title: B_WT_H1_r1

city: Washington

first: Mathilde

last: Biot

address: 800 22nd St NW

institute: George Washington University

description: HORMAD1 ChIP-seq of the B6 mouse, replicate 1

data_processing:
Reads were trimmed to 100bp and then filtered on the Phred score (> 28). Reads were mapped to the mm10 genome using Bowtie 2 with the following parameters: -N 1 -I 100 -X 1000 -no-mixed -no-discordant. Unmapped reads and duplicates were removed in order to obtain our final dataset for post-processing. Bigwig: Read enrichment along the genome with a bin size of 10bp in Count per Million, where the corresponding knockout have been subtracted. Peak detection: To detect regions significantly enriched along the genome and between our replicates, we used the IDR methodology. To do so, we called peaks between true replicate, pooled pseudo-replicates and self-pseudo-replicates with the following relaxed MACS2 parameters: --format BAMPE --p value 0.01, as advised by the authors and a negative control was included (the corresponding knockout, except for CTCF, where input was used). Then, IDR analyses were performed and replicates with an IDR rescue and self-consistency ratio below 4 were considered to be reproducible. Therefore, the final peak datasets were build by taking the N peaks from true replicates below the IDR threshold of 0.05, as recommende by the authors. If replicates do not satisfy those conditions, replicates were considered not reproducible, and thus only one replicate was considered. The one considered contained the highest percentage of peak satisfying IDR conditions. Therefore, the final peak datasets were build by taking the N peaks from pseudo-replicates below the IDR threshold of 0.01, as recommended by authors. For DMC1, reads were processed using the hotSSDS and hotSSDS-extra Nextflow pipelines (Auffret et al., MiMB Germ Cells Development,  2023.), available on github: (https://github.com/jajclement/hotSSDS.git; https://github.com/jajclement/hotSSDS-extra.git).
Assembly: mm10
Supplementary files format and content: bw: read enrichment along the genome where the corresponding knockout has been subtracted; bed: peak coordinates and enrichments

source_name: whole-testis

extract_protocol:
Testes were homogenized and fixed with 4% formaldehyde for 15 minutes. After quenching, cell suspension was washed and lysed to obtain a nuclei suspension. The nuclei suspension was filtered througth a 40µm cell strainer and sonicated. After a high speed of centrifugation, chromatin was collected and incubated with the antibody and then DNA-protein complexes were isolated.
Enriched DNA were prepared using the Next Gen DNA Library kit from Active Motif  following manufacturer's instructions. For DMC1, enriched DNA were prepared using the Illumina Trueseq protocol with an additional step of kinetic enrichment to titrate ssDNA.

treatment_protocol: 1.5dpp male pups were pipette feeding with WIN 18,466, an inhibitor of retinoic acid. Retinoic acid is a key component in the induction of spermatogonia into meiosis. Therefore, after pipette feeding pups for 7 to 10 consecutives days, a single dose of retinoic acid was intraperitonetealy injected to induce accumulated B type spermatogonia into meiosis in the whole testis. 8 days post-injection, testes were collected because enriched at 80-95% of Leptotene-Zygotene spermatocytes.

value: whole-testis

value: L/Z

value: wild-type

value: synchronization of spermatogenesis

tag: time

value: 8 days post-injection

tag: chip antibody


title: MUT_D7_p2_NFIAn_rep1

status: Public on Apr 23 2024

type: SRA

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

library_source: genomic

data_processing:
Data was processed using the nf-core atacseq pipeline (https://nf-co.re/atacseq) with the following options: --genome mm10  --skip_diff_analysis --min_reps_consensus 2 -r 1.2.1.
Assembly: mm10
Supplementary files format and content: normalised vsd values, columns are samples and rows are genomic intervals.

molecule: genomic DNA

organism: Mus musculus

source_name: neural progenitor differentiation

growth_protocol: 60-80,000 mouse ES cells were plated onto the pre-coated CellBIND dishes (Corning) in N2B27 medium (Advanced DMEM - F12 (Gibco, Cat. No. 21331-020) and Neurobasal medium (Gibco, Cat. No. A35829-01) (1:1), supplemented with 1xN2 (Gibco Cat no. 17502001), 1xB27 (Gibco Cat no. 17504001), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma-Aldrich, Cat No. A7979-50ML), and 0.1 mM 2-mercaptoethanol) supplemented with 10 ng/ml bFGF (R&D, Cat. No. 100-18B). On day 2, the media was changed to N2B27 supplemented with 5 μM CHIR99021 (GSK3β inhibitor; Axon, 1386). 20-21 h later, on day 3, the media was changed to N2B27 with 100 nM RA and 10 nM of Smoothened Agonist (SAG; Calbiochem, 566660). From day 5 onwards, cells were kept in N2B27 supplemented with 10 nM SAG. From day 3 onwards, media changes were performed daily.

extract_protocol:
CaTS-ATAC was performed as previously described (Delás et al., 2023) with in-house produced Tn5. A dead cell removal step was introduced to enrich for live cells prior to fixation and transposition. The details are as follows: at the differentiation timepoint of collection, cells were washed once with PBS and dissociated with Accutase (Gibco, A1110501) for 5 min at 37°C. Cells were collected in 1.5 ml LoBind Eppendorf tubes (Eppendorf cat. #Z666548) and spun down at 400xg for 4 min. Cell suspensions were supplemented with LIVE/DEADTM Fixable Dead Cell Stain Near-IR fluorescent reactive dye (Thermo Fisher, L34976), according to the manufacturer's instructions (1 µl dye/1 ml PBS for 1x106 cells) and incubated for 30 min on ice protected from light. During the incubation, the autoMACS® Pro Separator (Miltenyi Biotec) was set-up according to the manufacturer’s instructions. After the 30 min cell suspensions were divided into 15 ml falcon tubes and spun down for 10 min at 400xg at 4°C. Cells were resuspended, pooled into one tube, and counted. Cells were magnetically labelled with Dead Cell Removal Microbeads from the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101). For 1.0x107 cells, 100 µl beads were used. Cells and microbeads were mixed and incubated for 15 min at room temperature. If necessary, 1x Binding Buffer provided by the kit was added to the cell suspension to reach a minimum volume of 500 μl for separation. The samples were run through the autoMACS® Pro Separator (Miltenyi Biotec) using the ‘Depl05’ programme. The microbeads label dead cells, which are retained in the separation columns. Unlabelled live cells run through the column and were collected in a 15 ml falcon tube in PBS. Live cells were count and spun down for 4 min at 400xg at 4°C. Cell pellet was resuspended in 300 µl of PBS in 1.5 ml LoBind Eppendorf tubes. Cells were then fixed, transposed, stained for viability and intracellular markers (anti-SOX2-V450, anti-Nkx6.1-PE, goat anti-Olig2, rabbit anti-Nfia) and sorted. DNA of samples was isolated using the DNA Clean & Concentrator-5 kit (Zymo; D4013) as per manufacturer’s instructions.
Transposed DNA was first amplified with 2X PCR Master Mix NEB (Cat. No. M0541S), and 1 µl of constant forward primer and indexed reversed primer (Table S1) (both at 25 µM) in a total reaction volume of 50 ul. The program was as follows: 5 min at 72ºC, 30 s at 98ºC, followed by 7 cycles of 30 s at 98ºC, 30 s at 63 ºC and 60 s at 72 ºC, with a final extension of 5 min at 72 ºC. DNA was cleaned up with 1.8x volumes of AMPureXP beads (Beckman Coulter, Cat. No. A63882) and eluted in 18 µl of EB buffer. qPCR was carried out to determine the number of extra cycles using 2 µl of the amplified DNA in technical duplicates. Each 20 µl reaction contained 20 µl of 2X SYBR Green PCR assay, using PowerUP SYBR Green Master Mix (Thermo Fisher, Cat. No. A25742) and 2.5 µl of each primer (at 25 µM each). The qPCR program was as follows: initial activation for 2 min at 50ºC, 30 s at 98ºC, followed by 40 cycles of 10 s at 98ºC, 30 s at 63ºC and 60 s at 72ºC. The number of additional cycles was calculated as ¼ of the maximum amplification 86. The second amplification was done using 12.5 µl of amplified DNA, 2X PCR Master Mix NEB and 2.5 µl of each primer (at 25 uM) in a total volume of 50 ul. The program was the same as the first amplification without the initial extension and for the calculated number of cycles. Finally, re-amplified DNA was cleaned up using 1.8x volumes AMPureXP beads and eluted in 30 ul. Samples were quantified in the QuBit, size profiles examined in the Bioanalyzer using the DNA High Sensitivity DNA Kit (Agilent, Part No. 5067-4626).

tag: cell type

value: neural progenitor differentiation

tag: cell population

tag: genotype

value: MUT

tag: timepoint


title: LN-229, siControl_2_rep2

city: Los Angeles

first: Peggy

middle: J

last: Farnham

state: CA

address: 1450 Biggy St, NRT6514

department: Biochemistry and Molecular Medicine

country: USA

institute: University of Southern California

library_source: transcriptomic

data_processing:
RNA-seq results were aligned to the human genome GRCh38 using STAR
Counts quantified using HTseq and Rsem
Differentially expressed genes with absolute log2 fold change >0.5 and q-value cut-off of 0.05 were determined using DEseq2
Assembly: hg38
Supplementary files format and content: txt files containing output for reads per gene

molecule: total RNA

organism: Homo sapiens

source_name: brain

growth_protocol: LN-229 was grown using DMEM supplemented with 10% FBS and pen/strep.

extract_protocol:
Total RNA was extracted using trizol.
Libraries were constructed by Novogene using NEBNext Ultra™ II RNA Library Prep Kit for Illumina

tag: tissue

value: brain

tag: cell line

value: glioblastoma

value: wild type

tag: treatment

value: siControl


title: LN-229, siZFX siZNF593_rep1

value: siZFX siZNF593


title: M4_KO_M4_r2

description: MEI4 ChIP-seq of the Mei4KO mouse, replicate 2

value: Mei4tm1Bdm (Mei4KO)


title: MUT_D7_p1_NFIAn_rep3


title: 293T, DKO, pCMV6_rep2

source_name: kidney

value: kidney

value: human embryonic kidney

value: ZFX/ZNF711 knockout


title: LN-229, siControl_2_rep1


title: M4_KO_M4_r1

description: MEI4 ChIP-seq of the Mei4KO mouse, replicate 1


title: LN-229, siZNF593_rep3


title: RNAseq_DQ_2

city: Zhanjiang

first: Yiting

last: Guan

address: 236 Yuanzhu Road

department: Zhanjiang Institute of Clinical Medicine

country: China

institute: Guangdong Medical University

data_processing:
The sequencing adapters were removed from the raw RNA-seq reads, and the obtained clean data were aligned to the human reference genome (mm9) using HISAT2 software (version 2.1.0.).
For gene expression quantification, the sequencing reads within each gene were counted, and the counts were normalized using edgeR.
Differentially expressed genes (DEGs) were identified normalized according to DESeq2, |log2FC| > 1 and p < 0.05.
Assembly: mm9
Supplementary files format and content: wig or bedGraph index binary

source_name: ovary

extract_protocol:
For total RNA analysis and data processing, the total RNA was extracted using a TRIzol reagent following a standard protocol. The RNA integrity was checked on Agilent 2100 BioAnalyzer to conduct quality control (Agilent Technologies).
For RNA-seq data processing, the high-throughput RNA-Seq were performed with the NovaSeq 6000 platform to a depth of 1.5×107 reads.

value: ovary

value: cyclophosphamide, dasatinib and quercetin-treated


title: RNAseq_DQ_1


title: RNAseq_DQ_3


title: MCOHCF 17

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
Library strategy: 16S rDNA
Illumina HiSeq software used for basecalling.
Take the method of removing low quality by window, the specific operation is as follows: set a window of 25 bp, if the average quality value of the window is less than 20, the back-end bases will be truncated from the window; the read length after truncation is lower than the original read length For 75%, remove the entire sequence.
Remove linker contamination of reads (default adapter sequence and read sequence have an overlap of 15 bp, set to 15 bp, and allow the number of mismatches to be 3);
Remove reads containing N;Remove low-complexity reads (default reads with continuous base length ≥10 are low-complexity reads) finally, get the Cleandata
Splice the reads into tags through the overlap relationship between the reads; cluster the tags into OTUs and compare them with the database, and annotate species; based on the OTU and annotation results, perform sample species complexity analysis, analysis of species differences between groups, and association analysis. Model prediction, etc.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: colon

extract_protocol:
COLON were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

tag: strain

value: ICR

value: colon

tag: age

value: 10 weeks

value: High fat diet +control-FMT


title: MUT_D5_pM_NFIAn_rep3

value: neural progenitor differentiation

value: pMN


title: LN-229, siZFX siZNF593_rep2

value: brain


title: MUT_D7_p1_NFIAn_rep1

value: MUT


title: LN-229, siZNF593_rep2

value: glioblastoma

value: wild type


title: MCOHCF 13


title: RNAseq_Cy_3

value: cyclophosphamide-treated


title: RNAseq_Cy_2


title: LN-229, siZFX_rep3

value: siZFX


title: MCOHCF 11


title: RNAseq_Cy_1


title: MUT_D5_pM_NFIAn_rep2


title: MCOHCF 10


title: MUT_D5_p2_NFIAn_rep3


title: MCOHCF 12


title: RNAseq_Ctrl_2

value: WT


title: MUT_D5_pM_NFIAn_rep1


title: LN-229, siZFX_rep2


title: RNAseq_Ctrl_1


title: RNAseq_Ctrl_3


title: MUT_D7_p1_NFIAn_rep2


title: MUT_D5_p2_NFIAn_rep2


title: MCOHCF 7


title: MUT_D5_p2_NFIAn_rep1


title: LN-229, siControl_rep2

value: siControl


title: MCOHCF 6


title: LN-229, siZNF593_rep1


title: 3T3-L1 cells with ucMSCS 3

city: Taiyuan

first: Jingyi

last: Feng

address: Xinghualing

institute: The Second Hospital of Shanxi Medical University

data_processing:
Raw reads of fastq format were firstly processed using fastp  and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2  .
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count .
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene.

source_name: embryo

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: embryo

value: embryonic fibroblast

value: adipogenic differentiation. co-cultured with ucMSCS


title: MUT_D5_p1_NFIAn_rep3


title: LN-229, siControl_rep1


title: MUT_D5_p1_NFIAn_rep2


title: 3T3-L1 cells with ucMSCS 1


title: HEK293T, DKO, input (USC1563)

data_processing:
Data was analyzed using the ENCODE pipeline.
Reads were mapped to the genome using BWA
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigwig with total mapped reads

growth_protocol: LN-229 was grown in DMEM supplemented with 10% FBS and pen/strep

extract_protocol:
Chromatin was prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked using 1% formedelhyde for 10 mins and lysed. Chromatin was sonicated using a Bioruptor Pico.
Libraries were prepared using Roche KAPA Hyper Prep Kit (Roche# 07962347001) according to provided protocol

value: kidney

value: human embryonic kidney

value: ZFX/ZNF711 knockout


title: LN-229, siZFX_rep1


title: LN-229, siControl_rep3


title: MUT_D5_p1_NFIAn_rep1


title: MCOHCF 1

value: ICR

value: colon

value: 10 weeks

value: High fat diet +control-FMT


title: MCOHAF 23

value: High fat diet +AOS10mg/kg-FMT


title: MCOHCF 5


title: MCOHAF 19


title: MUT_D11_pM_NFIAn_rep3

value: neural progenitor differentiation

value: pMN

value: MUT


title: 3T3-L1 cells 3

value: adipogenic differentiation


title: HEK293T, DKO, wtZFX (USC1481)

value: wt ZFX

value: FLAG (CST #14793S)


title: 3T3-L1 cells 2

value: embryo

value: WT


title: Inp_B6

description: Input ChIP-seq of the B6 mouse, one replicate

value: whole-testis

value: L/Z

value: wild-type

value: synchronization of spermatogenesis

value: 8 days post-injection


title: 3T3-L1 cells 1

value: embryonic fibroblast


title: LN-229, siZFX, H3K4me3, Rep2 (USC1560)

value: brain

value: glioblastoma

value: wild type

value: siZFX


title: MCOHAF 18

value: ICR

value: colon

value: 10 weeks

value: High fat diet +AOS10mg/kg-FMT


title: LN-229, siZFX, ZNF593, Rep1 (USC1562)


title: MUT_D11_pM_NFIAn_rep1

value: neural progenitor differentiation

value: pMN

value: MUT


title: MUT_D11_pM_NFIAn_rep2


title: MCOHAF 17


title: LN-229, siControl, input, Rep1 (USC1559)


title: MUT_D11_p2_NFIAn_rep3


title: H1_KO_DMC1_r2

description: DMC1 ChIP-seq SSDS of the Hormad1KO mouse, replicate 2

value: whole-testis

value: Hormad1tm1.2Atot (Hormad1KO)


title: 3T3-L1 cells with ucMSCS 2

value: embryo

value: WT

value: adipogenic differentiation. co-cultured with ucMSCS


title: MCOHAF 15


title: MUT_D11_p2_NFIAn_rep2


title: H1_KO_DMC1_r1

description: DMC1 ChIP-seq SSDS of the Hormad1KO mouse, replicate 1

value: L/Z

value: synchronization of spermatogenesis

value: 8 days post-injection


title: LN-229, siControl, ZNF593, Rep1 (USC1558)

value: brain

value: glioblastoma

value: wild type

value: siControl


title: MCOHAF 14

value: ICR

value: colon

value: 10 weeks


title: HEK293T, DKO, ZFX12_13 (USC1528)

value: kidney

value: human embryonic kidney

value: ZFX/ZNF711 knockout

value: ZFX

value: FLAG (CST #14793S)


title: B_WT_DMC1_r2

description: DMC1 ChIP-seq SSDS of the B6 mouse, replicate 2

value: whole-testis

value: wild-type


title: MUT_D11_p2_NFIAn_rep1

value: neural progenitor differentiation

value: MUT


title: LN-229, siControl, H3K4me3, Rep2 (USC1556)


title: B_WT_DMC1_r1

description: DMC1 ChIP-seq SSDS of the B6 mouse, replicate 1

value: L/Z

value: synchronization of spermatogenesis

value: 8 days post-injection


title: LN-229, siControl, input, Rep1 (USC1555)

value: brain

value: glioblastoma

value: wild type


title: MCOHAF 5

value: ICR

value: colon

value: High fat diet +AOS10mg/kg-FMT


title: MUT_D11_p1_NFIAn_rep3


title: S11_KO_CTCF_r2

description: CTCF ChIP-seq of the Spo11KO mouse, replicate 2

value: Spo11tm1Mjn (Spo11KO)

value: anti-CTCF


title: MUT_D11_p1_NFIAn_rep2


title: MCOHAF 2

value: 10 weeks


title: MCOHAF 3


title: MUT_D11_p1_NFIAn_rep1


title: LN-229, siControl, H3K4me3, Rep1 (USC1553)

value: siControl


title: MCOHA10 12

value: High fat diet +AOS10mg/kg


title: P9_KO_CTCF_r2

description: CTCF ChIP-seq of the Prdm9KO mouse, replicate 2

value: whole-testis

value: B6;129P2-Prdm9tm1Ymat/J (Prdm9KO)


title: S11_KO_CTCF_r1

description: CTCF ChIP-seq of the Spo11KO mouse, replicate 1


title: LN-229, siZNF593, ZFX, Rep1 (USC1550)


title: P9_KO_CTCF_r1

description: CTCF ChIP-seq of the Prdm9KO mouse, replicate 1


title: MCOHA10 11


title: LN-229, siControl, ZFX, Rep1 (USC1548)


title: R3_N2_25C

city: Toronto

first: Julie

last: Claycomb

state: Ontario

address: 661 University Ave.

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: Isolated poly-adenylated RNA using oligo-dT beads

data_processing:
Cutadapt (Matrin 2011) was used to remove adapters using the adapter  “AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC” and discarding any reads not which were not trimmed or not within a 16-30 nucleotide range.
Reads were then mapped to the C. elegans genome (Wormbase release WS262) using STAR alignment tool (Dobin 2013).
A custom script was used for counting the number of reads for each feature from .bam files by STAR-aligner (Dobin, et al. 2013) and outputting counting data as .csv files. These were then converted to tables with an additional custom script [available at www.github.com/ClaycombLab/Charlesworth_2020], and detailing gene, feature, sequence, cigar, position, count, biotype, sample, feature type, total mapped reads, read length, matched read length and RPM for each sequence.
mRNA data quality was initially assessed via FASTQC, and any read that was sequenced into its adapters was trimmed via Cutadapt (adapter sequence “AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC”) All reads without adapters were retained for analysis. Reads were then mapped to the C. elegans genome (Wormbase release WS262) using STAR-aligner (Dobin, et al. 2013). The number of reads mapping to each gene feature was determined using summarizeOverlaps from the GenomicAlignment package (Lawrence, et al. 2013 - v1.22.1). Pre-filtering was used to remove all rows possessing only a single count or less across all samples. Differential expression and statistical analysis was performed using DESeq2 (Love, et al. 2014). mRNA differential gene expression changes were determined using DeSeq2. DE genes were >2-fold change (+/-) and <0.01 Padj.
Assembly: Wormbase release WS262
Supplementary files format and content: sRNA: mapping data, sequences and read counts for features of interest in the C. elegans genome (WS262). mRNA: read count matrix of number of detected reads per gene in N2 or csr-1a mutants at 20C and 25C.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole Worm

growth_protocol: All C. elegans strains were derived from the wild type Bristol N2 strain and cultured according to standard growth conditions <Brenner 1974> on Nematode Growth Medium (NGM) plates inoculated with E. coli OP50 at 20°C, unless otherwise stated.

extract_protocol:
For samples in which only RNA was isolated: Typical total RNA extraction and ethanol precipitation were performed, followed by quantification using a Nanodrop 1800C spectrophotometer. For samples in which Argonaute/sRNA complexes were isolated: Protein lysates were prepared by dounce homogenization of worm samples at 4°C, lysates were cleared by 10min 13,000xg centrifugation. Input (total small RNA) samples were taken first and total RNA was extracted using a typical Tri-Reagent protocol, followed by ethanol precipitation. IPs were performed with anti-GFP (Chromotek) or anti-CSR-1a (rabbit polyclonal). In the final step, beads with Argonaute-sRNA complexes were resuspended in Tri-Reagent, followed by RNA extraction as for other samples.
For sRNA libraries , RNA samples were treated with a 5' polyphosphatase prior to use in library prep with the  NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) per manufactuer instructions. For mRNA libraries, samples were DNAse treated prior to use with the NEBNext Ultra II Directional RNA Prep Kit for Illumina - with Poly-A selection per manufacterer instructions.

treatment_protocol: Synchronized staged animals were collected in 1X M9 and washed in M9 and MilliQ water. For samples in which only RNA was taken (PolyA RNA): Upon adding 4x volume Tri-Reagent (Molecular Research Center, Inc.), samples were flash frozen in a dry ice/ethanol bath and stored at -80°C for later RNA extraction. For samples in which Argonaute complexes were first isolated before RNA extraction (all other Input and IP samples for sRNA sequencing), all liquid was removed from samples, and samples were flash frozen in a dry ice/ethanol bath and stored at -80°C for later protein extraction.

value: Whole Worm

value: wild-type (N2)

tag: developmental stage

value: L4 Larval Stage

value: Wild-type C. elegans, Bristol Strain

tag: temperature


title: R2_N2_25C


title: B_WT_CTCF_r2

description: CTCF ChIP-seq of the B6 mouse, replicate 2

value: L/Z

value: wild-type

value: synchronization of spermatogenesis

value: 8 days post-injection


title: MCOHA10 9

value: ICR

value: colon


title: LN-229, siZNF593, input, Rep1 (USC1547)

value: brain

value: glioblastoma

value: wild type


title: B_WT_CTCF_r1

description: CTCF ChIP-seq of the B6 mouse, replicate 1

value: anti-CTCF


title: MCOHA10 10

value: 10 weeks

value: High fat diet +AOS10mg/kg


title: LN-229, siControl, input, Rep1 (USC1545)

value: siControl


title: R3_N2_20C

value: Whole Worm


title: MCOHA10 6


title: LN-229, siZFX, H3K4me3, Rep1 (USC1554)

value: siZFX


title: MCOHA10 5


title: S3_KO_S3

description: SYCP3 ChIP-seq of the Sycp3KO mouse, one replicate

value: whole-testis

value: Sycp3tm1Hoog (Sycp3KO)


title: LN-229, siZNF593, ZFX, Rep1 (USC1508)


title: H1_KO_S3_r2

description: SYCP3 ChIP-seq of the Hormad1KO, replicate 2

value: L/Z

value: Hormad1tm1.2Atot (Hormad1KO)


title: R2_N2_20C

value: wild-type (N2)

value: L4 Larval Stage

value: Wild-type C. elegans, Bristol Strain


title: R1_N2_20C


title: LN-229, siControl, ZFX, Rep1 (USC1506)


title: LN-229, siZNF593, input, Rep1 (USC1505)


title: MCOHA10 4

value: ICR

value: colon


title: MCOHA10 3


title: I1_KO_S3

description: SYCP3 ChIP-seq of the Iho1KO mouse, one replicate

value: Iho1tm1.2Atot (Iho1KO)

value: synchronization of spermatogenesis

value: 8 days post-injection


title: R3_JMC164_csr-1a(tor159)_25C


title: LN-229, siControl, input, Rep1 (USC1503)

value: brain

value: glioblastoma

value: wild type


title: MCOHA10 2

value: 10 weeks

value: High fat diet +AOS10mg/kg


title: R1_N2_25C

value: Whole Worm


title: M4_KO_S3_r2

description: SYCP3 ChIP-seq of the Mei4KO mouse, replicate 2

value: whole-testis

value: Mei4tm1Bdm (Mei4KO)


title: RNAseq_WCH01_relapse

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
Sequenced reads were mapped to hg19 whole genome using STAR
Sequenced reads were mapped to mm10 whole genome using STAR
Assembly: hg19; mm10
Supplementary files format and content: txt files with gene counts

source_name: BM cells

growth_protocol:
BM cells harvested from the patient.
APL cells from  murine sgUtx;SR.

extract_protocol:
RNA was extracted with Trizol
RNA-seq libraries were constructed by Illumina Stranded mRNA Sample Preparation Kit (NEB, Cat#E7770) according to the manufacturer’s protocol,

tag: subject status

value: acute promyelocytic leukemia (APL) patient

value: BM cells


title: R1_JMC164_csr-1a(tor159)_25C

value: L4 Larval Stage


title: MCOHA10 1


title: MCOHFD 20

value: High fat diet


title: R2_GR3039_csr-1(mg657)_CSR-1a_IP

description: Immunoprecipitated RNA using GFP conjugated chromtek GFP Trap MA beads


title: R1_JMC164_csr-1a(tor159)_20C


title: S11_KO_S3

description: SYCP3 ChIP-seq of the Spo11KO mouse,  one replicate

value: L/Z

value: Spo11tm1Mjn (Spo11KO)


title: RNAseq_WCH01_pretreat


title: MCOHFD 19

value: ICR

value: colon


title: DIS-24-T2

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

description:
21Feb18_H06
mature_counts.csv
hairpin_counts.csv

data_processing:
Reads were processed by the nf-core/smrnaseq (v 1.1.0) pipeline
Reads were trimmed with Trim Galore! (v 0.6.5). Reads were first clipped by 4 bases on the 5’ and 3’ ends followed by adapter trimming.
Reads were then mapped to annotated miRbase (release 22) miRNAs with Bowtie1(v 1.3.1). Reads were first mapped to annotated mature miRNAs with unmapped reads subsequently mapped to annotated hairpin miRNAs.
Count estimation was done using Samtools (v 1.12)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include hairpin and mature miRNA counts

source_name: serum

extract_protocol:
Serum EVs were then isolated via precipitation using “ExoQuick™ - Exosome Precipitation Kit” (#EXOQ20A-1, Biozol, Eching, Germany) according to manufacturer’s protocol from 500µL aliquots. The pellet containing precipitated EVs was suspended in 100µL of PBS. 50µL of this suspension were subjected to small RNA extraction using of the “SeraMir™ Exosome RNA Amplification Kit” (#RA808A-1, Biozol, Eching, Germany) with an adapted protocol for extracellular RNA isolation14. The isolates were eluted in 30µL elution buffer and miRNA concentration was quantified using the “Qubit™ microRNA Assay Kit” (#Q32880, Invitrogen™, Waltham, MA) according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared using the TruSeq® RNA seq Library Prep Kit v2 according to the Illumina TruSeq® messenger (mRNA) sequencing protocol. The RNA-seq libraries were sequenced on the Illumina HiSeq 3000/4000 (1 x 50bp).
miRNA-sequencing libraries were prepared according to the manufacturer’s protocol of the NEXTFLEX® Small RNA-Seq Kit v3 (#NOVA-5132-06, PerkinElmer, Waltham, MA) and sequenced on SP lanes on an Illumina NovaSeq 6000 (1 × 50 bp).

tag: time point

tag: patient id

value: serum

tag: diagnosis

value: CD

tag: fraction

value: small RNA


title: R1_GR3039_csr-1(mg657)_CSR-1a_IP


title: B_WT_S3_r2

description: SYCP3 ChIP-seq of the B6 mouse, replicate 2

value: wild-type

value: synchronization of spermatogenesis

tag: time

value: 8 days post-injection

tag: chip antibody


title: H1_KO_S3_r1

description: SYCP3 ChIP-seq of the Hormad1KO, replicate 1

tag: cell type

value: Hormad1tm1.2Atot (Hormad1KO)


title: R2_GR3039_csr-1(mg657)_CSR-1a_input

description: Total input RNA from lysate used for IPs

value: Whole Worm

tag: genotype


title: MCOHFD 18

value: 10 weeks


title: DIS-20-T2

description:
21Feb18_H05
mature_counts.csv
hairpin_counts.csv


title: R2_JMC164_csr-1a(tor159)_25C


title: B_WT_S3_r1

description: SYCP3 ChIP-seq of the B6 mouse, replicate 1

value: whole-testis


title: R1_GR3039_csr-1(mg657)_CSR-1a_input


title: DIS-12-T2

description:
21Feb18_H03
mature_counts.csv
hairpin_counts.csv

value: UC


title: MCOHFD 11


title: H1_KO_H1_r2

description: HORMAD1 ChIP-seq of the Hormad1KO mouse, replicate 2


title: R2_JMC161_CSR-1_IP

value: L4 Larval Stage

value: unc-119(ed3) III; mgTi11[rpl-28::csr-1a exon1::gfp]; csr-1(tm892)


title: DIS-08-T2

description:
21Feb18_H02
mature_counts.csv
hairpin_counts.csv


title: M4_KO_S3_r1

description: SYCP3 ChIP-seq of the Mei4KO mouse, replicate 1

value: L/Z

value: Mei4tm1Bdm (Mei4KO)


title: H1_KO_H1_r1

description: HORMAD1 ChIP-seq of the Hormad1KO mouse, replicate 1


title: MCOHFD 10

value: ICR

value: High fat diet


title: DIS-04-T2

description:
21Feb18_H01
mature_counts.csv
hairpin_counts.csv

value: serum


title: R1_JMC161_CSR-1_IP


title: MCOHFD 8

value: colon


title: DIS-24-T1

description:
21Feb18_G06
mature_counts.csv
hairpin_counts.csv

value: CD

value: small RNA


title: I1_KO_H1_r2

description: HORMAD1 ChIP-seq of the Iho1KO mouse, replicate 2

value: Iho1tm1.2Atot (Iho1KO)

value: synchronization of spermatogenesis


title: P9_KO_S3

description: SYCP3 ChIP-seq of the Prdm9KO mouse, one replicate

value: B6;129P2-Prdm9tm1Ymat/J (Prdm9KO)

value: 8 days post-injection


title: MCOHFD 7

value: 10 weeks


title: R1_JMC161_CSR-1_input

value: Whole Worm


title: R2_JMC161_CSR-1_input


title: M4_KO_H1_r2

description: HORMAD1 ChIP-seq of the Mei4KO mouse, replicate 2

value: whole-testis


title: R3_GR3043_input

value: L4 Larval Stage

value: csr-1(mg661[G120*]) mgIs75[rpn-2::gfp] IV; mgTi14[pbs-5::mcherry]


title: I1_KO_H1_r1

description: HORMAD1 ChIP-seq of the Iho1KO mouse, replicate 1

value: L/Z


title: MCOHFD 1


title: DIS-16-T2

description:
21Feb18_H04
mature_counts.csv
hairpin_counts.csv


title: MCOHFD 17


title: M4_KO_H1_r1

description: HORMAD1 ChIP-seq of the Mei4KO mouse, replicate 1

value: Mei4tm1Bdm (Mei4KO)


title: R2_GR3035_CSR-1a_IP

description: Immunoprecipitated RNA using GFP conjugated chromtek GFP Trap MA beads


title: DIS-12-T1

description:
21Feb18_G03
mature_counts.csv
hairpin_counts.csv

value: UC


title: MCOcon 12

value: ICR

value: control


title: S11_KO_H1_r2

description: HORMAD1 ChIP-seq of the Spo11KO mouse, replicate 2

value: Spo11tm1Mjn (Spo11KO)


title: DIS-08-T1

description:
21Feb18_G02
mature_counts.csv
hairpin_counts.csv

value: serum


title: MCOcon 11

value: colon


title: R1_GR3035_CSR-1a_IP


title: R2_GR3035_CSR-1a_input

description: Total input RNA from lysate used for IPs


title: MCOcon 10


title: S11_KO_H1_r1

description: HORMAD1 ChIP-seq of the Spo11KO mouse, replicate 1


title: DIS-04-T1

description:
21Feb18_G01
mature_counts.csv
hairpin_counts.csv

value: CD

value: small RNA


title: R1_GR3035_CSR-1a_input


title: DIS-20-T1

description:
21Feb18_G05
mature_counts.csv
hairpin_counts.csv


title: DIS-23-T2

description:
21Feb18_F06
mature_counts.csv
hairpin_counts.csv


title: P9_KO_H1_r2

description: HORMAD1 ChIP-seq of the Prdm9KO mouse, replicate 2

value: B6;129P2-Prdm9tm1Ymat/J (Prdm9KO)

value: synchronization of spermatogenesis


title: P9_KO_H1_r1

description: HORMAD1 ChIP-seq of the Prdm9KO mouse, replicate 1

value: 8 days post-injection


title: MCOHFD 5

value: 10 weeks

value: High fat diet


title: MCOcon 8


title: DIS-16-T1

description:
21Feb18_G04
mature_counts.csv
hairpin_counts.csv


title: R2_JMC223_WAGO-4_IP

value: Whole Worm

value: L4 Larval Stage

value: wago-4(tor117[gfp::3xflag::wago-4]) II


title: MCOcon 7


title: I1_KO_I1_r2

description: IHO1 ChIP-seq of the Iho1KO mouse, replicate 2

value: whole-testis

value: L/Z

value: Iho1tm1.2Atot (Iho1KO)


title: R1_JMC223_WAGO-4_IP


title: B_WT_H1_r2

description: HORMAD1 ChIP-seq of the B6 mouse, replicate 2

value: wild-type


title: DIS-15-T2

description:
21Feb18_F04
mature_counts.csv
hairpin_counts.csv


title: DIS-11-T2

description:
21Feb18_F03
mature_counts.csv
hairpin_counts.csv


title: R2_JMC223_WAGO-4_input


title: MCOcon 4

value: ICR

value: control


title: I1_KO_I1_r1

description: IHO1 ChIP-seq of the Iho1KO mouse, replicate 1


title: R1_JMC223_WAGO-4_input


title: DIS-07-T2

description:
21Feb18_F02
mature_counts.csv
hairpin_counts.csv

value: serum


title: H1_KO_I1_r2

description: IHO1 ChIP-seq of the Hormad1KO mouse, replicate 2

value: Hormad1tm1.2Atot (Hormad1KO)


title: R2_JMC248_WAGO-10_IP

description: Immunoprecipitated RNA using GFP conjugated chromtek GFP Trap MA beads

value: wago-10(tor162[3xflag::wago-10]) V


title: R1_JMC248_WAGO-10_IP


title: MCOcon 2

value: colon


title: H1_KO_I1_r1

description: IHO1 ChIP-seq of the Hormad1KO mouse, replicate 1

value: synchronization of spermatogenesis


title: DIS-23-T1

description:
21Feb18_E06
mature_counts.csv
hairpin_counts.csv

value: UC

value: small RNA


title: MCOcon 1

value: 10 weeks


title: DIS-19-T2

description:
21Feb18_F05
mature_counts.csv
hairpin_counts.csv

value: CD


title: M4_KO_I1_r2

description: IHO1 ChIP-seq of the Mei4KO mouse, replicate 2

value: Mei4tm1Bdm (Mei4KO)

value: 8 days post-injection


title: MCOA10 10


title: R2_JMC248_WAGO-10_input

description: Total input RNA from lysate used for IPs

value: Whole Worm

value: L4 Larval Stage


title: DIS-19-T1

description:
21Feb18_E05
mature_counts.csv
hairpin_counts.csv


title: R1_JMC207_ALG-4_IP

value: alg-4(tor143[gfp::3xflag::alg-4]) III


title: DIS-15-T1

description:
21Feb18_E04
mature_counts.csv
hairpin_counts.csv


title: MCOcon 5


title: M4_KO_I1_r1

description: IHO1 ChIP-seq of the Mei4KO mouse, replicate 1

value: whole-testis

value: L/Z


title: MCOA10 9

value: ICR


title: R2_JMC207_ALG-4_input


title: S11_KO_I1_r2

description: IHO1 ChIP-seq of the Spo11KO mouse, replicate 2

value: Spo11tm1Mjn (Spo11KO)


title: R1_JMC207_ALG-4_input


title: DIS-07-T1

description:
21Feb18_E02
mature_counts.csv
hairpin_counts.csv

value: serum


title: S11_KO_I1_r1

description: IHO1 ChIP-seq of the Spo11KO mouse, replicate 1


title: MCOA10 8


title: DIS-11-T1

description:
21Feb18_E03
mature_counts.csv
hairpin_counts.csv


title: MCOcon 3

value: control


title: MCOA10 7

value: colon


title: MCOHCF 2

value: High fat diet +control-FMT


title: P9_KO_I1_r2

description: IHO1 ChIP-seq of the Prdm9KO mouse, replicate 2

value: B6;129P2-Prdm9tm1Ymat/J (Prdm9KO)

value: synchronization of spermatogenesis


title: R2_JMC205_ALG-3_IP

value: alg-3(tor141[gfp::3xflag::alg-3]) IV


title: DIS-03-T1

description:
21Feb18_E01
mature_counts.csv
hairpin_counts.csv

value: CD

value: small RNA


title: DIS-03-T2

description:
21Feb18_F01
mature_counts.csv
hairpin_counts.csv


title: MCOA10 6

value: 10 weeks


title: P9_KO_I1_r1

description: IHO1 ChIP-seq of the Prdm9KO mouse, replicate 1

value: 8 days post-injection


title: DIS-26-T2

description:
21Feb18_D07
mature_counts.csv
hairpin_counts.csv


title: R1_JMC205_ALG-3_IP

description: Immunoprecipitated RNA using GFP conjugated chromtek GFP Trap MA beads

value: Whole Worm

value: L4 Larval Stage


title: DIS-22-T2

description:
21Feb18_D06
mature_counts.csv
hairpin_counts.csv


title: R2_JMC205_ALG-3_input


title: B_WT_I1_r2

description: IHO1 ChIP-seq of the B6 mouse, replicate 2

value: whole-testis

value: wild-type


title: MCOA10 5

value: ICR


title: MCOA10 4


title: B_WT_I1_r1

description: IHO1 ChIP-seq of the B6 mouse, replicate 1

value: L/Z


title: R1_JMC205_ALG-3_input

description: Total input RNA from lysate used for IPs


title: MCOA10 3

value: AOS 10mg/kg


title: DIS-14-T2

description:
21Feb18_D04
mature_counts.csv
hairpin_counts.csv

value: serum

value: UC


title: R2_JMC164_CSR-1b_IP


title: H1_KO_M4_r2

description: MEI4 ChIP-seq of the Hormad1KO mouse, replicate 2

value: Hormad1tm1.2Atot (Hormad1KO)


title: DIS-18-T2

description:
21Feb18_D05
mature_counts.csv
hairpin_counts.csv


title: H1_KO_M4_r1

description: MEI4 ChIP-seq of the Hormad1KO mouse, replicate 1


title: R1_JMC164_CSR-1b_IP


title: DIS-10-T2

description:
21Feb18_D03
mature_counts.csv
hairpin_counts.csv


title: R2_JMC164_CSR-1b_input


title: I1_KO_M4_r2

description: MEI4 ChIP-seq of the Iho1KO mouse, replicate 2

value: Iho1tm1.2Atot (Iho1KO)


title: DIS-06-T2

description:
21Feb18_D02
mature_counts.csv
hairpin_counts.csv


title: MCOA10 1

value: colon


title: DIS-02-T2

description:
21Feb18_D01
mature_counts.csv
hairpin_counts.csv


title: I1_KO_M4_r1

description: MEI4 ChIP-seq of the Iho1KO mouse, replicate 1

value: synchronization of spermatogenesis


title: S11_KO_M4_r2

description: MEI4 ChIP-seq of the Spo11KO mouse, replicate 2

value: Spo11tm1Mjn (Spo11KO)


title: s76075

city: Paris

first: Hafid

last: Ait-Oufella

address: 56, Rue Leblanc

country: France

institute: Inserm

data_processing:
Fastq files were aligned using STAR algorithm (version 2.7.6a), on the mm10 Ensembl 346 release 101 reference. Reads were then count using RSEM (v1.3.1).
Assembly: GRCm38
Supplementary files format and content: raw counts per gene, by sample

source_name: aorta

extract_protocol:
Total RNA was extracted from thoracic aorta samples with Qiagen columns (RNeasy MiniSpin Columns) using a polytron (T25 basic, IKA, Labortechnik)
RNA concentrations were obtained using nanodrop or a fluorometric Qubit RNA assay (Life Technologies, Grand Island, New York, USA). The quality of the RNA (RNA integrity number) was determined on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) as per the manufacturer’s instructions. RNA sequencing 344 libraries were prepared from 100 ng of total mRNA using the Illumina® Stranded Total RNA 345 Prep

value: aorta

tag: Sex

value: female

value: Ldlr-/-

tag: diet

value: Continuous HFD


title: DIS-26-T1

description:
21Feb18_C07
mature_counts.csv
hairpin_counts.csv

tag: tissue

value: CD

value: small RNA


title: R2_JMC151_CSR-1a_input

value: Whole Worm

value: L4 Larval Stage

value: csr-1(tor160[csr-1 exon1::gfp::3xflag IV:7957568]) IV


title: DIS-22-T1

description:
21Feb18_C06
mature_counts.csv
hairpin_counts.csv


title: s76006

value: Alternate


title: s76074


title: MCOA10 2

value: ICR

value: 10 weeks

tag: treatment

value: AOS 10mg/kg


title: RJ_M4

description: MEI4 ChIP-seq od the RJ2 mouse, one replicate

value: whole-testis

tag: cell line

value: L/Z

value: 8 days post-injection


title: DIS-18-T1

description:
21Feb18_C05
mature_counts.csv
hairpin_counts.csv

value: serum


title: YF_Tg_M4_r2

description: MEI4 ChIP-seq of the B6-Tg(YF) mouse, replicate 2

value: synchronization of spermatogenesis


title: s76005

value: aorta

value: female


title: DIS-14-T1

description:
21Feb18_C04
mature_counts.csv
hairpin_counts.csv

value: UC


title: R2_JMC101_CSR-1_IP

description: Immunoprecipitated RNA using GFP conjugated chromtek GFP Trap MA beads

tag: strain

value: csr-1(tor67[gfp::3xflag::csr-1]) IV


title: s76004

value: Ldlr-/-


title: R1_JMC151_CSR-1a_IP

value: Whole Worm

tag: developmental stage


title: YF_Tg_M4_r1

description: MEI4 ChIP-seq of the B6-Tg(YF) mouse, replicate 1


title: R2_JMC101_CSR-1_input

description: Total input RNA from lysate used for IPs

value: L4 Larval Stage

tag: temperature


title: DIS-10-T1

description:
21Feb18_C03
mature_counts.csv
hairpin_counts.csv

value: CD

value: small RNA


title: s76003

value: Alternate


title: P9_KO_M4_r2

description: MEI4 ChIP-seq of the Prdm9KO mouse, replicate 2

value: B6;129P2-Prdm9tm1Ymat/J (Prdm9KO)


title: s76076

value: Continuous HFD


title: R1_JMC101_CSR-1_input


title: DIS-06-T1

description:
21Feb18_C02
mature_counts.csv
hairpin_counts.csv


title: IgAN, Xenium

type: RNA

city: Oxford

first: Rui

last: Qi

state: Oxford

address: Old Road Campus

institute: University of Oxford

description: Xenium In Situ Spatial Gene Expression Profiling of Diseased Renal Tissue

hyb_protocol: The IgAN Xenium samples underwent cyclic rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer platform captured Z-stack of images every cycle of DNA-fluorescently tagged probes which were merged to create a spatially resoloved map of the transcripts across the renal tissue section. Decoding of transcripts was performed on the Xenium Analyzer platform using the assigned probe kit for select genes in the multi-tissue gene panel. Assignment of mRNAs to a given cell was done using the defined by the Z-stack of images nuclear expansion.

scan_protocol: See other protocols

data_processing:
Output files were generated by the Xenium Onboard Analysis pipeline to generate gene transcript by cell and transcript by tissue location data matrices.
barcodes.tsv.gz: list of spatial barcodes
features.tsv.gz: list of gene IDs
cells.csv.gz: list of cells information
matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
transcripts.csv.gz: list of transcript information
morphology.ome.tif: image of tissue
gene_panel.json: store and transmit information about gene testing panels

source_name: Renal Biopsy

label_protocol: Slides were imaged on a Xenium Analyzer 10X machine, with profiling regions selected to include the entire renal biopsy section. The tissue was profiled using the Xenium Human Multi-Tissue Probe Set (10x, 1000626).

extract_protocol: One 5 μm section from a IgAN diseased sample was processed for 10X Xenium In Situ Analyzer. Following the 10X Xenium workflow using stored human FFPE renal biopsy blocks, tissue was sectioned, and slides were prepared following the manufacturer-recommended Xenium In Situ for FFPE- Deparaffinization & Decrosslinking Demonstrated Protocol (CG000580). A 5µm FFPE renal biopsy section from an IgAN-diseased patient was placed within the imaging area on specialized Xenium slides. The slide then underwent subsequent staining and tissue processing according to manufacturer protocols outlined in Xenium In Situ Gene Expression User Guide RevE (CG000582). Slides were stained with 10X Human Multi-Tissue and Cancer Xenium Pre-Designed Gene Expression Panel (10x, 1000626) without a custom gene panel. Selected pre-designed padlock probes were incubated on the tissue overnight before rolling circle amplification and chemical autofluorescence quenching.

value: Renal Biopsy

value: Renal Disease Biopsy:IgAN


title: s76002


title: P9_KO_M4_r1

description: MEI4 ChIP-seq of the Prdm9KO mouse, replicate 1

value: whole-testis

value: L/Z

value: 8 days post-injection


title: DIS-02-T1

description:
21Feb18_C01
mature_counts.csv
hairpin_counts.csv

value: serum


title: S11_KO_M4_r1

description: MEI4 ChIP-seq of the Spo11KO mouse, replicate 1

value: Spo11tm1Mjn (Spo11KO)

value: synchronization of spermatogenesis


title: R1_JMC151_CSR-1a_input

value: csr-1(tor160[csr-1 exon1::gfp::3xflag IV:7957568]) IV


title: Yf_Tg_P9

description: PRDM9 ChIP-seq of the B6-Tg(YF) mouse, one replicate


title: s75935

value: aorta

value: female

value: Ldlr-/-


title: GBS_BEC_I_R3_total_RNA

city: Cologne

first: Till

middle: David

last: Sauerwein

address: Gleueler Str. 60

department: Data Science and Services

institute: ZB MED - Information Centre for Life Sciences

description: GBS infecting IPSC-BECs replicate 3

data_processing:
Adapter filtering: Illumina’s TruSeq “Read 1” adapter sequence using cutadapt version: 1.15
Trimming of reads with a Phred score below 20 using cutadapt version 1.15
Poly(A) clipping reads using READemption 0.4.3
Discarding of reads with a length below 20 using READemption version 0.4.3
Aligning of reads to both genomes using segemehl version 0.2.0
Gene quantification using READemption version 0.4.3
Differential gene expression analysis using DESeq2 version: 1.18.1, R version: 3.4.4
Genome_build: Human: GENCODE version: 26, NCBI assembly name: GRCh38.p10 / Streptococcus: accession number: HG939456.1, Genbank assembly accession number: GCA_000689235.1
Supplementary_files_format_and_content: csv files containing DESeq2 results

organism:
Streptococcus sp. 'group B'
Homo sapiens

source_name: Brain-like endothelial cells generated from induced pluripotent stem cells (iPSC-BECs) AND Group B Streptococcus (GBS)

growth_protocol: Human: Growth of hCMEC/D3 cell line: hCMEC/D3 cells were maintained on tissue culture flasks coated with 1% rat tail collagen in EndoGRO MV medium (Millipore-Sigma). Cells were split onto 24-well tissue culture plastic dishes for experiments and allowed to grow to confluency (4 days) before infection experiments were conducted. Streptococcus: Wild-type GBS strains were cultivated in Todd-Hewitt broth (THB) at 37C in static culture/

extract_protocol:
Total RNA was collected using the MirVana RNA (Thermo Scientific) isolation kit
Sequencing was performed on a NextSeq500 platform (Illumina) in single-end mode for 75 cycles

treatment_protocol: iPSC-BECs were differentiated and infected with GBS at an MOI of 10 for 5 hours

tag: disease state

value: infected


title: DIS-25-T2

description:
21Feb18_B07
mature_counts.csv
hairpin_counts.csv

tag: time point

value: CD

value: small RNA


title: P9_KO_P9_r2

description: Prdm9 ChIP-seq of the Prdm9KO mouse, replicate 2

value: B6;129P2-Prdm9tm1Ymat/J (Prdm9KO)


title: GBS_BEC_I_R2_total_RNA

description: GBS infecting IPSC-BECs replicate 2


title: R1_JMC101_CSR-1_IP

value: Whole Worm

value: L4 Larval Stage

value: csr-1(tor67[gfp::3xflag::csr-1]) IV


title: DIS-21-T2

description:
21Feb18_B06
mature_counts.csv
hairpin_counts.csv

tag: patient id

value: UC


title: s75934

value: Continuous HFD


title: antim6A_bound_2

city: New York

first: Longfei

last: Gao

state: NY

address: 650 West 168th Street

institute: Columbia University

description: P2 Cxcl12+ BMMSC antim6A elution

data_processing:
Raw reads were mapped to mouse genome (mm10) using RSubread (v2.10.4).
Due to low RNA input for library preparation, potential PCR duplicates were removed with Picard (http://broadinstitute.github.io/picard) as previously described (Lee et al., 2019).
Raw counts were generated with featureCounts. RPKM calculation and differential expression analysis were performed with edgeR (3.38.1).
Assembly: mm10

source_name: primary Cxcl12-Dsred+ BMMSCs

extract_protocol:
polyA RNA was isolated from sorted Cxcl12-DsRed+ cells using Dynabeads Oligo-(dT)25 magnetic beads (ThermoFisher Scientific, Cat# 61011) according to manufacturer’s instructions. 6% of eluted RNA was saved as input fraction. 1.25 μg of antim6A antibody (Synaptic Systems, Cat#202003) or IgG was pre-bound to Protein A/G magnetic beads (Millipore, Cat#16-663X) in IP buffer (20-mM Tris pH 7.5, 140-mM NaCl, 1% NP-40, 2-mM EDTA) for 1 h. Sample RNA was incubated with antibody-bound Protein A/G beads for 2 hours at 4 ℃. Samples were washed twice in low-salt-wash buffer (10 mM Tris, pH 7.5, 5 mM EDTA), twice with high-salt-wash buffer (20 mM Tris, pH 7.5, 1 M NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM EDTA), and then twice with RIPA buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM EDTA). All wash solutions for each sample were collected as the “unbound” fraction. RNA was eluted from the beads by incubating with 50 μl 20 mM N6-methyladenosine 5-monophosphate sodium salt (Sigma-Aldrich, Cat# M2780) for 1 hour at 4 ℃.
Following ethanol precipitation, input, unbound, and bound fractions was reverse transcribed, amplified, tagmented and indexed following Smart-seq2 method (Picelli et al., 2014)

value: bone marrow

value: mesenchymal stromal cells


title: P9_KO_P9_r1

description: Prdm9 ChIP-seq of the Prdm9KO mouse, replicate 1

value: whole-testis

value: L/Z

value: 8 days post-injection


title: GBS_BEC_I_R1_total_RNA

description: GBS infecting IPSC-BECs replicate 1


title: DIS-17-T2

description:
21Feb18_B05
mature_counts.csv
hairpin_counts.csv

value: serum

tag: diagnosis


title: IgG_bound_2

description: P2 Cxcl12+ BMMSC IgG elution


title: B_WT_P9_r2

description: PRDM9 ChIP-seq of the B6 mouse, replicate 2

value: wild-type

value: synchronization of spermatogenesis


title: DIS-13-T2

description:
21Feb18_B04
mature_counts.csv
hairpin_counts.csv

tag: fraction


title: B_WT_P9_r1

description: PRDM9 ChIP-seq of the B6 mouse, replicate 1

tag: time


title: antim6A_bound_1

description: P2 Cxcl12+ BMMSC antim6A elution


title: Input_2

description: P2 Cxcl12+ BMMSC Input


title: DIS-09-T2

description:
21Feb18_B03
mature_counts.csv
hairpin_counts.csv


title: 16_F4_#4_high

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

data_processing:
The raw reads from BRB-seq sequencing were demultiplexed with BRB-seq tools for each sample.
Reads were first adapter and polyA trimmed with cutadapt (v1.18) and those shorter than 30 bases were discarded
Reads  were aligned to the mouse genome GRCm38 and reads per gene were quantified using STARsolo (v2.7.9a)
The read counts were normalized and statistically analyzed with DESeq2 (v1.42.0).
Assembly: Mouse genome GRCm38
Supplementary files format and content: text file format for read count table

extract_protocol:
BRB-seq
Size Selection Method:i7 TM3 ver3
Adaptor:Nextera XT:706:TAGGCATG 506:ACTGCATA

value: embryonic stem cells

value: FOXA2 expression high

value: RA (18 hours)


title: 15_F4_#4_medium

value: FOXA2 expression medium


title: IgG_bound_1

description: P2 Cxcl12+ BMMSC IgG elution


title: DIS-05-T2

description:
21Feb18_B02
mature_counts.csv
hairpin_counts.csv

value: CD

value: small RNA


title: DIS-01-T2

description:
21Feb18_B01
mature_counts.csv
hairpin_counts.csv


title: Input_1

description: P2 Cxcl12+ BMMSC Input


title: DIS-25-T1

description:
21Feb18_A07
mature_counts.csv
hairpin_counts.csv


title: high fat diet + Aroclor1260 + PCB126, replicate 5

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
low quality sequence data and adapter sequences were trimmed using Trimmomatic v0.33
trimmed sequences were aligned to the genome using Mirdeep2 v0.0.7
mature miRNAs were quantified using Mirdeep2 v0.0.7
Genome_build: mm10

source_name: liver

growth_protocol: Male C57Bl/6J mice were fed a high fat diet (HFD, 42% kCal from fat) for 12 weeks and exposed to a single oral gavage of vehicle control (corn oil), Aroclor1260 (20 mg/kg), PCB126 (20 µg/kg), or the combination of the doses of Aroclor1260 + PCB126.

extract_protocol:
miRNA was isolated from five mouse livers/experimental exposure using Qiagen miRNA kits.
Libraries were prepared from 1 µg of mouse liver RNA using the QIAseq miRNA Library Kit (QIAGEN Cat. No. 331502), following manufacturer’s instructions.

value: high fat diet + Aroclor1260 + PCB126

value: male


title: 14_F4_#4_low

value: FOXA2 expression low


title: 13_F4_#4_negative

value: FOXA2 expression negative


title: DIS-21-T1

description:
21Feb18_A06
mature_counts.csv
hairpin_counts.csv

value: UC


title: 12_F4_#3_high


title: DIS-17-T1

description:
21Feb18_A05
mature_counts.csv
hairpin_counts.csv


title: 11_F4_#3_medium


title: high fat diet + Aroclor1260 + PCB126, replicate 3


title: DIS-13-T1

description:
21Feb18_A04
mature_counts.csv
hairpin_counts.csv


title: 06_siHSD17B14 3

city: Houston

first: Shaolin

last: Ma

state: Tx

address: 1881 East Road

institute: MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (SST+RMA) normalization procedures.

label: biotin

source_name: OVCAR8 cells

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: OVCAR8 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 0.1% gentamicin sulfate

extract_protocol: Total RNA was isolated using a Direct-zol kit (Zymo Research, Cat. # R2062)

treatment_protocol: OVCAR8 cells were transfected with siControl and siHD17B14 for 48 hours using lipofectamine RNAiMax.


title: 03_siControl 3

value: siControl


title: high fat diet + Aroclor1260 + PCB126, replicate 2


title: 10_F4_#3_low


title: high fat diet + Aroclor1260 + PCB126, replicate 1


title: 9_F4_#3_negative


title: 04_siHSD17B14 1


title: DIS-05-T1

description:
21Feb18_A02
mature_counts.csv
hairpin_counts.csv


title: high fat diet + PCB126, replicate 5

value: high fat diet + PCB126


title: 01_siControl 1


title: DIS-09-T1

description:
21Feb18_A03
mature_counts.csv
hairpin_counts.csv


title: 05_siHSD17B14 2


title: 02_siControl 2


title: 8_F4_#2_high


title: high fat diet + PCB126, replicate 4


title: 7_F4_#2_medium


title: RPE Normal2 [re-analysis]

city: New Haven

first: Hui

middle: Cong

last: Cai

state: CT

address: 300 George St, Suite 8100

institute: Yale University

description: Normal 5-1 Avg (log2)

hyb_protocol: All reactions and hybridizations were carried out according to the manufacturer's protocol (Affymetrix; Thermo Fisher Scientific). Affymetrix GeneChip Human Clariom S arrays (Thermo Fisher Scientific) were washed using the GeneChip® Fludics Station 450 (Thermo Fisher Scientific)

scan_protocol: Affymetrix GeneChip Human Clariom S arrays were scanned with the GeneChip Scanner 3000 (Thermo Fisher Scientific).

data_processing:
Raw data were processed to perform gene-level normalization and quality control using Affymetrix Expression Console Software (Thermo Fisher Scientific).
RMA expression value derived from Expression Console software Transcriptome Analysis Console (TAC)  4.0.1 (Applied Biosystems)
probe group file: Clariom_S_Human.r1.pgf
meta-probeset file: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv
Normal vs AMD,  Normal: 3 samples, AMD: 4 samples; Filter criteria:  Fold Change: > 2 or < -2; Total number of genes: 15606

source_name: non-AMD patient donor derived

label_protocol: GeneChip® WT Plus Reagent Kit were used for generating biotinylated ss-cDNA for hybridization.

growth_protocol: Fibroblasts from 4 donors with age-related macular degeneration and 3 controls with no history of AMD were grown and treated with modified messenger ribonucleic acid (mRNA) encoding reprogramming factors, Oct3/4, Sox-2, Klf4, and c-Myc, nanog and Lin28. Newly generated iPSC colonies were picked and expanded using Nutristem medium (Stemgent, Reprocell, MD, USA) or MTeSR™1 media. iPSC colonies were detached and grown as embryoid bodies (EB) in EB formation medium and STEMdiff™ Neural Induction Medium and RPE differentiation medium containing DMEM/F12, 2% B-27 supplement, minimum essential media, non-essential amino acids and antibiotics. At ~45 days, pigmented iPSC-derived RPE cells appeared in the cultures. Patches of pigmented iPSC-derived RPE cells were micro-dissected, dissociated with trypsin-ethylenediaminetetraacetic acid (EDTA, 0.05%), and plated onto laminin-coated plates until confluent as previously described.

extract_protocol: Total RNA was isolated from differentiated iPSC-derived RPE cells using Aurum™ Total RNA Mini Kit (Bio-Rad Laboratories, CA, USA) according to the manufacturer’s instructions, with Dnase I treatment. RNA quantity and quality were assessed by micro-volume spectrophotometry on the Nanodrop 2000 (Thermo Fisher Scientific) and by on-chip capillary electrophoresis on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: no special treatment

tag: donor status

value: non-AMD Patient

value: iPS derived RPE cells


title: RPE Normal1 [re-analysis]

description: Normal Patient 3 iPS RPE

tag: cell type


title: RNAseq_SR-3

data_processing:
Sequenced reads were mapped to hg19 whole genome using STAR
Assembly: hg19
Supplementary files format and content: txt files with gene counts

source_name: U937 cells

growth_protocol: GFP+ or GFP+mCherry+ U937 cells were sorted after infection. BM cells harvested from the patient.

value: U937 cells

value: pro-monocytic

tag: genotype


title: high fat diet + PCB126, replicate 3

tag: Sex


title: high fat diet + Aroclor1260 + PCB126, replicate 4


title: 6_F4_#2_low

value: embryonic stem cells


title: high fat diet + PCB126, replicate 2


title: RNAseq_SR-2


title: RPE Normal3 [re-analysis]

description: Normal 6-1 Avg (log2)


title: 5_F4_#2_negative


title: RPE AMD3 [re-analysis]

description: RPE AMD 3-1 Avg (log2)

source_name: AMD patient donor derived

value: advanced age-related macular degeneration (AMD)-patient


title: RPE AMD2 [re-analysis]

description: RPE AMD 2-1 Avg (log2)


title: RNAseq_SR-1


title: high fat diet + PCB126, replicate 1


title: RNAseq_sgUTX-SR-3


title: high fat diet + Aroclor1260, replicate 5

value: high fat diet + Aroclor1260


title: 4_F4_#1_high

value: FOXA2 expression high

value: RA (18 hours)


title: 3_F4_#1_medium

value: FOXA2 expression medium


title: high fat diet + Aroclor1260, replicate 4


title: RNAseq_sgUTX-SR-2


title: 2_F4_#1_low


title: iPSC Normal3

description: iPSC Normal 3 Avg (log2)

value: fibroblast derived iPSC


title: DIS-01-T1

description:
21Feb18_A01
mature_counts.csv
hairpin_counts.csv

value: serum

value: small RNA


title: RPE AMD4 [re-analysis]

description: RPE AMD 4-1 Avg (log2)


title: 1_F4_#1_negative

value: FOXA2 expression negative


title: iPSC Normal2

description: iPSC Normal 2 Avg (log2)


title: RNAseq_sgUTX-SR-1


title: RNAseq_sgUTX-pMIG-3

value: sgUTX


title: iPSC Normal1

description: iPSC Normal 1 Avg (log2)


title: high fat diet + Aroclor1260, replicate 2

value: male


title: RNAseq_Mouse_SR_Veh_2

source_name: murine sgUtx;SR APL cells

value: murine sgUtx;SR APL cells

value: APL cells

value: vehicle

value: 5 days


title: high fat diet + Aroclor1260, replicate 1


title: RNAseq_sgUTX-pMIG-2

value: U937 cells

value: pro-monocytic


title: iPSC AMD4

description: iPSC AMD 4 Avg (log2)

value: advanced age-related macular degeneration (AMD)-patient


title: RNAseq_Mouse_SR_Veh_1


title: iPSC AMD3

description: iPSC AMD 3 Avg (log2)


title: high fat diet control replicate 5

value: high fat diet, control


title: RNAseq_Mouse_SR_ATRA_2

value: 200nM ATRA


title: RNAseq_sgUTX-pMIG-1


title: high fat diet control replicate 4


title: RNAseq_Mouse_SR_ATRA_1


title: RPE AMD1 [re-analysis]

description: RPE AMD 1-1 Avg (log2)

value: iPS derived RPE cells


title: RNAseq_pMIG-3

value: WT


title: iPSC AMD1

description: iPSC AMD 1 Avg (log2)

value: fibroblast derived iPSC


title: RNAseq_pMIG-1


title: high fat diet control replicate 3


title: high fat diet + Aroclor1260, replicate 3

value: high fat diet + Aroclor1260


title: high fat diet control replicate 2


title: RNAseq_pMIG-2


title: LDN_3_Foxa2.pos_161044

description: RNA-expression for differential gene expression analysis in RA vs RA+BMP perturbations

data_processing:
The paired-end raw reads from TM3’ sequencing were first split
and the 12bp of UMI were extracted from Read2 with umi-tools (v1.0.0).
Read1 were then trimmed with cutadapt (v1.18) and mapped to the mouse genome (mm10) using star (v2.5.2a).
deduplicated read counts at gene levels were quantified by htseq (v0.11.2).
The read counts were normalized and statistically analyzed with DESeq2 (v1.26.0).
Assembly: mouse genome (mm10)
Supplementary files format and content: read count table from htseq

source_name: embryonic stem cells (R1)

extract_protocol:
SMART-Seq v2
Size Selection Method:i7 TM3 ver3
Adaptor:Unique Nextera 1: 7098:CACTCAATTC, 2: 5098:TTAAGTTGTG

value: embryonic stem cells (R1)

value: RA+LDN

value: 18 hours RA, 6 hours no treatment, 8 hours LDN


title: CUTTAG_SR-2

data_processing:
Sequenced reads were mapped to hg19 using bowtie2
peaks were called using SEACR
Assembly: hg19
Supplementary files format and content: bigwig, bed files
Library strategy: CUT&TAG

growth_protocol: U937 cells were cultured in medium and infected with virus.

extract_protocol:
GFP+ or GFP+mCherry+ U937 cells were sorted after infection
CUT&TAG assay was performed using NovoNGS® CUT&TAG 2.0 High-Sensitivity Kit (Novoprotein scientific Inc., Cat# N259-YH01-01A).

tag: chip antibody

value: Flag (proteintech, Cat# 20543-1-AP)


title: LDN_3_Foxa2.neg_161043


title: FB Normal3

description: FB Normal 3 Avg (log2)

value: non-AMD Patient

value: fibroblast


title: FB Normal2

description: FB Normal 2 Avg (log2)


title: high fat diet control replicate 1

value: male


title: CUTTAG_SR-1


title: LDN_2_Foxa2.pos_161042


title: CUTTAG_IgG-2

value: Goat Anti-Rabbit IgG H&L (novoprotein, Cat# N269-01A)


title: LDN_2_Foxa2.neg_161041


title: mRNA gingival tissues Cybb-/- (Naive) 3

data_processing:
sequencing runs were performed on the Illumina NextSeq 500 using the NextSeq 500/550 75 cycle High Output Kit v2.5 (Cat# 20024906).
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Gingival tissues

growth_protocol: Mice age less than 12 weeks were used in the 8 day long experiments.

extract_protocol:
RNA was extracted using Qiagen RNAeasy kits
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Cat# 20020594) along with TruSeq RNA CD Index Plate (Cat# 20019792).

treatment_protocol: For ligature group mice: A silk thread like ligature was tied around maxillary right molar. Mice were sacked after 8 days.

value: Naive

value: Cybb-/-


title: FB Normal1

description: FB Normal 1 Avg (log2)


title: iPSC AMD2

description: iPSC AMD 2 Avg (log2)

value: advanced age-related macular degeneration (AMD)-patient


title: mRNA gingival tissues Cybb-/- (Naive) 2


title: LDN_1_Foxa2.neg_161039


title: CUTTAG_IgG-1

value: pro-monocytic


title: mRNA gingival tissues Cybb-/- (Naive) 1


title: BMP_3_Foxa2.pos_161038

value: 18 hours RA, 6 hours no treatment, 8 hours BMP4


title: FB AMD2

description: FB AMD 2 Avg (log2)


title: FB AMD3

description: FB AMD 3 Avg (log2)


title: BatchA_SW1783_water extract of Poria Cocos (Low dose)_rep3 [2-3-3]

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human astrocytoma cell line, SW1783 (HTB-13) was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz’s L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, without CO2 incubator. The cells were subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Dulbecco's Modified Eagle Medium (DMEM), phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Leibovitz's L-15 medium was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO), wortmannin, LY294002, Thioridazine were purchased from Sigma-Aldrich (St. Louis, MO, USA) and QIAzol lysis reagents was purchased from Qiagen (Germantown, MD, USA). The Ez-Cytox cell viability assay kit was purchased from Dogen Bio (Seoul, Korea). The dried Poria cocos Wolf (Polyporaceae) were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea), and their morphology was carefully validated by Dr. Goya Choi, Herbal Medicine Resources Research Center Korea Institute of Oriental Medicine (KIOM), Republic of Korea. A voucher specimen (2-22-0221) was deposited in the Korean Herbarium of Standard Herbal Resources of KIOM (Naju, Republic of Korea). The crushed material was extracted at 100 ± 3℃ for 3 hours by water refluxed system (MS-DM609, Misung Scientific, Yangu, Republic of Korea) and filtered through 5 um cartridge filter (KOC Biotech, Daejeon, Republic of Korea). The filtrates were concentrated under 40℃ using a rotary evaporator (Ev-1020t, SciLab, Seoul, Republic of Korea), and then freeze dried (LP20, IlShin Biobase, Dongduchen, Republic of Korea). The yield of PC was 24.2 % and final extracts were homogenized and stored at air-tight container in 4℃ cold room. For the in vitro investigation, homogenous PC was vigorously vortexed for 30 min at room temperature in phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 um membrane. The stock solution of PC (10mg/mL) was aliquoted in 1.5mL tube and stored at -80°C until use.

value: Human astrocytoma cell line

value: PCW 20 μg/mL


title: FB AMD4

description: FB AMD 4 Avg (log2)


title: mRNA gingival tissues  WT mice (Naive) 3

value: C57BL/6 (wildtype)


title: BatchA_SW1783_water extract of Poria Cocos (Low dose)_rep2 [2-2-3]


title: Dark_Adapted_T24_C

city: Cambridge

first: Allison

last: Coe

state: MA

address: 15 Vassar St

department: Civil and Environmental Engineering

institute: Massachusetts Institute of Technology

data_processing:
Reads were trimmed and adapters were removed with BBDuk (from the BBTools package, V38.16) (parameters: ktrim=r, k=23, mink=11, hdist=1, qtrim=rl, trimq=6)
The trimmed reads were aligned to Prochlorococcus NATL2A (NC_007335.2) and Alteromonas macleodii MIT1002 (NZ_JXRW01000001.1) genomes using bowtie2 (parameters: default)
The number of reads that aligned to each annotated ORF in the “sense” orientation was determined using HTSeq (V0.11.2) (parameters: --nonunique all)
Assembly: NZ_JXRW01000001.1, NC_007335.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism:
Alteromonas macleodii
Prochlorococcus marinus str. NATL2A

growth_protocol: Prochlorococcus and Alteromonas were maintained on Pro99 amended natural seawater in a 13:11 light:dark incubator at 24C.

extract_protocol:
Total RNA was extracted using the mirVana microRNA (miRNA) extraction kit (Ambion, USA).
Ribosomal RNA was depleted using RiboZero kit (Illumina) and libraries prepared using the KAPA RNA HyperPrep kit (Illumina)


title: Dark_Adapted_T24_B


title: mRNA gingival tissues  WT mice (Naive) 2


title: BMP_3_Foxa2.neg_161037


title: BatchA_SW1783_water extract of Poria Cocos (Low dose)_rep1 [2-1-3]


title: Dark_Adapted_T24_A


title: BMP_2_Foxa2.pos_161036


title: FB AMD1

description: FB AMD 1 Avg (log2)


title: mRNA gingival tissues  WT mice (Naive) 1


title: BMP_2_Foxa2.neg_161035


title: BatchA_SW1783_water extract of Poria Cocos (Medium dose)_rep3 [2-3-2]

value: PCW 100 μg/mL


title: Dark_Adapted_T20_C


title: mRNA gingival tissues Cybb-/- (ligature) 3

value: Ligature


title: BMP_1_Foxa2.pos_161034

value: embryonic stem cells (R1)


title: Dark_Adapted_T20_B


title: BatchA_SW1783_water extract of Poria Cocos (Medium dose)_rep2 [2-2-2]


title: BMP_1_Foxa2.neg_161033


title: mRNA gingival tissues Cybb-/- (ligature) 2


title: BatchA_SW1783_water extract of Poria Cocos (Medium dose)_rep1 [2-1-2]


title: Dark_Adapted_T20_A


title: RAcontrol_3_Foxa2.pos_161032

value: RA

value: 18 hours


title: BatchA_SW1783_water extract of Poria Cocos (High dose)_rep1 [2-2-1]

value: PCW 500 μg/mL


title: mRNA gingival tissues WT mice (ligature) 3


title: RAcontrol_3_Foxa2.neg_161031


title: mRNA gingival tissues Cybb-/- (ligature) 1


title: BatchA_SW1783_water extract of Poria Cocos (High dose)_rep1 [2-1-1]


title: RAcontrol_2_Foxa2.neg_161029


title: mRNA gingival tissues WT mice (ligature) 1


title: mRNA gingival tissues WT mice (ligature) 2


title: Dark_Adapted_T16_A


title: RAcontrol_1_Foxa2.pos_161028


title: 2_KDH1 IP

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

data_processing:
NGMerge was used to automatically detect and remove sequencing adapters using options -a -n 18 -v
FastQ files were aligned to the dm3 genome using Bowtie2 v2.2.2 with options -N 1 -k 1.
Duplicated reads for generation of TDF tracks were identified and removed with sambamba 0.8.0. TDF tracks were generated with IGVTools2 and options count -z 5 -w 25 -e 250.
Peak calling between IP and Input samples was performed independently for individual and pooled replicates per group using MACS 1.4.2 with default options (duplicate removal) and genome=dm. Candidate called peaks from pooled replicates were defined as final peaks if they presented overlap with peaks identified in both their respective individual replicates.
Final peaks in all conditions were used to perform a Differential Binding analysis using the DiffBind package version 2.10.0, using functions: dba.count with options score=DBA_SCORE_RPKM_FOLD,bLog=TRUE,bRemoveDuplicates=TRUE,bScaleControl=TRUE; dba.contrast with options categories=DBA_CONDITION,block=DBA_REPLICATE,minMembers=2 and dba.analyze with options method=DBA_DESEQ2,bFullLibrarySize=TRUE,bSubControl=FALSE. Peaks were selected as significant based on a raw pvalue of 0.05 (column DiffBind.rej).
Peaks were annotated to dm3 genomic features using homer2 with the anntatePeaks function and default options.
Assembly: dm3
Supplementary files format and content: BED files with final peak calling results (pooled called peaks also present in both individual replicate peak calls)
Supplementary files format and content: Excel XLSX with DiffBind results

organism: Drosophila melanogaster

source_name: S2 cells

extract_protocol:
Cells were fixed with 1.8% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Twin Sonication System (Diagenode).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (Illumina)

value: S2 cells

value: αRNAPII

value: KD H1


title: Dark_Adapted_T13_B


title: BatchA_SW1783_Thioridazine_rep2 [1-2-6]

value: Thioridazine 10 uM


title: Dark_Adapted_T13_C


title: RAcontrol_2_Foxa2.pos_161030


title: BatchA_SW1783_Thioridazine_rep1 [1-1-6]


title: IP KDH1 1


title: Dark_Adapted_T13_A


title: IP LZ1

value: LacZ


title: BatchA_SW1783_LY294002_rep3 [1-3-5]


title: Dark_Adapted_T16_C


title: IL-23R stimulated

first: Jordan

last: Zhou

address: 413 E 69th St

institute: Weill Cornell Medical College

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small Intestine

extract_protocol:
Small intestine from IL-23R-eGFP mice were aseptically removed from the mice, cleaned by removing the fat tissues and Peyer’s patches were carefully removed. Afterwards, intestines were opened longitudinally, extensively cleaned with cold Dulbecco's PBS (Corning) and cut approximately into 0.5-cm sections. To dissociate epithelial cells, cut tissues were incubated in Hanks' balanced salt solution) containing 5 mM EDTA (Thermo Fisher Scientific), 1 mM dithiothreitol (Sigma-Aldrich) and 2% fetal bovine serum twice at 37 °C for 20 min. After incubation, the tissues were vortexed, transferred to digestion buffer containing collagenase III (1 mg mL-1; Worthington), dispase (0.4 U mL-1; Thermo Fisher Scientific), DNase I (20 μg mL-1 ;Sigma-Aldrich) and 10% FBS in RPMI 1640 (Corning), and incubated in a shaker at 200 rpm for 1 hour at 37°C. Leukocytes were enriched by 40/80% density gradient Percoll centrifugation (GE Healthcare). Live eGFP+ cells was sorted from enriched leukocytes and stimulated with rmIL-23 for 2 hours.
Library construction was performed by the epigenomics core at Weill Cornell Medical College.

tag: tissue

value: Small Intestine

value: Immune cells


title: IL-23R unstimulated

description: 10x Genomics

tag: treatment

value: Unstimulated


title: RAcontrol_1_Foxa2.neg_161027


title: BatchA_SW1783_water extract of Poria Cocos (High dose)_rep1 [2-3-1]

tag: cell line

value: Human astrocytoma cell line


title: BatchA_SW1783_LY294002_rep2 [1-2-5]


title: 2_KDH1 10% INPUT*


title: Dark_Adapted_T8_B

tag: strain


title: BatchA_SW1783_Wortmannin_rep3 [1-3-4]

value: wortmannin 10 uM


title: 2_LZ 10% INPUT*


title: Dark_Adapted_T4_C


title: 10% INPUT KDH1 1*


title: scRNAseq on cells from mutant mice - LL002

description: 10x Genomics

data_processing:
Raw reads were mapped to mm10 genome (mm10-2020A provided by 10x Genomics) and counted using CellRanger (version 5.0.1) with default parameter.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
CD45/Ter119-DAPI-Calcein-AM+ cells were sorted from three control and three Δ/Δ mice using a yield and then purity sorting mode on BD SORP FACSAria.
10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 were used to prepare the library, targeting ~5000 cells, according to manufacturer's instructions.

value: non-hematopoietic cells

value: bone marrow

tag: age


title: scRNAseq on cells from mutant mice - LL011

description: 10x Genomics

data_processing:
Raw reads were mapped to mm10 genome (mm10-2020A provided by 10x Genomics) and counted using CellRanger (version 6.1.2) with default parameter.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: mutant


title: scRNAseq on cells from control mice - LL010

description: 10x Genomics

value: control


title: BatchA_SW1783_Wortmannin_rep1 [1-1-4]


title: BatchA_SW1783_Thioridazine_rep3 [1-3-6]


title: 10% INPUT LZ 1*


title: Dark_Adapted_T8_C


title: Dark_Adapted_T4_A


title: spleen HCF-3

first: Yong

last: Zhao

address: 700 Changcheng Road

institute: Qingdao Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: spleen

extract_protocol:
Spleen were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: spleen

value: 10 weeks

value: High fat diet +control-FMT


title: RNH+_hrp48_2

description:
H12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx

data_processing:
NGMerge was used to automatically detect and remove sequencing adapters using options -a -n 18 -v
FastQ files were aligned to the dm3 genome using Bowtie2 v2.2.2 with options -N 1 -k 1.
Duplicated reads for generation of TDF tracks were identified and removed with sambamba 0.8.0. TDF tracks were generated with IGVTools2 and options count -z 5 -w 25 -e 250.
Peak calling between IP and Input samples was performed independently for individual and pooled replicates per group using MACS 1.4.2 with default options (duplicate removal) and genome=dm. Candidate called peaks from pooled replicates were defined as final peaks if they presented overlap with peaks identified in both their respective individual replicates.
Definition of final Rloops was performed using DESeq2 with lfcShrinkage fold change estimation (type=’normal’) to assess level of RNH+ depletion. Final Rloops were defined as those RNH- candidate Rloops with a DESeq2 lfcShrinkage FC RNH+/RNH- (RNH depletion) of -1.25 or less
Assembly: dm3
Supplementary files format and content: xlsx with DESeq2estimated intensities for candidate Rloops and lfcShrink RNH+ vs RNH- fold estimation
Library strategy: DRIP-Seq

extract_protocol:
Cells were lyzed and genomic DNA purified, using phenol-chloroform extractions followed by DNA precipitation. DNA was sonicated using a Bioruptor Twin Sonication System (Diagenode).
DRIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (Illumina)

value: S2 cells

value: primary culture of late stage (20-24 hours old)


title: 2_LZ IP

value: αRNAPII


title: RNH+_hrp36_2

description:
G12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: Dark_Adapted_T0_C


title: BatchA_SW1783_Vehicle(DMSO)_rep2 [A1-2-1]

value: 2% DMSO


title: spleen HCF-2


title: BatchA_SW1783_LY294002_rep1 [1-1-5]


title: Dark_Adapted_T0_B


title: RNH+_LacZ_2

description:
F12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: BatchA_SW1783_Wortmannin_rep2 [1-2-4]


title: spleen HCF-1


title: spleen HAF-3

value: High fat diet +AOS10mg/kg-FMT


title: RNH-_hrp48_2

description:
E12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: Parental_T24_C

source_name: Parental

value: Parental


title: scRNAseq on cells from control mice - LL001

description: 10x Genomics


title: Dark_Adapted_T0_A


title: BatchA_water extract of Poria Cocos (Low dose)_rep2 [2-2-3]

description:
sample 2-2-3
RCM_poria_cocos_HT29.txt

growth_protocol: Human colorectal adenocarcinoma cell line, HT29 (HTB-38) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HT29 cells were maintained in DMEM medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.

value: PCW 20 μg/mL


title: spleen HAF-2


title: spleen HA10-3

value: High fat diet +AOS10mg/kg


title: BatchA_water extract of Poria Cocos (Medium dose)_rep3 [2-3-2]

description:
sample 2-3-2
RCM_poria_cocos_HT29.txt

value: PCW 100 μg/mL


title: Parental_T24_A


title: Parental_T24_B


title: Parental_T20_C


title: INPUT_10%_hrp36_2

description:
A12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: INPUT_10%_hrp48_2

description:
B12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: Dark_Adapted_T8_A


title: spleen HA10-2


title: BatchA_water extract of Poria Cocos (Medium dose)_rep2 [2-2-2]

description:
sample 2-2-2
RCM_poria_cocos_HT29.txt


title: Parental_T20_B


title: spleen HA10-1


title: RNH-_hrp36_2

description:
D12
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: BatchA_water extract of Poria Cocos (Medium dose)_rep1 [2-1-2]

description:
sample 2-1-2
RCM_poria_cocos_HT29.txt


title: BatchA_water extract of Poria Cocos (Low dose)_rep3 [2-3-3]

description:
sample 2-3-3
RCM_poria_cocos_HT29.txt


title: INPUT_10%_LacZ_2

description:
H11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: RNH+_hrp48_1

description:
G11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: BatchA_water extract of Poria Cocos (High dose)_rep1 [2-3-1]

description:
sample 2-3-1
RCM_poria_cocos_HT29.txt

value: PCW 500 μg/mL


title: spleen HFD-3

value: High fat diet


title: Parental_T16_C


title: BatchA_water extract of Poria Cocos (Low dose)_rep1 [2-1-3]

description:
sample 2-1-3
RCM_poria_cocos_HT29.txt


title: RNH+_hrp36_1

description:
F11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: spleen HFD-2


title: BatchA_water extract of Poria Cocos (High dose)_rep1 [2-2-1]

description:
sample 2-2-1
RCM_poria_cocos_HT29.txt


title: RNH+_LacZ_1

description:
E11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: BatchA_water extract of Poria Cocos (High dose)_rep1 [2-1-1]

description:
sample 2-1-1
RCM_poria_cocos_HT29.txt


title: spleen HFD-1


title: Parental_T16_B


title: Parental_T16_A


title: RNH-_hrp48_1

description:
D11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: spleen con-3


title: BatchA_LY294002_rep3 [1-3-3]

description:
sample 1-3-3
RCM_poria_cocos_HT29.txt


title: Parental_T13_C


title: RNH-_hrp36_1

description:
C11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: BatchA_LY294002_rep2 [1-2-3]

description:
sample 1-2-3
RCM_poria_cocos_HT29.txt


title: spleen con-2


title: RNH-_LacZ_1

description:
B11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: Parental_T13_A


title: BatchA_LY294002_rep1 [1-1-3]

description:
sample 1-1-3
RCM_poria_cocos_HT29.txt


title: spleen A10-3

value: AOS 10mg/kg


title: Parental_T8_C


title: INPUT_10%_hrp48_1

description:
A11
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: BatchA_Wortmannin_rep3 [1-3-2]

description:
sample 1-3-2
RCM_poria_cocos_HT29.txt

value: wortmannin 10 uM


title: spleen con-1

value: ICR

value: control


title: INPUT_10%_hrp36_1

description:
H10
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx


title: spleen A10-2

value: spleen

value: 10 weeks


title: BatchA_Wortmannin_rep2 [1-2-2]

description:
sample 1-2-2
RCM_poria_cocos_HT29.txt


title: Parental_T8_B


title: spleen A10-1


title: INPUT_10%_LacZ_1

description:
G10
DESeq2_LacZ_lfcShrink.xlsx
DESeq2_hrp36_lfcShrink.xlsx
DESeq2_hrp48_lfcShrink.xlsx

value: S2 cells


title: Parental_T8_A


title: S2 H1 dep (2)

description:
gv204_peaks.bed
gv205_peaks.bed

data_processing:
NGMergewas used to automatically detect and remove sequencing adapters using options -a -n 10 -v.
Adapter cleaned FastQ files were downsampled to the library size of the smallest replicate/pair file (˜21.2 million reads) using setqtk (https://github.com/lh3/seqtk).
For analysis of THSS fragments, reads were aligned to dm3 with Bowtie2 using a maximum insert size of 100bp (options --very-sensitive -k 10 -X 100)
Genrich version 0.5 was used to detect putative ATAC peaks with options -j -y -r -e chrM.
Assembly: dm3
Supplementary files format and content: narrowPeak

extract_protocol:
Nuclei were obtained and treated with Tn5 fo 30 minutes, then DNA was purified using MinElute PCR Purification Kit (QIAGEN)
ATAC-seq libraries were prepared by PCR amplification and size selection using Ampure beads (Agencourt RNAClean XP Beads, S01307)

value: KD H1


title: testis HCF-3

source_name: testis

extract_protocol:
Testis were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testis

value: High fat diet +control-FMT


title: BatchA_Vehicle(DMSO)_rep3 [A1-3-1]

description:
sample A1-3-1
RCM_poria_cocos_HT29.txt

value: 2% DMSO


title: Parental_T4_C

value: Parental


title: S2 H1 dep (1)

description:
gv204_peaks.bed
gv205_peaks.bed


title: testis HCF-2


title: BatchA_Vehicle(DMSO)_rep2 [A1-2-1]

description:
sample A1-2-1
RCM_poria_cocos_HT29.txt


title: Parental_T4_B


title: BatchA_Vehicle(DMSO)_rep1 [A1-1-1]

description:
sample A1-1-1
RCM_poria_cocos_HT29.txt


title: S2 Control (2)

description:
gv204_peaks.bed
gv205_peaks.bed

value: LacZ


title: testis HCF-1


title: Parental_T4_A


title: testis HAF-3

value: High fat diet +AOS10mg/kg-FMT


title: S2 Control (1)

description:
gv204_peaks.bed
gv205_peaks.bed


title: KDH1_a48_2

description:
ChIP_10.05_KDH1_a36_peaks_filtered.bed
ChIP_10.05_KDH1_a48_peaks_filtered.bed
ChIP_10.05_LZ_a36_peaks_filtered.bed
ChIP_10.05_LZ_a48_peaks_filtered.bed

data_processing:
NGMerge was used to automatically detect and remove sequencing adapters using options -a -n 18 -v
FastQ files were aligned to the dm3 genome using Bowtie2 v2.2.2 with options -N 1 -k 1.
Duplicated reads for generation of TDF tracks were identified and removed with sambamba 0.8.0. TDF tracks were generated with IGVTools2 and options count -z 5 -w 25 -e 250.
Peak calling between IP and Input samples was performed independently for individual and pooled replicates per group using MACS 1.4.2 with default options (duplicate removal) and genome=dm. Candidate called peaks from pooled replicates were defined as final peaks if they presented overlap with peaks identified in both their respective individual replicates.
Assembly: dm3
Supplementary files format and content: bed


title: testis HAF-2


title: Parental_T0_C


title: Parental_T0_B


title: mouse kidney, spatial, IMQ, MM04032_part2

description:
MM04032_DP8400019634TR_L01_read_1.part_002
processed_data: 4032_1.txt
processed_data: 4032_2.txt
processed_data: 4032_3.txt
processed_data: 4032_4.txt

library_source: other

data_processing:
BGI's SAW pipeline was used to process fastq files into resulting gene expression matrices
Assembly: mm10
Supplementary files format and content: GEM formatted counts file including X/Y coordinates
Library strategy: spatial transcriptomics

molecule: other

source_name: Kidney

extract_protocol:
10 µm kidney tissue sections were cryosectioned from OCT embedded frozen blocks and adhered to the Stereo-seq chip surface, fixed in methanol and stained with nucleic acid dye for imaging. Then we performed permeabilization, reverse transcription, cDNA amplification and library preparation following Stereo-seq protocol.
After cDNA interruption, amplification and double-selection, libraries were subjected to Agilent 2100 quality inspection. Finally, the double-selection libraries were constructed into libraries suitable for the MGI DNBSEQ-Tx sequencing platform through circularization steps and were sequenced to collect data (50 bp for read 1 and 100 bp for read 2).

value: Kidney

value: imq


title: INPUT10%_KDH1_2


title: Parental_T0_A


title: mouse kidney, spatial, control_part2

description:
MM04025_DP8400019130BR_L01_read_1.part_002
processed_data: control_1.txt
processed_data: control_2.txt
processed_data: control_3.txt
processed_data: control_4.txt


title: Dark_Adapted_T4_B


title: KDH1_a48_1


title: Arabidopsis thaliana shoots, Pseudomonas Root401 in 100mMNaCl, replicate 3

first: Fantin

last: Mesny

address: Carl-von-Linné-Weg 10

department: Plant-Microbes interaction

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Read trimming with Trimmomatic PE v0.38 (parameters TRAILING:20 AVGQUAL:20 MINLEN:100)
Read mapping against genomic index with Hisat2 v2.2.1 (default parameters)
Per-gene read counting with featureCounts v2.0.0 (parameter -p, default settings)
Assembly: TAIR10.1
Supplementary files format and content: Output files from featureCounts, containing the number of reads mapped on each Arabidopsis thaliana gene as well as information regarding the genes (location in genome and length)

organism: Arabidopsis thaliana

source_name: Shoots

extract_protocol:
Qiagen RNeasy Plant Mini Kit
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

value: Shoots

value: Pseudomonas Root401 in 100mMNaCl


title: spleen HAF-1


title: mouse kidney, spatial, control_part1

description:
MM04025_DP8400019130BR_L01_read_1.part_001
processed_data: control_1.txt
processed_data: control_2.txt
processed_data: control_3.txt
processed_data: control_4.txt


title: KDH1_a36_1


title: INPUT10%_KDH1_1


title: testis HAF-1


title: Mouse_embryonic_brain_Apcdd1+/-_2

city: Beijing

first: Ying

last: Liu

address: 5 Summer Palace Road, Haidian District, Beijing

department: College of Future Technology

institute: Peking University

data_processing:
Scanpy (version: 1.9.1)74 was used for downstream analyses. Low-quality cells were filtered out considering the abnormal gene count and high mitochondrial read percentage.
We normalized the gene expression by scaling total UMIs to 10,000 in each cell followed by log transformation.
The BBKNN algorithm was used to remove batch effects across four samples.
 Then, principal component analysis (PCA) was performed and the top 50 principal components (PCs) were used for uniform manifold approximation and projection (UMAP) and Leiden clustering.
Because of the different file format of MGI and 10X, some cell IDs in our original barcodes file can be matched with more than one barcodes, which is also the reason for more lines than provided in matrix file.
Assembly: mm10
Supplementary files format and content: barcodes, features, and  matrix files

source_name: embryonic brain

extract_protocol:
The E10.5 mouse embryos were dissected from pregnant mice sacrificed by anesthesia and decapitation. The head part of embryo was dissected out by fine tweezers and stored in Shbio®Tissue Preservation Solution (21903-10) overnight, which were then dissociated using Shbio®Tissue Dissociation Kit (219517-10).
Briefly, tissues were incubated in 1 ml enzyme mix on a metal rotor at 37 °C for 15 min, during which specimens were gently mixed for 20 times using 1,000-ml tips every 7 min. Cell dissociations were terminated by adding 2 ml of complete medium and then suspensions were filtered through a 100-µm strainer and centrifuged for 10 min at 500g. The supernatant was discarded and the cell pellet was resuspended with 300 µl suspension buffer (1X DPBS containing 2% FBS). Dyed by 50 ng/ml DAPI for 3 min and refiltered with a 40-µm strainer, cell suspensions were then sorted with FACS BD Aria III sorter to remove dead cells, fragments and lumps. Cell numbers of suspensions were measured with fluorescence cell counter (Luna-FLTM, Logos biosystems) and hemocytometer using trypan blue staining. Cell suspensions were then adjusted to a proper cell concentration for library construction of scRNA-seq. scRNA-seq was then performed using the DNBelab C high throughput single cell RNA library prep kit (MGI) following the manufacturer’s protocol. The QubitTM Flex Fluorometer (Thermo Fisher Scientific) and Agilent Fragment Analyzer were used to determine the concentration and assess the quality of the libraries, which were then subjected to MGISEQ-2000 for sequencing. Cell barcode and unique molecular identifiers (UMI) sequences were parsed using DNBelab_C_Series_HT_scRNA-analysis-software (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software)

value: embryonic brain


title: Arabidopsis thaliana shoots, heat-killed Pseudomonas Root401 in 100mMNaCl, replicate 3


title: mouse kidney, spatial, IMQ, MM04032_part1

description:
MM04032_DP8400019634TR_L01_read_1.part_001
processed_data: 4032_1.txt
processed_data: 4032_2.txt
processed_data: 4032_3.txt
processed_data: 4032_4.txt


title: Mouse_embryonic_brain_WT-2

value: WT


title: testis HFD-3

city: Qingdao

value: ICR

value: High fat diet


title: testis HFD-2

value: 10 weeks


title: Mouse_embryonic_brain_WT-1


title: Arabidopsis thaliana shoots, heat-killed Pseudomonas Root401 in 100mMNaCl, replicate 2


title: ChIP_LZ_a36_2

value: S2 cells


title: testis HFD-1


title: LZ_a48_2


title: testis HA10-1

value: High fat diet +AOS10mg/kg


title: Mouse_embryonic_brain_Apcdd1+/-_1


title: Arabidopsis thaliana shoots, Pseudomonas Root401 in 100mMNaCl, replicate 1


title: Arabidopsis thaliana shoots, Pseudomonas Root401 in 0mMNaCl, replicate 3

value: Pseudomonas Root401 in 0mMNaCl


title: KDH1_a36_2

value: KD H1


title: testis con-3

value: testis

value: control


title: kidney HCF-3

source_name: kidney

extract_protocol:
Kidney were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: High fat diet +control-FMT


title: Arabidopsis thaliana shoots, Pseudomonas Root401 in 0mMNaCl, replicate 2


title: testis con-2


title: kidney HCF-2


title: Arabidopsis thaliana shoots, Pseudomonas Root401 in 0mMNaCl, replicate 1


title: Arabidopsis thaliana shoots, heat-killed Pseudomonas Root401 in 100mMNaCl, replicate 1


title: LZ_a36_1

value: LacZ


title: testis con-1


title: Arabidopsis thaliana shoots, heat-killed Pseudomonas Root401 in 0mMNaCl, replicate 3


title: INPUT10%_LZ_1


title: testis A10-3

value: AOS 10mg/kg


title: INPUT10%_LZ_2


title: LZ_a48_1


title: kidney HAF-3

value: High fat diet +AOS10mg/kg-FMT


title: ChIP 2 hrp36

description:
hrp36_peaks_eval.bed
hrp48_peaks_eval.bed

value: primary culture of late stage (20-24 hours old)


title: Arabidopsis thaliana shoots, heat-killed Pseudomonas Root401 in 0mMNaCl, replicate 2

value: Shoots


title: kidney HAF-2


title: Arabidopsis thaliana shoots, heat-killed Pseudomonas Root401 in 0mMNaCl, replicate 1


title: ChIP 2 hrp48


title: testis A10-1


title: kidney HAF-1


title: Arabidopsis thaliana roots, Pseudomonas Root401 in 100mMNaCl, replicate 3

source_name: Roots

value: Roots

value: Pseudomonas Root401 in 100mMNaCl


title: ChIP 2 INPUT 10%


title: kidney HCF-1

value: ICR


title: kidney HA10-3

value: 10 weeks


title: ChIP 1 hrp36

value: S2 cells


title: kidney HA10-2

value: High fat diet +AOS10mg/kg


title: kidney HA10-1


title: Arabidopsis thaliana roots, Pseudomonas Root401 in 100mMNaCl, replicate 1