title: PY53_eHHO_OSM_0h_input

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

data_processing:
raw reads were trimmed using cutadapt and mapped onto hg38 using Bowtie2 with “--very-sensitive” options
Picard was then used to remove duplicates using the MarkDuplicates tool.
Peak calling was performed using MACS2 with “--broad -B -- broad-cutoff 0.1” options. The peaks were filtered and by qvalue >5 and merged in triplicates.
The neighboring genes in which the peak resides in their TSS-centered 50 KB regions were extracted using ChIPpeakAnno package.
The BigWig files were created using the bamCoverage tool in deepTools.
Assembly: hg38
Supplementary files format and content: BigWig files of 0h and 0.5h after cytokine induction.

source_name: eHHO

growth_protocol: Human hepatocyte organoids derived from primary human hepatocytes (HHOs)  were expanded in expanding medium (EM).

extract_protocol:
Cells were
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (ILLUMINA) following manufacturer's protocols.

treatment_protocol: HHOs were cultureed in EM without OSM for 6 hrs and then induced by OSM. Cells were harvested at 0h and 0.5h after OSM induction.

value: eHHO

tag: patient

tag: antibody

value: input

value: male


title: Endoderm Ngn3Cre 21ss b2 067, scRNA-seq

status: Public on Jan 15 2025

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_067

library_source: transcriptomic single cell

data_processing:
For the Smart-seq3xpress scRNA-seq data, initial quality control was executed with FastQC version 0.11.9 under default settings. Index, primer, and adaptor sequences were then trimmed from paired-end reads using Trimmomatic version 0.39 with default parameters. Alignment of trimmed reads to the Mus musculus Genome assembly GRCm38 (mm10) was accomplished using HISAT version 2.1.0.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

molecule: total RNA

organism: Mus musculus

source_name: Endoderm

extract_protocol:
Endodermal and gut tissues from 9SS to 27SS, were enzymatically dissociated using 0.25% trypsin (Gibco, 25200-056) for roughly 4 minutes at 37°C. The reaction was halted by the addition of 0.4 volumes of fetal bovine serum (FBS). The resultant cell suspension was centrifuged at 1000 rpm for 5 minutes at 4°C, followed by supernatant removal. To prepare single-cell suspensions from endodermal and gut samples, cells were incubated with anti-EpCAM-APC antibody (Invitrogen, 17-5791-82, dilution 1:100) in FACS buffer (comprising HBSS buffer with 1% FBS) for 20 minutes at 4°C in darkness. Following incubation, cells were washed with FACS buffer and subjected to analysis and sorting using BD FACSAriaTM Fusion flow cytometers. Dead cells were excluded from the analysis through staining with 1 µg/mL DAPI (Macklin, D807022).
The Smart-seq3xpress libraries were prepared following Smart3-seq3xpress's protocols.

tag: tissue

value: Endoderm

tag: strain

tag: genotype

value: Ngn3-Cre; Ai6

tag: time


title: Sample 346

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description: Supratentorial ependymoma, NOS

library_source: transcriptomic

data_processing:
The Salmon (v 0.12.0) index was generated using the GRCh38 human genome (GENCODE 43/Ensembl 109) with --type quasi -k 31
Transcript quantification was performed using Salmon (v 0.12.0) with --validateMapping
Transcript quantifications were converted to gene-level counts in R using the tximport (v 1.32.0)
Assembly: Human GRCh38/hg38
Supplementary files format and content: tab-delimited text file with Gene ID and transcript per million (TPM) for all the samples

organism: Homo sapiens

source_name: Brain tumor

extract_protocol:
FFPE-tumor samples were deparaffined using Deparaffinization Solution (Qiagen) and total RNA was extracted using the RNeasy DSP FFPE kit (Qiagen). The concentration was assessed using the Qubit RNA Assay kit (Thermo Fisher) and the RNA quality was quantified by measuring the DV200 value, using the RNA ScreenTape Assay (Agilent, Santa Clara, CA, USA) in the Agilent 4200 TapeStation System. Only samples with a DV200 value of ≥ 31.6 were sequenced.
The starting amount of total RNA was 100 ng for preparing the sequencing library using the Illumina RNA Prep with Enrichment (L) Tagmentation and Illumina Exome panel – Enrichment Oligos Only (Illumina) following manufacturer's recommendations.

value: Brain tumor


title: TKO-F1295A-2

city: Gainesville

first: Jonathan

last: Licht

state: Florida

address: 2033 Mowry Road

department: UF Health Cancer Center

country: USA

institute: University of Florida

data_processing:
Trimming and quality control were performed on raw fastq files using Trimmomatic (v0.36) and FastQC (v0.11.4).
The reads were aligned to the transcriptome using STAR (v2.7.9a) and quantified using RSEM (v1.3.1)
Differential expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: RSEM raw gene counts in .csv file

source_name: TKO

growth_protocol: Cells were plated at a density of 0.2x10^6 cells/mL and harvest at 70-80% confluence

extract_protocol:
Total RNA was extracted with the Direct-zol RNA MiniPrep Plus Kit
Poly(A) RNA sequencing were performed by the University of Florida Interdisciplinary Center for Biotechnology Research core

tag: cell line

value: TKO

tag: cell type

value: plasma cell

tag: biological replicate

tag: vector

value: NSD2 p.F1295A expression vector


title: TKO-WT-3

value: NSD2 expression vector


title: Sample 66

description: Glioblastoma, IDH wildtype


title: PY39a_eHHO_OSM_0h_input

library_source: genomic

molecule: genomic DNA

tag: Sex

value: female

tag: treatment


title: TKO-WT-2


title: Sample 41

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 066, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_066


title: PM16_eHHO_OSM_0h_STAT3


title: Sample 36

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 064, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_064


title: Endoderm Ngn3Cre 21ss b2 065, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_065


title: TKO-D1240A-3

value: NSD2 p.D1240A expression vector


title: Sample 67

description: Glioblastoma, IDH wildtype


title: TKO-D1240A-2


title: Endoderm Ngn3Cre 21ss b2 063, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_063


title: Sample 227

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 068, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_068


title: PM16_eHHO_OSM_0h_input


title: TKO-D1240A-1


title: Sample 184

description: Oligodendroglioma, IDH-mutant  and  1p/19q-codeleted, grade 2


title: PY53_eHHO_OSM_0h_STAT3


title: Endoderm Ngn3Cre 21ss b2 062, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_062


title: Sample 128


title: TKO-3


title: Endoderm Ngn3Cre 21ss b2 061, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_061


title: PY39a_eHHO_OSM_0.5h_STAT3


title: TKO-2


title: Sample 110

description: Glioblastoma, IDH wildtype


title: PY39a_eHHO_OSM_0h_STAT3


title: TKO-1


title: Sample 105

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 060, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_060


title: K20191231-2,Adelaide,Liver

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

data_processing:
We used TEMP2-insertion (version 0.1.6) to identify new transposon insertions in Illumina and BGI DNA-seq data.
Assembly: phaCin_unsw_v4.1
Supplementary files format and content: tab-delimited text files contain the information of identified transposon insertions.
Library strategy: DNA-seq

organism: Phascolarctos cinereus

source_name: Liver

extract_protocol:
Total DNA was isolated from koala tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen).
Short fragment PCR-free DNA-seq libraries was constructed and sequenced in BGI China or the Broad Institute.

value: Liver

tag: Stage

value: adult

tag: location

value: Adelaide

tag: koala id


title: TKO-F1295A-1


title: PM16_eHHO_OSM_0.5h_STAT3


title: Endoderm Ngn3Cre 21ss b2 059, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_059


title: Sample 91

description: Supratentorial ependymoma, NOS


title: Sample 61

description: Pilocytic astrocytoma


title: Endoderm Ngn3Cre 21ss b2 058, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_058


title: Pool016_scRNA_10X [Batch2]

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
make fastq using cellranger-2.2.0.
create gene counts using cellranger-2.2.0.
Pipelines by the sc-eQTL-Gen Consortium for genotype imputation, demultiplexing of single cells to individual samples, doublet identification and cell-type classification were used.
Assembly: Genome_build: Grch38
Supplementary files format and content: Tab-separated value files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Blood

growth_protocol: Not applicable

extract_protocol:
total RNA
Chromium Single Cell Gene Expression v2 Single-cell RNA-seq.

treatment_protocol: Not applicable

value: Blood

tag: batch

tag: ethnicity

value: African


title: PY53_eHHO_OSM_0.5h_STAT3

value: eHHO

tag: patient


title: K20191231-2,Adelaide,Brain

source_name: Brain

value: Brain


title: Pool015_scRNA_10X [Batch2]


title: Sample 58

description: Glioblastoma, IDH wildtype


title: Pool014_scRNA_10X [Batch2]


title: K20190727,Adelaide,Liver


title: Sample 46

description: Glioblastoma, IDH wildtype


title: K20190727,Adelaide,Brain


title: Endoderm Ngn3Cre 21ss b2 057, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_057


title: Endoderm Ngn3Cre 21ss b2 055, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_055


title: Pool013_scRNA_10X [Batch2]


title: Sample 29

description: Oligodendroglioma, IDH-mutant  and  1p/19q-codeleted, grade 3


title: K98314,Currumbin,Testis

data_processing:
We used TEMP2-insertion (version 0.1.6) to identify new transposon insertions in Illumina and BGI DNA-seq data.
To leverage Nanopore long-read DNA-seq data for constructing transposon insertion sequences, we first employed Guppy-basecaller62 (version 5.0.16) with the high accuracy configuration to convert the Nanopore raw signals into raw reads. Subsequently, the raw reads were aligned to the koala genome using Minimap263 (version 2.17) with the parameters “-x map-ont”. Soft clipped reads (those with clipped 5´ or 3´ ends) and spanning reads (those containing internal deletions) were collected. A soft clipped read or spanning read was designated as supporting a transposon insertion if the soft clipped or deleted portion could be mapped back to transposon consensus sequences using Minimap2 with parameters “-x map-ont”. Adjacent reads supporting transposon insertions were clustered together and used for assembling the insertion sequence via wtdbg2 (version 2.5) with default parameters. An insertion with a sequence originating from both KoRV-A and PhER was classified as a recKoRV insertion, and the structure of recKoRV was defined accordingly for Currumbin and Sunshine Coast koalas. Hence, insertions with sequences solely from KoRV-A were deemed as full-length KoRV-A insertions.
Assembly: phaCin_unsw_v4.1
Supplementary files format and content: tab-delimited text files contain the information of identified transposon insertions.
Library strategy: DNA-seq

source_name: Testis

extract_protocol:
Total DNA was isolated from koala tissue samples using the DNeasy® Blood and Tissue Kit (Qiagen).
Short fragment PCR-free DNA-seq libraries was constructed and sequenced in BGI China or the Broad Institute. Long fragment DNA-seq libraries was constructed and sequenced in Cold Spring Harbor using the PromethION platform.

value: Testis

value: Currumbin


title: Pool012_scRNA_10X [Batch2]


title: K98224,Currumbin,Testis


title: Endoderm Ngn3Cre 21ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_054

value: Endoderm

value: Ngn3-Cre; Ai6


title: Pool011_scRNA_10X [Batch2]


title: Sample 19

description: Ganglioglioma

value: Brain tumor


title: Endoderm Ngn3Cre 21ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_053


title: Sample 16

description: Glioblastoma, IDH wildtype


title: Pool010_scRNA_10X [Batch2]


title: Endoderm Ngn3Cre 21ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_052


title: K98224,Currumbin,Brain


title: Sample 12

description: Supratentorial ependymoma, NOS


title: Pool009_scRNA_10X [Batch2]


title: Sample 3

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_051


title: K98214,Currumbin,Ovary

source_name: Ovary

value: Ovary


title: Pool008_scRNA_10X [Batch2]


title: Endoderm Ngn3Cre 21ss b2 056, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_056


title: Sample 466

description: Astrocytoma, IDH-mutant, grade 3


title: K94283,SunshineCoast,Liver

value: SunshineCoast


title: Pool007_scRNA_10X [Batch2]


title: K94283,SunshineCoast,Brain


title: Endoderm Ngn3Cre 21ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_049


title: Sample 416

description: Pilocytic astrocytoma


title: Pool006_scRNA_10X [Batch2]


title: Sample 253

description: Glioblastoma, IDH wildtype


title: Pool004_scRNA_10X [Batch2]


title: NPC, WEGS, male 7

city: Jakarta

first: Handoko

last: Handoko

address: Jl. Salemba Raya

country: Indonesia

institute: Faculty of Medicine, Universitas Indonesia

data_processing:
Basecalling with minKnow super accuracy mode with dna_r10.4.1_e8.2_400bps_sup@v5.0.0 basecalling model with 5mC and 5hmC detection mode
Alignment toward GRCh38 human reference genome
Metylation pileup using modkit
Assembly: hg38
Supplementary files format and content: bed

source_name: nasopharyngeal cancer biopsy

extract_protocol:
DNA extraction using Qiagen DNA Mini Kit for tissue
Ligation sequencing DNA V14 (SQK-LSK114)
Ligation

value: nasopharyngeal cancer biopsy


title: NPC, WEGS, male 6


title: Sample 249

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_047


title: NPC, WEGS, male 5


title: Pool003_scRNA_10X [Batch2]


title: Endoderm Ngn3Cre 21ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_046


title: K98224,Currumbin,Liver


title: Pool002_scRNA_10X [Batch2]


title: Sample 236

description: Astrocytoma, IDH-mutant, grade 2


title: NPC, WEGS, male 4


title: Endoderm Ngn3Cre 21ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_045


title: Pool001_scRNA_10X [Batch2]


title: NPC, WEGS, male 2


title: Sample 208

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_044


title: Pool016_scRNA_10X [Batch1]


title: Endoderm Ngn3Cre 21ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_043


title: NPC, WEGS, male 3

data_processing:
Basecalling with minKnow super accuracy mode with dna_r10.4.1_e8.2_400bps_sup@v5.0.0 basecalling model with 5mC and 5hmC detection mode
Alignment toward GRCh38 human reference genome
Methylation pileup using modkit
Assembly: hg38
Supplementary files format and content: bedgraph


title: Endoderm Ngn3Cre 21ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_042


title: Pool015_scRNA_10X [Batch1]


title: Sample 166

description: Glioblastoma, IDH wildtype


title: Sample 214

description: Glioblastoma, IDH wildtype


title: NPC, WEGS, male 1


title: Sample 199

description: Glioblastoma, IDH wildtype


title: Pool014_scRNA_10X [Batch1]


title: Endoderm Ngn3Cre 21ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_048


title: Endoderm Ngn3Cre 21ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_041


title: Sample 158

description: Astrocytoma, IDH-mutant, grade 2


title: Mock_WT_2

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

country: South Korea

institute: Kyungpook National University

data_processing:
Basecalls were performed for Illumina NovaSeq 6000 output.
ChIP-seq reads were trimmed using Trimmomatic v0.38.
ChIP-seq reads were aligned to the yeast reference genome sacCer3 using BowTie v1.1.2.
Peaks were called using MACS2 v2.1.1.20160309 and duplicate reads were processed using Picard v0.118.
Peaks annotated using ChIPseeker 1.16.1.
Normalized bedGraph files were generated using MACS2 and converted to bigwig files using bedGraphToBigWig program.
Assembly: sacCer3
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

extract_protocol:
Formaldehyde was add to mid-log phase cells at final concentration of 1% for 20 min. After quenching and cell lysis, sheared chromatin via sonication was incubated with anti-Flag M2 agarose beads and Protein A sepharose for mock IP control. Eluted chromatin fragments were treated with protease then DNA was extracted using a standard phenol/chloroform extraction method.
ChIP-seq libraries were constructed using TruSeq DNA Sample prep kits and sequenced on an Illumina Novaseq 6000.

value: UBC9 HisFlag-smt3


title: Pool013_scRNA_10X [Batch1]


title: Mock_WT_1


title: Sample 95

description: Glioblastoma, IDH wildtype


title: Pool012_scRNA_10X [Batch1]


title: Endoderm Ngn3Cre 21ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_039


title: ubc9_RR_INPUT_2

value: ubc9-K153/157R HisFlag-smt3


title: Sample 81

description: Pilocytic astrocytoma


title: Pool011_scRNA_10X [Batch1]


title: Endoderm Ngn3Cre 21ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_038


title: ubc9_RR_INPUT_1


title: Pool010_scRNA_10X [Batch1]


title: Sample 73

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_037


title: WT_INPUT_2


title: Pool009_scRNA_10X [Batch1]


title: WT_INPUT_1


title: Sample 42

description: Glioblastoma, IDH wildtype


title: Pool008_scRNA_10X [Batch1]


title: Sample 32

description: Pilocytic astrocytoma


title: Endoderm Ngn3Cre 21ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_035


title: Sample 31

description: Glioblastoma, IDH wildtype


title: ubc9_RR_Smt3_IP_1


title: Pool007_scRNA_10X [Batch1]


title: ubc9_RR_Smt3_IP_2


title: Endoderm Ngn3Cre 21ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_040


title: supT1, HIV 24h, rep3

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

data_processing:
RiboDoc package
Removed adaptor with cutadapt and kept only 10-40-mers
Reads are mapped using bowtie2 and Hisat2 on Hg38 and HIV-pNL4-3 XCS  (parameters: -v 2 -y -a -m 1 --best --strata -p 18)
Kept only the mapped reads - samtools (parameters: -F 4 -f 0,16 -h)
P-site offset is calculated using RiboWaltz program
Assembly: GRCh38.104 for human genome, and HIV-pNL4-3 XCS for HIV
Supplementary files format and content: csv file with TPM counts for each gene in human genome, the file contains the data for the three replicates
Supplementary files format and content: txt file with TPM counts for each gene in HIV genome, the file contains the data for the three replicates

growth_protocol: SupT1 CD4+ T cells were cultured with RPMI GlutaMax 1640 (Gibco) complemented with 10% FBS (Dutscher) and 1% penicillin/streptomycin.

extract_protocol:
24h post-infection, cycloheximide (CHX) was added to cell culture (100 µg/ml, 10 min, 37°C, Sigma). Cells were then washed in cold PBS containing CHX and lysed at 4°C (10 mM Tris-HCl pH7.5, 100 mM KCl, 10 mM Mg2+ acetate, 1% Triton X100 and 2 mM DTT).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA preparation kits

treatment_protocol: 1 billion SupT1 cell line were infected with 4 055 ng of HIVNL4-3 XCS HIV-Gagp24 for 3h in IMDM plus 10mM HEPES (Gibco/ThermoFisher Scientific) supplemented with 2 µg/ml of DEAE-dextran (Sigma).

value: 24h infection with HIV NL4-3 XCS


title: Endoderm Ngn3Cre 21ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_034


title: WT_Smt3_IP_2


title: Pool006_scRNA_10X [Batch1]


title: Endoderm Ngn3Cre 21ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_033


title: supT1, HIV 24h, rep2


title: Pool005_scRNA_10X [Batch1]


title: WT_Smt3_IP_1


title: Endoderm Ngn3Cre 21ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_032


title: Endoderm Ngn3Cre 21ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_050


title: Endoderm Ngn3Cre 21ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_031


title: endosperm10DAA; treated; replicate 3

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

description: endosperm10DAA; treated; replicate 3

data_processing:
The code for sequencing processing and mutation calling has been packaged, and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: IRGSP-1.0
Supplementary files format and content: TSV
Library strategy: BID-Seq

molecule: polyA RNA

organism: Oryza sativa

source_name: endosperm

extract_protocol:
Total RNA isolation: total RNA was isolated according to TRIzol reagent manufacturer’s protocol, followed by isopropanol precipitation. PolyA+ RNA isolation: Dynabeads™ mRNA Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment, from the purified total RNA.
With 10 ng synthetic RNA oligos carrying 0%, 20%, 40%, 60%, 80%, or 100% pseudouridine, 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). To perform 3′-adapter ligation, 10 µl 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNN AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 30 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 30 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 9.3 µl RNase-free water.  The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 10 µl RNase-free water.  A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 8.5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 8.5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 75 µl RNase-free H2O, 270 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Then the ‘Input’ was diluted to 10.5 µl with RNase-free water. Both ‘Input’ and ‘Treated’ samples were mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. To this was added 4 µl 5× SSIV Buffer, 2 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 h, followed by adding 1 µl RNase H (catalog no. M0297L, NEB) and incubating at 37 °C for 20 min. The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 with single-end 100 bp read length.

value: endosperm

tag: cultivar

value: Nipponbare


title: Pool004_scRNA_10X [Batch1]

tag: tissue

value: Blood


title: supT1, HIV 24h, rep1


title: RPE cell, Homo F6 mutate,rep2,bulk ATAC

city: La Jolla

first: Ying

last: Yuan

address: Palmilla Dr.

department: MATS

institute: UCSD

data_processing:
check quality with FastQC
trim adapter with trim_galore
mpping with bowtie2
sort to bam file with samtools
deduplicate with picard
generate bigwig file with deeptools
Assembly: hg38
Supplementary files format and content: hg38_sorted_rmdup.bw

source_name: eye

extract_protocol: bulk ATAC

value: eye

value: hTERT RPE-1

value: RPE cells

value: TMEM216 knockdown


title: Endoderm Ngn3Cre 21ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_036

tag: strain


title: Pool003_scRNA_10X [Batch1]

tag: genotype

value: African


title: endosperm10DAA; treated; replicate 2

description: endosperm10DAA; treated; replicate 2


title: Pool002_scRNA_10X [Batch1]


title: RPE cell, Homo F6 mutate,rep1,bulk ATAC


title: endosperm10DAA; treated; replicate 1

description: endosperm10DAA; treated; replicate 1


title: Pool001_scRNA_10X [Batch1]


title: Endoderm Ngn3Cre 21ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_028

value: Endoderm

tag: time


title: RPE cell, WT MOCK,rep1,bulk ATAC

tag: cell line

value: WT


title: RPE cell, WT MOCK,rep2,bulk ATAC

tag: cell type


title: embryo10DAA; treated; replicate 3

description: embryo10DAA; treated; replicate 3

source_name: embryo

value: embryo


title: resistant_rep3

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: rRNA depleted total RNA

data_processing:
Reads were mapped to the human genome GRCh38 using STAR aligner (v2.7.1a), allowing up to 100 multiple alignments and up to 200 loci anchors (--outFilterMultimapNmax 100 --winAnchorMultimapNmax 200).
Differential expression analysis of genes and transposable elements comparing triplicates of samples treated with normal or pathogenic concentrations of insulin was performed using TEtranscripts (v2.2.3).
Assembly: hg38
Supplementary files format and content: comma-separated values file contains differential expression data for annotated transcripts

extract_protocol:
Cells were washed with EMEM and RNA was then purified using TRIzolTMreagent following manufacturer’s instructions.
RNA-seq libraries were prepared using a KAPA RNA HyperPrep kit with RiboErase. Spike-ins were included but were not used for analysis.

treatment_protocol: HepG2 cells were treated with 0.1nM (normal) or 3nM (pathogenic) insulin concentrations in EMEM 0.125% BSA for three days.

value: Liver

value: Hepatocellular carcinoma

value: 3 nM insulin


title: Endoderm Ngn3Cre 21ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_027

value: Ngn3-Cre; Ai6


title: embryo10DAA; treated; replicate 2

description: embryo10DAA; treated; replicate 2


title: resistant_rep2

description: rRNA depleted total RNA


title: RPE cell, Hetero G1 mutate,rep1,bulk ATAC


title: Endoderm Ngn3Cre 21ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_026


title: flagleaf10DAA; treated; replicate 3

description: flagleaf10DAA; treated; replicate 3

source_name: flagleaf

value: flagleaf


title: resistant_rep1

description: rRNA depleted total RNA


title: flagleaf10DAA; treated; replicate 2

description: flagleaf10DAA; treated; replicate 2


title: RPE cell, Homo D4 mutate,rep2,bulk ATAC


title: sensitive_rep3

description: rRNA depleted total RNA

value: 0.1 nM insulin


title: Endoderm Ngn3Cre 21ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_024


title: Endoderm Ngn3Cre 21ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_030


title: Endoderm Ngn3Cre 21ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_023


title: flagleaf10DAA; treated; replicate 1

description: flagleaf10DAA; treated; replicate 1


title: sensitive_rep2

description: rRNA depleted total RNA


title: 8_3RHR-TAFRO

city: Philadelphia

first: David

middle: C

last: Fajgenbaum

state: PA

address: 3535 Market St.

department: Department of Medicine

institute: University of Pennsylvania

description: FFPE preserved lymph node tissue

data_processing:
Using STAR aligner (v 2.7.4a) reads were mapped to GRCh38 human genome to produce BAM files. BAM files were summerized using summarizeOverlaps function from the GeonomicAlignements (v 1.8.4) software suite.
Assembly: GRCh38
Supplementary files format and content: Processed data file consist of gene count matrix

source_name: lymph node

extract_protocol:
RNA was isolated from Formalin Fixed Paraffin Embedded (FFPE) tissue sections fixed on slides using the RNeasy DSP FFPE kit (Qiagen, Hilden, Germany). Briefly, sections 10 microns thick, were scraped from 5 slides of each sample and submerged in Deparaffinization Solution (DSP) as per protocol. During this process tissue digestion using Proteinase K was also done. DNAseI treated RNA was subsequently isolated using Qiagen’s proprietary spin column method as per protocol. RNA integrity was assessed using the TapeStation RNA ScreenTape (Agilent, Santa Clara, CA) and concentration was determined used the Qubit 2.0 Fluorometer (ThermoFisher, Waltham, MA). Since FFPE RNA is expected to be highly degraded, a DV200 value, which is the percentage of RNA fragments above 200bp, was determined for each sample.
Libraries for whole transcriptome RNA sequencing were prepared using the Stranded Total RNAseq with Ribo-zero Plus kit (Illumina, San Diego, CA) as per manufacturer’s instructions starting with an input of 100ng of RNA and 15 cycles of final PCR amplification. Library size was assessed using the 2100 Bioanalzyer and the High-Sensitivity DNA assay (Agilent, Santa Clara, CA). Concentration was determined using the Qubit Fluorometer 2.0. Next Generation Sequencing with a paired-end 2x100bp run length was done on the NextSeq2000 platform (Illumina, San Diego, CA). A minimum of 30M reads per sample was acquired for each sample.

value: lymph node

tag: phenotype

value: Idiopathic Multicentric Castleman Disease


title: sensitive_rep1

description: rRNA depleted total RNA


title: panicleHeading; treated; replicate 3

description: panicleHeading; treated; replicate 3

source_name: panicle

value: panicle

value: Nipponbare


title: Endoderm Ngn3Cre 21ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_022


title: Endoderm Ngn3Cre 21ss b2 029, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_029


title: 72_2BLN-2-2A

description: FFPE preserved lymph node tissue

value: large diffuse B cell lymphoma


title: SP, Sepsis, SP24

city: Daejeon

first: Taylor

last: Roh

address: 266, Munhwa-ro

department: Microbiology

institute: Chungnam National University

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform. Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality. The cleaned reads were aligned to the Homo sapiens (GRCh38) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations. The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively. Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016). Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Assembly: genome used for mapping: GRCh38
Supplementary files format and content: fastq

extract_protocol:
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen). To determine the DV200 (% of RNA fragments >200 bp) value, samples are run on the TapeStation RNA screentape (Agilent).
A total of 100 ng of total RNA was subjected to a sequencing library construction using the Agilent SureSelect RNA Direct_Human kit according to the manufacturer's protocol.

value: Blood

value: PBMCs

value: Sepsis


title: Endoderm Ngn3Cre 21ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_021

value: Endoderm


title: embryo10DAA; treated; replicate 1

description: embryo10DAA; treated; replicate 1


title: RPE cell, Hetero G1 mutate,rep2,bulk ATAC

value: eye

value: hTERT RPE-1

value: RPE cells

value: TMEM216 knockdown


title: 70_1BLN-6-1C

description: FFPE preserved lymph node tissue


title: SP, Sepsis, SP23


title: panicleHeading; treated; replicate 1

description: panicleHeading; treated; replicate 1


title: Endoderm Ngn3Cre 21ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_020


title: SP, Sepsis, SP22


title: Endoderm Ngn3Cre 21ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_025


title: Endoderm Ngn3Cre 21ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_019


title: 68_1BLN-3-1B

description: FFPE preserved lymph node tissue


title: SP, Sepsis, SP21


title: flagleafHeading; treated; replicate 2

description: flagleafHeading; treated; replicate 2


title: Endoderm Ngn3Cre 21ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_018


title: SP, Sepsis, SP20


title: 56_1XXL_NOS

description: FFPE preserved lymph node tissue


title: 67_1BLN-2-2A

description: FFPE preserved lymph node tissue


title: Endoderm Ngn3Cre 21ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_016


title: RPE cell, Homo D4 mutate,rep1,bulk ATAC


title: 54_1NGT_NOS

description: FFPE preserved lymph node tissue


title: SP, Sepsis, SP18


title: Endoderm Ngn3Cre 21ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_017


title: strawHeading; treated; replicate 3

description: strawHeading; treated; replicate 3

source_name: straw

value: straw


title: panicleHeading; treated; replicate 2

description: panicleHeading; treated; replicate 2


title: strawHeading; treated; replicate 2

description: strawHeading; treated; replicate 2


title: flagleafHeading; treated; replicate 1

description: flagleafHeading; treated; replicate 1


title: 48_BPN9_TAFRO_1

description: FFPE preserved lymph node tissue


title: Endoderm Ngn3Cre 21ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_015

value: Ngn3-Cre; Ai6


title: strawHeading; treated; replicate 1

description: strawHeading; treated; replicate 1


title: SP, Sepsis, SP17


title: 69_1BLN-6-2B

description: FFPE preserved lymph node tissue


title: 47_7MC4_TAFRO_1A

description: FFPE preserved lymph node tissue


title: flagleafHeading; treated; replicate 3

description: flagleafHeading; treated; replicate 3

value: flagleaf


title: seedling2W; treated; replicate 3

description: seedling2W; treated; replicate 3

source_name: seedling

value: seedling


title: 36_1SLN-8-3A

description: FFPE preserved lymph node tissue

value: lymph node

value: Sentinal lymph node


title: Endoderm Ngn3Cre 21ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_013

source_name: Endoderm


title: seedling2W; treated; replicate 2

description: seedling2W; treated; replicate 2


title: SP, Sepsis, SP15


title: Endoderm Ngn3Cre 21ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_012


title: 35_1SLN-7-1B

description: FFPE preserved lymph node tissue


title: SP, Sepsis, SP14


title: SP, Sepsis, SP19


title: seedling2W; treated; replicate 1

description: seedling2W; treated; replicate 1


title: Endoderm Ngn3Cre 21ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_011


title: SP, Sepsis, SP12


title: seedling8DAY; treated; replicate 3

description: seedling8DAY; treated; replicate 3


title: 33_1SLN-5-2A

description: FFPE preserved lymph node tissue


title: Endoderm Ngn3Cre 21ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_009


title: Endoderm Ngn3Cre 21ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_010


title: seedling8DAY; treated; replicate 2

description: seedling8DAY; treated; replicate 2


title: 31_1SLN-3-2A

description: FFPE preserved lymph node tissue


title: seedling8DAY; treated; replicate 1

description: seedling8DAY; treated; replicate 1


title: SP, Sepsis, SP16


title: Endoderm Ngn3Cre 21ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_008


title: SP, Sepsis, SP10


title: 30_1SLN-2-1A

description: FFPE preserved lymph node tissue


title: Endoderm Ngn3Cre 21ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_014


title: radicleLight; treated; replicate 3

description: radicleLight; treated; replicate 3

source_name: radicle

value: radicle


title: Endoderm Ngn3Cre 21ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_007


title: SP, Sepsis, SP09


title: 3_6LJ2-TAFRO

description: FFPE preserved lymph node tissue

value: Idiopathic Multicentric Castleman Disease


title: radicleLight; treated; replicate 2

description: radicleLight; treated; replicate 2

value: Nipponbare


title: Endoderm Ngn3Cre 21ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_006


title: 29_1SLN-1-1A

description: FFPE preserved lymph node tissue


title: SP, Sepsis, SP08

value: Blood


title: Endoderm Ngn3Cre 21ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_005


title: radicleLight; treated; replicate 1

description: radicleLight; treated; replicate 1


title: 27_1SLE-8-1A

description: FFPE preserved lymph node tissue

value: Systemic lupus erythematosus


title: SP, Sepsis, SP07

value: PBMCs

value: Sepsis


title: plumulelLight; treated; replicate 3

description: plumulelLight; treated; replicate 3

source_name: plumulel

value: plumulel


title: SP, Sepsis, SP13


title: 34_1SLN-6-1A

description: FFPE preserved lymph node tissue


title: SP, Sepsis, SP11


title: plumulelLight; treated; replicate 2

description: plumulelLight; treated; replicate 2


title: SP, Sepsis, SP06


title: 20_1SLE-1-1C

description: FFPE preserved lymph node tissue


title: 22_1SLE-3-1C

description: FFPE preserved lymph node tissue


title: Endoderm Ngn3Cre 21ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_004

value: Endoderm


title: Endoderm Ngn3Cre 21ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_003


title: SP, Sepsis, SP05


title: 17_1LJ7-NOS

description: FFPE preserved lymph node tissue


title: radicleDark; treated; replicate 3

description: radicleDark; treated; replicate 3


title: Endoderm Ngn3Cre 21ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_002


title: Endoderm Ngn3Cre 21ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_001


title: plumulelLight; treated; replicate 1

description: plumulelLight; treated; replicate 1


title: SP, Sepsis, SP04


title: 11_6RZ5-TAFRO

description: FFPE preserved lymph node tissue


title: SP, Sepsis, SP03


title: Endoderm Ngn3Cre 18ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_18ss_b2_003


title: 1_2LNH-TAFRO

description: FFPE preserved lymph node tissue


title: radicleDark; treated; replicate 1

description: radicleDark; treated; replicate 1


title: SP, Sepsis, SP01


title: sample755_GCB-DLBCL-NOS-MYC-R

city: Warszawa

first: Michalina

last: Zajdel

address: W. K. Roentgena 5

department: Department of Cancer Biology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

data_processing:
Raw sequencing results were analysed in Torrent Suite (version 5.6), including sequence reading, truncation of adapter sequences and assignment of reads to the correct samples.
Unmapped BAM files were converted to fastq files using the bamToFastq script from the BEDTools package (version 2.225).
NGS reads were mapped to the human genome (hg19) using the BWA software (version 0.7.17).
Reads included in the miRBase database (version 21), and new microRNAs were counted with the miRDeep2 application (version 2.0.1.2).
Assembly: hg19
Supplementary files format and content: Comma-delimited CSV file includes a matrix of raw counts

source_name: GCB-DLBCL-NOS-MYC-R

extract_protocol:
Total RNA containing microRNA fraction was isolated using Trizol
The concentration of miRNA in total RNA was estimated with a Bioanalyser (Agilent 2100) using the Agilent Small RNA Kit. MicroRNA libraries were prepared using the Ion Total RNA-seq Kit v2 for Small RNA Libraries reagent kit (Thermo Fisher Scientific) according to the manufacturer's procedure.

value: GCB-DLBCL-NOS-MYC-R

value: cell aspirates of tumours obtained by fine-needle aspiration biopsy


title: plumulelDark; treated; replicate 3

description: plumulelDark; treated; replicate 3


title: Endoderm Ngn3Cre 18ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_18ss_b2_001


title: sample302_GCB-DLBCL-NOS-MYC-R


title: plumulelDark; treated; replicate 2

description: plumulelDark; treated; replicate 2


title: Endoderm Wnt5b 27ss b2, scRNA-seq

description:
Wnt5b_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Wnt5bCreER-RFP; Ai6


title: HC, Healthy, HC12

source_name: Blood

value: HC


title: SP, Sepsis, SP02


title: sample351_GCB-DLBCL-NOS-MYC-R


title: plumulelDark; treated; replicate 1

description: plumulelDark; treated; replicate 1


title: sample751_GCB-DLBCL-NOS-MYC-R


title: HC, Healthy, HC11


title: Endoderm Wnt5b 27ss b1, scRNA-seq

description:
Wnt5b_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos


title: endosperm10DAA; input; replicate 2

description: endosperm10DAA; input; replicate 2

value: endosperm


title: radicleDark; treated; replicate 2

description: radicleDark; treated; replicate 2


title: HC, Healthy, HC09


title: endosperm10DAA; input; replicate 1

description: endosperm10DAA; input; replicate 1


title: sample35_GCB-DLBCL-NOS-MYC-R


title: HC, Healthy, HC08


title: sample1263_GCB-DLBCL-NOS-MYC-R


title: Endoderm Wnt5b 24ss b2, scRNA-seq

description:
Wnt5b_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: Endoderm Ngn3Cre 18ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_18ss_b2_002

value: Ngn3-Cre; Ai6


title: HC, Healthy, HC07


title: embryo10DAA; input; replicate 2

description: embryo10DAA; input; replicate 2

value: embryo


title: Endoderm Wnt5b 24ss b1, scRNA-seq

description:
Wnt5b_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: Endoderm Wnt5b 21ss b2, scRNA-seq

description:
Wnt5b_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: Endoderm Wnt5b 21ss b1, scRNA-seq

description:
Wnt5b_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: flagleaf10DAA; input; replicate 2

description: flagleaf10DAA; input; replicate 2

value: flagleaf


title: Endoderm Wnt5b 18ss b2, scRNA-seq

description:
Wnt5b_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: HC, Healthy, HC06


title: sample758_GCB-DLBCL-NOS

source_name: GCB-DLBCL-NOS

value: GCB-DLBCL-NOS


title: sample763_GCB-DLBCL-NOS


title: HC, Healthy, HC10


title: HC, Healthy, HC05


title: flagleaf10DAA; input; replicate 1

description: flagleaf10DAA; input; replicate 1


title: sample762_GCB-DLBCL-NOS


title: Endoderm Wnt5b 18ss b1, scRNA-seq

description:
Wnt5b_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: HC, Healthy, HC04


title: Endoderm Wnt5b 15ss b2, scRNA-seq

description:
Wnt5b_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: panicleHeading; input; replicate 2

description: panicleHeading; input; replicate 2

value: panicle


title: sample115_BL

source_name: BL

value: BL


title: Endoderm Wnt5b 15ss b1, scRNA-seq

description:
Wnt5b_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: embryo10DAA; input; replicate 1

description: embryo10DAA; input; replicate 1

value: Nipponbare


title: HC, Healthy, HC02

value: Blood


title: panicleHeading; input; replicate 1

description: panicleHeading; input; replicate 1


title: sample466_GCB-DLBCL-NOS-MYC-R


title: HC, Healthy, HC03

value: PBMCs


title: sample611_BL


title: flagleafHeading; input; replicate 2

description: flagleafHeading; input; replicate 2


title: flagleafHeading; input; replicate 1

description: flagleafHeading; input; replicate 1


title: Endoderm Wnt5b 12ss b2, scRNA-seq

description:
Wnt5b_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: Endoderm Wnt5b 12ss b1, scRNA-seq

description:
Wnt5b_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: HC, Healthy, HC01


title: sample123_BL


title: strawHeading; input; replicate 2

description: strawHeading; input; replicate 2

value: straw


title: strawHeading; input; replicate 1

description: strawHeading; input; replicate 1


title: seedling2W; input; replicate 2

description: seedling2W; input; replicate 2

value: seedling


title: sample165_BL


title: Endoderm Sox2 27ss b1, scRNA-seq

description:
Sox2_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Endoderm

value: Sox2-CreER; Rosa-RFP


title: sample752_BL

value: cell aspirates of tumours obtained by fine-needle aspiration biopsy


title: sample753_BL


title: seedling2W; input; replicate 1

description: seedling2W; input; replicate 1


title: seedling8DAY; input; replicate 2

description: seedling8DAY; input; replicate 2


title: Endoderm Sox2 27ss b2, scRNA-seq

description:
Sox2_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos


title: sample71_BL


title: sample441_HGBCL-11q


title: sample610_HGBCL-11q


title: radicleLight; input; replicate 2

description: radicleLight; input; replicate 2

value: radicle


title: Endoderm Sox2 21ss b2, scRNA-seq

description:
Sox2_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: Endoderm Sox2 21ss b1, scRNA-seq

description:
Sox2_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: sample339_HGBCL-11q


title: Endoderm Sox2 24ss b1, scRNA-seq

description:
Sox2_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: radicleLight; input; replicate 1

description: radicleLight; input; replicate 1


title: Endoderm Wnt5b 09ss b2, scRNA-seq

description:
Wnt5b_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos

value: Wnt5bCreER-RFP; Ai6


title: Endoderm Sox2 18ss b2, scRNA-seq

description:
Sox2_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: plumulelLight; input; replicate 1

description: plumulelLight; input; replicate 1

value: plumulel


title: sample185_HGBCL-11q


title: sample402_HGBCL-11q


title: plumulelLight; input; replicate 2

description: plumulelLight; input; replicate 2


title: Endoderm Wnt5b 09ss b1, scRNA-seq

description:
Wnt5b_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: Endoderm Sox2 18ss b1, scRNA-seq

description:
Sox2_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: sample452_BL


title: sample289_HGBCL-11q


title: Endoderm Sox2 15ss b2, scRNA-seq

description:
Sox2_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: radicleDark; input; replicate 2

description: radicleDark; input; replicate 2


title: radicleDark; input; replicate 1

description: radicleDark; input; replicate 1


title: H1,S6 WY14643 3

city: Ann Arbor

first: Anne

last: Lietzke

state: MI

address: 1000 Wall Street

institute: University of Michigan

data_processing:
FastQC (v0.11.8) was used to ensure the quality of data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1).
Alignment options followed ENCODE standards for RNA-seq.
FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Data were pre-filtered to remove genes with 0 counts in all samples.
Differential gene expression analysis was performed using DESeq2, using a negative binomial generalized linear model (thresholds: log2(fold change) >0.5 or <-.5, FDR (Padj) <0.05). Plots were generated using variations of DESeq2 plotting functions and other packages with Genialis (Boston, MA, USA).
Assembly: Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1).
Supplementary files format and content: Processed data file for each sample contain the following columns in order: Feature ID, Gene Symbol, Raw Count, TPM, and CPM.

growth_protocol: HUES8 and H1 cell lines were differentiated to SC-islets in a 6 stage differentiation protocol (Hogrebe et al. 2021, PMID: 34349281). Primary human islets were received and cultured per protocol (Prodo Labs).

extract_protocol:
Total RNA was isolated from human islet and stem cell samples and DNase treated using commercially available kits (Omega Biotek and Ambion, respectively).
Libraries were constructed and subsequently subjected to 151bp paired-end cycles on the NovaSeq-6000 platform (Illumina).

treatment_protocol: H1 Stage 6 cells were treated for 7 days starting at stage 6 day 3 with vehicle or WY14643.

value: Human embryonic stem


title: Endoderm Sox2 15ss b1, scRNA-seq

description:
Sox2_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos

data_processing:
For the Smart-seq3xpress scRNA-seq data, initial quality control was executed with FastQC version 0.11.9 under default settings. Index, primer, and adaptor sequences were then trimmed from paired-end reads using Trimmomatic version 0.39 with default parameters. Alignment of trimmed reads to the Mus musculus Genome assembly GRCm38 (mm10) was accomplished using HISAT version 2.1.0.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files


title: H1,S6 WY14643 2


title: plumulelDark; input; replicate 2

description: plumulelDark; input; replicate 2


title: Endoderm Sox2 24ss b2, scRNA-seq

description:
Sox2_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: IntactMouseProstate_C57BL6_rep1

first: Arul

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

description:
Library name: SI_32219
10x chromium 3′ gene expression V3.1

data_processing:
After sequencing, read demultiplexing, alignment and gene quantification were conducted with the 10X Genomics Cell Ranger pipeline (v5.0) and the pre-built reference genome (mm10 for mouse and GRCh38 for human libraries).
Assembly: mm10
Supplementary files format and content: filtered_ feature_matrix.h5: Per-sample non-zero count matrix files in H5 format.
Supplementary files format and content: sc.annotation.GEO.csv : Metadata table containing cell annotation for each sample.

source_name: prostate

extract_protocol:
Prostate tissues were harvested from these animals two weeks after surgical procedure. All four prostate lobes were pooled and minced using a pair of spring scissors. Subsequently, the minced tissues were digested with 5mg/mL collagenase Type II (Gibco, 17101015) for 1 hour at 37°C followed by TryLE (Gibco, 17101015) digestion for 10 min. After TryLE digestion, samples were inactivated with an excess of DMEM containing 10% fetal bovine serum (FBS), and samples were sequentially passed through 100 mm and 40 mm cell strainers to remove debris, followed by a 0.5% BSA in 1xPBS wash. Cell suspensions were then processed for scRNAseq.
The 10x barcoding and complementary DNA (cDNA) synthesis were performed using 10x chromium 3′ scRNA-seq V2 or V3.1 chemistry according to the manufacturer’s instructions. Briefly, an appropriate volume of single-cell suspension/enzyme mix, barcoded beads, and partitioning oil were loaded in distinct lanes on the chip and processed in a 10x chromium controller instrument. The 10x GemCode Technology uses a droplet-based method to partition thousands of cells to generate nanoliter-scale Gel Bead-In-Emulsions (GEMs). Inside each GEM, cDNA generated from an individual cell shares a common 10x barcode. The prepared GEMs were incubated in a thermomixer to produce cDNA. Recovered cDNA was cleaned up and amplified by polymerase chain reaction to generate enough quantity for library construction. The size and yield were evaluated using a high-sensitivity bioanalyzer assay chip (Agilent). A set of recommended primers (P5, P7, and R2) in the manufacturer’s standard protocol were added to prepare the Illumina-ready sequencing library. The final library was evaluated for size and yield using a high-sensitivity bioanalyzer assay chip (Agilent). The final libraries were sequenced with the Illumina Hiseq2500 according to recommended specifications.

treatment_protocol: All animal work was done in compliance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at University of Michigan. C57BL/6 or FVB mice were purchased from Jackson Laboratory (Bar Harbor, ME). The mice were either sham-operated or castrated at 8 weeks of age.

value: prostate

value: mixed


title: seedling8DAY; input; replicate 1

description: seedling8DAY; input; replicate 1


title: Endoderm Sox2 12ss b2, scRNA-seq

description:
Sox2_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos

extract_protocol:
Endodermal and gut tissues from 9SS to 27SS, were enzymatically dissociated using 0.25% trypsin (Gibco, 25200-056) for roughly 4 minutes at 37°C. The reaction was halted by the addition of 0.4 volumes of fetal bovine serum (FBS). The resultant cell suspension was centrifuged at 1000 rpm for 5 minutes at 4°C, followed by supernatant removal. To prepare single-cell suspensions from endodermal and gut samples, cells were incubated with anti-EpCAM-APC antibody (Invitrogen, 17-5791-82, dilution 1:100) in FACS buffer (comprising HBSS buffer with 1% FBS) for 20 minutes at 4°C in darkness. Following incubation, cells were washed with FACS buffer and subjected to analysis and sorting using BD FACSAriaTM Fusion flow cytometers. Dead cells were excluded from the analysis through staining with 1 µg/mL DAPI (Macklin, D807022).
The Smart-seq3xpress libraries were prepared following Smart3-seq3xpress's protocols.


title: NormalMouseProstate_FVB_rep2

description:
Library name: SI_22785
10x chromium 3′ gene expression V2

value: FVB


title: plumulelDark; input; replicate 1

description: plumulelDark; input; replicate 1


title: H1,S6 WY14643 1


title: H1,S6 Vehicle 4

value: Vehicle


title: NormalMouseProstate_C57BL6_rep1

description:
Library name: SI_18283
10x chromium 3′ gene expression V2


title: 606_lung_M_28_R thorax_uninf [24868]

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: 606_lung_M_28_R thorax_uninf

data_processing:
Adapter sequences were trimmed from raw reads usingCutadapt
The remaining reads were then filtered to remove low quality bases and low-quality reads using theFASTX-Toolkit
Remaining reads were mapped to GCF_000009645.1(CC5 reference strain),GCF_004118995.1(CC8 reference strain), andGCF_000412775.1(CC45 reference strain) usingBowtie2
Reads mapping to genes were counted usingHTSeq-count
Differential expression analysis was performed using the Bioconductor packageDESeq2
Assembly: GCA_014825515.1
Supplementary files format and content: matrix text files include raw read counts
Supplementary files format and content: normalized text files include DESEQ2 normalized read counts

organism: Artibeus jamaicensis

source_name: lung

growth_protocol: Virus propagation was performed in Vero E6 cells (ATCC CRL-1586) in DMEM supplemented with 2% fetal bovine serum (FBS), 1 mM L-glutamine, 50 U/mL penicillin, and 50 μg/mL streptomycin (DMEM2).

extract_protocol:
RNA extracted using Qiagen AllPrep DNA/RNA 96-well system
Illumina Stranded mRNA prep

treatment_protocol: Twenty-one animals were intranasally and orally inoculated with a total of 1.5 x 105 TCID50 of hCoV19/USA/MD/HP05647/2021 (B.1.617.2/Delta, EPI_ISL_2331496), and four animals were inoculated with DMEM as controls

value: lung

value: uninf


title: Endoderm Sox2 09ss b2, scRNA-seq

first: Cheng-ran

last: Xu

description:
Sox2_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: H1,S6 WY14643 4


title: Endoderm Sox2 09ss b1, scRNA-seq

description:
Sox2_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: H1,S6 Vehicle 3


title: H1,S6 Vehicle 2


title: Progenitor_Foxg1_LOF_Mutant_3

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: B304 TIFR Homi Bhabha road

department: Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description:
Mut_Ctx3
Foxg1_Progenitor_countsMatrix.csv
Foxg1_Progenitor_DESeq2_results.csv

data_processing:
Read alignment software - HISAT2
Read mapping tool - FeatureCounts
Read normalization - DESeq2
Assembly: mm10
Supplementary files format and content: CSV file format; Raw Counts
Supplementary files format and content: CSV file format; Normalized Counts

source_name: Cerebral Cortex

growth_protocol: in vivo cortical progenitors or neurons isolated using microdissection and FACS purification.

extract_protocol:
Trypsin-based tissue dissociation and PCI-based RNA isolation
NEBNext RNA Ultra II directional protocol 2x150bp

treatment_protocol: FACS purification of recombined cells using 561 or 488 lazers.

value: Cerebral Cortex

value: hGFAPCreERT2/+; Foxg1lox/lox; Ai9

value: Tamoxifen injection


title: 596_NT_M_4_R thorax_D4 [24866]

description: 596_NT_M_4_R thorax_D4

source_name: NT (nasal turbinates)

value: NT (nasal turbinates)


title: Endoderm Pdx1 27ss b2, scRNA-seq

city: Beijing

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

institute: Peking University

description:
Pdx1_27ss_b2
Smart-seq3xpress

value: Endoderm


title: Progenitor_Foxg1_LOF_Mutant_4

description:
Mut_Ctx4
Foxg1_Progenitor_countsMatrix.csv
Foxg1_Progenitor_DESeq2_results.csv


title: Progenitor_Foxg1_LOF_Mutant_2

description:
Mut_Ctx2
Foxg1_Progenitor_countsMatrix.csv
Foxg1_Progenitor_DESeq2_results.csv


title: 593_NT_M_1_L thorax_D1 [24865]

description: 593_NT_M_1_L thorax_D1


title: CastratedD15MouseProstate_C57BL6_rep1

description:
Library name: SI_32220
10x chromium 3′ gene expression V3.1

value: castration


title: Endoderm Pdx1 24ss b2, scRNA-seq

description:
Pdx1_24ss_b2
Smart-seq3xpress


title: Hues8,S6 3


title: 595_NT_M_4_R flank_D4 [24864]

description: 595_NT_M_4_R flank_D4


title: Progenitor_Foxg1_LOF_Mutant_1

description:
Mut_Ctx1
Foxg1_Progenitor_countsMatrix.csv
Foxg1_Progenitor_DESeq2_results.csv


title: 594_NT_M_4_L flank_D4 [24863]

description: 594_NT_M_4_L flank_D4


title: Endoderm Pdx1 27ss b1, scRNA-seq

description:
Pdx1_27ss_b1
Smart-seq3xpress


title: Hues8,S6 2


title: Progenitor_Foxg1_LOF_Control_3

description:
Ctrl_Ctx3
Foxg1_Progenitor_countsMatrix.csv
Foxg1_Progenitor_DESeq2_results.csv

value: FlashTag Injection


title: Endoderm Pdx1 24ss b1, scRNA-seq

description:
Pdx1_24ss_b1
Smart-seq3xpress


title: Hues8,S6 1


title: Endoderm Sox2 12ss b1, scRNA-seq

description:
Sox2_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos

value: Sox2-CreER; Rosa-RFP


title: Progenitor_Foxg1_LOF_Control_2

description:
Ctrl_Ctx2
Foxg1_Progenitor_countsMatrix.csv
Foxg1_Progenitor_DESeq2_results.csv


title: 592_NT_F_1_L thorax_D1 [24861]

description: 592_NT_F_1_L thorax_D1


title: Progenitor_Foxg1_LOF_Control_1

description:
Ctrl_Ctx1
Foxg1_Progenitor_countsMatrix.csv
Foxg1_Progenitor_DESeq2_results.csv


title: 600_NT_pregnant_1_R thorax_D1 [24862]

description: 600_NT_pregnant_1_R thorax_D1


title: Endoderm Pdx1 21ss b1, scRNA-seq

description:
Pdx1_21ss_b1
Smart-seq3xpress


title: H1,S6 Vehicle 1


title: WT_IL33-IFNb_24h_A

city: MONTREAL

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: rRNA-depleted total RNA

data_processing:
The quality of sequence reads was assessed with the FastQC tool (Babraham Bioinformatics)
Low-quality bases were trimmed and adapter sequences were removed using Trimmomatic v.0.33 (Bolger et al., 2014) using the following arguments: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:4 LEADING:3 TRAILING:3 SLIDINGWINDOW:6:25 MINLEN:30.
Sequence reads were mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 with Bowtie v1.0.0 algorithms (Kim et al., 2013; Langmead et al., 2009)
The number of reads mapping onto gene exons was quantified by counting the number of strand-specific reads using featureCounts (Liao et al., 2014).
The differential gene expression analysis was performed by comparing IL-33-treated with non-stimulated ILC2 using the edgeR Bioconductor package (Robinson and Oshlack, 2010). First, residual rRNA reads were excluded and genes with an expression level > 10 counts per million reads (CPM) in at least 3 of the samples were retained for TMM normalization and differential gene expression.
For data visualization in IGV genome browser, bigwig scaled per million reads mapping onto gene exons were generated using a succession of genomeCoverageBed and wigToBigWig tools.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)
Supplementary_files_format_and_content: Bigwig files scaled per million reads mapping onto gene exons

source_name: lung ILC2

growth_protocol: C57BL/6J wild-type mice were bred and housed under specific pathogen-free conditions with ad libitum access to food and water. Unless otherwise stated, experiments were conducted using adult female age-matched mice (8 – 16 weeks) in accordance with the guidelines and policies of the Canadian Council on Animal Care and those of McGill University. To obtain single cell suspensions, mouse lungs were processed as described previously (Duerr et al., 2016). Briefly, lungs were perfused with cold PBS, isolated and were finely minced. Lung pieces were digested in RPMI-1640 supplemented with 5% FBS, 0.2 mg/ml  LiberaseTM (Roche) and 0.1 mg/ml DNase I (Roche) for 50 min. Digested lungs were homogenized using a syringe and passed through a 70 μm cell strainer to obtain single cell suspensions. Cells were washed with PBS and red blood cells were lysed using Red Blood Cell Lysing Buffer Hybri-MaxTM (Sigma). Lung single cell suspensions were blocked with 2.4G2 hybridoma supernatant followed by antibody and Fixable Viability DyeTM (eBioscience) staining. ILC2 were sorted into on a BD FACSAriaTM Fusion cell sorter based on surface marker expression as viable lineage negative CD45+CD90+CD25+ST2+ cells. Isolated ILC2 were incubated for 18h in complete medium (RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, 50 μg/mL gentamicin  and 55 μM 2-mercaptoethanol) containing recombinant murine (rm) IL-7 (10 ng/ml), washed and rested for 4 h in complete medium without cytokines before use in experiments.

extract_protocol:
Total RNA was extracted using the MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems) as per the manufacturer’s protocol. RNA integrity was assessed using a Bioanalyzer RNA Pico kit (Agilent).
Ribosomal RNAs were depleted and libraries were prepared with the KAPA stranded total RNA kit (Roche), then multiplexed and sequenced on an Illumina HiSeq 2500 flow cell in a paired-end 50bp configuration.
rRNA-depleted stranded RNA-Seq

treatment_protocol: Purified lung ILC2 were left untreated or stimulated for 4 and 24 h with rm-IL-33 (10 ng/ml) in the presence or absence of IFN-b (500 U/ml).

value: female

tag: mouse strain

value: IL33 + IFNb 24h


title: 599_NT_pregnant_28_R thorax_uninf [24860]

description: 599_NT_pregnant_28_R thorax_uninf


title: Hues8,S5 4

value: Human embryonic stem


title: WT_IL33-IFNb_24h_B

description: rRNA-depleted total RNA

tag: Sex


title: Hues8,S5 3


title: Endoderm Pdx1 18ss b2, scRNA-seq

description:
Pdx1_18ss_b2
Smart-seq3xpress


title: Hues8,S5 2


title: Hues8,S5 1


title: 591_NT_pregnant_28_L thorax_uninf [24859]

description: 591_NT_pregnant_28_L thorax_uninf

tag: treatment


title: WT_IL33_24h_B

description: rRNA-depleted total RNA


title: Endoderm Pdx1 18ss b1, scRNA-seq

description:
Pdx1_18ss_b1
Smart-seq3xpress


title: 581_NT_pregnant_4_none_D4 [24858]


title: Endoderm Pdx1 15ss b2, scRNA-seq

description:
Pdx1_15ss_b2
Smart-seq3xpress


title: WT_IL33_24h_A

description: rRNA-depleted total RNA


title: Hues8,S4 5


title: 579_NT_F_1_L flank_D1 [24856]

description: 579_NT_F_1_L flank_D1


title: Hues8,S4 4


title: WT_IL33-IFNb_4h_B

description: rRNA-depleted total RNA

value: IL33 + IFNb 4h


title: 580_NT_F_4_R flank_D4 [24857]

description: 580_NT_F_4_R flank_D4


title: Endoderm Pdx1 15ss b1, scRNA-seq

description:
Pdx1_15ss_b1
Smart-seq3xpress


title: Endoderm Pdx1 12ss b2, scRNA-seq

description:
Pdx1_12ss_b2
Smart-seq3xpress


title: WT_IL33-IFNb_4h_A

description: rRNA-depleted total RNA


title: Hues8,S4 2


title: WT_IL33_4h_B

description: rRNA-depleted total RNA

value: IL33 4h


title: Hues8,S4 3


title: Endoderm Pdx1 12ss b1, scRNA-seq

description:
Pdx1_12ss_b1
Smart-seq3xpress


title: 578_NT_F_1_R thorax_D1 [24855]

description: 578_NT_F_1_R thorax_D1


title: 577_NT_F_1_L thorax_D1 [24854]

description: 577_NT_F_1_L thorax_D1


title: WT_IL33_4h_A

description: rRNA-depleted total RNA


title: Endoderm Pdx1 09ss b1, scRNA-seq

description:
Pdx1_09ss_b1
Smart-seq3xpress


title: Endoderm Pdx1 09ss b2, scRNA-seq

description:
Pdx1_09ss_b2
Smart-seq3xpress


title: WT_UT_B

description: rRNA-depleted total RNA

value: non treated


title: Hues8,S3 5


title: 605_lung_M_28_L thorax_uninf [24852]

description: 605_lung_M_28_L thorax_uninf


title: Hues8,S4 1


title: Hues8,S3 4


title: Endoderm Pdx1 21ss b2, scRNA-seq

description:
Pdx1_21ss_b2
Smart-seq3xpress


title: 606_NT_M_28_R thorax_uninf [24853]

description: 606_NT_M_28_R thorax_uninf


title: 596_lung_M_4_R thorax_D4 [24851]

description: 596_lung_M_4_R thorax_D4


title: WT_UT_A

description: rRNA-depleted total RNA


title: Endoderm Pax9 27ss b1, scRNA-seq

description:
Pax9_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Pax9-CreER-EGFP; Rosa-RFP


title: PBMCs, Fu-Hp, rep2

description: Library name: GD_41

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome. The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes. Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010). The RC (Read Count) data were processed based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020) using Bioconductor (Gentleman et al.,2004). Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Assembly: genome used for mapping: hg19
Supplementary files format and content: fastq

source_name: Peripheral Blood Mononuclear Cell

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. In brief, each 500ng total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, Inc., USA).

value: Peripheral Blood Mononuclear Cell

value: wildtype

value: Haptoglobin


title: Hues8,S3 3


title: Endoderm Pax9 24ss b2, scRNA-seq

description:
Pax9_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: PBMCs, Fu-Hp, rep1

description: Library name: GD_40


title: 605_NT_M_28_L thorax_uninf [24867]

description: 605_NT_M_28_L thorax_uninf

value: uninf


title: Hues8,S3 2


title: 595_lung_M_4_R flank_D4 [24849]

description: 595_lung_M_4_R flank_D4

value: lung


title: Endoderm Pax9 24ss b1, scRNA-seq

description:
Pax9_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: Hues8,S3 1


title: 594_lung_M_4_L flank_D4 [24848]

description: 594_lung_M_4_L flank_D4


title: PBMCs, HC-Hp, rep2

description: Library name: HC_41


title: Endoderm Pax9 21ss b2, scRNA-seq

description:
Pax9_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: PBMCs, HC-Hp, rep1

description: Library name: HC_40


title: 600_lung_pregnant_1_R thorax_D1 [24847]

description: 600_lung_pregnant_1_R thorax_D1


title: Endoderm Pax9 27ss b2, scRNA-seq

description:
Pax9_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos


title: Hues8,S2 5


title: Endoderm Pax9 21ss b1, scRNA-seq

description:
Pax9_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: PBMCs, Untreated, rep2

description: Library name: UT_41


title: Hues8,S2 4


title: 592_lung_F_1_L thorax_D1 [24846]

description: 592_lung_F_1_L thorax_D1


title: PBMCs, Untreated, rep1

description: Library name: UT_40


title: Endoderm Pax9 18ss b2, scRNA-seq

description:
Pax9_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: Endoderm Pax9 18ss b1, scRNA-seq

description:
Pax9_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: APBY_23

city: London

first: Anton

last: Patrikeev

state: London

address: Chester Beatty Laboratories, 237 Fulham Rd.

department: Targeted Therapy

country: United Kingdom

institute: The Institute of Cancer Research

description:
Library name: APBY_23
TAM (M1)

data_processing:
Computational anlaysis steps included: 1. Mapping on a reference genome (using BWA v0.7.5a and SAMTOOLS v1.2). 2. Quantification of annotated features (number of aligned reads); merging of the counts into one single file (using RSEM). 3. Normalization of the counts and computation of comparison scores between pairs of groups (using DESeq2 v2.13).
Assembly: MiRBase human miRNAs (http://mirbase.org, v22.1)
Supplementary files format and content: two comma-delimited text files with raw and normalized counts for each sample

source_name: PBMC

growth_protocol: PBMC were isolated from leukapheresis cones purchased from the NHS blood and transplant service. PBMC were isolated from whole blood by density gradient centrifugation on Lymphoprep (StemCell Technology®). PMBC were cultures with indicated tumour cells at a ratio of (50:1) for seven days to generate TAM

extract_protocol:
RNA was isolated from cells using Trizol Reagent following manufactures instructions
Small RNA-Seq Gel Free

treatment_protocol: Day 7 CD14 cells (TAM) were isolated by magnetic bead isolation then treated +/- LPS-IFNg overnight. No co-culture CD14 were isolated on day of PBMC processing following magnetic bead isolation.

value: PBMC

value: CD14 positive

value: Co--culture +LPS/IFNG


title: 599_lung_pregnant_28_R thorax_uninf [24845]

description: 599_lung_pregnant_28_R thorax_uninf


title: Hues8,S2 3


title: 593_lung_M_1_L thorax_D1 [24850]

description: 593_lung_M_1_L thorax_D1


title: APBY_22

description:
Library name: APBY_22
TAM (M2)

value: Co-culture


title: Hues8,S2 2


title: 591_lung_pregnant_28_L thorax_uninf [24844]

description: 591_lung_pregnant_28_L thorax_uninf


title: Hues8,S2 1


title: 581_lung_pregnant_4_none_D4 [24843]


title: Hues8,S1 5


title: Endoderm Pax9 12ss b2, scRNA-seq

description:
Pax9_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos

value: Endoderm


title: Endoderm Pax9 15ss b1, scRNA-seq

description:
Pax9_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: 580_lung_F_4_R flank_D4 [24842]

description: 580_lung_F_4_R flank_D4


title: APBY_19

description:
Library name: APBY_19
TAM (M2)


title: Endoderm Pax9 12ss b1, scRNA-seq

description:
Pax9_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: 579_lung_F_1_L flank_D1 [24841]

description: 579_lung_F_1_L flank_D1


title: APBY_20

description:
Library name: APBY_20
TAM (M1)


title: 578_lung_F_1_R thorax_D1 [24840]

description: 578_lung_F_1_R thorax_D1


title: Hues8,S1 4


title: Hues8,S1 3


title: APBY_18

description:
Library name: APBY_18
Monocyte

value: No Co-culture


title: Endoderm Pax9 09ss b2, scRNA-seq

description:
Pax9_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: Endoderm Pax9 09ss b1, scRNA-seq

description:
Pax9_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: Hues8,S1 2


title: APBY_6

description:
Library name: APBY_6
TAM (M1)


title: Endoderm Pax9 15ss b2, scRNA-seq

description:
Pax9_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: Hues8,S1 1


title: Endoderm Nkx2_3 27ss b2, scRNA-seq

description:
Nkx2_3_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Nkx2.3-CreER-EGFP; Rosa-RFP


title: Endoderm Nkx2_3 27ss b1, scRNA-seq

description:
Nkx2_3_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos


title: APBY_5

description:
Library name: APBY_5
TAM (M2)


title: APBY_17

description:
Library name: APBY_17
Monocyte


title: 606_spleen_M_28_R thorax_uninf [24838]

description: 606_spleen_M_28_R thorax_uninf

source_name: spleen

value: spleen


title: 605_spleen_M_28_L thorax_uninf [24837]

description: 605_spleen_M_28_L thorax_uninf


title: Hues8,S0 3

value: Human embryonic stem


title: Endoderm Nkx2_3 24ss b2, scRNA-seq

description:
Nkx2_3_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: Hues8,S0 4


title: APBY_21

description:
Library name: APBY_21
Monocyte


title: Endoderm Nkx2_3 24ss b1, scRNA-seq

description:
Nkx2_3_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: APBY_3

description:
Library name: APBY_3
TAM (M1)


title: Hues8,S0 2


title: 594_spleen_M_4_L flank_D4 [24834]

description: 594_spleen_M_4_L flank_D4


title: APBY_2

description:
Library name: APBY_2
TAM (M2)


title: Hues8,S0 1


title: Endoderm Nkx2_3 21ss b2, scRNA-seq

description:
Nkx2_3_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: APBY_1

description:
Library name: APBY_1
Monocyte


title: 577_lung_F_1_L thorax_D1 [24839]

description: 577_lung_F_1_L thorax_D1


title: H1,S6 6


title: Endoderm Nkx2_3 21ss b1, scRNA-seq

description:
Nkx2_3_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: 591_spleen_pregnant_28_L thorax_uninf [24832]

description: 591_spleen_pregnant_28_L thorax_uninf


title: Sample_6_iMGL_Xenon

city: Boston

first: Wesley

last: Nogueira Brandao

state: Massachusetts

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: salmon plaint text quantification file (quant.sf)

source_name: iMGL

growth_protocol: The cells were plated in coated 6-well plates (350,000 cells/well) and cultured in complete iMG medium containing DMEM/F12 (Gibco 10565-018), IL-34 (100 ng/mL, PeproTech 200-34), TGF-β1 (50 ng/mL, Miltenyi Biotec 130-095-067), and M-CSF (25 ng/mL, PeproTech 300-25). The cells were maintained in culture for 3 days.

extract_protocol:
The microglia cells were isolated by cell sorter, and 1000 cells have their RNA extracted by Broad Institute using TCL buffer containing 1% Beta-Mercaptoethanol.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
cDNA libraries were generated from sorted cells using the Smart-seq2 protocol65. RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2× 25bp reads.

treatment_protocol: Cells were treated with  Xenon 75% exposure for 24 hours.

value: iMGL

value: Xenon

value: Chamber


title: 599_spleen_pregnant_28_R thorax_uninf [24833]

description: 599_spleen_pregnant_28_R thorax_uninf


title: Sample_5_iMGL_Xenon


title: H1,S6 4


title: Endoderm Nkx2_3 18ss b2, scRNA-seq

description:
Nkx2_3_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: Endoderm Nkx2_3 18ss b1, scRNA-seq

description:
Nkx2_3_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: H1,S6 3


title: 596_spleen_M_4_R thorax_D4 [24836]

description: 596_spleen_M_4_R thorax_D4


title: 595_spleen_M_4_R flank_D4 [24835]

description: 595_spleen_M_4_R flank_D4


title: 581_spleen_pregnant_4_none_D4 [24831]


title: H1,S6 2


title: Endoderm Nkx2_3 15ss b2, scRNA-seq

description:
Nkx2_3_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: Sample_3_iMGL_Air

value: Air


title: Endoderm Nkx2_3 15ss b1, scRNA-seq

description:
Nkx2_3_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: H1,S6 1


title: Sample_2_iMGL_Air


title: 605_blood_M_28_L thorax_uninf [24828]

description: 605_blood_M_28_L thorax_uninf

source_name: blood

value: blood


title: Sample_1_iMGL_Air


title: Endoderm Nkx2_3 12ss b2, scRNA-seq

description:
Nkx2_3_12ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos

source_name: Endoderm


title: H1,S5 6


title: Endoderm Nkx2_3 12ss b1, scRNA-seq

description:
Nkx2_3_12ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 12SS embryos


title: Sample_10_IPSMG_XENON

data_processing:
Count files (fastq) were preprocessed for quality control and adapter trimming using fastp. High quality reads were aligned using Salmon (v1.7).
Biological outliers were determined using PCA and heatmap visualization and removed for final analysis. Technical outliers were removed for further analysis.
Downstream differential gene expression analysis was carried out using DESeq2 (v.1.34.00). Comparisons were run using LRT, and the cutoff for significant genes was either P < 0.01 or P < 0.05.
Assembly: mm10
Supplementary files format and content: tar file of salmon outputs including plaint text  quantification file (quant.sf), transcripts used for quantification, parameter settings, version of Salmon, and estimated bias parameters
Supplementary files format and content: Bigwig file format, which was created from sorted BAM files and normalization against mouse genome length using deeptools.

source_name: IPSMG

growth_protocol: Human iMGL were transplanted into the brains of early postnatal (P1) immunodeficient MITRG mice. The cells were isolated after Xe treatment with animals at 6 months of age.

treatment_protocol: Xe treatment (Xe 30%, 40 minutes once a week) was initiated in 5xFAD-MITRG mice at 4 months of age and continued once a week until the animals reached 6 months of age.

value: IPSMG

value: Female

value: XENON

tag: age

value: 6 Months


title: H1,S6 5


title: 593_blood_M_1_L thorax_D1 [24826]

description: 593_blood_M_1_L thorax_D1


title: Endoderm Nkx2_3 09ss b2, scRNA-seq

description:
Nkx2_3_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: Sample_4_iMGL_Xenon

tag: location


title: 580_spleen_F_4_R flank_D4 [24830]

description: 580_spleen_F_4_R flank_D4


title: Sample_9_IPSMG_XENON


title: H1,S5 4


title: 595_blood_M_4_R flank_D4 [24825]

description: 595_blood_M_4_R flank_D4


title: Sample_8_IPSMG_XENON


title: H1,S5 3


title: 594_blood_M_4_L flank_D4 [24824]

description: 594_blood_M_4_L flank_D4


title: 606_blood_M_28_R thorax_uninf [24829]

description: 606_blood_M_28_R thorax_uninf

value: uninf


title: Sample_7_IPSMG_XENON


title: 600_blood_pregnant_1_R thorax_D1 [24823]

description: 600_blood_pregnant_1_R thorax_D1


title: Endoderm Ngn3GFP HZ 27ss b1, scRNA-seq

description:
Ngn3GFP_HZ_27ss_b1
Smart-seq3xpress


title: Endoderm Ngn3GFP HZ 24ss b1, scRNA-seq

description:
Ngn3GFP_HZ_24ss_b1
Smart-seq3xpress


title: Endoderm Nkx2_3 09ss b1, scRNA-seq

description:
Nkx2_3_09ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: H1,S5 1


title: 592_blood_F_1_L thorax_D1 [24822]

description: 592_blood_F_1_L thorax_D1


title: Sample_5_IPSMG_AIR

value: AIR


title: 596_blood_M_4_R thorax_D4 [24827]

description: 596_blood_M_4_R thorax_D4


title: H1,S4 6


title: Endoderm Ngn3GFP HZ 18ss b1, scRNA-seq

description:
Ngn3GFP_HZ_18ss_b1
Smart-seq3xpress


title: 599_blood_pregnant_28_R thorax_uninf [24821]

description: 599_blood_pregnant_28_R thorax_uninf


title: Sample_4_IPSMG_AIR


title: H1,S5 5


title: H1,S4 5


title: 591_blood_pregnant_28_L thorax_uninf [24820]

description: 591_blood_pregnant_28_L thorax_uninf


title: Endoderm Ngn3GFP HZ 15ss b1, scRNA-seq

description:
Ngn3GFP_HZ_15ss_b1
Smart-seq3xpress


title: Sample_3_IPSMG_AIR


title: H1,S4 4


title: 581_blood_pregnant_4_none_D4 [24819]


title: Endoderm Ngn3GFP HM 27ss b1, scRNA-seq

description:
Ngn3GFP_HM_27ss_b1
Smart-seq3xpress


title: Sample_2_IPSMG_AIR


title: H1,S4 3


title: H1,S5 2


title: Sample_1_IPSMG_AIR


title: Endoderm Ngn3GFP HM 24ss b1, scRNA-seq

description:
Ngn3GFP_HM_24ss_b1
Smart-seq3xpress


title: Sample_6_IPSMG_XENON


title: 578_blood_F_1_R thorax_D1 [24816]

description: 578_blood_F_1_R thorax_D1


title: Endoderm Ngn3GFP HZ 21ss b1, scRNA-seq

description:
Ngn3GFP_HZ_21ss_b1
Smart-seq3xpress


title: H1,S4 1


title: H1,S4 2


title: Endoderm Ngn3GFP HM 18ss b1, scRNA-seq

description:
Ngn3GFP_HM_18ss_b1
Smart-seq3xpress


title: TLN-3

data_processing:
the sequencing reads were 5’, 3’-adaptor trimmed and filtered reads (length < 18nt or length > 40nt) with cutadapt, and aligned to the cytoplasmic mature-tRNA sequences getting from GtRNAdb and the mitochondrial tRNA sequences getting from mitotRNAdb using BWA software (0.7.12-r1039). For tRNA alignment, the maximum mismatch was 2
Assembly: Hg38
Supplementary files format and content: csv file contains all reads counts for each replicate in the two conditions.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).  tRNAs were purified from total RNA and m1A&m3C demethylated then partially hydrolyzed according to the Hydro-tRNAseq method.
Fragments of ~19-35 nt for partially hydrolyzed and re-phosphorylated tRNAs were converted to small RNA sequencing libraries using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit


title: Endoderm Ngn3GFP HM 21ss b1, scRNA-seq

description:
Ngn3GFP_HM_21ss_b1
Smart-seq3xpress


title: TLN-2


title: Endoderm Ngn3GFP HM 15ss b1, scRNA-seq

description:
Ngn3GFP_HM_15ss_b1
Smart-seq3xpress


title: TLN-1


title: H1,S3 3


title: Expi-3


title: 577_blood_F_1_L thorax_D1 [24815]

description: 577_blood_F_1_L thorax_D1


title: H1,S3 2


title: Endoderm Ngn3Cre 27ss b1, scRNA-seq

description:
Ngn3Cre_27ss_b1
Smart-seq3xpress

value: Ngn3-Cre; Ai6


title: CP_14_3

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

data_processing:
CASAVA  bcl2fastq-1.8.4 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Assembly: reference sequence used for read alignment
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Cervus nippon

source_name: antler

growth_protocol: Reserve mesenchyme cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
Collect total RNA from chondrocytes and RMCs induced chondrogenic differentiation for 0, 7, 14 days  using Rneasy mini plus kit (Qiagen). A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
the small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 500,000 cells were placed in centrifuge tubes. Then the culture medium was changed from maintenance medium to chondrogenic medium, changing every 2 days for a course of 0, 7, 14 days.

value: antler

value: reserve mesenchyme cells

value: mesenchymal stem cell

value: WT

value: RMCs induced chondrogenic differentiation for 14 days


title: Expi-2


title: 580_blood_F_4_R flank_D4 [24818]

description: 580_blood_F_4_R flank_D4


title: H1,S3 1

value: Human embryonic stem


title: CP_14_2


title: CP_14_1


title: Endoderm Ngn3Cre 21ss b1, scRNA-seq

description:
Ngn3Cre_21ss_b1
Smart-seq3xpress

value: Endoderm


title: Expi-1


title: H1,S2 5


title: FMRP-cTag CLIP, CA1, noCre, replicate 3

city: New York

first: Ruth

last: Singer

state: NY

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

description:
Library name: FMRP_noCre_rep3
FMRP_noCre_rep3

data_processing:
Filter for quality of reads using fastq_filter.pl (CTK, fastq_filter.pl -f min:0-15:20,mean:16-39:20)
Trim 3' linker sequence (Cutadapt, -m 20 -a GTGTCAGTCACTTCCAGCGG)
Collapse exact duplicates using fastq2collapse.pl (CTK)
Trim 5' barcode and linker (CTK, stripBarcode.pl -len 9)
Remove reads less than 17 nt prior to mapping (cutadapt -m 17)
Mapped reads with STAR to UCSC mm10 transcriptome
Collapse PCR duplicates (CTK, tag2collapse.pl -EM 30 -random-barcode --seq-error-model em-local --weight-in-name --keep-max-score --keep-tag-name)
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain quantification of the numer of FMRP tags mapped per transcript

source_name: CA1 hippocampus

extract_protocol:
After optogenetic activation and UV-crosslinking, tissue was dissected from acute hippocampal slices in HBSS with 0.1 mg/mL cycloheximide. Tissue was homogenized in lysis buffer (1x PBS, 0.1% SDS, 0.5% NP-40, 0.5% Sodium deoxycholate supplemented, 1X cOmplete Mini EDTA-free Protease Inhibitor (Roche) and 0.1 mg/mL cycloheximide) by mechanical homogenization. FMRP-cTag-CLIP was performed as described previously (see associated paper for details).
RNA tags were isolated and cloned using the BrdU-CLIP method as described in associated paper.

value: CA1 hippocampus

value: Camk2a-Cre x Fmr1 cTag

value: noCre


title: CP_7_3

value: RMCs induced chondrogenic differentiation for 7 days


title: H1,S2 4


title: 579_blood_F_1_L flank_D1 [24817]

description: 579_blood_F_1_L flank_D1

value: blood


title: CP_7_2


title: Endoderm Nepn 27ss b2, scRNA-seq

description:
Nepn_27ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos

value: Nepn-CreER-EGFP; Rosa-RFP


title: FMRP-cTag CLIP, CA1, noCre, replicate 2

description:
Library name: FMRP_noCre_rep2
FMRP_noCre_rep2


title: Endoderm Nepn 27ss b1, scRNA-seq

description:
Nepn_27ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 27SS embryos


title: H1,S3 4


title: H1,S2 3


title: CP_7_1


title: FMRP-cTag CLIP, CA1, noCre, replicate 1

description:
Library name: FMRP_noCre_rep1
FMRP_noCre_rep1


title: Endoderm Nepn 24ss b2, scRNA-seq

description:
Nepn_24ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: H1,S2 1


title: Endoderm Ngn3Cre 24ss b1, scRNA-seq

description:
Ngn3Cre_24ss_b1
Smart-seq3xpress


title: FMRP-cTag CLIP, CA1, Control, replicate 4

description:
Library name: FMRP_CLIP_Control_rep4
FMRP_Control_rep4

value: AAV-Control


title: CP_0_2

value: RMCs induced chondrogenic differentiation for 0 days


title: FMRP-cTag CLIP, CA1, Control, replicate 3

description:
Library name: FMRP_CLIP_Control_rep3
FMRP_Control_rep3


title: Endoderm Nepn 24ss b1, scRNA-seq

description:
Nepn_24ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 24SS embryos


title: CP_0_1


title: H1,S1 5


title: H1,S1 4


title: FMRP-cTag CLIP, CA1, Control, replicate 2

description:
Library name: FMRP_CLIP_Control_rep2
FMRP_Control_rep2


title: Endoderm Nepn 21ss b2, scRNA-seq

description:
Nepn_21ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: Endoderm Nepn 21ss b1, scRNA-seq

description:
Nepn_21ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 21SS embryos


title: Endoderm Ngn3Cre 18ss b1, scRNA-seq

description:
Ngn3Cre_18ss_b1
Smart-seq3xpress


title: CC_3

value: chondrocyte


title: FMRP-cTag CLIP, CA1, Control, replicate 1

description:
Library name: FMRP_CLIP_Control_rep1
FMRP_Control_rep1


title: H1,S1 3


title: CC_1


title: FMRP-cTag CLIP, CA1, Opto, replicate 3

description:
Library name: FMRP_CLIP_Opto_rep3
FMRP_ChR1_rep3


title: Endoderm Nepn 15ss b2, scRNA-seq

description:
Nepn_15ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: Endoderm Nepn 18ss b2, scRNA-seq

description:
Nepn_18ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: Endoderm Nepn 18ss b1, scRNA-seq

description:
Nepn_18ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 18SS embryos


title: H1,S1 1


title: FMRP-cTag CLIP, CA1, Opto, replicate 4

description:
Library name: FMRP_CLIP_Opto_rep4
FMRP_ChR1_rep4


title: CP_0_3


title: H1,S1 2


title: FMRP-cTag CLIP, CA1, Opto, replicate 2

description:
Library name: FMRP_CLIP_Opto_rep2
FMRP_ChR1_rep2


title: T30.4_NA

type: RNA

city: Oullins-Pierre-Bénite

first: Marion

last: Debombourg

address: 165 chemindu grand revoyet

institute: biomerieux

hyb_protocol: NanoString nCounter, a hybridization-based multiplex assay.

scan_protocol: Data were collected and analyzed using the nCounter Digital Analyze according to the manufacturer instructions (NanoStrings Technologies, Seattle, WA).

data_processing: Normalization was performed using internal controls and 3 housekeeping genes (DECR1, HPRT1, POLR2A)

label: biotin

source_name: whole blood

label_protocol: Biotin & color-coded tag, 300 ng of total RNA from each sample was analyzed for the detection of a 144-gene panel according to the manufacturers instructions.

growth_protocol: Patient's blood was directly collected in a PaxGene tube and then stabilized at room temperature for 2H

extract_protocol: Total RNA was extracted using the PaxGene Blood RNA kit (PreAnalytiX/QIAGEN) according to manufacturer instructions

treatment_protocol: After the 2h stabilization, the tube was stored at -80°C

tag: cohort

value: FIGHT

tag: status

value: Healthy Volunteer

tag: support

value: PaxGene

tag: stimulus


title: H1,S0 3


title: Endoderm Nepn 15ss b1, scRNA-seq

description:
Nepn_15ss_b1
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 15SS embryos


title: FMRP-cTag CLIP, CA1, Opto, replicate 1

description:
Library name: FMRP_CLIP_Opto_rep1
FMRP_ChR1_rep1


title: H1,S0 4


title: T28.4_NA


title: H1,S0 2


title: CC_2

value: antler


title: Endoderm Nepn 09ss b2, scRNA-seq

description:
Nepn_09ss_b2
Smart-seq3xpress
Tamoxifen was administered to pregnant mice at E8.0, with analysis conducted on 9SS embryos


title: H1,S0 1


title: Human Islet 6

source_name: Primary human islets

value: Primary human islets


title: T21.4_NA


title: H1,S2 2