title: testis rep_4 from the 3 months old mice

source_name: testis rep_4 from the 3 months old mice


title: initial segment rep_1 from the 3 months old mice

status: Public on Mar 02 2022

type: SRA

city: Guangzhou

first: Yun

last: Xie

state: China

address: No. 58 Zhongshan 2nd Road, Yuexiu District, 0080, China.

country: China

institute: sun yat-sen university

library_source: transcriptomic

data_processing:
Cutadapt was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2.
The reads mapped the genome were calculated using HTseq.
Genome_build: mm10
Supplementary_files_format_and_content: read counts table

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
The library was prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit (Illumina Inc., San Diego, CA, USA)

tag: tissue

value: initial segment

tag: age

value: 3 months

tag: strain


title: Ct-rep2

type: RNA

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

description: Gene expression in Hela cells transfected with C-terminal truncated mutation HBx

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard protocol. Washing and staining was performed on Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000.

data_processing: The data were processed with Expression Console Software. Normalization was performed by the Signal Space Transformation-Robust multi-array average method (sst-RMA).

label: biotin

organism: Homo sapiens

source_name: Hela_C-terminal truncated mutation HBx

label_protocol: Labeling was performed according to manufacturer's standard protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HeLa cell lines expressing wild-type and mutant HBx stably was constructed.

tag: cell line

value: HeLa

tag: genotype/variation


title: 7

first: Jinfei

last: Zhang

state: Guangdong

address: 483 Wushan Road

institute: SCAU

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: RNA was extracted from clones cultured in LB broth after 4 h mating

extract_protocol:
Bacterial cells were collected by 8000×g centrifugation for 10 min
The library was constructed using an Illumina TruSeq RNA sample Prep Kit v2

treatment_protocol: In the absence of antibiotics

tag: evolved lins

value: Evolved clone

tag: antibiotics treatment

value: no

tag: plasmid-bearing

value: yes


title: 20


title: Neural progenitor cells (low passage) - PTHS patient #1 - replicate 2

city: Campinas

first: Fabio

last: Papes

state: SP

address: Rua Carl Von Linaeus

country: Brazil

institute: University of Campinas

data_processing:
Transcript-level quantification using Salmon (version 0.14.1)
Genome_build: GENCODE 32 basic annotation (GRCh38)
Supplementary_files_format_and_content: Salmon quantification outputs

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells (passage 5) were cultured in DMEM/F12 medium containing N2 and SM1 suplements, along with FGF-2 (20 ng/mL).

extract_protocol:
Total RNA was extracted using Rneasy Mini Plus kit (Qiagen).
Libraries were made using the TruSeq Stranded mRNA kit (Illumina) and sequenced on a NovaSeq6000 S4 instrument to produce 150 PE read at ~40M reads per library (6Gb production)

treatment_protocol: Cells were not treated.

tag: cell type

value: iPSC-derived neural progenitor cells

tag: treatment

tag: genotype

value: PTHS patient


title: Neural progenitor cells (low passage) - parent #1 - replicate 2

value: parental control


title: 161_VD_17

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

country: USA

institute: Texas A&M University

description:
mRNA count data
AWO22587-0191-161-VD-17

hyb_protocol: NanoString nCounter PrepStation

scan_protocol: NanoString SPRINT Profiler set to high resolution (550)

data_processing: NanoString nSolver Analysis Software v4.0 was utilized for quality assessment and raw gene count accession. Four housekeeping, six positive spike-in, and eight negative control genes were used for intersample count normalization.

label: Biotin

organism: Bos taurus

source_name: Whole blood

label_protocol: NanoString nCounter mRNA Bovine Custom Panel

extract_protocol: Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit

tag: treatment group

value: Healthy

tag: study

tag: location

value: MS

tag: animal info

value: Bull

tag: vaccinated

tag: dewormed


title: syngeneic heart graft 2

first: Yunhua

last: Tang

address: No. 58 Zhongshan Er Road, Guangzhou, China

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10_Ensembl92
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: heart

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

tag: tissue

value: heart

tag: time

value: day 5 posttransplant


title: 12_DG_17

description:
mRNA count data
AWO22587-0188-12-DG-17

value: MO


title: 107_DG_18

description:
mRNA count data
AWO22587-0187-O107-DG-18


title: testis rep_1 from the 3 months old mice

source_name: testis rep_1 from the 3 months old mice

value: testis

tag: age

tag: strain


title: Neurons - PTHS patient #4 - replicate 3

source_name: Neurons

growth_protocol: Neural progenitor cells were culture in DMEM/F12 medium containing N2 and SM1 suplements, along with FGF-2 (20 ng/mL). Neurons were cultured in Neurobasal medium containing GEM21 suplement.

value: iPSC-derived neurons

tag: disease


title: testis rep_2 from the 3 months old mice

source_name: testis rep_2 from the 3 months old mice


title: 105_MH_19

description:
mRNA count data
AWO22587-0190-105-MH-19


title: 142_MH_19

description:
mRNA count data
AWO22587-0192-142-MH-19

value: Heifer


title: 2

tag: evolved lins


title: 3

tag: antibiotics treatment


title: 15

tag: plasmid-bearing


title: S.L.24h.7

city: Wuhan

first: Zhaohui

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm39 whole genome using hisat2
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: 176_VD_17

description:
mRNA count data
AWO22587-0189-176-VD-17


title: allogeneic  heart graft 2

value: Balb/C


title: Neural progenitor cells (low passage) - parent #1 - replicate 3

tag: cell type


title: Neurons - PTHS patient #4 - replicate 2

tag: treatment


title: 1

value: Evolved clone


title: syngeneic heart graft 1


title: BA4396

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: WT mice with 28-day Angiotensin-II (500ng/kg/min) and QDG (1.145 g/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Genome_build: GCRmm38/mm10(UCSC)
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: renal

growth_protocol: The renal were dissected and  stored in liquid nitrogen and stored in low temperature.Total RNA was extracted with TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by KAPA Library Quantification Kit (KAPA Biosystem, Wilmington, MA, USA).

extract_protocol: A total amount of 1 μg RNA per sample was used. In brief, the NEB Next rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit  (NEB,Ipswich, MA, USA)for Illumina was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: renal

tag: genotype

value: WT

value: Angiotensin-II

value: Qingda granule

tag: group

value: AngII+QDG


title: AT+P

value: Ancestral clone

value: no

value: yes


title: 166_VD_17

description:
mRNA count data
AWO22587-0182-166-VD-17

tag: treatment group

tag: study

value: MS

value: Steer


title: allogeneic  heart graft 1

value: heart

value: day 5 posttransplant


title: BA4395


title: 231_TA_20

description:
mRNA count data
AWO22587-0185-231-TA-20

tag: location

tag: animal info


title: X.L.24h.3


title: 130_MH_19

description:
mRNA count data
AWO22587-0186-130-MH-19

tag: vaccinated

tag: dewormed


title: Neurons - parent #4 - replicate 1

value: iPSC-derived neurons

value: parental control


title: S.L.24h.5

tag: tissue

value: liver


title: Neurons - PTHS patient #4 - replicate 1

value: PTHS patient


title: BA4372

description: WT mice with 28-day Angiotensin-II (500ng/kg/min) and QDG  (1.145 g/kg/d) treatment


title: BA4414


title: Neural progenitor cells (low passage) - parent #1 - replicate 1

value: iPSC-derived neural progenitor cells


title: 241_PS_19

description:
mRNA count data
AWO22587-0184-241-PS-19

value: Heifer


title: Neurons - parent #4 - replicate 2


title: Neural progenitor cells - PTHS patient #4 - replicate 3


title: X.L.24h.1


title: 143_PS_19

description:
mRNA count data
AWO22587-0183-143-PS-19


title: Neurons - parent #4 - replicate 3


title: Neural progenitor cells - PTHS patient #4 - replicate 2


title: Y55_DG_18

description:
mRNA count data
AWO22587-0180-Y55-DG-18

value: Healthy

value: MO


title: C.L.24h.21


title: C.L.24h.19


title: 148_MH_19

description:
mRNA count data
AWO22587-0178-148-MH-19


title: 237_TA_20

description:
mRNA count data
AWO22587-0181-237-TA-20


title: 76_DG_17

description:
mRNA count data
AWO22587-0177-76-DG-17


title: Neural progenitor cells - PTHS patient #4 - replicate 1


title: BA4413

description: WT mice with 28-day Angiotensin-II (500ng/kg/min) treatment

value: renal

value: WT

value: Angiotensin-II

value: Saline

value: AngII


title: Pex5_KO_male_rep6

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus.GRCm38.98 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Genome_build: Mus musculus.GRCm38.98
Supplementary_files_format_and_content: raw gene counts for every gene in every sample

source_name: Whole kidney

growth_protocol: The three mouse lines used in this study are inbred strains, bred on the genetic background of the C57BL/6J mouse. Before all experiments, mice were adapted to a 12-hour light/ dark cycle. All experiments were performed at circadian time ZT3 (ZT0 is the time when light is switched on and ZT12 is the time when light is switched off).

extract_protocol:
Tissue acollection was performed from mice sacrificed at ZT9 (ZT – Zeitgeber time units; ZT0 is the time of light on and ZT12 is the time of light off). RNA from whole kidneys was isolated with the standard method of Chomczynski and Sacchi (Anal Biochem, 162: 156-159, 1987).
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA)

treatment_protocol: The Pex5 deletion in the renal tubule of adult mice was induced by 2-week treatment with DOX of 8-week-old Pex5lox/lox/Pax8-rtTA/LC1 male and female mice. In parallel, the same DOX treatment was provided to their littermate controls (Pex5lox/lox mice). All experiments on adult mice were performed 4 weeks after the end of DOX treatment.

value: Whole kidney

value: PEX5 cKO

tag: Sex

value: Male


title: 173_MH_19

description:
mRNA count data
AWO22587-0179-173-MH-19

value: MS


title: Pex5_KO_male_rep4


title: BA4371

tag: strain

value: Qingda granule

value: AngII+QDG


title: Pex5_KO_male_rep5


title: Neural progenitor cells - parent #4 - replicate 3

tag: disease

value: parental control


title: Pex5_KO_male_rep3


title: BA4398


title: Pex5_KO_male_rep2


title: BA4336


title: Neural progenitor cells - parent #4 - replicate 2


title: BA4441

description: WT mice with 28-day Saline treatment

value: Control


title: Pex5_KO_male_rep1


title: 212_TA_20

description:
mRNA count data
AWO22587-0174-212-TA-20


title: BA4334


title: Neural progenitor cells - PTHS patient #3 - replicate 3

value: iPSC-derived neural progenitor cells

value: PTHS patient


title: Neural progenitor cells - PTHS patient #3 - replicate 2


title: 297_PS_19

description:
mRNA count data
AWO22587-0176-297-PS-19

value: Bull


title: Neural progenitor cells - parent #4 - replicate 1


title: Pex5_KO_female_rep6

value: Female


title: BA4437

description: WT mice with 28-day Saline treatment

value: renal


title: Neural progenitor cells - PTHS patient #3 - replicate 1


title: BA4407

value: WT


title: 225_PS_19

description:
mRNA count data
AWO22587-0173-225-PS-19

value: Healthy

value: Steer


title: 267_TA_20

description:
mRNA count data
AWO22587-0172-267-TA-20

value: Heifer


title: Pex5_KO_female_rep4

value: Whole kidney


title: 252_TA_20

description:
mRNA count data
AWO22587-0171-252-TA-20


title: Neural progenitor cells - parent #3 - replicate 3


title: BA4333

description: WT mice with 28-day Saline treatment

value: Saline


title: Pex5_KO_female_rep3

value: PEX5 cKO


title: BA4335

description: WT mice with 28-day Saline treatment


title: Neural progenitor cells - parent #3 - replicate 1


title: 166_MH_19

description:
mRNA count data
AWO22587-0170-166-MH-19

value: MS


title: 161_DG_17

description:
mRNA count data
AWO22587-0175-161-DG-17

value: MO


title: PHF20L1_Input_rep2

city: Houston

first: Margarida

last: Albuquerque Almeida Santos

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description:
C_3HA_PHF20L1_Input
PHF20L1_peaks.bed

library_source: genomic

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
Sequenced DNA reads were mapped to the human genome (hg38) using Bowtie (version 1.1.2) and only the reads that were mapped to unique position were retained.
To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained for further analysis.
The peaks in each ChIP sample were detected by MACS2 (version 2.2.7.1) by comparing to the corresponding input sample. The --extsize was set as 200 bp. The peaks that overlapped ENCODE blacklist regions were removed.
The peaks were called in the replicate of PHF20 or PHF20L1 with best signal at pvalue≤0.01 and in the other replicate(s) at pvalue≤0.05. The peaks that were called in the best replicate and overlapped the peaks called in the other replicate(s) were identified as the final list of PHF20 or PHF20L1 binding sites.
PHF20_ChIP_rep1 has the best signal among PHF20 replicates, and PHF20L1_ChIP_rep1 has the best signal among PHF20L1 replicates.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Peak locations in bed format.

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were made from ChIP DNA NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (#E7645S, NEB).

value: Osteosarcoma

tag: cell line

value: C-3xHA PHF20L1 Over-expressed

tag: chip antibody


title: 188_PS_19

description:
mRNA count data
AWO22587-0169-188-PS-19


title: Pex5_KO_female_rep2


title: PHF20L1_Input_rep1

description:
PHF20L1_HA_Input
PHF20L1_peaks.bed

value: N-3xHA PHF20L1 Over-expressed


title: Neural progenitor cells - PTHS patient #2 - replicate 2

value: iPSC-derived neural progenitor cells


title: Pex5_KO_female_rep1


title: 250_TA_20

description:
mRNA count data
AWO22587-0168-250-TA-20


title: Neural progenitor cells - PTHS patient #2 - replicate 1

value: PTHS patient


title: Pex5_Ctrl_male_rep6

value: Control

value: Male


title: PHF20L1_ChIP_rep3

description:
C_3HA_PHF20L1_HA_Rep2
PHF20L1_peaks.bed


title: 233_PS_19

description:
mRNA count data
AWO22587-0166-233-PS-19


title: Neural progenitor cells - parent #2 - replicate 3

value: parental control


title: 279_TA_20

description:
mRNA count data
AWO22587-0167-279-TA-20


title: Pex5_Ctrl_male_rep5


title: Pex5_Ctrl_male_rep4


title: Pex5_KO_female_rep5

value: Female


title: 262_TA_20

description:
mRNA count data
AWO22587-0165-262-TA-20


title: BA4373

description: WT mice with 28-day Saline treatment

value: renal

value: WT


title: Neural progenitor cells - parent #3 - replicate 2


title: PHF20L1_ChIP_rep1

description:
N_3HA_PHF20L1_HA_Rep2
PHF20L1_peaks.bed


title: R9_DG_18

description:
mRNA count data
AWO22587-0164-R9-DG-18

value: Healthy


title: PHF20_Input

description:
PHF20_HA_Input
PHF20_peaks.bed

value: N-3xHA PHF20 Over-expressed


title: PHF20_ChIP_rep2

description:
N_3HA_PHF20_HA_Rep1
PHF20_peaks.bed


title: Neural progenitor cells - parent #2 - replicate 1


title: 225_TA_20

description:
mRNA count data
AWO22587-0163-225-TA-20

value: Steer


title: Neural progenitor cells - PTHS patient #2 - replicate 3


title: Pex5_Ctrl_male_rep2

value: Whole kidney


title: Neural progenitor cells - PTHS patient #1 - replicate 3


title: PHF20_ChIP_rep1

description:
N_3HA_PHF20_HA_Rep2
PHF20_peaks.bed


title: Pex5_Ctrl_male_rep1


title: Neural progenitor cells - PTHS patient #1 - replicate 2


title: 138_MH_19

description:
mRNA count data
AWO22587-0162-138-MH-19

value: MS

value: Heifer


title: 167_MH_19

description:
mRNA count data
AWO22587-0161-167-MH-19

value: Bull


title: Neural progenitor cells - PTHS patient #1 - replicate 1


title: PHF20L1_ChIP_rep2

description:
C_3HA_PHF20L1_HA_Rep1
PHF20L1_peaks.bed

value: Osteosarcoma

value: C-3xHA PHF20L1 Over-expressed


title: Pex5_Ctrl_female_rep5


title: Neural progenitor cells - parent #1 - replicate 3

value: iPSC-derived neural progenitor cells


title: 242_PS_19

description:
mRNA count data
AWO22587-0160-242-PS-19


title: F9721_6h_1

city: Beijing

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Adapter trimming and low-quality read removing were performed using fastp software. Reads were aligned to the B73 AGPv4 reference genome (Zm-B73-REFERENCE-GRAMENE-4.0) using the Hisat2 aligner, removing the 5’ and 3’ low-quality bases. A python module HTSeq was used to quantify the number of reads mapped on a gene with union mode. Raw gene count data were filtered with at least one read was counted across all samples for each gene. Transcripts per million (TPM) values were generated using R software, and gene length for each gene were calculated from Zm-B73-REFERENCE-GRAMENE-4.0_Zm00001d.2.gff3. Differential gene expression analysis between samples was performed using DESeq2 with padj ≤ 0.01 and fold change of |log2 Ratio| ≥ 2.
Genome_build: maize B73 (Zm-B73-REFERENCE-GRAMENE-4.0)
Supplementary_files_format_and_content: comma-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Zea mays

source_name: seed

growth_protocol: For the germination test, 50 uniform seeds from the middle of the ear were first sterilized with 0.1% H2O2 for 10 minutes and then rinsed with sterilized water three times. After that, the seeds with embryo upwards were evenly placed in a Petri dish (diameter = 15 cm) on four layers of sterile filter paper moistened with 15 ml sterilized water. The Petri dishes were then incubated in a light incubator with a constant temperature of 28℃ under a 16/8 h (light/dark) photoperiod. Additional 5 ml sterilized water was added to the Petri dishes every 12 hours during the germination process. The seeds were recognized as germination after radicle emergence of 0.5 mm

extract_protocol:
To prepare for the transcriptome sequencing, we performed a germination test of the two lines under the same conditions. For 72-3, germinating seeds at four-time points (0, 6, 12, 24 HAI) were sampled, while 6-time points (0, 6, 12, 24, 36, 48 HAI) of F9721 were sampled for RNA extraction. Three biological replicates were set for each time point of the two lines. Total RNA was extracted using RNA Easy Fast kit DP452 (TianGen BioTech Beijing Corporation). RNA purity, concentration, and integrity were determined using Nano-Drop TM 2000 spectrophotometer (Thermo Scientific, USA)
Libraries of each RNA sample were constructed using Illumina Truseq RNA Sample Prep kits. The paired-end of 125 bp sequencing was performed with an Illumina HiSeq2500 sequencer

tag: seed condition

value: germinated seed 6h

value: seed

tag: inbred line

tag: phenotype

value: slow germination


title: F9721_6h_3


title: Pex5_Ctrl_female_rep4

tag: genotype

value: Control


title: 234_TA_20

description:
mRNA count data
AWO22587-0159-234-TA-20


title: Neural progenitor cells - parent #1 - replicate 2

tag: cell type

tag: treatment

value: parental control


title: F9721_6h_2


title: 34_DG_17

description:
mRNA count data
AWO22587-0158-34-DG-17

tag: treatment group

tag: study

value: MO


title: Pex5_Ctrl_female_rep3

value: Female


title: Neural progenitor cells - parent #2 - replicate 2


title: Pex5_Ctrl_male_rep3

value: Male


title: SindbislibraryP1 input pool Sample 21

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

description: SindbislibraryP1 input pool

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, these represent artificial microRNAs encoded by different Sindbis viruses in a sample
Counts of forward and reverse compliment artificial microRNA sequences are reported
Genome_build: Not relevant
Supplementary_files_format_and_content: count values for each Sample

organism: Sindbis virus

source_name: Unknown

extract_protocol:
Total RNA was extracted from 1 million cells cultured in vitro using Qiagen's RNAeasy kit
Following the recommended protocol for tailed amplicon sequencing with Miseq illumina we perform PCR amplification with primers corresponding to common sequences outside amiRNA

value: ATCC

tag: sample type

value: Input pool

value: wild type


title: Neural progenitor cells - parent #1 - replicate 1


title: PanCO2 Sample 20

value: Pancreatic cancer


title: Pex5_Ctrl_female_rep2

value: Whole kidney


title: F9721_48h_2

value: germinated seed 48h


title: Pex5_Ctrl_female_rep1


title: F9721_48h_1


title: PanCO2 Sample 19


title: Pex5_Ctrl_female_rep6


title: 30m_GAS_CR_rep6

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

institute: University of Basel

description:
direction:
direction_1st_mate: antisense, direction_2nd_mate: sense

data_processing:
RNA-seq reads were subjected to 3’ adapter and poly(A)/poly(T) tail trimming using Cutadapt v1.9.1 from Martin et al., EMBnet.journal, 2011. The following 3’ adapter sequences were utilized for generating RNA-Seq libraries and subsequently trimmed: mate1 5’-AGATCGGAAGAGCACACGTC-3’, mate2 5’-AGATCGGAAGAGCGTCGTGT-3’.
Reads shorter than 30 nucleotides were discarded.
The kallisto v0.43.1 software from Bray et al., Nature Biotechnology, 2016 was used for building transcriptome index and aligning filtered reads. The default options of kallisto were utilized for building transcriptome index. For aligning filtered reads we used options “--rf-stranded” and “--pseudobam”.
Mapped reads were assigned to transcripts in a weighted manner: if a read was uniquely mapped to a transcript, then the transcript’s read count was incremented by 1; if a read was mapped to n different transcripts, each transcript’s read count was incremented by 1/n.
The expression of each transcript was estimated in transcripts per million (TPM) units by dividing its read count by the transcript length and normalizing to the library size. The expression of a gene was obtained by summing up the normalized expression of the transcripts associated with it. For every gene, read counts of transcripts associated with this gene were also summed up and further used for the differential expression analysis.
Genome_build: As the reference mouse transcriptome, we considered sequences of protein coding transcripts with the support level 1-3 based on genome assembly GRCm38 (release 92) and transcript annotations from Ensembl database (see Hubbard et al., Nucleic Acids Research, 2002).
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values at the gene level for each sample

molecule: polyA RNA

source_name: Gastrocnemius muscle

growth_protocol: Mice were singly caged throughout the treatment period.

extract_protocol:
Snap frozen muscles were pulverized and lysed in RLT buffer (Qiagen). RNA was extracted using an AccuPure Tissue RNA Mini Kit (R20096) with an iColumn 24 (AccuBioMed). TruSeq Stranded mRNA HT Sample Prep Kit was used for the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were subjected to calorie restriction (70% of AIN93M diet with 1.43x(vitamins + minerals)) for 15 months from the age of 15 months.

value: Gastrocnemius muscle

tag: age

value: post natal month 30

value: calorie restriction


title: F9721_36h_3

value: germinated seed 36h


title: PanCO2 Sample 18


title: 30m_GAS_CR_rep5


title: F9721_36h_2

value: seed


title: PanCO2 Sample 17


title: 30m_GAS_CR_rep3


title: 30m_GAS_CR_rep4


title: PanCO2 Sample 16


title: F9721_36h_1

value: slow germination


title: MiaPACA2 Sample 15


title: F9721_48h_3


title: 30m_GAS_CR_rep2


title: F9721_24h_2

value: germinated seed 24h


title: MiaPACA2 Sample 13


title: F9721_24h_1


title: MiaPACA2 Sample 12


title: F9721_12h_3

value: germinated seed 12h


title: 30m_TRI_CR_rep6

source_name: Triceps brachii muscle

value: Triceps brachii muscle


title: 30m_TRI_CR_rep5


title: F9721_12h_2


title: 30m_TRI_CR_rep4


title: F9721_24h_3


title: F9721_12h_1


title: PCaCAF Sample 10

description: PCaCAF

source_name: PCaCAF


title: MiaPACA2 Sample 11


title: F9721_0h_3

value: dry seed


title: MiaPACA2 Sample 14


title: 30m_GAS_CR_rep1


title: PCaCAF Sample 9

description: PCaCAF


title: 30m_TRI_CR_rep2


title: F9721_0h_2


title: PCaCAF Sample 8

description: PCaCAF


title: PCaCAF Sample 7

description: PCaCAF


title: 72-3_6h_3

value: germinated seed 6h

value: fast germination


title: PCaCAF Sample 6

description: PCaCAF

value: ATCC


title: 30m_TA_CR_rep5

source_name: Tibialis anterior muscle

value: Tibialis anterior muscle

value: wild type


title: GM38 Sample 5

value: Normal fibroblasts


title: 30m_TA_CR_rep4


title: 72-3_6h_2


title: F9721_0h_1


title: 30m_TRI_CR_rep3


title: GM38 Sample 4


title: 30m_TA_CR_rep6


title: 30m_TA_CR_rep3


title: 72-3_24h_3


title: GM38 Sample 3


title: 72-3_24h_2


title: GM38 Sample 2


title: 72-3_24h_1


title: 30m_TA_CR_rep1


title: GM38 Sample 1


title: 30m_Sol_CR_rep6

source_name: Soleus muscle

value: Soleus muscle


title: alys-4

first: Chen

last: Zhu

address: 300 Feng Lin Road, Shanghai 200032, China

institute: CAS Center for Excellence in Molecular Plant Sciences

description: For sRNA-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Remove the 3' linker sequence in the reads, and remove the reads without inserts due to the connector self-ligation. Remove the reads with low-quality sequence and reads containing the unknown base N, too short(<18nt) or too long(> 32 nt).
Useing fastx_tool 0.04 to ffilter the low quality data , and using bowtie version 1.1.1 for genome mapping.
The expression level of each transcript was calculated according to the (TPM) method. miRDeep2 was used to quantify gene abundances
Differential gene expression analysis was done using R package DEGseq
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample (sRNA-seq), miRNA target gene annotation text file

organism: Arabidopsis thaliana

source_name: Arabidopsis seedling

extract_protocol:
Total RNA was extracted from each tissue using  TRIzol® Reagent (Plant RNA Purification Reagent for  plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library.
Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >2μg) was used to construct sequencing library

value: seedling

tag: developmental stage

value: 12 day

tag: eco-type

value: Columbia

value: alys


title: 72-3_12h_3

tag: tissue

value: seed


title: 30m_Sol_CR_rep5

tag: strain

value: post natal month 30

value: calorie restriction


title: 72-3_12h_2

value: germinated seed 12h


title: UM-MCC-29

type: genomic

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

country: Germany

institute: DKZF

description: DNA methylation measured by the Infinium EPIC BeachChip

hyb_protocol: The infinium EPIC BeachChip assay was performed at the microarray unit of the DKFZ Genomics and Proteomics Core Facility with > 1000ng of input DNA and following  the standard illumina protocol

data_processing:
Raw IDAT files were processed in R following the cross-package workflow described by Maksimovic et al. This included the Bioconductor packages minfi  and limma . Quality of the data was assessed with the minfi qcReport function. Data were normalized using functional normalization  implemented in minfi. Probes with a detection p-value above 0.01 in at least one sample were removed. Additionally, probes located on sex chromosomes, probes with SNPs at CpG sites and cross-reactive probes were discarded
normalized beta values (functional normalization using the preprocessFunnorm function of the minfi R-package)

label: Cy5 and Cy3

source_name: cell line

growth_protocol: The cell lines (MCC13, MCC26 , UISO, WaGa, PeTa, MKL-1, MKL-2, UKE-MCC-1a, UKE-MCC-4a) were maintained in RPMI-1640 (Pan Biotech, Aidenbach, Germany). The squamous cell carcinoma  and fibroblast cell lines were maintained in DMEM medium (Pan Biotech, Aidenbach, Germany). Both were supplemented with 10% fetal bovine serum (Sigma, St. Lous, MO, USA) and 1% penicillin/streptomycin (Pan Biotech, Aidenbach, Germany). The cell lines (UM-MCC-52, UM-MCC-13, UM-MCC-29, UM-MCC-623, UM-MCC-9, UM-MCC-34 and UM-MCC-32) were maintained in chicken embryonic extract medium.

extract_protocol: DNA isolation from cell lines was performed using Qiagen QiAamp DNA mini Kit according to the manufacturer’s protocol

treatment_protocol: no treatment

value: VP-MCC


title: alys-3

description: For sRNA-seq


title: UM-MCC-32

scan_protocol: The infinium EPIC BeachChip assay was performed at the microarray unit of the DKFZ Genomics and Proteomics Core Facility with > 1000ng of input DNA and following  the standard illumina protocol

value: UV-MCC


title: Fibros-LK3

label_protocol: The infinium EPIC BeachChip assay was performed at the microarray unit of the DKFZ Genomics and Proteomics Core Facility with > 1000ng of input DNA and following  the standard illumina protocol

value: Fibroblast


title: 30m_TRI_CR_rep1

value: Triceps brachii muscle


title: 30m_Sol_CR_rep4


title: SCC-13

value: SCC


title: UM-MCC-9


title: 30m_TA_CR_rep2

value: Tibialis anterior muscle


title: 72-3_12h_1

value: fast germination


title: 72-3_0h_3

value: dry seed


title: HSC-1


title: 30m_Sol_CR_rep3

value: Soleus muscle

value: wild type


title: SSR1-4

description: For sRNA-seq

value: seedling

value: 12 day

value: SSR1 overexpression


title: 72-3_6h_1

value: germinated seed 6h

value: seed


title: Met-4


title: PeTa


title: 30m_Sol_CR_rep2

value: post natal month 30

value: calorie restriction


title: SSR1-3

description: For sRNA-seq

value: Columbia


title: 72-3_0h_2


title: Fibros-LK4


title: Col-4

description: For sRNA-seq

value: WT


title: 30m_Sol_CR_rep1


title: 72-3_0h_1


title: Col-3

description: For sRNA-seq


title: SCL-1


title: DSP-1010200000014-D12

status: Public on Mar 01 2022

city: Seattle

first: Stephanie

last: Zimmerman

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies

data_processing:
library strategy: GeoMx Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: tonsil_SampleAnnotations: txt file containing sample annotations
Supplementary_files_format_and_content: tonsil_RawCounts: txt file containing raw probe counts per sample
Supplementary_files_format_and_content: tonsil_CollapsedTargetCounts: txt file containing collapsed gene-level target counts per sample

source_name: Human FFPE tonsil

extract_protocol:
Samples were incubated with the mouse Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: FFPE

tag: segment

tag: roi

tag: slide

tag: molecule subtype

value: RNA ISH


title: MKL-2

value: VP-MCC


title: DSP-1010200000014-E01

value: PanCK


title: DSP-1010200000014-D10


title: DSP-1010200000014-D11


title: DSP-1010200000014-D09


title: SCL-2

value: SCC


title: DSP-1010200000014-D07


title: DSP-1010200000014-D06


title: UKE-MCC-1a


title: DSP-1010200000014-D05


title: DSP-1010200000014-D03


title: MCC13

value: vMCC


title: UM-MCC-34

value: UV-MCC


title: DSP-1010200000014-D02


title: DSP-1010200000014-D01


title: DSP-1010200000014-D04


title: UM-MCC-623


title: UISO


title: DSP-1010200000014-D08


title: DSP-1010200000014-C11


title: DSP-1010200000014-C12


title: DSP-1010200000014-C06


title: DSP-1010200000014-C07


title: DSP-1010200000014-C10


title: DSP-1010200000014-C09


title: DSP-1010200000014-C05


title: DSP-1010200000014-C04


title: UM-MCC-52


title: DSP-1010200000014-C03


title: DSP-1010200000014-C01

source_name: Human fresh frozen tonsil

value: FF


title: DSP-1010200000014-B12


title: DSP-1010200000014-C02


title: DSP-1010200000014-B11


title: DSP-1010200000014-B09


title: DSP-1010200000014-B07


title: DSP-1010200000014-B08


title: DSP-1010200000014-B10


title: DSP-1010200000014-B05


title: MKL-1


title: DSP-1010200000014-B01


title: DSP-1010200000014-A11


title: DSP-1010200000014-B03


title: DSP-1010200000014-A10


title: UM-MCC-13


title: UKE-MCC-4a


title: DSP-1010200000014-A06


title: DSP-1010200000014-A07


title: DSP-1010200000014-A12


title: DSP-1010200000014-B02


title: Fibro-1.7

value: Fibroblast


title: DSP-1010200000014-A03


title: DSP-1010200000014-B04


title: WaGa


title: DSP-1010200000014-B06


title: DSP-1010200000014-A02


title: DSP-1010200000014-A05


title: DSP-1010200000014-A08


title: DSP-1010200000014-A09


title: DSP-1010200000014-A04


title: Met-1


title: Fibro-1.2


title: CFBE ALI rep2 (RNA-seq)

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
Paired raw reads were trimmed and mapped on Banana Slug Analytics Platform (http://sluganalysis.ucsc.edu).
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with FPKM values for each sample

source_name: Epithelial cells

growth_protocol: Human bronchial epithelial CFBE41o- cells stably expressing F508del-CFTR (CFBE) or wild-type CFTR (WTBE) were cultured in MEM medium, supplemented with 10% fetal bovine serum (Hyclone), 0.5% Penicillin/Streptomycin and 2mM L-glutamine. 0.5µg/mL puromycin (InvivoGen) were added for WTBE while 25µg/mL puromycin for CFBE cells to select stably transfected cells. Cells were maintained in a humidified chamber with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and quantified by Qubit RNA HS Assay Kit (ThermoFisher).
The library was prepared using illumina TruSeq Stranded mRNA sample prep kit

treatment_protocol: For transwell-cultured (ALI) condition, cells were seeded on Millicell cell culture insert (Millipore) placed in 24-well plates. Media on the apical surface was removed daily until complete confluency (dry membrane) and basolateral media were replaced every other two days. Confluent cells were cultured for at least another 10days for polarization. For submerged cells, cells were also cultured in 24well plates and cultured till fully confluent.

tag: culture condition

value: Air-liquid interface

tag: cell line

value: CFBE (CFBE41o- cells stably expressing F508del mutant CFTR)

value: Cystic fibrosis (CF) bronchial epithelial cells


title: CFBE ALI rep1 (RNA-seq)


title: WTBE ALI rep2 (RNA-seq)

value: WTBE (CFBE41o- cells stably expressing wild-type CFTR)


title: WTBE ALI rep3 (RNA-seq)


title: CFBE SUB rep2 (RNA-seq)

value: Submerge


title: WTBE SUB rep3 (RNA-seq)


title: WTBE SUB rep1 (RNA-seq)


title: WTBE ALI rep1 (RNA-seq)


title: WTBE SUB rep2 (RNA-seq)


title: CFBE SUB rep3 (RNA-seq)


title: CFBE ALI rep3 (ATAC-seq)

data_processing:
Paired-end reads were aligned to the human hg19 database (GRCh37.p13) using BWA.
The mitochondrial reads and reads with mapQuality <30 were removed. Duplicate reads were cleaned by MarkDuplicates tool. The narrowpeaks were called using MACS2 from the converted BED files. Normalized bigwig files were generated by Wig/BedGraph-to-BigWig tool on Galaxy platform
Peak annotations and feature distributions were performed by ChipSeeker (Bioconductor) and KEGG pathways were analyzed by PathfindR in R studio.
Genome_build: hg19
Supplementary_files_format_and_content: callpeak normalized reads

extract_protocol:
60,000 cells (>95% viability) were trypsinized and lysed in 50L cold lysis buffer (10mm Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 10% Tween-20, and 0.01% Digitonin) and incubated on ice for 5min. Then 1mL wash buffer (10mm Tris-HCl, 10mM NaCl, 3mM MgCl2 and 10% Tween-20) was added and tube were inverted 3 times gently.
Nuclei were pelleted at 500g for 5min at 4°C and resuspended in 50 µL of transposition mixture (TDE1 tagment DNA enzyme and TD buffer, illumina) and incubated for 30 min at 37 °C. Isolated DNA samples were purified using DNA Clean and Concentrator-5 (Zymo Research), which can be stored in -20°C. Purified DNA products were pre-amplified for 5 cycles with NEBNext High-Fidelity 2x PCR MasterMix (NEB). Additional cycles were added based on qPCR results of partially-amplified library. PCR reactions were purified and qualified using an Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent).  The libraries were quantified using a sensitive fluorescence dye-based Qubit dsDNA HS Assay Kit (ThermoFisher). Libraries were pooled at a final concentration of 650pM


title: CFBE SUB rep1 (RNA-seq)


title: Triple combination [Sample7]

city: Bethesda

first: Anusara

last: Daenthanasanmak

state: MD

address: 10 Center Dr

department: Lymphoid Malignancies Branch

institute: National Institutes of Health

description:
Sample7
Adult T cell leukemia cell lines
mRNA-seq

data_processing:
The sequencing quality of the reads was assessed per sample using FastQC (version 0.11.5).
Preseq (version 2.0.3), Picard tools (version 1.119) and RSeQC (version 2.6.4).
Sequencing reads were trimmed of low quality bases and adapter sequences were removed using Cutadapt (version 1.18).
The trimmed reads were aligned to the GRCh38 (GENCODE hg38, version 30).
Gene and isoform expression levels are quantified using RSEM (version 1.3.0).
Genome_build: Human_hg38 (GRCh38)
Supplementary_files_format_and_content: RawCountFile_rsemgenes.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: TreatedvsVehical_voom_deg.csv: Comma-separated text file includes DEG table.

source_name: Human ATL43Tb (-) cell lines

growth_protocol: The xenograft tumor model was established by subcutaneous injection of 1×10^7 ATL43Tβ (-) cells into the flank of NSG mice for 10 days.

extract_protocol:
Total RNA was extracted from ATL43Tβ (-) tumor isolated from NSG mice after 5-day treatment with the triple combination using an RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: IBET762+Copanlisib+Bardoxolone methyl were administered for 5 days (alternate days).

value: ATL43Tbeta (-) xenograft tumor

tag: mouse strain

value: NOD scid gamma

value: IBET762+Copanlisib+Bardoxolone methyl


title: DSP-1010200000014-C08

value: FFPE


title: WTBE ALI rep3 (ATAC-seq)

tag: cell type


title: Triple combination [Sample8]

description:
Sample8
Adult T cell leukemia cell lines
mRNA-seq

tag: treatment


title: Vehicle [Sample3]

description:
Sample3
Adult T cell leukemia cell lines
mRNA-seq

value: Vehicle


title: Triple combination [Sample6]

description:
Sample6
Adult T cell leukemia cell lines
mRNA-seq


title: Vehicle [Sample2]

description:
Sample2
Adult T cell leukemia cell lines
mRNA-seq


title: DSP-1010200000014-A01

source_name: blank sample

value: No Template Control

value: RNA ISH


title: CFBE ALI rep1 (ATAC-seq)


title: CFBE ALI rep3 (RNA-seq)


title: WTBE ALI rep1 (ATAC-seq)


title: CFBE ALI rep2 (ATAC-seq)


title: Vehicle [Sample4]

description:
Sample4
Adult T cell leukemia cell lines
mRNA-seq


title: WTBE ALI rep2 (ATAC-seq)


title: Triple combination [Sample5]

description:
Sample5
Adult T cell leukemia cell lines
mRNA-seq


title: Vehicle [Sample1]

description:
Sample1
Adult T cell leukemia cell lines
mRNA-seq


title: 6DR: wafer 6, 19900-20000 μm, rep2

city: Saint Paul

first: Jonathan

last: Schilling

state: MN

address: 1500 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota

data_processing:
Read trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/) with parameters qtrim=rl, trimq=10, minlen=100, maq=10. Reads were aligned to the Postia placenta MAD 698-R v1.0 genome (https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Pospl1) using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with parameters --local --sensitive-local. The “NH” field of multi-mapping reads in the SAM files was edited to 1, allowing multi-mapping reads to be randomly assigned to one mapping loci. This procedure allows duplicated/paralogous genes to be represented in the data. Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Aligned reads were mapped to genes using htseq-count (PMID: 25260700) with parameters -a 1, -t “exon” -i “name”.
Genome_build: Postia placenta MAD 698-R v1.0 from JGI (mycocosm.jgi.doe.gov/Pospl1/Pospl1.home.html).
Supplementary_files_format_and_content: Text file (.txt) is a matrix of raw read counts for every gene and every sample

organism: Rhodonia placenta

source_name: brown rot decayed aspen wood

growth_protocol: Using Rhodonia placenta (MAD698R, ATCC44394) maintained on malt extract agar, modified soil-block microcosms (1:1:1 soil:peat:vermiculite, 50% moisture content) containing birch “feeder” strips were inoculated and incubated in the dark at 26 °C and 70% relative humidity until a fungal mat was formed (approx. 2 weeks). Aspen wafers (60 × 20 × 2.5 mm), cut with the cross section as the largest face and wood rays oriented across the shorter 20-mm dimension, were placed in microcosms such that R. placenta would grow vertically up the wafer. After 26 days of incubation (dark, 26 °C, 70% RH), wafers with horizontal hyphal fronts were harvested and 2 samples (7 x 5 x 2.5 mm) were cut from the newest 5 mm of the fungal growth (0-5 mm). To maintain the orientation, a notch was cut out of the top corner of the hyphal front edge. This process was repeated at the 15-20 mm distance.

extract_protocol:
The RNAs from the cryo-sectioned samples were isolated using RNAqueous™-Micro Total RNA Isolation Kit (cat#AM1931), followed by full-length cDNA synthesis using SMARTer® Ultra® Low RNA Kit for Illumina® Sequencing (cat# 634936).
Nextera XT DNA Library Preparation Kit (FC-131-1096) and IDT® for Illumina® 233 DNA/RNA UD Indexes Set A, Tagmentation (cat#20027213) were used to generate the template library for sequencing according to the manufacture’s protocol.

treatment_protocol: Samples were prepared for cryo-sectioning by submerging the sample in a fixative solution (pure HPLC grade methanol containing 0.1% (v/v) Triton X-100) to stabilize RNA, followed by a gradual equilibration to optimum cutting temperature (OCT) medium using 100% methanol, 70% (v/v) ethanol, 96% (v/v) ethanol, 100% ethanol and 50% (v/v) 1X phosphate buffered saline in OCT medium. Samples were then embedded in OCT medium and frozen at -80 °C. Previously embedded samples in OCT were cryo-sectioned on a Cryostar NX70 cryostat at 12 μm from the leading edge of the sample until the full span of approximately 100 μm was cut. The cryo-sectioned samples were transferred to a 1.5 mL microcentrifuge tube and were kept frozen to ensure RNA integrity.

tag: synonymn

value: Rhodonia placenta

value: MAD 698-R

tag: wafer location


title: 6CR: wafer 6, 19900-20000 μm, rep1


title: 6DN: wafer 6, 15000-15100 μm, rep2


title: 6CN: wafer 6, 15000-15100 μm, rep1


title: 6BR: wafer 6, 4900-5000 μm, rep2


title: 6BN: wafer 6, 0-100 μm, rep2


title: 6AR: wafer 6, 4900-5000 μm, rep1


title: 5DR: wafer 5, 19900-20000 μm, rep2


title: MCC26

value: vMCC


title: 5DN: wafer 5, 15000-15100 μm, rep2


title: 5CN: wafer 5, 15000-15100 μm, rep1


title: 4BR: wafer 4, 4900-5000 μm, rep1


title: 4DN: wafer 4, 15000-15100 μm, rep2


title: 5AN: wafer 5, 0-100 μm, rep1


title: 5CR: wafer 5, 19900-20000 μm, rep1


title: 4CR: wafer 4, 19900-20000 μm, rep1


title: 3DR: wafer 3, 19900-20000 μm, rep2


title: 4CN: wafer 4, 15000-15100 μm, rep1


title: 5BN: wafer 5, 0-100 μm, rep2


title: 4DR: wafer 4, 19900-20000 μm, rep2


title: 3DN: wafer 3, 15000-15100 μm, rep2


title: 3CN: wafer 3, 15000-15100 μm, rep1


title: 3CR: wafer 3, 19900-20000 μm, rep1


title: 3BN: wafer 3, 0-100 μm, rep2


title: 3AN: wafer 3, 0-100 μm, rep1


title: 3AR: wafer 3, 4900-5000 μm, rep1


title: 2DR: wafer 2, 19900-20000 μm, rep2


title: 2DN: wafer 2, 15000-15100 μm, rep2


title: 6AN: wafer 6, 0-100 μm, rep1


title: 2CR: wafer 2, 19900-20000 μm, rep1


title: 5BR: wafer 5, 4900-5000 μm, rep2


title: 2CN: wafer 2, 15000-15100 μm, rep1


title: 4BN: wafer 4, 0-100 μm, rep1


title: 5AR: wafer 5, 4900-5000 μm, rep1


title: 2AR: wafer 2, 4900-5000 μm, rep1


title: 3BR: wafer 3, 4900-5000 μm, rep2


title: 1CR: wafer 1, 19900-20000 μm, rep1


title: 1AN: wafer 1, 0-100 μm, rep1


title: 2AN: wafer 2, 0-100 μm, rep1


title: DSP-1010910372679-A-H06

data_processing:
Library strategy: GeoMx Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: RawCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, probe information, and raw probe count matrix for each probe and sample
Supplementary_files_format_and_content: CollapsedTargetCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and target-level count matrix for each gene target and sample
Supplementary_files_format_and_content: NormalizedTargetCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and Q3 normalized target-level count matrix for each gene target and sample

source_name: FxF E13.5 embryo

tag: slide name

value: BRK086 G5S5

tag: scan name

tag: panel

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

tag: area

value: Midgut

value: Neuron

value: Herniated

tag: molecule

value: other:mRNA ISH


title: DSP-1010910372679-A-H04

tag: tissue

value: Epithelium


title: DSP-1010910372679-A-H03


title: DSP-1010910372679-A-H09


title: DSP-1010910372679-A-H02

value: Mesenchyme


title: DSP-1010910372679-A-H07


title: DSP-1010910372679-A-H12

value: Lung

value: Distal


title: DSP-1010910372679-A-H05


title: DSP-1010910372679-A-H10


title: DSP-1010910372679-A-H08


title: DSP-1010910372679-A-G10

value: Duodenum

value: Liver Distal


title: DSP-1010910372679-A-H01


title: DSP-1010910372679-A-G09


title: DSP-1010910372679-A-G07


title: DSP-1010910372679-A-G08


title: 1CN: wafer 1, 15000-15100 μm, rep1

tag: strain


title: DSP-1010910372679-A-G06

tag: roi

value: Liver Proximal


title: DSP-1010910372679-A-G05


title: 1DR: wafer 1, 19900-20000 μm, rep2


title: DSP-1010910372679-A-G04


title: DSP-1010910372679-A-G02

value: BRK086 G4S3

value: Heart

value: Wall

value: Atrium


title: DSP-1010910372679-A-G03


title: DSP-1010910372679-A-G11

value: BRK086 G5S5


title: DSP-1010910372679-A-G01

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1010910372679-A-H11


title: DSP-1010910372679-A-F10

value: Trabecula

value: Ventricle


title: DSP-1010910372679-A-G12

value: Neuron


title: DSP-1010910372679-A-F11

value: other:mRNA ISH


title: DSP-1010910372679-A-F09


title: DSP-1010910372679-A-F12


title: DSP-1010910372679-A-F06


title: DSP-1010910372679-A-F07


title: DSP-1010910372679-A-F05


title: DSP-1010910372679-A-F04


title: DSP-1010910372679-A-F02


title: DSP-1010910372679-A-F08


title: DSP-1010910372679-A-E11


title: DSP-1010910372679-A-F01


title: DSP-1010910372679-A-F03


title: DSP-1010910372679-A-E09


title: DSP-1010910372679-A-E10


title: DSP-1010910372679-A-E08


title: DSP-1010910372679-A-E07


title: DSP-1010910372679-A-E05

value: Epithelium


title: DSP-1010910372679-A-E04


title: DSP-1010910372679-A-E01


title: DSP-1010910372679-A-E03


title: DSP-1010910372679-A-E02


title: DSP-1010910372679-A-D10


title: DSP-1010910372679-A-D11


title: DSP-1010910372679-A-D08


title: DSP-1010910372679-A-D06


title: DSP-1010910372679-A-D05


title: DSP-1010910372679-A-D12


title: DSP-1010910372679-A-D04


title: DSP-1010910372679-A-D03


title: DSP-1010910372679-A-D09


title: DSP-1010910372679-A-E12

value: Mesenchyme


title: DSP-1010910372679-A-D01

value: Lung


title: DSP-1010910372679-A-D02

value: Distal


title: DSP-1010910372679-A-C11


title: DSP-1010910372679-A-C10


title: DSP-1010910372679-A-C07

value: Right Metanephros

value: Cortex


title: DSP-1010910372679-A-C03

value: Nephron


title: DSP-1010910372679-A-E06

value: BRK086 G4S3


title: DSP-1010910372679-A-C08


title: DSP-1010910372679-A-C04


title: DSP-1010910372679-A-C02


title: DSP-1010910372679-A-C06


title: DSP-1010910372679-A-B11


title: DSP-1010910372679-A-B10


title: DSP-1010910372679-A-D07


title: DSP-1010910372679-A-C01


title: DSP-1010910372679-A-B09


title: DSP-1010910372679-A-B08


title: DSP-1010910372679-A-B07

value: Medulla


title: DSP-1010910372679-A-B12


title: DSP-1010910372679-A-B02

value: Midgut

value: Herniated


title: DSP-1010910372679-A-B06


title: DSP-1010910372679-A-B04


title: DSP-1010910372679-A-C12


title: DSP-1010910372679-A-B01


title: DSP-1010910372679-A-B03


title: DSP-1010910372679-A-C09


title: DSP-1010910372679-A-B05


title: DSP-1010910372679-A-A11

value: Body


title: DSP-1010910372679-A-A12

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1010910372679-A-A10


title: DSP-1010910372679-A-C05


title: DSP-1010910372679-A-A09


title: DSP-1010910372679-A-A07

value: Duodenum

value: Liver Distal


title: DSP-1010910372679-A-A05

value: Neuron

value: Liver Proximal


title: DSP-1010910372679-A-A04

value: other:mRNA ISH


title: DSP-1010910372679-A-A06

value: Epithelium


title: DSP-1010910372679-A-A03

value: Mesenchyme


title: DSP-1010910372678-B-D02

value: BRK086 G5S5

value: Heart

value: Wall

value: Ventricle


title: DSP-1010910372679-A-A01

value: No Template Control

value: NTC


title: DSP-1010910372678-B-C11

value: Atrium


title: DSP-1010910372678-B-C08

value: Trabecula


title: DSP-1010910372678-B-C09

value: Valve


title: DSP-1010910372678-B-C10

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1010910372678-B-C12


title: DSP-1010910372678-B-C07


title: DSP-1010910372678-B-D01


title: DSP-1010910372678-B-C04


title: DSP-1010910372678-B-B12


title: DSP-1010910372678-B-B11


title: DSP-1010910372678-B-C01


title: DSP-1010910372678-B-B10


title: DSP-1010910372678-B-C06


title: DSP-1010910372678-B-C03


title: DSP-1010910372678-B-C02


title: DSP-1010910372679-A-A08

value: BRK086 G4S3

value: Duodenum


title: DSP-1010910372678-B-B06

value: Lung

value: Distal


title: DSP-1010910372678-B-B05

value: other:mRNA ISH


title: DSP-1010910372678-B-B09


title: DSP-1010910372679-A-A02

value: Epithelium

value: Liver Proximal


title: DSP-1010910372678-B-B07

value: BRK086 G5S5

value: Mesenchyme


title: DSP-1010910372678-B-B08


title: DSP-1010910372678-B-B04


title: DSP-1010910372678-B-B01


title: DSP-1010910372678-B-A12


title: DSP-1010910372678-B-A11


title: DSP-1010910372678-B-B02


title: DSP-1010910372678-B-B03


title: DSP-1010910372678-B-A10


title: DSP-1010910372678-B-A09

value: Misplaced


title: DSP-1010910372678-B-C05

value: Heart

value: Ventricle


title: DSP-1010910372678-B-A05


title: DSP-1010910372678-B-A07


title: DSP-1010910372678-B-A04


title: DSP-1010910372678-B-A06


title: DSP-1010910372678-B-A01

value: No Template Control

value: NTC


title: DSP-1010910372678-B-A02


title: DSP-1010910372664-E-H12

value: AEL026 S2 G9S4 FxF mouse embryo E13 NBF full ROIs

value: Trabecula


title: DSP-1010910372664-E-H11

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1010910372664-E-H10


title: DSP-1010910372664-E-H05

value: Wall

value: Atrium


title: DSP-1010910372664-E-H08


title: DSP-1010910372664-E-H07


title: DSP-1010910372664-E-H06


title: DSP-1010910372664-E-H02

value: Stomach

value: Neuron


title: DSP-1010910372664-E-H03

value: other:mRNA ISH


title: DSP-1010910372664-E-G11

value: Esophagus

value: Abdominal


title: DSP-1010910372678-B-A08

value: BRK086 G5S5

value: Lung

value: Epithelium

value: Distal


title: DSP-1010910372664-E-G06


title: DSP-1010910372664-E-G07


title: DSP-1010910372678-B-A03


title: DSP-1010910372664-E-G09


title: DSP-1010910372664-E-H09

value: Heart

value: Ventricle


title: DSP-1010910372664-E-G10

value: Mesenchyme


title: DSP-1010910372664-E-F11

value: AEL026 S2 G9S4 FxF mouse embryo E13 NBF full ROIs


title: DSP-1010910372664-E-G08


title: DSP-1010910372664-E-G05


title: DSP-1010910372664-E-F12


title: DSP-1010910372664-E-G01


title: DSP-1010910372664-E-F07


title: DSP-1010910372664-E-G04


title: DSP-1010910372664-E-F08


title: DSP-1010910372664-E-G02


title: DSP-1010910372664-E-F09


title: DSP-1010910372664-E-F10


title: DSP-1010910372664-E-G03


title: DSP-1010910372664-E-H04


title: DSP-1010910372664-E-F06


title: DSP-1010910372664-E-H01


title: DSP-1010910372664-E-F04


title: DSP-1010910372664-E-F01


title: DSP-1010910372664-E-F02


title: DSP-1010910372664-E-F05


title: DSP-1010910372664-E-F03


title: DSP-1010910372664-E-E12


title: DSP-1010910372664-E-G12


title: DSP-1010910372664-E-E11


title: DSP-1010910372664-E-E10

value: AEL026 S1 G8S4 FxF mouse embryo E13 NBF full ROIs

value: Metanephros

value: Cortex


title: DSP-1010910372664-E-E08

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1010910372664-E-E09


title: DSP-1010910372664-E-E07


title: DSP-1010910372664-E-E04

value: Nephron


title: DSP-1010910372664-E-E01


title: DSP-1010910372664-E-D12


title: DSP-1010910372664-E-E03


title: DSP-1010910372664-E-E05

value: Medulla


title: DSP-1010910372664-E-D09

value: other:mRNA ISH


title: DSP-1010910372664-E-D06


title: DSP-1010910372664-E-D11


title: DSP-1010910372664-E-D08


title: DSP-1010910372664-E-D10


title: DSP-1010910372664-E-C11

value: Trabecula


title: DSP-1010910372664-E-D01


title: DSP-1010910372664-E-C08

value: Wall

value: Atrium


title: DSP-1010910372664-E-E02


title: DSP-1010910372664-E-C10


title: DSP-1010910372664-E-C06


title: DSP-1010910372664-E-C09


title: DSP-1010910372664-E-D04


title: DSP-1010910372664-E-C05


title: DSP-1010910372664-E-D03


title: DSP-1010910372664-E-C07


title: DSP-1010910372664-E-C04


title: DSP-1010910372664-E-D05


title: DSP-1010910372664-E-D02


title: DSP-1010910372664-E-E06


title: DSP-1010910372664-E-C03


title: DSP-1010910372664-E-C01

value: Esophagus

value: Abdominal


title: DSP-1010910372664-E-C12


title: DSP-1010910372664-E-B10

value: Stomach

value: Neuron


title: DSP-1010910372664-E-B12

value: Epithelium


title: DSP-1010910372664-E-B09

value: Mesenchyme


title: DSP-1010910372664-E-B08


title: DSP-1010910372664-E-B11


title: DSP-1010910372664-E-B04

value: Lung

value: Distal


title: DSP-1010910372664-E-B05

value: AEL026 S1 G8S4 FxF mouse embryo E13 NBF full ROIs


title: DSP-1010910372664-E-B06


title: DSP-1010910372664-E-B07


title: DSP-1010910372664-E-A11


title: DSP-1010910372664-E-B01


title: DSP-1010910372664-E-B03


title: DSP-1010910372664-E-A12


title: DSP-1010910372664-E-A06


title: DSP-1010910372664-E-A09


title: DSP-1010910372664-E-A10


title: DSP-1010910372664-E-A07


title: DSP-1010910372664-E-A08


title: DSP-1010910372664-E-B02


title: DSP-1010910372664-E-A05


title: DSP-1010910372664-E-A04


title: DSP-1010910372664-E-C02


title: DSP-1010910372664-E-A02


title: DSP-1010910372664-E-A03


title: DSP-1010910372664-E-A01

value: No Template Control

value: NTC


title: DSP-1010910372663-F-B09

value: AEL026 S2 G9S4 FxF mouse embryo E13 NBF full ROIs

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA

value: Metanephros

value: Cortex


title: DSP-1010910372663-F-B08

value: other:mRNA ISH


title: DSP-1010910372663-F-B07


title: DSP-1010910372663-F-B06


title: DSP-1010910372664-E-D07

value: Nephron


title: DSP-1010910372663-F-B03


title: DSP-1010910372663-F-B02


title: DSP-1010910372663-F-B01

value: Medulla


title: DSP-1010910372663-F-A11


title: DSP-1010910372663-F-A12


title: DSP-1010910372663-F-A10


title: DSP-1010910372663-F-A08


title: DSP-1010910372663-F-A07


title: DSP-1010910372663-F-A09


title: DSP-1010910372663-F-A01


title: DSP-1010910372663-F-A05


title: DSP-1010910372663-F-A06


title: DSP-1010910372663-F-A02


title: DSP-1010910372663-F-A03


title: DSP-1002500002688-D-A08

value: Pancreas


title: DSP-1002500002688-D-A10


title: DSP-1010910372663-F-B05


title: DSP-1002500002688-D-A05


title: DSP-1002500002688-D-A06


title: DSP-1002500002688-D-A07


title: DSP-1002500002688-D-A04

value: Esophagus

value: Entrance


title: DSP-1002500002688-D-A03


title: DSP-1002500002688-D-A01


title: DSP-1002500002688-D-A02


title: DSP-1002500002677-C-H12

value: Epithelium


title: DSP-1002500002677-C-H11

value: Heart

value: Wall

value: Ventricle


title: DSP-1010910372663-F-B04

value: Mesenchyme


title: DSP-1002500002677-C-H10

value: Trabecula


title: DSP-1002500002677-C-H08


title: DSP-1002500002677-C-H09


title: DSP-1010910372663-F-A04


title: DSP-1002500002677-C-H06


title: DSP-1002500002677-C-H05


title: DSP-1002500002677-C-H04


title: DSP-1002500002677-C-H07


title: DSP-1002500002677-C-G08

value: Midgut

value: Herniated


title: DSP-1002500002677-C-G10

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1002500002677-C-G12

value: Neuron


title: DSP-1002500002677-C-G07


title: DSP-1002500002677-C-G11


title: DSP-1002500002677-C-G06

value: Lung

value: Proximal


title: DSP-1002500002688-D-A09

value: other:mRNA ISH


title: DSP-1002500002677-C-H02

value: Atrium


title: DSP-1002500002677-C-G09


title: DSP-1002500002677-C-G02


title: DSP-1002500002677-C-H01


title: DSP-1002500002677-C-G03


title: DSP-1002500002677-C-G05


title: DSP-1002500002677-C-F12

value: Trachea


title: DSP-1002500002677-C-F11


title: DSP-1002500002677-C-F10


title: DSP-1002500002677-C-G01


title: DSP-1002500002677-C-G04


title: DSP-1002500002677-C-F07

value: Esophagus

value: Body


title: DSP-1002500002677-C-F06


title: DSP-1002500002677-C-F05


title: DSP-1002500002677-C-F04

value: Epithelium


title: DSP-1002500002677-C-F03


title: DSP-1002500002677-C-F09


title: DSP-1002500002677-C-E12

value: Stomach


title: DSP-1002500002677-C-F02


title: DSP-1002500002677-C-E10


title: DSP-1002500002677-C-E08


title: DSP-1002500002677-C-E06


title: DSP-1002500002677-C-E07


title: DSP-1002500002677-C-H03

value: Heart

value: Valve


title: DSP-1002500002677-C-E05


title: DSP-1002500002677-C-E04

value: Mesenchyme


title: DSP-1002500002677-C-E03

value: Entrance


title: DSP-1002500002677-C-F01


title: DSP-1002500002677-C-F08

value: Midgut


title: DSP-1002500002677-C-D12

value: Wall

value: Ventricle


title: DSP-1002500002677-C-D09

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1002500002677-C-E02


title: DSP-1002500002677-C-D11


title: DSP-1002500002677-C-D07


title: DSP-1002500002677-C-E01

value: Trabecula


title: DSP-1002500002677-C-D08


title: DSP-1002500002677-C-D06


title: DSP-1002500002677-C-D04


title: DSP-1002500002677-C-D02


title: DSP-1002500002677-C-D03


title: DSP-1002500002677-C-C11


title: DSP-1002500002677-C-C12


title: DSP-1002500002677-C-E11


title: DSP-1002500002677-C-C08


title: DSP-1002500002677-C-C05

value: Conductive Fibers


title: DSP-1002500002677-C-C07

value: other:mRNA ISH


title: DSP-1002500002677-C-E09


title: DSP-1002500002677-C-C03

value: Duodenum

value: Liver Proximal


title: DSP-1002500002677-C-C02


title: DSP-1002500002677-C-C01


title: DSP-1002500002677-C-C06


title: DSP-1002500002677-C-B12


title: DSP-1002500002677-C-B08

value: Atrium


title: DSP-1002500002677-C-B07


title: DSP-1002500002677-C-B11


title: DSP-1002500002677-C-D10


title: DSP-1002500002677-C-C04


title: DSP-1002500002677-C-B10


title: DSP-1002500002677-C-B03


title: DSP-1002500002677-C-B04


title: DSP-1002500002677-C-B05


title: DSP-1002500002677-C-B06


title: DSP-1002500002677-C-B01

value: Neuron

value: Herniated


title: DSP-1002500002677-C-C10


title: DSP-1002500002677-C-D05

value: Trachea

value: Epithelium


title: DSP-1002500002677-C-C09

value: Heart


title: DSP-1002500002677-C-A11


title: DSP-1002500002677-C-B02


title: DSP-1002500002677-C-A10

value: Lung

value: Proximal


title: DSP-1002500002677-C-A09


title: DSP-1002500002677-C-D01

value: Esophagus

value: Body


title: DSP-1002500002677-C-A02

value: Mesenchyme


title: DSP-1002500002677-C-A07

value: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA


title: DSP-1002500002677-C-A01

value: No Template Control


title: DSP-1002500002677-C-A06


title: DSP-1002500002677-C-A04


title: DSP-1002500002677-C-A08


title: DSP-1002500002677-C-A05


title: DSP-1002500002677-C-B09

value: Wall

value: Ventricle


title: DSP-1002500002677-C-A03

value: other:mRNA ISH


title: DSP-1002500002677-C-A12

value: Midgut


title: PD-1 + CTLA-4 rep5

city: Hamilton

first: Karen

last: Mossman

address: 1280 Main St West

department: Department of Medicine

institute: McMaster University

description: Gene expression data from tumours.

hyb_protocol: Fragmented sample was hybridized to Affymetrix Clariom S human arrays at 45 °C overnight.

scan_protocol: Arrays were imaged using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data was analyzed using the Transcriptome Analysis Console software, Thermo Fischer. Data were processed using RMA (with Quantile Normalization), HDF5 output.

source_name: MC38 subcutaneous tumor from C57Bl/6 mouse

label_protocol: RNA was normalized to an input amount of 100 ng and underwent reverse transcription. sscDNA was purified using magnetic beads and fragmented using UDG.

growth_protocol: 2 x 10^5 MC38 cells were implanted subcutaneously on the left flank.

extract_protocol: 4 days after the start of treatment mice were sacrificed and tumours harvested. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: On the first day of treatment (10 days after implanting tumors), 0.1 mg of Mitomycin C, 250µg of αPD-1 and αCTLA-4 antibodies were administered by i.t. and i.p. injections, respectively. For the following 3 days, 2 x 10^7 pfu of oHSV was administered by i.t. injection (total of 3 doses). Experimental groups receiving αPD-1/CTLA-4 followed a dosing schedule of 250 µg treatments every 3 days for a total of 8 doses.

value: MC38 subcutaneous tumor

value: anti-PD-1 + anti-CTLA-4


title: mito + HSV + PD-1 + CTLA-4 rep 4

description: Gene expression data from tumours.

value: Mitomycin C + oncolytic HSV-1 + anti PD-1 + anti-CTLA-4


title: mito + HSV rep 3

description: Gene expression data from tumours.

value: Mitomycin C + oncolytic HSV-1


title: mito + HSV rep 4

description: Gene expression data from tumours.


title: PD-1 + CTLA-4 rep3

description: Gene expression data from tumours.


title: PD-1 + CTLA-4 rep1

description: Gene expression data from tumours.


title: mito + HSV + PD-1 + CTLA-4 rep 3

description: Gene expression data from tumours.


title: mito + HSV rep 5

description: Gene expression data from tumours.


title: mito + HSV + PD-1 + CTLA-4 rep 2

description: Gene expression data from tumours.


title: PD-1 + CTLA-4 rep4

description: Gene expression data from tumours.


title: mito + HSV + PD-1 + CTLA-4 rep 5

description: Gene expression data from tumours.


title: oncolytic HSV rep 2

description: Gene expression data from tumours.

value: oncolytic HSV-1


title: mito + HSV + PD-1 + CTLA-4 rep 1

description: Gene expression data from tumours.


title: oncolytic HSV rep 4

description: Gene expression data from tumours.


title: oncolytic HSV rep 3

description: Gene expression data from tumours.


title: Mitomycin rep 5

description: Gene expression data from tumours.

value: Mitomycin C


title: oncolytic HSV rep 1

description: Gene expression data from tumours.


title: PD-1 + CTLA-4 rep2

description: Gene expression data from tumours.


title: Mitomycin rep 2

description: Gene expression data from tumours.


title: mito + HSV rep 2

description: Gene expression data from tumours.


title: PBS rep 5

description: Gene expression data from tumours.

value: Saline


title: oncolytic HSV rep 5

description: Gene expression data from tumours.


title: PBS rep4

description: Gene expression data from tumours.


title: PBS rep 2

description: Gene expression data from tumours.


title: Mitomycin rep 4

description: Gene expression data from tumours.


title: PBS rep 1

description: Gene expression data from tumours.


title: Mitomycin rep 1

description: Gene expression data from tumours.


title: Mitomycin rep 3

description: Gene expression data from tumours.


title: RNA-seq Liver Refed Foxk1KO4

city: Charlottesville

first: Shun

last: Fujinuma

state: Virginia

address: Jordan Hall, RM 4061B, 1340 Jefferson Park Ave

institute: University of Virginia

data_processing:
Read QC, trimming and filtering were performed using fastp
Raw reads were aligned using HISAT2 against mm10/GRCm38 as reference genome with default parameters
Read counting was performed using featureCounts
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized counts

source_name: Liver

extract_protocol:
Livers were removed and flash frozen. Total RNA was extracted from liver tissue with the use of a TRIzol Plus RNA Purification Kit (Life Technologies).
RNA-seq libraries were prepared with the use of a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol:
NASH models: Alb-Cre/Foxk1(F/+) and Alb-Cre/Foxk1(F/F) mice fed ND (31 kcal% protein, 54 kcal% carbohydrate, 15 kcal% fat; CLEA) or CDAHFD (18 kcal% protein, 20 kcal% carbohydrate, 62 kcal% fat; Research Diets) for 12 weeks from 6 weeks of age.
Fasted/Refed models: 10-week-old mice were fasted for 24 hours or refed for 2 hours after 24-hour fasting.

value: Liver

tag: protocol

value: RNA-seq

tag: genotype

tag: age

value: 10 week-old

value: Refed for 2 hours after a 24-hour fasting


title: RNA-seq Liver Refed Foxk1KO6


title: RNA-seq Liver Refed Foxk1KO5


title: RNA-seq Liver Refed Foxk1KO3


title: RNA-seq Liver Refed Foxk1KO2


title: Epi_YesFGF2_biological_rep1

city: Albany

first: Nicholas

last: Moskwa

state: New York

address: 1400 Washington Avenue

institute: University at Albany

description: Epithelial portion of organoids grown for 7 days

hyb_protocol: Samples were hybridized to the Affymetrix Clariom D Assay, Mouse for 16-18 h at 45°C.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000

data_processing:
Data were processed using Transcriptome Analysis Console software and R/Rstuio. The data were analyzed with the robust multichip analysis (RMA) algorithm using default analysis settings and global scaling as a normalization method. Values are presented according to log2 RMA signal intensity. We defined the genes with a fold-change of more than 1.99 or less than 1.99 and a p-value of less than 0.05 as different expression genes
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.r1.mps

label_protocol: Samples were enzymatically fragmented and biotinylated by terminal deoxynucleotidyl transferase (TdT) (Clariom D Kit)

growth_protocol: Organoids were cultured for 7 days with a 4 day media change

extract_protocol: Total RNA was extracted using RNeasy Mini-Kit (Qiagen), then cDNA synthesis and amplification (Clariom D Kit)

treatment_protocol: Grown with or without FGF2 containing media

value: organoids

value: Epithelial


title: Epi_YesFGF2_biological_rep3


title: HSPC_endogenous_WT_Irradiated_leg_3

city: Fontenay aux Roses

first: Daniel

last: LEWANDOWSKI

state: Ile-de-France

address: 18 route du Panorama

department: IBFJ/iRCM

country: France

institute: CEA

description: Gene expression data from endogenous WT HSPC in irradiated leg of recipient mice transplanted with JAK2V617F hematopoieitc cells.

hyb_protocol: Following fragmentation, 5.5 ug of Labeled ss-cDNA were hybridized with rotation at 60rpm  for 16 hr at 45C on GeneChip Clariom S array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with TAC 4.0.1.36 software, normalized with SST-RMA algorithm (ThermoFisher) and corrected by global scaling.

label_protocol: Biotinylated cDNA were prepared according to the GeneChip whole Transcript (WT) Pico Reagent Kit protolcol (Affymetrix).

growth_protocol: Mouse hematopoietic stem and progenitor cells (HSPC) from non- and irradiated BM legs were sorted based on Lin-cKit+Sca+CD48- phenotype expressing or not the GFP (reporter of JAK2V617F expression)

extract_protocol: Total RNA was extracted according to the protocol of RNeasy Plus Micro Kit (QIAGEN) and The RNA integrity (RNA Integrity Score≥7.0) was checked on the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: ND

value: Bone marrow

value: WT

tag: location

value: irradiated leg


title: Epi_YesFGF2_biological_rep2


title: mito + HSV rep 1

description: Gene expression data from tumours.


title: HSPC_JAK2V617F_Irradiated_leg_2

description: Gene expression data from JAK2V617F HSPC in irradiated leg of recipient mice transplanted with JAK2V617F hematopoieitc cells.

source_name: hematopoietic stem and progenitor cells (HSPC)


title: Epi_NoFGF2_biological_rep1

value: control


title: HSPC_endogenous_WT_non_irradiated_leg_3

description: Gene expression data from endogenous WT HSPC in non-irradiated leg of recipient mice transplanted with JAK2V617F hematopoieitc cells.

value: hematopoietic stem and progenitor cells (HSPC)

value: non-irradiated leg


title: RNA-seq Liver Refed Control5


title: RNA-seq Liver Refed Control4


title: RNA-seq Liver Refed Foxk1KO1


title: RNA-seq Liver Refed Control6


title: RNA-seq Liver Refed Control3


title: RNA-seq Liver Refed Control2


title: HSPC_JAK2V617F_non_irradiated_leg

description: Gene expression data from JAK2V617F HSPC in non-irradiated leg of recipient mice transplanted with JAK2V617F hematopoieitc cells.


title: RNA-seq Liver Fasted Foxk1KO6

value: Fasted for 24 hours


title: RNA-seq Liver Refed Control1


title: RNA-seq Liver Fasted Foxk1KO2


title: HSPC_JAK2V617F_non_irradiated_leg_2


title: RNA-seq Liver Fasted Foxk1KO4


title: RNA-seq Liver Fasted Foxk1KO3


title: RNA-seq Liver Fasted Control6


title: HSPC_endogenous_WT_Irradiated_leg_1


title: RNA-seq Liver Fasted Control3


title: RNA-seq Liver Fasted Foxk1KO1


title: HSPC_JAK2V617F_non_irradiated_leg_1


title: HSPC_JAK2V617F_Irradiated_leg_1


title: HSPC_endogenous_WT_Irradiated_leg_2


title: RNA-seq Liver Fasted Control1


title: HSPC_endogenous_WT_non_irradiated_leg_1


title: Epi_NoFGF2_biological_rep2


title: HSPC_endogenous_WT_non_irradiated_leg_2


title: Epi_NoFGF2_biological_rep3


title: RNA-seq Liver Fasted Control4


title: RNA-seq Liver CDAHFD12wks Foxk1KO5

value: 18 week-old

value: Fed CDAHFD for 12 weeks


title: RNA-seq Liver CDAHFD12wks Foxk1KO6


title: RNA-seq Liver CDAHFD12wks Foxk1KO2


title: RNA-seq Liver CDAHFD12wks Foxk1KO1


title: RNA-seq Liver Fasted Foxk1KO5


title: RNA-seq Liver Fasted Control2


title: RNA-seq Liver CDAHFD12wks Control6


title: RNA-seq Liver CDAHFD12wks Foxk1KO4


title: RNA-seq Liver CDAHFD12wks Control5


title: RNA-seq Liver CDAHFD12wks Control4


title: RNA-seq Liver Fasted Control5


title: RNA-seq Liver CDAHFD12wks Foxk1KO3


title: RNA-seq Liver CDAHFD12wks Control2


title: RNA-seq Liver ND12wks Foxk1KO4

value: Fed ND for 12 weeks


title: RNA-seq Liver ND12wks Control5


title: RNA-seq Liver ND12wks Control4


title: RNA-seq Liver ND12wks Control6


title: RNA-seq Liver ND12wks Foxk1KO2


title: RNA-seq Liver ND12wks Foxk1KO5


title: RNA-seq Liver ND12wks Control3


title: RNA-seq Liver ND12wks Foxk1KO1


title: RNA-seq Liver ND12wks Control2


title: RNA-seq Liver ND12wks Control1


title: Nkx2.2ko_d3,5

city: Solna

first: Zhanna

last: Alekseenko

state: Stockholm

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

data_processing:
Clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.2.38/RTA 1.18.61) with a 1x51 setup in RapidHighOutput mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
Reads were mapped with Tophat/2.0.4 to the Mouse genome assembly, build GRCm38 using default parameters settings.
Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
FPKMs for genes and transcripts were generated using cufflinks/2.1.1 on bamfiles
Voom normalized logCPM values were obtained using voom function from R limma package
Genome_build: mm10

source_name: Neural progenitor cells

growth_protocol: mESCs were differentiated in monolayer condition in N2B27 medium in different conditions.

extract_protocol:
Total RNA was extracted using Quick-RNA Mini Prep Plus kit (Zymo Research). For samples collected at 3.5 days in culture or later, neural progenitors were isolated using prominin-based MACs-sorting, and total RNA was extracted from prominin-positive isolated population.
Illumina TruSeq Stranded mRNA
poly-A selection

treatment_protocol: Cells were treated with RA for the first 3.5 days of culture and with the activator of SHH signaling SAG1.3 during the entire experimental period for the Foxa2-/- cell line and corresponding WT control, or during the first 3.5 days of differentiation for the Nkx2.2-/- cell line and corresponding WT control.

tag: line

tag: Stage

value: 3.5 days


title: PBS rep 3

description: Gene expression data from tumours.

value: MC38 subcutaneous tumor

tag: treatment

value: Saline


title: Nkx2.2ko_d5,5


title: WT_d5,5


title: Foxa2ko_d7,5_Ag_2

value: 7.5 days


title: Foxa2ko_d7,5_Ag_1


title: Foxa2ko_d6,5_Ag_2

value: 6.5 days


title: RNA-seq Liver CDAHFD12wks Control3

value: Liver

value: RNA-seq


title: Foxa2ko_d5,5_Ag_3

value: 5.5 days


title: Foxa2ko_d6,5_Ag_1


title: RNA-seq Liver ND12wks Foxk1KO6


title: RNA-seq Liver CDAHFD12wks Control1


title: Foxa2ko_d5,5_Ag_2


title: Foxa2ko_d4,5_Ag_3

value: 4.5 days


title: Foxa2ko_d4,5_Ag_2


title: RNA-seq Liver ND12wks Foxk1KO3


title: Foxa2ko_d5,5_Ag_1


title: Foxa2ko_d4,5_Ag_1


title: Foxa2ko_d2_3

value: 2 days

value: RA d0-2; SAG d0-2


title: Foxa2ko_d2_1


title: Foxa2ko_d1_3

value: 1 day

value: RA d0-1; SAG d0-1


title: Foxa2ko_d3,5_3


title: Foxa2ko_d3,5_1


title: Foxa2koko_mESCs_2

source_name: Embryonic stem cells

value: undifferentiated cells

value: No


title: WT_d3,5


title: Foxa2ko_d2_2


title: Foxa2ko_mESCs_3


title: Foxa2ko_d1_2


title: Foxa2ko_d1_1


title: WT_d7,5_3


title: WT_d7,5_1


title: WT_d6,5_3


title: Foxa2koko_mESCs_1


title: WT_d7,5_2


title: WT_d4,5_3


title: WT_d6,5_1


title: WT_d5,5_3


title: WT_d5,5_2


title: WT_d5,5_1


title: WT_d6,5_2


title: WT_d3,5_2


title: WT_d4,5_2


title: WT_d3,5_1


title: Foxa2ko_d3,5_2


title: WT_d2_2


title: WT_d4,5_1


title: WT_d3,5_3


title: WT_d2_1


title: WT_mESC_2


title: WT_mESC_1


title: Puro_24hrs_Rep2

city: Lexington

first: John

middle: Kyle

last: Friend

state: VA

address: A427 Science Addition, 204 W Washington St

department: Chemistry and Biochemistry

institute: Washington and Lee University

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 24 hrs after switch to uridine containing medium with puromycin

data_processing:
Raw reads were filtered with quality cut-off set to 20 and 90% bases with minimum cut-off (Filter by quality, Galaxy).
Reads were aligned to the mm10 transcriptome (Bowtie2, Galaxy)
Custom software was used to count C-->U conversion events in the aligned sam files and to determine the percentage of read with these conversions (https://github.com/Kyle-Friend/DecayKinetics).
Percentage C-->U conversions were then fit to an exponential decay curve to calculate mRNA half-lives in the samples (https://github.com/Kyle-Friend/DecayKinetics).
Genome_build: mm10 (GRCm39)
Supplementary_files_format_and_content: Tab-delimited text file with transcript name, three columns with experimental half-lives (control, G418-treated, and puromycin-treated), and average number of RNA-seq reads.

source_name: Mouse embryonic stem cells

growth_protocol: mESCs (E14Tg2a) were maintained in 2i medium under normal growth conditions

extract_protocol:
mESCs were trypsinized to remove them from plates and washed with PBS twice. The cell pellet was then treated with TRIzol reagent to prepare total RNA for sequencing. RNA quality was verified on an Agilent Bioanalyzer.
Poly(A) selection, fragmentation, adapter ligation.

treatment_protocol: 100 μM 4-thiouracil was included in 2i medium over 24 hours with medium exchanges every 8 hours. Cells were then incubated with 10 mM uridine in 2i medium for the indicated time points with no antibiotic, G418 (0.1 μg/mL), or puromycin (0.1 μg/mL).

tag: cell type

value: E14Tg2a mouse embryonic stem cells

value: Labeled thiouracil, uridine chase 24 hours

tag: antibiotic

value: Puromycin (0.1 μg/mL)


title: Puro_4hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 4 hrs after switch to uridine containing medium with puromycin

value: Labeled thiouracil, uridine chase 4 hours


title: WT_d1_2


title: Puro_8hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 8 hrs after switch to uridine containing medium with puromycin

value: Labeled thiouracil, uridine chase 8 hours


title: Puro_2hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 2 hrs after switch to uridine containing medium with puromycin

value: Labeled thiouracil, uridine chase 2 hours


title: Puro_0hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 0 hrs after switch to uridine containing medium with puromycin

value: Labeled thiouracil, uridine chase 0 hours


title: Puro_1hr_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 1 hr after switch to uridine containing medium with puromycin

value: Labeled thiouracil, uridine chase 1 hour


title: Puro_4hrs_Rep1


title: Puro_8hrs_Rep1


title: Puro_24hrs_Rep1


title: Puro_1hr_Rep1


title: Puro_0hrs_Rep1


title: G418_24hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 24 hrs after switch to uridine containing medium with G418


title: Puro_2hrs_Rep1


title: G418_1hr_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 1 hr after switch to uridine containing medium with G418


title: G418_0hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 0 hrs after switch to uridine containing medium with G418


title: G418_2hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 2 hrs after switch to uridine containing medium with G418


title: G418_8hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 8 hrs after switch to uridine containing medium with G418


title: G418_4hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 4 hrs after switch to uridine containing medium with G418


title: G418_8hrs_Rep1


title: G418_24hrs_Rep1


title: G418_1hr_Rep1


title: G418_2hrs_Rep1


title: G418_4hrs_Rep1


title: Control_24hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 24 hrs after switch to uridine containing medium


title: G418_0hrs_Rep1


title: WT_d1_1


title: Control_8hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 8 hrs after switch to uridine containing medium


title: Control_0hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 0 hrs after switch to uridine containing medium


title: Control_2hrs_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 2 hrs after switch to uridine containing medium


title: Control_1hr_Rep2

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 1 hr after switch to uridine containing medium


title: Control_2hrs_Rep1


title: Control_1hr_Rep1


title: Control_8hrs_Rep1


title: Control_4hrs_Rep1

description: mESCs grown in 2i medium, labeled with thiouracil, and harvested 4 hrs after switch to uridine containing medium


title: Control_0hrs_Rep1


title: 26m_IHC_4

city: Omaha

first: David

middle: ZZ

last: He

state: Nebraska

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

data_processing:
All data processing was performed using the CLC Genomics Workbench (version 20.0.2) including trimming of reads, alignment, read counts, and normalization using the default paramaters.
Genome_build: mm10, build name GRCm38
Supplementary_files_format_and_content: Normalized RPKM values and relevant statistics were exported to Excel.

source_name: Inner hair cells

extract_protocol:
Approximately 1,000 cells of each type were separately suspended in RNALater (~100 µL in total volume) and total RNA, including small RNAs (> ~18 nucleotides), were extracted and purified using the Qiagen RNeasy mini plus Kit (Qiagen, Germantown, MD). On-column DNase digestion was performed to eliminate DNA contamination in the collected RNA.
Libraries were prepared using the SMARTer Low Input RNA kit (Clontech Laboratories, Mountain View, CA) to generate cDNA in combination with the Nextera Library preparation kit (Illumina, San Diego, CA). Library size and concentration were assessed using an Agilent 2100 Bioanalyzer and a Quibit fluorometer (Invitrogen, Thermo Fisher Scientific) to ensure the inserts were the appropriate size and determine concentration prior to sequencing. Transcriptome libraries were sequenced using the HiSeq 2500 Sequencing System (Illumina).

value: CBA

value: 26 months old

tag: biological sample

value: Organ of Corti, ~1000 isolated inner hair cells


title: 26m_IHC_2


title: 9m_OHC_2

source_name: Outer hair cells

value: 9 months old

value: Organ of Corti, ~1000 isolated outer hair cells


title: 9m_OHC_3


title: 26m_OHC_4


title: 26m_OHC_3


title: 9m_IHC_1


title: 26m_OHC_2


title: 9m_OHC_1


title: 9m_IHC_4


title: 26m_OHC_1


title: 26m_IHC_1


title: 9m_IHC_2


title: 26m_IHC_3


title: 9m_OHC_4


title: Control_4hrs_Rep2


title: 9m_IHC_3


title: NK cell - Lung - Treated #3

city: AMSTERDAM

first: Kevin

last: Kos

email: k.kos@nki.nl, k.d.visser@nki.nl

state: NOORD-HOLLAND

address: PLESMANLAAN 121

department: Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description:
5-10K NK cells from Lungs (treated)
6062_15_NK_cell_-_Lung_-_Treated_3_GCTCATGA-CCTAGAGT_S15

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using HiSat2
Hisat2 was supplied with a known set of gene models (Ensembl version 87).
In order to count the number of reads per gene, a custom script, Itreecount (https://github.com/NKI-GCF/itreecount), has been used. This script is based on the same ideas as HTSeq-count. A list of the total number of uniquely mapped sequencing reads for each gene that is present in the provided Gene Transfer Format (GTF) file was generated.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample; differential expression results

source_name: NK cell - Lung - Treated

growth_protocol: Single cells suspensions were prepared from axillary TDLNs and lungs from Cdh1F/F;Trp53F/F;Foxp3GFP-DTR mice bearing 100mm2  orthotopically transplanted mammary tumors, treated with difteria toxin (DT) or PBS. Lungs were enzymatically digested in 100 µg/mL Liberase Tm (Roche) under continuous rotation for 30 minutes at 37 °C. Erilysis was performed for lungs

extract_protocol:
NK cells were flow cytometrically sorted in RLT buffer (qiagen) +1% b-mercapto-ethanol for the subsequent extraction of total RNA using RNAeasy mini kit (Qiagen). Total RNA was extracted using according to the manufacturer’s protocol.
Library preparation was performed as previously described (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014). https://doi.org/10.1038/nprot.2014.006), using 2100 Bioanalyzer System for library quality control.

treatment_protocol: single cells were stained with fluorescencently conjugated monoclonal atibodies against CD45,CD3 ,NKp46,DX5, and live/dead marker to identify their cell surface expression. NK cells were identified as live, CD45+, CD3-, NKp46+, DX5+

tag: strain background

value: FVB/N

tag: tumor stage

value: 100mm2 orthotopically transplanted KEP tumor

value: Lungs


title: Control_24hrs_Rep1


title: Embryonic Salivary Gland scRNA Sequencing

data_processing:
Clean reads were analyzed with mouse reference genome using the Cell Ranger v4.0
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: tsv and mtx files containing cell barcodes and gene count matrix

source_name: Salivary Gland Stroma

extract_protocol:
Capture 12,359 cells using the 10x Chromium System done by Singulomics
Libraries were prepared according to 10x Genomics Chrmoium Next GEM Single Cell 3' GEM Kit instructions (Cat# 1000130). Briefly, single cells were emulsified in 10X Chromium system and each cell's RNA was barcoded. cDNA was amplified, fragmented and indexed primers 10-13 cycles and library fragments of ~400 bp. The cDNA was flowed onto a Illumina flow cell for cluster generation. Libraries were sequenced on 1 lane of a Illumina HiSeq for 400 million PE150 reads following the manufacturer's protocols.
scRNA-Seq / Drop-Seq

value: Salivary Gland

value: Embryonic day 16


title: NK cell - Lung - Untreated #2

description:
5-10K NK cells from Lungs (untreated)
6062_10_NK_cell_-_Lung_-_Untreated_2_TAGGCATG-CTAAGCCT_S3

source_name: NK cell - Lung - Untreated

value: PBS T=0 & T=7


title: NK cell - Lung - Untreated #4

description:
5-10K NK cells from Lungs (untreated)
6062_12_NK_cell_-_Lung_-_Untreated_4_CGAGGCTG-TCTCTCCG_S12


title: NK cell - Lung - Treated #4

description:
5-10K NK cells from Lungs (treated)
6062_16_NK_cell_-_Lung_-_Treated_4_ATCTCAGG-GCGTAAGA_S16


title: NK cell - Lung - Treated #2

description:
5-10K NK cells from Lungs (treated)
6062_14_NK_cell_-_Lung_-_Treated_2_GTAGAGGA-TTCTAGCT_S14


title: NK cell - LN - Treated #4

description:
5-10K NK cells from axillary lymph nodes (treated)
6062_8_NK_cell_-_LN_-_Treated_4_TCCTGAGC-ACTGCATA_S11

source_name: NK cell - LN - Treated

value: Axillary TDLN


title: NK cell - Lung - Untreated #1

description:
5-10K NK cells from Lungs (untreated)
6062_9_NK_cell_-_Lung_-_Untreated_1_GGACTCCT-AAGGAGTA_S1


title: NK cell - Lung - Untreated #3

description:
5-10K NK cells from Lungs (untreated)
6062_11_NK_cell_-_Lung_-_Untreated_3_CTCTCTAC-CGTCTAAT_S6


title: NK cell - LN - Treated #3

description:
5-10K NK cells from axillary lymph nodes (treated)
6062_7_NK_cell_-_LN_-_Treated_3_AGGCAGAA-GTAAGGAG_S10


title: NK cell - Lung - Treated #1

description:
5-10K NK cells from Lungs (treated)
6062_13_NK_cell_-_Lung_-_Treated_1_AAGAGGCA-TCGACTAG_S13


title: NK cell - LN - Treated #1

description:
5-10K NK cells from axillary lymph nodes (treated)
6062_5_NK_cell_-_LN_-_Treated_1_TAAGGCGA-CTCTCTAT_S9


title: NK cell - LN - Untreated #1

description:
5-10K NK cells from axillary lymph nodes (untreated)
6062_1_NK_cell_-_LN_-_Untreated_1_ACTCGCTA-CTATTAAG_S2

source_name: NK cell - LN - Untreated


title: NK cell - LN - Untreated #2

description:
5-10K NK cells from axillary lymph nodes (untreated)
6062_2_NK_cell_-_LN_-_Untreated_2_GGAGCTAC-AAGGCTAT_S5


title: NK cell - LN - Treated #2

description:
5-10K NK cells from axillary lymph nodes (treated)
6062_6_NK_cell_-_LN_-_Treated_2_CGTACTAG-TATCCTCT_S7


title: NK cell - LN - Untreated #3

description:
5-10K NK cells from axillary lymph nodes (untreated)
6062_3_NK_cell_-_LN_-_Untreated_3_GCGTAGTA-GAGCCTTA_S4


title: 4967_34_WT_Treg_MG_-_30_8_18_TAGCTTA

description:
4967_34_WT_Treg_MG_-_30_8_18_TAGCTTA_S48
4,5 K Tregs isolated from WT mammary gland (n = 3)

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample; differential expression results

source_name: WT MG Treg

growth_protocol: Single cells suspensions were prepared from the WT and K14cre;Cdh1F/F;Trp53F/F mice bearing 225mm2  mammary tumors from blood, spleen, lungs, TDLNs, tumor and healthy mammary gland. Tumors were subjected to digestion for 1h, 37 degrees: 3mg/mL Collagenase A (Roche) in serum free DMEM (Dulbecco), Deoxyribonuclease I from bovine  pancreas (DNAse) 25μg/mL (Sigma-Aldrich). Lungs were enzymatically digested in 100 µg/mL Liberase Tm (Roche) under continuous rotation for 30 minutes at 37 °C. Erilysis was performed for lungs/blood

extract_protocol:
Tregs were flow cytometrically sorted in RLT buffer (qiagen) +1% b-mercapto-ethanol for the subsequent extraction of total RNA using RNAeasy mini kit (Qiagen). Total RNA was extracted using according to the manufacturer’s protocol.
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0 as assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared using standard Illumina protocols, analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: single cells were stained with fluorescencently conjugated monoclonal atibodies against CD3, CD4, CD25,CD45, CD8 and live/dead marker to identify their cell surface expression. Tregs were identified as live, CD45+, CD3+, CD4+, CD8-, CD25+

value: WT

value: mammary gland (CD3+CD4+CD25+)


title: NK cell - LN - Untreated #4

description:
5-10K NK cells from axillary lymph nodes (untreated)
6062_4_NK_cell_-_LN_-_Untreated_4_CGGAGCCT-TTATGCGA_S8