title: 4C_WT_for_g_del_GA7_rep2

data_processing:
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or the human genome (H. sapiens, UCSC hg19) using Bowtie (version 1.2.3).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Assembly: M. musculus, UCSC mm9 or H. sapiens UCSC hg19
Supplementary files format and content: zipped bedGraph files include RPM values for each Sample
Library strategy: QHR4C-seq

extract_protocol:
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 2% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions. The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).


title: 4C_WT_for_g_del_GA3_rep2

status: Public on Oct 31 2023

type: SRA

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

country: China

institute: Shanghai JiaoTong University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: cortex

tag: tissue

value: cortex

tag: cell line

value: cortex-neuron

tag: cell type

value: neuron

tag: genotype

value: wildtype


title: 4C_WT_for_g_del_GA7_rep1


title: 4C_WT_for_g_del_GB1_rep1


title: 4C_WT_for_g_del_CBSh_rep1


title: 4C_WT_for_g_del_B6_rep2


title: 4C_WT_for_g_del_GA3_rep1


title: 4C_WT_for_g_del_CBSh_rep2


title: 4C_BC_del_E_rep1

data_processing:
library strategy: QHR4C-seq
Paired-end reads were aligned to the human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input. Peaks were called using macs14
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or the human genome (H. sapiens, UCSC hg19) using Bowtie (version 1.2.3).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Assembly: M. musculus, UCSC mm9 or H. sapiens UCSC hg19
Supplementary files format and content: zipped bedGraph files include RPM values for each Sample

extract_protocol:
1 × 10^6 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 2% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions. The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

value: BC del


title: 4C_WT_for_g_del_GB1_rep2


title: 4C_WT_for_g_del_B22_rep2


title: 4C_WT_for_g_del_B6_rep1


title: 4C_BC_del_D_rep1


title: 4C_WT_for_g_del_B21_rep2


title: 4C_WT_for_g_del_B22_rep1


title: 4C_WT_for_g_del_B16_rep2


title: 4C_WT_for_g_del_B16_rep1


title: 4C_WT_for_g_del_B13_rep2


title: 4C_WT_for_g_del_B18_rep1


title: 4C_WT_for_g_del_B18_rep2


title: 4C_WT_for_g_del_B21_rep1


title: 4C_WT_for_g_del_B13_rep1


title: 4C_g_del_GA7_rep1

value: CBSg del -/-


title: 4C_g_del_GB1_rep2


title: 4C_g_del_GA7_rep2


title: 4C_WT_for_g_del_B10_rep2


title: 4C_WT_for_g_del_B10_rep1


title: 4C_g_del_GA3_rep2


title: 4C_g_del_B6_rep2


title: 4C_g_del_CBSh_rep1


title: 4C_g_del_GA3_rep1


title: 4C_g_del_CBSh_rep2


title: 4C_g_del_B6_rep1


title: 4C_g_del_B22_rep2


title: 4C_g_del_B22_rep1


title: 4C_g_del_B18_rep2


title: 4C_g_del_B21_rep1


title: 4C_g_del_B21_rep2


title: 4C_g_del_B18_rep1


title: 4C_g_del_B16_rep2


title: 4C_g_del_B16_rep1


title: 4C_g_del_GB1_rep1


title: 4C_g_del_B13_rep2


title: 4C_g_del_B13_rep1


title: RNA_g_del_rep2

library_source: transcriptomic

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.

molecule: total RNA

extract_protocol:
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.

value: g_del -/-


title: RNA_wt_for_g_del_rep1


title: RNA_g_del_rep4


title: RNA_g_del_rep3


title: 4C_g_del_B10_rep2


title: RNA_g_del_rep1


title: 4C_g_del_B10_rep1


title: RAW264.7 cells, DMSO-LPS-2

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

country: USA

institute: University of Florida

description:
raw_counts.txt
DMSO-LPS_DMSO_RNAseq_results.xlsx
DMSO-LPS-2_S4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic and QC was performed using FastQC.
Reads were mapped to the mouse transcriptome using the STAR aligner.
Differential gene expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: Excel files containing results of differential gene expression analysis

growth_protocol: RAW264.7 cells (250,000 cells/well) were seeded in 6-well plates and allowed to attach overnight. After overnight incubation, the media (DMEM, 10% FBS) in each well were replaced with fresh media prior to treatment with compound

extract_protocol:
RNA was extracted after 12h using RNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Illumina RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF).

treatment_protocol: Cells were treated with solvent control (DMSO, 0.5%) and LPS (1 µg/mL), solvent control (DMSO, 0.5%) alone, 7(E)-9-keto-hexadec-7-enoic acid (32, 10, 3.2 µM) and LPS (1 µg/mL).

value: Mouse Macrophage

tag: biorep

tag: treatment

value: Vehicle control (0.5%DMSO) + LPS (1 µg/mL)


title: RAW264.7 cells, FA-1-52-3-10-2

description:
raw_counts.txt
DMSO-LPS_FA-1-52-3-10_RNAseq_results.xlsx
FA-1-52-3-10-2_S8

value: Compound (10 µM) + LPS (1 µg/mL)


title: RAW264.7 cells, DMSO-LPS-1

description:
raw_counts.txt
DMSO-LPS_DMSO_RNAseq_results.xlsx
DMSO-LPS-1_S3


title: RAW264.7 cells, DMSO-2

description:
raw_counts.txt
DMSO-2_S2

value: Vehicle control (0.5%DMSO)


title: RAW264.7 cells, FA-1-52-3-3-2-1

description:
raw_counts.txt
DMSO-LPS_FA-1-52-3-3_RNAseq_results.xlsx
FA-1-52-3-3-2-1_S9

value: Compound (3.2 µM) + LPS (1 µg/mL)


title: RAW264.7 cells, FA-1-52-3-3-2-2

description:
raw_counts.txt
DMSO-LPS_FA-1-52-3-3_RNAseq_results.xlsx
FA-1-52-3-3-2-2_S10


title: Control_input

city: Kobe

first: Weijia

last: Zang

address: Hyogo, Kobe, Chuo Ward, Minatojima Minamimachi, 6 Chome−３−7

department: Department of Hematology-Oncology

country: Japan

institute: Foundation for Biomedical Research and Innovation at Kobe

description: genomic DNA immunoprecipitated without antibody

data_processing:
The adapter sequences were removed from the FASTQs using Trimmomatic (0.39).
The cleaned FASTQs were aligned using Bowtie2 (2.4.4) to the mouse reference genome mm10.
The duplicated reads were removed using picard (2.26.2) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Lineage- bone marrow cells in femora and tibiae

extract_protocol:
Cells were fixed with 2mM DSG (Thermo Fisher Scientific, 20593) for 30 min at room temperature and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1 mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 10 min at 37°C.Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4°C. Cells were pelleted, and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4°C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated.Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 ml of 10% Triton X-100 and 30 ml of 5M NaCl were added. The sample was then incubated with 20 ml of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4°C. Primary antibodies were added to each tube and immunoprecipitation (IP) was conducted overnight in the cold room. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4°C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4°C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65°C. RNA and protein were digested with 0.2 mg/ml RNase A for 30 min at 37C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: Four weeks after BMT, the recipient mice received 20 mg/kg pIpC injection every other day for a total of 3 doses.

tag: strain

tag: donor genotype

value: CD45.2(+) Brd9fl/fl

tag: recipient genotype

tag: timing of preparation

value: 5 months after pIpC injection

tag: chip antibody


title: Control_sample

description: genomic DNA immunoprecipitated with previous antibody

value: anti-CTCF (Millipore, 07-729)


title: Input_KO_S [mouse_Brd9_H3K27Ac-ChIP-seq]

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

value: CD45.2(+) Mx1-Cre Brd9fl/fl


title: H3K27Ac_WT2 [mouse_Brd9_H3K27Ac-ChIP-seq]

value: anti-H3K27Ac (Abcam, ab4729)


title: RAW264.7 cells, FA-1-52-3-10-1

description:
raw_counts.txt
DMSO-LPS_FA-1-52-3-10_RNAseq_results.xlsx
FA-1-52-3-10-1_S7


title: RAW264.7 cells, FA-1-52-3-32-2

description:
raw_counts.txt
DMSO-LPS_FA-1-52-3-32_RNAseq_results.xlsx
FA-1-52-3-32-2_S6

value: Compound (32 µM) + LPS (1 µg/mL)


title: Input_WT_S [mouse_Brd9_H3K27Ac-ChIP-seq]


title: Brd9KO_2 [mouse_Brd9_ATAC-seq]

source_name: Lineage-  bone marrow cells in femora and tibiae

extract_protocol: Cells harvest was followed by a transposition reaction and purification followed the manual of ATAC-seq kit from Active motif (#13150)

treatment_protocol: Four weeks after birth, the recipient mice received 20 mg/kg pIpC injection every other day for a total of 3 doses.

value: Five months after pIpC injection


title: Brd9KO_input


title: Brd9KO_sample


title: Brd9KO_1 [mouse_Brd9_ATAC-seq]

value: Lineage-  bone marrow cells in femora and tibiae


title: Control_1 [mouse_Brd9_ATAC-seq]


title: E.Coli Nissle 1917 expressing aldafermin, replicate 4, adipose tissue

city: kuopio

first: Valeria

last: Iannone

address: Yliopistonranta 1

department: Clinical Nutrition

country: Finland

institute: University of Eastern Finland

data_processing:
Raw reads of FASTQ format were processed through fastp. Reads with adaptor contamination, poly-N sequences, with low quality nucleotides (Base Quality less than 5), with low uncertain nucleotides (N>10%) were removed.
Reference genome and gene model annotation files were downloaded from https://www.ensembl.org/index.html. Paired-end clean reads were mapped using the Spliced Transcripts Alignment to a Reference software. FeatureCounts software were used to count the read numbers mapped to each gene.
Supplementary files format and content: tab-delimited text files include gene counts values for each Sample

source_name: adipose tissue

extract_protocol:
The liver was homogenized in Buffer RLT (Cat. No./ID:79216, Qiagen, Germany) and extracted with RNeasy minikit (Qiagen, Germany). The RNase-free DNase I (Qiagen, Germany) treatment was performed for removing genomic DNA contaminants.
For sequencing library preparation 1μg RNA per sample was used generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

value: adipose tissue

tag: Sex

value: male

tag: age

value: 26- to 29 -week-old

value: WT


title: RAW264.7 cells, DMSO-1

description:
raw_counts.txt
DMSO-1_S1

value: Mouse Macrophage


title: RAW264.7 cells, FA-1-52-3-32-1

description:
raw_counts.txt
DMSO-LPS_FA-1-52-3-32_RNAseq_results.xlsx
FA-1-52-3-32-1_S5


title: Control_2 [mouse_Brd9_ATAC-seq]


title: E.Coli Nissle 1917 expressing aldafermin, replicate 3, adipose tissue


title: H3K27Ac_KO1 [mouse_Brd9_H3K27Ac-ChIP-seq]


title: E.Coli Nissle 1917 expressing aldafermin, replicate 1, adipose tissue


title: ATAC MP

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
Adapters were detected and removed using fastq-mcf of ea-utils  (https://expressionanalysis.github.io/ea-utils, version 1.04.738) and mapped to chromosomes 1-19, X, Y and M of the mouse mm10 using bowtie (version 1.3.1), with the options ‘-y -m 1 -S -X 2000 --allow-contain’. Mapped paired-end reads were converted to a bed file by generating the original fragment using a custom perl script and duplicates were removed such that only one fragment with the same starting and end position was retained. Due to the repetitive nature of the Y chromosome and non-informative mitochondrial genome, reads mapped to either of them removed were and .wig files were generated using BEDtools and converted to bigwig format.
Assembly: mm10
Supplementary files format and content: *.bw: tag denisty files of ChIP data in bigWig format
Supplementary files format and content: *.narrowPeak: peak files for ChIP-Seq tracks used in analysis obtained by MACS
Supplementary files format and content: RNA_FPKM.txt: normalized per gene abundance measurements (FPKM) for RNA-Seq samples obtained by Cuffdiff

source_name: FACS sorted T+/Noto-/Foxa2- from caudal ends of TS12/TS13 embryos obtained from tatraploid complementation of embryonic stem cells

growth_protocol: ES cell lines were cultured according to standard conditions. Cells were maintained on gelatinized plates and mitotically inactive primary mouse embryo fibroblasts with standard ESC medium, refreshed daily, containing 15% FCS and 1000 U/ml leukemia inhibitory factor. ES cells were used to generate embryos via the tetraploid complementation assay.

extract_protocol:
In total, 2000 cells were used per ATAC-Seq experiment. After spinning down the FACS sorted cells, the pellets were resuspended in 50ul of lysis buffer (10mM Tris pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) and immediately spun down at 500g and 4°C for 10 min. The supernatant was discarded and each pellet was resuspended in the transposition reaction mix (25ul 2x TD buffer, 2.5ul Tn5 transposase, 22ul H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
To prepare the ATAC-Seq libraries, the purified tagmented DNA was combined with the Nextera PCR primers and 2x Kapa HiFi Hotstart Readymix and pre-amplified (98°C 30 seconds, 8x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50ul volume. To determine the remaining cycles to avoid potential overamplification, 5ul of the preamplification mix was combined with the primers, 1x Evagreen Sybr green (Jena Biosciences) and 2x Kapa HiFi Hotstart Readymix in a 15ul total volume and run for 30 cycles on a StepOne Plus. The remaining 45ul pre-amplified samples were amplified for a further 7 cycles, resulting in a total of 15 cycles. The libraries were purified using MiElute column (Qiagen) and the concentration was measured using the DNA HS Qubit assay (life). Approximately 4ng of each library were run on a DNA HS Bioanalyzer chipto verify library size and calculate molarities.

value: genetically modified F1G4 (C57BL/6N x SV129) mES cells

value: mesodermal progenitors

value: T::H2B-Venus (BAC), Noto::H2B-mCherry (BAC), Foxa2::H2B-mTurquoise (BAC)

value: In order to obtain single cell suspensions from embryo tissue for FACS sorting, 10ul of 5% BSA in PBS was added to the pooled samples and 100ul of ice-cold 0.05% trypsin was added. A homogenous suspension was achieved by slow pipetting and the reaction was stopped with the addition of 200ul of 5% BSA in PBS. Before cell sorting on a FACS Aria II (Becton Dickinson), the cell suspension was filtered through a 35µm mesh. Cells were sorted into FACS-tubes containing 5% BSA in PBS, which had previously been rotating for several hours to pre-coat the tube walls with BSA. Sorted cells were centrifuged at 1000rpm and 4°C for 10 minutes, transferred to Eppendorf tubes containing PBS with 0.05% Triton X-100 and centrifuged at 1000rpm and 4°C for 10 minutes. The supernatant was removed and cells were directly processed for ATAC-Seq.


title: ATAC NotoP

source_name: FACS sorted Noto+/T+/Foxa2+ from caudal ends of TS12/TS13 embryos obtained from tatraploid complementation of embryonic stem cells

value: notochord progenitors


title: E.Coli Nissle 1917 expressing aldafermin, replicate 2, adipose tissue


title: control_2_E.Coli Nissle 1917, replicate 5, adipose tissue

value: control_2_E.Coli Nissle 1917


title: E.Coli Nissle 1917 expressing aldafermin, replicate 5, adipose tissue


title: Mop_5D_rep2 (Multiome Gene Expression)

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
replication of Mop_5D
Mop_5D_rep2_barcodes.tsv.gz
Mop_5D_rep2_features.tsv.gz
Mop_5D_rep2_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Raw sequencing was processed using cellranger-arc (10x Genomics), generating snRNA-seq UMI count matrices for intronic and exonic reads mapping in the sense direction of a gene.
Cells were filtered for low quality nuclei by requiring ≥1000 ATAC fragments and ≥500 genes detected per nuclei.
Genes were annotated with hg38 Gencode v33 for human, mm10 Gencode vM22 for mouse, ensembl release 104 (and Refseq GCF_003339765.1 for 10x multiome) for macaque, and GCA_009663435.2 for marmoset. To maximize the number of orthologous protein-coding quantified in macaque 10x multiome RNA data, we supplemented any missing protein coding genes in GCF_003339765.1 gtf with annotations present in Ensembl release 104.
Assembly: hg38 GRCh38
Assembly: mm10 GRCm38
Assembly: Mmul_10 (rheMac10)
Assembly: cj1700_1.1 (calJac4)
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.   Files provided in tar archives.

source_name: primary motor cortex

extract_protocol:
[nuclei preparation protocol]  Brain tissue was pulverized using a mortar and pestle on dry ice and pre-chilled with liquid nitrogen. Pulverized brain tissue was resuspended in 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was Dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until solution was uniform. Nuclei were filtered using a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellet was resuspended in 1 mL NIM-DP buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1x Protease Inhibitor, 1U/μL Recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4˚C). Pelleted nuclei were resuspended in 400uL 2μM 7-AAD (Invitrogen, A1310) in Sort Buffer (1mM EDTA, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor, 1% fatty acid-free BSA in PBS).
120,000 nuclei were sorted (Sony, SH800S) into a LoBind tube containing Collection Buffer (5U/uL Recombinant RNase inhibitor, 1X Protease Inhibitor, 5% fatty acid-free BSA in PBS). 5X Permeabilization Buffer (50mM Tris-HCl pH 7.4, 50mM NaCl, 15mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U/μL Recombinant RNase inhibitor, 5X Protease Inhibitor) was added for a final concentration of 1X. Nuclei were incubated on ice for 1 minute, then centrifuged (500 rcf, 5min at 4C). Supernatant was discarded and 650uL of Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%.Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor) was added without disturbing the pellet followed by centrifuging (500 rcf, 5 min at 4˚C). Supernatant was removed, and the pellet was resuspended in 7uL of 1X Nuclei Buffer (Nuclei Buffer (10x Genomics), 1mM DTT, 1 U/μL Recombinant RNase inhibitor). 1 μL of nuclei was diluted in 1X Nuclei Buffer, stained with Trypan Blue (Invitrogen, T10282) and counted. 16-20k nuclei were used for tagmentation reaction and controller loading and libraries were generated following manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).
10x multiome ATAC-seq and RNA-seq libraries were paired-end sequenced on NextSeq 500 and NovaSeq 6000 to a depth of ~50,000 reads per cell for each modality.

value: primary motor cortex

tag: species

value: Mouse

tag: donor id

value: 4 mice are pooled

value: M

tag: mouse strain

tag: library type

value: 10x Genomics Multiome Gene Expression


title: Mop_5D_rep2 (Multiome ATAC)

library_source: genomic single cell

tag: tissue

value: 10x Genomics Multiome ATAC


title: control_2_E.Coli Nissle 1917, replicate 3, liver

source_name: liver

value: liver


title: control_1, replicate 1, liver

value: male


title: control_1, replicate 3,adipose tissue

value: adipose tissue

value: 26- to 29 -week-old


title: E.Coli Nissle 1917 expressing aldafermin, replicate 4, liver

value: WT


title: E.Coli Nissle 1917 expressing aldafermin, replicate 2, liver


title: control_1, replicate 5, liver


title: control_1, replicate 5, adipose tissue


title: control_2_E.Coli Nissle 1917, replicate 2, liver


title: E.Coli Nissle 1917 expressing aldafermin, replicate 5, liver


title: control_2_E.Coli Nissle 1917, replicate 5, liver


title: control_2_E.Coli Nissle 1917, replicate 4, liver


title: control_1, replicate 2, liver


title: control_2_E.Coli Nissle 1917, replicate 3,adipose tissue


title: E.Coli Nissle 1917 expressing aldafermin, replicate 1, liver


title: control_2_E.Coli Nissle 1917, replicate 1, adipose tissue


title: control_2_E.Coli Nissle 1917, replicate 2, adipose tissue


title: control_1, replicate 1,adipose tissue


title: control_2_E.Coli Nissle 1917, replicate 4, adipose tissue


title: E.Coli Nissle 1917 expressing aldafermin, replicate 3, liver


title: control_1, replicate 4, adipose tissue


title: control_1, replicate 2, adipose tissue


title: control_1, replicate 3, liver


title: Mop_4B_rep2 (Multiome Gene Expression)

description:
replication of Mop_4B
Mop_4B_rep2_barcodes.tsv.gz
Mop_4B_rep2_features.tsv.gz
Mop_4B_rep2_matrix.mtx.gz


title: control_1, replicate 4, liver


title: Mop_4B_rep2 (Multiome ATAC)


title: control_2_E.Coli Nissle 1917, replicate 1, liver


title: Mop_4B_rep1 (Multiome ATAC)

description:
Mop_4B_rep1_barcodes.tsv.gz
Mop_4B_rep1_features.tsv.gz
Mop_4B_rep1_matrix.mtx.gz


title: Mop_2C_rep2 (Multiome ATAC)

description:
replication of Mop_2C
Mop_2C_rep2_barcodes.tsv.gz
Mop_2C_rep2_features.tsv.gz
Mop_2C_rep2_matrix.mtx.gz


title: Mop_5D_rep1 (Multiome Gene Expression)

description:
Mop_5D_rep1_barcodes.tsv.gz
Mop_5D_rep1_features.tsv.gz
Mop_5D_rep1_matrix.mtx.gz


title: Mop_3C_rep2 (Multiome ATAC)

description:
replication of Mop_3C
Mop_3C_rep2_barcodes.tsv.gz
Mop_3C_rep2_features.tsv.gz
Mop_3C_rep2_matrix.mtx.gz


title: Mop_3C_rep1 (Multiome Gene Expression)

description:
Mop_3C_rep1_barcodes.tsv.gz
Mop_3C_rep1_features.tsv.gz
Mop_3C_rep1_matrix.mtx.gz


title: Mop_5D_rep1 (Multiome ATAC)


title: NCR+ ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 4

city: Manchester

first: Matthew

last: Hepworth

address: AV Hill Building

country: United Kingdom

institute: University of Manchester

description:
SI_NCR_KO_4
SI_NCR_KO_4

data_processing:
CASAVA based recognition was used to convert raw reads into FASTQ files
Reads with adapter contamination, reads with >10 % of uncertain nucleotides and reads with base quality <5 in over 50% of the read were filtered out.
The remaining reads were aligned with HISAT2.
Assembly: mm10
Supplementary files format and content: comma-separated-values (.csv) files include gene counts for each sample

source_name: Small intestine lamina propria

growth_protocol: Littermate mice aged 12 weeks were housed in individually ventilated cages at the University of Manchester, under specific pathogen free conditions, standard chow and water provided ad libitum, constant temperature and a 12 hour light and dark cycle.

extract_protocol:
For small intestine lymphocyte isolation, fat and Peyer’s patches were removed and the small intestine was opened longitudinally and washed vigorously in PBS. Tissue was incubated for two concurrent rounds in PBS containing 1 mM EDTA, 1 mM dithiothreitol and 5 % FBS for 25 min at 37 °C with constant mixing. Then, tissues were washed in PBS and digested in complete RPMI with in 1 mg/ml collagenase VIII (Sigma-Aldrich) and 20 μg/ml DNase (Sigma-Aldrich) for 25 min at 37 °C. For mLN, fat was removed and lymph node was digested in 0.33mg/mL Liberase TL (Roche) and 1mg/ml DNase (Sigma-Aldrich)  for 25min at 37ºC on agitation. All the digested tissues were filtered through a 70 μm nylon strainer and stained for fluorescence-activated cell sorting. Live CD45+ B220- CD11c- CD11b- CD3- CD5- NK1.1- Ter119- TCRgd- TCRb- CD90.2+ CD127+ KLRG1- ILC were sorted as NCR+ ILC3 (NKp46+), or LTi-like ILC3 (CCR6+ ckit+)  into 250uL RL buffer using a BD FACS Aria II. Lysates were spun and frozen at -20ºC  overnight. Then, RNA was extracted using the Single Cell RNA Purification Kit (Norgen), including in-column DNA digestion, and frozen at -80ºC. RNA was amplified using SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara Bio USA, Inc., Mountain View, USA) following manufacturer's instructions.
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit (New England Biolabs, Ipswich, USA) following the manufacturer’s recommendations.

value: Small intestine lamina propria

value: NCR+ ILC3

value: Rorc-Cre x Bcl6-fl/fl


title: NCR+ ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 5

description:
SI_NCR_KO_5
SI_NCR_KO_5


title: Mop_2C_rep1 (Multiome ATAC)

description:
Mop_2C_rep1_barcodes.tsv.gz
Mop_2C_rep1_features.tsv.gz
Mop_2C_rep1_matrix.mtx.gz


title: NCR+ ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 1

description:
SI_NCR_WT_1
SI_NCR_WT_1


title: NCR+ ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 4

description:
SI_NCR_WT_4
SI_NCR_WT_4


title: LTi-like ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 1

description:
SI_LTi_WT_1
SI_LTi_WT_1

value: LTi-like ILC3


title: NCR+ ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 2

description:
SI_NCR_WT_2
SI_NCR_WT_2


title: LTi-like ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 3

description:
SI_LTi_WT_3
SI_LTi_WT_3


title: LTi-like ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 5

description:
SI_LTi_WT_5
SI_LTi_WT_5


title: Mop_3C_rep2 (Multiome Gene Expression)


title: Mop_3C_rep1 (Multiome ATAC)


title: NCR+ ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 3

description:
SI_NCR_KO_3
SI_NCR_KO_3


title: NCR+ ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 1

description:
SI_NCR_KO_1
SI_NCR_KO_1


title: NCR+ ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 2

description:
SI_NCR_KO_2
SI_NCR_KO_2


title: NCR+ ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 5

description:
SI_NCR_WT_5
SI_NCR_WT_5


title: NCR+ ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 3

description:
SI_NCR_WT_3
SI_NCR_WT_3


title: LTi-like ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 5

description:
SI_LTi_KO_5
SI_LTi_KO_5


title: LTi-like ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 2

description:
SI_LTi_KO_2
SI_LTi_KO_2


title: Mop_2C_rep2 (Multiome Gene Expression)


title: LTi-like ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 2

description:
SI_LTi_WT_2
SI_LTi_WT_2


title: LTi-like ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 1

description:
SI_LTi_KO_1
SI_LTi_KO_1


title: LTi-like ILC3 from the small intestine of Bcl6-fl/fl mice, biol rep 4

description:
SI_LTi_WT_4
SI_LTi_WT_4


title: Mop_2C_rep1 (Multiome Gene Expression)


title: LTi-like ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 3

description:
SI_LTi_KO_3
SI_LTi_KO_3


title: LTi-like ILC3 from the small intestine of Rorc-Cre x Bcl6-fl/fl mice, biol rep 4

description:
SI_LTi_KO_4
SI_LTi_KO_4


title: LTi-like ILC3 from the mLN of Bcl6-fl/fl control mice, biol rep 4

description:
mLN_LTi_WT_4
mLN_LTi_WT_4

source_name: mLN

value: mLN


title: LTi-like ILC3 from the mLN of Bcl6-fl/fl control mice, biol rep 2

description:
mLN_LTi_WT_2
mLN_LTi_WT_2


title: LTi-like ILC3 from the mLN of Bcl6-fl/fl control mice, biol rep 3

description:
mLN_LTi_WT_3
mLN_LTi_WT_3


title: LTi-like ILC3 from the mLN of Bcl6-fl/fl control mice, biol rep 1

description:
mLN_LTi_WT_1
mLN_LTi_WT_1


title: LTi-like ILC3 from the mLN of Rorc-Cre x Bcl6-fl/fl mice, biol rep 3

description:
mLN_LTi_KO_3
mLN_LTi_KO_3


title: LTi-like ILC3 from the mLN of Rorc-Cre x Bcl6-fl/fl mice, biol rep 4

description:
mLN_LTi_KO_4
mLN_LTi_KO_4


title: LTi-like ILC3 from the mLN of Rorc-Cre x Bcl6-fl/fl mice, biol rep 2

description:
mLN_LTi_KO_2
mLN_LTi_KO_2


title: LTi-like ILC3 from the mLN of Rorc-Cre x Bcl6-fl/fl mice, biol rep 1

description:
mLN_LTi_KO_1
mLN_LTi_KO_1


title: 4C_H_f_del_rep2 [QHR4C-seq]

data_processing:
library strategy: QHR4C-seq
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or the human genome (H. sapiens, UCSC hg19) using Bowtie (version 1.2.3).
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Assembly: M. musculus, UCSC mm9 or H. sapiens UCSC hg19
Supplementary files format and content: zipped bedGraph files include RPM values for each Sample

extract_protocol:
1 × 10^6 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase. Collagenase was quenched with 2-fold volumes of 10%FBS in NeuroBasal Medium and the suspended cells were used for library construction.
The neuron suspension or cultured cell were cross-linked using 2% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions. The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

value: cortex

tag: cell line

value: cortex-neuron

value: neuron

value: CBSf del -/-


title: 4C_H_f_del_rep1 [QHR4C-seq]

tag: cell type


title: 4C_B21_WT_for_f_del_rep1 [QHR4C-seq]

tag: genotype

value: wildtype


title: 4C_H_WT_for_f_del_rep1 [QHR4C-seq]


title: 4C_B21_f_del_rep2 [QHR4C-seq]


title: 4C_B21_WT_for_f_del_rep2 [QHR4C-seq]


title: 4C_B21_f_del_rep1 [QHR4C-seq]


title: RNA_cortex_WT_rep10

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.
Supplementary files format and content: GSE225162

molecule: polyA RNA


title: RNA_cortex_WT_rep8


title: RNA_cortex_WT_rep7


title: RNA_cortex_WT_rep9


title: RNA_cortex_WT_rep6


title: RNA_cortex_WT_rep5


title: RNA_cortex_WT_rep3


title: 4C_H_WT_for_f_del_rep2 [QHR4C-seq]


title: RNA_cortex_WT_rep12


title: RNA_cortex_WT_rep11


title: cerebellar endothelial cells - chronic model - Ccm3 knock-out 2

city: Uppsala

first: Ross

last: Smith

address: Skrindvägen 20

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
The quality control and prepossessing of the raw reads were done using Trim Galore.
Reads were mapped to the mm10 mouse genome using default settings of STAR (version 2.5.3a)for both the acute model and chronic models.
The number of reads per gene were counted while mapping by STAR.
Reads normalization was done using the DESeq2 Bioconductor package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with normalized counts for each acute model sample
Supplementary files format and content: tab-delimited text files with normalized counts for each chronic model sample

source_name: brain

extract_protocol:
For acute disease model: Endothelial cells were isolated from the cerebella of 3 wild-type and 3 Ccm3 knock-out mice with the Adult Brain Dissociation kit (130-107-677; MiltenyiBiotech), CD45 MicroBeads (30-052-301; MiltenyiBiotech) and CD31 MicroBeads (30-097-418; MiltenyiBiotech) according to the manufacturer’s instructions. Total RNA was extracted from each sample with the RNeasy Micro Kit (Qiagen) in the automated QIACube (Qiagen) platform. For chronic disease model: Endothelial cells were similarly isolated from the cerebella of 5 wild-type and 5 Ccm3 knock-out mice.
For acute model: RNA sequencing libraries were prepared with SMARTer Stranded Total RNA Sample Prep kit - Mammalian kit (Clontech), according to the manufacturer’s instructions. This kit includes depletion of ribosomal RNA prior to library synthesis, barcoding and amplification. 1 μl of each library was analyzed in the Agilent 2100 bioanalyzer for validation of fragment size and quality control of the amplified RNA-seq library, using the High Sensitivity DNA kit (Agilent).  For chronic model: Libraries were prepared with the stranded RNA library prep kits (Collibri; for Illumina), with rRNA depletion kits used according to the manufacturer instructions (#A39003024, A39003096; Invitrogen)

value: brain

value: Ccm3 knock-out


title: 4C_WT_GB5_rep1 [QHR4C-seq]


title: 4C_WT_GA1_rep2 [QHR4C-seq]


title: 4C_WT_GB5_rep2 [QHR4C-seq]


title: 4C_WT_GB2_rep1 [QHR4C-seq]


title: RNA_cortex_WT_rep4


title: 4C_WT_GA9_rep2 [QHR4C-seq]


title: 4C_WT_HS7L_rep2 [QHR4C-seq]


title: 4C_WT_B2_rep1 [QHR4C-seq]


title: 4C_WT_B8_rep2 [QHR4C-seq]


title: RNA_cortex_WT_rep1


title: RNA_cortex_WT_rep2


title: 4C_WT_B8_rep1 [QHR4C-seq]


title: 4C_WT_B19_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_H_rep2 [QHR4C-seq]


title: 4C_WT_B2_rep2 [QHR4C-seq]


title: 4C_WT_GA1_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GB7_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_H_rep1 [QHR4C-seq]


title: 4C_WT_HS7L_rep1 [QHR4C-seq]


title: 4C_WT_GB2_rep2 [QHR4C-seq]


title: 4C_WT_GA9_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA7_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GB7_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GB1_rep2 [QHR4C-seq]


title: 4C_WT_B19_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA7_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_GB1_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA6_rep2 [QHR4C-seq]


title: 4C_WT_B12_rep2 [QHR4C-seq]


title: 4C_WT_B12_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA6_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA4_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA1_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA1_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA3_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA4_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_B18_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_B9_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_B22_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_B22_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_B6_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_B6_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_B16_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_B18_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_B16_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_B9_rep1 [QHR4C-seq]


title: 4C_WT_for_fg_del_B13_rep2 [QHR4C-seq]


title: 4C_FG_H_rep1 [QHR4C-seq]

value: CBSfg del -/-


title: 4C_WT_for_fg_del_B13_rep1 [QHR4C-seq]


title: 4C_FG_H_rep2 [QHR4C-seq]


title: 4C_FG_GB7_rep2 [QHR4C-seq]


title: 4C_WT_for_fg_del_GA3_rep2 [QHR4C-seq]


title: 4C_FG_GB1_rep1 [QHR4C-seq]


title: 4C_FG_GB1_rep2 [QHR4C-seq]


title: 4C_FG_GA7_rep1 [QHR4C-seq]


title: 4C_FG_GA7_rep2 [QHR4C-seq]


title: 4C_FG_GA6_rep1 [QHR4C-seq]


title: 4C_FG_GB7_rep1 [QHR4C-seq]


title: 4C_FG_GA4_rep2 [QHR4C-seq]


title: 4C_FG_B9_rep2 [QHR4C-seq]


title: 4C_FG_GA3_rep1 [QHR4C-seq]


title: 4C_FG_GA1_rep1 [QHR4C-seq]


title: 4C_FG_GA3_rep2 [QHR4C-seq]


title: 4C_FG_GA1_rep2 [QHR4C-seq]


title: 4C_FG_B22_rep2 [QHR4C-seq]


title: 4C_FG_B18_rep1 [QHR4C-seq]


title: 4C_FG_B9_rep1 [QHR4C-seq]


title: 4C_FG_B18_rep2 [QHR4C-seq]


title: 4C_FG_B22_rep1 [QHR4C-seq]


title: 4C_FG_B6_rep1 [QHR4C-seq]


title: 4C_FG_B6_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_GA7_rep2 [QHR4C-seq]


title: 4C_FG_B16_rep1 [QHR4C-seq]


title: 4C_FG_GA6_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_GB1_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_GB1_rep2 [QHR4C-seq]


title: 4C_FG_B13_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_GA7_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_GA3_rep2 [QHR4C-seq]


title: 4C_FG_GA4_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_GA3_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_B6_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B22_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B18_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B6_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_B22_rep1 [QHR4C-seq]


title: 4C_FG_B13_rep2 [QHR4C-seq]


title: 4C_FG_B16_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B18_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_B16_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B13_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B16_rep1 [QHR4C-seq]


title: 4C_WT_for_f_del_B10_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B10_rep1 [QHR4C-seq]


title: 4C_F_GB1_rep1 [QHR4C-seq]


title: 4C_F_GB1_rep2 [QHR4C-seq]


title: 4C_F_GA3_rep2 [QHR4C-seq]


title: 4C_F_GA7_rep1 [QHR4C-seq]


title: 4C_F_B6_rep1 [QHR4C-seq]


title: 4C_F_B18_rep2 [QHR4C-seq]


title: 4C_F_B16_rep2 [QHR4C-seq]


title: 4C_F_B6_rep2 [QHR4C-seq]


title: 4C_F_B22_rep1 [QHR4C-seq]


title: 4C_F_B18_rep1 [QHR4C-seq]


title: 4C_F_B22_rep2 [QHR4C-seq]


title: 4C_F_B16_rep1 [QHR4C-seq]


title: 4C_F_B13_rep2 [QHR4C-seq]


title: 4C_WT_for_f_del_B13_rep1 [QHR4C-seq]


title: RNA_Whole_Brain_WT_rep1

value: HS7L_del -/-


title: RNA_Whole_Brain_WT_rep3


title: 4C_F_B10_rep2 [QHR4C-seq]


title: 4C_F_B13_rep1 [QHR4C-seq]


title: 4C_F_B10_rep1 [QHR4C-seq]


title: RNA_Whole_Brain_HS7L_del_rep6


title: RNA_Whole_Brain_WT_rep4


title: RNA_Whole_Brain_WT_rep2


title: 4C_F_GA3_rep1 [QHR4C-seq]


title: RNA_Whole_Brain_HS7L_del_rep4


title: RNA_Whole_Brain_HS7L_del_rep5


title: 4C_F_GA7_rep2 [QHR4C-seq]


title: RNA_Whole_Brain_HS7L_del_rep3


title: RNA_Whole_Brain_HS7L_del_rep2


title: RNA_Whole_Brain_HS7L_del_rep1


title: RNA_Olfactory_Bulb_WT_rep4


title: RNA_Olfactory_Bulb_WT_rep3


title: RNA_Olfactory_Bulb_HS7L_del_rep5


title: RNA_Olfactory_Bulb_WT_rep1


title: RNA_Olfactory_Bulb_HS7L_del_rep6


title: RNA_Olfactory_Bulb_HS7L_del_rep3


title: RNA_WT_for_fg_del_rep1


title: RNA_Olfactory_Bulb_WT_rep2


title: RNA_Olfactory_Bulb_HS7L_del_rep4


title: RNA_Olfactory_Bulb_HS7L_del_rep1


title: RNA_WT_for_fg_del_rep2


title: RNA_fg_del_rep4


title: RNA_Olfactory_Bulb_HS7L_del_rep2


title: RNA_fg_del_rep1


title: RNA_f_del_rep4


title: RNA_fg_del_rep3


title: RNA_WT_for_f_del_rep1


title: RNA_WT_for_f_del_rep2


title: RNA_WT_for_HS7L_del_rep2


title: RNA_f_del_rep2


title: RNA_f_del_rep3


title: RNA_fg_del_rep2


title: RNA_f_del_rep1


title: RNA_WT_for_HS7L_del_rep1


title: RNA_HS7L_del_rep3


title: RNA_HS7L_del_rep1


title: RNA_HS7L_del_rep2


title: P9_male_rep2


title: P9_female_rep1


title: P9_female_rep2


title: P9_male_rep1


title: P6_male_rep2


title: P6_male_rep1


title: P6_female_rep2


title: P3_male_rep2


title: P6_female_rep1


title: P3_female_rep1


title: P3_male_rep1


title: P21_male_rep2


title: P3_female_rep2


title: P21_female_rep2


title: RNA_HS7L_del_rep4


title: P21_female_rep1


title: P18_female_rep2


title: P15_male_rep2


title: P18_male_rep1


title: P18_female_rep1


title: P18_male_rep2


title: P15_male_rep1


title: P15_female_rep2


title: P12_female_rep2


title: P15_female_rep1


title: P12_male_rep2


title: P12_female_rep1


title: P0_male_rep1


title: P12_male_rep1


title: P0_male_rep2


title: P0_female_rep1


title: E18.5_RNA_rep3


title: E18.5_RNA_rep4


title: P0_female_rep2


title: E16.5_RNA_rep3


title: E16.5_RNA_rep4


title: E18.5_RNA_rep2


title: E18.5_RNA_rep1


title: E16.5_RNA_rep1


title: E14.5_RNA_rep3


title: E14.5_RNA_rep2


title: E16.5_RNA_rep2


title: E14.5_RNA_rep1


title: E12.5_RNA_rep2


title: E12.5_RNA_rep1


title: E12.5_RNA_rep3


title: E12.5_RNA_rep4


title: P21_male_rep1


title: E18-5-5

city: Hefei

first: LU

last: Qingshuang

address: 111 Kowloon Road

department: Institute of Physical Science and Information Technology

institute: Anhui University

data_processing:
Quality Control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq Alignment: format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment:Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis:In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Pregnant C57 mice with lung mesenchymal cell specific knockdown of Prmt5 were housed in a germ-free rat room at 60% humidity and 20℃ temperature

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Lung

value: Prmt5 knockdown


title: E18-5-8


title: E18-5-3


title: E18-5-10

value: WT


title: E18-5-9


title: E18-5-1


title: FXRKOUDCA-1

city: Beijing

first: Chunpan

last: Zhang

address: No. 95 Yong-An Road

institute: Beijing Friendship Hospital

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Assembly: mm8
Supplementary files format and content: Count values for each Sample

source_name: DNT cells

extract_protocol:
Preparing DNT cells by in vitro conversion of wild type mouse-derived CD4+ cells, then these converted DNT cells (CD3+NK1.1-CD4-CD8-) were sorted using FACS Aria II, and then stimulated with or without UDCA (60uM) for 2 days. And then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

tag: developmental stage

value: adult

value: UDCA stimulated


title: FXRKOcontrol-2

tag: treatment

value: Without UDCA stimulated


title: FXRKOcontrol-1

tag: strain


title: FXRKOUDCA-2


title: FXRKOUDCA-3


title: WTUDCA-3


title: WTUDCA-2


title: WTcontrol-3


title: WTcontrol-1


title: WTcontrol-2


title: FXRKOcontrol-3


title: run_2827_s_2_withindex_sequence.txt_(8h)CTTGGAA [Anomalous Q400]

city: St. Louis

first: Antonietta

last: Franco

state: MO

address: 1 Brookings Dr, St. Louis

department: Pharmacogenomics

institute: Washington Univeristy school of medicine in St. Louis

data_processing:
Partek Flow software was used to process data, trimmed base on quality score with default setting
RNA-seq reads were aligned to the mm10 -esembl Transcript relase_95 assembly with STAR
CPM (counts per million) were calculated by using Refseq as annotation mode and normalized by adding 0.0001 to CPM
Supplementary files format and content: mm10_esembl transcripts relase 95
Supplementary files format and content: text files including cpm for each samples

source_name: E18.5 Pups hearts

extract_protocol:
Total RNA from HEART TISSUE was isolated using TRIzol Reagent (Cat: 15596-026, Ambion RNA Life technologies) and treated with DNase I (Invitrogen, Cat: 18068015).
mRNA sequencing was performed using the RiboErase protocol, with indexing and pooled sequencing on a NovaSeq S4. Sequencing depth was 30M reads per sample.

value: E18.5 Pups hearts

value: tissue

value: Mfn2R400Q KNOCK-IN

value: Anomalous Q400


title: E14.5_RNA_rep4

value: cortex

value: cortex-neuron

value: neuron


title: run_2827_s_2_withindex_sequence.txt_(12h)GATAGTT [Q400]


title: run_2827_s_2_withindex_sequence.txt_(8c)AGACTGA [wt]

value: wt mouse

value: wt


title: run_2827_s_2_withindex_sequence.txt_(7h)TATCTTA [Anomalous Q400]


title: run_2827_s_2_withindex_sequence.txt_(5h)TTTTCGG [Q400]


title: run_2827_s_2_withindex_sequence.txt_(6c)CCAGGCA [wt]


title: run_2827_s_2_withindex_sequence.txt_(5c)AGGACCT [wt]


title: run_2827_s_2_withindex_sequence.txt_(7c)TTCGCTG [wt]


title: run_2827_s_2_withindex_sequence.txt_(4h)TCCGGGA [Q400]


title: run_2827_s_2_withindex_sequence.txt_(6h)TTTCAGA [Q400]


title: run_2827_s_2_withindex_sequence.txt_(3c)TGTGCCA [wt]


title: run_2827_s_2_withindex_sequence.txt_(2h)AAACCTT [Anomalous Q400]


title: run_2827_s_2_withindex_sequence.txt_(4c)CATTTAG [wt]


title: run_2827_s_2_withindex_sequence.txt_(1h)ACAGATA [Anomalous Q400]


title: run_2827_s_2_withindex_sequence.txt_(1c)GAGTACG [wt]


title: WTUDCA-1


title: run_2827_s_1_withindex_sequence.txt_(2c)TGCCCAT [wt]


title: run_2827_s_1_withindex_sequence.txt_(3h)AACGGAG [Q400]


title: neuron_wt_sac_rpf_rep1

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

data_processing:
Adapter trimming by Cutadapt.
Reads mapping by STAR to the transcriptome.
Reads calculation with RSEM.
Assembly: For [Dataset 1], mm10. For [Dataset 2], hg38.
Supplementary files format and content: posterior_mean_estimate.xlsx: For [Dataset 1] and [Dataset 2], Excel file with reads mapped to individual genes by RSEM algorithm.
Library strategy: Ribo-seq

source_name: cerebral hemispheres

growth_protocol: The human iPSC lines were reprogrammed from skin biopsy samples of three FXS male patients and three age-matched healthy males at Emory University. All iPSC lines were cultured on irradiated MEFs in human iPSC medium consisting of D-MEM/F12 (Invitrogen), 20% Knockout Serum Replacement (KSR, Invitrogen), 1X Glutamax (Invitrogen), 1X MEM Non-essential Amino Acids (Invitrogen), 100 µM β-Mercaptoethanol (Invitrogen), and 10 ng/ml human basic FGF (PeproTech). Forebrain-specific organoids were generated using established protocols as previously described. Briefly, human iPSC colonies were detached from the MEF feeder layer with 1 mg/ml collagenase treatment for 1 hour and suspended in embryonic body (EB) medium, consisting of FGF-2-free iPSC medium supplemented with 2 µM Dorsomorphin and 2 µM A-83 in non-treated polystyrene plates for 4 days with a daily medium change. On days 5-6, half of the medium was replaced with induction medium consisting of DMEM/F12, 1X N2 Supplement (Invitrogen), 10 μg/ml Heparin (MilliporeSigma), 1X Penicillin/Streptomycin, 1X Non-essential Amino Acids, 1X Glutamax, 4 ng/ml WNT-3A (R&D Systems), 1 μM CHIR99021 (Tocris), and 1 μM SB-431542 (Tocris). On day 7, organoids were embedded in Matrigel (BD Biosciences) and continued to grow in induction medium for 6 more days. On day 14, embedded organoids were mechanically dissociated from Matrigel by pipetting up and down onto the plate with a 5 ml pipette tip. Typically, 10-20 organoids were transferred to each well of a 12-well spinning bioreactor (SpinΩ) containing differentiation medium, consisting of DMEM/F12, 1X N2 and B27 Supplements (Invitrogen), 1X Penicillin/Streptomycin, 100 µM β-Mercaptoethanol (Invitrogen), 1X MEM NEAA, 2.5 μg/ml Insulin (MilliporeSigma). All media was changed every other day.

extract_protocol:
For [Dataset 1] and [Dataset 2], CHX (cycloheximide, Milliporesigma C7698-1G) was added to a final concentration of 100 μg/ml to the medium and incubated for 7 minutes. Then spin down the cells, wash once with cold DPBS with 100 μg/ml CHX and spin down again, flash-freeze with LN2 and store at -80C. RPFs were prepared according to the manufacturer's instructions with riboLace kit (IMMAGINA, RL001). Total RNAs were extracted with standard TRIzol protocol.
For [Dataset 1] and [Dataset 2], RNA libraries for input samples were constructed by SMARTer Stranded Total RNA-Seq Kit v2 (TaKaRa, 634417) with total RNA as input. RNA libraries for RPFs were constructed with NEBNext® Small RNA Library Prep Set for Illumina® (NEB, E7330L) with end-repaired RPFs extracted as inputs.

treatment_protocol:
For [Dataset 1], KCl depolarization was performed as follows: Replace half medium with fresh medium+100 mM KCl (to make final 50 mM). After ten minutes, replace half medium for 3 times. After two hours, harvest cells. SAC incubation was performed as follows: (SAC) at 20 μM for 24 hours.
For [Dataset 2], SAC incubation was performed as follows: (SAC) at 20 μM from day 49 to 56.

value: cerebral hemispheres

value: cortical neurons

value: 20 uM SAC


title: neuron_wt_sac_mRNA_rep1

description:
input_wt_sac_r1
RiboMinus RNA

data_processing:
Adapter trimming by Cutadapt.
Reads mapping by STAR to the transcriptome.
Reads calculation with RSEM.
Assembly: For [Dataset 1], mm10. For [Dataset 2], hg38.
Supplementary files format and content: posterior_mean_estimate.xlsx: For [Dataset 1] and [Dataset 2], Excel file with reads mapped to individual genes by RSEM algorithm.

value: WT


title: neuron_wt_sac_mRNA_rep2

description:
input_wt_sac_r2
RiboMinus RNA


title: run_2827_s_2_withindex_sequence.txt_(10h)CTCAATG [Anomalous Q400]


title: neuron_wt_dmso_mRNA_rep1

description:
input_wt_dmso_r1
RiboMinus RNA

value: DMSO


title: neuron_wt_dmso_rpf_rep1


title: neuron_ko_sac_rpf_rep1


title: neuron_ko_sac_rpf_rep2


title: neuron_ko_sac_mRNA_rep1

description:
input_ko_sac_r1
RiboMinus RNA


title: run_2827_s_1_withindex_sequence.txt_(11h)ACCATAC [Q400]


title: neuron_ko_sac_mRNA_rep2

description:
input_ko_sac_r2
RiboMinus RNA


title: neuron_ko_dmso_rpf_rep1


title: neuron_ko_dmso_mRNA_rep1

description:
input_ko_dmso_r1
RiboMinus RNA


title: ATAC_f

data_processing:
For ATAC-seq and ATAC-seq data, paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. Macs1.4 was then used to call peaks and generate .wig files.
Assembly: M. musculus, UCSC mm9
Supplementary files format and content: bigwig files suitable for viewing on UCSC

extract_protocol:
cortex was dissected and digested with 0.00625% collagenase followed by filtering using a 100μm cell strainer to prepare single neuron resuspension. Cells were washed twice with PBS solution and then counted.
For each reaction, 10^5 neurons were used and resuspended in 50μl RSB buffer containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin in EP tube for lysis by incubating on ice for 3 minutes. After lysis the product was washed with 1ml RSB buffer containing 0.1% Tween-20 and was centrifuged 800rpm at 4℃. Supernatant was discarded and nuclei were resuspended for transposition mixture containing 25μl 2× TD buffer, 3μl transposase, 16μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween-20 and 5μl H2O. Transposition reactions were performed by incubating at 37 ℃ for 30 min in a thermo shaker at 1000 rpm. Transposition products were immediately cleaned up with 1× Ampure XP Beads (Beckman) and the purified DNA were then prepared into library using TruePrep DNA Library Prep kit for Illumina (Vazyme) according to the manufacturer’s instructions. The ATAC-seq libraries were then pooled and finally sequenced using an Illumina Novaseq6000 platform.

value: F del -/-


title: neuron_ko_dmso_mRNA_rep2

description:
input_ko_dmso_r2
RiboMinus RNA


title: ATAC_WT_rep2

value: wildtype


title: ATAC_fg

value: FG del -/-


title: D8-WT1

city: BEIJING

first: HAO

last: wenyan

department: School of Basic Medical Sciences

institute: Peking University Health Science Center

data_processing:
Illumina Casava2.19 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 hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>].
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell, Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample.

source_name: kidney

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: kidney

value: wild type

value: glyoxylate


title: D8-WT8


title: D5_4

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample


title: ATAC_WT_rep1


title: D8-HET5

value: Vhl mutant


title: D8-HET2-1


title: neuron_wt_sac_rpf_rep2


title: D5_3


title: neuron_wt_dmso_mRNA_rep2

description:
input_wt_dmso_r2
RiboMinus RNA


title: UT3

value: control (saline)


title: UT2


title: neuron_wt_dmso_rpf_rep2


title: Brd9_KO_HSPC

data_processing:
Gene counts were generated by running cellranger count (6.0.2) with mm10-2020A as the transcriptome dataset.
Assembly: mm10
Supplementary files format and content: tsv

source_name: Lineage- cKit+ bone marrow cells in femora and tibiae

extract_protocol:
RNA was extracted using RNeasy columns (Qiagen) per manufacturer’s instructions.
RNA was poly(A)-selected, and unstranded Illumina libraries were prepared with the standard TruSeq protocol

tag: donor genotype

value: CD45.2(+) Mx1-Cre Brd9fl/fl

value: Eight weeks after pIpC injection


title: pIpC_3

data_processing:
RNA-seq rawdata was cleaned by FastP(PE mode) and aligned to GRCm38 by Hisat2(2.2.1)
Data were  filtered using Samtools and converted to BAM files
Read counted by FeatureCount from Subreads Packages(R)
Counts data was normalized by edgeR and used for GSEA analysis
Assembly: GRCm38
Supplementary files format and content: raw gene counts

source_name: GFP+ bone marrow cells in femora and tibiae

treatment_protocol: The next day after BMT, the recipient mice received 20 mg/kg pIpC or PBS injection every other day for a total of 3 doses.

value: CD45.2(+) Mx1-Cre Brd9fl/fl MA9

tag: recipient genotype

value: 10 days after pIpC injection


title: pIpC_2

tag: timing of preparation


title: pIpC_1


title: PBS_1

value: 10 days after PBS injection


title: PBS_2


title: PBS_3


title: Ctrl_MA9_ATAC

data_processing:
rawData Fastq Data passed FastQC then was merged and removed sequencing adapters under NGmerge(paired-end)
aligning the reads to reference genome(mm10) under Bowtie2
Peak Calling under Genrich with Removal of mitochondrial reads and PCR duplicates together.
Deeptools convert BAM files to IGV visualizable bigwig files.
HOMER is used for motif discovery
Assembly: mm10
Supplementary files format and content: bigwig

value: CD45.2(+) Mx1-Cre Brd9fl/fl MLL-AF9


title: KO_MA9_ATAC


title: WT_input_PFA

data_processing:
The adapter sequences were removed from the FASTQs using Trimmomatic (0.39).
The cleaned FASTQs were aligned using Bowtie2 (2.4.4) to the mouse reference genome mm10.
The duplicated reads were removed using picard (2.26.2) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
cells were fixed with 1% paraformaldehyde for 10 min at room temperature.Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4°C. Cells were pelleted, and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4°C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated.Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 ml of 10% Triton X-100 and 30 ml of 5M NaCl were added. The sample was then incubated with 20 ml of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4°C. Primary antibodies were added to each tube and immunoprecipitation (IP) was conducted overnight in the cold room. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4°C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4°C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4°C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65°C. RNA and protein were digested with 0.2 mg/ml RNase A for 30 min at 37C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

value: CD45.2(+) Brd9fl/fl

value: 5 months after pIpC injection

tag: chip antibody


title: WT_H3K4me1

value: Anti-Histone H3  (mono methyl K4) antibody (Abcam, ab8895)


title: WT_H3K27Ac

value: Anti-Histone H3 (acetyl K27) antibody (Abcam, ab4729)


title: KO_H3K4me3

value: Anti-Histone H3  (tri methyl K4) antibody (Abcam, ab8580)


title: KO_H3K27Ac


title: Brd9_KO_03

data_processing:
Raw FASTQs were processed using nf-core/rnaseq (3.0).
Assembly: mm10
Supplementary files format and content: txt


title: Brd9_KO_01


title: Brd9_Cont_03


title: KO_H3K4me1


title: Brd9_KO_02


title: Brd9_Cont_02


title: WT_HSPC


title: WT_H3K4me3


title: neuron_ko_dmso_rpf_rep2

value: cerebral hemispheres

value: cortical neurons

value: DMSO


title: Brd9_Cont_01


title: Brain-scRNAseq

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

description: Young

data_processing:
Ror RNAseq data, alignment to the Ensembl reference genome mm9 was performed using the Tophat and bowtie2. Alignment files were sorted using SAMtools v.1.10.2. Count tables were generated using HTSeq-0.6.1.
ATAC-seq data were aligned using Bowtie2 and removed PCR duplicates using Picard. We called Peaks using MACS2. Peaks from the biological replicates were merged using Samtools and Bedtools.
For scRNAseq, the Cell Ranger Software (version 1.2.0) was used to perform the first preprocessing step. ‘cellranger count’ was used to performing read filtering, alignment, and count matrix generation from fastq files per sample. The reads were aligned to the mm10 (refdata-gex-mm10-2020-A) reference genome provided by 10xGenomics. The gene-barcode matrix was generated using only confidently mapped reads with valid barcodes and unique molecular identifiers
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: txt file include count and peak signal for each sample;txt file  include  barcode and gene count.

source_name: Endothelial cells

extract_protocol:
Mice were deeply anaesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). After perfusion, whole brain, lung and liver were immersed in ice-cold PBS, which were minced with a razor blade and disaggregated in Type IV collagenase (400 U/ml, Worthington,Lakewood, NJ), Dispase (1.2 U/ml, Worthington, Lakewood, NJ) and DNase I (32 U/ml, Worthington, Lakewood, NJ) in 6 mL 1× PBS with Ca2+ and Mg2+ (GIBCO) at 37 °C for 60 min, with gentle trituration every 10 min. After adequate disaggregation, 1 ml of FBS was added to the disaggregation reaction then the disaggregated cells were washed with 1× ice-cold PBS and filtered through a 40-μm mesh. After centrifugation at 400g for 5 min, cell pellets were resuspended in 10 ml 20% BSA and centrifuged at 1,000 g at 4 °C for 25 min to remove the myelin (only for brain).   The pellets were then resuspended in 1× PBS/3% FBS/0.1% NaN3/2 mM EDTA and blocked with rat anti-mouse CD16/32 (Mouse BD Fc Block, BD Pharmingen) for 10 min on ice. Endothelial cells were labeled with PE-Cyanine7 rat anti-mouse CD31 (cat. # 25-0311-82, eBiosciences, CA), and pericytes were labeled with APC rat anti-mouse PDGFRβ (cat. #17-1402-82, eBiosciences, CA). PE rat anti-mouse CD45 (cat. #516087, BD Pharmingen, CA) and 7-AAD (Invitrogen) were added to exclude hematopoietic lineage cells and dead cells. Staining was done for 1 h at 4 °C. Cells were washed and PE-cyanine7-CD31+/APC-PDGFRβ−/PE-CD45−/7-AAD− cells were sorted into EGM-2/MV medium (cat. #CC3202, Clontech, Mountain View, CA) with an Aria III sorter (BD). ECs were centrifuged at 2,000 g at 4 °C for 10 min and resuspended in Trizol (Life Technologies) or extraction buffer for RNA , DNA, protein extraction.
RNAseq:RNA-seq was performed as we previously reported (PMID:28288111). The RNA-seq data were generated from EC cells after FACS purification. Each RNA-seq analysis was conducted on three biological replicates. ECs total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). In brief, mRNA was first enriched from total RNA by poly-A. Oligo-dT-directed reverse transcription generated complementary DNAs corresponding to the 3′end of poly-A transcripts; the complementary DNA was amplified by PCR using the Ovation 3′-DGE System kit (NuGen Technologies, San Carlos, CA). Amplified cDNA was sheared using a Covaris ultrasonicator and then libraries were prepared using the Ovation SP + Ultralow DR Multiplex System (NuGen Technologies, San Carlos, CA). Deep sequencing was then performed on the Illumina Hiseq-2500 platform (Illumina, Hayward, CA) in single-end 50 bp format.  ATAC-seq:Briefly, ECs were lysed in cold lysis buffer (10 mM Tris-HCl, Ph7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal) and tagmentation performed using Illumina Nextera DNA kit (FC-121-1030) for 30 min at 37 °C on a shaking thermomixer. Tagmented DNA was purified using Qiagen MinElute kit (Cat no. 28004) and amplified using NEB Next High-Fidelity 2X PCR Mast Mix (Cat no. M0543S) for 11 cycles as follows: 72 °C, 5 min; 98 °C, 30 s; 98 °C, 10 s; 63 °C, 30 s; 72 °C, 1 min. Library preparation was complete after further clean up using Qiagen PCR MinElute kit (Cat no. 28004) and Beckman Coulter XP AMPpure beads (A63880). Tagmentation size was assessed using Agilent 2100 Bioanalyser. Libraries were quantified with Qubit 2.0 (Life Technologies) and sequenced using paired-end 150 bp reads on the Illumina HiSeq4000 platform at XX. Three biological replicates were used for analysis.scRNAseq:Single-cell RNA-seq libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kit 3.1(10X Genomics, US). Briefly, Brain ECs (1~2 x105) were isolated by FCAS from young, middle and aged mice (n=2 each group). Single-cell suspension at a density of 500-1000 cells/µL in FACS buffer was added to 10X Genomics GefmCode Single-cell instrument that generateed single-cell Gel Bead-In-EMlusion (GEMs). RNA transcripts from single cells were uniquely barcoded (16 nt) and reverse-transcribed within droplets. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. All libraries were quantified by using High Sensitivity DNA assay Kit (Agilent, US). All single-cell libraries were sequenced on a Novaseq 6000 system (Illumina, US).

value: brain

value: Endothelial cells

value: 2-4 months


title: KO_input_PFA

value: CD45.2(+) Mx1-Cre Brd9fl/fl


title: malignant_PCa_tissue_patient7

type: RNA

city: Exeter

first: Zhuofan

last: Mou

address: Heavitree Road

department: Department of Clinical and Biomedical Sciences

institute: University of Exeter

hyb_protocol: Following fragmentation (Encore Biotin Kit), cDNAs were hybridized for 18 hr at 45C on Thermofisher Human Clariom D Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 430 according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 7G scanner according to the manufacturer's instructions.

data_processing: Raw data were imported from CEL files and analysed in the R programming language using the 'oligo' package. The parameter 'target=core' was set, and the Robust Multichip Average (RMA) algorithm was applied. This process included steps of background correction, normalization, and expression calculation, with results converted to a log2 scale.

label: biotin

organism: Homo sapiens

source_name: malignant prostate cancer tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen WT Pico kit in combinations with the Nugen Encore Biotin kit according to the manufacturer's instructions.

extract_protocol: RNA was extracted using the Qiagen blood mini kit (Hilden, Germany), adapted by the use of a Qiashredder column (Hilden, Germany) on the Qiacube platform (Hilden, Germany). RNA concentration and integrity were assessed using the Agilent Bioanalyser 2100 platform (Agilent, Santa Clara, CA, USA).

tag: Sex

value: Male

tag: tnm

tag: gleason

tag: smoking status

value: No

tag: family history


title: malignant_PCa_tissue_patient9

tag: age

value: Yes

value: Father with breast cancer


title: benign_tissue_patient17

source_name: benign prostate tissue

value: Former smoker (6 weeks ago)

value: Strong family history of bowel cancer


title: benign_tissue_patient15

value: Father with prostate cancer


title: benign_tissue_patient12

value: Former smoker (17 years ago)


title: malignant_PCa_tissue_patient10


title: malignant_PCa_tissue_patient15


title: Biological rep 1 Dox-induced MIO-M1-CTG(648)

city: Mexico City

first: Oscar

last: Hernández-Hernández

state: Mexico City

address: Calz. México Xochimilco 289

department: Genetics

country: Mexico

institute: Instituto Nacional de Rehabilitación

description: Mutant cells Dox-induced

hyb_protocol: The hybridization, wash and stain kit (Affymetrix) was used. GeneChip Hybridation Oven 645 and GeneChip Fluidics Station 450 were used.

scan_protocol: GeneChip Scanner 3000 7G

data_processing:
The raw intensity values were background corrected and normalized using Robust Multiarray Average (RMA) method and Quantile Normalization, respectively
probe group file: Clariom_D_Human.na36.hg38.probeset.csv
meta-probeset file: Clariom_D_Human.na36.hg38.probeset.csv

source_name: Dox-induced MIO-M1-CTG(648)

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were grown in presence of Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen, Carlsbad, CA, USA), supplemented with 10% tetracycline free fetal bovine serum, 100 U/ml penicillin and 100 μg/ml streptomycin, 350 μg/ml G418 and 0.35 μg/ml puromycin. Cultures were maintained at 37°C in a 5% humidified CO2 atmosphere.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Valencia, CA, USA) and RNase-Free DNase Set, according to the manufacturer’s protocol. The RNA concentration was determined using a NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and the RNA integrity number (RIN) was determined in an Agilent 2100 Bioanalyzer.

treatment_protocol: MIO-M1-CTG(0) and MIO-M1-CTG(648) cells were cultured in absence (-Dox) or presence (+Dox) of doxycycline (1 μg/ml) during 8 days, replacing culture medium every 48 hours. For each of the four experimental groups, 3 biological replicates were used.

tag: cell line background

tag: genotype/variation

value: Dox-induced MIO-M1-CTG(648)

value: doxycycline (1 μg/ml)

tag: days of dox treatment


title: benign_tissue_patient14


title: malignant_PCa_tissue_patient14


title: Biological rep 3 Dox-induced MIO-M1-CTG(0)

description: Control cells Dox-induced

source_name: Dox-induced MIO-M1-CTG(0)

value: Dox-induced MIO-M1-CTG(0)


title: Biological rep 2 Dox-induced MIO-M1-CTG(648)

description: Mutant cells Dox-induced


title: Biological rep 2 non-induced MIO-M1-CTG(648)

description: Mutant cells non-induced

source_name: non-induced MIO-M1-CTG(648)

value: non-induced MIO-M1-CTG(648)


title: Biological rep 2 non-induced MIO-M1-CTG(0)

description: Control cells non-induced

source_name: non-induced MIO-M1-CTG(0)

value: non-induced MIO-M1-CTG(0)


title: benign_tissue_patient9


title: Cochlear ZB20_KO rep4

city: Shanghai

first: zhifang

last: xie

address: 1665 Kongjiang Road

department: Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
Single end 50 bases reads were generated on DNBSEQ platform (BGI-Shenzhen, China)
The sequencing data was filtered with SOAPnuke(V1.5.2) by removing reads containing adaptors, removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%, removing reads whose unknown base ratio is more than 5%.
The clean reads were aligned to the reference genome using HISAT2 (v2.0.4) and aligned to reference coding gene set using Bowtie2 (v2.2.5), then expression levels of gene was calculated by RSEM (v1.2.12).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include read counts and FPKM values for each Sample

source_name: cochleae

extract_protocol:
Total RNA was extracted from cochleae using Trizol combined with Qiagen RNeasy Micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: cochleae

value: postnatal day 10

tag: genotype

value: Zbtb20 F/F,FoxG1-cre


title: Biological rep 1 non-induced MIO-M1-CTG(0)

description: Control cells non-induced


title: malignant_PCa_tissue_patient13


title: Cochlear ZB20_KO rep3

data_processing:
Single end 50 bases reads were generated on DNBSEQ platform (BGI-Shenzhen, China)
The sequencing data was filtered with SOAPnuke(V1.5.2) by removing reads containing adaptors, removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%, removing reads whose unknown base ratio is more than 5%.
The clean reads were aligned to the reference genome using HISAT2 (v2.0.4) and aligned to reference coding gene set using Bowtie2 (v2.2.5), then expression levels of gene was calculated by RSEM (v1.2.12).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

value: Zbtb20 F/F,FoxG3-cre


title: Biological rep 1 Dox-induced MIO-M1-CTG(0)

description: Control cells Dox-induced

tag: treatment


title: benign_tissue_patient13

value: Male


title: Biological rep 3 non-induced MIO-M1-CTG(0)

description: Control cells non-induced


title: Biological rep 1 non-induced MIO-M1-CTG(648)

description: Mutant cells non-induced


title: Cochlear ZB20_KO rep2

tag: strain

value: Zbtb20 F/F,FoxG2-cre


title: benign_tissue_patient10

value: No


title: malignant_PCa_tissue_patient12


title: Biological rep 3 non-induced MIO-M1-CTG(648)

description: Mutant cells non-induced


title: Biological rep 2 Dox-induced MIO-M1-CTG(0)

description: Control cells Dox-induced


title: malignant_PCa_tissue_patient8


title: Biological rep 3 Dox-induced MIO-M1-CTG(648)

description: Mutant cells Dox-induced


title: Cochlear WT rep2

value: Zbtb20 +/+,FoxG2-cre


title: benign_tissue_patient7


title: Cochlear ZB20_KO rep1


title: PFB_DRK7024_S_biol rep3

city: Toulouse

first: Anis

last: Djari

address: 6 All. Emile Monso

country: France

institute: INPT

data_processing:
raw reads were trimmed with trimgalore
trimmed reads were mapped using STAR
raw read count was made using featurecounts
Assembly: SLYMIC v1.0 - Solanum lycopersicum - Micro-Tom cultivar https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_012431665.1/
Supplementary files format and content: tab-delimited text includes raw count for per sample

organism: Solanum lycopersicum

source_name: Floral bud pollen stage

growth_protocol: Plant material consisted in of five different tomato (Solanum lycopersicum) cultivars: Clodano (Syngenta™),  DRK7024 (De Ruiter™), JAG8810 (Bayer™), M82 and West Virginia 106 (WVA106). In NS conditions, plants were cultivated in a greenhouse with a photoperiod of 16h/8h with a mean temperature of 24°C during the day and a mean temperature of 18°C during the night.

extract_protocol:
5-10 floral buds for each stage were sampled before and 20 days after the start of the heat stress from 20-25 plants per genotype for the RNAseq analysis (Figure S1B). Total RNAs were isolated from 200 and 500 mg of floral buds at different developmental stages using TRIzol Reagent (Life Technologies). Total RNA extract was purified with the Qiagen RNAeasy mini kit RNA. After DNase treatment (DNA-free Kit, Life Technologies), the total RNA quantity and quality (RNA integrity number, RIN) were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA extracts with a RIN of 10 were used for sequencing.
The RNA libraries were constructed as described in the Illumina TruSeq Stranded mRNA guide. mRNAs were sequenced in a HiSeq 3000 sequencing system with 2 × 125 bp paired-end sequences (Illumina HiSeq SBS Kit v4) by the Genotoul bioinformatics platform, Toulouse (http://bioinfo.genotoul.fr/index.php).

treatment_protocol: For heat-stress treatments, the plants at bolting stage have been submitted during 3 weeks to a mean temperature of 35°C during the day (16h) and 25°C during the night (8h) using the main and two auxiliary heaters and the temperature has been monitored all along the HS. In both conditions, the hygrometry was around 55% all day and plants had a daily watering.

value: Floral bud pollen stage

value: Stressed

tag: replicate

value: biol rep3


title: PFB_Clodano_S_biol rep3

value: Clodano


title: Cochlear WT rep3

value: Zbtb20 +/+,FoxG3-cre


title: benign_tissue_patient8


title: malignant_PCa_tissue_patient17

value: Former smoker (6 weeks ago)

value: Strong family history of bowel cancer


title: PFB_DRK7024_NS_biol rep3

value: Non-stressed


title: PFB_JAG8810_S_biol rep3


title: PFB_Clodano_NS_biol rep3


title: PFB_JAG8810_NS_biol rep3


title: PFB_M82_NS_biol rep3


title: TFP_DRK7024_S_biol rep3

source_name: Floral bud tetrad stage

value: Floral bud tetrad stage


title: PFB_WVA106_NS_biol rep3


title: PFB_M82_S_biol rep3


title: TFP_Clodano_S_biol rep3


title: TFP_M82_S_biol rep3


title: TFP_JAG8810_S_biol rep3


title: TFP_WVA106_S_biol rep3


title: TFP_DRK7024_NS_biol rep3


title: Cochlear ZB20_KO rep5

value: cochleae


title: PFB_WVA106_S_biol rep3


title: TFP_JAG8810_NS_biol rep3


title: PFB_Clodano_S_biol rep2

value: biol rep2


title: PFB_M82_S_biol rep2


title: PFB_DRK7024_S_biol rep2


title: PFB_DRK7024_NS_biol rep2


title: TFP_WVA106_NS_biol rep3


title: PFB_JAG8810_S_biol rep2


title: PFB_Clodano_NS_biol rep2


title: TFP_DRK7024_S_biol rep2


title: PFB_WVA106_NS_biol rep2


title: PFB_M82_NS_biol rep2


title: PFB_WVA106_S_biol rep2


title: PFB_JAG8810_NS_biol rep2


title: TFP_M82_S_biol rep2


title: TFP_JAG8810_S_biol rep2


title: TFP_Clodano_NS_biol rep3


title: TFP_M82_NS_biol rep3


title: TFP_Clodano_NS_biol rep2


title: TFP_DRK7024_NS_biol rep2


title: TFP_M82_NS_biol rep2


title: Cochlear WT rep1

value: postnatal day 10

value: Zbtb20 +/+,FoxG1-cre


title: TFP_WVA106_NS_biol rep2


title: PFB_Clodano_S_biol rep1

value: biol rep1


title: PFB_M82_S_biol rep1


title: Cochlear WT rep5


title: PFB_DRK7024_S_biol rep1


title: PFB_JAG8810_S_biol rep1


title: TFP_Clodano_S_biol rep2


title: PFB_DRK7024_NS_biol rep1


title: PFB_WVA106_S_biol rep1


title: PFB_M82_NS_biol rep1


title: TFP_WVA106_S_biol rep2


title: PFB_JAG8810_NS_biol rep1


title: TFP_DRK7024_S_biol rep1


title: PFB_Clodano_NS_biol rep1


title: PFB_WVA106_NS_biol rep1


title: TFP_JAG8810_S_biol rep1


title: TFP_M82_S_biol rep1


title: TFP_Clodano_S_biol rep1


title: TFP_M82_NS_biol rep1


title: TFP_WVA106_S_biol rep1


title: Cochlear WT rep4


title: TFP_DRK7024_NS_biol rep1


title: TFP_JAG8810_NS_biol rep1


title: TFP_JAG8810_NS_biol rep2


title: TFP_Clodano_NS_biol rep1


title: hiPSC-derived NPC, Fast, Day7, Rep3, ID77

city: Stanford

first: Sarah

middle: Christine

last: Heilshorn

address: 476 Lomita Mall

department: Materials Science and Engineering

institute: Stanford University

data_processing:
All data processing was performed by Lexogen through their 'Gene Expression Profiling' sequencing and data analysis service. The full pipeline is available here: https://github.com/Lexogen-Tools/quantseqpool_analysis
10N long unique molecular identifier sequences were extracted with umi_tools (v1.01) and reads were trimmed with Cutadapt (v2.5) to remove artifacts and adapter sequences. Reads which result in a length <20 or consist entirely of adapter sequences are removed.
Trimmed sequences were mapped to a human reference transcriptome (Ensembl GRCh38.93) with STAR Aligner (2.7.5a).
Reads with identical mapping coordinates and UMI sequences were collpased, MultiQC of the resultant alignment was performed, and featureCounts (subread v1.6.4) was used to generate a gene abundance file.
Assembly: hg38
Supplementary files format and content: Data table containing number of molecules per gene per sample

source_name: Induced pluripotent stem cells

growth_protocol: hiPSCs were differentiated with dual SMAD inhibition into NPCs.

extract_protocol:
RNA was extracted by Lexogen with the SPLIT RNA Extraction Kit (Lexogen) with prior gel dissociation with a MiniG Automated Tissue Homogenizer (1400 RPM). At least 300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared by Lexogen with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen).

treatment_protocol: NPCs were encapsulated into three protein enginereed biomaterials with distinct stress relaxation profiles.

value: Induced pluripotent stem cells

tag: cell line

tag: cell type

value: Neural progenitor cell

value: WT

value: Fast

tag: time

value: Day 7


title: hiPSC-derived NPC, Fast, Day7, Rep1, ID75


title: hiPSC-derived NPC, Fast, Day7, Rep2, ID76


title: hiPSC-derived NPC, Slow, Day7, Rep3, ID74

value: Slow


title: TFP_WVA106_NS_biol rep1


title: hiPSC-derived NPC, Slow, Day7, Rep1, ID72


title: hiPSC-derived NPC, Static, Day7, Rep3, ID71

value: Static


title: hiPSC-derived NPC, Static, Day7, Rep2, ID70


title: hiPSC-derived NPC, Fast, Day0, Rep2, ID58

value: Day 0


title: hiPSC-derived NPC, Fast, Day0, Rep3, ID59


title: hiPSC-derived NPC, Fast, Day0, Rep1, ID57


title: hiPSC-derived NPC, Static, Day0, Rep2, ID52


title: hiPSC-derived NPC, Slow, Day0, Rep1, ID54


title: hiPSC-derived NPC, Slow, Day0, Rep2, ID55


title: hiPSC-derived NPC, Static, Day0, Rep3, ID53


title: hiPSC-derived NPC, Slow, Day0, Rep3, ID56


title: hiPSC-derived NPC, Slow, Day7, Rep2, ID73


title: hiPSC-derived NPC, Static, Day0, Rep1, ID51


title: hiPSC-derived NPC, Static, Day7, Rep1, ID69


title: D melanogaster, M luteus injected, 3 hours, biol rep 5

city: London

first: Marc

last: Dionne

address: Level 0, Flowers Building

department: Life Sciences

institute: Imperial College London

description: Libraries were sequenced on an Illumina NextSeq 500 using v1 chemistry.

data_processing:
Reads were assigned to transcripts (Flybase Dmel 6.33) using Kallisto 0.46.1
Transcript assignments were converted to genes and differentially expressed genes were identified using Sleuth
Assembly: FlyBase release 6.33
Supplementary files format and content: wt_gene-level_TPMs_6.33.csv is a csv showing TPM (transcripts per million) values for each gene in each sample, generated using Kallisto and Sleuth. Genes are listed with two identifiers, a gene name and a FlyBase identifier (FBGn).

organism: Drosophila melanogaster

source_name: whole male Drosophila melanogaster

growth_protocol: Drosophila melanogaster were kept on 10% yeast, 8% fructose, 2% polenta, 0.8% agar, supplemented with nipagin and propionic acid. Bacteria were cultured in LB.

extract_protocol:
Trizol (Life Technologies) was used according to the manufacturer's instructions.
Libraries were prepared using Illumina TruSeq Stranded mRNA v2, with the following changes from the manufacturer’s protocol: starting samples were 250ng total RNA; fragmentation was performed for 10 minutes at 94°; no spike-ins were used; and 14 cycles of PCR were used to enrich libraries.

treatment_protocol: Bacteria were injected as suspensions in PBS at OD600=1. Flies were then kept at 29° for 3 hours before being homogenized in TRIzol for RNA extraction.

value: whole male Drosophila melanogaster


title: D melanogaster, M luteus injected, 3 hours, biol rep 3


title: D melanogaster, M luteus injected, 3 hours, biol rep 4


title: D melanogaster, M luteus injected, 3 hours, biol rep 1


title: D melanogaster, E coli injected, 3 hours, biol rep 5


title: D melanogaster, E coli injected, 3 hours, biol rep 4


title: D melanogaster, E coli injected, 3 hours, biol rep 3


title: Untreated moDC  Rep2

first: Chrysanthi

last: Ainali

address: Strand, London WC2R 2LS, UK

institute: King's College London

description:
moDC Rep2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Human blood

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

extract_protocol: Cell populations were sorted as indicated and flash-frozen as cell pellet. RNA was then extracted using Macherey-Nagel NucleoSpin RNA XS kit, in accordance with the manufacturer's protocol provided. Quality control was performed with Agilent Bioanalyzer.

value: Blood

value: dendritic cell

tag: cell population

value: moDC


title: CD141+ Dermal DC Rep3

description:
CD141+ DDC Rep3
replicate 3

source_name: Human Skin

value: Skin

value: CD141+ DDC


title: D melanogaster, E coli injected, 3 hours, biol rep 2


title: CD141High sorted from VitD3-treated moDC  Rep1

description:
CD141-High Rep1
replicate 1


title: Untreated moDC  Rep3

description:
moDC Rep3
replicate 3


title: CD1c+ Dermal DC Rep2

description:
CD1c+ DDC Rep2
replicate 2

value: CD1c+ DDC


title: CD1c+ Dermal DC Rep1

description:
CD1c+ DDC Rep1
replicate 1


title: CD141+ Dermal DC Rep2

description:
CD141+ DDC Rep2
replicate 2


title: CD141Low sorted from VitD3-treated moDC  Rep2

description:
CD141-Low Rep2
replicate 2


title: CD141Low sorted from VitD3-treated moDC  Rep1

description:
CD141-Low Rep1
replicate 1


title: CD1c+ Dermal DC Rep3

description:
CD1c+ DDC Rep3
replicate 3


title: CD141High sorted from VitD3-treated moDC  Rep3

description:
CD141-High Rep3
replicate 3


title: Untreated moDC  Rep1

description:
moDC Rep1
replicate 1


title: CD141Low sorted from VitD3-treated moDC  Rep3

description:
CD141-Low Rep3
replicate 3


title: CD141High sorted from VitD3-treated moDC  Rep2

description:
CD141-High Rep2
replicate 2


title: CD141+ Dermal DC Rep1

description:
CD141+ DDC Rep1
replicate 1


title: D melanogaster, PBS-injected, 3 hours, biol rep 4


title: D melanogaster, PBS-injected, 3 hours, biol rep 5


title: D melanogaster, E coli injected, 3 hours, biol rep 1


title: D melanogaster, PBS-injected, 3 hours, biol rep 3


title: D melanogaster, M luteus injected, 3 hours, biol rep 2


title: D melanogaster, PBS-injected, 3 hours, biol rep 1


title: D melanogaster, PBS-injected, 3 hours, biol rep 2


title: D melanogaster, uninjected, 3 hours, biol rep 3


title: D melanogaster, uninjected, 3 hours, biol rep 2


title: D melanogaster, uninjected, 3 hours, biol rep 4


title: D melanogaster, uninjected, 3 hours, biol rep 5


title: D melanogaster, uninjected, 3 hours, biol rep 1


title: Ripk1_KO aTreg

first: Xiaoxue

last: Deng

address: 320 Yueyang Road, Shanghai, China

institute: University of Chinese Academy of Sciences

description:
counts.txt
vst_table.txt

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCm38 using  hisat2(v2.2.1)
Gene expression was quantified with featureCounts (v 2.0.1)
Supplementary files format and content: GrCm38
Supplementary files format and content: tab-delimited text files include raw oounts values and variance stabilizing transformation normalized values for each Sample

source_name: spleen and lymph nodes

extract_protocol:
RNA was harvested using TRIZOL reagent (Life technologies). 300 to 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: spleen and lymph nodes

value: primary Treg cell

value: Treg

value: Ripk1 knockout

value: no treatment


title: Ripk_KO rTreg

description:
counts.txt
vst_table.txt


title: WT_rTreg

description:
counts.txt
vst_table.txt

value: WT


title: WT_aTreg

description:
counts.txt
vst_table.txt