title: WT female mouse blood animal6

description:
PM_mWT_Cistr_F3_blood_S54_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT female


title: scRNAseq_8cell_R43_4

status: Public on Nov 18 2025

type: SRA

city: Bethesda

first: Guanghui

last: Yang

state: Maryland

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

country: USA

institute: National Institutes of Health

library_source: transcriptomic single cell

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference genome contains sequences of GRCm38 and ERCC spike-in.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 101) and ERCC spike-in product page.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM, TPM values for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Blastomere

extract_protocol:
Znhit3+/- female mice were injected intraperitoneally with eCG (5 IU) followed 46 h to 48 h with hCG (5 IU) and then co-caged with Znhit3+/- males. Fertilized zygotes were flushed from plugged females 16 h post hCG injection and cultured in M2 medium containing hyaluronidase to remove the cumulus mass. Zygotes without cumulus were then washed and cultured in advanced KSOM until 8-cell stage. When collecting samples, embryos were first washed in PBS and transferred into acidic Tyrode’s solution to remove zonae pellucidae. Single zona-free embryo was then pipetted into a capillary tube with a diameter of 1.5 to 2 times of the diameter of single blastomeres to physically dissociate single blastomeres. Single blastomeres that remained intact were transferred into PCR strips  containing 2.5 µl of RLT plus buffer.
RNAs in each sample were captured by oligo-dT beads and then processed following the G&T-seq protocol to construct the scRNA-Seq library.

tag: strain

tag: developmental stage

tag: cell type

value: Blastomere


title: 4 Gy, protons, organoids, 6 days, mouse 3

city: Groningen

first: Davide

last: Cinat

address: Hanzeplein 1

country: Netherlands

institute: University Medical Center Groningen

description: Lexogen

library_source: transcriptomic

data_processing:
For the alignment of the fastq files the mouse genome GRCm39 was used. The gene counts per sample were detected with the QuantSeq 3' mRNA-seq Integrated Data Analysis Pipeline on the BlueBee Genomics Platform provided by Lexogen with default settings. Rstudion v4.1.3 was used for downstream analysis and for the generation of CPM files. The R package edgeR was used for normalization and identification of differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files including the raw counts and tab-delimited text files including the CPM for all timepoints, replicates and doses are provided.

source_name: Submandibular salivary gland

growth_protocol: Organoids from all animals and conditions were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
For the cDNA library preparation, total RNA was extracted from organoids at 2 and 6 days post irradiation using Rneasy Mini Kit according to the manufacturer`s instructions and its quality was determined using High Sensitivity RNA ScreenTapes on an Agilent 2100 Bioanalyzer. 100 ng of RNA was used as an input for all samples.
100 ng of highly intact RNA (RIN values > 9) was processed for the cDNA library preparation using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following the manufacturers protocol.

treatment_protocol: Organoids were irradiated with either 4, 7 and 15 Gy photons or 4, 7 and 15 Gy (plateau) protons at day 5. Organoid media of all conditions was refreshed after irradiation. Organoids were collected at either day 2 (48 hr) or day 6 post irradiation. Since photon and proton irradiations were performed on different days, each irradiation type and timepoint has its own control (non-irradiated).

tag: tissue

value: Submandibular salivary gland

tag: age

value: 8-12 weeks old

value: Salivary gland cells derived from organoids

tag: treatment

value: Proton-irradiated 4 Gy


title: Control, protons, organoids, 6 days, mouse 2

description: Lexogen

value: Non-irradiated


title: WT female mouse blood animal5

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
PM_mWT_Cistr_F3_blood_S54_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

data_processing:
We aligned reads to hg38 using STAR aligner, version 2.7.0f. We used FeatureCounts to count reads aligning to genes in GENCODE v32 (human), vM33 (mouse).
Assembly: hg38, mm39
Supplementary files format and content: text files include RPKM values for each sample

molecule: total RNA

source_name: blood

extract_protocol:
RNA was harvested and purified using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following manufacturer's protocols.

value: blood

tag: genotype


title: WT male mouse blood animal2 lane1

description:
PM_mWT_Cistr_M3_blood_S72_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT male


title: WT female mouse blood animal4

description:
PM_mWT_Cistr_F2_blood_S24_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: Control, protons, organoids, 6 days, mouse 1

description: Lexogen


title: EZHIP_mHet_Bl_RNAseq_rep2

city: Beijing

first: Feng

last: Kong

address: Qinghuayuan Street

country: China

institute: Tsinghua University

description:
Library name: Sample 29
EZHIP_KO_E3.5_1_FPKM.txt

data_processing:
All mRNA-seq data were trimmed by Trim Galore v0.4.2 and subsequently mapped to the mm9 transcriptome using HISAT2 v.2.2.1 (Kim et al., 2019). The gene expression level was calculated by StringTiev2.1.2 (Pertea et al., 2016). based on the annotation of mm9/hg19 refFlat database from UCSC genome browser. HTSeq v.0.6.0 (Anders et al., 2015) was applied to calculate counts per gene with default parameters.
Assembly: mm9
Supplementary files format and content: fpkm

source_name: mouse pre-implantation embryos, E3.5

extract_protocol:
Oocytes or embryos were lysed and used directly as input materials for subsequent RNA-seq library preparation
All RNA-seq libraries followed the smart-seq2 protocol as previously describeb (Picelli et al., 2014) and were sequenced by the DNBSEQ-T7 system according to the manufacturer's instructions.

treatment_protocol: GSK343 was dissolved in DMSO as 10uM stock. To block EZH2 activity in embryos, PN3 stage zygotes were collected and cultured in KSOM containing 2.5μM GSK343 or DMSO as control, and then collected at the 8C stage for the following experiments.

value: mouse pre-implantation embryos, E3.5

value: Ezhip mHet


title: EZHIP_mKO_8C_RNAseq_rep3

description:
Library name: Sample 25
EZHIP_KO_8C_FPKM.txt

source_name: mouse pre-implantation embryos, 8 cell

value: mouse pre-implantation embryos, 8 cell

value: Ezhip mKO


title: scRNAseq_8cell_R43_2


title: scRNAseq_8cell_R43_3


title: EZHIP_WT_Bl_RNAseq_rep1

description:
Library name: Sample 26
EZHIP_KO_E3.5_1_FPKM.txt

value: wide type


title: scRNAseq_8cell_R43_6


title: WT male mouse blood animal1 lane1

description:
PM_mWT_Cistr_M2_blood_S66_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT female mouse blood animal3

description:
PM_mWT_Cistr_F2_blood_S24_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_8C_RNAseq_rep2

description:
Library name: Sample 24
EZHIP_KO_8C_FPKM.txt


title: scRNAseq_8cell_R43_1


title: 15 Gy, protons, organoids, 2 days, mouse 3

description: Lexogen

value: Proton-irradiated 15 Gy


title: 15 Gy, protons, organoids, 2 days, mouse 2

description: Lexogen


title: EZHIP_mKO_8C_RNAseq_rep2

description:
Library name: Sample 23
EZHIP_KO_8C_FPKM.txt


title: WT female mouse blood animal2

description:
PM_mWT_Cistr_F1_blood_S18_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: 15 Gy, protons, organoids, 2 days, mouse 1

description: Lexogen


title: scRNAseq_8cell_R43_5


title: scRNAseq_8cell_R42_8


title: EZHIP_mKO_8C_RNAseq_rep1

description:
Library name: Sample 22
EZHIP_KO_8C_FPKM.txt


title: Control, protons, organoids, 6 days, mouse 3

description: Lexogen


title: scRNAseq_8cell_R42_7


title: EZHIP_mHet_8C_RNAseq_rep1

description:
Library name: Sample 21
EZHIP_KO_8C_FPKM.txt


title: Cistr KO male mouse bone marrow animal4

description:
PM_mKO_Cistr_M5_bmarrow_S606_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

source_name: bone marrow

value: bone marrow

value: Cistr-/- male


title: Cistr KO male mouse bone marrow animal3

description:
PM_mKO_Cistr_M4_bmarrow_S599_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_8C_RNAseq_rep1

description:
Library name: Sample 20
EZHIP_KO_8C_FPKM.txt


title: 7 Gy, protons, organoids, 2 days, mouse 2

description: Lexogen

value: Proton-irradiated 7 Gy


title: scRNAseq_8cell_R42_6

value: Blastomere


title: scRNAseq_8cell_R42_5


title: Cistr KO male mouse bone marrow animal2 lane2

description:
PM_mKO_Cistr_M2_bonem_S37_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R42_4


title: EZHIP_mKO_L2C_RNAseq_rep1

description:
Library name: Sample 18
EZHIP_KO_L2C_FPKM.txt

source_name: mouse pre-implantation embryos, late 2 cell


title: 4 Gy, protons, organoids, 2 days, mouse 2

description: Lexogen

value: Submandibular salivary gland


title: EZHIP_mHet_L2C_RNAseq_rep2

description:
Library name: Sample 17
EZHIP_KO_L2C_FPKM.txt

value: mouse pre-implantation embryos, late 2 cell


title: scRNAseq_8cell_R42_3


title: EZHIP_mKO_L2C_RNAseq_rep2

description:
Library name: Sample 19
EZHIP_KO_L2C_FPKM.txt


title: Cistr KO male mouse bone marrow animal2 lane1

description:
PM_mKO_Cistr_M2_bonem_S37_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT female mouse blood animal1

description:
PM_mWT_Cistr_F1_blood_S18_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT female


title: 4 Gy, protons, organoids, 2 days, mouse 1

description: Lexogen

value: 8-12 weeks old

value: Salivary gland cells derived from organoids

value: Proton-irradiated 4 Gy


title: scRNAseq_8cell_R42_2


title: Cistr KO male mouse bone marrow animal1 lane2

description:
PM_mKO_Cistr_M1_bonem_S31_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R42_1


title: Cistr KO male mouse bone marrow animal1 lane1

description:
PM_mKO_Cistr_M1_bonem_S31_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_mHet_L2C_RNAseq_rep1

description:
Library name: Sample 16
EZHIP_KO_L2C_FPKM.txt


title: Cistr KO female mouse bone marrow animal3 lane2

description:
PM_mKO_Cistr_F3_bonem_S25_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: Cistr-/- female


title: Control, protons, organoids, 2 days, mouse 3

description: Lexogen

value: Non-irradiated


title: scRNAseq_8cell_R40_8


title: 7 Gy, protons, organoids, 2 days, mouse 3

description: Lexogen


title: EZHIP_WT_L2C_RNAseq_rep2

description:
Library name: Sample 15
EZHIP_KO_L2C_FPKM.txt


title: EZHIP_WT_L2C_RNAseq_rep1

description:
Library name: Sample 14
EZHIP_KO_L2C_FPKM.txt


title: Cistr KO female mouse bone marrow animal3 lane1

description:
PM_mKO_Cistr_F3_bonem_S25_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: 4 Gy, protons, organoids, 2 days, mouse 3

description: Lexogen


title: 7 Gy, protons, organoids, 2 days, mouse 1

description: Lexogen


title: Cistr KO female mouse bone marrow animal2 lane2

description:
PM_mKO_Cistr_F2_bonem_S7_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_mKO_PN5_RNAseq_rep2

description:
Library name: Sample 13
EZHIP_KO_PN5_FPKM.txt

source_name: mouse pre-implantation embryos, 1 cell

value: mouse pre-implantation embryos, 1 cell


title: Control, protons, organoids, 2 days, mouse 1

description: Lexogen


title: scRNAseq_8cell_R40_6


title: 15 Gy, photons, organoids, 6 days, mouse 3

description: Lexogen

value: Photon-irradiated 15 Gy


title: Control, protons, organoids, 2 days, mouse 2

description: Lexogen


title: EZHIP_mHet_PN5_RNAseq_rep2

description:
Library name: Sample 12
EZHIP_KO_PN5_FPKM.txt

value: Ezhip mHet


title: Cistr KO female mouse bone marrow animal1 lane2

description:
PM_mKO_Cistr_F1_bonem_S1_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R40_5


title: scRNAseq_8cell_R40_4


title: 15 Gy, photons, organoids, 6 days, mouse 1

description: Lexogen


title: 15 Gy, photons, organoids, 6 days, mouse 2

description: Lexogen


title: Cistr KO female mouse bone marrow animal1 lane1

description:
PM_mKO_Cistr_F1_bonem_S1_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_PN5_RNAseq_rep2

description:
Library name: Sample 11
EZHIP_KO_PN5_FPKM.txt

value: wild type


title: scRNAseq_8cell_R40_3


title: EZHIP_mHet_PN5_RNAseq_rep1

description:
Library name: Sample 9
EZHIP_KO_PN5_FPKM.txt


title: WT male mouse bone marrow animal4

description:
PM_mWT_Cistr_M3_bonem_S67_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT male


title: EZHIP_mKO_PN5_RNAseq_rep1

description:
Library name: Sample 10
EZHIP_KO_PN5_FPKM.txt

value: Ezhip mKO


title: scRNAseq_8cell_R40_2


title: 7 Gy, photons, organoids, 6 days, mouse 3

description: Lexogen

value: Photon-irradiated 7 Gy


title: 7 Gy, photons, organoids, 6 days, mouse 2

description: Lexogen


title: scRNAseq_8cell_R40_1


title: EZHIP_WT_PN5_RNAseq_rep1

description:
Library name: Sample 8
EZHIP_KO_PN5_FPKM.txt


title: WT male mouse bone marrow animal3

description:
PM_mWT_Cistr_M3_bonem_S67_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: bone marrow


title: 7 Gy, photons, organoids, 6 days, mouse 1

description: Lexogen


title: WT male mouse bone marrow animal2

description:
PM_mWT_Cistr_M2_bonem_S61_L002
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R40_7

value: Blastomere


title: EZHIP_KO_FGO_RNAseq_rep3

description:
Library name: Sample 7
EZHIP_KO_FGO_FPKM.txt

source_name: mouse oocytes, FGO

value: mouse oocytes, FGO

value: Ezhip KO


title: scRNAseq_8cell_R39_8


title: 4 Gy, photons, organoids, 6 days, mouse 3

description: Lexogen

value: Submandibular salivary gland

value: Photon-irradiated 4 Gy


title: EZHIP_Het_FGO_RNAseq_rep2

description:
Library name: Sample 6
EZHIP_KO_FGO_FPKM.txt

value: Ezhip Het


title: Cistr KO female mouse bone marrow animal2 lane1

description:
PM_mKO_Cistr_F2_bonem_S7_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: WT male mouse bone marrow animal1

description:
PM_mWT_Cistr_M2_bonem_S61_L001
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: scRNAseq_8cell_R39_7


title: 4 Gy, photons, organoids, 6 days, mouse 2

description: Lexogen

value: 8-12 weeks old

value: Salivary gland cells derived from organoids


title: WT female mouse bone marrow animal2

description:
PM_mWT_Cistr_F5_bmarrow_S629_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus

value: WT female


title: WT female mouse bone marrow animal1

description:
PM_mWT_Cistr_F4_bmarrow_S622_L004
Mouse_CISTR.GENCODEvM33.RPKM.genPos.consensus


title: EZHIP_WT_FGO_RNAseq_rep2

description:
Library name: Sample 5
EZHIP_KO_FGO_FPKM.txt


title: scRNAseq_8cell_R39_6


title: 4 Gy, photons, organoids, 6 days, mouse 1

description: Lexogen


title: EZHIP_KO_FGO_RNAseq_rep2

description:
Library name: Sample 4
EZHIP_KO_FGO_FPKM.txt


title: scRNAseq_8cell_R39_5


title: scRNAseq_8cell_R39_4


title: Control, photons, organoids, 6 days, mouse 3

description: Lexogen

value: Non-irradiated


title: scRNAseq_8cell_R39_3


title: EZHIP_KO_FGO_RNAseq_rep1

description:
Library name: Sample 3
EZHIP_KO_FGO_FPKM.txt


title: Control, photons, organoids, 6 days, mouse 1

description: Lexogen


title: CH12F3_Ligase4-KO_Valemetostat_3

city: Boston

first: Roberto

last: Chiarle

state: Ma

address: Longwood 333

institute: Boston Childrens Hospital

data_processing:
Docker4seq (https://github.com/kendomaniac/docker4seq) rnaseqCount function default parameter
Assembly: mm9
Supplementary files format and content: tab delimited

growth_protocol: Cells were cultured at 37 °C with 5% CO2

extract_protocol:
Total RNA was isolated from indicated cells with RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and genomic DNA was removed by genomic DNA binding columns in the kit.
Libraries were generated and sequenced by Novogene Corporation Inc. Briefly, Poly(A)-containing mRNA was purified from total RNA using poly(T) oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification; then was sequenced through Illumina NovaSeq (PE150) to obtain ~40 million paired-end reads (12G) per sample.

treatment_protocol: RNA-seq libraries were prepared from CH12F3 Ligase4-deficient cells stimulated with anti-CD40–IL-4–TGF-β for 24 h

tag: cell line

value: Mouse B-lymphoma cells

value: Ligase4 KO

value: anti-CD40–IL-4–TGF-Beta + valemetostat


title: CH12F3_Ligase4-KO_Valemetostat_1

description: Libraries were generated and sequenced by Novogene Corporation Inc.


title: Control, photons, organoids, 6 days, mouse 2

description: Lexogen


title: EZHIP_Het_FGO_RNAseq_rep1

description:
Library name: Sample 2
EZHIP_KO_FGO_FPKM.txt


title: CH12F3_Ligase4-KO_Valemetostat_2


title: scRNAseq_8cell_R39_1


title: WT_D14_oocytes

description: Library name: Sample 1

data_processing:
Raw reads were trimmed with cutadapt v1.14 with parameters , and the trimmed reads were sequentially mapped to mouse rRNAs sequences (mm9) using Bowtie2 v2.2.2 (Langmead and Salzberg, 2012). Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a (Dobin et al., 2013). The gene expression level was then calculated by Cufflinks v2.2.1 (Trapnell et al., 2010) based on the annotation of CDS region, defined by mm9/hg19 refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: fpkm
Library strategy: Ribo-Seq

source_name: mouse oocytes, D14

extract_protocol:
Oocytes or embryos were lysed and used directly as input materials for subsequent RNA-seq library preparation
All Ribo-lite libraries were subjected to sequencing library preparation by D-Plex Small RNA-seq Kit (Diagenode; C05030001) and were sequenced by the DNBSEQ-T7 system according to the manufacturer's instructions.

value: mouse oocytes, D14

value: wild type


title: scRNAseq_8cell_R39_2


title: EZHIP_WT_FGO_RNAseq_rep1

description:
Library name: Sample 1
EZHIP_KO_FGO_FPKM.txt


title: 1167 Cell Line,120h,Replicate 3 , GridION

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Library name: Sample72
1167_120h_3

data_processing:
RNA Sequencing (both short and long reads) was performed at the National Institute on Aging. Nanopore was base-called using Guppy v. 6.0.1. Short-read data were processed by checking quality (FastQC v. 0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trimming (BBDuk, https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), and mapping to the human genome 38 and annotation version 104 using STAR (v. 2.7.10a). Minimap version 2.17 was used for mapping long-read data.
Stringtie2 (v. 2.2.1) was used for quantification and assembly.
Assembly: HG38 v. 104
Supplementary files format and content: Data at the isoform level generated by stringtie2.
Supplementary files format and content: Tab delimited .txt file containing counts for all samples.

organism: Homo sapiens

growth_protocol: Human myoblast cell lines AB1167 and AB678 were cultured in Hamm's F10 media with 20% fetal bovine serum (FBS) and Promocell Skeletal Muscle Cell Growth Medium. AB678 and AB1167 myoblasts were cultured in proliferative conditions (day 0).

extract_protocol:
RNA was collected every 24 hours over the 5-day differentiation period. Total RNA collection included a digestion step using DNase I, extracted using Direct-zol™ RNA MiniPrep kit (Zymo Research). RNA quality and quantity were checked using Agilent RNA Screen Tape on the Agilent Tapestation.
For Illumina (short-read) sequencing libraries were prepared from 150 ng RNA, using an Illumina TruSeq Stranded mRNA Library prep kit following the manufacturer’s protocol (Illumina, Cat#20020594). For Nanopore (long-read) sequencing, 75 ng of RNA were used to prepare the sequencing library using a cDNA-PCR Sequencing Kit (SQK-PCS109) following the manufacturer’s protocol (Oxford Nanopore).

treatment_protocol: This study has no chemical treatment to the cells. However, in this study we investigated molecular processes during muscle differentiation , therefore the intervention applied was aimed to differentiate the cell lines. We induced AB678 and AB1167 myoblasts to differentiate by culturing them to high density and replacing the growth medium with differentiation medium, Dulbecco’s modified Eagle medium, (DMEM) containing 2% horse serum.

value: Muscle

tag: time


title: 15 Gy, photons, organoids, 2 days, mouse 3

description: Lexogen

value: Photon-irradiated 15 Gy


title: scRNAseq_8cell_R35_8

value: Blastomere


title: scRNAseq_8cell_R35_7


title: CH12F3_Ligase4-KO_Tazemetostat_2

value: anti-CD40–IL-4–TGF-Beta + tazemetostat


title: 1167 Cell Line,120h,Replicate 1 , GridION

description:
Library name: Sample70
1167_120h_1


title: 1167 Cell Line,120h,Replicate 2 , GridION

description:
Library name: Sample71
1167_120h_2


title: 7 Gy, photons, organoids, 2 days, mouse 3

description: Lexogen

value: Photon-irradiated 7 Gy


title: CH12F3_Ligase4-KO_DMSO_3

value: anti-CD40–IL-4–TGF-Beta + DMSO


title: 7 Gy, photons, organoids, 2 days, mouse 2

description: Lexogen

value: Submandibular salivary gland


title: 1167 Cell Line,96h,Replicate 3 , GridION

description:
Library name: Sample69
1167_96h_3


title: 15 Gy, photons, organoids, 2 days, mouse 1

description: Lexogen


title: 15 Gy, photons, organoids, 2 days, mouse 2

description: Lexogen


title: CH12F3_Ligase4-KO_DMSO_2


title: CH12F3_Ligase4-KO_Tazemetostat_1


title: 1167 Cell Line,96h,Replicate 2 , GridION

description:
Library name: Sample68
1167_96h_2


title: CH12F3_Ligase4-KO_DMSO_1


title: scRNAseq_8cell_R35_4


title: scRNAseq_8cell_R35_5


title: CH12F3_Ligase4-KO_Tazemetostat_3


title: 7 Gy, photons, organoids, 2 days, mouse 1

description: Lexogen


title: 1167 Cell Line,96h,Replicate 1 , GridION

description:
Library name: Sample67
1167_96h_1


title: 4 Gy, photons, organoids, 2 days, mouse 3

description: Lexogen

value: Photon-irradiated 4 Gy


title: 4 Gy, photons, organoids, 2 days, mouse 2

description: Lexogen

value: 8-12 weeks old


title: 1167 Cell Line,72h,Replicate 3 , GridION

description:
Library name: Sample66
1167_72h_3


title: 4 Gy, photons, organoids, 2 days, mouse 1

description: Lexogen

value: Salivary gland cells derived from organoids


title: 1167 Cell Line,72h,Replicate 2 , GridION

description:
Library name: Sample65
1167_72h_2


title: Hippocampus, sham, scRNA-seq

city: Xi’an

first: Jiaxi

last: Xu

address: 76 West Yanta Road

institute: Xi’an Jiaotong University

description: single-cell sequencing

data_processing:
fastp software(V:0.23.1) was used for quality control of sequencing data
STAR software (V:2.7.1a) was used for comparison analysis
subread software (V:1.6.4) was used for quantitative analysis
seeksoul tools software (V:1.0.0) was used for single-cell data quality control and matrix data generation
seurat software (V:4.0.5) was used for cell dimensionality reduction clustering
Assembly: GRCm38
Supplementary files format and content: include gene count values for each sample

source_name: Hippocampus

extract_protocol:
DOCA-salt- or sham-treated WT mice (n=3 mice/group) were euthanized, and their sensory cortex and hippocampus were rapidly dissected on ice.
SeekOne® Digital Droplet Single Cell 3’ library preparation kit (SeekGene Catalog No.K00202)

value: Hippocampus

value: WT

value: DOCA-salt treatment


title: scRNAseq_8cell_R35_6


title: scRNAseq_8cell_R35_1


title: scRNAseq_8cell_R35_2


title: 1167 Cell Line,72h,Replicate 1 , GridION

description:
Library name: Sample64
1167_72h_1


title: Hippocampus, DOCA-salt treatment,scRNA-seq

description: single-cell sequencing


title: scRNAseq_8cell_R34_7


title: Control, photons, organoids, 2 days, mouse 1

description: Lexogen

value: Non-irradiated


title: AR10-3

city: Guangzhou

first: Xiang

last: Li

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-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.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.

source_name: Heart

extract_protocol:
Snap frozen heart tissues were ground to powder under liquid nitrogen. Pulverized samples were used for total RNA extraction using TRIzol reagent (Thermo Fisher Scientific, USA), and RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Heart

value: Minimally invasive surgery-induced aortic regurgitation (heart failure phase)

tag: time point

value: 10 weeks


title: Control, photons, organoids, 2 days, mouse 2

description: Lexogen


title: Cortex, sham, scRNA-seq

description: single-cell sequencing

source_name: Cortex

value: Cortex

value: sham


title: 1167 Cell Line,48h,Replicate 3 , GridION

description:
Library name: Sample63
1167_48h_3

value: Muscle


title: scRNAseq_8cell_R34_8

value: Blastomere


title: AR10-4


title: 1167 Cell Line,48h,Replicate 2 , GridION

description:
Library name: Sample62
1167_48h_2


title: scRNAseq_8cell_R35_3


title: AR10-2


title: scRNAseq_8cell_R34_6


title: U87/Compound A

type: RNA

city: Charlottesville

first: Zhongqiu

last: Xie

state: VA

address: 1574 Broad Crossing Rd, , Charlottesville

institute: university of virginia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized

label_protocol: not provided

growth_protocol: U87 grow in MEM medium

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Compound A or DMSO trearment

value: Compound A


title: 1167 Cell Line,48h,Replicate 1 , GridION

description:
Library name: Sample61
1167_48h_1


title: AR10-1


title: scRNAseq_8cell_R34_4


title: scRNAseq_8cell_R34_5


title: U87/DMSO

value: DMSO


title: AR4-4

value: Minimally invasive surgery-induced aortic regurgitation (compensatory phase)

value: 4 weeks


title: MLN1

first: Jiao

last: Fan

address: Fuxing road

institute: 301 hospital

description: Library name: MLN1

data_processing:
The quality control of RNA-seq data was done by FastQC (v0.11.8).
The RNA-seq data was trimmed by Trim Galore (v0.6.1) with default parameters for pair-end data to remove the low-quality reads and adaptors.
The trimmed RNA-seq data were aligned to the mm10 mouse transcriptome using STAR (v2.5.0a) with default parameters.
Gene expression was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using HTSeq.
Assembly: mm10
Supplementary files format and content: gene_count.txt

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol.
Use Oligo dT magnetic beads to enrich mRNA from total RNA.

value: peripheral blood

value: Monocytic cell line


title: 1167 Cell Line,24h,Replicate 2 , GridION

description:
Library name: Sample59
1167_24h_2


title: MLN2

description: Library name: MLN2


title: Cortex, DOCA-salt treatment,scRNA-seq

description: single-cell sequencing


title: 1167 Cell Line,24h,Replicate 1 , GridION

description:
Library name: Sample58
1167_24h_1


title: Control, photons, organoids, 2 days, mouse 3

description: Lexogen

value: Submandibular salivary gland

value: 8-12 weeks old

value: Salivary gland cells derived from organoids


title: AR4-3


title: scRNAseq_8cell_R34_3


title: scRNAseq_8cell_R34_2


title: AR4-2


title: scRNAseq_8cell_R34_1


title: oxLDL1

description: Library name: oxLDL1


title: 1167 Cell Line,24h,Replicate 3 , GridION

description:
Library name: Sample60
1167_24h_3


title: S3

value: Sham


title: oxLDL3

description: Library name: oxLDL3


title: 1167 Cell Line,0h,Replicate 1 , GridION

description:
Library name: Sample55
1167_0h_1


title: 678 Cell Line,120h,Replicate 3 , GridION

description:
Library name: Sample54
678_120h_3


title: 1167 Cell Line,0h,Replicate 3 , GridION

description:
Library name: Sample57
1167_0h_3


title: oxLDL2

description: Library name: oxLDL2


title: AR4-1

value: Heart


title: S4


title: scRNAseq_8cell_R33_8


title: scRNAseq_8cell_R33_6


title: Supermere, series D

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

description: Library name: D5

data_processing:
The reads were trimmed for adapters and polyX tails, then filtered by sequencing Phred quality (>= Q15) using fastp. We then aligned reads to the human transcriptome (Ensembl version 104) using kallisto and converted transcript counts to gene counts using tximport.
Assembly: Ensembl version 104
Supplementary files format and content: CSV of gene counts

source_name: Supermere

extract_protocol:
Total RNA was isolated from EVs and NVEPs using Qiagen microRNA isolation kit as recommended by manufacturer.
Total RNA, either 40–200 ng of EV/ NVEPs RNA, or 2 μg of cellular RNA, was rRNA-depleted using the Ribo-Zero rRNA Removal Kits (Illumina, CA). One quarter of the rRNA-depleted RNA was fragmented to 100–500 nt using the 5× First-Strand Buffer (Clontech, CA), and utilized for the RNA library construction by SMARTer Stranded RNA-Seq Kit (Clontech). The quality of libraries were examined using the Agilent DNA 1000 kit at the Agilent 2100 Bioanalyzer instrument, and cDNA quantified by qRT-PCR. The libraries were sequenced on HiSeq 2000 (Illumina).

value: Supermere

tag: series

value: D


title: Supermere, series E

description: Library name: E5

value: E


title: scRNAseq_8cell_R33_7


title: Supermere, series C

description: Library name: C5

value: C


title: 678 Cell Line,120h,Replicate 1 , GridION

description:
Library name: Sample52
678_120h_1

value: Muscle


title: scRNAseq_8cell_R33_4

value: Blastomere


title: B16F10 tongue xenograft, LN-nociceptive nerve inhibition-3

city: Shanghai

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: tongue xenograft

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: tongue xenograft

value: murine melanoma

value: WT

value: inhibition of LN-innervating nociceptive nerves


title: S2


title: scRNAseq_8cell_R33_5


title: S1


title: Supermere, series A

description: Library name: A5

value: A


title: B16F10 tongue xenograft, LN-nociceptive nerve inhibition-2


title: 678 Cell Line,96h,Replicate 3 , GridION

description:
Library name: Sample51
678_96h_3


title: 1167 Cell Line,0h,Replicate 2 , GridION

description:
Library name: Sample56
1167_0h_2


title: scRNAseq_8cell_R33_3


title: Exomere, series D

description: Library name: D4

source_name: Exomere

value: Exomere


title: 678 Cell Line,96h,Replicate 1 , GridION

description:
Library name: Sample49
678_96h_1


title: B16F10 tongue xenograft, LN-nociceptive nerve inhibition-1


title: Exomere, series E

description: Library name: E4


title: scRNAseq_8cell_R33_1

source_name: Blastomere


title: Morula_KO_3

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed with Cutadapt ver. 4.2 using AAAAAAAAAA as the adapter sequence, then mapped to the reference genome with STAR ver. 2.7.6a. The mouse rDNA (GenBank: BK000964.3) was used as the reference genome.
PCR duplicates were removed from the aligned bam file which was then transferred into sam format. The 5' end of each read in the sam file was examined with a home-made C++ program.
Assembly: BK000964.3
Supplementary files format and content: Statistics of rRNA bases at the 5' end of sequencing reads as well as their RiboMeth scores

source_name: embryos

extract_protocol:
Znhit3KI/- female mice were injected intraperitoneally with eCG (5 IU) followed 46 h to 48 h with hCG (5 IU) and then co-caged with Znhit3KI/- males. Fertilized zygotes were flushed from plugged females 16 h post hCG injection and cultured in M2 medium containing hyaluronidase to remove the cumulus mass. Zygotes without cumulus were then washed and cultured in advanced KSOM until intended developmental stages. Before sample collection, embryos were first examined by immunofluorescence (IF) staining to confirm expression of the HA tag fused to Znhit3 in the knock-in (KI) allele. All IF reagents were supplied with 0.5U/μl RNase inhibitor. Embryos without the knock-in allele were treated as KO and others as control. 15~20 zona-free KO or control embryos were used as one group which were washed in PBS and then transferred into acidic Tyrode’s solution to remove zonae pellucidae before collecting into PCR strips with 5 µl RLT plus lysis buffer.
9 μl RNAclear beads (1:1.8 ratio) were used to purify RNA in each group. 10 μl 50 mM Na2CO3/NaHCO3 buffer (pH 9.2) were used for elution with 5min incubation before heating at 95 °C for 10min in a PCR cycler to finish hydrolysis. 1μl 1N HCl was added to bring down the pH. 22 ul RNAclear XP beads and 28ul 100% isopropanol were then added to bind the fragmented RNA in each group. The beads were washed twice with 180ul 85% ethanol and eluted with 10μl Antarctic phosphatase reaction mix containing 7.5μl H2O, 1μl 10x Antarctic phosphatase reaction buffer, 1μl Antarctic phosphatase (NEB M0289S) and 0.5μl 20U/μl RNase inhibitor. Incubation at 37 °C for 30min and then 70 °C for 5min was performed to finish de-phosphorylation and enzyme inactivation. After de-phosphorylation, RNA fragments were purified again by adding 18ul RNAclear XP beads and 27ul 100% isopropanol. The RNAclear XP beads were eluted with 10μl poly-adenylation mix from the SMARTer smRNA-Seq kit (Takara 635029) after washing. Other steps of the product manual were followed to finish the library preparation with 14 PCR cycles for library amplification.

value: embryos

value: Morula


title: 678 Cell Line,72h,Replicate 3 , GridION

description:
Library name: Sample48
678_72h_3


title: scRNAseq_8cell_R33_2


title: 678 Cell Line,120h,Replicate 2 , GridION

description:
Library name: Sample53
678_120h_2


title: Exomere, series A

description: Library name: A4


title: Exomere, series C

description: Library name: C4


title: B16F10 tongue xenograft, control-3

value: vehicle-treated


title: SEV, series E

description: Library name: E3

source_name: SEV

value: SEV


title: B16F10 tongue xenograft, control-1


title: Morula_KO_1


title: B16F10 tongue xenograft, control-2


title: 678 Cell Line,72h,Replicate 2 , GridION

description:
Library name: Sample47
678_72h_2


title: SF1CreSRBIfl/fl, liver, CLP6h, rep3

city: Lexington

first: Xiang-An

address: 741 S Limestone

institute: University of Kentucky

data_processing:
3 steps for Data Quality Control: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Hisat2 v2.0.5 - mapping reads to reference genome
featureCounts v1.5.0-p3-quantification of gene expression level
DESeq2 R package (1.20.0)/edgeR R package (3.22.5) - Differential expression analysis
Ensembl release 94
Assembly: tab-delimited text file include raw count of sequencing reads
Supplementary files format and content: tab-delimited text file include the FPKM value with the annotation of each gene

source_name: Liver

extract_protocol: Paired-end 150bp on Illumina platform, 250-300bp insert cDNA library, output is 30 Million each direction

treatment_protocol:
CLP (25G, half ligation) treatment for 6h
Isolate RNA by using RNeasy Kits from Qiagen and following manufacturer's instructions

value: Liver

value: CLP 6h


title: 678 Cell Line,72h,Replicate 1 , GridION

description:
Library name: Sample46
678_72h_1


title: 678 Cell Line,48h,Replicate 3 , GridION

description:
Library name: Sample45
678_48h_3


title: Morula_KO_2


title: SEV, series D

description: Library name: D3

value: D


title: Morula_Ctrl_3

value: Znhit3KI/KI or Znhit3KI/-


title: SF1CreSRBIfl/fl, liver, CLP6h, rep2


title: 678 Cell Line,48h,Replicate 2 , GridION

description:
Library name: Sample44
678_48h_2


title: SEV, series C

description: Library name: C3

value: C


title: Morula_Ctrl_2


title: SF1CreSRBIfl/fl, liver, CLP6h, rep1


title: 678 Cell Line,96h,Replicate 2 , GridION

description:
Library name: Sample50
678_96h_2

value: Muscle


title: SEV, series A

description: Library name: A3


title: 678 Cell Line,24h,Replicate 3 , GridION

description:
Library name: Sample42
678_24h_3


title: Morula_Ctrl_1


title: 678 Cell Line,48h,Replicate 1 , GridION

description:
Library name: Sample43
678_48h_1


title: 8C_KO_3


title: LEV, series D

description: Library name: D2

source_name: LEV

value: LEV


title: SRBIfl/fl, liver, CLP6h, rep3

value: SRBIfl/fl


title: SRBIfl/fl, liver, CLP6h, rep2


title: 678 Cell Line,24h,Replicate 2 , GridION

description:
Library name: Sample41
678_24h_2


title: LEV, series E

description: Library name: E2

value: E


title: 8C_KO_2


title: 678 Cell Line,24h,Replicate 1 , GridION

description:
Library name: Sample40
678_24h_1


title: LEV, series C

description: Library name: C2


title: SRBIfl/fl, liver, CLP6h, rep1


title: LEV, series A

description: Library name: A2


title: L3

first: yao

last: shan

address: Xinzao

institute: guangzhou

data_processing:
For transcriptome analysis, fastp software (https://github.com/OpenGene/fastp) was used to exclude the reads containing adaptor contamination, base with low quality, and undetermined bases with default parameters and verify the quality of the sequence. The reads were mapped with HISAT2 (https://ccb.jhu.edu/software/hisat2) and assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. All transcriptomes from all samples were then merged to reconstruct a comprehensive transcriptome with gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts.
Assembly: GRCm38
Supplementary files format and content: gene fpkm for each Sample

source_name: brain

extract_protocol:
In brief, total RNA was extracted from PrL tissue using TRIzol reagent (Invitrogen, Carlsbad, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: brain

tag: group

value: sexual motivation low group mice


title: 8C_Ctrl_3


title: Cell, series E

description: Library name: E1

source_name: Cell

value: Cell


title: L2


title: 8C_Ctrl_2


title: Cell, series D

description: Library name: D1


title: 678 Cell Line,0h,Replicate 2 , GridION

description:
Library name: Sample38
678_0h_2


title: L1


title: 678 Cell Line,0h,Replicate 1 , GridION

description:
Library name: Sample37
678_0h_1


title: 8C_Ctrl_1


title: Cell, series C

description: Library name: C1


title: H3

value: sexual motivation high group mice


title: efferocytic macrophages

city: ANN ARBOR

first: Hernan

last: Roca

state: MI

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

description:
Library name: sample 2
10X Genomics

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
RNA-seq reads were aligned with STARsolo (v2.7.10) and background subtraction and cell detection were done using cellbender (v0.3.0)
https://github.com/porchard/snRNAseq-NextFlow
Assembly: mm10
Supplementary files format and content: .h5 files generated by cellbender

source_name: Bone marrow derived macrophages

extract_protocol:
All samples were then stained with F4/80-APC (ThermoFisher) and flow cytometric sorting was performed. F4/80+(APC)/CT+ (efferocytic) macrophages and control F4/80-APC+ (non-engulfing) macrophages were sorted, and each cell population was subsequently processed for single-cell RNA sequencing
Briefly, cells were combined with an RT-mix and up to eight samples loaded in wells of a Chromium chip. Partitioning oil and beads (each containing a polydT sequence, a 10x barcode sequence, and a unique molecular identifier sequence for each barcode), were also loaded on the chip. The 10x Chromium machine captures a single barcoded bead in an oil droplet, along with zero, one, or two cells according to a Poisson distribution, such that 60% of the loaded cells are captured. Following capture in the oil droplet, the mRNA was reverse transcribed into cDNA, and a portion was then amplified by PCR and fragmented. Adaptors were ligated and the product amplified again, using one of 96 indexing primer sets. Invitrogen Dynabeads and Beckman Coulter SPRI select beads were used to purify the product and ensure the final size range of the library to be sequenced was 200-800bp.  V3 chemistry was used.

value: Bone marrow derived macrophages

value: macrophage

value: efferocytotic


title: CH12F3_Ligase4-KO_Valemetostat_2

description:
PE38
CH12F3_Lig4-KO_Valemetostat.bw
CH12F3_Lig4-KO_Valemetostat.bedgraph

library_source: other

data_processing:
The adapter was removed using cutadapt software
Duplicates were removed using Picard software
Index and alignment was performed using Bowtie software --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 20
Assembly: GRCm37/mm9
Supplementary files format and content: Bigwig
Supplementary files format and content: Bedgraph
Library strategy: Cut&Tag

molecule: other

extract_protocol:
The library preparation was performed with the CUT&Tag-IT™ Assay Kit (Active Motif, cat. no. 53160).
The CUT&Tag for H3K27ac libraries were sequenced through Illumina MiniSeq (PE38)

treatment_protocol: CUT&Tag for H3K27ac libraries were prepared from CH12F3 Ligase4-deficient cells stimulated with anti-CD40–IL-4–TGF-β for 24 h

value: Mouse B-lymphoma cells

value: Ligase4 KO

value: anti-CD40–IL-4–TGF-Beta + valemetostat


title: H2


title: CH12F3_Ligase4-KO_Valemetostat_1


title: Cell, series A

description: Library name: A1

value: A


title: CH12F3_Ligase4-KO_Valemetostat-5

data_processing:
GEAT_docker(https://github.com/alessandriLuca/HTGTS_alignment) default parameters
Assembly: mm9
Supplementary files format and content: bedfiles tab separated
Library strategy: LAM-HTGTS

extract_protocol:
The library preparation was performed as previously described in Zhang, X. et al, Nature 575, 385-389 (2019).
12-16 samples were pooled and sequenced through Illumina MiSeq (PE250) by the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

treatment_protocol: LAM-HTGTS libraries were prepared from different CH12F3 mutants stimulated with anti-CD40–IL-4–TGF-β for 72 h

value: anti-CD40–IL-4–TGF-Beta + Valemetostat


title: control macrophages

description:
Library name: sample 1
10X Genomics

value: control


title: POc04478_3

city: Nanning

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

data_processing:
The original file sequenced by the MGI high-throughput sequencer is an image file. After base calling and Bcl2Fastq conversion, the original sequenced reads in FASTQ (fq for short) format can be obtained, which is called raw data or raw reads.
The original sequencing data will contain linker information, low-quality bases, and undetected bases (represented by N). These information will cause great interference to subsequent information analysis. These interference information will be removed by fine filtering methods. The final data is valid data, we call it Clean data or Clean read.
Use SOAPnuke software (v2.1.0) to filter Raw reads to get Clean reads. The main parameters are: –lowQual=20, –nRate=0.005, –qualRate=0.5, other parameters are default. The steps of data processing are as follows: 1) Filter out the paired reads containing the linker sequence.2) Remove paired reads with a ratio of N (N means that the base information cannot be determined) greater than 0.5%.3) Remove low-quality paired reads (reads with Qphred<=20 bases accounting for more than 50% of the entire read length).
Image recognition, decontamination, and adapter removal of sequencing results. Statistical results include the number of sequencing reads, data yield, Q20 content, Q30 content, GC content, etc
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: Penicillium oxalicum strains were cultured on PDA at 28°C for 4 days, and the spores were washed with 0.2% Tween-80 to obtain fresh spore fluid.

extract_protocol:
RNA was extracted with Trizol,  the purity of RNA (OD260/280) was detected by Nanodrop2000. The integrity of RNA were accurately detected by Agilent 2100,the detection indicators include: RIN value, 28S/18S, whether the map baseline is raised, 5S peak, and electrophoresis to detect whether the RNA sample is diffuse or has a genome DNA contamination.
After the sample is qualified, the library is constructed. The main process is as follows: 1) mRNA enrichment for total RNA by mRNA enrichment method: Enrich mRNA with polyA tail using magnetic beads with Oligo dT. 2) Fragment the RNA obtained by interrupting the buffer, perform reverse transcription with random N6 primers, and synthesize the double-stranded cDNA to form double-stranded DNA. 3) Fill in the end of the synthesized double-stranded DNA and phosphorylate the 5' end, form a sticky end with a protruding "A" at the 3' end, and then connect a bubbling linker with a protruding "T" at the 3' end. 4) The ligation product is amplified by PCR with specific primers. 5) The PCR product is thermally denatured into single-stranded DNA, and then a single-stranded circular DNA library is obtained by circularizing the single-stranded DNA with a bridge primer.

treatment_protocol: Fresh spore fluid was inoculated into the glucose medium for 24 hours and then transferred to the enzyme-producing medium containing Avicel as the only carbon source for 24 hours.

value: Mycelium

value: Silencing of POc04478 gene after adding 5 microM of copper ions

value: Culture in enzyme production medium with raw starch after transfer 24h


title: H1


title: 678 Cell Line,0h,Replicate 3 , GridION

description:
Library name: Sample39
678_0h_3

value: Muscle


title: 8C_KO_1

value: embryos


title: CH12F3_Ligase4-KO_Tazemetostat_2

description:
PE38
CH12F3_Lig4-KO_Tazemetostat.bw
CH12F3_Lig4-KO_Tazemetostat.bedgraph

value: anti-CD40–IL-4–TGF-Beta + tazemetostat


title: POc04478_2


title: CH12F3_Ligase4-KO_Tazemetostat_1


title: CH12F3_Ligase4-KO_Valemetostat-3


title: Treat_2

city: Shenzhen

first: Xiaodong

last: Wang

address: Xueyuan Avenue

institute: Shenzhen University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), and low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: MDA-MB-231 cells

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen). 2 μg total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina (Wuhan Seqhealth Co., Ltd.) following manufacturer's protocols.

value: MDA-MB-231 cells

value: tumor cells

value: WT

value: treated by BN1 for 24 h


title: CH12F3_Ligase4-KO_DMSO_2

description:
PE38
CH12F3_Lig4-KO_DMSO.bw
CH12F3_Lig4-KO_DMSO.bedgraph

value: anti-CD40–IL-4–TGF-Beta + DMSO


title: Treat_1


title: CH12F3_Ligase4-KO_Valemetostat-2

value: Mouse B-lymphoma cells


title: PoxKu70_3


title: CH12F3_Ligase4-KO_DMSO_1

value: Ligase4 KO


title: Control_3

value: no treatment


title: CH12F3_Ligase4-KO_Tazemetostat-5

value: anti-CD40–IL-4–TGF-Beta + Tazemetostat


title: Control_2


title: PoxKu70_1


title: 786-O cells, shRNA METTL3, replicate 3

city: Birmingham

first: Chen

last: Huang

state: AL

address: 720 20th St S

institute: University of Alabama at Birmingham

description: Library name: Sample 6

data_processing:
Reads were aligned to the human reference genome (GRCh38 p13, Release 39) from Gencode using STAR (version 2.7.10b) with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All. The aligned reads were assembled into genes, and their abundance was estimated as fragments/kilobase of exon/million fragments mapped using Salmon.
Assembly: GRCh38 p13, Release 39
Supplementary files format and content: tab-delimited text files including raw count for each samples
Supplementary files format and content: tab-delimited text files including fpkm for each samples

source_name: kidney

extract_protocol:
For RNA sequencing from control and METTL3-knockdown 786-O cells, total RNAs isolated from 786-O cells stably expressing either control shRNA or METTL3-targeted shRNA were subjected to RNA sequencing using the DNBSEQ platform from BGI Genomics (San Jose, CA, USA). Briefly, high-quality (RIN>8) total RNAs isolated from cultured cells by the RNA miniprep kit (Zymo Research) were rRNA-depleted, fragmented (~200 bp), and converted to ds-cDNA.
After adapter ligation, size-selected (~200-300 bp) sequencing libraries were prepared, which were then used to produce DNA nanoballs (DNBs), following BGI’s DNBSEQ protocol. Sequencing was performed in the DNBSEQ-G400 platform, generating >50 million reads/samples with paired-end 150 bp reads.

value: kidney

value: epithelial cells


title: 786-O cells, shRNA METTL3, replicate 2

description: Library name: Sample 5


title: PoxKu70_2

value: Mycelium


title: Control_1


title: cle_acc_3

city: Singapore

first: Sally

last: Koh

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

description: Library name: Sample 20

data_processing:
STAR ver. 2.7.10a for genome mapping
Assembly: Lactuca sativa reference genome (V8)
Supplementary files format and content: Raw read counts, with one sample per column in the compiled .xlsx file.

organism: Lactuca sativa

source_name: Whole seedling

growth_protocol: Four-day-old whole seedlings of Lactuca sativa var. Little Gem were grown on MS basal medium under continuous light (24 h) at 22 °C

extract_protocol:
The seedlings are first removed from treatment solution, and then snap frozen in liquid nitrogen. RNA was extracted using the Rneasy Plant Mini Kit (Qiagen) according to the manufactuere's instructions. Dnase digestion was carried out during the RNA extraction procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four-day-old seedlings were transferred to the following treatment for 2 h incubation: control (H2O), vehicle control (0.02% ethanol), 10 µM ABA, 10 µM ACC, 10 µM CLE12p, 10 µM ABA + CLE12p and 10 µM ABA + ACC.

value: Whole seedling

value: 10 µM CLE12p + 10 µM ACC

value: 2 h


title: CH12F3_Ligase4-KO_Tazemetostat-4


title: 786-O cells, shRNA METTL3, replicate 1

description: Library name: Sample 4


title: CH12F3_Ligase4-KO_Tazemetostat-3


title: CH12F3_Ligase4-KO_Valemetostat-4

value: anti-CD40–IL-4–TGF-Beta + Valemetostat


title: Anableps eye - adult 2

city: Baton Rouge

first: Patricia

last: Schneider

state: Louisiana

address: LSU 131 Life Sciences Building

department: Biological Sciences

institute: Louisiana State University

description:
Library name: D1_Aa_eye_adult2
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequences were aligned to Anableps anableps genome (GCA_014839685.1) to gene expression count using Space Ranger's default settings - version 3.1.3.
Gene Expression level of RefSeq coding genes were quantified using Spacer Ranger's default settings - version 3.1.3.
The data analysis was made in the Loupe browser software - version 8.1.2.
Assembly: GCA_014839685.1
Supplementary files format and content: Aa_Eye_A1_Aa_Eye_A11_Merged_Resize002_ch00.tif: Imagem of tissue.
Supplementary files format and content: A1_Aa_head_barcodes.tsv.gz: list of spatial barcodes.
Supplementary files format and content: A1_Aa_head_features.tsv.gz: list of genes.
Supplementary files format and content: A1_Aa_head_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format.
Supplementary files format and content: Aa_Eye_B1_Aa_Eye_B11_Merged_Resize002_ch00.tif:  Imagem of tissue.
Supplementary files format and content: B1_Aa_head_eye_barcodes.tsv.gz: list of spatial barcodes.
Supplementary files format and content: B1_Aa_head_eye_features.tsv.gz: list of genes.
Supplementary files format and content: B1_Aa_head_eye_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format.
Supplementary files format and content: Aa_Eye_C1_Aa_Eye_C11_Merged_Resize002_ch00.tif:  Imagem of tissue.
Supplementary files format and content: C1_Aa_eye_adult1_barcodes.tsv.gz: list of spatial barcodes.
Supplementary files format and content: C1_Aa_eye_adult1_features.tsv.gz: list of genes.
Supplementary files format and content: C1_Aa_eye_adult1_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format.
Supplementary files format and content: Aa_Eye_D1_Aa_Eye_D11_Merged_Resize002_ch00.tif: Imagem of tissue.
Supplementary files format and content: D1_Aa_eye_adult2_barcodes.tsv.gz: list of spatial barcodes.
Supplementary files format and content: D1_Aa_eye_adult2_features.tsv.gz: list of genes.
Supplementary files format and content: D1_Aa_eye_adult2_matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format.
Library strategy: Spatial Transcriptomics

organism: Anableps anableps

source_name: Eye

extract_protocol:
Fresh frozen head and eye were OCT embedded, and 10µm frozen sections were cut with cryostat (Leica).
Spatial transcriptome sequencing libraries were prepared with the 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to the manufacturer's instructions.

value: Eye

tag: batch


title: 786-O cells, shRNA Control, replicate 3

description: Library name: Sample 3


title: POc04478_1

value: Silencing of POc04478 gene after adding 5 microM of copper ions

value: Culture in enzyme production medium with raw starch after transfer 24h


title: CH12F3_Ligase4-KO_Tazemetostat-2


title: Anableps eye - adult 1

description:
Library name: C1_Aa_eye_adult1
Fresh frozen Spatial transcriptome sequencing


title: cle_acc_1

description: Library name: Sample 18


title: cle_acc_2

description: Library name: Sample 19


title: CH12F3_Ligase4-KO_Tazemetostat-1


title: Anableps head - stage 3 and eye - stage 5

description:
Library name: B1_Aa_head_eye
Fresh frozen Spatial transcriptome sequencing

source_name: Head and eye

value: Head and eye


title: CH12F3_Ligase4-KO_Valemetostat-1


title: CH12F3_Ligase4-KO_DMSO-5


title: cle_aba_3

description: Library name: Sample 17

value: 10 µM CLE12p + 10 µM ABA


title: Anableps head - stage 4

description:
Library name: A1_Aa_head_S4
Fresh frozen Spatial transcriptome sequencing

source_name: Head

value: Head


title: 786-O cells, shRNA Control, replicate 1

description: Library name: Sample 1


title: H2122.DPP4.DMSO_H2122.DPP4.DMSO1_R2

city: Asahikawa

first: Hiraku

last: Yanada

country: Japan

institute: Asahikawa Medical University

description: Library name: Sample4

data_processing:
The obtained raw reads were trimmed and quality-filtered using Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and Cutadapt (version 1.16). The trimmed reads were mapped to the human GRCh38 genome using STAR (version 2.7.2b). Reads on the annotated genes were counted using featureCounts (version 1.6.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and featurecount values for each samples.

source_name: Lung

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Cat.# 74106).
Isolation Module (New England BioLabs), double-stranded cDNA libraries (RNA-seq libraries) were prepared using the SMARTer stranded RNA-Seq kit v2 (Clontech) and the DNBSEQ MGIEasy Universal Library Conversion Kit (MGI Tech) according to the manufacturer’s instructions.

value: Lung


title: Aa retina, rep2_1

description:
Library name: Aa_retina2_1
Parse

data_processing:
snRNA-seq FASTQ files were processed using the TrailmakerTM piping module (https://app.trailmaker.parsebiosciences.com/) pipeline v1.4.0, Parse Biosciences, 2024).
The heatmaps and UMAP were generated using the Seurat v5 R package.
Assembly: GCA_014839685.1
Supplementary files format and content: Aa_retina_all_genes.csv.gz: list of genes.
Supplementary files format and content: Aa_retina_cell_metadata.csv.gz: list of barcodes.
Supplementary files format and content: Aa_retina_count_matrix.mtx.gz: Gene expression count matrix.

source_name: Retina

extract_protocol:
Nucleus suspensions from adult retina were fixed and frozen using the Evercode Nuclei Fixation Kit v3 from Parse Biosciences following the manufacturer’s protocol.
Fixed nuclei were processed with the Evercode WT Mini v3 Kit (Parse Biosciences) targeting 5,000 nuclei/sample. Libraries were sequenced to ~20,000 reads/nucleus on an Illumina NovaSeq X Plus (paired-end, 150 bp).

value: Retina

value: multiple


title: cle_aba_1

description: Library name: Sample 15


title: H2122.DPP4.DMSO_H2122.DPP4.DMSO1_R1

description: Library name: Sample3


title: CH12F3_Ligase4-KO_DMSO-3

first: Roberto

institute: Boston Childrens Hospital

value: Mouse B-lymphoma cells

value: Ligase4 KO

value: anti-CD40–IL-4–TGF-Beta + DMSO


title: cle_3

description: Library name: Sample 14

value: 10 µM CLE12p


title: cle_2

description: Library name: Sample 13

value: Whole seedling


title: H2122.LUC.DMSO_H2122.LUC.DMSO1_R2

description: Library name: Sample2


title: H2122.LUC.DMSO_H2122.LUC.DMSO1_R1

description: Library name: Sample1


title: CH12F3_Ligase4-KO_DMSO-1


title: 786-O cells, shRNA Control, replicate 2

description: Library name: Sample 2

value: kidney

value: epithelial cells


title: KO-BMDM-3

first: Jin

address: Yanchang Road

institute: Shanghai Tongji Stomatological Hospital and Dental School

description:
Library name: Sample6
Column name in gene_count.txt: K_3

data_processing:
NovaSeq Reagent Kit (NovaSeq X Plus)
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: gene_count.txt: gene count expression quantification and annotation for each sample

source_name: bone marrow-derived macrophages

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library,
The  RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego,CA) using 1μg of total RNA.

value: bone marrow-derived macrophages

value: lincRNA-EPS knockout

value: RANKL induced


title: L3 sample 3

city: Cologne

first: Walter

last: Sandt

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: CECAD

description: Library name: L3.3

data_processing:
fastp processing followed by salmon alignment
Assembly: caenorhabditis_elegans.PRJNA13758.WBPS15.mRNA_transcripts.fa caenorhabditis_elegans.PRJNA13758.WBPS15.genomic.fa (decoy)
Supplementary files format and content: raw_counts.csv

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
Each condition contained three biological replicates of 8000 worms, collected in ice-cold 1x M9 buffer from plates seeded with OP50. The samples were washed three times with 1x M9 buffer, resuspended in Trizol (Invitrogen) and 0.7 mm zirconia beads (Roth), and quick-frozen in liquid nitrogen at -80°C until RNA extraction was performed. The samples were disrupted using a Precellys24 homogenizer (Bertin) and 1-Bromo-3-chloropane (Sigma-Aldrich) was added for phase separation.
The purification of RNA was performed using the RNeasy Mini Kit (Qiagen) according to the provided instructions. The isolated RNA was eluted in RNase-free H2O and quantified using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific).

value: Whole worm

value: daf-2 constitutive mutant of N2 strain

value: reference


title: CH12F3_AID-WT_Valemetostat-8

last: Chiarle

address: Longwood 333

value: anti-CD40–IL-4–TGF-Beta + Valemetostat


title: cle_1

description: Library name: Sample 12

value: 2 h


title: L3 sample 2

description: Library name: L3.2


title: cle_aba_2

description: Library name: Sample 16

value: 10 µM CLE12p + 10 µM ABA


title: KO-BMDM-1

description:
Library name: Sample4
Column name in gene_count.txt: K_1


title: acc_2

description: Library name: Sample 10

value: 10 µM ACC


title: L3 sample 1

description: Library name: L3.1


title: CH12F3_AID-WT_Valemetostat-6

value: Mouse B-lymphoma cells


title: WT-BMDM-3

description:
Library name: Sample3
Column name in gene_count.txt: W_3

value: WT


title: CH12F3_Ligase4-KO_DMSO-4

value: Ligase4 KO

value: anti-CD40–IL-4–TGF-Beta + DMSO


title: acc_1

description: Library name: Sample 9

value: Whole seedling


title: Dauer Day30, exit 24h, sample 3

description: Library name: D30.24.3

value: Dauer Day30, exit 24h


title: Aa retina, rep2

description:
Library name: Aa_retina2
Parse

value: Retina

value: multiple


title: CH12F3_AID-WT_Valemetostat-5


title: Aa retina, rep1

description:
Library name: Aa_retina1
Parse


title: CH12F3_Ligase4-KO_DMSO-2


title: WT-BMDM-2

description:
Library name: Sample2
Column name in gene_count.txt: W_2

value: bone marrow-derived macrophages


title: aba_3

description: Library name: Sample 8

value: 10 µM ABA


title: Dauer Day30, exit 24h, sample 2

description: Library name: D30.24.2

value: Whole worm


title: CH12F3_AID-WT_Valemetostat-4


title: WT-BMDM-1

description:
Library name: Sample1
Column name in gene_count.txt: W_1

value: RANKL induced


title: acc_3

description: Library name: Sample 11


title: CH12F3_AID-WT_Valemetostat-3


title: aba_2

description: Library name: Sample 7


title: CH12F3_AID-WT_Valemetostat-7


title: KO-BMDM-2

description:
Library name: Sample5
Column name in gene_count.txt: K_2

value: lincRNA-EPS knockout


title: MiceConj1_ADT

first: Pablo

last: Argüeso

address: 800 Washington St

department: Ophthalmology

institute: Tufts Medical Cener

description:
Library name: Mice3_ADT
lectin-derived oligonucleotide (ADT-like)
MiceConj1_filtered_feature_bc_matrix.h5
mCornea_joint.clean.rds

data_processing:
Raw sequencing data were aligned, filtered, and normalized using Cell Ranger (v7.2.0).
Assembly: GRCh38 - human, mm10 - mice
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: Seurat object with merged and processed samples: hCornea.joint.rds
Supplementary files format and content: Seurat object with merged and processed samples: mCornea.joint.rds
Library strategy: CITE-seq

molecule: protein

source_name: Conjunctiva

extract_protocol:
Human corneal–limbal and conjunctival tissues were incubated separately at 37 °C for 2 hours in DMEM/F12 containing 2.4 IU/mL Dispase II (Thermo Fisher Scientific, Waltham, MA, USA). The epithelia were scraped, collected, and further digested with Gibco™ TrypLE (Thermo Fisher Scientific) for 5 minutes. The remaining stromal and conjunctival fragments were cut into small pieces, placed each in a MACS C tube (Miltenyi Biotec, Bergisch Gladbach, Germany) containing 4 mg/mL collagenase A (Sigma-Aldrich, St. Louis, MO, USA) in DMEM, and digested for 1 hour at 37 °C using a gentleMACS dissociator (Miltenyi Biotec). After digestion, single cells from all individual compartments were pooled, filtered through a 70 µm cell strainer (Miltenyi Biotec), washed in PBS supplemented with 0.04% bovine serum albumin (BSA; Sigma-Aldrich), and counted. Cells were resuspended in cold 0.04% BSA-PBS, and cold methanol was added dropwise to a final concentration of 80%. Samples were incubated at –20 °C for 30 minutes before storage at –80 °C.  Mouse conjunctival and corneal tissues were digested separately in DMEM containing 2 mg/mL collagenase A and 10 mg/mL Dispase II at 37 °C for 1 hour. During digestion, tissues were gently triturated by passing them through a 20G syringe needle five times every 20 minutes. Following enzymatic digestion, samples were rinsed with DMEM and incubated in TrypLE (Thermo Fisher Scientific) for 10 minutes at 37 °C. Cell suspensions were filtered through a 70 µm cell strainer, washed in 0.04% BSA-PBS, and counted. Cells were resuspended in cold 0.04% BSA–PBS, and cold methanol was added dropwise to a final concentration of 80%. Samples were incubated at –20 °C for 30 minutes before storage at –80 °C.
Single-cell suspensions (1 mL, approx. 106 cells/mL) were thawed and washed in wash-resuspension buffer containing 3× SSC, 1 mM DTT, 0.04% ultrapure BSA, and 0.2 U/μL RNase inhibitor. Cells were incubated on ice for 30 minutes with a mixture of DNA-labeled lectins and biotinylated SNA I, each at 0.5 μg/mL (equivalent to 0.05 μg of lectin per million cells). After three washes in wash-resuspension buffer, cells were incubated with TotalSeq™-B0975 Streptavidin (BioLegend, San Diego, CA) at 0.5 μg/mL (0.05 μg per million cells) for 30 minutes on ice. Cells were then washed three times, counted, and adjusted to a final concentration of ~1,000 cells/μL. Single cells were captured using the Chromium Controller, and single-cell RNA sequencing libraries were prepared with the Chromium Next GEM Single Cell 3′ v3.1 Kit and the 3′ Feature Barcode Kit (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions to generate both the gene expression and cell surface feature libraries. For sequencing, gene expression and cell surface feature libraries from each sample were pooled at a 4:1 ratio and sequenced using either the Illumina NovaSeq 6000 or NovaSeq X Plus platforms, targeting 20,000 reads per cell.

value: Conjunctiva

tag: adt

value: Lectin_MPA, Lectin_PNA, Lectin_ECA, Lectin_AAL, Lectin_MAA-I, Lectin_SNA-I, Lectin_ConA, Lectin_DSA, Lectin_WGA

tag: library type

value: ADT


title: aba_1

description: Library name: Sample 6

value: 2 h


title: Dauer Day30, exit 6h, sample 3

description: Library name: D30.6.3

value: daf-2 constitutive mutant of N2 strain

value: Dauer Day30, exit 6h


title: CH12F3_AID-WT_Valemetostat-2

value: Mouse B-lymphoma cells

value: anti-CD40–IL-4–TGF-Beta + Valemetostat


title: c_water_3

description: Library name: Sample 5

value: Whole seedling

value: water


title: Dauer Day30, exit 6h, sample 2

description: Library name: D30.6.2


title: Mice4_ADT

description:
Library name: Mice2_ADT
lectin-derived oligonucleotide (ADT-like)
Mice4_filtered_feature_bc_matrix.h5
mCornea_joint.clean.rds

source_name: Cornea-conjunctiva

value: Cornea-conjunctiva


title: CH12F3_AID-WT_Valemetostat-1


title: MiceConj1_mRNA

description:
Library name: Mice3_mRNA
polyA RNA
MiceConj1_filtered_feature_bc_matrix.h5
mCornea_joint.clean.rds

value: mRNA


title: Dauer Day30, exit 6h, sample 1

description: Library name: D30.6.1


title: c_water_2

description: Library name: Sample 4


title: CH12F3_AID-WT_Tazemetostat_5

value: anti-CD40–IL-4–TGF-Beta + Tazemetostat


title: c_water_1

description: Library name: Sample 3


title: Dauer Day30, exit 0h, sample 3

description: Library name: D30.0.3

value: Dauer Day30, exit 0h


title: Dauer Day30, exit 0h, sample 2

description: Library name: D30.0.2

value: Whole worm


title: Mice1_ADT

description:
Library name: Mice1_ADT
lectin-derived oligonucleotide (ADT-like)
Mice1_filtered_feature_bc_matrix.h5
mCornea_joint.clean.rds


title: CH12F3_AID-WT_Tazemetostat_4


title: c_ethanol_2

description: Library name: Sample 2

value: 0.02% ethanol


title: Dauer Day30, exit 24h, sample 1

description: Library name: D30.24.1

value: Dauer Day30, exit 24h


title: CH12F3_AID-WT_Tazemetostat_3


title: c_ethanol_1

description: Library name: Sample 1


title: Mice1_mRNA

description:
Library name: Mice1_mRNA
polyA RNA
Mice1_filtered_feature_bc_matrix.h5
mCornea_joint.clean.rds


title: CH12F3_AID-WT_Tazemetostat_2


title: Dauer Day30, exit 0h, sample 1

description: Library name: D30.0.1


title: HD_rep10

first: Qin

last: Qiao

address: Tsinghua Garden

institute: Tsinghua University

description: Library name: HD10-SA

data_processing:
Read quality was verified using FastQC. Clean reads were aligned to the human GRCh38 reference genome using Hisat2, and uniquely mapped reads were summarized by feature Counts from the Subread package. Differentially expressed genes (DEG) were identified with edgeR and limma packages in R version 3.6.3, with criteria of at least log2(FC) > 1 and (false discovery rate) FDR < 0.05. Gene ontology analysis and pathway enrichment were conducted by Metascape online analysis platform and https://www.bioinformatics.com.cn (last accessed on 10 Dec 2024), an online platform for data analysis and visualization.
Assembly: GRCh38
Supplementary files format and content: CSV  file includes FPKM for each Sample

source_name: peripheral blood cells

extract_protocol:
Total RNA from whole blood cells was extracted by TRIzol (Invitrogen) according to manufacturer’s instruction.
The RNA samples were sent to BGI genomics for library construction (DNBSEQ Eukaryotic mRNA library) and sequencing (DNBseq), with a read length of 150 bp for paired-end reads.

value: peripheral blood cells

tag: disease

value: healthy donor


title: liver.NK.cell.control.3

city: Munich

first: Kevin

last: Schmid

state: Bavaria

address: Ismaninger Str. 22

institute: TU Munich

description: Library name: A6_EKDL240003925-1A_22HNYVLT3_L1

library_source: genomic

data_processing:
Trimmomatic (Bolger, Lohse, & Usadel, 2014)
Aligmment using Bowtie2 ((Langmead & Salzberg, 2012)
Assembly: mm10
Supplementary files format and content: .txt

molecule: genomic DNA

source_name: liver

extract_protocol:
Transposed DNA was isolated using MiniElute Kit (Qiagen)
Library prep was perfomed according to Buenrostro et al. (PMID: 25559105)

value: liver

value: liver NK cells


title: CH12F3_AID-WT_Tazemetostat_1


title: liver.NK.cell.control.2

description: Library name: A5_EKDL240003924-1A_22HNYVLT3_L1


title: Dauer Day15, exit 24h, sample 2

description: Library name: D15.24.2

value: daf-2 constitutive mutant of N2 strain

value: Dauer Day15, exit 24h


title: HD_rep9

city: Beijing

description: Library name: HD09-SA


title: CH12F3_AID-WT_Idelalisib_Valemetostat-5

city: Boston

value: Mouse B-lymphoma cells

value: anti-CD40–IL-4–TGF-Beta + Idelalisib + Valemetostat


title: liver.NK.cell.control.1

description: Library name: A4_EKDL240003923-1A_22HNYVLT3_L1


title: HD_rep8

description: Library name: HD08-SA


title: CH12F3_AID-WT_Idelalisib_Valemetostat-4


title: Dauer Day15, exit 24h, sample 1

description: Library name: D15.24.1


title: Mice4_mRNA

description:
Library name: Mice2_mRNA
polyA RNA
Mice4_filtered_feature_bc_matrix.h5
mCornea_joint.clean.rds


title: HD_rep7

description: Library name: HD07-SA


title: Dauer Day15, exit 6h, sample 3

description: Library name: D15.6.3

value: Dauer Day15, exit 6h


title: CH12F3_AID-WT_Idelalisib_Valemetostat-3


title: Dauer Day15, exit 24h, sample 3

description: Library name: D15.24.3


title: HD_rep6

description: Library name: HD06-SA


title: CH12F3_AID-WT_Idelalisib_Valemetostat-2


title: liver.ILC1s.control.1

description: Library name: A1_EKDL240003920-1A_22HNYVLT3_L1

value: liver ILC1


title: HD_rep5

description: Library name: HD05-NSA


title: CH12F3_AID-WT_Idelalisib_Valemetostat-1


title: HD_rep4

description: Library name: HD04-NSA


title: Dauer Day15, exit 6h, sample 1

description: Library name: D15.6.1


title: Response of the thermotolerant strain GT48 strain at 47 °C in relation to thermotolerant strain GT48 at 37 °C

city: Cuernavaca

first: Gilberto

last: Pérez Morales

state: Morelos

address: Avenida Universidad 2001, Colonia Chamilpa

department: Cellular Engineering Department

country: Mexico

institute: Instituto de Biotecnología - Universidad Nacional Autónoma de México

description: Analysis was performed using the experimental samples of the thermotolerant strain GT48 at 47 degrees Celcius compared with the control samples of the same strain at 37 degrees Celcius as reference .

hyb_protocol: Incorporation of fluorophore was analyzed by using the absorbance at 555 nm and 647 respectively. Equal quantities of labeled cDNA were hybridized using hybridization solution HybIT2 (TeleChem International INC). The arrays were incubated for 14 h at 42 °C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images were performed in GenePix 4100-A reader with its accompanying software. For each spot, the mean density, mean background, and mean normalized signal values were calculated with the Array-Pro Analyzer software from Media Cybernetics.

data_processing:
Microarray data analysis was performed as follows. The data obtained from the quantification of the images were analyzed with Genarise in SWAP mode. The free software genArise, was developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes. The goal of genArise is to identify which of the genes show good evidence of being differentially expressed. The software identifies differential expressed genes by calculating an intensity-dependent z-score. Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point, and define a z-score where z measures the number of standard deviations a data point is from the mean.
zi = (Ri – mean(R)) / sd(R) Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 1.5 standard deviations would be the significantly differentially expressed genes.

label: Alexa555, Alexa647

organism: Escherichia coli

source_name: Control samples of the thermotolerant strain GT48 at 37 °C

label_protocol: 10 ug of total RNA were used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647, employing the SuperScript Plus direct labeling kit (Invitrogen).

growth_protocol: Samples of parental JU15 and thermally evolved strain GT48 were collected during mid-exponential growth at 37 °C, 45 °C, and 47 °C.

extract_protocol: 10 mL of culture were mixed with 500 µL of RNAlaterTM (Thermo Fisher Scientific, Baltics, UAB), then gently mixed by inversion. The samples were centrifugated at 5,000 rpm for 5 minutes, the supernatant was discarded, and the pellet was frozen at -70 °C until further analysis. Total RNA was isolated using the hot phenol method (Flores et al. 2005). Chromosomal DNA was removed with the turbo-DNA free kit (cat no. AM1907, Thermo Fisher Scientific, Baltics, UAB).

treatment_protocol: The strains were grown in a AM1 minimal medium supplemented with 40 g/L glucose, 0.1 g/L sodium citrate, and 10% (v/v) LB components. Cells were harvested at mid-exponential phase at 37 °C, 45 °C, and 47 °C.

value: GT48 (Thermally evolved from  JU15 strain)

source_name: Experimental samples of the thermotolerant strain GT48 at 45 °C


title: Dauer Day15, exit 0h, sample 3

description: Library name: D15.0.3

value: Dauer Day15, exit 0h


title: Response of the thermotolerant strain GT48 strain at 45 °C in relation to thermotolerant strain GT48 at 37 °C

description: Analysis was performed using the experimental samples of the thermotolerant strain GT48 at 45 degrees Celcius compared with the control samples of the same strain at 37 degrees Celcius as reference .


title: HD_rep3

description: Library name: HD03-NSA


title: Dauer Day15, exit 0h, sample 2

description: Library name: D15.0.2


title: Response of the parental JU15 strain at 45 °C in relation to thermotolerant strain GT48 at 45 °C

description: Analysis was performed using the experimental samples of the parental strain JU15 at 45 degrees Celcius compared with the control samples of the thermally evolved GT48 strain at 45 degrees Celcius as reference .

source_name: Control samples of the thermotolerant strain GT48 at 45 °C

source_name: Experimental samples of the parental strain JU15 at 45 °C

value: JU15 (MG1655:ΔpflB, ΔfrdA, ΔadhA ΔxylFGH, Δreg 27.3 kpb, gatCS184L)


title: CH12F3_AID-WT_Idelalisib_Tazemetostat-4

value: anti-CD40–IL-4–TGF-Beta + Idelalisib +Tazemetostat


title: HD_rep2

description: Library name: HD02-NSA


title: Dauer Day15, exit 0h, sample 1

description: Library name: D15.0.1

value: Whole worm


title: liver.ILC1s.control.3

description: Library name: A3_EKDL240003922-1A_22HNYVLT3_L1


title: Response of the parental JU15 strain at 37 °C in relation to thermotolerant strain GT48 at 37 °C

description: Analysis was performed using the experimental samples of the parental strain JU15 at 37 degrees Celcius compared with the control samples of the thermally evolved GT48 strain at 37 degrees Celcius as reference .

source_name: Experimental samples of the parental strain JU15 at 37 °C


title: CH12F3_AID-WT_Idelalisib_Tazemetostat-5


title: Dauer Day4, exit 24h, UV, sample 3

description: Library name: D4.24.UV.3

value: Dauer Day4, exit 24h, UV


title: HD_rep1

description: Library name: HD01-NSA


title: CH12F3_AID-WT_Idelalisib_Tazemetostat-2


title: CH12F3_AID-WT_Idelalisib_Tazemetostat-3


title: pilo3

city: nanjing

first: jiurong

last: yang

institute: 东南大学

data_processing:
DEseq2(Love, et al., 2014) was used to analyze the differential expression of circRNA
Assembly: mm10
Supplementary files format and content: tab-delimited text files and SRPBM value of each sample

source_name: cortex

extract_protocol:
A starting dose of 3µg total RNA was taken from each sample. rRNA was removed from the sample using the Ribo-Zero™ Gold Kits
According to the operation instructions of NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA), select different index tags to build the library

value: cortex

tag: Sex

value: male


title: CH12F3_AID-WT_Idelalisib_Tazemetostat-1


title: liver.ILC1s.control.2

description: Library name: A2_EKDL240003921-1A_22HNYVLT3_L1


title: COPD_stage34_rep7

description: Library name: COPD24-4

value: peripheral blood cells

value: COPD

tag: Stage


title: Dauer Day4, exit 24h, UV, sample 2

description: Library name: D4.24.UV.2


title: Dauer Day15, exit 6h, sample 2

description: Library name: D15.6.2


title: pilo2

tag: strain


title: Dauer Day4, exit 24h, sample 3

description: Library name: D4.24.3

value: Dauer Day4, exit 24h


title: COPD_stage34_rep6

description: Library name: COPD19-4

tag: cell type


title: Dauer Day4, exit 24h, UV, sample 1

description: Library name: D4.24.UV.1

tag: tissue

value: daf-2 constitutive mutant of N2 strain


title: COPD_stage34_rep5

description: Library name: COPD17-4


title: CH12F3_AID-WT_Idelalisib_DMSO-5

value: anti-CD40–IL-4–TGF-Beta + Idelalisib + DMSO


title: pilo1


title: CH12F3_AID-WT_Idelalisib_DMSO-4

value: Mouse B-lymphoma cells


title: control3


title: COPD_stage34_rep4

description: Library name: COPD102-4


title: Dauer Day4, exit 24h, sample 2

description: Library name: D4.24.2


title: COPD_stage34_rep3

description: Library name: COPD73-4


title: CH12F3_AID-WT_Idelalisib_DMSO-3


title: control2


title: Dauer Day4, exit 24h, sample 1

description: Library name: D4.24.1


title: CH12F3_AID-WT_Idelalisib_DMSO-2


title: COPD_stage34_rep2

description: Library name: COPD77-3


title: control1


title: CH12F3_AID-WT_Idelalisib_DMSO-1


title: Dauer Day4, exit 6h, UV, sample 3

description: Library name: D4.6.UV.3

value: Dauer Day4, exit 6h, UV


title: COPD_stage2_rep12

description: Library name: COPD95-2


title: Dauer Day4, exit 6h, UV, sample 1

description: Library name: D4.6.UV.1


title: COPD_stage34_rep1

description: Library name: COPD76-3


title: CH12F3_AID-WT_DMSO_4

value: anti-CD40–IL-4–TGF-Beta + DMSO


title: COPD_stage2_rep11

description: Library name: COPD80-2


title: Stimulated-02, stimulated with S. aureus

city: Talas

first: Ghulam Asghar

last: Sajid

state: Kayseri

address: Yenidoğan, Turhan Baytop Sokak No:1

department: Animal Science Department

country: Turkey

institute: Erciyes University

description:
Library name: Sample 5
Column name in raw_reads.txt = T2

data_processing:
Preprocessed with FastQC; cleaned using HTStream; alignment to chicken genome using Salmon; DESeq2 for normalization and differential expression analysis.
Assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016772045.1
Supplementary files format and content: Tab-delimited text file contains raw reads of all samples

organism: Ovis aries

source_name: Mammay gland

growth_protocol: Ovine mammary epithelial cell culture was established in 40 mL of Dulbecco's modified Eagle's medium (DMEM, 500 mL, high glucose, Sigma-Aldrich, USA) with addition of 20% bovine serum (FBS, 10 mL, Sigma-Aldrich, USA), insulin (5 µL, Sigma-Aldrich, USA), amphotericin B (500 µL, Sigma-Aldrich, USA) and penicillin-streptomycin (250 µL, Sigma-Aldrich, USA). The cells were cultured on uncoated polystyrene Petri dishes with surface modifications designed to enhance cell culture (35 mm). Cultures were maintained in a 5% CO2 atmosphere at 37 °C until monolayer confluence was achieved.

extract_protocol:
Total RNA isolation was performed from the control and treatment groups (three samples per group) using the Trizol isolation kit (TransZol Up Plus, ER501-01-V2, China) according to the manufacturer's instructions
Prepared using TruSeq RNA Sample Preparation Kit v2 Guide (Illumina, San Diego, CA, USA).

treatment_protocol: A field strain of S. aureus was isolated at the Microbiology Laboratory of the Veterinary Faculty at Erciyes University, from a diseased animal with known mastitis pathogenesis. A fresh microbial culture was prepared in Tryptic Soy Broth (TSB) by overnight incubation and was subsequently washed twice with PBS before the planned treatment. The microbial stimulation solution was prepared in Dulbecco's modified Eagle's medium (DMEM, 500 mL, high glucose, Sigma-Aldrich, USA) without antibiotics. A concentration of 1.5×108 microbial cells/mL was obtained by using the 1 OD at 620 nm. Multiplicity of infection (MOI) was determined using our early pilot studies, 600:1 MOI was used to challenge oMECs in wells containing 2 mL of culture (up to 2.5×105 cells/well). Control well with the same quantity of cells and volume of Dulbecco's modified Eagle's medium (DMEM, 500 mL, high glucose, Sigma-Aldrich, USA) were incubated at 37 °C for 24 hours, along with treated wells.

value: Mammay gland

value: Mammary epithelial cells

tag: breed

value: Aakraman

value: stimulated with S. aureus


title: Dauer Day4, exit 6h, sample 2

description: Library name: D4.6.2

tag: treatment

value: Dauer Day4, exit 6h


title: Stimulated-01, stimulated with S. aureus

description:
Library name: Sample 4
Column name in raw_reads.txt = T1


title: CH12F3_AID-WT_DMSO_3

tag: genotype


title: CH12F3_AID-WT_DMSO_2

tag: cell line


title: Control-02, non-stimulated

description:
Library name: Sample 2
Column name in raw_reads.txt = C2

value: non-stimulated


title: COPD_stage2_rep9

description: Library name: COPD71-2


title: Control-03, non-stimulated

description:
Library name: Sample 3
Column name in raw_reads.txt = C3


title: Dauer Day4, exit 6h, sample 3

description: Library name: D4.6.3

value: Whole worm


title: Control-01, non-stimulated

description:
Library name: Sample 1
Column name in raw_reads.txt = C1


title: COPD_stage2_rep8

description: Library name: COPD68-2


title: Dauer Day4, exit 0h, UV, sample 3

description: Library name: D4.0.UV.3

value: Dauer Day4, exit 0h, UV


title: CH12F3_AID-WT_DMSO_1


title: Stimulated-03, stimulated with S. aureus

description:
Library name: Sample 6
Column name in raw_reads.txt = T3


title: CH12F3_AID-KO_Valemetostat-3

value: AID-KO

value: anti-CD40–IL-4–TGF-Beta + Valemetostat


title: N2, wrt-10, day 8, early adult, replicate 3

city: Durham

first: Ivan

last: Falsztyn

state: NC

address: French Science Center

department: Biology

institute: Duke University

description: Library name: N2_wrt-10_rep4_S20_L001_R1_001.fastq

data_processing:
WS273 was used in mapping and analysis
bowtie2-2.3.3.1-linux-x86_64 was used to map paired-end reads (bowtie2 -p 2 -k 1 -S)
HTSeq python-htseq 0.6.1p1-4build1 (amd64 binary) in ubuntu bionic was used to count reads
Assembly: WS273
Supplementary files format and content: COUNTS file with raw counts for each sample

source_name: Early adult, hermaphrodite, whole animal

growth_protocol: L1 larvae were starved in virgin s-basal medium for 8 days at 20°C. Arrested larvae were plated onto the indicated food source (RNAi) and grown for 68 hours prior to collection.

extract_protocol:
100 μL of acid-washed sand and 1 mL of TRIzol were added to frozen worm pellets, and the tubes were vortexed vigorously for 10 minutes to homogenize samples. 200 μL of phenol-chloroform was added, and the mixture was vigorously vortexed for an additional 3 minutes. Tubes were centrifuged for 3 minutes at 21,000 rpm. A p200 micropipette was used to extract the aqueous layer, which was transferred to a new 1.5 mL Eppendorf tube and mixed with 500 μL of isopropanol. The mixture was incubated for 8 minutes at room temperature followed by 2 minutes on ice. Tubes were subsequently centrifuged for 10 minutes at 21,000 rpm. RNA pellets were washed with 75% ethanol twice, after which they were allowed to air dry prior to resuspension in 10 μL of water.
Libraries were prepared for sequencing using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs #E7775) starting with 1 μg of total RNA per sample as input and seven cycles of PCR.

treatment_protocol: 15 µL of the indicated RNAi strain in E. coli HT115 was transferred and spread  onto nematode growth medium plates with Carbenicillin (50 mg/ml) and IPTG (1 mM) and incubated overnight at room temperature

value: wild type

value: wrt-10 RNAi


title: COPD_stage2_rep7

description: Library name: COPD64-2

value: peripheral blood cells

value: COPD


title: Dauer Day4, exit 6h, sample 1

description: Library name: D4.6.1

value: daf-2 constitutive mutant of N2 strain


title: Dauer Day4, exit 0h, UV, sample 2

description: Library name: D4.0.UV.2


title: Dauer Day4, exit 6h, UV, sample 2

description: Library name: D4.6.UV.2

value: Dauer Day4, exit 6h, UV


title: CH12F3_AID-WT_DMSO_5

data_processing:
GEAT_docker(https://github.com/alessandriLuca/HTGTS_alignment) default parameters
Assembly: mm9
Supplementary files format and content: bedfiles tab separated
Library strategy: LAM-HTGTS

extract_protocol:
The library preparation was performed as previously described in Zhang, X. et al, Nature 575, 385-389 (2019).
12-16 samples were pooled and sequenced through Illumina MiSeq (PE250) by the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

value: Mouse B-lymphoma cells

value: anti-CD40–IL-4–TGF-Beta + DMSO


title: COPD_stage2_rep6

description: Library name: COPD53-2


title: CH12F3_AID-KO_Valemetostat-1


title: COPD_stage2_rep10

description: Library name: COPD72-2


title: COPD_stage2_rep5

description: Library name: COPD48-2


title: Dauer Day4, exit 0h, sample 3

description: Library name: D4.0.3

value: Dauer Day4, exit 0h


title: N2, wrt-10, day 8, early adult, replicate 1

description: Library name: N2_wrt-10_rep2_S4_L001_R1_001.fastq

value: Early adult, hermaphrodite, whole animal


title: CH12F3_AID-KO_Tazemetostat-4

value: anti-CD40–IL-4–TGF-Beta + Tazemetostat


title: COPD_stage2_rep4

description: Library name: COPD49-2


title: Dauer Day4, exit 0h, sample 2

description: Library name: D4.0.2


title: N2, wrt-1, day 8, early adult, replicate 3

description: Library name: N2_wrt-1_rep4_S19_L001_R1_001.fastq

value: wrt-1 RNAi


title: N2, wrt-1, day 8, early adult, replicate 2

description: Library name: N2_wrt-1_rep3_S11_L001_R1_001.fastq


title: Dauer Day4, exit 0h, sample 1

description: Library name: D4.0.1


title: COPD_stage2_rep3

description: Library name: COPD44-2


title: N2, wrt-1, day 8, early adult, replicate 1

description: Library name: N2_wrt-1_rep2_S3_L001_R1_001.fastq


title: Dauer Day1, exit 24h, UV, sample 3

description: Library name: D1.24.UV.3

value: Dauer Day1, exit 24h, UV


title: CH12F3_AID-KO_Tazemetostat-2


title: COPD_stage2_rep2

description: Library name: COPD37-2


title: CH12F3_AID-KO_Valemetostat-2


title: N2, wrt-10, day 8, early adult, replicate 2

description: Library name: N2_wrt-10_rep3_S12_L001_R1_001.fastq


title: COPD_stage2_rep1

description: Library name: COPD34-2


title: Dauer Day4, exit 0h, UV, sample 1

description: Library name: D4.0.UV.1

value: Whole worm


title: Dauer Day1, exit 24h, UV, sample 2

description: Library name: D1.24.UV.2


title: CH12F3_AID-KO_DMSO-5


title: N2, tra-1, day 8, early adult, replicate 3

description: Library name: N2_tra-1_rep4_S22_L001_R1_001.fastq

value: tra-1 RNAi


title: N2, tra-1, day 8, early adult, replicate 2

description: Library name: N2_tra-1_rep3_S14_L001_R1_001.fastq


title: CH12F3_AID-KO_Tazemetostat-1

value: AID-KO


title: COPD_stage1_rep6

description: Library name: COPD74-1


title: Dauer Day1, exit 24h, UV, sample 1

description: Library name: D1.24.UV.1


title: CH12F3_AID-KO_DMSO-4


title: Dauer Day1, exit 24h, sample 3

description: Library name: D1.24.3

value: Dauer Day1, exit 24h


title: CH12F3_AID-KO_Tazemetostat-3


title: COPD_stage1_rep5

description: Library name: COPD70-1


title: CH12F3_AID-KO_DMSO-3


title: Dauer Day1, exit 24h, sample 2

description: Library name: D1.24.2


title: COPD_stage1_rep4

description: Library name: COPD56-1


title: N2, tra-1, day 8, early adult, replicate 1

description: Library name: N2_tra-1_rep2_S6_L001_R1_001.fastq

value: wild type


title: N2, ptr-23, day 8, early adult, replicate 2

description: Library name: N2_ptr-23_rep3_S13_L001_R1_001.fastq

value: ptr-23 RNAi


title: COPD_stage1_rep3

description: Library name: COPD54-1

value: peripheral blood cells


title: Dauer Day1, exit 24h, sample 1

description: Library name: D1.24.1


title: CH12F3_AID-KO_DMSO-1


title: COPD_stage1_rep2

description: Library name: COPD52-1

value: COPD


title: N2, ptr-23, day 8, early adult, replicate 1

description: Library name: N2_ptr-23_rep2_S5_L001_R1_001.fastq


title: COPD_stage1_rep1

description: Library name: COPD51-1


title: Dauer Day1, exit 6h, UV, sample 2

description: Library name: D1.6.UV.2

value: daf-2 constitutive mutant of N2 strain

value: Dauer Day1, exit 6h, UV


title: CH12F3_AID-KO_Valemetostat_2

description:
PE75
CH12F3_AID-KO_Valemetostat.bw
CH12F3_AID-KO_Valemetostat.bedgraph

data_processing:
The adapter was removed using cutadapt software
Duplicates were removed using Picard software
Index and alignment was performed using Bowtie software --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 20
Assembly: GRCm37/mm9
Supplementary files format and content: Bigwig
Supplementary files format and content: Bedgraph
Library strategy: Cut&Tag

extract_protocol:
The library preparation was performed with the CUT&Tag-IT™ Assay Kit (Active Motif, cat. no. 53160).
The CUT&Tag for H3K27me3 libraries were sequenced through Illumina MiSeq (PE75)

treatment_protocol: CUT&Tag for H3K27me3 libraries were prepared from CH12F3 AID-deficient cells stimulated with anti-CD40–IL-4–TGF-β for 24 h

value: Mouse B-lymphoma cells

value: anti-CD40–IL-4–TGF-Beta + valemetostat


title: Dauer Day1, exit 6h, UV, sample 3

description: Library name: D1.6.UV.3


title: CH12F3_AID-KO_Valemetostat_1


title: Dauer Day1, exit 6h, sample 3

description: Library name: D1.6.3

value: Dauer Day1, exit 6h


title: N2, empty vector, day 8, early adult, replicate 3

description: Library name: N2_ev_rep4_S17_L001_R1_001.fastq

value: Early adult, hermaphrodite, whole animal

value: empty vector


title: AMO-BZB cells, shMFF - 1

city: Catanzaro

first: Claudia

last: Veneziano

address: Viale Europa, Località Germaneto

department: Department of Experimental and Clinical Medicine

country: Italy

institute: "Magna Graecia" University of Catanzaro

description: Library name: shMFF_sample1

data_processing:
Torrent Suite software v5.14.0 was used to align and process the raw sequences. Output normalized counts (in read per milion) were generated as .chp files.
Assembly: hg19
Supplementary files format and content: .chp file for each Sample

source_name: AMO-BZB

growth_protocol: H929 MM cells, stably overexpressing MFF or an empty vector as a control, were collected and immediately resuspended in TRIzol Reagent, followed by RNA extraction for RNA sequencing analysis. Similarly, AMO-BZB MM cells, stably silenced for MFF or a scrambled control, were collected, resuspended in TRIzol Reagent, and RNA was extracted for RNA sequencing analysis.

extract_protocol:
RNA was extracted with the fenol/chloroform method, quality and quantity controlled with the NanoDrop system (Invitrogen).
Libraries preparation was manually performed using the Ion AmpliSeq Transcriptome Human Gene Expression Core Panel, according to the Ion AmpliSeq Library Kit Plus.

treatment_protocol: H929 MM cells were stably transduced with lentiviral vectors to overexpress MFF or an empty vector as a control. AMO-BZB MM cells were stably transduced with lentiviral vectors to silence MFF or a scrambled control. After positive selection using puromycin, the silencing and the overexpression of MFF were evaluated.

value: AMO-BZB

value: Multiple Myeloma plasma cells

value: shMFF


title: Dauer Day1, exit 6h, UV, sample 1

description: Library name: D1.6.UV.1

value: Whole worm