title: Hi-C E13.5 fibroblast, male, rep1

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

description: hic E13.5 fibroblast male rep1

data_processing:
Illumina Casava1.8 software was used for basecalling.
Hi-C reads were processed using HiCPro v2.7.1b and replicates of same stage were pooled together
Cmpartment and TAD analysis were done with  cooltools (v0.3.2) (Venev et al., 2020)
Hi-C data was visulalized with Juicebox (v1.11.08) (Durand et al., 2016)
Assembly: mm9
Supplementary files format and content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: fibroblast

extract_protocol:
Embryos were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Formaldehyde was then quenched with glycine for 10 min at RT.
sisHi-C libraries were produced as previously described (Du et al., 2017). Crosslinked embryos were washed with 1 × PBS and lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min, the chromatin was solubilized with 0.5% SDS at 62 °C for 5 min. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP (Invitrogen, #19518018), the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, #65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Kapa HiFi PCR mix (Roche, #KK2602), and the products were purified and size-selected with AMPure XP beads (Beckman Coulter, #A63881).

value: fibroblast

value: C57BL/6N X PWK/PhJ

value: wild type


title: 20170221_WT_ES

status: Public on Sep 10 2024

type: SRA

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

description:
20170221_WT_ES
RNA isolated from long spermatides sorted out from testes obtained from Tent5c +/+ mice

library_source: transcriptomic

data_processing:
Obtained datasets were mapped to the mouse GRCm39 genome using STAR on default program settings. Read summarization was processed by featureCounts in the short-read mode (-p –O) including only features covered by at least 20% (–fracOverlapFeature 0.2). Differential expression analysis was preformed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: DESeq2_table_long_spermatides_wt_and_Tent5c_mut.csv.gz: CSV file with differential expression analysis of elongated spermatides, WT vs TENT5C KO
Supplementary files format and content: DESeq2_table_round_spermatides_wt_and_Tent5c_mut.csv.gz: CSV file with differential expression analysis of round spermatides, WT vs TENT5C KO
Supplementary files format and content: DESeq2_table_round_long_spermatides_wt.csv.gz: : CSV file with differential expression analysis of WT spermatides, round vs elongated
Supplementary files format and content: DESeq2_table_testis_wt_and_Tent5c_mut.csv.gz: CSV file with differential expression analysis of whole testes sequencing, WT vs TENT5C KO

molecule: total RNA

organism: Mus musculus

source_name: testis

extract_protocol:
For male germ cells isolation from testis, a protocol adapted from the work of Bastos et al. (2005)was used, as described in Brouze et al. (2024). Total RNA from testes and collected spermatides was isolated with TRI Reagent (Sigma) following manufacturer’s protocol. Tissues were homogenizedin TRI Reagent using glass Dounce homogenizer while collected cell pellets were suspended in TRI Reagent and lysed by pipetting. DNA traces from final RNA samples were removed using TURBO DNA free kit (Thermo Fisher Scientific) before further experiments.
rRNAs were removed from total DNA-free RNA samples with Ribo-Zero Gold rRNA-removal Kit (Illumina). rRNA-free samples were cleaned-up by 3M sodium acetate precitipation method. KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems) was used for sequencing libraries preparation, with random primers used for cDNA synthesis step. On each step of the procedure samples were cleaned-up using AMPure XP Reagent magnetic beads. Quality and fragment size distribution of the libraries was determined by electrophoresis on Agilent 2100 Bioanalyzer (Agilent Technologies Inc.).

tag: tissue

value: testis

tag: cell type

value: long spermatids

tag: genotype

value: WT


title: 20170221_FamC_ES

description:
20170221_FamC_ES
RNA isolated from long spermatides sorted out from testes obtained from Tent5c -/- mice

value: Tent5c -/-


title: Hi-C E9.5 fibroblast, female, rep1

country: China

description: hic E9.5 fibroblast female rep1

library_source: genomic

molecule: genomic DNA

tag: strain


title: MV-4-11 cells, 2 days, DMSO_rep1

city: Guangzhou

first: Huahui

last: Guo

address: 190 Kaiyuan Avenue, Huangpu District, Guangzhou

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence using Trim Galore.
Fastp v0.21.0 was used to remove potential adapters and low-quality reads (parameter: fastp -w 10)
STAR v2.7.9a was applied to map the clean reads to both the human genome (GRCh38) and the ERCC spike-in sequences
Gene counts and the normalized expression value (TPM, transcripts per kilobase million) were computed by StringTie v2.1.4
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: MV-4-11 cells were maintained in IMDM medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated from cell pallets using RNAiso Plus reagent (Takara) and 1 μg total RNA was used to generate cDNA with the PrimeScript™ RT Master Mix (Takara). RNA was quantified with NanoDrop followed by integrity evaluation via Agilent 5400 TapeStation analysis according to manufacturer's protocol.
RNA libraries for RNA-seq were prepared using mRNA-Seq library kit following manufacturer's protocol.

treatment_protocol: Cells were incubated for 2 days in the presence of DMSO or GSK032 (100 nM) or SAHA (100 nM) or combination of GSK032 and SAHA (COMBO, 100nM) or (R)-23a (100 nM or 200 nM) before performing RNA extraction.

value: Peripheral blood

tag: cell line

tag: treatment

value: DMSO


title: FLOXP+DOX2

city: Jinan, Shandong

first: Lin

last: Xie

address: No.107, Wen Hua Xi Road

institute: Qilu Hospital of Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCm39.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: heart

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MKO mice and their littermates FLOXP mice were selected and randomly divided into four groups : FLOXP+NS, FLOXP+DOX, MKO+NS, MKO+DOX. The mice in the FLOXP+DOX and MKO+DOX groups were injected with an accumulative dose of 20 mg/kg doxorubicin (MCE, USA, cat# HY-15142) [5 mg/kg intraperitoneal (i.p.) injection at day 0, 7, 14, and 21], whereas an equivalent volume of normal saline was administered by intraperitoneal injection to the FLOXP+NS and MKO+NS groups.

value: heart

value: doxorubicin


title: Hi-C E13.5 fibroblast, female, rep1

description: hic E13.5 fibroblast female rep1


title: 20170221_WT_RS

description:
20170221_WT_RS
RNA isolated from round spermatides sorted out from testes obtained from Tent5c +/+ mice

value: round spermatids


title: Hi-C E9.5 fibroblast, male, rep1

description: hic E9.5 fibroblast male rep1


title: Mouse_testis_spermatids_WT_18

description:
19_Mouse_18WT_Testis
RNA isolated from testes obtained from Tent5c+/+ mice

value: whole testes


title: MV-4-11 cells, 2 days, GSK032_100nM_rep2


title: MV-4-11 cells, 2 days, DMSO_rep2


title: 20170221_FamC_RS

description:
20170221_FamC_RS
RNA isolated from round spermatides sorted out from testes obtained from Tent5c -/- mice


title: T27 RNAseq

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
ChIP-seq reads were aligned to the reference genome (hg38) using BWA 0.7.17. Reads with mapping quality < 10 were not counted, and reads aligned to the same position and strand were only counted once. H3K27ac peaks were called using HOMER12, with style ‘histone’ for variable length. Density signals were calculated by deeptools’s bamCoverage.
RNA-seq reads were mapped to the hg38 reference genome using STAR 2.7.10a (Ref. 17) and Ensembl release 99 annotations. Reads were counted with featureCounts, discarding reads with mapping quality < 10. Density signals were calculated by deeptools’s bamCoverage11 with BPM normalization.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: polyA RNA

source_name: Lung neuroendocrine tumor

growth_protocol: NCI-H727, NCI-H1770 and NCI-H835 cell lines were acquired from ATCC. The cell lines were cultured in complete RPMI 1640 media (Gibco, Thermo Fisher Scientific, Massachusetts, USA) supplemented with 10% or 5% fetal bovine serum (FBS; HyClone, Utah, UK), 1% penicillin streptomycin (Diagnovum, Tilburg, Netherlands), 1% L-glutamine (Sartorius, Göttingen, Germany), 1% sodium pyruvate (Sartorius), and 1% non-essential amino acids (Diagnovum). LNET xenografts were established 5 days following the subcutaneous injection of 4*106 NCI-H727 cells to the back of athymic nude mouse (FOXN1NU NU/NU mouse).

extract_protocol:
2 mm tissue sample was homogenized in tri-reagent and RNA was extracted flowing the standard tri-reagent protocol. After precipitation RNA was resuspended in appropriate volume of Rnase free water supplemented with RNA inhibitors (New England Biolabs).
RNA-seq libraries were generated using the KAPA mRNA Hyperprep Kit according to the manufacturer's instructions. ChIP DNA was used to generate sequencing libraries using KAPA Hyper Prep Kit.

treatment_protocol: A51 treated cells were treated with 150nM BTX-A51.

value: Lung neuroendocrine tumor

value: Neuroendocrine


title: MV-4-11 cells, 2 days, GSK032+SAHA_100nM_rep2


title: MV-4-11 cells, 2 days, GSK032_100nM_rep1


title: Hi-C E7.5 ectoderm, female, rep1

description: hic E7.5 Ect female rep1

source_name: ectoderm

value: ectoderm


title: T26 RNAseq


title: Mouse_testis_spermatids_TENT5C_KO_17

description:
15_Mouse_17mutant_Testis
RNA isolated from testes obtained from Tent5c -/- mice


title: KO MII RNA-seq_r3

city: Shanghai

first: Xinyu

last: Wang

address: Siping Road 1239

institute: Tongji University

description: KO MII oocytes RNA-seq replicate3

data_processing:
For raw paired-end transcriptome sequencing data, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. STAR v2.6.1c was used to align the clean sequence data to the mouse reference genome (mm10), and RSEM v1.3.1 was used to quantify gene expression from the aligned sequences for each gene. The gene annotation file was obtained from the mouse GENCODE release (GRCm38.99). The R package DESeq2 v1.42.1 was used to identify differentially expressed genes between distinct Isca2 groups in mice. GSEA analysis was performed using the R package clusterProfiler v4.10.1, providing normalized enrichment scores and nominal p-values. KEGG functional annotation was conducted using the KOBAS online tool (http://bioinfo.org/kobas).
Assembly: mm10
Supplementary files format and content: aligned sequence file(bam) and gene expression quantification file(genes.results)

source_name: MII oocytes

growth_protocol: Animal welfare and the experimental procedures adhered to the ethical provisions on the Care and Use of Experimental Animals of Wenzhou Medical University and were approved and authorized by the Animal Experimental Committee of the University (No. xmsq2021-0068). Animals were maintained under a 12 h light/dark cycle and provided with food and water ad libitum in individually ventilated units.

extract_protocol:
To collected pre-implantation embryos, Isca2+/- female mouse intraperitoneal with 6.5 international unit of pregnant mares’ serum gonadotropin and, 45 to 47 h later, with 5 IU of human chorionic gonadotropin and crossed to Isca2+/- males. Embryos were isolated in M2 medium (Sigma: M7167) and cultured in potassium-supplemented optimised medium (Merck: MR-121-D) at 37℃ in 5% CO2.
The RNA-seq procedure was performed as previously described. Briefly, E4.5 blastocysts were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the single cell full length mRNA-amplification kit (N712, Vazyme). Library preparation was performed using the TruePrep DNA Library Prep Kit (TD501, Vazyme) according to the manufacturer’s instructions. All libraries were sequenced using the NovaSeq X Plus (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: MII oocytes

value: Isca2 -/-


title: T25 RNAseq


title: Mouse_testis_spermatids_WT_16

description:
11_Mouse_16WT_Testis
RNA isolated from testes obtained from Tent5c+/+ mice


title: KO MII RNA-seq_r2

description: KO MII oocytes RNA-seq replicate2


title: T23 RNAseq


title: Hi-C E7.5 ectoderm, male, rep1

description: hic E7.5 Ect male rep1

value: C57BL/6N X PWK/PhJ


title: Med1_IM15KO_rep2

city: Vancouver

first: Francis

middle: C

last: Lynn

state: BC

address: 950 28th Ave W

department: Surgery

country: Canada

institute: University of British Columbia

description:
Med1 ChIP-seq
Illumina NextSeq500
KO_Med1.bigwig

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using BWA and filtered for PCR duplicates.
For MIN6 cells, treatment samples were called using input as control with a q value of 0.05 in MACS2v2.2.1. For islets, EaSeq v1.111 "find peak" function was used with adaptive threshold function for control versus knockout islets (Med15) and control versus input (Med1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Mouse islets

extract_protocol:
Johnson et al., 2007, Science 316: 1497- 1502
SMARTer® ThruPLEX® DNA-Seq Kit
Paired end (MIN6) and single reads (islets)

tag: passage/age

value: 8 weeks

tag: chip antibody

value: MED1 (A300-793A, Bethyl)


title: KO MII RNA-seq_r1

description: KO MII oocytes RNA-seq replicate1


title: Hi-C E6.5 epiblast, female, rep2

description: hic E6.5 Epi female rep2

source_name: epiblast

value: epiblast

value: wild type


title: T24 RNAseq


title: WT MII RNA-seq_r3

description: WT MII oocytes RNA-seq replicate3


title: Med15_IM15KO_rep2

description:
Med15 ChIP-seq
Illumina NextSeq500
KO_Med15.bigwig

value: MED15 (11566-AP; ProteinTech)


title: T27 H3K27ac


title: Input_IM15KO_rep2

description:
Input
Illumina NextSeq500


title: Hi-C E6.5 epiblast, male, rep2

description: hic E6.5 Epi male rep2


title: WT MII RNA-seq_r2

description: WT MII oocytes RNA-seq replicate2


title: T26 H3K27ac


title: Hi-C E6.5 epiblast, female, rep1

description: hic E6.5 Epi female rep1


title: WT MII RNA-seq_r1

description: WT MII oocytes RNA-seq replicate1


title: Med15_CTRL_rep2

description:
Med15 ChIP-seq
Illumina NextSeq500
WT_Med15.bigwig


title: T25 H3K27ac


title: Hi-C E6.5 epiblast, male, rep1

description: hic E6.5 Epi male rep1


title: Hi-C E6.5 extraembryonic ectoderm, reciprocal cross, female, rep2

description: hic b6Xi E6.5 ExE female rep2

source_name: extraembryonic ectoderm

value: extraembryonic ectoderm

value: PWK/PhJ X C57BL/6N


title: Med1_IM15KO_rep1


title: Input_CTRL_rep2

description:
Input
Illumina NextSeq500


title: T23 H3K27ac


title: Hi-C E6.5 visceral endoderm, reciprocal cross, female, rep2

description: hic b6Xi E6.5 VE female rep2

source_name: visceral endoderm

value: visceral endoderm


title: Hi-C E6.5 extraembryonic ectoderm, reciprocal cross, female, rep1

description: hic b6Xi E6.5 ExE female rep1


title: Hi-C E7.5 ectoderm, male, rep2

description: hic E7.5 Ect male rep2


title: Med15_IM15KO_rep1


title: NCI-H727 + A51 RNAseq


title: Med1_CTRL_rep1

description:
Med1 ChIP-seq
Illumina NextSeq500
WT_Med1.bigwig


title: Input_IM15KO_rep1

description:
Input
Illumina NextSeq500


title: Hi-C E6.5 visceral endoderm, reciprocal cross, female, rep1

description: hic b6Xi E6.5 VE female rep1


title: Med1_CTRL_rep2


title: Hi-C E9.5 yolk sac, female, rep1

description: hic E9.5 yolk sac female rep1

source_name: yolk sac

value: yolk sac


title: NCI-H727 RNAseq

value: DMSO


title: Med15_CTRL_rep1


title: NCI-H835 RNAseq


title: Input_CTRL_rep1

description:
Input
Illumina NextSeq500


title: Hi-C E7.5 extraembryonic ectoderm, mix of gender, rep2

description: hic E7.5 ExE rep2


title: Med1_MIN6_rep3

description:
Med1 ChIP-seq
Illumina NextSeq500
Med1_bigwig

value: Passage 31-32


title: T24 H3K27ac

value: Lung neuroendocrine tumor


title: T16 RNAseq

value: Neuroendocrine


title: T19 RNAseq


title: Hi-C E7.5 extraembryonic ectoderm, mix of gender, rep1

description: hic E7.5 ExE rep1


title: Hi-C E6.5 extraembryonic ectoderm, female, rep2

description: hic E6.5 ExE female rep2


title: Med15_MIN6_rep3

description:
Med15 ChIP-seq
Illumina NextSeq500
Med15_bigwig


title: T14 RNAseq


title: Hi-C E6.5 extraembryonic ectoderm, female, rep3

description: hic E6.5 ExE female rep3


title: Hi-C E6.5 extraembryonic ectoderm, female, rep1

description: hic E6.5 ExE female rep1


title: Input_MIN6_rep3

description:
Input
Illumina NextSeq500


title: NCI-H835 + A51 RNAseq


title: Hi-C E6.5 visceral endoderm, female, rep2

description: hic E6.5 VE female rep2


title: T19 H3K27ac


title: Med15_MIN6_rep2


title: T18 H3K27ac


title: Hi-C E6.5 visceral endoderm, female, rep1

description: hic E6.5 VE female rep1


title: Med1_MIN6_rep2


title: Input_MIN6_rep2

description:
Input
Illumina NextSeq500


title: Hi-C Trophectoderm of E3.5 blastocyst, mix of gender, rep2

description: hic E3.5 TE rep2

source_name: trophectoderm

value: trophectoderm


title: T17 H3K27ac


title: Hi-C Trophectoderm of E3.5 blastocyst, mix of gender, rep1

description: hic E3.5 TE rep1


title: T16 H3K27ac


title: Med1_MIN6_rep1


title: T15 RNAseq


title: Hi-C Morula, mix of gender, rep2

description: hic morula rep2

source_name: morula

value: morula


title: T15 H3K27ac


title: T14 H3K27ac


title: Med15_MIN6_rep1


title: M2 oocytes,L/L cre,6 months_KO_2

status: Public on Sep 09 2024

city: Hangzhou

first: Xiaoling

last: Deng

address: Xihu District

institute: Westlake university

data_processing:
kallisto/0.46.2 + sleuth/0.30.1
Sequence reads were pseudoaligned and quantified by kallisto
Differential expression analysis was performed with the sleuth R package
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Ovary

extract_protocol:
The merged oocytes were placed in 5 µl of cell lysis buffer from Huada
Smart-seq2

value: Ovary

tag: Stage

value: oocytes

value: KO

tag: age

value: 6 months


title: M2 oocytes,L/L cre,6 months_KO_1


title: M2 oocytes,L/L,6 months_Ctrl_4

value: WT


title: M2 oocytes,L/L cre,6 months_KO_4


title: M2 oocytes,L/L,6 months_Ctrl_3


title: Hi-C Morula, mix of gender, rep1

description: hic morula rep1

value: C57BL/6N X PWK/PhJ

value: wild type


title: M2 oocytes,L/L cre,6 months_KO_3


title: M2 oocytes,L/L,6 months_Ctrl_2


title: M2 oocytes,L/L,6 months_Ctrl_1


title: ebf3a wt, 5 dpf, rep 1

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

country: USA

institute: UMass Chan Medical School

data_processing:
Paired-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.

organism: Danio rerio

source_name: head with eyes, 10-12 embryos pooled

extract_protocol:
Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit (Qiagen). 10-12 for 6 dpf and 15-20 for 2 dpf.
Libraries were constructed by GENEWIZ Azenta with standard protocols

value: head with eyes

value: 5 dpf

value: ebf3a wild types


title: ebf3a hom, 5 dpf, rep 2

value: ebf3a homozygotes


title: ebf3a hom, 5 dpf, rep 1


title: ebf3a wt, 5 dpf, rep 2


title: ebf3a het, 2 dpf, rep 2

source_name: upper body with eyes, 15-20 embryos pooled

value: upper body with eyes

value: 2 dpf

value: ebf3a heterozygotes


title: ebf3a wt, 2 dpf, rep 1


title: ebf3a wt, 2 dpf, rep 2


title: ebf3a hom, 2 dpf, rep 2


title: ebf3a hom, 2 dpf, rep 1


title: ebf3a het, 2 dpf, rep 1


title: Input_MIN6_rep1

description:
Input
Illumina NextSeq500

value: Passage 31-32


title: Y_1779

city: La Jolla

first: Farhoud

last: Faraji

state: CA

address: 3855 Health Sciences Drive, Floor 2, Room 2345, Bay KK

department: Moores Cancer Center

institute: UC San Diego Health

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene count, and aggregation were performed using the CellRanger softward v6.
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: tongue epithelium

extract_protocol:
Sorted, vialbe tongue epithelium-derived single cells were encapsulated in gel-beads-in emulsion (GEMs) using the 10x controller with a chromium single cell 3' GEM library and gel bead kit (v2)
Library preparation was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics).

value: tongue epithelium


title: EY_1774


title: N_1778_1401


title: E_2145


title: EY_1775


title: N_1400


title: Y_1972


title: K14_YAP mouse 3

data_processing:
Paired-end reads were aligned using STAR v2.7.9 using default settings. STAR index was created using the GRCm39 primary genome FASTA and annotation files. The resulting BAM files were sorted by name using samtools v1.7 then gene counts were quantified using HTSeq-count v0.13.5. Pairwise differential expression was calculated and principal component analysis plots were created using DESeq2 v1.34.0. DEGs were defined at thresholds of padj<0.01 and log2FC>1.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes transcript per million (TPM) counts for each gene and sample

extract_protocol:
RNA was prepared by homogenization of whole tongue epithelia in TRIzol®  (Invitrogen) followed by phenol:chloroform extraction and RNeasy Mini Kt based column purification with on-column DNase treatment (Qiagen)
Messenger RNA 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


title: Control mouse 4

value: LSL-rtTA


title: K14_YAP mouse 1


title: E_1776


title: K14_YAP mouse 2


title: Control mouse 3


title: K14_E6-E7_YAP mouse 6


title: Control mouse 1


title: K14_E6-E7_YAP mouse 5


title: K14_E6-E7_YAP mouse 4


title: K14_E6-E7_YAP mouse 2


title: K14_E6-E7_YAP mouse 1


title: K14_E6-E7 mouse 5


title: K14_E6-E7 mouse 4


title: K14_E6-E7 mouse 3


title: N4172 cell line sample 4.

data_processing:
Paired-end reads were aligned using STAR v2.7.9 using default settings. STAR index was created using the GRCm39 primary genome FASTA and annotation files. The resulting BAM files were sorted by name using samtools v1.7 then gene counts were quantified using HTSeq-count v0.13.5. Pairwise differential expression was calculated and principal component analysis plots were created using DESeq2 v1.34.0. DEGs were defined at thresholds of padj<0.01 and log2FC>1.
Assembly: GRCm39
Supplementary files format and content: Comma separated values file includes transcript per million (TPM) counts for each gene and sample

extract_protocol:
RNA was prepared by lysis of cells in TRIzol®  (Invitrogen) followed by phenol:chloroform extraction and RNeasy Mini Kt based column purification with on-column DNase treatment (Qiagen)
Messenger RNA 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

value: tongue epithelium primary culture


title: K14_E6-E7 mouse 1


title: N4172 cell line sample 3.


title: N4172 cell line sample 2.


title: N4172 cell line sample 1.


title: EY3960 cell line sample 2.


title: EY4174 cell line sample 2.


title: Control mouse 5


title: Control mouse 2


title: EY4028 cell line sample 2.


title: EY4174 cell line sample 1.


title: EY3960 cell line sample 1.


title: K14_E6-E7_YAP mouse 3


title: EY H3K27me3 experiment 4 sample 3

data_processing:
Raw reads were aligned using Bowtie2 (version 2.2.5; PMID: 22388286) to build version mm10 of the mouse genome. Peaks were called independently in each replicate against the corresponding IgG control using SEACR (version 1.3, PMID: 31300027) in relaxed mode. Peaks with RPKM < 10 were filtered out. Consensus peaks were merged for each genotype, EY or N, by combining all filtered peaks using bedtools merge (version 2.27.1; PMID: 20110278). Tornado plots were generated using deeptools (version 3.3.5; PMID: 24799436). Differential acetylation was called using DESeq2 (version 1.42.0; PMID: 25516281, PMID: 30395178) and apeglm (version 1.24.0) in R (version 4.3.2). Peaks with adjusted p-values less than 0.05 were considered significant. Motif enrichment was performed using the findMotifsGenome.pl script in the HOMER package (version 4.11; PMID: 20513432). Peaks were annotated using the annotatePeaks.pl script in the HOMER package. Peaks were annotated if they lie within the gene body or closer than 10 kb to the annotated TSS.
Assembly: mm10
Supplementary files format and content: Unfiltered deduplicated BigWig files
Library strategy: CUT&TAG

source_name: EY

extract_protocol:
CUT&TAGseq was performed on primary cultured cell suspensions using the Active Motif CUT&TAG-seq Kit according the the manufacturer's protocol
Library construction was performed using the Active Motif CUT&TAG-seq Kit according the the manufacturer's protocol

value: EY


title: EY H3K27ac experiment 4 sample 3


title: N H3K27me3 experiment 4

source_name: N

value: N


title: EY H3K27me3 experiment 4 sample 2


title: EY H3K27me3 experiment 1


title: K14_E6-E7 mouse 2


title: N H3K27me3 experiment 2


title: EY H3K27me3 experiment 4 sample 1


title: EY H3K27ac experiment 4 sample 1


title: EY H3K27ac experiment 4 sample 2


title: EY H3K27ac experiment 1


title: N H3K27ac experiment 4


title: EY H3K27ac experiment 2


title: N H3K27ac experiment 2


title: N H3K27ac experiment 1


title: EY YAP experiment 4 sample 3


title: EY YAP experiment 4 sample 2


title: EY4028 cell line sample 1.


title: EY H3K27me3 experiment 2


title: N YAP experiment 1


title: N YAP experiment 4


title: N YAP experiment 2


title: EY isotype experiment 4 sample 2


title: EY YAP experiment 4 sample 1


title: EY YAP experiment 1


title: EY isotype experiment 4 sample 3


title: EY isotype experiment 2


title: EY isotype experiment 1


title: N H3K27me3 experiment 1


title: N isotype experiment 4


title: EY isotype experiment 4 sample 1


title: N isotype experiment 1


title: N isotype experiment 2


title: N4172 cell line sample 6

data_processing:
Raw reads were aligned using BWA (version 0.7.17; PMID: 19451168) to build version mm10 of the mouse genome. Peaks were called using MACS2 (version 2.2.7.1; PMID: 18798982) in narrow peak mode with a False Discovery Rate threshold of less than 0.01. Consensus peaks were merged for all samples by combining all called peaks using bedtools merge (version 2.27.1). Reads were recounted in consensus peaks using bedtools coverage (version 2.27.1). DESeq2 (version 1.42.0) and apeglm (version 1.24.0) in R (version 4.3.2) were used to call differential chromatin accessibility, peaks with adjusted p-value of less than 0.05 were considered significant. Motifs and peak annotation was performed as with the CUT&Tag data using HOMER.
Assembly: mm10
Supplementary files format and content: Unfiltered deduplicated BigWig files

extract_protocol:
ATACseq was performed on primary cultured cell suspensions using the Active Motif ATAC-seq Kit according the the manufacturer's protocol
Library construction was performed using the Active Motif ATAC-seq Kit according the the manufacturer's protocol


title: N4172 cell line sample 1


title: N4172 cell line sample 2


title: N4172 cell line sample 5


title: N4172 cell line sample 3


title: EY4028 cell line sample 2


title: EY4028 cell line sample 1


title: EY3960 cell line sample 2


title: EY YAP experiment 2


title: iXEN, rep2 [scRNA-Seq]

city: New York

first: Yang

last: Yang

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using the seqc software (https://github.com/dpeerlab/seqc).
Assembly: mm10
Supplementary files format and content: csv file (gene expression, cells along rows, genes along columns)

source_name: iXEN

extract_protocol:
Reprogramming XEN cells were collected at Day 7, Day 14, Day 28 of reprogramming using fluorescence-activated cell sorting (FACS) to enrich for cells undergoing lineage conversion based on key lineage marker expression. Starting XEN and fully reprogrammed XEN-iPS cells were also assayed. ES cells converting to iXEN cells were also collected at 9h, 24h and 48h of reprogramming. A similar FACS enrichment strategy was used for the 9h timepoint as was used for reprogramming XEN cells. Starting ES and fully converted iXEN cells were additionally sampled. All reprogramming XEN cells were dissociated using 0.25% Trypsin-EDTA, and other cells using 0.05% Trypsin-EDTA (i.e. starting and end XEN, ES, iPS and iXEN populations, and converting ES-to-iXEN cells). Cells taken for sorting were filtered through a 0.35um nylon mesh strainer to achieve single cell suspensions. Cells were centrifuged at 400g for 5 mins at room temperature and washed twice with wash buffer (5% FBS in PBS without Ca2++ and Mg2++). Cell pellets were then resuspended in 100 µl staining buffer (wash buffer with diluted antibodies) and incubated at room temperature for 30 mins protected from light. Following incubation, cells were washed twice with wash buffer. Cell pellets were finally resuspended in wash buffer containing 1µg/ml 4′,6-diamidino-2-phenylindole (DAPI). Finally, cells were resuspended at a final concentration of 5-10x106/ml in wash buffer and sorted using SORP FACSAria IIu (BD Biosciences) with a 100µm nozzle at 20psi. Dissociated or sorted cells were counted and diluted in DMEM + 10% FBS. Final cell suspensions were loaded on a Chromium Controller targeting a 5,000 – 8,000 cell range, depending on the sample, to generate single-cell 3’ RNA-seq libraries in duplicate.
Libraries were generated following the manufacturer’s instructions (10x Genomics Chromium Single Cell 3′ Reagent Kit User Guide v2 Chemistry). Briefly, cells were resuspended in master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate in every single GEM was retrotranscripted to cDNA, which contains Illumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: iXEN

value: iGata4-Gata6-Venus iXEN

value: Induced XEN cell


title: iXEN, rep1 [scRNA-Seq]


title: ES,  48h,  rep2 [scRNA-Seq]

source_name: ES

value: ES

value: iGata4-Gata6-Venus ES

value: Embyronic stem cell


title: ES,  24h, rep2 [scRNA-Seq]


title: ES,  48h,  rep1 [scRNA-Seq]


title: ES,  24h,  rep1 [scRNA-Seq]


title: XEN-iPS, rep2 [scRNA-Seq]

source_name: XEN-iPS

value: XEN-iPS

value: 3F-4 XEN-iPS

value: Induced pluripotent stem cell


title: ES,  0h, rep2 [scRNA-Seq]


title: N4172 cell line sample 4


title: ES,  9h, rep2 [scRNA-Seq]


title: XEN, Day 28, rep1 [scRNA-Seq]

source_name: XEN

value: XEN

value: 3F-4 XEN

value: Extraembryonic endoderm stem cell


title: EY4174 cell line sample 1


title: XEN, Day 14, rep1 [scRNA-Seq]


title: XEN, Day 7, rep2 [scRNA-Seq]


title: ES,  9h, rep1 [scRNA-Seq]


title: XEN, Day 28, rep2 [scRNA-Seq]


title: XEN, Day 14, rep2 [scRNA-Seq]


title: XEN, Day 0, rep2 [scRNA-Seq]


title: XEN, Day 7, rep1 [scRNA-Seq]


title: EY3960 cell line sample 1


title: KYSE150, shNC, replicate3

city: Zhengzhou

first: Renle

address: No.40 Daxue North Road

department: Henan Institute of Medical and Pharmaceutical Sciences

institute: Zhengzhou University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set;
The expression level of gene was calculated by RSEM.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes row counts for each sample
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

extract_protocol:
Total RNA was extracted using Trizol
RNA transcriptome profiles were generated by the Beijing Genomics Institute (BGI) using the DNA Nanoball sequence (DNBSEQ) platform.

value: human esophageal squamous cell carcinoma

value: shNC


title: EY4174 cell line sample 2

value: tongue epithelium primary culture


title: KYSE150, shNC, replicate2


title: KYSE150, shSPP1#2, replicate3


title: KYSE150, shSPP1#2, replicate1


title: KYSE150, shNC, replicate1


title: ES,  0h, rep1  [scRNA-Seq]


title: XEN-iPS, rep1 [scRNA-Seq]


title: input_HW04_1hr_auxin_L3_rep2_1

first: Jun

last: Kim

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

data_processing:
Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 with default parameters. Bam sorting and indexing was performed using samtools version 1.11. BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage with a bin size of 10 bp and 200 bp read extension. Only reads with a minimum mapping quality of 20 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed. The average coverage data was generated by averaging ChIP-Input enrichment scores per 10 bp bins across the genome.  ChIP-seq peaks are identified using MACS2 version 2.1.1 (https://github.com/macs3-project/MACS). Peaks are called using both the individual replicates and combined bam files with minimum false discovery rate of 0.05. The peaks shown below average ChIP-seq tracks are peaks called using the combined bam files, whereas the peaks shown below individual replicates are peaks called using the corresponding replicate.
Assembly: WS220
Supplementary files format and content: bw file contains signal track, input subtracted enrichment at each binned genomic loci
Supplementary files format and content: bed file contains binarized chip enrichment across the genome

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. L3 worms were kept on plates with or without auxin prior to collection.

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

treatment_protocol: collected worms were treated with auxin using NGM media containing 1 mM auxin. The worms were left on NGM plate to crawl around for an hour.

value: whole worms

tag: development stage

value: input


title: input_HW04_noauxin_L3_rep2


title: input_HW04_1hr_auxin_L3_rep1


title: ES,  48h,  rep1

library_source: genomic single cell

data_processing:
Demultiplexing,barcode processing, and fragment curation were performed using Cell Ranger ATAC.
Assembly: mm10
Supplementary files format and content: tsv file (fragment files)
Supplementary files format and content: tbi format file (tabix index of fragment files)

extract_protocol:
Reprogramming XEN cells were collected at Day 7, Day 14, Day 28 of reprogramming using fluorescence-activated cell sorting (FACS) to enrich for cells undergoing lineage conversion based on key lineage marker expression. Starting XEN and fully reprogrammed XEN-iPS cells were also assayed. ES cells converting to iXEN cells were also collected at 9h, 24h and 48h of reprogramming. A similar FACS enrichment strategy was used for the 9h timepoint as was used for reprogramming XEN cells. Starting ES and fully converted iXEN cells were additionally sampled. All reprogramming XEN cells were dissociated using 0.25% Trypsin-EDTA, and other cells using 0.05% Trypsin-EDTA (i.e. starting and end XEN, ES, iPS and iXEN populations, and converting ES-to-iXEN cells). Cells taken for sorting were filtered through a 0.35um nylon mesh strainer to achieve single cell suspensions. Cells were centrifuged at 400g for 5 mins at room temperature and washed twice with wash buffer (5% FBS in PBS without Ca2++ and Mg2++). Cell pellets were then resuspended in 100 µl staining buffer (wash buffer with diluted antibodies) and incubated at room temperature for 30 mins protected from light. Following incubation, cells were washed twice with wash buffer. Cell pellets were finally resuspended in wash buffer containing 1µg/ml 4′,6-diamidino-2-phenylindole (DAPI). Finally, cells were resuspended at a final concentration of 5-10x106/ml in wash buffer and sorted using SORP FACSAria IIu (BD Biosciences) with a 100µm nozzle at 20psi. Dissociated or sorted cells were washed in PBS + 0.04% BSA and processed for nuclei isolation following manufacturer’s instructions (Demonstrated Protocol: Nuclei Isolation for Single Cell ATAC Sequencing; Document CG000169 Rev D). Final nuclei preparations were loaded on a Chromium Controller targeting 10,000 nuclei, and processed in singlicate.
Libraries were generated following the manufacturer’s instructions (10x Genomics Chromium Next GEN Single Cell ATAC Reagent Kit Guide v1.1). Briefly, isolated nuclei were resuspended in diluted nuclei buffer and taken for the transposition reaction. Transposed nuclei were then diluted in master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The DNA fragments from the nuclei in every single GEM were PCR linear amplified and appended with an Illumina P5 primer sequence, a Read 1N sequence, and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, and the appropriated size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: ES,  48h,  rep2


title: ES,  24h, rep2


title: ES,  24h,  rep1


title: KYSE150, shSPP1#2, replicate2


title: H4K20me1_HW04_1hr_auxin_L3_rep1

value: H4K20me1 (abcam, ab9051)


title: input_HW04_noauxin_L3_rep1


title: ES,  9h, rep1


title: ES,  0h, rep1


title: H4K20me1_HW04_1hr_auxin_L3_rep2


title: H4K20me1_HW04_noauxin_L3_rep1


title: XEN, Day 28, rep1


title: H4K20me1_HW04_noauxin_L3_rep2


title: XEN, Day 0, rep1 [scRNA-Seq]


title: XEN-iPS, rep1


title: PQN85_HW04_1hr_auxin_L3_rep2


title: XEN, Day 14, rep1


title: PQN85_HW04_noauxin_L3_rep2


title: XEN, Day 0, rep1


title: XEN, Day 7, rep1


title: PQN85_HW04_noauxin_L3_rep1


title: iXEN, rep1

value: iXEN

value: iGata4-Gata6-Venus iXEN


title: pDEMYELINsMMrCorpusCallosumAAiM102d201110rerun

city: Cambridge

first: Evan

last: Macosko

address: 75 Ames St

institute: Broad Institute

description: 10x Genomics v3.1

data_processing:
Cellranger
Assembly: GRCm38.102-5.0.1
Supplementary files format and content: h5ad, processed single cell counts matrices
Supplementary files format and content: h5Seurat, processed single cell counts matrices
Library strategy: Fragmentation and A-tailing

source_name: corpus callosum

extract_protocol:
Stereotaxic surgery and injection of LPC or saline into corpus callosum. Brains were isolated and frozen, lesions were microdissected
10x Genomics v3.1

treatment_protocol: saline or LPC

value: corpus callosum

value: Brain cells

value: Stereotaxic injection of LPC or saline control


title: SMC3_HW04_1hr_auxin_L3_rep2

value: SMC3 (SDIX,Q4469)


title: pDEMYELINsMMrCorpusCallosumZiM101d201110rerun

description: 10x Genomics v3.1


title: SMC3_HW04_1hr_auxin_L3_rep1


title: pDEMYELINsMMrCorpusCallosumYiM142d201110rerun

description: 10x Genomics v3.1


title: SMC3_HW04_noauxin_L3_rep2


title: pDEMYELINsMMrCorpusCallosumXiM141d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumWiM138d201110rerun

description: 10x Genomics v3.1


title: SMC3_HW04_noauxin_L3_rep1


title: pDEMYELINsMMrCorpusCallosumViM137d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumUiM100d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumTiM146d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumQiM133d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumNiM114d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumSiM145d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumRiM134d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumOiM125d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumPiM126d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumMiM113d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumKiM121d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumJiM118d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumIiM117d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumHiM124d201110rerun

description: 10x Genomics v3.1


title: pDEMYELINsMMrCorpusCallosumGiM123d201110rerun

description: 10x Genomics v3.1


title: RIV A8 803 bp 5mC template 2 µM dGTP and 200 µM d(A/T/C)TP (MiSeq)

city: Konstanz

first: Melanie

last: Henkel

state: Baden-Württemberg

address: Universitätsstraße 10

department: Department of Chemistry

country: Germany

institute: University of Konstanz

description: 803 bp 5mC template

library_source: other

data_processing:
Sequencing data were processed by using the open source software KNIME 4.6.2
Raw sequence and quality values were extracted from the FASTQ file format and Phred quality scores (Q scores) were transformed into base calling error probabilities (P)
The data was preprocessed by defining the unique molecular identifier (UMI) sequence context and translating Read 1 sequence and P into the reverse complement orientation
Read 1 and Read 2 were aligned to give the expected size of the template (bisulfite converted samples 95 bp, 5mC detection samples 109 bp) and merged into one sequence for which base calls with the lower error probability were transferred for the Read 1 and Read 2 overlay segment
High quality data was filtered by removal of reads containing a base within the UMI contexts with a P value above the threshold or removal of merged reads with a mean error probability over all bases in the sequence context above the threshold value
For each filtered read, a deletion and insertion correction was performed to adjust frameshifts by employing the Levenshtein distance between the read and reference template (OR10A2 olfactory receptor family 10 subfamily A member 2 [ Homo sapiens (human) ])
N base calls were replaced by reference bases to prevent false positive error detection
Reads were aligned to the reference template sequence and reads with a misalignment higher as 6% or 12% were removed from the data set
Reads were sorted into UMI family groups with identical UMIs and analysis was proceeded with UMI families containing a minimum of three reads
Error calculation of UMI families was performed by averaging over the error for each sequence position of each read in one UMI family
By employing an error cut-off of 0.9, true KlenTaq DNA polymerase derived errors were then set to 1 and errors below the cut-off were set to 0 for each UMI family
The mean error was calculated over all UMI families at each sequence position, yielding the KTq based error rate
5mC detection was facilitated by comparing the error rates of the unmodified C template data set with the error rates of the 5mC template sequencing data using the Microsoft Excel software
Error rates, calculated from sequencing data of human genomic DNA based NGS libraries; were processed further for 5mC detection using the Microsoft Excel software. Errors were standardised using an adapted z-score which only includes error rates at C positions but values from CpG sites were excluded
Assembly: OR10A2 olfactory receptor family 10 subfamily A member 2 [ >NC_000011.10 Homo sapiens chromosome 11, GRCh38.p14 Primary Assembly ]
Supplementary files format and content: excel-files include position, reference DNA sequence and error rates
Library strategy: DNA Amplicon-Seq

molecule: other

organism: synthetic construct

source_name: DNA template generated by PCR

extract_protocol: Reaction mixtures for linear PCR contained 2 µM dGTP and 200 µM d(A/T/C)TP (each), 100 nM 109 bp forward primer, 50 pM 803 bp C or 5mC template and 250 nM KTq variant in 1x KTq reaction buffer (50 mM Tris HCl (pH 9.2), 16 mM (NH4)2SO4, 2.5 mM MgCl2, 0.1% (v/v) Tween 20). PCR was performed in 25 µL with an initial denaturation at 95°C for 3 min followed by amplification over 20 cycles with denaturation at 95°C for 10 s, annealing at 62°C for 30 s and elongation at 72°C for 4 min. Final elongation was performed for 10 min at 72°C. Single-stranded (ssDNA) PCR product from 109 to 364 nt was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) in combination with the NTC binding buffer according to the manufacturer’s instructions with elution in 22 µL Milli-Q water. To verify that no original template DNA was extracted, 1 µL of purified PCR product was subsequently applied in a PCR for purity verification. Reaction mixtures contained 200 µM dNTPs (each), 500 nM 803 bp forward and reverse primer, 10% (v/v) PCR product as template and 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase in 1x Q5® Reaction Buffer (New England Biolabs). PCR was performed in 10 µL reaction mixtures with an initial denaturation at 98°C for 1 min followed by amplification over 25 cycles with denaturation at 98°C for 10 s, annealing at 62°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. The absence of the 803 bp PCR product was verified by agarose gel electrophoresis. 17.5 µL of purified linear PCR product ssDNA was treated with the PreCR® Repair Mix (New England Biolabs) in 20 µL according to the manufacturer’s instructions. Without further purification, the reaction mixture was applied in a 2-cycle UMI PCR. Reaction mixtures for UMI introduction contained 200 µM dNTPs (each), 200 nM forward and reverse UMI primer, 0.02 U/µL Q5® Hot Start High-Fidelity DNA Polymerase and 0.2x Q5® Reaction Buffer (New England Biolabs) in 25 µL end volume. PCR was performed with an initial denaturation at 98°C for 1 min followed by primer elongation over 2 cycles with denaturation at 98°C for 10 s, annealing at 48°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 183 bp UMI PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) according to the manufacturer’s instructions. To improve purification, NTI binding buffer was 1:1.5 diluted with Milli-Q water for solubilising agarose gel slices and the dissolved mixture was diluted in total to 1:2.5 prior to DNA binding on the purification column. Purified UMI PCR product was eluted in 15 µL Milli-Q water. DNA concentration was determined by qPCR using previously prepared 183 bp reference DNA in decadic dilution series for the quantification based on standard amplification curves. Reaction mixtures contained 0.96x NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs), 400 nM 183 bp forward and reverse primer, 1x SYBR Green I (Sigma-Aldrich) and 1.85 µL reference template or UMI PCR product elution in 5 µL end volume. qPCR was performed in a Light Cycler® 96 instrument (Roche Diagnostics) with an initial denaturation at 98°C for 1 min followed by amplification over 30 cycles with denaturation at 98°C for 10 s, annealing at 60°C for 30 s and elongation at 72°C for 30 s. High resolution melting curves were measured immediately after PCR amplification. For absolute quantification, Cq values of reactions with reference template were plotted against the logarithm of their DNA concentrations and the linear regression function was used to calculate the concentration of the UMI PCR product. Calculated concentrations were multiplied by two, because applied reference template DNA was double stranded and only one strand of UMI PCR product carried both primer binding sites. Reactions for reference and UMI DNA were performed twice and a no template control reaction was performed to determine side product signals. The minimum reaction efficiency for the standard curve was 0.9 to 1.1 and the cut-off for the correlation coefficient of linear regression was 0.98. 67.63 fM of purified UMI PCR product was treated with the PreCR® Repair Mix (New England Biolabs) in 11.25 µL according to the manufacturer’s instructions. Without further purification, the reaction mixture was applied in the Amplicon PCR. Reaction mixtures for Amplicon library preparation contained 1x NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs), 400 nM forward and reverse Amplicon primer (containing Illumina TruSeq adapter and indexes sequences) and 26.57 fM UMI PCR product (for final analysis of approximately 100 000 UMI families) in 25 µL end volume. PCR was performed with an initial denaturation at 98°C for 1 min followed by amplification over 35 cycles with denaturation at 98°C for 10 s, annealing at 70°C for 30 s and elongation at 72°C for 30 s. Final elongation was performed for 2 min at 72°C. 263 bp Amplicon PCR product was purified by preparative agarose gel electrophoresis using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel) according to the manufacturer’s instructions. To improve purification, NTI binding buffer was 1:1.5 diluted with Milli-Q water for solubilising agarose gel slices and the solved mixture was diluted in total to 1:6.5 prior to DNA binding on the purification column. The PCR product was eluted in 20 µL Milli-Q water and treated with the PreCR® Repair Mix (New England Biolabs) in 20 µL according to the manufacturer’s instructions. Repaired product DNA was purified using the QIAEX II system (Qiagen) according to the manufactures instructions and was eluted in 18 µL Milli-Q water. DNA library concentrations were determined using the Quantus™ Fluorometer (Promega). After quality control by electrophoresis with the Bioanalyzer 2100 system (Agilent), DNA libraries were pooled equimolarly and sequencing was performed in paired-end mode on an Illumina MiSeq™ or NextSeq 2000 system with 2 x 75 bp read length. Each prepared NGS library was prepared and sequenced once.

value: DNA template generated by PCR


title: GAT29_TNFa+IL1b+IFNg

type: RNA

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.

source_name: GAT29, gastric mucosoid, TNFɑ, IL1β and IFNɣ

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: 250,000 cells derived from Stomach antrum organoids were seeded in 200μL culture medium into collagen-coated (A10644-0, 12.5–15μg/cm2; Gibco) Transwell inserts (PIHP01250; Millipore) placed in a 24-well plate at 37°C, 5% CO2 in a humidified incubator. The space between filter and well was filled with 400μL culture medium (Boccellato et al., GUT 2019). At day 3 post seeding, the medium overlying the cells was removed from the well insert to start the air–liquid interface culture. Subsequently, the 500μL medium below the filter was replaced twice a week. Experiment with mucosoids are done bewteen week 2 and 3 after seeding.

extract_protocol: total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany). The procedure was performed according to the manufacturer’s specification. The total RNA concentration was quantified using a NanoDrop spectrophotometer

treatment_protocol: Samples were treated with TNFa (5 ng/mL), IL1n (2.5 ng/mL), and IFNg (10 ng/mL) combined or individually (as indicated), for 5 days before extracting RNA for transcriptomic profile by microarray

tag: patient

value: TNFɑ, IL1β and IFNɣ


title: GAT29_IL1b

source_name: GAT29, gastric mucosoid, IL1β


title: RIV A8 803 bp C template 2 µM dGTP and 200 µM d(A/T/C)TP (MiSeq)

description: 803 bp C template


title: pDEMYELINsMMrCorpusCallosumFiM112d201110rerun

description: 10x Genomics v3.1


title: GAT29_IFNg

source_name: GAT29, gastric mucosoid, IFNɣ

value: IFNɣ


title: GAT27_IFNg

source_name: GAT27, gastric mucosoid, IFNɣ


title: GAT27_TNFa

source_name: GAT27, gastric mucosoid, TNFɑ

value: TNFɑ


title: GAT23_TNFa+IL1b+IFNg

source_name: GAT23, gastric mucosoid, TNFɑ, IL1β and IFNɣ


title: pDEMYELINsMMrCorpusCallosumEiM111d201110rerun

description: 10x Genomics v3.1


title: GAT29_NT

source_name: GAT29, gastric mucosoid, NT

value: NT


title: GAT27_IL1b

source_name: GAT27, gastric mucosoid, IL1β


title: Bisulfite converted 5'-3' strand 803 bp 5mC template

description: 803 bp 5mC template


title: Bisulfite converted 5'-3' strand 803 bp C template

description: 803 bp C template


title: GAT23_IFNg

source_name: GAT23, gastric mucosoid, IFNɣ


title: pDEMYELINsMMrCorpusCallosumDiM120d201110rerun

description: 10x Genomics v3.1


title: GAT29_TNFa

source_name: GAT29, gastric mucosoid, TNFɑ


title: pDEMYELINsMMrCorpusCallosumCiM119d201110rerun

description: 10x Genomics v3.1


title: GAT23_IL1b

source_name: GAT23, gastric mucosoid, IL1β


title: GAT27_TNFa+IL1b+IFNg

source_name: GAT27, gastric mucosoid, TNFɑ, IL1β and IFNɣ


title: GAT27_NT

source_name: GAT27, gastric mucosoid, NT


title: iRFP, 5 hr TNFα, rep3

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
NIJK04_iRFP_bccounts_final.txt
NIJK04_iRFP_bccounts_reseq.txt

data_processing:
Illumina sequencing reads were trimmed with cutadapt to obtain barcodes and UMIs
Barcodes were counted using the custom “bc-umi” program, which collapses highly similar barcodes and performs UMI de-duplication
barcode counts were then collected into a matrix using the custom “bc-tabulate” program
Assembly: Custom, dual-barcoded sgRNA library
Supplementary files format and content: Tab-delimited text file containing raw, unnormalized read counts for each sample.
Library strategy: CiBER-seq

extract_protocol:
Cells were harvested for by centrifugation and lysed in TRI reagent (Sigma-Aldrich, T9424). To isolate RNA, 200 uL chloroform per 1 mL TRI reagent was added, shaken vigorously, incubated at RT for 5 min, then centrifuged at 12,000 g for 15 min at 4°C. The aqueous phase was transferred to a new tube, and 1 uL GlycoBlue (ThermoFisher, AM9515) and 500 uL 2-propanol per 1 mL TRI reagent was added. Samples were incubated at RT for 10 min then centrifuged at 12,000 g for 10 min at 4°C. The supernatant was removed from the RNA pellet, and the pellet was washed by adding at least 1 mL 75% ethanol. Samples were vortexed and centrifuged at 7500 g for 5 min at 4°C. The RNA pellet was briefly dried and then resuspended in water
400 ug of RNA was treated with Turbo DNase (ThermoFisher Scientific, AM2238) for 30 min at 37°C. 100 ug of RNA was reverse transcribed using Protoscript II and two gene-specific primers with UMIs at a 1:1 ratio. cDNA was treated with 1 L each of RNase A and RNase H (NEB M0297S and ThermoFisher, EN0531) for 30 min at 37°C. cDNA from each sample was purified by spin column then quantified by qPCR. cDNA was then split in half and used as input for two step-1 PCR reactions.

treatment_protocol: treated with 1 mg/mL doxycycline (Sigma-Aldrich, D9891) for 48 hrs; or treated with 5 ng/mL TNF-alpha (Sigma-Aldrich, H8916) for indicated time

value: iRFP barcode

value: 3x-NF-kB vs p(SFFV)

value: 5 hours TNF-a


title: mCherry, 5 hr TNFα, rep3

description:
NIJK04_mCherry_bccounts_final.txt
NIJK04_mCherry_bccounts_reseq_final.txt

value: mCherry barcode


title: pDEMYELINsMMrCorpusCallosumBiM116d201110rerun

description: 10x Genomics v3.1


title: GAT23_NT

source_name: GAT23, gastric mucosoid, NT


title: GAT23_TNFa

source_name: GAT23, gastric mucosoid, TNFɑ


title: mCherry, 2 hr TNFα, rep3

value: 2 hours TNF-a


title: pDEMYELINsMMrCorpusCallosumAiM115d201110rerun

description: 10x Genomics v3.1

source_name: corpus callosum


title: iRFP, 2 hr TNFα, rep3


title: SI, B6, allogeneic BMT

first: Alan

last: Hanash

state: New York

institute: MSKCC

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the seqc software (https://github.com/dpeerlab/seqc)
Assembly: mm10
Supplementary files format and content: csv file (cells along rows, genes along columns)

source_name: Small Intestine

extract_protocol:
Intestinal crypt cells were isolated from normal mice or from transplant recipients as follows. In brief, after euthanasia with CO2, either the entire small intestine (SI) or the terminal 10 cm of ileum was collected, opened longitudinally, and washed with PBS. The tissue was then incubated at 4 °C in EDTA (10 mM) for 20 min to dissociate the crypts. To isolate single cells from crypts, the pellet was further incubated in 1× TrypLE express (Gibco, Life Technologies) supplemented with 2 kU/ml DNase1 (Roche). To isolate single cells from intestinal organoids, crypts, organoids were dissociated using 1× TrypLE express at 37°C. After vigorously pipetting through a p200 pipette causing mechanical disruption, the crypt suspension was washed with 10 ml of DMEM/F12 medium containing 10% FBS and 2 kU/ml DNase1 and passaged through a 40 mm cell strainer. Dissociated crypt cells or intestinal organoids were stained with DAPI and then sorted to purify DAPI-negative cells. The single cell RNA sequencing (scRNA-seq) of FACS-sorted cell suspensions was performed on a Chromium instrument (10X genomics) following the user guide manual CG00052 Rev E and Single Cell 3’ Reagent Kit (v2). Each sample, containing approximately 5000 cells at a final dilution of 66–70 cells/µl was loaded onto the cartridge according to the manual. The viability of cells was between 83-99%, as confirmed with 0.2% Trypan Blue staining using a Countess II cell counter.
The individual transcriptomes of encapsulated cells were barcoded during the reverse transcription (RT) step. The resulting cDNA was purified with DynaBeads. This was followed by amplification with 14 cycles of PCR: 98 ̊C for 180s, 14x (98 ̊C for 15s, 67 ̊C for 20s, 72 ̊C for 60s), and 72 ̊C for 60s. Next, 50 ng of PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to the sequencing adapters, and indexed by PCR: 98 ̊C for 45s; 12x (98 ̊C for 20s, 54 ̊C for 30s, 72 ̊C for 20s), and 72 ̊C for 60s. The indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on the Illumina NovaSeq S4 platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher). Sequencing depth was 198 million reads per sample on average (31,900 reads per cell). The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package48. Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis. After barcode correction and filtering, we recovered 11,427 unique transcripts per cell, with a median read per transcript of 1.83.

value: Small Intestine

tag: group


title: mCherry, untreated, rep3

value: untreated


title: SI, B6, syngeneic BMT

description: 10x Genomics


title: SI, BM, replicate 1

description: 10x Genomics


title: SI, BM, replicate 2

description: 10x Genomics


title: SI, BM + treatment

description: 10x Genomics


title: iRFP, untreated, rep2


title: mCherry, 5 hr TNFα, rep2


title: SI, BM + treatment2

description: 10x Genomics


title: mCherry, 2 hr TNFα, rep2


title: iRFP, 2 hr TNFα, rep2


title: SI, B6, replicate 1

description: 10x Genomics


title: mCherry, untreated, rep2


title: SI, day 5 + 6h IFNg, scRNAseq

description: 10x Genomics


title: iRFP, 5 hr TNFα, rep1


title: SI, B6, replicate 2

description: 10x Genomics


title: mCherry, 5 hr TNFα, rep1


title: SI, day 5 + 48h IFNg, scRNAseq

description: 10x Genomics


title: iRFP, untreated, rep3


title: SI, day 5, scRNAseq

description: 10x Genomics


title: Liver, G108 treatment, high protein diet, mouse 4

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC (v0.11.8)
Reads were aligned to the reference genome GRCm38_snp_tran using HISAT2 (v2.0.5)
Readcounts were generated using the Rsubread FeatureCounts module (v2.0.0)
Transcripts per million (TPM) were calculated based on the number of reads count mapped to each gene over the exon length of the respective gene x 1 million, divided by the total number of mapped reads.
Differential expressed (DE) genes were determined with DESeq2 (v 1.36.0). Shrinkage of effect size was performed on Deseq2 results using theapeglmmethod.
Assembly: GRCm38
Supplementary files format and content: tab delimited text file includes TPM values for each sample
Supplementary files format and content: xlsx file includes Deseq2 comparisons between groups

source_name: Liver

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
Sequencing libraries were prepared using the NGS RNA Library Prep Set (PT042, Novogene). RNA sequencing procedures were performed by NovoGene UK.

treatment_protocol: Lean 10-week-old C57BL/6 mice were provided ad libitum a 60 kcal% high fat diet (diet D12492) for 8 weeks prior to the start of the study. The cohort of mice were individually housed and randomly divided into treatment groups: The high fat, standard protein diet (SP diet) (D08091803) and high fat, high protein diet (HP diet) (D08091801). All mice had ad libitum access to water and their allocated diets. Mice were subcutaneously administered with vehicle or G108 at a dose of 2.5 nmol/kg at 9 am each day for 22 days. Following a 4 h fast on day 25 all mice were culled, with tissues snap frozen in liquid nitrogen prior to storage at −80°C.

value: Liver

tag: Sex

value: male

tag: dietary protein_content

value: High protein


title: iRFP, untreated, rep1


title: Liver, G108 treatment, high protein diet, mouse 2


title: Liver, G108 treatment, high protein diet, mouse 3


title: mCherry, unreated, rep1


title: SI, B6, naive

description: 10x Genomics


title: SI, day 5 + 24h IFNg, scRNAseq

description: 10x Genomics


title: mCherry, 2 hr TNFα, rep1


title: mCherry, pre, rep3

value: dual p(SFFV)


title: iRFP, 5 hr TNFα, rep2


title: mCherry, post, rep3

value: tetracycline


title: iRFP, 2 hr TNFα, rep1


title: iRFP, post, rep3


title: Liver, G108 treatment, standard protein diet, mouse 3

value: Standard protein


title: Liver, G108 treatment, standard protein diet, mouse 4


title: iRFP, pre, rep3


title: mCherry, pre, rep2


title: Liver, G108 treatment, standard protein diet, mouse 2


title: Liver, G108 treatment, high protein diet, mouse 1


title: iRFP, pre, rep2


title: Liver, vehicle treatment, high protein diet, mouse 2

value: Vehicle


title: mCherry, post, rep1


title: Liver, vehicle treatment, high protein diet, mouse 4


title: Liver, vehicle treatment, high protein diet, mouse 1


title: iRFP, pre, rep1


title: Liver, vehicle treatment, standard protein diet, mouse 4


title: Liver, vehicle treatment, high protein diet, mouse 3


title: iRFP, post, rep1


title: Liver, vehicle treatment, standard protein diet, mouse 2


title: Liver, vehicle treatment, standard protein diet, mouse 1


title: Liver, vehicle treatment, standard protein diet, mouse 3


title: S8-scDNA-seq_prot

city: Houston

first: Yijune

state: Texas

address: 1901 East Rd

institute: MD Anderson

data_processing:
FASTQ files generated by the sequencer were processed using the Tapestri Pipeline V2, which included adapter trimming and sequence alignment (Burrows-Wheeler Aligner) to the human genome (GRCh37/hg19), barcode correction, and cell find. For variant calling and genotyping, we processed as previously described 1.
Assembly: hg19
Supplementary files format and content: Raw read counts and filtered genotype calls for single-cell DNA seq
Supplementary files format and content: Raw and normalized read counts for single-cell antibody seq
Library strategy: Multiomic single-cell DNA and antibody seqeuncing (DAbseq)

source_name: Bone Marrow

extract_protocol:
Mononuclear cells (MNCs) were isolated from each sample using the standard gradient separation approach with Ficoll-Paque PLUS (GE Healthcare Lifesciences, Marlborough, MA).
According to the manufacturer's protocol, single-cell library DNA preparation was performed using the Tapestri Platform and reagents (MissionBio). Briefly, cryopreserved bone marrow mononuclear cells were thawed, washed with RPMI1640 supplemented with 40% FBS, 1% BSA, and 5 mM EDTA, and counted using a Countess cell counter (Invitrogen). BMNCs were normalized to 25,000 cells/μL in 40 μL and incubated with Human TruStain FcX (BioLegend, catalog# 422301), Blocking buffer in 1× staining buffer for 15 minutes on ice. Next, cells were stained with TotalSeq™-D Human Heme Oncology Cocktail (Biolegend, catalog# 399906), CD70 (Biolegend, catalog# 355127), CD99 (Biolegend, catalog# 371325), and CD366 (Biolegend, catalog# 345057) AOCs for 30 minutes on ice. Following staining, cells were washed three times in wash buffer and were loaded onto the Tapestri instrument for single-cell encapsulation, lysis, and barcoding with 2 μmol/L antibody tag forward primer. The DNA from barcoded cells was amplified via multiplex PCR using a targeted myeloid panel that included 279 amplicons across 37 genes associated with myeloid malignancies (https://designer.missionbio.com/catalogpanels/Myeloid-MDACC). DNA libraries were extracted from the droplets, followed by purification with Ampure XP beads (Beckman Coulter). The purified DNA libraries were indexed and then sequenced on Illumina's NovaSeq 6000 SP with 250-bp paired-end multiplexed runs. Protein PCR products, which exist in the supernatant from the Ampure XP bead purification step, were isolated by a 5-minute incubation with 2 μL 5′ biotin oligo for 5 minutes at 96°C, followed by a 5-minute incubation on ice. Isolated proteins were washed using 2× binding and washing buffer and streptavidin beads. Protein libraries were generated using the washed proteins, library template, and i5/i7 indices via PCR. The protein library PCR product was cleaned again using Ampure XP beads. Protein libraries were quantified, quality checked, and sequenced on Illumina's NovaSeq 6000 S4 with 150-bp paired-end multiplexed runs.

value: Bone Marrow

value: Mononuclear cells


title: S13-scDNA-seq_prot


title: mCherry, post, rep2


title: S15-scDNA-seq_prot


title: S10-scDNA-seq_prot

source_name: Peripheral Blood

value: Peripheral Blood


title: Ctrl4, scRNA

city: San Antonio

first: Gek Ming

last: Sia

address: 7703 Floyd Curl Drive, MED 237B

institute: University of Texas Health at San Antonio

description: 10x Genomics

data_processing:
10x Genomics Cell Ranger v7.0.1 was used for sample demultiplexing, barcode processing, UMI filtering, gene counting, and genome mapping.
Assembly: mm10-2020-A (10x Genomics) reference genome
Supplementary files format and content: 10x Genomics Cell Ranger Count output feature barcode matrices

source_name: cerebral cortex

extract_protocol:
Briefly, microglia were isolated by cold dounce homogenization followed by FACS for Cd11b/CD45/Cx3cr1, as described in Tillmon et. al. 2024
10x Genomics Chromium 3' library v3.1 kit

treatment_protocol: Male C57BL/6J mice received either corticosterone (0.1 mg/ml in 1% ethanol) or control (1% ethanol) drinking water for 21 days

value: cerebral cortex

value: microglia

value: wildtype

value: Ctrl


title: Cort4, scRNA

description: 10x Genomics

value: Corticosterone


title: S7-scDNA-seq_prot


title: Cort3, scRNA

description: 10x Genomics


title: Ctrl3, scRNA

description: 10x Genomics


title: iRFP, post, rep2

value: iRFP barcode


title: mCherry, pre, rep1

value: mCherry barcode

value: untreated


title: S5 DMSO_input [2674725_N6-S5-D-input]

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

data_processing:
Raw ChIP-seq reads were mapped to GRCh38 using bwa-mem (Version 0.7.16a) sorting, indexing and duplicates were marked using samtools (Version 1.7). MACS2 (Version 2.1.1) were used for peak calling on unique mapped reads and ENCODE blacklist regions were used to filter the peaks. bamCoverage command from deeptools (Version 3.5.4) were used to generate RPGC normalized bigwig tracks.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: lymphocyte

extract_protocol:
Cell were fixed with 1%formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris)
DNA was quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher). Libraries were prepared with HyperPrep Library Preparation Kit (Roche PN 07962363001). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).

value: lymphocyte

value: B cell

tag: antibody

value: DMSO


title: Ctrl2, scRNA

description: 10x Genomics


title: S5 EHT 1610_input [2674727_N6-S5-SNS_500nm_input]


title: S2 EHT 1610_input [2674726_N6-S2-SNS_500nm_input]


title: p-Ser5_Pol II_THAL-SNS-032_2 [2674723_N6-S5-SNS_500nm_2]

value: p-Ser5 Pol II (Millipore, # 04-1572)


title: Ctrl1, scRNA

description: 10x Genomics


title: S2 DMSO input [2674724_N6-S2-D-input]


title: Liver, G108 treatment, standard protein diet, mouse 1

value: Liver

value: male

value: Standard protein


title: p-Ser5_Pol II_THAL-SNS-032_1 [2674722_N6-S5-SNS_500nm_1]


title: p-Ser2_Pol II_THAL-SNS-032_1 [2674720_N6-S2-SNS_500nm_1]

value: p-Ser2 Pol II (Millipore, # 04-1571)


title: p-Ser2_Pol II_THAL-SNS-032_2 [2674721_N6-S2-SNS_500nm_2]


title: thymus, Con, replicate2, scRNAseq

first: wang

last: my

address: Cangqian Street, Cangxing Street

institute: BoYu Intelligent Health Innovation Laboratory, Hangzhou, 311100, P. R. China.

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thymus

extract_protocol:
For sample preparation of scRNA-seq, thymus were prepared from mice of Con group (treatment with saline), EB group (0.1 mg per time), and EB plus high-dose RGLS treatment (RGLSH, 1.4 g/kg) group.
Libraries were prepared according to the manufacturer’s protocol.

value: thymus

value: Con


title: thymus, EB, replicate 2, scRNAseq

description: 10X Genomics

value: EB


title: p-Ser5_Pol II_DMSO_2 [2674719_N6-S5-D-2]


title: p-Ser5_Pol II_DMSO_1 [2674718_N6-S5-D-1]


title: p-Ser2_Pol II_DMSO_2 [2674717_N6-S2-D-2]


title: thymus, Con, replicate1, scRNAseq

description: 10X Genomics


title: MTR4_H3K4me3_rep2

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
Pair-end CUT&Tag reads were trimmed with trim_galore and then aligned to mm10 reference by bowtie2 software using arguments: bowtie2 --end-to-end --very-sensitive --no-mixed --phred33 -I 10 -X 1000 -p 8 -x reference -1 sample_R1.fq.gz -2 sample_R2.fq.gz -S sample.raw.sam. All unmapped reads, none-uniquely mapped reads, PCR duplicated reads, mitochondrial reads were removed before following analyses. Read counts were normalized by RPKM method and macs2 software was used to call peaks in the downstream analyses.
Assembly: mm10
Supplementary files format and content: bw files
Library strategy: CUT&Tag

source_name: Oocyte

extract_protocol:
Oocytes were collected from Day-21 mice with indicated genotypes.120 oocytes were collected per sample.
NovoNGS CUT&Tag 3.0 High sensitivity Kit (for Illumina) (Novoprotein; N259) was used for library construction. Protocol used in this study followed the manufacture’s instructions with several modifications, including antibody concentration 1:100 for primary antibody (CST: 9751) and 1:200 for secondary antibody and 16 PCR cycles for amplification.

value: Oocyte


title: Cort1, scRNA

description: 10x Genomics

value: cerebral cortex

value: microglia

value: wildtype


title: thymus, EB, replicate1, scRNAseq

description: 10X Genomics


title: p-Ser2_Pol II_DMSO_1 [2674716_N6-S2-D-1]


title: Cort2, scRNA

description: 10x Genomics

value: Corticosterone


title: thymus, RGLSH, replicate 1, scRNAseq

description: 10X Genomics

value: RGLSH


title: NALM6_THAL-SNS-032_3 [2652861_N6_SNS032]

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.3a --twopassMode Basic
read counts quantified by RSEMv1.3.1
Assembly: GRCh38
Supplementary files format and content: TPM counts are provided in csv files for each library

extract_protocol:
Takara NucleoSpin® RNA Plus XS (740990.50) according to manufacturer instructions
TruSeq Stranded mRNA Library Prep Kit, Illumina, PN 20020595

value: lymphocyte

value: WT


title: NALM6_THAL-SNS-032_2 [2652860_N6_SNS032]

value: B cell


title: NALM6_THAL-SNS-032_1 [2652859_N6_SNS032]


title: WT_H3K4me3_rep2


title: WT_H3K4me3_rep1


title: thymus, RGLSH, replicate 2, scRNAseq

description: 10X Genomics


title: ATAC-MTR4-rep1

data_processing:
The pair-end ATAC-seq reads were aligned to mm10 reference genome by bowtie2 software. All unmapped reads, none-uniquely mapped reads, PCR duplicated reads, mitochondrial reads were removed before following analyses. Read counts were normalized by RPKM method and macs2 software was used to call narrow peaks in the downstream analysis.
Assembly: mm10
Supplementary files format and content: bw files

extract_protocol:
Oocytes were collected from Day-21 mice with indicated genotypes.120 oocytes were collected per sample.
Samples were extracted from Day-21 ovaries with 50 oocytes per sample. Oocytes were lysed in a buffer containing 0.05% Digitonin, 0.5% NP-40 and 0.5% Tween20. Tn5 enzyme in Chromatin Profile Kit for Illumina (Novoprotein; N248) was used to fragment chromatin at 37℃ for 30 minutes and stopped by stop buffer immediately. After purifying DNA using DNA clean beads, PCR was performed to amplify the library for 15 cycles using the following PCR conditions: 72℃ for 3 min; 98℃ for 30 s; and thermocycling at 98℃ for 15 s, 60℃ for 15 s and 72℃ for 8 s; following by 72℃ 2 min. After the PCR reactions, libraries were purified with the 1.2X DNA cleaning beads.


title: 32kPa, rep2

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
An alignment reference was generated from the hg38 human genome and GENCODE comprehensive gene annotations (v26), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter.
About 41-116 million uniquely mapped reads were acquired per sample. DESeq2 package v1.36.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: ER+ MCF7

growth_protocol: MCF7s were cultured in DMEM (Gibco) and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (PS). Prior to plating on CytoSoft Rigidity Plates, the media was changed  to phenol-red free DMEM (Gibco), 10% charcoal-stripped  supplemented with 10% charcoal-stripped FBS and 1% penicillin-streptomycin. At plating on the CytoSoft Rigidity Plates, MCF7s were supplemented  with complete Phenol-Red Free media with 10 nM 17-B estradiol (Invitrogen).

extract_protocol:
mRNA samples were harvested from cells using QIAzol (Qiagen).
RNA libraries for RNA-Seq were prepared using NEBNext® Poly(A) selection.

treatment_protocol: Cells  cultured at 37 C at 5% CO2 for 48 hours on either 0.5 kPa, 32 kPa or normal tissue culture plates.

value: ER+ MCF7


title: 32kPa, rep1


title: TC, rep3

value: TC


title: ATAC-MTR4-rep2


title: TC, rep2


title: ATAC-WT-rep1


title: ATAC-WT-rep2


title: TC, rep1


title: Pancreas, Peptide, CD45-, sample7

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (v2.20.0.422)
files were aligned to Mus musculus GRCm38 reference using STAR aligner (2.7.9a)
Assembly: Mouse reference, mm10
Supplementary files format and content: Processed data files are gzipped STAR output directory (Solo.out).

source_name: Pancreas

growth_protocol: Animals were housed in a specific pathogen-free environment and kept under standard conditions with a 12-h day/night cycle and access to food and water ad libitum.

extract_protocol:
The pancreatic tail was digested in a two-step enzymatic process. First, the pancreatic tail was digested with RPMI 1640 (Nacalai Tesque) containing 2% FBS, 1mg/mL collagenase type XI (Sigma-Aldrich) and 10U/ml DNase I (TaKaRa) for 10 minutes at 37℃, and then with Accumax (Nacalai Tesque) for 5 minutes at 37℃. The single-cell suspension was obtained by passing through a 70 µm cell strainer. The resulting cell suspensions were washed with MEM α (Thermo Fisher Scientific) containing 2% FBS.
RNA-seq library was constructed using a modified sciRNA-seq protocol. The CD45 negative cells were sorted into 384-well plates with barcoded oligo dT primer for each well (1 cell / well). After reverse transcription in each well, cDNA was pre-amplified using the xGen™ ssDNA & Low-Input DNA Prep (IDT). Purified cDNAs were tagmentationed with Amplicon Tagment enzyme (Illumina) and PCR for library construction was done by using NEBNext High-Fidelity 2× PCR Master Mix (NEB).

treatment_protocol: Chronic pancreatitis model mice were induced by repetitive intraperitoneal injections of caerulein (50 μg/kg body weight/h) six times a day, three times a week, for 4 weeks, as previously described.  Normal mice were given saline intraperitoneal injections. At the same time as caerulein administration, normal saline (control group; 5 μl/g) or HMGB1 fragment treatment (HMGB1 group; 5 mg/kg) was administered via the tail vein three times a week for 8 weeks.

value: Pancreas

value: Caerulein + Peptide


title: 0.5kPa, rep3


title: 0.5kPa,  rep2


title: MTR4_H3K4me3_rep1


title: Pancreas, Peptide, CD45-, sample6


title: 32kPa, rep3


title: 0.5kPa, rep1


title: Pancreas, Peptide, CD45-, sample5


title: Pancreas, Peptide, CD45-, sample3


title: Pancreas, Peptide, CD45-, sample2


title: Pancreas, Peptide, CD45-, sample4


title: Pancreas, Peptide, CD45-, sample1


title: Endometrial cells,Set2,1622,non-pregnant

city: beijing

first: Yumeng

last: Ren

state: Beijing

address: Xicheng District

institute: Peking university people’s hospital

data_processing:
Use the fastp tool for quality control of sequencing data. Remove sequences with the following low-quality criteria: Sequences with unknown bases numbering 5 or more. Sequences with a length less than 75bp. Sequences with an average base quality value less than 15. The resulting data after this step is termed Clean Data.
Use the sortmerna tool to align the Clean Data against a ribosomal database. Exclude sequences that align to the ribosomal database. The data obtained after this step is termed de-rRNA Clean Data.
Use the STAR tool to align the de-rRNA Clean Data to the reference genome.
Use the RSeQC tool to assess the quality of the alignment results from STAR.
Use the featureCounts tool to quantify gene expression from the alignment results. Use the edgeR tool for differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited rawcount files for each samples
Supplementary files format and content: tab-delimited FPKM files for each samples

source_name: endometrium tissue

growth_protocol: All endometrial biopsy samples were obtained with disposable uterine-cavity tissue-suction tubes (Runting), and all the collected samples were stored in All protect Tissue Reagent (QIAGEN). The samples were transported to our laboratory on ice packs and stored at -80°C before processing.

extract_protocol:
RNA was extracted from endometrial tissue using RNAprep Pure Tissue Kit (DP341; Tiangen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using a KAPA Stranded RNA-Seq Library Preparation Kit (KR0934, KAPA Biosystems), following the manufacturer’s instructions.

treatment_protocol: The estradiol administration of all patients was started from the second day of menstruation with 4 mg estradiol valerate (Progynova; Bayer, Leverkusen, Germany) per day. When endometrial thickness was at least 7 mm and endogenous progesterone level was less than 1.5 ng/ml, 90 mg progesterone sustained-release vaginal gel (Crinone; Merck-Serono, Darmstadt, Germany) was applied transvaginally per day. The initial day of progesterone administration was recognized as “P+0” and endometrial biopsies were respectively taken on days P+3, P+5, and P+7 for each patient by a dedicated physician.

value: endometrium tissue

value: non-pregnant


title: Endometrial cells,Set2,0592,non-pregnant


title: Endometrial cells,Set2,1416,non-pregnant


title: Pancreas, Saline, CD45-, sample8

value: Caerulein + Saline


title: Endometrial cells,Set2,0067,non-pregnant


title: Endometrial cells,Set2,0615,non-pregnant


title: Endometrial cells,Set2,1835,non-pregnant


title: Pancreas, Saline, CD45-, sample6


title: pDEMYELINsMMrCorpusCallosumLiM122d201110rerun

description: 10x Genomics v3.1

value: corpus callosum

value: Brain cells

value: Stereotaxic injection of LPC or saline control


title: Pancreas, Peptide, CD45-, sample8


title: Pancreas, Saline, CD45-, sample7


title: Pancreas, Saline, CD45-, sample5


title: Pancreas, Saline, CD45-, sample4


title: Pancreas, Saline, CD45-, sample3


title: Endometrial cells,Set2,0840,non-pregnant


title: Endometrial cells,Set2,0636,non-pregnant


title: Pancreas, Saline, CD45-, sample2


title: Endometrial cells,Set2,0639,non-pregnant


title: Pancreas, Saline, CD45-, sample1


title: Pancreas, Healthy, CD45-, sample8

value: Non Treat


title: Endometrial cells,Set2,0756,non-pregnant


title: Pancreas, Healthy, CD45-, sample7


title: Endometrial cells,Set2,0611,non-pregnant


title: Endometrial cells,Set2,1376,non-pregnant


title: Endometrial cells,Set1,1229,pregnant

value: pregnant


title: Pancreas, Healthy, CD45-, sample3


title: Endometrial cells,Set2,1064,non-pregnant


title: Endometrial cells,Set1,1346,pregnant


title: Endometrial cells,Set1,0995,pregnant


title: Endometrial cells,Set1,0286,pregnant


title: Pancreas, Healthy, CD45-, sample6


title: Endometrial cells,Set2,0497,non-pregnant


title: Pancreas, Healthy, CD45-, sample5


title: SOD1G93A/PHD1-/-, replicate 3, snRNA-seq

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: 10x Genomics 3'

data_processing:
Fastq files from 10x experiments were mapped to the mouse genome (mm10-2020-A, provided by 10x genomics) using cellranger count (v5.0.2), the includeIntrons option was enabled.
Filtered count matrices were loaded into Scanpy (v1.8.1) and cells with more than 15% reads associated to mitochondrial genes or less than 250 genes expressed were filtered out, next Scrublet (v0.2.2) was used to remove doublets with thresholds being determined automatically.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lumbar spinal cord

extract_protocol:
To extract nuclei from frozen mouse lumbar spinal cords, we used a slightly modified version of the protocol described previously by Swiech et al, 2015, Nat Biotech. In brief, lumbar spinal cords from three 110 days-old littermate pairs (six samples in total) were dissected and frozen immediately in precooled RNAse-free eppendorfs. Tissue was stored at -80°C until nuclei were extracted. At the day of nuclei extraction, frozen tissues were left in homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg Acetate, 10 mM Tris pH8, 0.1 mM EDTA, 0.1% Igepal/NP-40, 0.1 mM PMSF, 1 mM β-mercaptoethanol in H2O) for 5 minutes on ice to prevent nuclei from breaking. Next, tissue was homogenized by 100 gentle manual strokes using a dounce homogenizer (Sigma-Aldrich). Subsequently, a 1:1 volume of gradient medium (5 mM CaCl2, 3 mM Mg Acetate, 10 mM Tris pH8, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 50% Optiprep, in water) was layered on top of the homogenized sample before ultracentrifugation (7,700 rpm for 30 min at 4°C using a SW41Ti rotor). Subsequently, the nuclei-containing pellet was resuspended in 150 μL resuspension buffer (BSA 1%, nuclease free water 340 mM, RNasin Plus 0.2 U/ μL in 1X PBS). Number and quality of purified nuclei was controlled using a LUNA-FL Dual fluorescence cell counter (Logsbio)
After single nuclei preparation, samples were immediately processed for the single nuclei whole transcriptome analysis (WTA). The single-nucleus RNA sequencing analysis was performed using 10X genomics 3’ WTA suite, according to the manufacturer recommendation. In brief, single nuclei were encapsulated in droplets for lysis and subsequent reverse transcription of polyadenylated mRNA species. After the first cDNA amplification, the library was subjected to Truseq based library preparation to incorporate the Illumina sequencing adaptors and indices. The final library obtained at the end of the single cell RNA-sequencing workflow was sequenced on either of the Illumina Hiseq 4000 or Illumina NovaSeq6000 platforms as per the sequencing specification mentioned in the 10X scRNAseq workflow. Each lane was pooled with multiple 10X libraries which were indexed separately.

value: lumbar spinal cord

value: 110 days


title: Pancreas, Healthy, CD45-, sample1


title: Endometrial cells,Set1,1700,pregnant


title: Endometrial cells,Set1,1879,pregnant


title: SOD1G93A/PHD1-/-, replicate 2, snRNA-seq

description: 10x Genomics 3'


title: Pancreas, Healthy, CD45-, sample2


title: SOD1G93A/PHD1+/+, replicate 3, snRNAseq

description: 10x Genomics 3'


title: Endometrial cells,Set1,1550,pregnant


title: Endometrial cells,Set1,0882,pregnant


title: SOD1G93A/PHD1+/+, replicate 2, snRNAseq

description: 10x Genomics 3'


title: Endometrial cells,Set2,1610,non-pregnant


title: Aorta Control, scRNAseq

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

description: 3' scRNA10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Integration and analysis performed with Partek Flow analysis software  (https://www.partek.com/partek-flow/)
Assembly: mm10
Supplementary files format and content: cell ranger h5 formatted and comma separated value count matrix files; annotated cell barcode comma separated value files

source_name: Aorta

extract_protocol:
Aortae from 4 control and 4 diabetic mice were collected in DMEM media containing 10 % fetal calf serum (FCS) on ice. Aortae were then individually cut into small pieces and digested for 1 hour at 37 °C on a thermomixer in PBS containing LiberaseTM (0.1 mg/mL, Sigma), 1.4 mM CaCl2, Hyaluronidase (60 U/mL Sigma), DNase I (Qiagen 120U/mL). The aortic suspension after digestion was filtered through a 40 µM cell strainer and washed with FCS containing DMEM media. Cells from the experimental groups (control and diabetes) were pooled and resuspended in the FCS containing DMEM media and incubated at 37 °C with 5% CO2 in a cell culture incubator for 30 minutes. Aortic cells were resuspended in FACS buffer containing 1X HBSS, 0.05 mM EDTA, and 5 g BSA and incubated with fluorochrome-coupled antibodies (7AAD-PE/Cy5 and Calcein-FITC) to sort viable and metabolically active cells using FACS Fusion (BD Biosciences).
scRNA-seq libraries prepared according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, sorted aortic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into  10X chip chip to generate droplets or gel bead in emulsions (GEMs). Poly-A RNA transcripts from lysed cells captured in GEMs were retrotranscribed to cDNA, and barcoded according to embedded bead functional oligos which contain an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Barcoded cDNA was amplified by PCR, enzymatically fragmented and sized selected with SPRIselect reagent for subsequent library construction. During final library construction unique sample indexes were included from the 10X genomics "Single Index Kit T Set A".

treatment_protocol: To induce diabetes, 6-week-old male Apoe-/- were rendered diabetic by daily intraperitoneal (IP) injections of streptozotocin (STZ) (55 mg/kg body weight/day) or citrate vehicle (controls) on 5 consecutive days and followed for 10 weeks

value: Aortic

value: Aorta

value: Apoe -/-

value: 17 weeks

tag: sample group

value: control


title: Endometrial cells,Set1,0751,pregnant

tag: tissue


title: Aorta Diabetes, scRNAseq

description: 3' scRNA10x Genomics

tag: cell type

value: diabetic (streptozotocin induced)


title: Endometrial cells,Set1,0649,pregnant


title: mTEChi DRKO 4

city: Minneapolis

first: Christine

middle: H

last: O'Connor

address: 117 Pleasant St. SE

department: Minnesota Supercomputer Institute

institute: University of Minnesota

data_processing:
trimmomatic version 0.33 was used to clean reads for adapter contamination and low-quality sequence.
HISAT2 version 2.1.0 was used to align samples to the genome reference consortium mouse build 38 reference genome.
featureCounts v1.6.2 was used to count mapped reads to genes.
Differential Gene Expression was done using raw read counts in edgeR (via CLCGWB).
Expression heatmaps from raw counts were done using the Morpheus software (https://software.broadinstitute.org/morpheus).
Genome_build: GRCm38
Supplementary_files_format_and_content: Hogquist_thymocytes_bulkRNAseq_rawcounts.txt: Tab-delimited text file with gene expression count data.

source_name: murine thymocytes

extract_protocol:
Qiagen RNeasy micro kit was used to extract RNA from each sample.
Library creation was performed using the SMARTer Stranded Total RNA Pico Mammalian v2 kit (Takara Bio), according to manufacturer’s instruction. Sequencing was performed on a NovaSeq6000 using paired-end 150-base chemistry.

value: MHC-II-hi mTECs

tag: genotype

value: IFNAR1-KO IFNLR-KO


title: Pancreas, Healthy, CD45-, sample4

value: Pancreas


title: mTEChi DRKO 3


title: Endometrial cells,Set1,1891,pregnant

value: endometrium tissue


title: mTEChi DRKO 1


title: Endometrial cells,Set1,1026,pregnant


title: Endometrial cells,Set1,0815,pregnant


title: EDI27, differentiated by PROT#4, tumor_r3

city: Los Angeles

first: Miller

last: Huang

address: 4640 West Sunset Blvd Off Campus

department: Pediatrics

institute: Keck School of Medicine of Usc

data_processing:
RNA-sequencing reads were mapped to the human hg38 primary assembly reference genome using the HISAT2 aligner v2.2.0
Gene expression was quantified as reads per Gene using featureCounts v2.0.2
Assembly: Ensembl Homo_sapiens.GRCh38_genome release 109
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: Neuroblastoma

growth_protocol: EDI27 iPSC were maintained on GelTrex coated 6-well plates in StemFlex media(Thermo Fisher) in a humidified 37°C incubator with 5% CO2. Cells were passaged every 4-5days using Accutase (and plated at 20-30,000 cells/cm2) StemFlex media with 2uM of ROCK inhibitor Thiazovivin.

extract_protocol:
Total RNA was extracted from flash frozen tissue using the Tissuelyzer (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen).
Extracted RNA were sent to Novogene (https://en.novogene.com/) for library preparation (polyA enrichment)

treatment_protocol: 4 different differentiation protocol, from iPSC to tNCC, were used.

value: Neuroblastoma

value: sympathoadrenal cell


title: mTEChi DRKO 2


title: mTEChi WT 4

value: WT


title: Endometrial cells,Set1,0725,pregnant


title: EDI27, differentiated by PROT#4, tumor_r1


title: mTEChi WT 2


title: mTEChi WT 3


title: mTEChi WT 1


title: EDI27, differentiated by PROT#3, tumor_r3


title: mTEChi STAT1KO 4


title: EDI27, differentiated by PROT#4, tumor_r2


title: mTEChi STAT1KO 3


title: mTEChi STAT1KO 2


title: EDI27, differentiated by PROT#2, tumor_r2


title: XCR1 WT 8

value: XCR1+ DCs


title: EDI27, differentiated by PROT#2, tumor_r3


title: EDI27, differentiated by PROT#3, tumor_r1


title: EDI27, differentiated by PROT#2, tumor_r1