title: RD29A:DREB1a CS Rep2

city: Ahmedabad

first: Bhuvan

last: Pathak

state: Gujarat

address: m303 School of Arts and Sciences, Ahmedabad University, Commerce Six Road

department: Biological and Life Sciences Division

institute: Ahmedabad University

data_processing:
Transcriptome analysis was carried out in the galaxy platform (galaxy.org)
Sequence reads were trimmed for adapter sequence using trimmomatic tool, mapped to Oryza sativa japonica genome (plant ensemble v 48) using STAR (RNA-STAR), using TranscriptomeSAMGeneCounts; as separate tabular "Junctions" output, NH HI AS, nM, XS and cH parameters.
The gene expression abundance was performed using featurecount version 1.6.4 and differential gene analysis using edgeR
Genome_build: Oryza sativa japonica (plant ensemble v. 48- uses IRGSP 1.0 build)
Supplementary_files_format_and_content: matrix table with read counts  for every gene and every sample

organism: Oryza sativa Japonica Group

source_name: seedling

growth_protocol: fourty four seedlings representing four homozygous and seven hemizygous lines (4/line)  containing rd29a:AtDREB1a and twelve wild-type (Taipei 309) seedlings were germinated on 1/2MS media for 10 days.

extract_protocol:
The whole seedlings without roots following the treatment were flash frozen in liquid nitrogen, RNA was isolated using trizol, were DNAase treated and were screened for AtDREB1a induction in response to cold-stress. Based on the  similar AtDREB1a transcript induction levels (compared to WT), RNA from three homozygous lines representing six biological replicates  (line # 11,20 and 29) at room-temperature and cold-stress and six seedlings from WT room-temperature and cold-stressed  were pooled as one sample.Later two technical replicates of each of the four pooled samples were used for transcriptome analysis
All library construction were prepared according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library average size was about 390bp with an insert size of about 270bp. Illumina® 8-nt dual-indices were used

treatment_protocol: twenty two seedlings each of the RD29A:AtDREB1a and six wild-type were kept on ice for 20 hours and other six were maintained at room-temperature as controls.

value: 10 days old

value: cold stress


title: GMC_BL6J_ 8M_ET2_c1358_brain

status: Public on Oct 05 2022

type: SRA

city: Bonn

first: Dan

last: Ehninger

state: NRW

address: Venusberg-Campus 1/99

department: AG Ehninger

country: Germany

institute: DZNE

library_source: transcriptomic

data_processing:
Demultiplexing and data transformation to generate fastq files was done using bcl2fastq2 (v2.20).
Sequencing reads were trimmed using CutAdapt (https://usegalaxy.org/) to remove adapter sequences. Trimmed reads were mapped to the mouse transcriptome (GRCm38, mm10) using HISAT2 (v2.1.0).
Bam files were indexed using Samtools and count matrices generated by Genomic Alignments in R. Gene count matrices were generated using annotation information from a Mus_musculus.GRCm38.102.chr.gtf file imported with the rtracklayer (Lawrence et al., 2009) package into R. All downstream analyses were performed using R (Version 3.5.1, https://cran.r-project.org/). Library normalization and expression differences between samples were quantified using the DESeq2 package (Love et al., 2014). A false discovery rate (FDR) < 0.05 was used as a cutoff in differential expression analyses.
3  and 5 months old mice were used as the "young adult baseline" for Ageing-Brain, Ageing-Spleen and Ageing-mTOR-Spleen datasets, respectively
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Mouse tissues were harvested, flash frozen on dry ice and total RNA isolated from the tissues with TRI-Reagent. Total RNA was purified with the Monarch RNA Cleanup kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using a ligation mediated RNA sequencing protocol published by Huo et al. 2015

tag: tissue

value: brain

tag: genotype

value: WT

tag: age

value: 8 months

tag: Sex

value: male


title: GMC_BL6J_20M_ET5_c3054_brain

value: 20 months


title: Ts65Dn iPSCs Rep3

city: Pune

first: Nishant

last: Singhal

state: Maharashtra

address: Ganeskhind Road

country: India

institute: National Centre for Cell Science

data_processing:
Basecalling performed with CASAVA ver. 1.8.2
Reads mapped against mouse (mm10) genome using the TopHat application on Illumina BaseSpace
Differential gene analysis performed using CuffLinks application on Illumina BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited textfile, contains differential gene expression analysis from CuffDiff results on normalized gene count values (FPKM)

source_name: Ts65Dn induced Pluripotent Stem Cell

growth_protocol: Mouse embryos were collected, eviscerated, decapitated and then further treated with trypsin to obtain the MEFs. Retroviral overexpression of Oct4, Sox2, Klf4 and c-Myc was used to generated iPSCs.

extract_protocol:
Subconfluent MEFs were harvested in Trizol lysis buffer (Qiagen RNAeasy). Single cell suspension of mouse iPSCs were prepared and feeder cells were depleted. Total RNA  was collected using the RNAeasy reagent (Qiagen) following the manufacturer’s instructions.
mRNA-seq libraries were prepared from 1 ug of total RNA using the Illumina mRNA-seq Sample Preparation kit following the manufacturer’s instructions

treatment_protocol: MEFs were cultured at least two passages in classical DMEM (Gibco) medium supplemented with antibiotics, glutamine and 10% fetal calf serum. IPSCs were cultured in ES medium in the presence of 2000 unit of LIF.

value: Mouse pluripotent stem cells

value: Passage 15


title: RD29A:DREB1a CS Rep1

tag: developmental stage

tag: treatment


title: GMC_BL6J_ 3M_ET55_c1030_brain

value: 3 months


title: Ts65Dn iPSCs Rep2


title: RD29A:DREB1a RT Rep2

value: room temperature


title: Ts65Dn iPSCs Rep1


title: GMC_BL6J_14M_ET2_c568_brain

value: 14 months


title: RD29A:DREB1a RT Rep1


title: genomic DNA from normal sample SG 1962-1-37

type: genomic

city: Shanghai

first: Bin

last: Li

address: 1200 Cailun Road, Pudong New Area

country: China

institute: Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine

description: normal sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina EPIC Human Methylation850 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: MethylationEPIC array targets 862,927 CpG sites  across the genome. All DNA methylation analysis of MethylationEPIC array was performed in R  v.3.6.2. The IDAT intensity files were analyzed in minfi R package. Raw intensity values were  normalized with minfi preprocesser Noob.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: normal sample SG 1962-1-37

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Illumina Infinium® HumanMethylation850 BeadChip according to standard instructions

tag: gender

value: Female

tag: pasi score

tag: disease state

value: Normal


title: GMC_BL6J_ 8M_ET66_c2295_brain


title: genomic DNA from normal sample SG 1962-1-36

description: normal sample

source_name: normal sample SG 1962-1-36


title: WT CS Rep2


title: genomic DNA from normal sample SG 1962-1-39

description: normal sample

source_name: normal sample SG 1962-1-39

value: Male


title: 2N iPSCs Rep2

source_name: 2N induced Pluripotent Stem Cells


title: 2N iPSCs Rep3


title: GMC_BL6J_ 26M_ET0_c3667_brain

value: 26 months


title: GMC_BL6J_5M_ET80_c2231_brain

value: 5 months


title: genomic DNA from normal sample SG 1962-1-42

description: normal sample

source_name: normal sample SG 1962-1-42


title: genomic DNA from blood stasis syndrome sample SG 1962-1-29

description: blood stasis syndrome sample

value: BSS


title: genomic DNA from normal sample SG 1962-1-40

description: normal sample

source_name: normal sample SG 1962-1-40


title: 2N iPSCs Rep1


title: GMC_BL6J_3M_ET2_c953_brain


title: genomic DNA from blood stasis syndrome sample SG 1962-1-20

description: blood stasis syndrome sample


title: genomic DNA from blood stasis syndrome sample SG 1962-1-22

description: blood stasis syndrome sample


title: genomic DNA from blood stasis syndrome sample SG 1962-1-27

description: blood stasis syndrome sample


title: genomic DNA from blood stasis syndrome sample SG 1962-1-33

description: blood stasis syndrome sample


title: genomic DNA from blood stasis syndrome sample SG 1962-1-21

description: blood stasis syndrome sample


title: GMC_BL6J_26M_ET65_c3775_brain


title: genomic DNA from blood stasis syndrome sample SG 1962-1-19

description: blood stasis syndrome sample


title: WT RT  Rep2

value: 10 days old


title: WT RT  Rep1


title: genomic DNA from normal sample SG 1962-1-44

description: normal sample

source_name: normal sample SG 1962-1-44


title: GMC_BL6J_20M_ET0_c2140_brain

value: brain


title: Ts65Dn MEFs Rep3

source_name: Ts65Dn Mouse Embryonic Fibroblasts

value: Mouse embyronic fibroblasts


title: Ts65Dn MEFs Rep1


title: genomic DNA from blood stasis syndrome sample SG 1962-1-11

description: blood stasis syndrome sample


title: GMC_BL6J_14M_ET0_c2600_brain

value: WT


title: genomic DNA from blood stasis syndrome sample SG 1962-1-35

description: blood stasis syndrome sample


title: 2N MEFs Rep3

source_name: 2N Mouse Embryonic Fibroblasts


title: genomic DNA from blood stasis syndrome sample SG 1962-1-34

description: blood stasis syndrome sample


title: GMC_BL6J_8M_ET0_c3662_brain

value: 8 months

value: male


title: genomic DNA from blood stasis syndrome sample SG 1962-1-12

description: blood stasis syndrome sample


title: genomic DNA from blood heat syndrome sample SG 1962-1-32

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-32

value: BHS


title: GMC_BL6J_5M_ET6_c3670_brain


title: MC2_d8 vs OMM

type: RNA

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: color-swap: polarity(-)

hyb_protocol: Whole mouse genome 8x60K microarrays were done according to the supplier’s protocol (Agilent Technologies).

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

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA  Version A.11.5.1.1 and the GE2_1200_Dec17  extraction protocol (Agilent Technologies). Interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

source_name: primary colon epithelial cells

label_protocol: RNA labeling was performed with the Low Input  Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: Germ-free (GF) C57BL/6 mice were kept in isolators under sterile conditions.

extract_protocol: Primary murine eithelial cells from colon were isolated by CD45 + cell depletion followed by CD31 + ( Pecam1) positive selection. Total RNA from epithelial cells was isolated with RNeasy (Qiagen) according the supplier's instructions.

treatment_protocol: GF mice were reconstitutted with Oligo-Maus-Mikrobiota (OMM, https://pubmed.ncbi.nlm.nih.gov/27869789/) or minimal consortium (MC2, OMM + E-coli + C. amalonaticus) .

tag: strain

value: Germ-free (GF) C57BL/6

tag: cell type

value: primary colon epithelial cells

value: MC2 (OMM + minimal consortium of 2 additional strains, OMM + E.coli + C. amalonaticus)

tag: time

value: d8 (day 8) post colonialization

value: OMM (Oligo-Mouse-Microbiota, community of 12 strains)


title: OMM vs MC2_d8

description: color-swap: polarity(+)


title: 2N MEFs Rep1


title: GMC_BL6J_3M_ET4_c940_brain

value: 3 months


title: 2N MEFs Rep2


title: Rice Root RNA-seq Rep 2

status: Public on Oct 04 2022

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

country: USA

institute: University of Georgia

data_processing:
Sequences were quality trimmed and adaptors were identified and filtered using CutAdapt v2.8
UMI sequences were extracted from processed fasta files using UMI-tools v1.0.1
Sequences were aligned to their respective genome using STAR v2.7.2
Sequences were deduplicated using the UMI and mapping location using UMI-tools v1.0.1
Transcriptoinal start sites were determined using the R library TSRchitect v1.2.0 in R v4.0.0
Genome_build: Maize genome = AGPv4.38, Sorghum genome = NCBIv3.52, Rice genome = IRGSP-1.0.51, Wheat genome = IWGSC.51, Soy genome = Wm82.a4.v1
Supplementary_files_format_and_content: Text file containing single nucleotide position of transcription start site, read count, and strand

molecule: polyA RNA

organism: Oryza sativa

source_name: Rice root

growth_protocol: Plants grown for four weeks with standard 16H daylight conditions at room temperature

extract_protocol:
RNA was extracted using Monarch Total RNA Extraction and Purification kit (NEB #T2010)
Libraries where prepared using the novel smar2C2 method described in the related manuscript

value: Japonica

tag: technique

value: RNA-seq

value: Root


title: genomic DNA from blood stasis syndrome sample SG 1962-1-9

description: blood stasis syndrome sample

value: Male

value: BSS


title: genomic DNA from blood stasis syndrome sample SG 1962-1-28

description: blood stasis syndrome sample

value: Female


title: Rice Root RNA-seq Rep 1


title: MC2_d4 vs OMM

description: color-swap: polarity(-)

value: d4 (day 4) post colonialization


title: Rice Shoot RNA-seq Rep 2

source_name: Rice shoot

value: Shoot


title: Rice Root smar2C2 Rep 2


title: Rice Root smar2C2 Rep 1


title: Rice Shoot smar2C2 Rep 1


title: S4KO_EE_3

city: Farmington

first: Linda

middle: S

last: Cauley

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

data_processing:
Sickle was used to perform quality control and trim the sequences when necessary with a minimum QC score of 25 and basepair length of 45 after trimming
Trimmed sequences were aligned to mm10 genome assembly using Hisat2
Using samtools aligned sequences were sorted and converted to BAM files
Stringtie was used to assemble RNA-seq alignments to previously annotated gene transcripts and its quantification
Ballgown was used to determine the differential expression in R
Assembly: mm10
Supplementary files format and content: GTF file used in stringtie for transcript quantification is uploaded

source_name: lungs

growth_protocol: Primary cells were isolated from the lungs of WT and S4KO mice and sorted for CD44+CD103-KLRG1-CD127-

extract_protocol:
RNA was extracted using Qiagen Rneasy mini plus using manufacturer’s instruction
RNA libraries were prepared using Illumina TruSeeq RNA Library Prep Kit following manufacturer’s protocol

value: lungs

tag: cell line

value: early effector

value: CD8 T


title: S4KO_EE_2


title: Rice Shoot RNA-seq Rep 1


title: S4KO_EE_1


title: OMM vs MC2_d4

description: color-swap: polarity(+)

value: Germ-free (GF) C57BL/6


title: WT_EE_2


title: Rice Shoot smar2C2 Rep 2


title: WT_EE_1


title: genomic DNA from blood heat syndrome sample SG 1962-1-31

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-31

value: BHS


title: Ts65Dn MEFs Rep2

value: Mouse embyronic fibroblasts


title: genomic DNA from blood heat syndrome sample SG 1962-1-30

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-30


title: L21_SGC0946_M1_LPS

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

data_processing:
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b with default settings
BAM files were indexed and filtered on MAPQ>15 with SAMtools v1.3.1
Raw tag counts and reads per kilobase million (RPKM) per gene were summed using HOMER2′s analyzeRepeats.pl script with default settings and the -noadj or -rpkm options for raw counts and RPKM reporting
Assembly: mm10
Supplementary files format and content: Metadata table, RPKM, and raw gene counts for every gene and every sample

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow (BM) was isolated from femurs and tibias of C57BL/6 mice by flushing. BM was cultured in RPMI 1640 containing 25 mM HEPES, 2 mM L-glutamine, 10% FCS, penicillin (100 U/ml), streptomycin (100 µg/ml), and 15% L929-conditioned medium (M-CSF source) for 7-8 days.

extract_protocol:
RNA was isolated from 500K BMDMs using the RNeasy Mini Kit (QIAGEN) with DNase treatment.
700 ng RNA was used for Illumina library construction. RNA amplification, cDNA generation, and adaptor ligation were performed using the KAPA mRNA HyperPrep Kit (Roche) following the manufacturer’s instructions. Samples were pooled, diluted to 10 nM, and sequenced single-end on an Illumina HiSeq 4000 system (Illumina) to a depth of ±20 million reads with a length of 50 base pairs.

treatment_protocol: During differentiation, 1 µM SGC0946 (Sigma) or Dimethyl sulfoxide (DMSO; Sigma) as control was administered to the BMDMs. LPS samples: 10 ng/mL LPS (from Escherichia coli; O111:B4; Sigma) for 3 hours. GW3965 samples: 2µM GW3965 (Sigma) for 17 hours.

value: Bone marrow-derived macrophages


title: L20_SGC0946_M4_notx


title: L1_DMSO_M1_notx reanalyzed

value: DMSO


title: L19_SGC0946_M3_notx


title: L17_SGC0946_M1_notx


title: L18_SGC0946_M2_notx


title: L16_DMSO_M3_GW3965 reanalyzed


title: genomic DNA from blood heat syndrome sample SG 1962-1-26

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-26


title: L5_DMSO_M1_LPS

value: DMSO+LPS


title: L14_DMSO_M1_GW3965 reanalyzed


title: L15_DMSO_M2_GW3965 reanalyzed


title: WT CS Rep1

source_name: seedling

value: 10 days old

value: WT

value: cold stress


title: L6_DMSO_M2_LPS


title: L4_DMSO_M4_notx


title: genomic DNA from blood heat syndrome sample SG 1962-1-25

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-25

value: Male


title: L7_DMSO_M3_LPS


title: genomic DNA from blood heat syndrome sample SG 1962-1-23

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-23


title: L32_SGC0946_M3_GW3965


title: L30_SGC0946_M1_GW3965


title: L3_DMSO_M3_notx reanalyzed


title: L31_SGC0946_M2_GW3965


title: L2_DMSO_M2_notx reanalyzed


title: PTEN T cell-specific knockout VDJ1, experiment 2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

library_source: transcriptomic single cell

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotations for scTCR-seq

source_name: Sort purified TCRb-CD69- pre-selection CD4+CD8+ double-positive (DP), TCRb-CD69- post-selection DP, and CCR6+CD127+TCRb+ thymocytes from Cd4CrePtenfl/fl mice

growth_protocol: 5-week-old WT and Cd4CrePtenfl/fl mice were used

extract_protocol:
TCRb-CD69-CD4+CD8+, TCRb-CD69-CD4+CD8+, and CCR6+CD127+TCRb+ thymocytes were sorted from thymus and loaded onto the Chromium Controller according to their respective cell counts (2,000; 2,000; and 12,500) per sample.
Libraries were prepared using the Chromium Single Cell Immune Profiling v2 Library and Gel Bead Kit (10x Genomics)
scRNA-seq and scTCR-seq

value: Cd4CrePtenfl/fl mice


title: wild-type VDJ2, experiment 2

source_name: Sort purified TCRb-CD69- pre-selection CD4+CD8+ double-positive (DP), TCRb-CD69- post-selection DP, and CCR6+CD127+TCRb+ thymocytes from WT mice


title: PTEN T cell-specific knockout GEX1, experiment 2

value: Sort purified TCRb-CD69- pre-selection CD4+CD8+ double-positive (DP), TCRb-CD69- post-selection DP, and CCR6+CD127+TCRb+ thymocytes


title: genomic DNA from blood heat syndrome sample SG 1962-1-10

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-10

value: Female


title: L23_SGC0946_M3_LPS


title: wild-type VDJ1, experiment 2


title: wild-type GEX2, experiment 2


title: wild-type GEX1, experiment 2


title: L22_SGC0946_M2_LPS


title: KO 10d NTN [6499]

last: Labes

department: Institute of Translational Physiology

institute: Charité - Universitätsmedizin Berlin

data_processing:
Demultiplexing was performed using Bcl2FASTQ conversion software from Illumina according to the manufacturer's recommendations.
Reads were mapped to the Mouse genome GRCm38 v. 80 and annotated using the ENSEMBL GRCm38 v. 86 gene annotation.

source_name: kidney

extract_protocol:
Kidneys were ground to fine powder under liquid nitrogen. RNA from whole kidneys was extracted using the trizol-chloroform extraction method
NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol

treatment_protocol: Nephrotoxic serum (sheep serum raised against rat glomerular basement membrane constituents) was injected in wildtype and AnxA1 knockout animals

value: kidney

value: male

value: AnxA1 knockout

value: NTN serum, 10d


title: KO 10d NTN [6498]


title: KO 10d NTN [6500]


title: KO 10d NTN [6496]


title: KO 10d NTN [6497]


title: WT 10d NTN [6495]


title: WT 10d NTN [6493]


title: WT 10d NTN [6494]


title: genomic DNA from blood heat syndrome sample SG 1962-1-6

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-6


title: WT 10d NTN [6490]


title: WT 10d NTN [6492]


title: WT 10d NTN [6489]


title: WT_rep3_ZLPS

data_processing:
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b with default settings
BAM files were indexed and filtered on MAPQ>15 with SAMtools v1.3.1
Raw tag counts and reads per kilobase million (RPKM) per gene were summed using HOMER2′s analyzeRepeats.pl script with default settings and the -noadj or -rpkm options for raw counts and RPKM reporting
Genome_build: mm10
Supplementary_files_format_and_content: Metadata table, RPKM, and raw gene counts for every gene and every sample

growth_protocol: Bone marrow (BM) was isolated from femurs and tibias of myeloid DOT1L WT/KO C57BL/6 (Lyz2) mice by flushing. BM was cultured in RPMI 1640 containing 25 mM HEPES, 2 mM L-glutamine, 10% FCS, penicillin (100 U/ml), streptomycin (100 µg/ml), and 15% L929-conditioned medium (M-CSF source) for 7-8 days.

treatment_protocol: LPS samples (MLPS): 10 ng/mL LPS (from Escherichia coli; O111:B4; Sigma) for 3 hours.

tag: lps treatment (yes/no)

value: no


title: WT_rep3_MLPS

value: yes


title: WT_rep2_ZLPS


title: WT_rep2_MLPS


title: WT_rep1_MLPS


title: KO_rep1_MLPS

value: KO


title: KO_rep3_ZLPS


title: KO_rep1_ZLPS


title: KO_rep3_MLPS


title: DMSO_BMDM_M3

library_source: genomic

data_processing:
Reads were aligned to mouse genome mm10 using HISAT2.
HOMER (v4.11.1) findPeaks was used for H3K79me2 peak calling with the setting -style histone.
Merged peak files were created using bedtools (v2.27.0) merge, and read coverage under peaks was calculated using coverageBed.
Merged peak files were combined with coverage files using bedtools unionbedg.
ChIPseeker (v1.20.0) was used for peak annotation in an R 3.6.3 environment.
Methylation score was calculated by counting reads in a 3 kb window around the TSS. TSS regions were annotated by org.Mm.eg.db v3.8.2
Genome_build: mm10
Supplementary_files_format_and_content: The combined peak file (readcount_H3K79me2_BMDMs_SGC0946.txt) was generated by using bedtools (v2.27.0) merge, and read coverage under peaks was calculated using coverageBed. Subsequently, merged peak files were combined with coverage files using bedtools. unionbedg.
Supplementary_files_format_and_content: HOMER_tagDirs were created by using Hisat2.

growth_protocol: Bone marrow (BM) was isolated from femurs and tibias of WT and KO mice by flushing. BM was cultured in RPMI 1640 containing 25 mM HEPES, 2 mM L-glutamine, 10% FCS, penicillin (100 U/ml), streptomycin (100 µg/ml), and 15% L929-conditioned medium (M-CSF source) for 7-8 days.

extract_protocol:
Briefly, 10-20 million BMDMs were lifted using TrypLE (ThermoFisher) and crosslinked with 1% formaldehyde (ThermoFisher) for 10 min. Chromatin was pulled down overnight using an anti-H3K79me2 antibody (Clone: NL59, Merck).
Illumina libraries were created from 10 ng ChIP chromatin using the KAPA HyperPrep (Roche) kit.  Libraries were pooled to a concentration of 10 nM and sequenced single-ended on an Illumina HiSeq 4000 instrument (Illumina) to a depth of ±40 million 50 bp reads per sample.

treatment_protocol: During differentiation, 1 µM SGC0946 (Sigma) or Dimethyl sulfoxide (DMSO; Sigma) as control was administered to the BMDMs.

tag: chip antibody

value: H3K79me2 antibody (Clone:NL59, Merck).

value: Bone marrow-derived macrophages


title: KO_rep2_ZLPS


title: PTEN T cell-specific knockout VDJ1

data_processing:
Library strategy: TCR-seq
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotationsn for scTCR-seq

source_name: CCR6+CD127+TCRb+ thymocytes

growth_protocol: Wild-type, Cd4-Cre;Pten flox/+ and Cd4-Cre;Pten flox/flox mice of up to 6 weeks of age without signs of tumorigenesis (i.e. without disrupted CD4, CD8 thymic populations) were used

extract_protocol:
CCR6+CD127+TCRb+ thymocytes cells were sorted from thymus and loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell Immune Profiling v2 Library and Gel Bead Kit (10x Genomics)
scRNA-seq and scTCR-seq

value: CCR6+CD127+TCRb+ thymocytes

value: PTEN T cell-specific knockout


title: DMSO_BMDM_M1

value: DMSO


title: SGC0946_BMDM_M3


title: PTEN T cell-specific knockout VDJ2


title: genomic DNA from blood heat syndrome sample SG 1962-1-1

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-1

value: BHS


title: Input_BMDM


title: PTEN T cell-specific knockou GEXt2

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample for scRNAseq and filtered contig annotationsn for scTCR-seq


title: genomic DNA from blood heat syndrome sample SG 1962-1-13

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-13

value: Male


title: SGC0946_BMDM_M1


title: genomic DNA from blood heat syndrome sample SG 1962-1-2

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-2


title: wild-type VDJ2

value: wild-type


title: PTEN T cell-specific knockout GEX1


title: genomic DNA from blood heat syndrome sample SG 1962-1-4

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-4


title: KO_rep2_MLPS


title: wild-type GEX1


title: wild-type GEX2


title: WT_rep1_ZLPS

value: WT


title: tumor organoid Csf1rKO_1

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Strasse 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

data_processing:
alignment: CLC Genomics Workbench (QIAGEN) using default settings
expression levels: CLC Genomics Workbench (QIAGEN) using default settings
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample

source_name: tumor organoid

extract_protocol:
Intestinal adenoma cells from 3-5 tumors for each ApcMin/+ mouse were isolated. 1.5 ×104 single cells per sample were embedded in matrigel and grown for 3-4 passages. RNA was harvested using Rneasy Mini Kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ApcMin/+; Csf1rDIEC; Mir34afl/fl

value: mouse :18-20 weeks; 3-4 passages


title: DMSO_BMDM_M2


title: tumor organoid MiR34aKO_Csf1rKO_2

value: ApcMin/+; Csf1rDIEC; Mir34aDIEC


title: SGC0946_BMDM_M2


title: tumor organoid MiR34aKO_Csf1rKO_1


title: tumor organoid MiR34aKO_1

value: ApcMin/+; Csf1rfl/fl; Mir34aDIEC


title: genomic DNA from blood heat syndrome sample SG 1962-1-24

description: blood heat syndrome sample

source_name: blood heat syndrome sample SG 1962-1-24

value: Female


title: tumor organoid wt_1

value: ApcMin/+; Csf1rfl/fl; Mir34afl/fl


title: tumor organoid MiR34aKO_2


title: adenoma Csf1rKO_2

source_name: Adenoma

extract_protocol:
Adenomas were isolated from small intestine, flash frozen into liquid nitrogen, and RNA was harvested using RNeasy Mini Kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 18 weeks


title: adenoma Csf1rKO_3


title: adenoma MiR34aKO_Csf1rKO_3


title: adenoma MiR34aKO_Csf1rKO_2


title: adenoma Csf1rKO_1


title: adenoma MiR34aKO_3


title: adenoma wt_2


title: adenoma wt_1


title: TP+hucMSC-Exs group 2

city: chengdu

first: Ruiwu

last: Dai

state: Sichuan

address: No.270 Rongdu Rd, Jinniu District

institute: General Hospital of Western Theater

description: Exo 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Rattus norvegicus

source_name: hucMSC-Exs (10 μg/100 g) were injected via the tail veins of rats in the TP+hucMSC-Exs group

growth_protocol: Pancreatic tissue atmosphere with air at -80C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 1 ml normal saline or hucMSC-Exs (10 μg/100 g)

value: Sprague-Dawley

value: pancreas

tag: condition

value: Traumatic pancreatitis

value: hucMSC-Exs (10 μg/100 g)


title: TP+hucMSC-Exs group 1

description: Exo 1

tag: tissue


title: TP group 2

description: TP 2

source_name: Traumatic pancreatitis

value: 1 ml normal saline


title: adenoma MiR34aKO_1

tag: genotype


title: tumor organoid Csf1rKO_2

tag: age


title: TP group 1

description: TP 1


title: Control group 1

description: Control 1

source_name: Sprague-Dawley Rat pancreas

value: control


title: Quiescent 1, Roots, Plate, Replicate 2

city: Gainesville

last: Ferl

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

description:
Q1P2
Q1P_Q1A_RNAseq_results.xlsx    Q1P_Q1C_RNAseq_results.xlsx    Q1P_Q1D_RNAseq_results.xlsx   Q1P_Q1B_RNAseq_results.xlsx

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program (Martin, 2011) to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis. The genome of Arabidopsis thaliana (version TAIR10.51) from TAIR (The Arabidopsis Information Resource) was used as the reference sequences for RNA-seq analysis. The cleaned reads of each sample were mapped to the reference sequences using the read mapper of the STAR package (Spliced Transcripts Alignment to a Reference, v2.7.9a) (Dobin et al., 2013). The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2) (Anders, Pyl and Huber, 2015) samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates, choose and count uniquely mapped reads for gene expression analysis. The counted reads of each gene were analyzed by a DESeq2-based R pipeline. Significant up- and down-regulated genes were selected using the threshold of -1.0 < Log2FoldChange < 1.0 and p-value <= 0.05.
Assembly: TAIR10.51
Supplementary files format and content: .xls spreadsheets containing lists of genes,  FPKM values, and CPM values.

organism: Arabidopsis thaliana

source_name: Roots, Q1, plate

growth_protocol:
plant grown on petri plate of solid 0.5x MS media, 7 day old plants harvested and stored in RNAlater™ until RNA extraction
plants were grown on a phytagel matrix-encased coupon then placed in Kennedy Fixation Tubes for multiple timepoints with a clinorotation substitute for microgravity to simulate a suborbital flight pattern.

extract_protocol:
RNA extraction was performed using Qiagen RNeasy Plant mini kit (Qiagen, Hilden, Germany catalog # 74904) according to the manufacturer’s guidelines. RNA concentration was determined on Qubit 2.0 Fluorometer and RNA quality was assessed using the Agilent 2100 Bioanalyzer (AgiRNA extraction was performed using Qiagen RNeasy Plant mini kit (Qiagen, Hilden, Germany catalog # 74904) according to the manufacturer’s guidelines. RNA concentration was determined on Qubit 2.0 Fluorometer and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
First, 100 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) with 2/3 of poly A enriched RNA and 1/10 reaction volume using SPT Labtech mosquito LV liquid handling instrument. Briefly, RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. This step was followed by first-strand cDNA synthesis using reverse transcriptase and random hexamer primer.  Synthesis of ds-cDNA was performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation. At this point, Illumina adaptors were ligated to the sample.  Finally, each library (uniquely barcoded) was enriched by 15 cycles of amplification, and purified with Agencourt AMPure beads (Beckman Coulter, catalog # A63881). Barcoded libraries were sized on the Bioanalyzer and quantified with the Qubit 2.0 Fluorometer. Finally, these individual libraries were pooled in equimolar concentration for sequening aiming for 60 million reads per sample with total of 1 lane of NovaSeq S4 2x150 cycles run. RNASeq libraries were constructed at the UF ICBR Gene Expression Core (https://biotech.ufl.edu/gene-expression-genotyping/, RRID:SCR_019145). The Illumina NovaSeq 6000 was used to sequence the libraries for 2 x 150 cycles. Sequencing was performed at the ICBR NextGen Sequencing (https://biotech.ufl.edu/next-gen-dna/, RRID:SCR_019152).
Sequencing was performed at the ICBR NextGen Sequencing Core (https://biotech.ufl.edu/next-gen-dna/, RRID:SCR_019152). Normalized libraries were submitted to the “Free Adapter Blocking Reagent” protocol (FAB, Cat# 20024145) in order to minimize the presence of adaptor-dimers and index hopping rates.  The library pool was diluted to 0.8 nM and sequenced on one S4 flow cell lane (2x150 cycles) of the Illumina NovaSeq6000. The instrument’s computer utilized the NovaSeq Control Software v1.6. Cluster and SBS consumables were v1.5. The final loading concentration of the library was 120 pM with 1% PhiX spike-in control. One lane generated 2.5-3 billion paired-end reads (~950Gb) with an average Q30%>= 92.5% and Cluster PF= 85.4%. FastQ files were generated using the BCL2fastQ function in the Illumina BaseSpace portal.

treatment_protocol: plants placed into Kennedy Fixation Tubes for various timepoints with select samples having a clinorotation treatment

tag: ecotype

value: Wild Type

value: Roots

tag: organism part

value: All roots from 7 day-old seedling

value: 7 day-old plants

value: 24 hour light cycle, 8 hour dark storage

tag: biosource type

value: RNAlater fixed_sample


title: tumor organoid wt_2

value: mouse :18-20 weeks; 3-4 passages


title: Quiescent 1, Roots, Plate, Replicate 3

description:
Q1P3
Q1P_Q1A_RNAseq_results.xlsx    Q1P_Q1C_RNAseq_results.xlsx    Q1P_Q1D_RNAseq_results.xlsx   Q1P_Q1B_RNAseq_results.xlsx

tag: treatment


title: Quiescent 1, Roots, KFT D, Replicate 3

description:
Q1D3
Q1C_Q1D_RNAseq_results.xlsx    Q1A_Q1D_RNAseq_results.xlsx    Q1B_Q1D_RNAseq_results.xlsx    Q1P_Q1D_RNAseq_results.xlsx

source_name: Roots, Q1, KFT D

growth_protocol:
plant grown on coupon of solid 0.5x MS media, Placed in Kennedy Fixation Tube for 4 hours, 7 day old plants harvested and stored in RNAlater™ until RNA extraction
plants were grown on a phytagel matrix-encased coupon then placed in Kennedy Fixation Tubes for multiple timepoints with a clinorotation substitute for microgravity to simulate a suborbital flight pattern.

value: 24 hour light cycle, 8 hour dark storage, Placed in KFT for 4 hours


title: Quiescent 1, Roots, KFT D, Replicate 1

description:
Q1D1
Q1C_Q1D_RNAseq_results.xlsx    Q1A_Q1D_RNAseq_results.xlsx    Q1B_Q1D_RNAseq_results.xlsx    Q1P_Q1D_RNAseq_results.xlsx


title: Quiescent 1, Roots, KFT D, Replicate 2

description:
Q1D2
Q1C_Q1D_RNAseq_results.xlsx    Q1A_Q1D_RNAseq_results.xlsx    Q1B_Q1D_RNAseq_results.xlsx    Q1P_Q1D_RNAseq_results.xlsx


title: adenoma MiR34aKO_Csf1rKO_1

value: ApcMin/+; Csf1rDIEC; Mir34aDIEC


title: Quiescent 1, Roots, KFT C, Replicate 2

description:
Q1C2
Q1C_Q1D_RNAseq_results.xlsx    Q1A_Q1C_RNAseq_results.xlsx    Q1B_Q1C_RNAseq_results.xlsx    Q1P_Q1C_RNAseq_results.xlsx

source_name: Roots, Q1, KFT C


title: Quiescent 1, Roots, KFT C, Replicate 1

description:
Q1C1
Q1C_Q1D_RNAseq_results.xlsx    Q1A_Q1C_RNAseq_results.xlsx    Q1B_Q1C_RNAseq_results.xlsx    Q1P_Q1C_RNAseq_results.xlsx


title: adenoma wt_3

value: ApcMin/+; Csf1rfl/fl; Mir34afl/fl


title: Quiescent 1, Roots, KFT B, Replicate 3

description:
Q1B3
Q1B_Q1C_RNAseq_results.xlsx    Q1B_Q1D_RNAseq_results.xlsx    Q1P_Q1B_RNAseq_results.xlsx   Q1A_Q1B_RNAseq_results.xlsx

source_name: Roots, Q1, KFT B


title: adenoma MiR34aKO_2

value: ApcMin/+; Csf1rfl/fl; Mir34aDIEC

value: 18 weeks


title: Quiescent 1, Roots, KFT A, Replicate 3

description:
Q1A3
Q1A_Q1B_RNAseq_results.xlsx    Q1A_Q1C_RNAseq_results.xlsx    Q1A_Q1D_RNAseq_results.xlsx    Q1P_Q1A_RNAseq_results.xlsx

source_name: Roots, Q1, KFT A


title: Quiescent 1, Roots, KFT A, Replicate 2

description:
Q1A2
Q1A_Q1B_RNAseq_results.xlsx    Q1A_Q1C_RNAseq_results.xlsx    Q1A_Q1D_RNAseq_results.xlsx    Q1P_Q1A_RNAseq_results.xlsx


title: Quiescent 1, Roots, KFT A, Replicate 1

description:
Q1A1
Q1A_Q1B_RNAseq_results.xlsx    Q1A_Q1C_RNAseq_results.xlsx    Q1A_Q1D_RNAseq_results.xlsx    Q1P_Q1A_RNAseq_results.xlsx


title: Clinostat (Q6), Roots, Replicate 3

description:
CR3
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q1R_Q6R_RNAseq_results.xlsx    Q3R_Q6R_ratio_RNAseq_results.xlsx

source_name: Roots, C(Q6)

growth_protocol:
plant grown on coupon of solid 0.5x MS media, Placed in Kennedy Fixation Tube for 4 hours and 14 minutes, 7 day old plants harvested and stored in RNAlater™ until RNA extraction, Placed on Clinostat at 1 RPM for 4 minutes
plants were grown on a phytagel matrix-encased coupon then placed in Kennedy Fixation Tubes for multiple timepoints with a clinorotation substitute for microgravity to simulate a suborbital flight pattern.

value: 24 hour light cycle, 8 hour dark storage, Placed in KFT for 4 hours and 14 minutes, Clinorotated for 4 minutes


title: Clinostat (Q6), Roots, Replicate 2

description:
CR2
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q1R_Q6R_RNAseq_results.xlsx    Q3R_Q6R_ratio_RNAseq_results.xlsx


title: Quiescent 1, Roots, KFT B, Replicate 2

description:
Q1B2
Q1B_Q1C_RNAseq_results.xlsx    Q1B_Q1D_RNAseq_results.xlsx    Q1P_Q1B_RNAseq_results.xlsx   Q1A_Q1B_RNAseq_results.xlsx


title: Clinostat (Q6), Leaves, Replicate 3

description:
CL3
Q1_3L_Q6L_RNAseq_results.xlsx    Q123L_Q6L_RNAseq_results.xlsx    Q3L_Q6L_ratio_RNAseq_results.xlsx

source_name: Leaves, C(Q6)

value: Leaves

value: All leaves from 7 day-old seedling


title: Clinostat (Q6), Roots, Replicate 1

description:
CR1
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q1R_Q6R_RNAseq_results.xlsx    Q3R_Q6R_ratio_RNAseq_results.xlsx


title: Quiescent 1, Roots, KFT C, Replicate 3

description:
Q1C3
Q1C_Q1D_RNAseq_results.xlsx    Q1A_Q1C_RNAseq_results.xlsx    Q1B_Q1C_RNAseq_results.xlsx    Q1P_Q1C_RNAseq_results.xlsx


title: Clinostat (Q6), Leaves, Replicate 2

description:
CL2
Q1_3L_Q6L_RNAseq_results.xlsx    Q123L_Q6L_RNAseq_results.xlsx    Q3L_Q6L_ratio_RNAseq_results.xlsx


title: Quiescent 1, Roots, KFT B, Replicate 1

description:
Q1B1
Q1B_Q1C_RNAseq_results.xlsx    Q1B_Q1D_RNAseq_results.xlsx    Q1P_Q1B_RNAseq_results.xlsx   Q1A_Q1B_RNAseq_results.xlsx


title: Clinostat (Q6), Leaves, Replicate 1

description:
CL1
Q1_3L_Q6L_RNAseq_results.xlsx    Q123L_Q6L_RNAseq_results.xlsx    Q3L_Q6L_ratio_RNAseq_results.xlsx


title: Quiescent 4, Roots, Replicate 2

description:
Q4R2
Q1R_Q4R_RNAseq_results.xlsx

source_name: Roots, Q4

growth_protocol:
plant grown on coupon of solid 0.5x MS media, Placed in Kennedy Fixation Tube for 4 hours and 28 minutes, 7 day old plants harvested and stored in RNAlater™ until RNA extraction
plants were grown on a phytagel matrix-encased coupon then placed in Kennedy Fixation Tubes for multiple timepoints with a clinorotation substitute for microgravity to simulate a suborbital flight pattern.

value: 24 hour light cycle, 8 hour dark storage, Placed in KFT for 4 hours and 28 minutes


title: Quiescent 4, Roots, Replicate 3

description:
Q4R3
Q1R_Q4R_RNAseq_results.xlsx


title: Quiescent 1, Roots, Plate, Replicate 1

description:
Q1P1
Q1P_Q1A_RNAseq_results.xlsx    Q1P_Q1C_RNAseq_results.xlsx    Q1P_Q1D_RNAseq_results.xlsx   Q1P_Q1B_RNAseq_results.xlsx


title: Quiescent 4, Roots, Replicate 1

description:
Q4R1
Q1R_Q4R_RNAseq_results.xlsx


title: Quiescent 4, Leaves, Replicate 2

description:
Q4L2
Q1L_Q4L_RNAseq_results.xlsx

source_name: Leaves, Q4


title: Quiescent 4, Leaves, Replicate 1

description:
Q4L1
Q1L_Q4L_RNAseq_results.xlsx

source_name: Leaves, Q3


title: Quiescent 4, Leaves, Replicate 3

description:
Q4L3
Q1L_Q4L_RNAseq_results.xlsx


title: Quiescent 3, Roots, Replicate 3

description:
Q3R3
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q3R_Q6R_ratio_RNAseq_results.xlsx

source_name: Roots, Q3

growth_protocol:
plant grown on coupon of solid 0.5x MS media, Placed in Kennedy Fixation Tube for 4 hours and 18 minutes, 7 day old plants harvested and stored in RNAlater™ until RNA extraction
plants were grown on a phytagel matrix-encased coupon then placed in Kennedy Fixation Tubes for multiple timepoints with a clinorotation substitute for microgravity to simulate a suborbital flight pattern.

value: 24 hour light cycle, 8 hour dark storage, Placed in KFT for 4 hours and 18 minutes


title: Quiescent 3, Roots, Replicate 2

description:
Q3R2
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q3R_Q6R_ratio_RNAseq_results.xlsx

value: Wild Type


title: Quiescent 3, Leaves, Replicate 3

description:
Q3L3
Q1_3L_Q6L_RNAseq_results.xlsx    Q123L_Q6L_RNAseq_results.xlsx    Q3L_Q6L_ratio_RNAseq_results.xlsx


title: Quiescent 3, Leaves, Replicate 2

description:
Q3L2
Q1_3L_Q6L_RNAseq_results.xlsx    Q123L_Q6L_RNAseq_results.xlsx    Q3L_Q6L_ratio_RNAseq_results.xlsx


title: Quiescent 3, Leaves, Replicate 1

description:
Q3L1
Q1_3L_Q6L_RNAseq_results.xlsx    Q123L_Q6L_RNAseq_results.xlsx    Q3L_Q6L_ratio_RNAseq_results.xlsx


title: Quiescent 2, Roots, Replicate 3

description:
Q2R3
Q123R_Q6R_RNAseq_results.xlsx   Q1R_Q2R_RNAseq_results.xlsx

source_name: Roots, Q2

growth_protocol:
plant grown on coupon of solid 0.5x MS media, Placed in Kennedy Fixation Tube for 4 hours and 14 minutes, 7 day old plants harvested and stored in RNAlater™ until RNA extraction
plants were grown on a phytagel matrix-encased coupon then placed in Kennedy Fixation Tubes for multiple timepoints with a clinorotation substitute for microgravity to simulate a suborbital flight pattern.

value: Roots

value: 24 hour light cycle, 8 hour dark storage, Placed in KFT for 4 hours and 14 minutes


title: Quiescent 2, Roots, Replicate 1

description:
Q2R1
Q123R_Q6R_RNAseq_results.xlsx   Q1R_Q2R_RNAseq_results.xlsx

value: All roots from 7 day-old seedling

value: 7 day-old plants


title: Quiescent 2, Roots, Replicate 2

description:
Q2R2
Q123R_Q6R_RNAseq_results.xlsx   Q1R_Q2R_RNAseq_results.xlsx

value: RNAlater fixed_sample


title: Quiescent 2, Leaves, Replicate 2

description:
Q2L2
Q123L_Q6L_RNAseq_results.xlsx   Q1L_Q2L_RNAseq_results.xlsx

source_name: Leaves, Q2


title: Quiescent 2, Leaves, Replicate 3

description:
Q2L3
Q123L_Q6L_RNAseq_results.xlsx   Q1L_Q2L_RNAseq_results.xlsx


title: Quiescent 2, Leaves, Replicate 1

description:
Q2L1
Q123L_Q6L_RNAseq_results.xlsx   Q1L_Q2L_RNAseq_results.xlsx


title: Quiescent 1, Roots, Replicate 3

description:
Q1R3
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q1R_Q6R_RNAseq_results.xlsx    Q1R_Q2R_RNAseq_results.xlsx    Q1R_Q3R_RNAseq_results.xlsx

source_name: Roots, Q1


title: Quiescent 1, Leaves, Replicate 1

description:
Q1L1
Q1_3L_Q6L_RNAseq_results.xlsx     Q123L_Q6L_RNAseq_results.xlsx  Q1L_Q2L_RNAseq_results.xlsx    Q1L_Q3L_RNAseq_results.xlsx    Q1L_Q4L_RNAseq_results.xlsx    Q1L_Q6L_RNAseq_results.xlsx

source_name: Leaves, Q1


title: Quiescent 1, Leaves, Replicate 3

description:
Q1L3
Q1_3L_Q6L_RNAseq_results.xlsx     Q123L_Q6L_RNAseq_results.xlsx  Q1L_Q2L_RNAseq_results.xlsx    Q1L_Q3L_RNAseq_results.xlsx    Q1L_Q4L_RNAseq_results.xlsx    Q1L_Q6L_RNAseq_results.xlsx


title: T235

city: Singapore

first: Neerja

last: Karnani

address: 30 Medical drive

country: Singapore

institute: Singapore Institute for Clinical Sciences, A*STAR

data_processing:
Raw sequencing reads were first assessed using FastQC v0.10.1. Average length of sequenced reads was 100nt. All adaptors sequences had been removed.
Reads with low-quality scores and short sequences of less than 50 bases were removed using Trimmomatic v0.36
Surviving reads were aligned against GRCh37 (hg19) human genome assembly (Ensembl) using STAR (version 2.7.2c) and unique reads were quantified using –quantmode function embedded within STAR
Read counts were read into R (edgeR, limma package) and transcripts with an average read count of greater than or equals to 5 across all samples and CPM of greater than 1 in more than 50 samples were retained. To account for library size differences, a Trimmed-Mean of M values (TMM) normalization was implemented.
Genome_build: hg19
Supplementary_files_format_and_content: Tab.delimited file comprising of raw counts for 238 samples
Supplementary_files_format_and_content: Tab.delimited file comprising of log-CPM values for 237 samples. (1 sample removed after TMM normalization due to missing ppBMI/booking BMI value).Transcripts with an average read count of greater than or equals to 5 across all samples and CPM of greater than 1 in more than 50 samples were retained.

source_name: Maternal Whole Blood_Chinese

extract_protocol:
Total RNA extraction was performed using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) as per the manufacturer’s protocol. Briefly, 400µl of mid gestation maternal whole blood was mixed thoroughly with Qiazol and chloroform and incubated at room temperature for 10 minutes. The mixture was centrifuged (12000 x g) for 20 minutes at 4°C and the upper aqueous layer was removed and mixed with ethanol. Sample was then added to RNeasy spin column and centrifuged for 30 seconds (8000 x g) at room temperature. After on-column DNase digestion, the spin column was washed with supplied buffers. Total RNA was eluted with 50µl RNase-free water and stored at -80°C. RNA concentration and purity was assessed by Nanodrop ND-8000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA), while RNA integrity was determined using Agilent 2100 Bioanalyzer and RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA).
Approximately 200ng of total RNA was used as input for whole transcriptome library preparation, which was performed using Globin-Zero Gold rRNA removal kit followed by Illumina TruSeq kit according to the manufacturer’s protocols. The concentration of the libraries with inserts ranging in size from 160-180bp was quantified by quantitative PCR before multiplexing for sequencing. The final concentration and size distribution of the pooled library was determined using Agilent 2100 Bioanalyzer before sequencing on the Illumina HiSeq 4000 platform (BGI Tech Solutions Co Ltd, Hongkong).

tag: ethnicity

value: Chinese

value: Maternal Whole Blood


title: T237

source_name: Maternal Whole Blood_Malay

value: Malay


title: T234

source_name: Maternal Whole Blood_Indian

value: Indian


title: T238


title: T233


title: T232


title: Quiescent 3, Roots, Replicate 1

description:
Q3R1
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q3R_Q6R_ratio_RNAseq_results.xlsx


title: T229


title: T231


title: T224


title: T226


title: Quiescent 1, Roots, Replicate 2

description:
Q1R2
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q1R_Q6R_RNAseq_results.xlsx    Q1R_Q2R_RNAseq_results.xlsx    Q1R_Q3R_RNAseq_results.xlsx

value: 24 hour light cycle, 8 hour dark storage, Placed in KFT for 4 hours


title: T221


title: Quiescent 1, Leaves, Replicate 2

description:
Q1L2
Q1_3L_Q6L_RNAseq_results.xlsx     Q123L_Q6L_RNAseq_results.xlsx  Q1L_Q2L_RNAseq_results.xlsx    Q1L_Q3L_RNAseq_results.xlsx    Q1L_Q4L_RNAseq_results.xlsx    Q1L_Q6L_RNAseq_results.xlsx


title: T220


title: T222


title: Quiescent 1, Roots, Replicate 1

description:
Q1R1
Q1_3R_Q6R_RNAseq_results.xlsx    Q123R_Q6R_RNAseq_results.xlsx    Q1R_Q6R_RNAseq_results.xlsx    Q1R_Q2R_RNAseq_results.xlsx    Q1R_Q3R_RNAseq_results.xlsx


title: T223


title: T236


title: T217


title: T219


title: T216


title: T215


title: Control group 2

description: Control 2

source_name: Sprague-Dawley Rat pancreas

value: Sprague-Dawley

value: pancreas

value: control

value: 1 ml normal saline


title: T213


title: T212


title: T209


title: T211


title: T210


title: T230


title: T228


title: T214


title: T208


title: T225


title: T227


title: wild-type VDJ1

source_name: CCR6+CD127+TCRb+ thymocytes

value: CCR6+CD127+TCRb+ thymocytes

value: wild-type


title: T207


title: T206


title: T205


title: T218


title: T204


title: T202


title: T203


title: T201


title: T200


title: T198


title: T196


title: T199


title: T197


title: T195


title: T194


title: T193


title: T192


title: T191


title: T188


title: T189


title: T185


title: T187


title: T186


title: T184


title: T181


title: T183


title: T182


title: T180


title: T177


title: T176


title: T175


title: T174


title: T173


title: T172


title: T169


title: T170


title: T168


title: T171


title: T166


title: T167


title: T164


title: T190


title: T161


title: T162


title: T163


title: T160


title: T159


title: T156


title: T158


title: T179


title: T178


title: T155


title: T153


title: T157


title: T154


title: T150


title: T151


title: T152


title: T147


title: T165


title: T145


title: T146


title: T148


title: T144


title: T142


title: T141


title: T143


title: T140


title: T139


title: T138


title: T136


title: T137


title: T132


title: T133


title: T134


title: T135


title: T131


title: T130


title: T149


title: T128


title: T129


title: T127


title: T124


title: T126


title: T125


title: T123


title: T121


title: T122


title: T120


title: T119


title: T116


title: T118


title: T113


title: T114


title: T115


title: T111


title: T106


title: T110


title: T108


title: T107


title: T104


title: T102


title: T103


title: T097


title: T096


title: T098


title: T094


title: T095


title: T101


title: T099


title: T100


title: T093


title: T091


title: T092


title: T090


title: T117


title: T088


title: T085


title: T112


title: T109


title: T084


title: T087


title: T086


title: T089


title: T083


title: T105


title: T079


title: T082


title: T080


title: T081


title: T076


title: T077


title: T074


title: T072


title: T073


title: T075


title: T070


title: T068


title: T067


title: T065


title: T066


title: T064


title: T063


title: T062


title: T061


title: T056


title: T055


title: T060


title: T058


title: T059


title: T057


title: T078


title: T053


title: T071


title: T054


title: T049


title: T050


title: T052


title: T051


title: T044


title: T047


title: T045


title: T046


title: T042


title: T043


title: T040


title: T041


title: T036


title: T037


title: T039


title: T034


title: T032


title: T038


title: T035


title: T031


title: T029


title: T030


title: T028


title: T033


title: T026


title: T048


title: T027


title: T024


title: T025


title: T022


title: T023


title: T021


title: T020


title: T019


title: T012


title: T015


title: T016


title: T013


title: T014


title: T011


title: T010


title: T009


title: T008


title: T002


title: T007


title: T001


title: T003


title: M2_Chronic_ETOH_S75

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC v0.11.8
Reads aligned to the hg19 human genome using the STAR aligner version 2.5.3a. Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads. The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection and sjdbOverhang value of 100. When necessary, Illumina barcodes were trimmed using trimgalore21.
Raw or TPM (transcripts per million) gene expression was quantified across all gene exons with HOMER using the top-expressed isoform as proxy for gene expression, and differential gene expression was carried out on the raw counts using the DeSeq2 package version 1.22.2 using duplicates to compute within-group dispersion and treating cell-line identity as a batch variable to account for cell-line technical bias. Differentially expressed genes were defined as having a false discovery rate (FDR) <0.1 and a log2 fold change >0.585 (~1.5 fold) when comparing two experimental conditions.
Principal component analysis (PCA) was carried out using the prcomp R function on the top 2000 expressed TPM gene values.
Overrepresentation analysis was carried out using MetaScape with default parameters. We looked for significant overrepresentation of Gene Ontology (GO) biology process, Reactome, and MSigDB Canonical Pathways.
Genome_build: hg19
Supplementary_files_format_and_content: Raw count tables

growth_protocol: Fibroblasts were derived from skin punch biopsies and converted to iPSCs by virally introducing reprogramming factors SOX2, KLF9, OCT3/4, and c-Myc as previously described15. GPCs were derived from iPSCs as previously described16. Briefly, iPSC colonies were lifted enzymatically, transferred to ultra-low-attachment plates, and placed on an orbital shaker for 3 weeks as embryoid bodies. Embryoid bodies were dissociated into GPCs and passaged 4-6 times to eliminate neuronal cells. GPCs were differentiated on Matrigel coated plates in serum-free differentiation media for 4 weeks. Serum-free differentiation media contained DMEM F12 + Glutamax (Thermo Fisher; Waltham, MA), 10% KOSR (Thermo Fisher; Waltham, MA), N-2 supplement (Thermo Fisher; Waltham, MA), 20ng/mL CNTF (Proteintech; Rosemont, IL), 20ng/mL BMP4 (PeproTech; Rocky Hill, NJ), 20ng/mL FGF2 (Joint Protein Central, Korea), and 20 ng/mL EGF (Humanzyme; Chicago, IL).

extract_protocol:
Bulk RNA was collected using TriZol (Invitrogen; Carlsbad, CA) and kept at -80°C before extraction. Briefly, chloroform was incubated with TriZol samples for 10 min on ice. Samples were centrifuged at 12,000 rcf for 15 min at 4°C. Clear liquid phase was transferred to new tube with isopropanol and incubated for 10 min at room temperature. Precipitate was pelleted with centrifugation at 12,000 rcf for 10 min at 4°C. Pellet was washed with cold 75% EtOH followed by 100% EtOH before removing liquid and drying at room temperature for 20 min. Dry pellet was dissolved in 20uL nuclease-free water.
Stranded RNA-Seq

treatment_protocol: Cortisol (Sigma Aldrich, St Louis, MO) was reconstituted in Ethanol (EtOH) to a stock concentration of 100mM kept at 20°C. Cells were treated with 50µM cortisol (0.005% EtOH) or 5µM cortisol (0.0005% EtOH) for acute treatment. Chronic cortisol treated cells received 5µM cortisol or 0.0005% EtOH every 48 hours for 7 days and were collected 24 hours after the last dose.

value: Chronic Ethanol

tag: disease state

value: Healthy

value: patient-derived astrocytes


title: M2_Chronic_Cortisol_S76

value: Chronic Cortisol


title: T006


title: T004


title: M2_Acute_Cortisol_S74

value: Acute Cortisol


title: M1_Chronic_Cortisol_S72


title: M2_Acute_ETOH_S73

value: Acute Ethanol


title: M1_Chronic_ETOH_S71


title: T069


title: meg-1 meg-2 (biological replicate)

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 N. Wolfe St. PCTB 706

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

data_processing:
Reads were aligned to the genome with HISAT2.
Reads were counted with HTSeq-count.
Differential expression analysis was done with DESeq2
Assembly: ce10
Supplementary files format and content: text file containing fpkm values for each sample.

organism: Caenorhabditis elegans

source_name: embryos

extract_protocol:
RNA was extracted with Trizol/chloroform and purified with Zymo RNA Clean and Concentrator kit.
Libraries were prepared with 1 µg of total RNA using TruSeq stranded total RNA library prep kit with 12 cycles of PCR amplification.

treatment_protocol: Synchronized L1s were fed on RNAi bacteria at 20˚C until reaching adult stage.

value: embryos

value: meg-1(vr10) meg-2 RNAi

value: meg-2 RNAi


title: M1_Acute_Cortisol_S70


title: Wild type (biological replicate)

value: L4440 RNAi


title: M1_Acute_ETOH_S69


title: T017

value: Chinese

value: Maternal Whole Blood


title: Wild type


title: T005

value: Indian


title: T018

value: Malay


title: H1 CoV2

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

data_processing:
Fastq files were generated with cellranger-4.0.0 mkfastq. We used “cellranger-4.0.0 mkgtf” to make a gtf file containing human protein coding genes, antisense genes, lincRNAs as well as exon coding for the TCR and BRC, as recommended by 10x Genomics. We added annotations for viral genes and the 3 prime viral UTR to the gtf file. To be able to detect where on the negative strand viral reads were mapping we also added annotation for viral genes where the strand was set to “-“.  We created a reference genome with “cellranger-4.0.0 mkref” using as input the gtf file described above and a fasta file containing the human genome sequence from ENSEMBL release 93 (ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz) concatenated to the SARS-CoV-2 sequence, GenBank ID: MN988713.1.
Read mapping and assigning reads to genes was done with “cellranger-4.0.0 count”
Supplementary files format and content: Filtered_gene_bc_matrices text output files from Cell Ranger count.

source_name: hPSC derived liver organoid

extract_protocol:
liver organoids were disociated into single cells using trypsin. Single cell suspension was  resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).
scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kit (10x Genomics). Samples were sequenced using a HiSeq 2500 system.

value: hPSC derived liver organoid

value: human liver

value: live SARS-CoV-2


title: 1016 CoV2

value: DiPS 1016 SevA


title: 1016 H1

value: heat-inactivated SARS-CoV-2


title: Ast_M9_EtOH_S89

value: Chronic Ethanol

value: MDD Responsive

value: patient-derived astrocytes


title: Ast_M9_Cont_S61

value: Control


title: Ast_M8_Cont_S59


title: Ast_M8_Cort_S88

value: Chronic Cortisol


title: Ast_M7_EtOH_S85


title: Ast_M7_Cort_S86


title: Ast_M8_EtOH_S87


title: Ast_M5_Cort_S82

value: MDD Non-responsive


title: Ast_M7_Cont_S57


title: Ast_M5_EtOH_S81


title: Ast_M4_Cort_S80


title: Ast_M6_EtOH_S83


title: Ast_M4_Cont_S51


title: meg-1 meg-2

value: embryos

value: meg-1(vr10) meg-2 RNAi

value: meg-2 RNAi


title: Ast_M6_Cort_S84


title: Ast_M6_Cont_S55


title: Ast_M5_Cont_S53


title: Ast_M3_Cort_S78

value: Healthy


title: Ast_M3_Cont_S49


title: Ast_M2_EtOH_S75


title: H1 HI


title: Ast_M2_Cort_S76


title: Ast_M2_Cont_S47


title: Ast_M9_Cort_S90


title: Ast_M1_EtOH_S73


title: Ast_M1_Cont_S45


title: Ast_M1_Cort_S74


title: Ast_M4_EtOH_S79


title: FUL-SOC1_Round5

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

institute: German Federal Institute for Risk Assessment

data_processing:
Fastq reads that did not pass the filter quality of CASAVA 1.8 or mapped with no mismatches to the phix174 genome using SOAPv2.21  were eliminated
The remaining sequences in fasta format were extracted and grouped according to library specific barcodes, allowing no mismatches. Barcodes were removed leading to 40 bp sequence libraries used in the data analysis. The 40 bp sequences that were present in libraries in an unexpected high number (>1000) were eliminated, as well as 40 bp reads containing the sequence “TCGTATGCCG” which is part of the Illumina adapter sequence used for sequencing. Data analysis was essentially performed as described before (Slaterry et al 2011). We based our analysis in  14-mer sequences. Frequencies of kmer sequences in each round except Round 0 was calculated directly from the data using the function oligonucleotideFrequency from the Bioconductor R package: Biostrings. Sequences in Round 0 represent a set of randomly synthesized oligonucleotides and their complexity did not allow for the direct calculation of  14-mer frequencies. Therefore, the sequence frequency in Round 0 was estimated by the sixth-order Monte Carlo model, as proposed before (Slattery et al., 2011). We chose the sixth-order Monte Carlo model because when the model was trained using 75% of the sequencing data, it resulted in the highest prediction value as measured by the Pearson correlation coefficient between the predicted and observed frequencies in the other 25% of the sequencing data. Relative affinity for each Kmer was calculated as the ratio between its frequency in Round 5 versus Round 0 to the power of ⅕.  Kmers with less than 10 reads in Round 5 were eliminated. Finally, relative affinities were normalized to 1 by dividing for the highest affinity-predicted Kmer.
Supplementary files format and content: CSV file, with 4 columns: 14-mer sequence, DNA binding speficicity, SE of the estimation, Number of reads supporting this Kmer In Round5

organism: synthetic construct

source_name: in vitro generated 40bp dsDNA sequences

extract_protocol: SELEX-seq dsDNA libraries were generated from ssDNA sequences by a single-cycle PCR amplification round with complementary primers essentially as described by Jolma et al. (2010). dsDNA sequences contain a 40 bp random sequence flanked by barcodes needed for later characterization after multiplex sequencing. In addition, the dsDNA sequences contained all features needed for direct sequencing on an HiSeq 2000 sequencer (Illumina).  First, purified FUL antibodies resuspended in 1X PDS were coupled to magnetic beads according to manufacturer’s instructions (MyOne, Invitrogen). As for EMSA, proteins were synthesized using TNT SP6 Quick Coupled Transcription/ Translation System (Promega) according to manufactures instructions in a total volume of 20 µl. Binding reaction mix was prepared essentially as for EMSA experiments with a total volume of 120 µl (Smaczniak et al., 2012b), the mix contained 20 µl in vitro synthesized protein and 50-100 ng dsDNA. The binding mix was incubated on ice for 1 hour. Followed by immunoprecipitation using 0.5 mg FUL-antibody coupled to magnetic beads (MyOne, Invitrogen) in a thermomixer at 4ºC at 700 rpm. After immunoprecipitation, magnetic beads were washed 5 times with 150 µl binding buffer without salmon-sperm DNA. Bound DNA was elucidated in 50 µl 1X TE in a 90ºC thermomixer at full speed. Next, magnetic beads were immobilized and supernatant transferred to a new tube. To allow a second round of SELEX, DNA fragments were amplified with 8 to 16 cycles of PCR with SELEX round specific primers (Jolma et al., 2010). The amplification efficiency was checked on agarose gel by comparison to a sample of known concentration. The total amplicon was used for a subsequent round of SELEX. Round for sequencing were cut out from gel after PCR amplification using MinElute Gel Extraction Kit (Qiagen). Multiple SELEX samples were multiplexed in quimolar amounts, sequencing was performed in a HiSeq 2000 sequencer (Illumina).

tag: protein complex interrogated

tag: round of selex enrichment

value: Round 5


title: Ast_M3_EtOH_S77

tag: cell type


title: FUL-SOC1_Round6

value: Round 6


title: FUL-SOC1_Round4

value: Round 4


title: FUL-SOC1_Round3

value: Round 3


title: FUL-SOC1_Round0

value: Round 0


title: FUL-SEP4_Round5


title: FUL-SEP4_Round6


title: FUL-SEP1_Round6


title: FUL-SEP4_Round0


title: FUL-SEP3_Round6


title: FUL-SEP3_Round0


title: FUL-SEP3_Round3


title: FUL-SEP1_Round0


title: FUL-SEP1_Round5


title: FUL-SEP3_Round4


title: FUL-FUL_Round6

value: FUL-FUL


title: FUL-SEP3_Round5


title: FUL-FUL_Round3


title: FUL-FUL_Round4


title: FUL-FUL_Round1

value: Round 1


title: FUL-FUL_Round2

value: Round 2


title: FUL-FUL_Round5


title: FUL-FUL_Round0


title: FUL-AG_Round6

value: FUL-AG


title: FUL-AG_Round5


title: FUL-AG_Round3


title: FUL-AG_Round0


title: Sorghum Root RNA-seq Rep 2

data_processing:
Sequences were quality trimmed and adaptors were identified and filtered using CutAdapt v2.8
UMI sequences were extracted from processed fasta files using UMI-tools v1.0.1
Sequences were aligned to their respective genome using STAR v2.7.2
Sequences were deduplicated using the UMI and mapping location using UMI-tools v1.0.1
Transcriptoinal start sites were determined using the R library TSRchitect v1.2.0 in R v4.0.0
Genome_build: Maize genome = AGPv4.38, Sorghum genome = NCBIv3.52, Rice genome = IRGSP-1.0.51, Wheat genome = IWGSC.51, Soy genome = Wm82.a4.v1
Supplementary_files_format_and_content: Text file containing single nucleotide position of transcription start site, read count, and strand

organism: Sorghum bicolor

source_name: Sorghum root

tag: strain

tag: technique

value: RNA-seq

value: Root


title: Sorghum Root RNA-seq Rep 1


title: Sorghum Shoot RNA-seq Rep 1

source_name: Sorghum shoot

value: Shoot


title: Sorghum Shoot RNA-seq Rep 2


title: Sorghum Root smar2C2 Rep 1


title: Sorghum Shoot smar2C2 Rep 1


title: A15248_Thalamus(N944)

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description:
N944
counts.txt

data_processing:
FASTQ files were aligned against the NCBI M. fascicularis transcriptome using the salmon aligner (v1.2.1), using the following arguments: --validateMappings --incompatPrior 1 -p 30 --useVBOpt --gcBias --posBias --biasSpeedSamp 10
Transcript counts were read into R using the Bioconductor tximport package, summarizing transcript (NCBI RefSeq transcript) counts at the gene (NCBI Gene ID) level using length scaled TPM abundances (e.g., using countsFromAbundance = “lengthScaledTPM”).
Genome_build: GCF_000364345.1 (Macaca_fascicularis_5.0, downloaded on 22 November 2019).
Supplementary_files_format_and_content: counts.txt: Matrix of read counts per gene. The first column is the NCBI Gene ID, and the remaining columns are the counts/gene for each sample. First row lists the sample IDs.

organism: Macaca fascicularis

source_name: Thalamus

growth_protocol: Adult female fascicularis macaque monkeys between 5.5-11 years of age (mean: 7 years) and 2.8-4.2 kg in body weight (mean: 3.5 kg) were enrolled in the original study designed to assess the reproductive and neurodevelopmental effects of exposure to low-level DA (Burbacher et al., 2019). Animals were singly housed in stainless steel caging equipped with metabolic pans and a wide mesh that provided daily contact with an adjacent social partner in the Infant Primate Research Laboratory at the Washington National Primate Research Center (WaNPRC) in Seattle, WA, USA. The room was maintained 24 ± 4°C on a 12-hr light/dark schedule. Animals were given Lab Diet High Protein Monkey Diet (St. Louis, MO, USA) biscuits 2x/day, regular environmental enrichment (fresh and frozen fruit, vegetables, cereals, toys, puzzle balls, etc.) daily, and provided filtered water ad libitum. All research protocols strictly adhered to the guidance of the Animal Welfare Act and the Guide for Care and Use of Laboratory Animals of the National Research Council and were approved by the University of Washington Institutional Animal Care and Use Committee. Observers were experimentally blinded to the exposure conditions of the macaques and employed positive reinforcement techniques to train animals to drink out of a syringe to allow for controlled dosing of DA or vehicle control. Following training, animals underwent a baseline period of assessment designed to asses clinical signs of toxicity prior to starting daily oral exposure of 0 (n=10), 0.075 (n=11), or 0.15 (n=11) mg/kg of DA (BioVectra, Charlottetown, PE, Canada) in 5% sucrose water. Animals continued to be assessed 3-5x per week throughout a 2-month pre-breeding period, a 1-8-month breeding period, a 6-month pregnancy, and a 2-12-month postpartum period. Exposure ceased postpartum for 8 animals, and for 24 animals dosing continued until necropsy. In all animals, behavioral assessment continued at least 3x/week until necropsy.

extract_protocol:
Between 30-50 mg of amygdala, hippocampus, or thalamus of non-human primate tissues were added to 1mL TRIzol with 5mm stainless steel beads (Qiagen, Germantown, MD). Tissues were homogenized using Qiagen’s TissueLyser LT for 2 mins at 40Hz. Homogenized tissues were centrifuged at 10,000 RPM for 2 mins. The supernatant was transferred to a new tube and an equal volume of 100% ethanol was added. Total RNAs, including small and micro RNAs, were extracted using Direct-zol RNA Miniprep Plus (Zymo Research, Irvine, CA) according to manufacturer’s protocol. Extracted RNAs were quantified on a Qubit 4 Fluorometer using the RNA HS Assay Kit (Thermo Fisher Scientific, Grand Island, NY) and qualified using a Bioanalyzer 2100 (Agilent, Santa Clara, CA).
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II). Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103). All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput. Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474). Samples where adapter dimers constitute more than 4% of the electropherogram area are failed prior to sequencing. Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized. Successful libraries are normalized to 10nM for submission to sequencing.

treatment_protocol: Animals were fasted for 12 hrs and sedated under 20 mg/kg ketamine, before transportation to the necropsy room at the WaNRPC. Sedated animals were euthanized with an intravenous overdose of sodium pentobarbital, as per the AMVA Panel on Euthanasia recommendations (Leary et al., 2020). Euthanasia was confirmed and the brain quickly excised from the skull. The brain was bisected along the midsagittal plane. ROIs, including the HIP and THA, were identified by a certified veterinary pathologist. From the left hemisphere, dissected tissue was sliced into small, approximately 3 cm sections (representing 1-3 sections/ROI), placed in a 2 ml cryostat tube, immediately frozen in liquid nitrogen, and stored at -80°C.

tag: individual

tag: weight

value: 5.87 years

tag: Sex

value: Female

value: Thalamus

tag: dose

value: 0 (mg/kg/day)

tag: total dosing time

value: 717 days


title: A15236_Hippocampus(N909)

description:
N909
counts.txt

source_name: Hippocampus

tag: age

value: 7.33 years

tag: tissue

value: Hippocampus

value: 724 days


title: A16103_Hippocampus(N843)

description:
N843
counts.txt

value: 7.23 years

value: 448 days


title: A16117_Thalamus(N812)

description:
N812
counts.txt

value: 6.21 years

value: 477 days


title: A16112_Hippocampus(N777)

description:
N777
counts.txt

value: 6.96 years

value: 454 days


title: A15248_Hippocampus(N942)

description:
N942
counts.txt


title: A15236_Amygdala(N910)

description:
N910
counts.txt

source_name: Amygdala

value: Amygdala


title: A16113_Hippocampus(N610)

description:
N610
counts.txt

value: 6.69 years

value: 420 days


title: A16117_Amygdala(N811)

description:
N811
counts.txt


title: A16113_Thalamus(N612)

description:
N612
counts.txt


title: A14392_Hippocampus(N577)

description:
N577
counts.txt

value: 4 kg

value: 10.35 years

value: 413 days


title: A15238_Hippocampus(N744)

description:
N744
counts.txt

value: 6.36 years

value: Female

value: 0 (mg/kg/day)

value: 678 days


title: A16106_Amygdala(N511)

description:
N511
counts.txt

value: 7.09 years

value: 392 days


title: A15242_Amygdala(N477)

description:
N477
counts.txt

value: 6.52 years

value: 598 days


title: A16106_Thalamus(N512)

description:
N512
counts.txt

value: Thalamus


title: FUL-AG_Round4

value: FUL-AG

value: Round 4


title: A15234_Hippocampus(N170)

description:
N170
counts.txt

value: 7.72 years

value: Hippocampus

value: 268 days


title: A15247_Hippocampus(N975)

description:
N975
counts.txt

value: 6.35 years

value: 653 days


title: Sorghum Shoot smar2C2 Rep 2

extract_protocol:
RNA was extracted using Monarch Total RNA Extraction and Purification kit (NEB #T2010)
Libraries where prepared using the novel smar2C2 method described in the related manuscript

value: Shoot


title: A15248_Amygdala(N943)

description:
N943
counts.txt

value: 5.87 years

value: Amygdala

value: 717 days


title: A15244_Hippocampus(N136)

description:
N136
counts.txt

value: 5.53 years

value: Female

value: 294 days


title: Sorghum Root smar2C2 Rep 2

value: Root


title: A15238_Thalamus(N746)

description:
N746
counts.txt

value: 6.36 years

value: 0 (mg/kg/day)

value: 678 days


title: A15238_Amygdala(N745)

description:
N745
counts.txt


title: E_D13d_3

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: TAIR10

source_name: Shoot

growth_protocol: Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 9 days. Seedlings were then transferred to ceramics granular soil (SAKATA SEED CORPORATION, Japan) and grown for 5 days.

extract_protocol:
Seedlings were flash-frozen on liquid nitrogen, and RNA was extracted using  RNeasy Plant Mini Kit (QIAGEN K.K.).
Lasy-Seq v1.1 (Kamitani et al., 2019, Sci. Rep. see also　https://sites.google.com/view/lasy-seq/ )

treatment_protocol: Ethanol pretreatment was performed by immersing the pots in trays containing 10 mM Ethanol for 3 days. Drought treatment was then started by removing excess water from the trays and stopping subsequent watering. Shoots were harvested at 0 day Ethanol pretreatment and 0, 10 and 13 days after the onset of drought treatment.

tag: genotype

tag: organ

value: shoot


title: E_D13d_5

tag: treatment


title: E_D13d_1


title: E_D13d_4


title: E_D10d_3


title: E_D10d_4


title: MCF7 cells, shTRIB3 rep4

city: Utrecht

first: Miguel

last: Hernandez-Quiles

address: Heidelberglaan 100

institute: UMC Utrecht

data_processing:
Analysis was performed using R v4.1.0 and Bioconductor v3.13.
Reads were subjected to quality control (FastQC v0.11.9 and dupRadar v1.12.1), trimmed using Trimmomatic v0.39 and aligned to the genomes using HISAT2 (v2.2.1).
Counts were obtained using HTSeq (v0.11.0) using the corresponding GTFs (Mus_musculus.GRCm39.105.gtf). Genes were reannotated using biomaRt, using Ensembl (v105)
The count data was transformed to log2-counts per million (logCPM) using voom, estimating the mean-variance relationship.
Differential expression was assessed using a moderated t-test using the linear model framework from the limma package.
Assembly: h38
Supplementary files format and content: .txt files contain counts of sequencing reads for each ENSEMBL transcript.

extract_protocol:
RNA isolation from these cultured cells was performed using TRI Reagent (Sigma) according to manufacturer’s protocol.
Libraries were generated using Truseq RNA stranded polyA (Illumina)

tag: cell line

value: Mammary epithelial cell adenocarcinoma


title: E_D13d_2


title: MCF7 cells, shTRIB3 rep1


title: E_D10d_2


title: MCF7 cells, shControl rep4

value: shControl


title: A14400_Amygdala(N375)

description:
N375
counts.txt

value: 11.12 years

value: 371 days


title: A14400_Hippocampus(N374)

description:
N374
counts.txt

value: Hippocampus


title: E_D0d_3


title: MCF7 cells, shTRIB3 rep3


title: MCF7 cells, shTRIB3 rep2


title: E_D0d_5


title: E_D10d_1


title: E_D0d_4


title: MCF7 cells, shControl rep3


title: E_D0d_2


title: MCF7 cells, shControl rep2


title: Hybrid poplar apex

first: Daniel

last: Conde

state: FL

address: 2033 Mowry road

data_processing:
When using the 10× Genomics Chromium single-cell RNA-seq technology, sequencing data are initially preprocessed by the Cell Ranger v3.1.0 pipeline. Cell Ranger integrates a series of bioinformatic tools that align sequencing reads, generate feature-barcode matrices, and the output files for further clustering and gene expression analysis.
Genome_build: P. tremula × alba INRA clone 717-1B4 genome and annotation files were used in these analyses.
Supplementary_files_format_and_content: The processed data files correspond with the 3 outputs of the Cell Ranger: barcodes.tsv, features.tsv and matrix.mtx

organism: Populus tremula x Populus alba

source_name: leaf primordia

growth_protocol: Shoot tips and stem cuttings from in vitro grown hybrid poplar (Populus tremula × alba INRA clone 717 1B4) were used as explants for shoot multiplication. The explants were cut into small pieces (about 10–15 mm long) and placed aseptically on Murashige and Skoog media with vitamins (PhytoTech Labs, catalog number: M519) supplemented with 0.1 g/L myo-inositol (PhytoTech Labs, catalog number: I703), 0.25 g/L MES (PhytoTech Labs, catalog number: M825), 2% (w/v) sucrose (PhytoTech Labs, catalog number: S391) and solidified with 0.8% agar (PhytoTech Labs, catalog number: A296). The pH of the medium was adjusted to 5.8 with KOH before autoclaving. Explants were grown in a growth chamber under long-day conditions (16 hours light/8 hours dark), 22°C, 65% relative humidity, and 100 μmol m−2 s−1 photosynthetic photon flux. After three weeks in culture, a 5 mm-long portion of the shoot apex from 20 plants was excised, and leaves were removed, leaving only leaf primordia.

extract_protocol:
To perform nuclei isolation, we followed the protocol that we previously developed for poplar shoot apices (https://doi.org/10.1371/journal.pone.0251149).
20k nuclei were loaded to the 10X Genomics Chromium to generate the snRNA-seq library following the 10X Genomics Chromium Single Cell v3.1 protocol. The cDNA reaction was prepared as described previously (https://doi.org/10.1371/journal.pone.0251149).
Prior to full-scale sample sequencing, a preliminary run was performed in an Illumina iSeq (~ 4M reads) to allow the evaluation of parameters that are indicative of the quality of the single-cell RNA-seq library, including the estimated number of cells captured and the fraction of reads in cells (i.e., percentage of ambient or "leaked" RNA). The sequencing was performed using a standard program as follows: 28 bp (Cell barcode and UMI) for read 1, 90 bp (cDNA) for read 2, 10 bp for I7 Index, and 10 bp for I5 Index. The assessment of RNA leakage was derived from the profile of the relationship between UMI counts and cell barcodes detected. If the library was considered suitable for full-scale sequencing (reads in cells > 50% and at least 3,000 cells captured at low sequencing depth) we proceeded to sequencing in an Illumina NovaSeq6000. For full-scale sequencing we targeted 150-200M reads mapped to the genome per sample, which in our experience resulted in a sequencing saturation >70% and an average of 43,000 reads per nucleus.

value: leaf primordia


title: E_D0d_1


title: W_D13d_5


title: MCF7 cells, shControl rep1


title: W_D13d_4


title: E_D10d_5


title: W_D13d_3


title: W_D13d_2


title: W_D10d_3


title: W_D10d_2


title: W_D13d_1


title: W_D10d_1


title: W_D10d_5


title: W_D0d_5


title: W_D0d_4


title: W_D0d_3


title: W_D0d_2


title: C_D0d_5


title: W_D0d_1


title: PWL056

description: TCRb+CD69+CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRictorfl/fl chimeras

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: post PtenRicdKO

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: Cells were sort-purified using specificed markers from thymus of WT, Cd4CrePtenfl/fl Cd4CrePtenfl/fl Raptorfl/fl, Cd4CrePtenfl/flRictorfl/fl chimeras

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.


title: PWL045

description: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRictorfl/fl chimeras

source_name: pre PtenRicdKO


title: PWL044

value: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRictorfl/fl chimeras


title: W_D10d_4


title: PWL053

description: TCRb+CD69+CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRaptorfl/fl chimeras

source_name: post PtenRapdKO


title: PWL054

value: TCRb+CD69+CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRaptorfl/fl chimeras


title: PWL055

value: TCRb+CD69+CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRictorfl/fl chimeras


title: PWL040

description: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRaptorfl/fl chimeras

source_name: pre PtenRapdKO


title: PWL051


title: PWL037

description: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/fl chimeras

source_name: pre PtenKO


title: C_D0d_4


title: PWL035

description: TCRb-CD69–CD4+CD8+ cells from thymus of WT chimeras

source_name: pre WT


title: PWL049

description: TCRb+CD69+CD4+CD8+ cells from thymus of Cd4CrePtenfl/fl chimeras

source_name: post PtenKO


title: PWL048

value: TCRb+CD69+CD4+CD8+ cells from thymus of Cd4CrePtenfl/fl chimeras


title: PWL041

value: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRaptorfl/fl chimeras


title: C_D0d_1


title: C_D0d_2


title: E_7D_3

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: TAIR10
Supplementary files format and content: raw or normalized counts

growth_protocol: Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 10 days. Seedlings were then transferred to ceramics granular soil (SAKATA SEED CORPORATION, Japan) and grown for 5 days.

extract_protocol:
Seedlings were flash-frozen on liquid nitrogen, and RNA was extracted using mirVana miRNA Isolation Kit AM1561 (Thermo Fisher Scientific K.K.).
Lasy-Seq v1.1 (Kamitani et al., 2019, Sci. Rep. see also　https://sites.google.com/view/lasy-seq/ )

treatment_protocol: Ethanol pretreatment was performed by immersing the pots in trays containing 10 mM Ethanol for 3 days. Drought treatment was then started by removing excess water from the trays and stopping subsequent watering. Shoots were harvested at 0, 1, 3, 5, and 7 days after the onset of drought treatment.


title: C_D0d_3


title: PWL043


title: PWL042


title: PWL036

value: TCRb-CD69–CD4+CD8+ cells from thymus of WT chimeras


title: E_7D_1


title: E_7D_2


title: PWL032


title: E_5D_3


title: E_5D_1


title: E_5D_2


title: PWL028


title: PWL029


title: PWL030


title: E_3D_3


title: PWL031


title: PWL027


title: E_3D_2


title: E_3D_1


title: PWL026

description: TCRb+CD69+CD4+CD8+ cells from thymus of WT chimeras

source_name: post WT


title: E_1D_3


title: E_1D_2


title: E_1D_1


title: E_0D_2


title: E_0D_1


title: E_0D_3


title: PWL020


title: PWL019


title: PWL016


title: PWL017

value: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/fl chimeras


title: C_7D_3


title: PWL014

description: TCRb+CD69+CD4+CD8+ cells from thymus of Cd4CrePtenfl/flRictorfl/flchimeras


title: PWL015


title: C_7D_2


title: PWL025

value: TCRb+CD69+CD4+CD8+ cells from thymus of WT chimeras


title: PWL018


title: PWL022


title: C_5D_3


title: C_5D_1


title: C_3D_3


title: C_3D_2


title: C_3D_1


title: PWL021


title: C_7D_1


title: C_5D_2


title: C_1D_3


title: C_0D_3


title: C_0D_2


title: C_0D_1


title: C_1D_1


title: PWL003


title: PWL012


title: PWL005

description: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/fl Rictorfl/fl chimeras


title: PWL007

value: TCRb-CD69–CD4+CD8+ cells from thymus of Cd4CrePtenfl/fl Rictorfl/fl chimeras


title: PWL004


title: PWL009


title: PWL002


title: C_1D_2


title: PWL008


title: PWL006


title: PWL013


title: PWL011


title: JLR826

description: Sort-purified TCRb+CD69+ post-selection CD4+CD8+ double-positive (DP) thymocytes from Cd4CrePtenfl/flStat3fl/fl mice

source_name: post-selection DP; PTEN/Stat3 dKO

growth_protocol: Cells were sort-purified using specified markers from thymus of WT, Cd4CrePtenfl/fl, and Cd4CrePtenfl/flStat3fl/fl mice

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen

treatment_protocol: Sorted cells were lysed with lysis buffer from RNeasy Micro kit from Qiagen

value: Cd4CrePtenfl/flStat3fl/fl mice


title: JLR818

description: Sort-purified TCRb+CD69+ post-selection CD4+CD8+ double-positive (DP) thymocytes from WT mice

source_name: post-selection DP; WT

value: WT mice


title: JLR822

value: Sort-purified TCRb+CD69+ post-selection CD4+CD8+ double-positive (DP) thymocytes


title: JLR824


title: JLR812

description: Sort-purified TCRb+CD69+ post-selection CD4+CD8+ double-positive (DP) thymocytes from Cd4CrePtenfl/fl mice

source_name: post-selection DP; PTEN KO

value: Cd4CrePtenfl/fl mice


title: JLR820


title: PWL001


title: JLR804


title: JLR808


title: JLR810


title: JLR806


title: JLR816


title: DBR910: Post-Selection DP (B) Pten-KO #3

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: cells from sort-purified post-selection TCRb+CD69+CD4+CD8+

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were sort-purified using specificed markers from thymus of WT, Cd4CrePtenfl/fl, and Cd4CrePten+/fl

tag: cell population


title: DBR909: Post-Selection DP (B) Pten-KO #2

value: cells from sort-purified post-selection TCRb+CD69+CD4+CD8+


title: Soy Leaf RNA-seq

last: Schmitz

organism: Glycine max

source_name: Soy Leaf

growth_protocol: Plants grown for four weeks with standard 16H daylight conditions at room temperature

value: RNA-seq

value: Leaf


title: Soy Leaf 40pg Rep 2

source_name: Soy leaf


title: JLR814


title: DBR902: Post-Selection DP (B) WT #1


title: DBR906: Post-Selection DP (B) Pten-Het #2


title: Soy Leaf 40pg Rep 1


title: DBR907: Post-Selection DP (B) Pten-Het #3


title: DBR908: Post-Selection DP (B) Pten-KO #1


title: DBR903: Post-Selection DP (B) WT #2


title: Soy Leaf 400pg Rep 1


title: Soy Root RNA-seq

source_name: Soy Root

value: Root


title: Soy Leaf 400pg Rep 2


title: DBR900: Pre-selection DP (A) Pten- KO#2

source_name: cells from sort-purified pre-selection TCRb–CD69–CD4+CD8+


title: DBR905: Post-Selection DP (B) Pten-Het #1


title: DBR899: Pre-selection DP (A) Pten-KO #1

value: cells from sort-purified pre-selection TCRb–CD69–CD4+CD8+


title: Soy Leaf 4ng Rep 2


title: DBR895: Pre-selection DP (A) WT #3


title: DBR897: Pre-selection DP (A) Pten-Het #2


title: DBR898: Pre-selection DP (A) Pten-Het #3


title: DBR904: Post-Selection DP (B) WT #3


title: DBR896: Pre-selection DP (A) Pten-Het #1


title: Soy Leaf 40ng Rep 2


title: Soy Leaf 4ng Rep 1


title: Soy Root smar2C2 Rep 2

source_name: Soy root


title: Soy Leaf 40ng Rep 1


title: DBR894: Pre-selection DP (A) WT #2


title: DBR893: Pre-selection DP (A) WT #1


title: DBR901: Pre-selection DP (A) Pten-KO #9


title: Soy Root smar2C2 Rep 1


title: Soy Leaf smar2C2 Rep 2


title: Soy Leaf smar2C2 Rep 1


title: Gp1-2_T_3

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

description: processed data file: all_sample_cnt.tsv

data_processing:
The raw data is preprocessed by trimmomatic (version 0.36).
The clean reads were aligned to the TAIR 10 reference genome using hisat2 (version 2.1.0) with parameters "--rna-strandness RF -p 30 --dta”.
Reads count matrix was produced by htseq-count (version 0.9.1).
Genome_build: TAIR10
Supplementary_files_format_and_content: all_sample_cnt.tsv: Tab-delimited text file includes reads count values for each Sample.

source_name: 7-day-old seedling

growth_protocol: Col-0 and gp1-2 (SAIL_209_D07) were grown on ½ MS medium containing 1% sucrose at 22°C, 16h light/8h dark.

extract_protocol:
The total RNA was extracted using the Trizol reagent.
The library constructs and sequencing were performed by the Core Facilities of Genomics in Shanghai Center for Plant Stress Biology.

treatment_protocol: 5-day-old seedlings were transferred to a Y plate (containing the same medium) and treated with GB03 bacteria for 2 days before the seedlings were harvested. Control was performed by no GB03 treatment.

tag: ecotype/background

tag: genotype/variation

value: T-DNA insertion mutant SAIL_209_D07

value: Full seedlings

value: 7 days

value: Treated with GB03-emitted microbial volatiles (GMVs)


title: R-o-18-1

city: Anseong-Si

first: adji baskoro

last: dwi nugroho

state: Gyeonggi-do

address: Daedeok-myeon, Naeri, Chung-Ang University

country: South Korea

institute: Chung-Ang University

description: replicate 1

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software.
The raw reads were trimmed and quality-filtered before genome alignment using Trimmomatic (ver0.36) with more than 90% portion (Q>30) were only used in the mapping.
Reference genome of Brassica rapa plants was obtained from Ensembl (https://plants.ensembl.org/info/website/ftp/index.html) and mapped using TopHat2 software with default parameters.
Aligned reads were converted to digital counts using FeatureCounts and analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a p-value < 0.05 and two-fold difference cut-off.
Assembly: B. rapa reference genome was obtained from Ensembl (https://plants.ensembl.org/info/website/ftp/index.html)
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Brassica rapa

source_name: whole plant

extract_protocol:
Total RNA was extracted from 2 week-old seedling samples using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contaminant.
RNA-seq libraries were constructed using NovaSeq 6000 platform system (Macrogen Co., South Korea) according to the manufacturer’s instructions.

value: whole plant

value: Wild type


title: Brclf-1

description: replicate 1

value: CLF Mutant


title: R-o-18-3

description: replicate 3


title: Brclf-2

description: replicate 2


title: Gp1-2_T_2

city: Shanghai

description: processed data file: all_sample_cnt.tsv


title: Gp1-2_C_3

description: processed data file: all_sample_cnt.tsv

value: Regular


title: Gp1-2_C_1

description: processed data file: all_sample_cnt.tsv


title: Gp1-2_C_2

description: processed data file: all_sample_cnt.tsv


title: Gp1-2_T_1

description: processed data file: all_sample_cnt.tsv


title: Col-0_T_2

description: processed data file: all_sample_cnt.tsv


title: Col-0_T_1

description: processed data file: all_sample_cnt.tsv


title: Col-0_T_3

description: processed data file: all_sample_cnt.tsv


title: Col-0_C_2

description: processed data file: all_sample_cnt.tsv


title: Col-0_C_1

description: processed data file: all_sample_cnt.tsv


title: Col-0_C_3

description: processed data file: all_sample_cnt.tsv


title: P5-9

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Normalization (TMM), and differential expression analysis using EdgeR
Genome_build: mm10

source_name: Immunopanned retinal ganglion cells

extract_protocol:
RGCs were purified from mouse retinas by sequential immunopanning. Retinas were dissociated with papain, cleared of macrophages by anti-macrophage antibodies, and RGCs purified by anti-CD90 antibodies as described previously ( Meyer-Franke et al, 1995).
RNA libraries were prepared for sequencing using standard Illumina protocols
TrueSeq +RiboZero gold

tag: cell type

value: early postnatal mouse RGCs


title: P5-8

tag: strain


title: E18-3

value: embryonic mouse RGCs


title: E18-4


title: P5-6


title: Brclf-3

description: replicate 3


title: XO_iPSC_p35_2

first: Stefan

middle: F

last: Pinter

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

description:
3' polyA RNA
d156

data_processing:
Adapters were trimmed using cutadapt v2.7
Reads were aligned to the human genome (hg38) using hisat v2.2.1
Reads were quantified against GENCODE version 36 using featureCounts v2.0 from the Rsubread package.
Assembly: hg38
Supplementary files format and content: raw counts for each gene for each sample of hiPSCs and TBLs

source_name: hIPSC

growth_protocol: hiPSCs were grown on Geltrex in mTeSR media.

extract_protocol:
RNA was extracted using the PureLink RNA Minit Kit (Thermo Fisher).
3'mRNA hiPSC libraries were prepared using the Quant-seq 3’ mRNA Library Prep Kit FWD (Lexogen).
For the hiPSCs, 75bp single-end reads were sequenced on the NextSeq500.

value: hIPSC

tag: chromosome composition

value: XO


title: XY_iPSC_p17_2

description:
3' polyA RNA
d154

value: XY


title: XO_iPSC_p35_1

description:
3' polyA RNA
d155


title: XO_iPSC_p37

description:
3' polyA RNA
d158


title: XY_iPSC_p16

description:
3' polyA RNA
d153


title: XO_iPSC_p36

description:
3' polyA RNA
d157


title: R-o-18-2

description: replicate 2


title: XO9_iPSC_p13

description:
3' polyA RNA
d144


title: XO9_iPSC_p14_2

description:
3' polyA RNA
d145


title: XY_iPSC_p12

description:
3' polyA RNA
d151


title: XY_iPSC_p15

description:
3' polyA RNA
d152


title: XY_iPSC_p17_1

description:
3' polyA RNA
d150


title: XO9_iPSC_p14_1

description:
3' polyA RNA
d143


title: XO9_iPSC_p12

description:
3' polyA RNA
d142


title: XO8_iPSC_p14_2

description:
3' polyA RNA
d140


title: XO8_iPSC_p13

description:
3' polyA RNA
d139