title: BA induction after 72h

city: Sinjuku-ku

first: Kumiko

last: Saeki

address: 1-21-1 Toyama

institute: National Center for Global Health and Medicine

hyb_protocol: 0.60 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression Microarray 8x60K Ver.2.0 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. GeneSpring software (Agilent) was used for normalization. We set 75 percentile for it, and followed by the instruction.

source_name: ES cell, BA induction after 72h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 µg Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacture's instructions, followed by Rneasy Column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND1000.

growth_protocol: human ES cell (KhES-3) was cultured on the layer of 46-Gy irradiated mouse embyonic fibroblast (MEF) cells with ES culture medium (DMEM/F12 (1:1) supplemented with 20% KSR, 0.1 mM 2-ME, 1% NEAA, and 5 ng/mL human recombinant basic fibroblast growth factor (hbFGF)

extract_protocol: Cells were dissolved in TRIZOL, and total RNA were extracted with standard protocol. RNA was further purified with Rneasy kit.

treatment_protocol: ES cells were cultured in a 6 cm low-attachment culture dish using a serum-free BA differentiation medium composed of 1:1 ratio of IMDM (Sigma) and Ham’s F12 (WAKO), 5 mg/ml bovine serum albumin (Sigma), 1:100 synthetic lipids (Invitrogen), 450 mM a- monothioglycerol (WAKO), 1:100 insulin-transferrin-selenium (ITS-A, Invitrogen), 2 mM Glutamax II (Invitrogen), 5% protein-free hybridoma mix (PFHMII, Invitrogen), 50 mg/ml ascorbic acid-2-phosphate (Sigma), and the hematopoietic cytokine cocktail I (5 ng/ml IGF-II, 20 ng/ml BMP4, 5 ng/ml VEGFA, 20 ng/ml KITLG, 2.5 ng/ml FLT3LG, 2.5 ng/ml IL-6) for each indicated time.

value: BA induction

tag: time


title: C1HTsmall_s5_1911004005_Col11_S179

status: Public on Dec 10 2019

type: SRA

city: Barcelona

first: Atefeh

last: Lafzi

address: Baldiri Reixac 4

department: CNAG

country: Spain

institute: Center for Genomic Regulation

description:
cryopreserved HCA reference
C1HTsmall_human_exp_mat.tsv, C1HTsmall_human_metada.tsv, C1HTsmall_mouse_exp_mat.tsv, C1HTsmall_mouse_metada.tsv

library_source: transcriptomic

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11), R2 = cDNA

molecule: polyA RNA

organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

growth_protocol: NIH3T3-GFP, MDCK-TurboFP650 and HEK293-RFP were cultured at 37ºC in an atmosphere of 5% (v/v) carbon dioxide in Dulbecco’s Modified Eagle’s Medium, supplemented with 10% (w/v) fetal bovine serum, 100 U penicillin, and 100 µg/L streptomycin (Invitrogen).

extract_protocol:
PBMCs were isolated according to the manufacturer’s instructions for FICOLL extraction (pluriSelect).Minced mouse colon was digested in 1X HBSS and 83 µl of collagenase IV (final concentration 166 U/ml) for 15 min at 37ºC and filtered through a 70 µm nylon mesh.
Sequencing librraries were prepared according to the respective single-cell RNA-seq protocols as detailed in the Methods and referenced in TableS1.
Library selection and sequencing was performed following recommendations of to the respective single-cell RNA-seq protocols as detailed in the Methods.

treatment_protocol: Untreated cells and donors.

tag: protocol

tag: centre

value: Stanford

tag: cell type

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: DMSO_1

city: South San Francisco

first: Peichuan

last: Zhang

state: CA

address: 1070 Veterans Blvd

country: USA

institute: Calico Life Sciences

description:
cells treated with DMSO (0.1%)
sample name:
cjopb8gwh000r3h5yfvr662f2

data_processing:
Illumina bcl2fastq v2.20.0 was used for basecalling.
Salmon v0.9.1 was used to pseudo-align reads to GRCh38, producing transcripts-per-million (TPM) estimates.
Isoform-level TPM estimates were aggregated to get genes-per-million (GPM) estimates.
Gene counts were de-noised by clamping low count values to the 5th percentile value, then log2-transformed, to produce normalized gene counts.
Differential expression analysis was performed using Sleuth v0.29.0, producing gene-level effect sizes and Q-values.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-separated text files including genes-per-million values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: cells treated with DMSO (0.1%)

growth_protocol: WI-38 cells of mid-age (PDL ~32) were cultured in OptiMEM (Invitrogen) supplemented with 10% FBS in a 37C incubator (5% CO2, 21% O2) to ~70%.

extract_protocol:
Cells were rinsed briefly with PBS and frozen with liquid nitrogen and stored at -80C before processed for the isolation of total RNA.  Total RNA was isolated and purified using the RNeasy kit (Qiagen), with on-column DNase digest.
Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries from 375 ng of total RNA.

treatment_protocol: Cells were then subjected to treatment with 0.1% DMSO (control), or 10uM Gr-4D (Gr-4D-CB, from ChemBridge; or Gr-4D-MP, from MolPort), or no treatment for 24 hours.

tag: treatment

value: mock

tag: cell line


title: A0370-130712

city: Brisbane

first: Jonathan

last: Ellis

state: Queensland

address: 37 Kent Street, Woolloongabba

country: Australia

institute: Queensland University of Technology

data_processing:
Data aligned to GRCh37 with STAR v2.4.2a and quantified against GENCODE v23 using the following STAR parameters --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMmapqUnique 100 --outSAMattributes All --quantMode GeneCounts --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab separated gene raw count table

source_name: PBMC

extract_protocol:
Total RNA extracted from PBMCs
Illumina TruSeq Stranded total RNA

tag: subject

value: PRE

tag: Sex

value: Male

tag: b27 status

value: Positive

tag: age at collection

tag: basdai

tag: esr

tag: crp

tag: anti-tnf

value: N


title: piwi_CRISPR_line2_F9_sRNA-seq

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

description: total sRNA

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.15)
The trimmed reads were sorted by sequence using fastq-sort (from fastq-tools version 0.8) with option -s and deduplicated using a custom haskell program, keeping the highest quality among duplicates, at any given position
The 5' and 3' 4 nt UMIs were removed from the deduplicated reads using cutadapt (version 1.15) with options -u 4 and -u -4
After removing UMIs, the reads from 18 to 24 nt were selected using bioawk version 20110810
The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.1) with options -L 6 -i S,1,0.8 -N 0
The reads that failed to map were inspected using grep -E -B 1 -A 2 "^G[ACGTN]{20,25}T+$" to detect possible reads starting with G with 20 to 25 nt followed by a poly-U tail that might have prevented the mapping, and this tail was removed from such reads using a custom haskell program before re-mapping them.
Mapped and remapped reads were used to estimate the abundance of small RNAs derived from structural RNAs using featureCounts (version 1.5.2) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as “si_22G” if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The “si_22G” reads were re-mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.1) with options -L 6 -i S,1,0.8 -N 0
The resulting alignment was used to generate the normalized bigwig file using millions of non-structural RNAs as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.26) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of “si_22G” RNAs along the genome

organism: Caenorhabditis elegans

source_name: nematodes

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching. The harvested animals were washed three times with M9 buffer and 40 µl of worm pellet was frozen in dry ice with TRI Reagent (MRC, Inc.). After five repetitions of freeze and thaw, total RNA was isolated according to the TRI Reagent protocol. Ten micrograms of RNA were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by phenol-extraction and isopropanol precipitation. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. 10 µg of total DNase treated RNAs with RIN > 8 was size seleceted from 15% UREA PAGE gel and used to generate small RNA libraries.
The library preparation was performed as essentially described by Jayaprakash et al., 2011, except that a 5’ polyphosphatase (lucigen RP8092H) treatment was performed to be able to clone tri-phosphate small RNAs, and that the PAGE gel extraction after each ligation was substitute with purification by 1.8 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) and 3 volumes of isopropanol. The multiplexed amplified libraries were further purified using PippinPrep DNA size selection with 3% gel cassettes and the following parameters for the selection: BP start (115) and the BP end (165). The purified libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced either on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005) or Illumina MiniSeq platform using MiniSeq High Output Reagent Kit 75-cycles (FC-420-1001).

treatment_protocol: RNAi treatment was performed using worms grown on 15 cm Petri dishes seeded with concentrated RNAi food. The Arhinger RNAi library was used to pick the selected bacteria clones.

tag: genotype

value: CRISPR-cas9 piwi mutant line 2

tag: tissue

value: whole worm

tag: developmental stage

value: young adult, 48 hours post hatching


title: A0076-121007

tag: time

value: Female

value: ND


title: C1HTsmall_s5_1911004005_Col12_S163

tag: protocol


title: WT_CRISPR_line2_F12_sRNA-seq

description: total sRNA

value: WT derived from CRISPR-cas9 piwi mutant line 2


title: A0075-121007


title: BA induction after 66h

type: RNA

state: Tokyo

country: Japan

source_name: ES cell, BA induction after 66h


title: WT_CRISPR_line1_F12_sRNA-seq

description: total sRNA

value: WT derived from CRISPR-cas9 piwi mutant line 1


title: piwi_CRISPR_line1_F9_sRNA-seq

description: total sRNA

value: CRISPR-cas9 piwi mutant line 1


title: BA induction after 54h

source_name: ES cell, BA induction after 54h


title: A0369-211212

value: POST

value: Y


title: BA induction after 42h

source_name: ES cell, BA induction after 42h

value: BA induction


title: WT_CRISPR_line2_F9_sRNA-seq

description: total sRNA


title: A0368-220612


title: BA induction after 48h

source_name: ES cell, BA induction after 48h


title: BA induction after 60h

source_name: ES cell, BA induction after 60h


title: C1HTsmall_s5_1911004005_Col10_S164

tag: centre

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: A0369-220612

value: PRE


title: BeWo_IGF_TNF100n_rep1

type: genomic

city: Mitaka

first: Kei

last: Tanaka

department: Medicine

institute: Kyorin University

description: SAMPLE 11

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip Kit using standard Illumina protocol.

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

data_processing: GenomeStudio software V2010.3

label: Cy5 and Cy3

molecule: genomic DNA

source_name: BeWo, IGF-I, TNF-alpha 100ng/ml, replicate1

label_protocol: Standard Illumina Protocol

growth_protocol: BeWo cells were incubated with Ham F-12 medium supplemented with 10% fetal calf serum at 5% CO2 and 95% air at 37°C.

extract_protocol: genomic DNA was extracted from BeWo cells using Quiagen AllPrep DNA/RNA Mini Kit according to standard instructions.

treatment_protocol: Bewo cells were incubated with TNF-α (100pg/ml, 100ng/ml) and IGF-I (100ng/ml) for 48  hrs.

value: BeWo

tag: cell type

value: choriocarcinoma cell line


title: WT_CRISPR_line1_F9_sRNA-seq

description: total sRNA

tag: treatment


title: A0368-170912

value: Positive


title: BA induction after 32h

source_name: ES cell, BA induction after 32h

tag: cell line


title: prg-1_n4357_rep2_sRNA-seq

description: total sRNA


title: C1HTsmall_s5_1911004005_Col09_S180


title: C1HTsmall_s5_1911004005_Col05_S168


title: BeWo_IGF_TNF100p_rep1

description: SAMPLE 9

source_name: BeWo, IGF-I,TNF-alpha 100pg/ml, replicate1


title: A0334-180512

tag: subject

value: Male


title: C1HTsmall_s5_1911004005_Col08_S165


title: BeWo_IGF_TNF100n_rep2

description: SAMPLE 12

source_name: BeWo, IGF-I, TNF-alpha 100ng/ml, replicate2


title: C1HTsmall_s5_1911004005_Col06_S167


title: C1HTsmall_s5_1911004005_Col07_S166


title: BA induction after 36h

source_name: ES cell, BA induction after 36h


title: BA induction after 20h

source_name: ES cell, BA induction after 20h


title: BeWo_IGF_TNF100p_rep2

description: SAMPLE 10

source_name: BeWo, IGF-I, TNF-alpha 100pg/ml, replicate2


title: A0331-311011

tag: Sex

value: N


title: BeWo_IGF_rep2

description: SAMPLE 8

source_name: BeWo, IGF-I, replicate2


title: BA induction after 28h

source_name: ES cell, BA induction after 28h


title: BeWo_TNF100n_rep1

description: SAMPLE 5

source_name: BeWo, TNF-alpha 100ng/ml, replicate1


title: A0331-230514

source_name: PBMC

tag: b27 status


title: BA induction after 16h

source_name: ES cell, BA induction after 16h


title: A0334-251111

tag: age at collection


title: prg-1_n4357_rep1_sRNA-seq

description: total sRNA

source_name: nematodes

value: whole worm

value: young adult, 48 hours post hatching


title: N2_rep2_sRNA-seq

description: total sRNA


title: A0323-080811

tag: basdai


title: piwi_CRISPR_line1_F12_mut16_RNAi_RNA-seq

description: total RNA, rRNA-depleted

data_processing:
Reads were mapped on the C. elegans genome (WBcel235) using hisat2 (version 2.0.4) with default parameters
Mapped reads were used to estimate the abundance of protein coding genes using featureCounts (version 1.5.2) with options -O -M --primary -s 2 --fracOverlap 0 and annotations corresponding to protein coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The alignment was used to generate the normalized bigwig file using millions of summed forward reads per kilobase in protein coding genes as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.26) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of RNAs along the genome

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching. The harvested animals were washed three times with M9 buffer and 40 µl of worm pellet was frozen in dry ice with TRI Reagent (MRC, Inc.). After five repetitions of freeze and thaw, total RNA was isolated according to the TRI Reagent protocol. Ten micrograms of RNA were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by phenol-extraction and isopropanol precipitation. Agilent 2200 TapeStation System was used to evaluate the RIN indexes of all the RNA preps, and only samples with RIN > 8 was used for downstream applications. For the preparation of total RNA extracted from generation F4 of wild-type and piwi mutant worms 10 manually picked worms were used.
DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. We developed an RNase H based method to degrade C. elegans and mitochondrial ribosomal RNAs (rRNAs) using 50nt oligos complementary to rRNA and mtRNA C. elegans sequences. The sequences of the oligos used are provided in supplementary table S3. 1 µg of DNase-treated total RNA was mixed with 1 µg of oligos at equimolar concentration and 1X probe hybridization buffer (200 mM NaCl, 10 mM Tris pH 7.5) and incubated in a thermocycler using the following parameters: 2 minutes at 95°C followed by 0.1°C/sec at 95-45°C, and 2 minutes hold at 45°C. Next 2 µl of Thermostable RNase H (epicentre) was added to the reactions together with 1X RNase H reaction buffer 50 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2) and incubated for 30 minutes at 45°C. Next, digested RNAs were treated with 2 U of Turbo DNase (Ambion) at 37°C for 30 minutes followed by purification using 2.2 volumes of Agencourt RNAClean XP Beads (Beckman Coulter, NC0068576) following the manufacturer’s instructions. 100 ng of Ribosomal-depleted RNAs were then used to generate strand-specific RNA libraries using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760S). Multiplexed RNA libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).

value: RNAi treatment mut-16


title: BA induction after 24h

source_name: ES cell, BA induction after 24h


title: BeWo_IGF_rep1

description: SAMPLE 7

source_name: BeWo, IGF-I, replicate1


title: N2_rep1_sRNA-seq

description: total sRNA


title: C1HTsmall_s5_1911004005_Col04_S178

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK


title: BeWo_TNF100n_rep2

description: SAMPLE 6

source_name: BeWo, TNF-alpha 100ng/ml, replicate2


title: C1HTsmall_s5_1911004005_Col03_S162


title: A0323-210314

tag: esr


title: piwi_CRISPR_line2_F12_mut16_RNAi_RNA-seq

description: total RNA, rRNA-depleted

value: CRISPR-cas9 piwi mutant line 2


title: C1HTsmall_s4_1911011082_Col20_S109


title: BA induction after 12h

source_name: ES cell, BA induction after 12h


title: C1HTsmall_s5_1911004005_Col01_S161


title: C1HTsmall_s5_1911004005_Col02_S177


title: piwi_CRISPR_line1_F12_RNA-seq

description: total RNA, rRNA-depleted


title: BeWo_control_rep2

description: SAMPLE 2

source_name: BeWo, control, replicate2


title: piwi_CRISPR_line2_F12_RNA-seq

description: total RNA, rRNA-depleted


title: A0301-051110

value: Negative

tag: crp


title: A0070-170907

tag: anti-tnf


title: BeWo_TNF100p_rep1

description: SAMPLE 3

source_name: BeWo, TNF-alpha 100pg/ml, replicate1


title: C1HTsmall_s4_1911011082_Col19_S110


title: BeWo_TNF100p_rep2

description: SAMPLE 4

source_name: BeWo, TNF-alpha 100pg/ml, replicate2


title: A0292-230810

value: Female


title: WT_CRISPR_line2_F12_RNA-seq

description: total RNA, rRNA-depleted

tag: genotype

value: WT derived from CRISPR-cas9 piwi mutant line 2


title: WT_CRISPR_line1_F12_RNA-seq

description: total RNA, rRNA-depleted

value: WT derived from CRISPR-cas9 piwi mutant line 1

tag: tissue


title: piwi_CRISPR_line2_F9_RNA-seq

description: total RNA, rRNA-depleted

tag: developmental stage


title: A0283-220210

tag: time


title: P30 Stria Vascularis whole cells capture 2

city: Bethesda

first: Michael

last: Hoa

state: MD

address: 35 Convent Dr, Rm 1F-226

institute: National Institutes on Deafness and Other Communication Disorders, NIH

description: Single cell RNA-seq

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the CellRanger v2.0.0 pipeline using default settings.
Secondary analysis was performed using the Seurat2 package
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger v2.0.0 gene counts matrices.

organism: Mus musculus

source_name: Stria Vascularis

extract_protocol:
single cell RNA-Seq: Single cell suspension from stria vascularis: Inner ears from ~12 P30 mice were removed and stria vascularis from the cochleae were collected into 200ul DMEM F-12 media. The tissue was lysed in 0.5mg/ml trypsin at 37c for 7 minutes. The media was carefully removed and replaced with 5% FBS to stop the lysis. The tissue was triturated and filtered through a 20um filter. The filtered cells were let to sit on ice for 35 minutes. 150ul of the supernatant was removed and cell pellet was suspended in the remaining 50ul. Cells were counted on a Luna automated cell counter and a cell density of 1x106 cells/ml was used to load onto the 10X genomics chip.
single nucleus RNA-Seq: Single nucleus suspension from stria vascularis: Published single nucleus suspension protocol from 10x genomics was used to isolate the nuclei. Briefly, stria vascularis from ~10 P30 animals were isolated and collected in 3ml DMEM F-12 media. Following collection, the media was replaced with 3ml chilled lysis buffer (10mM Tris-HCl, 10mM Nacl, 3mM MgCl2,0.005% Nonidet P40 in Nuclease free water) and the tissue were lysed at 4c for 25 minutes. The lysis buffer was then replaced with 1.5ml DMEM F-12 media. The tissues were triturated and filtered through a 20um filter. The filtrate was centrifuged at 500rcf for 5 minutes at 4c. The supernatant was removed, and the cell pellet was resuspended in 1ml nuclei wash and resuspension buffer (1xPBS with 1% BSA and 0.2U/ul RNase Inhibitor). The cells were filtered through a 10um filter and centrifuged at 500rcf for 5 minutes at 4c. The supernatant was removed, and pellet resuspended in 50ul of nuclei wash and resuspension buffer. Nuclei were counted in a Luna cell counter and a nuclear density of 1x106 cells/ml was used to load onto the 10X genomics chip.
Library preparation was performed according to the manufacturer’s instructions for the 10x Genomics Chromium platform (10x Genomics). The libraries were sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: Stria Vascularis

tag: strain

value: CBA/J mice (strain 000656)


title: C1HTsmall_s4_1911011082_Col18_S116

tag: protocol

tag: centre

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: A0283-230913

value: POST

value: Y


title: P30 Stria Vascularis whole cells capture 1

description: Single cell RNA-seq


title: A0128-221010

value: Positive


title: C1HTsmall_s4_1911011082_Col14_S112

tag: cell type


title: C1HTsmall_s4_1911011082_Col13_S111


title: C1HTsmall_s4_1911011082_Col16_S114


title: C1HTsmall_s4_1911011082_Col12_S103


title: A0292-050911


title: NS58.FF.Pi.PancT6

city: Chapel Hill

first: Xianlu

middle: Laura

last: Peng

state: NC

address: 450 West Dr.

institute: The University of North Carolina at Chapel Hill

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing: Digital count from each individual samples were combined as a matrix.

source_name: PrimaryPDAC

extract_protocol: RNA and DNA was harvested from FFPE samples using the Roche High Pure RNA Paraffin Kit (CAT#3270289001) following manufacturer's instructions. RNA and DNA was harvested from FF and FNA samples using the Qiagen AllPrep DNA/RNA Mini Kit (CAT#80204) following manufacturer's instructions.

tag: sample type

value: FF

tag: extraction method

value: Qiagen AllPrep DNA/RNA Mini Kit


title: NS57.FF.Pi.0818T1


title: piwi_CRISPR_line1_F9_RNA-seq

description: total RNA, rRNA-depleted

value: CRISPR-cas9 piwi mutant line 1

value: whole worm

tag: treatment


title: WT_CRISPR_line2_F9_RNA-seq

description: total RNA, rRNA-depleted

value: young adult, 48 hours post hatching


title: BA induction after 10h

source_name: ES cell, BA induction after 10h

tag: cell line

value: BA induction


title: C1HTsmall_s4_1911011082_Col17_S115


title: NS56.FF.Pi.1129T1


title: piwi_CRISPR_line2_F4_RNA-seq

description: total RNA, rRNA-depleted

value: CRISPR-cas9 piwi mutant line 2


title: WT_CRISPR_line1_F9_RNA-seq

description: total RNA, rRNA-depleted


title: C1HTsmall_s4_1911011082_Col15_S113


title: piwi_CRISPR_line1_F4_RNA-seq

description: total RNA, rRNA-depleted


title: C1HTsmall_s4_1911011082_Col11_S119


title: BA induction after 14h

source_name: ES cell, BA induction after 14h


title: WT_CRISPR_line2_F4_RNA-seq

description: total RNA, rRNA-depleted


title: NS55.FF.Pi.1118T1


title: A0128-020710

tag: subject

value: PRE

tag: Sex

value: Male

tag: b27 status

tag: age at collection

value: N


title: C1HTsmall_s4_1911011082_Col10_S104


title: BA induction after 8h

source_name: ES cell, BA induction after 8h


title: C1HTsmall_s4_1911011082_Col09_S120


title: WT_CRISPR_line1_F4_RNA-seq

description: total RNA, rRNA-depleted

value: WT derived from CRISPR-cas9 piwi mutant line 1


title: BA induction after 4h

source_name: ES cell, BA induction after 4h


title: A0126-220711

source_name: PBMC

tag: basdai

tag: esr

tag: crp

tag: anti-tnf


title: A0126-160309

tag: time


title: BA induction after 6h

source_name: ES cell, BA induction after 6h


title: BA induction after 3h

source_name: ES cell, BA induction after 3h


title: A0124-020209


title: C1HTsmall_s4_1911011082_Col08_S105


title: prg-1_n4357_rep2_RNA-seq

description: total RNA, rRNA-depleted

source_name: nematodes

tag: genotype

tag: tissue

tag: developmental stage


title: A0120-121208


title: prg-1_n4357_rep1_RNA-seq

description: total RNA, rRNA-depleted


title: C1HTsmall_s4_1911011082_Col07_S106

tag: protocol

tag: centre

tag: cell type


title: BeWo_control_rep1

description: SAMPLE 1

source_name: BeWo, control, replicate1

value: BeWo

value: choriocarcinoma cell line


title: NS53.FF.Pi.0806T1

tag: sample type

tag: extraction method


title: C1HTsmall_s4_1911011082_Col06_S107

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

value: Stanford

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: NS52.FF.Pi.0523T1


title: A0117-180610

tag: subject


title: A0069-240807

tag: Sex


title: N2_rep2_RNA-seq

description: total RNA, rRNA-depleted

tag: treatment


title: NS51.FF.Pi.1109T1


title: A0124-191110

value: POST

tag: b27 status

tag: age at collection

value: Y


title: C1HTsmall_s4_1911011082_Col05_S108


title: NS50.FF.Pi.0614T1

value: FF


title: C1HTsmall_s4_1911011082_Col04_S118


title: prg-1_n4357_rep2_GRO-seq

description: biotinylated RNA

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) was trimmed from the raw reads using cutadapt (version 1.15). The reads where the adaptor was not found were nonetheless kept ("untrimmed")
The 5' and 3' 4 nt UMIs were removed from the trimmed reads using cutadapt (version 1.15) with options -u 4 and -u -4
The 5' 4 nt UMIs as well as 7 nt in 3' (to be sure to eliminate possibly unrecognized first adaptor bases, as well as preceding 3' 4 nt UMIs) were removed from the "untrimmed" reads using cutadapt (version 1.15) options -u 4 and -u -7
Both types of reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.1) with default parameters, and the resulting alignment files were merged using samtools (version 1.3.1)
Mapped reads were used to estimate the abundance of protein coding genes using featureCounts (version 1.5.2) with options -O -M --primary -s 1 --fracOverlap 0 and annotations corresponding to protein coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
The merged alignment was used to generate the normalized bigwig file using millions of summed forward reads per kilobase in protein coding genes as normalizer. This was done with a custom bash script using bedtools (version 2.27.1), bedops (version 2.4.26) and bedGraphToBigWig (version 4)
Genome_build: C. elegans ce11 (WBcel235)
Supplementary_files_format_and_content: bigwig files allowing to display the normalized abundance of nascent RNAs along the genome

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching. The harvested animals were washed three times with M9 buffer and nuclei were extracted as described by Cecere et al., 2014.
GRO-seq experiments were performed as described by Cecere et al., 2014 except that biotin-UTP was used to label nascent RNAs.


title: NS54.FF.Pi.0119T1

value: Qiagen AllPrep DNA/RNA Mini Kit


title: A0111-180213

value: Female

value: Positive

tag: basdai

tag: esr


title: prg-1_n4357_rep1_GRO-seq

description: biotinylated RNA

value: whole worm

value: young adult, 48 hours post hatching


title: NS49.FF.Pi.0607T1


title: A0086-280809

tag: crp

tag: anti-tnf


title: C1HTsmall_s4_1911011082_Col03_S102


title: C1HTsmall_s4_1911011082_Col02_S117


title: N2_rep2_GRO-seq

description: biotinylated RNA

tag: genotype


title: C1HTsmall_s4_1911011082_Col01_S101


title: A0086-290413

tag: time


title: NS47.FF.Pi.1012T1


title: NS48.FF.Pi.0503T1


title: N2_rep1_GRO-seq

description: biotinylated RNA

tag: tissue

tag: developmental stage


title: A0079-221007


title: NS46.FF.Pi.1214T1


title: C1HTsmall_s3_1911011081_Col20_S89

tag: protocol

tag: centre


title: NS45.FF.Pi.0524T1

tag: sample type


title: A0008-170907


title: N2_rep1_RNA-seq

description: total RNA, rRNA-depleted


title: NS44.FF.Pi.0327T1

tag: extraction method


title: C1HTsmall_s3_1911011081_Col19_S90

tag: cell type


title: NS43.FF.Pi.0517T1


title: DT.99

city: Athens

first: Aristotelis

last: Chatziioannou

address: 48 Vassileos Constantinou Avenue

country: Greece

institute: National Hellenic Research Foundation

data_processing:
Sequence alignment was performed with Tophat2
Cufflinks was used to quantify expression
Cuffdiff was used to compare the level of gene expression
Genome_build: GRCm.38

source_name: Liver

extract_protocol:
Isolation was performed using commercial kit of QIAGEN (Cat.No.73404), and Quality control of the RNA samples was tested by 2100 BioAnalyzer (Agilent). Illumina TruSeq Stranded RNA Sample Prep Kit was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver cells

tag: strain line

tag: Sex

value: M

tag: obesity

value: Yes

tag: diabetes

value: No


title: A0008-180711

tag: subject

tag: b27 status

tag: age at collection

tag: basdai


title: A0076-131114

tag: esr

tag: crp

tag: anti-tnf


title: DT.98

value: F


title: NS42.FFPE.Pi.0422T1

value: FFPE

value: Roche High Pure RNA Paraffin Kit


title: C1HTsmall_s3_1911011081_Col17_S95

value: Stanford


title: A0075-080909

tag: time

value: Male


title: C1HTsmall_s3_1911011081_Col18_S96

tag: protocol

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: A0370-030513

value: POST

value: Y


title: A0301-150711

value: Negative


title: C1HTsmall_s3_1911011081_Col16_S94

tag: centre


title: WT_pombe_Rapid-1

city: Eugene

first: Jeffrey

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

description: Nucleosomal DNA

library_source: genomic

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Genome_build: S. cerevisiae genome build sacCer3 (R64)
Genome_build: S. pombe genome build ASM294v2
Genome_build: N. crassa genome build NC12, but with the large inversion on LGVI corrected (see Series-level supplementary files neurospora_crassa_or74a_12_genome_FIXED.fasta and neurospora_crassa_or74a_12_transcripts_FIXED.gtf)
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

organism: Schizosaccharomyces pombe

source_name: exponentially-growing S. pombe

growth_protocol: exponentially-growing yeast were grown in YPD until OD600 was between 0.6 and 1.0. Yeast patches were grown overnight on YPD or selective agar. S. pombe was grown to OD600=0.8 in YES(5) media. N. crassa conidia (2.5*10^7 cells) were grown in Vogel's solution plus 1.5% sucrose for 3.5 hours until >70% of conidia were germinated.

extract_protocol:
cells were crosslinked with 1% formaldehyde for 15 min (10min for N. crassa), spheroplasted,  digested with micrococcal nuclease and quenched. For "standard" protocol, crosslinks reversed overnight at 65 degrees with proteinase K treatment, phenol-chloroform extracted, RNase-treated, mononucleosome band gel-extracted and CIP-treated. For Rapid protocol, RNase was added for 30 minutes, then crosslinks were reversed at 65 degrees with proteinase K treatment for 45 minutes. DNA was recovered by MinElute column (eluted into 1x cutsmart buffer) and incubated with Quick CIP for 10 minutes.
CIP-treated nucleosome-sized DNA footprints were converted to libraries with NuGEN Ovation Ultralow kit

tag: strain background

value: WT


title: C1HTsmall_s3_1911011081_Col15_S93


title: DT.96


title: NS41.FNA.Pi.1009T1

tag: sample type

value: FNA

tag: extraction method

value: Qiagen AllPrep DNA/RNA Mini Kit


title: NS39.FNA.Pi.0614T1


title: NS40.FNA.Pi.0523T1


title: C1HTsmall_s3_1911011081_Col14_S92

tag: cell type


title: A0070-151010

tag: Sex


title: WT_E1h_ICI_ER

city: Durham

first: Yukitomo

last: Arao

address: 111 TW Alexandr Dr.

institute: NIEHS

data_processing:
Raw sequencing reads were trimmed to 36bp then filtered to retain only those with average base quality score > 20.
Reads were mapped against the mm9 reference assembly via Bowtie2 (v2.1.0) with parameters "--end-to-end --sensitive", then filtered via samtools to require a minimum mapping score of 30.
Duplicate reads within a given library were removed via Picard MarkDuplicates.jar.
For samples with two libraries, mapped deduplicated hits were aggregated via Picard MergeSamFiles.jar.
Peaks were called via HOMER (v4.10.3) findPeaks with parameters "-style factor -fdr 0.00001 -F 12" using GSM894057 as the corresponding input.  Peaks were then re-defined as 200bp regions centered on the called peak midpoint.
To generate depth tracks the mapped non-duplicate reads were extended to the estimated average fragment size of 150bp, converted to bedGraph via BEDtools (v2.24.0) genomeCoverageBed, normalized to 20M reads, then converted to bigWig format by UCSC utility bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks in BED format; normalized depth tracks in bigWig format.

source_name: mouse uterus

growth_protocol: Animals were maintained on a NIH-31 regular diet.

extract_protocol:
Frozen mouse tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: OVX 12-wk-old AF2ERKI or WT littermate female mice (six animals per group) were injected intraperitoneally with 2 mg/kg fulvestrant/ICI182780 (ICI) or 2 mg/kg tamoxifen (Tam) dissolved in DMSO respectively. 50 µl DMSO was injected as vehicle (Veh). After 1h injection, animals were euthanized with carbon dioxide, then uterus was collected. Collected tissues were stored at -70 ˚C until processed.

tag: tissue

value: uterus

tag: strain

tag: chip antibody

value: ER[alpha] Santa Cruz SC-542

tag: genotype/variation

value: wild type

tag: treatment

value: 2 mg/kg fulvestrant/ICI182780 (ICI)


title: A0120-180909

tag: subject

tag: b27 status

value: Positive

tag: age at collection

tag: basdai


title: DT.94

value: Liver cells

tag: strain line

value: F

tag: obesity

value: No

tag: diabetes


title: NS38.FNA.Pi.1129T1


title: C1HTsmall_s3_1911011081_Col13_S91

tag: protocol

tag: centre

value: Stanford


title: DT.93

value: M


title: DT.92

value: Yes


title: A0117-240715

tag: time

value: POST

value: Male

tag: esr

tag: crp

tag: anti-tnf


title: C1HTsmall_s3_1911011081_Col11_S99

tag: cell type

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: A0111-311008

value: PRE

tag: Sex

value: Female

value: N


title: A0069-040909

value: Y


title: NS37.FNA.Pi.0806T1

tag: sample type

value: FNA

tag: extraction method

value: Qiagen AllPrep DNA/RNA Mini Kit


title: NS36.FNA.Pi.0524T1


title: A0079-130309

tag: subject


title: NS34.FNA.Pi.0119T1


title: DT.91


title: NS35.FNA.Pi.0327T1


title: DT.90


title: DT.89


title: NS33.FNA.Pi.1214T1


title: C1HTsmall_s3_1911011081_Col12_S83


title: NS32.FNA.Pi.1109T1


title: smNPCP21C21_S2_L002

city: LA JOLLA

first: Matteo

last: D'Antonio

address: 9500 Gilman Drive #0761

institute: UCSD

data_processing:
RNA-seq reads were aligned to the human genome (hg19) with STAR 2.4.0h (outFilterMultimapNmax 20, outFilterMismatchNmax 999, outFilterMismatchNoverLmax 0.04, outFilterIntronMotifs RemoveNoncanonicalUnannotated, outSJfilterOverhangMin 6 6 6 6, seedSearchStartLmax 20, alignSJDBoverhangMin 1) using a gene database constructed from Gencode v19
Reads that overlap with exon coordinates were counted using HTSeqcount (-s reverse -a 0 -t exon -i gene_id -m union)
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated file created using featureCounts v1.5.0 (number of reads mapped to each Gencode V.19 gene)

growth_protocol: human iPSCs at 70%–80% confluency were dissociated using accutase (Innovative Cell Technologies) and resuspended at 1x106 cells/ml in N2B27 medium (DMEM/F12 with GlutaMAX (Thermo Fisher Scientific), 1 x N-2 supplement (Thermo Fisher Scientific), 1 x B-27 supplement (Thermo Fisher Scientific), 150 mM ascorbic acid (Tocris), and 1% Penicillin/Streptomycin) supplemented with 1 µM Dorsomorphin (Tocris), 10 µM SB431542 (Tocris), 3 µM CHIR99021, 0.5 µM Purmorphamine and 5 mM Y-26732 (Stemcell Technologies).  Three million cells were transferred into one well of an uncoated 6-well tissue culture plate and incubated at 37ºC, 5% CO2 on a shaker at 90 rpm.  Uniform small EBs formed within 24h and increased in size over the following days.  After 48h, a full media change was performed with N2B27 medium supplemented with Dorsomorphin, SB431542, CHIR99021, and Purmorphamine.  At this time, about 2/3 of EBs were either discarded or EBs were split across 3 wells of a 6-well plate to reduce the high cell density required initially to ensure uniform formation of embryoid bodies.  On days 3-5, half media change was performed with fresh N2B27 media supplemented with Dorsomorphin, SB431542, CHIR99021, and Purmorphamine.  On day 6, Dorsomorphin and SB431542 were withdrawn and a full media change with smNPC media (N2B27 media supplemented with 3 µM CHIR99021 and 0.5 µM Purmorphamine) was performed.  At this stage, neuroepithelial folds were clearly visible in all EBs.  On day 8, EBs were triturated by pipetting 10-15 times with a P1000 pipette and plated onto matrigel-coated 10 cm plates.  After 3-4 days, attached EB fragments and outgrown cells were dissociated to single cells with accutase (Innovative Cell Technologies) and split at a 1:6 to 1:8 ratio onto matrigel-coated plates.  After the first passage, cells were passaged at a 1:10 to 1:15 ratio every 3-6 days.

extract_protocol:
Total RNA was extracted from the differentiated smNPCs using RNeasy Plus Mini Kit and was reverse transcribed using RNA to cDNA EcoDry Premix according to the manufacturer’s instruction.
RNA libraries were generated using llumina’s TruSeq Stranded mRNA Sample Prep Kit (Illumina) following manufacturer’s instructions.

tag: tissue

value: iPSC-derived induced glioblastoma (iGBM) model

value: iPSC-derived neural progenitor cells

tag: iPSc passage

tag: differentiation day

tag: genotype


title: smNPCP21C21_S2_L003


title: C1HTsmall_s3_1911011081_Col06_S87


title: DT.88

value: Liver cells

tag: strain line

tag: obesity


title: DT.97

tag: diabetes


title: C1HTsmall_s3_1911011081_Col09_S100

tag: protocol

tag: centre


title: C1HTsmall_s3_1911011081_Col07_S86


title: DT.85


title: C1HTsmall_s3_1911011081_Col05_S88


title: smNPCWT_S1_L003

source_name: ctrl

value: wildtype


title: C1HTsmall_s3_1911011081_Col04_S98


title: smNPCT9A35_S3_L003


title: C1HTsmall_s3_1911011081_Col08_S85


title: NS31.FNA.Pi.1118T1


title: smNPCT9A35_S3_L002


title: DT.86

value: No


title: NS30.FNA.Pi.0818T1


title: C1HTsmall_s3_1911011081_Col10_S84

value: Stanford


title: DT.84

value: M


title: C1HTsmall_s3_1911011081_Col02_S97


title: DT.82

value: F


title: C1HTsmall_s3_1911011081_Col03_S82


title: DT.87

value: Yes


title: C1HTsmall_s3_1911011081_Col01_S81


title: NS27.FNA.Pi.0417T1


title: NS29.FNA.Pi.0921T1


title: DT.83


title: NS25.FF.PDX.0411T1

source_name: PDX

value: FF


title: NS24.FF.PDX.0806T1


title: siRNA.1: 24hr siRNA; MDA-MB-231 cell

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

data_processing:
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.36). Next, the reads were mapped to the Homo sapiens reference genome from Ensembl database and aligned using the STAR alignment tool (Version 2.5.3). After this, the read counts were generated from SUBREAD (Version 1.5.2) and featured counts were outputted for statistical analysis in R. Quality control and normalization was conducted in R using edgeR (Version 3.20.9).
Statistical Analysis and DEGs: Statistical analysis was conducted in R using limma (Version 3.34.9). Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >1.5 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37
Supplementary_files_format_and_content: Normalized expressions and differentially expressed genes

source_name: MDA-MB-231 cell

growth_protocol: MCF-7 cells were cultured in RPMI medium +5%FBS+pen/strep.  MDA-MB-231 cells were cultured in L15 medium+5%FBS + pen/strep

extract_protocol:
RNA was extracted using Trizol protocol, followed by DNase treatment.  RNA was then re-purified with an aqueous column-based protocol followed by gel analysis to analyze purity and quality of the RNA.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).

treatment_protocol: Cells were treated with vehicle or inhibitors while in growth phase, for times indicated. Cells were treated with siRNA for 72 hrs. prior to harvest.

tag: cell line

value: MDA-MB-231 cell

tag: treatment

value: 24hr siRNA


title: siRNA.2: 24hr siRNA; MDA-MB-231 cell


title: NB73.2: 24hr NB73; MDA-MB-231 cell

value: 24hr NB73


title: NB73.1: 24hr NB73; MDA-MB-231 cell


title: NS26.FNA.Pi.1012T1

source_name: PrimaryPDAC


title: DT.81


title: C1HTsmall_s2_1911011072_Col20_S69

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: DT.80


title: NS22.FF.PDX.1108T1


title: DT.77


title: VEH.2: 24hr Vehicle; MDA-MB-231 cell

value: 24hr Vehicle


title: NS23.FF.PDX.1222


title: FDI6.2: 24hr FDI-6; MCF-7 cells

source_name: MCF-7 cells

value: MCF-7 cells

value: 24hr FDI-6


title: C1HTsmall_s2_1911011072_Col19_S70


title: C1HTsmall_s2_1911011072_Col16_S74


title: DT.74


title: VEH.1: 24hr Vehicle; MDA-MB-231 cell


title: DT.76


title: NS28.FNA.Pi.0607T1

value: FNA

value: Qiagen AllPrep DNA/RNA Mini Kit


title: NS21.FF.PDX.0113T1


title: NS20.FF.PDX.0616T1


title: C1HTsmall_s2_1911011072_Col18_S76


title: NB73.2: 24hr NB73; MCF-7 cells


title: DT.71

value: Liver cells


title: C1HTsmall_s2_1911011072_Col15_S73


title: NB73.1: 24hr NB73; MCF-7 cells


title: smNPCWT_S1_L002

value: iPSC-derived induced glioblastoma (iGBM) model

value: iPSC-derived neural progenitor cells

value: wildtype


title: FDI6.1: 24hr FDI-6; MCF-7 cells


title: C1HTsmall_s2_1911011072_Col14_S72

value: Stanford


title: C1HTsmall_s2_1911011072_Col13_S71


title: NS19.FF.PDX.0523T1


title: DT.70

value: F

value: No


title: NS18.FF.PDX.0218T2

value: FF


title: DT.39

value: Yes


title: DT.41

value: M


title: VEH.2: 24hr Vehicle; MCF-7 cells


title: C1HTsmall_s2_1911011072_Col12_S63


title: C1HTsmall_s2_1911011072_Col11_S79


title: NS16.FF.PDX.1125T2


title: C1HTsmall_s2_1911011072_Col10_S64


title: FDI6.2: 9hr FDI-6; MCF-7 cells

value: 9hr FDI-6


title: NS15.FF.PDX.1112T1


title: FDI6.1: 9hr FDI-6; MCF-7 cells


title: C1HTsmall_s2_1911011072_Col17_S75

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: C1HTsmall_s2_1911011072_Col08_S65


title: C1HTsmall_s2_1911011072_Col09_S80


title: NB55.3: 9hr NB55; MCF-7 cells

value: 9hr NB55


title: FDI6.3: 9hr FDI-6; MCF-7 cells

value: MCF-7 cells


title: DT.155


title: NS14.FF.PDX.0902T1B


title: VEH.1: 24hr Vehicle; MCF-7 cells

value: 24hr Vehicle


title: DT.154


title: NS17.FF.PDX.PancT6


title: NS13.FF.PDX.1109


title: NS12.FF.PDX.0319


title: C1HTsmall_s2_1911011072_Col07_S66


title: DT.153


title: NB55.2: 9hr NB55; MCF-7 cells


title: C1HTsmall_s2_1911011072_Col06_S67


title: DT.95


title: NS11.FF.PDX.1108


title: DT.30


title: NS10.FF.PDX.0119T1


title: DT.156


title: C1HTsmall_s2_1911011072_Col05_S68


title: NB73.3: 9hr NB73; MCF-7 cells

value: 9hr NB73


title: NB55.1: 9hr NB55; MCF-7 cells


title: DT.150


title: C1HTsmall_s2_1911011072_Col04_S78


title: NB73.2: 9hr NB73; MCF-7 cells


title: NS09.FF.PDX.0508T1

value: Qiagen AllPrep DNA/RNA Mini Kit


title: NB73.1: 9hr NB73; MCF-7 cells


title: DT.149

value: Liver cells


title: NS08.FF.PDX.0225T1


title: C1HTsmall_s2_1911011072_Col03_S62


title: DT.147


title: C1HTsmall_s2_1911011072_Col02_S77


title: NS07.FFPE.PDX.1108T1

value: FFPE

value: Roche High Pure RNA Paraffin Kit


title: NS05.FFPE.PDX.0417T1


title: DT.152


title: C1HTsmall_s2_1911011072_Col01_S61


title: NS06.FFPE.PDX.1109T1


title: C1HTsmall_s1_1911011069_Col20_S49


title: VEH.2: 9hr Vehicle; MCF-7 cells

value: 9hr Vehicle


title: DT.151


title: DT.146


title: NS04.FFPE.PDX.0910T1


title: VEH.1: 9hr Vehicle; MCF-7 cells


title: C1HTsmall_s1_1911011069_Col19_S50

value: Stanford


title: DT.145


title: DT.144

value: F


title: C1HTsmall_s1_1911011069_Col18_S56


title: Total_oligo_rep2

city: Madrid

first: Irene

last: Diaz-Lopez

address: C/Nicolas Cabrera 1

institute: Centro de biologia molecular Severo Ochoa

description: Total RNA

data_processing:
Illumina Sequencing Analysis Viewer, Illumina run specifications and FastQC were using for base-calling (external service)
Remove rRNA sequences using GRCh38 release and bowtie software with parameters --un -x index -1 reads_1 -2 reads_2 -S output.sam
Alignment with hisat2 using GRCh38 release as reference genome with parametes --min-intronlen 20 --max-intronlen 11000 --known-splicesites-infile splicesites.txt -x genome_file -1 samplefile_1 -2 samplefile_2 -S outputfile.sam
Counts per transcript were calculated using featurecounts with parameters -T 4 -p -t gene -g gene_id -a Homo_sapiens.gtf -o data_matrix
Differential expression and translation efficiency were calculated with Deseq2 software (different parameters depending on the comparative). Sizefactors were calculated used the spike percentaje of aligments and the library size of each sample (in TOTAL samples only the library size were took in account)
Genome_build: GRCh38
Supplementary_files_format_and_content: [processed_data_oligo.xlsx]  Deseq2 normalized counts and analysis for all samples

growth_protocol: Adherent cells grown in DMEM with 10%FBS  in P100 culture plaques during 24h

extract_protocol:
Lysates were obtained using standard mammalian lysis buffer, clarified and fractionated in a 10%-40% sucrose gradient after ultracentifugation for the monosomes and polysomes samples, or directly from the clarified for the total samples
RNA libraries were prepared for sequencing using standard Illumina protocols. ERCC RNA spike-in mix (Thermo Fisher) were added to track the dilutions on the mRNA due to the technique
Stranded  libraries

treatment_protocol: Transfection with 100µmol of problem oligo (4VIC) or control oligo (4) with turbofect, extraction at 16 hours post transfection

value: Human kidney (embryonic)

tag: transfection

value: oligo (4VIC)

tag: fraction

value: total RNA


title: NS03.FFPE.PDX.0113T1


title: Total_oligo_rep1

description: Total RNA


title: VEH.3: 9hr Vehicle; MCF-7 cells


title: Polysomes_oligo_rep2

description: mRNA

value: Polysomes


title: C1HTsmall_s1_1911011069_Col17_S55

tag: cell type


title: single-cell RNA-seq dataset: PR8-infected MDCK cells at a MOI of 0.2 harvested at 6hpi

city: New York

first: Chang

last: Wang

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: Illumina NextSeq 500 and HiSeq 2500

data_processing:
For the single-cell RNA-seq datasets generated in the time course infection assay, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment and gene counting with the processed UMIs for each cell. Then the UMI counts for all the viral reads including the gapped reads with the CIGAR string containing a large gap (i.e., “MNM”) were merged into the expression matrix.
For the bulk RNA-seq datasets, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment.
For the single-cell RNA-seq datasets generated from PR8-infected A549 and MDCK cells at different MOIs, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment.
Genome_build: hg19 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1)
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets generated in the time course infection assay, each tab-delimited text file contains the raw gene expression matrix for individual cells harvested at a given time point. For the bulk RNA-seq datasets, each tab-delimited text file contains the raw gene counts for a given sample.

organism:
Canis lupus familiaris
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: Madin-Darby canine kidney cells

growth_protocol: Madin-Darby canine kidney (MDCK) cells were maintained in minimum essential medium (MEM) supplemented with 5% FBS. MDCK cells were infected in MDCK infection media (MEM supplemented with 2% bovine serum albumin (BSA), 1% antibiotic-antimycotic, and 1.5ug/mL TPCK-Trypsin)

extract_protocol:
Cells were trypisinized, extensively washed, and re-suspended in PBS containing 0.04% BSA.
Cells were subject to 10X Genomics single cell library preparation with Chromium 3’ v2 chemistry following the manufacturer’s protocol.

treatment_protocol: MDCK cells were infected with PR8 virus at a MOI of 0.2.

tag: cell types

value: MDCK

tag: infection time points

value: 6 hours post-infection

tag: virus strain


title: NS01.FFPE.PDX.1109T1

tag: sample type

tag: extraction method


title: C1HTsmall_s1_1911011069_Col15_S53

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: Polysomes_oligo_rep1

description: mRNA

tag: tissue


title: DT.141

tag: Sex

value: No


title: C1HTsmall_s1_1911011069_Col13_S51


title: DT.142

tag: strain line

value: M

value: Yes


title: DT.139

tag: obesity


title: Monosomes_oligo_rep2

description: mRNA

value: Monosomes


title: Viral genome sequencing dataset: PR8 virus stock

data_processing:
Library strategy: amplicon sequencing
For the single-cell RNA-seq datasets generated in the time course infection assay, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment and gene counting with the processed UMIs for each cell. Then the UMI counts for all the viral reads including the gapped reads with the CIGAR string containing a large gap (i.e., “MNM”) were merged into the expression matrix.
For the bulk RNA-seq datasets, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.5.3a) was used for the alignment.
For the single-cell RNA-seq datasets generated from PR8-infected A549 and MDCK cells at different MOIs, the Cell Ranger (v2.1.0) single cell software suite was applied to convert the BCL files and perform the alignment.
Genome_build: hg19 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1)
Supplementary_files_format_and_content: For the single-cell RNA-seq datasets generated in the time course infection assay, each tab-delimited text file contains the raw gene expression matrix for individual cells harvested at a given time point. For the bulk RNA-seq datasets, each tab-delimited text file contains the raw gene counts for a given sample.

molecule: other

organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: PR8 virus stock

growth_protocol: PR8 virus stock was plaque purified and propagated in MDCK cells.

extract_protocol:
Viral genomic RNA (vRNA) of the virus stocks used in the infection assay was extracted using RNeasy Mini Kit (Qiagen).
vRNA was amplified using multi-segment reverse-transcription PCR (M-RT-PCR) and then subject to Illumina library preparation with Nextera DNA library prep kit.


title: C1HTsmall_s1_1911011069_Col12_S43

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11), R2 = cDNA

extract_protocol:
PBMCs were isolated according to the manufacturer’s instructions for FICOLL extraction (pluriSelect).Minced mouse colon was digested in 1X HBSS and 83 µl of collagenase IV (final concentration 166 U/ml) for 15 min at 37ºC and filtered through a 70 µm nylon mesh.
Sequencing librraries were prepared according to the respective single-cell RNA-seq protocols as detailed in the Methods and referenced in TableS1.
Library selection and sequencing was performed following recommendations of to the respective single-cell RNA-seq protocols as detailed in the Methods.


title: Monosomes_oligo_rep1

description: mRNA


title: DT.140

value: Liver cells

tag: diabetes


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 12hpi batch #2 replicate #2

organism:
Homo sapiens
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: primary human bronchial epithelial cells

growth_protocol: HBEpC cells (PromoCell) were maintained and infected in PromoCell airway epithelial cell growth media with SupplementMix.

extract_protocol:
Cells were trypisinized, extensively washed, and re-suspended in PBS containing 0.04% BSA. The total RNA was extracted using RNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen), followed by poly(A) mRNA enrichment.
The enriched poly(A) mRNAs were subject to bulk RNA-seq library preparatin with NEBNext Ultra II RNA library prep kit for Illumina following the manufacturer’s protocol.

treatment_protocol: HBEpC cells were infected with PR8 virus at a MOI of 5.

value: HBEpC

value: 12 hours post-infection


title: C1HTsmall_s1_1911011069_Col14_S52

tag: protocol


title: Total_control_rep2

description: Total RNA

value: control (4)


title: DT.137


title: C1HTsmall_s1_1911011069_Col11_S59

tag: centre

value: Stanford


title: DT.138


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 12hpi batch #2 replicate #1


title: DT.136


title: C1HTsmall_s1_1911011069_Col10_S44


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 24hpi batch #1 replicate #2

value: 24 hours post-infection


title: Total_control_rep1

description: Total RNA

value: Human kidney (embryonic)

tag: cell line


title: Polysomes_control_rep2

description: mRNA


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 24hpi batch #1 replicate #1


title: Polysomes_control_rep1

description: mRNA


title: NS02.FFPE.PDX.1222T1

value: FFPE

value: Roche High Pure RNA Paraffin Kit


title: single-cell RNA-seq dataset: PR8-infected A549 cells at a MOI of 0.2 harvested at 6hpi

description: Illumina NextSeq 500 and HiSeq 2500

source_name: adenocarcinomic human alveolar basal epithelial cells

growth_protocol: A549 cells (ATCC) were maintained in Kaighn’s modified Ham’s F-12 medium (F-12K) supplemented with 10% fetal bovine serum (FBS) prior to infection. A549 cells were infected in A549 infection media (F-12K supplemented with 2% bovine serum albumin (BSA), 1% antibiotic-antimycotic, and 1ug/mL TPCK-Trypsin). A549 cells in this dataset was from another batch of cells comparing to those in the time course infection datasets.

treatment_protocol: A549 cells were infected with PR8 virus at a MOI of 0.2.


title: DT.135

value: F


title: C1HTsmall_s1_1911011069_Col09_S60


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 12hpi batch #1 replicate #2


title: DT.134


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 12hpi batch #1 replicate #1


title: Monosomes_control_rep1

description: mRNA


title: C1HTsmall_s1_1911011069_Col08_S45


title: DT.133


title: 28 hours APF rep4

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description:
ctrl_genitilia_wpp_28h_4
processed data file: counts.txt

data_processing:
Sequencing reads from 3 lanes of 51-base Hi-seq data were aligned with tophat (2.0.13) to the dm3 assembly from UCSC with annotations from Flybase 5.57.
Reads were counted in unioned exons using bedtools count.
Genes expressed were compared to the FlyTF.org list of annotated transcription factors.
Genome_build: dm3
Supplementary_files_format_and_content: counts.txt: Tab-delimited text with raw counts for each sample.

organism: Drosophila melanogaster

source_name: Male pupal terminalia

growth_protocol: Male D. melanogaster white pre-pupa were collected at room temperature and incubated in a petri dish containing a moistened Kimwipe at 25˚C for 24 hours or 28 hours prior to dissection.

extract_protocol:
After incubation, pupae were impaled in their anterior region and immobilized within a glass dissecting well containing cold phosphate buffered saline. The posterior tip of the pupa was separated and washed with a P200 pipette to flush the pupal terminalia into solution.
Poly-A RNA-seq libraries were generated using a Clontech library preparation kit (040215).

tag: genotype

value: male

value: pupal terminalia

tag: developmental stage

value: 28h after puparium formation


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 6hpi batch #1 replicate #2

value: 6 hours post-infection


title: C1HTsmall_s1_1911011069_Col06_S47

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: C1HTsmall_s1_1911011069_Col07_S46


title: DT.132

value: Yes

value: No


title: Bulk RNA-seq dataset: PR8-infected HBEpC cells at 6hpi batch #1 replicate #1


title: 28 hours APF rep3

description:
ctrl_genitilia_wpp_28h_3
processed data file: counts.txt


title: DT.131

value: Liver cells

value: M


title: Bulk RNA-seq dataset: PR8-infected A549 cells at 24hpi replicate #1

growth_protocol: A549 cells (ATCC) were maintained in Kaighn’s modified Ham’s F-12 medium (F-12K) supplemented with 10% fetal bovine serum (FBS) prior to infection. A549 cells were infected in A549 infection media (F-12K supplemented with 2% bovine serum albumin (BSA) and 1% antibiotic-antimycotic).

treatment_protocol: A549 cells were infected with PR8 virus at a MOI of 5.


title: 28 hours APF rep2

description:
ctrl_genitilia_wpp_28h_2
processed data file: counts.txt


title: 28 hours APF rep1

description:
ctrl_genitilia_wpp_28h_1
processed data file: counts.txt


title: C1HTsmall_s1_1911011069_Col04_S58


title: DT.129


title: Bulk RNA-seq dataset: PR8-infected A549 cells at 12hpi replicate #1

value: 12 hours post-infection


title: DT.130


title: Monosomes_control_rep2

description: mRNA

tag: transfection

value: control (4)

tag: fraction

value: Monosomes


title: 24 hours APF rep3

description:
ctrl_genitilia_wpp_24h_3
processed data file: counts.txt

value: 24h after puparium formation


title: C1HTsmall_s1_1911011069_Col03_S42

value: Stanford

tag: cell type


title: Bulk RNA-seq dataset: PR8-infected A549 cells at 12hpi replicate #2

tag: cell types

tag: infection time points


title: C1HTsmall_s1_1911011069_Col05_S48


title: DT.128


title: C1HTsmall_s1_1911011069_Col01_S41


title: DT.127


title: DT.143


title: C1HTsmall_s1_1911011069_Col02_S57


title: DT.125


title: DT.126


title: DT.148


title: 24 hours APF rep2

description:
ctrl_genitilia_wpp_24h_2
processed data file: counts.txt


title: Bulk RNA-seq dataset: PR8-infected A549 cells at 6hpi replicate #1

tag: virus strain


title: C1HTmedium_m7_1912014300_Col20_S289

description:
cryopreserved HCA reference
C1HTmedium_human_exp_mat.tsv, C1HTmedium_human_metada.tsv, C1HTmedium_mouse_exp_mat.tsv, C1HTmedium_mouse_metada.tsv

data_processing:
zUMIs was used to filtering, mapping and quantification of reads.
Low quality reads were removed (barcodes and UMI sequences with more than 1 base below the Phred quality threshold of 20) .
We also excluded barcodes with less than 100 reads.
For techniques with known barcodes, we provided zUMIs with these barcode sequences, and used the automatic barcode detection function to detect the sequenced cells for other techniques.
cDNA reads were mapped to the human GRCh38, mouse GRCm38, and a human-mouse-dog mixed (for species level doublet detection) reference genomes using STAR
Reads were then assigned to exonic and intronic features using featureCounts and counted using the default parameters of zUMIs for human-only, mouse-only and mixed bam-files, separately.
The output expression matrix of reads mapping to both exonic and intronic regions was selected for the downstream analysis.
Genome_build: human GRCh38, mouse GRCm38
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols except SMARTseq2 which contains read counts. For each expression matrix there is a corresponding metadata file.
R1 = BC (1-6), UMI (7-11); R2 = cDNA


title: 24 hours APF rep1

description:
ctrl_genitilia_wpp_24h_1
processed data file: counts.txt


title: Bulk RNA-seq dataset: PR8-infected A549 cells at 24hpi replicate #2

value: 24 hours post-infection


title: DT.124


title: C1HTmedium_m7_1912014300_Col18_S296


title: single-cell RNA-seq dataset: PR8-infected HBEpC cells at 24hpi

value: HBEpC


title: 24 hours APF rep4

description:
ctrl_genitilia_wpp_24h_4
processed data file: counts.txt


title: single-cell RNA-seq dataset: PR8-infected A549 cells at a MOI of 5 harvested at 6hpi


title: C1HTmedium_m7_1912014300_Col17_S295


title: A1023C18: H3K27me3_EGF-1

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

description:
H3K27me3_EGF-1
A1023C18

data_processing:
Raw sequencing reads were first aligned with the bowtie2 software (v2.2.9) on the Drosophila Melanogaster (dmel-R6,21) reference genome to extract reads coming from spike-in chromatin. Remaining reads were then aligned on the Human hg38 reference genome using bowtie2 very-sensitive mode. PCR duplicates were removed from aligned data using Picard tools, and genome-browser tracks files were generated using the Deeptools suite (v3.1.0) and the bamCoverage function. In order to validate the overall H3K9me2 profile, large genomic domains were called with the EPIC software  (v0.2.9, https://github.com/biocore-ntnu/epic, --window-size 500 --gaps-allowed 5 --false-discovery-rate-cutoff 0.01), and LOCKs were defined as previously proposed (McDonald et al. 2017).
Raw sequencing reads were first aligned with the bowtie2 software (v2.2.9) on the Drosophila Melanogaster (dmel-R6,21) reference genome to extract reads coming from spike-in chromatin. Remaining reads were then aligned on the Human hg38 reference genome using bowtie2 very-sensitive mode. PCR duplicates were removed from aligned data using Picard tools, and genome-browser tracks files were generated using the Deeptools suite (v3.1.0) and the bamCoverage function. Input samples per condition have been merged in a single coverage WIG file.
In order to validate the overall H3K9me2 profile, large genomic domains were called with the EPIC software [3] (v0.2.9, https://github.com/biocore-ntnu/epic, --window-size 500 --gaps-allowed 5 --false-discovery-rate-cutoff 0.01), and LOCKs were defined as previously proposed (McDonald et al. 2017).
Counts of aligned reads per human gene have been generated using the FeatureCounts software [4] and the gene coordinates extracted from the GENCODE annotation file (v26). Genes with less than 10 reads were discarded from the analysis. The raw count table was then normalized using the TMM method from the edgeR R package [5] (v3,22,3), and the limma voom (v3.36.3)  functions were applied to detect genes with differential binding between untreated and EGF samples. Finally, genes with an adjusted pvalue < 0,05 and a log2 fold-change > 0,3 were called significant.
Genome_build: hg38
Supplementary_files_format_and_content: wig file of ChIP signal

source_name: Basal breast cancer  cells

growth_protocol: MDA-MB-468 cells grown in 145 mm2 dishes until ~ 70% confluence were treated with EGF (100 ng mL-1) for 72h in biological triplicate and untreated cells were used as an appropriate control.

extract_protocol:
The pelleted cells were washed twice with ice-cold PBS1x by centrifuging at 500 x g for 5 min at 4°C.  For lysis of crosslinked chromatin, the pellet was resuspended in lysis buffer A (50 mM Tris HCl pH8, 10 mM EDTA, 1% SDS, 50 x protease inhibitor cocktail) at room temperature and incubated for 5 min on rotating wheel. Next, lysate was centrifuged at 300 x g for 10 min at 8°C to prevent SDS precipitation and the supernatant was discarded. For chromatin shearing, the pellet was sheared in buffer B (25 mM Tris HCl pH8, 3 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl, 50 x protease inhibitor cocktail) to approximatively 200-600 base-pair average size using the Bioruptor Pico (Diagenode). After centrifugation at 20 000 x g, 4ºC for 15 min, the supernatant containing sheared chromatin was used for immunoprecipitation. 25 µL (10%) of sheared chromatin was used as input DNA to normalize sequencing data. As supplement control for normalization, we used spike-in chromatin Drosophila and spike-in antibody (Active motif). For chromatin immunoprecipitation (1 million cells per ChIP), it was carried out using sheared chromatin and antibody H3K9me2 complexed to Dynal Protein G magnetic beads (Thermo Fisher). Briefly, 6 µL of H3K9me2 antibody was mixed with 1 µg of spike-in antibody. 23 µL of magnetic beads were washed three times in ice-cold buffer C (20 mM Tris HCl pH8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl, 50 x protease inhibitor cocktail) and incubated with the mix of H3K9me2 and spike-in antibody for 4h at room temperature on rotating wheel in buffer C (494 µL). After the quick-spin and the removal of supernatant, the beads were resuspended in 100 µL buffer C. Each 50 µL of the latter was incubated with 250 µL of sheared chromatin mixed previously with 50 ng of spike-in chromatin Drosophila (250 µL chromatin of interest: 2,5 µL of spike-in chromatin, v:v) at 4°C on rotating wheel, overnight (~ 16h).  After quick-spin, the supernatant was discarded and the beads were successively washed in buffer C, buffer D (20 mM Tris-HCl pH8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), buffer E (10 mM Tris-HCl pH8, 0.25 M LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1 mM EDTA) and buffer F (10 mM Tris-HCl pH8, 1 mM EDTA, 50 mM NaCl).  Finally, input and immunoprecipitated chromatin samples were resuspended in solution containing TE buffer/ 1% SDS, decrosslinked by heating at 65°C overnight and subjected to both RNase A and Proteinase K treatments.
Illumina compatible libraries were prepared from input and immunoprecipitated DNAs using the Illumina TruSeq ChIP library preparation kit according to the manufacturer’s protocol. Briefly, 4 to 10ng of DNA were subjected to subsequent steps of end-repair, dA-tailing and ligation of TruSeq indexed Illumina adapters. After a final PCR amplification step, the 24 resulting barcoded libraries were equimolarly pooled in 2 groups quantified using a qPCR method (KAPA library quantification kit, Roche) before sequencing on the Illumina HiSeq2500 instrument. Each pool was loaded on 1 rapid flow cell (11pM) and sequenced using a single read mode (SR50). This sequencing configuration was set to reach an average of 25 million reads (50-base long) per sample.

treatment_protocol: Cells were harvested by trypsinization. After adding media to stop trypsin, cells were centrifuged at 500 x g for 5 min at room temperature. The pelleted cells were resuspended in media, counted and crosslinked with 37% formaldehyde (final concentration 1%) for 10 min at room temperature. The crosslinking was stopped by addition of 2.5 M glycine (final concentration 0.125 M) for 5 min at room temperature followed by centrifugation at 500 x g for 5 min at 4°C.

value: MDA-MB-468 cells

tag: passages used

value: From  6 to 14

tag: chip antibody


title: A1023C22: H3K27me3_EGF-2

description:
H3K27me3_EGF-2
A1023C22


title: C1HTmedium_m7_1912014300_Col19_S290


title: Bulk RNA-seq dataset: PR8-infected A549 cells at 6hpi replicate #2


title: single-cell RNA-seq dataset: PR8-infected HBEpC cells at 12hpi


title: C1HTmedium_m7_1912014300_Col15_S293


title: DT.120

tag: Sex

value: F


title: DT.121

tag: strain line


title: single-cell RNA-seq dataset: PR8-infected A549 cells at 24hpi


title: single-cell RNA-seq dataset: PR8-infected HBEpC cells at 6hpi


title: A1023C17: H3K27me3_untreated-1

description:
H3K27me3_untreated-1
A1023C17


title: A1023C21: H3K27me3_untreated-2

description:
H3K27me3_untreated-2
A1023C21


title: DT.119

tag: obesity


title: C1HTmedium_m7_1912014300_Col16_S294


title: A1023C16: H3K9me3_EGF-2

description:
H3K9me3_EGF-2
A1023C16


title: C1HTmedium_m7_1912014300_Col14_S292


title: DT.118

tag: diabetes


title: DT.122


title: C1HTmedium_m7_1912014300_Col13_S291

tag: protocol


title: A1023C15: H3K9me3_untreated-2

description:
H3K9me3_untreated-2
A1023C15


title: single-cell RNA-seq dataset: PR8-infected A549 cells at 12hpi


title: DT.117


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep10]

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

description:
Ad5-FMDV-ISA206VG_T24_rep10
Total blood sample (replicate 10) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.12.
Tophat2 (v 2.1.1), with parameters "-N 2 --read-edit-dist 2 --b2-sensitive --no-coverage-search", was used for alignment on the reference genome/transcriptome (Ensembl90 database).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1).
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. Genes, whose sum of all samples counts was less than 10, were filtered out. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed.
Genome_build: Oar_v3.1 from Ensembl database version 90
Supplementary_files_format_and_content: counts_table_all_samples.txt : Tab-delimited text file containing the table of raw counts for all samples (3 vaccination types, 3 timepoints, 10 replicates), as established after mapping using TopHat and gene counts using featureCounts.

organism: Ovis aries

source_name: blood

extract_protocol:
RNA was extracted from the PAXgene Blood RNA tubes using the PAXgene Blood RNA kit and purified with the RNeasy MinElute Cleanup kit (QIAGEN). The quality of the total RNA was assessed on an Agilent Bioanalyzer 2100, using RNA 6000 pico kit (Agilent Technologies). Directional RNA-Seq Libraries were constructed from 1 µg of total RNA using the TruSeq mRNA Stranded library prep kit (Illumina), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Vaccination

tag: animal id

tag: breed

value: Prealpes

tag: tissue

value: blood

tag: Stage

value: adult (6 months)

value: male

tag: treatment

tag: time point


title: C1HTmedium_m7_1912014300_Col12_S283

city: Barcelona

first: Atefeh

last: Lafzi

institute: Center for Genomic Regulation

tag: centre

tag: cell type

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: DT.116

value: Liver cells

value: No

value: Yes


title: A1014C07: H3K9me3_untreated-1

description:
H3K9me3_untreated-1
A1014C07

tag: cell line


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep10]

description:
Ad5-FMDV-ISA206VG_T4_rep10
Total blood sample (replicate 10) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m7_1912014300_Col11_S299


title: DT.115


title: A1014C12: H3K4me3_EGF-2

description:
H3K4me3_EGF-2
A1014C12


title: C1HTmedium_m7_1912014300_Col10_S284


title: DT.114


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep10]

description:
Ad5-FMDV-ISA206VG_T0_rep10
Total blood sample (replicate 10) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: A1014C11: H3K4me3_untreated-2

description:
H3K4me3_untreated-2
A1014C11


title: A1014C08: H3K9me3_EGF-1

description:
H3K9me3_EGF-1
A1014C08


title: C1HTmedium_m7_1912014300_Col09_S300


title: DT.113

value: M


title: single-cell RNA-seq dataset: PR8-infected A549 cells at 6hpi

tag: cell types

tag: infection time points

value: 6 hours post-infection

tag: virus strain


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep9]

description:
Ad5-FMDV-ISA206VG_T24_rep9
Total blood sample (replicate 9) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

tag: Sex


title: C1HTmedium_m7_1912014300_Col08_S285


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep9]

description:
Ad5-FMDV-ISA206VG_T0_rep9
Total blood sample (replicate 9) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep9]

description:
Ad5-FMDV-ISA206VG_T4_rep9
Total blood sample (replicate 9) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: A1014C03: H3K4me3_untreated-1

description:
H3K4me3_untreated-1
A1014C03

tag: passages used

tag: chip antibody


title: C1HTmedium_m7_1912014300_Col05_S288


title: DT.110

tag: strain line

tag: obesity

tag: diabetes


title: DT.112


title: DT.111


title: week4_PH_ATAC_rep3

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Sequencing reads were mapped to the human hg19 reference genome assembly using bowtie2 (Langmead and Salzberg, 2012) with default parameters. Peak calling was performed using MACS2 (Zhang et al., 2008) with default parameters, “--nomodel --shift 37 --extsize 73” to bypass building a ChIP-based shifting model and instead shift read 5’-ends and extend in the 5'->3' direction by a half-nucleosome size (73bp), and  “--broad --qvalue 0.01” to composite broad regions of read enrichment with a minimum FDR q-value cutoff of 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited file with peak coordinates

source_name: HUES 8 hESC line

growth_protocol: Undifferentiated stem cells were maintained as aggregates in supplemented mTeSR1 medium (StemCell Technologies) using spinner flasks (Corning) set at a 70rpm rotation rate in a 37ºC 5% CO2 incubator. Directed hPSC differentiation into islet cells was conducted as described in the methods of (Alvarez-Dominguez et al. 2019).

extract_protocol:
Live cells (typically ~50,000) were pelleted and tagmentation was performed at 37ºC for 30min as described in (Buenrostro et al., 2013). Briefly, cell pellets were resuspended in buffer containing Tn5 Transposase (Nextera DNA Sample Preparation kit; Illumina), incubated at 37ºC for 30min, and DNA was isolated using the MinElute PCR purification kit (Qiagen).
Tagmented DNA was PCR-amplified for 10 cycles and purified using AMPure XP magnetic beads (Beckman Coulter). Double-sided AMPure cleanup to remove high-molecular-weight fragments was conducted by incubation of double-concentrated AMPure beads added at 0.55x volume to the PCR reactions, followed by cleanup with a 1x AMPure volume. Sequencing libraries were pooled and sequenced on a HiSeq 2500 instrument.

value: HUES 8 hESC line

value: hPSC-derived poly-hormonal cell

tag: developmental stage

value: Stage 6 week 4


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep8]

description:
Ad5-FMDV-ISA206VG_T24_rep8
Total blood sample (replicate 8) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

tag: animal id

tag: breed

tag: tissue


title: C1HTmedium_m7_1912014300_Col06_S287

address: Baldiri Reixac 4

source_name: human PBMC, mouse colon, HEK293, NIH3T3, MDCK

growth_protocol: NIH3T3-GFP, MDCK-TurboFP650 and HEK293-RFP were cultured at 37ºC in an atmosphere of 5% (v/v) carbon dioxide in Dulbecco’s Modified Eagle’s Medium, supplemented with 10% (w/v) fetal bovine serum, 100 U penicillin, and 100 µg/L streptomycin (Invitrogen).

tag: protocol

value: Stanford


title: week4_PH_ATAC_rep2


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep8]

description:
Ad5-FMDV-ISA206VG_T4_rep8
Total blood sample (replicate 8) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

tag: Stage

tag: treatment

tag: time point


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep7]

description:
Ad5-FMDV-ISA206VG_T24_rep7
Total blood sample (replicate 7) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: DT.107

source_name: Liver

tag: cell type


title: C1HTmedium_m7_1912014300_Col02_S297

tag: centre


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep7]

description:
Ad5-FMDV-ISA206VG_T4_rep7
Total blood sample (replicate 7) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: DT.109


title: A1014C04: H3K4me3_EGF-1

description:
H3K4me3_EGF-1
A1014C04

tag: cell line

value: MDA-MB-468 cells


title: week4_PH_ATAC_rep1


title: DT.106

tag: Sex


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep8]

description:
Ad5-FMDV-ISA206VG_T0_rep8
Total blood sample (replicate 8) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: week3_PH_ATAC_rep3

value: Stage 6 week 3


title: C1HTmedium_m7_1912014300_Col04_S298


title: C1HTmedium_m7_1912014300_Col01_S281


title: C1HTmedium_m7_1912014300_Col03_S282


title: C1HTmedium_m6_1912014299_Col20_S269


title: week3_PH_ATAC_rep2


title: week2_PH_ATAC_rep3

value: Stage 6 week 2


title: C1HTmedium_m7_1912014300_Col07_S286


title: week3_PH_ATAC_rep1


title: DT.108


title: C1HTmedium_m6_1912014299_Col19_S270


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep6]

description:
Ad5-FMDV-ISA206VG_T24_rep6
Total blood sample (replicate 6) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

value: Prealpes


title: DT.105


title: week2_PH_ATAC_rep1


title: week1_PH_ATAC_rep3

value: Stage 6 week 1


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep6]

description:
Ad5-FMDV-ISA206VG_T4_rep6
Total blood sample (replicate 6) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

value: blood

value: adult (6 months)


title: DT.103


title: C1HTmedium_m6_1912014299_Col18_S276

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: week1_PH_ATAC_rep2


title: DT.102

value: Liver cells


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep6]

description:
Ad5-FMDV-ISA206VG_T0_rep6
Total blood sample (replicate 6) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

value: male


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep7]

description:
Ad5-FMDV-ISA206VG_T0_rep7
Total blood sample (replicate 7) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: C1HTsmall_s1_1911011069_Col16_S54

description:
cryopreserved HCA reference
C1HTsmall_human_exp_mat.tsv, C1HTsmall_human_metada.tsv, C1HTsmall_mouse_exp_mat.tsv, C1HTsmall_mouse_metada.tsv


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep5]

description:
Ad5-FMDV-ISA206VG_T24_rep5
Total blood sample (replicate 5) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: week1_PH_ATAC_rep1


title: C1HTmedium_m6_1912014299_Col16_S274

description:
cryopreserved HCA reference
C1HTmedium_human_exp_mat.tsv, C1HTmedium_human_metada.tsv, C1HTmedium_mouse_exp_mat.tsv, C1HTmedium_mouse_metada.tsv


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep5]

description:
Ad5-FMDV-ISA206VG_T4_rep5
Total blood sample (replicate 5) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: DT.101

value: F

value: No


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep5]

description:
Ad5-FMDV-ISA206VG_T0_rep5
Total blood sample (replicate 5) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: DT.104

value: Yes


title: week0_PH_ATAC_rep2

value: HUES 8 hESC line

value: Stage 6 week 0


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep4]

description:
Ad5-FMDV-ISA206VG_T24_rep4
Total blood sample (replicate 4) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m6_1912014299_Col15_S273


title: week0_PH_ATAC_rep3

value: hPSC-derived poly-hormonal cell


title: week0_PH_ATAC_rep1


title: C1HTmedium_m6_1912014299_Col14_S272

value: Stanford


title: XEN rep3

city: Hangzhou

first: Shihao

state: Zhejiang

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting RNA-seq reads were trimmed using Trimmomatic (Version 0.33, AVGQUAL:20TRAILING:20MINLEN:50) to remove the adaptor sequence and low-quality bases.
The clean paired-end reads of each sample were mapped to the annotated genome of Musmusculus (GRCm38) (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/) using HISAT2 aligner (Version 2.0.4)
Cufflinks counted the expression of each gene and reported them in FPKM (Trapnell et al., 2014), and then differentially expressed genes were assessed using Cuffdiff (cutoff, p-value≤0.05).
Genome_build: Mus musculus (GRCm38)
Supplementary_files_format_and_content: abundance measurements

source_name: Extra-embryonic endoderm cells

growth_protocol: Undifferentiated mESCs were cultured on mitomycin-inactivated mouse embryonic fibroblasts (MEFs) in DMEM supplemented with 15% fetal bovine serum and 1000 U/mL LIF at 37℃ in 5% CO2. SMCs and XEN cells cultured in DMEM supplemented with 15% fetal bovine serum.

extract_protocol:
Total RNA was prepared using TRIzol Reagent (ambion), Sequencing libraries were prepared from 3 μg of each RNA sample using TruSeq RNA Sample Prep Kit (Illumina).
mRNA with polyA tail was purified from total RNA with poly-T oligo attached magnetic beads and carried out fragmentation into about 200 bp using divalent cations at elevated temperature.The RNA fragments were converted into first strand cDNA using random primers, and then second strand synthesis was performed using DNA polymerase I and RNase H treatment. After end repair, Illumina PE adaptors were ligated to the ends of cDNA fragments. Adaptor-tagged cDNA fragments were size selected on low-range ultra-agarose gel and enriched using Illumina PCR Primer Cocktail and 10-cycle PCR. The qualities of the libraries were checked on a Bioanalyzer2100 system (Agilent) to ensure the proper insert length. Finally, the libraries were diluted, mixed and sequenced to a depth of ~25M 150bp paired-end reads using an Illumina HiSeq 2000 system.

treatment_protocol: ESCs were resuspended and plated onto gelatin-coated dishes at a density of 4Χ104/cm2 in DMEM+15% serum supplemented with 10 μM atRA or 10 μM atRA+5μM CHIR for 10 days, then DMEM with 10% serum for 6 days, to perform induced differentiation.

tag: strain

value: Extra-embryonic endoderm cells

value: control

tag: time (differentiation)


title: week4_SCbeta_ATAC_rep3

value: hPSC-derived beta cell

value: Stage 6 week 4


title: XEN rep1


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep4]

description:
Ad5-FMDV-ISA206VG_T0_rep4
Total blood sample (replicate 4) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

value: Prealpes


title: week4_SCbeta_ATAC_rep2


title: C1HTmedium_m6_1912014299_Col13_S271


title: XEN rep2


title: C1HTmedium_m6_1912014299_Col17_S275


title: C1HTmedium_m6_1912014299_Col12_S263


title: RA/CHIR-16d rep3

source_name: Differentiated ESCs

value: ES-derived XEN-like cells

value: RA/CHIR-induced


title: C1HTmedium_m6_1912014299_Col11_S279

value: human PBMC (60%) and mouse colon (30%), HEK293T (6%), NIH3T3 (3%), MDCK (1%)


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep3]

description:
Ad5-FMDV-ISA206VG_T24_rep3
Total blood sample (replicate 3) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

value: blood

value: adult (6 months)


title: week4_SCbeta_ATAC_rep1


title: RA/CHIR-16d rep2


title: C1HTmedium_m6_1912014299_Col10_S264


title: DT.100

value: Liver cells

tag: strain line

value: F


title: week3_SCbeta_ATAC_rep3

value: Stage 6 week 3


title: RA/CHIR-16d rep1


title: C1HTmedium_m6_1912014299_Col09_S280


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep3]

description:
Ad5-FMDV-ISA206VG_T0_rep3
Total blood sample (replicate 3) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

value: male


title: RA/CHIR-10d rep3


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep4]

description:
Ad5-FMDV-ISA206VG_T4_rep4
Total blood sample (replicate 4) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: week3_SCbeta_ATAC_rep2

value: HUES 8 hESC line


title: week3_SCbeta_ATAC_rep1


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep2]

description:
Ad5-FMDV-ISA206VG_T24_rep2
Total blood sample (replicate 2) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep2]

description:
Ad5-FMDV-ISA206VG_T4_rep2
Total blood sample (replicate 2) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: C1HTmedium_m6_1912014299_Col07_S266


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep2]

description:
Ad5-FMDV-ISA206VG_T0_rep2
Total blood sample (replicate 2) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: week2_SCbeta_ATAC_rep3

value: Stage 6 week 2


title: RA/CHIR-10d rep2


title: RA/CHIR-7d rep3


title: week2_SCbeta_ATAC_rep2


title: RA/CHIR-10d rep1


title: Sheep whole blood - T24 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T24_rep1]

description:
Ad5-FMDV-ISA206VG_T24_rep1
Total blood sample (replicate 1) collected 24h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: week2_SCbeta_ATAC_rep1


title: C1HTmedium_m6_1912014299_Col05_S268

value: Stanford


title: C1HTmedium_m6_1912014299_Col06_S267


title: C1HTmedium_m6_1912014299_Col04_S278


title: RA/CHIR-7d rep2


title: week1_SCbeta_ATAC_rep3

value: Stage 6 week 1


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep3]

description:
Ad5-FMDV-ISA206VG_T4_rep3
Total blood sample (replicate 3) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: RA/CHIR-4d rep3


title: RA/CHIR-7d rep1


title: Sheep whole blood - T4 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T4_rep1]

description:
Ad5-FMDV-ISA206VG_T4_rep1
Total blood sample (replicate 1) collected 4h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt


title: week1_SCbeta_ATAC_rep1


title: week1_SCbeta_ATAC_rep2


title: C1HTmedium_m6_1912014299_Col08_S265


title: RA/CHIR-4d rep2


title: C1HTmedium_m6_1912014299_Col02_S277


title: Sheep whole blood - T24 - Ad5-FMDV [Ad5-FMDV_T24_rep10]

description:
Ad5-FMDV_T24_rep10
Total blood sample (replicate 10) collected 24h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt

value: Adenovirus 5-FMDV (Ad5-FMDV)


title: C1HTmedium_m6_1912014299_Col01_S261


title: Sheep whole blood - T4 - Ad5-FMDV [Ad5-FMDV_T4_rep10]

description:
Ad5-FMDV_T4_rep10
Total blood sample (replicate 10) collected 4h after vaccination with Adenovirus 5-FMDV (Ad5-FMDV).
processed data file: counts_table_all_samples.txt


title: week0_SCbeta_ATAC_rep3

value: hPSC-derived beta cell

value: Stage 6 week 0


title: Sheep whole blood - T0 - Ad5-FMDV-ISA206VG [Ad5-FMDV-ISA206VG_T0_rep1]

description:
Ad5-FMDV-ISA206VG_T0_rep1
Total blood sample (replicate 1) collected 0h after vaccination with Adenovirus 5-FMDV+Adjuvant ISA206VG (Ad5-FMDV-ISA206VG).
processed data file: counts_table_all_samples.txt

value: Prealpes