomic DNA from Patient70_week25

value: Breast cancer


title: GLO1KO1


title: ALDH3A1KO5


title: PBS9


title: ctr.3R

description: right side region from sham animal

source_name: right side region from sham animal

value: sham

tag: time point


title: PBS8


title: ALDH3A1KO4


title: ctr.5L

description: left contralateral sham region

tag: strain


title: PBS7


title: genomic DNA from Patient32_week25

value: Chemotherapy


title: PBS6


title: genomic DNA from Patient19_week25

value: Chemotherapy+bevacizumab


title: ATAC_muscle_WT_0h_rep1

value: muscle

tag: cell line

value: muscle satellite cell

value: cell proliferation


title: ctr.1R

description: right side region from sham animal

value: cerebral


title: ctr.2R

description: right side region from sham animal

value: male


title: ALDH3A1KO2

tag: cell type


title: ctr.3L

description: left contralateral sham region


title: PBS5

tag: genotype


title: genomic DNA from Patient118_week25


title: hour4.2R

description: right focal region 4 hour after stroke

value: photothrombotic cerebral ischemia


title: ctr.1L

description: left contralateral sham region


title: genomic DNA from Patient99_week25


title: PBS4


title: WT5


title: PBS3


title: ALDH3A1KO1


title: genomic DNA from Patient78_week25


title: WT4


title: genomic DNA from Patient55_week25


title: ALDH3A1KO3


title: WT2


title: Vancomycin11

value: Vancomycin


title: WT1

value: larvae


title: genomic DNA from Patient60_week25


title: PBS1

value: Colon


title: WT3

value: WT


title: genomic DNA from Patient126_week25


title: Vancomycin9


title: L2_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.6), Trimmomatic (ver. 0.39) and cutadapt (ver. 3.1) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.104) using STAR (ver. 2.7.9a).
The read count of gene features was performed with the featureCounts tool (ver. 2.0.1)
Assembly: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

organism: Caenorhabditis elegans

source_name: Whole worms

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for six hours on mNGM plates covered with OP50 (control group) or L. lactis.

value: Whole worms

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding L2


title: genomic DNA from Patient129_week25

value: Female

value: Tumor biopsy

value: Breast cancer

value: Chemotherapy


title: S48 PLC7_OE shoot drought replicate3

city: Amsterdam

first: Max

last: van Hooren

state: Noord Holland

address: Science park 904

department: Plant Cell biology

country: Netherlands

institute: University of Amsterdam

data_processing:
Data was cleaned using FastQC, filtering out all reads smaller than 25 nucleotides and any reads where >75% of the read had a quality score of 17 or less
Reads were aligned to the TAIR10_cdna_20101214_updated reference genome using the Kallisto package
For the number of alignments, 500 was chosen.
The Sleuth package (Pimentel et al., 2017) was used to determine differential gene expression (DEG), the Wald-test was used to determine fold-change difference between conditions or genotypes. Significance was deemed at q<0.05 as determined by the Likelihood-ratio test.
Assembly: TAIR10_cdna_20101214
Supplementary files format and content: abundance.tsv contain est count and tpm for each arabidpsis gene.
Supplementary files format and content: abundance.h5 contain est count and tpm for each of the 500 allignments performed by kallisto. Can be used by the Sleuth package to get average and confidence intervals for the est_counts and tpm

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: 9 days on agar, 12 days on vermiculite with growth media

extract_protocol:
Plant tissues were grinded with mortar and pestle in liquid nitrogen. RNA used for sequencing was extracted using the RNeasy Plant Mini Kit from Qiagen, following the manufacturer’s instructions. The quality of the RNA, i.e. RNA integrity, for sequencing was checked by RIN measurement by ‘Dutch Genomics Service and Support Provider’ (MAD, Science Park, University of Amsterdam, The Netherlands), for which all root samples scored at least 6.5, and all shoot samples at least 9.0.
The total RNA was mixed with ERCC RNA Spike-In Control mix 1 (Thermo Fisher Scientific) and afterwards a poly- A enrichment was performed using Dynabeads mRNA DIRECT Micro Purification Kit (Invitrogen). With the Ion Total RNA-Seq kit v2 and the Ion Xpress RNA-Seq barcoding kit, bar-coded RNA libraries were generated by following the manufacturer’s instructions (Thermo Fisher Scientific)

treatment_protocol: 7 days on vermiculite with or without growth media

value: shoot

value: drought


title: genomic DNA from Patient77_week25

value: Chemotherapy+bevacizumab


title: Vancomycin8


title: L2_rep1


title: Vancomycin7


title: melanophore_72hpf_rep2

type: RNA

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

hyb_protocol: Labeled cRNA sample were fragmented at 60oC and hybridized on to Agilent Zebrafish Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65o C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D). Raw data extraction from Images was obtained using Agilent Feature Extraction software

data_processing: Images were quantified using Feature Extraction Software (Version-11.5 Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift normalization is a global normalization, where the locations of all the spot intensities in an array are adjusted. [This normalization takes each column in an experiment independently, and computes the percentile of the expression values for this array, across all spots (where n has a range from 0-100 and n=75 is the median). It subtracts this value from the expression value of each entity.

source_name: zebrafish pigmented melanophores

label_protocol: The microarray hybridization and scanning were performed at the Agilent certified microarray facility of Genotypic Technology, Bengaluru, India. The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000

growth_protocol: Zebrafish were bred, raised and maintained at 28.5 °C according to standard protocols (Westerfield M, 2000) and were housed at the CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road New Delhi, India. Embryos were staged both using timing (hours post fertilization (hpf); days post fertilization (dpf)) and morphological features according to (Kimmel, 1995)

extract_protocol: RNA was isolated from each of these sorted populations according to manufacturer’s protocols (Nucleospin RNA XS kit; MachereyNagel)

treatment_protocol: No treatment

value: pigmented melanophores

tag: developmental stage


title: L1_rep2

value: feeding L1


title: S46 PLC7_OE shoot drought replicate1


title: PBS2

value: PBS


title: genomic DNA from Patient16_week25

tag: gender


title: S47 PLC7_OE shoot drought replicate2


title: Vancomycin10

value: Colon

value: Vancomycin


title: mitfa_24hpf_rep2

source_name: zebrafish mitfa:GFP positive cells

value: mitfa:GFP pigment lineage cells


title: mitfa_34hpf_rep2


title: mitfa_34hpf_rep1


title: mitfa_24hpf_rep1


title: melanophore_72hpf_rep1


title: Vancomycin6

value: WT


title: genomic DNA from Patient105_week25

tag: sample type


title: genomic DNA from Patient33_week25

tag: agent


title: Vancomycin5


title: S43 PLC7_OE root drought replicate1

source_name: root

value: root


title: S44 PLC7_OE root drought replicate2


title: OP_rep2

value: Whole worms

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding OP50


title: genomic DNA from Patient40_week25

value: Female

value: Tumor biopsy

value: Breast cancer

tag: timepoint


title: S42 PLC5_OE shoot drought replicate3

value: shoot

value: drought


title: S41 PLC5_OE shoot drought replicate2


title: OP_rep1


title: genomic DNA from Patient80_week25

value: Chemotherapy+bevacizumab


title: genomic DNA from Patient82_week25


title: Vancomycin3


title: genomic DNA from Patient73_week25

value: Chemotherapy


title: Vancomycin2

value: Colon


title: Vancomycin1

value: Vancomycin


title: S40 PLC5_OE shoot drought replicate1


title: genomic DNA from Patient125_week25


title: L1_rep1

value: feeding L1


title: S39 PLC5_OE root drought replicate3


title: Vancomycin4

value: WT


title: genomic DNA from Patient50_week25


title: IRF8KO P14 microglia - ATAC_rep2

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

country: USA

institute: NIH/NICHD

data_processing:
Basecalls performed using bcl2fastq without the acceptance of index mismatch
After removing the adapter and low-quality sequences, the data were aligned to the mm10 genome with Bowtie2.
Peaks were called on aligned sequences using MACS2 v2.2.7.1 with -p 0.01 --nomodel --shift -37 --extsize 73 -B --SPMR --keep-dup all options.
All peaks were further filtered with less than 0.01 irreversible differential rates.
The bigwig files were generated with Deeptools to visualize the RPGC-normalized, average peaks of each genotype.
Assembly: mm10
Supplementary files format and content: Peak files (.narrowpeak) consist of peak regions and tag density generated by MACS2
Supplementary files format and content: A bigwig file contains RPGC-normalized, average peaks of each genotype.

source_name: FACS-sorted microglia

growth_protocol: Microglia were non-enzymatically isolated from a WT, 5xFAD, and IRF8KO brain.

extract_protocol:
FACS-sorted microglia were lysed in NP-40 lysis buffer.
As manufacturer's protocol, the isolated nuclei were tagmented using the Nextera DNA library prep kit (Illumina). The library was amplified by 9-14-cycle PCR and size-selected.

value: FACS-sorted microglia

value: untreated


title: genomic DNA from Patient127_week25


title: IRF8KO P14 microglia - ATAC_rep1


title: genomic DNA from Patient109_week25


title: IRF8KO P9 microglia - ATAC_rep3


title: B16_Sema3E_8hrs-Rep2

hyb_protocol: Labeled cRNA sample were fragmented at 60°C and hybridized on to Agilent Mouse Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent Technologies(In situ Hybridization kit, Part Number 5188-5242).

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D). Raw data extraction from Images was obtained using Agilent Feature Extraction software.

data_processing: Images were quantified using Feature Extraction Software (Version-11.5 Agilent). Feature extracted raw data was normalized using GeneSpring GX software from Agilent. Intra-array normalization was done which deals with variability within a single array. gProcessed signal (dye normalized background subtracted signal intensity) was log transformed and then for each of the array the 75th percentile value was calculated separately. In each sample the log transformed intensity values for each probe were subtracted by the calculated 75th percentile value of the respective array and expression values were obtained.

source_name: B16, Sema3E treatment, 8hrs

label_protocol: The microarray hybridization and scanning were performed at the Agilent certified microarray facility of Genotypic Technology, Bengaluru, India. The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: B16 cells were grown in Dulbecco's Modified Eagle Medium - High glucose, supplemented with 5% fetal bovine serum at 37 °C, 5% CO2

extract_protocol: RNA was isolated according to manufacturer’s protocols (Nucleospin Triprep kit; MachereyNagel).

treatment_protocol: Total RNA was extracted from Control, SEMA3E treated (2 hrs and 8hrs) and cytochalasin D (8h) treated B16 cells. The RNA was quality controlled and quantified using agilent bioanalyzer. The samples were analyzed by Agilent_mouse_GXP_8X60K array. Two biological replicates of each sample were analyzed. We acknowledge Genotypic Technology Private Limited Bangalore for the microarray processing and data analysis reported in this publication.

value: B16 mouse melanoma cell line

value: 8 hrs


title: B16_Cytochalasin_Rep2

source_name: B16, Cytochalasin D treatment, 8hrs

value: Cytochalasin D


title: B16_Cytochalasin_Rep1


title: B16_Sema3E_8hrs-Rep1


title: genomic DNA from Patient108_week25


title: S36 PLC3_OE shoot drought replicate3


title: S35 PLC3_OE shoot drought replicate2


title: Z12 open choroid chk236

city: Boston

first: Debora

last: Nickla

state: MA

address: 424 Beacon St

department: Dept. of Biosciences and Disease

institute: New England College of Optometry

data_processing:
raw data was processed by the standard Illumina pipeline to yeild trimmed fastq files
fastq data counted against transcripts (ensembl v105) with salmon
data summarized to gene-level with tximeta (bioconductor)
Assembly: GRCg6a (gene models – ensembl v105)
Supplementary files format and content: gzipped tab-delimited text – raw counts per ensembl gene ID per sample

organism: Gallus gallus

source_name: choroid

extract_protocol:
RNA was extracted from choroid and retinal tissues using the QIAgen RNAeasy kit
NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: chick eyes were occluded (goggled) or open

value: choroid

tag: eye treatment

value: open

value: M


title: S34 PLC3_OE shoot drought replicate1


title: IRF8KO P9 microglia - ATAC_rep1


title: S37 PLC5_OE root drought replicate1

value: root


title: IRF8KO P9 microglia - ATAC_rep2


title: B16_Sema3E_2hrs-Rep2

source_name: B16, Sema3E treatment, 2hrs

value: 2 hrs


title: WT P14 microglia - ATAC_rep2


title: Z12 open retina chk236

source_name: retina

value: retina


title: WT P14 microglia - ATAC_rep1


title: B16_Control_Rep2

source_name: B16, Non targeted control

value: 0 hrs

value: Control


title: genomic DNA from Patient15_week25

value: Female

value: Tumor biopsy

value: Breast cancer

value: Chemotherapy


title: genomic DNA from Patient22_week25


title: S38 PLC5_OE root drought replicate2

value: drought


title: S32 PLC3_OE root drought replicate2


title: B16_Sema3E_2hrs-Rep1


title: B16_Control_Rep1


title: Z12 occluded choroid chk236

value: occluded


title: genomic DNA from Patient8_week25

value: Chemotherapy+bevacizumab


title: WT P9 microglia - ATAC_rep2

value: FACS-sorted microglia

value: WT

value: untreated


title: genomic DNA from Patient43_week25


title: S31 PLC5_OE root control replicate3

value: control


title: S33 PLC3_OE root drought replicate3


title: genomic DNA from Patient42_week25


title: WT P9 microglia - ATAC_rep1


title: genomic DNA from Patient58_week25


title: Z12 occluded choroid chk235

value: choroid

value: M


title: genomic DNA from Patient113_week25


title: S29 PLC2_OE shoot drought replicate2

value: shoot


title: WT microglia, control for X4MG - ATAC_rep2


title: Z12 open retina chk235

value: retina

value: open


title: S28 PLC2_OE shoot drought replicate1


title: Z12 open choroid chk235


title: Z12 occluded retina chk235


title: MetX04 positive microglia (X4MG) - ATAC_rep1


title: genomic DNA from Patient84_week25


title: S26 PLC2_OE root drought replicate2

value: root


title: Z12 open choroid chk234

value: F


title: genomic DNA from Patient5_week25

value: Female

value: Tumor biopsy


title: S27 PLC2_OE root drought replicate3


title: 5xFAD MetX04 negative microglia - ATAC_rep2

description: 5xFADMG_10m_F_ATAC_merge_SeqDepthNorm.bw


title: genomic DNA from Patient12_week25

value: Breast cancer

value: Chemotherapy


title: S25 PLC2_OE root drought replicate1

value: drought


title: Z12 open retina chk234


title: genomic DNA from Patient101_week25


title: 5xFAD MetX04 negative microglia - ATAC_rep1


title: Z12 occluded retina chk236

value: occluded


title: S24 AtWT shoot drought replicate4

value: AtWT


title: genomic DNA from Patient36_week25

value: Chemotherapy+bevacizumab


title: Z12 occluded choroid chk234


title: S30 PLC2_OE shoot drought replicate3


title: WT

city: Fukushima

first: Kazuhiko

last: Ikeda

state: Fukushima

address: 1 Hikariga-oka

department: Blood Transfusion and Transplantation Immunology

institute: Fukushima Medical University

data_processing:
Following SPRI bead cleanup (Beckman Coulter, Brea, CA), the resulting DNA libraries were quantified and sequenced
Reads were aligned using the BWA algorithm (mem mode; default settings)
Duplicate reads were removed, and only reads that mapped uniquely (mapping quality ≥ 1) and as matched pairs were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome.
Assembly: The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Supplementary files format and content: signal bigWIG (BW) files
Library strategy: CUT & Tag

source_name: bone marrow

extract_protocol: Active Motif CUT&Tag kit, catalog number 53160 was used.

value: bone marrow

value: LSK cells

value: WT

tag: antibody


title: S23 AtWT shoot drought replicate3


title: MetX04 positive microglia (X4MG) - ATAC_rep2

value: FACS-sorted microglia


title: WT microglia, control for X4MG - ATAC_rep1


title: genomic DNA from Patient120_week25


title: Z12 open choroid chk233

value: choroid

tag: Sex


title: Z12 occluded retina chk234

value: retina


title: genomic DNA from Patient27_week25


title: S22 AtWT shoot drought replicate2

value: shoot


title: ParBF, S.typhi LT2, F, IP1

city: Toulouse

first: Jean-Yves

last: Bouet

address: 169 avenue Marianne Grunberg-Manago

country: France

institute: CNRS

description: Mapped reads: 9809234; average fragment size: 191

data_processing:
Basecalls and alignment performed using Torrent_Suite 5.12.1
ChIP-seq reads were aligned to the corresponding genomes of reference, including the plasmids content.
The F plasmid reads were counted in the centre of DNA fragment according to each average librairy size.
The F plasmid reads, substracted from background, were binned with a window and a step of 40 and 20, respectively.
Assembly: Escherichia coli str. K-12 substr. MG1655ASM584v2
Supplementary files format and content: The counting of reads over the genomic sequences was performed using bedtools 2.26.0 with the tool genomecov and the options -d, -s, -strand and -ibam

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: plasmid

growth_protocol: Samples were prepared from exponential growing phase cultures in LB media (OD600 ~0.5) at 37°C or 30°C for E. coli or S. Thy LT2, respectively.

extract_protocol:
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti ParBF antibody
A maximum of 2 ng of ChIP DNA was used to synthetize the library as described in manufacturer’s instructions (Ion ChIP-Seq Library Preparation on the Ion Proton™ System - revision B - Step10). The last size selection was modified by a double size selection (0.55X/0.25X) of binding to AMPure® XP beads followed by a step of wash and elution. Then, qualification and quantification were made with the Bioanalyzer - Agilent, Santa Clara, CA

treatment_protocol: Cells were treated with formalhedyde (1 %)

tag: strain name

value: plasmid

tag: plasmid f

tag: dna topology

value: CCC

tag: chip antibody

value: anti ParBF


title: Z12 open retina chk233

tag: tissue

tag: time point

value: open

value: F


title: S21 AtWT shoot drought replicate1

tag: treatment


title: S19 AtWT root drought replicate3

value: root


title: ParBF, S.typhi LT2, F, input

description: Mapped reads: 6554227; average fragment size: 149


title: Z12 occluded choroid chk233


title: Z12 occluded retina chk233


title: ParBF, S.typhi LT2 gyrB, F, IP1

description: Mapped reads: 8627520; average fragment size: 189

value: LT2 gyrB652ts


title: genomic DNA from Patient3_week25

value: Female

value: Tumor biopsy

tag: disease state

value: Breast cancer

value: Chemotherapy


title: genomic DNA from Patient111_week25


title: ParBF, S.typhi LT2 gyrB, F, IP2

description: Mapped reads: 1489543; average fragment size: 187

tag: genotype


title: S18 AtWT root drought replicate2

value: AtWT

value: drought


title: genomic DNA from Patient114_week25


title: ParBF, S.typhi LT2 gyrB, F, input

description: Mapped reads: 3869340; average fragment size: 187


title: Z12 open choroid chk232


title: genomic DNA from Patient26_week25


title: S17 AtWT root drought replicate1


title: efp mutant, biological replicate 2

city: Chuncheon-si

first: Yong-Joon

last: Cho

state: Gangwon-do

address: 1, Kangwondaehak-gil

department: Department of Molecular Bioscience

country: South Korea

institute: Kangwon National University

data_processing:
Sequencing was performed using Illumina HiSeq 2500 with 50 bp single end platform.
Generated raw data were quality- and linker-trimmed using bbduk with the parameters; ‘minlen=10 qtrim=rl trimq=10 ktrim=r k=25 mink=11 hdist=1 tpe tbo’.
Cleaned reads were mapped to the reference genome by hisat2 v.2.2.1 with --no-spliced-alignment option.
Mapped result was converted to bedGraph using genomeCoveragebed in bedtools v.2.29.2 with ‘-bg -3’ parameters to calculate the coverage of 3’ positions of the mapped reads.
All mapped reads in a sample were summed and normalized to a fixed value of 10 million in a bedGraph file.
Assembly: GCF_000022165.1
Supplementary files format and content: bedGraph file includes the normalized ribosomal tags for forward and reverse strand of DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: efp mutant

growth_protocol:
Wild-type and Δefp mutant Salmonella strains were grown overnight in N-minimal medium containing 10 mM MgCl2.
1/100 dilution of overnight was used to inoculate 200 ml of the same medium and grown until OD600 = 0.3. .

extract_protocol:
The cultures were harvested by rapid filtration and freezing in liquid nitrogen. Cells were lysed with 1 M NaCl-containing lysis buffer and 25 AU of extracted RNA lysates was pelleted over a 1-ml sucrose cushion (20 mM Tris [pH 7.5], 500 mM NH4Cl, 0.5 mM EDTA, 1.1 M sucrose) using a TLA 100.3 rotor at 65,000 rpm for 2 h.
Pellets were resuspended in 200 ml of lysis buffer and the RNA was digested with MNase.
We followed the described protocol to construct libraries (Mohammad F, Green R, Buskirk AR: A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution. Elife 2019, 8.)
Ribo-Seq

treatment_protocol: Cells were then washed and transferred to 200 ml N-minimal medium containing 0.5 mM MgCl2 and grown for 1 h.

tag: cell type

value: efp mutant


title: Z12 open retina chk232


title: Uhrf2 KO

value: bone marrow

value: LSK cells

value: KO


title: genomic DNA from Patient41_week25

extract_protocol: DNA was isolated using the QIAcube and AllPrep DNA/RNA Mini Kit 350 or 600 for biopsies from the first two or the last time point, respectively (Qiagen) according to the company’s standard protocol.

tag: gender


title: efp mutant, biological replicate 1


title: Z12 occluded choroid chk232

value: choroid

value: occluded


title: S16 PLC5_OE shoot control replicate4

value: shoot

value: control


title: S20 AtWT root drought replicate4


title: Z12 occluded retina chk232

value: retina

value: F


title: genomic DNA from Patient110_week25

tag: sample type

value: Chemotherapy+bevacizumab


title: wild-type, biological replicate 2

source_name: wild type

value: wild type


title: Z12 open choroid chk231

value: open

value: M


title: S15 PLC5_OE shoot control replicate3


title: wild-type, biological replicate 1


title: genomic DNA from Patient37_week25

value: Female

value: Tumor biopsy

value: Breast cancer

tag: agent


title: Z12 open retina chk231


title: genomic DNA from Patient71_week25

tag: timepoint


title: S13 PLC5_OE shoot control replicate1


title: S11 PLC3_OE root drought replicate1

value: root

value: drought


title: genomic DNA from Patient24_week25


title: S10 PLC5_OE root control replicate2


title: Z12 occluded retina chk231

tag: eye treatment


title: genomic DNA from Patient122_week25


title: S09 PLC5_OE root control replicate1


title: Z08 open choroid chk230


title: genomic DNA from Patient20_week25


title: genomic DNA from Patient74_week25


title: S08 AtWT shoot control replicate4

value: AtWT


title: S14 PLC5_OE shoot control replicate2


title: Z08 open retina chk230


title: APP-PS1_UA-WASHOUT_replicate_5

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Mice were maintained at the NIA under standard conditions and fed standard chow ad libitum. The APP/PS1 strain was from Jackson Laboratory (stock 004462) was originally from Dr. Mark Mattson (NIA).

extract_protocol: RNA was purified with the Nucleospin RNA isolation kit (catalog no. 740955 250, Macherey-Nagel) and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific). The quality was also inspected using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For those mice treated with urolithin A (UA), mice were treated with UA (200 mg/kg/day) by gavage starting at 2 and ending at 7 months after which tissue was collected. If the mice were subjected to washout, mice were treated or not with UA, then UA was stopped for one month then tissues were collected.

value: hippocampus

value: Urolithin A_5m+washout_1m

value: Male

tag: age

value: 9 months

tag: strain

value: + APP + PSEN


title: genomic DNA from Patient7_week12

data_processing:
Touleimat and Tost, Epigenomics 2012
Average Beta


title: Z08 occluded choroid chk230

value: choroid

value: occluded

tag: Sex


title: S07 AtWT shoot control replicate3

value: shoot

value: control


title: genomic DNA from Patient112_week12

value: Chemotherapy+bevacizumab


title: APP-PS1_UA-WASHOUT_replicate_4


title: Z08 occluded retina chk230

value: retina

value: M


title: Z12 occluded choroid chk231


title: APP-PS1_UA-WASHOUT_replicate_3


title: S06 AtWT shoot control replicate2


title: genomic DNA from Patient119_week12

value: Female

value: Tumor biopsy


title: Z08 open choroid chk229

value: open


title: S05 AtWT shoot control replicate1


title: genomic DNA from Patient23_week12

value: Breast cancer


title: S04 AtWT root control replicate4

value: root

value: AtWT


title: Z08 open retina chk229


title: APP-PS1_UA-WASHOUT_replicate_1

value: hippocampus

value: Urolithin A_5m+washout_1m


title: genomic DNA from Patient66_week12


title: APP-PS1_WASHOUT_replicate_3

value: water+washout

value: Male

value: 9 months


title: S03 AtWT root control replicate3


title: Z08 occluded choroid chk229

value: choroid

value: occluded


title: genomic DNA from Patient28_week12


title: APP-PS1_UA-WASHOUT_replicate_2

value: + APP + PSEN


title: APP-PS1_WASHOUT_replicate_1


title: Z08 occluded retina chk229


title: genomic DNA from Patient51_week12

value: Chemotherapy+bevacizumab


title: S01 AtWT root control replicate1

value: control


title: Z08 open choroid chk228

value: F


title: WT_WASHOUT_replicate_5

value: - APP - PSEN


title: S02 AtWT root control replicate2


title: Z08 open retina chk228

value: retina


title: genomic DNA from Patient90_week12

value: Female

value: Tumor biopsy


title: WT_WASHOUT_replicate_4


title: U251-COL8A1, rep1

city: Guangzhou

first: Mingkai

last: Liu

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South China University of Technology

data_processing:
TrimGalore v0.6.9, Hisat2 v2.2.1, featureCounts v.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore.
Trimmed sequence reads were mapped to hg38 using Hisat2
Read count extraction and normalization were performed using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: cell line

growth_protocol: The cell lines U251-MG were cultured at 37˚C, 5% CO2, and 10% fetal bovine serum in DMEM.

extract_protocol:
U251-COL8A1 and U251-NC were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For lentiviral vectors expressing COL8A1 and negative control (NC), the corresponding cDNAs were cloned into the pCDH-CMV-MCS-EF1-puro overexpression vector, then U251-MG were infected with lentivirus-mediated COL8A1 overexpression vector and negative control vector

value: cell line

tag: cell line

value: glioma cell

value: WT

value: COL8A1 overexpressed


title: U251-COL8A1, rep2


title: genomic DNA from Patient81_week12

value: Breast cancer


title: Z08 occluded choroid chk228


title: genomic DNA from Patient94_week12


title: U251-NC, control, rep2


title: genomic DNA from Patient45_week12


title: APP-PS1_WASHOUT_replicate_2

value: hippocampus

value: water+washout

value: Male


title: WT_WASHOUT_replicate_2

value: 9 months


title: U251-NC, control, rep1


title: WT_WASHOUT_replicate_3


title: genomic DNA from Patient48_week12


title: Healthy control replicate 5

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38

source_name: Peripheral blood NK cells

extract_protocol:
Total RNA was isolated from purified NK cells using RNA Isolation Kit (Dongsheng, R1061) according to the manufacturer’s instructions.
RNA-Sequencing was conducted using the Illumina HiSeq X Ten platform (Novogene Bioinformatics Technology Co., Ltd.) with paired-end 150-bp reads.

value: Peripheral blood NK cells

value: No treatment

value: Healthy control

tag: biomaterial provider

value: Cui Hua Liu's lab

tag: ethnicity

value: Colored

tag: bmi

tag: smoking status

value: Never

tag: bcg scar

value: Present

tag: previous diagnosis_of_tb

value: No

tag: igra

value: Negative

tag: pulmonary cavitation

tag: mtb culture

tag: drug resistant_tb


title: Z08 open retina chk227

tag: tissue

value: retina

tag: time point

value: open

value: F


title: WT_WASHOUT_replicate_1

tag: treatment

tag: genotype

value: - APP - PSEN


title: genomic DNA from Patient130_week12

tag: gender

value: Female

tag: sample type

value: Tumor biopsy

tag: disease state

value: Breast cancer

tag: agent

value: Chemotherapy+bevacizumab

tag: timepoint


title: APP-PS1_UA_replicate_2

value: hippocampus

value: Urolithin A_5m

tag: Sex

value: Male

tag: age

value: 8 months

tag: strain

value: + APP + PSEN


title: Z08 occluded choroid chk227

value: choroid

tag: eye treatment

value: occluded


title: Z08 occluded retina chk227


title: Healthy control replicate 3

value: Peripheral blood NK cells

value: No treatment

value: Healthy control

tag: biomaterial provider

value: Cui Hua Liu's lab

tag: ethnicity

value: Colored

tag: bmi

tag: smoking status

value: Former

tag: bcg scar

value: Present

tag: previous diagnosis_of_tb

value: No

tag: igra


title: Healthy control replicate 4

tag: tissue

tag: treatment

value: Female

value: Never

value: Unknown

value: Negative

tag: pulmonary cavitation

tag: mtb culture

tag: drug resistant_tb


title: APP-PS1_UA_replicate_3

value: hippocampus

value: Urolithin A_5m

value: Male

tag: genotype


title: APP-PS1_UA_replicate_1

tag: Sex

value: 8 months

value: + APP + PSEN


title: Z08 occluded retina chk228

value: retina

tag: time point

value: occluded

value: F


title: Z08 open choroid chk226

value: choroid

value: open

value: M


title: Healthy control replicate 2

value: Peripheral blood NK cells

value: No treatment

tag: disease state

value: Healthy control

tag: age

value: Cui Hua Liu's lab

value: Colored

value: Present


title: Z08 open retina chk226

tag: eye treatment


title: genomic DNA from Patient121_week12

tag: gender

value: Female

tag: sample type

value: Tumor biopsy

value: Breast cancer

tag: agent

value: Chemotherapy+bevacizumab

tag: timepoint


title: genomic DNA from Patient76_week12


title: genomic DNA from Patient75_week12


title: Latent tuberculosis infection replicate 5

value: Latent tuberculosis infection

tag: biomaterial provider

value: Male

tag: ethnicity

tag: bmi

tag: smoking status

value: Never

tag: bcg scar

value: Unknown

tag: previous diagnosis_of_tb

value: No

value: Positive


title: Healthy control replicate 1

tag: tissue

tag: treatment

tag: igra

value: Negative

tag: pulmonary cavitation

tag: mtb culture

tag: drug resistant_tb


title: Z08 occluded choroid chk226

value: choroid

tag: time point

tag: eye treatment

value: occluded

tag: Sex

value: M


title: genomic DNA from Patient11_week12

tag: gender

tag: sample type

tag: disease state

tag: agent


title: APP-PS1_CTR_replicate_3

value: hippocampus

value: water

tag: age

value: 8 months

tag: strain

tag: genotype

value: + APP + PSEN


title: Latent tuberculosis infection replicate 4

value: Peripheral blood NK cells

value: No treatment

tag: biomaterial provider

value: Cui Hua Liu's lab

value: Female

tag: ethnicity

value: Colored

tag: bmi

tag: smoking status

tag: bcg scar

value: Present

tag: previous diagnosis_of_tb


title: Z08 open choroid chk227

tag: tissue

value: open

value: F


title: Z08 occluded retina chk226

value: retina

tag: time point


title: APP-PS1_UA_replicate_4

tag: treatment

value: Urolithin A_5m

value: Male


title: APP-PS1_CTR_replicate_1

tag: Sex


title: genomic DNA from Patient83_week12

tag: gender

value: Tumor biopsy

value: Breast cancer

value: Chemotherapy

tag: timepoint


title: genomic DNA from Patient79_week12

tag: sample type

tag: disease state

value: Chemotherapy+bevacizumab


title: WT_CTR_replicate_4

value: hippocampus

value: water

tag: age

value: 8 months

value: - APP - PSEN


title: Z08 open choroid chk225

value: choroid

tag: eye treatment

value: M


title: genomic DNA from Patient124_week12

value: Female

tag: agent


title: Latent tuberculosis infection replicate 3

value: Peripheral blood NK cells

value: No treatment

value: Latent tuberculosis infection

tag: biomaterial provider

value: Cui Hua Liu's lab

value: Colored

value: Never

value: Present

value: No

tag: igra

value: Positive

tag: pulmonary cavitation

tag: mtb culture

tag: drug resistant_tb


title: Z08 open retina chk225

value: retina

value: open


title: WT_CTR_replicate_3

value: hippocampus

value: water

value: Male

tag: strain

tag: genotype


title: APP-PS1_CTR_replicate_2

tag: tissue

value: 8 months

value: + APP + PSEN


title: GS3

city: Hangzhou

first: Tianyi

last: Gu

address: No.268, Kaixuan Road

institute: Zhejiang University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9

organism: Rattus norvegicus

source_name: Blood

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Blood

tag: treatment

value: GS


title: Z08 occluded choroid chk225

value: choroid

tag: time point

value: occluded

tag: Sex

value: M


title: Latent tuberculosis infection replicate 1

value: Peripheral blood NK cells

value: No treatment

value: Latent tuberculosis infection

value: Cui Hua Liu's lab

tag: ethnicity

value: Colored

tag: bmi

tag: smoking status

tag: bcg scar

tag: previous diagnosis_of_tb


title: GS2


title: genomic DNA from Patient62_week12

first: Thomas

address: Ullernchausséen 70

institute: Oslo University Hospital

tag: gender

value: Female

tag: sample type

value: Tumor biopsy

tag: disease state

value: Breast cancer

tag: agent

value: Chemotherapy+bevacizumab

tag: timepoint


title: Active tuberculosis infection replicate 5

value: Active tuberculosis infection

tag: age

tag: biomaterial provider

value: Male

value: Former

value: Present

value: Unknown

tag: igra

value: Positive

tag: pulmonary cavitation

value: No

tag: mtb culture

value: Yes

tag: drug resistant_tb


title: genomic DNA from Patient14_week12


title: WT_CTR_replicate_2

tag: tissue

value: hippocampus

tag: treatment

value: water

tag: Sex

value: 8 months

tag: strain

tag: genotype

value: - APP - PSEN


title: GS1

value: Blood

value: GS


title: WT_CTR_replicate_1


title: Z08 occluded retina chk225

value: retina

tag: time point

tag: eye treatment

value: occluded

value: M


title: Z20 open choroid chk224

value: choroid

value: open


title: genomic DNA from Patient1_week12

tag: gender

value: Female

tag: sample type

value: Tumor biopsy

value: Breast cancer

value: Chemotherapy+bevacizumab


title: DNAgel3

value: DNAgel


title: genomic DNA from Patient85_week12

tag: disease state

tag: agent


title: Active tuberculosis infection replicate 4

value: Peripheral blood NK cells

value: No treatment

value: Active tuberculosis infection

tag: age

value: Cui Hua Liu's lab

value: Male

tag: ethnicity

value: Colored

tag: bmi

tag: smoking status

value: Never

tag: bcg scar

value: Present

tag: previous diagnosis_of_tb

value: No

value: Positive

value: Yes


title: Active tuberculosis infection replicate 3

tag: tissue

tag: biomaterial provider

tag: igra

tag: pulmonary cavitation

tag: mtb culture

tag: drug resistant_tb


title: genomic DNA from Patient38_week12

tag: timepoint


title: Z20 open retina chk224

value: retina

tag: time point

tag: eye treatment

value: open

tag: Sex

value: M


title: Active tuberculosis infection replicate 2

tag: treatment

tag: disease state

value: Female

value: Unknown


title: Latent tuberculosis infection replicate 2

value: Latent tuberculosis infection

tag: age

tag: ethnicity

value: Former


title: DNAgel2

value: Blood

value: DNAgel


title: Z20 occluded choroid chk224

value: choroid

value: occluded


title: genomic DNA from Patient103_week12

tag: gender

tag: sample type

value: Tumor biopsy

value: Breast cancer

tag: agent

value: Chemotherapy+bevacizumab


title: Z20 occluded retina chk224

tag: tissue


title: Active tuberculosis infection replicate 1

value: Peripheral blood NK cells

value: No treatment

value: Active tuberculosis infection

tag: biomaterial provider

value: Cui Hua Liu's lab

value: Male

value: Colored

tag: bmi

tag: smoking status

value: Never

tag: bcg scar

value: Present

tag: previous diagnosis_of_tb

value: No


title: Control3

value: Control


title: DNAgel1

value: Blood


title: genomic DNA from Patient52_week12

value: Female

tag: timepoint


title: Control2


title: genomic DNA from Patient87_week12

value: Chemotherapy


title: 116_siSP1SP3

city: Shanghai

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic ( 0.36 ), then mapped to GR38p7 whole genome using Hisat2 ( 2.0.5 ) with parameters ( --rna-strandness RF --fr  )
FPKM value of each gene was calculated using cufflinks ( 2.2.1 ),and the read counts of each gene were obtained by htseq-count (  0.9.1 )
Genome_build: GR38p7

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: genotype/variation

value: SP1 and SP3 knockdown


title: 116_siSP3

value: SP3 knockdown


title: genomic DNA from Patient44_week12

city: Oslo

last: Fleischer

value: Tumor biopsy

value: Breast cancer


title: Z20 open choroid chk223

value: choroid

tag: time point

tag: eye treatment

value: open

tag: Sex

value: F


title: Control1

tag: treatment


title: Z20 open retina chk223

value: retina


title: 116_siSP1

value: SP1 knockdown


title: Z20 occluded choroid chk223

value: occluded


title: Kidney, infected C57BL/6 mouse, day 21, biol rep 3

city: Glasgow

first: John

last: Ogunsola

state: State

address: 243 Henry Wellcome Building

country: United Kingdom

institute: University of Glasgow

data_processing:
Filtered, high-quality reads were aligned to the Mus musculus genome GRCm38.p6.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM to calculate the gene expression level of each sample.
Differential gene expression analysis was performed using DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: readcounts

source_name: Kidney

extract_protocol:
RNA was harvested from 30mg kidney lysate using Rneasy mini plus kit (Qiagen), followed by poly-A enrichment. 1 ug of total RNA was used for the construction of sequencing libraries.
DNA nanoball synthesis followed rounds of PCR amplification of the cDNA

value: Kidney

tag: strain

tag: genotype

value: WT

tag: infection

value: T. brucei-infected

tag: time

value: Day 21


title: genomic DNA from Patient115_week12

tag: gender

tag: sample type

tag: disease state

tag: agent


title: genomic DNA from Patient17_week12

value: Chemotherapy+bevacizumab


title: Z20 occluded retina chk223

tag: tissue


title: 116_NC_2

value: control


title: 116_NC_1


title: Z20 open choroid chk222

value: M


title: genomic DNA from Patient70_week12

value: Female

value: Chemotherapy


title: Elys-KD RNA-seq, rep 2

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

data_processing:
Reads were aligned to dm3/R5 genome assembly, counted for genes (BDGP5.78 annotation) and converted to transcripts per million (TPM) values using Salmon (Patro et al. 2017) or  mapped on dm3 genome using HISAT2 (Pertea et al. 2016). Differential expression was revealed by DESeq2 (Love et al. 2014) package for R with the cutoff parameters P < 0.05 and TPM fold change > 2.
Assembly: dm3
Supplementary files format and content: sf files are  read counts per gene of each RNA-seq replica which were obtained via Salmon software; xlsx file contains table with data regarding differential expression in S2 cells upon Elys-KD

organism: Drosophila melanogaster

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Approximately 107 control and Elys-KD S2 cells were collected. Poly(A)+ RNA purified on the oligo(dT) column was isolated (in two biological replicates) using Trizol reagent (Invitrogen).
Purification of poly(A)+ RNA on the oligo(dT) column, cDNA library preparation with random primers and single-end deep sequencing on Illumina Novaseq 6000 were carried out by GENEWIZ (https://www.genewiz.com) resulting in the 77.5-88.5 million 150 nt paired-end reads.


title: Z20 open retina chk222


title: Kidney, infected C57BL/6 mouse, day 21, biol rep 1


title: Kidney, infected C57BL/6 mouse, day 7, biol rep 4

value: Day 7


title: genomic DNA from Patient67_week12

value: Tumor biopsy

value: Breast cancer


title: Kidney, infected C57BL/6 mouse, day 7, biol rep 3


title: Control-KD RNA-seq, rep 2


title: Z20 occluded retina chk222


title: Elys-KD RNA-seq, rep 1


title: genomic DNA from Patient19_week12


title: Control-KD RNA-seq, rep 1


title: genomic DNA from Patient118_week12


title: Z20 open choroid chk221

value: choroid

value: open


title: Kidney, infected C57BL/6 mouse, day 21, biol rep 2


title: ParBF, E.coli WT, F_telRL3.5, IP2

description: Mapped reads: 9535898; average fragment size: 181

organism: Escherichia coli

tag: strain name

value: plasmid

tag: plasmid f

tag: prophage

tag: dna topology

value: Linear

tag: chip antibody

value: anti ParBF


title: Kidney, uninfected C57BL/6 mouse, day 0, biol rep 3

value: Kidney

value: naïve

value: Day 0


title: genomic DNA from Patient99_week12

tag: timepoint


title: Kidney, infected C57BL/6 mouse, day 7, biol rep 1

value: WT

value: T. brucei-infected


title: ParBF, E.coli WT, F_telRL3.5, IP1

description: Mapped reads: 15493504; average fragment size: 173


title: Z20 occluded choroid chk221

tag: time point

tag: eye treatment

value: occluded

tag: Sex


title: Kidney, uninfected C57BL/6 mouse, day 0, biol rep 2

tag: strain

tag: genotype


title: ParBF, E.coli WT, F_telRL3.5, input

description: Mapped reads: 4412379; average fragment size: 182


title: genomic DNA from Patient39_week12


title: Z20 occluded retina chk221

value: retina

value: M


title: Kidney, uninfected C57BL/6 mouse, day 0, biol rep 1

tag: infection

tag: time


title: genomic DNA from Patient32_week12

tag: gender

value: Female

tag: sample type

value: Chemotherapy


title: Z20 occluded choroid chk222


title: ParBF, E.coli WT, F_telRL13, IP2

description: Mapped reads: 13693419; average fragment size: 194


title: Z20 open retina chk221


title: Z20 open choroid chk220

value: F


title: genomic DNA from Patient56_week12

value: Tumor biopsy

tag: disease state

value: Breast cancer

tag: agent

value: Chemotherapy+bevacizumab


title: Kidney, infected BALB/c mouse, day 21, biol rep 3

tag: tissue

value: BALB/c

value: Day 21


title: ParBF, E.coli WT, F_telRL13, IP1

description: Mapped reads: 21906102; average fragment size: 164

tag: strain name

value: plasmid

tag: plasmid f

value: Linear

value: anti ParBF


title: genomic DNA from Patient91_week12


title: genomic DNA from Patient78_week12


title: Z20 open retina chk220

value: open


title: Kidney, infected C57BL/6 mouse, day 7, biol rep 2

value: Kidney

value: WT

value: Day 7


title: Kidney, infected BALB/c mouse, day 21, biol rep 2

value: T. brucei-infected


title: Z20 occluded choroid chk220

value: choroid

value: occluded


title: genomic DNA from Patient60_week12

value: Female


title: Kidney, infected BALB/c mouse, day 21, biol rep 1


title: genomic DNA from Patient55_week12


title: Z20 occluded retina chk220

value: retina

value: F


title: Kidney, infected BALB/c mouse, day 7, biol rep 3


title: Z20 open choroid chk219


title: ParBF, E.coli WT, F_telRL47, input

description: Mapped reads: 7835823; average fragment size: 164

tag: prophage

tag: dna topology


title: Z20 open retina chk219


title: genomic DNA from Patient129_week12

value: Tumor biopsy

value: Breast cancer

tag: timepoint


title: Kidney, infected BALB/c mouse, day 7, biol rep 1

value: BALB/c


title: ParBF, E.coli WT, F, IP1

description: Mapped reads: 18000450; average fragment size: 162

value: CCC

tag: chip antibody


title: ParBF, E.coli WT, F, input

description: Mapped reads: 5518379; average fragment size: 151

value: plasmid


title: genomic DNA from Patient126_week12

value: Chemotherapy


title: Z20 occluded choroid chk219

tag: time point

tag: eye treatment


title: genomic DNA from Patient73_week12


title: genomic DNA from Patient98_week12


title: ParBF, E.coli WT, F_telRL13, input

description: Mapped reads: 6470513; average fragment size: 162

value: Linear


title: ParBF, E.coli topA, F, IP1

description: Mapped reads: 26075208; average fragment size: 186

value: W3110 rpsL topA31::miniTn10

value: anti ParBF


title: ParBF, E.coli topA, F, IP2

description: Mapped reads: 20939631; average fragment size: 187


title: Z16 open choroid chk218

value: open

tag: Sex


title: Kidney, uninfected BALB/c mouse, day 0, biol rep 3

value: Kidney

tag: strain

tag: genotype

value: WT

value: naïve

value: Day 0


title: Z20 occluded retina chk219

value: occluded


title: Kidney, uninfected BALB/c mouse, day 0, biol rep 2

tag: infection

tag: time


title: ParBF, E.coli topA, F, input

description: Mapped reads: 10887278; average fragment size: 169


title: genomic DNA from Patient77_week12

tag: gender

value: Female

tag: sample type


title: Kidney, uninfected BALB/c mouse, day 0, biol rep 1


title: Z16 open retina chk218

value: retina

value: F


title: ParBF, E.coli WT, F_telRL47, IP1

description: Mapped reads: 22545774; average fragment size: 158


title: IRF8KO_adult_rep2_batch#2

data_processing:
Basecalls performed using bcl2fastq without the acceptance of index mismatch
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.2b.
Sequence duplicates were removed using Picard v2.17.11. Aligned tags were counted with Subread featureCounts. All steps are packaged in CCBR/Pipeliner.
Assembly: mm10
Supplementary files format and content: tab-delimited text files consist of Read count per gene

growth_protocol: In vivo microglia from each brain were non-enzymatically isolated.

extract_protocol:
Microglia were FACS-sorted directly in TRIzol and stored until usage. Total RNA was purified by phase extraction.
The cDNA was synthesized using SMART-Seq v4 Ultra Low Input RNA Kit (Takara bio USA, CA) with 15-cycle amplification. Adaptors were added to 1ng cDNA using the Nextera XT library prep kit (Illumina, CA).

value: female

tag: age

tag: cell type

value: FACS-sorted microglia

tag: treatment


title: Z16 occluded choroid chk218

tag: tissue

value: choroid


title: D39_D-pptAB-D-ami_planktonic_biol-rep-1

city: Pittsburgh

first: N.

middle: Luisa

last: Hiller

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description: D39 D-pptAB-D-ami biol-rep-1

data_processing:
Data processing performed on Galaxy platform
Sequence reads were mapped to Spn D39 genome using bowtie2 on Galaxy (version 2.5.3) with default parameters
Read count extraction was performed using featureCounts on Galaxy (version 2.0.3) (parameters - GFF feature type filter: gene)
Read count normalization was performed using DESeq2 on Galaxy
Assembly: GCF_000014365.2
Supplementary files format and content: Comma separated CSV file includes raw counts for each sample. Rows are genes that can be identified by a new gene ID, corresponding old gene ID or a locus tag. Some old gene IDs have no corresponding new gene ID, hence they are identified solely by their locus tag (genome accession and coordinates).

organism: Streptococcus pneumoniae

growth_protocol: Spn strains were grown in chemically-defined media supplemented with 55mM final concentration glucose at 37C, 5%CO2 until OD600 reached 0.3, 2mL cultures were collected.

extract_protocol:
Pelleted samples were treated with proteinase K, lysozyme and mutanulysin and samples were extracted using Quick-RNA™ MiniPrep Kit (Zymo Research Cooperation Cat. no. R1055).
Using manufacturer's protocol, RNA libraries for RNA-seq were prepared with NEB E7770 (NEBNext® Ultra™ II RNA Library Prep Kit for Illumina) on ribosomal RNA (rRNA) depleted RNA.

treatment_protocol: No treatments were added to the cultures, the collected culture were mixed 1:1 with in-house RNA-later, spun down for 5 min at max speed.

value: pptAB amiA-F double deletion


title: Kidney, infected BALB/c mouse, day 7, biol rep 2

value: BALB/c

value: T. brucei-infected

value: Day 7


title: IRF8KO_adult_rep1_batch#2


title: genomic DNA from Patient29_week12

value: Tumor biopsy

tag: disease state

value: Breast cancer

tag: agent

value: Chemotherapy


title: D39_D-phrA_planktonic_biol-rep-2

description: D39 D-phrA biol-rep-2

value: phrA deletion


title: Z16 occluded retina chk218


title: WT_adult_rep2_batch#2

value: WT


title: genomic DNA from Patient40_week12

tag: timepoint


title: D39_D-phrA_planktonic_biol-rep-1

description: D39 D-phrA biol-rep-1


title: Z16 open choroid chk217

value: open

value: M


title: genomic DNA from Patient93_week12

value: Female


title: WT_adult_rep1_batch#2


title: D39_D-pptAB_planktonic_biol-rep-2

description: D39 D-pptAB biol-rep-2

value: pptAB deletion


title: D39_D-pptAB_planktonic_biol-rep-1

description: D39 D-pptAB biol-rep-1


title: Z16 occluded retina chk217

value: retina

value: occluded


title: IRF8KO_P14_rep2

value: female

value: FACS-sorted microglia


title: genomic DNA from Patient102_week12


title: Z16 occluded choroid chk217

value: choroid


title: genomic DNA from Patient21_week12


title: D39_WT_planktonic_biol-rep-2

description: D39 WT biol-rep-2


title: IRF8KO_P14_rep1


title: IRF8KO_P14_rep3


title: D39_D-pptAB-D-ami_planktonic_biol-rep-2

description: D39 D-pptAB-D-ami biol-rep-2

value: pptAB amiA-F double deletion


title: D39_WT_planktonic_biol-rep-1

description: D39 WT biol-rep-1


title: Z16 open choroid chk216


title: genomic DNA from Patient116_week12


title: genomic DNA from Patient16_week12


title: Z16 open retina chk216


title: WT_P14_rep3


title: genomic DNA from Patient105_week12


title: genomic DNA from Patient69_week12

value: Chemotherapy+bevacizumab


title: Z16 occluded retina chk216


title: genomic DNA from Patient86_week12


title: ADP_UA_5

description: ADP

hyb_protocol: Purified RNA was hybridized for 16 to 24 hours at 65°C in nCounter hybridization buffer with NanoString Reporter and Capture probes, using 8 μL Master Mix, 5 µL sample, and 2 µL Capture ProbeSet per sample.

scan_protocol: Once the hybridization reactions have been removed from the thermal cycler, proceed immediately to an nCounter Prep Station. This step can process up to 12 samples per run in approximately 2.5 to 3 hours. Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: The raw data as RCC files format were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform.

label: NanoString barcodes

source_name: hippocampus

label_protocol: Per manufacturer recommendations, https://nanostring.com/products/ncounter-assays-panels/oncology/metabolic-pathways/ . The purified RNA is diluted in nuclease-free water to 20 ng/uL. RNA (~100 ng) added for hybridization assay.

extract_protocol: The hippocampus tissue (5 mg) of 3xTg and 3xTg/Polβ+/- AD mice were prepared for the extraction of total RNA using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, #12183018A) according to the manufacturer’s protocol.

treatment_protocol: Mice were treated according to animal study protocol 361-OSD-2023. Mice were group housed and fed ad libitum. WT (C57BL6/J), 3xTgAD, 3xTgAD/PolB +/- transgenic mice were treated with Urolithin A (200 mg kg day−1) by oral gavage for 5 months.

value: hippocampus

tag: strain/background

value: Urolithin A

value: 5 months


title: Z16 open retina chk215

tag: time point


title: genomic DNA from Patient8_week12

value: Tumor biopsy

value: Breast cancer

value: Chemotherapy


title: ADP_UA_3

description: ADP


title: IRF8KO_P9_rep2


title: IRF8KO_P9_rep3


title: ADP_UA_2

description: ADP


title: genomic DNA from Patient108_week12


title: IRF8KO_P9_rep1


title: genomic DNA from Patient22_week12


title: Z16 occluded retina chk215

tag: eye treatment


title: ADP_UA_4

description: ADP

tag: Sex

value: Male


title: Z16 occluded choroid chk215

value: M


title: WT_P9_rep3

value: WT


title: Z16 open choroid chk214

value: open


title: WT_P9_rep2


title: ADP_UA_1

description: ADP


title: genomic DNA from Patient123_week12

value: Female


title: Z16 occluded choroid chk216

value: occluded


title: AD_UA_5

description: AD

value: Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm


title: Z16 open choroid chk215


title: AD_UA_4

description: AD


title: Z16 open retina chk214

value: retina


title: WT_P9_rep1

value: female

value: FACS-sorted microglia


title: genomic DNA from Patient50_week12

value: Chemotherapy+bevacizumab


title: WT_P14_rep2


title: Z16 occluded choroid chk214

value: choroid


title: genomic DNA from Patient113_week12


title: AD_UA_3

description: AD

value: hippocampus

value: Urolithin A


title: Duo3_11cLow_PM

city: New York

first: Tomasz

last: Ahrends

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Reads were aligned and annotated using STAR (v2.7.10b)
Differential expressionanalysis was performed using DESEq2 (v1.38.3) and gene set enrichment analyses using fgsea (v 1.24.0) onGene Onthology biological process dataset (c5.go.bp.v7.5.1.symbols)
Assembly: GRCm39 genome
Supplementary files format and content: Processed files iclude all genes differentially expressed between ZT3 and ZT15 for both eosinophil subsets.

source_name: intestinal lamina propria

extract_protocol:
Sorted eosinophils (1000 cells) were lysed in guanidine thiocyanate buffer (TCL buffer, QIAGEN) supplemented with 1% β-mercaptoethanol. RNA was isolated by solid-phase reversible immobilization bead cleanup using RNAClean XP beads (Beckman Coulter), reverse-transcribed and amplified
Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq500 for a total yield of 400M reads

treatment_protocol: Eosinophil subsets were isolated from lamina propria at ZT3 or ZT15.

value: intestinal lamina propria

value: eosinophil


title: Duo4_11cLow_PM


title: genomic DNA from Patient34_week12

value: Tumor biopsy

value: Breast cancer

value: Chemotherapy


title: Z16 occluded retina chk214

value: M


title: Z16 open retina chk217

value: open


title: genomic DNA from Patient5_week12

value: Female


title: WT_P14_rep1

source_name: FACS-sorted microglia

value: WT


title: Z16 open retina chk213

value: F


title: ADP_Veh_4

description: ADP

value: Vehicle

value: 5 months


title: Duo1_11cLow_PM


title: AD_UA_1

description: AD

value: Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm

value: Male


title: genomic DNA from Patient27_week12


title: Z16 open choroid chk213

value: choroid


title: genomic DNA from Patient42_week12


title: Z16 occluded choroid chk213

value: occluded


title: AD_UA_2

description: AD

value: hippocampus

value: Urolithin A


title: Duo4_11cHi_PM

value: intestinal lamina propria

value: eosinophil


title: ADP_Veh_2

description: ADP


title: genomic DNA from Patient3_week12

value: Tumor biopsy

value: Breast cancer


title: genomic DNA from Patient58_week12

value: Chemotherapy


title: Z16 occluded retina chk213

value: retina


title: Duo3_11cHi_PM


title: ADP_Veh_1

description: ADP


title: Duo2_11cLow_PM


title: genomic DNA from Patient111_week12

value: Female


title: Z04 open choroid chk212

value: open

value: M


title: genomic DNA from Patient114_week12


title: Z04 open retina chk212


title: Duo1_11cHi_PM


title: ADP_Veh_3

description: ADP

value: Vehicle


title: genomic DNA from Patient110_week12


title: Z04 occluded choroid chk212


title: AD_Veh_2

description: AD

value: 5 months


title: genomic DNA from Patient37_week12


title: Duo4_11cLow_AM


title: AD_Veh_1

description: AD

value: Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm


title: Duo3_11cLow_AM


title: genomic DNA from Patient89_week12


title: Z04 occluded retina chk212


title: AD_Veh_4

description: AD

value: Male


title: Duo1_11cLow_AM


title: genomic DNA from Patient128_week12


title: Duo2_11cLow_AM


title: AD_Veh_5

description: AD


title: Z04 open retina chk211


title: genomic DNA from Patient71_week12


title: Z04 open choroid chk211

value: choroid


title: Duo4_11cHi_AM


title: Z04 occluded choroid chk211

value: occluded


title: Duo2_11cHi_PM


title: AD_Veh_3

description: AD

value: hippocampus


title: genomic DNA from Patient47_week12


title: Duo3_11cHi_AM


title: WT_Veh_4

value: WT


title: Z04 occluded retina chk211


title: Duo2_11cHi_AM

value: intestinal lamina propria


title: Z04 open choroid chk210


title: WT_Veh_1


title: WT_Veh_2


title: genomic DNA from Patient52_week25


title: Duo1_11cHi_AM

value: eosinophil


title: Z04 open retina chk210


title: E14_mutant_rep2

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

description: mutant replicate 2

data_processing:
Reads were aligned to mm10 genome using Hisat2 (with parameters --no discordant and --no-mixed)
Raw counts were determined using the Rsubread package featurecounts
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: dorsal telencephalon

extract_protocol:
Dorsal telencephalon was dissected, and RNA was extracted using Trizol.
Total RNA library was prepared by Illumina TruSeq Stranded Total RNA Library Sample Prep Kit (RS-122-2201) with Ribo-Zero to remove ribosomal RNA

value: dorsal telencephalon

tag: developmental stage

value: Embryonic day 14


title: mycelium tissue, Swd3.2

first: Zhongling

last: Wu

address: Building 2, No. 1518 Jiangchang West Road, Jing'an District, Shanghai

institute: Bright Dairy & Food Co., Ltd.

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Fastqc.
Trimmed sequence reads were mapped to  the reference genome of Monascus purpureus V1.0(JGI assembly ) using Hisat2.
Stringtie was used for the assemble transcripts and remap and quality gene-expression level,which is estimated by FPKM values.
Assembly: Monascus purpureus v1.0
Supplementary files format and content: tab-delimited text file includs FPKM values for each Sample

organism: Monascus purpureus

source_name: mycelium

growth_protocol: The WT, Set1 and Swd3 mutant strains were cultured in PDB medium for 2 d, and the mycelium were collected for the total RNA extraction.

extract_protocol:
RNA was extracted using RNA prep Pure Kit (TIANGEN), 1 ug total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep kit following manufacturer's protocals.

value: mycelium

tag: genotype

value: Swd3 knockout


title: Z04 occluded choroid chk210

data_processing:
raw data was processed by the standard Illumina pipeline to yeild trimmed fastq files
fastq data counted against transcripts (ensembl v105) with salmon
data summarized to gene-level with tximeta (bioconductor)
Assembly: GRCg6a (gene models – ensembl v105)
Supplementary files format and content: gzipped tab-delimited text – raw counts per ensembl gene ID per sample

source_name: choroid

extract_protocol:
RNA was extracted from choroid and retinal tissues using the QIAgen RNAeasy kit
NEBNext Ultra II Directional RNA Library Prep Kit


title: mycelium tissue, Swd3.1


title: Z04 occluded retina chk210

value: retina


title: mycelium tissue, Set1.3

value: Set1 knockout


title: E14_mutant_rep1

description: mutant replicate 1


title: Z04 open choroid chk209

value: open

value: M


title: mycelium tissue, Set1.2


title: E14_wt_rep2

description: control replicate 2


title: Z04 open retina chk209


title: E14_wt_rep1

description: control replicate 1

source_name: dosal telencephalon

value: dosal telencephalon


title: genomic DNA from Patient18_week12

value: Female

value: Tumor biopsy

value: Breast cancer

value: Chemotherapy


title: mycelium tissue, Swd3.3


title: genomic DNA from Patient89_week25


title: CCR6+RORγt- Treg rep3

city: Hamburg

first: Georg

middle: R

last: Herrnstadt

address: Martininstraße 52

department: III. Department of Medicine

institute: University clinic Hamburg-Eppendorf

data_processing:
Illumina RTA 2 software was used for base-calling
Gene abundance was quantified using salmon (v1.2.0)42 and mouse gene annotations from ENSEMBL (version 97) for GRCm38 genome assembly, and imported using R package tximport
Counts normalization and differential gene expression analysis were performed using DESeq2 package.44
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file including normalized count values for each Sample

extract_protocol:
Spleens were harvested in HBSS and passed through 70-mm nylon meshes. After lysis of erythrocytes with ammonium chloride, cells were washed and passed through 40-mm meshes. FACS sorting was performed from splenic single cell suspensions pre-enriched for CD4+ T cells by MACS sorting. Tregs were isolated by FACSorting. Surface staining and reporter fluorescence was used to separate CCR6+RORγtneg Treg17 cells (CD3+CD4+Foxp3(RFP)+RORγt(GFP)negCCR6+) and biTregs (CD3+CD4+Foxp3(RFP)+RORγt(GFP)+)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: splenic Treg

tag: strain

tag: sorted cell


title: CCR6+RORγt- Treg rep2


title: mycelium tissue, control.3

value: WT


title: Z04 occluded retina chk209

first: Debora

last: Nickla

address: 424 Beacon St

institute: New England College of Optometry

source_name: retina

value: occluded


title: mycelium tissue, control.2


title: CCR6+RORγt- Treg rep1


title: Z04 open choroid chk208

value: choroid

value: F


title: mycelium tissue, control.1


title: RORγt+ Treg rep3

source_name: biTreg


title: Z04 open retina chk208


title: OPNisin_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.7), Trimmomatic (ver. 0.39) and cutadapt (ver. 3.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.104) using STAR (ver. 2.7.10a).
The read count of gene features was performed with the featureCounts tool (ver. 2.0.1)
Assembly: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the QIAseq Stranded mRNA Lib Kit UDI (QIAGEN, 180440). (Clontech)

treatment_protocol: Three-day-old worms were cultured for one day on mNGM plates covered with OP50 (control group) or OP50 + nisin.

value: Whole

tag: cell line

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding OP50+nisin


title: Z04 occluded choroid chk208

city: Boston


title: RORγt+ Treg rep2


title: mycelium tissue, Set1.1

value: mycelium

value: Set1 knockout


title: Z04 occluded choroid chk209

value: M


title: RORγt+ Treg rep1


title: Z04 occluded retina chk208

value: retina


title: Opcont_rep2

value: feeding OP50


title: Z04 open choroid chk207

value: open


title: OPcont_rep1


title: Z04 open retina chk207


title: SMXL7d53-GR hypocotyl, dex, rep4

city: Heidelberg

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

data_processing:
Reads were mapped by STAR-2.7.8a with "--alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterMultimapNmax 1" option.
Reads per gene were counted by summarizeOverLaps function (GenomicAlignments v1.30.0 package in R) with "mode="union", ignore.strand = TRUE" option.
Raw counts were normalized by DESeq2 (v1.34.0 package)
Assembly: tair10 / araport11 annotation
Supplementary files format and content: rawCounts.csv is a csv format table provides raw counts for each sample and each gene.
Supplementary files format and content: normalized_counts.csv is a csv format table provides normalized counts for each sample and each gene.

source_name: Hypocotyl

growth_protocol: Plants were grown on soil at 21-22 degrees in short day conditions (10 h light and 14 h darkness) for three weeks and then transferred to long day conditions (16 h light and 8 h darkness) for one weak.

extract_protocol:
The hypocotyls were immediately harvested and pulverized with pestle and mortar. RNA was isolated with RNeasy Mini Kit (QIAGEN, Netherland) and genomic DNA contamination was removed by referring to the protocol of TURBO DNA-free™ Kit (Thermo Scientific; USA). Subsequent clean-up of RNA was performed by using RNeasy Mini Kit.
1.2 µg of total RNA/sample was used for the library preparation using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) with polyA mRNA workflow and Unique Dual Index primers (NEB). 12 cycles of amplification were performed.

treatment_protocol: 15 µM dex or equal volume of DMSO (mock) was treated by directly watering to 4-week-old plants. Plants were harvested 5 hours after the treatment.

value: Hypocotyl

value: dex


title: SMXL7d53-GR hypocotyl, dex, rep3

value: WT


title: Z04 occluded retina chk207

value: occluded


title: OPNisin_rep1


title: SMXL7d53-GR hypocotyl, dex, rep2


title: Z00 open retina chk206


title: SMXL7d53-GR hypocotyl, mock, rep4

value: mock


title: Z04 occluded choroid chk207

value: choroid

value: F


title: SMXL7d53-GR hypocotyl, mock, rep3


title: SMXL7d53-GR hypocotyl, dex, rep1


title: Z00 open choroid chk206