title: NEUROG3-HA-P2A-Venus - H3K4me3_CR

value: 18,000 freshly sorted Venus+ cells

value: H3K4me3 (Diagenode,PAb 003-05)


title: UN rep2 [A-46]

status: Public on Aug 04 2021

type: SRA

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

country: Canada

institute: University of British Columbia

description:
A-46_S4
10x v2

library_source: transcriptomic

data_processing:
Reads were aligned using Cellranger v.2.2.0
Exon and intron counts were tabulated using Velocyto
Data were analyzed using Seurat v3
Genome_build: mm10-1.2.0 (GRCm38.93)
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each cell with tab delimeters

molecule: total RNA

organism: Mus musculus

source_name: control_Lumbar spinal cord

extract_protocol:
Single nucleus dissociation was completed with a modified protocol based on our previous work. Briefly, animals were euthanized by isoflurane inhalation and cervical dislocation. The lumbar spinal cord was rapidly dissected and frozen on dry ice. Spinal cords were dounced in 500 µl sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg-acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was added and filtered through a µm cell strainer. The lysate was subsequently centrifuged at 3200 g for 10 min at 4°C. The supernatant was decanted, and 3 mL of sucrose buffer added to the pellet and incubated for 1 min. The pellet was homogenized using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg-acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant immediately poured off. The nuclei on the bottom half of the tube wall were collected with 100 µl PBS with 0.04% BSA and 0.2 U/µl RNase inhibitor. Resuspended nuclei were filtered through a 30 µm strainer. The nuclei suspension was finally adjusted to 1000 nuclei/µl.
Library preparation was carried out with 10X Genomics Chromium Single Cell Kit Version 2. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 5000. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed.

tag: strain

tag: genotype

value: wild type

tag: condition

value: uninjured control

tag: tissue

value: Lumbar spinal cord


title: SCI rep1 [F-12]

description:
F-12_S1
10x v2

source_name: SCI_Lumbar spinal cord

value: SCI (severe contusion of the thoracic spinal cord)


title: Total RNA from primary myoblasts CP5

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

country: USA

institute: Northwestern University & Rehabilitation Institute of Chicago

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC. Adapters were trimmed and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the human genome (hg19) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg19 obtained from UCSC (University of California Santa Cruz; http://genome.ucsc.edu)
Normalization was determined using DESeq2
After normalization, the Statistics and Machine Learning Toolbox function anova2 in MATLAB was used to perform a two-way analysis of variance (ANOVA) of RNA-seq data to identify differentially regulated transcripts in CP and TD myoblasts (cell group effect), treated and non-treated with AZA (treatment effect).
Genome_build: human genome (hg19)
Supplementary_files_format_and_content: RNA_SEQ reads_normalized.csv

organism: Homo sapiens

source_name: From contractured muscle in a child with cerebral palsy

growth_protocol: Satellite cell-derived myoblasts were cultured at 37°C in a 5% CO2 atmosphere using a high-serum medium containing Ham’s F10 (Corning) with 20% Fetal Bovine Serum (FBS, from Gibco), 10 mg/ml streptomycin and 100 units/ml penicillin (Gibco) and human recombinant bFGF (5 ng/ml) (BD). Myoblasts were seeded at ~5,000 cells/cm2 and were maintained in the same high-serum medium up to 20-30% of confluence before 5-azacytidine (AZA) treatment. Cells were treated with AZA (5 μM) (Sigma-Aldrich) for 24 hours to induce DNA demethylation, or not treated with AZA as a control. After 24h, the AZA-containing medium was removed, cells were rinsed twice with high-serum medium and then cultured until they reached 70-80% confluence in high-serum medium before RNA extraction.

extract_protocol:
Total RNA was isolated and purified from 70-80% confluent myoblast cell culture preparations (passage 4) using Trizol reagent (Ambion - Life Technologies) and a Qiagen RNeasy Mini Kit according to manufacturer's recommendations.
Total RNA examples were checked for quality using RINs generated from Agilent Bioanalyzer 2100. RNA quantity was determined using a Qubit fluorometer. The Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 1 ug of high-quality RNA samples (RIN>7). The Kit procedure was performed without modifications. This procedure included mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation. An IlluminaIllumina  NextSeq 500 sequencer was used to sequence the libraries with the production of single-end, 75 bp reads at the depth of 20-25 M reads per sample.

treatment_protocol: Cells were treated with AZA (5 μM) (Sigma-Aldrich) for 24 hours to induce DNA demethylation, or not treated with AZA as a control. After 24h, the AZA-containing medium was removed, cells were rinsed twice with high-serum medium and then cultured until they reached 70-80% confluence in high-serum medium before DNA extraction.

tag: gmfcs scale

tag: limbs

value: Quadriplegic

tag: gender

value: Female

tag: age

value: Hamstring muscle biopsy

tag: cell type

value: primary myoblasts

value: contractured cerebral palsy (CP)

tag: treatment

value: control


title: Total RNA from primary myoblasts CP2_AZA

source_name: From contractured muscle in a child with cerebral palsy, treated with 5-azacytidine

value: Diplegic

value: Male

value: AZA


title: NEUROG3-HA-P2A-Venus-positive#0

city: Illkirch

first: Valerie

last: SCHREIBER

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were identified and mapped onto the hg38 assembly of the human genome using STAR version 2.7.5a
Quantification of gene expression was performed using HTSeq version 0.6.1 and gene annotations from Ensembl release 98.
Normalization of read counts and differential expression analysis between Venus-negative and Venus-positive samples were performed using the method implemented in the DESeq2 Bioconductor library version 1.16.1
A negative binomial GLM fit, having the condition as variable, and a Wald significance test were implemented for the differential expression analysis. Differentially expressed genes were defined as those having a Benjamini – Hochberg-adjusted Wald test P < 0.05 and a log2 Fold-Change greater than 1
Genome_build: hg38
Supplementary_files_format_and_content: Excel file showing the genes differentially expressed between NEUROG3-Venus positive and negative hiPSC line differentiated to pancreatic endocrine progenitors

molecule: polyA RNA

source_name: Venus-positive sorted pancreatic endocrine progenitors

growth_protocol: Cells were seeded at 3x10e5 cells/cm2 on Growth Factor Reduced Matrigel (Corning)-coated 24wells in mTESR1 + 5µM Y27632 (Stem Cell Technologies). Differentiation was initiated 24 hours after and performed following exactly the protocol described by Petersen et al, Stem cell reports:1-37 (2017) until the end of Stage 5 (day 13).

extract_protocol:
Total RNA was prepared with RNeasy micro kit (Qiagen).
Full length cDNA were generated from 2 ng of total RNA using SMART-SeqX v4 UltraX Low Input RNA Kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, USA) followed by 12 cycles of library amplification. Following purification with SPRIselect beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: At day 13 of differentiation, cells were harvested with TrypLE Select (Life Technologies), quenched with 3 volumes of MCDB131-3 medium (Petersen et al (2017) Stem cell reports:1-37)  containing 5 mM Y27632 , centrifuged 4 min at 200g, resuspended at 5M/ml in MCDB131-3 medium containing 5 mM Y27632 and sorted using a FACS Fusion/Aria in 350 µl RLT buffer (RNeasy micro kit, Qiagen).

tag: differentiation stage

value: hiPSC derived pancreatic endocrine progenitors, end of stage 5 (day 13)

tag: differentiation

value: Differentiation #29

tag: number of cells

value: 20,000 sorted Venus-positive cells


title: NEUROG3-HA-P2A-Venus - NEUROG3_CR

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were trimmed using cutadapt v1.9.1 with option: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -m 5 -e 0.1
Paired-end reads were mapped to Homo Sapiens genome (assembly hg38) using Bowtie2 (release 2.3.4.3, parameter: -N 1 -X 1000)
Reads overlapping with ENCODE hg38 blacklisted region V2 were removed using Bedtools
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig tracks were generated using bamCoverage from deepTools for ≤120 bp and ≥150 bp fragments separately. Tracks were normalized with RPKM method. The bin size is 20. ≤120 bp fragments for samples VLSR27, VLSR28, VLSR29. ≥150 bp fragments for samples VLSR32, VLSR41, VLSR44.

molecule: genomic DNA

source_name: Venus+-sorted pancreatic endocrine progenitors

growth_protocol: Cells were seeded at 3x10e5 cells/cm2 on Growth Factor Reduced Matrigel (Corning)-coated 24wells- or 6wells-plates (CellBind Corning) in mTESR1 + 5µM Y27632 (Stem Cell Technologies). Differentiation was initiated 24 hours after and performed following exactly the protocol described by Petersen et al, Stem cell reports:1-37 (2017) until the end of Stage 5 (day 13).

extract_protocol:
We followed the protocol of Hainer and Fazzio (2019) Current Protocols 126 (1):e85 (2019) with minor modifications. Fresh or thawed cells were washed once with 1mL cold PBS and resuspended in nuclear extraction buffer (NE, 20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% Triton X-100, 20% glycerol, freshly added protease inhibitors)). After 3 min spinning at 4°C at 600g, cells were resuspended in 600 μL NE buffer. Concanavalin A beads (Polysciences, 25 μL bead slurry/sample) were washed twice with ice-cold Binding buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and resuspended in 300 μL Binding buffer. Nuclei were added to beads with gentle vortexing and incubated for 10 min at 4°C with gentle rocking. Bead-bound nuclei were blocked with 1 mL cold Blocking buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, 2mM EDTA, freshly added protease inhibitors) by gentle pipetting, incubated 5 min at RT and washed in 1mL cold Wash buffer (WB, 20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, freshly added protease inhibitors) and resuspended in 250 μL cold WB. 250 μL of primary antibody diluted 1:100 in cold WB were added with gentle vortexing, and samples were incubated overnight with gentle rocking at 4°C. Samples were washed twice in 1 mL cold WB, and resuspended in 250 μL cold WB. When indicated, incubation with a secondary antibody (Donkey anti Sheep IgG, 1:200) was performed for 1h at 4°C in WB under gentle rocking. After 2 washes with 1 ml WB, and resuspension in 250 μl WB, 200 μL of pA-MN (diluted at 1.4 ng/mL in cold WB, in-house production using the pK19pA-MN plasmid, obtained from Ulrich Laemmli (Addgene plasmid # 86973; http://n2t.net/addgene:86973 ; RRID:Addgene_86973) was added with gentle vortexing, and samples were incubated with rotation at 4°C for 1 hour. Samples were washed twice in 1 mL cold WB and resuspended in 150 μL cold WB. Three μL of 100 mM CaCl2 was added upon gentle vortexing to activate the MN. After 30 min of digestion, reactions were stopped by addition of 150 μL 2XSTOP buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/mL RNaseA, 40ug/mL glycogen) and DNA fragments were released by passive diffusion during incubation at 37°C for 20 min. After centrifugation for 5 min at 16,000g at +4°C to pellet cells and beads, 3 μL 10% SDS and 2.5 μL Proteinase K 20mg/ml were added to the supernatents, and samples were incubated 10 min at 70°C. DNA purification was done with phenol/chloroform/isoamyl alcohol extraction followed by chloroform extraction using MaxTract tubes (Qiagen). DNA was precipitated with ethanol after addition of 20 µg glycogene, and resuspended in 25µl 0.1XTE.
Illumina sequencing libraries were prepared at the Genomeast facility (IGBMC, Illkirch). CUT&RUN samples were purified using Agencourt SPRIselect beads (Beckman-Coulter). Libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (Diagenode) following the manufacturer's protocol with some modifications. Illumina compatible indexes were added through a PCR amplification (3 min at 72°C, 2 min at 85°C, 2 min at 98°C; [20 sec at 98°C, 10 sec at 60°C] x 13 cycles). Amplified libraries were purified and size-selected using Agencourt SPRIselect beads (Beckman Coulter) by applying the following ratio: volume of beads / volume of libraries = 1,4 / 1. The libraries were sequenced on Hiseq 4000 as Paired-End 2x100 base reads following Illumina’s instructions.

treatment_protocol: At day 13 of differentiation, cells were harvested with TrypLE Select (Life Technologies), quenched with 3 volumes of MCDB131-3 medium (Petersen et al (2017) Stem cell reports:1-37)  containing 5 mM Y27632 , centrifuged 4 min at 200g, resuspended at 5M/ml in MCDB131-3 medium containing 5 mM Y27632 and sorted using a FACS Fusion/Aria in the same medium, at +4°C. Sorted cells were either used directly for CUT&RUN or cryostored in Cryostor10 (Stem Cell Technologies) at -80°C until use.

tag: cell line

tag: cell number

value: 75,000 freshly sorted Venus+ cells

tag: cut&run antibodies (primary)

value: Sheep anti NGN3 (R&D Systems, AF2765) + Donkey anti Sheep-Alexa Fluor-488 (Jackson ImmunoRes, 713-545-147)


title: Total RNA from primary myoblasts CP5_AZA


title: NEUROG3-HA-P2A-Venus - HA_CR

value: Rabbit anti HA (Abcam, ab9110)


title: NEUROG3-HA-P2A-Venus-positive#4

value: Differentiation #30

value: 3,900 sorted Venus-positive cells


title: Total RNA from primary myoblasts TD8

source_name: From typically developing muscle (control)

value: typically developing (TD) control


title: Total RNA from primary myoblasts TD8_AZA

source_name: From typically developing muscle (control), treated with 5-azacytidine

value: Female


title: NEUROG3-HA-P2A-Venus-positive#2

value: 8,000 sorted Venus-positive cells


title: SCI rep3 [F-14]

description:
F-14_S9
10x v2

value: wild type

value: SCI (severe contusion of the thoracic spinal cord)

value: Lumbar spinal cord


title: Total RNA from primary myoblasts CP1_AZA

value: Quadriplegic

value: Hamstring muscle biopsy

value: primary myoblasts

value: contractured cerebral palsy (CP)


title: Total RNA from primary myoblasts TD1

value: Male

value: control


title: NEUROG3-HA-P2A-Venus-negative#2

source_name: Venus-negative sorted pancreatic endocrine progenitors

value: hiPSC derived pancreatic endocrine progenitors, end of stage 5 (day 13)

value: 100,000 sorted Venus-negative cells


title: MMS mem1 rep1

city: Nanjing

first: gui

middle: Hong

last: La

address: XuanWu

country: China

institute: Nanjing Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using hisat2 version 2.1.0
Reads counts were calculated using featureCounts version 1.6.3
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: the whole plant

growth_protocol: soil,16 hour light, 8 hour dark cycle

extract_protocol:
10-day-old seeding of mem1-1 mutant and Col-0 plants were grown in soil
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mem1 mutant and Col-0 1 under normal and 200ppm MMS treatment conditions, respectively

tag: cultivar

value: Col

value: 10-day-old seeding

tag: agent

value: 200ppm MMS


title: NEUROG3-HA-P2A-Venus - H3K27me3_CR

value: 15,000 frozen Venus+ sorted cells

value: H3K27me3 (Millipore, 07-449)


title: Total RNA from primary myoblasts CP6

value: Diplegic


title: Total RNA from primary myoblasts TD1_AZA

value: typically developing (TD) control

value: AZA


title: MMS mem1 rep2

tag: genotype


title: Total RNA from primary myoblasts TD2_AZA

tag: condition


title: Total RNA from primary myoblasts CP1

tag: tissue


title: MMS wildtype rep2

value: wild type


title: Total RNA from primary myoblasts TD2

tag: gmfcs scale


title: THP1_sgIRF8_2_Rep2.txt

city: Cold Spring Harbor, Syosset

first: Chrsitopher

last: Vakoc

state: NEW YORK

address: 1 Bungtown Rd

institute: CSHL

data_processing:
Raw sequence files were mapped to reference human genome hg38 using Tophat2, Cuffdiff was used to analyzed dfferentially expressed genes with structural RNAs maked, and normalized to total mapped reads.
Genome_build: hg38
Supplementary_files_format_and_content: txt, normalized RPKM

source_name: leukemia cell line

growth_protocol: MOLM13, MV4-11 and THP1 were grown at RPMI-1640 supplemented with 10% FBS, OCI-AML3 was cultured under alpha-MEM plus 20% FBS.

extract_protocol:
TRIzol was used to extract total RNA according manufacture's protocol. RNA-seq library was contructed using Illumina TruSeq sample prep kit V2.Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.
Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: All cells were infected with lentivirus expressing sgROS, sgIRF8_1 and sgIRF8_2 with two replicates, samples were collected 4 days post infection.

tag: post infection

value: day 4 after infection


title: Total RNA from primary myoblasts TD5_AZA

tag: limbs

tag: gender

value: Hamstring muscle biopsy


title: THP1_sgROSA_Rep2.txt

value: sgROSA


title: Control mem1 rep2

tag: age

value: Control


title: THP1_sgIRF8_1_Rep2.txt

tag: treatment


title: Total RNA from primary myoblasts TD5

value: Male

tag: cell type

value: primary myoblasts


title: THP1_sgIRF8_1_Rep1.txt


title: Control wildtype rep2


title: MMS wildtype rep1


title: 2429_cerebellum_male_ethanol

city: Bryan

first: Rajesh

last: Miranda

state: Texas

address: 8441 Riverside Pkwy

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University School of Medicine

description: 2429 cbl

data_processing:
Trimmomatic read trimmer was used to evaluate and trim all adapter sequences and low quality bases. Reads were scanned with a sliding window of 5, cutting when the average quality per base drops below 20, then trimming reads at the beginning and end if base quality drops below 25, and then if the read length is less than 35.
HISAT2 was used for read mapping
HTSeq generated transcript-wise counts
DESeq2 was used for normalizing counts, calculating fold change, and initial differential analysis. In order to perform sex x treatment analysis, we used the DESeq2 normalized counts and ran multiple 2-way ANOVAs with subsequent FDR correction.
Genome_build: mm10
Supplementary_files_format_and_content: htseq-count_refGene_on_*tabular: raw counts

source_name: Brain

growth_protocol: Adult C57BL/6J mice were purchased from The Jackson Laboratory and a breeding colony was established to produce neonates for experiments.

extract_protocol:
On P10, 24 hours following the final E or V treatment, animals were anesthized using isoflurane vapor, transcardially perfused with phosphate buffered saline containing 5 U/mL heparin, brains were removed, and the hippocampus and cerebellum were microdissected, flash frozen in liquid nitrogen, and stored at -80 degrees Celcius. Hippocampus and cerebellum were homogenized according to manufacturer specification using a Next Advance BBX24B Bullet Blender homogenizer and 0.5 mm glass beads.  RNA was isolated using the Qiagen RNeasy Mini Kit plus on-column DNase Removal Kit.
RNA quantity was assessed using the Qubit 3.0 fluorometer with the Qubit Broad-Range RNA Assay Kit and an Agilent Fragment Analyzer with the Standard Sensitivity RNA Gel Kit was used to assess RNA quality.  All samples had an RNA Quality No. ≥ 8.9 (Mean 9.7, Median 10.0).  RNA-seq libraries were prepared using the Illumina TruSeq mRNA Library Prep Kit with TruSeq Unique Dual Indexed adapters and were quantified with the Qubit 1X dsDNA High-Sensitivity NGS Gel Kit.  Libraries were further characterized for functionality with the KAPA Library Quantification Kit and for fragment size using the Agilent Fragment Analyzer with the High-Sensitivity NGS Gel Kit.  Library molarities were calculated followed by dilution and denaturation all according to manufacturer’s specification for clustering.  An initial set of n = 5V and 5E were clustered on a cBot and paired-end sequenced on a HiSeq 3000 with a 150-cycle SBS kit for 2X75 reads.  A supplemental set of n = 2V and 2E were clustered on a high-output NextSeq 500 flow cell and paired-end sequenced with a 150-cycle SBS kit for 2X75 reads.

treatment_protocol: Experimental neonates were distributed between treatment groups, ethanol (E) or vehicle control (V) and were separated according to sex as evenly as possible over multiple litters. On P4-9 intragastric gavage was utilized to administer ethanol at 4g/kg/day in 20% Intralipid  or 20% Intralipid vehicle equivalent alone.

tag: strain

value: Cerebellum

value: Postnatal Day 10

value: Ethanol

tag: Sex

value: male


title: 2524_cerebellum_male_ethanol

description: 2524 cbl


title: SMAD3_CPC_SMC

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

data_processing:
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were aligned to the human genome and transcriptome annotation (GRCh38) using STAR v.2.5 with parameters --sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted. Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix.txt files contain the gene expression profiles in each sample.
Supplementary_files_format_and_content: Cell_barcodes.txt files contain the ordered cell barcodes for each cell in the gene expression matrix.

source_name: CPC-SMC

extract_protocol:
mRNA molecules were captured using bead-bound oligo dT(30).
Captured mRNA molecules were reverse transcribed with template switching to obtain cDNA. cDNA was amplified by PCR reactions (12 cycles). Aliquots of amplified cDNA from each sample were pooled, and purified with AMPure XP beads. The purified PCR products were used as input for the Nextera XT reactions to generate the sequencing libraries.

value: CPC-SMC

value: SMAD3 c.652delA/+

tag: number of cells


title: 2438_cerebellum_male_ethanol

description: 2438 cbl


title: Control wildtype rep1

value: Col

value: 10-day-old seeding


title: THP1_sgROSA_Rep1.txt

tag: cell line


title: 2430_cerebellum_female_ethanol

description: 2430 cbl

value: female


title: 2470_cerebellum_male_vehicle

description: 2470 cbl

value: Vehicle


title: THP1_sgIRF8_2_Rep1.txt


title: Control  mem1 rep1


title: 2442_cerbellum_male_vehicle

description: 2442 cbl


title: XB-BY4742 vs. Suppressor#5-P1

type: RNA

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan) * Priming: 5xSSC, 0.1%SDS * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul * Hybridization: 45 min at 42C. * Wash 2x: milliQ * Wash: 5xSSC, 0.1%SDS * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul) * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC at 23C * Drying: blow with nitrogen for 3min at 30C.

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. ImaGene feature extraction: Features were extracted using ImaGene software from Biodiscovery.

data_processing: Genes, no bg corr, dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

organism: Saccharomyces cerevisiae

source_name: XB-ref

label_protocol:
Robot amplification and labeling v1.0: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).
mRNA amplification protocol description: * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 10^6 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul. * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturer's protocol. * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.
Labeling protocol description: * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).   All subsequent steps are performed by the robot script: * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines Cy3 and Cy5 labeled material). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturer's protocol. * RNA concentration and labeling incorporation are measured (SpectraMax 190). * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. * Samples are stored at -20C until hybridization.

growth_protocol: XB-grow: Three independent cho2opi3 suppressor strains (cho2opi3S #3, #4, #5) that were obtained after prolonged culture of the cho2opi3 parent in choline-free synthetic defined medium containing 2% glucose as carbon source (SD medium). Wild-type and cho2opi3S strains were precultured in SD medium (w/o choline, w/o inositol) to mid-log phase (OD600 ~1.0), and transferred to 15 ml of the corresponding medium at OD600 of 0.05. The cho2opi3 parent strain was precultured to OD600 ~1.0 in SD medium containing 1 mM choline; cells were collected by filtration, washed with choline-free SD medium (30°C), and used to inoculate 15 ml fresh SD medium without choline to an OD600 of 0.1. All strains were cultured at 30°C in replicate and harvested in early mid-log phase (OD600 of 0.55-0.65).

extract_protocol:
Yeast RNA isolation for robotic amplification v1.0: use autoclaved MQ: 1. Take Frozen cells (-80C) and resuspend in 500 ul Acid Phenol Chloroform (From Sigma, 5:1, pH 4.7). Immediately add the same volume TES-buffer (TES: 10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). Vortex very hard for 20 seconds (10 sec upright, 10 sec at an angle) to resuspend pellet. 2. Incubate in water bath for 10 minutes at 65C and vortex again. 3. Transfer to 1.5 ml Eppendorf-tubes. Put tubes in the thermomixer (65C, 1400RPM) for 50 minutes. 4. Spin for 20 minutes at 14000 rpm at 4C. 5. Take new Eppendorf-tube, fill with 500 ul Phenol Chloroform (5:1, pH 4.7). Add water-phase from point 5. Vortex hard for 20 seconds. Spin down for 10 minutes at 14000 rpm at 4C. 6. Take new Eppendorf-tube, fill with 500 ul Chloroform:Isoamyl-alcohol (25:1). Add water-phase from point 6. Vortex hard for 20 seconds. Spin down for 10 minutes at 14000 rpm at 4C. 7. Take new Eppendorf-tube, fill with 50 ul Sodium Acetate (NaAc 3M, pH 5.2). Add water-phase from point 7. Fill tube with Ethanol (100%, -20C). Flip tubes three times. Incubate at 20C for longer than 30 minutes. 8. Spin tubes down for 5 minutes at room temperature, 14000 rpm. Remove fluid with pipette. Be careful not to touch RNA-pellet. 9. Wash pellet with Ethanol 500 ul (80%, -20C). Spin down shortly. 10. Remove Ethanol, do not air dry but directly proceed to 11.11. Dissolve RNA-pellet in 100ul sterile water (MQ, autoclaved). Pipet untill the pellet is released from the side of the tube. wait 5 minutes and pipet up and down 5 more times. Yield will be around 150ug. (Make sure all RNA is dissolved completely!) 12. measure concentration (dilute 100 times). 13. freeze in liquid N2 store at -80C.
Purification procedure: Take 50 µg total RNA; adjust volume to 300 µl with MQ; add 160 µl RLT buffer; add 240 µl 96% ethanol, mix by pipetting and directly apply to the RNeasy column; centrifuge 8000 rpm 15 sec; add 350 µl buffer RW1; centrifuge 8000 rpm 15 sec; add 10 µl DNase to 70 µl RDD buffer and apply to the column, incubate 15 min at room temperature; add 350 µl buffer RW1; centrifuge 8000 rpm 15 sec; Add 500 µl RPE buffer; Wait 1 minute and centrifuge 8000 rpm 15 sec; Add 500 µl RPE buffer; Wait 1 minute and centrifuge 8000 rpm 15 sec; Discard flowthrough and centrifuge 10,000 rpm 2 min; Transfer column to a 1.5 ml tube; Add 35 µl MQ; Wait for 4min and centrifuge 10,000 rpm 1 min; Add the same 35 µl MQ; Wait for 4min and centrifuge 10,000 rpm 1 min; Transfer eluate to a new tube as some column material may stick to the bottom of your tube; Measure concentration, (dilute 50 times (4 µl in 196 µl)) + bioanalyser (50 ng); Directly make 1 aliquot of 30 µl with a concentration of 0.6 µg/µl; Measure the concentration of this aliquot again (4 µl in 96 µl MQ), must be 0.6 µg/µl. Adjust or remake if necessary; Split into 2 aliquots of > 10 µl each; Freeze in liquid N2 and store at -80C.

tag: strain/background

tag: genotype/variation

value: wild type

tag: sample type

value: reference

tag: genotype/background

value: suppressor


title: cho2opi3_parent-P2 vs. XB-BY4742

value: parental knockout


title: XB-BY4742 vs. BY4742-P1

source_name: XB-wt

value: wild type control


title: 2472_cerebellum_female_vehicle

description: 2472 cbl


title: 2431_cerebellum_female_ethanol

description: 2431 cbl


title: XB-BY4742 vs. cho2opi3_parent-P1


title: XB-BY4742 vs. Suppressor#3-P1


title: OCI-AML3_sgIRF8_1_Rep2.txt

value: day 4 after infection


title: 2438_hippocampus_male_ethanol

description: 2438 hip

value: Hippocampus


title: OCI-AML3_sgIRF8_2_Rep2.txt


title: 2469_cerebellum_male_vehicle

description: 2469 cbl

value: Cerebellum


title: OCI-AML3_sgROSA_Rep2.txt

value: sgROSA


title: XB-BY4742 vs. Suppressor#4-P1


title: 2524_hippocampus_male_ethanol

description: 2524 hip

value: Postnatal Day 10

value: Ethanol


title: OCI-AML3_sgIRF8_1_Rep1.txt


title: 2431_hippocampus_female_ethanol

description: 2431 hip


title: 2470_hippocampus_male_vehicle

description: 2470 hip

value: male


title: Suppressor#5-P2 vs. XB-BY4742


title: OCI-AML3_sgIRF8_2_Rep1.txt


title: Suppressor#4-P2 vs. XB-BY4742


title: 2472_hippocampus_female_vehicle

description: 2472 hip


title: OCI-AML3_sgROSA_Rep1.txt


title: MSK PCa16

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and then aligned to human assembly hg19 with STAR v2.6 using default parameters to generate BAM alignment files.
TPMcalculator software was to generate TPM (transcripts per million) for each gene in each BAM file.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: comma delimited text file containing TPM of genes

source_name: prostate cancer organoid

growth_protocol: Organoid culture and seeding experiments were performed as described previously (PMID: 25201529, 26797458)

extract_protocol:
RNA extraction was performed according to manufacture's instuction in PureLinkTM RNA Mini Kit (Thermo Fisher Scientific #12183025)
RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA, at the Genome Technology Center (GTC) at NYU.

tag: primary site

value: Prostate

tag: biopsy site

value: Liver


title: MSK PCa17


title: 2445_hippocampus_female_vehicle

description: 2445 hip

tag: tissue


title: Suppressor#3-P2 vs. XB-BY4742


title: MV4-11_sgIRF8_2_Rep2.txt

tag: post infection


title: MV4-11_sgIRF8_1_Rep2.txt


title: 2429_hippocampus_male_ethanol

description: 2429 hip


title: 2469_hippocampus_male_vehicle

description: 2469 hip


title: MV4-11_sgIRF8_2_Rep1.txt


title: MV4-11_sgROSA_Rep2.txt


title: 2430_hippocampus_female_ethanol

description: 2430 hip


title: MSK PCa14

value: Lymph Node


title: BY4742-P2 vs. XB-BY4742


title: 2442_hippocampus_male_vehicle

description: 2442 hip


title: HES0003_rep1

city: Kyoto

first: Ying

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University

data_processing:
Reads were trimmed by TrimGalore-0.6.6
Reads were aligned to human reference genome using tophat2 v2.1.1 with bowtie2 v2.2.5
gene counts were generated by featureCounts v1.5.0-p2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each Sample

source_name: ESC

growth_protocol: iPSCs were first cultured on SNL cells  in either primate ES cell medium or DMEM/F-12 medium supplemented with 20% KSR, 0.1mM NEAA and 0.1mM 2-Mercaptoethanol. Both mediums were supplemented with 5 ng/ml human basic fibroblast growth factor. iPSCs were then passaged to feeder-free cell-culture medium StemFit AK02N  with 0.1% Y-27632 and  0.25% iMatrix-511, and maintained in freeder-free condition for at least two passages.  All cell lines were passaged by washing in PBS, incubating in TrypLE Select for 3 min at 37 °C, detaching, harvesting, and reseeding at a split ratio of 1:2 or 1:3 in StemFit AK02N  with 0.1% Y-27632  and 0.25% iMartix-511. Medium was changed every 1-2 days

extract_protocol:
RNA was harvested from cell using RLT plus 2-mercaptethanol reagent. Illumina TruSeq stranded mRNA Library Prep Kit was used with 350 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment

value: ESC

tag: disease state

value: untreated

tag: derived from

value: Embryonic stem cells


title: Mouse_72hr_Untreated [1.CGTACTAG_ATAGCCTT]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
Reads were aligned against the GRCm38 mouse and GRCh38 human genomes and quantified using Kallisto
Genome_build: GRCm38/GRCh38
Supplementary_files_format_and_content: abundance h5 and tsv files

growth_protocol: Human DCs were magnetically isolated from fresh healthy human donor leuko paks using the Miltenyi Blood Dendritic Cell Isolation kit II. For murine DCs, spleens were harvested from 10 naïve C57BL6/J mice and pooled, then DCs were magnetically isolated using the Miltenyi Pan DC Isolation kit. DCs were then incubated with ITE or ledft untreated at 37C and 5% CO2 for 6 hours, 18 hours, or 72 hours before being lysed for RNA extraction.

extract_protocol:
Arcturus® PicoPure®
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)

treatment_protocol: DCs were treated with 100nM ITE for 6, 18 or 72 hours or left untreated and collected at the same timepoints for use as a control.

value: Female

tag: age

value: 8 weeks

value: spleen

value: Dendritic cells

value: untreated for 72hrs


title: MOLM13_sgIRF8_2_Rep2.txt

value: day 4 after infection

tag: treatment


title: hyb-L1

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

institute: Cancer Research Center of Toulouse

description:
Gene expression in normal cell culture conditions
E6E7RSTp40

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Gene expression analysis was carried out by using Agilent Whole Human 44K Genome Oligo Array (G4112F and G4845A, for training and validation sets, respectively; Agilent Technologies), according to the manufacturer’s protocol. For each series, all microarrays were simultaneously normalized by using the Quantile algorithm.

source_name: Hybrid-fibroblast

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from frozen tumor samples by using the miRNeasy Mini Kit (Qiagen, Germantown, MD) and was purified by using the RNeasy Min EluteTMCleanup Kit (Qiagen), according to the manufacturer’s instructions. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies).

tag: phenotype

value: Hybrid

tag: cell type

value: Cell line


title: MSK PCa9


title: Parental-immort-rep1

description:
Gene expression in normal cell culture conditions
E6E7.1

source_name: Embryonic-lung-fibroblast

value: Immortalized


title: Parental-transformed-rep1

description:
Gene expression in normal cell culture conditions
RST.1

value: transformed


title: Mouse_18hr_Untreated [1.CGTACTAG_TCTTACGC]

tag: strain

tag: Sex

value: untreated for18hrs


title: Mouse_18hr_Untreated [1.TAAGGCGA_TCTTACGC]


title: hyb-cl1.4

description:
Gene expression in normal cell culture conditions
cl2.4p10


title: MSK PCa6

value: Prostate


title: hyb-cl2.2

description:
Gene expression in normal cell culture conditions
cl.2.2p10


title: MV4-11_sgIRF8_1_Rep1.txt

tag: cell line


title: HES0003_rep2


title: hyb-cl2.3

description:
Gene expression in normal cell culture conditions
cl.2.3p10


title: MV4-11_sgROSA_Rep1.txt

value: sgROSA


title: Mouse_6hr_Untreated [1.CGTACTAG_CTAGTCGA]

value: untreated for 6hrs


title: Mouse_18hr_Untreated [1.AGGCAGAA_TCTTACGC]


title: Parental-transformed-rep2

description:
Gene expression in normal cell culture conditions
RST.2


title: HES0001_rep2

value: ESC


title: HPS0009_rep2

source_name: iPSC

value: iPSC

value: Healthy:RIKEN 2A

value: untreated

value: Umbilical cord


title: HES0001_rep1

value: Embryonic stem cells


title: MOLM13_sgIRF8_1_Rep2.txt


title: Mouse_72hr_ITE [1.AGGCAGAA_TAAGGCTC]

value: Female

value: 8 weeks

value: spleen

value: Dendritic cells

value: AhR ligand ITE for 72hrs


title: Mouse_72hr_Untreated [1.AGGCAGAA_ATAGCCTT]

value: untreated for 72hrs


title: Parental-immort-rep3

description:
Gene expression in normal cell culture conditions
E6E7.3

value: Immortalized

value: Cell line


title: Parental-transformed-rep3

description:
Gene expression in normal cell culture conditions
RST.3

value: transformed


title: Mouse_6hr_Untreated [1.TAAGGCGA_CTAGTCGA]


title: Mouse_72hr_Untreated [1.TAAGGCGA_ATAGCCTT]


title: Mouse_6hr_Untreated [1.AGGCAGAA_CTAGTCGA]


title: HPS0003_rep2

value: Healthy:RIKEN 1A


title: Freshly isolated postnatal human thymocytes library 1

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
Sequence reads were aligned to a combination of the human genome reference (GRCh38) using Bowtie and the inDrops pipeline
Counts per gene were summarized after filtering and identification of abundant barcodes using the inDrops pipeline
Single cell data anlysis was conducted using the Seurat pipeline, regularized negative binomial for normalization (SCTransform), Louvain algorithm for clustering
Genome_build: GRCh38
Supplementary_files_format_and_content: spring.data.tsv.gz: processed count matrix, spring.groupings.csv: metadata with clustering; all.barcode.mappings.txt: equivalence between cell barcode and cell names

source_name: human thymocytes

growth_protocol: For differentiation to hematopoietic progenitors, iPSCs were plated at low confluency (~30-50x103/well) on matrigel (corning cat#354234) coated 6-well plates in mTeSR™.  Two days later, differentiations were begun by removing the mTeSR™ completely and adding the differentiation media for day 0.  Specific media components: day 0-1: BMP4, VEGF, Chir, day 2-3: BMP4, VEGF, bFGF, day 4-5: VEGF, bFGF, day 6-12: BMP4, VEGF, bFGF, SCF, FLT3L, TPO  IL-11, IGF-1, SHH, Transferrin.  Doxycycline was added from day 0-2 to activate Notch1 where indicated.  T cell differentiation was accomplished using the OP9-hDLL4:hMHCII feeder layer.  Co-cultures were initiated in 10cm plates in T cell differentiation media containing αMEM, 20%FBS, glutamax, aMTG, ascorbic acid, 5ng/ml IL-7, 5ng/ml FLT3L, and 50ng/ml SCF.  Cultures were passaged onto new feeder cells every 7 days.  After the first 7 days, SCF was removed and 10υM dexamethasone was added.

extract_protocol:
after FACS isolation of live CD45 positive cells, cells were taken to the InDrops machine and Harvard Medical School and 2000 cells captured per sample.
Library prep was done by the core facility at Harvard.

treatment_protocol: with or without dox from day 0-2

tag: developmental stage

value: mix of hematopoietic progenitors and developing T cells

tag: culture media

value: feshly isolated and analyzed the same day.

tag: isolation method

value: FACS for live, CD45+ cells


title: MOLM13_sgROSA_Rep2.txt

value: day 4 after infection

value: sgROSA


title: MOLM13_sgIRF8_1_Rep1.txt


title: MOLM13_sgIRF8_2_Rep1.txt


title: Mouse_6hr_ITE [1.CGTACTAG_AGCTAGAA]

value: AhR ligand ITE for 6hrs


title: HPS0003_rep1

value: iPSC

value: untreated

value: Umbilical cord


title: 2445_cerebellum_female_vehicle

description: 2445 cbl

value: Cerebellum

value: Postnatal Day 10

value: Vehicle

value: female


title: Mouse_72hr_ITE [1.CGTACTAG_TAAGGCTC]

value: Female

value: 8 weeks

value: spleen

value: Dendritic cells

value: AhR ligand ITE for 72hrs


title: Day 42 hematopoietic cells + dox 0-2 sample 2

source_name: bBU1c2 TetOn:NICD1 iPSC line

value: maturing T/NK cells

value: aMEM, 20% FBS, IL-7, FLT3L, dexamethsone, AA

value: dox


title: HPS0334_rep1

value: Chronic granulomatous disease

value: Peripheral blood, CD34 positive


title: HPS0334_rep2

value: iPSC


title: HPS0009_rep1

value: Healthy:RIKEN 2A

value: untreated


title: Mouse_6hr_ITE [1.AGGCAGAA_AGCTAGAA]

value: AhR ligand ITE for 6hrs


title: Freshly isolated postnatal human thymocytes library 2

value: mix of hematopoietic progenitors and developing T cells

value: feshly isolated and analyzed the same day.

value: FACS for live, CD45+ cells


title: Mouse_18hr_ITE [1.CGTACTAG_CTTAATAG]

value: Female

value: AhR ligand ITE for18hrs


title: HPS0265_rep2

value: Primary immunodeficiency syndrome

value: Bone marrow


title: Mouse_18hr_ITE [1.AGGCAGAA_CTTAATAG]

value: 8 weeks

value: spleen

value: Dendritic cells


title: MOLM13_sgROSA_Rep1.txt

value: day 4 after infection

value: sgROSA


title: HPS0265_rep1


title: Monocyte_ITE_MOG_L [TCGACGTC_TACTCCTT]

data_processing:
Reads were aligned against the GRCm38 mouse genome using STAR (v.2.7.2) with parameters --twopassMode Basic --alignIntronMax 1000000 --sjdbOverhang 37 --alignMatesGapMax 1000000
Reads were counted using FeatureCounts from Subread (1.5.0) in pair-end mode
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file containing Gene IDs and number of reads mapping to that gene

growth_protocol: The brain and spinal cord were harvested from NOD EAE mice approximately 100 days after immunization and digested with papain and collagenase D. Myelin was removed using a Percoll gradient and cells were stained with surface antibodies.  Astrocytes, Microglia, and Moncytes were isolated by flow cytometry.

treatment_protocol: Mice were treated once per week with ITE+MOG liposomes or plain liposomes starting 35 days after EAE induction in NOD mice, during the chronic phase of disease.

value: NOD/ShiLtJ

value: 20 weeks

value: Monocytes


title: Mouse_6hr_ITE [1.TAAGGCGA_AGCTAGAA]


title: Mouse_18hr_ITE [1.TAAGGCGA_CTTAATAG]


title: Monocyte_ITE_MOG_L [CGATCAGT_TACTCCTT]


title: Day 20 hematopoietic cells + dox 0-2 sample 2

value: early T/NK cells

value: aMEM, 20% FBS, IL-7, FLT3L, SCF, AA

value: dox


title: Day 42 hematopoietic cells + dox 0-2 sample 1

value: maturing T/NK cells

value: aMEM, 20% FBS, IL-7, FLT3L, dexamethsone, AA


title: Mouse_72hr_ITE [1.TAAGGCGA_TAAGGCTC]

value: Female

value: AhR ligand ITE for 72hrs


title: Day 20 hematopoietic cells + dox 0-2 sample 1

value: FACS for live, CD45+ cells


title: Monocyte_MOG_L [TAGCGCTC_TACTCCTT]


title: Day 16 hematopoietic cells + dox 0-2 sample 2


title: Day 16 hematopoietic cells + dox 0-2 sample 1


title: Monocyte_ITE_L [GCGTAGTA_TACTCCTT]


title: HPS0174_rep2

value: iPSC

value: Dermatomyositis

value: untreated

value: Skin


title: Monocyte_ITE_L [GGAGCTAC_TACTCCTT]


title: HPS0270_rep1

value: Atopic dermatitis

value: PBMC/T


title: Monocyte_ITE_MOG_L [CCTAAGAC_TACTCCTT]

value: NOD/ShiLtJ


title: Monocyte_ITE_MOG_L [TGCAGCTA_TACTCCTT]

value: 20 weeks


title: Monocyte_MOG_L [ATGCGCAG_TACTCCTT]

value: Monocytes


title: HPS0174_rep1


title: Monocyte_Plain_L [TGCAGCTA_TATGCAGT]


title: Day 13 hematopoietic cells + dox 0-2 sample 1

value: early T/NK cells


title: Monocyte_Plain_L [TCGACGTC_TATGCAGT]


title: Monocyte_MOG_L [ACTGAGCG_TACTCCTT]


title: HPS0184_rep2

value: Systematic Sclerosis (SSc)


title: Day 13 hematopoietic cells + dox 0-2 sample 2

value: aMEM, 20% FBS, IL-7, FLT3L, SCF, AA

value: dox


title: Monocyte_ITE_L [CGGAGCCT_TACTCCTT]


title: Day 12 hematopoietic progenitors no dox sample 2

value: hematopoietic progenitors

value: Stempro34 plus BMP4, VEGF, bFGF, SCF, FLT3L, TPO, IL-11, IGF-1, SHH, Transferrin, AA

value: no dox


title: HPS0270_rep2


title: Monocyte_ITE_L [ACTCGCTA_TACTCCTT]

value: Female


title: Monocyte_MOG_L [TACGCTGC_TACTCCTT]


title: HPS0214_rep2

value: iPSC

value: Ehlers-Danlos syndrome, Kosho Type


title: Monocyte_Plain_L [CGATCAGT_TATGCAGT]


title: Monocyte_Vehicle [TAGCGCTC_TATGCAGT]

value: Vehicle


title: HPS0214_rep1

value: untreated

value: Skin


title: Day 12 hematopoietic progenitors + dox 0-2 sample 1

value: FACS for live, CD45+ cells


title: HPS0064_rep1

value: Glycogen storage disease, Type 1b


title: Monocyte_Plain_L [CCTAAGAC_TATGCAGT]

value: NOD/ShiLtJ

value: 20 weeks


title: Day 12 hematopoietic progenitors + dox 0-2 sample 2


title: Microglia_ITE_MOG_L [GCGTAGTA_TATGCAGT]

value: Microglia


title: Microglia_MOG_L [TCGACGTC_CTCCTTAC]


title: Microglia_ITE_MOG_L [ACTCGCTA_TATGCAGT]


title: Donor OA

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

country: Italy

institute: IRCCS, Ospedale San Raffaele

data_processing:
FASTQ files were demultiplexed from the raw base call (BCL) files using 10x Genomics 'cellranger demux' (CellRanger v3.0.2).
The whitelist of cell barcodes was identified with 'umi_tools whitelist --set-cell-number N --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNNNN' (umi_tools v1.0.0); with N = 2000 for donor1 and donor2, 5000 for donor3 and 1500 for donorOA.
Reads of the whitelisted cells were extracted with 'umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNNNN --filter-cell-barcode --whitelist=whitelist.txt' (umi_tools v1.0.0).
Extracted reads were aligned with STAR aligner (v2.5.3a) to the primary assembly of human genome (GRCh38) with parameter '--outFilterMultimapNmax 1' (to exclude multi-mapping reads).
Mapped reads were assigned to gene_name attributes from GENCODE basic annotation for GRCh38 (version 31) using Subread featureCounts (v1.6.4). Results were save in BAM files with option 'featureCounts -R BAM' and succesively sorted and indexed with samtools (v1.9).
Per gene counts were summarized for each cell using 'umi_tools count --per-gene --gene-tag=XT --assigned-status-tag=XS --per-cell' (umi_tools v1.0.0).
Genome_build: hg38 (GRCh38 - v31)
Supplementary_files_format_and_content: Tab separated files of raw counts;  table with three columns: the gene_id, the cell barcode and the count of deduplicated UMIs. One file per sample, gzipped (.gz).

source_name: freshly isolated testis parenchyma

extract_protocol:
Fresh testes parenchyma was washed twice in PBS and subjected to enzymatic digestion (collagenase type I, collagenase type IV, hyaluronidase, trypsin, Deoxyribonuclease I; all enzymes at 1 mg/ml in DMEM-F12 without serum) for 10 minutes at 37°C with gentle agitation, repeated twice (1ml of digestion medium each time). The cell suspension was filtered through strainers with mesh size 70µm, washed twice with 0.4% BSA/PBS and filtered through a 40µm cell strainer to obtain single cell.
Chromium Single Cell 3′ Library & Gel Bead Kit v2 kit (10xGenomics).

value: testis

tag: disease

value: obstructive azoospermia


title: Monocyte_Vehicle [ACTGAGCG_TATGCAGT]

value: Monocytes


title: Microglia_MOG_L [TGCAGCTA_CTCCTTAC]


title: Day 12 hematopoietic progenitors no dox sample 1

value: hematopoietic progenitors


title: HPS0184_rep1

value: Systematic Sclerosis (SSc)


title: HPS0064_rep2


title: HPS0049_rep1

value: Wilson’s disease


title: Microglia_ITE_L [TAGCGCTC_CTCCTTAC]

value: Female


title: HPS0224_rep2

value: iPSC

value: amyloid neuropathy, Familial type


title: Microglia_ITE_L [ATGCGCAG_CTCCTTAC]


title: Microglia_ITE_L [TACGCTGC_CTCCTTAC]


title: Microglia_ITE_MOG_L [GGAGCTAC_TATGCAGT]


title: Microglia_ITE_L [ACTGAGCG_CTCCTTAC]


title: K562 Cells, PAS Sequencing Sample 1

city: Irvine

first: Whitney

last: England

state: CA

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

data_processing:
Reads were aligned to GRCh38 using STAR 2.5.2a.
Per-position read depth was quantified using samtools 1.8-11.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tsv is a tab separated text file of per-position read depth with 3 columns: Chromosome, Position, Depth.

source_name: K562 cells

growth_protocol: K562 cells were grown in RPMI 1640 supplemented with 10% FBS, and 1% penicillin streptomycin

extract_protocol:
10 μg total RNA extracted with Trizol (Ambion) was fragmented with fragmentation reagent (Ambion) at 70 o C for 10 minutes followed by precipitation with ethanol.
Reverse transcription was performed with PASSEQ7-2 RT oligo: [phos]NNNNAGATCGGAAGAGCGTCGTGTTCGGATCCATTAGGATCCGAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTT[V-Q] and Superscript III (Invitrogen). cDNA was recovered by ethanol precipitation and 120-200 nucleotides of cDNA was gel-purified from 8% Urea-PAGE. Recovered cDNA was circularized with Circligase TM II (Epicentre) at 60 o C overnight. Buffer E (Promega) was added in cDNA and heated at 95 o C for 2 minutes, and then cool to 37 o C slowly. Circularized cDNA was linearized by BamH I (Promega). cDNA was collected by centrifugation after ethanol precipitation. PCR was carried out with primers PE1.0 and PE2.0 containing index (Illumina). Around 200 bp of PCR products was gel-purified.

value: bone marrow chronic myelogenous leukemia


title: Microglia_ITE_MOG_L [CGGAGCCT_TATGCAGT]


title: Monocyte_Vehicle [TACGCTGC_TATGCAGT]

value: Vehicle


title: Microglia_Plain_L [GCGTAGTA_CTCCTTAC]


title: Microglia_MOG_L [CGATCAGT_CTCCTTAC]


title: HPS0224_rep1

value: untreated

value: Skin


title: Monocyte_Vehicle [ATGCGCAG_TATGCAGT]


title: HPS0049_rep2


title: HPS0070_rep1

value: Mitochondrial myopathy, Encephalopathy


title: HPS0175_rep2

value: Pompe’s disease


title: Microglia_Plain_L [ACTCGCTA_CTCCTTAC]

value: NOD/ShiLtJ

value: 20 weeks


title: Microglia_Vehicle [TGCAGCTA_AGAGGATA]

value: Microglia


title: Microglia_MOG_L [CCTAAGAC_CTCCTTAC]


title: Microglia_Plain_L [CGGAGCCT_CTCCTTAC]


title: Microglia_Plain_L [GGAGCTAC_CTCCTTAC]


title: Microglia_Vehicle [CGATCAGT_AGAGGATA]


title: Microglia_Vehicle [CCTAAGAC_AGAGGATA]


title: Microglia_Vehicle [TCGACGTC_AGAGGATA]


title: HPS0070_rep2


title: HPS0175_rep1


title: Astrocytes_ITE_MOG_L [TAGCGCTC_AGAGGATA]

value: Astrocytes


title: Parental-immort-rep2

description:
Gene expression in normal cell culture conditions
E6E7.2

value: Immortalized

value: Cell line


title: HPS0254_rep2

value: Alzheimer’s disease


title: fungi growth on 1% polygalacturonic acid for 8 hour rep2

first: Ronald

last: de vries

address: Uppsalalaan 8

institute: westerdijkinstitute

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized to Affymetrix A. niger Genome GeneChips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Microarray data was analyzed using the Bioconductor tool package version 2.8 (http://www.bioconductor.org/) together with house-made Perl (version .5.0) and Python (version 3.0) scripts. Probe intensities were normalized for background by the robust multi-array average (RMA) method using the R statistical language and environment. This method makes use of only perfect match (PM) probes. Normalization was processed by the quantiles algorithm. The median polish summary method was used to calculate the gene expression values.

label: biotin

organism: Aspergillus niger

source_name: Mycelium

label_protocol: Biotin-labeled antisense cRNA was produced from 2 µg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com)

growth_protocol: Aspergillus niger N402 was propagated and grown on complete medium (CM) or minimal medium (MM). Liquid cultures were grown in a rotary shaker at 250 rpm and 30C. Transfer experiment was performed by growing the strain for 16 h in 1 L Erlenmeyer flasks that contained 250 mL CM supplemented with 2% D-fructose as carbon source. The mycelium was harvested by filtration and washed with MM without a carbon source.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: One gram (wet weight) of the mycelium was transferred to 250 mL Erlenmeyer flasks containing 50 mL MM supplemented with 1% SBP or PGA (Sigma-Aldrich) and incubated for 8 h and 24 h.

value: grown on PGA after 8 hour incubation


title: Astrocytes_MOG_L [CGGAGCCT_AGAGGATA]

value: Female


title: Astrocytes_ITE_MOG_L [ATGCGCAG_AGAGGATA]


title: fungi growth on 1% polygalacturonic acid for 24 hour rep1

value: grown on PGA after 24 hour incubation


title: HPS0240_rep1

value: iPSC

value: Lysosomal storage disease( Metachromatic leukodystrophy (MLD)


title: fungi growth on 1% polygalacturonic acid for 8 hour rep1


title: Astrocytes_MOG_L [GCGTAGTA_AGAGGATA]


title: Astrocytes_ITE_MOG_L [TACGCTGC_AGAGGATA]


title: HPS0240_rep2


title: HPS0200_rep2

value: Muscular dystrophy,Limb-girdle type


title: Astrocytes_ITE_MOG_L [ACTGAGCG_AGAGGATA]


title: Astrocytes_ITE_L [TCGACGTC_ATAGAGAG]


title: Astrocytes_MOG_L [ACTCGCTA_AGAGGATA]


title: Astrocytes_MOG_L [GGAGCTAC_AGAGGATA]


title: Astrocytes_ITE_L [CGATCAGT_ATAGAGAG]


title: HPS0200_rep1

value: untreated


title: Astrocytes_ITE_L [TGCAGCTA_ATAGAGAG]


title: Astrocytes_ITE_L [CCTAAGAC_ATAGAGAG]


title: HPS0143_rep2

value: Congenital fiber type disproportion disease

value: Skin


title: HPS0254_rep1


title: submerged growth on sugar beet pulp for 24 hours biological rep2

value: during SBP degradation after 24 hour incubation


title: HPS0143_rep1


title: Astrocytes_Plain_L [TAGCGCTC_ATAGAGAG]

value: NOD/ShiLtJ


title: fungi growth on 1% polygalacturonic acid for 24 hour rep2


title: Astrocytes_Plain_L [ACTGAGCG_ATAGAGAG]

value: 20 weeks


title: HPS0183_rep2

value: Inclusion body myositis


title: submerged growth on sugar beet pulp for 8 hours biological rep1

value: during SBP degradation after 8 hour incubation


title: Astrocytes_Plain_L [TACGCTGC_ATAGAGAG]

value: Astrocytes


title: Astrocytes_Plain_L [ATGCGCAG_ATAGAGAG]


title: Astrocytes_Vehicle [GCGTAGTA_ATAGAGAG]

value: Vehicle


title: HPS0183_rep1


title: submerged growth on sugar beet pulp for 8 hours biological rep2


title: Hippocampus_GRMREmx1-cre_rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression for hippocampus, GRMREmx1-cre, 2.5 month

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.0), using the 1-color defaults for all parameters.

source_name: hippocampus, GRMREmx1-cre, 2.5 month

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit and RNase-Free DNase Kit (Qiagen) from the whole hippocampus isolated from both hemispheres of male dflox control and GREmx1-cre, MREmx1-cre, and GRMREmx1-cre knockout mice.  Mice were approximately 2.5 months old.

tag: gender

value: male


title: Astrocytes_Vehicle [GGAGCTAC_ATAGAGAG]


title: Astrocytes_Vehicle [CGGAGCCT_ATAGAGAG]


title: Hippocampus_GRMREmx1-cre_rep1


title: Astrocytes_Vehicle [ACTCGCTA_ATAGAGAG]


title: Hippocampus_GRMREmx1-cre_rep3


title: WT 24 hours light replicate 3

city: Philadelphia

first: Diep

middle: R

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

data_processing:
Raw read quality was first diagnosed using FastQC (v0.11.7).
Trim Galore! (v0.4.4) was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Transcript abundance was quantified as TPM using Kallisto with flags --bias --single -b 10 -l 300 -s 100 (Bray et al 2016).
Kallisto index was used to build the an index from transcripts defined by AtRTDv2_QUASI_19April2016.fa (Zhang et al 2017 Plant Cell)
Genome_build: AtRTDv2_QUASI_19April2016.fa; https://ics.hutton.ac.uk/atRTD/ (Zhang et al 2017 Plant Cell)
Supplementary_files_format_and_content: h5: HDF5 file containing run info, abundance esimates (TPM), bootstrap estimates, and transcript length information length ; tsv: plaintext file of the abundance estimates (TPM).

source_name: WT seedlings harvested at 24h light replicate 3

growth_protocol: About 50 mg (5 mL) Arabidopsis thaliana seeds of genotype: WT (Col-0), atg2, atg5, and atg9 seeds were surface-sterilized (Desfeux et al 2000 Plant Physiology), washed five times with sterilized water, and sown on a mesh platform (mesh size 1 mm; 3 cm x3 cm x 3 cm) layered with 1% sterilized agarose. Plants were grown in a round plastic vessel (diameter 120 mm, height 140 mm) containing approximately 300 ml liquid medium (¼x Murashige & Skoog medium without vitamins, ¼x Gamborg B5 vitamins solution, 2 mM MES, 1% [w/v] sucrose, pH 5.8) (Lee et al 2008 Molecular & Cellular Proteomics). Seeds were grown for five days in the dark, then transferred to light (100-125 µE) at 22oC. Samples were collected at 0 hours (0 h), 12 hours (12 h), and 24 hours (24 h) of growth in light.

extract_protocol:
Total RNA was extracted using an adapted CTAB/chloroform/LiCl extraction protocol (Chang et al 1993 Plant Mol Biol Rep). Full details are available on protocols.io: dx.doi.org/10.17504/protocols.io.3f6gjre.
Total RNA-sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, CA, USA) as per manufacterers instructions but with reaction volumes adjusted 1/3x.

treatment_protocol: Seeds were grown for five days in the dark, then transferred to light (100-125 µmolm-2s-1) at 22oC. Samples were collected at 0 hours (0 h), 12 hours (12 h), and 24 hours (24 h)of growth in light.

tag: ecotype

tag: genotype

value: WT

value: light

tag: time (hrs)

value: seedlings


title: HPS0263_rep1

value: iPSC

tag: disease state

value: Huntington’s disease


title: Hippocampus_MREmx1-cre_rep4

description: Gene expression for hippocampus, MREmx1-cre, 2.5 month

source_name: hippocampus, MREmx1-cre, 2.5 month


title: WT 24 hours light replicate 1

source_name: WT seedlings harvested at 24h light replicate 1

tag: tissue


title: WT 12 hours light replicate 3

source_name: WT seedlings harvested at 12h light replicate 3


title: HPS0264_rep2

value: Parkinson’s disease (PD)

tag: derived from


title: WT 12 hours light replicate 2

source_name: WT seedlings harvested at 12h light replicate 2

tag: treatment


title: HPS0264_rep1

value: untreated


title: Hippocampus_MREmx1-cre_rep3


title: WT 12 hours light replicate 1

source_name: WT seedlings harvested at 12h light replicate 1


title: HPS0059_rep2

value: Amyotrophic lateral sclerosis (ALS)


title: WT control (dark) replicate 3

source_name: WT seedlings harvested at 0h light (dark) replicate 3

value: dark (control)


title: HPS0263_rep2

value: Skin


title: Hippocampus_MREmx1-cre_rep2


title: WT control (dark) replicate 1

source_name: WT seedlings harvested at 0h light (dark) replicate 1


title: Hippocampus_GREmx1-cre_rep4

description: Gene expression for hippocampus, GREmx1-cre, 2.5 month

source_name: hippocampus, GREmx1-cre, 2.5 month


title: WT control (dark) replicate 2

source_name: WT seedlings harvested at 0h light (dark) replicate 2


title: Hippocampus_MREmx1-cre_rep1


title: WT 24 hours light replicate 2

source_name: WT seedlings harvested at 24h light replicate 2


title: atg9 24 hours light replicate 3

source_name: atg9 seedlings harvested at 24h light replicate 3


title: HPS0059_rep1

source_name: iPSC


title: atg9 24 hours light replicate 1

source_name: atg9 seedlings harvested at 24h light replicate 1


title: atg9 12 hours light replicate 2

source_name: atg9 seedlings harvested at 12h light replicate 2


title: Hippocampus_GREmx1-cre_rep2


title: Hippocampus_GREmx1-cre_rep3


title: atg9 12 hours light replicate 3

source_name: atg9 seedlings harvested at 12h light replicate 3


title: atg9 24 hours light replicate 2

source_name: atg9 seedlings harvested at 24h light replicate 2


title: atg9 12 hours light replicate 1

source_name: atg9 seedlings harvested at 12h light replicate 1


title: atg9 control (dark) replicate 3

source_name: atg9 seedlings harvested at 0h light (dark) replicate 3


title: Hippocampus_GREmx1-cre_rep1


title: WD.37322 [19191_WD.37323_S28]

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
reads were aligned to hg19 genome assembly using Tophat2 with default settings
gene expression levels of Refseq genes were counted with Htseq-count
For miRNA, reads were trimmed to remove adapter and aligned to hg19 using Bowtie
miRNAs in miRBase v21 were counted using customized R scripts
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing the raw count

extract_protocol: RNAseq libraries were prepared from Illumina TruSeq miRNA for miRNA-seq

tag: disease/tissue type

value: Normal


title: WD.37320 [19189_WD.37320_S12]


title: WD.37322 [19190_WD.37322_S20]


title: atg9 control (dark) replicate 1

source_name: atg9 seedlings harvested at 0h light (dark) replicate 1


title: S16.1854.A2 [11859_S16.1854A2_CTTGTA]

description: 11859_S16-1854A2_CTTGTA_L999_cutadapt.fastq.gz

value: Plaque


title: atg9 control (dark) replicate 2

source_name: atg9 seedlings harvested at 0h light (dark) replicate 2


title: atg5 24 hours light replicate 3

source_name: atg5 seedlings harvested at 24h light replicate 3


title: Hippocampus_dflox_rep4

description: Gene expresson for hippocampus, dflox, 2.5 month

source_name: hippocampus, dflox, 2.5 month


title: Hippocampus_dflox_rep3


title: S16.1596.A1 [11858_S16.1596A1_GGCTAC]

description: 11858_S16-1596A1_GGCTAC_L999_cutadapt.fastq.gz


title: MSK PCa7

source_name: prostate cancer organoid

tag: primary site

value: Prostate

tag: biopsy site

value: Lymph Node


title: S15.13213.A2 [11460_S15.13213_B1_TACAGC]

value: Tumor


title: MSK PCa5

value: Circulating Tumor Cells


title: atg5 12 hours light replicate 2

source_name: atg5 seedlings harvested at 12h light replicate 2


title: Hippocampus_dflox_rep1

value: male

tag: strain


title: S15.11353.B1 [11459_S15.11353_A2_TAATCG]


title: atg5 12 hours light replicate 3

source_name: atg5 seedlings harvested at 12h light replicate 3


title: atg5 24 hours light replicate 1

source_name: atg5 seedlings harvested at 24h light replicate 1


title: S15.6546.A1 [11458_S15.6546.A1_GACGAC]


title: atg5 control (dark) replicate 2

source_name: atg5 seedlings harvested at 0h light (dark) replicate 2


title: atg5 control (dark) replicate 3

source_name: atg5 seedlings harvested at 0h light (dark) replicate 3


title: MSK PCa3


title: atg5 12 hours light replicate 1

source_name: atg5 seedlings harvested at 12h light replicate 1


title: MSK PCa4

value: Pleural Effusion


title: atg5 control (dark) replicate 1

source_name: atg5 seedlings harvested at 0h light (dark) replicate 1


title: atg5 24 hours light replicate 2

source_name: atg5 seedlings harvested at 24h light replicate 2

value: light


title: MSK PCa2

value: Bone


title: MSK PCa1


title: submerged growth on sugar beet pulp for 24 hours biological rep1

source_name: Mycelium

value: during SBP degradation after 24 hour incubation


title: atg2 24 hours light replicate 1

source_name: atg2 seedlings harvested at 24h light replicate 1

value: seedlings


title: S15.8104.C [11456_S15.8104.C_CTATAC]


title: atg2 24 hours light replicate 2

source_name: atg2 seedlings harvested at 24h light replicate 2


title: S15.13213.B1 [11457_S15.13213.A2_CTCAGA]


title: Human_72hr_Untreated [1.AAGAGGCA_ATAGCCTT]

tag: subject status

value: healthy human donor

tag: Sex

value: not collected

tag: age

value: peripheral blood

tag: cell type

value: Dendritic cells

value: untreated for 72hrs


title: atg2 12 hours light replicate 1

source_name: atg2 seedlings harvested at 12h light replicate 1


title: atg2 12 hours light replicate 2

source_name: atg2 seedlings harvested at 12h light replicate 2


title: Human_72hr_Untreated [1.CGAGGCTG_ATAGCCTT]


title: atg2 24 hours light replicate 3

source_name: atg2 seedlings harvested at 24h light replicate 3


title: S15.11076.B1 [11451_S15.11076.B1_CATGGC]


title: S15.1874.A [11453_S15.1874.A_CCAACA]


title: Human_18hr_Untreated [1.AAGAGGCA_TCTTACGC]

value: untreated for18hrs


title: atg2 control (dark) replicate 2

source_name: atg2 seedlings harvested at 0h light (dark) replicate 2

value: dark (control)


title: 1326: Primary Human MSCs - #6 donor - preconditioned with Vadadustat

city: Warsaw

first: Katarzyna

last: Zielniok

address: Nowogrodzka 59

department: Department of Clinical Immunology

country: Poland

institute: Medical University of Warsaw

description: *** Raw data not submitted due to patient privacy concerns (currently under IRB review) ***

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end sequencing (2x100 bp) performed using the HiSeq1500 platform with an average of 16 - 20 million read pairs generated for each library.
Quality control checks of the sequencing raw data conducted with FastQC, and adapter-trimming with BBDUK2 tool.
Quantification of transcript abundance and gene expression was performed using Salmon software.
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample.
Supplementary_files_format_and_content: Matrix table with normalized gene counts generated by DESeq2 used for GSEA analysis

source_name: Mesenchymal Stromal Cells

growth_protocol: Routine MSCs cultures were maintained under conditions of 5% CO2, 95% humidified air at 37°C. For the analyses, we used six BM-MSCs populations that were between passage 4 and 6 and that fulfilled acknowledged identification criteria for MSCs.

extract_protocol:
The incubation lasted for 6 h, after which we removed the medium from the cell cultures, washed cells with PBS and disrupted them by scraping in 350 μL of RLT isolation buffer from Qiagen RNeasy Mini Kit according to the protocol provided by the manufacturer.
cDNA libraries construction was carried out with 1μg of total RNA using TruSeq Stranded mRNA Library Prep Kit ( Illumina, San Diego, CA, USA) according to the manufacturer’s instruction.

treatment_protocol: Two methods of hypoxic preconditioning were used. The first, "physical" hypoxia was achieved by culturing cells for 6h in a gas mixture composed of 2% O2 (balanced with N2) and 5% CO2. The second, "pharmacological" hypoxia was obtained by culturing cells for 6h with the PHDs inhibitor, Vadadustat (AKB-6548, Akebia, Cambridge, MA, USA) in a concentration of 40 μM. Vadadustat was prepared as a 5 mM stock solution in DMSO according to the manufacturer's instructions, meaning that no more than 0.8 % (v/v) DMSO was present in the culture medium. After 6 h of incubation, cells were harvested, washed with PBS and frozen at -80°C for further analysis.

tag: cells

value: primary MSCs (Mesenchymal Stromal Cells)

value: bone marrow-derived

value: 6h incubation with 40 μM Vadadustat

tag: donor sex

tag: donor age


title: atg2 12 hours light replicate 3

source_name: atg2 seedlings harvested at 12h light replicate 3

tag: ecotype

tag: genotype


title: Human_72hr_Untreated [1.CTCTCTAC_ATAGCCTT]


title: 1325: Primary Human MSCs - #6 donor - preconditioned in hypoxia

value: 6h incubation in 2% O2 (hypoxia)


title: 1322: Primary Human MSCs - #5 donor - preconditioned in hypoxia

value: male


title: Human_18hr_Untreated [1.CGAGGCTG_TCTTACGC]


title: atg2 control (dark) replicate 3

source_name: atg2 seedlings harvested at 0h light (dark) replicate 3

tag: time (hrs)


title: 1323: Primary Human MSCs - #5 donor - preconditioned with Vadadustat

tag: tissue


title: atg2 control (dark) replicate 1

source_name: atg2 seedlings harvested at 0h light (dark) replicate 1


title: S15.8957.A1 [11454_S15.8957_CGGAAT]

value: Plaque


title: 1320: Primary Human MSCs - #4 donor - preconditioned with Vadadustat


title: 1324: Primary Human MSCs - #6 donor - untreated

value: untreated/control


title: S15.12438.B1 [11450_S15.12438.B1_CAGGCG]

value: Tumor


title: 1317: Primary Human MSCs - #3 donor - preconditioned with Vadadustat

value: female


title: S15.5743.B [11452_S15.5743.B_CATTTT]


title: S15.11353.A2 [11448_S15.11353_B1_CACGAT]


title: S15.11600.A1 [11455_S15.11600.A1_CTAGCT]


title: 1319: Primary Human MSCs - #4 donor - preconditioned in hypoxia


title: Human_18hr_Untreated [1.CTCTCTAC_TCTTACGC]


title: S15.5029.A [11446_S15.5029.A_CAACTA]


title: 1321: Primary Human MSCs - #5 donor - untreated


title: 1313: Primary Human MSCs - #2 donor - preconditioned in hypoxia


title: 1314: Primary Human MSCs - #2 donor - preconditioned with Vadadustat


title: Human_6hr_Untreated [1.AAGAGGCA_CTAGTCGA]

value: untreated for 6hrs


title: 1310: Primary Human MSCs - #1 donor - preconditioned in hypoxia


title: Human_72hr_ITE [1.CGAGGCTG_TAAGGCTC]

value: healthy human donor

value: AhR ligand ITE for 72hrs


title: 1311: Primary Human MSCs - #1 donor - preconditioned with Vadadustat


title: 1318: Primary Human MSCs - #4 donor - untreated


title: Human_72hr_ITE [1.CTCTCTAC_TAAGGCTC]

value: not collected

value: peripheral blood


title: 1315: Primary Human MSCs - #3 donor - untreated


title: Human_72hr_ITE [1.AAGAGGCA_TAAGGCTC]

value: Dendritic cells


title: S15.12439. [11449_S15.12439_CACTCA]


title: S15.9737.B1 [11445_S15.9737.B1_CAAAAG]


title: 1316: Primary Human MSCs - #3 donor - preconditioned in hypoxia


title: S15.9737.A1 [11444_S15.9737.A1_ATTCCT]


title: S15.5029.B [11447_S15.5029.B_CACCGG]


title: 1309: Primary Human MSCs - #1 donor - untreated


title: 1312: Primary Human MSCs - #2 donor - untreated


title: Human_18hr_ITE [1.AAGAGGCA_CTTAATAG]

value: AhR ligand ITE for18hrs


title: Human_18hr_ITE [1.CGAGGCTG_CTTAATAG]


title: Human_6hr_Untreated [1.CGAGGCTG_CTAGTCGA]


title: S15.11601.A2 [11442_S15.11601.A2_ACTGAT]


title: Human_18hr_ITE [1.CTCTCTAC_CTTAATAG]


title: S15.11580.A1 [11441_S15.11580.A1_GGTAGC]


title: S15.7535.B [11440_S15.7535.B_GAGTGG]


title: S15.7247.B1 [11443_S15.7247.B1_ATGAGC]


title: Human_6hr_ITE [1.AAGAGGCA_AGCTAGAA]

value: AhR ligand ITE for 6hrs


title: Sample 24 - lung normal tissue (control)

city: Sao Paulo

first: Tabatha

middle: Gutierrez

last: Prieto

state: Sao Paulo

address: Av Dr Arnaldo 455, room 1143

department: Pathology

country: Brazil

institute: Faculty of Medicine of University of Sao Paulo

description:
control
226N

data_processing:
The data were then analyzed in the StepOne software (v. 2.0, Applied Biosystems) using the Δ threshold cycle (Ct) method (2^−ΔΔCt) (Livak and Schmittgen, 2001). All data were normalized by the housekeeping genes, and normal lung tissue specimens were used as case control. For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Avg. Ct_HKG).
Matrix normalized file reports normalized signal (against housekeeping genes); normalized differences in cycle thresholds against housekeeping genes, where both tumor samples (test) and normal tissue samples (control) were normalized following the same protocol (i.e. DeltaCt = [Ct_Target − Avg. Ct_HKG]). Fold Change worksheet reports test/control (i.e., mRNA of tumor tissue (SCLC)/mRNA of Normal lung tissue (SCLC) ratios; Fold Change =  2^-ΔΔCt, where -ΔΔCt = -[ΔCttest - Avg. ΔCtcontrol].

label: RT2 SYBR® Green qPCR

source_name: mRNA of Normal lung tissue (SCLC)

label_protocol: Complementary DNA was synthesized using the c-DNA – RT² First Strand Kit (Qiagen Sample & Assay Technologies) according to the manufacturer’s protocol. The difference of expression in EMT genes was evaluated by the real-time PCR method. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed using the RT² Profiler PCR Array System (PAHS-090Z; Qiagen, Dusseldorf, Germany) kit for the human epithelial-to-mesenchymal transition (EMT) pathway with 84 target genes. The array includes a total of 84 EMT genes, 5 housekeeping genes (ACTB, B2M, GAPDH, HPRT1, RPLP0), 1 genomic DNA control (GDC) to assess contamination, 3 reverse transcriptase controls (RTC) that certify the efficiency of the reverse transcription step, and 3 positive PCR controls (PPC) consisting of an artificial DNA sequence certifying the test accuracy. Each 96-well plate  includes SYBR® Green-optimized primer assays for a thoroughly researched panel of 84 EMT genes, that also are included the collagen and integrin genes. Furthermore, the high-quality primer design and RT2 SYBR® Green qPCR Mastermix formulation enable the PCR array to amplify 96 gene-specific products simultaneously under uniform cycling conditions. The samples were amplified using Applied Biosystems Step One Plus (Applied Biosystems, California, USA). The cycling conditions were as follows: 95°C for 10 minutes, 40 cycles at 95°C for 15 seconds, 60°C for 1 minute, followed by the dissociation period.

extract_protocol: The neoplastic area was micro dissected during the frozen section procedure to ensure the inclusion of neoplastic tissue and distant non-neoplastic tissue as control. Total mRNA was extracted from fresh-frozen tumor and normal tissues using the QIAsymphony miRNA CT 400 kit (Qiagen, CA, USA) according to the manufacturer’s instructions. RNA integrity and quality were determined using the Bioanalyzer 2100 (Agilent Technologies).

value: normal lung

tag: gender

value: Not applicable

tag: tobacco history

tag: histological subtype

value: SCLC

tag: pathological stage

tag: status

tag: survival


title: Sample 23 - lung normal tissue (control)

description:
control
223N


title: Sample 21 - lung normal tissue (control)

description:
control
214N


title: Human_6hr_Untreated [1.CTCTCTAC_CTAGTCGA]

tag: subject status

tag: treatment


title: Sample 20 - lung normal tissue (control)

description:
control
213N

tag: age


title: Human_6hr_ITE [1.CGAGGCTG_AGCTAGAA]

tag: Sex

tag: cell type


title: S15.6736.A1 [11439_S15.6736.A1_CGTACG]

tag: disease/tissue type


title: Sample 19 - lung normal tissue (control)

description:
control
211N


title: S15.5741.A6 [11438_S15.5741.A6_GTTTCG]


title: S15.5743.A [11437_S15.5743.B_GTGGCC]


title: Sample 16 - lung normal tissue (control)

description:
control
207N


title: Sample 17 - lung normal tissue (control)

description:
control
209N


title: Sample 18 - lung normal tissue (control)

description:
control
210N


title: Human_6hr_ITE [1.CTCTCTAC_AGCTAGAA]


title: Sample 22 - lung normal tissue (control)

description:
control
220N


title: S15.4787.A1 [11436_S15.4787.A1_GTGAAA]


title: Sample 13 - lung normal tissue (control)

description:
control
202N


title: Sample 11 - lung normal tissue (control)

description:
control
199N


title: S15.4306.A1 [11434_S15.4306.A1_GTAGAG]


title: Sample 12 - lung normal tissue (control)

description:
control
201N


title: Hippocampus_dflox_rep2

source_name: hippocampus, dflox, 2.5 month

tag: strain


title: Sample 5 - lung normal tissue (control)

description:
control
188N


title: Sample 6 - lung normal tissue (control)

description:
control
189N


title: Sample 7 - lung normal tissue (control)

description:
control
192N


title: Sample 10 - lung normal tissue (control)

description:
control
198N


title: S15.4629.A1 [11433_S15.4629.A1_CCGTCC]


title: Sample 15 - lung normal tissue (control)

description:
control
204N


title: Sample 14 - lung normal tissue (control)

description:
control
203N


title: Mus musculus P-I

city: Chiyoda-ku

first: Kento

last: Mio

state: Tokyo

address: 12 Sanban-cho

department: Studies in Human Life Sciences

institute: Otsuma Womenʼs University

description: Gene expression data of ileum extracted from Mus musculus fed a paramylon diet.

hyb_protocol: cDNA were hybridized to the GeneArray Mouse 2.0ST Array. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific, Inc.) according to the manufacturer’s recommendations.

data_processing: Expression values were generated using Expression Console software, version 1.3 (Thermo Fisher Scientific, Inc.) with default robust multichip analysis parameters.

source_name: ileum in Mus musculus fed a paramylon diet

label_protocol: The resultant single-strand cDNA was fragmented and labeled with biotin.

extract_protocol: Total RNA in each organs were extracted by using protocol of RNeasy Mini kit (Qiagen, Hilden, Germany).

value: ileum


title: Mus musculus C-L

description: Gene expression data of liver extracted from Mus musculus fed a cellulose diet.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G (Thermo Fisher Scientific, Inc.) according to the manufacturer’s recommendations.

source_name: liver in Mus musculus fed a cellulose diet

value: liver


title: Sample 9 - lung normal tissue (control)

description:
control
196N


title: Mus musculus P-L

description: Gene expression data of liver extracted from Mus musculus fed a paramylon diet.

source_name: liver in Mus musculus fed a paramylon diet


title: Sample 4 - lung normal tissue (control)

description:
control
185N


title: Sample 3 - lung normal tissue (control)

description:
control
183N


title: PBS treated murine liver non parenchymal cells

city: Atlanta

first: James

middle: E

last: Dahlman

state: GA

address: 313 Ferst Dr NW

department: BME

institute: Georgia Institute of Technology

description:
LSL-Tomato/Ai14 (#007914)
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5

data_processing:
Sample demultiplexing, barcode processing, and single-cell 3’ gene counting was performed with the Cell Ranger Single Cell 30 Software Suite CR3.0.2. Each droplet partition’s contents were tagged with a unique molecule identifier (UMI), which was read as the second read of each sequenced read-pair, along with Illumina barcodes. 98 nucleotides of Read1s were aligned to the mouse genome (mm10) using STAR aligner. Only confidently mapped non-PCR duplicates with valid barcodes and UMIs were used for further analysis (>97%)
To compare single cell populations, the Cell Ranger matrix file was imported into Seurat. Cells were log-normalized to a scale factor of 10,000 then scaled using a linear transformation. This was followed by PCA dimensional reduction, t-SNE clustering and then exported using rBCS for further analysis in BBrowser2 (v2.9.23). Once in BBrowser2, the cell search tool was used to identify the cell types within each cluster and gene expression profiles were compared within cell types of interest.
In order to find differentially expressed genes between groups of cells, the asymptotic beta test used in edgeR was used. For each cluster, the algorithm is run on  that cluster versus all other cells, yielding lists of genes that are differentially expressed in that cluster relative to the rest of the sample. Only genes with a P adjusted value (false-discovery rate) or less than 0.05 and a fold change greater than 1.5, and genes that have an average occurrence greater than one count per cell across the condition were included within the subsequent gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis
To understand the functions of the differentially expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by the Enrichr web server and KEGGMapper (https://www.kegg.jp/) respectively
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalised gene counts for every gene and every sample

source_name: Murine liver non parenchymal cells

extract_protocol:
Cells were isolated 3 hours after injection with PBS or LNPs. Mice were perfused with 20 mL of 1X PBS through the right atrium. Liver tissues were finely minced, and then placed in a digestive enzyme solution with Collagenase Type I (Sigma Aldrich), Collagenase XI (Sigma Aldrich) and Hyaluronidase (Sigma Aldrich) at 37C at 550 rpm for 45 minutes. Cell suspension was filtered through 70μm mesh and red blood cells were lysed. Cells were stained to identify specific cell populations and sorted using the BD FacsFusion.
Individually barcoded single-cell RNA-Seq libraries were prepared using the Chromium instrument and the Single Cell 3’ Reagent kit (v3) following the manufacturer’s protocol (10X Genomics). ~2000 cells were loaded for each of the three conditions. Library sequencing was performed on an Illumina Nextseq platform, using the 150-cycle High Output kit (Illumina)
10X Genomics 3' Gene Expression v3

tag: agent

value: PBS

value: FACS sorted liver

tag: time point

value: 3 hours after injection


title: 20mix-LNP treated murine liver non parenchymal cells


title: S15.9248.A1 [11430_S15.9248_A1_AGTCAA]

value: Plaque


title: S15.10296. [11429_S15.10296_A1_CTTGTA]


title: Sample 8 - lung normal tissue (control)

description:
control
195N


title: Sample 24 - lung tumor tissue (test)

description:
test
PU 242T

source_name: mRNA of tumor tissue (TC)

value: lung tumor

value: Male

value: Smoker

value: Typical carcinoid

value: Lack information

value: Alive


title: Sample 2 - lung normal tissue (control)

description:
control
182N


title: Sample 1 - lung normal tissue (control)

description:
control
156N


title: 714-MB: WT_midbrain rep3

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

data_processing:
RNA-Seq read level data was processed using the bcbio-nextgen (v1.1.5-b pipeline). Using salmon (v0.14.0, options(  -l SR   --seqBias  --validateMappings --numBootstraps 30) )  against mm10 transcriptome
Gene level quantification carried out in R (3.6.0) bioconductor package bcbioRNASeq  ( 0.3.25) and tximport (1.12.3)
Raw read counts transformed using variance stabilizing transformation (VST)  using the DESeq2 Bioconductor package (1.30.1)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with vst transformed gene counts for every gene and every sample
Supplementary_files_format_and_content: salmon quant tab delimited output files

source_name: midbrain

extract_protocol:
Total RNA was extracted from dissected fore brain, mid brain and hind brain of 3 biological replicates P-25 wild type and Fmr1CRE knockin mutant mice from same litter using the RNeasy kit (QIAGEN) combined with QIAshredder (QIAGEN), following the manufacturer’s instructions.
Random primed cDNA from poly(A) selected RNA was converted into an Illumina sequencing library using RNA Library Prep Kit from Illumina (E7420, NEB, USA) in conjunction with NEBNext® Multiplex Oligos for Illumina (E7335/E7500, NEB, USA).
Single-end 50-base pair (bp) reads were generated using a NextSeq 500 (Illumina Inc, SY-415-1002)

value: midbrain

tag: genotype

value: wildtype


title: 715-MB: Fmr1CRE_midbrain rep3

tag: tissue

value: Fmr1 Mut


title: Sample 23 - lung tumor tissue (test)

description:
test
PU 237T

tag: gender

value: Non-smoker


title: Mus musculus C-I

description: Gene expression data of ileum extracted from Mus musculus fed a cellulose diet.

source_name: ileum in Mus musculus fed a cellulose diet


title: Sample 20 - lung tumor tissue (test)

description:
test
NE 03

value: Female

tag: tobacco history

value: IIB


title: S15.4554.A1 [11427_S15.4554.A1_TAGCTT]


title: Sample 22 - lung tumor tissue (test)

description:
test
PU 235T

tag: histological subtype

value: IA


title: Sample 21 - lung tumor tissue (test)

description:
test
PU 234T

tag: pathological stage

value: IIIB


title: S15.4303.A1 [11426_S15.4303.A1_GATCAG]


title: 713-MB: WT_midbrain rep2


title: S15.11356.A1 [11425_S15.11356.A1_ACTTGA]

value: Tumor


title: 711-MB: Fmr1CRE_midbrain rep2


title: Sample 19 - lung tumor tissue (test)

description:
test
PU 239T

source_name: mRNA of tumor tissue (AC)

value: Atypical carcinoid

tag: status


title: Sample 17 - lung tumor tissue (test)

description:
test
PU 236T

tag: survival


title: 702-MB: WT_midbrain rep1


title: S15.6746.B [11428_S15.6746_B1_GGCTAC]


title: S15.6993.A1 [11424_S15.6993.A1_CAGATC]

value: Plaque


title: Sample 15 - lung tumor tissue (test)

description:
test
NE 02

value: lung tumor

value: Dead


title: Sample 16 - lung tumor tissue (test)

description:
test
PU 232T


title: S15.5295.B1 [11421_S15.5295_B1_TGACCA]


title: Sample 14 - lung tumor tissue (test)

description:
test
PU240T

source_name: mRNA of tumor tissue (LCNEC)

value: Former

value: Large cell neuroendocrine carcinoma

value: IB


title: Mummified human remains A.C.B.

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: found in Basel, Switzerland

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium EPICBeadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Analysis was performed on RAW idat files using the R package minfi and the ssNoob normalization. Detection p values were calculated using the R sesame package.

label: Cy5 and Cy3

source_name: colon tissue

extract_protocol: Sample preparation and DNA extraction was performed in a dedicated pre-PCR area with protective clothing, UV-light exposure of the equipment, and bleach sterilization of surfaces, and filtered pipette tips at the ancient DNA laboratory of the EURAC Institute for Mummy Studies in Bolzano, Italy. DNA was extracted from the tissue samples using a chloroform-based DNA extraction method (DOI: 10.1016/j.mimet.2008.07.014)

value: female

value: colon


title: Sample 10 - lung tumor tissue (test)

description:
test
NE 19

source_name: mRNA of tumor tissue (SCLC)

value: Smoker

value: Small cell lung carcinoma

value: IV


title: Sample 13 - lung tumor tissue (test)

description:
test
NE 13

value: Female


title: Sample 11 - lung tumor tissue (test)

description:
test
NE 04

value: Male


title: Sample 9 - lung tumor tissue (test)

description:
test
NE 18


title: Sample 18 - lung tumor tissue (test)

description:
test
PU 238T

value: Non-smoker

value: IA

value: Alive


title: 715-HB: Fmr1CRE_hindbrain rep3

source_name: hindbrain

value: hindbrain

value: Fmr1 Mut


title: 711-HB: Fmr1CRE_hindbrain rep2


title: S15.5295.A1 [11420_S15.5295_A1_TTAGGC]

value: Tumor


title: Mummified human remains T.H.

description: found in Vác, Hungary

source_name: lung tissue

label_protocol: Standard Infinium HD Methylation Assay protocol

value: lung


title: 702-HB: WT_hindbrain rep1

value: wildtype


title: 701-MB: Fmr1CRE_midbrain rep1

value: midbrain


title: S15.6955.A [11011_S15.6599]

value: Plaque


title: S15.5509. [11419_S15.5509_A1_CGATGT]


title: Sample 8 - lung tumor tissue (test)

description:
test
NE 17

value: lung tumor

value: IIIB

value: Dead


title: Sample 2 - lung tumor tissue (test)

description:
test
NE 05

value: Smoker

value: Small cell lung carcinoma


title: Sample 4 - lung tumor tissue (test)

description:
test
NE 10

value: Female

value: IV


title: Sample 7 - lung tumor tissue (test)

description:
test
NE 15

value: Male


title: S15.7535.A [11013_S15.7535]


title: 713-HB: WT_hindbrain rep2


title: Sample 12 - lung tumor tissue (test)

description:
test
NE 12

value: Large cell neuroendocrine carcinoma

value: IIIA


title: Sample 3 - lung tumor tissue (test)

description:
test
NE 06


title: Sample 1 - lung tumor tissue (test)

description:
test
NE 01


title: 701-HB: Fmr1CRE_hindbrain rep1

value: hindbrain


title: S15.6746.A [11418_S15.6746_A1_ATCACG]


title: MSK PCa22

first: Yu

address: 1275 York Ave, Box 20

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA sequencing reads were 3’ trimmed for base quality 15 and adapter sequences using version 0.4.5 of TrimGalore, and then aligned to human assembly hg19 with STAR v2.6 using default parameters to generate BAM alignment files.
TPMcalculator software was to generate TPM (transcripts per million) for each gene in each BAM file.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: comma delimited text file containing TPM of genes

source_name: prostate cancer organoid

extract_protocol:
RNA extraction was performed according to manufacture's instuction in PureLinkTM RNA Mini Kit (Thermo Fisher Scientific #12183025)
RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA, at the Genome Technology Center (GTC) at NYU.

tag: primary site

value: Prostate

tag: biopsy site

value: Lymph Node


title: 714-HB: WT_hindbrain rep3


title: MSK PCa24


title: Sample 6 - lung tumor tissue (test)

description:
test
NE 14

tag: age


title: 715-FB: Fmr1CRE_forebrain rep3

source_name: forebrain

value: forebrain

value: Fmr1 Mut


title: S15.8147.A1 [11009_S15.8417]

value: Tumor


title: Sample 5 - lung tumor tissue (test)

description:
test
NE 11


title: S15.10848.A [11010_S15.10848]


title: 714-FB: WT_forebrain rep3

value: wildtype


title: 12-treatment-BK [miRNA-seq]

description:
28842_12-treatment-BK_S19_L999
BK_treated_miRNA

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
reads were aligned to hg19 genome assembly using Tophat2 with default settings
gene expression levels of Refseq genes were counted with Htseq-count
For miRNA, reads were trimmed to remove adapter and aligned to hg19 using Bowtie
miRNAs in miRBase v21 were counted using customized R scripts
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file containing the raw count

source_name: CTCL patient_Skin_Baseline

extract_protocol:
QIAGEN RNAeasy FFPE
Kappa mRNA Hyperprep kit for mRNA-seq, and Illumina TruSeq miRNA for miRNA-seq

treatment_protocol: Cobomarsen given via intralesional injection (75 mg/dose), subcutaneous (SC), IV rapid bolus injection, or 2-hour IV infusion (300, 600 or 900 mg/dose)

tag: subject status

value: CTCL patient

value: Skin

tag: timepoint

value: Baseline


title: 20a-LNP treated murine liver non parenchymal cells

value: FACS sorted liver

value: 3 hours after injection