title: Mouse-striatum-cKO-Rep3

city: Nan Jing

first: Wen

middle: hua

last: Liu

state: Jiang Su

address: 2 Sipailou Road

institute: Southeast university

data_processing:
The clean reads were subjected to further analysis based on the RNA-seq pipeline, by Bowtie, TopHat, CuffLinks, and CummeRbund software suite
The Cuffdiff program within Cufflinks was used to test for statistically significant differences between w1118 and dnlg3KO88/dnlg3KO127. The downstream statistical analyses and plots were performed in R (v3.1.1; http://www.r-project.org/).
Volcano plots, MA plots and bubble plots were generated in R with the function pheatmap of the gplots package. GO analysis was conducted using DAVID and Cytoscape (v3.4.0) with the BiNGO plugin (v3.0.3)
Assembly: GRCm38, release-98
Supplementary files format and content: csv file include count values for all 6 Samples

source_name: Brain

extract_protocol:
Total RNA was extracted from FACS by sorting strong GFP-positive cells using RNAiso Plus (TaKaRa). RNA-seq data were obtained by the service provided by Genergy Biotechnology Co. Ltd. (Shanghai, China).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Isolating the strong GFP-positive striatal IPs at E15.5  Pqbp1+/Y;Dlx5/6-Cre-IRES-EGFP and Pqbp1fl/Y;Dlx5/6-Cre-IRES-EGFP mice by using fluorescence-activated cell sorting (FACS)

value: Brain

value: Striatal intermediate progenitors

value: fluorescence-activated cell sorting


title: Human iPSCs, mesoderm differentiation day 2, TCF21 overexpression, biol rep 2

status: Public on Feb 21 2023

type: SRA

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

country: USA

institute: Harvard University

description:
Column TCF21
TF_gene_expression.csv

library_source: transcriptomic

data_processing:
For the first six samples (sorted FOXL2+, COV434, iPSCs), kallisto v0.46.2 was used to determine transcript abundances based on the Ensembl GRCh38 v96 reference transcriptome, with additional TF transgenes added.
For the mesoderm differentiation samples (with and without TF expression), reads were aligned to the GrCh38 genome assembly using STAR v2.7.9a, and differential expression analysis was performed using DESeq2 1.28.1 with the iPSC samples as a reference.
Assembly: GrCh38
Supplementary files format and content: Abundance tables (abundance.tsv) are output from kallisto and contain TPM abundances for transcripts.
Supplementary files format and content: TF_gene_expression.csv is output from DESeq2 and contains: the basal gene expression (in iPSCs), the log2 fold change from iPSCs to the other samples, and the adjusted p-values for changes in gene expression.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: iPSCs containing integrated transcription factor expression transposons were dissociated with TRYPLE, and plated in DK10 medium (DMEM-F12, 15 mM HEPES, 1X GlutaMax, 10% KSR) with Y-27632 (10 µM), CHIR99021 (3 µM), and doxycycline (1 µg/mL) at a cell density of 12,500/cm2 on Matrigel-coated polystyrene plates. The medium volume per well of 6-well plate was 2 mL. RNA was extracted 48 hours after plating.

extract_protocol:
Monarch Total RNA Miniprep kit (NEB).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (with PolyA Enrichment Beads)

tag: cell line

tag: cell type

value: induced pluripotent stem cell, mesoderm differentiation

tag: genotype

tag: treatment


title: Mouse-striatum-cKO-Rep2

country: China

molecule: total RNA

organism: Mus musculus

tag: tissue


title: Human iPSCs, mesoderm differentiation day 2, TCF21 overexpression, biol rep 1

description:
Column TCF21
TF_gene_expression.csv

value: TCF21 overexpression


title: Human iPSCs, biol rep 2

growth_protocol: hiPSCs were cultured in mTESR Plus medium (Stemcell Technologies) on standard polystyrene plates coated with hESC-qualified Matrigel (Corning).

value: induced pluripotent stem cell

value: wild-type

value: No TFs


title: NSC-60C

type: RNA

city: Tokyo

first: Masayuki

last: Komatsu

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National Cancer Center Research Institute

description: Parental line

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring version 14.9 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

label: biotin

source_name: Gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: Cells were maintained in 10% FBS-containing Ham's F12 medium under an atmosphere of 5% CO2 and 95% air at 37˚C.

extract_protocol: Cultured cells were washed by D-PBS and lysed by ISOGEN solution. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No specific treatment.


title: NSC-58C

description: Parental line


title: NSC-57C

description: Parental line


title: Mouse-striatum-cKO-Rep1


title: NSC-61C

description: Parental line


title: NSC-64C

description: Parental line


title: Human iPSCs, biol rep 1


title: Mouse-striatum-WT-Rep2

value: WT


title: COV434, biol rep 2

growth_protocol: COV434 cells were cultured in DMEM + 10% FBS + 1X GlutaMax (Gibco).

value: small cell carcinoma of the ovary, hypercalcemic type


title: NSC-56C-2

description: Parental line


title: COV434, biol rep 1


title: Mouse-striatum-WT-Rep3


title: NSC-54C

description: Parental line


title: Sorted FOXL2+ granulosa-like cells, biol rep 1

growth_protocol: For differentiation of granulosa-like cells, iPSCs containing integrated transcription factor expression transposons were dissociated with TRYPLE, and plated in DK10 medium (DMEM-F12, 15 mM HEPES, 1X GlutaMax, 10% KSR) with Y-27632 (10 µM), CHIR99021 (3 µM), and doxycycline (1 µg/mL) at a cell density of 12,500/cm2 on Matrigel-coated polystyrene plates. The medium volume per well of 6-well plate was 2 mL. 48 hours after plating, the medium was changed to DK10 + doxycycline (1 µg/mL), and the medium was subsequently changed every 24 hours. Cells were harvested on day 5 and sorted based on FOXL2-T2A-tdTomato reporter expression.

extract_protocol:
Arcturus PicoPure kit (Thermo Fisher)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (with PolyA Enrichment Beads)

value: granulosa-like cell

value: NR5A1, RUNX1, TCF21, GATA4


title: Sorted FOXL2+ granulosa-like cells, biol rep 2


title: 203866300034_R06C01

type: genomic

city: Berlin

first: David

last: Kaul

address: Augustenburger Platz 1

department: Department of Radiation Oncology

country: Germany

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
The calculations were carried out in R, version 4.2.0 "Virgorous Calesthenics"
Average beta-Values after normalization using detection p values

label: cy3, cy5

molecule: genomic DNA

source_name: Tumor

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

tag: Sex

value: Male

tag: age

tag: incoming diagnosis

value: Anaplastic ependymoma (WHO grade III)

tag: tumor location

value: supratentorial

tag: progression-free survival (months)

tag: progression (0=no, 1=yes)

tag: overall survival (months)

tag: death (0=no, 1=yes)

tag: material type

value: FFPE


title: Mouse-striatum-WT-Rep1


title: AP19

city: miami

first: RIMPI

last: KHURANA

state: FL

address: Room 6112B, Rosenstiel Medical Science Building (RMSB),1600 NW 10th Avenue

institute: University of miami

description: Non-Response

data_processing:
FASTQ raw files were generated by the sequencer, further pre-processed to discard the adaptor sequences using Cutadapt, and low-quality reads were eliminated
filtered reads were mapped to mouse genome-mm9 using STAR aligner (RRID:SCR_004463).  STAR counts were used for differential expression analysis using DESeq
Assembly: Mus Musculus mm9
Supplementary files format and content: CSV

source_name: Prostate tumors

extract_protocol:
Prostate tumors were harvested following treatment and RNA isolated using RNeasy plus micro kit
Paired end sequencings were performed for 30 million reads on mRNA

treatment_protocol: Pb-Cre; PTENfl/fl Trp53fl/fl mice with established prostate tumors were treated with degarelix (0.625 mg/mouse, sc, single dose) + copanlisib (14 mg/kg, iv, every alternate day) + aPD-1 (200 μg/mouse, ip, every alternate day) combination for 28 days

value: Prostate tumors

value: Pb-Cre; PTENfl/fl Trp53fl/fl

value: Untreated

tag: response status

value: Non-Response

tag: condition


title: AP20

description: Non-Response


title: AP18

description: Non-Response


title: SH-SY5Y FUSKO DIFF 3 (smallRNA-seq)

city: Poznan

first: Kishor

last: Gawade

address: Uniwersytetu Poznańskiego 10

department: Faculty of Biology

country: Poland

institute: Adam Mickiewicz University

description:
FUSKO_DIFF3
counts_file_differentiated.txt

data_processing:
Quality check with FastQC v0.11.4. Then, fastx-toolkit/0.0.14 was used for adapter removal and quality filtering.
Aligned to ribosomal RNA sequences using Bowtie 2 (v2.2.3) and discarding of mapped reads.
Mapping against the human genome (GRCh38 downloaded from Ensembl) with Bowtie 2 (v2.2.3).
SAM files to BAM format using samtools then applied with an R package Rsubread featureCounts to get raw read counts with the parameters featureType=gene allowMultiOverlap=TRUE and countMultiMappingReads=TRUE.
A GTF file was created from Homo_sapiens.GRCh38.100.gtf (Ensembl) that consists of only snoRNAs, miRNAs, and snRNAs used in featureCounts as an annotation file. Differentially expressed genes (DEGs) using DESeq2 with default settings and a threshold of 0.05 for adjusted P-value.
Assembly: Homo_sapiens.GRCh38 from Ensembl version 100
Supplementary files format and content: .text file consisting of raw read count matrix

growth_protocol: SH-SY5Y cells were grown in Dulbecco’s modified Eagle’s medium containing L-glutamine and 4.5 g/L glucose (DMEM; Lonza) and supplemented with 10% fetal calf serum (Gibco) and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin (Sigma-Aldrich)) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated using the Quick-RNA MiniPrep Kit (Zymo Research, R1055) according to the manufacturer's protocol.
500 ng of total RNA were used to prepare small RNA sequencing libraries using Small RNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) following the manufacturer’s protocol. Library quality was analyzed with High Sensitivity DNA Kit on Agilent Bioanalyzer 2100, and quantification was done using Qubit dsDNA HS (High Sensitivity) Assay kit (InvitrogenTM) with Qubit fluorometer. Quantified libraries were sent to the Lexogen sequencing facility (Vienna, Austria). Single-end read sequencing was carried out with 75 bp sequencing length on the Illumina NextSeq500 platform.

treatment_protocol: SH-SY5Y wild-type and FUS knockout cells were subjected to retinoic acid (RA) treatment for 10 days. All-trans RA (USP, Tretinoin, 1674004) at a final concentration of 75 µM was added to DMEM with 10% FBS. The media, along with the RA, were replaced every 3 days.

value: thrice-cloned sub-line of bone marrow biopsy-derived line SK-N-SH

value: FUS knock-out

value: Differentiation using Retinoic Acid for 10 days


title: NSC-52C

description: Parental line


title: AP16

description: Response

value: Response


title: AP17

description: Non-Response


title: NSC-50C

description: Parental line


title: SH-SY5Y FUSKO DIFF 1 (smallRNA-seq)

description:
FUSKO_DIFF1
counts_file_differentiated.txt


title: SH-SY5Y WT DIFF 2 (smallRNA-seq)

description:
WT_DIFF2
counts_file_differentiated.txt

value: wild-type


title: NSC-47C

description: Parental line


title: NSC-51C

description: Parental line


title: SH-SY5Y WT DIFF 3 (smallRNA-seq)

description:
WT_DIFF3
counts_file_differentiated.txt


title: AP15

description: Response


title: NSC-49C

description: Parental line


title: 203774250049_R06C01

value: Ependymoma (WHO grade II)


title: NSC-46C

description: Parental line


title: SH-SY5Y FUSKO PROLI 3 (smallRNA-seq)

description:
FUSKO3_Proli
counts_file_proliferating.txt


title: AP14

description: Response


title: NSC-44CF

description: Parental line


title: NSC-53C

description: Parental line


title: SH-SY5Y FUSKO DIFF 2 (smallRNA-seq)

description:
FUSKO_DIFF2
counts_file_differentiated.txt


title: 203810690062_R06C01

value: Female


title: NSC-40C

description: Parental line


title: NSC-39C

description: Parental line


title: NSC-37C

description: Parental line


title: SH-SY5Y WT DIFF 1 (smallRNA-seq)

description:
WT_DIFF1
counts_file_differentiated.txt


title: SH-SY5Y FUSKO PROLI 1 (smallRNA-seq)

description:
FUSKO1_Proli
counts_file_proliferating.txt


title: anti-HA WT rep2

city: Ottawa

first: Marjorie

last: Brand

state: Onatrio

address: 501 Smyth Road

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

description: GATA2-expressing mutant

library_source: genomic

data_processing:
Raw reads data were aligned to mouse reference genome (mm10) using Bowtie2. Reads that were duplicated or mapped to the black list regions were removed from the analysis. The resulted bam files were sorted, and subjected to MACS3 for peak calling. For visualization of the bind profiles, deepTools bamCoverage was used to generate coverage track (bigWig).
Peaks were called using MACS3 with recommended CUT&Tag settings as follows: macs3 callpeak -t sample_rep1.bam sample_rep2.bam -f BAMPE --gsize 2308125349 -q 1e-6 --nolambda --nomodel --outdir sample_MACS3_Output.
Assembly: mm10
Library strategy: CUT&Tag

source_name: Fetal liver

growth_protocol: Cells were cultured in expansion media containing β-estradiol

extract_protocol: Cells were incubated with retroviruses for 3 d and washed and resuspended in PBS with 2% FBS prior to FACS isolation.

value: Fetal liver

value: Hematopoietic progenitors

value: Infected with GATA2 vector

tag: chip antibody

value: HA-tag mAb rabbit (Cell Signaling Technology, 3724)


title: anti-HA 9aa-Ins rep1

description: 9aa-Ins-expressing mutant

value: Infected with 9aa-Ins vector


title: anti-HA WT rep1

description: GATA2-expressing mutant


title: SH-SY5Y FUSKO PROLI 2 (smallRNA-seq)

description:
FUSKO2_Proli
counts_file_proliferating.txt

tag: cell line


title: anti-HA 9aa-Ins rep2

description: 9aa-Ins-expressing mutant

tag: cell type


title: 203740910036_R04C01

value: Anaplastic ependymoma (WHO grade III)

value: supratentorial

value: FFPE


title: NSC-38C-1

description: Parental line


title: SH-SY5Y WT PROLI 3 (smallRNA-seq)

description:
WT3_Proli
counts_file_proliferating.txt

tag: genotype


title: SH-SY5Y WT PROLI 2 (smallRNA-seq)

description:
WT2_Proli
counts_file_proliferating.txt

tag: treatment


title: anti-GATA2 9aa-Ins rep1

description: 9aa-Ins-expressing mutant

tag: tissue

value: GATA2 pAb rabbit (custom)


title: 203927450065_R06C01

tag: Sex

value: Male


title: anti-GATA2 WT rep1

description: GATA2-expressing mutant


title: SH-SY5Y WT PROLI 1 (smallRNA-seq)

description:
WT1_Proli
counts_file_proliferating.txt

value: thrice-cloned sub-line of bone marrow biopsy-derived line SK-N-SH


title: NSC-36C

description: Parental line


title: TA-/-, thymus tissue, sample3

city: Guangzhou

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

description:
TA-/-_Thy3
thymus_tissue_rpkm.txt

data_processing:
STAR-2.5.2b software was used to map reads to the reference genome.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for bulk RNA-seq Samples

source_name: murine thymus tissue

extract_protocol:
Total RNA was extracted utilizing RNA iso Plus (TaKaRa, 9109) from liver tissues or 5×10^5 CD8+ T cells that were isolated using a FACS Aria II cell sorter
RNA libraries were prepared for sequencing using standard Illumina protocols or BGI protocols.

value: murine thymus tissue

tag: age

value: 2-4 weeks

tag: strain

value: TG Aire-/-

value: thymus total cells

value: no treatment


title: NSC-35C-1

description: Parental line


title: NSC-34C

description: Parental line


title: KEN_OSKM_hiTSC_C2_rep2

city: Jerusalem

first: Yosef

last: Buganim

address: Hadassah Medical School

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

data_processing:
Raw reads were quality-trimmed and adapters removed using trim_galore (version 0.6.5)
The processed fastq files were mapped to the mouse transcriptome and genome using HISAT2 (v2.1.0). The genome version was GRCh38.
Quantification was done using htseq-count (version 0.13.5)
Differential analysis was done using the R package DESeq2  (version 1.28.1)
Genome_build: GRCh38

source_name: Human induced trophoblast stem cells

growth_protocol: hiTSC and hbdTSC cells were grown on a layer of Mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells and cultured in human TSC medium (Okae et al, 2018). HFFs were grown in DMEM containing 10%FBS, 1% L-glutamine and 1% penicillin-streptomycin. hESCs and hiPSCs were grown in human embryonic stem cell (hES) medium comprised of Knockout DMEM containing 15% KnockOut serum replacement, 0.1 mM 2-mercaptoethanol, 1% L-glutamine, 1% non-essential amino acids and 1% Penicillin-Streptomycin, supplemented with freshly added 4ng/ml bFGF.

extract_protocol:
Total RNA was isolated using the Macherey-Nagel RNA NucleoSpin kit (Ornat)
mRNA libraries were prepared using the SENSE mRNA-seq library prep kit V2 (Lexogen)

value: OSKM-Induced trophoblast stem cells, line #2


title: anti-GATA2 9aa-Ins rep2

description: 9aa-Ins-expressing mutant

value: Fetal liver


title: TA-/-, thymus tissue, sample2

description:
TA-/-_Thy2
thymus_tissue_rpkm.txt


title: KEN_OSKM_hiTSC_C2_rep1


title: 204776820085_R07C01

value: Female

tag: incoming diagnosis

value: Ependymoma (WHO grade II)

tag: tumor location

value: infratentorial


title: TA+/-, thymus tissue, sample3

description:
TA+/-_Thy3
thymus_tissue_rpkm.txt

value: TG Aire+/-


title: TA-/-, thymus tissue, sample1

description:
TA-/-_Thy1
thymus_tissue_rpkm.txt


title: NSC-29C

description: Parental line


title: TA+/-, thymus tissue, sample2

description:
TA+/-_Thy2
thymus_tissue_rpkm.txt


title: KEN_OSKM_hiTSC_C1_rep2

value: OSKM-Induced trophoblast stem cells, line #1


title: GM2_hiTSCs_C16_rep2

value: Induced trophoblast stem cells, line #16


title: NSC-26C-1

description: Parental line


title: NSC-28C

description: Parental line


title: GM2_hiTSCs_C16_rep1


title: GM2_hiTSCs_C15_rep2

value: Induced trophoblast stem cells, line #15


title: TA+/-, thymus tissue, sample1

description:
TA+/-_Thy1
thymus_tissue_rpkm.txt


title: A-/-, thymus tissue, sample3

description:
A-/-_Thy3
thymus_tissue_rpkm.txt

value: Aire-/-


title: GM2_hiTSCs_C15_rep1


title: NSC-32C

description: Parental line


title: NSC-24C

description: Parental line


title: MKN45

description: Parental line


title: NSC-23C-1

description: Parental line


title: 203740910036_R03C01

value: Anaplastic ependymoma (WHO grade III)

value: supratentorial

tag: progression-free survival (months)

tag: progression (0=no, 1=yes)

value: FFPE


title: A-/-, thymus tissue, sample2

description:
A-/-_Thy2
thymus_tissue_rpkm.txt

value: murine thymus tissue

value: 2-4 weeks


title: KEN_OSKM_hiTSC_C1_rep1


title: GM2_hiTSCs_C13_rep2

value: Induced trophoblast stem cells, line #13


title: A-/-, thymus tissue, sample1

description:
A-/-_Thy1
thymus_tissue_rpkm.txt

value: thymus total cells

value: no treatment


title: HSC-60

description: Parental line


title: TA-/-, liver tissue, batch2, sample2, CD8 depleted

description:
TA-/-CD8del_L2
liver_tissue_CD8del_rpkm.txt

source_name: murine liver tissue

value: murine liver tissue

value: TG Aire-/-

value: liver total cells

value: CD8+ T depleted


title: HSC-59

description: Parental line


title: AP21

description: Non-Response

value: Prostate tumors

value: Pb-Cre; PTENfl/fl Trp53fl/fl

value: Untreated

value: Non-Response


title: PCS_hiTSC_C11_rep1

value: Induced trophoblast stem cells, line #11


title: GM2_hiTSCs_C13_rep1


title: PCS_hiTSC_C11_rep2


title: TA-/-, liver tissue, batch2, sample2

description:
TA-/-_L2
liver_tissue_CD8del_rpkm.txt


title: HSC-58

description: Parental line


title: HSC-44

description: Parental line


title: A+/+, liver tissue, batch2, sample1

description:
A+/+_L1
liver_tissue_CD8del_rpkm.txt

value: Aire+/+


title: KEN_hiTSC_C7_rep2

value: Induced trophoblast stem cells, line #7


title: TA-/-, liver tissue, batch2, sample1

description:
TA-/-_L1
liver_tissue_CD8del_rpkm.txt


title: KEN_hiTSC_C7_rep1


title: KEN_hiTSC_C1_rep2

value: Induced trophoblast stem cells, line #1


title: TA+/-, liver tissue

description:
TA+/-
liver_tissue_rpkm.txt

value: TG Aire+/-


title: KEN_hiTSC_C1_rep1


title: A-/-, liver tissue

description:
A-/-
liver_tissue_rpkm.txt

value: 2-4 weeks

value: Aire-/-


title: KEN_hiTSC_C4_rep2

value: Induced trophoblast stem cells, line #4


title: KATO-III

description: Parental line

value: KATO-III


title: A+/+, liver tissue, batch2, sample2

description:
A+/+_L2
liver_tissue_CD8del_rpkm.txt

value: murine liver tissue

value: no treatment


title: HSC-43

description: Parental line


title: TA-/-, liver tissue, batch2, sample1, CD8 depleted

description:
TA-/-CD8del_L1
liver_tissue_CD8del_rpkm.txt

value: TG Aire-/-

value: liver total cells


title: HSC-39

description: Parental line


title: KEN_hiTSC_C4_rep1


title: GM2_fib_rep2

source_name: Human skin fibroblasts

value: Adult female skin fibroblasts


title: HGC-27

description: Parental line


title: TA-/-, liver tissue

description:
TA-/-
liver_tissue_rpkm.txt


title: GSU

description: Parental line

value: GSU


title: NSC-22C

description: Parental line


title: FU97

description: Parental line


title: GCIY

description: Parental line

value: GCIY


title: A+/+, liver tissue

description:
A+/+
liver_tissue_rpkm.txt


title: No TrpABX_004

city: New York

first: Nicholas

last: Arpaia

state: NY

address: 701 West 168th Street, Hammer Health Sciences Center 906

department: Microbiology and Immunology

institute: Columbia University Irving Medical Center

data_processing:
Reads were aligned to the Mus musculus reference transcriptome (Mouse:GRCm38) using kallisto (0.44.0) Bray et al, Nature Biotech. 2016
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Estimated Counts (Est_Counts) and Transcripts Per Million (TPM)

source_name: Intestinal Ileum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Poly-A+ mRNAs were enriched from total RNA using oligo d(T) beads, followed by cDNA library construction

treatment_protocol: Mice were fed Control or Tryptophan deficient diet for three weeks.  ABX treated animals were fed a cocktail of Ampicillin, Vancomycin, Gentamycin, Metronidizole and Neomycin.

value: Intestinal Ileum

value: Tryptophan Deficient Diet + Antibiotics


title: GM2_fib_rep1


title: KEN_hFF_rep1

source_name: Human foreskin fibroblasts

value: Foreskin fibroblasts


title: No TrpABX_005


title: NSC-17CA

description: Parental line


title: NSC-20C

description: Parental line


title: NSC-18C-1

description: Parental line


title: NSC-16C

description: Parental line


title: KEN_hFF_rep2


title: No TrpABX_003


title: hiPSC_rep1

source_name: Human induced pluripotent stem cells

value: Induced pluripotent stem cells


title: hiPSC_rep2


title: NSC-48CA

description: Parental line


title: ControlABX_005

value: Control Diet + Antibiotics


title: NSC-15CF

description: Parental line


title: ControlABX_004


title: NSC-10C

description: Parental line


title: No TrpABX_001


title: ID116GV_Infected

city: Belo Horizonte

first: Ana Maria

last: Caetano Faria

state: Minas Gerais

address: Av. Antônio Carlos, 6627, Pampulha

department: Bioquímica e Imunologia

country: Brazil

institute: Universidade Federal de Minas Gerais

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: minfi package from Bioconductor on R environment

label: Cy5 and Cy3

label_protocol: Standard Illumina labelling protocol

growth_protocol: Whole Blood collected from patients

extract_protocol: DNA was extracted using salting out methodology

treatment_protocol: Leukocytes purified from whole blood

value: whole blood

value: Leukocytes

value: M

tag: ID

tag: infection

value: Infected

tag: disease state

value: leprosy


title: NSC-14C

description: Parental line


title: ControlABX_003


title: hbdTSC_E9_rep2

value: Blastocyst-derived trophoblast stem cells, line #9


title: CR17_Infected

value: F


title: NSC-11C

description: Parental line


title: ID77GV_Infected


title: NSC-9C

description: Parental line


title: ID97GV_Infected


title: No TrpABX_002


title: hESCs_rep2

source_name: Embryonic stem cells

value: Embryonic stem cells


title: hbdTSC_E9_rep1

source_name: Blastocyst-derived trophoblast stem cells


title: hESCs_rep1


title: hbdTSC_E2_rep2

value: Blastocyst-derived trophoblast stem cells, line #2


title: No Trp_004

value: Tryptophan Deficient Diet


title: H3K4me2_OSKM_72h_KEN_hFF_rep2

data_processing:
For analysis of the H3K4me2 activity data, raw reads (FastQ files) were quality-trimmed using Trim Galore (v0.6.5, default parameters) and aligned to the human genome GRCh38 using burrows-wheeler aligner (BWA v 0.7.17, 59 )
Peaks were called with MACS2 (v 2.2.7.1 60 ). Differential peak analysis was performed using the DESeq2 package (v 1.28.1, DOI:10.18129/B9.bioc.DESeq2)
Peaks were defined specifically for each group of cells and the R package (Venn v 1.9) was used to construct all Venn diagrams
Peaks that are specific to OSKM D3 and OGKM D3 were differentially identified with FDR<0.05
Intersection of these peaks with hbdTSCs and hESCs allowed for the identification of specific set of peaks that were investigated for possible regulation of nearby genes
GREAT was used to associate these peaks with genes within 250 kb. Extracted genes were then intersected with a specific set of genes that were differentially expressed in hbdTSCs and not in fibroblasts or hESCs, or set of genes that were differentially expressed in hESCs and not in fibroblasts or hbdTSCs
Genome_build: GRCh38

source_name: Foreskin fibroblasts

growth_protocol: hbdTSC cells were grown on a layer of Mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells and cultured in human TSC medium (Okae et al, 2018). HFFs were grown in DMEM containing 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin. hESCs were grown in human embryonic stem cell (hES) medium comprised of Knockout DMEM containing 15% KnockOut serum replacement, 0.1 mM 2-mercaptoethanol, 1% L-glutamine, 1% non-essential amino acids and 1% Penicillin-Streptomycin, supplemented with freshly added 4ng/ml bFGF. HFFs infected with lentiviral vectors GOKM or OSKM were grown in DMEM containing 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin and treated with 2ug/ml doxycycline for 3 days.

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Mendenhall et al., 2013). Briefly, cells from two biological replicates per line were fixed for 10min at RT with a final formaldehyde concentration of 0.8%. Formaldehyde was quenched with glycine at a final concentration of 125mM. The cells were then lysed with lysis buffer (100mM Tris-HCl, 300mM NaCl, 2% Triton X-100, 0.2%v sodium deoxycholate and 10mM Cacl2) supplemented with EDTA-free protease inhibitor (Roche, 11873580001) for 20min on ice. The chromatin was digested by adding MNase (Thermo Scientific, 88216) for 20min at 37C and MNase was inactivated by adding 20mM EGTA. The fragmented chromatin was added to pre-bounded Dynabeads (A and G mix, Invitrogen, 10004D/ 10002D) using H3K4me2 antibody (Millipore, 07-030) at 2 ug per reaction. Samples were then washed twice with RIPA buffer, twice with RIPA high salt buffer (NaCl 360mM), twice with LiCl wash buffer (10mM Tris-Hcl, 250mM LiCl, 0.5% DOC, 1mM EDTA, 0.5% IGEPAL) and twice with 10mM Tris-HCl pH = 8. DNA was purified by adding RNase A (Thermo Scientific, EN0531) and incubated for 30 min at 37C and then with Proteinase K (Invitrogen, 25530049) for 2h. The DNA was eluted by adding 2X concentrated elution buffer (10mM Tris-HCl, 300mM NaCl, 1% SDS, 2mM EDTA) and reverse crosslinked overnight at 65C. The DNA was then extracted using AMPure XP beads (Beckman Coulter Genomics, A63881).
ChIP sample libraries were prepared according to Illumina Genomic DNA protocol.

value: OSKM-induced Foreskin fibroblasts


title: ControlABX_002


title: CR10_Infected


title: NSC-6C

description: Parental line


title: NSC-4X1a

description: Parental line


title: NSC-7C

description: Parental line


title: ControlABX_001


title: ID100_Healthy

value: Healthy


title: hbdTSC_E2_rep1


title: No Trp_005

value: Intestinal Ileum


title: CR07_Infected


title: H3K4me2_OSKM_72h_KEN_hFF_rep1


title: No Trp_003


title: ID101_Healthy


title: CR13_Infected


title: No Trp_002


title: CR03_Infected


title: paps1-1 rep1

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

description: mutant

data_processing:
Adapter clipping was done by LGC Genomics. Reads shorter than 20 bp were discarded.
Reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using STAR (Dobin et al., 2013; doi:10.1093/bioinformatics/bts635) version 2.7.3a with the –quantMode GeneCounts option to get mapping counts at gene level.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Raw gene read counts for each sample.

organism: Arabidopsis thaliana

source_name: pollen tube/style complex

extract_protocol:
For RNA isolation the Arcturus® PicoPure® RNA Isolation Kit was used. The cut portions of the style with grown pollen tubes were flash-frozen in supplied Extraction Buffer directly after the experiment. RNA extraction was performed following the manufacturer’s instructions, including on-column DNAse digestion.
RNA were processed at LGC Genomics for mRNA library preparation and subsequent RNA-Seq on an Illumina HiSeq2000.

value: pollen tube/style complex

value: paps1-1 (Col-0)


title: CR14_Infected


title: NSC-8CM

description: Parental line


title: H3K4me2_GOKM_72h_KEN_hFF_rep2

value: GOKM-induced Foreskin fibroblasts


title: No Trp_001


title: paps1-1 rep 2

description: mutant


title: H3K4me2_GOKM_72h_KEN_hFF_rep1


title: H3K4me2_KEN_hFF_rep2

value: Foreskin fibroblasts


title: WT biol rep 3

description: wild type


title: WT biol rep 2

description: wild type


title: Control_005

value: Control Diet


title: H3K4me2_KEN_hFF_rep1


title: Control_004


title: WT biol rep 1

description: wild type


title: Control_003


title: H3K4me2_hbdTSC_E2_rep2


title: GM2_hiTSCs_C16_rep3 [RRBS]

data_processing:
Raw reads were quality-trimmed and adapters removed.
BSMAP V 2.9 was used to align the paired-end reads to the human genome (hg19)
The methylation ratio of CpGs with sequencing depth of at least 10 reads were computed based on 100bp tiles.
Differential analysis was done using the R package Methylkit  (version 1.14.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Bed CpG file

source_name: iTSCs

growth_protocol: hiTSC and hbdTSC cells were grown on a layer of Mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells and cultured in human TSC medium (Okae et al, 2018). HFFs were grown in DMEM containing 10%FBS, 1% L-glutamine and 1% penicillin-streptomycin. hiTSC and hbdTSC cells were passaged twice on matrigel in order to minimize the presence of MEF feeder cells. hESCs and hiPSCs were grown in human embryonic stem cell (hES) medium comprised of Knockout DMEM containing 15% KnockOut serum replacement, 0.1 mM 2-mercaptoethanol, 1% L-glutamine, 1% non-essential amino acids and 1% Penicillin-Streptomycin, supplemented with freshly added 4ng/ml bFGF.

extract_protocol:
DNA was isolated from samples and incubated in lysis buffer (25mM Tris-HCl at pH8, 2mM EDTA, 0.2%SDS, 200mM NaCl) supplemented with 300μg/mL proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. hiTSC colonies and hbdTSC colonies were passaged twice on matrigel in order to eliminate the presence of MEF feeder cells.
Libraries were prepared as previously described in Boyle et al., 2012.

tag: tag

value: Induced trophoblast stem cells, line #16


title: Control_002


title: GM2_hiTSCs_C16_rep2 [RRBS]


title: KEN_D3_OSKM_rep2 [ATAC-Seq]

data_processing:
For analysis of the accessibility data, raw reads (FastQ files) were quality-trimmed using Trim Galore (v0.6.5, default parameters) and aligned to the human genome GRCh38 using burrows-wheeler aligner (BWA v 0.7.17, 59 )
Peaks were called with MACS2 (v 2.2.7.1 60 ). Differential peak analysis was performed using the DESeq2 package (v 1.28.1, DOI:10.18129/B9.bioc.DESeq2)
Peaks were defined specifically for each group of cells and the R package (Venn v 1.9) was used to construct all Venn diagrams
Peaks that are specific to OSKM D3 and OGKM D3 were differentially identified with FDR<0.05
Intersection of these peaks with hbdTSCs and hESCs allowed for the identification of specific set of peaks that were investigated for possible regulation of nearby genes
GREAT was used to associate these peaks with genes within 250 kb. Extracted genes were then intersected with a specific set of genes that were differentially expressed in hbdTSCs and not in fibroblasts or hESCs, or set of genes that were differentially expressed in hESCs and not in fibroblasts or hbdTSCs
Genome_build: GRCh38

extract_protocol:
50,000 cells per replicate (two biological replicates per line) were incubated with 0.1% NP-40 to isolate nuclei.
ATAC-Seq library preparation was performed as previously described (Buenrostro et al., 2013). After nuclei isolation, nuclei were then transposed for 30 min at 37C with adaptor-loaded Nextera Tn5 (Illumina, Fc-121-1030). Transposed fragments were directly PCR amplified and Sequenced on an Illumina NextSeq 500 platform to generate 2 x 36-bp paired-end reads.


title: Control_001


title: H3K4me2_hbdTSC_E2_rep1


title: GM2_hiTSCs_C16_rep1 [RRBS]


title: CR20_Infected

value: whole blood

value: Leukocytes


title: CR16_Infected

value: M

value: Infected

value: leprosy


title: ID94_Healthy


title: ID109_Healthy


title: CR15_Infected


title: PCS_hiTSC_C11_rep3 [RRBS]

value: Induced trophoblast stem cells, line #11


title: GF WT mouse colorectal polyps

first: Ce

last: Tang

address: No.58, Zhong Shan Er Lu

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Illumina Novaseq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (mm10) whole genome.
BAM files resulting from the alignments were summarized to genes using the Stringtie algorithm.
Transcript per million (TPM) were calculated.
Genome_build: mm10
Assembly: Supplementary_files_format_and_content: Excel file includes FPKM and TPM values for each sample.

source_name: colorectal polyps

extract_protocol: RNA libraries were prepared for sequencing using NEBNext® Ultra RNA Library Prep Kit for Illumina® (E7530).

treatment_protocol: After mice were dissected, polyps and non-polyp tissues from colon were removed and flash frozen on liquid nitrogene. Total RNA was harvested using Mammalian Total RNA Miniprep kit (MilliporeSigma, USA).

value: colorectal polyps

value: WT


title: ID227_Healthy

value: F


title: KEN_D3_GOKM_rep2 [ATAC-Seq]


title: GF WT mouse colorectal nonpolyp tissues

source_name: colorectal non-polyp

value: colorectal non-polyp


title: paps1-1 rep 3

description: mutant


title: PCS_hiTSC_C11_rep2 [RRBS]


title: CR19_Infected


title: KEN_D3_GOKM_rep1 [ATAC-Seq]


title: GF KO mouse colorectal polyps


title: PCS_hiTSC_C11_rep1 [RRBS]


title: ID37_Healthy

value: Healthy


title: GF KO mouse colorectal nonpolyp tissues


title: ID262_Healthy


title: KEN_hFF_rep1 [ATAC-Seq]


title: KEN_hiTSC_C4_rep2 [RRBS]

value: Induced trophoblast stem cells, line #4


title: KEN_hFF_rep2 [ATAC-Seq]


title: KO mice treated with AOM-3DSS

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Colonic tumor/ non-tumor tissue-infiltrating cells were prepared as follows. Briefly, tissue pieces were cut into 1 mm slices, then they were shaken for 40 min in Hanks‘ Balanced Salt Solution (HBSS) containing 3 mM EDTA at 37℃. Intra-epithelial lymphocytes and colonic epithelial cells in the culture supernatant were discarded, and the gut slices were washed twice with HBSS. Then, they were shaken at 37℃ for 120 min in RPMI containing 10% FBS and 1% streptomycin+penicillin, 200 U/ml collagenase (C2139; Sigma-Aldrich), and 5 U/ml Dnase 1 (Sigma-Algrich). After the incubation, the samples were vortexed for 10 sec, and single cell suspension was harvested after sterile gauze-filtration. To prepare lymphocytes, tissue-infiltrating cells were further purified on a 45%/66.6% discontinuous Percoll (Pharmacia, Uppsala, Sweden) gradient at 2200 rpm for 20 min. Colonic polyp-infiltrating myeloid cells for scRNA-seq analysis were stained with anti-mouse CD11b and CD11c antibodies for flow cytometry and were sorted by FACS Aria Fusion (BD Biosciences).
After colonic polyp-infiltrating myeloid-derived cells were harvested, cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent. Fresh cells were resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albumin. Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3’ library preparation kit (SeekGene Catalog No.SO01V3.1). Briefly, appropriate number of cells were loaded into the flow channel of SeekOne® MM chip which had 170,000 microwells and allowed to settle in microwells by gravity. After removing the unsettled cells, sufficient Cell Barcoded Magnetic Beads (CBBs) were pipetted into flow channel and were also allowed to settle in microwells with the help of a magnetic field. Next excess CBBs were rinsed out and cells in MM chip were lysed to release RNA which was captured by the CBB in the same microwell. Then all CBBs were collected and reverse transcription were performed at 37℃ for 30 minutes to label cDNA with cell barcodes on the beads. Further Exonuclease I treatment were performed to remove unused primer on CBBs. Subsequently, barcoded cDNA on the CBBs was hybridized with random primer which had reads 2 SeqPrimer sequence on the 5’ end and could extend to form the second strand DNA with cell barcode on the 3’ end. The resulting second strand DNA were denatured off the CBBs, purified and amplified in PCR reaction. The amplified cDNA product was then cleaned to remove unwanted fragment and added to full length sequencing adapter and sample index by indexed PCR. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length.

value: CD11b+ & CD11c+ myeloid cells

value: 26 weeks old


title: hESCs_rep2 [ATAC-Seq]

value: Embryonic stem cells


title: KEN_hiTSC_C4_rep3 [RRBS]


title: KEN_hiTSC_C4_rep1 [RRBS]


title: ID194_Healthy


title: WT mice treated with AOM-3DSS

description: 10x Genomics


title: hESCs_rep1 [ATAC-Seq]


title: KEN_hiTSC_C2_rep3 [RRBS]

value: Induced trophoblast stem cells, line #2


title: PFC, female, ethanol, 6

city: Richmond

first: JENNIFER

last: WOLSTENHOLME

state: VA

address: 1217 E Marshall Street, KMSB Rm 536

institute: Virginia Commonwealth University

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P21

data_processing:
Quality of FastQC files were assessed with FastQC.
FastQC files were aligned to the GRCm38/mm10 genome using STAR (v2.7.8a). Only reads that mapped to a single location were used in subsequent analysis.
Raw read counts were compiled using featureCounts within the Bioconductor package Subread (v2.0.2).
A GFF annotation file containing collapsed exon counting bins was prepared and the number of reads overlapping each exon bin was counted using the DEXSeq (v1.38.0)
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited featureCount text files include raw counts for each sample
Supplementary files format and content: tab-delimited exonHTcount text files include raw exon bin counts for each sample
Supplementary files format and content: fastq files (for reads 1 and 2) include raw RNA sequencing data

source_name: brain

extract_protocol:
Total RNA was isolated from prefrontal cortex tissue using STAT60 Reagent (Tel-Test, Friendswood, TX) and miRNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
polyA-enriched cDNA libraries were prepared following standard protocols using NEBNext Ultra™ II Directional RNA Library Prep Kit (Illumina)

treatment_protocol: Adolescent male and female DBA/2J mice were dosed with 4 g/kg ethanol (25% w/v in water by gavage) or water intermittently (2 days on/2 days off) on PND 29, 30, 33, 34, 37, 38, 41, and 42. Prefrontal cortex tissue from three mice of the same sex and treatment were pooled, homogenized, and divided in half 24 hours after the last dose. Half of each pooled sample was subjected to RNA-Seq, and the other half was subjected to ChIP-Seq (n = 22).

value: brain

value: female

value: ethanol

tag: biological replicate


title: KEN_hiTSC_C2_rep2 [RRBS]


title: PFC, female, ethanol, 4

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P15


title: CR12_Infected

value: whole blood

value: Leukocytes


title: hbdTSC_E2_rep2 [ATAC-Seq]

value: Blastocyst-derived trophoblast stem cells, line #2


title: Osteoarthritic chondrocytes2

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Raw sequencing reads were processed using Partek Flow Analysis Software (build version 10.0.21.0210). Briefly, raw reads were checked for their quality and trimmed. Reads with an average base quality score per position >30 were considered for alignment. Trimmed reads were aligned to the human genome version hg38-Gencode Genes- release 30 using STAR -2.6.1d with default parameters. Reads with alignment percentage >75% were de-duplicated based on their unique molecular identifiers (UMIs). Reads mapping to the same chromosomal location with duplicate UMIs were removed. Thereafter ‘Knee’ plot was constructed using the cumulative fraction of reads/UMIs for all barcodes. Barcodes below the cut-off defined by the location of the knee were assigned as true cell barcodes and quantified. Further noise filtration was done by removing cells having >3% mitochondrial counts and total read counts >24,000. Genes not expressed in any cell were also removed as an additional clean-up step. Cleaned up reads were normalized using counts per million (CPM) method followed by log transformation generating count matrices for each sample. Samples were batch corrected on the basis of expressed genes and mitochondrial reads percent.
Genome_build: hg38-Gencode Genes- release 30
Supplementary_files_format_and_content: Sparse matrix files with genes in columns and cells in rows

source_name: Chondrocytes isolated from osteoarthritis samples

extract_protocol:
Single cell samples were prepared using Single Cell 3/ Library & Gel Bead Kit v2 and Chip Kit (10X Genomics) according to the manufacturer’s protocol. Briefly samples were FACS sorted using DAPI to select live cells followed by resuspension in 0.04% BSA-PBS. Nearly 1,200 cells/µl were added to each well of the chip with a target cell recovery estimate of 8,000 cells. Thereafter Gel bead-in Emulsions (GEMs) were generated using GemCode Single-Cell Instrument. GEMs were reverse transcribed, droplets were broken and single stranded cDNA was isolated. cDNAs were cleaned up with DynaBeads and amplified. Finally, cDNAs were ligated with adapters, post-ligation products were amplified, cleaned up with SPRIselect. Purified libraries were submitted to UCLA Technology Center for Genomics & Bioinformatics for quality check and sequencing. The quality and concentration of the purified libraries were evaluated by High Sensitivity D5000 DNA chip (Agilent) and sequencing was performed on NextSeq500.
Single Cell 3/ Library & Gel Bead Kit v2

value: chondrocytes


title: PFC, female, ethanol, 3

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P11


title: hbdTSC_E2_rep1 [ATAC-Seq]


title: CR02_Infected

value: M

value: Infected

value: leprosy


title: CR08_Infected

value: F


title: Osteoarthritic chondrocytes1


title: CR04_Infected


title: PFC, female, ethanol, 2

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P5


title: ID219_Healthy

value: Healthy


title: KEN_hiTSC_C1_rep2 [RRBS]

value: Induced trophoblast stem cells, line #1


title: ID189_Healthy


title: PFC, female, ethanol, 1

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P1


title: Osteoarthritic chondrocytes2_IgG

data_processing:
Library strategy: Cut&Run
UMI-tools ‘extract’ function was used to remove UMIs from each read of the raw fastq files and append them to the read name. The initial quality of the raw fastq files were checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were trimmed using Cutadapt v2.10 in paired-end mode. Trimmed reads were aligned to human genome build hg19 using bowtie2. Next, aligned reads were deduplicated and PCR duplicates were removed by UMI-tools ‘dedup’ function followed by sorting and indexing of the deduplicated bam files by SAMtools v1.11. Bam coverage maps were generated using bamCoverage from the deepTools suite v3.5.0. Heatmaps were generated using computeMatrix and plotHeatmap from the deepTools suite v3.5.0. Significant peaks (p-value<0.05) were called from the deduplicated reads using MACS2 and annotated using the R package ChIPseeker.
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 peak files

extract_protocol:
In situ chromatin profiling using CUT & RUN was performed according to Skene et al 34. Briefly samples were FACS sorted using DAPI to select live cells and 10,000 cells were collected in 10%FBS-PBS media. Cell nuclei were immobilized on Concanavalin A beads after washing. pSTAT3 or normal rabbit IgG antibodies (Cell signaling technology) were incubated with the nuclei overnight in the presence of 0.02% digitonin at 4°. The next day, 700ng/mL of proteinA-micrococcal nuclease (pA-Mnase purified in house with vector from Addgene 86973 76) were incubated with the nuclei at 4 degrees for an hour. After washing, the tubes were placed in heat blocks on ice set to 0 degrees, CaCl2 (1mM) was added and incubated for 30 min before 2X Stop buffer containing EDTA was added. DNA was extracted using Qiagen DNA isolation kit according to manufacturer’s protocol Purified DNA was quantified in Qubit and Bioanalyzer (2100) traces using D5000 high sensitivity chip were run to determine the size of the cleaved products. UMI-coded libraries were generated using Swift Biosciences-ACCEL-NGS® 2S PLUS DNA LIBRARY KITS according to manufacturer’s protocol. Pair-end (75bp) Illumina sequencing was performed on the UMI-coded and amplified libraries using NextSeq platform.
Swift Biosciences-ACCEL-NGS® 2S PLUS DNA LIBRARY KITS

tag: antibody

value: IgG antibody


title: WT rep 4 random hexamers

description: Wild type, random hexamer priming

data_processing:
Reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using STAR (Dobin et al., 2013; doi:10.1093/bioinformatics/bts635) version 2.7.3a with the –quantMode GeneCounts option to get mapping counts at gene level.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Raw gene read counts for each sample.

source_name: pollen tubes

extract_protocol:
RNA from semi-in vivo grown pollen tubes were isolated using the Arcturus® PicoPure® RNA Isolation Kit.
Sequencing libraries were generated using the Ovation RNA-Seq System 1-16 for Arabidopsis, which includes an rRNA depletion step and allows for adjusting the balance between random-hexamer and oligo(dT) primers in the initital reverse transcription. For each pollen-tube sample, we split the extracted RNA and generated one library using only random-hexamer primers and one library using only oligo(dT) primers. The libraries were sequenced on an Illumina NextSeq550 instrument using a high-output flow cell.

value: pollen tubes

tag: ecotype

value: WT

tag: priming

value: random hexamer


title: KEN_hiTSC_C1_rep1 [RRBS]


title: Osteoarthritic chondrocytes1_IgG

tag: cell type


title: hESCs_rep3 [RRBS]

value: Embryonic stem cells


title: PFC, female, water, 5

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P16

tag: tissue

value: brain

value: female

tag: treatment

value: water


title: WT rep 4 oligo(dT)

description: Wild type, oligo(dT) priming

tag: genotype

value: oligo(dT)


title: Osteoarthritic chondrocytes2_STAT3

value: STAT3 antibody


title: ID214_Healthy

value: whole blood

value: Leukocytes

tag: age

tag: Sex


title: KEN_D3_OSKM_rep1 [ATAC-Seq]

value: OSKM-induced Foreskin fibroblasts


title: hESCs_rep2 [RRBS]


title: Osteoarthritic chondrocytes1_STAT3

value: chondrocytes


title: PFC, female, water, 3

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P9


title: PFC, female, water, 4

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P12


title: hESCs_rep1 [RRBS]


title: Adult chondrocytes2_IgG

source_name: Chondrocytes isolated from adult tissue samples


title: CR09_Infected

value: M

value: Infected

value: leprosy


title: WT rep 3 oligo(dT)

description: Wild type, oligo(dT) priming


title: CR21_Infected


title: GM2_fibs_rep3 [RRBS]

source_name: Adult Skin fibroblasts

value: Adult female skin fibroblasts


title: WT rep 2 random hexamers

description: Wild type, random hexamer priming

value: pollen tubes


title: ID117_Healthy

value: F

value: Healthy


title: KEN_hiTSC_C2_rep1 [RRBS]

value: Induced trophoblast stem cells, line #2


title: GM2_fibs_rep2 [RRBS]


title: Adult chondrocytes1_IgG

value: IgG antibody


title: WT rep 2 oligo(dT)

description: Wild type, oligo(dT) priming

value: WT


title: Adult chondrocytes2_STAT3


title: KEN_hiTSC_C1_rep3 [RRBS]

value: Induced trophoblast stem cells, line #1


title: PFC, male, ethanol, 6

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P22

value: brain

value: male

value: ethanol


title: ID43_Healthy

value: whole blood

value: Leukocytes


title: GM2_fibs_rep1 [RRBS]


title: Adult chondrocytes1_STAT3

value: STAT3 antibody

value: chondrocytes


title: KEN_hFF_rep3 [RRBS]

value: Foreskin fibroblasts


title: WT rep 1 random hexamers

description: Wild type, random hexamer priming

value: random hexamer


title: CR11_Infected

value: Infected

value: leprosy


title: ID151_Healthy

value: M


title: PFC, male, ethanol, 5

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P20


title: Fetal chondrocytes2_IgG

source_name: Chondrocytes isolated from fetal tissue samples


title: PFC, male, ethanol, 4

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P17


title: CR05_Infected

value: F


title: PFC, female, water, 1

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P2

value: female

value: water


title: KEN_hFF_rep2 [RRBS]


title: Fetal chondrocytes1_IgG

value: IgG antibody


title: ID11_Healthy

value: Healthy


title: paps1-1 rep 4 random hexamers

description: Mutant, random hexamer priming

value: pollen tubes

value: paps1-1 mutant


title: WT rep 1 oligo(dT)

description: Wild type, oligo(dT) priming

value: WT

value: oligo(dT)


title: WT rep 3 random hexamers

description: Wild type, random hexamer priming


title: paps1-1 rep 4 oligo(dT)

description: Mutant, olidgo(dT) priming


title: CR06_Infected

value: whole blood

value: Leukocytes


title: PFC, male, ethanol, 2

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P7

value: brain

value: male

value: ethanol


title: PFC, male, ethanol, 3

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P13


title: Fetal chondrocytes1_STAT3

value: STAT3 antibody

value: chondrocytes


title: hbdTSC_E9_rep3 [RRBS]

value: Blastocyst-derived trophoblast stem cells, line #9


title: PFC, male, ethanol, 1

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P3


title: paps1-1 rep 3 random hexamers

description: Mutant, random hexamer priming

value: random hexamer


title: hbdTSC_E9_rep2 [RRBS]


title: Fetal chondrocytes2_STAT3


title: ID261_Healthy

value: F


title: paps1-1 rep 3 oligo(dT)

description: Mutant, olidgo(dT) priming


title: Human Mammary Epithelial Cells - ATAC

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore v0.6.4 (Cutadapt v3.1)
Reads were then aligned to hg19 (mm9 for DF) whole genome using bowtie2 v2.3.3.1, alignment files were sorted and indexed using samtools v1.9, duplicate removal done using Picard v2.9.0
deepTools bamCoverage v3.5.0 was used to convert bam to bigWig
macs2 v2.2.7.1 was used to call peaks (to convert bam to bed)
Genome_build: hg19 (mm9 for DF)
Supplementary_files_format_and_content: bigWig (as produced by deepTools bamCoverage)
Supplementary_files_format_and_content: bed (as produced by macs2)

source_name: Human Mammary Epithelial Cells

growth_protocol: Normal Human Melanocytes (NHM) were cultures in Dermal Cell Basal Medium (ATCC) with the addition of 5 µg/mL Insulin, 50 µg/mL Ascorbic Acid, 6 mM L-Glutamine, 1.0 µM Epinephrine, 1.5 mM Calcium Chloride, Peptide Growth Factor and M8 Supplement. MCF-7, DFs and MDA-MB-231L cells were grown in DMEM (Gibco) with 4.5 g/L D-glucose, 110 mg/L sodium pyruvate, 10% FBS and 1% Penicillin/Streptomycin (Hyclone). HMEC cells were grown in complete Mammary Epithelial Cell Growth Media.

extract_protocol:
DNA for ATAC-seq  was prepared from 20,000 cells following the OMNI-ATAC procedures from Corces et al. (Nature Methods 2017) and Buenrostro et al. (Curr Protoc Mol Biol 2016), with modifications, using the Nextera kit (Illumina).  The cells were lysed for 3 minutes on ice and transposed for 30 minutes at 37C.  DNA was cleaned-up using procedures of a DNA extraction column.
The DNA libraries were prepared with 5-9 cycles of PCR amplification with the NEB High Fidelity Master Mix (New England Biolabs).  Clean up was done using the Zymo DNA Clean and Concentrator kit (Zymo Research) and followed with AMPure XP (Beckman Coulter) bead cleanup to remove primer dimers and under-digested chromatin.

treatment_protocol: MCF7 cells were treated with estradiol (E2) treatment MCF-7 cells were grown for 5 days in modified DMEM without phenol-red (Hyclone) with 4.5 g/L D-glucose, 4.0 L-glutamine, 10% charcoal-dextran–stripped FBS, 1% Penicillin/Streptomycin and 1nM of 17-β-estradiol or EtOH.

tag: cell line

value: Human Mammary Epithelial Cells

tag: ectopic expression


title: ID21_Healthy


title: PFC, male, water, 5

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P23

value: water


title: PFC, male, water, 4

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P18


title: hbdTSC_E9_rep1 [RRBS]


title: paps1-1 rep 2 random hexamers

description: Mutant, random hexamer priming


title: paps1-1 rep 2 oligo(dT)

description: Mutant, olidgo(dT) priming


title: hbdTSC_E2_rep3 [RRBS]

value: Blastocyst-derived trophoblast stem cells, line #2


title: PFC, female, water, 2

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P6

value: female


title: PFC, male, water, 3

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P14


title: hbdTSC_E2_rep2 [RRBS]


title: paps1-1 rep 1 random hexamers

description: Mutant, random hexamer priming

value: pollen tubes

value: paps1-1 mutant


title: PFC, male, water, 2

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P8


title: hbdTSC_E2_rep1 [RRBS]


title: CR01_Infected

value: Infected

value: leprosy


title: paps1-1 rep 1 oligo(dT)

description: Mutant, olidgo(dT) priming

value: oligo(dT)


title: CR18_Infected

value: whole blood

value: Leukocytes

value: M


title: PFC, female, ethanol, 5

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P19

value: brain

value: ethanol


title: PFC, male, water, 1

description:
featureCounts matrix column names: Geneid, Chr, Start, End, Strand, Length, P11, P12, P13, P14, P15, P16, P17, P18, P19, P1, P20, P21, P22, P23, P2, P3, P4, P5, P6, P7, P8, P9; exon count matrix column names: exonID, count
P4

value: male


title: Fetal chondrocytes3

data_processing:
The initial quality of the raw fastq files were checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were trimmed using Cutadapt v2.10 in paired-end mode. Trimmed reads were aligned to human genome build hg19 using bowtie2. PCR duplicates were removed  from the aligned reads followed by sorting and indexing of the bam files by SAMtools v1.11. Bam coverage maps were generated using bamCoverage from the deepTools suite v3.5.0. Significant peaks (p-value<0.05) were called using MACS2 and annotated using R.
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 peak files

extract_protocol:
Samples were washed, lysed followed by nuclei tagmentation and adapter ligation by Tn5 using the Nextera DNA Sample Preparation kit (Illumina). Transposed DNA fragments were amplified using the NEBNext Q5 HotStart HiFi PCR Master Mix with regular forward and reverse barcoded primers. The final product was purified with MinElute PCR Purification kit (Qiagen), and quality checked on 2100 Bioanalyzer (Agilent). Sequencing was performed on Illumina HiSeq 2500 with single-end 50 base pair reads.
Nextera DNA Sample Preparation kit

value: chondrocytes


title: KEN_hFF_rep1 [RRBS]

value: Foreskin fibroblasts


title: Fetal chondrocytes2


title: eIF4E1B_CKO_rep2

city: Beijing

first: Hailian

last: Zhao

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: replicates were merged for processing

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences at the 3' end were removed using Cutadapt v1.15 with the parameter: -a ATCTCGTATGCCGTCTTCTGCTT
After filtering, the LACE-seq reads were aligned to mouse pre-rRNA by bowtie with default parameters.
The unmapped reads to mouse pre-rRNA were then aligned to the mm9 reference genome.
Assembly: mm9
Supplementary files format and content: LACE-seq reads coverage in bigwig format

source_name: oocyte

extract_protocol:
Cells were lysed on ice using 50 μl wash buffer for 10 min.
The preparation of protein A/G beads observed the instructions of the manufacturer, and their coupling with either anti-eIF4E or -eIF4E1B antibody took place. The lysate of oocytes was pre-treated with RQ1 DNase and incubated with antibody-coated beads. After extensive wash steps, the immunoprecipitated RNAs were fragmented, and experienced 3’-dephosphorylation and linker ligation, followed by reverse transcription on-beads. Then, first-strand cDNAs were derived from protein A/G beads and further captured by streptavidin C1 beads for pre-PCR and poly(A)-tailing to produce dsDNA as the template for IVT. IVT products were purified by the removal of DNA template using Turbo DNase and further purified by Agencourt RNA Clean beads based on the instructions of the manufacturer. Then, linear amplified RNA was transformed into cDNA and amplified by PCR with P7 and barcoded P5 index primers. Final PCR products with a size of 130-300 bp were excised from a 2% agarose gel and purified by use of Qiagen gel purification kit as per the instructions of the manufacturer. Illumina HiSeq 2500 at BerryGenomics was used for the single-end sequencing of all LACE-seq libraries.

treatment_protocol: 0.1% PFA was used for the 10-min crosslink of 100 mouse oocytes at room temperature for 10 min, followed by their quenching via 150 mM glycine

value: oocyte

tag: developmental stage

value: GV

value: anti-eIF4E1B(Shanghai Youke Biotechnology, custom antibody specific to 1-244aa of eIF4E1B)

tag: protocol

value: LACE-seq


title: eIF4E1B_CKO_rep1

description: replicates were merged for processing


title: Sugar medium (glucose, mannose and xylose), 18h of fed-batch, biological rep. 2

city: LUND

first: Daniel

middle: P

last: Brink

address: Naturvetarvagen 14

department: Applied Microbiology

country: Sweden

institute: Lund University

description: Gene expression data from a sample taken after 18h of fed-batch cultivation with sugar medium (glucose, mannose and xylose with sugar concentrations similar to those in the spruce hydrolysate), biological replicate 2

hyb_protocol: Fifteen micrograms of the biotin labeled cRNA was fragmented in to strands of 35 to 200 bases in length, 10 micrograms of which were hybridised onto the GeneChip® Yeast Genome 2.0 Array overnight in the GeneChip® Hybridisation oven 6400 using standard procedures.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing:
R (v 4.2.1) was used to process the data using the Affy (v 1.74.0) and Limma (v 3.52.4) Bioconductor packages. The raw data was processed using RMA normalized. The treat() function of Limma was used to select for a logFC cutof of log(2). Statistical analysis was performed with Benjamini-Hochberg adjusted p-value using decidetests(p = 0.05, adjust.method='BH',method=global).
RMA norm. - RMA normalized data from the different samples; AveExpr - average expression per probe calculated by Limma (treat); log2FC - log2 fold change per probe  calculated by Limma (treat);  t value calculated by Limma (treat); P.value - p-value calculated by Limma (treat); adj.P.value (global) - false discovery rate adjusted p-value (Benjamini-Hochberg) calculated by Limma (decidetests(method=global)); decideTests(global) results - outcome of the statistical test : 1 = significantly upregulated; 0 = non-significant; -1 = significantly downregulated

label: Biotin

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae sugars fed-batch (18h)

label_protocol: Two micrograms total RNA was processed following the GeneChip® Expression 3′-Amplification Reagents One-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA. This was used as template to generate biotin-targeted cRNA, following the manufacturer’s specifications.

growth_protocol: The yeast cells were pre-cultured in 300 mL cotton plugged shakeflasks for 24h at 30°C in a rotary incubator at 160rpm. 100 mL media was used, containing 16.5 g/L glucose, 7.5 g/L (NH4)2SO4, 3.5 g/L KH2PO4, 0.74 g/L MgSO2·7H2O, trace metals and vitamins at pH 5. Aerobic batch cultivation was performed at 30°C, pH 5 and 750 rpm with a working volume of 0.7 L using a 2.5 L fermentor (Biostat A, B. Braun Biotech International, Melsungen, Germany) aerated with 1000 mL/min. The cultivation was initiated by adding 20 ml inoculum. The temperature and pH were automatically controlled (30°C, pH 5) .The stirring speed and aeration were 750 rpm and 1400 mL/min, respectively. The batch medium was supplemented with 20 g/L glucose, 20 g/L (NH4)2SO4, 10 g/L KH2PO4, 2 g/L MgSO2·7H2O, trace metals and vitamins. The reactors were either fed with non-detoxified spruce hydrolysate (adjusted pH 4.7 with NaOH) or a sugar mixture (glucose, mannose and xylose with sugar concentrations similar to those in the spruce hydrolysate). The  feed started at 0.04 L/h and was linearly increased to 0.10 L/h during 16h. After 16h, 1 L had been added, giving a final volume of 1.7 L.

extract_protocol: RNA extraction was performed using Trizol reagent (Invitrogen) following the recommendations of the supplier.

treatment_protocol: Samples for microarray analysis were immediately centrifuged at 4ºC for 3 minutes and the cells were frozen in liquid nitrogen and stored at -80ºC.

tag: strain


title: Fetal chondrocytes1


title: Sugar medium (glucose, mannose and xylose), 18h of fed-batch, biological rep. 1

description: Gene expression data from a sample taken after 18h of fed-batch cultivation with sugar medium (glucose, mannose and xylose with sugar concentrations similar to those in the spruce hydrolysate), biological replicate 1


title: Sugar medium (glucose, mannose and xylose), 9h of fed-batch, biological rep. 2

description: Gene expression data from a sample taken after 9h of fed-batch cultivation with sugar medium (glucose, mannose and xylose with sugar concentrations similar to those in the spruce hydrolysate), biological replicate 2

source_name: S. cerevisiae sugars fed-batch (9h)


title: GM12878, H3K4me1 biol rep 2

city: Montréal

first: Guillaume

last: Bourque

state: QC

address: 740, Dr. Penfield Avenue Room 6103

department: Human Genetics

institute: McGill University

data_processing:
paired-end interleaved fastq files
Basecalls were performed using bcl2fastq for Novaseq output.
Reads were aligned with vg map
Peaks were called with Graph Peak Caller
Assembly: genome graph with hg19 coordinates
Supplementary files format and content: narrowPeak

growth_protocol: Biomaterial provider GM12878 lymphoblastoid cell line; Coriell http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878

extract_protocol:
ChIPmentation library preparation was performed on 5 million cross-linked cells (1% formaldehyde).
Sonication of nuclei was performed on a BioRuptor UCD-300 targeting 150-500 bp size. Library preparation was performed following the Auto-ChIPmentation protocol for Histones (Diagenode inc, Denville, USA) according to the manufacturer’s indications.
ChIPmentation

value: lymphoblastoid cell line

tag: infection

value: influenza

tag: chip antibody

value: H3K4me1 cat # CST5326


title: GM12878, H3K4me1 biol rep 3


title: Sugar medium (glucose, mannose and xylose), 9h of fed-batch, biological rep. 1

description: Gene expression data from a sample taken after 9h of fed-batch cultivation with sugar medium (glucose, mannose and xylose with sugar concentrations similar to those in the spruce hydrolysate), biological replicate 1


title: GM12878, H3K27ac biol rep 3


title: Hydrolysate, 18h of fed-batch, biological rep. 2

description: Gene expression data from a sample taken after 18h (end of cultivation) of fed-batch cultivation with non-detoxified liquid spruce hydrolysate, biological replicate 2

source_name: S. cerevisiae hydrolysate fed-batch (18h)


title: R1 cells, sh-Lin41-3, EB formation, 6D

city: Zhengzhou

first: Ruijie

last: Wang

state: Henan

address: Fengchan Road Street

department: Academy of Medical Sciences

institute: Zhengzhou University

description:
sh-L-3
ctrl-vs-SH-L.all.annot.txt

data_processing:
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China)
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides  (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome (Ensembl 104) was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software
Assembly: Ensembl 104
Supplementary files format and content: Tab-delimied txt files include Count and FPKM values for each Sample

source_name: R1 cell

growth_protocol: Mouse R1 ES cells (ATCC, SCRC-1011)  were cultured in DMEM supplemented with 15% fetal bovine serum, 2 mM L-glutamine, 100 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM sodium pyruvate (Gibco) and 1,000 U/mL LIF (Millipore) on gelatin-coated plates.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, USA) according to the manufacturer’s protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England  Biolabs,  Ipswich,  MA,  USA) following manufacturer's protocols.

treatment_protocol: R1 cells were cultured in suspension without LIF for 6 days to form embryoid bodies (EBs)

value: R1 cell

value: Mouse embryonic stem cell

tag: shRNA

value: Lin41 knockdown

value: EB formation, 6D


title: Hydrolysate, 18h of fed-batch, biological rep. 1

description: Gene expression data from a sample taken after 18h (end of cultivation) of fed-batch cultivation with non-detoxified liquid spruce hydrolysate, biological replicate 1


title: GM12878, H3K27ac biol rep 2


title: R1 cells, sh-Lin41-1, EB formation, 6D

description:
sh-L-1
ctrl-vs-SH-L.all.annot.txt


title: GM12878, H3K27ac biol rep 1


title: R1 cells, sh-Pfkp-3, EB formation, 6D

description:
sh-P-3
ctrl-vs-SH-P.all.annot.txt

value: sh-Pfkp

value: Pfkp knockdown


title: Hydrolysate, 9h of fed-batch, biological rep. 1

description: Gene expression data from a sample taken after 9h of fed-batch cultivation with non-detoxified liquid spruce hydrolysate, biological replicate 1

source_name: S. cerevisiae hydrolysate fed-batch (9h)


title: Hydrolysate, 9h of fed-batch, biological rep. 2

description: Gene expression data from a sample taken after 9h of fed-batch cultivation with non-detoxified liquid spruce hydrolysate, biological replicate 2


title: R1 cells, sh-Pfkp-2, EB formation, 6D

description:
sh-P-2
ctrl-vs-SH-P.all.annot.txt


title: GM12878, H3K4me1 biol rep 1


title: AGO1 mRNA rep2

city: Riverside

first: Ye

last: Xu

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Raw reads were analyzed by a homemade pipeline pRNASeqTools v0.8 (https://github.com/grubbybio/pRNASeqTools).
The raw reads were aligned to the genome using STAR. Transcript levels were measured in reads per million total read counts.
Differentially expressed genes were identified using DEseq2 with fold change of 2 and p < 0.01 as the parameters.
Genes are annotated based on Araport11.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files including raw read count for each gene

source_name: seedling

growth_protocol: 16 hr light and 8 hr dark at 22 ˚C on MS medium

extract_protocol:
12-day-old seedlings of AGO1 truncation mutants in the ago1-36 background were ground to a fine powder in liquid nitrogen and subjected to RNA extraction using TRI Reagent, polyadenylated RNA was isolated from total RNA using the Magnetic mRNA Isolation Kit (NEB).
RNA-seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB7420) and sequenced on an Illumina Novaseq  platform to generate high-quality paired-end reads of 150bp in length.

value: seedling

tag: transgene

tag: time

value: 12 days old seedlings


title: ago1-36 mRNA rep2

tag: ecotype


title: ago1-36 mRNA rep1


title: ago1-36 mRNA rep3


title: Control sample from start of fed-batch (0h), biological rep. 2

description: Gene expression data from a control sample taken at start of fed-batch (0h), biological replicate 2

source_name: S. cerevisiae start of fed-batch (0h)


title: AGO1 mRNA rep3


title: AGO1 mRNA rep1


title: Control sample from start of fed-batch (0h), biological rep. 1

description: Gene expression data from a control sample taken at start of fed-batch (0h), biological replicate 1


title: GM12878, ATAC biol rep 1

extract_protocol:
ATAC-Seq library preparation was performed according to the Omni-ATAC protocol.50,000 GM12878 cultured cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 g for 5 min in a pre-chilled (4 ∘C) fixed-angle centrifuge. After centrifugation, supernatant was aspirated and cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% IGEPAL, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL and digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 rcf in a pre-chilled (4 ^∘C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 μL transposition mix (2x TD Buffer, 100 nM final transposase, 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, 5 μL H2O ).
Transposition reactions were incubated at 37∘C for 30 min in a thermomixer with shaking at 1000 rpm. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns. Primers (i5 and i7) were added by amplification (12 cycles) using NEBNext 2x MasterMix.
ATAC-seq Omni-ATAC

tag: cell type


title: GM12878, ATAC biol rep 2


title: AGO1_91_mRNA_rep3

description: AGO1 delete 91-189AA

source_name: 12 days old seedlings

value: AGO1::3XHA-AGO1 del 91-189AA

tag: tissue


title: R1 cells, sh-ctrl-3, EB formation, 6D

description:
sh-c-3
ctrl-vs-SH-L.all.annot.txt

value: sh-ctrl

value: WT

tag: treatment


title: R1 cells, sh-Pfkp-1, EB formation, 6D

description:
sh-P-1
ctrl-vs-SH-P.all.annot.txt

tag: genotype


title: R1 cells, sh-Lin41-2, EB formation, 6D

description:
sh-L-2
ctrl-vs-SH-L.all.annot.txt


title: AGO1_91_mRNA_rep2

description: AGO1 delete 91-189AA


title: R1 cells, sh-ctrl-2, EB formation, 6D

description:
sh-c-2
ctrl-vs-SH-L.all.annot.txt


title: GM12878, ATAC biol rep 3


title: S23_229E_48hpi

first: Edwin

middle: A

last: Rosado-Olivieri

address: 1230 York Ave

institute: The Rockefeller University

description: S23_229E_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam

data_processing:
QUALITY FILTER AND ADAPTER TRIM READS by trim_galore
MAPPING on combined host/viral genome by STAR
COUNT READS by featureCounts() in R
DGE analysis by DESeqDataSetFromMatrix in R
Assembly: combined human genome (GRCh38.p13), HCoV-229E genome (GenBank: NC_002645.1), HCoV-OC43 genome (GenBank: NC_006213), and SARS-CoV-2 genome (GenBank: MN985325.1)
Supplementary files format and content: count matrix

source_name: Lung

growth_protocol: in vitro differentiation of hPSCS into lung buds

extract_protocol:
RNA extration by Qiaegen RNAeasy kit
Poly(A) selection and library preparation using an Illumina TrueSeq mRNA kit

treatment_protocol: Infection by SARS-CoV-2, 229E or OC43

value: Lung

value: lung buds

value: wild-type


title: S22_229E_48hpi

description: S22_229E_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: AGO1_91_mRNA_rep1

description: AGO1 delete 91-189AA


title: R1 cells, sh-ctrl-1, EB formation, 6D

description:
sh-c-1
ctrl-vs-SH-L.all.annot.txt


title: S21_229E_48hpi

description: S21_229E_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: CD4+ T cells, ERα KO, EAE, day 9, 5

city: Urbana

first: Makoto

last: Inoue

state: Il

address: 2001 S Lincoln Ave

institute: University of Illinois at Urbana-Champaign

description: Sample 9

data_processing:
Samples were demultiplexed and adapter sequences were removed along with any reads shorter than 35 nt.
Salmon version 1.2.0 was used to quasi-map reads to the GRCm39 Annotation 109 transcriptome and quantify the counts for each transcript, then summed to gene level after adjusting for transcript lengths using the tximport package (v1.18.0) in R (v4.0.3).
Assembly: NCBI GRCm39, Annotation Release 109
Supplementary files format and content: Summed gene-level counts: Inoue_GeneCounts_forGEO.txt

source_name: CD4+ T cells

extract_protocol:
Total RNA was extracted from CD4+ T cells with QIAGEN RNeasy kit
Library construction and sequencing was done at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign using the Ovation RNASeq kit from Tecan and sequencing 100 bp single end reads on one SP lane in a NovaSeq 6000

value: CD4+ T cells

value: ER{alpha} KO

tag: batch


title: CD4+ T cells, ERα KO, EAE, day 9, 4

description: Sample 8


title: AGO1_189_mRNA_rep3

description: AGO1 delete 1-189AA

value: AGO1::3XHA-AGO1 del 1-189AA


title: AGO1_189_mRNA_rep2

description: AGO1 delete 1-189AA


title: S20_OC43_48hpi

description: S20_OC43_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: S19_OC43_48hpi

description: S19_OC43_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: CD4+ T cells, ERα KO, EAE, day 9, 2

description: Sample 6


title: S17_Mock_24hpi

description: S17_Mock_24hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam

value: Mock


title: CD4+ T cells, ERα KO, EAE, day 9, 3

description: Sample 7


title: AGO1_189_mRNA_rep1

description: AGO1 delete 1-189AA


title: AGO1_90_mRNA_rep3

description: AGO1 delete 1-90AA

value: AGO1::3XHA-AGO1 del 1-90AA


title: AGO1_90_mRNA_rep2

description: AGO1 delete 1-90AA


title: CD4+ T cells, ERα KO, EAE, day 9, 1

description: Sample 5


title: Knockout postnatal day 42 replicate 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Comparisons: developmental age+ genotype effect on lung gene expression

hyb_protocol: The biotinylated RNA was fragmented and hybridized to the Affymetrix array for 16 hr at 45 degree C in a hybridization oven rotating at 60 rpm. The array was washed and stained with streptavidin–phycoerythrin using an Affymetrix Fluidics Station 450.

scan_protocol: The array was scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The chip data was analyzed using Affymetrix GeneChip Operating Software (GCOS) version 1.2.

source_name: Homogenized lung tissue

label_protocol: cDNA was synthesized from RNA using a one-cycle cDNAsynthesis kit. Biotinylated RNA was then synthesized from cDNA using an IVT labeling kit after incubating at 37◦C for 16 hr.

extract_protocol: Total RNA was extracted from lung homogenates of each lung (n=3 samples per group, for E13.5, 2-3 lungs were combined for one sample.) using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA). Quality and quantity of RNAs were evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mice were time mated. Water and feed (AIN-76A) were provided ad libitum to time-pregnant dams and postnatal mice. The temperature (72±3 degree F) and humidity (50±15 percent) of the room were monitored and mice were exposed to a 12-hr light-dark cycle. Embryos were taken from pregnant dams by surgery and embryonic lungs were harvest at designated ages. At designated postnatal age, mouse lungs were harvested. All lungs were snap frozen in liquid nitrogen and stored at -70C until used.

tag: developmental age

value: adult PND42


title: Knockout postnatal day 42 replicate 1


title: S16_SARS2_12hpi

description: S16_SARS2_12hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam

tag: cell line


title: Knockout postnatal day 42 replicate 3


title: Knockout postnatal day 14 replicate 3

value: juvenile PND14


title: S15_SARS2_24hpi

description: S15_SARS2_24hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: AGO1_90_mRNA_rep1

description: AGO1 delete 1-90AA


title: Knockout postnatal day 4 replicate 3

value: neonate PND4


title: Knockout postnatal day 14 replicate 2


title: Knockout postnatal day 4 replicate 2


title: Knockout postnatal day 4 replicate 1


title: CD4+ T cells, wildtype, EAE, day 9, 3

description: Sample 3

value: wildtype


title: S18_SARS2_12hpi

description: S18_SARS2_12hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: S14_SARS2_24hpi

description: S14_SARS2_24hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: CD4+ T cells, wildtype, EAE, day 9, 2

description: Sample 2


title: S13_Mock_12hpi

description: S13_Mock_12hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: Knockout postnatal day 3 replicate 3

value: neonate PND3


title: Knockout postnatal day 14 replicate 1


title: S12_Mock_24hpi

description: S12_Mock_24hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: CD4+ T cells, wildtype, EAE, day 9, 4

description: Sample 4


title: S11_Mock_12hpi

description: S11_Mock_12hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: Knockout postnatal day 3 replicate 2


title: IMX2816 grown in SMD in aerobic glucose limited chemostat-2

city: Delft

first: Marcel

last: van den Broek

address: Van der Maasweg 9

country: Netherlands

institute: Delft University of Technology

data_processing:
RNA-seq reads were aligned to the CEN.PK113-7D reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
TMM (edgeR) normalized counts.
Assembly: CEN.PK113-7D ASM257140v2
Supplementary files format and content: Comma delimited file, TMM normalized transcript counts

growth_protocol: Growth protocol: An oxic batch culture with 20 g L-1 glucose was followed by an oxic, carbon-limited chemostat culture at a dilution rate of 0.10 h−1 with 7.5 g L-1 glucose in the medium as previously described (Daran-Lapujade et al., 2009; Tai et al., 2005). The temperature was controlled at 30°C, and the pH was maintained at 5.0 by automatic addition of 2.0 M KOH. To maintain oxic conditions, air at a rate of 0.5 L min−1 was sparged through the culture which was stirred at 800 rpm. CEN.PK113-7D cultures were grown on SMD only whil the strain IMX2816 (MATa MAL2-8c Sccan1Δ::Spycas9-natNT2 Δx-2::ScPGK1p-ScSNO1-ScSSA1t::ScTDH3p-ScTHI4-ScTDH1t::ScCCW12p-ScABZ2-ScENO2t Scsga1Δ::ScTEF1p-ScFMS1-ScADH1t::ScTDH3p-ScINO1-ScTDH1t::ScCCW12p-ScSNZ1-ScENO2t YPRcTau3Δ::ScPYK1p-CfBIO1-ScBIO1t::ScTDH3p-ScABZ1-ScTDH1t) was grown on SMD or vitamin-free SMD (SMDΔvitamins) supplemented with 0.2 g L−1 sterile pluronic PE6100 (BASF, Ludwigshafen, Germany) to avoid foam formation.

extract_protocol:
RNA was extracted with hot-phenol method as described by Schmitt et al. (1990)
cDNA libraries were prepared using the TruSeq stranded mRNA kit (illumina) and sequenced on NovaSeq 6000 (illumina) at Novogen

treatment_protocol: Cultures were sampled into liquid nitrogen and processed as described by Piper et al. (2002)

value: engineered


title: IMX2816 grown in SMDminus vitamins in aerobic glucose limited chemostat-1


title: IMX2816 grown in SMD in aerobic glucose limited chemostat-1


title: Bex_3 [T6956]

city: East Lansing

first: Lyndsey

last: Reich

state: Michigan

address: 1355 Bogue St.

department: Pharmacology & Toxicology

institute: Michigan State University

description:
fpkm_genename.xls
readcount_genename.xls
DE_sort_padj.xls
DE_fold_change_cutoff2_sort_padj.xls
DE_Bex_vs_control.xls

data_processing:
FeatureCounts software v1.5.0-p3 was used for quantification
Read counts are filtered from raw data: (1)Remove reads with adaptor contamination.  (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).  (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
STAR software v2.6.1d was used to map reads to the reference genome
read counts are normalized to fpkm
PCA analysis was used for analysis of outliers
DESeq2 was used for differential expression analysis between treatment groups
Supplementary files format and content: XLS files containing counts and fpkm

source_name: Mammary tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the polyA enrichment procedure.

value: Mammary tumor

value: MMTV-Neu

value: Bexarotene 100mg/kg diet


title: Bex_4 [T7020]


title: Knockout postnatal day 2 replicate 3

value: neonate PND2


title: CEN.PK113-7D grown in SMD in aerobic glucose limited chemostat-3

value: host

value: MATa ura3-52 MAL2-8c


title: Bex_2 [T6991]


title: IMX2816 grown in SMDminus vitamins in aerobic glucose limited chemostat-2


title: S10_Mock_24hpi

description: S10_Mock_24hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam

value: Lung

value: lung buds

value: wild-type


title: S09_SARS2_12hpi

description: S09_SARS2_12hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: CEN.PK113-7D grown in SMD in aerobic glucose limited chemostat-2


title: S08_Mock_48hpi

description: S08_Mock_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam

value: Mock


title: Bex_1 [T6973]


title: M42011_4 [T7007]

description:
fpkm_genename.xls
readcount_genename.xls
DE_sort_padj.xls
DE_fold_change_cutoff2_sort_padj.xls
DE_42011_vs_control_outlier_removed.xls

value: MSU 42011 100mg/kg diet


title: M42011_3 [T6983]


title: CEN.PK113-7D grown in SMD in aerobic glucose limited chemostat-1


title: PBMC, Groupe3, J15, animal 683

city: Paris

first: Sylvain

last: Baize

address: 25-28 rue du Docteur Roux, CEDEX 15

country: France

institute: Institut Pasteur

data_processing:
Bioinformatics analysis was performed using the RNA-seq pipeline from Sequana. Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences of at least 25 nucleotides in length were considered for further analysis. STAR version 2.5.0a, with default parameters, was used for alignment against the reference genome (Macaca Fascicularis 5 from ENSEMBL version 95). Reads were assigned to genes using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -O -s 2).
Assembly: Macaca Fascicularis 5 from ENSEMBL version 95
Supplementary files format and content: Table of read counts normalized by TPM

organism: Macaca fascicularis

source_name: blood

extract_protocol:
Total RNA was extracted from PBMCs collected on days 0, 3, 6, 9, and 12 using the RNeasy Mini Kit with DNase treatment (Qiagen).
The libraries were prepared using the NEXTflex Rapid Directional RNA-seq (RNA sequencing) Kit (Bioo Scientific) and were quantified and qualified using a Quantus quantification kit (Promega) and a fragment analyzer advanced analytical (AATI).

value: blood

value: peripheral blood mononuclear cell

value: PBMC


title: PBMC, Groupe3, J12, animal 683


title: M42011_2 [T6931]


title: PBMC, Groupe3, J12, animal 598


title: M42011_1 [T6928]


title: S05_Mock_12hpi

description: S05_Mock_12hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: PBMC, Groupe3, J9, animal 683


title: S06_Mock_48hpi

description: S06_Mock_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: PBMC, Groupe3, J9, animal 598


title: Control4 [T7001]

description:
fpkm_genename.xls
readcount_genename.xls
DE_sort_padj.xls
DE_fold_change_cutoff2_sort_padj.xls

value: Control


title: S04_SARS2_48hpi

description: S04_SARS2_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: S03_SARS2_24hpi

description: S03_SARS2_24hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: S07_Mock_48hpi

description: S07_Mock_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: Control3 [T6943]


title: Knockout postnatal day 1 replicate 3

description: Comparisons: developmental age+ genotype effect on lung gene expression

value: neonate PND1


title: S02_SARS2_48hpi

description: S02_SARS2_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: PBMC, Groupe3, J9, animal 269


title: Knockout postnatal day 1 replicate 2


title: Knockout postnatal day 2 replicate 2


title: Knockout postnatal day 2 replicate 1


title: Control2 [T6890]


title: Knockout embryonic day 18.5 replicate 2

value: embryo E18.5


title: Knockout postnatal day 1 replicate 1


title: Knockout postnatal day 0 replicate 3

value: neonate PND0


title: S01_SARS2_48hpi

description: S01_SARS2_48hpi_L001_L002_merged_Aligned.sortedByCoord.ReadGroups.out.bam


title: PBMC, Groupe3, J6, animal 598


title: Knockout embryonic day 18.5 replicate 3


title: PBMC, Groupe3, J6, animal 269


title: PBMC, Groupe3, J3, animal 683


title: Knockout postnatal day 0 replicate 1


title: Ovaroids, day 14, biol rep 2

city: Boston

first: Merrick

last: Smela

address: 3 Blackfan Circle

institute: Harvard University

data_processing:
The Parse biosciences analysis pipeline (v. 0.9.6) was used to call cell barcodes and align reads to the GrCh38 reference.
MTX files were exported using scanpy (v. 1.8.2)
Assembly: GrCh38
Supplementary files format and content: MTX files are the counts tables for gene expression with cells as rows and genes as columns.
Supplementary files format and content: cell_metadata.csv files are the row labels for the counts tables, and all_genes.csv is the column labels.

source_name: ovarian organoid

growth_protocol: To form ovaroids, granulosa-like cells were harvested with TRYPLE, counted, and mixed with F2 hPGCLCs. For each ovaroid, 100,000 granulosa-like cells and 10,000 hPGCLCs were added to each well of a 96-well U-bottom low-bind plate (Corning #7007) in 200 µL of GK15 medium (GMEM, 15% KSR, with 1X GlutaMax, sodium pyruvate, and non-essential amino acids) supplemented with 10 mM Y-27632, 0.1 mM 2-mercaptoethanol, 1 µg/mL doxycycline, 100 ng/mL SCF, and 50 µg/mL primocin. The plate was centrifuged (100 g, 2 min) and incubated (37 °C, 5% CO2) for two days. Subsequently, ovaroids were transferred to Transwells (collagen-coated PTFE, 3 µm pore size, 24 mm diameter, Corning #3492) for air-liquid interface culture with aMEM, 10% KSR, 55 µM 2-mercaptoethanol, 500 ng/mL doxycycline, and 50 µg/mL primocin. Typically 5-6 ovaroids were cultured on each 6-well Transwell. The medium (1.5 mL) was changed every 2 days.

extract_protocol:
Parse Fixation Kit and WT Mega Kit
Parse Biosciences WT Mega Kit

value: ovarian organoid

value: F2 PGCLC and D4 granulosa-like cell

value: primordial germ cell-like cell and granulosa-like cell

tag: day


title: Knockout postnatal day 0 replicate 2


title: PBMC, Groupe3, J3, animal 598


title: Knockout embryonic day 18.5 replicate 1


title: MP46

city: Turku

first: Arfa

last: Mehmood

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology, UTU

data_processing:
The Transcript per million values were calculated using Kallisto v 0.48.0
The transcipt counts of each gene was summed to produce gene-level data.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

extract_protocol:
RNA was harvested using RNeasy® Mini Kit (Qiagen)
Illumina Stranded mRNA Library Preparation, Illumina (1000000124518)

value: Uveal melanoma

value: BAP1 negative


title: Mel285

value: WT


title: Knockout embryonic day 17.5 replicate 3

value: embryo E17.5


title: PBMC, Groupe3, J6, animal 683


title: PBMC, Groupe3, J3, animal 269


title: Ovaroids, day 14, biol rep 1


title: Ovaroids, day 8, biol rep 2


title: PBMC, Groupe3, J0, animal 683


title: Knockout embryonic day 17.5 replicate 2


title: Knockout embryonic day 15.5 replicate 3

value: embryo E15.5


title: Control1 [T6933]

value: Mammary tumor

value: MMTV-Neu


title: PBMC, Groupe3, J0, animal 598

value: blood


title: Ovaroids, day 8, biol rep 1


title: Ovaroids, day 4, biol rep 2


title: Ovaroids, day 4, biol rep 1


title: PBMC, Groupe3, J0, animal 269

value: peripheral blood mononuclear cell


title: Knockout postnatal day 3 replicate 1

value: neonate PND3


title: Knockout embryonic day 15.5 replicate 2


title: Knockout embryonic day 17.5 replicate 1


title: PBMC, Groupe2, J15, animal 644

value: PBMC


title: Ovaroids, day 2, biol rep 2


title: PBMC, Groupe2, J15, animal 852


title: Ovaroids, day 2, biol rep 1


title: Knockout embryonic day 13.5 replicate 3

value: embryo E13.5


title: PBMC, Groupe2, J12, animal 852


title: Knockout embryonic day 13.5 replicate 1


title: Knockout embryonic day 13.5 replicate 2


title: PBMC, Groupe2, J12, animal 895


title: PBMC, Groupe2, J12, animal 644