title: i22-UCH1-KDO1-48H-r3_S10

source_name: Chordoma cell line

tag: donor

tag: time


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_chronic ATL_2

status: Public on Sep 01 2020

type: genomic

city: Saga

first: Tatsuro

last: Watanabe

state: Saga

address: 5-1-1 Nabeshima, Saga

country: Japan

institute: Saga University

description:
C2_P
Clinical specimen, T-cells

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 or HumanMethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
Genome Studio software (V2011.1 Methylation module 1.9.0) was used. Beta values were obtained after background correction and normalization to internal controls.
The GSE136189_GPL13534_beta_and_raw_data.txt and GSE136189_GPL23976_beta_and_raw_data.txt files include normalized Beta values, unmethylated signal intensities, methylated signal intensitites, and detection p-values.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: T-cell 18

label_protocol: Standard Illumina Protocol.

growth_protocol: RPMI-1640 containing 10% FBS and Pen/Str was used for T-cell lines.

extract_protocol: Genomic DNA samples were isolated using QIAamp DNA Kit (Qiagen).

tag: diagnosis

value: Chronic ATL

tag: cell type

value: T cells

tag: gender

value: Female

tag: age

tag: wbc (/ul)

tag: lym (%)

tag: abn. lym (%)

tag: sil-2r (u/ml)


title: i21-UCH1-KDO1-24H-r3_S9

type: SRA

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample

molecule: total RNA

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

tag: treatment

tag: cell line


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_chronic ATL_1

description:
C1_N
Clinical specimen, T-cells

source_name: T-cell 17


title: i20-UCH1-KDO1-6H-r3_S8


title: i18-UCH1-DMSO1-r3_S6

value: DMSO


title: ATAC_Tumor_Hi_2

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

library_source: genomic

data_processing:
Conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard).
Trimming: Trimmomatic (version 0.32).
Alignment: Bowtie2 (version 2.2.4) with the ‘very-sensitive-local’ parameter, later duplicate reads were removed using sambamba markdup (version 0.5.5) and only primary alignments with mapping quality >30 were retained.
Peak calling: Peaks were called using MACS2 (version 2.1.1.20160309) on each individual sample using the function callpeak with narrow peak setting (using the --nomodel --extsize 147 --p 1e-09 parameters). Peaks overlapping with blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/) were discarded.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: bigWig generation: Coverage files were generated from reads extended to 130bp using bedtools (version 2.26.0), using the following command: bamtobed | slop -s -l 0 -r 130 | genomeCoverageBed -bg. bigWig files containing counts of reads per basepair per million were created by the UCSC Genome Browser’s bedGraphToBigWig tool.

organism: Mus musculus

source_name: CD8+ T cells

growth_protocol: TILs were isolated from Yumm1.7 melanoma tumors 18 days after engraftment based on mitotracker staining. In vitro-generated CD8 T cells were activated from OT-1 splenocytes.

extract_protocol: DNA were collected by Qiagen MinElute kit.

treatment_protocol: In vitro-generated CD8 T cells were treated with Oligomycin A and Mdivi-1 for 6 hours followed by the collection of MDR/MG-Hi and -Lo population.

value: CD8+ intratumoral T cells (in vivo FACS purified cells)


title: ATAC_Tumor_Hi_3


title: i23-UCH1-ISRIB-1-48h-r1_S11

value: ISRIB+DMSO


title: ATAC_Tumor_Lo_1


title: i19-UCH1-KDO1-3H-r3_S7


title: SMCX_KO_mES_C7_GROSEQ

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

country: USA

institute: University of Michigan

description:
anti-BrdU enriched RNA
in vitro transcription (GRO)

data_processing:
Library strategy: GRO-Seq
Full length reads were mapped to mm9 using Bowtie (v1.1.2)
Adaptor sequence was trimmed off from unmapped reads.
Adaptor-trimmed unmapped reads were mapped again using Bowtie
Reads from both alignments were merged
BAM Files were converted to Bigwig files in a strand specific manner. Bigwigs were normalized to 25 million non-rRNA and non-mitochondrial reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to 25 million non-rRNA non-mtRNA reads.

source_name: mouse embryonic stem cells

growth_protocol: mES were cultured on gelatin-coated dishes in high-glucose DMEM containing 15% ES-qualified FBS (Chemicon), 2 mM glutamine, 1 × penicillin-streptomycin, 1 × NEAA, 10 mM HEPES, 143 μM β-mercaptoethanol (Sigma) and 1,000 U ml−1 of LIF (Chemicon) in a humidified incubator at 37°C with 5% CO2. Medium was replaced every day and Trypsin-EDTA was used for dissociation during passaging.

extract_protocol:
Nuclei in Trizol were homogenized with a qiashredder.
Split 3' Adaptor
BrU containing fragmented RNA were enriched using anti-BrdU beads followed by 3' dephosphorylation, polyadenylation, reverse-transcription, Rnase digestion, circular ligation, linearization with USER and gel purification. Libraries were amplified by PCR.

treatment_protocol: Nuclei were isolated as described in PMID:19056941 and PMID:21572438 with minor modifications. Nuclei were resuspended in 80µl of Nuclei Resuspension Buffer (25 mM Tris pH 7.5, 5 mM MgCl2, 0.1 mM EDTA, 0.15% IGEPAL CA-630, 25% glycerol, 50 mM KCl, 0.5 mM DTT and 40 U/ml of Superase.In). Global Run-On reaction was started by adding 80 µl of GROmix (30 mM Tris pH 8, 10 mM MgCl2, 250 mM KCl, 0.05 mM EDTA, 0.3% IGEPAL CA-630, 0.5% Sarkosyl (L7414, Sigma), 2.5 mM DTT, 15% glycerol, 12 µM CTP and 0.8 mM each of ATP, GTP and Br-UTP).

tag: strain

value: 129S1/SvImJ + C57BL/6J

tag: strain of origin


title: SMCX_KO_mES_C5_GROSEQ


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_chronic ATL_1

description:
C1_P
Clinical specimen, T-cells

source_name: T-cell 15


title: WGBS_Tumor_Hi_3

data_processing:
Bisulfite alignment of the WGBS reads to the mm10/GRCm38 assembly of the mouse reference genome and methylation calling was performed using gemBS (version 3.3.0) (https://doi.org/10.1093/bioinformatics/bty690) with the following parameters: sampling_rate = 4, non_stranded = False, remove_individual_bams = True, mapq_threshold = 10, qual_threshold = 13, reference_bias = 2, left_trim = 5, right_trim = 0, keep_improper_pairs = True, keep_duplicates = False, haploid = False, conversion = auto, remove_individual_bcfs = True, contig_pool_limit = 100000000, phred_threshold = 10.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: *bed: Bed files include CpG methylation calls for each sample.

growth_protocol: TILs were isolated from Yumm1.7 melanoma tumors 18 days after engraftment based on mitotracker staining.

extract_protocol: None provided


title: i17-UCH1-KDO1-48H-r1_S5


title: i16-UCH1-KDO1-24H-r1_S4


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_chronic ATL_1

description:
C1_D
Clinical specimen, T-cells

source_name: T-cell 16


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_smoldering ATL_3

description:
S3_N
Clinical specimen, T-cells

source_name: T-cell 14

value: Smoldering ATL


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_smoldering ATL_3

description:
S3_P
Clinical specimen, T-cells

source_name: T-cell 12


title: ATAC_Tumor_Hi_1


title: SMCX_WT_mES_F9_GROSEQ


title: LSD1_GT_mES_03_rep2_GROSEQ


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_HTLV-1 asymptomatic carrier_3

description:
AC3_N
Clinical specimen, T-cells

source_name: T-cell 11

value: HTLV-1 asymptomatic carrier

value: Male


title: LSD1_GT_mES_03_rep1_GROSEQ


title: SMCX_WT_mES_F8_GROSEQ


title: i15-UCH1-KDO1-6H-r1_S3


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_HTLV-1 asymptomatic carrier_3

description:
AC3_D
Clinical specimen, T-cells

source_name: T-cell 10


title: LSD1_WT_mES_17_rep1_GROSEQ


title: i14-UCH1-KDO1-3H-r1_S2


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_HTLV-1 asymptomatic carrier_3

description:
AC3_P
Clinical specimen, T-cells

source_name: T-cell 09


title: i13-UCH1-DMSO1-r1_S1


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_HTLV-1 asymptomatic carrier_2

description:
AC2_N
Clinical specimen, T-cells

source_name: T-cell 08


title: J24-8

city: Christchurch

first: Amber

middle: Rose

last: Paulson

address: Lincoln Research Centre, Cnr Springs Road And Gerald Street, Private Bag 4749

department: Forage Science

country: New Zealand

institute: AgResearch Litmited

data_processing:
Flexbar (v2.4) - barcode and adapter trimming in 'ANY' mode
BBMap (v12.2015) screen to remove rRNA using custom host and bacterial rRNA reference
Rockhopper alignment (v2.03)
Predicted asRNA and ncRNA removed
Filtered out non-expressed features, with less than five aligned reads in two or fewer libraries.
Upper quartile normalization and voom transformation with Limma (v3.38.3) R package (Note: Sample O20-3 omitted as outlier and not included in this dataset)
Genome_build: GCA_001656035.1/ASM165603v1/GI: 1034308998
Supplementary_files_format_and_content: raw read counts; tab deliminated
Supplementary_files_format_and_content: normalized/transformed expression values represented as log2 counts-per-million; tab deliminated

organism: Yersinia entomophaga

source_name: exponential_37C_bacteria from host

extract_protocol:
ScriptSeq RNA-Seq Library Preparation Kit (Illumina)
RNA was extracted with RNeasy mini kit (Qiagen), including both on-column and off-column DNAse (Qiagen) digestion, followed by isopropanol precipitation

treatment_protocol: RNA was stabilized with RNAprotect Bacterial Reagent (Qiagen) and stored at -80 °C.

tag: growth phase

value: exponential

tag: temperature

tag: growth protocol

value: in vivo

tag: rrna depletion kit

value: ScriptSeq Complete Gold Kit (Epidemiology) (Illumina)


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_HTLV-1 asymptomatic carrier_2

description:
AC2_P
Clinical specimen, T-cells

source_name: T-cell 07


title: J24-7


title: i47-UM-Chor-KDOBA67-2_S13

source_name: UM-Chor

value: Chordoma cell line

value: UM-Chor

tag: donor


title: i46-UM-Chor-KDOBA67-1_S14


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_smoldering ATL_3

description:
S3_D
Clinical specimen, T-cells

source_name: T-cell 13

tag: diagnosis


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_HTLV-1 asymptomatic carrier_1

description:
AC1_N
Clinical specimen, T-cells

source_name: T-cell 06

tag: cell type

value: No Data


title: i45-UM-Chor-vehicle3_S9


title: i44-UM-Chor-vehicle2_S15


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_HTLV-1 asymptomatic carrier_1

description:
AC1_D
Clinical specimen, T-cells

source_name: T-cell 05

tag: gender


title: J24-5


title: D4-2

source_name: stationary_25C_bacteria from host

value: stationary


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_HTLV-1 asymptomatic carrier_1

description:
AC1_P
Clinical specimen, T-cells

source_name: T-cell 04

tag: age


title: i43-UM-Chor-vehicle1_S2


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_healthy volunteer_3

description:
HC3_P
Clinical specimen, T-cells

source_name: T-cell 03

value: Healthy

tag: wbc (/ul)


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_healthy volunteer_2

description:
HC2_P
Clinical specimen, T-cells

source_name: T-cell 02

value: T cells

tag: lym (%)


title: i40-MUG-Chor-KDOBA67-3_S16

source_name: MUG-Chor

value: MUG-Chor


title: RNA-seq, mice, dentate gyrus (right side), shCCK, replicate 2

city: Atlanta

first: Feiran

last: Zhang

state: GA

address: 615 Michael St NE

department: Human Genetics

institute: Emory University

description: Illumina HiSeq

data_processing:
Paired-end reads were first aligned to mouse genome (mm9) by Tophat v2.1.1 with default settings.
FPKM values were calculated by Cufflinks v2.2.1.
Differential expression was analyzed by Cuffdiff v2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression values are in Cufflinks-normalized fpkm_tracking format.

molecule: polyA RNA

source_name: Dentate gyrus

extract_protocol:
Total RNA was extracted from fresh DG using TRIzol Reagent (Invitrogen) and Direct-zol RNA mini prep kit (Zymo Research)
Bulk mRNA-seq libraries were generated from total RNA isolated from triplicated samples per condition. The library construction was performed by Novogene. An Agilent 2100 BioAnalyzer and DNA1000 kit were used to quantify amplified cDNA and to control the quality of the libraries.

treatment_protocol: 12-week-old, wild-type, C57BL/6J mice were anesthetized under 1-2% isoflurane in oxygen at 0.6-0.8 LPM flow rate throughout the duration of the surgery. 500nL of either AAV5-shScrambled-eGFP or AAV5-shCCK-eGFP was unilaterally injected to the dentate gyrus (DG) using the following stereotaxic coordinates: AP -2.0 mm, ML +/- 1.5 mm, DV -2.3 mm from Bregma, with a microsyringe (Hamilton, 33GA) and microinjection pump (Hamilton) at a speed of 75nl/min. The needle then remained in place for 5 min before being withdrawn and the mouse allowed to recover from the surgery. 2 months post injection, mice were anesthetized under 5% isoflurane in oxygen and then sacrificed by decapitation. The whole brain was then removed from the skull and immediately placed in cold PBS. Still in cold PBS, the brain was then bisected, and DG was then dissected out from the injected hemisphere. DGs from each hemisphere were then pooled and placed in RNAlater Stabilization Solution (Thermo Fisher).

tag: tissue

value: dentate gyrus (right side)

tag: background strain

tag: knockdown

value: shCCK

value: 5 months

tag: treatment of rna sample

value: Poly(A) selection

tag: biological replicate no.


title: RNA-seq, mice, dentate gyrus (right side), shCCK, replicate 3

description: Illumina HiSeq


title: RNA-seq, mice, dentate gyrus (right side), shCCK, replicate 1

description: Illumina HiSeq


title: O20-4

tag: strain


title: LSD1_WT_mES_17_rep2_GROSEQ

source_name: mouse embryonic stem cells

tag: strain of origin


title: O20-3B

tag: growth phase

tag: temperature


title: i48-UM-Chor-KDOBA67-3_S1

tag: treatment

tag: cell line


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_healthy volunteer_1

description:
HC1_P
Clinical specimen, T-cells

source_name: T-cell 01

tag: diagnosis

tag: abn. lym (%)

tag: sil-2r (u/ml)


title: J24-6

tag: growth protocol

tag: rrna depletion kit


title: i37-MUG-Chor-vehicle3_S4

tag: cell type

value: DMSO

tag: donor


title: O18-8

source_name: exponential_25C_bacteria from host


title: Bear340BH

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

data_processing:
The reads were first evaluated for their overall quality using FastQC (REF: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ION Torrent read qualities converted to Illumina phred scores. The reads were then filtered for average base quality scores below 15.  UMIs are removed from sequences and appended to the read name to group and remove PCR duplicates. 3’ adapter is left on the sequence to remove later in the pipeline. The PCR duplicates are then removed using UMITools 0.5.4 (PMID:28100584)
Quantify miRNAs that shows high similarity to human miRNAs for mRNA target prediction. To quantify known human miRNAs we used Kraken v13-274 (REF: PMID:23816787). First Reaper in Kraken is used to strip low quality bases and low complexity sequence and trim 3’ adapter.  Then the sequences were aligned using bowtie with --time -v 2 --best -k 21 --strata -m 20 parameters to all known smallRNA sequences. All smallRNA features were quantified using annotation set v12-164 in kraken. A consolidated table were generated for miRNA quantifications for differential miRNA analysis.
Differential miRNA analysis:
We used generated tables from two strategies above to discover differentially expressed miRNAs using DEBrowser v1.9.16 (REF: https://doi.org/10.1101/399931).
For differential gene expression we use DESeq2 package (PMID: 25516281) in DEBrowser. The goal of differential miRNA expression analysis is to detect miRNAs whose difference in expression, when accounting for the variance within condition, is higher than expected by chance. DESeq2 then computes the probability whether a miRNA is differentially expressed (DE) or not. DESeq2 calculates both a nominal and a multiple hypothesis corrected p-value (padj). To find significant DE miRNAs, the ones has lower padj values and higher fold changes are selected to perform downstream analysis. Here we use 0.01< for padj value and > 2 fold change cutoffs to detect differentially expressed miRNAs.
Supplementary_files_format_and_content: bear_miRNA_hsa.tsv: include miRNA quantifications in tab separated format.
Supplementary_files_format_and_content: all_detected.csv: Differential miRNA analysis results in comma separated format.

organism: Ursus americanus

source_name: hibernating black bear

extract_protocol:
Total RNA (including small RNAs) isolated by miRNeasy Serum/Plasma kit (Qiagen, USA) on QIAcube Instrument (Qiagen, USA)
QIAseq miRNA Library Kit (IonTorrent version, Qiagen, USA) used for library preperation. Manufacturer's protocol followed. Then libraries sequenced at Proton System (ThermoFisher Scientific, USA).
Small RNA library preperation made

tag: condition

value: during hybernation

tag: tissue

value: plasma sample


title: i39-MUG-Chor-KDOBA67-2_S7


title: RNA-seq, mice, dentate gyrus (right side), shScrambled, replicate 1

description: Illumina HiSeq

tag: background strain

tag: knockdown

value: shScrambled

tag: age

tag: treatment of rna sample


title: O20-1

tag: strain

tag: growth phase

value: in vivo


title: Bear321BH


title: i36-MUG-Chor-vehicle2_S5

tag: treatment


title: i38-MUG-Chor-KDOBA67-1_S3

tag: cell line


title: RNA-seq, mice, dentate gyrus (right side), shScrambled, replicate 2

description: Illumina HiSeq

tag: biological replicate no.


title: RNA-seq, mice, dentate gyrus (right side), shScrambled, replicate 3

description: Illumina HiSeq


title: Zbtb18_OE_Day2_r3

first: Irina

last: Udalova

state: Oxfordshire

address: The Kennedy Institute of Rheumatology, Roosevelt Drive, Headington

institute: Kennedy Institute

description: Zbtb18 over expression activated B cells (Non-plasma cells) at day2

data_processing:
Reads were trimmed with Cutadapt prior to mapping with Bowtie2 with the options: "--local --X 2000"
Duplicates were removed with PicardTools markDuplicates, as were reads with MAPQ scores < 10 or insert sizes > 150 bp
Peak calling was conducted using MACS2 with the following settings: "--format BAMPE --nomodel --keep-dup-all --mfold 5,50".
DeepTools was used to generate normalised (FPKM) bigWigs of ATAC signal
Genome_build: mm10
Supplementary_files_format_and_content: bigWig - ATAC signal (FPKM)

growth_protocol: Mice primary splenocytes were harvested and primed 1 day with 0.25 µg/ml anti-CD180 (RP-105; clone RP14; BD) in 1640 RPMI medium with 10% FBS, 10mM Hepes and 100 units/ml penicillin, and then spinfected twice with retrovius expressing either control with RFP repoter or Zbtb18 with GFP reporter before seeding on the irradiated 40LB stroma cell line for another 2 days and mixing by 1:1.

extract_protocol:
Nuclei isolated and accessible DNA tagmented and purified following Omni-ATAC protocol (Corces, 2017).
DNA fragments 100 bp - 1 kb were selected with AMPure XP beads and amplified by PCR prior to pooling and sequencing

treatment_protocol: anti-CD40 (10ug/ml, FGK4.5; BioXcell) and IL-4 (10ng/ml, ebiosciences)

value: Sorted B cells (Fixable Viability Dye eFluor 780- B220+ CD138- RFP+)

tag: overexpression

tag: day of differentiation

tag: replicate


title: O18-7

value: exponential

tag: temperature

tag: growth protocol

tag: rrna depletion kit

value: ScriptSeq Complete Gold Kit (Epidemiology) (Illumina)


title: O18-3


title: Bear341BH

tag: condition


title: Zbtb18_OE_Day0_r2

description: Zbtb18 over expression activated B cell at day0

tag: cell type


title: O19-1

source_name: lag_25C_bacteria from host

value: lag


title: Bear342BH

tag: tissue


title: i32-UCH1-KDOBA67-3_S6

value: Chordoma cell line

tag: donor


title: i30-UCH1-KDOBA67-1_S18


title: i35-MUG-Chor-vehicle1_S10


title: Bear343BH


title: Zbtb18_OE_Day2_r2

source_name: Zbtb18 over expression activated B cells (Non-plasma cells) at day2


title: Zbtb18_OE_Day0_r1

source_name: Zbtb18 over expression activated B cell at day0


title: Bear339BH


title: O15-3


title: i31-UCH1-KDOBA67-2_S17


title: i29-UCH1-vehicle3_S8


title: O15-1


title: Bear310BH


title: i28-UCH1-vehicle2_S11


title: O18-4


title: Bear338BH


title: Control_OE_Day2_r2

description: Control over expression activated B cells (Non-plasma cells) at day2

value: Control


title: Control_OE_Day2_r3

source_name: Control over expression activated B cells (Non-plasma cells) at day2


title: i27-UCH1-vehicle1_S12


title: MF

source_name: stationary_25C_bacterial culture

extract_protocol:
TruSeq stranded mRNA (Illumina)
RNA was extracted with RNeasy mini kit (Qiagen), including both on-column and off-column DNAse (Qiagen) digestion, followed by isopropanol precipitation

value: stationary

value: in vitro

value: Ribo-Zero rRNA removal kit for Bacteria (Epicentre)


title: Control_OE_Day2_r1


title: BearBB345DH

source_name: their summer active counter part

value: before hybernation


title: Zbtb18_OE_Day2_r1


title: Control_OE_Day0_r2

description: Control over expression activated B cell at day0


title: O15-2


title: BearBB316DH


title: H3

source_name: exponential_37C_bacterial culture


title: UK3

source_name: Chordoma cell line

value: chordoma


title: Bear343DH


title: BearBB342DH


title: UK2


title: Control_OE_Day0_r1

source_name: Control over expression activated B cell at day0


title: E3

source_name: lag_25C_bacterial culture


title: MG


title: Bear341DH


title: UK1


title: E1


title: UD3


title: F22-2

source_name: exponential_25C_bacterial culture


title: Bear302DH


title: UD2


title: Bear335DH


title: 3xdelta-relQ-30min-mit-AHT-f_S12_R1_001

city: Tübingen

first: Christiane

last: Wolz

address: Elfriede-Aulhorn-Strasse 6

country: Germany

institute: University Tübingen

data_processing:
Data were processed using CLC Genomic Workbench from Qiagen
Reads were trimmed for adaptor and reads shorter than 15bp were discarded . Trimmed reads were aligned to reference genome HG001. Calculation of RPKM was automatically performed by CLC Genomic Workbench. Statistical analysis was also performed by CLC Genomic workbench. Genes with p>0.001 and 3-fold difference were included
Genome_build: Refence genome: HG001 provided by Ulrike Mäder
Supplementary_files_format_and_content: RPKM

organism: Staphylococcus aureus

growth_protocol: Strain were grown over night in CDM. OD600 was measured and diluted to an OD600 =0.05 for day cultures and grown until early exponential phase (OD600=0.3)

extract_protocol:
Pellet was solved in Trizol. Strains were lysed using 0.5mm circonia silicia beads. Chloroform was used seperate RNA from DNA and proteins. RNA extraction was performed following the protocol by Amp Tech ExpressArt® RNA ready
RNA was examined by a capillary electrophoresis on a Shimadzu MultiNA microchip followed by rRNA depletion using Ribo-Zero rRNA removel Kit from Illumina. RNA was converted to cDNA by fragmenting RNA samples by ultrasound and ligating an oligonucleotide adapter to the 3’end of the RNA. Using M-MLV reverse transcriptase first strand cDNA was created using 3’ adapter as primer. The 5’Illumina TruSeq sequencing adapter was ligated to the 3’end of the purified (Agencourt AMPure XP kit) cDNA and PCR was performed. Samples were pooled in equimolar amounts and fractionated in a size range of 200-500 bp using a preparative agarose gel and Illumina sequencing was performed using 75bp reads.

treatment_protocol: At OD600=0.3 strains were split into two groups. One remained the untreated control and the second RSH or RelQ were induced using 0.1µg/ml anhydrotetracycline (AHT or Atc)

tag: genotype

value: [delta]rshsyn[delta]relP[delta]relQ

tag: induction of rsh-syn or relq

value: yes


title: 3xdelta-relQ-30min-mit-AHT-e_S10_R1_001

tag: strain


title: 3xdelta-relQ-30min-mit-AHT-d_S8_R1_001


title: MK3

value: MUG


title: F22-1

tag: growth phase


title: Bear310DH

value: plasma sample


title: H1


title: 3xdelta-relQ-30min-ohne-AHT-e_S9_R1_001

value: no


title: SON siRNA 2

city: Birmingham

first: Erin

last: Ahn

state: Alabama

address: 1824 6th Ave S

department: Pathology

institute: University of Alabama in Birmingham

data_processing:
1) mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA
2) RNA fragment and reverse transcription
3) End repair, add A and adaptor ligation
4) RCR amplification
5) Single strand separation and cyclization
6) DNA nanoball synthesis
7) Sequencing on DNBseq platform
Genome_build: hg38

growth_protocol: MEG-01 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 4mM L-glutamine

extract_protocol: The RNA was poly(A)-selected and the libraries were prepared using TruSeq stranded total RNA Library Prep kit (Illumina, San Diego, CA) and sequenced (150 bp paired-end) using DNA nanoball sequencing (DNBseq) technology (BGI, Cambridge, MA).

treatment_protocol: MEG-01 AMKL cells were transfected with negative control siRNA or SON siRNA (100 pmol/106 cells) and harvested after 48 h for total RNA isolation using the RNeasy Mini Kit (Qiagen).

value: Human AMKL cell line

value: Megakaryocyte

tag: treatment

value: 48-hour SON siRNA


title: 3xdelta-RSHshortHyd-30min-mit-AHT-c_S6_R1_001


title: 3xdelta-relQ-30min-ohne-AHT-d_S7_R1_001


title: Bear337DH


title: SON siRNA 1

tag: cell line


title: Bear300DH


title: MK1


title: Bear337BH

value: during hybernation


title: UD1

value: DMSO


title: Control 3

value: control


title: Bear345BH


title: MD2


title: Control 2


title: Bear344BH


title: 3xdelta-relQ-30min-ohne-AHT-f_S11_R1_001


title: SON siRNA 3


title: 3xdelta-RSHshortHyd-30min-ohne-AHT-c_S5_R1_001


title: MD1


title: 3xdelta-RSHshortHyd-30min-mit-AHT-b_S4_R1_001


title: UCH7_KDOBA67_1


title: 3xdelta-RSHshortHyd-30min-ohne-AHT-b_S3_R1_001


title: MD3


title: MUG_DMSO_2


title: 3xdelta-RSHshortHyd-30min-ohne-AHT-a_S1_R1_001


title: MUG_DMSO_1


title: RNA_Tumor_Lo_2

data_processing:
conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard)
trimming: Trimmomatic (version 0.32)
alignment: STAR aligner version 2.5.2b
defining genes: Ensembl annotation of mm10/GRCm38
read counts: function summarizeOverlaps from the GenomicAlignments package (version 1.16.0) in R/Bioconductor (version 3.5.1)
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: read counts files: Gene expression was quantified by counting primary alignments to exons using the function summarizeOverlaps from the GenomicAlignments package (version 1.16.0) in R/Bioconductor (version 3.5.1)

source_name: CD8+ T cells

value: CD8+ intratumoral T cells (in vivo FACS purified cells)


title: Patient_54_AL_m3

city: Tampere

first: Lena

last: Möbus

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling.
Illumina standard primers were trimmed using cutadapt (version 1.15)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 91) using Tophat2 (version 2.1.1) and Bowtie2 (version 2.3.2)
Mapped reads were cleaned and sorted using Samtools (version 1.5)
Number of reads for each gene was counted using HTSeq (version 0.10.0) and annotated according to the Gencode version 27 annotation gtf file
Genome_build: GRCh38, Ensembl release 91
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts as generated by HTSeq

extract_protocol:
RNAlater fixed skin tissue samples were disrupted using innuSPEED Lysis Tubes W (1.4 – 1.6 mm steel beads & 3.5 mm ceramic beads) (Analytik Jena, Jena, Germany) in a SpeedMill Plus (3x 1min intervals) (Analytik Jena) in Lysis/Binding Buffer (Lifetechnologies). Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Lifetechnologies, Carlsbad, CA) following the manufacturers specifications with an additional on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA)

tag: patient id

tag: disease state

value: atopic dermatitis

tag: timepoint

value: 3 months post-treatment (m3)

tag: therapy

value: cyclosporine

value: skin


title: Patient_46_AN_m3

value: dupilumab


title: RNA_Tumor_Lo_3

value: CD8+ intratumoral T cells (in vitro FACS purified cells)


title: Patient_48_AN_m3


title: RNA_Tumor_Hi_4


title: UCH7_DMSO_1

value: chordoma


title: 3xdelta-RSHshortHyd-30min-mit-AHT-a_S2_R1_001

value: [delta]rshsyn[delta]relP[delta]relQ

value: yes


title: Saline 2

city: New York

first: Zhi

last: Li

state: NY

address: 435 East 30th St, 9th Floor  New York, NY 10016

institute: NYU School of Medicine

description: transcriptome

data_processing:
Alignment with Star
Quantification with HT-seq
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Primary chondrocytes

growth_protocol: Sprague dawley rat were raised in the same facility (Science Building Animal Facility, NYU Langone Medical Center), receiving the same food and care.

extract_protocol: RNA was extracted from pooled chondrocytes harvested from the knee cartilage (3 animals for each sample). RNA was extracted from trypsinized primary cells using QUIAGEN’s RNeasy Mini Kit (cat. No. 74104) according to manufacturer’s instructions.  Isolated RNA was submitted to and processed by the Genome Technology Center (GTC) at NYU Langone Health using Illumina HiSeq 4000 to acquire chondrocytes transcriptome.

value: Sprague Dawley


title: RNA_Tumor_Hi_3


title: UCH7_KDOAB67_3


title: Patient_46_AL_m3


title: Control 1

value: Human AMKL cell line


title: Saline 1

description: transcriptome


title: Patient_44_AN_m3


title: Patient_48_AL_m3


title: Lipo-CGS 3

description: transcriptome


title: MUG_KDOBA67_3

value: MUG


title: Lipo-CGS 2

description: transcriptome


title: UCH7_KDOBA67_2


title: RNA_Tumor_Hi_2


title: Patient_44_AL_m3


title: Lipo-CGS 1

description: transcriptome


title: Saline 3

description: transcriptome


title: N4 OVA-UFP 5 [U_S47]

city: Boston

first: KLaus

last: Schmitz-Abe

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

data_processing:
fastq file to bam file to count file: Rsubread (feature Counts) using default parameters
Count file to Gene differential expression file: edgeR (version 3.28), DESeq2 (version 1.26.0) using default parameters
Join results; Results_RNASeq.xlsx
Genome_build: GRCm38/mm10 (UCSC reference)
Supplementary_files_format_and_content: vcf files and excel file

source_name: N4 OVA-UFP_Treg cells

extract_protocol:
The cells were sorted our using Foxp3YFP reporter, then they were lysed using RLT buffer. The RNA was extracted using the Qiagen miniRNasy kit as per manufacturer's protocol
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol

tag: genotype/variation

value: N4 OVA-UFP

value: lung

value: Teff cells

tag: sequencing batch

value: B


title: UCH7_DMSO_2

value: DMSO


title: Patient_42_AL_m3

value: atopic dermatitis


title: Liposome 3

description: transcriptome


title: MUG_KDOBA67_2


title: N4 OVA-UFP 4 [T_S46]


title: RNA_Tumor_Lo_4


title: RNA_Tumor_Hi_1

value: CD8+ intratumoral T cells (in vivo FACS purified cells)


title: Patient_42_AN_m3

value: 3 months post-treatment (m3)


title: MK2


title: Liposome 1

description: transcriptome


title: N4 OVA-UFP 2 [R_S44]

value: A


title: Patient_41_AL_m3

value: dupilumab

value: skin


title: MUG_KDOBA67_1

value: chordoma


title: Uninvolved knee 3

description: transcriptome


title: Liposome 2

description: transcriptome


title: N4 OVA-UFP 3 [S_S45]


title: Patient_40_AL_m3


title: MUG_DMSO_3


title: N4 OVA 4 [P_S42]

source_name: N4 OVA_Treg cells

value: N4 OVA


title: Patient_40_AN_m3


title: Patient_39_AN_m3


title: s8_D21_R303

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

data_processing:
Quality filtering of the Illumina HiSeq2500 fastq files was not required
Reads of the fastq files were aligned to the reference sequence using Tophat 2.0.14 combined with Bowtie 2.1.0 (yielding 93.4 - 95.7 % aligned reads/sample). The default mismatch rate of 2% was used (3 mismatches in a read of 150 bases). The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package.
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files. The amount of reads mapped on genes was 69.9-78.6 %/sample (as a % of all reads initially aligned to the genome).
Genome_build: Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalized per sample).

source_name: Oral PMNs

extract_protocol:
PMNs were isolated flash frozen on dry ice, and RNA  was purified using an RNA Purification Method/Kit (RNABee, Machery Nagel).
Strand-specific mRNA-seq libraries for the Illumina platform were generated using Illumina protocols and sequenced at BaseClear BV (Leiden, The Netherlands).

tag: subject

tag: time point


title: N4 OVA-UFP 1 [Q_S43]

tag: cell type


title: Uninvolved knee 2

description: transcriptome


title: Uninvolved knee 1

description: transcriptome


title: s8_D09_R268


title: s8_D14_R290


title: Patient_41_AN_m3

tag: tissue


title: N4 OVA 3 [O_S41]


title: s8_D00_R224


title: N4 OVA 1 [M_S39]


title: UCH7_DMSO_3

tag: donor


title: Patient_38_AL_m3


title: Patient_39_AL_m3


title: Faecalicatena fissicatena D5 Porphyran 2

first: Eric

last: Martens

state: MI

address: 1150 W. Medical Center Dr.

description:
FfissicatenaD5 DEseq
126113_ATTACTCG-TAATCTTA_S6_L004_R1_001

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in seaweed polysaccharides was compared to gene expression in galactose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1%
Genome_build: B. thetaiotaomicron 3731 is NZ_CVOY00000000.1 (B. xylanisolvens 18002P, F contorta 548 and 588 are de novo assemblies)
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample

organism: Faecalicatena fissicatena

source_name: Bacterial Total RNA

growth_protocol: Strains were grown to mid-log on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro.

extract_protocol:
Qiagen Rneasy kit and rRNA depleted with Microbe Express Kit (Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were centrifuged to remove negatively charged polysaccharides and cell pellets were treated with two volumes of RNA Protect (Qiagen) of the original culture volume then frozen at -80C until RNA was extracted

tag: carbon source

value: Porphyran


title: Faecalicatena fissicatena D5 Porphyran 1

description:
FfissicatenaD5 DEseq
126112_ATTACTCG-AGGCGAAG_S5_L004_R1_001


title: N4 PBS 2 [K_S37]

source_name: N4 PBS_Treg cells

value: N4 PBS


title: N4 OVA 2 [N_S40]


title: Faecalicatena fissicatena D5 Agarose 1

description:
FfissicatenaD5 DEseq
126110_AGCGATAG-CCTATCCT_S3_L004_R1_001

value: Low-melt agarose


title: Patient_16_AN_m3


title: s7_D21_R288


title: N4 PBS 3 [L_S38]


title: Faecalicatena fissicatena D5 Agarose 2

description:
FfissicatenaD5 DEseq
126111_AGCGATAG-GGCTCTGA_S4_L004_R1_001


title: s7_D14_R262


title: s7_D09_R248


title: Faecalicatena fissicatena D5 Galactose 2

description:
FfissicatenaD5 DEseq
126109_TCTCGCGC-GGCTCTGA_S2_L004_R1_001

value: Galactose


title: Patient_15_AN_m3


title: s7_D00_R222


title: WT OVA-UFP 4 [H_S34]

source_name: WT OVA-UFP_Treg cells

value: WT OVA-UFP


title: N4 PBS 1 [J_S36]

value: lung


title: WT OVA-UFP 5 [I_S35]

value: Teff cells


title: Faecalicatena fissicatena D5 Galactose 1

description:
FfissicatenaD5 DEseq
126108_TCTCGCGC-CCTATCCT_S1_L004_R1_001


title: Patient_15_AL_m3


title: s6_D14_R296


title: s6_D21_R309


title: Patient_36_AL_m3


title: Patient_13_AN_m3


title: Bacteroides thetaiotaomicron 3731 Carrageenan 2

description:
Bthetaiotaomicron3731 DEseq
104693_TTAGGC_S14_L004_R1_001

organism: Bacteroides thetaiotaomicron

value: Lambda-Carrageenan


title: Bacteroides thetaiotaomicron 3731 Carrageenan 1

description:
Bthetaiotaomicron3731 DEseq
104692_CCGTCC_S13_L004_R1_001


title: WT OVA-UFP 2 [F_S32]


title: WT OVA-UFP 3 [G_S33]


title: Patient_12_AL_m3


title: Bacteroides thetaiotaomicron 3731 Galactose 2

description:
Bthetaiotaomicron3731 DEseq
104691_CTTGTA_S12_L004_R1_001


title: Patient_13_AL_m3


title: s6_D00_R234


title: WT OVA-UFP 1 [E_S31]


title: Patient_16_AL_m3


title: Bacteroides thetaiotaomicron 3731 Galactose 1

description:
Bthetaiotaomicron3731 DEseq
104690_ATGTCA_S11_L004_R1_001


title: s5_D21_R314


title: Patient_12_AN_m3


title: WT OVA 5 [D_S30]

source_name: WT OVA_Treg cells

value: WT OVA

value: B


title: s5_D14_R301


title: Patient_7_AL_m3

value: atopic dermatitis


title: WT OVA 4 [C_S29]


title: Patient_7_AN_m3

value: 3 months post-treatment (m3)


title: Patient_34_AL_m3


title: s5_D09_R275


title: s6_D09_R271


title: s5_D00_R233


title: s4_D21_R305


title: Patient_34_AN_m3


title: s4_D14_R293


title: N4 OVA-UFP 5 [26_S26]

value: N4 OVA-UFP

value: Treg cells


title: N4 OVA-UFP 4 [25_S25]


title: Patient_32_AL_m3

value: cyclosporine

value: skin


title: WT OVA 3 [B_S28]

value: A


title: N4 OVA-UFP 3 [24_S24]


title: s4_D09_R265


title: Ex-TAQed diploid strain ExTQ014

city: Nagakute

first: Hidenori

last: Tanaka

state: Aichi

address: 41-1 Yokomichi

department: Genome Engineering Program

institute: Toyota Central R&D Labs., Inc

description: Ex-TAQing treated strain ExTQ014. Leaves from progeny of Ex-TAQing treated plant

hyb_protocol: Oligo aCGH/ChIP-on-chip Hybridization Kit and Oligo aCGH/ChIP Wash Buffer Kit

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).

organism: Arabidopsis thaliana

source_name: leaves from progeny of Ex-TAQing treated plant

label_protocol: 100 ng of genomic DNA was fluorescently labeled using SureTag DNA Labeling Kit according to the manufaturer instructions (Agilent).  Initially, the DNA was denaturede in the presence of the random primer at 95 ºC for 10 minutes in a heatblock, and then quickly cooled on ice. Labeling occurred with the addition of dNTP, Cy5-dUTP(sample) or Cy3-dUTP(control) and Klenow. Incubation took place 2 hours at 37ºC in a heatblock. The unincorporated nucleotides were removed using a Microcon YM-30 ultra-fltration column (Millipore) and the labeled probe was concentrated to 25 µL.

growth_protocol: Plants were grown in corner dishes on germinaton medium (MS medium containing 1% sucrose and 0.8% agar) for 4weeks under a 16 h light/8 h dark regime.

extract_protocol: Genomic DNA was isolated using DNeasy  plant Mini Kit according to the manufacturer instructions (Qiagen).

treatment_protocol: Progeny of Ex-TAQing treated plant. Ex-TAQing treated plant was introduced of Mse I reatriction enzyme gene, and the heat treatment for activation of Taq I incubated for 3 hours at 33ºC.

value: leaves

tag: agent

value: progeny of Ex-TAQing treated plant

tag: ecotype

source_name: Wild type (Col-0)


title: Ex-TAQed diploid strain ExTQ016

description: Ex-TAQing treated strain ExTQ016. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ013

description: Ex-TAQing treated strain ExTQ013. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ015

description: Ex-TAQing treated strain ExTQ015. Leaves from progeny of Ex-TAQing treated plant


title: WT OVA 2 [A_S27]


title: Ex-TAQed diploid strain ExTQ012

description: Ex-TAQing treated strain ExTQ012. Leaves from progeny of Ex-TAQing treated plant


title: N4 OVA 4 [21_S21]

value: N4 OVA


title: s3_D14_R295


title: s4_D00_R226


title: Patient_28_AL_m3

value: dupilumab


title: WT OVA-UFP 5 [23_S23]

value: WT OVA-UFP


title: Patient_28_AN_m3


title: s3_D09_R270


title: Patient_30_AN_m3


title: Patient_30_AL_m3


title: s3_D21_R306


title: Patient_32_AN_m3


title: N4 OVA 3 [20_S20]

value: lung


title: N4 OVA-UFP 1 [22_S22]


title: s3_D00_R225


title: Ex-TAQed diploid strain ExTQ011

description: Ex-TAQing treated strain ExTQ011. Leaves from progeny of Ex-TAQing treated plant


title: s2_D21_R312


title: s2_D14_R299


title: s2_D09_R274


title: Ex-TAQed diploid strain ExTQ010

description: Ex-TAQing treated strain ExTQ010. Leaves from progeny of Ex-TAQing treated plant


title: Patient_26_AL_m3


title: s2_D00_R228


title: Patient_23_AN_m3


title: N4 OVA 2 [19_S19]


title: Ex-TAQed diploid strain ExTQ009

description: Ex-TAQing treated strain ExTQ009. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ007

description: Ex-TAQing treated strain ExTQ007. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ008

description: Ex-TAQing treated strain ExTQ008. Leaves from progeny of Ex-TAQing treated plant


title: Patient_26_AN_m3


title: s1_D14_R292


title: N4 OVA 1 [18_S18]


title: N4 PBS 2 [14_S14]

value: N4 PBS


title: Ex-TAQed diploid strain ExTQ006

description: Ex-TAQing treated strain ExTQ006. Leaves from progeny of Ex-TAQing treated plant


title: Patient_24_AN_m3


title: N4 PBS 5 [17_S17]


title: Ex-TAQed diploid strain ExTQ005

description: Ex-TAQing treated strain ExTQ005. Leaves from progeny of Ex-TAQing treated plant


title: Ex-TAQed diploid strain ExTQ004

description: Ex-TAQing treated strain ExTQ004. Leaves from progeny of Ex-TAQing treated plant


title: s1_D09_R266


title: Patient_24_AL_m3


title: Ex-TAQed diploid strain ExTQ002

description: Ex-TAQing treated strain ExTQ002. Leaves from progeny of Ex-TAQing treated plant


title: Patient_21_AN_m3


title: N4 PBS 4 [16_S16]


title: Ex-TAQed diploid strain ExTQ003

description: Ex-TAQing treated strain ExTQ003. Leaves from progeny of Ex-TAQing treated plant


title: Patient_21_AL_m3


title: s1_D21_R308


title: N4 PBS 3 [15_S15]


title: Patient_11_AL_m3


title: WT OVA-UFP 3 [11_S11]


title: BM-Tetrasporophyte

city: 56, Gongjudaehak-ro, Gongju-si, Republic of Korea

first: EUNYOUNG

last: SHIM

address: Department of Biological Sciences 205

country: South Korea

institute: Kongju National University

data_processing:
Primary sequencing data (raw reads) produced by the Illumina/Hiseq-2000 platform.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then Transcriptome de-novo assembly was carried out using CLC assembler and CAP3.
Reads Per Kilobase Million (RPKM) were calculated using CLCAssemblyCell.

organism: Bostrychia moritziana

source_name: Tetrasporophyte

growth_protocol: The thalli were maintained in unialgal cultures in IMR medium (Klochkova et al. 2006) at 20°C in a 16:8-h light and dark cycles with illumination of >20 µmol photons m-2s-1providedbycool white fluorescent lights. The plants were transferred every 1-2 weeks to new IMR medium. Male and female gametophytes actively developing spermatangial clusters and carpogonial branches, respectively, were harvested.

extract_protocol:
Total RNA from the different life history stages (male, female, tetrasporophyte) was extracted using TRI Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To prepare carposporophytes, male and female gametophytes were placed in the same dish for one week, the males were then removed. After 20 days, female gametophytes that had many cystocarps were harvested, and are referred to as ‘carposporophytes’ (female with cystocarps). Released carpospores developed into mature tetrasporophytes in a month. Tetrasporophytes were harvested when they had mature sporangia.

tag: strain

tag: life stage

value: Tetrasporophyte


title: BIBB-515 sample 11

first: Daniel

middle: Michael

last: Jordan

address: 1 Gustave L Levy Place, box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Inhibition of Lss expression
lss_11

data_processing:
Quality control metrics were calculated using RNA-SeQC v1.1.7
Sequenced reads were aligned using STAR v2.5.3a
Reads were quantified using the featureCounts tool from the Subread package v1.6.3
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files output from featureCounts using various options. Options used to generate each file are shown in the first line of the file.

source_name: liver

growth_protocol: Six-week-old female C57BL/6J (B6) mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and acclimated for two weeks prior to initiation of experiments. Mice were housed three or four per cage and maintained at 22ºC under a 12-hour light cycle. Mice were maintained in accordance with University of California, Los Angeles Institution Animal Care and Use Committee protocols. Three days prior to initiation of experiments, all mice were switched from a chow diet (Ralston Purina Company) to the control diet (Research Diets D111112201) (kcal= 15% fat, 65% carbohydrate, 20% protein).

extract_protocol:
Flash frozen hepatic samples were homogenized in Qiazol (QIAGEN) and RNA isolated according to the manufacturer’s protocol with RNeasy columns (QIAGEN). Isolated RNA was converted to cDNA using a High Capacity cDNA Synthesis Kit (ThermoFisher) according to the manufacturer’s instructions.
Primers targeted at genes of interest were designed and reactions were run in triplicate using KAPA SYBR FAST qPCR Master Mix (Roche) with 8 ng of cDNA per reaction.

treatment_protocol: At experiment initiation, mice (n = 11/group) were randomized to control diet or a matched diet containing BIBB-515 (dosed at 55 mg/kg body weight).

value: liver

tag: diet

value: BIBB-515 55 mg/kg


title: WT OVA-UFP 2 [10_S10]

tag: treatment


title: WT OVA-UFP 1 [9_S9]


title: H08_2

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

institute: Queen's University Belfast

description:
Fluidigm_2_expression_matrix.csv
Cell 100

data_processing:
Base call files were generated on board the nextseq 500 sequencer using real time analysis (RTA) and then converted to fastq format post-run using bcl2fastq2 in BaseSpace which also removed illumina adapters
Sequencing QC was assessed using Fastqc (v0.11.3) to ensure good quality sequencing and that adapters were successfully removed
Sequenced reads (fastq format) were  aligned to bovine genome UMD3.1 (Bos Tau4) using STAR (v2.5.3a) with default settings
Alignment QC was assessed using multiQC
Gene counts calculated using HTseq (v0.6.1p1) with default settings
Created expression matrix from HTseq output
Genome_build: UMD 3.1 (bos Tau4)
Supplementary_files_format_and_content: csv files with expression matrices created from HTseq output with genes in rows and single cells in columns

organism: Bos taurus

source_name: Retinal microvascular endothelial cells

extract_protocol:
RMECs were isolated from bovine retinas according to (Stitt, Chakravarthy, Archer, & Gardiner, 1995). RMECs were maintained in DMEM supplemented with 0.1mg/ml Primocin, 0.38μg/ml insulin, 1mg/ml heparin and 10% (v/v) porcine serum (PS). BRECs were passaged at approximately 80% confluency in a 1:3 ratio and grown until confluency at passage 3 for Fluidigm C1 runs . RMECs were dissociated form flask using TryPLE Express dissociation reagent and single cells were captured on Fluidigm C1 Microfluidics chip.
Clontech modified Illumina® Nextera® XT DNA sample preparation protocol was used for single-cell mRNA sequencing library preparation from cDNA acquired using the C1 system which was miniaturised using the Labcyte Access Robotic System in conjunction with Echo 525 Acoustic Dispenser

tag: passage


title: H07_2

description:
Fluidigm_2_expression_matrix.csv
Cell 99


title: BIBB-515 sample 9

description:
Inhibition of Lss expression
lss_9


title: BIBB-515 sample 10

description:
Inhibition of Lss expression
lss_10


title: N4 PBS 1 [13_S13]


title: BM-Female

source_name: Female gametophyte

value: Female gametophyte


title: Patient_8_AL_m3

tag: patient id

tag: disease state

value: atopic dermatitis

tag: timepoint

value: 3 months post-treatment (m3)


title: Patient_23_AL_m3

tag: therapy


title: WT OVA-UFP 4 [12_S12]

tag: genotype/variation

value: Treg cells

tag: sequencing batch

value: B


title: Ex-TAQed diploid strain ExTQ001

description: Ex-TAQing treated strain ExTQ001. Leaves from progeny of Ex-TAQing treated plant


title: BIBB-515 sample 7

description:
Inhibition of Lss expression
lss_7


title: Patient_4_AN_m3

value: cyclosporine

value: skin


title: WT OVA 1 [6_S6]

value: WT OVA

tag: cell type

value: A


title: BM-Male

source_name: Male gametophyte

value: Male gametophyte


title: BIBB-515 sample 6

description:
Inhibition of Lss expression
lss_6

tag: tissue


title: Patient_4_AL_m3


title: G02_2

description:
Fluidigm_2_expression_matrix.csv
Cell 95


title: WT PBS 4 [4_S4]

source_name: WT PBS_Treg cells

value: WT PBS


title: s1_D00_R235

tag: subject

tag: time point


title: F09_2

description:
Fluidigm_2_expression_matrix.csv
Cell 93


title: Control sample 4

value: control


title: Patient_11_AN_m3

value: dupilumab


title: G09_2

description:
Fluidigm_2_expression_matrix.csv
Cell 96


title: SARS-CoV-2 Infected Vero cells, untreated

city: Cambridge

first: Silvi

last: Rouskin

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were aligned to the genome of SARS-CoV-2 strain USA-WA1/2020 (GenBank: MN985325.1) using Bowtie2 v2.3.4.1 with the parameters --local --no-unal --no-discordant --no-mixed -L 12 -X 1000.
Mutations with respect to the reference genome were identified using DREEM software.
Average mutational frequencies ber base were computed and normalized (setting the median of the top 5% of frequences to 1, scaling linearly, and winsorizing all values >1 to 1) using DREEM software.
The structure of the entire genome was folded in ten segments using the Fold program from RNAstructure v6.0.1 with the normalized mutational frequencies as folding constraints.
Reads were filtered using DREEM if they had a pair of mutations closer than 4 bases, had a mutation next to a position with no information, or had a number of mutations greater than 3 standard deviations above the median among all reads.
Filtered reads were clustered and the mutation rate per position in each cluster was computed and normalized (setting the median of the top 5% of frequences to 1, scaling linearly, and winsorizing all values >1 to 1) with DREEM.
The structure of the frameshift element was folded using the ShapeKnots program from RNAstructure v6.0.1 with the normalized cluster mutation rates as constraints in folding.
Genome_build: USA-WA1/2020 (GenBank: MN985325.1)

organism:
Chlorocebus aethiops aethiops
Severe acute respiratory syndrome coronavirus 2

source_name: Vero cells

growth_protocol: Vero cells (ATCC CCL-81) were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) plated into 100 mm dishes and infected at a MOI of 0.01 with 2019-nCoV/USA-WA1/2020 (Passage 6). Infected cells  were incubated at 37 °C, 5% CO2 and harvested 2 days post infection. Infected cell pellets were centrifuged at 5000xg for 5 min at 4 °C and resuspended in Trizol (Ambion).

extract_protocol:
The cells were centrifuged at 1,000g for 5 min at 4 °C. The cells were washed twice by resuspending the pellet with 15 ml PBS with 30% β-mercaptoethanol and centrifugation to pellet then just once with 15 ml PBS. After washes, the pellet was resuspended in 1 ml Trizol (ThermoFisher Scientific) and RNA was extracted following the manufacturer’s specifications. Total RNA was purified using RNA Clean and Concentrator -25 kit (Zymo).
rRNA was subtracted from the RNA extracted from Vero cells using rRNA subtraction mix and RNase H (Lucigen). RNA was fragmented at 70 °C for 2.5 min. The ends were dephosphorylated and repaired with Shrimp Alkaline Phosphatase at 37 °C for 1 h. Linker was added with T4 RNA ligase at 22 °C for 18 h. RNA was reverse-transcribed with TGIRT-III (Ingex) at 60 °C for 1.5 h. RT product was gel-purified and size-selected for ~250 nt, circularized with CircLigase (Lucigen), and PCR-amplified with Phusion High-Fidelity DNA Polymease (NEB) for up to 16 cycles. The product was run on a gel to select for fragments ~300 nt and sequenced on an iSeq100 (Illumina).

treatment_protocol: 200 μl DMS (or 2% v/v) was added dropwise to the plated Vero cells 48 h post SARSCoV-2 infection and incubated for 4 min at 37 °C. DMS was neutralized by adding 15 ml PBS (ThermoFisher Scientific) with 30% β-mercaptoethanol.

value: Kidney epithelial cell

tag: cell line

value: ATCC CCL-81

tag: sars-cov-2 strain

value: SARS-CoV-2 strain USA-WA1/2020 (Passage 6)

tag: dms treatment

value: no DMS


title: Patient_9_AN_m3


title: H02_2

description:
Fluidigm_2_expression_matrix.csv
Cell 98


title: WT OVA 3 [8_S8]

value: lung


title: BIBB-515 sample 8

description:
Inhibition of Lss expression
lss_8

value: liver

tag: strain

value: BIBB-515 55 mg/kg


title: Patient_1_AN_m3

value: atopic dermatitis

value: 3 months post-treatment (m3)


title: WT PBS 1 [1_S1]

value: Treg cells


title: Control sample 6

tag: diet


title: Control sample 3


title: WT OVA 2 [7_S7]

tag: treatment

value: B


title: F02_2

description:
Fluidigm_2_expression_matrix.csv
Cell 90

tag: passage


title: H01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 97


title: Treg cells KO rep4 [Err-Treg-5]

city: Gainesville

first: Minghao

last: Gong

state: Florida

address: 1395 Center Drive, D6-18c

institute: University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Alignment of RNA-seq reads were mapped to the Mus musculus genome mm10 using STAR aligner (v2.7)
Significantly altered genes (FDR P < 0.05) were identified by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Combined Matrix table with raw gene counts for every gene and every sample

source_name: KO_Splenic regulatory T cells

extract_protocol:
Total RNA was extracted from CD4+Foxp3+ TREGS isolated from each individual mouse from WT and KO using RNeasy Kit.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded RNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol.

tag: age

value: 2-3 months old

tag: gender

value: female

value: spleen

value: Regulatory T cells


title: Patient_8_AN_m3

tag: patient id

tag: disease state

tag: timepoint

value: cyclosporine

value: skin


title: Patient_9_AL_m3

tag: therapy

value: dupilumab


title: Patient_57_AL_m0

value: baseline (m0)


title: G01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 94


title: WT PBS 5 [5_S5]

tag: genotype/variation

value: WT PBS

tag: cell type

tag: sequencing batch


title: Control sample 5

tag: tissue

value: control


title: Treg cells KO rep3 [Err-Treg-4]


title: F01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 89


title: WT PBS 3 [3_S3]

value: lung


title: Treg cells KO rep2 [Err-Treg-3]


title: Patient_3_AL_m3


title: E09_2

description:
Fluidigm_2_expression_matrix.csv
Cell 88


title: sample.mp_hi_run_2_180206

city: SAINT LOUIS

first: Regina

last: Clemens

state: MO

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine in St. Louis

description: ionomycin-stimulated, sorted neutrophils

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Bone marrow neutrophils

extract_protocol:
Cells were sorted directly into RNA lysis buffer (Qiagen RNeasy plus) and RNA isolated per protocol.
Clontech SMARTer Ultra-Low RNA kit

treatment_protocol: Bone marrow neutrophils were labeled with 250nM DIBAC4(3) then stimulated with 100nM ionomycin. Change in membrane potential as indicated by DIBAC4(3) fluorescence was measured on an Aria Fusion cell sorter. 20,000 cells from the depolarized and polarized populations between 2-4 minutes after stimulation.

value: Bone marrow neutrophils

tag: response

value: depolarized


title: sample.mp_lo_run_2_180206

value: polarized


title: Patient_56_AN_m0

value: atopic dermatitis


title: WT PBS 2 [2_S2]

value: Treg cells

value: A


title: Treg cells KO rep1 [Err-Treg-1]

value: 2-3 months old


title: F06_2

description:
Fluidigm_2_expression_matrix.csv
Cell 92


title: Patient_3_AN_m3

value: 3 months post-treatment (m3)


title: Treg cells WT rep5 [B6-N-Treg-5]

source_name: WT_Splenic regulatory T cells

value: female

value: spleen


title: F05_2

description:
Fluidigm_2_expression_matrix.csv
Cell 91


title: Control sample 2

value: liver


title: E07_2

description:
Fluidigm_2_expression_matrix.csv
Cell 86


title: sample.mp_lo_run_2_180214


title: Treg cells WT rep4 [B6-N-Treg-4]

value: Regulatory T cells


title: E06_2

description:
Fluidigm_2_expression_matrix.csv
Cell 85


title: sample.mp_hi_run_2_180220


title: Treg cells WT rep3 [B6-N-Treg-3]


title: Patient_57_AN_m0

value: skin


title: Control sample 1


title: Patient_1_AL_m3

value: dupilumab


title: Patient_54_AL_m0

value: baseline (m0)


title: E08_2

description:
Fluidigm_2_expression_matrix.csv
Cell 87


title: sample.mp_hi_run_1_180214


title: Patient_56_AL_m0


title: E01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 83


title: Patient_53_AN_m0


title: Patient_55_AN_m0


title: Patient_55_AL_m0


title: WGBS_Tumor_Lo_4

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

institute: CeMM, Vienna

data_processing:
Bisulfite alignment of the WGBS reads to the mm10/GRCm38 assembly of the mouse reference genome and methylation calling was performed using gemBS (version 3.3.0) (https://doi.org/10.1093/bioinformatics/bty690) with the following parameters: sampling_rate = 4, non_stranded = False, remove_individual_bams = True, mapq_threshold = 10, qual_threshold = 13, reference_bias = 2, left_trim = 5, right_trim = 0, keep_improper_pairs = True, keep_duplicates = False, haploid = False, conversion = auto, remove_individual_bcfs = True, contig_pool_limit = 100000000, phred_threshold = 10.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: *bed: Bed files include CpG methylation calls for each sample.

source_name: CD8+ T cells

extract_protocol: None provided

value: CD8+ intratumoral T cells (in vivo FACS purified cells)


title: E05_2

description:
Fluidigm_2_expression_matrix.csv
Cell 84


title: sample.mp_lo_run_2_180220


title: Treg cells WT rep2 [B6-N-Treg-2]


title: D08_2

description:
Fluidigm_2_expression_matrix.csv
Cell 80


title: Patient_52_AN_m0


title: Ob_d7-1

city: Philadelphia

first: Fanxin

last: Long

state: PENNSYLVANIA

address: 3615 Civic Center Boulevard, Abramson Research Center Room#904

department: Orthopedics

institute: Children's Hospital of Philadelphia

description:
d7_Sample#1
Ob_d0&7_all_gene_CPM.txt; Ob_d0&7_all_gene_RPKM.txt
d7 Osteoblast

source_name: Calvarial Osteoblast

growth_protocol: Calvarial osteoblasts were isolated and cultured to confluency, then subjects to mineralization medium for days as indicated.

extract_protocol:
Total RNAs were isolated with QIAGEN RNeasy Mini Kit.
Ribo-Zero Gold

treatment_protocol: Cultured cells were subjected to daily medium change. On day of sample collections, non-mineralized or mineralized cells were isolated without or with collagenase I, respectively, then with 0.05% Typsin.

value: Calvaria

value: Postnatal day 2-3 cells with 7 days differentiation


title: Patient_53_AL_m0


title: Ob_d7-3

description:
d7_Sample#3
Ob_d0&7_all_gene_CPM.txt; Ob_d0&7_all_gene_RPKM.txt
d7 Osteoblast


title: D12_2

description:
Fluidigm_2_expression_matrix.csv
Cell 82


title: Patient_51_AN_m0


title: Ob_d7-2

description:
d7_Sample#2
Ob_d0&7_all_gene_CPM.txt; Ob_d0&7_all_gene_RPKM.txt
d7 Osteoblast


title: Patient_51_AL_m0


title: Ob_d4-3

description:
d4_Sample#3
Ob_d4_all_gene_CPM.txt; Ob_d4_all_gene_RPKM.txt
d4 Osteoblast

value: Postnatal day 2-3 cells with 4 days differentiation


title: Treg cells WT rep1 [B6-N-Treg-1]


title: D07_2

description:
Fluidigm_2_expression_matrix.csv
Cell 79


title: D11_2

description:
Fluidigm_2_expression_matrix.csv
Cell 81


title: ATAC_OM_Lo_2

data_processing:
Conversion and demultiplexing: IlluminaBasecallsToMultiplexSam to generate one bam file per lane from the data on the Illumina machine, IlluminaSamDemux to demultiplex the bam file into multiple samples (https://github.com/DanieleBarreca/picard).
Trimming: Trimmomatic (version 0.32).
Alignment: Bowtie2 (version 2.2.4) with the ‘very-sensitive-local’ parameter, later duplicate reads were removed using sambamba markdup (version 0.5.5) and only primary alignments with mapping quality >30 were retained.
Peak calling: Peaks were called using MACS2 (version 2.1.1.20160309) on each individual sample using the function callpeak with narrow peak setting (using the --nomodel --extsize 147 --p 1e-09 parameters). Peaks overlapping with blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/) were discarded.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: bigWig generation: Coverage files were generated from reads extended to 130bp using bedtools (version 2.26.0), using the following command: bamtobed | slop -s -l 0 -r 130 | genomeCoverageBed -bg. bigWig files containing counts of reads per basepair per million were created by the UCSC Genome Browser’s bedGraphToBigWig tool.

extract_protocol: DNA were collected by Qiagen MinElute kit.

value: CD8+ intratumoral T cells (in vitro FACS purified cells)


title: Patient_50_AL_m0

value: atopic dermatitis


title: ATAC_OM_Lo_1


title: Ob_d4-2

description:
d4_Sample#2
Ob_d4_all_gene_CPM.txt; Ob_d4_all_gene_RPKM.txt
d4 Osteoblast


title: Ob_d4-1

description:
d4_Sample#1
Ob_d4_all_gene_CPM.txt; Ob_d4_all_gene_RPKM.txt
d4 Osteoblast


title: D06_2

description:
Fluidigm_2_expression_matrix.csv
Cell 78


title: D05_2

description:
Fluidigm_2_expression_matrix.csv
Cell 77


title: Ob_d0-2

description:
d0_Sample#2
Ob_d0&7_all_gene_CPM.txt; Ob_d0&7_all_gene_RPKM.txt
d0 Osteoblast

value: Postnatal day 2-3 cells without differentiation


title: WGBS_Tumor_Hi_1


title: Ob_d0-1

description:
d0_Sample#1
Ob_d0&7_all_gene_CPM.txt; Ob_d0&7_all_gene_RPKM.txt
d0 Osteoblast


title: Patient_49_AL_m0


title: Ob_d0-3

description:
d0_Sample#3
Ob_d0&7_all_gene_CPM.txt; Ob_d0&7_all_gene_RPKM.txt
d0 Osteoblast


title: D02_2

description:
Fluidigm_2_expression_matrix.csv
Cell 76


title: Patient_50_AN_m0


title: Patient_49_AN_m0


title: Patient_52_AL_m0


title: ATAC_OM_Hi_3


title: Patient_48_AL_m0


title: ATAC_OM_Hi_2


title: Patient_48_AN_m0


title: WGBS_Tumor_Hi_2


title: ATAC_OM_Lo_3


title: Liver1

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

description: mRNA of leukemia stem cells isolated from liver

data_processing:
Raw reads generated from the Illumina HiSeq2500 sequencer were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal are performed using Trimmomatic-0.36 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35".
Processed/cleaned reads were then mapped to reference sequence (Mg38/M17) with STAR-2.6.0c given the following parameters: "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05 on each set of raw expression measures. The ‘lfcShrink’ method was applied, which moderates log2 fold-changes for lowly expressed genes.
Genome_build: Mg38/M17
Supplementary_files_format_and_content: normalized count matrix generated by DESeq2

growth_protocol: Leukemia stem cells were isolated from mice at day 13 after transplantation with leukemia cells

extract_protocol:
QIAGEN RNeasy Plus
Clontech SMARTer + Nextera XT (Low Input Library)

treatment_protocol: No treatment

value: Leukemia stem cells

value: Male

tag: technical replicates

value: replicate 1


title: C10_2

description:
Fluidigm_2_expression_matrix.csv
Cell 73


title: Liver3

value: replicate 3


title: Liver2

value: replicate 2


title: ATAC_OM_Hi_1


title: C09_2

description:
Fluidigm_2_expression_matrix.csv
Cell 72


title: D01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 75


title: C06_2

description:
Fluidigm_2_expression_matrix.csv
Cell 71


title: C11_2

description:
Fluidigm_2_expression_matrix.csv
Cell 74


title: Patient_47_AN_m0


title: Patient_46_AL_m0


title: BM2

description: mRNA of leukemia stem cells isolated from bone marrow

source_name: bone marrow

value: bone marrow


title: BM1


title: BM3


title: Patient_45_AN_m0


title: Patient_47_AL_m0


title: C05_2

description:
Fluidigm_2_expression_matrix.csv
Cell 70


title: C02_2

description:
Fluidigm_2_expression_matrix.csv
Cell 69


title: C01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 68


title: B12_2

description:
Fluidigm_2_expression_matrix.csv
Cell 67


title: HG4

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: mouse corpus cavernous tissue

growth_protocol: Growth in complement medium 199 (M199) contained with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin, 0.5 mg/ml heparin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: Treatment with glucose for 72 hours

value: cavernous endothelial cells

tag: glucose status

value: high glucose


title: B11_2

description:
Fluidigm_2_expression_matrix.csv
Cell 66


title: Patient_44_AN_m0

extract_protocol:
RNAlater fixed skin tissue samples were disrupted using innuSPEED Lysis Tubes W (1.4 – 1.6 mm steel beads & 3.5 mm ceramic beads) (Analytik Jena, Jena, Germany) in a SpeedMill Plus (3x 1min intervals) (Analytik Jena) in Lysis/Binding Buffer (Lifetechnologies). Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Lifetechnologies, Carlsbad, CA) following the manufacturers specifications with an additional on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA)

value: skin


title: NG2

value: normal glucose


title: HG2


title: Patient_44_AL_m0

value: baseline (m0)


title: Patient_45_AL_m0


title: Patient_43_AL_m0


title: B09_2

description:
Fluidigm_2_expression_matrix.csv
Cell 64


title: B08_2

description:
Fluidigm_2_expression_matrix.csv
Cell 63


title: B07_2

description:
Fluidigm_2_expression_matrix.csv
Cell 62


title: SpleenRep2

first: Donna

middle: L

last: Farber

address: 650 West 168th Street, BB1701

department: Surgery

institute: Columbia University

data_processing:
Read mapping to annotated transcriptome was done using kallisto (version 0.44). Mouse transcriptome Mus_musculus.GRCm38.cdna.all.fa.gz (Ensembl Relsease 94) was donwloaded from https://useast.ensembl.org/index.html
quant function of kallisto was used with arguments '--single -l 180 -s 20' for the single-end sequenced batch
Estimated counts generated with tximport(countsFromAbundance="lengthScaledTPM") for protein-coding genes
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file includes estimated counts for each sample

source_name: spleen influenza-specific mouse CD4+ T cells

extract_protocol:
After sorting using a BD Influx (BD Biosciences) sorter, cells were centrifuged and transferred into microcentrifuge tubes for extraction of RNA. Pellets of sorted cells were resuspended in 700ul of QIAzol Lysis Reagent (QIAGEN) and vortexed. Lysed samples were homogenated in the TissueLyser LT (QIAGEN) by shaking for 5min at 50Hz. Samples were left to rest for additional 5min at room temperature for complete dissociation of nucleoprotein complexes. Homogenized lysates were centrifuged through QIAshredder filters (QIAGEN). 100ul of gDNA eliminator solution was added. Samples received 140μl of chloroform followed by vortexing. Finally, samples were spun at 12,000 x g for 15min at 4°C. After centrifugation, the two phase solution contains RNA in the top transparent phase. The RNA phase was collected and transferred into a new microcentrifuge tube. An equivalent volume of 70% ethanol was added to the RNA-containg solution. The RNA/ethanol solution was transferred to an RNeasy MinElute spin column (QIAGEN) and washed with Buffer RWT and two rounds of Buffer RPE (QIAGEN). Following a final wash of the column with 80% ethanol, the RNA was eluted using RNase-Free water and stored at -80°C. Quality and quantity of total RNA was determined using the RNA 6000 Pico chip run on 2100 Bioanalyzer (Agilent Technologies).
Library preparation and RNA sequencing was performed by the Columbia University Genome Center. Total RNA samples were submitted and enriched for mRNA using a poly-A pull down strategy.

treatment_protocol: Lung tissue was mechanically disrupted using the gentleMACS tissue dissociator (Milteny Biotech). Tissue homogenates were then incubated for 30-60min at 37°C with digestion medium RPMI (Thermo Fisher) containing 10% fetal bovine serum (FBS) (Thermo Fisher), L-glutamate (Thermo Fisher), sodium pyruvate (Thermo Fisher), nonessential amino acids (Thermo Fisher), penicillin-streptomycin (Thermo Fisher), collagenase D (1 mg/ml, Roche), trypsin inhibitor (1 mg/ml, Thermo Fisher) and DNase I (0.1 mg/ml, Roche). After digestion, samples were once again mechanically disrupted using the gentleMACS dissociator, followed by a passing through a 100μm filter. After centrifugation, samples were depleted for red blood cells using ACK Lysing Buffer (Thermo Fisher) for 5min at room temperature. After washing and resuspending in RPMI containing 5% FBS, samples are filtered through a 70μm filter and kept on ice in the dark.   Lymphocytes from spleens were isolated by first pressing the tissues through a 100μm filter with a plunger of a 1mL syringe to generate cell suspensions in RPMI containing 5% FBS. Spleen cell suspensions were further depleted for red blood cells using ACK Lysing Buffer as described above. Cells were then washed, resuspended, filtered through a 70μm filter and kept on ice until processing for flow cytometric analysis.

value: Spleen

value: CD4+ OT-II T cell


title: SpleenRep1


title: Patient_42_AL_m0

first: Lena

last: Möbus

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling.
Illumina standard primers were trimmed using cutadapt (version 1.15)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 91) using Tophat2 (version 2.1.1) and Bowtie2 (version 2.3.2)
Mapped reads were cleaned and sorted using Samtools (version 1.5)
Number of reads for each gene was counted using HTSeq (version 0.10.0) and annotated according to the Gencode version 27 annotation gtf file
Genome_build: GRCh38, Ensembl release 91
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts as generated by HTSeq


title: 21_Inulin, acute T. muris mouse

type: RNA

city: Frederiksberg

first: Laura

middle: J

last: Myhill

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: InulinTmuris 3

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Standard Affymetrix normalization.

label: biotin

source_name: Mouse inulin diet, T. muris infected

label_protocol: Standard Affymetrix protocol.

growth_protocol: Mice were housed in cages.

extract_protocol: At 21 days post infection mice were euthanised and the caecal blind end dissected, washed and stored in RNAlater at -20°C.

treatment_protocol: Mice were 7 weeks old at study start and fed respective diets. At 9 weeks old respective mice were infected with Trichuris muris or not.

tag: strain/background

value: Caecum

value: Inulin-supplemented

tag: infection

value: Trichuris muris


title: LungRep2

source_name: lung-resident influenza-specific mouse CD4+ T cells

value: Lung


title: Patient_42_AN_m0

address: Arvo Ylpön katu 34

institute: Tampere University

value: atopic dermatitis


title: B10_2

description:
Fluidigm_2_expression_matrix.csv
Cell 65


title: 24_Inulin, acute T. muris mouse

description: InulinTmuris 6

tag: diet


title: 23_Inulin, acute T. muris mouse

description: InulinTmuris 5


title: NG1


title: 16_Control, acute T. muris mouse

description: Tmuris 4

source_name: Mouse control diet, T. muris infected

value: Control


title: Test_rep2

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

description: processed data file: Processed_file.txt

data_processing:
RNA-seq data files were trimmed using the Trimmomatic tool.
Reads were aligned against Mus musculus reference genome (mm10) using Tophat v2.0.9 and gene-, cds-, and transcripts-level expression were computed through Cufflinks.
The transcript expression counts generated using “classic-FPKM” normalization method Cuffnorm.
Genome_build: Mus musculus reference genome mm10 (GRCm38)
Supplementary_files_format_and_content: Processed_file.txt: Normalized count file generated by cuffnorm; matrix table with counts-per-million from all samples in a tab-delimited text file.

source_name: Lens

extract_protocol:
Mouse lenses at stage P4 (n = 15 lenses per biological replicate) were collected from  Tdrd7-/- or control mice. RNA isolation was performed using the mirVanaTM RNA isolation kit (Life Technologies, Grand Island, NY). Total RNA isolation, followed by removal of small molecular weight RNA was performed according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tdrd7 -/-

tag: developmental stage

value: Postnatal day P4

value: Lens


title: Patient_41_AL_m0


title: 22_Inulin, acute T. muris mouse

description: InulinTmuris 4


title: 18_Control, acute T. muris mouse

description: Tmuris 6


title: 19_Inulin, acute T. muris mouse

description: InulinTmuris 1


title: Patient_43_AN_m0


title: 17_Control, acute T. muris mouse

description: Tmuris 5


title: 20_Inulin, acute T. muris mouse

description: InulinTmuris 2


title: B01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 59

source_name: Retinal microvascular endothelial cells

tag: passage


title: B05_2

description:
Fluidigm_2_expression_matrix.csv
Cell 60


title: 15_Control, acute T. muris mouse

description: Tmuris 3


title: Test_rep1

description: processed data file: Processed_file.txt


title: Patient_41_AN_m0


title: Patient_40_AL_m0


title: A12_2

description:
Fluidigm_2_expression_matrix.csv
Cell 58


title: B06_2

description:
Fluidigm_2_expression_matrix.csv
Cell 61


title: LungRep1


title: Patient_40_AN_m0


title: A11_2

description:
Fluidigm_2_expression_matrix.csv
Cell 57


title: Control_rep1

description: processed data file: Processed_file.txt

value: Wild type control


title: 14_Control, acute T. muris mouse

description: Tmuris 2


title: A08_2

description:
Fluidigm_2_expression_matrix.csv
Cell 55


title: Patient_38_AN_m0


title: mCN_LSD1_shRNA_B_DLAR_BRUSEQ_rep2

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

description: anti-BrdU enriched RNA

data_processing:
Library strategy: Bru-Seq
Full length reads were mapped to mm9 using TopHat2 (v2.1.0) with Bowtie2 (v2.2.6)
Adaptor sequence was trimmed off from unmapped reads.
Adaptor-trimmed unmapped reads were mapped again
Reads from both alignments were merged
BAM Files were converted to Bigwig files in a strand specific manner. Bigwigs were normalized to 10 million non-rRNA and non-mitochondrial reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to 10 million non-rRNA non-mtRNA reads.

source_name: E16.5 mouse embryonic cortex

growth_protocol: Cortices from E16.5 male mouse embryos were collected in HHGN dissection solution (Hanks' Balanced Salt Solution supplemented with 2.5 mM Hepes, 35 mM Glucose, 4 mM sodium bicarbonate). Cortices were incubated with 0.1% trypsin (Life Technologies) in HHGN for 20 min. at room temperature, quenched in Neurobasal media (Life Technologies) containing 10% fetal bovine serum (FBS), and triturated in Neurobasal media containing 0.01 mg/ml DNaseI.  Dissociated cells were suspended in Neurobasal media supplemented with 1x B27 solution (Life Technologies), 1x penicillin-streptomycin , 0.5 mM L-glutamine, and 25 mM 2-mercaptoethanol. Cells from one cortex were plated in a 10-cm tissue culture dish treated with 50 mg/ml Poly-D-lysine hydrobromide (Sigma, MW 30,000-70,000). Cultured are maintained in humidified incubators with 5% CO2 at 37°C. Half of culture media was replaced with new culture media every 3 days in vitro (DIV).

extract_protocol:
Nuclei in Trizol were homogenized with a qiashredder.
Direct ligation of 3' adaptors to RNA and cDNA (DLAR). 3' adaptor ligation to the fragmented RNA followed by anti-BrdU enrichment and reverse transcription. Second adaptor ligation to 3' of cDNA.
Purified RNA was fragmented and reverse adaptor was ligated to the 3' end of RNA. BrU containing RNA were enriched and reverse transcribed. After treatment with RNAses to remove hybrid RNA, splinted forward adaptor was ligated to the 3' ends of cDNA. Libraries were amplified by PCR.

treatment_protocol: Lentiviral delivery of shRNA on DIV 7 and incubation with 2mM Bromouridine on DIV 11.

tag: strain

tag: strain of origin

value: 11 days in vitro

tag: shRNA

value: Lsd1 shRNA B on DIV 7

tag: Sex

value: male


title: mCN_LSD1_shRNA_B_DLAR_BRUSEQ_rep1

description: anti-BrdU enriched RNA


title: mCN_LSD1_shRNA_A_DLAR_BRUSEQ_rep1

description: anti-BrdU enriched RNA

value: Lsd1 shRNA A on DIV 7


title: Control_rep2

description: processed data file: Processed_file.txt


title: A06_2

description:
Fluidigm_2_expression_matrix.csv
Cell 53


title: 13_Control, acute T. muris mouse

description: Tmuris 1


title: Patient_37_AN_m0

city: Tampere

tag: patient id

tag: disease state

tag: timepoint

value: baseline (m0)

value: skin


title: mCN_LSD1_shRNA_A_DLAR_BRUSEQ_rep2

description: anti-BrdU enriched RNA


title: A07_2

description:
Fluidigm_2_expression_matrix.csv
Cell 54


title: Patient_38_AL_m0


title: Patient_37_AL_m0


title: Patient_36_AN_m0


title: mCN_control_shRNA_DLAR_BRUSEQ_rep2

description: anti-BrdU enriched RNA

value: Control shRNA on DIV 7


title: A02_2

description:
Fluidigm_2_expression_matrix.csv
Cell 51


title: A01_2

description:
Fluidigm_2_expression_matrix.csv
Cell 50


title: mCN_control_shRNA_DLAR_BRUSEQ_rep1

description: anti-BrdU enriched RNA


title: Patient_39_AL_m0


title: 10_Inulin, uninfected mouse

description: Inulin 4

source_name: Mouse inulin diet, uninfected

value: Caecum

value: Uninfected


title: 11_Inulin, uninfected mouse

description: Inulin 5

value: Inulin-supplemented


title: 12_Inulin, uninfected mouse

description: Inulin 6


title: 6_Control, uninfected mouse

description: Control 6

source_name: Mouse control diet, uninfected


title: 8_Inulin, uninfected mouse

description: Inulin 2


title: Patient_36_AL_m0


title: 7_Inulin, uninfected mouse

description: Inulin 1


title: Patient_35_AN_m0


title: mCN_Untreated_DLAR_BRUSEQ_rep2

description: anti-BrdU enriched RNA

value: No shRNA Treatment


title: A05_2

description:
Fluidigm_2_expression_matrix.csv
Cell 52


title: mCN_Untreated_DLAR_BRUSEQ_rep1

description: anti-BrdU enriched RNA


title: 4_Control, uninfected mouse

description: Control 4


title: H08_1

description:
Fluidigm_1_expression_matrix.csv
Cell 48


title: H07_1

description:
Fluidigm_1_expression_matrix.csv
Cell 47


title: 5_Control, uninfected mouse

description: Control 5


title: 9_Inulin, uninfected mouse

description: Inulin 3


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_smoldering ATL_2

city: Saga

first: Tatsuro

last: Watanabe

address: 5-1-1 Nabeshima, Saga

institute: Saga University

description:
S2_N
Clinical specimen, T-cells

data_processing:
Genome Studio software (V2011.1 Methylation module 1.9.0) was used. Beta values were obtained after background correction and normalization to internal controls.
The GSE136189_GPL13534_beta_and_raw_data.txt and GSE136189_GPL23976_beta_and_raw_data.txt files include normalized Beta values, unmethylated signal intensities, methylated signal intensitites, and detection p-values.

source_name: T-cell 40

growth_protocol: RPMI-1640 containing 10% FBS and Pen/Str was used for T-cell lines.

extract_protocol: Genomic DNA samples were isolated using QIAamp DNA Kit (Qiagen).

tag: diagnosis

value: Smoldering ATL

tag: cell type

value: T cells

tag: gender

value: Male

tag: age

tag: wbc (/ul)

tag: lym (%)

tag: abn. lym (%)

tag: sil-2r (u/ml)

value: No Data


title: Patient_35_AL_m0

value: atopic dermatitis

tag: tissue


title: 15580X4 Cornea rep4

city: Loma Linda

first: Hironori

last: Uehara

state: California

address: 11021 Campus st

department: Ophthalmology

institute: Loma Linda University

description: One month post Ad-Cas9-Col8a2gRNA injection

data_processing:
Fastq files were loaded into Galaxy (https://galaxyproject.org/).
The sequences having CTTCTCCCTG and CTGCCTTCGC were extracted using the Select feature,
The number of bases between CTTCTCCCTG and CTGCCTTCGC were counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: 15580R_IndelRate_MsCornealEndothelium.xlsx

source_name: Corneal Endothelium

extract_protocol:
Genomic DNA from the corneal endothelium/stroma was purified by Quick-DNA Microprep Plus Kit (Zymo research).
PCRs were performed on the locus using TTCTTCTTCTCCCTGCAGCC and GCACATACTTTACCGGGGCA (30 cycles, the product size: 155bp).  The deep sequencing was performed by the HSC core at University of Utah. The library was prepared using the Swift Biosciences Accel-NGS 1S Plus DNA Library Kit.
The sequence protocol used MiSeq Nano 150 Cycle Paired End Sequencing v2.

treatment_protocol: Intracameral injection of Ad-Cas9-Col8a2gRNA

value: Corneal Endothelium


title: Patient_34_AL_m0


title: 15580X3 Cornea rep3


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_smoldering ATL_2

description:
S2_D
Clinical specimen, T-cells

source_name: T-cell 39


title: Patient_34_AN_m0


title: H06_1

description:
Fluidigm_1_expression_matrix.csv
Cell 46

tag: passage


title: 15580X1 Cornea rep1

tag: strain


title: H05_1

description:
Fluidigm_1_expression_matrix.csv
Cell 45


title: H04_1

description:
Fluidigm_1_expression_matrix.csv
Cell 44


title: 3_Control, uninfected mouse

description: Control 3

tag: strain/background

tag: diet

value: Control

tag: infection


title: Patient_33_AL_m0

tag: patient id


title: H09_1

description:
Fluidigm_1_expression_matrix.csv
Cell 49


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_smoldering ATL_2

description:
S2_P
Clinical specimen, T-cells

source_name: T-cell 38


title: Patient_33_AN_m0

tag: disease state


title: T-cells_(CD3+/CD4+/CD7-/CADM1+)_smoldering ATL_1

description:
S1_N
Clinical specimen, T-cells

source_name: T-cell 37

value: Female


title: 2_Control, uninfected mouse

description: Control 2


title: H03_1

description:
Fluidigm_1_expression_matrix.csv
Cell 43


title: Patient_32_AL_m0

tag: timepoint


title: T-cells_(CD3+/CD4+/CD7dimly+/CADM1+)_smoldering ATL_1

description:
S1_D
Clinical specimen, T-cells

source_name: T-cell 36

tag: diagnosis


title: 15580X2 Cornea rep2


title: H02_1

description:
Fluidigm_1_expression_matrix.csv
Cell 42


title: T-cells_(CD3+/CD4+/CD7+/CADM1-)_smoldering ATL_1

description:
S1_P
Clinical specimen, T-cells

source_name: T-cell 35

tag: cell type


title: Patient_32_AN_m0


title: Patient_31_AN_m0


title: G08_1

description:
Fluidigm_1_expression_matrix.csv
Cell 40


title: Patient_30_AN_m0


title: G06_1

description:
Fluidigm_1_expression_matrix.csv
Cell 38


title: 1_Control, uninfected mouse

description: Control 1


title: Patient_30_AL_m0


title: G05_1

description:
Fluidigm_1_expression_matrix.csv
Cell 37


title: Patient_29_AN_m0


title: Patient_29_AL_m0


title: G09_1

description:
Fluidigm_1_expression_matrix.csv
Cell 41


title: Patient_31_AL_m0


title: pCTSH1 cells, 6h, replicate 3

city: Gentofte

first: Flemming

last: Pociot

address: Niels Steensens Vej 2

department: T1D Biology

institute: Steno Diabetes Center Copenhagen

hyb_protocol: A total of 7.5 µg of labeled cRNA was fragmented, and a hybridization cocktail was prepared, plated, and loaded into an Affymetrix GeneTitan system. Hybridization was performed for 16h on HT Rat230+PM microarrays. The GeneTitan system was used to perform the microarray hybridization, washing, and scanning.

scan_protocol: Image acquisition and quantification were performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Cel files were read into an AffyBatch object, quantile normalized and corrected for background using RMA background correction in the affy package in R statistical environment. Differential expression analysis was carried out on non-control probes with an empirical Bayes approach using LIMMA package in R. Principal Component Analysis (PCA) method was employed for the initial interpretation of the data. P-values were adjusted for multiple comparisons using the FDR correction. Differentially expressed genes were identified using the double-filtering criterion: FDR-adjusted p-value < 0.05 and an absolute log2 fold change > 1.2. For transcripts targeted by more than one probe only those probes that were changing in the same direction and the probes with highest fold change values were retained for further analysis.

source_name: INS1 cells, transfected with pCTSH vector, treated with IL-1β and IFNγ for 6 hours

label_protocol: Briefly, double-stranded cDNA was synthesized for each of the 21 samples from 100ng of total RNA, and biotin-labeled cRNA was transcribed using the IVT Express Kit (Affymetrix, Santa Clara, California).

growth_protocol: The generation of INS-1 cells stably transfected with a plasmid encoding CTSH (pCTSH) or an empty control vector (pcDNA) has been described previously (Floyel et al. PNAS 2014). Untransfected INS-1 cells, pcDNA cells, and two CTSH-overexpressing clones (pCTSH#1, pCTSH#2) were cultured as previously described (Floyel et al. PNAS 2014).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA quantity and purity was determined by UV absorbance using a NanoDrop 2000 (Thermo Scientific) and the RNA integrity was evaluated using the 2100 Bioanalyzer RNA 6000 Nanochips (Agilent Technologies, CA, USA). All samples had RNA Integrity Number (RIN) above 8.5.

treatment_protocol: Cells were seeded in 12-well culture plates (0.25x106 cells/well) and precultured for 3 days before exposure to 150 pg/ml recombinant mouse IL-1β (BD Pharmingen) and 5 ng/ml recombinant rat IFNγ (R&D Systems) for 0, 6, and 16 hours.

tag: cell line

value: Rat insulin secreting INS1 cells

tag: treatment


title: F07_1

description:
Fluidigm_1_expression_matrix.csv
Cell 35

extract_protocol:
RMECs were isolated from bovine retinas according to (Stitt, Chakravarthy, Archer, & Gardiner, 1995). RMECs were maintained in DMEM supplemented with 0.1mg/ml Primocin, 0.38μg/ml insulin, 1mg/ml heparin and 10% (v/v) porcine serum (PS). BRECs were passaged at approximately 80% confluency in a 1:3 ratio and grown until confluency at passage 3 for Fluidigm C1 runs . RMECs were dissociated form flask using TryPLE Express dissociation reagent and single cells were captured on Fluidigm C1 Microfluidics chip.
Clontech modified Illumina® Nextera® XT DNA sample preparation protocol was used for single-cell mRNA sequencing library preparation from cDNA acquired using the C1 system which was miniaturised using the Labcyte Access Robotic System in conjunction with Echo 525 Acoustic Dispenser


title: pcDNA cells, 6h, replicate 3

source_name: INS1 cells, transfected with empty pcDNA vector, treated with IL-1β and IFNγ for 6 hours


title: G07_1

description:
Fluidigm_1_expression_matrix.csv
Cell 39


title: Patient_28_AN_m0


title: pCTSH1 cells, 0h, replicate 3

source_name: INS1 cells, transfected with pCTSH vector, no treatment


title: pcDNA cells, 0h, replicate 3

source_name: INS1 cells, transfected with empty pcDNA vector, no treatment


title: pcDNA cells, 16h, replicate 3

source_name: INS1 cells, transfected with empty pcDNA vector, treated with IL-1β and IFNγ for 16 hours


title: pCTSH1 cells, 16h, replicate 2

source_name: INS1 cells, transfected with pCTSH vector, treated with IL-1β and IFNγ for 16 hours


title: F04_1

description:
Fluidigm_1_expression_matrix.csv
Cell 34

source_name: Retinal microvascular endothelial cells


title: INS1 cells, 0h, replicate 3

source_name: INS1 cells, no treatment

value: no treatment


title: day 0 lung, Vit D deficient mother replicate 2

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

description: RMA expression value derived from Expression Console software; gene level (SST-RMA) analysis

hyb_protocol: Samples were hybridized with Clariom D Rat Arrays (also known as the GeneChip Rat Transcriptome Array 1.0, ThermoFisher) and scanned at the University of Colorado Anschutz Medical Campus Microarray and Genomics Core Facility. Samples were hybridized for 16 hours at 4°C.  cRNA was purified and 15 ug cRNA product was added to prepare 2nd-cycle single-stranded cDNA (ss-cDNA) synthesis by reverse transcription of cRNA.  RNase H was added to remove template RNA. 5ug purified ss-cDNA was obtained for fragmentation.  UDG and APE 1 were added to break the DNA strand.  The fragmented cDNA was labeled with TdT and biotinylated labeling reagents.  5.2 ug (in 60µl) of fragmented and biotinylated ss-cDNA was added to 160 µl hybridization master mix.  The hybridization cocktails were heated at 99° for 5 minutes and 45°C before injecting 200 µl into the Clariom D Rat array.  The arrays were incubated in the GeneChip Hybridization Oven 640 and rotated at 60 rpm for 16 hours at 45°C.  Immediately after the completion of hybridization, the arrays were stained and washed using GeneChip Hybridization, wash, and stain kit (Thermo Fisher Scientific REF 901240) and GeneChip Fluidics Station 450. Array was scanned using GeneChip Scanner 3000 7G.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA Normalization was done using RMA express (http://rmaexpress.bmbolstad.com/).  The full list of 68,842 RMA normalized probesets is provided with this submission.   This list was reduced to 22,133 by removing probesets that had no annotation, were annotated to ESTs, or were annotatated to non coding RNAs.  Differential gene expression was determined using Significance Analysis of Microarrays in BRB Array Tools v 4.5.1. and the following settings: exclude genes with log-ratio variation < 50%; 500 permutations; FDR = 5%, and 90% false negative rate (type II error). 11066 probesets met the exclusion criteria.  Following statistical analysis, probesets that represented duplicate analysis of genes were removed to create the final results (this list is provided with the submission).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = RTA-1_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: newborn pup from vitamin D deficient mother

label_protocol: Samples were prepared according to the standard GeneChip Whole Transcript Expression protocol.  In the reverse transcription procedure, high quality total RNA was primed with primers containing a T7 promoter sequence.  The reaction synthesized first-strand cDNA with T7 promoter sequence at the 5’ end. The second –strand cDNA was synthesized using DNA polymerase and RNAase H.  The second-strand cDNA was converted to double-stranded cDNA, which acted as a template for in vitro transcription.

growth_protocol: The whole lungs of offspring from vitamin D adequate or vitamin D deficent mothers were harvested on day of life 1.

extract_protocol: Lung tissue was homogenized in TRIzol reagent (Invitrogen) using a PowerGen 500 homogenizer (Fisher Scientific). Total RNA was extracted using the Qiagen miRNeasy Mini Kit as per the manufacturer’s instructions.

tag: maternal status

value: vitamin D deficient mother

tag: age

value: day 0 newborn

value: lung


title: day 0 lung, Vit D deficient mother replicate 4


title: day 0 lung, Vit D deficient mother replicate 3


title: pCTSH1 cells, 16h, replicate 3

value: transfected with pCTSH vector, treated with IL-1β and IFNγ for 16 hours


title: Patient_28_AL_m0

value: baseline (m0)

value: skin


title: day 0 lung, control, replicate 4

source_name: newborn pup from vitamin D adequate mother

value: vitamin D adequate mother


title: F08_1

first: David

last: Simpson

institute: Queen's University Belfast

description:
Fluidigm_1_expression_matrix.csv
Cell 36

data_processing:
Base call files were generated on board the nextseq 500 sequencer using real time analysis (RTA) and then converted to fastq format post-run using bcl2fastq2 in BaseSpace which also removed illumina adapters
Sequencing QC was assessed using Fastqc (v0.11.3) to ensure good quality sequencing and that adapters were successfully removed
Sequenced reads (fastq format) were  aligned to bovine genome UMD3.1 (Bos Tau4) using STAR (v2.5.3a) with default settings
Alignment QC was assessed using multiQC
Gene counts calculated using HTseq (v0.6.1p1) with default settings
Created expression matrix from HTseq output
Genome_build: UMD 3.1 (bos Tau4)
Supplementary_files_format_and_content: csv files with expression matrices created from HTseq output with genes in rows and single cells in columns


title: F02_1

description:
Fluidigm_1_expression_matrix.csv
Cell 33


title: Patient_27_AL_m0