title: ChIP-seq_PM 1

data_processing:
Paired-end ChiP-Seq reads were aligned using BWA mem (v.0.7.8) (Li and Durbin, 2009) against the GRCm39/mm10 mouse genome assembly with default settings.
For peak calling, MACS2 callpeak (v2.1.1) (Zhang et al., 2008) were called on individual replicates for each ChIP (treatment) and Input (control) pair, using q value < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. Peaks were annotated by the function of annotatePeak of ChIPseeker.
Reads distributions (from bigwig) across gene are presented as an average plot (average of reads signals across the targeted genes).
The deeptools tool is used for this analysis. Differential peaks were then selected with the absolute value of the log2 fold change was 1 at an Pvalue < 0.05 using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS

extract_protocol:
Microglia treated with PM and PBS
Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the NEB/NEBNext® Library Quant Kit for Illumina®(E7630S).

tag: treatmnet

value: PM

tag: chip antibody

value: NF- kB p65 (Cell Signaling Technology, Cat. No. 8242s)


title: S49a-RCB

status: Public on Feb 23 2022

type: SRA

city: Faridabad

first: Prasenjit

last: Guchhait

state: Haryana

address: Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad-Gurgaon Expressway, 3rd Milestone,

country: India

institute: Prasenjit Guchhait

library_source: transcriptomic

data_processing:
We have used FastQC and MultiQC for quality check
STAR was used for alignment
DESeq2 was used for normalization and quantification of reads
DAVID, METASCAPE was used for pathway enrichment analysis
Galaxy was also used for raw count calculation
Genome_build: Hg19
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Platelet rich plasma was separated from whole blood by centrifugation. Platelet pellet in Trizol was then used for RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols (NEB, USA)

tag: cell type

value: Platelets

tag: disease

tag: disease state

value: Asymptomatic

tag: tissue

value: whole blood


title: S44-RCB

value: Symptomatic


title: input_Ctrl 1

city: Xi'an

first: Yuan

last: Zhang

address: No. 620, West Chang'an Avenue, Chang'an District

country: China

institute: Shaanxi Normal University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: microglia

value: control (PBS)

tag: strain

value: microglia

value: none (input)


title: S42-RCB


title: Induced pluripotent stem cells on D1 after lentiviral transduction, wPRE

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description:
D1.wPRE
Single cell RNA-Seq
cDNA
counts.mtx

data_processing:
Quality of fastq files was assessed with Fastqc v0.11.3 and summarised with MultiQC v1.8.
Alignment and protein-coding gene quantification were performed using 10x cellranger v3.1.0.
To maintain consistency between sequencing runs, alignment was performed by using only R2 strands, trimmed to 91 nt.
Cells with fewer than 200 unique features and cells with more than 25% of counts from mitochondrial genes were discarded from count matrix.
The processing was performed with regard to the regular gene expression library (GSE160604).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.mtx: MatrixMarket of raw expression levels for cells.
Supplementary_files_format_and_content: meta.csv: Comma-separated metadata for cells.

source_name: A1ATD1 induced pluripotent stem cells

growth_protocol: Moreau et al., 2016. Megakaryocyte forward programming by lentiviral transduction with 3 transcription factors and two cytokine combinations.

extract_protocol:
10X library preparation.
10X VDJ protocol.

treatment_protocol: Cells were methanol fixed, as per 10X protocol, and stored at -80 degrees C. They were then rehydrated as per 10X protocol and submitted for library preparation.

tag: cell line

tag: day of differentiation

value: Induced pluripotent stem cells

tag: transgene library

value: wPRE

tag: library batch

value: Batch 1


title: A1ATD1 36

description: raw.csv

data_processing:
The quality of the data was assessed using FastQC, MultiQC
Reads were aligned using STAR v2.7.3a (parameters --outSAMtype BAM SortedByCoordinate)
Protein-coding gene quantification was performed using Subread featureCounts v2.0.0 (default parameters)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: csv file of raw expression levels

molecule: polyA RNA

source_name: Forward programmed megakaryocytes

growth_protocol: The hiPSC line A1ATD1c was forward programmed towards the megakarycoyte lineage using method describes in Moreau et al. 2016 (PMID: 27052461) and cell material collected after 40 days of standard culture. Rainbow vectors allowing fluorescence reporting of transcription factor expression (as described in Dalby et al. 2018) have been used to programme the cells.

extract_protocol:
The single cells were sorted in 96-well plates containing cell lysis buffer (2.3mL of 0.2% Triton X-100 with RNase inhibitor) and frozen to -80°C before library preparation.
The method for single cell cDNA library making has been adapted from Smartseq2 for full-length RNAseq from single cells and Fluidigm (PMID: 24385147). Briefly, the reverse transcription was initiated with oligo-dT primers using SuperScript-II reverse transcriptase (Thermo Scientific) and supplemented with ERCC RNA Spike-In. The cDNA was then PCR amplified for 21 cycles using the KAPA HiFi Hotstart ReadyMix and IS primers (Kappa biosystems). After purification of the amplified cDNA, the indexed library was made using the Illumina Nextera XT DNA kit, 96 cells eventually pooled and library quality checked on an Agilent high sensitivity DNA chip before sequencing on one lane of an HiSeq-4000 (Illumina).

treatment_protocol: The megakaryocytes have been sorted by FACS at day40 and 24 single cells of each rainbow transgene pattern (GFT, GF, GT, FT, G, F, T, Neg; G:GATA1, F:FLI1, T:TAL1) directly lysed in 0.2% Triton-X before NGS library preparation (see detailed methods in Dalby et al. 2018)

tag: hipsc line

tag: differentiation day

value: Day 40

tag: transgene pattern

value: GT


title: S53a-RCB


title: A1ATD1 35

description: raw.csv


title: Induced pluripotent stem cell derived megakaryocytes on D20, run 3

description:
cDNA
Single-cell RNA-Seq

data_processing:
Quality of fastq files was assessed with Fastqc v0.11.3 and summarised with MultiQC v1.8.
Alignment and protein-coding gene quantification was performed using 10x cellranger v3.1.0.
To maintain consistency between sequencing runs, alignment was performed by using only R2 strands, trimmed to 91 nt.
Cells with fewer than 200 unique features and genes detected in fewer than 3 cells were discarded from count matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw.mtx: MatrixMarket of raw expression levels for cells.
Supplementary_files_format_and_content: cell-meta.csv: Metadata for cells.

tag: sequencing run

value: Run 3


title: S36-RCB


title: S33-RCB


title: Ctrl 1

data_processing:
STAR is used to align clean reads to reference genome.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: excel file of dif expression analysis result with read count and fpkm

extract_protocol:
RNA from microglia was extracted using RNA Easy Fast Tissue/Cell Kit (Cat.#DP451)
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: A1ATD1 34

description: raw.csv


title: A1ATD1 33

description: raw.csv

value: GF


title: RRS-NKp46+ ILC3-ATACseq KO2

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Quality control was the first step for processing raw sequence reads by FastQC.
Then adapter sequences and poor-quality reads were removed.
Quality filtered reads were then mapped to mouse genome (mm10) by Bowtie2, and only uniquely mapped reads were saved.
Peak calling was done using MACS2 with an initial threshold q-value of 0.01 as cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: Excel, raw counts of sequencing reads from duplicates samples with chromosome ID, chromosome start and end positions.

source_name: lamina proprial lymphocytes

extract_protocol:
Library preparation was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme, Nanjing, China. 1.2X Agencourt AMPure XP beads(Beckman Coulter) were used to purify libraries for sequencing.
150 paired-end sequencing was performed with Illumina NovaSeq 6000.

value: cells were isolated from small intestinal lamina propria.

value: KO-NKp46+ ILC3s

tag: gender

value: pooled male and female

tag: genotype


title: RRS-NKp46+ ILC3-ATACseq KO1


title: Differentiating mesoderm on D3, run 3

description:
cDNA
Single-cell RNA-Seq

value: Differentiating mesoderm


title: RRS-NKp46- ILC3-ATACseq KO1

value: KO-NKp46- ILC3s

value: male


title: input_PM 1

tag: treatmnet

value: PM


title: Induced pluripotent stem cells on D1 after lentiviral transduction, TAL1

description:
D1.TAL1
Single cell RNA-Seq
cDNA
counts.mtx


title: RRS-NKp46+ ILC3-ATACseq CTRL1

value: CTRL-NKp46+ ILC3s


title: S19-RCB

value: Platelets

value: Symptomatic

value: whole blood


title: S21-RCB


title: A1ATD1 30

description: raw.csv


title: Differentiating megakaryocytes on D8, run 3, batch 2

description:
cDNA
Single-cell RNA-Seq

value: Differentiating megakaryocytes

value: Batch 2


title: A1ATD1 28

description: raw.csv

value: Day 40


title: S24a-RCB

value: Asymptomatic


title: S20-RCB


title: S18-RCB


title: A1ATD1 31

description: raw.csv


title: Differentiating megakaryocytes on D10, run 2

description:
cDNA
Single-cell RNA-Seq

value: Run 2

value: Batch 1


title: Differentiating megakaryocytes on D5, run 3, batch 2

description:
cDNA
Single-cell RNA-Seq

value: Run 3


title: ChIP-seq_Ctrl 1

value: control (PBS)

value: microglia

tag: chip antibody

value: NF- kB p65 (Cell Signaling Technology, Cat. No. 8242s)


title: Differentiating megakaryocytes on D10, run 3

description:
cDNA
Single-cell RNA-Seq

tag: cell type


title: RRS-NKp46- ILC3-ATACseq CTRL2

value: cells were isolated from small intestinal lamina propria.

value: CTRL-NKp46- ILC3s

value: pooled male and female


title: A1ATD1 29

description: raw.csv

value: GF


title: Induced pluripotent stem cell derived megakaryocytes on D15, run 2

description:
cDNA
Single-cell RNA-Seq


title: Induced pluripotent stem cell derived megakaryocytes on D20, run 2

description:
cDNA
Single-cell RNA-Seq


title: A1ATD1 32

description: raw.csv


title: Differentiating megakaryocytes on D9, run 2, batch 2

description:
cDNA
Single-cell RNA-Seq


title: S28a-RCB

value: Platelets

tag: disease


title: RRS-NKp46- ILC3-ATACseq CTRL1

value: male


title: S12-RCB

tag: disease state

value: Symptomatic

value: whole blood


title: RRS-NKp46+ ILC3-ATACseq CTRL2

tag: tissue

value: CTRL-NKp46+ ILC3s


title: RRS-NKp46- ILC3-ATACseq KO2

value: KO-NKp46- ILC3s


title: A1ATD1 26

description: raw.csv

value: Day 40


title: A1ATD1 27

description: raw.csv


title: Differentiating megakaryocytes on D8, run 2, batch 2

description:
cDNA
Single-cell RNA-Seq

value: Differentiating megakaryocytes

value: Run 2

value: Batch 2


title: Differentiating megakaryocytes on D7, run 2

description:
cDNA
Single-cell RNA-Seq

value: Batch 1


title: S9a-RCB

value: Asymptomatic


title: A1ATD1 25

description: raw.csv


title: S11a-RCB


title: S6a-RCB


title: A1ATD1 23

description: raw.csv


title: A1ATD1 24

description: raw.csv


title: LLC-p53+ sgCtrl rep3

city: Nanjing

first: Wang

last: Yafeng

state: Jiangsu

address: 12 Xuefu-Road, Pukou District

institute: Nanjing University

data_processing:
The illumina high-throughput sequencing results initially existed as original image data files and were converted into original sequencing sequence (raw read) by BCL2FastQ2
The raw read were filtrated through removing adaptor, low-quality and N ratio greater than 5% sequence.
The filtrated read was mapped to mouse reference transcripts (GENCODE Release version M21) using softwave Salmon (version0.14.0)
Gene expression value was quantitatively estimated through Fragments per Kilobase per Million Mapped Fragments (FPKM)
Gene differential expression between the three groups was analyzed by DESeq2 (version1.30.0).
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse Lewis lung carcinoma (LLC) cell line

extract_protocol:
RNA was harvested using Takara Trizol reagent and standard RNA lsolation protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse lung carcinoma cell line

value: LLC

tag: guide rna

value: Control sgRNA


title: LLC-p53+ sgmIfng rep3

tag: cell line

value: Ifng-activating sgRNA


title: LLC-p53+ sgCtrl rep2


title: Differentiating megakaryocytes on D5, run 2, batch 2

description:
cDNA
Single-cell RNA-Seq

tag: day of differentiation


title: Day 27 plate 2 [UMC-HS-033]

city: Utrecht

first: Maria

middle: Christine

last: Heinz

address: Heidelberglaan 100

department: Molecular Cancer Research

country: Netherlands

institute: University Medical Center Utrecht

description: Single RFP+ CRC cells were sorted from murine livers at indicated time points and processed for single cell sequencing.

data_processing:
Paired-end reads were aligned to the transcriptome assembly mm10 including DTR-eGFP and tDimer2 reporter transcripts using the BWA-MEM algorithm.
Reads mapping to multiple loci were discarded.
Left reads contain barcodes and unique molecular identifiers (UMIs) (read length of 26 bp) and were not used for quantification.
Transcript counts were obtained by counting the number of UMIs for each cell barcode and each transcript and aggregating the number across all transcripts of the same locus.
Downstream analysis of processed data file in the linked study included: exclusion of spike-in RNAs, inclusion of cells with > 200 unique transcripts and < 10 % mitochondrial reads.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files containing transcript counts

source_name: Liver metastases of colorectal cancer

growth_protocol: The murine CRC model of the genetic background VillinCre-ERT2; ApcFL/FL; KrasLSL-G12D/+; Tp53KO/KO; R26R-Confetti; Lgr5DTR-eGFP was generated as previously described, while RFP+ confetti clones were isolated by FACS in order to generate the corresponding organoid line (Fumagalli et al., Cell Stem Cell, 2020). This line was cultured in BME (AMS Bio) and growth media containing Advanced DMEM/F12 (Invitrogen) supplemented with 10 mM Hepes (Invitrogen), 1% GlutaMAX (Invitrogen), 1% Penicillin-Streptomycin (Lonza) as well as 1x B27 supplement (Invitrogen), 1.25 mM N-Acetyl-L-cysteine (Sigma-Aldrich), and 10 % Noggin conditioned medium was refreshed every 2-3 days. Lgr5+ and Lgr5- cells were collected by FACS and injected in 100 µl PBS into recipient mice (strain: NOD.Cg-PrkdcSCID Il2rgtm1Wjl/SzJ). Approximately, 400k, 200k, 200k, and 50k cells were injected into the portal vein and harvested after 1, 7, 13, and 27 days, respectively. Animals were kept at animal facilities of the Central Laboratory Animal Research Facility (Gemeenschappelijk Dierenlaboratorium, GDL).

extract_protocol:
RNA isolation and library preparation was performed according to the previously published SORT-seq tecnique, an implemented version of the CEL-seq2 technique (Muraro et al., Cell Syst, 2016).
Library preparation was performed according to the SORT-seq technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: For the isolation of CRC cells, a two-step liver perfusion protocol was adopted and modified (Klaunig et al., in vitro, 1981). In brief, the portal vein or subhepatic vena cava was cannulated with a 24G IV catheter (BD Insyte Autoguard Shielded IV catheter; BD 381412) to perfuse first, 70 mL HBSS (Gibco) with 0.5 mM EGTA, 25 mM HEPES, and NaOH to reach a pH of 7.4 at 37°C. Next, 80 mL digestion medium consisting of DMEM-low glucose (Corning) with 15 mM HEPES, Penn-Strep, collagenase type IV (Gibco) in sufficient quantity for 120 Collagenase Digestive Units (CDU)/ml at 37°C) was perfused. The liver was excised, minced in a 15 cm petri dish with 10 mL digestion medium, resuspended in 25 mL isolation medium (DMEM-High/F-12, Gibco with 10% FBS), and filtered through a 70 µm strainer. The supernatant of two initial washing steps (centrifugation at 50xg for 2 minutes) was washed twice more with 25 mL isolation medium (centrifugation at 500xg for 3 min). Then, DRAQ7 (Cell Signaling Technology) was added and single, alive, RFP+ cells were FACS-sorted into 384-well collection plates for scRNA-seq. Plates were stored at -80°C until processed further.

tag: confetti clone

value: RFP+

tag: time of harvest

value: Day 27

tag: lgr5 status of injected cells

value: Lgr5- and Lgr5+ for cells 1-192 and 193-384, resp.


title: LLC-p53+ sgmIfng rep1


title: A1ATD1 21

description: raw.csv

tag: hipsc line

tag: differentiation day

value: GF


title: LLC-p53+ sgmIfng rep2


title: Differentiating megakaryocytes on D6, run 2

description:
cDNA
Single-cell RNA-Seq

tag: sequencing run

tag: library batch


title: S1a-RCB

value: Platelets

value: whole blood


title: A1ATD1 20

description: raw.csv

tag: transgene pattern


title: LLC-p53+ sgCtrl rep1

tag: genotype


title: Day 27 plate 1 [UMC-HS-031]

value: VillinCre-ERT2; ApcFL/FL; KrasLSL-G12D/+; Tp53KO/KO; R26R-Confetti; Lgr5DTR-eGFP


title: Differentiating megakaryocytes on D5, run 2

description:
cDNA
Single-cell RNA-Seq


title: A1ATD1 22

description: raw.csv

value: Day 40


title: LLC sgmIfng rep3


title: Differentiating mesoderm on D3, run 2

description:
cDNA
Single-cell RNA-Seq

value: Differentiating mesoderm


title: Day 13 plate 1 [UMC-HS-027]

value: Day 13


title: A1ATD1 19

description: raw.csv


title: LLC sgmIfng rep2


title: Differentiating mesoderm on D2, run 2

description:
cDNA
Single-cell RNA-Seq

value: Run 2


title: A1ATD1 18

description: raw.csv


title: Day 7 plate 1 [UMC-HS-021]

value: Day 7


title: LLC sgmIfng rep1


title: Induced pluripotent stem cells on D1 after lentiviral transduction, run 2

description:
cDNA
Single-cell RNA-Seq

value: Induced pluripotent stem cells

value: Batch 1


title: Differentiating megakaryocytes on D4, run 2

description:
cDNA
Single-cell RNA-Seq

value: Differentiating megakaryocytes


title: A1ATD1 17

description: raw.csv


title: LLC sgCtrl rep2

value: mouse lung carcinoma cell line

value: LLC

value: Control sgRNA


title: LLC sgCtrl rep3


title: PA14_PL_3

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

description: Cells were passaged in LB medium for 5 days and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

data_processing:
mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.

organism: Pseudomonas aeruginosa

growth_protocol: Cells were either grown in LB to an OD600 =2 (planktonic) or inoculated at a starting OD600 of 0.002 in LB and grown statically in half-area 96-well µClear microtiter plates at 37 °C in humid atmosphere for 48 h.

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
Total RNA was fragmented (150-350 bp) in Fast AP-Buffer (Thermo Scientific), DNA was digested by TURBO™ DNase (Invitrogen), and RNA fragments were phosphorylated by FastAP alkaline phosphatase (Thermo Scientific). Custom-made barcodes were ligated to the RNA using the T4 ligase (New England Biolabs) and fragments were subsequently purified and concentrated using the RNA Clean & Concentrator™-25 Kit (Zymo Research) following the manufacturer’s instructions. Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Directly after cultivation the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C

tag: treatment

value: planktonic

tag: geographical location


title: Induced pluripotent stem cells plated as single cells

description:
cDNA
Single-cell RNA-Seq

tag: cell type


title: Induced pluripotent stem cells plated at beginning of timecourse

description:
cDNA
Single-cell RNA-Seq


title: Lung_CUT_TAG_PRMK_rep2_H3K4me1

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
Library strategy: CUT-TAG
Sequenced reads were mapped to mm10 whole genome using bowtie2
peaks were called using SEACR
mm10
bigwig files

source_name: replicates: PRMK_rep2

growth_protocol: The PRM and PRMK mouse were developed on recipient mice after transplantation through injection into the left lobe of lung.

extract_protocol:
PRM lung, PRM liver and PRMK lung organoids were harvested from the recipient mice.
CUT&TAG assay was performed using NovoNGS® CUT&TAG 2.0 High-Sensitivity Kit (Novoprotein scientific Inc., Cat# N259-YH01-01A).

value: lung

tag: plasmids

tag: antibody

value: H3K4me1(Abcam, Cat# ab8895)


title: Lung_CUT_TAG_PRMK_rep1_H3K4me1

source_name: replicates: PRMK_rep1

tag: tissue


title: A1ATD1 14

description: raw.csv

value: G


title: Induced pluripotent stem cells from clumps, run 2

description:
cDNA
Single-cell RNA-Seq

tag: cell line


title: PA14_PL_1

description: Cells were grown in LB to an OD600 =2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.


title: A1ATD1 16

description: raw.csv


title: Induced pluripotent stem cell derived megakaryocytes on D15

description:
cDNA
Single-cell RNA-Seq

tag: day of differentiation

value: Run 1


title: LLC sgCtrl rep1

tag: guide rna


title: Induced pluripotent stem cell derived megakaryocytes on D20

description:
cDNA
Single-cell RNA-Seq


title: A1ATD1 13

description: raw.csv


title: PA14_DrhlR_PL_R3


title: A1ATD1 12

description: raw.csv


title: PA14_DrhlR_PL_R2


title: Lung_CUT_TAG_PRM_rep2_H3K4me1

source_name: replicates: PRM_rep2


title: PA14_DrhlR_PL_R1


title: Differentiating megakaryocytes on D10

description:
cDNA
Single-cell RNA-Seq


title: Day 1 plate 1 [UMC-HS-019]

value: VillinCre-ERT2; ApcFL/FL; KrasLSL-G12D/+; Tp53KO/KO; R26R-Confetti; Lgr5DTR-eGFP

tag: confetti clone

value: RFP+

tag: time of harvest

value: Day 1

value: Lgr5- and Lgr5+ for cells 1-192 and 193-384, resp.


title: A1ATD1 11

description: raw.csv

tag: hipsc line

value: Day 40


title: A1ATD1 15

description: raw.csv

tag: differentiation day


title: Lung_CUT_TAG_PRM_rep1_H3K4me1

source_name: replicates: PRM_rep1


title: A1ATD1 10

description: raw.csv


title: PA14_PL_2


title: Differentiating megakaryocytes on D9

description:
cDNA
Single-cell RNA-Seq

tag: sequencing run


title: Liver_CUT_TAG_PRM_rep2_H3K4me1

source_name: replicates: PRM_liver_rep2

value: liver


title: PA14_DrhlR_DlasR_PL_R2


title: Differentiating megakaryocytes on D8

description:
cDNA
Single-cell RNA-Seq

tag: library batch


title: Differentiating megakaryocytes on D6

description:
cDNA
Single-cell RNA-Seq


title: Lung_RNA_seq_PRM_rep5

description:
1_RNAseq4_PRMK_VS_PRM_result_all.csv
1_RNAseq4_PRMK_VS_PRM_result_DEGs.csv

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM)
GRCm38
txt files with gene TPM

source_name: replicates: PRM_rep5

extract_protocol:
PRM lung, PRM liver and PRMK lung organoids were harvested from the recipient mice. RNA was extracted with Trizol
RNA-seq libraries were constructed by Illumina Stranded mRNA Sample Preparation Kit (NEB, Cat#E7770) according to the manufacturer’s protocol,


title: Lung_RNA_seq_PRM_rep4

source_name: replicates: PRM_rep4


title: Liver_CUT_TAG_PRM_rep1_H3K4me1

source_name: replicates: PRM_liver_rep1


title: A1ATD1 9

description: raw.csv

tag: transgene pattern


title: A1ATD1 8

description: raw.csv


title: PA14_DrhlR_DlasR_BF_R2

description: Biofilms were inoculated at a starting OD600 of 0.002 in LB and grown statically in half-area 96-well µClear microtiter plates (Greiner Bio-One) at 37 °C in humid atmosphere. After 48 h, mature biofilms (10 wells per replicate) were resuspended and harvested in an equal volume of RNAlater (Qiagen).

value: biofilm


title: PA14_DrhlR_DlasR_PL_R1


title: PA14_DrhlR_DlasR_BF_R3


title: PA14_DrhlR_DlasR_BF_R1


title: A1ATD1 7

description: raw.csv


title: A1ATD1 5

description: raw.csv


title: Lung_RNA_seq_PRM_rep3

source_name: replicates: PRM_rep3


title: Differentiating megakaryocytes on D7

description:
cDNA
Single-cell RNA-Seq

value: Batch 1


title: Differentiating megakaryocytes on D5

description:
cDNA
Single-cell RNA-Seq

value: Differentiating megakaryocytes


title: Differentiating megakaryocytes on D4

description:
cDNA
Single-cell RNA-Seq


title: PA14_DrhlR_DlasR_PL_R3


title: Differentiating mesoderm on D3

description:
cDNA
Single-cell RNA-Seq

value: Differentiating mesoderm


title: PA14_DrhlR_BF_R3


title: A1ATD1 4

description: raw.csv


title: Differentiating mesoderm on D2

description:
cDNA
Single-cell RNA-Seq


title: PA14_DrhlR_BF_R1


title: NP group_1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: high fat/high cholesterol/high sucrose/bile acid diet with pemafibrate 0.1 mg/kg for three weeks

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform in a 101-base single-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

extract_protocol:
Total RNA was isolated from the liver tissues using the Rneasy® Mini Kit (QIAGEN, Hilden, Germany)。
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: heart


title: PA14_DrhlR_BF_R2


title: A1ATD1 3

description: raw.csv


title: A1ATD1 6

description: raw.csv


title: N group_2

description: high fat/high cholesterol/high sucrose/bile acid diet for three weeks


title: A1ATD1 2

description: raw.csv


title: N group_1

source_name: high fat/high cholesterol/high sucrose/bile acid diet for three weeks


title: PA14_DphoB_PL_R3


title: A1ATD1 1

description: raw.csv


title: Induced pluripotent stem cells from clumps

description:
cDNA
Single-cell RNA-Seq


title: Induced pluripotent stem cells on D1 after lentiviral transduction

description:
cDNA
Single-cell RNA-Seq

value: Induced pluripotent stem cells


title: PA14_DphoB_PL_R2

value: planktonic


title: I-BET151_ATAC_1

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the human hg38 reference genome assembly using Bowtie2 (v2.2.5) (Langmead et al., 2012) with options: --no-discordant --no-unal --no-mixed -X 2000 --local.
The BAM files were removed the null and not unmapped reads using sambamba(v0.7.1)(Tarasov et al., 2015) view with the default parameter settings.
The BAM files were removed the duplicated reads using sambamba(v0.7.1)(Tarasov et al., 2015) markdup with the default parameter settings.
For peak calling, parameters used were macs2 (v2.1.2) (Zhang et al., 2008) callpeak with parameter settings: -q 0.05 --nomodel --shift -100 --extsize 200. The peaks visualization in genome was showed by IGV software (Robinson et al., 2011).
The peaks annotations were performed with R package ChIPseeker (Yu et al., 2015) from the bioconductor project. Motif enrichment was done using HOMER with options: -fdr 0.05 -len 8,10,12.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamcoverage
Supplementary_files_format_and_content: peak text files

source_name: MEL1 hESC line

growth_protocol: PP cells were cultured in  basal medium (EF6): DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF and 10 μM 616452.

extract_protocol:
5×10^4 cells were collected and lysed using lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to collect cell nuclei. Then, nuclei were resuspended in the mixture containing 10 μl 5× TTBL, 5 μl TTE Mix V50 and 35 μl ddH2O. The mixture were incubated at 37°C for 30 min. Then, the fragments were purified by the standard processing of TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and VAHTS DNA Clean Beads (Vazyme N411).
The standard processing was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep Index Kit V2 for Illumina ® (Vazyme TD202). The library concentration was measured using Qubit dsDNA BR Assay Kit (Invitrogen) by Qubit (Invitrogen).

treatment_protocol: DMSO samples were treated with DMSO and I-BET151 samples were treated with 1 μM I-BET151 for 7 days.

tag: cell line background

tag: source cell tye

value: human embryonic stem cell (hESC) line

value: hPSC-derived pancreatic progenitor cells

value: 1 μM I-BET151 for 7 days


title: C group_2

description: normal chow diet for three weeks

source_name: normal chow diet for three weeks


title: PA14_DphoB_PL_R1

tag: treatment

tag: geographical location


title: iMAC_single cell RNA seq

city: Cheongju-si

first: Sang Cheol

last: Kim

address: Osong Health Technology Administration Complex, 187, Osongsaengmyeong 2-ro, Osong-eup

country: South Korea

institute: Korea National Institute of Health

data_processing:
The reads of each library were processed separately using the “cellranger count” pipeline to generate a gene-barcode matrix for each library. In this step, the reads were aligned to a human reference genome (version: hg19, GRCh37.p13).
The concatenated gene matrix, barcode matrix and count matrix were imported into Seurat (http://satijalab.org/seurat/) to undergo data preprocessing.
We filtered genes whose expression was detected in fewer than 3 cells. We filtered cells whose expression was detected in less than 100 genes and less than 10 percent mitochondrial genes.
We normalized the read counts for each cell are divided by the total counts for that cell and multiplied by the scale factor. After normalization, the read count data was log- transformed (log (read count + 1)), data scaling using linear models, focused on each minus the mean expression of the gene in all cells.
Genome_build: hg19, GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: stem cell

growth_protocol: The human ESCs were differentiated into macrophages following a previous protocol with some modifications (PLoS One. 2011;6(7):e22261. doi: 10.1371/journal.pone.0022261). Briefly, ESCs were plated onto matrigel-coated plates. When colonies grew up to 500μm in diameter, cell culture media was replaced with mesoderm differentiation medium (APEL 2 supplemented with 1X Insulin-Transferrin-Selenium-X (ITX, Invitrogen), 100ng/ml BMP4). After 48hrs, 100ng/ml BMP4 was replaced by 20ng/ml BMP4. On day 4, BMP4 was replaced by 40ng/ml VEGF and 50ng/ml SCF. After 2 days, medium was changed by hematopoietic differentiation medium (APEL 2 supplemented with 1X ITX, 50ng/ml SCF, 10ng/ml TPO, 50ng/ml IL-3, 50ng/ml IL-6 and 50ng/ml Flt-3L). On day 15, floating cells were collected, and incubated in macrophage differentiation medium (RPMI 1640 supplemented with 100ng/ml M-SCF).

extract_protocol:
Single cell capturing and barcoding to generate single-cell Gel Beads-in Emulsion (GEMs) was performed using the 10x Genomics Chrominum platform following the manufacturer’s protocol. In Brief, cell suspensions were loaded onto 10x Genomics Single Cell 3’ Chips with the reverse transcription master mix with RT Primer (TSO) (PN-310354). In this step, cells were separated into the GEMs along with gel beads coated with oligonucleotides which allow the mRNA capture inside the droplets by 30 bp oligo-dT after cell lysis and, provide barcodes to index cells (16 bp) with transcripts (10 bp UMI). After reverse transcription (RT), the barcoded cDNAs were amplified.
library was generated using the Single Cell 3’ Reagent Kit (v2 chemistry). We used illumine Hiseq 4000 system in stand-alone mode to sequence the libraries to obtain pair end sequencing 26 bp (read1) X 98 bp (read2). To process the barcodes, UMI counting and demultiplexing, we used the official 10x Genomics pipeline Cell Ranger v2.1.1. The raw base call files generated by Illumina sequencers were demultiplexed into reads in FASTQ format using the bcl2fastq v.2.20 (GEO number, Data Citation 1). The raw reads were then trimmed from the 3’ end and, get the recommended number of cycles for read pairs (Read1: 26 bp; Read2: 98 bp). The reads of each library were processed separately using the “cellranger count” pipeline to generate a gene-barcode matrix for each library. In this step, the reads were aligned to a human reference genome (version: hg19, GRCh37.p13).

tag: cell type

value: ESCs


title: DMSO_ATAC_1

value: DMSO


title: NP group_2

source_name: high fat/high cholesterol/high sucrose/bile acid diet with pemafibrate 0.1 mg/kg for three weeks


title: PA14_DphoB_DlasR_PL_R3


title: S2 cells - Insulin-treated, RNA-seq, rep3

city: Salt Lake City

first: Adrian

last: Rothenfluh

state: Utah

department: Psychiatry

country: USA

institute: University of Utah

data_processing:
ATAC-seq Fastq files were aligned to the dm6 genome assembly (http://ftp.flybase.net/releases/FB2018_06/dmel_r6.25/fasta/) using Novocraft Novoalign with the following settings: --NonC -o SAM -r Random. SAM files were processed to BAM format, sorted, and indexed using Samtools [38]. BAM files were reads per million-normalized and converted to bigWig files using the Bio-ToolBox ‘bam2wig.pl’ program (https://github.com/tjparnell/biotoolbox/blob/master/scripts/bam2wig.pl). Peak calling was performed on the bigWig files by utilizing the Multi-Replicate Macs ChIPseq pipeline (https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPseq) with the following settings: --dupfrac 0.2 --size 200 --cutoff 2 --peaksize 300 --peakgap 200. Called peaks were annotated in R with the ChIPseeker package [39]. Count data for called peaks was collected from processed BAM files using the Bio-ToolBox ‘get_datasets.pl’ program (https://metacpan.org/pod/distribution/Bio-ToolBox/scripts/get_datasets.pl). The count data was then used to identify differentially accessible regions with the R package DEseq2
RNA-seq fastq files were aligned to the BDGP6 genome assembly using the STAR aligner [41] with the following settings: --twopassMode Basic --outSAMtype BAM SortedByCoordinate -- outWigType bedGraph --outWigStrand Unstranded --clip3pAdapterseq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. The resulting sorted BAM files were indexed using Samtools (Li et al., 2009). FeatureCounts was used to collect count data for BDGP6 genes using the following command: -T 16 -s 2 [42]. Count data for all replicates and experimental conditions were combined into a single count matrix in R. The count matrix was subsequently used to identify differentially expressed genes with the R package DEseq2 [40].
Genome_build: dm6
Genome_build: BDGP6
Supplementary_files_format_and_content: peak files include peak coordinates for peaks called from merged replicates
Supplementary_files_format_and_content: peak annotation file includes closest gene and type of gene regulator
Supplementary_files_format_and_content: pathways file includes GO pathways significant for genes annotated to differentially open peaks
Supplementary_files_format_and_content: bigWig files include data to visualize each sample
Supplementary_files_format_and_content: DESeq files include results from count differences in the two conditions
Supplementary_files_format_and_content: metrics file includes quality results for RNA sequencing run

organism: Drosophila melanogaster

source_name: S2 Cells

extract_protocol:
Total RNA was isolated from S2 cells using a PureLink RNA purification kit
RNA libraries were constructed using a NEBNext Ultra II RNA Library Kit for Illumina and NEBNext Multiplex Oligos for Illumina, Primer Set 1

value: 10 M insulin for 4 hours

tag: breed

value: Oregon-R

tag: Sex

value: Male

value: Schneider 2


title: PA14_DphoB_DlasR_PL_R2


title: S-ADSCs DB/DB

first: Yao

last: Xie

address: 88 Jiefang Road

department: Department of Cardiology

institute: Zhejiang University School of Medicine Second Affiliated Hospital

description: subcutaneous

data_processing:
Cell ranger software provided by 10XGenomics was used to align reads and generate feature-barcode matrices
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: adipose-derived stem cells

extract_protocol:
Adipose tissue was digested by 2 mg/ml collagenase type I (Gibico,17100017) and 1mg/ml dispase II (Sigma, D4693) in Hanks’ balanced salt solution (HBSS) at 37°C for 30 to 45 minutes with occasional vortex. The digestion was stopped by DMEM/F12 with 10% FBS. The digestion was subsequently passed through 100-μm filter and then another 70-μm filter, followed by a centrifugation at 300g for 5 minutes. The suspension or so-called SVF was mixed with red blood cell lysis buffer (Biolegend, 420301) for 5 minutes on ice. The cells were then centrifuged and resuspended.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: adipose tissue

tag: genotype

value: DB/DB


title: I-BET151_ChIP_input_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the human hg38 reference genome assembly using Bowtie2 (v2.2.5) (Langmead et al., 2012) with options: -3 5 --local.
The BAM files were removed the null and not unmapped reads using sambamba(v0.7.1)(Tarasov et al., 2015) view with the default parameter settings.
The BAM files were removed the duplicated reads using sambamba(v0.7.1)(Tarasov et al., 2015) markdup with the default parameter settings.
For peak calling, parameters used were macs2 (v2.1.2) (Zhang et al., 2008) callpeak with the default parameter settings. The peaks visualization in genome was showed by IGV software (Robinson et al., 2011).
The peaks annotations were performed with R package ChIPseeker (Yu et al., 2015) from the bioconductor project. Motif enrichment was done using HOMER with options: -fdr 0.05 -len 8,10,12.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamcoverage
Supplementary_files_format_and_content: peak text files

growth_protocol: 3*10^6 PPs were cultured in 10-cm dishes with basal medium (EF6):DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF and 10 μM 616452.

extract_protocol:
Cells cultured in a 10-cm dish (about 10^7 cells) were collected and fixed in 1% formaldehyde at RT for 10 min. Then, 0.125 M glycine was used to quench the reaction. After washed with 1× PBS twice, cells were harvested and lysed by Lysis Buffer and Cell Lysis Buffer in Magna ChIP A/G One-Day Chromatin Immunoprecipitation Kit (EMD Millipore Corp, Cat. #17-10086) step by step. Thereafter, the nuclear pellets were resuspended in Nuclear Lysis Buffer in Magna ChIP A/G One-Day Chromatin Immunoprecipitation Kit. The mixture was sonicated as 30s on, 30s off with 20 cycles. The sonication samples were centrifuged at 12000 rpm for 20 min at 4°C to harvest supernatant. 20 μl Protein A/G magnetic beads (EMD Millipore Corp) for each immunoprecipitation were washed with block buffer (1× PBST and 0.5% BSA) for 2 times. Before immunoprecipitation, Protein A/G magnetic beads and 2 μg antibodies were incubated at 4°C overnight followed by washed using block solution for 3 times. Moreover, the sonication supernatant was diluted in dilution buffer to 1 ml total volume and 20 μl of the mixture was left as input samples. Next, the sonication supernatant was incubated with beads at 4°C for 6-10 hours. After incubation, the Protein A/G beads, antibodies and chromatin formed the complex. And the complex was stepwise washed in 1 ml wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), high NaCl buffer (Wash supplemented with 500 mM NaCl) and TE buffer (10 mM Tris-HCl pH 8, 50 mM NaCl, 1 mM EDTA) at 4°C for 5min. Then, DNA fragments were eluted by incubating with 200 μl elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) at 65°C for 30 min followed by reversed in elution buffer with 0.2 M NaCl at 65°C overnight. Finally, RNA in these samples was digested with 0.2 mg/ml RNase A at 37°C for 2 h and protein was digested with 0.2 mg/ml proteinase K at 62°C for 2h and 95°C for 10 min. DNA was extracted by using DNA Clean & Concentrator-5 Kit (ZYMO, Cat. D4014).
ChIP and input DNA were quantified by Qubit before library preparation using the VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme).


title: S2 cells - Insulin-treated, RNA-seq, rep1

tag: cell line


title: I-BET151_ChIP_rep2

tag: chip antibody


title: PV-ADSCs DB/DB

description: perivascular


title: S-ADSCs WT

description: subcutaneous

value: wild type


title: PA14_DphoB_DlasR_PL_R1


title: I-BET151_ChIP_input_rep1


title: PV-ADSCs WT

description: perivascular


title: S2 cells - Vehicle-treated, RNA-seq, rep3

value: 25 mM HEPES, pH 8.2 for 4 hours


title: I-BET151_ChIP_rep1


title: C group_1

description: normal chow diet for three weeks


title: GSK126-treated cells rep3

city: BEIJING

first: Qianqian

last: Yin

address: 49 North Garden Road, Haidian District

department: Center of Basic Medical Research

institute: Peking University Third Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
aligned to the GRCm38.p4 (mm10) genome assembly using Hisat2（version:2.0.4）
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
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: GRCm38.p4 (mm10)
Supplementary_files_format_and_content: files include counts and RPKM values for each Sample

source_name: mouse B16F10 melanoma cells

growth_protocol: B16F10 melanoma cells were grown in Dulbecco's modified Eagle's medium (DMEM) or RPMI-1640 supplemented with 10% fetal bovine serum (FBS, GIBCO, CA, USA), 50 IU/mL penicillin, and 50 mg/mL streptomycin (Invitrogen, CA, USA). All cells were cultured at 37 ℃ in a humidified incubator in the presence of 5% CO2.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B16F10 melanoma cells were treated with GSK126 at 10 μM

value: mouse B16F10 melanoma cells


title: DMSO_ChIP_Input_rep2


title: PA14_DphoB_DlasR_BF_R3

value: biofilm


title: S2 cells - Vehicle-treated, RNA-seq, rep2


title: GSK126-treated cells rep2


title: PA14_DphoB_DlasR_BF_R2


title: PA14_DphoB_DlasR_BF_R1


title: DMSO_ChIP_rep2


title: GSK126-treated cells rep1


title: PA14_DphoB_BF_R3


title: DMSO_ChIP_Input_rep1


title: DMSO-treated cells rep3


title: S2 cells - Insulin-treated, ATAC-seq, rep2

description:
ATAC_Insulin.narrowPeak.gz
ATAC_Peak_Annotation.xlsx

extract_protocol:
S2 cells were incubated with 3 μM DAPI for 10 min. 60,000 cells per sample were sorted using a BD FACS Aria flow cytometer (BD Biosciences, San Jose, CA, USA). DAPI-negative cells were collected into ice-cold PBS (pH 7.4). After sorting, the samples were washed once with ice-cold PBS and centrifuged at 500 g for 5 min at 4 °C
Briefly, 50 μL lysis buffer (10 mM Tris-HCl 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) was added to each sample, and the sample was centrifuged at 500 g for 10 min at 4 °C. The supernatant was removed, and the nuclei pellet was tagmented using a Nextera DNA Library Prep kit (Illumina, Inc., San Diego, CA, USA) as previously described. Then, the tagmented DNA was purified using a Qiagen MinElute PCR Purification Kit (Qiagen, Germantown, MD, USA). The purified DNA was PCR amplified for 5 cycles using a Nextera DNA Library Index kit (Illumina) and Phusion HF Master Mix (New England BioLabs, Inc., Ipswich, MA, USA) with the following protocol: 72 °C for 5 min, 98 °C for 30 sec, and 5 cycles of 98 °C for 10 sec, 63 °C for 30 sec, and 72 °C for 1 min. A 5-μL aliquot of the pre-amplified reaction was analyzed by qPCR using SsoFast EvaGreen Supermix (Bio-Rad Life Science, Inc., Hercules, CA, USA) and an Applied Biosystems 7900HT qPCR instrument (ThermoFisher) using the following protocol: 1 cycle of 98 °C for 30 sec and 40 cycles of 98 °C for 10 sec, 63 °C for 30 sec, and 72 °C for 1 min. Then, the pre-amplified PCR mixture was amplified for another 10 cycles (corresponding to 1/3 maximum fluorescence from the qPCR assay) using the same thermocycling parameters. After amplification, the libraries were purified using AMPure XP beads (Beckman Coulter Life Sciences, Indianapolis, IN, USA)


title: PA14_DphoB_BF_R2


title: S2 cells - Insulin-treated, RNA-seq, rep2


title: DMSO_ChIP_rep1


title: S2 cells - Vehicle-treated, RNA-seq, rep1


title: DMSO-treated cells rep2


title: S2 cells - Insulin-treated, ATAC-seq, rep1


title: I-BET151_rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the human hg38 reference genome assembly using HISAT2(v2.1.0)(Kim et al., 2015) with the default parameter settings.
Gene expression based on GENCODE v34 annotations (Harrow et al., 2012) was determined using stringrie (Pertea et al., 2015) with the default parameter settings.Transcripts per million reads (TPM) were calculated for represented the expression of each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene TPM for every gene and every sample

growth_protocol: Undifferentiated MEL1 human embryonic stem cells were cultured in hPSC medium: DMEM/F12 (Life Technologies) supplemented with 20% KnockOut Serum Replacement (KSR) (Life Technologies), 1× Non-Essential Amino Acids (NEAA) (Life Technologies), 1× Penicillin/Streptomycin, 0.055 mM 2-Mercaptoethanol (Sigma), and 10 ng/ml bFGF (Peprotech). hPSCs were maintained on CF1 feeder cells in humidified incubator at 37°C and 5% CO2.  hPSCs were seeded into 10-cm dishes and cultured for four days before differentiation. The medium was changed every day. Then, hPSCs were washed by DPBS (Life Technologies) followed by dissociated into single cells using Accutase. The cells were counted and seeded at 5.5×10^6 cells per well of low-attached 6-well plates (Corning) in 5.5 ml hPSC medium supplemented with 10 ng/ml activin A (Peprotech) and 10 ng/ml heregulin B (Peprotech). The plates were plated on a shaker at 100 rpm in incubator to promote cell aggregates formation. The media were changed every day. The differentiation media are as follows: Day 1: RPMI (Life Technologies) including 1:5000 ITS-X (Gibco), 0.2% FBS, 100 ng/ml activin A, and 3 μM CHIR99021 (TargetMol). Day 2: RPMI containing 0.2% FBS, 1:2000 ITS-X, and 100 ng/ml activin A. Day 3: RPMI containing 0.2% FBS, 1:1000 ITS-X, 25 ng/ml KGF (Peprotech), and 2.5 μM A83-01 (TargetMol). Day 4-5: RPMI containing 0.4% FBS, 1:1000 ITS-X, and 25 ng/ml KGF. Day 6-7: DMEM containing 1:50 B27 (Gibco) and 3 nM TTNPB (Sigma). Day 8: DMEM containing 1:50 B27, 3 nM TTNPB and 50 ng/ml EGF (Peprotech). Day 9-11: DMEM containing 1:50 B27, 50 ng/ml KGF, and 50 ng/ml EGF. Day 12-18 (R6 medium): DMEM containing 1:50 B27, 0.05% BSA (Yeasen), 10 μM zinc sulfate (Vetec), 10 μg/ml heparin (Sigma), 10 μM 616452 (TargetMol), 1 μM T3 (Sigma), 0.2 μM LDN-193189 (Tocris), 0.2 μM Compound E (MedChem Express), 0.5 mM vitamin C, and 10 μM forskolin (TargetMol). Day 19-24 (R7 medium): DMEM containing 1:50 B27, 0.05% BSA, 10 μM zinc sulfate, 10 μg/ml heparin, 10 μM 616452, 1 μM T3, 1 mM N-acetyl cysteine (Sigma), 1 μM Trolox (Sigma), and 0.5 mM vitamin C. ePPs were cultured on feeder in EF6I medium: DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF, 10 μM 616452, and 1 μM I-BET151 (APExBIO). PPs were cultured in basal medium (EF6): DMEM containing 1:50 B27, 50 ng/ml EGF, 10 ng/ml bFGF and 10 μM 616452.

extract_protocol:
Cells were havested and total RNA was isolated using Quick-RNA MiniPrep Kit (ZYMO).
3 μg RNA per sample were used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: PA14_DphoB_BF_R1


title: PA14_DlasR_PL_R3


title: I-BET151_rep1


title: DMSO-treated cells rep1


title: S2 cells - Vehicle-treated, ATAC-seq, rep2

description:
ATAC_Vehicle.narrowPeak.gz
ATAC_Peak_Annotation.xlsx


title: S2 cells - Vehicle-treated, ATAC-seq, rep3


title: PA14_DlasR_PL_R2


title: DMSO_rep2


title: S2 cells - Vehicle-treated, ATAC-seq, rep1


title: Lung_Organoids_scRNAseq_MLL3_KO

data_processing:
ScRNA-seq alignment process was completed by cellranger(version 3.0.0)
Seurat V3 workflow
mm10
txt files with gene counts for scRNA-seq

source_name: replicates: MLL3_KO_Lung_Organoids

extract_protocol: Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform

treatment_protocol: Preparation: Collect 3ml herprized peripheral blood from patient. Put all regent, 1×ACK, 0.04% PBS-BSA, and sample on ice;Lyse RBCs;Centrifuge at 300g, RT for 3min;Collect the plasma (around 1.5ml) in an EP tube;Add 30ml 1×ACK to resuspend blood by inverting the tube;Put the mixed ACK-sample on ice and lysis for <7min (keep inverting the tube during lysis);Centrifuge at 300g, RT for 3min;Discard the supernatant;Add 10ml 1×ACK to lysis again;Lysis on ice for <5min (keep inverting the tube during lysis);Centrifuge at 300g, RT for 3min;Discard the supernatant.;Wash and count (get rid of dead cells);Resuspend cells by 5ml 0.04% PBS-BSA pre-cold buffer;Mix throughout by pipetting;Suck out 10ul for counting (add 10ul Typan Blue);Suck out 2×106 cells into EP tube and put the remaining cells on ice;Centrifuge the EP tube at 100g, RT for 3min;Discard the supernatant;Resuspend the cells using 1ml 0.04%PBS-BSA buffer;Centrifuge at 100g, RT for 3min;Discard the supernatant;Resuspend the cells using 830ul 0.04%PBS-BSA buffer;Count (both living and dead cells) twice;Keep the density of living cells between 0.7~1.2×106/ml;Freeze the remaining cells

value: Lung

tag: plasmids


title: Lung_Organoids_scRNAseq_scram

source_name: replicates: scram_Lung_Organoids


title: S2 cells - Insulin-treated, ATAC-seq, rep3


title: Liver_scRNAseq_PRM

source_name: replicates: PRM_Liver

value: Liver


title: SC-β

value: human embryonic stem cell (hESC) line

value: hPSC-derived pancreatic beta-like cells


title: PA14_DlasR_BF_R2


title: PA14_DlasR_BF_R3


title: ePP-β_rep2

value: ePP-derived pancreatic beta-like cells


title: Left_lung_scRNAseq_PRM

source_name: replicates: PRM_Left_lung


title: PA14_DlasR_BF_R1


title: Lung_WGBS_seq_PRMK_rep2

data_processing:
WGBS reads were aligned to the mm10 genome assembly using BS-Seeker2(v2.1.8)
Bismark was used to call methylation
mm10
CGmap.gz files for WGBS

source_name: replicates: PRMK_rep2

extract_protocol:
genomic DNA
After in situ transplantation, lung organoids carrying Trp53 and Rb1 mutations and Myc overexpression lead to single primary PRM in recipient mice. And lung organoids carrying Trp53, Rb1 and kmt2c mutations and Myc overexpression lead to single primary PRMK in recipient mice.

treatment_protocol: PRM and PRMK tumor tissue  were harvested from the recipient mice. The PRM and PRMK tumor tissue  were harvested from the recipient mice at ~3-4 mouths after transplantation.


title: ePP-β_rep1


title: Lung_WGBS_seq_PRMK_rep1

source_name: replicates: PRMK_rep1


title: PA14_BF_3


title: Lung_WGBS_seq_PRM_rep2

source_name: replicates: PRM_rep2


title: PA14_DlasR_PL_R1

value: planktonic


title: ePP-P21_rep1

value: expandable pancreatic progenitor cells


title: DMSO_rep1

value: hPSC-derived pancreatic progenitor cells


title: PA14_BF_2


title: ePP-P21_rep2


title: PA14_BF_1


title: Lung_WGBS_seq_PRM_rep1

source_name: replicates: PRM_rep1

extract_protocol:
genomic DNA
After in situ transplantation, lung organoids carrying Trp53 and Rb1 mutations and Myc overexpression lead to single primary PRM in recipient mice. And lung organoids carrying Trp53 ，Rb1 and kmt2c mutations and Myc overexpression lead to single primary PRMK in recipient mice.


title: Lung_RNA_seq_PRMKScramble_rep3

description:
1_RNAseq3_sgMeis2_VS_sgScr_result_all.csv
1_RNAseq3_sgMeis2_VS_sgScr_result_DEGs.csv

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM)
GRCm38
txt files with gene counts, TPM

source_name: replicates: PRMKScramble_rep3

extract_protocol: RNA was extracted with Trizol

treatment_protocol: PRM lung,PRM liver and PRMK lung organoids were harvested from the recipient mice.


title: PA14rsmAsfa3_R3

city: London

first: Luke

last: Allsopp

address: Emmanuel Kaye Building, 1B Manresa Roa

institute: Imperial College

data_processing:
The NGS library pool was single-read sequenced on an Illumina NextSeq 500 system using 75 bp read length. Greater than 10 million reads were obtained for each sample.
Trimmed and rRNA depleted RNA-seq reads were mapped to the Pseudomonas aeruginosa UCBPP-PA14, complete genome ('NC_008463') using CLC Genomics Workbench and more than 99% of reads matched. Greater than 8 million reads were obtained for each sample post depletion.
Expression values in RPKM (Reads Per Kb exon (contig) per Million mapped reads) were calculated following (Mortazavi et al. 2008, Nat Methods. 5(7):621-8) and can be directly compared to each other.
A matrix of read counts was generated. DESeq2 package was used to assess differential gene expression (Love, M.I., Huber, W. and Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15, 550). All statistical analyses were performed in R version x64 4.0.2 (Team, R.C. (2020), Vienna, Austria.). Statistically significant differences in gene expression were assessed by the Wald test and adjusted for multiple comparisons using the Benjamini–Hochberg false-discovery rate correction. P-adjusted <0.05 was deemed significantly differentially expressed.
Genome_build: Pseudomonas aeruginosa UCBPP-PA14, complete genome ('NC_008463')

source_name: Shaking culture

growth_protocol: All strains were grown overnight and sub-cultured in TSB. Strains were grown at 37°C to log phase (OD600nm of 0.8).

extract_protocol:
Volumes containing 0.75 OD units (approximately 10^8 bacteria) of each sample were collected, spun down, and resuspended in directly 100 μl of formamide (95%) containing 1% Beta-mercaptoethanol, 18 mM EDTA and 0.025% SDS. Total RNA was isolated from the resuspended cell pellets using the RNAsnap protocol developed by Stead et al. (2012). The RNA extracted was examined by capillary electrophoresis before rRNA depletion using Vertis Biotechnologie depletion probes.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The TruSeq barcode sequences, which are part of the 5' and 3' TruSeq sequencing adapters. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The cDNA pool was eluted in the size range of 200– 500 bp from a preparative agarose gel. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis (Fig. 3). The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.


title: ePP-P9_rep1


title: ePP-P9_rep2


title: PA14rsmAsfa3_R2


title: Whole body except venom gland, rep3

city: Goyang-si

first: Jungsuk

last: Sung

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

institute: Life science

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated. In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
The trimmed reads for all samples that should be compared each other are merged into one file to do transcriptome assembly. Merged data is assembled using Trinity program, a generally utilized for de novo reconstruction of transcriptomes, combining read sequences of a certain length of overlap to form longer fragments without N gaps, called contigs.
For assembled genes, the longest contig of the assembled contigs are filtered and clustered into the non-redundant transcripts using CD-HIT-EST program. We defined these transcripts as unigenes. Obtained unigenes are used for the subsequent annotation and ORF prediction. The abundance of unigenes across samples is estimated by RSEM algorithm. The expression level is calculated as read count.
Genome_build: In order to build a reference for Agelena koreana RNA-seq analysis, sequencing reads from this study were merged and assembled by Trinity.
Supplementary_files_format_and_content: Fasta files include assembled gene, unigenes, and predicted open read frame by trinity and transdecoder software.
Supplementary_files_format_and_content: tsv file include raw gene counts and FPKM values for every gene and every sample.

organism: Agelena koreana

source_name: whole body without venom gland

growth_protocol: The spider Agelena koreana was collected from Chungbuk, Korea. The venom glands of the spider were separated from the chelicerae and stored after washing in phosphate buffered saline.

extract_protocol:
TRIzol reagent (Life Technologies, Grand Island, NY, USA) was used for extracting total RNA and subsequent RNA sequencing using NGS method was followed (Macrogen, Seoul, Korea). The sequencing was performed in triplicates for both venom gland and body, producing 6 data pools.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

value: whole body without venom gland


title: Whole body except venom gland, rep2


title: cont_SLN_#11R

type: RNA

city: Fukuoka

first: Tomoko

last: Tanaka

address: 7-45-1 Nanakuma, Jonan-ku

institute: Fukuoka University

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay Mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: submandibular lymph node, 3days, PBS

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from SLNs using TRIzol Reagent (Thermo Fisher Scientific) and purified using Purelink RNA Purification Kit (Thermo Fisher Scientific)  according to the manufacturer's instructions.

value: submandibular lymph node

value: SLNs injected with PBS


title: cont_SLN_#9R


title: cont_SLN_#10L


title: meta_SLN_#1R

source_name: submandibular lymph node, 3days, B16-F10

value: SLNs implanted with B16-F10


title: Whole body except venom gland, rep1


title: meta_SLN_#8R


title: meta_SLN_#3R


title: PP2


title: DE

value: hPSC-derived definitive endoderm cells


title: Lung_RNA_seq_PRMKMeis2_rep3

source_name: replicates: PRMKMeis2_rep3


title: Lung_RNA_seq_PRMKScramble_rep1

source_name: replicates: PRMKScramble_rep1


title: hPSC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed low-complexity or low-quality sequence.
Sequencing reads were mapped to the human hg38 reference genome assembly using HISAT2(v2.1.0)(Kim et al., 2015) with the default parameter settings.
Gene expression based on GENCODE v34 annotations (Harrow et al., 2012) was determined using stringrie (Pertea et al. 2015) with the default parameter settings.Transcripts per million reads (TPM) were calculated for represented the expression of each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene TPM for every gene and every sample

value: MEL1 hESC line


title: Lung_RNA_seq_PRMKMeis2_rep2

source_name: replicates: PRMKMeis2_rep2


title: Venom gland, rep2

source_name: venom gland

value: venom gland


title: PA14rsmAsfa2_R3


title: N_5

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: ftp://mirbase.org/pub/mirbase/CURRENT/
Supplementary_files_format_and_content: normalized counts

organism: Camelus bactrianus

source_name: Normal camels

growth_protocol: On July, 27th, 2020, thin camels (n = 5) and normal camels (n = 5) were obtained from Shibatai Township, Zhuozishan Town, Wulanchabu, Inner Mongolia, and the blood (80 mL) were taken from each camel.

extract_protocol:
Total RNA was extracted from the plasma-derived exosomes of thin camels and normal camels using mirVANA miRNA Isolation kit (Takara Biomedical Technology Co., Ltd., Beijing, China) according to the manufacturer’s recommendations, and then the quality and concentrations of the total RNA were assessed using a microplate reader (OD260/280). After that, the total RNA was sent to OBiO Technology (Shanghai) Corp., Ltd (China) for small RNA sequencing.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Exosomes were obtained by supercentrifugation

tag: group

value: Normal camels

tag: weight

value: Plasma

tag: molecule type

value: Small RNA


title: PA14rsmAsfa2_R2


title: PA14rsmAsfa3_R1


title: Lung_RNA_seq_PRMKMeis2_rep1

source_name: replicates: PRMKMeis2_rep1

value: Lung


title: Lung_RNA_seq_PRMK_rep3

description:
1_RNAseq2_PRMK_VS_PRM_result_all.csv
1_RNAseq2_PRMK_VS_PRM_result_DEGs.csv

source_name: replicates: PRMK_rep3


title: N_4


title: PA14rsmAsfa2_R1


title: PA14rsmArpoN_R3

value: rsmArpoN


title: Venom gland, rep1


title: Venom gland, rep3


title: N_3


title: Lung_RNA_seq_PRMKScramble_rep2

source_name: replicates: PRMKScramble_rep2


title: N_2


title: Gargle_inactivation

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

description: Inactivated viral particles and synthetic RNA (IVT spike-in control) were added to saline gargle samples to test the sensitivity of Swab-Seq at various concentrations.

data_processing:
Library strategy: Swab-Seq
BCL files converted to fastq files with bcl2fastq2.
Reads with appropriate barcodes demultiplexed with custom python script.
Fastq files mapped to reference sequences and concatenated by barcodes using kallisto and BUStools.
Further filtering, calculation of S2/Spike-in ratio, and data visualization performed in R.
Genome_build: Custom reference that includes SARS-CoV-2 S2 sequence, spike-in control sequence, and RPP30 gene.
Supplementary_files_format_and_content: Two kinds of processed data files are provided: *.data.txt and *.metadata.txt. *.data.txt files are tab-separated files with 4 columns. Column 1 is a barcode sequence that addresses a specific well in the experiment. Column 2 is a placeholder (represents a UMI sequence for BUStools) that lists "A" for all samples. Column 3 is an indicator of which target sequence is quantified (0 = S2, 1 = spike-in control, 4 = RPP30). Column 4 provides the counts of reads mapping to the indicated target sequence. *.metadata.txt are tab-separated files that provide information about the conditions of each well in the experiment. The first 5 columns of metadata files are standard. Column 1 is the well barcode (consistent with the well barcodes in the *.data.txt files). Column 2 is the i7 portion of the barcode. Column 2 is the i5 portion of the barcode. Column 4 indicates the plate ID (just "Plate1" if there was only one plate in the experiment). Column 5 indicates the well of the plate that the barcode represents (wells A01 through H12). A variable number of additional columns are provided, depending on the experiment. The column header indicates the information provided.

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Saline gargle samples with heat-inactivated SARS-CoV-2 viral particles

extract_protocol: An extraction-free protocol was used to amplify viral RNA from inactivated particles in this experiment. Barcoded primers targeting human RPP30 and SARS-CoV-2 S genes amplify targets in parallel. Samples contain S spike-in control RNA for normalization.

tag: experimental design ("serial dilution" or "positive/negative")

value: Serial dilution

tag: pcr kit

value: TaqPath Multiplex

tag: pcr cycles

tag: viral inactivation

value: 65C for 30min or 95C for 10, 20, or 30min


title: N_1


title: PA14rsmArpoN_R2


title: Lung_RNA_seq_PRMK_rep2

source_name: replicates: PRMK_rep2


title: Lung_RNA_seq_PRMK_rep1

source_name: replicates: PRMK_rep1


title: Saliva_dilutions_96_vs_384

description: Inactivated viral particles and synthetic RNA (IVT spike-in control) were added to saliva samples to test the sensitivity of Swab-Seq at various concentrations.

source_name: Heat-inactivated SARS-CoV-2 viral particles from ATCC in saliva samples

value: 95C for 30min


title: RNA_vs_virus

description: Viral RNA (synthetic RNA and IVT spike-in control) or inactivated viral particles and human DNA (RPP30 sequence) were combined to test the sensitivity of Swab-Seq at various concentrations.

source_name: Synthetic SARS-CoV-2 RNA from Twist Bioscience or heat-inactivated SARS-CoV-2 viral particles from ATCC

extract_protocol:
Either synthetic RNA  or an extraction-free protocol to amplify viral RNA from inactivated particles was used in this experiment
Barcoded primers targeting human RPP30 and SARS-CoV-2 S genes amplify targets in parallel. Samples contain S spike-in control RNA for normalization.


title: Liver_ATAC_seq_PRM_Liver_rep2

data_processing:
ATAC-Seq reads were aligned to the mm10 genome assembly using Bowtie2(2.2.1)
HMMRATAC was used to call peaks
mm10
gappedPeak files for ATAC-Seq

source_name: replicates: PRM_Liver_rep2

extract_protocol:
genomic DNA
The organoids were harvested at 3 days after culture, and were gently digested into single cell suspension using TrypLE. 20,000 cells were used for ATAC-seq.  Library preparation was performed as previously described (2013 Buenrostro). Briefly, cells were washed lysed using lysis buffer followed by transposase reaction  (Novoprotein). Transposed DNA was purified using MinElute PCR Purification kit (Qiagen) and amplified using NEBNext High-Fidelity 2X PCR Master Mix(NEB) followed by purified using MinElute PCR Purification kit (Qiagen).

treatment_protocol: PRM lung，PRM liver and PRMK lung organoids were harvested from the recipient mice.

value: Liver


title: PA14rsmA_R3

source_name: Shaking culture

value: rsmA


title: Liver_ATAC_seq_PRM_Liver_rep1

source_name: replicates: PRM_Liver_rep1


title: Saliva_dilutions_various_conditions

value: TaqPath Multiplex/TaqPath CG


title: PA14rsmA_R2


title: T_4

source_name: Thin camels

value: Thin camels


title: Lung_ATAC_seq_PRMK_rep2


title: PA14rsmA_R1


title: Lung_ATAC_seq_PRMK_rep1


title: RNA_samples_50cycles

description: Viral and human RNA

source_name: Extracted RNA from Nasopharyngeal Swabs

extract_protocol: Nasopharyngeal swab samples were collected from the upper respiratory system of each participant under the supervision of a health care professional and placed into 3ml of the CDC formulation Viral Transport Media (VTM, https://www.cdc.gov/csels/dls/locs/2020/new_sop_for_creating_vtm.html). Swabs in VTM were stored at 4C until RNA extraction, which was performed within 72 hours of collection for all samples. For testing, 200 μl of VTM was used for RNA extraction using Zymo Quick-RNA 96 Viral kit and eluted in 30 μl. Barcoded primers targeting human RPP30 and SARS-CoV-2 amplify targets in parallel. Samples contain S2 spike-in control for normalization.

value: Positive/negative

value: RNA extraction


title: T_3


title: RNA_samples

description: Viral and human RNA


title: T_2


title: PA14_R2

value: wild type


title: PA14rsmArpoN_R1


title: Stability_test

description: Inactivated viral particles and synthetic RNA (IVT spike-in control) were added to saliva and saline gargle samples to test the stability of viral particles in collected samples for Swab-Seq.

source_name: Saline gargle or saliva samples with heat-inactivated SARS-CoV-2 viral particles

extract_protocol: An extraction-free protocol for either saliva or saline gargle was used to amplify viral RNA from inactivated particles in this experiment. Barcoded primers targeting human RPP30 and SARS-CoV-2 S genes amplify targets in parallel. Samples contain S spike-in control RNA for normalization.

value: 95C or 65C for 30min


title: LungATAC_seq_PRM_rep2

source_name: replicates: PRM_rep2


title: Multiplex_vs_CG

description: Viral RNA (synthetic RNA and IVT spike-in control) and human DNA (RPP30 sequence) were combined to test the sensitivity of Swab-Seq at various concentrations.

source_name: Synthetic SARS-CoV-2 RNA from Twist Bioscience

extract_protocol: Synthetic RNA and DNA were used in this experiment. Barcoded primers targeting human RPP30 and SARS-CoV-2 S genes amplify targets in parallel. Samples contain S spike-in control RNA for normalization.


title: Luna_vs_Taqpath

value: Luna/TaqPath Multiplex


title: LungATAC_seq_PRM_rep1

source_name: replicates: PRM_rep1


title: T_5

value: Plasma


title: IfngKO Hematopoietic stem cell RNA-seq 3

status: Public on Feb 22 2022

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

data_processing:
For RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4
For RNA-seq gene counts were derived with  htseq-count v0.8.0
RNA-seq quantification, normalization, and differnetial gene expression as performed using EdgeR release 3.9
Genome_build: mm10
Supplementary_files_format_and_content: cpm tables

source_name: IfngKO HSC RNA-seq 3

extract_protocol:
For RNA-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-) and Rps (Lin-, cKit+, Sca1+, C-150- CD48+) were sorted from a pooled sample of 2 male and 2 female 8-week old mice HSCs were purified from three or four biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE: Dnmt3a+/+; Tet2+/+ or Vav-CRE:Dnmt3afl/fl or + or Vav-CRE:Tet2fl/fl  mice.  Total RNA was isolated from the samples using the NucleoSpin RNA XS kit
The SMARTer Ultra Low RNA kit (Clontech) was used to prepare the libraries from 3-5ng of total RNA.

treatment_protocol: Mice of different genotype were treated with two doses of 10ug of recombinant mouse IFNg or volume-equivalent PBS. A 24h resting peroid was included between the two doses. Mice were sacrificed 2h post-second dose.

value: IfngKO

tag: age

tag: cre-driver

value: Vav

value: Hematopoietic stem cell

tag: treatment

value: PBS


title: Dnmt3a IFNg Hematopoietic stem cell RNA-seq 7

source_name: Dnmt3a IFNg HSC RNA-seq 7

tag: cell type

value: IFNg


title: IfngKO Hematopoietic stem cell RNA-seq 2

source_name: IfngKO HSC RNA-seq 2

tag: strain


title: PA14_R1


title: IfngKO Hematopoietic stem cell RNA-seq 1

source_name: IfngKO HSC RNA-seq 1


title: Dnmt3a IFNg Hematopoietic stem cell RNA-seq 6

source_name: Dnmt3a IFNg HSC RNA-seq 6


title: Dnmt3a IFNg Hematopoietic stem cell RNA-seq 5

source_name: Dnmt3a IFNg HSC RNA-seq 5


title: Dnmt3aKO-IfngrKO Hematopoietic stem cell RNA-seq 2

source_name: Dnmt3aKO-IfngrKO HSC RNA-seq 2


title: Dnmt3aKO-IfngrKO Hematopoietic stem cell RNA-seq 3

source_name: Dnmt3aKO-IfngrKO HSC RNA-seq 3


title: PA14_R3


title: Dnmt3aKO-IfngrKO Hematopoietic stem cell RNA-seq 1

source_name: Dnmt3aKO-IfngrKO HSC RNA-seq 1


title: Control IFNg Hematopoietic stem cell RNA-seq 5

source_name: Hematopoietic Stem Cell

value: Wild-type


title: Control IFNg Hematopoietic stem cell RNA-seq 6


title: T_1

tag: tissue

value: Small RNA


title: Tet2KO Restricted Progenitor RNA-seq 4

source_name: Restricted Progenitor

tag: genotype

value: Restricted Progenitor


title: Tet2KO Restricted Progenitor RNA-seq 5


title: Tet2KO Restricted Progenitor RNA-seq 2


title: Control IFNg Hematopoietic stem cell RNA-seq 3


title: Control Restricted Progenitor RNA-seq 5


title: Control Restricted Progenitor RNA-seq 3


title: IfngKO Hematopoietic stem cell RNA-seq 5

source_name: IfngKO HSC RNA-seq 5


title: Tet2KO Hematopoietic stem cell RNA-seq 4


title: Control Restricted Progenitor RNA-seq 1


title: Tet2KO Restricted Progenitor RNA-seq 1


title: Control Restricted Progenitor RNA-seq 2


title: Dnmt3a IFNg Hematopoietic stem cell RNA-seq 8

source_name: Dnmt3a IFNg HSC RNA-seq 8


title: Tet2KO Hematopoietic stem cell RNA-seq 1


title: Tet2KO Hematopoietic stem cell RNA-seq 3


title: Tet2KO Hematopoietic stem cell RNA-seq 2


title: Dnmt3aKO Hematopoietic stem cell RNA-seq 4


title: Dnmt3aKO-IfngrKO Hematopoietic stem cell RNA-seq 4

source_name: Dnmt3aKO-IfngrKO HSC RNA-seq 4


title: Control Hematopoietic stem cell RNA-seq 4


title: Control Hematopoietic stem cell RNA-seq 2


title: Control Hematopoietic stem cell RNA-seq 3


title: dp-1

city: Beijing

first: Hao

last: Dong

address: Huatuo road NO.31

institute: National Institutes for Food and Drug Control

description: Gram-negative bacteria

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GCA_000054005
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Brucella abortus 2308

source_name: B. abortus dp-1

growth_protocol: B. abortus 2308 and the clpP mutant were grown in TSB at 37℃ until the log phase was reached

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately, The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B. abortus 2308 was obatined from IVDC, and the clpP mutant was constructed by homologous recombination

value: clpP mutant


title: Control IFNg Hematopoietic stem cell RNA-seq 2


title: dp-3

description: Gram-negative bacteria


title: A2308_1

description: Gram-negative bacteria

source_name: B. abortus A2308

value: control


title: A2308_3

description: Gram-negative bacteria


title: CRH_Hu600

city: Toronto

first: Etienne

last: Sibille

state: Ontario

address: RM,133, 250 college street

department: Neuroscience of Aging and Depression

country: Canada

institute: Center for Addiction and Mental Health

data_processing:
2x100 bp paired-end reads were aligned to GRCh38 human reference genome (ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/dna/) using HiSat2 (default settings) and Genomic-Alignments (Lawrence et al., 2013).
Noise was corrected by removing low expressing genes if 1) they had less than ten reads and 2) were not detected in more than two thirds of samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: .csv (count matrix)

extract_protocol:
For cell collection, 12 µm-thick fresh-frozen sgACC sections were thaw-mounted onto polyethylene naphthalate-membrane slides (Leica Microsystems, Concord, ON, Canada; 11600289) and stored at -80°C. CRH-expressing inhibitory neurons were visualized using FISH labeling with RNAScope Multiplex Fluorescent V2 Assay (Advanced Cell Diagnostics; catalog no. 323100) with some modification. On the day of experiment, slides were taken from -80°C and immediately immersed in chilled 4% PFA diluted in PBS for 5 minutes. Sections were dehydrated by dipping slides serially in 50%, 70%, 100% ethanol and a hydrophobic barrier was drawn around each tissue section.  Sections were treated with hydrogen peroxide for 7 minutes to inactivate endogenous peroxidase and further treated with Protease 3 for 7 minutes at room temperature. After PBS wash, human CRH probe was applied on the section and incubated at 40°C for 1 hour. Excessive probes were removed by rinsing sections twice with wash buffer for several seconds and selective signal amplification was achieved by sequential incubation of Amp 1-3, HRP-C1, TSA Plus Fluorescein (PerkinElmer; catalog no. NEL741E001KT) and HRP blocker. After the final wash, tissue sections were counterstained with Neurotrace red (Thermo Fisher Scientific; catalog no. N21482) and dehydrated with 100% ethanol. ~150 cells were collected from layer 1-3 of gray matter per each subject using a LMD7 system (Leica Microsystems) and processed for RNA extraction using Picopure RNA isolation kit (Thermo Fisher Scientific; catalog no. KIT0204).
Sequencing libraries are prepared using the SMARTer Stranded Total RNA-Seq Kit Pico Input Mammalian (Clontech, Mountain View, CA, USA; catalog no. 634413). cDNA fragment size distribution of each library was determined with Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to check the presence of adapter dimers and gDNA contamination. Libraries were pooled and sequenced using Illumina MiSeq system (Illumina, San Diego, CA, USA) for quality check (QC), and then Illumina NovaSeq 6000 sequencer at Donnelly Sequencing Center at the University of Toronto (ccbr.utoronto.ca/donnelly-sequencing-centre).

value: Major Depressive Disorder (MDD)

tag: pair

tag: pmi

tag: ph

tag: rna ratio

tag: rin

tag: suicide

tag: recurrent

tag: antidepressant

tag: alcohol

value: Subgenual anterior cingulate cortex (sgACC)


title: CRH_Hu1001

tag: group


title: CRH_Hu943

tag: age


title: CRH_Hu863


title: CRH_Hu809


title: A2308_2

description: Gram-negative bacteria


title: CRH_Hu1047

value: Control


title: CRH_Hu1031


title: CRH_Hu852


title: Dnmt3aKO Hematopoietic stem cell RNA-seq 2

tag: cre-driver


title: CRH_Hu615


title: Dnmt3aKO Hematopoietic stem cell RNA-seq 1

tag: treatment


title: CRH_Hu789


title: dp-2

description: Gram-negative bacteria


title: C2C12 cells, Neg siRNA, 1

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

data_processing:
Real time Analysis (RTA):  HiSeq 2000
Base-calling: bcl2fastq v1.8.4
Alignment: Reads in gzipped fastq format were aligned using Tophat2 version-2.0.12 with --mate-inner-dist 100 --mate-std-dev 50  to the Mouse genome GRCm38, Ensembl release 76.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 76 were counted  with HTSeq-count and reads mapping to exons were counted using an exon level flattened GTF wile with dexseq-count.py
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: gene_level_counts.txt: Gene expression counts using reads aligning to annotated exon features of 41388 genes
exon_level_counts.txt: Exon level expression counts using reads aligning to annotated exon features. 3,74,286 exons from 41,388 genes quantified
Rbm_siRNA_vs_Neg_siRNA_edgeR_results_annotated.txt: Gene level differential expression in Rbm39 siRNA transfected cells vs negative control siRNA cells. Genewise statistical tests for higher expression in Rbm39 siRNA samples calculated using edgeR's glmLRT. Genes with at least 10 reads across three samples, total 13334 genes, were classified as expressed and used in the model.
Rbm_siRNA_vs_Neg_siRNA_DEXseq_results.txt: Exon level differential expression results calculated with DEXseq. All comparisons( total 374429 comparisons)  included in the results

source_name: C2C12 cells, Neg siRNA

extract_protocol:
RNA was extracted with RNeasy Micro kit (Qiagen)
Libraries were prepared with a TruSeq Stranded mRNA Library Prep Kit (Illumina)
Paired-end stranded RNAseq

value: Non targeting control siRNA

tag: cell line

value: C2C12 mouse myoblast

value: cells transfected with siRNA for 24 hrs


title: C2C12 cells, Rbm siRNA, 1

source_name: C2C12 cells, Rbm siRNA

value: RBM39 siRNA

value: RBM39 knockdown


title: C2C12 cells, Neg siRNA, 3


title: C2C12 cells, Rbm siRNA, 3


title: C2C12 cells, Neg siRNA, 2


title: KO_ENU_rep3

first: Jian

last: Mao

address: 2318 Yuhangtang Rd

institute: Hangzhou Normal University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 and paired-end clean reads were aligned to the reference genome using Hisat2.
HTSeq was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen). A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Age-matched WT and G1 Tert-/- mouse cohorts were treated with 150 μg g-1 ENU (Sigma-Aldrich) or saline by intraperitoneal, livers were extracted after 24 h of injection.

tag: strain

value: Liver

value: G1 Tert-/-

value: ENU


title: KO_Control_rep3

tag: tissue

value: Saline (Control)


title: KO_Control_rep2

tag: genotype


title: C2C12 cells, Rbm siRNA, 2


title: KO_Control_rep1


title: CRH_Hu513

tag: pair


title: WT_ENU_rep3

value: WT


title: CRH_Hu1086

tag: pmi


title: WT_ENU_rep1


title: Cultivated peanut 180930I_SY01_P1_H20_SAAS_339_191127

type: genomic

city: Jinan

first: rz

last: Tian

state: Shandong

address: 202 North Industrial Road

institute: SAAS

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
As per manufacturer (Affymetrix)
Genotype Call (SNP call): 'ATCG' type or '---' (means NoCall)

organism: Arachis hypogaea

source_name: Cultivated peanut

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Field collection or laboratory cultivation

extract_protocol: Unkown

value: leaf


title: WT_Control_rep3


title: WT_ENU_rep2


title: WT_Control_rep1


title: Cultivated peanut 180930I_SY01_P1_H18_SAAS_338_191127


title: Cultivated peanut 180930I_SY01_P1_H16_SAAS_337_191127


title: WT_Control_rep2


title: Cultivated peanut 180930I_SY01_P1_H14_SAAS_336_191127


title: Cultivated peanut 180930I_SY01_P1_H10_SAAS_334_191127


title: Cultivated peanut 180930I_SY01_P1_H12_SAAS_335_191127


title: Cultivated peanut 180930I_SY01_P1_H04_SAAS_302_191127


title: Cultivated peanut 180930I_SY01_P1_H08_SAAS_333_191127


title: KO_ENU_rep2


title: Cultivated peanut 180930I_SY01_P1_H02_SAAS_177_191127


title: Cultivated peanut 180930I_SY01_P1_H06_SAAS_331_191127


title: Cultivated peanut 180930G_SY01_P1_P19_SAAS_036_191127


title: KO_ENU_rep1


title: Cultivated peanut 180930G_SY01_P1_P13_SAAS_006_191127


title: Cultivated peanut 180930G_SY01_P1_F16_SAAS_223_191127


title: Cultivated peanut 180930G_SY01_P1_F18_SAAS_226_191127


title: Cultivated peanut 180930G_SY01_P1_P15_SAAS_007_191127


title: Cultivated peanut 180930G_SY01_P1_P21_SAAS_040_191127


title: Cultivated peanut 180930G_SY01_P1_F22_SAAS_229_191127


title: Cultivated peanut 180930G_SY01_P1_P23_SAAS_050_191127


title: Cultivated peanut 180930I_SY01_P1_F24_SAAS_133_191127


title: Cultivated peanut 180930G_SY01_P1_F14_SAAS_222_191127


title: Cultivated peanut 180930G_SY01_P1_F06_SAAS_217_191127


title: Cultivated peanut 180930G_SY01_P1_F12_SAAS_221_191127


title: Cultivated peanut 180930G_SY01_P1_F04_SAAS_215_191127


title: Cultivated peanut 180930G_SY01_P1_F10_SAAS_220_191127


title: Cultivated peanut 180930G_SY01_P1_F02_SAAS_214_191127


title: Cultivated peanut 180930G_SY01_P1_D24_SAAS_213_191127


title: Cultivated peanut 180930G_SY01_P1_D22_SAAS_212_191127


title: Cultivated peanut 180930G_SY01_P1_D16_SAAS_202_191127


title: Cultivated peanut 180930G_SY01_P1_P17_SAAS_021_191127


title: Cultivated peanut 180930G_SY01_P1_D06_SAAS_191_191127


title: Cultivated peanut 180930G_SY01_P1_D20_SAAS_210_191127


title: Cultivated peanut 180930G_SY01_P1_F20_SAAS_228_191127


title: Cultivated peanut 180930G_SY01_P1_D18_SAAS_208_191127


title: Cultivated peanut 180930G_SY01_P1_D12_SAAS_197_191127


title: Cultivated peanut 180930G_SY01_P1_D10_SAAS_195_191127


title: Cultivated peanut 180930G_SY01_P1_D14_SAAS_198_191127


title: Cultivated peanut 180930G_SY01_P1_D08_SAAS_194_191127


title: Cultivated peanut 180930G_SY01_P1_B18_SAAS_143_191127


title: Cultivated peanut 180930G_SY01_P1_B20_SAAS_144_191127


title: Cultivated peanut 180930G_SY01_P1_D02_SAAS_167_191127


title: Cultivated peanut 180930G_SY01_P1_B16_SAAS_132_191127


title: Cultivated peanut 180930G_SY01_P1_B24_SAAS_146_191127


title: Cultivated peanut 180930G_SY01_P1_B10_SAAS_090_191127


title: Cultivated peanut 180930G_SY01_P1_D04_SAAS_169_191127


title: Cultivated peanut 180930G_SY01_P1_B14_SAAS_104_191127


title: Cultivated peanut 180930G_SY01_P1_B08_SAAS_085_191127


title: Cultivated peanut 180930G_SY01_P1_F08_SAAS_219_191127


title: Cultivated peanut 180930G_SY01_P1_B22_SAAS_145_191127


title: Cultivated peanut 180930F_SY01_P1_P07_SAAS_317_191127


title: Cultivated peanut 180930G_SY01_P1_B12_SAAS_103_191127


title: Cultivated peanut 180930G_SY01_P1_B02_SAAS_055_191127


title: Cultivated peanut 180930G_SY01_P1_B04_SAAS_057_191127


title: Cultivated peanut 180930F_SY01_P1_P03_SAAS_315_191127


title: Cultivated peanut 180930F_SY01_P1_P09_SAAS_318_191127


title: Cultivated peanut 180930F_SY01_P1_P11_SAAS_319_191127


title: Cultivated peanut 180930F_SY01_P1_P05_SAAS_316_191127


title: Cultivated peanut 180930F_SY01_P1_P01_SAAS_314_191127


title: Cultivated peanut 180930F_SY01_P1_N21_SAAS_312_191127


title: Cultivated peanut 180930F_SY01_P1_N23_SAAS_313_191127


title: Cultivated peanut 180930E_SY01_P1_N17_GAAS_309_191127


title: Cultivated peanut 180930E_SY01_P1_N15_GAAS_308_191127


title: Cultivated peanut 180930E_SY01_P1_N13_GAAS_307_191127


title: Cultivated peanut 180930E_SY01_P1_N11_GAAS_306_191127


title: Cultivated peanut 180930E_SY01_P1_N09_GAAS_305_191127


title: Cultivated peanut 180930E_SY01_P1_N01_GAAS_300_191127


title: Cultivated peanut 180930E_SY01_P1_N05_GAAS_303_191127


title: Cultivated peanut 180930E_SY01_P1_L23_GAAS_299_191127


title: Cultivated peanut 180930E_SY01_P1_L15_GAAS_295_191127


title: Cultivated peanut 180930E_SY01_P1_L17_GAAS_296_191127


title: Cultivated peanut 180930E_SY01_P1_L13_GAAS_294_191127


title: Cultivated peanut 180930G_SY01_P1_B06_SAAS_061_191127


title: Cultivated peanut 180930E_SY01_P1_L19_GAAS_297_191127


title: Cultivated peanut 180930E_SY01_P1_L11_GAAS_293_191127


title: Cultivated peanut 180930E_SY01_P1_L07_GAAS_291_191127


title: Cultivated peanut 180930E_SY01_P1_L09_GAAS_292_191127


title: Cultivated peanut 180930E_SY01_P1_L03_GAAS_289_191127


title: Cultivated peanut 180930E_SY01_P1_L05_GAAS_290_191127


title: Cultivated peanut 180930E_SY01_P1_L01_GAAS_288_191127


title: Cultivated peanut 180930E_SY01_P1_J21_GAAS_286_191127


title: Cultivated peanut 180930E_SY01_P1_J23_GAAS_287_191127


title: Cultivated peanut 180930E_SY01_P1_J15_GAAS_283_191127


title: Cultivated peanut 180930E_SY01_P1_J13_GAAS_282_191127


title: Cultivated peanut 180930E_SY01_P1_J19_GAAS_285_191127


title: Cultivated peanut 180930E_SY01_P1_J17_GAAS_284_191127


title: Cultivated peanut 180930E_SY01_P1_J09_GAAS_280_191127


title: Cultivated peanut 180930E_SY01_P1_J07_GAAS_279_191127


title: Cultivated peanut 180930E_SY01_P1_N07_GAAS_304_191127


title: Cultivated peanut 180930E_SY01_P1_J05_GAAS_278_191127


title: Cultivated peanut 180930E_SY01_P1_J11_GAAS_281_191127


title: Cultivated peanut 180930E_SY01_P1_H23_GAAS_275_191127


title: Cultivated peanut 180930E_SY01_P1_J03_GAAS_277_191127


title: Cultivated peanut 180930E_SY01_P1_J01_GAAS_276_191127


title: Cultivated peanut 180930E_SY01_P1_N03_GAAS_301_191127


title: Cultivated peanut 180930E_SY01_P1_H17_GAAS_272_191127


title: Cultivated peanut 180930E_SY01_P1_H19_GAAS_273_191127


title: Cultivated peanut 180930E_SY01_P1_L21_GAAS_298_191127


title: Cultivated peanut 180930E_SY01_P1_H21_GAAS_274_191127


title: Cultivated peanut 180930D_SY01_P1_O24_SAAS_014_191127


title: Cultivated peanut 180930E_SY01_P1_H15_GAAS_271_191127


title: MB66_I

city: La Jolla

first: Caroline

middle: R

last: McKeown

state: CA

address: 10550 N. Torrey Pines Rd., DNC-216

department: Dorris Neuroscience Center

institute: The Scripps Research Institute

data_processing:
Reads were aligned using STAR v2.5.2a to the Xenbase 9.2 transcriptome with parameters outReadsUnmapped=Fastx, outFilterMismatchNmax=10, seedSearchStartLmax=30
Reads were counted using HTSeq v0.11.1 with parameters -m intersection-nonempty -s no -a 20 -t exon
Counts were normalized using the DESeq2 v1.22.2 package
Genome_build: Xenbase v9.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Xenopus laevis

source_name: stage 66 midbrain

extract_protocol:
Brain regions were collected from the appropriate stage and total RNA was extracted using the mirVana kit (Life Technologies, USA). DNase treatment was used to remove genomic DNA and was followed by clean-up using RNeasy mini kit (Qiagen, USA).
1µg of cDNA was sheared in microTube (Covaris) and then used for library preparation (KAPA Taq PCR kits). The next generation sequencing was done using HiSeq2000 platform (Illumina; RRID:SCR_020132)

value: midbrain

tag: Stage


title: MB61_III

source_name: stage 61 midbrain


title: MB61_II


title: Cultivated peanut 180930D_SY01_P1_O20_SAAS_010_191127


title: Cultivated peanut 180930D_SY01_P1_H13_SAAS_234_191127


title: Cultivated peanut 180930D_SY01_P1_O22_SAAS_013_191127


title: MB55_II

source_name: stage 55 midbrain


title: Cultivated peanut 180930D_SY01_P1_H11_SAAS_233_191127


title: MB61_I


title: MB55_I


title: MB55_III


title: Cultivated peanut 180930D_SY01_P1_O18_SAAS_009_191127


title: Cultivated peanut 180930D_SY01_P1_H07_SAAS_231_191127


title: Cultivated peanut 180930D_SY01_P1_H09_SAAS_232_191127


title: SC49_II

source_name: stage 49 spinal cord

value: spinal cord


title: MB49_II

source_name: stage 49 midbrain


title: Cultivated peanut 180930D_SY01_P1_H01_SAAS_225_191127


title: SC49_I


title: Cultivated peanut 180930D_SY01_P1_H05_SAAS_230_191127


title: Cultivated peanut 180930D_SY01_P1_H03_SAAS_227_191127


title: Cultivated peanut 180930D_SY01_P1_F23_SAAS_224_191127


title: Cultivated peanut 180930D_SY01_P1_F21_SAAS_218_191127


title: MB49_I


title: Cultivated peanut 180930D_SY01_P1_F19_SAAS_216_191127


title: HB49_I

source_name: stage 49 hindbrain

value: hindbrain


title: FB49_II

source_name: stage 49 forebrain

value: forebrain


title: Cultivated peanut 180930D_SY01_P1_F17_SAAS_211_191127


title: FB49_I


title: SC46_III

source_name: stage 46 spinal cord


title: SC46_II


title: Cultivated peanut 180930D_SY01_P1_F13_SAAS_205_191127


title: Cultivated peanut 180930D_SY01_P1_F11_SAAS_204_191127


title: SC46_I


title: MB46_III

source_name: stage 46 midbrain


title: Cultivated peanut 180930D_SY01_P1_F09_SAAS_203_191127


title: Cultivated peanut 180930D_SY01_P1_F05_SAAS_166_191127


title: Cultivated peanut 180930D_SY01_P1_F07_SAAS_201_191127


title: MB46_I


title: Cultivated peanut 180930D_SY01_P1_F03_SAAS_165_191127


title: HB46_III

source_name: stage 46 hindbrain


title: HB46_II


title: Cultivated peanut 180930D_SY01_P1_F01_SAAS_164_191127


title: HB46_I


title: FB46_III

source_name: stage 46 forebrain


title: FB46_II


title: HB49_II


title: Cultivated peanut 180930D_SY01_P1_D23_SAAS_163_191127


title: Cultivated peanut 180930D_SY01_P1_D19_SAAS_161_191127


title: Cultivated peanut 180930D_SY01_P1_D17_SAAS_158_191127


title: MB44_III

source_name: stage 44 midbrain