title: Tibialis Anterior,GDF5-treated mdx,8weeks,rep3

city: Paris

first: Aly

last: BOURGUIBA

state: France

address: 105 bd de l'hôpital

country: France

institute: Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie,

description: Library name: MDX-GDF5-16

data_processing:
Data were generared using Cell  Ranger  8.0.1
Assembly: Mouse mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 : UMI count matrix in h5 format

source_name: skeletal muscle

extract_protocol:
Tibialis anterior muscles were isolated from mice immediately following euthanasia, minced, snap frozen in liquid nitrogen and cryoconserved at - 80°C. Nuclei from n=3 (mdx and mdx-GDF5) and n=2 (WT) were isolated following Chromium Nuclei Isolation Kits (10x Genomics) according to the manufacturer’s instruction. For counting, nuclei were labeled with Acridine Orange and Propidium Iodide and counted using a Luna FL automatic cell counter. Nuclei from each sample were loaded onto separate lanes of the 10x Genomics Chromium with the aim to recover 20,000 nuclei per sample, using loading volumes recommended by the manufacturer
Libraries were prepared and sequenced according to manufacturer’s instructions on a NextSeq 2000 instrument.

value: skeletal muscle

value: 9 weeks

value: 8 weeks


title: Tibialis Anterior,GDF5-treated mdx,3weeks,rep3

status: Public on Jul 29 2026

type: SRA

description: Library name: MDX-GDF5-15

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: age

value: 3 weeks

tag: genotype

tag: treatment

tag: time

value: 2 weeks


title: Control2

city: Guangzhou

first: Zhiwen

last: Zhang

address: Lujing Road 2

country: China

institute: Southern Medical University

description:
Library name: Sample2
Count2

library_source: transcriptomic

data_processing:
Sequencing output was normalized and expressed as RPKM (reads per kilobase of exon per million mapped reads). Raw reads were adapter-trimmed with cutadapt v1.18 and aligned to the GENCODE v30 mouse reference genome using HISAT2 v2.1.0 (default settings).
Assembly: mm10
Supplementary files format and content: gene_fpkm

molecule: total RNA

source_name: spleen

growth_protocol: CD8⁺ T cells were isolated from mouse spleens using a positive selection kit (Miltenyi Biotec, 130‑104‑075). Purified CD8⁺ T cells were seeded onto culture plates pre‑coated with anti‑CD3 (5 µg/mL) and anti‑CD28 (2 µg/mL) antibodies at 4 °C for 24 h. Cells were cultured in RPMI‑1640 medium supplemented with 30 U/mL recombinant murine IL‑2, 1% non‑essential amino acids, 1% sodium pyruvate, and 50 µM 2‑mercaptoethanol. According to experimental grouping, PYG, ECCS, BSSC, acetate, or CUCPT 4a was added, and cells were incubated at 37 °C in 5% CO₂ for 72 h. Activated T cells were then used for subsequent functional assays.

extract_protocol:
Total RNA was extracted from mouse CD8⁺ T cells (acetate-treated and control) using TRIzol reagent (Thermo Fisher Scientific).
Qualified RNA samples were submitted to Novogene (Beijing) for paired-end sequencing on an Illumina NovaSeq 6000 platform. Libraries were prepared with the TruSeq RNA Sample Prep Kit (Illumina).

treatment_protocol: Final concentration of 5mm mol/L acetate treatment for 48 hours

value: spleen

tag: cell line

value: mice primary cells

tag: cell type

value: CD8+T cell

value: WT

value: No treatment


title: 203991400166_R08C01_20185937_PFC

type: genomic

city: Exeter

first: Joshua

last: Harvey

state: Devon

address: RILD Building, RD&E, Barrack Road

department: Clinical and Biomedical Sciences

country: United Kingdom

institute: University of Exeter

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

label: Cy3 & Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Prefrontal cortex

label_protocol: Standard Illumina Protocol

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Prefrontal cortex

tag: regiondescription

tag: plate

tag: centre

value: Newcastle Brain Tissue Resource

tag: Sex

value: female

tag: thal

value: FALSE


title: Tibialis Anterior,WT,9weeks,rep2

description: Library name: WT-12

value: no treatment


title: Tibialis Anterior,mdx,9weeks,rep3

description: Library name: MDX-14

value: AAV-SCR


title: Tibialis Anterior,WT,9weeks,rep1

description: Library name: WT-11


title: 203991400166_R02C01_20010014_PFC


title: Control1

description:
Library name: Sample1
Count1


title: CD49d-deficient TCL1-tg pc rep4

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Library name: 110_PC_Tanja

data_processing:
Read count per gene was estimated with Salmon.
Assembly: mm10
Supplementary files format and content: raw count per gene in tab delimited file

source_name: Peritoneal cavity

extract_protocol:
Total RNA extracted using Rneasy Mini Kit (Qiagen)
TruSeq Stranded Total RNA LP (Illumina)

treatment_protocol: Untreated

value: Peritoneal cavity

value: CLL

value: TCL1 T/+ CD19 Cre/+ ITGA4 fl/fl


title: Tibialis Anterior,WT,3weeks,rep2

description: Library name: WT-10

value: skeletal muscle


title: Tibialis Anterior,WT,3weeks,rep1

description: Library name: WT-09

value: 3 weeks


title: 203991400166_R01C01_P23/12_PFC

value: QSBB


title: Tibialis Anterior,GDF5-treated mdx,8weeks,rep2

description: Library name: MDX-GDF5-8

value: 9 weeks

value: 8 weeks


title: 203991400142_R08C01_20110891_PFC

value: male


title: CD49d-deficient TCL1-tg spleen rep5

description: Library name: 110_SP_Tanja

source_name: Spleen

value: Spleen


title: Tibialis Anterior,mdx,9weeks,rep2

description: Library name: MDX-6


title: Tibialis Anterior,GDF5-treated mdx,8weeks,rep1

description: Library name: MDX-GDF5-7


title: CD49d-deficient TCL1-tg pc rep3

description: Library name: 112_PC_Tanja


title: 203991400142_R05C01_20110645_PFC


title: Tibialis Anterior,GDF5-treated mdx,3weeks,rep2

description: Library name: MDX-GDF5-4

value: 2 weeks


title: CD49d expressing TCL1-tg spleen rep5

description: Library name: 56_SP_Tanja

value: TCL1 T/+ CD19 Cre +/+ ITGA4 fl/fl


title: Tibialis Anterior,mdx,9weeks,rep1

description: Library name: MDX-5


title: Tibialis Anterior,mdx,3weeks,rep2

description: Library name: MDX-2


title: Tibialis Anterior,mdx,3weeks,rep1

description: Library name: MDX-1


title: CD49d expressing TCL1-tg pc rep4

description: Library name: 108_PC_Tanja


title: Tibialis Anterior,GDF5-treated mdx,3weeks,rep1

description: Library name: MDX-GDF5-3


title: 203991400143_R06C01_PD944_PFC

value: Prefrontal cortex

value: Imperial Brain Bank


title: 203991400143_R03C01_PD988_PFC

value: FALSE


title: Input 5

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

country: USA

institute: University of Virginia

data_processing:
eCLIP reads begin with the UMI and, in the first step of analysis, UMIs were pruned from read sequences using umi_tools (v0.5.1) [Ref: PMID: 28100584]. UMI sequences were saved by incorporating them into the read names in the FASTQ files to be utilized in subsequent analysis steps. Next, 3-adapters were trimmed from reads using cutadapt (v2.7) [Ref: http://journal.embnet.org/index.php/embnetjournal/article/view/200], and reads shorter than 18 bp in length were removed.
Reads were then mapped to a database of human repetitive elements and rRNA sequences compiled from Dfam [Ref: PMID: 26612867] and Genbank [Ref: PMID: 23193287]. All non-repeat mapped reads were mapped to the human genome (hg38) using STAR (v2.6.0c) [Ref: PMID: 23104886]. PCR duplicates were removed using umi_tools (v0.5.1) by utilizing UMI sequences from the read names and mapping positions.
Peaks were identified within eCLIP samples using the peak caller CLIPper
(https://github.com/YeoLab/clipper) [Ref: PMID: 24213538]. For each peak, IP versus input fold enrichment values were calculated as a ratio of counts of reads overlapping the peak region in the IP and the input samples (read counts in each sample were normalized against the total number of reads in the sample after PCR duplicate removal). A p-value was calculated for each peak by the Yates’ Chi-Square test, or Fisher Exact Test if the observed or expected read number was below 5.
Comparison of different sample conditions was evaluated in the same manner as IP versus input enrichment; for each peak called in IP libraries of one sample type we calculated enrichment and p-values relative to normalized counts of reads overlapping these peaks in another sample type.
Assembly: mm10
Supplementary files format and content: bam

source_name: Whole heart

extract_protocol:
eCLIP studies were performed according to the published single-end seCLIP protocol [pubmed ID 28766298] with the following modifications. For each sample (N=2), approximately 66 mg of frozen mouse heart tissue was cryoground into a powder, UV crosslinked (254 nm radiation, 400 mJoules/cm2), and lysed using 500 µL eCLIP lysis mix. Samples were then subjected to two rounds of sonication for 4 minutes with 30 second ON/OFF at 75% amplitude. 1% of lysate was removed for assessing RNA quality and quantity. Lysate volume equivalent to 50 ug of RNA was DNased and enzymatically fragmented using a 1:100 dilution of RNase-I (Ambion). Pre-validated anti-PTBP1 antibody (Eclipsebio) was then precoupled to Anti-Rabbit IgG Dynabeads (ThermoFisher), added to lysate, and incubated overnight at 4˚C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with eCLIP high stringency wash buffers. IP and input samples were cut from the membrane at 50 kDa to 125 kDa. RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as previously described.
The eCLIP cDNA adapter contains a sequence of 10 random nucleotides at the 5 end. This random sequence serves as a unique molecular identifier (UMI) [Ref: PMID: 22101854] after sequencing primers are ligated to the 3 end of cDNA molecules.

treatment_protocol: WT C57BL/6 mice were used for this study.

value: Whole heart

value: WT C57Bl/6


title: Input 6


title: IP6 replicate 2


title: 203991400143_R02C01_PD020_PFC


title: CD49d expressing TCL1-tg pc rep3

description: Library name: 106_PC_Tanja

value: Peritoneal cavity


title: CD49d expressing TCL1-tg pc rep2

description: Library name: 102_PC_Tanja

value: CLL


title: IP5 replicate 1


title: 203991390124_R08C01_P02/14_PFC

value: female


title: Embryo_pool_16, control

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description: Library name: Embryo_pool_16

library_source: genomic

data_processing:
The libraries were prepared with the EZ DNA Methylation Direct kit from Zymo, followed by the Pico Methyl kit for whole genome amplification, adapter ligation and PCR amplification (Zymo Research).
The libraries were pooled; quantitated by qPCR and sequenced on one 10B and 25B lane for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 seque
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors have been trimmed from the 3'-end of the reads.
The quality-scores line in fastq files use an ASCII offset of 33 known as Sanger scores
Trimming (TrimGalore), Alignment (Bismark)
Differential methylation analysis (methylKit R package), Functional annotation
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: bismark coverage files / methylation counts

organism: Ovis aries

source_name: Embryo

extract_protocol:
Genomic DNA was extracted from sperm samples using the Quick-DNA Miniprep Plus (Zymo Research).
Embryo pools were processed for whole-genome bisulfite sequencing (WGBS) using the EZ DNA Methylation Direct Kit (Zymo Research, Irvine, CA, USA). Following bisulfite conversion, library preparation was performed using the Pico Methyl Kit (Zymo Research).

treatment_protocol: Treatment group rams were supplemented with 3g of methionine per day from weaning to puberty.

value: Embryo

value: control


title: CD49d-deficient TCL1-tg pc rep2

description: Library name: 101_PC_Tanja

value: TCL1 T/+ CD19 Cre/+ ITGA4 fl/fl


title: Embryo_pool_15, control

description: Library name: Embryo_pool_15


title: Embryo_pool_14, control

description: Library name: Embryo_pool_14


title: 203991390124_R01C01_PDC085_PFC


title: 203991410071_R07C01_20000064_PFC

value: Newcastle Brain Tissue Resource


title: Embryo_pool_13, control

description: Library name: Embryo_pool_13


title: CD49d expressing TCL1-tg rep1

description: Library name: 81_PC_Tanja


title: Embryo_pool_12, control

description: Library name: Embryo_pool_12


title: CD49d-deficient TCL1-tg pc rep1

description: Library name: 26_PC_Tanja


title: Embryo_pool_10, control

description: Library name: Embryo_pool_10


title: 203991410071_R04C01_20174968_PFC


title: Embryo_pool_8, methionine supplemented

description: Library name: Embryo_pool_8

value: methionine supplemented


title: CD49d-deficient TCL1-tg spleen rep4

description: Library name: 112_SP_Tanja


title: Embryo_pool_6, methionine supplemented

description: Library name: Embryo_pool_6


title: 203991410071_R02C01_PD229_PFC


title: Embryo_pool_5, methionine supplemented

description: Library name: Embryo_pool_5


title: CD49d expressing TCL1-tg spleen rep4

description: Library name: 108_SP_Tanja


title: 203991410070_R08C01_20185918_PFC

value: male


title: Fusarium graminearum inoculation, rachis, 4d, biol rep 3

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

description: Library name: FHB_rachis_4d_R3

data_processing:
Raw reads quality filtering and trimming for adapter contaminants with Trimmomatic v0.39 (Bolger et al., 2014)
High quality reads were mapped to the Triticum durum cv. Svevo Rel 2.0 genome and annotation using STAR 2.7.10b (Dobin et al., 2013).
Read counts and transcripts per million TPM were calculated per gene using RSEM v1.3.3 (Li and Dewey, 2011).
Assembly: Svevo Rel2.0 genome assembly
Supplementary files format and content: tab delimited text file including rawcounts for each sample
Supplementary files format and content: tab delimited text file including TPM values for each sample

organism: Triticum turgidum subsp. durum

source_name: spike rachis

growth_protocol: Durum wheat plants (Triticum turgidum L. ssp. durum) cv. Svevo were grown in pots filled with loam-based potting soil, plus 1/3 of sand and perlite (in 1:1 volume ratio) in a controlled environment (16/8 hours day/night length at 24/20 °C).

extract_protocol:
Total RNA was extracted from 100 mg frozen material using RNeasy Plant Mini Kit (Qiagen) with the optional on-column DNase treatment for genomic DNA removal.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: Fusarium graminearum strain CS3005 was point inoculated at early-anthesis (Zadoks growth stage 61): two florets of the two central spikelets in the main tiller were inoculated with 10 μL of inoculum (5 × 105 conidia mL−1 ). Mock plants were inoculated with 10 μL of sterilized water. Inoculated spikelets were marked with a marker pen to facilitate the sampling. Inoculated and mock spikes were covered with plastic bags to maintain high humidity and promote disease development. Inoculated/mock spikelets and the three flanking spike internodes were sampled 2 and 4 days after inoculation from at least 4 spikes per replicate and immediately frozen in liquid nitrogen.

value: spike rachis

value: Svevo cultivar

value: F. graminearum inoculation

value: 4 days


title: CD49d expressing TCL1-tg spleen rep3

description: Library name: 106_SP_Tanja

value: Spleen

value: TCL1 T/+ CD19 Cre +/+ ITGA4 fl/fl


title: 203991410070_R07C01_19940144_PFC

value: Prefrontal cortex

value: FALSE


title: Fusarium graminearum inoculation, rachis, 4d, biol rep 1

description: Library name: FHB_rachis_4d_R1


title: Fusarium graminearum inoculation, rachis, 2d, biol rep 3

description: Library name: FHB_rachis_2d_R3

value: 2 days


title: CD49d-deficient TCL1-tg spleen rep3

description: Library name: 101_SP_Tanja

value: CLL

value: TCL1 T/+ CD19 Cre/+ ITGA4 f/f


title: Fusarium graminearum inoculation, rachis, 2d, biol rep 2

description: Library name: FHB_rachis_2d_R2


title: CD49d expressing TCL1-tg spleen rep1

description: Library name: 81_SP_Tanja


title: Fusarium graminearum inoculation, spikelets, 4d, biol rep 2

description: Library name: FHB_spikelets_4d_R2

source_name: spikelet

value: spikelet


title: CD49d-deficient TCL1-tg spleen rep2

description: Library name: 59_SP_Tanja


title: Fusarium graminearum inoculation, spikelets, 4d, biol rep 1

description: Library name: FHB_spikelets_4d_R1


title: Fusarium graminearum inoculation, spikelets, 2d, biol rep 3

description: Library name: FHB_spikelets_2d_R3


title: Fusarium graminearum inoculation, spikelets, 2d, biol rep 2

description: Library name: FHB_spikelets_2d_R2


title: CD49d-deficient TCL1-tg spleen rep1

description: Library name: 26_SP_Tanja


title: Fusarium graminearum inoculation, spikelets, 2d, biol rep 1

description: Library name: FHB_spikelets_2d_R1


title: 203991400128_R06C01_PD775_PFC

value: Imperial Brain Bank

value: female


title: Mock, rachis, 4d, biol rep 3

description: Library name: Mock_rachis_4d_R3

value: mock


title: Mock, rachis, 4d, biol rep 2

description: Library name: Mock_rachis_4d_R2


title: MEF Blm -/- Recql -/- Rep3

city: Baltimore

first: Robert

last: Brosh

state: Maryland

address: NIH Biomedical Research Center, 251 Bayview Blvd

institute: National Institute on Aging, NIH

description: Library name: DKO3

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: primary MEF cells

growth_protocol: Primary MEF cells were maintained in DMEM supplemented with 10% FBS and antibiotics and they were grown in humidified atmosphere at 37C with 5% CO2 and  3% O2

extract_protocol:
Cell pellets from MEF cultures were lysed in RLT buffer (Qiagen), and lysates were processed with the QIAcube (Qiagen) for automated RNA extraction.
library was constructed using the KAPA Stranded mRNA library preparation kit

value: primary MEF cells

value: Blm Recql KO


title: 203991400128_R03C01_P24/14_PFC

value: QSBB

value: male


title: Mock, rachis, 4d, biol rep 1

description: Library name: Mock_rachis_4d_R1

value: spike rachis

value: Svevo cultivar


title: MEF Blm -/- Recql -/- Rep2

description: Library name: DKO2


title: Mock, rachis, 2d, biol rep 3

description: Library name: Mock_rachis_2d_R3


title: 203991400128_R02C01_PD016_PFC


title: Mock, rachis, 2d, biol rep 2

description: Library name: Mock_rachis_2d_R2


title: MEF Blm -/- Recql -/- Rep1

description: Library name: DKO1


title: 203991400153_R06C01_NP17/021_PFC

value: Oxford Brain Bank


title: Mock, spikelets, 4d, biol rep 3

description: Library name: Mock_spikelets_4d_R3

value: 4 days


title: Mock, spikelets, 4d, biol rep 2

description: Library name: Mock_spikelets_4d_R2


title: MEF Recql -/- Rep3

description: Library name: REC3

value: Recql KO


title: 203991400153_R05C01_PD034_PFC

value: Prefrontal cortex

value: FALSE


title: Mock, spikelets, 4d, biol rep 1

description: Library name: Mock_spikelets_4d_R1


title: MEF Recql -/- Rep2

description: Library name: REC2


title: Mock, spikelets, 2d, biol rep 2

description: Library name: Mock_spikelets_2d_R2

value: 2 days


title: 203991400153_R02C01_PD286_PFC


title: Mock, spikelets, 2d, biol rep 1

description: Library name: Mock_spikelets_2d_R1


title: 203991400153_R01C01_P28/12_PFC


title: NH4NO3 application, shoot, 24h, biol rep 3

description: Library name: NH4NO3_shoot_24h_R3

source_name: shoot/leaves

growth_protocol: Durum wheat seeds (Triticum turgidum L. ssp. durum) cv. Svevo were pre-germinated in Petri dishes with wet filter paper, at 4 °C for 5 days to obtain a synchronous germination. Germinating seeds were transferred into pots filled with a mixture of vermiculite and sand (4:1 ratio), placed in a growth chamber set at 14/10 hours day/night length at 14/8 °C for 10 days. Temperatures were then changed to 23/18°C and plants were watered with half strength Hoagland solution until plants reached the third leaf stage.

extract_protocol:
Total RNA was extracted from 100 mg frozen material using NucleoSpin RNA Plant, Mini kit (Macherey-Nagel) including the on-column DNase treatment for genomic DNA removal.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: The following growth conditions were then applied: i) heat stress [HS; 37/30 °C], ii) simulated drought/osmotic [DS; half strength Hoagland plus 300 mM Mannitol], iii) salinity [SS; half strength Hoagland plus 150 mM NaCl) and iv) nitrogen application [half strength Hoagland plus 3 mM NH4NO3]. Root and shoot samples were collected from treated and control plants at 4h and 24 after application of the treatment, in three biological replicates, each consisting of at least five individual plants, and immediately frozen in liquid nitrogen.

value: shoot/leaves

value: nitrogen application, 3mM NH4NO3


title: Embryo_pool_3, methionine supplemented

description: Library name: Embryo_pool_3

value: Embryo

value: methionine supplemented


title: Fusarium graminearum inoculation, rachis, 4d, biol rep 2

description: Library name: FHB_rachis_4d_R2

value: F. graminearum inoculation


title: NH4NO3 application, shoot, 24h, biol rep 2

description: Library name: NH4NO3_shoot_24h_R2


title: MEF Blm -/- Rep3

description: Library name: BLM3

value: primary MEF cells

value: Blm KO


title: NH4NO3 application, shoot, 24h, biol rep 1

description: Library name: NH4NO3_shoot_24h_R1


title: 203991410070_R05C01_P10/02_PFC

value: QSBB

value: female


title: CD49d expressing TCL1-tg spleen rep2

description: Library name: 102_SP_Tanja

value: Spleen

value: CLL

value: TCL1 T/+ CD19 Cre +/+ ITGA4 fl/fl


title: 203991390154_R07C01_C076_PFC

value: Imperial Brain Bank

value: male


title: NH4NO3 application, shoot, 4h, biol rep 3

description: Library name: NH4NO3_shoot_4h_R3

value: Svevo cultivar


title: MEF Blm -/- Rep2

description: Library name: BLM2


title: Fusarium graminearum inoculation, rachis, 2d, biol rep 1

description: Library name: FHB_rachis_2d_R1

value: spike rachis


title: 203991400127_R08C01_20100745_PFC

value: Prefrontal cortex

value: Newcastle Brain Tissue Resource

value: FALSE


title: 203991400127_R04C01_PD970_PFC


title: NH4NO3 application, shoot, 4h, biol rep 2

description: Library name: NH4NO3_shoot_4h_R2

value: shoot/leaves

value: nitrogen application, 3mM NH4NO3


title: 203991390154_R06C01_P20/14_PFC


title: NH4NO3 application, shoot, 4h, biol rep 1

description: Library name: NH4NO3_shoot_4h_R1


title: MEF Blm -/- Rep1

description: Library name: BLM1


title: NH4NO3 application, root, 24h, biol rep 3

description: Library name: NH4NO3_root_24h_R3

source_name: root

value: root


title: 203991390154_R04C01_20110932_PFC


title: NH4NO3 application, root, 24h, biol rep 2

description: Library name: NH4NO3_root_24h_R2


title: 203991400128_R07C01_19900205_PFC


title: MEF WT Rep 3

description: Library name: WT3

value: primary MEF cells

value: WT


title: NH4NO3 application, root, 24h, biol rep 1

description: Library name: NH4NO3_root_24h_R1


title: 203991390154_R02C01_PD357_PFC


title: MEF WT Rep 2

description: Library name: WT2


title: NH4NO3 application, root, 4h, biol rep 2

description: Library name: NH4NO3_root_4h_R2


title: 203991390154_R01C01_NP12/060_PFC

value: Oxford Brain Bank


title: NH4NO3 application, root, 4h, biol rep 3

description: Library name: NH4NO3_root_4h_R3


title: NH4NO3 application, root, 4h, biol rep 1

description: Library name: NH4NO3_root_4h_R1


title: MEF WT Rep 1

description: Library name: WT1


title: 203991410102_R06C01_NP14/133_PFC


title: Salinity stress, shoot, 24h, biol rep 3

description: Library name: Salinity_shoot_24h_R3

value: salinity stress, 150 mM NaCl


title: Wild-type [WGBS]

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
Bismark was used to perform read mapping (standard parameters) and methylation calling. Samtools was used to perform SAM/BAM coversion.
MethylDackel was used to merge context and create final methylation matrix.
Assembly: mm10
Supplementary files format and content: BedGraph containing CpG methylation levels.

growth_protocol: Embryonic stem E14tg2a Dnmt1wt/wt, Dnmt1wt/N1580A, Dnmt1N1580A /N1580A and Dnmt1 KO cell lines were grown on 0.15% gelatin-coated 6-well plates at a density of 2.5x10^5 cells per well in Dulbecco‘s modified Eagle‘s medium (Gibco) containing 15% fetal bovine serum (Gibco) and 1000 U/ml mouse leukemia inhibitory factor (Millipore).

extract_protocol:
Genomic DNA was purified from cell lysates using Zymo Genomic DNA Clean & Concentrator-10 Kit.
100 ng of genomic DNA was bisulfite converted using Zymo EZ DNA Methylation-Lightning Kit according to the manufacture’s protocol. This was followed by a second strand synthesis reaction and then addition of adapters through tagmentation using Illumina’s Nextera® kit. PCR was performed with Illumina Nextera Unique Dual Indices. Library quality control was performed on the Agilent 2200 TapeStation. Libraries were sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Genomic DNA was isolated following 48 h of cell growth in DMEM medium supplemented with 15% fetal bovine serum and 1000 U/mL mLIF.

value: Embryonic stem cells

value: Wild-type


title: Salinity stress, shoot, 24h, biol rep 1

description: Library name: Salinity_shoot_24h_R1


title: Salinity stress, shoot, 24h, biol rep 2

description: Library name: Salinity_shoot_24h_R2


title: 203991410102_R03C01_PD945_PFC


title: Salinity stress, shoot, 4h, biol rep 3

description: Library name: Salinity_shoot_4h_R3


title: Heterozygous Dnmt1 N1580A knock-in [WGBS]

value: Heterozygous Dnmt1 N1580A knock-in


title: Salinity stress, shoot, 4h, biol rep 2

description: Library name: Salinity_shoot_4h_R2


title: 203991410102_R02C01_PD784_PFC

value: Imperial Brain Bank

value: female


title: Salinity stress, shoot, 4h, biol rep 1

description: Library name: Salinity_shoot_4h_R1

value: Svevo cultivar


title: Homozygous Dnmt1 N1580A knock-in [WGBS]

value: Homozygous Dnmt1 N1580A knock-in


title: 203991410115_R05C01_PD918_PFC

value: Prefrontal cortex

value: male


title: Mock, rachis, 2d, biol rep 1

description: Library name: Mock_rachis_2d_R1

value: spike rachis

value: mock

value: 2 days


title: Salinity stress, root, 24h, biol rep 3

description: Library name: Salinity_root_24h_R3

value: root


title: Salinity stress, root, 24h, biol rep 2

description: Library name: Salinity_root_24h_R2


title: Salinity stress, root, 24h, biol rep 1

description: Library name: Salinity_root_24h_R1


title: 203991410115_R04C01_PD079_PFC

value: FALSE


title: Salinity stress, root, 4h, biol rep 3

description: Library name: Salinity_root_4h_R3


title: Dnmt1 KO [WGBS]

value: Dnmt KO


title: Homozygous Dnmt1 N1580A knock-in

data_processing:
Bismark was used to perform read mapping (standard parameters) and methylation calling. Samtools was used to perform SAM/BAM coversion.
MethylDackel was used to merge context and create final methylation matrix.
Assembly: mm10
Supplementary files format and content: bedgraph

growth_protocol: For the analysis of heterozygous and homozygous Dnmt1 N1580A knock-in substitution cells, embryonic stem E14tg2a Dnmt1wt/N1580A and Dnmt1 N1580A/N1580A cell lines were grown on 0.15% gelatin-coated 6-well plates at a density of 2.5x10^5 cells per well in Dulbecco‘s modified Eagle‘s medium (Gibco) containing 15% fetal bovine serum (Gibco), 1000 U/ml mouse leukemia inhibitory factor (Millipore). For the analysis of ground state transition from naïve to "primed" cells, naïve embryonic stem E14tg2a Dnmt1wt/N1580A cell lines were grown on 0.15% gelatin-coated 6-well plates at a density of 2.5x10^5 cells per well in Dulbecco‘s modified Eagle‘s medium (Gibco) containing 15% fetal bovine serum (Gibco), 1000 U/ml mouse leukemia inhibitory factor (Millipore), 3 µM CHIR99021 (Sigma-Aldrich, USA) and 1 µM PD0325901 (Sigma-Aldrich, USA) kinase inhibitors.

extract_protocol:
Genomic DNA was purified from cell lysates using Zymo Genomic DNA Clean & Concentrator-10 Kit.
500 ng of starting input genomic DNA was digested with 30 units of MspI (NEB). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥50 bp in size were recovered using the Zymo DNA Clean & Concentrator™-5. The fragments were then bisulfite-treated using the Zymo EZ DNA Methylation-Lightning™ Kit. Preparative-scale PCR was performed and the resulting products were purified with Zymo DNA Clean & Concentrator™-5 for sequencing on an Illumina NovaSeq 6000 platform.

treatment_protocol: For the analysis of heterozygous and homozygous Dnmt1 N1580A knock-in substitution cells, genomic DNA was isolated following 48 h of cell growth in DMEM medium supplemented with 15% fetal bovine serum and 1000 U/mL mLIF. For the analysis of ground state transition from naïve to "primed" cells, the cellular shift to the “primed” state was promoted by passaging mESC cells at the same density in DMEM media (15% FBS, 1000 U/mL mLIF) for the subsequent 8 days without the presence of 2i. Genomic DNA was isolated on day 0 (naïve cell state), day 2, day 4 and day 8 of mESC “priming”.


title: Salinity stress, root, 4h, biol rep 2

description: Library name: Salinity_root_4h_R2


title: 203991410115_R01C01_PD341_PFC


title: Salinity stress, root, 4h, biol rep 1

description: Library name: Salinity_root_4h_R1


title: 203968030135_R08C01_PD134_PFC


title: Heterozygous Dnmt1 N1580A knock-in


title: Osmotic stress, shoot, 24h, biol rep 3

description: Library name: Drought_shoot_24h_R3

value: shoot/leaves

value: osmotic stress, 300mM Mannitol


title: Osmotic stress, shoot, 24h, biol rep 2

description: Library name: Drought_shoot_24h_R2


title: Osmotic stress, shoot, 24h, biol rep 1

description: Library name: Drought_shoot_24h_R1


title: Day 8

value: Embryonic stem cells


title: 203968030135_R07C01_P47/11_PFC

value: QSBB


title: Osmotic stress, shoot, 4h, biol rep 3

description: Library name: Drought_shoot_4h_R3


title: Day 4

value: Heterozygous Dnmt1 N1580A knock-in


title: 203968030135_R02C01_PD022_PFC

value: Imperial Brain Bank


title: Osmotic stress, shoot, 4h, biol rep 2

description: Library name: Drought_shoot_4h_R2


title: MEF Recql -/- Rep1

description: Library name: REC1

value: primary MEF cells

value: Recql KO


title: Osmotic stress, shoot, 4h, biol rep 1

description: Library name: Drought_shoot_4h_R1

value: Svevo cultivar


title: Day 2


title: Osmotic stress, root, 24h, biol rep 3

description: Library name: Drought_root_24h_R3


title: 203968030072_R08C01_PD099_PFC

value: Prefrontal cortex


title: Osmotic stress, root, 24h, biol rep 2

description: Library name: Drought_root_24h_R2


title: 203968030072_R06C01_20140969_PFC

value: Newcastle Brain Tissue Resource

value: male


title: 203968030072_R03C01_P10/15_PFC

value: female


title: Osmotic stress, root, 4h, biol rep 3

description: Library name: Drought_root_4h_R3


title: Tbx4CreER;Atg5f/f mice, bleomycin, tracheal injection

city: Tianjin

first: guiying

last: xu

address: No.890 Jinggu Road

institute: Tianjin Haihe Hospital

data_processing:
Utilizing Cell Ranger software, the resultant FASTQ files were quantified and filtered, and mapped to mouse official gene symbols according to Genome Reference Consortium Mouse Reference 38 (GRCm38). The differentially expressed genes (DEGs) between two groups were analyzed by FindMarkers function of Seurat package with the conditions that FC > 1.5 and adjusted p-value < 0.05. Subsequently, the enrichment analysis of the DEGs were conducted using the online tool (v2021) of DAVID website (https://david.ncifcrf.gov/). Additonally, the module scoring analysis were conducted with AddModuleScore function of Seurat package. The gene sets using in the module scoring analysis were all downloaded from GSEA mouse molecular signatures database (http://www.gsea-msigdb.org/gsea/msigdb/).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
The mice were euthanised to remove the lung tissue. Mouse lungs were digested with 3mL elastase and then were incubated with 5mL 0.5% DNase I at 37 °C for 15 minutes. Lung cell suspensions were filtered through a 100 μm strainer and were collected into a 50 mL centrifuge tube. Red blood cell lysis buffer was used to remove the erythrocytes. Cells were resuspended in Hank’s balanced saline solution (HBSS) with 2% FBS, 1% PS, and 10 mmol/L HEPES.
The protoplast suspension was loaded into Chromium microfluidic chips with 30 (v3.1) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30(v3.1) reagent kit (10X Genomics) according to the  manufacturer’s instructions.

value: Lung

value: Lung cells

value: BLM


title: Osmotic stress, root, 24h, biol rep 1

description: Library name: Drought_root_24h_R1

value: root


title: Osmotic stress, root, 4h, biol rep 2

description: Library name: Drought_root_4h_R2


title: Day 0


title: Osmotic stress, root, 4h, biol rep 1

description: Library name: Drought_root_4h_R1


title: Heat stress, shoot, 24h, biol rep 3

description: Library name: Heat_shoot_24h_R3

value: shoot/leaves

value: heat stress, 37/30 °C


title: 203968030080_R07C01_PD334_PFC

value: FALSE


title: Heat stress, shoot, 24h, biol rep 2

description: Library name: Heat_shoot_24h_R2


title: Tbx4CreER;Atg5f/f mice, PBS, tracheal injection

value: PBS


title: WT mice, bleomycin, tracheal injection

value: WT


title: 203968030080_R01C01_20160306_PFC


title: Heat stress, shoot, 24h, biol rep 1

description: Library name: Heat_shoot_24h_R1


title: Heat stress, shoot, 4h, biol rep 3

description: Library name: Heat_shoot_4h_R3


title: WT mice, PBS, tracheal injection


title: 203968030071_R07C01_20163932_PFC


title: Heat stress, root, 24h, biol rep 3

description: Library name: Heat_root_24h_R3


title: Heat stress, shoot, 4h, biol rep 1

description: Library name: Heat_shoot_4h_R1


title: Heat stress, shoot, 4h, biol rep 2

description: Library name: Heat_shoot_4h_R2


title: 203968030071_R01C01_P29/12_PFC

value: QSBB


title: Heat stress, root, 24h, biol rep 2

description: Library name: Heat_root_24h_R2


title: mIMCD3 cells, SFN_Ctrl_rep1

first: xudan

last: dou

state: Tianjin

address: No.22 Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Bowtie2 was utilized to align sequence reads to the mm10 reference genome sequence. Samtools was employed to sort the aligned reads, and read counts per gene were acquired from the mapped reads through FeatureCounts. Mfuzz algorithm were used to analyze dynamic gene expression.
Assembly: mm10
Supplementary files format and content: rawcount.txt

extract_protocol:
Total RNAs were extracted from primary TEC using TRIzol (Invitrogen, 15596018) according to the manufacturer’s instructions.
For all RNA samples, libraries were constructed and sequenced on the on the Illumina NovaSeq platform.

value: Mouse inner medullary collecting duct

value: SFN


title: Heat stress, root, 24h, biol rep 1

description: Library name: Heat_root_24h_R1

value: Svevo cultivar


title: 203991410033_R05C01_20050124_PFC

value: Prefrontal cortex


title: mIMCD3 cells, SFN_Ctrl_rep2


title: mIMCD3 cells, SFN_6h_rep2

value: HS 6h SFN


title: Heat stress, root, 4h, biol rep 3

description: Library name: Heat_root_4h_R3


title: Heat stress, root, 4h, biol rep 2

description: Library name: Heat_root_4h_R2


title: 203991410033_R03C01_C074_PFC

value: Imperial Brain Bank


title: Heat stress, root, 4h, biol rep 1

description: Library name: Heat_root_4h_R1


title: mIMCD3 cells, SFN_6h_rep1


title: 203991410033_R02C01_PD969_PFC

value: male


title: Control, shoot, 24h, biol rep 2

description: Library name: Control_shoot_24h_R2

value: NTC


title: 203991410077_R08C01_PD309_PFC


title: Control, shoot, 24h, biol rep 1

description: Library name: Control_shoot_24h_R1


title: Control, shoot, 24h, biol rep 3

description: Library name: Control_shoot_24h_R3


title: mIMCD3 cells, SFN_1h_rep2

value: HS 1h SFN


title: Control, shoot, 4h, biol rep 2

description: Library name: Control_shoot_4h_R2


title: 203991410077_R07C01_PD125_PFC


title: Control, shoot, 4h, biol rep 3

description: Library name: Control_shoot_4h_R3


title: mIMCD3 cells, SFN_1h_rep1


title: Control, shoot, 4h, biol rep 1

description: Library name: Control_shoot_4h_R1


title: mIMCD3 cells, Nrf2KO_SFN_HS1h_rep2


title: Control, root, 24h, biol rep 3

description: Library name: Control_root_24h_R3


title: 203991410077_R06C01_19960064_PFC

value: Newcastle Brain Tissue Resource

value: female


title: Control, root, 24h, biol rep 2

description: Library name: Control_root_24h_R2

value: root


title: mIMCD3 cells, Nrf2KO_SFN_HS1h_rep1


title: 203991410077_R05C01_RI03/208_PFC

value: Oxford Brain Bank

value: TRUE


title: mIMCD3 cells, Nrf2KO_SFN_rep2


title: Control, root, 24h, biol rep 1

description: Library name: Control_root_24h_R1


title: Control, root, 4h, biol rep 3

description: Library name: Control_root_4h_R3


title: Control, root, 4h, biol rep 2

description: Library name: Control_root_4h_R2


title: 203991410077_R04C01_PD844_PFC

value: FALSE


title: Control, root, 4h, biol rep 1

description: Library name: Control_root_4h_R1


title: 203991410077_R02C01_PDC128_PFC


title: 3cm spike peduncle, 30DPA, biol rep 3

description: Library name: Pedunc_30DPA_R3

source_name: 3cm spike peduncle sampled at 30DPA

growth_protocol: Durum wheat seeds (Triticum turgidum L. ssp. durum) cv. Svevo were pre-germinated in Petri dishes with wet filter paper, at 4 °C for 5 days to obtain a synchronous germination. Germinating seeds were then transferred into pots filled with loam-based potting soil, plus 1/3 of sand and perlite (in 1:1 volume ratio) in a controlled environment starting with a 14/10 hours day/night length at 14/8 °C and progressively reaching 16/8 hours day night length at 24/20 °C

extract_protocol:
Total RNA was extracted from 100 mg fresh weight material; the Direct-Zol RNA Miniprep Kits Zymo Research) was used for leaf, root, meristem and ovary samples, while the RNeasy Plant Mini Kit (Qiagen) was used for seed samples. In both protocols genomic DNA contamination was removed using the on-column DNase treatment
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: 3cm spike peduncle

tag: Stage

tag: cultivar

value: Svevo


title: 3cm spike peduncle, 30DPA, biol rep 2

description: Library name: Pedunc_30DPA_R2


title: mIMCD3 cells, DMSO_Ctrl_rep2

value: Mouse inner medullary collecting duct

value: WT

value: DMSO


title: 3cm spike peduncle, 30DPA, biol rep 1

description: Library name: Pedunc_30DPA_R1


title: 203977090028_R06C01_20141164_PFC

value: Prefrontal cortex


title: 3cm spike peduncle, 16DPA, biol rep 3

description: Library name: Pedunc_16DPA_R3

source_name: 3cm spike peduncle sampled at 16DPA


title: 3cm spike peduncle, 16DPA, biol rep 2

description: Library name: Pedunc_16DPA_R2


title: mIMCD3 cells, DMSO_Ctrl_rep1


title: 203977090028_R04C01_PD687_PFC


title: mIMCD3 cells, DMSO_6h_rep2

value: HS 6h DMSO


title: 3cm spike peduncle, 5DPA, biol rep 3

description: Library name: Pedunc_5DPA_R3

source_name: 3cm spike peduncle sampled at 5DPA


title: 3cm spike peduncle, 16DPA, biol rep 1

description: Library name: Pedunc_16DPA_R1


title: 3cm spike peduncle, 5DPA, biol rep 2

description: Library name: Pedunc_5DPA_R2


title: mIMCD3 cells, DMSO_6h_rep1


title: 203977090028_R01C01_20000117_PFC


title: 3cm spike peduncle, 5DPA, biol rep 1

description: Library name: Pedunc_5DPA_R1


title: 203977090014_R07C01_19960171_PFC


title: Lamina flag leaf, 30DPA, biol rep 3

description: Library name: FlagL_30DPA_R3

source_name: Lamina flag leaf sampled at 30DPA

value: Lamina flag leaf


title: mIMCD3 cells, DMSO_1h_rep2

value: HS 1h DMSO


title: Embryo_pool_4, methionine supplemented

description: Library name: Embryo_pool_4

value: Embryo

value: methionine supplemented


title: Lamina flag leaf, 30DPA, biol rep 2

description: Library name: FlagL_30DPA_R2


title: 203977090014_R06C01_NP14/148_PFC

value: male


title: 203977090014_R04C01_20174903_PFC

value: Newcastle Brain Tissue Resource


title: mIMCD3 cells, DMSO_1h_rep1


title: Lamina flag leaf, 16DPA, biol rep 3

description: Library name: FlagL_16DPA_R3

source_name: Lamina flag leaf sampled at 16DPA


title: Lamina flag leaf, 16DPA, biol rep 2

description: Library name: FlagL_16DPA_R2


title: Lamina flag leaf, 30DPA, biol rep 1

description: Library name: FlagL_30DPA_R1


title: 203977090014_R01C01_PD800_PFC

value: Imperial Brain Bank

value: female


title: mIMCD3 cells, Nrf2_SFN_HS1h

data_processing:
The Bowtie2 algorithm was employed to align paired-end reads obtained from ChIP-seq and ATAC-seq experiments to the mouse reference genome mm10. To eliminate PCR duplicates and reads aligned to mtDNA, the "mark duplicates" command from Picard (http://broadinstitute.github.io/picard/) was utilized. Subsequently, ChIP-seq and ATAC-seq peaks were identified using HOMER's findPeaks algorithm. Bigwig files were generated based on the deepTools output5. Statistical differences in normalized read counts across peaks between sets of ChIP-seq experiments were determined using HOMER's getDifferentialPeaks.pl, which leverages the statistical modeling functions of DESeq2. ChromHMM algorithm was then applied to define chromatin states, while the AnnotatePeaks.pl algorithm was utilized to analyze the distribution of peaks around the transcription start site (TSS). Additionally, the FindMotifsGenome.pl algorithm was employed to assess motif enrichment.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.
Library construction was effected with a VAHTS Universal DNA Library Prep Kit for Illumina V3, and sequencing was carried out on the Illumina platform.

tag: chip antibody

value: anti-Nrf2 (Abcam, ab62352)

value: SFN HS1h


title: Lamina flag leaf, 5DPA, biol rep 2

description: Library name: FlagL_5DPA_R2

source_name: Lamina flag leaf sampled at 5DPA


title: mIMCD3 cells, Nrf2_SFN

value: SFN


title: mIMCD3 cells, Nrf2_DMSO_HS1h

value: DMSO HS1h


title: 203976760067_R05C01_PD740_PFC

source_name: Prefrontal cortex

value: FALSE


title: mIMCD3 cells, Nrf2_DMSO

value: Mouse inner medullary collecting duct


title: 3cm spike peduncle, W10, biol rep 1

description: Library name: Pedunc_W10_R1

source_name: 3cm spike peduncle sampled at W10

value: 3cm spike peduncle

value: Svevo


title: Lamina flag leaf, W10, biol rep 2

description: Library name: FlagL_W10_R2

source_name: Lamina flag leaf sampled at W10


title: 3cm spike peduncle, W10, biol rep 2

description: Library name: Pedunc_W10_R2


title: 203976760067_R04C01_20050099_PFC

value: Prefrontal cortex


title: 203976760067_R02C01_PD405_PFC


title: Lamina flag leaf, W10, biol rep 1

description: Library name: FlagL_W10_R1

value: Lamina flag leaf


title: mIMCD3 cells, NFAT5-SFN

value: anti-Nfat5 (Abcam, ab3446)


title: mIMCD3 cells, NFAT5-DMSO-1h


title: 203976760067_R01C01_P67/12_PFC

value: QSBB


title: Endosperm+tegument, 30DPA, biol rep 2

description: Library name: Endosperm_30DPA_R2

source_name: Endosperm+tegument sampled at 30DPA

value: Endosperm+tegument


title: Endosperm+tegument, 30DPA, biol rep 3

description: Library name: Endosperm_30DPA_R3


title: Endosperm+tegument, 30DPA, biol rep 1

description: Library name: Endosperm_30DPA_R1


title: Embryo, 30DPA, biol rep 2

description: Library name: Embryo_30DPA_R2

source_name: Embryo sampled at 30DPA

value: Embryo


title: mIMCD3 cells, NFAT5-ChIP-HS-1h-SFN


title: 203977090024_R01C01_20185942_PFC

value: Newcastle Brain Tissue Resource

value: male


title: Embryo, 30DPA, biol rep 1

description: Library name: Embryo_30DPA_R1


title: mIMCD3 cells, K9me3_SFN

value: H3K9me3 (Abcam, ab3446)


title: 203968030120_R05C01_20174960_PFC


title: Endosperm+tegument, 21DPA, biol rep 2

description: Library name: Endosperm_21DPA_R2

source_name: Endosperm+tegument sampled at 21DPA


title: 203991390151_R04C01_20150639_PFC

value: female


title: 203968030120_R04C01_20152906_PFC


title: Embryo, 21DPA, biol rep 3

description: Library name: Embryo_21DPA_R3

source_name: Embryo sampled at 21DPA


title: Embryo, 21DPA, biol rep 2

description: Library name: Embryo_21DPA_R2


title: 203968030120_R02C01_20150975_PFC


title: Embryo, 21DPA, biol rep 1

description: Library name: Embryo_21DPA_R1


title: mIMCD3 cells, K9ac-DMSO

value: H3K9ac (Abcam, ab3446)

value: DMSO


title: Kernel, 16DPA, biol rep 3

description: Library name: Kernel_16DPA_R3

source_name: Kernel sampled at 16DPA

value: Kernel


title: 203960330128_R07C01_PD808_PFC

value: Imperial Brain Bank

value: FALSE


title: mIMCD3 cells, K4me3_SFN

value: H3K4me3 (Abcam, ab3446)

value: Mouse inner medullary collecting duct

value: SFN


title: Kernel, 16DPA, biol rep 2

description: Library name: Kernel_16DPA_R2

value: Svevo


title: 203991410066_R04C01_C073_PFC

value: Prefrontal cortex


title: C57BL/6 mice, kidney, adenine diet & AA, 5

city: Suzhou

first: liwei

last: zhu

state: Jiangsu

address: 77th, Changan South Street

institute: Zhangjiagang TCM Hospital Affiliated to Nanjing University ofChinese Medicine

description: Library name: AA_5

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: kidney

growth_protocol: Eight-week-old male C57BL/6 mice (20 ± 2 g)

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The CKD model was established by administering adenine-enriched chow for 4 week, AA groups received daily oral gavage of AA, while the control animals were maintained on adenine-free chow. Weeks 5–8, all groups were transitioned to standard diet while AA treatment continued.

value: kidney

tag: strain

value: adenine diet & AA


title: C57BL/6 mice, kidney, adenine diet, 3

description: Library name: M_3

value: adenine diet


title: C57BL/6 mice, kidney, adenine diet, 5

description: Library name: M_5


title: Kernel, 16DPA, biol rep 1

description: Library name: Kernel_16DPA_R1


title: 203960330128_R05C01_C054_PFC


title: mIMCD3 cells, K4me3_DMSO


title: Kernel, 11DPA, biol rep 3

description: Library name: Kernel_11DPA_R3

source_name: Kernel sampled at 11DPA


title: 203960330128_R01C01_PD089_PFC


title: mIMCD3 cells, K4me1_SFN

value: H3K4me1 (Abcam, ab3446)


title: Kernel, 11DPA, biol rep 1

description: Library name: Kernel_11DPA_R1


title: 203960330097_R06C01_PD172_PFC

value: male


title: Kernel, 5DPA, biol rep 2

description: Library name: Kernel_5DPA_R2

source_name: Kernel sampled at 5DPA


title: Kernel, 5DPA, biol rep 1

description: Library name: Kernel_5DPA_R1


title: mIMCD3 cells, K4me1_DMSO


title: 203960330097_R05C01_PD411_PFC


title: Kernel, 3DPA, biol rep 3

description: Library name: Kernel_3DPA_R3

source_name: Kernel sampled at 3DPA


title: 203968030060_R03C01_PDC005_PFC

value: TRUE


title: Brain immune cells from aged mice, Sham, Day 3

city: Durham

first: Vaibhav

last: Jain

state: North Carolina

address: 300 N Duke St

department: Duke Molecular Physiology Institute

institute: Duke University

description:
Library name: A_Sham
10X Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the 10X Cellranger software version 7.1.0
Assembly: mm10-2020-A
Supplementary files format and content: Tab separated barcode, gene and matrix files

source_name: Brain

extract_protocol:
Mice were intubated, anesthetized with isoflurane, and transcardially perfused. Brains were immediately harvested and dissociated mechanically. Immune cells were enriched using Percoll. Cell suspensions were resuspended in FACS buffer and subjected to FACS sorting to collect CD45⁺ cells. The sorted cells were then processed for library preparation and sequencing.
10x Genomics CG000315 Chromium NextGEM Single Cell 3’ Gene Expression v3.1, Dual Index, Rev. E

treatment_protocol: Young and aged mice were subjected to a KCl-mediated mouse model of cardiac arrest and resuscitation. Sham-operated mice underwent the same surgical procedures without the experimental intervention.

value: Brain

value: CD45+ cells

value: Wild-type

value: Sham surgery


title: C57BL/6 mice, kidney, normal diet, 5

description: Library name: C_5

value: normal diet


title: 203968030090_R03C01_20140182_PFC

value: Newcastle Brain Tissue Resource

value: FALSE


title: mIMCD3 cells, K36me3_SFN

value: H3K36me3 (Abcam, ab3446)

value: Mouse inner medullary collecting duct


title: Kernel, 3DPA, biol rep 2

description: Library name: Kernel_3DPA_R2

value: Kernel

value: Svevo


title: 203960330097_R04C01_P82/15_PFC

value: Prefrontal cortex

value: QSBB

value: female


title: Pistil, W10/well-developed stigmatic hairs stage, biol rep 3

description: Library name: Pistil_W10_R3

source_name: Pistil sampled at W10/well-developed stigmatic hairs stage

value: Pistil


title: 203960330127_R07C01_20090012_PFC

value: male


title: Pistil, W10/well-developed stigmatic hairs stage, biol rep 2

description: Library name: Pistil_W10_R2


title: Pistil, W10/well-developed stigmatic hairs stage, biol rep 1

description: Library name: Pistil_W10_R1


title: Kernel, 11DPA, biol rep 2

description: Library name: Kernel_11DPA_R2


title: Pistil, W9/Stigmatic hairs differentiating stage, biol rep 3

description: Library name: Pistil_W9_R3

source_name: Pistil sampled at W9/Stigmatic hairs differentiating stage


title: mIMCD3 cells, K27me3_DMSO

value: H3K27me3 (Abcam, ab3446)

value: DMSO


title: Pistil, W9/Stigmatic hairs differentiating stage, biol rep 2

description: Library name: Pistil_W9_R2


title: Kernel, 5DPA, biol rep 3

description: Library name: Kernel_5DPA_R3


title: mIMCD3 cells, K27ac-SFN

value: H3K27ac (Abcam, ab3446)

value: SFN


title: Pistil, W7.5/Stigmatic Branches Elongating stage, biol rep 3

description: Library name: Pistil_W7.5_R3

source_name: Pistil sampled at W7.5/Stigmatic Branches Elongating stage


title: 203960330127_R05C01_PDC028_PFC

value: Imperial Brain Bank


title: Pistil, W9/Stigmatic hairs differentiating stage, biol rep 1

description: Library name: Pistil_W9_R1


title: 203960330127_R04C01_C046_PFC


title: Pistil, W7.5/Stigmatic Branches Elongating stage, biol rep 1

description: Library name: Pistil_W7.5_R1


title: mIMCD3 cells, K27ac-DMSO


title: Spike primordia, W4/Stamen primordia stage, biol rep 3

description: Library name: Infl_W4_R3

source_name: Spike primordia sampled at W4/Stamen primordia stage

value: Spike primordia

value: W4/Stamen primordia stage


title: mIMCD3 cells, Input-SFN

value: IgG


title: 203960330127_R03C01_P64/09_PFC

source_name: Prefrontal cortex

value: TRUE


title: Spike primordia, W4/Stamen primordia stage, biol rep 2

description: Library name: Infl_W4_R2


title: 203960330127_R02C01_PD917_PFC

value: FALSE


title: Spike primordia, W4/Stamen primordia stage, biol rep 1

description: Library name: Infl_W4_R1


title: mIMCD3 cells, Input-DMSO

value: Mouse inner medullary collecting duct


title: Spike primordia, W3.5/Floret primordia stage, biol rep 3

description: Library name: Infl_W3.5_R3

source_name: Spike primordia sampled at W3.5/Floret primordia stage

value: W3.5/Floret primordia stage

value: Svevo


title: 203960330125_R08C01_PDC059_PFC

value: Prefrontal cortex


title: Spike primordia, W3.5/Floret primordia stage, biol rep 2

description: Library name: Infl_W3.5_R2


title: mIMCD3 cells, Nrf2KO_SFN_rep1


title: mIMCD3 cells, ATAC_SFN-2

extract_protocol:
mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.mIMCD3 cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Crosslinking was halted by adding 150 mM of glycine for 5 minutes at room temperature.
DNA was subsequently purified for the final library construction using the TruePrep TM DNA Library Prep Kit V2 for Illumina.


title: Spike primordia, W3.5/Floret primordia stage, biol rep 1

description: Library name: Infl_W3.5_R1


title: 203960330125_R07C01_20150829_PFC

value: Newcastle Brain Tissue Resource


title: Spike primordia, W3.25/lemma primordia stage, biol rep 3

description: Library name: Infl_W3.25_R3

source_name: Spike primordia sampled at W3.25/lemma primordia stage

value: W3.25/lemma primordia stage


title: mIMCD3 cells, ATAC_DMSO-2


title: Spike primordia, W3.25/lemma primordia stage, biol rep 2

description: Library name: Infl_W3.25_R2


title: 203960330125_R05C01_PD793_PFC

value: female


title: G422TN-GBM, Ctrl, Day 7, rep1

city: Wuhan

first: Hai-Feng

last: Jiang

state: Hubei

address: No.13, Hanghang Road, Baofeng Street, Qiaokou District, Wuhan City, Hubei Province

institute: Huazhong University of Science and Technology

description: Fresh frozen Spatial transcriptome sequencing

library_source: other

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Spatial Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.gz.json.gz.gz: scalefactors in json.gz format
Supplementary files format and content: tissue_hires_image.png.gz.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

molecule: other

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10 μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: G422TN cells

value: tumor cells


title: Spike primordia, W3.25/lemma primordia stage, biol rep 1

description: Library name: Infl_W3.25_R1


title: Spike primordia, W2.5/late double ridge stage, biol rep 3

description: Library name: Infl_W2.5_R3

source_name: Spike primordia sampled at W2.5/late double ridge stage

value: W2.5/late double ridge stage


title: Kernel, 3DPA, biol rep 1

description: Library name: Kernel_3DPA_R1

value: Kernel


title: mIMCD3 cells, K36me3_DMSO

value: H3K36me3 (Abcam, ab3446)

value: DMSO


title: mIMCD3 cells, K27me3_SFN

value: H3K27me3 (Abcam, ab3446)

value: SFN


title: 203960330125_R04C01_19950019_PFC

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.


title: 203960330125_R01C01_20130827_PFC

value: male


title: Spike primordia, W2.5/late double ridge stage, biol rep 2

description: Library name: Infl_W2.5_R2

value: Spike primordia


title: Spike primordia, W2.5/late double ridge stage, biol rep 1

description: Library name: Infl_W2.5_R1


title: WT (Dp1Tyb cohort), 4

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

institute: Francis Crick Institute

description: 10x Genomics

data_processing:
Fastq samples were processed with CellRanger v 6.1.2
Normalization, scaling, dimensional reduction and cluster detection was carried out using Seurat v 4.1.0 in an R enviroment version v 4.1.1
Differential expression analysis was carried out using glmGamPoi v 1.12.2
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: tar file containing tab separated features, tab separated barcodes and matrix (cell ranger output)

source_name: Heart

extract_protocol:
E13.5 mouse hearts were dissected and subsequently dissociated into single cells using the Neonatal Heart Dissociation kit and gentleMACS Octo dissociator (Miltenyi Biotec). Cells were resuspended in PBS, 0.04% BSA, filtered through 40 um FLowmi cell strainer and kept on ice until loaded.
Approximately 20,000 cells were loaded on Chromium Chip and partitioned in nanolitre scale droplets using the Chromium Controller and Chromium. Next GEM Single Cell Reagents (CG000315 Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index)). Within each droplet the cells were lysed and the RNA was reverse transcribed. All of the resulting cDNA within a droplet shared the same cell barcode. Illumina compatible libraries were generated from the cDNA using Chromium Next GEM Single Cell library reagents in accordance with the manufacturers instructions (10x Genomics, CG000315 Chromium Single Cell 3' Reagent Kits User Guide (v3.1 - Dual Index)). Final libraries are QC’d using the Agilent TapeStation and sequenced using the Illumina NovaSeq 6000. Sequencing read configuration: 28-10-10-90

value: Heart

tag: developmental stage

value: M

value: WT (Dp1Tyb cohort)


title: Lamina flag leaf, 5DPA, biol rep 3

description: Library name: FlagL_5DPA_R3

source_name: Lamina flag leaf sampled at 5DPA

tag: tissue

value: Lamina flag leaf

value: Svevo


title: Lamina flag leaf, 16DPA, biol rep 1

description: Library name: FlagL_16DPA_R1

source_name: Lamina flag leaf sampled at 16DPA


title: 3rd leaf, 3rd leaf stage, biol rep 3

description: Library name: 3rdLeaf_R3

source_name: 3rd leaf sampled at 3rd leaf stage

value: 3rd leaf

value: 3rd leaf stage


title: 3rd leaf, 3rd leaf stage, biol rep 2

description: Library name: 3rdLeaf_R2


title: 203960330127_R06C01_PD772_PFC

value: Prefrontal cortex

value: Imperial Brain Bank

value: FALSE


title: Dp1Tyb, 5

description: 10x Genomics

value: F


title: Lamina flag leaf, 5DPA, biol rep 1

description: Library name: FlagL_5DPA_R1


title: 203976760067_R07C01_20150691_PFC

value: Newcastle Brain Tissue Resource


title: 203968030148_R02C01_PD017_PFC


title: 3cm spike peduncle, W10, biol rep 3

description: Library name: Pedunc_W10_R3

source_name: 3cm spike peduncle sampled at W10

value: 3cm spike peduncle


title: 3rd leaf, 3rd leaf stage, biol rep 1

description: Library name: 3rdLeaf_R1


title: WT (Dp1Tyb cohort), 3

description: 10x Genomics


title: Root maturation zone (2mm), the 1st leaf stage, biol rep 3

description: Library name: Root_Maturation_Zone_R3

source_name: Root maturation zone (2mm) sampled at the 1st leaf stage

value: Root maturation zone (2mm)

value: the 1st leaf stage


title: Lamina flag leaf, W10, biol rep 3

description: Library name: FlagL_W10_R3

source_name: Lamina flag leaf sampled at W10


title: Root maturation zone (2mm), the 1st leaf stage, biol rep 1

description: Library name: Root_Maturation_Zone_R1


title: Root elongation zone (2mm), 1st leaf stage, biol rep 3

description: Library name: Root_Elongation_Zone_R3

source_name: Root elongation zone (2mm) sampled at 1st leaf stage

value: Root elongation zone (2mm)

value: 1st leaf stage


title: 203968030148_R01C01_P15/10_PFC

value: QSBB

value: male


title: Root maturation zone (2mm), the 1st leaf stage, biol rep 2

description: Library name: Root_Maturation_Zone_R2


title: 203968030168_R08C01_20152936_PFC


title: Dp1Tyb, 4

description: 10x Genomics

value: Heart

value: M


title: WT (Dp1TybDyrk1aKO cohort), 5

description: 10x Genomics

value: WT (Dp1TybDyrk1aKO cohort)


title: WT (Dp1TybDyrk1aKO cohort), 4

description: 10x Genomics


title: 203968030168_R02C01_PD180_PFC

value: female


title: Root elongation zone (2mm), 1st leaf stage, biol rep 1

description: Library name: Root_Elongation_Zone_R1

value: Svevo


title: 203968030168_R01C01_20174940_PFC

value: Prefrontal cortex


title: Root tip/apex (1mm), 1st leaf stage, biol rep 3

description: Library name: RootApex_R3

source_name: Root tip/apex (1mm) sampled at 1st leaf stage

value: Root tip/apex (1mm)


title: Root elongation zone (2mm), 1st leaf stage, biol rep 2

description: Library name: Root_Elongation_Zone_R2


title: Pistil, W7.5/Stigmatic Branches Elongating stage, biol rep 2

description: Library name: Pistil_W7.5_R2

value: Pistil


title: Root tip/apex (1mm), 1st leaf stage, biol rep 1

description: Library name: RootApex_R1


title: Root tip/apex (1mm), 1st leaf stage, biol rep 2

description: Library name: RootApex_R2


title: WT (Dp1Tyb cohort), 2

description: 10x Genomics

value: WT (Dp1Tyb cohort)


title: 203991460130_R08C01_20150242_PFC

value: Newcastle Brain Tissue Resource

value: FALSE


title: Dp1Tyb, 3

description: 10x Genomics

value: F


title: 203991460130_R06C01_20040022_PFC


title: 1st leaf, 1st leaf stage, biol rep 3

description: Library name: 1stLeaf_R3

source_name: 1st leaf sampled at 1st leaf stage

value: 1st leaf


title: 1st leaf, 1st leaf stage, biol rep 1

description: Library name: 1stLeaf_R1


title: 1st leaf, 1st leaf stage, biol rep 2

description: Library name: 1stLeaf_R2


title: WT (Dp1Tyb cohort), 1

description: 10x Genomics


title: Primary root, seedling stage, biol rep 3

description: Library name: Seedling_Root_R3

source_name: Primary root sampled at seedling stage

value: Primary root

value: seedling stage


title: 203991460130_R05C01_PD493_PFC

value: Imperial Brain Bank


title: Primary root, seedling stage, biol rep 2

description: Library name: Seedling_Root_R2


title: WT (Dp1TybDyrk1aKO cohort), 3

description: 10x Genomics


title: Primary root, seedling stage, biol rep 1

description: Library name: Seedling_Root_R1


title: WT (Dp1TybDyrk1aKO cohort), 2

description: 10x Genomics


title: Coleoptile/shoot, seedling stage, biol rep 2

description: Library name: Seedling_Shoot_R2

source_name: Coleoptile/shoot sampled at seedling stage

value: Coleoptile/shoot


title: 203991460107_R05C01_PDC081_PFC


title: Coleoptile/shoot, seedling stage, biol rep 1

description: Library name: Seedling_Shoot_R1


title: WT (Dp1TybDyrk1aKO cohort), 1

description: 10x Genomics

value: Heart


title: Dp1Tyb, 2

description: 10x Genomics

value: M


title: Primary and secondary buds of colony stage A1 - ML245-A1

first: Marie

last: Lebel

address: Stocker Road

department: Biosciences

description:
Library name: Sample 5
10X Genomics, ACME fixed cells, filtered matrix

data_processing:
Individual 10X sample libraries were demultiplexed using Cell Ranger Makefastq v7.0.0 with default settings.
Reads were quality-checked using FASTQC. For the buds samples (samples 1-8): Reads were mapped with CellRanger count (v7.1.0). The archived processed files were filtered for empty droplets. using CellRanger count automatic filtering. For the circulating cells samples (sample 9-10): Reads were mapped with CellRanger count (v6.1.2). The archived processed files are not filtered for empty droplets.
Assembly: The reference genome was prepared by concatenating: (1) the nuclear genome (BioProject PRJNA1225683), with the addition of a manually annotated Piwi2 gene (Boschl.Bs14.g18242-nested) to the GTF and (2) the published mitochondrial genome (sc6a-b isolate, GenBank: HF548551.1, GTF filtered to only the protein coding genes).
Supplementary files format and content: For the buds samples (samples 1-8):  Tab-separated files and matrixes.
Supplementary files format and content: For the circulating cells samples (sample 9-10): H5 files.

organism: Botryllus schlosseri

source_name: Primary and secondary buds

extract_protocol:
For the buds samples (samples 1-8): buds were microdissected along with their surrounding tunic and some ampullae and washed twice in in calcium- and magnesium-free artificial sea water (CMFASW; 31g/L NaCl, 0.8g/L KCl, 0.29g/L NaHCO3, 1.6g/L Na2SO4, pH 8.0) with 40U/ml RNAsin Plus (Promega). Buds were then detunicated and dissociated by pipetting in 0.2µm-filtered 1% Trypsin (m./v.) in CMFASW with 40 U/ml RNAsin Plus for 20-30 min. Cell suspensions with over 85% cell viability were fixed in ACME (10% acetic acid, 15% methanol, 10% glycerol in molecular grade water) with 40U/ml RNAsin Plus for 1h on ice, gently shaking, then stored at -20°C for up to a few days. Fixative was removed from cell suspensions by washing and centrifugating cells in 0.2µm-filtered 1% BSA in PBS, then stored at -80°C with 10% (v./v.)  DMSO. On the day of library preparation, cryopreserved samples were slowly thawed on ice, centrifuged and  resuspended in 1% BSA-PBS with 40U/ml RNAsin Plus. They were then filtered with 40µm cell strainer to remove largest aggregates, stained with Draq5 and sorted by FACS to select only single cells. For the circulating cells samples (sample 9-10): colonies were cleaned a couple hours before dissections and kept in 0.22µm filtered ASW until blood collection. At collection time, colonies were dried gently with a Kim wipe, then 100-200 µL of PBS-M-DTT (0.7M D-mannitol in 1X PBS with 0.01 M dithiothreitol, added fresh each day) was added on top. Blood was extracted by making multiple cuts in vascularized regions of the colony, and gently pressing on it. The PBS-M-DTT with suspended blood cells was collected and kept in a microcentrifuge tube on ice. Blood cells from several colonies at the same stage were pooled. Each cell suspension was filtered through a 40µm strainer into a microcentrifuge tube which had been coated with 10% (v./v.) bovine serum albumin in Dulbecco’s phosphate-buffered saline and washed by centrifugation before resuspension in PBS-M-DTT. The cell viability prior to encapsulation was 79% (Sample 9 -A1) and 80% (Sample 10 - B2).
Cell encapsulation, RT, cDNA amplification, and library preparation were carried out using the Chromium Next GEM Single Cell 3′ v3.1 Kits (10X Genomics 1000123, 1000127, and 1000190). For the buds samples (samples 1-8): The manufacturer’s guidelines were followed. The libraries were then sequenced (paired-end) on an Illumina NextSeq2000. When necessary, resequencing was performed to achieve a sequencing saturation of approximately 40% or higher. FASTQ files in this archive contain the concatenated reads from all sequencing of the same library. For the circulating cells samples (sample 9-10): The manufacturer’s guidelines were followed except for one step. To prepare the RT mix prior to cell encapsulation, the manufacturer protocol instructs to add nuclease-free water, then to add the cell suspension; we added PBS-M instead of nuclease-free water to adjust for live cells osmolarity.

value: Primary and secondary buds

value: colony stage A1

value: WT isogenic clone FC*


title: Secondary buds of colony stage D - ML245-D

description:
Library name: Sample 6
10X Genomics, ACME fixed cells, filtered matrix

source_name: Secondary buds

value: Secondary buds

value: colony stage D


title: Dp1Tyb, 1

description: 10x Genomics


title: Primary and secondary buds of colony stage B1 - ML232-B2

description:
Library name: Sample 4
10X Genomics, ACME fixed cells, filtered matrix

value: colony stage B2


title: Primary and secondary buds of colony stage C2 - ML263-C2

description:
Library name: Sample 7
10X Genomics, ACME fixed cells, filtered matrix

value: colony stage C2


title: 203991460127_R01C01_20090067_PFC

source_name: Prefrontal cortex

value: Prefrontal cortex

value: Newcastle Brain Tissue Resource

value: female


title: Primary and secondary buds of colony stage B2, replicate 2  - ML232-B1

description:
Library name: Sample 3
10X Genomics, ACME fixed cells, filtered matrix

value: colony stage B1


title: Primary and secondary buds of colony stage A2, ML232-A2

description:
Library name: Sample 2
10X Genomics, ACME fixed cells, filtered matrix

value: colony stage A2


title: Primary and secondary buds of colony stage B2, replicate 1  - ML231-B2

description:
Library name: Sample 1
10X Genomics, ACME fixed cells, filtered matrix


title: MSC-i.v

city: TIANJIN

first: HAO

last: YU

address: Building B3, TianDa Science and Technology Park, No. 80 Fourth Avenue, TEDA,Tianjin，China

institute: Tianjin AmcellGene Engineering Co., Ltd.

description:
Library name: MSC-i.v
MSC i.v (3×10000000 cells/kg), scRNAseq

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 mRatBN7.2  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mRatBN7.2
Supplementary files format and content: tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: blood

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cells culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: blood


title: 203991460154_R03C01_20110715_PFC

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

value: male

value: FALSE


title: 203991460154_R01C01_20163918_PFC


title: SCI

description:
Library name: SCI
SCI sample, scRNAseq


title: Sham

description:
Library name: Sham
sham sample, scRNAseq


title: RAW264.7, Guanine, input

first: Yueyu

last: Kong

address: Wuhan University

institute: Wuhan University

description: ChIP-seq

data_processing:
Sequencing adapters were trimmed by Trim galore (v0.6.7)
The chimeric Mus musculus genome (Mm10) was generated by STAR (v2.7.10a)
The clean reads were mapped to chimeric genome using STAR
Peaks were called by Macs2 (v2.1.1)
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: Ascites

growth_protocol: DMEM +10%FBS

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the sonication was performed using a Bioruptor (Minichiller 300, Diagenode) with 30 cycles (30 s on, 30 s off).
ChIP-seq libraries were generated using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607, Vazyme)

treatment_protocol: PBS/guanine (10μg/mL) for 24h

value: Ascites

value: Abelson murine leukemia virus-induced tumor

value: WT

value: Guanine treatment


title: MSC-i.t

description:
Library name: MSC-i.t
MSC i.t groups (1×10000000 cells/kg), scRNAseq


title: RAW264.7, PBS, rep2

description: ChIP-seq

value: PBS treatment


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, 100 ng/ml FGF8b, not DLX5 activated, rep 3

city: Helsinki

first: Shrinidhi

last: Madhusudan

state: Uusimaa

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Library name: F21_C

data_processing:
Raw reads (FASTQ) were quality-filtered using fastp; reads containing adapters, poly-N, or low-quality bases were removed to obtain clean reads. Q20, Q30, and GC content were calculated on the clean data.
Clean reads were aligned to the reference genome using HISAT2 v2.0.5
Gene-level read counts were quantified using featureCounts v1.5.0-p3, counting reads mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: Gene count matrices in Excel sheets (.xls, first column contains gene identifiers (Ensembl gene IDs)); each subsequent column contains the raw read counts for one sample, with column headers corresponding to the sample library names.

source_name: WA09 (WiCell)

growth_protocol: Human embryonic stem cells were differentiated to GnRH neurons using our previously established protocol, please refer those publications for details. PMID: 27426041, PMID: 31996360

extract_protocol:
Total RNA was extracted using NucleoSpin RNA (Machery-Nagel, Cat. 740955.250). Poly-T-oligo attached beads were used to isolate messenger RNA (mRNA) from total RNA. RNA integrity and quality were assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: For this publication, a DLX5 activation line was generated and this line was differentiated to GnRH neurons. For all conditions, cell were always DLX5 activated between Day10-Day20. Only for conditions stated, no FGF8b was given during Day10-Day20. Samples A and B are day20 all treated with 100 ng/ml FGF8b from day10-day20. Samples J and K are day25 neurons all treated with 100 ng/ml FGF8b from day10-day20. Samples B and K were additionally DLX5 activated from day10-day20. Samples, N#_A, F#_A and F#_C were all FACS-sorted day25 TdT positive GnRH neurons. Samples N#_A, F#_A were additionally DLX5 activated from day10-day20. Samples N#_A were NOT treated with FGF8b from day10-day20.

value: WA09 (WiCell)

value: human embryonic stem cells


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, 100 ng/ml FGF8b, not DLX5 activated, rep 2

description: Library name: F20_C


title: RAW264.7, PBS, rep1

description: ChIP-seq


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, 100 ng/ml FGF8b, not DLX5 activated, rep 1

description: Library name: F19_C


title: 203977090026_R07C01_PD801_PFC

first: Joshua

last: Harvey

address: RILD Building, RD&E, Barrack Road

value: Imperial Brain Bank


title: RAW264.7, PBS, input

description: ChIP-seq


title: LRS_polyA_U2OS_Rep2

first: Yulong

last: Song

address: No.1, Xinzao Road, Xinzao Town, Panyu District

institute: Guangzhou Medical University

description:
Library name: Sample 16
LRS polyA-selected RNA-seq

data_processing:
CLC Genomics Workbench v 11.0.1
The RNA-seq raw data was initially processed by Cutadapt (version v4.0; -q 30,30 --trim-n --length-tag 'length=' -m 36 -e 0.1), including removing the adapter sequences from the 3' end of reads and trimming the bases with quality scores lower than 30 from both 5’ and 3’ ends
Subsequently, the clean reads were aligned to the human reference genome (hg19) using STAR (version v2.7.10b) with the default parameters. And the corresponding Gencode v19 annotation files were obtained from UCSC table browser
Then, a custom perl script was used to calculate the editing level of each site, which is the percentage of reads with G bases in all reads
Only sites with a minimum coverage depth of 30 were retained for further analysis, and the cutoff of base quality is ≥ 30
Assembly: hg19
Supplementary files format and content: tab-delimited text file with the A-to-I RNA editing level

growth_protocol: HEK293T and U2OS cells were cultured in DMEM, supplemented with 10% fetal bovine serum and 100 U/ml penicillin G and 100 μg/ml streptomycin at 37°C under 5% CO2.

extract_protocol:
Total RNAs were then extracted using the FastPure® Cell/Tissue Total RNA Isolation Kit V2 (Vazyme Biotech Co., Ltd., RC112-01).
For the polyA-based mRNA enrichment, mRNAs were captured using VAHTS mRNA Capture Beads (Vazyme Biotech Co., Ltd., N401). For the rRNA-depleted method, ribosomal-depleted RNA was purified with Ribo-off rRNA Depletion kit (Vazyme Biotech Co., Ltd., N406). Then, the RNA-seq libraries were constructed with VAHTS Universal V8 RNA-Seq Library Prep Kit (Vazyme Biotech Co., Ltd., NRM605).

treatment_protocol: Without any treatment

value: Human osteosarcoma cell line derived from a bone tumour of a 15-year-old girl in 1964


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, 100 ng/ml FGF8b, DLX5 activated, rep 3

description: Library name: F21_A


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, 100 ng/ml FGF8b, DLX5 activated, rep 2

description: Library name: F20_A


title: AB20834

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample 20
element screen

data_processing:
bases2fastq version 2.2.0.1940753917 arguments --legacy-fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Tumor

extract_protocol:
Tumors were finely minced on ice and enzymatically digested in RPMI containing 1 mg/mL Collagenase IV and 0.05 mg/mL DNase I at 37°C for three cycles of 8 minutes each. Between incubations, tissues were mechanically dissociated using a gentleMACS dissociator.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were inoculated with 1M MCA205-hTREM2 cell line. On day 7 received 4-5M armored CAR TREM2 cells (24h post cyclo treatment) . On day 15 tumors were collected.

value: Tumor

value: tumor-infiltrating CAR T cell

tag: sorting gate

value: CAR

tag: batch


title: LRS_polyA_U2OS_Rep1

description:
Library name: Sample 15
LRS polyA-selected RNA-seq

tag: genotype


title: 203977090026_R05C01_20070105_PFC

institute: University of Exeter

value: Prefrontal cortex

value: Newcastle Brain Tissue Resource


title: AB20833

description:
Library name: Sample 19
element screen

tag: treatment


title: 203991390076_R07C01_19900113_PFC


title: 203991390105_R07C01_PD055_PFC

value: female


title: AB20832

description:
Library name: Sample 18
element screen


title: LRS_polyA_HEK293T_Rep1

description:
Library name: Sample 7
LRS polyA-selected RNA-seq

tag: cell line

value: Epithelial-like cell of Kidney


title: 203977090026_R03C01_PD502_PFC

value: male

value: FALSE


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, no FGF8b, DLX5 activated, rep 2

description: Library name: N20_A

tag: cell type


title: AB20831

description:
Library name: Sample 17
element screen


title: 203977090026_R02C01_NP14/017_PFC

tag: regiondescription

value: Oxford Brain Bank


title: C57BL/6J 8-10 weeks female, Liver, 36dpi, Biological replicate 4

city: Boston

first: Yuko

last: Hasegawa

state: MA

address: 181 Longwood Ave.

institute: Brigham and Women's Hospital

description:
Library name: Liver-day36-4
Liver_featureCounts.txt

data_processing:
Low-quality bases and the adaptors were trimmed using Trim Galore. The reads were mapped to the mouse reference genome (mm10) using STAR with default parameters, and the gene-level raw read count matrix was obtained using the featureCounts function in the subread using mouse GENCODE annotation M25 (GRCm38.p6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Liver

extract_protocol:
RNA was harvested by bead-beating the tissue in TRIzol
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Mice were orally gavaged with 5 × 10⁹ Citrobacter rodentium

value: Liver

value: WT

value: Cr infection

tag: time


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, no FGF8b, DLX5 activated, rep 1

description: Library name: N19_A

value: WA09 (WiCell)


title: C57BL/6J 8-10 weeks female, Liver, 36dpi, Biological replicate 3

description:
Library name: Liver-day36-3
Liver_featureCounts.txt


title: 203976760069_R06C01_NP12/136_PFC

tag: plate

tag: centre


title: WA09 cells, Day25, 100 ng/ml FGF8b, DLX5 activated, rep 5

description: Library name: K17

value: human embryonic stem cells


title: C57BL/6J 8-10 weeks female, Liver, 36dpi, Biological replicate 2

description:
Library name: Liver-day36-2
Liver_featureCounts.txt


title: 203968030087_R05C01_PD002_PFC

value: Imperial Brain Bank

tag: Sex

tag: thal

value: TRUE


title: AB20828

description:
Library name: Sample 14
element screen

value: Tumor


title: 203976760069_R01C01_PD717_PFC


title: C57BL/6J 8-10 weeks female, Liver, 36dpi, Biological replicate 1

description:
Library name: Liver-day36-1
Liver_featureCounts.txt


title: WA09 cells, Day25, 100 ng/ml FGF8b, DLX5 activated, rep 3

description: Library name: K15


title: AB20827

description:
Library name: Sample 13
element screen

value: tumor-infiltrating CAR T cell


title: C57BL/6J 8-10 weeks female, Liver, 21dpi, Biological replicate 4

description:
Library name: Liver-day21-4
Liver_featureCounts.txt


title: AB20826

description:
Library name: Sample 12
element screen

value: CAR


title: 203977090007_R05C01_NP10/011_PFC

value: Prefrontal cortex


title: WA09 cells, Day25, 100 ng/ml FGF8b, DLX5 activated, rep 1

description: Library name: K10


title: AB20825

description:
Library name: Sample 11
element screen


title: C57BL/6J 8-10 weeks female, Liver, 21dpi, Biological replicate 2

description:
Library name: Liver-day21-2
Liver_featureCounts.txt


title: WA09 cells, Day25, 100 ng/ml FGF8b, DLX5 activated, rep 2

description: Library name: K14


title: 203977090007_R01C01_PD1016_PFC


title: C57BL/6J 8-10 weeks female, Liver, 21dpi, Biological replicate 3

description:
Library name: Liver-day21-3
Liver_featureCounts.txt


title: 203991460130_R01C01_PD864_PFC


title: WA09 cells, Day25, 100 ng/ml FGF8b, not DLX5 activated, rep 5

description: Library name: J17


title: AB20824

description:
Library name: Sample 10
element screen


title: 203991460127_R06C01_20141901_PFC

value: Newcastle Brain Tissue Resource


title: 203977090008_R06C01_PD899_PFC


title: C57BL/6J 8-10 weeks female, Liver, 21dpi, Biological replicate 1

description:
Library name: Liver-day21-1
Liver_featureCounts.txt


title: Coleoptile/shoot, seedling stage, biol rep 3

first: Cristian

last: Forestan

address: Viale Fanin 44

description: Library name: Seedling_Shoot_R3

data_processing:
Raw reads quality filtering and trimming for adapter contaminants with Trimmomatic v0.39 (Bolger et al., 2014)
High quality reads were mapped to the Triticum durum cv. Svevo Rel 2.0 genome and annotation using STAR 2.7.10b (Dobin et al., 2013).
Read counts and transcripts per million TPM were calculated per gene using RSEM v1.3.3 (Li and Dewey, 2011).
Assembly: Svevo Rel2.0 genome assembly
Supplementary files format and content: tab delimited text file including rawcounts for each sample
Supplementary files format and content: tab delimited text file including TPM values for each sample

value: Coleoptile/shoot

tag: Stage

value: seedling stage

tag: cultivar

value: Svevo


title: AB20823

description:
Library name: Sample 9
element screen


title: C57BL/6J 8-10 weeks female, Liver, 17dpi, Biological replicate 4

description:
Library name: Liver-day17-4
Liver_featureCounts.txt


title: RAW264.7, Guanine, rep1

description: ChIP-seq

value: Ascites

value: Abelson murine leukemia virus-induced tumor

value: Guanine treatment


title: Primary and secondary buds of colony stage C1 - ML275-C1

description:
Library name: Sample 8
10X Genomics, ACME fixed cells, filtered matrix

value: Primary and secondary buds

value: colony stage C1

value: WT isogenic clone FC*


title: WA09 cells, Day25, 100 ng/ml FGF8b, not DLX5 activated, rep 4

description: Library name: J16

value: WA09 (WiCell)

value: human embryonic stem cells


title: RAW264.7, Guanine, rep2

description: ChIP-seq

value: WT


title: 203991460127_R05C01_PD880_PFC

value: Imperial Brain Bank

value: female

value: FALSE


title: 203991460154_R08C01_PD936_PFC

value: Prefrontal cortex


title: 203977090026_R08C01_20080081_PFC

value: Newcastle Brain Tissue Resource


title: 203977090008_R05C01_PD794_PFC

value: male


title: WA09 cells, Day25, 100 ng/ml FGF8b, not DLX5 activated, rep 3

description: Library name: J15


title: AB20822

description:
Library name: Sample 8
element screen

value: Tumor

value: tumor-infiltrating CAR T cell


title: C57BL/6J 8-10 weeks female, Liver, 17dpi, Biological replicate 3

description:
Library name: Liver-day17-3
Liver_featureCounts.txt

value: Liver

value: Cr infection


title: 203977090008_R04C01_P10/14_PFC

value: QSBB


title: 203977090005_R08C01_PD706_PFC


title: WA09 cells, Day25, 100 ng/ml FGF8b, not DLX5 activated, rep 2

description: Library name: J14


title: C57BL/6J 8-10 weeks female, Liver, 17dpi, Biological replicate 2

description:
Library name: Liver-day17-2
Liver_featureCounts.txt


title: AB20821

description:
Library name: Sample 7
element screen


title: AB20820

description:
Library name: Sample 6
element screen


title: WA09 cells, Day25, 100 ng/ml FGF8b, not DLX5 activated, rep 1

description: Library name: J10


title: 203977090026_R06C01_20030007_PFC


title: C57BL/6J 8-10 weeks female, Liver, 17dpi, Biological replicate 1

description:
Library name: Liver-day17-1
Liver_featureCounts.txt


title: 203977090005_R07C01_20080109_PFC


title: AB20819

description:
Library name: Sample 5
element screen


title: WA09 cells, Day20, 100 ng/ml FGF8b, DLX5 activated, rep 5

description: Library name: B17


title: C57BL/6J 8-10 weeks female, Liver, 10dpi, Biological replicate 4

description:
Library name: Liver-day10-4
Liver_featureCounts.txt


title: 203977090005_R05C01_20050096_PFC


title: WA09 cells, Day25, FACS-sorted TdT positive neurons, 100 ng/ml FGF8b, DLX5 activated, rep 1

description: Library name: F19_A


title: 203977090005_R04C01_20100979_PFC


title: C57BL/6J 8-10 weeks female, Liver, 10dpi, Biological replicate 3

description:
Library name: Liver-day10-3
Liver_featureCounts.txt


title: WA09 cells, Day20, 100 ng/ml FGF8b, DLX5 activated, rep 4

description: Library name: B16


title: AB20818

description:
Library name: Sample 4
element screen


title: WA09 cells, Day20, 100 ng/ml FGF8b, DLX5 activated, rep 3

description: Library name: B15


title: LRS_polyA_HEK293T_Rep2

city: Guangzhou

description:
Library name: Sample 8
LRS polyA-selected RNA-seq

value: Epithelial-like cell of Kidney


title: C57BL/6J 8-10 weeks female, Liver, 10dpi, Biological replicate 2

description:
Library name: Liver-day10-2
Liver_featureCounts.txt


title: AB20817

description:
Library name: Sample 3
element screen


title: 203977090005_R03C01_RI04/042_PFC

city: Exeter

value: Oxford Brain Bank


title: WA09 cells, Day20, 100 ng/ml FGF8b, DLX5 activated ,rep 2

description: Library name: B14


title: AB20815

description:
Library name: Sample 2
element screen


title: C57BL/6J 8-10 weeks female, Liver, 10dpi, Biological replicate 1

description:
Library name: Liver-day10-1
Liver_featureCounts.txt


title: WA09 cells, Day20, 100 ng/ml FGF8b, DLX5 activated, rep 1

description: Library name: B10


title: AB20814

description:
Library name: Sample 1
element screen


title: 203977090005_R02C01_PDC091_PFC


title: 203977090004_R08C01_PD163_PFC


title: C57BL/6J 8-10 weeks female, Liver, 6dpi, Biological replicate 4

description:
Library name: Liver-day6-4
Liver_featureCounts.txt


title: WA09 cells, Day20, 100 ng/ml FGF8b, not DLX5 activated, rep 5

description: Library name: A17


title: C57BL/6J 8-10 weeks female, Liver, 6dpi, Biological replicate 3

description:
Library name: Liver-day6-3
Liver_featureCounts.txt


title: WA09 cells, Day20, 100 ng/ml FGF8b, not DLX5 activated, rep 4

description: Library name: A16


title: 203977090004_R06C01_19970112_PFC


title: C57BL/6J 8-10 weeks female, Liver, 6dpi, Biological replicate 2

description:
Library name: Liver-day6-2
Liver_featureCounts.txt


title: XRN1_DMSO_4h_r2

first: Folkert

last: van Werven

description: Library name: sample 65

data_processing:
FASTQ files were processed using the nf-core/rnaseq pipeline (version 3.10.1; 10.5281/zenodo.1400710), executed using Nextflow (v23.10.0) (Di Tommaso et al., 2017). Reads were aligned to the Saccharomyces cerevisiae strain SK1 reference genome (SK1_SGD_2018_NCSL00000000) using STAR (2.7.10a)47, and gene-level quantification was performed with RSEM (v1.3.1).  Differential expression analysis was carried out with DESeq2 (1.48.1) using a simple design formula (~ group). Wald tests were used to assess differential expression. Multiple-testing correction was performed using Independent Hypothesis Weighting (IHW)50; genes with an IHW-adjusted p-value below 0.05 were considered significant. ashr 51 was used for effect-size shrinkage.
Assembly: SK1-MvO-V1
Supplementary files format and content: txt and counts

organism: Saccharomyces cerevisiae

source_name: diploid

growth_protocol: Cells were arrested in early meiosis as described previously 9. Briefly, yeast cells were inoculated in yeast extract peptone dextrose (YPD) media [1% weight/volume (w/v) yeast extract, 2% w/v bacto peptone, 2% w/v glucose, uracil (24 mg/l) and adenine (12 mg/l)] for approximately 24 hours, before being diluted to OD600 0.4 in buffered, yeast extract, tryptone, acetate (BYTA, (1.0% w/v yeast extract, 2.0% w/v peptone, 1% potassium acetate, 50 mM potassium phthalate monobasic) and incubated for 16-18 hours. OD600 1.8 of yeast cells were then washed and transferred to SPO (0.3% Potassium acetate, Acetic acid to pH 7.0, 0.02% D-(+)-Raffinose pentahydrate).

extract_protocol:
24 OD units were collected by centrifugation, and snap frozen in liquid nitrogen. Per 10 OD units, RNA was extracted with Tris-EDTA-SDS (TES) buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and Acid Phenol:Chloroform:Isoamyl alcohol (125:24:1, Ambion) at 65°C for 45 minutes. Precipitation was carried out. rDNase (Machery-Nagel) treatment was carried out, before spin column purification (Machery-Nagel).
For degron strains, libraries from 100 ng of RNA were generated using the NEBNext Ultra II Directional PolyA mRNA Kit (modules K0105 and K0078), following the manufacturer’s protocols. Paired-end sequencing (100 bp) was performed on an Illumina NovaSeq X platform, with a minimum depth of 20 million reads per sample.

treatment_protocol: 3 hours after transfer to sporulation medium, copper (II) sulphate (CuSO4, 50 μM) and indole-3-acetic acid (IAA, 500 μM) were added to induce auxin-induced protein depletion. In all steps yeast were grown at 30°C at 300 rpm, and a 1:10 culture volume to flask total volume ratio was maintained.

value: diploid yeast cell

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 XRN1-3V5-IAA7:KanMX10

value: DMSO


title: XRN1_DMSO_4h_r1

description: Library name: sample 64

value: MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, trp1::hisG his3:p550 XRN1-3V5-IAA7:KanMX9


title: C57BL/6J 8-10 weeks female, Liver, 6dpi, Biological replicate 1

description:
Library name: Liver-day6-1
Liver_featureCounts.txt

value: WT


title: 203977090004_R01C01_PD1030_PFC

value: Imperial Brain Bank

value: female


title: 203977090004_R02C01_NP15/007_PFC

value: Prefrontal cortex

value: FALSE


title: WA09 cells, Day20, 100 ng/ml FGF8b, not DLX5 activated, rep 2

description: Library name: A14

value: WA09 (WiCell)

value: human embryonic stem cells