title: GW2580 3

city: Urbana

first: Katiria

last: Soto Diaz

state: IL

address: 1201 W Gregory Dr

institute: University of Illinois at Urbana-Champaign

data_processing:
Genome index was prepared using STAR and the Mus musculus DNA FASTA file from e!Ensembl. The reads were aligned to the reference genome to both reads.
Reads were counted using a FeatureCount in STAR.
Statistical analysis of differentially expressed genes (DEG) was performed using R studio.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include cell counts
Supplementary_files_format_and_content: Table with gene counts for every sample

source_name: CD11b+ positively selected microglia

growth_protocol: Cells were isolated from mice after treatment, and RNA was isolated the same day, no growing protocol was needed for the cells

extract_protocol:
Animals were euthanized,  perfused and their brains isolated. Brain tissue was enzymatically digested with Accutase and filtered through a 70micron filter. Microglia were enriched by percoll gradient centrifugation then magnetically isolated using a CD11b positive selection kit. RNA was extracted using a GeneJet RNA purification kit and then SMART-Seq v4 PLUS kit was used to generate high-quality cDNA libraries.
high-quality Illumina sequencing-ready libraries were prepared and sequencing was performed using with Illumina Hi-seq lane which generated an average of 47.9 million 150nt paired-end reads per sample with a minimum FastQC score of 34.

treatment_protocol: Animals were either orally gavaged with 80mg/kg/d GW2580 or vehicle alone for 8 days.

value: brain

value: CD11b+ positively selected microglia

tag: treatment method and duration

value: orally gavage for 8 day

value: 0.1% Tween 80, 0.5% Hydroxymethyl Propyl-cellulose+ 80mg/kg/d of GW2580

tag: Sex

value: female


title: JGHL45

status: Public on Oct 12 2021

type: SRA

city: Los Angeles

first: Mehdi

last: Bouhaddou

state: CA

address: 611 Charles E Young Drive, Boyer Hall 530

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
Unaligned reads were mapped to human reference for expression counting; all mouse reads were discarded. Reads were classified as "human", "mouse", "both", "neither", and "ambiguous" using Xenome (v1.0.0).
Adapters were trimmed and reads failing QC were removed using fastp (v0.20.0).
Remaining reads were mapped against an Ensembl GRCh38.90 reference.
Expression counts were estimated using RSEM (v1.3.1).
mRNA sequencing data (in units of FPKM) was median centered across patients by dividing by the median expression value for each gene. The log2 of these values were then calculated to generate the final RNA expression values used for subsequent analyses.
Genome_build: Ensembl GRCh38.90 reference
Supplementary_files_format_and_content: Processed data file contains transcripts per million (TPM) counts per gene isoform for all samples.

molecule: polyA RNA

organism: Homo sapiens

source_name: Patient-derived xenograph sample

growth_protocol: PDX samples were grown in NOD-SCID gamm mice as previously described (Li H et al 2014)

extract_protocol:
Total RNA was extracted using the RNAeasy kit from Qiagen.
Standard library preps were created by QB3-Berkeley Genomics core.

treatment_protocol: PDX tumors were treated as described in the manuscript.

tag: disease state

value: Head and neck cancer patient

tag: cetuximab response

value: not tested

tag: predicted cetuximab response

value: Sensitive


title: Unt_k27ac_rep1

city: SEVENOAKS

first: Anna

middle: Rita

last: Lamstaes

state: Kent

address: 99 Solefields Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Library strategy: ChIPmentation
Fastq files were quality checked, paired and trimmed using trimmomatic and aligned using Bowtie2. SAMtools were used to filter low quality and duplicate reads. Samples were spike-in normalized, or normalized based on sequencing depth. MACS2 was used to call peaks using input reads as a control.
Genome_build: hg38
Supplementary_files_format_and_content:
Spike-in normalized Bigwig

molecule: genomic DNA

source_name: Hepatocellular Carcinoma

growth_protocol: Hep3B cells grown in DMEM with 10% FBS and 1xP/S, 37oC, 5% CO2

extract_protocol:
Cells were washed and collected in PBS. The cell pellet was resuspended in RT PBS and fixed for 5min with 1% formaldehyde before quenching with 0.125M Glycine. 5000 fixed drosophila sg4 cells (0.05%) were added as a spike-in control. The cell pellet was obtained, washed in cold PBS and incubated in swelling buffer. The subsequent nuclear pellet was resuspended in lysis buffer and sonicated to fragments of ~200bp. One tenth of the sample was taken as input control. Samples were incubated overnight with the required antibody, 5ul of H2AV drosophila Ab and blocked ProteinA dynabeads. IPs were stingically washed. IPs were tagmented (Nextera DNA Library Prep Kit) and tagmented DNA eluted off the beads. The eluted IPs, and Input controls were decrosslinked, RNase and proteinase K treated. The input controls were tagmented.
Nextera DNA library prep kit and Nextera index kit (Illumina)

treatment_protocol: Untreated

tag: cell line

tag: treatment

value: Untreated

tag: spike-in

value: Drosophila spike in

tag: chip antibody


title: iPSC-RPE-3_CC-HS_L-475_RS14 [HM7FMBBXX_16496349_S45_L005]

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

data_processing:
salmon 0.9.1
gencode.v27.basic.annotation.gtf.gz
tximport with tx2gene collapse
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, tximport collapsed to genes

molecule: total RNA

growth_protocol: mature iPSC-RPE were cultured in MEM based media supplemented with FBS and other growth factors

extract_protocol:
Total RNA
Total RNAs (5 μg) from two biological replicates were pooled for cDNA library construction. cDNA library preparation and sequencing were carried out on an Illumina HiSeq 4000 platform

treatment_protocol: RPE cells were treated with CI-HS, CC-HS and two drugs.

tag: cell type

value: iPSC derived RPE


title: GW2580 2

organism: Mus musculus

tag: tissue

tag: strain

value: male


title: 2hr_k27ac_rep1

treatment_protocol: 2hr 10ng/ml IFNγ

value: 2hr IFNγ


title: 24hr_ATAC-seq_rep3

data_processing:
Fastq files were quality checked, paired and trimmed using trimmomatic and aligned using Bowtie2. SAMtools were used to filter low quality, duplicate reads and mitochondrial reads. MACS2 was used to call peaks.
Genome_build: hg38
Supplementary_files_format_and_content:
Bigwig

extract_protocol:
Cells were washed in cold PBS (containing IFNg for treated groups) and resuspended in lysis buffer (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl_2, 0.1% IGEPAL). The nuclei were pelleted and resuspended in 1x TD with 2.5ul TDE1 (Nextera DNA library prep kit, Illumina). These were incubated for 30min at 37oc. The tagmented DNA was purified using the MinElute PCR purification kit (Qiagen, 28004).
Nextera DNA library prep kit and Nextera index kit (Illumina)

treatment_protocol: 24hr 10ng/ml IFNγ

value: 24hr IFNγ


title: JGHL38

value: Resistant


title: 24hr_ATAC-seq_rep2


title: GW2580 1


title: JGHL37


title: GW2580 5


title: GW2580 4


title: Vehicle 5

value: 0.1% Tween 80, 0.5% Hydroxymethyl Propyl-cellulose


title: iPSC-RPE-1_CC-HS_ACA_RS7 [HMLLWBBXX_16496350_S59_L006]


title: JGHL36


title: 24hr_ATAC-seq_rep1

description: Two sequencing runs were performed to obtain the desired sequencing depth


title: JGHL40


title: Vehicle 4


title: JGHL35


title: iPSC-RPE-2_CC-HS_L475_RS13 [HMLLWBBXX_16496353_S62_L007]


title: Vehicle 2


title: JGHL34


title: iPSC-RPE-2_CC-HS_L475_RS13 [HM7FMBBXX_16496353_S49_L005]


title: iPSC-RPE-1_CC-HS_L475_RS6 [HMLLWBBXX_16496344_S53_L007]


title: 2hr_ATAC-seq_rep3


title: iPSC-RPE-2_CC-HS_L475_RS13 [HMLLWBBXX_16496353_S62_L006]


title: iPSC-RPE-1_CC-HS_L475_RS6 [HM7FMBBXX_16496344_S40_L005]


title: Vehicle 3


title: iPSC-RPE-2_CC-HS_L475_RS13 [HMLLWBBXX_16496353_S62_L008]


title: JGHL31


title: Vehicle 1


title: 2hr_ATAC-seq_rep2


title: 0.5hr_ATAC-seq_rep2

treatment_protocol: 0.5hr 10ng/ml IFNγ

value: 0.5hr IFNγ


title: iPSC-RPE-1_CC-HS_L475_RS6 [HMLLWBBXX_16496344_S53_L006]


title: JGHL30


title: 0.5hr_ATAC-seq_rep3


title: JGHL29


title: iPSC-RPE-1_CC-HS_L475_RS6 [HMLLWBBXX_16496344_S53_L008]


title: 0.5hr_ATAC-seq_rep1


title: Superemere_2

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v2.10
Reads were aligned to the GENCODE GRCm38.p5 genome using STAR v2.7.3a. GENCODE vM24 gene annotations were provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
featureCounts v2.0.0 was used to count the number of mapped reads to each gene.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Raw gene count matrix

source_name: liver tissue_supermeres

extract_protocol:
Liver tissue samples were immediately stored in RNAlater (Ambion) until homogenization with ceramic beads using the PowerLyzer (Qiagen) and RNA extracted using the RNeasy Kit (Qiagen) according to the manufacturer’s instructions.
polyA-selection

treatment_protocol: Mice were injected with PBS or exomeres (100 µg or 300 ug) or supermeres (100 µg or 300 µg) derived from DiFi cells diluted in 100 µl phosphate buffered saline pH 7.4 (PBS, Gibco, 70011-044,) into the tail vein. Mice received daily injections for 3 consecutive days and were sacrificed 24 h after the last injection.

tag: genotype

value: wild type

value: supermeres

value: liver


title: Superemere_1


title: JGHL33


title: iPSC-RPE-3_CC-HS_RS17 [HMLLWBBXX_16496345_S54_L008]

value: CC-HS


title: Superemere_3


title: PBS_3

source_name: liver tissue_PBS control

value: PBS control


title: 2hr_ATAC-seq_rep1


title: Unt_ATAC-seq_rep2


title: iPSC-RPE-3_CC-HS_RS17 [HM7FMBBXX_16496345_S41_L005]


title: Unt_ATAC-seq_rep3


title: JGHL26

value: Head and neck cancer patient


title: iPSC-RPE-3_CC-HS_RS17 [HMLLWBBXX_16496345_S54_L006]


title: JGHL28

value: not tested


title: JGHL27


title: XBP1U_INDUCED

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling.
STAR version 2.5.3a was used to align the fastq files to reference genome using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using Cufflinks version 2.2.1 with parameters -G -L.
Cuffmerge/quant/diff/norm were all run using default parameters.
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: FPKM-counts values.xlsx: Excel file includes Cuffnorm output containing FPKM and count values for each gene in each sample.

source_name: HeLa cells with inducible expression of XBP1u (24h, doxycycline)

growth_protocol: Cells were cultured in Minimum Essential Modified Eagle's Medium (Thermo Fisher Scientific, Waltham, MA, USA) with 2 mM l‐glutamine (Millipore Sigma, Burlington, MA, USA), antibiotics (100 U/ml of penicillin and 100 µg/ml of streptomycin (Millipore Sigma)), and 10% fetal bovine serum in a humidified incubator at 37°C in 5% CO2 in 6‐well plates. Cells were allowed to grow to 70–80% confluence before the start of the experiments.

extract_protocol: Total RNA (containing both mRNA and miRNA) was isolated using miRNeasy kit (Qiagen). RNA concentrations were calculated based on the absorbance at 260 nm. RNA samples were stored at -70°C until use.

treatment_protocol: Following hygromycin b selection (300 µg/ml, Sigma) and qPCR verification of 24 h doxycycline induction (400 µg/ml, D3072 Millipore Sigma) of XBP1s and XBP1u mRNAs in HeLa S3 cells, two stable clonal cell lines capable of stable inducible expression of XBP1s (Hela-XBP1s) and XBP1u (HeLa-XBP1u) were obtained. These cell lines were cultured in Minimum Essential Modified Eagle's Medium with 2 mM l‐glutamine, hygromycin B (300 µg/ml) and 10% tetracycline free fetal bovine serum (Takara Bio, USA) in a humidified incubator at 37°C in 5% CO2 in 6‐well plates. Cells were allowed to grow to 70–80% confluence before the start of the experiments.

value: HeLa CCL-2.2

value: Doxycycline induction (400 ug/ml) for 24 h

tag: induction


title: PBS_1


title: iPSC-RPE-2_CC-HS_RS10 [HM7FMBBXX_16496341_S37_L005]


title: iPSC-RPE-3_CC-HS_RS17 [HMLLWBBXX_16496345_S54_L007]


title: CTRL

source_name: HeLa cells with no transgene inducible expression activated


title: JGHL25

value: Sensitive


title: Exomere_2

source_name: liver tissue_exomeres

value: exomeres


title: Unt_ATAC-seq_rep1

value: Untreated


title: Exomere_3


title: JGHL32


title: iPSC-RPE-1_CC-HS_RS3 [HMLLWBBXX_16496359_S68_L007]

value: iPSC derived RPE


title: JGHL22


title: TEC03d505wtFOXN1wk0510XGEX

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

description:
Foxn1TECwtd505_10X.counts.gz
Foxn1TECwtd505_10X_metadata.txt.gz

data_processing:
RNA-seq: reads were aligned against the Ensembl transcriptome and genome (GRCh38.EBVB95-8wt.ERCC) using STAR (version 2.5.3a). The allocation of reads to protein coding gene meta-features was done using HTSeq.
ChIP-seq: Contaminating adaptor sequences were removed from fastq sequences using Trimmomatic (version 0.32). Reads were aligned against the human genome (GRCh38.EBVB95-8wt.ERCC) using STAR (version 2.5.3a). Peaks were called on deduplicated aligned sequences (paired ChIP and input samples) using MACS2 (version 2.0.10) with a relaxed P value setting of 0.1. Peaks from replicates were then pooled and analyzed using irreproducible discovery rate analysis (IDR < 0.05). Peaks were filtered against the ENCODE blacklist regions.
10X GEX: Single cell libraries were processed using Cellranger (version 3.1.0). Cells were excluded from analysis if the total UMI count was <1,000 or >32,000, the number of detectable features was <562 or >7,943 or the proportion of UMIs mapping to mitochondrial genes was >10%.
Genome_build: Homo sapiens: GRCh38.EBVB95-8wt.ERCC. Mus musculus: mm10
Supplementary_files_format_and_content: Processed data includes count matrices for RNA-seq/10X GEX, meta-data for 10X GEX and IDR<0.05 peaks for ChIP-seq data.

source_name: EpCAM+ CD45- TEC

growth_protocol: 4D6 cells  were grown in RPMI 1640 (Sigma-Aldrich) supplemented with 10% (v/v) heat inactivated fetal bovine serum (FBS) (SLS), 10 mM HEPES buffer, 1% (v/v) non-essential amino acids (NEAA) (Lonza), 2mM L-glutamine (Lonza), 100U/ml penicillin, and 100μg/ml streptomycin (Lonza) at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
RNA-seq: 4D6 thymic epithelial cells were transfected with plasmids encoding 1) wild type-FOXN1 alone 2) Δ550-FOXN1 mutant alone, 3) wild type and Δ550 οr 4) empty vector only, along with a GFP-expressing vector in a 4:1 ratio to facilitate sorting of positively transfected cells. Three biological replicates were prepared for each sample. A total of 75,000 GFP-positive cells were FACS sorted and RNA was extracted using the Rneasy Plus Micro kit (Qiagen). ChIP-seq: 4D6 cells were transfected with either wild type or Δ550 mutant FOXN1 construct tagged with a FLAG and three biological replicates of each transfected cell population were collected for ChIP-Seq analyses. The chromatin immunoprecipitation was performed using the iDeal ChIP-seq kit for Transcription Factors (Diagenode) as per manufacturer’s recommendations. Briefly, 2.5 x106 transfected cells were collected and subjected to protein-DNA crosslinking for 20 min. Cells were then lysed and chromatin was sheared for 8 sonication cycles (30’’ ON/30’’ OFF). Sheared chromatin was immunoprecipitated using M2 anti-FLAG antibody (Sigma) while parallel input samples from non-immunoprecipitated chromatin were prepared for each sample. 10X GEX: EpCAM+ CD45- live TEC were loaded onto the 10X Chromium system.
RNA-seq: RNA was processed using the RNA-Seq Poly A method and indexed using Nextera indexes. ChIP-seq: DNA libraries for all 12 samples were prepared using the MicroPlex Library Preparation Kit (12 indexes; Diagenode) following the manufacturer’s recommendations. 10X GEX: libraries were prepared as per manufacturer's protocol for 3' gene expression libraries.

value: EpCAM+ CD45- live TEC

value: wt Foxn1/d505 Foxn1

tag: age

value: 5 weeks

tag: method

value: 10X 3' gene expression


title: iPSC-RPE-2_CC-HS_RS10 [HMLLWBBXX_16496341_S50_L008]


title: iPSC-RPE-2_CC-HS_RS10 [HMLLWBBXX_16496341_S50_L006]


title: PBS_2

value: wild type


title: TEC03wtwtFOXN1wk0510XGEX

value: wt Foxn1/wt Foxn1


title: JGHL21


title: Exomere_1

value: liver


title: d23 rep 2

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
RNA-seq reads were trimmed using cutadapt, aligned with STAR, and alignments overlapping exons were enumerated using featureCounts. Differential gene expression was computed in R using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix

source_name: human iPSCs

growth_protocol: Human beta-like cells were generated using a previously described protocol (https://doi.org/10.1038/s41556-018-0271-4 and https://protocolexchange.researchsquare.com/article/nprot-7247/v1).

extract_protocol:
Total RNA was isolated from cell cultures using RNeasy kits from Qiagen
NEBNext Ultra II Directional RNA Library with NEBNext rRNA depletion

value: hPSC-eBCs


title: d23 rep 3


title: JGHL20


title: JGHL23

value: Resistant


title: d23 rep 1


title: XBP1S_INDUCED

source_name: HeLa cells with inducible expression of XBP1s (24h, doxycycline)


title: d30 rep 3


title: iPSC-RPE-1_CC-HS_RS3 [HM7FMBBXX_16496359_S55_L005]

value: CC-HS


title: d30 rep 2


title: iPSC-RPE-2_CC-HS_RS10 [HMLLWBBXX_16496341_S50_L007]


title: JGHL18

value: Head and neck cancer patient


title: iPSC-RPE-1_CC-HS_RS3 [HMLLWBBXX_16496359_S68_L008]


title: JGHL17

value: not tested


title: iPSC-RPE-3_CI-HS_RS18 [HMLLWBBXX_16496347_S56_L006]

value: CI-HS


title: TEC02wtwtFOXN1wk0510XGEX


title: TEC03d505wtFOXN1wk1610XGEX

value: 16 weeks


title: JGHL16


title: JGHL19

value: Sensitive


title: JGHL24


title: d30 rep 1


title: TEC01d505wtFOXN1wk0510XGEX


title: TEC01wtwtFOXN1wk0510XGEX


title: TEC03wtwtFOXN1wk1610XGEX


title: iPSC-RPE-1_CC-HS_RS3 [HMLLWBBXX_16496359_S68_L006]


title: JGHL15


title: entpd3_pos_rep4

growth_protocol: Self-enriched human beta-like cells were generated with modification to a previous described protocol (https://doi.org/10.1038/s41556-018-0271-4 and https://protocolexchange.researchsquare.com/article/nprot-7247/v1). Specifically, after day 20 of culture, the cultures were not subjected to dissociationg and enrichment via FACS. The cultures were allowed to continue maturation until day 28.

value: ENTPD3+ hPSC-seBCs


title: iPSC-RPE-3_CI-HS_RS18 [HMLLWBBXX_16496347_S56_L008]

value: iPSC derived RPE


title: TEC02d505wtFOXN1wk0510XGEX

value: EpCAM+ CD45- live TEC


title: entpd3_neg_rep4

value: ENTPD3- hPSC-seBCs


title: iPSC-RPE-2_CI-HS_RS11 [HMLLWBBXX_16496348_S57_L008]


title: entpd3_neg_rep3


title: TEC02wtwtFOXN1wk1610XGEX


title: TEC01d505wtFOXN1wk1610XGEX

value: wt Foxn1/d505 Foxn1


title: iPSC-RPE-2_CI-HS_RS11 [HM7FMBBXX_16496348_S44_L005]


title: entpd3_pos_rep2


title: JGHL11


title: iPSC-RPE-2_CI-HS_RS11 [HMLLWBBXX_16496348_S57_L006]


title: iPSC-RPE-2_CI-HS_RS11 [HMLLWBBXX_16496348_S57_L007]


title: entpd3_pos_rep1


title: entpd3_pos_rep3


title: DGRP_55031

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

data_processing:
cleaning with fastqc (1.1.2)
mapping with bowtie2 (2.2.6) on the sample's genome (i.e. mutating the default dm6 according to the VCF of the DGRP line)
peak calling with MACS2 (20160920) - per sample
features counted using Subread (1.4.6) on the merged peaks without repeats
counts normalized based on size-factors with DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: count matrix: read-counts per peak and sample (size-factor normalized)
Supplementary_files_format_and_content: count matrix + genotypes: The first 47 columns are the read counts in peaks, the remaining columns are the genotypes for the overlapping SNPs

organism: Drosophila melanogaster

source_name: Whole fly brain

extract_protocol:
Brains were dissected from one male and one female fly in PBS. Next, 50μl cold lysis buffer was added (10 mM Tris‐HCl pH  7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA‐630). After spinning down at 800g, supernatant was discarded and transposition mix was addded, followed by general omniATAC-seq
omniATAC-seq

value: Brain

value: Young adults (1-3 days)


title: JGHL9


title: iPSC-RPE-3_CI-HS_RS18 [HMLLWBBXX_16496347_S56_L007]


title: JGHL14


title: iPSC-RPE-3_CI-HS_RS18 [HM7FMBBXX_16496347_S43_L005]


title: JGHL13


title: TEC02d505wtFOXN1wk1610XGEX

value: 10X 3' gene expression


title: entpd3_neg_rep2


title: JGHL12


title: JGHL8


title: TEC01wtwtFOXN1wk1610XGEX

value: wt Foxn1/wt Foxn1


title: entpd3_neg_rep1


title: DGRP_55026_s2


title: E_GMP_SC

city: Vancouver

first: Elizabeth

last: Bulaeva

state: BC

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: British Columbia Cancer Agency

description: experimental leukemia

data_processing:
Sample demultiplexing was performed using “cellranger mkfastq” (v3.0.2) prior to TSO sequence trimming from the 5’ end of R2, allowing up to 1 mismatch using “cutadapt” (v2.3).
Alignment to hg19, read counting, and cell calling were performed using “cellranger count” (v3.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: .tsv files with barcode gene and feature information and .mtx files contain the gene id, cell id and total UMI counts per cell/gene.

source_name: hematopoietic cells

growth_protocol: human cord blood derived cells were transduced with MYC-GFP and transplanted into xenograft NRG-3GS mice. After the mice deveoped leukemia, leukemic cells were extracted and sorted from mouse spleens and sent for RNA-seq.

extract_protocol:
Sorted cells were loaded onto a 10X Genomics single-cell controller
Libraries were generated using the Chromium Single Cell 3’ Reagent v3 Chemistry kit and the manufacturer protocols were followed for all steps. Libraries were sequenced on an Illumina NextSeq machine.

value: hematopoietic cells

tag: phenotype

tag: xenograft strain

tag: type

value: single cell


title: iPSC-RPE-1_CI-HS_RS4 [HMLLWBBXX_16496357_S66_L006]


title: iPSC-RPE-1_CI-HS_RS4 [HMLLWBBXX_16496357_S66_L007]


title: DGRP_28275


title: JGHL10

tag: disease state


title: DGRP_28243


title: JGHL6

tag: cetuximab response


title: DGRP_29652


title: JGHL5

tag: predicted cetuximab response

value: Resistant


title: iPSC-RPE-1_CI-HS_RS4 [HMLLWBBXX_16496357_S66_L008]


title: 2045_VDJ

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

country: Switzerland

institute: Ludwig Institute for Cancer Research / CHUV

data_processing:
Library strategy: VDJ-seq
The V(D)J + 5' Gene Expression libraries were sequenced using Illumina HiSeq 4000 targeting the recommended by 10x Genomics read length and depth. The fastq files were generated and demultiplexed either by cellranger mkfastq from 10x Genomics (version 3.0.2) or by BaseCalling in Illumina RTA 1.18.66.3 and post processed via Illumina pipeline 2.19.1. The quality control of sequencing was confirmed by FastQC software (Andrews, 2010). Alignment, filtering, barcode and UMI counting was performed using GRCh38-3.1.0 reference genome and cellranger count from 10x Genomics, version 3.1.0. Multiple gene expression libraries were combined and normalized to the same sequencing depth (post-normalization mean reads per cell 28,950) using cellranger aggr. Two libraries were excluded from normalization step and were added to the analysis using their total reads per cell of 18,600 and 21,00, respectively. For all of the downstream analysis, filtered feature-barcode matrix containing gene expression data for only detected cellular barcodes was used. The single-cell V(D)J sequences and annotations were generated using cellranger vdj and vdj_GRCh38_alts_ensembl-3.1.0 reference genome. On average, 64.3% of reads were mapped to any V(D)J gene and only full length and productive TCRs (79.1% of total mapped) were considered for the analysis.
The downstream analysis was performed using Seurat (version 3.1.0; (Butler et al., 2018; Stuart et al., 2019) package in R language for statistical computing (R Core Team, 2020). Starting from the initial 44,718 cells, we filtered out potential doublets and debris by keeping only the cells with the number of genes between 300 and 5000 and whose UMI count ranged between 500 and 8000. By the same reasoning, we subsetted to the cells with mitochondrial content less than 15% and ribosomal content between 15% and 50%. This reduced the total number of cells by 15%. We then further filtered the remaining 37,658 cells to CD8+ population based on the expression of the known markers. Namely, cells had to have positive expression (> 0) of CD8A and/or CD8B, and to have minimal expression (< 1) of the non-T-cell markers – SLAMF7, PECAM1, KLRC3, KLRC1, TYROBP, CD4, SPI1, VWF, FCER1G, FOXP3, CD19, CD79A, IGKC, FCGR2A, CSF1R, FLT3, CLEC4C, COL1A2, MCAM, MYLK, FAP, PDPN, EPCAM, TP63. This further reduced the number of cells by 39% to a total of 22,963.
Genome_build: GRCh38-3.1.0
Supplementary_files_format_and_content: Comma separated, matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Comma separated, TCR sequencing

source_name: ovarian tumor-digest

extract_protocol:
After FACS sorting and before encapsulation, cells were manually counted with hemacytometer and viability was also checked using Trypan blue exclusion. For each sample, 1,000-10,000 cells were loaded into the Chromium machine with the aimed recovery of 600-8,000 cells. Single cells were encapsulated into droplets with reagents and gel bead containing a unique molecular identifier (UMI) from 10x.
cDNAs obtained after droplets break were purified with Dynabeads MyOne SILANE and amplified by 16 cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, 72°C for 1min] x 16; 72°C for 1min). Resulting amplified cDNAs were used for both 5’Gene Expression Library construction and V(D)J enriched libraries (TCR enrichment). Quantification of the resulting libraries was performed with the Qubit HS dsDNA assay kit and quality control was performed with the Fragment Analyzer (Agilent).

treatment_protocol: Cells from tumor digested specimens were adjusted to 2x10^6/well in 24-well plates and cultured overnight with WT1, hTERT and NY-ESO-1 PepTivator (by Miltenyi). The next day, the cells were collected and washed in wash solution prepared with 0.09% NaCl solution (Bichsel AG), with Fish Gelatin 1% (Sigma Aldrich) and RNasin 0.1% (Promega). After wash, the cells were resuspended in wash solution in the presence of human Fc Block (Miltenyi Biotech), 50nM Calcein AM (ThermoFisher) and Zombie UV Fixable Viability Kit (BioLegend). After incubation, cells were stained in wash solution in the presence of CD45 PerCP Cy5.5 (clone 2D1), CD3 BV711 (clone UCHT1), and CD8 BV650 (clone SK1) (all the Abs are from BioLegend). Cells belonging to the same tumor specimen were pooled together and sorted on a MoFlo Astrios (Beckman Coulter). Sorted cells were collected in 0.2mL PCR tubes with 10 µL PBS with 0.4% BSA (Sigma Aldrich) and RNasin 0.1%. Live cells were gated as Calcein AM positive and Zombie UV negative and further gated for CD45+CD3+CD8+ markers. Collected cells were then immediately encapsulated using 10x protocol.

tag: raw file name tag

tag: cell barcode appendix

value: ovarian tumor

value: CD8+ T cells


title: DGRP_29651


title: 2296_VDJ


title: iPSC-RPE-1_CI-HS_RS4 [HM7FMBBXX_16496357_S53_L005]

tag: treatment

value: CI-HS


title: B_CD34+38-_SC

description: experimental leukemia


title: JGHL7

value: Head and neck cancer patient


title: A_CD34+38-_SC

description: experimental leukemia


title: High_4

type: RNA

city: Val-de-Reuil

first: Cécilia

last: Brun

address: Campus de Maigremont

department: Translational Science - Essential Health

country: France

institute: Johnson & Johnson Santé Beauté France

hyb_protocol: Samples were finally sent to Genex (Longjumeau, France) for transcriptomic profiling.

scan_protocol: not provided

data_processing: A background correction followed by a quantile normalization (QN) was applied using the RMA framework as implemented in the limma R package. Quality-check was performed to properly evaluate the impact of the QN and filtering using extensive data visualization before and after normalization.

source_name: Fibroblasts - Biopsy

label_protocol: Total RNAs were sent to Genotypic Technology (India) for transcriptomic microarray profiling.

growth_protocol: Fibroblasts were obtained and isolated as described by Sauvaigo et al. Caucasian females were recruited by Dermscan (Lyon, France). Biopsy removal was performed in accordance with ethical procedures (Helsinki Guidelines) after approval by a Medical Ethics Committee (CCPPRB). Briefly, donors were divided into two groups (group 1 – age range 20–33 years ‘young donors’, n=9; group 2 – age range 61-68 years ‘old donors’, n=9). Cells were isolated from outgrowth of two 3mm-punch biopsies taken on the volar forearm and were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 1% fungizone, 0.04% de Gentamycin and 1% Glutamax in a 90% humidified incubator with 5% CO2 at 37°C. Cells were amplified and weekly passaged until passage 5. They were then harvested at 80-90% confluence and stored in liquid nitrogen. For this study, cells were used at passage 7.

extract_protocol: Cells from the young donor group were harvested at 80-90% confluence, pelleted and frozen. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, France) with a Qiacube according to the manufacturer’s instructions.

value: Fibroblasts

tag: proliferative capacity

value: High

value: Young (20-33 yrs)

tag: gender

value: Female

tag: population

value: Caucasian


title: DGRP_28136

tag: tissue


title: JGHL4

value: not tested

value: Sensitive


title: 1932_VDJ

tag: cell type


title: High_3


title: High_2


title: DGRP_28123

value: Brain

tag: genotype

value: Young adults (1-3 days)


title: High_1

tag: age


title: D_GMP_SC

description: experimental leukemia


title: DGRP_28222


title: DGRP_25199


title: DGRP_28224


title: Calu-3 cells, SR9009(2)

first: Xiaodong

last: Zhuang

state: Oxfordshire

address: Old Road Campus, Roosevelt Drive

data_processing:
Sequence adapters were removed and reads were quality trimmed by Trim Galore v0.5.0 (2). The reads were mapped against the reference human genome (hg38/GRCm38) using STAR v2.5.3 (3). Counts per gene were calculated using Rsubread v1.28.1 (4). Reads were analysed by edgeR v3.30.0 (5), first normalised using TMM and then counts per million were calculated and differential expression analysis was performed.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Calu-3 cells were lysed in RLT buffer and RNA was extracted using Qiagen RNAeasy kit. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Lung epithelial cell line Calu-3


title: DGRP_28153


title: 1784_VDJ


title: 1743_VDJ


title: JGHL1


title: 2312_VDJ


title: Calu-3 cells, SR9009(1)


title: JGHL2


title: DGRP_25193


title: 2246_VDJ


title: 2251_VDJ


title: h-APPDP-Neurons-TERT-3

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

description: h-APPDP-Neurons-TERT replicate 3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 using STAR software.
The HTSeq-count program was used to generate raw read counts for each gene
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: APP DP iPSC-derived neurons

extract_protocol:
RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSC-derived neurons

tag: transduction

value: TERT

tag: group

value: Treated


title: 1911_VDJ

value: ovarian tumor


title: 1934_VDJ

value: CD8+ T cells


title: Calu-3 cells, SR9009(3)


title: h-APPDP-Neurons-TERT-1

description: h-APPDP-Neurons-TERT replicate 1


title: Low_5

value: Low


title: Low_1


title: DGRP_25187


title: 2209_VDJ


title: JGHL3

value: Head and neck cancer patient


title: Low_4

value: Fibroblasts


title: 2060_VDJ


title: DGRP_25194


title: DGRP_55018


title: Calu-3 cells, shBmal1(3)


title: 2062_VDJ


title: Low_3


title: h-APPDP-Neurons-EGFP-2

description: h-APPDP-Neurons-EGFP replicate 2

value: EGFP

value: Control


title: Calu-3 cells, Control(1)


title: h-APPDP-Neurons-TERT-2

description: h-APPDP-Neurons-TERT replicate 2


title: DGRP_55015


title: Calu-3 cells, shBmal1(2)


title: DGRP_28239


title: DGRP_55028


title: Calu-3 cells, Control(2)


title: h-APPDP-Neurons-EGFP-3

description: h-APPDP-Neurons-EGFP replicate 3


title: Calu-3 cells, shBmal1(1)


title: Calu-3 cells, Control(3)


title: 1787_VDJ


title: Low_2

value: Young (20-33 yrs)

value: Female


title: DGRP_55030


title: DGRP_25185


title: 2273_VDJ


title: DGRP_28235


title: 2267_VDJ


title: 2045_RNA

data_processing:
The V(D)J + 5' Gene Expression libraries were sequenced using Illumina HiSeq 4000 targeting the recommended by 10x Genomics read length and depth. The fastq files were generated and demultiplexed either by cellranger mkfastq from 10x Genomics (version 3.0.2) or by BaseCalling in Illumina RTA 1.18.66.3 and post processed via Illumina pipeline 2.19.1. The quality control of sequencing was confirmed by FastQC software (Andrews, 2010). Alignment, filtering, barcode and UMI counting was performed using GRCh38-3.1.0 reference genome and cellranger count from 10x Genomics, version 3.1.0. Multiple gene expression libraries were combined and normalized to the same sequencing depth (post-normalization mean reads per cell 28,950) using cellranger aggr. Two libraries were excluded from normalization step and were added to the analysis using their total reads per cell of 18,600 and 21,00, respectively. For all of the downstream analysis, filtered feature-barcode matrix containing gene expression data for only detected cellular barcodes was used. The single-cell V(D)J sequences and annotations were generated using cellranger vdj and vdj_GRCh38_alts_ensembl-3.1.0 reference genome. On average, 64.3% of reads were mapped to any V(D)J gene and only full length and productive TCRs (79.1% of total mapped) were considered for the analysis.
The downstream analysis was performed using Seurat (version 3.1.0; (Butler et al., 2018; Stuart et al., 2019) package in R language for statistical computing (R Core Team, 2020). Starting from the initial 44,718 cells, we filtered out potential doublets and debris by keeping only the cells with the number of genes between 300 and 5000 and whose UMI count ranged between 500 and 8000. By the same reasoning, we subsetted to the cells with mitochondrial content less than 15% and ribosomal content between 15% and 50%. This reduced the total number of cells by 15%. We then further filtered the remaining 37,658 cells to CD8+ population based on the expression of the known markers. Namely, cells had to have positive expression (> 0) of CD8A and/or CD8B, and to have minimal expression (< 1) of the non-T-cell markers – SLAMF7, PECAM1, KLRC3, KLRC1, TYROBP, CD4, SPI1, VWF, FCER1G, FOXP3, CD19, CD79A, IGKC, FCGR2A, CSF1R, FLT3, CLEC4C, COL1A2, MCAM, MYLK, FAP, PDPN, EPCAM, TP63. This further reduced the number of cells by 39% to a total of 22,963.
Genome_build: GRCh38-3.1.0
Supplementary_files_format_and_content: Comma separated, matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Comma separated, TCR sequencing


title: Monoculture

city: Madison

first: Martha

last: Floy

state: Wi

address: 1415 Engineering Hall

institute: University of Wisconsin-Madison

data_processing:
Single cell sequencing data was processed using the CellRanger Pipeline (4.0.0-released July 7, 2020). Reads were mapped against the human genome (genome assembly version 2020-A) and annotated with the ENCODE gene annotations for the GRCh38 genome assembly (GENCODE v32). GFP and RFP construct sequences, as provided by the Allen Institute for Cell Science, were added to the genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw feature matrix

source_name: Monocultured stem cell derived-cardiac progenitor cells and epicardial cells

extract_protocol:
Cells were lifted for flow cytometry with Accutase, and resuspended in PBS (Ca2+/Mg2+ free) supplemented with 0.5% BSA and 5μM DAPI. Dead cells were gated out based on DAPI staining. For single cell sequencing, two samples were prepared of live cells from CMs and EpiCs monocultured or cocultured.
Two cellular suspension (monoculture and coculture) were loaded into two separate wells (estimated loading of 6,000 cells/well) in a 10X Chromium instrument using the Single Cell 3’ reagent kit according to the manufacturer’s instructions. MiSeq analysis confirmed greater than 90% of droplets contained cells compared to empty droplets, so we continued with paired-end sequencing performed on Illumina NovaSeq6000. Each fraction generated approximately 390 million raw reads which corresponded to approximately 71,000 reads per cell.


title: Coculture

source_name: Cocultured stem cell derived-cardiac progenitor cells and epicardial cells


title: DG_SCIDplusWT_Tcells_engram

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: GFP positive, Hoechst positive, NeuN positive sorted nuclei, from fear trained SCID (severe combined immunodeficiency)  mice (3 mice pooled)

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline. Fastq files from each run were specified using the --fastqs flag and files for each well index were specified using --samples flag.  The cellranger count pipeline, resulted in one count matrix for each of our 8 sample conditions.
Genome_build: mm10
Supplementary_files_format_and_content: raw UMI count matrices for each sample as well as matrices with cell barcodes and gene symbols.

source_name: Dentate Gyrus

growth_protocol: standard 12 h light/dark cycle conditions in rooms equipped with control for temperature and humidity. WT mice, IL-4KO and SCID mice were purchased from the Jackson Laboratory

extract_protocol:
10x Genomics Chromium single nuclei preparation
NGS Illumina Next Seq 500

treatment_protocol: 3-week old SCID mice were repopulated with T cells. 3 weeks later mice were feed with doxycycline food for 1week. Then mice were injected with AAV-cfos-tTA, and AAV-TRE-H2B-GFP in retrosplenial cortex and dentate gyrus. 2 weeks later, mice were taken off Dox for 24hr, and trained with contextual fear conditioning. 24hr after training, mice were euthanized and retrosplenial cortex and DG were dissected out for single cell sequencing experiment.

tag: strain

value: Jax strain 01913 (B6.CB17-Prkdcscid/SzJ)

value: neurons

value: 9 weeks

tag: Sex

value: male

value: SCIDplusWT

tag: activation state

value: engram

value: Dentate Gyrus


title: 1786_VDJ

value: r4s1vVDJ, r9s3vVDJ


title: DGRP_28238

value: Brain

value: Young adults (1-3 days)


title: Supermere_P3

data_processing:
Reads were processed using the TIGER informatics pipeline doi: 10.1080/20013078.2018.1506198
Reads were trimmed to remove adapter sequences with Cutadapt v2.5
Reads were aligned to GRCh37 using Bowtie1 v1.2.3
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw gene count matrix

source_name: Supermere

extract_protocol:
Total small RNA was extracted from pelleted cells or extracellular samples using the miRNeasy Mini Kit (QIAGEN, 217004) according to the manufacturer’s protocol.
Total RNA from each sample was taken into small RNA library preparation protocol using Automated NEXTflex® Small RNA-Seq Kit v3 (Bioo Scientific, PerkinElmer) for Illumina® Libraries on PerkinElmer® Scilone® G3 NGS workstation according to manufacturer’s protocol.

value: DiFi

value: Colorectal cancer cells

tag: compartment

value: extracelluar nanoparticle

tag: molecule subtype

value: small RNA


title: DG_SCIDplusIL4KO_Tcells_nonengram

description: GFP negative, Hoechst positive, NeuN positive sorted nuclei, from fear trained wildtype mice (3 mice pooled)

value: nonengram


title: DGRP_28233


title: DG_SCIDplusIL4KO_Tcells_engram


title: 1932_RNA

tag: raw file name tag

tag: cell barcode appendix

value: ovarian tumor

value: CD8+ T cells


title: DGRP_28202


title: Supermere_P1


title: h-APPDP-Neurons-EGFP-1

description: h-APPDP-Neurons-EGFP replicate 1

value: iPSC-derived neurons

value: EGFP

value: Control


title: DG_Cre.Pos_Engram

growth_protocol: standard 12 h light/dark cycle conditions in rooms equipped with control for temperature and humidity. Gad2cre+::IL-4Rfl/fl and Gad2cre-::IL-4Rfl/fl mice were bred in-house.

treatment_protocol: 8 week old mice were feed with doxycycline food for 1week. Then mice were injected with AAV-cfos-tTA, and AAV-TRE-H2B-GFP in retrosplenial cortex and dentate gyrus. 2 weeks later, mice were taken off Dox for 24hr, and trained with contextual fear conditioning. 24hr after training, mice were euthanized and retrosplenial cortex and dentate gyrus were dissected out for single cell sequencing experiment.

value: Jax strain 028867 (B6J.Cg-Gad2tm2(cre)Zjh/MwarJ)

value: neurons

value: 11 weeks

value: male

value: Engram


title: Exomere_P3

source_name: Exomere


title: 2296_RNA


title: Supermere_P2


title: DGRP_28212

value: Brain


title: 1784_RNA


title: DG_Cre.Neg_Engram

value: Dentate Gyrus


title: DGRP_28198

value: Young adults (1-3 days)


title: Exomere_P2

value: DiFi

value: Colorectal cancer cells


title: 1911_RNA


title: 2312_RNA


title: Exomere_P1

value: extracelluar nanoparticle

value: small RNA


title: DGRP_28194


title: sEV-P_P3

source_name: sEV pellet

value: extraceullar vesicle


title: DG_Cre.Neg_Nonengram

value: Nonengram


title: DG_SCIDplusWT_Tcells_nonengram

value: Jax strain 01913 (B6.CB17-Prkdcscid/SzJ)

value: 9 weeks

value: SCIDplusWT

value: nonengram


title: DG_Cre.Pos_Nonengram

value: Jax strain 028867 (B6J.Cg-Gad2tm2(cre)Zjh/MwarJ)

value: neurons


title: 2251_RNA

value: ovarian tumor

value: CD8+ T cells


title: DGRP_28189

value: Brain


title: WT Engram DG

description: GFP positive, Hoechst positive, NeuN positive sorted nuclei, from fear trained WT  mice (3 mice pooled)

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline with a premrna reference. Fastq files from each run were specified using the --fastqs flag and files for each well index were specified using --samples flag.  The cellranger count pipeline, resulted in one count matrix for each of our 4 sample conditions ( WT engram, SCID engram, WT nonengram, and SCID nonengram)
Genome_build: mm10
Supplementary_files_format_and_content: raw UMI count matrices for each sample as well as matrices with cell barcodes and gene symbols.

growth_protocol: standard 12 h light/dark cycle conditions in rooms equipped with control for temperature and humidity. WT mice and SCID mice were purchased from the Jackson Laboratory.

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

treatment_protocol: 6-7-week old mice were feed with doxycycline food for 1week. Then mice were injected with AAV-cfos-tTA, and AAV-TRE-H2B-GFP in dentate gyrus. 2 weeks later, mice were taken off Dox for 24hr, and trained with contextual fear conditioning. 24hr after training, mice were euthanized and dentate gyrus was dissected out for single cell sequencing experiment.

value: Jax strain 000664 (C57BL6)

value: Male

value: WT

value: Engram

value: Dentate Gyrus


title: 2062_RNA


title: DGRP_28176

value: Young adults (1-3 days)


title: WT Nonengram DG

description: GFP negative, Hoechst positive, NeuN positive sorted nuclei, from fear trained WT  mice (3 mice pooled)


title: 1743_RNA


title: sEV-P_P1

value: DiFi

value: Colorectal cancer cells

value: extraceullar vesicle

value: small RNA


title: Cell_P3

source_name: cell

value: cell


title: DGRP_28177


title: 2246_RNA


title: SCID Nonengram DG

description: GFP negative, Hoechst positive, NeuN positive sorted nuclei, from fear trained SCID (severe combined immunodeficiency)  mice (3 mice pooled)

value: Jax strain 01913 (B6.CB17-Prkdcscid/SzJ)

value: 9 weeks

value: SCID

value: Nonengram


title: DGRP_28141


title: DGRP_28140


title: Cell_P2


title: 2273_RNA

value: ovarian tumor

value: CD8+ T cells


title: 1934_RNA


title: mTEC4D6WT3input

description: mTEC4D6WT1_merged_vs_input_merged_IDR_0.05_MAPQ_10_minus_blacklist.narrowPeak.gz

value: mTEC4D6 cell line

value: WT FOXN1-flag

tag: method

value: ChIP-seq anti-flag

tag: chip antibody

value: M2 anti-FLAG antibody (Sigma)


title: sEV-P_P2


title: mTEC4D6WT3

value: ChIP-seq input

value: none (input)


title: CBSi+NaHS+HS rep1

city: Nanjing

first: jia long

last: tian

address: 1 Weigang

country: China

institute: Nanjing Agricultural University

data_processing:
Illumina Casava software used for basecalling.
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: PRJNA71455
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Ganoderma lucidum

source_name: G. lucidum

extract_protocol:
Total RNA was extracted using the Total RNA Extractor（Trizol）kit (B511311, Sangon, China) and treated with RNase-free DNase I to remove genomic DNA contamination. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ganoderma lucidum G.260125-1

value: cultured for 7 days

value: CBS-silenced


title: CBSi+NaHS+HS rep2


title: DGRP_28138

value: Brain

value: Young adults (1-3 days)


title: 2209_RNA


title: 2060_RNA


title: Cell_P1

value: DiFi

value: Colorectal cancer cells

value: cell

value: small RNA


title: DGRP_28128


title: DGRP_25201


title: CBSi+HS rep3


title: SCID Engram DG

value: Jax strain 01913 (B6.CB17-Prkdcscid/SzJ)

value: neurons

value: 9 weeks

value: Male

value: SCID

value: Engram

value: Dentate Gyrus


title: mTEC4D6WT2input

value: mTEC4D6 cell line

value: WT FOXN1-flag

value: ChIP-seq anti-flag

value: M2 anti-FLAG antibody (Sigma)


title: 2267_RNA

value: ovarian tumor

value: CD8+ T cells


title: CBSi+HS rep2

value: Ganoderma lucidum G.260125-1

value: cultured for 7 days

value: CBS-silenced


title: DGRP_25198

value: Brain

value: Young adults (1-3 days)


title: mTEC4D6WT2

value: ChIP-seq input

value: none (input)


title: 1787_RNA


title: CBSi+NaHS+HS rep3


title: CBSi+HS rep1


title: mTEC4D6WT1input


title: DGRP_25189


title: DGRP_25186


title: mTEC4D6WT1


title: DGRP_28265


title: mTEC4D6mut2IP

description: mTEC4D6mut1IP_merged_vs_input_merged_IDR_0.05_MAPQ_10_minus_blacklist.narrowPeak.gz

value: d550 FOXN1-flag


title: mTEC4D6mut3input


title: CBSi rep3


title: CBSi rep2


title: 1786_RNA

value: 4s1, r9s3GEX


title: IPF_5

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: 2 µg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 8.2.5

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: AT-II cells_IPF

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2 µg amplified cDNA was Cy3-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

extract_protocol: Qiagen RNeasy Mini Kit

tag: tissue source

value: fibrotic (IPF) lungs

value: AT-II cells


title: DGRP_25191

tag: tissue


title: mTEC4D6mut3IP

value: mTEC4D6 cell line


title: Sicontrol+NaHS+HS rep2

value: Sicontrol


title: DGRP_28262


title: DGRP_25208


title: Sicontrol+HS rep3


title: IPF_3

tag: cell type


title: DGRP_28260

tag: genotype


title: mTEC4D6mut1IP

tag: age

value: ChIP-seq anti-flag


title: CBSi rep1


title: IPF_6


title: IPF_1


title: mTEC4D6mut2input


title: Sicontrol+NaHS+HS rep1


title: Sicontrol+NaHS+HS rep3


title: IPF_4


title: Sicontrol+HS rep2


title: A549_hRSV_48hpi_rep2

city: St. Louis

first: Jacqueline

last: Payton

address: 660 S. Euclid Ave

institute: Washington University School of Medicine

data_processing:
Sequence reads were aligned to the Human GRCh38 primary assembly and annotated with the Ensembl release 76 (GRCh38) transcriptome.
Genome_build: Human GRCh38 primary assembly and annotated with the Ensembl release 76 (GRCh38) transcriptome

source_name: A549 cell line

extract_protocol:
RNA was isolated from 1-2x106 cells stored in TRIzol reagent following manufacturer's instruction.
cDNA from total RNA was synthesized with a Clontech SMARTer low input RNA kit. An Illumina TruSeq preparation kit was used for library constructon per manufacturer's instructions.

value: lung cancer cell line

tag: treatment

value: hRSV A2 strain infection

tag: timepoint

value: 48 hours post-infection


title: IPF_2


title: A549_hRSV_24hpi_rep2

value: 24 hours post-infection


title: mTEC4D6mut1input


title: Sicontrol rep2

value: Ganoderma lucidum G.260125-1

value: cultured for 7 days


title: Donor_6

source_name: AT-II cells_donor

value: donor lungs


title: A549_hRSV_48hpi_rep1


title: Donor_8


title: Sicontrol rep1


title: Donor_5


title: Sicontrol+HS rep1


title: mTEC4D6FOXN1WTD3RNA

value: WT FOXN1/d550 FOXN1

value: RNA-seq


title: mTEC4D6FOXN1Empty2RNA

value: Empty


title: Sicontrol rep3


title: mTEC4D6FOXN1Empty3RNA


title: mTEC4D6FOXN1WTD2RNA


title: mTEC4D6FOXN1Empty1RNA


title: mTEC4D6FOXN1WTD1RNA


title: A549_hRSV_24hpi_rep1


title: A549_EV_anti-Mediator_ChIP

data_processing:
Reads were aligned to hg19 with bowtie2 (v2.2.5) with default settings (Langmead and Salzberg, 2012).
Peaks were called with HOMER (version v4.10.1 ) with the settings tbp = 1 and findPeaks cmd = findPeaks ns1_ha_align_tbp1/ -style factor -o auto -i ns1_input_align_tbp1/ (Heinz et al., 2010).
Genome_build: Human GRCh37/hg19

extract_protocol:
Cells were cross-linked sequentially with 1.25mM EGS (ethylene glycol-bis(succinic acid N-hydroxysuccinimide ester)) and 1% formaldehyde in PBS. Sonication and ChIP were performed as described previously (Koues et al., Immunity, 2015).
At least 10 ng of ChIP, or input DNA was used for indexed library preparation. Samples were indexed and pooled (9-11 per lane) and subjected to 50 bp single-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA, USA) by the Genome Technology Access Center at Washington University in St. Louis.

tag: cell line

value: Empty vector transfection

tag: time

value: 24 hours post-transfection

value: anti-Mediator (TRAP1/CRSP220, A300-739A, Bethyl Laboratories


title: A549_mock_rep2

value: mock infection


title: A549_EV_anti-HA_ChIP

value: anti-HA, ab9110, Abcam


title: WT+NaHS+HS rep3

tag: strain

value: WT


title: WT+NaHS+HS rep1


title: WT+NaHS+HS rep2


title: A549_EV_input


title: Donor_2

value: AT-II cells


title: mTEC4D6FOXN1D2RNA

data_processing:
RNA-seq: reads were aligned against the Ensembl transcriptome and genome (GRCh38.EBVB95-8wt.ERCC) using STAR (version 2.5.3a). The allocation of reads to protein coding gene meta-features was done using HTSeq.
ChIP-seq: Contaminating adaptor sequences were removed from fastq sequences using Trimmomatic (version 0.32). Reads were aligned against the human genome (GRCh38.EBVB95-8wt.ERCC) using STAR (version 2.5.3a). Peaks were called on deduplicated aligned sequences (paired ChIP and input samples) using MACS2 (version 2.0.10) with a relaxed P value setting of 0.1. Peaks from replicates were then pooled and analyzed using irreproducible discovery rate analysis (IDR < 0.05). Peaks were filtered against the ENCODE blacklist regions.
10X GEX: Single cell libraries were processed using Cellranger (version 3.1.0). Cells were excluded from analysis if the total UMI count was <1,000 or >32,000, the number of detectable features was <562 or >7,943 or the proportion of UMIs mapping to mitochondrial genes was >10%.
Genome_build: Homo sapiens: GRCh38.EBVB95-8wt.ERCC. Mus musculus: mm10
Supplementary_files_format_and_content: Processed data includes count matrices for RNA-seq/10X GEX, meta-data for 10X GEX and IDR<0.05 peaks for ChIP-seq data.

value: mTEC4D6 cell line

value: d550 FOXN1


title: Donor_3


title: Donor_1


title: HMA-1

city: New York

first: Bi-Sen

last: Ding

state: NY

address: York Avenue

institute: Weill Cornell

description: one sample form pig liver

data_processing:
The sequences from scRNA-Seq of pig and minipig liver NPCs were aligned to pig (Sus scrofa) transcriptome (Sscrofa11.1) using Hisat2 v2.0.5
Low-quality cells expressing less than 200 genes as well as genes expressed in less than 3 cells were filtered. Mitochondrial gene content percentage thresholds were set to filter pig liver NPCs.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: matrix files

organism: Sus scrofa

source_name: Biopsy operation liver

extract_protocol:
Liver tissues  minipig were washed twice with cold PBS, minced, and incubated in a digestive mixture (1 mg/ml collagenase I and 1mg/ml dispase II in PBS) on an orbital shaker at 37 °C, for 15 min. After 15 min, liver tissues were suspended to ensure complete dissociation. Digested liver sample was homogenous with minimal chunks. Digested tissues were filtered through cell strainer multiple times, and cells were collected at 400 g for 5 min. After red blood cells were removed with RBC lysis buffer ( Solarbio) and washed once, hepatocytes and NPCs were separated by an additional centrifugation step at 50 g for 5 min at 4 °C.
Single cells were processed in the following steps: GEM generation & Barcoding, GEM-RT cleanup & cDNA amplification, and library construction, and finally were sequenced on an Illumina Nova-seq 6000 (Illumina).

value: Non-Parenchymal Cells (NPC)

value: MGCD&AZA treatment after  fibrosis


title: WT+HS rep2

value: Ganoderma lucidum G.260125-1


title: mTEC4D6FOXN1D3RNA

extract_protocol:
RNA-seq: 4D6 thymic epithelial cells were transfected with plasmids encoding 1) wild type-FOXN1 alone 2) Δ550-FOXN1 mutant alone, 3) wild type and Δ550 οr 4) empty vector only, along with a GFP-expressing vector in a 4:1 ratio to facilitate sorting of positively transfected cells. Three biological replicates were prepared for each sample. A total of 75,000 GFP-positive cells were FACS sorted and RNA was extracted using the Rneasy Plus Micro kit (Qiagen). ChIP-seq: 4D6 cells were transfected with either wild type or Δ550 mutant FOXN1 construct tagged with a FLAG and three biological replicates of each transfected cell population were collected for ChIP-Seq analyses. The chromatin immunoprecipitation was performed using the iDeal ChIP-seq kit for Transcription Factors (Diagenode) as per manufacturer’s recommendations. Briefly, 2.5 x106 transfected cells were collected and subjected to protein-DNA crosslinking for 20 min. Cells were then lysed and chromatin was sheared for 8 sonication cycles (30’’ ON/30’’ OFF). Sheared chromatin was immunoprecipitated using M2 anti-FLAG antibody (Sigma) while parallel input samples from non-immunoprecipitated chromatin were prepared for each sample. 10X GEX: EpCAM+ CD45- live TEC were loaded onto the 10X Chromium system.
RNA-seq: RNA was processed using the RNA-Seq Poly A method and indexed using Nextera indexes. ChIP-seq: DNA libraries for all 12 samples were prepared using the MicroPlex Library Preparation Kit (12 indexes; Diagenode) following the manufacturer’s recommendations. 10X GEX: libraries were prepared as per manufacturer's protocol for 3' gene expression libraries.


title: WT rep3

value: cultured for 7 days


title: Donor_7

value: donor lungs


title: Donor_4


title: A549_hRSV_mockinfected_input

value: lung cancer cell line

value: mock infected

value: 48 hours post-mock-infection


title: A549_mock_rep1


title: BEAS2B KRAS/p53

city: Lexington

first: Fan

last: Chen

state: Kentucky

address: 1095 V.A. Drive, HSRB 461

department: Toxicology and Cancer Biology

institute: University of Kentucky

data_processing:
Sequencing and base-calling were performed by BGI (Beijing Genomics Institute).
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads were mapped to Ensembl GRCh38 transcripts annotation (release 98), using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Genome_build: GRCh38 release 98
Supplementary_files_format_and_content: tab-delimited text files including TPM, FPKM and expected_count for each gene

source_name: Human normal lung epithelial cells

growth_protocol: BEAS-2B were propagated in RPMI-1640 media containing 1x penicillin/streptomycin, 4mM L-glutamine, 10% fetal bovine serum in 10 cm gelatin-coated petri-dishes.

extract_protocol:
RNA from treated cell lines was extracted using Absolutely RNA Mini-prep kits (Agilent).
RNA libraries were prepared for sequencing using BGI protocols.

treatment_protocol: KRAS G12V and p53 R175H lentiviruses and PIK3CA E545K retroviruses were used to establish the BEAS2B stable cell lines. Cell lines were infected with viral-containing supernatants for a period of 4-8 hours, and then the infected cultures were selected by puromycin (PIK3CA vectors), GFP-sorting (KRASG12V) or blasticidin (p53R175H).

tag: genotyping

value: p53 R175H+KRAS G12V

tag: tissue origin

value: 2D cell line


title: WT rep2


title: WT rep1


title: BEAS2B


title: mTEC4D6FOXN1WT1RNA

institute: University of Oxford

value: WT FOXN1

value: RNA-seq


title: A549_hRSV_mockinfected_anti-Mediator_ChIP

value: anti-Mediator (TRAP1/CRSP220, A300-739A, Bethyl Laboratories


title: WT+HS rep1

value: WT


title: A549_HA-NS1_anti-HA_ChIP

value: HA-NS1 transfection

value: 24 hours post-transfection

value: anti-HA, ab9110, Abcam


title: mTEC4D6FOXN1WT3RNA

value: mTEC4D6 cell line


title: mTEC4D6FOXN1D1RNA

value: d550 FOXN1


title: WT+HS rep3

value: Ganoderma lucidum G.260125-1


title: A549_hRSV_48hpi_input

value: hRSV A2 strain infection

value: 48 hours post-infection


title: SKNBE2-sg2-3

status: Public on Oct 11 2021

city: Wuhan

first: Rongfu

last: Tu

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

institute: Wuhan University

data_processing:
The main steps of applying Seqtk for filtering are as follows:1、Remove the sequence of joints contained in reads；2、Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01，among,Q=-10logerror_ratio；3、Remove reads with length less than 25；4、Remove ribosome RNA reads of the species。
Spliced mapping algorithm of Hisat2 (version:2.0.4) was applied to Genome mapping of preprocessed reads，Take default parameters. The alignment result generated by Mapping is BAM file
Application Stringtie (version: 1.3.0)in Hisat2 than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
EdgeR was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value.Meanwhile, we calculate Fold-change according to FPKM.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: USP29_gene_expression.txt (FPKMs, counts)

growth_protocol: Ramos and SK-N-BE2 cells were grown in complete RPMI-1640 (Hyclone) supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% penicillin/ streptomycin (Hyclone)

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with control sgRNA and USP29 sgRNA respectively, and selected with puromycin for 48 hours.

value: tumor cell

tag: infection

value: USP29 sgRNA


title: A549_hRSV_48hpi_anti-Mediator_ChIP

value: lung cancer cell line


title: BEAS2B PIK3CA/p53

value: p53 R175H+PIK3CA E545K


title: eBCs

data_processing:
FASTQs were processed using the 10x genomics cellranger pipeline (v2). Individual matrices were processed in R using Seurat (v2). Cells were fewer than 250 or greater than 75000 UMIl, or greater than 20% of UMIs derived from mitochondria were excluded. UMIs were log (+1) normalized, projected into 2 dimensions using PCA followed by tSNE and clustered using Seurat's graph based clustering on the top 20 principal components. Cells were annotated by manual inspection of marker genes. Pseudotemporal ordering and RNA velocities were examined using Monocle and Veloctyo respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix

source_name: human iPSCs

extract_protocol:
INS-eGFP positive cells were isolated by flow cytometry and single cells were captured on the 10x genomics chromium controller
10x Genomics 3' scRNA-seq v2 kit

value: hPSC-eBCs


title: A549_HA-NS1_anti-Mediator_ChIP


title: seBCs

data_processing:
FASTQs were processed using the 10x genomics cellranger pipeline (v2). Individual matrices processed in R using Seurat (v2). Cells were fewer than 250 or greater than 75000 UMIl, or greater than 20% of UMIs derived from mitochondria were excluded. UMIs were log (+1) normalized, projected into 2 dimensions using PCA followed by tSNE and clustered using Seurat's graph based clustering on the top 20 principal components. Cells were annotated by manual inspection of marker genes. Pseudotemporal ordering and RNA velocities were examined using Monocle and Veloctyo respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix

value: hPSC-seBCs


title: mTEC4D6FOXN1WT2RNA

value: WT FOXN1

value: RNA-seq


title: Ctrl

description: one sample form pig liver

value: Non-Parenchymal Cells (NPC)

value: Oil


title: SKNBE2-sg2-1


title: HC-1

description: one sample form pig liver

value: Oil with Ccl4


title: SKNBE2-NC-2

value: control sgRNA


title: SKNBE2-NC-3


title: Ramos-sg2-1

source_name: Ramos

value: Ramos


title: Ramos-sg2-2


title: BEAS2B p53

value: 2D cell line


title: ONT_cDNA_WT2

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

institute: Ludwig Maximilian University of Munich

description: ONT_cDNA_WT_flair.gtf and ONT_cDNA_WT_stringTie.gtf

data_processing:
ONT reads were aligned to Ensembl mouse genome assembly GRCm38 using minimap2 v2.17- r941. Following recommendations at https://github.com/lh3/minimap2, we used option -axsplice to allow spliced alignments and provided splice junctions extracted from the corresponding Ensembl release 95 transcriptome annotation with parameter --junc-bed. In the alignment of native RNA reads, we additionally used options -k14 -uf as recommended.
We used FLAIR v1.5.1 to identify and StringTie2 to assemble transcripts from ONT reads. We ran FLAIR with default settings on pooled reads from both WT and KO replicates and extracted condition-specific transcripts that had an estimated count of at least 1 in at least one of the 2 replicates per condition.
GRCm38/mm10
gtf files contain all identified transcripts per sample

source_name: Neural progenitor cells

growth_protocol: Mouse NPCs were isolated from Mettl14 WT and cKO mouse embryonic cortices and cultured in Neurobasal medium (GIBCO BRL) containing 20 ng/ml FGF2, 20 ng/ml EGF, 5 mg/ml heparin, 2% B27 (v/v, GIBCO BRL), Glutamax (Invitrogen), Penicillin/Streptomycin (Invitrogen) on culture dishes precoated with Matrigel matrix (2%, Corning).

extract_protocol:
Total RNA was extracted using TRIzol from cell pellets following the manufacturer's protocol.
For native RNA sequencing libraries were prepared by the standard kit (SQK-RNA002, Oxford Nanopore Technologies). The libraries were loaded onto R9.4.1 flowcells (FLO-MIN106D, Oxford Nanopore Technologies) and sequenced using four MinION Mk1b devices separately in parallel (MinKNOW 4.1.2, Oxford Nanopore Technologies). For direct cDNA sequencing, Each 1.5 μg of purified total RNA with 0.1 μl of RCS from direct RNA sequencing kit (SQK-RNA002) and 0.1 ng of the SIRV set 3 (Lexogen) control was prepared as a sequencing library following manufacturers instruction (SQK-DCS109, Oxford Nanopore Technologies).
ONT long-read RNA sequencing

value: Wild type

value: Neural progenitor cells

tag: sequencing technology

value: Oxford Nanopore Technology direct cDNA long-read sequencing


title: A549_HA-NS1_input

value: HA-NS1 transfection

value: 24 hours post-transfection


title: Ramos-NC-1

value: tumor cell


title: Ramos-NC-2


title: Ramos-sg2-3

value: USP29 sgRNA


title: SKNBE2-sg2-2


title: SKNBE2-NC-1


title: ONT_cDNA_KO2

description: ONT_cDNA_KO_flair.gtf and ONT_cDNA_KO_stringTie.gtf

value: Mettl14 knock out


title: ONT_cDNA_KO1


title: ONT_native_WT2

description: ONT_native_WT_flair.gtf and ONT_native_WT_stringTie.gtf

value: Oxford Nanopore Technology Native RNA long-read sequencing


title: Ramos-NC-3


title: EK_H3K36me3_ChIPSeq

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
H3K36me3 ChIP-seq, B6.Prdm9EK/EK; mutation is glu360lys, a severe catalytic hypomorph
EKHom_H3K36me3_ChIP_RPM.bedgraph
H3K4me3_H3K36me3Peaks_EKHom.bed

data_processing:
Single-end ChIP-Seq reads were trimmed with Trimmomatic and aligned to the mm10 genome assembly using BWA v0.7.9a
ChIP-Seq reads were filtered to remove duplicates and to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph, bed

source_name: spermatocytes

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. Cross-links were reversed and chromatin eluted by incubation at 68 degrees Celsius. After high-speed spin soluble chromatin was removed and used for ChIP with anti-H3K4me3.
Libraries were prepared for sequencing using standard Illumina protocols.

value: spermatocytes

value: 14 days post-partum


title: ONT_native_WT1


title: EP_H3K4me3_ChIPSeq Rep 2 (re-analysis)

description:
H3K4me3 ChIP-seq, B6.Prdm9EP/EP; mutation is glu360pro, a severe catalytic hypomorph
H3K4me3Peaks_EPHom.bed
H3K4me3_H3K36me3Peaks_EPHom.bed


title: EK_H3K4me3_ChIPSeq Rep 2

description:
H3K4me3 ChIP-seq, B6.Prdm9EK/EK; mutation is glu360lys, a severe catalytic hypomorph
EKHom_H3K4me3_ChIP_Merge_RPM.bedgraph
H3K4me3Peaks_EKHom.bed


title: ONT_cDNA_WT1


title: EP_H3K4me3_ChIPSeq Rep 1 (re-analysis)


title: ONT_native_KO1

description: ONT_native_KO_flair.gtf and ONT_native_KO_stringTie.gtf


title: ONT_native_KO2


title: NPC_rep1

data_processing:
kallisto was used for transcript quantification
GRCm38/mm10
tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA fraction was isolated from cultured NPC samples with Trizol reagent (Thermo Fisher) followed by total RNA extraction using the RNA Clean and Concentrator-25 (Zymo Research). mRNA was isolated from total RNA with Dynabeads mRNA purification kit (Thermo Fisher).
Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina and sequenced in Illumina HiSeq 2500 yielding approximately 30 million 50 bp single-end reads.
Illumina short-read RNA-seq

value: Illumina short read sequencing


title: NPC_rep3


title: KO3

data_processing:
Reads were aligned to the mouse genome (build GRCm38/mm10) using STAR aligner version 2.5.4b
StringTie-ls was used to assemble transcripts
kallisto-ls was used for transcript quantification
Isoform switching analysis was performed using the R package IsoformSwitchAnalyzeR version 1.4.0
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA fraction was isolated from cultured NPC samples with Trizol reagent (Thermo Fisher) followed by total RNA extraction using the RNA Clean and Concentrator-25 (Zymo Research). mRNA was isolated from total RNA with Dynabeads mRNA purification kit (Thermo Fisher).
For samples WT1 through WT4 and KO1 through KO4, RNA sequencing libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina, and each band of each sample used a unique index PCR primer (NEBNext Multiplex Oligos for Illumina). Libraries were multiplexed 1:1 for sequencing in the NextSeq 500 (Illumina) yielding approximately 100 million 2×75-bp paired-end reads per sample. For sample WT_control, libraries was prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina and sequenced in Illumina HiSeq 2500 yielding approximately 30 million 50 bp single-end reads.

tag: genotype/variation

value: neural progenitor cells (NPCs)


title: KO4


title: KO2


title: WT4


title: EP_H3K36me3_ChIPSeq

description:
H3K36me3 ChIP-seq, B6.Prdm9EP/EP; mutation is glu360pro, a severe catalytic hypomorph
EPHom_H3K36me3_ChIP_RPM.bedgraph
H3K4me3_H3K36me3Peaks_EPHom.bed


title: KO1


title: WT3


title: Trophoblast Giant Cells_3

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description:
TGC-3
mRNA
processed data file: all_FPKM.txt

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat-2 v2.1.1 with parameters -g 2.
HTSeq-count was used to count the aligned reads on a per gene basis (Version: HTSeq-0.11.2). The count data were normalized, fragments per kilobase of transcript per million of sequencing reads (FPKM) values were calculated using the DESeq2 package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all_FPKM.txt: Tab-delimited text file includes FPKM values.

source_name: TGCs

growth_protocol: TGCs were obtained following 3 days of culture of E4.5 laser dissected mural trophectoderm in IVC2 medium.

extract_protocol:
Lysis buffer from NEB Next Single Cell/Low Input cDNA Synthesis and Amplification Module (NEB) was directly added to the wells and the samples were frozen to lyse the cells.
3ul of the lysate was used to prepare library using NEB Next Single Cell/Low Input cDNA Synthesis and Amplification Module (NEB).

treatment_protocol: No specific treatment.

value: Trophoblast Giant Cells

value: Wild Type


title: E4.75 mural Trophectoderm_1

description:
E4-75_TE-1
mRNA
processed data file: all_FPKM.txt

source_name: E4.75 Embryo

growth_protocol: E4.75 embryos were laser dissected for collecting the mural trophectoderm.

extract_protocol:
Laser dissected samples were directly lysed in the lysis buffer provided by the NEB Next Single Cell/Low Input cDNA Synthesis and Amplification Module (NEB).
3ul of the lysate was used to prepare library using NEB Next Single Cell/Low Input cDNA Synthesis and Amplification Module (NEB).

value: E4.75 mural Trophectoderm


title: E4.75 mural Trophectoderm_2

description:
E4-75_TE-2
mRNA
processed data file: all_FPKM.txt


title: E4.5 mural Trophectoderm_3

description:
E4-5_TE-3
mRNA
processed data file: all_FPKM.txt

source_name: E4.5 Embryo

growth_protocol: E4.5 embryos were laser dissected for collecting the mural trophectoderm.

value: E4.5 mural Trophectoderm


title: E4.5 mural Trophectoderm_1

description:
E4-5_TE-1
mRNA
processed data file: all_FPKM.txt


title: E4.5 mural Trophectoderm_2

description:
E4-5_TE-2
mRNA
processed data file: all_FPKM.txt


title: bEnd5 Endothelial cells_3

description:
bEnd5-3
mRNA
processed data file: all_FPKM.txt

source_name: bEnd5 cell line

growth_protocol: bEnd5 cells were cultured in IVC2 medium for 3 days.

extract_protocol:
The cells were trypsinised and RNA was isolated using RNeasy Mini Kit (Qiagen).
10ng of RNA was used to prepare library using NEB Next Single Cell/Low Input cDNA Synthesis and Amplification Module (NEB).

value: bEnd5 Endothelial cells

value: bEnd5 cells transfected with tdTomato

tag: passage


title: Endothelial cells E5.5_Decidua_1

description:
E5-5_EC-1
mRNA
processed data file: all_FPKM.txt

source_name: E5.5 Decidua

growth_protocol: Primary cells isolated from decidua.

extract_protocol:
Cell lysate of the endometrial tissue was labelled for CD31 and CD45 and FACS sorted for CD31+ and CD45- cells. RNA was isolated from the FACS sorted cells using RNeasy Mini Kit (Qiagen).
10ng of RNA was used to prepare library using NEB Next Single Cell/Low Input cDNA Synthesis and Amplification Module (NEB).

value: Endothelial cells E5.5 Decidua


title: Endothelial cells E5.5_Decidua_3

description:
E5-5_EC-3
mRNA
processed data file: all_FPKM.txt


title: bEnd5 Endothelial cells_2

description:
bEnd5-2
mRNA
processed data file: all_FPKM.txt


title: EK_H3K4me3_ChIPSeq Rep 1 (re-analysis)

tag: chip antibody


title: Trophoblast Giant Cells_2

description:
TGC-2
mRNA
processed data file: all_FPKM.txt


title: WT1

value: Wild type


title: WT2


title: Trophoblast Giant Cells_1

description:
TGC-1
mRNA
processed data file: all_FPKM.txt


title: bEnd5 Endothelial cells_1

description:
bEnd5-1
mRNA
processed data file: all_FPKM.txt


title: E4.75 mural Trophectoderm_3

description:
E4-75_TE-3
mRNA
processed data file: all_FPKM.txt


title: Neural Progenitor Cells Fe-E - RNA_seq_rep3

city: Cambridge

first: Hiruy

last: Meharena

state: MA

address: 43 Vassar St

department: The Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

data_processing:
Hi-C - fastq.gz.gz paired-end reads were processed through Juicer as previously described (Rao et al., 2014). In Brief, paired-end read pairs were aligned separately to the human genome (hg19) using BWA, then, duplicates/invalid pairs were removed, and the remaining reads were filtered based on mapping quality score of 30 (Li and Durbin, 2009). Interaction matrices were generated at resolutions of 2.5Mb, 1Mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, and 5kb and normalized interactions matrices were produced at all resolutions using Knight and Ruiz.
ChIP-seq - fastq.gz.gz reads for each replicate were aligned using Bowtie 2.0  (bowtie2 --very-sensitive -k 30) to hg19 (human) and dm6 (drosophila) (Langmead and Salzberg, 2012).  Samtools was used to sort (samtools sort), remove duplicates (samtools markdup), remove mitochondrial reads (samtools view) and index BAM files (samtools index) (Li et al., 2009). Bigwigs were generated from BAM files adjusted to the scale-factor for each sample using the percentage of mapped reads from the drosophila genome (dm6) to total reads over input utilizing deepTools (3.5.0) bamCoverage (Egan et al., 2016; Ramirez et al., 2016). Peak regions were identified using homer (4.11), with the function findPeaks utilizing the reads generated from input samples as background.
ATAC-seq - fastq.gz.gz paired-end reads for each replicate were aligned using Bowtie 2.0  (bowtie2 --very-sensitive -k 30) to hg19 (Langmead and Salzberg, 2012).  Samtools was used to sort (samtools sort), remove duplicates (samtools markdup), remove mitochondrial reads (samtools view), index BAM files (samtools index), and BAM files were shifted by +4bp and -5bp using an in-house algorithm (Li et al., 2009). Accessible chromatin peak calling was performed using Model-based Analysis of ChIP-Seq (macs2 callpeak -f BAMPE -g hs -q 0.05) (Zhang et al., 2008). Differential peaks analysis between the isogenic pairs was performed using Diffbind v1.16.3 (Ross-Innes et al., 2012).
RNA-seq - fastq.gz.gz paired- and single-end reads were aligned using STAR (v.2.6.1a) to GRCh37 reference genome (GENCODE 19) (Dobin et al., 2013). Transcripts were quantified using HTSeq, data was normalized utilizing RUV-seq and differential gene-expression analysis was performed through DESeq2 (Anders et al., 2015; Love et al., 2014; Risso et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: hic files were generated utilizing juicer
Supplementary_files_format_and_content: bigwig files were generated utilizing deepTools

source_name: Neural Progenitor Cells

growth_protocol: iPSC - Fibroblasts of the derived from individuals with Down syndrome and euploid controls were utilized to generate iPSCs using Sendai virus to overexpress OCT4, SOX2, KLF4, and c-MYC, utilizing the CytoTune-iPS Sendai Reprogramming kit (Thermofisher scientific, A16518) as previously described (Raja et al., 2016). iPSCs were cultured on irradiated mouse embryonic fibroblasts (MEFs, Thermo Fisher Scientific, A34181) in DMEM/F12 media supplemented with knockout serum replacement (KSR, 20% v/v), MEM non-Essential amino acid solution (Sigma-Aldrich M7145), Glutamax (Thermo Fisher Scientific 35050-079), 8 ng/μl recombinant human FGF-basic (FGF2, PeproTech, 100-18B) and 71.5µM 2-mercaptoethanol (Sigma-Aldrich M6250). The quality of cells was monitored daily and differentiated cells were mechanically removed under a light microscope in a biosafety hood. iPSCs were cultured to 80% confluence and non-differentiated colonies were transferred to a feeder-free system and grown on Matrigel hESC-Qualified Matrix coated plates (VWR, 354277) using mTeSR1 medium (Stemcell technologies, 85850). iPSCs for RNA-seq, ATAC-seq, and Hi-C grown under feeder-free conditions.    NPC - iPSCs were grown to 80% confluence on feeder-free conditions in mTeSR1 medium. iPSCs were then dissociated into single cell suspension using ReLeSR™ (Stemcell Technology, 05872) following the manufacturers guidelines. 3 million cells were then transferred into a single well of AggreWell™800 (Stemcell Technology, 34811) to form 300 embryoid bodies of 10,000 iPSCs each in NPC-differentiation medium [1:1 of DMEM/F12 Glutamax and Neurobasal (Life Technologies 10565-042 and Thermo Fisher Scientific 21103049), N-2 Supplement (Invitrogen,17502-048), B-27 Serum-Free Supplement (Gibco, 12587010), 2.5µg/l insulin (Thermo Fisher Scientific, 41400045), Glutamax (Thermo Fisher Scientific, 35050-079), MEM non-Essential amino acid solution (Sigma-Aldrich, M7145), 71.5µM 2-mercaptoethanol, Pen/strep (Gemini Bio-Products, 400-109), Dorsomorphin (PeproTech, 8666430) and SB431542 (Tocris,1614)]. Half NPC-induction medium replacement was performed daily for 5 days and on day 6 EBs were washed and transferred onto Matrigel coated plates. Complete NPC-induction medium replacement was performed daily for 7 days, and on day 12 STEMdiff™ Neural Rosette Selection Reagent (Stemcell technologies, 05832) was utilized to isolate NPC-rosettes and re-plated on onto fresh Matrigel coated plates in NPC-induction medium. Complete NPC-induction medium replacement was performed for 7 days and on day 20 NPCs were transferred onto fresh Matrigel coated plates in NPC-expansion medium [1:1 of DMEM/F12 Glutamax and Neurobasal (Life Technologies 10565-042 and Thermo Fisher Scientific 21103049), N-2 Supplement (Invitrogen,17502-048), B-27 Serum-Free Supplement (Gibco, 12587010), 2.5µg/l insulin (Thermo Fisher Scientific, 41400045), Glutamax (Thermo Fisher Scientific, 35050-079), MEM non-Essential amino acid solution (Sigma-Aldrich, M7145), 71.5µM 2-mercaptoethanol, Pen/strep (Gemini Bio-Products, 400-109) and 8 ng/μl recombinant human FGF-basic (FGF2, PeproTech, 100-18B)]. NPCs were passaged ones a week and NPCs for RNA-seq, ATAC-seq, ChIP-seq and Hi-C were used between passage 3-5.

extract_protocol:
RNA was extracted utilizing RNeasy Plus Mini Kit (Qiagen).
In situ Hi-C - Hi-C libraries were generated from 2 million iPSCs and NPCs using the Arima Hi-C kit (Arima Genomics, San Diego) following to the manufacturer’s instructions without any modifications. Briefly, the Arima Hi-C kit consists of 6 steps: (i) cells were crosslinked with 1% formaldehyde, (ii) DNA was digested using the Arima restriction enzyme cocktail within intact permeabilized nuclei, (iii) ends were filled and biotinylated, (iv) blunt ends were ligated, (v) ligated fragments were purified, sheared and a biotin pull down was performed using streptavidin, and (vi) adapters were ligated, barcoded and amplified using the Kappa Hyperprep Kit (Roche, KK8502).    ChIP-seq - Library preparation consists of 8 steps: (i) cells were crosslinked with 1% formaldehyde, (ii) chromatin was sheared (Covaris E220 Focused-ultrasonicator) after lysing cells, (iii) digested chromatin was incubated with 2ug of LMNB1 antibody (Abcam, ab8982), samples were also incubated without any antibody for input and Spike-in chromatin was incubated with Spike-in antibody (Active motif). (iv) same amount of Spike-in chromatin/antibody was added to each sample. (V) antibody-bound DNA/protein complexes and input samples were captured and washed using Protein G magnetic beads. (vi) cross-links were reversed and protein was digested using proteinase K. (vii) DNA was purified utilizing QIAquick PCR Purification Kit (Qiagen, 28104) (viii) libraries were prepared utilizing the Kappa Hyperprep Kit (Roche, KK8502).    ATAC-seq - Libraries were prepared as previously described (Buenrostro et al., 2015).    RNA-seq - 150 ng of RNA was used to prepare libraries using the Kapa mRNA hyperprep kit for standard RNA libraries (Roche, KK8540) on a TecanEvo 150s (Tecan).

treatment_protocol: NPCs were treated daily for 5 days with vehicle (DMSO) or a combination of 400nM of dasatinib and 15uM of quercetin

value: Neural Progenitor Cells

value: Control

value: untreated

value: H9 WA09


title: Neural Progenitor Cells Iso-E - RNA_seq_DQ_rep1

value: Dasatinib+Quercetin


title: Neural Progenitor Cells Iso-T - RNA_seq_DMSO_rep3

value: Down syndrome

value: DMSO


title: Neural Progenitor Cells Iso-T - RNA_seq_DQ_rep1


title: Neural Progenitor Cells Iso-E - RNA_seq_DQ_rep3


title: Neural Progenitor Cells Fe-E - RNA_seq_rep2


title: Neural Progenitor Cells Iso-E - RNA_seq_DMSO_rep3


title: 6-48 control_24556

city: Taipei

first: Ting-Shuan

address: 5F ,No 1, Sec 1, Jen-Ai Rd

country: Taiwan

institute: ntu

description: mRNA expression after 0 ng/mL Aflatoxin B1 treated embryos from 6-48 hpf

hyb_protocol: 1.65 mg of Cy3-labled cRNA is then pooled and hybridized to Agilent Zebrafish V3 array 4´44K Microarray (Agilent Technologies, USA) at 65℃ for 17h.

scan_protocol: After washing and drying by nitrogen fun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535nm for Cy3.

data_processing: The scanned images were analyzed with Feature Extraction 10.5.1.1 Software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Danio rerio

source_name: embryos

label_protocol: 0.2 mg of total RNA was amplified by a low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Vy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: zebrafish embryos were selected at 6 hph with normal development.

extract_protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).

treatment_protocol: 6 hpf embryos  were treated with Aflatoxin B1 (150 ng/mL) till 48 hpf.

value: embryos


title: Neural Progenitor Cells Iso-T - RNA_seq_DMSO_rep1


title: Endothelial cells E5.5_Decidua_2

description:
E5-5_EC-2
mRNA
processed data file: all_FPKM.txt


title: 6-48 150 ng/mL AFB1_24554

description: mRNA expression after 150 ng/mL Aflatoxin B1 treated embryos from 6-48 hpf


title: Neural Progenitor Cells Iso-T - RNA_seq_DMSO_rep2


title: Neural Progenitor Cells Iso-E - RNA_seq_DMSO_rep2


title: Neural Progenitor Cells Fe-T - RNA_seq_rep1


title: Neural Progenitor Cells Ma-E - RNA_seq_rep2


title: Neural Progenitor Cells Iso-E - RNA_seq_DQ_rep2


title: MSCs at passage 4, biological replicate 1

city: Seoul

first: Seong-Who

last: Kim

address: 88, Olympic-ro 43-gil

country: South Korea

institute: University of Ulsan

description: Gene expression data from passage 4 (pre-senescent) MSCs.

hyb_protocol: Following fragmentation, 50-500 ng of cRNA were hybridized on Affymetrix GeneChip® Human Gene 2.0 ST Array X 4. GeneChips were washed and stained in the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Raw data files were processed by R/Bioconductor, using oligo package. The worlflow descripted in https://www.bioconductor.org/packages/release/workflows/vignettes/maEndToEnd/inst/doc/MA-Workflow.html was followed.

label: biotin

source_name: mesenchymal stem cells derived from human umbilical cord blood, passage 4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in α MEM supplemented with 10% FBS and 1% penicillin & streptomycin.

extract_protocol: Total RNA extraction were performed by TRIzol® (Invitrogen) as manufacturer's instruction.

treatment_protocol: Cells were subcultured by designated passage. Cells were trypsinized and subcultured every 4 days.


title: MSCs at passage 4, biological replicate 2


title: Neural Progenitor Cells Iso-E - RNA_seq_DMSO_rep1


title: MSCs at passage 9, biological replicate 2

description: Gene expression data from passage 9 (senescent) MSCs.

source_name: mesenchymal stem cells derived from human umbilical cord blood, passage 9


title: Neural Progenitor Cells Iso-T - RNA_seq_rep2


title: Neural Progenitor Cells Fe-T - RNA_seq_rep2


title: Neural Progenitor Cells Iso-E - RNA_seq_rep3


title: Neural Progenitor Cells Iso-E - RNA_seq_rep2


title: Neural Progenitor Cells Iso-T - RNA_seq_rep3


title: Neural Progenitor Cells Ma-E - RNA_seq_rep1


title: MSCs at passage 9, biological replicate 1


title: Neural Progenitor Cells Iso-T - RNA_seq_DQ_rep3


title: Induced pluripotent stem cell Iso-T - RNA_seq_rep2

source_name: Induced Pluripotent Stem Cells

value: Induced Pluripotent Stem Cells


title: Induced pluripotent stem cell Iso-T - RNA_seq_rep3


title: Neural Progenitor Cells Fe-T - RNA_seq_rep3


title: Neural Progenitor Cells Fe-E - RNA_seq_rep1


title: Neural Progenitor Cells Ma-T - RNA_seq_rep2


title: Neural Progenitor Cells Iso-T - ATAC_rep2


title: Induced pluripotent stem cell Iso-E - RNA_seq_rep1


title: Neural Progenitor Cells Iso-T - RNA_seq_DQ_rep2


title: Neural Progenitor Cells Iso-E - ATAC_rep1


title: Neural Progenitor Cells Ma-T - RNA_seq_rep1


title: Neural Progenitor Cells Ma-T - RNA_seq_rep3


title: Neural Progenitor Cells Ma-E - RNA_seq_rep3


title: Induced pluripotent stem cell Iso-E - ATAC_rep3


title: Induced pluripotent stem cell Iso-T - ATAC_rep1


title: Neural Progenitor Cells Ma-T - HiC_rep1


title: Neural Progenitor Cells Iso-T - HiC_rep3


title: Neural Progenitor Cells Ma-E - HiC_rep1


title: Neural Progenitor Cells Iso-T - RNA_seq_rep1


title: Induced pluripotent stem cell Iso-E - ATAC_rep1


title: Neural Progenitor Cells Iso-E - RNA_seq_rep1


title: Neural Progenitor Cells Iso-E - ATAC_rep3


title: Neural Progenitor Cells Iso-T - ATAC_rep3


title: Induced pluripotent stem cell Iso-T - ATAC_rep3


title: Neural Progenitor Cells Iso-E - ATAC_rep2


title: Neural Progenitor Cells Iso-T - HiC_rep1


title: Induced pluripotent stem cell Iso-T - ATAC_rep2


title: Induced pluripotent stem cell Iso-T - HiC_rep3


title: Induced pluripotent stem cell Iso-E - RNA_seq_rep3


title: Induced pluripotent stem cell Iso-E - RNA_seq_rep2


title: Neural Progenitor Cells Ma-T - HiC_rep2


title: Induced pluripotent stem cell Iso-T - RNA_seq_rep1


title: Induced pluripotent stem cell Iso-E - HiC_rep3


title: Neural Progenitor Cells Iso-T - ATAC_rep1


title: Induced pluripotent stem cell Iso-E - HiC_rep1


title: Neural Progenitor Cells Iso-E - HiC_rep1


title: 10 endogenous pre-miRNAs - HCT116

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description: Cloning of 10 endogenous pre-miRNAs from HCT116 cells

data_processing:
The resulting DNA sequences obtained from NGS were treated with cutadapt (cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC) (Martin, 2011) to remove the adapter sequences.
The trimmed paired-end sequencing reads were then joined using fastq-join (with default parameters).
Low quality reads were discarded using fastq_quality_filter (-q 30 -p 90) (FASTX- Toolkit, http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13).
The remaining sequencing reads were then aligned to the pre-generated reference sequences using Bowtie (local alignment mode) (Langmead and Salzberg, 2012). Only perfectly mapped reads were selected for further analysis.
Genome_build: Pre-generated reference sequences contained the pre-miRNA sequences and their variants.
Supplementary_files_format_and_content: Bed files containing read count number for each mapped reference sequence.

source_name: HCT116 cells

growth_protocol: The HCT116 cells were cultured in McCoyʼs 5A medium (Gibco, 16600082). The HEK293T cells were cultured in DMEM medium (Gibco, 12100061). The above mediums were supplemented with 10% fetal bovine serum (FBS) (Gibco, 10270106) and 1% of  Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
The total RNAs were isolated from the cells, which reached 80% confluency in a 100 mm dish, using 800 μL TRIzol Reagent (Invitrogen, 15596018) following the manufacturer's mannual.
2500 ng of total RNA from human cells or 250 fmol of synthesized pre-miRNAs were ligated by T4 RNA ligase 1. The ligated pre-miRNAs were then reverse-transcribed by Superscripts IV (Invitrogen, 18090010) and RT primers that formed 25–30 base pairs with pre-miRNAs. The reverse complementary sequence of the 3'-adapter (5'- TGGAATTCTCGGGTGCCAAGG-3') was included in the RT primers. The resulting cDNAs were first amplified using the reverse primer (5'-CCTTGGCACCCGAGAATTCCA-3') and the forward primer containing the 5'-adapter sequence (5'- GTTCAGAGTTCTACAGTCCGACGATC-3'). The resulting PCR products were then amplified using RPIx and RP1 primers to generate the DNA libraries for next-generation sequencing (NGS). The DNA libraries were sequenced by Illumina Nextseq 500 sequencer using Nextseq Mid Output 1250 (2x75) cycles kit.


title: 10 endogenous pre-miRNAs - HEK293T

description: Cloning of 10 endogenous pre-miRNAs from HEK293T cells

source_name: HEK293T cells


title: Neural Progenitor Cells Ma-E - HiC_rep2


title: Induced pluripotent stem cell Iso-E - ATAC_rep2


title: Induced pluripotent stem cell Iso-E - HiC_rep2


title: human fetal brown adipose tissue day 125

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

country: Italy

institute: Humanitas

data_processing:
STAR (v2.7.3a) for reads mapping
featureCounts (v2.0.1) for reads count
DESeq2 (v 1.22.2) for gene expression analysis
Genome_build: ENSEMBL GRCh38 release 77
Supplementary_files_format_and_content: raw count matrix and excel tables containing the results of the differential expression analysis + normalized counts

source_name: primary tissue

extract_protocol:
RNA was isolated using NucleoSpin RNA kit (Macherey and Nagel, 740955) with on-column DNA digestion following the manufacturer’s protocol.
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples received were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: primary tissue

tag: age + media

value: day 125


title: brown adipocyte differentiation on day +40 replicate 3

source_name: iPSC cell culture

value: iPSC

value: day +40


title: brown adipocyte differentiation on day +40 replicate 1