title: Knockout Rep 3

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

data_processing:
Base Calling was done using RTA v(2.4.1.1)
Alignment was done using TopHat v(2.0.7)
Peak Calling was performed using Picard
The Bioconductor package DESeq2 was used to generate normalised estimates of transcript abundance
Assembly: mm10
Supplementary files format and content: comma separated file including RPKM values for each Sample.

source_name: Spleen

extract_protocol:
Splenocyte suspensions were prepared from 4 week old Wildtype (WT), Dhh heterozygous (Dhh+/-) and Dhh knockout (Dhh-/-) mice spleen.  Cells were stained against Ter119 and CD71 and facs sorted to purify CD71+Ter119+ cells.  RNA was extracted from this CD71+Ter119+ cells defined as erythroblast population II.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD71+Ter119+ Splenocytes

tag: age

value: 4 weeks

value: Spleen

value: Dhh-/-


title: Heterozygous Rep 3

status: Public on May 31 2022

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain

tag: tissue

tag: genotype

value: Dhh+/-


title: CUT&RUNseq_H3K27me3_K27me3_MpPm_hermaphrodite_germline_rep2

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

country: USA

institute: UC Santa Cruz

description:
CRseq_rawCounts.matrix.txt
CRseq_zscores.matrix.txt

library_source: genomic

data_processing:
library strategy: Cut&Run
Libraries sequenced on the NovaSeq platform were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries sequenced on the NextSeq platform were sequenced and demultiplexed at UC Santa Cruz.
Illumina reads longer than 50 bp were trimmed to 50 bp. 50 bp reads were mapped to the Bristol (N2) genome version WS220 using tophat2 (v2.1.1) with bowtie2 (2.3.5.1).
For RNA-seq samples, R1 and R2 reads were mapped 3 ways: as single-end reads allowing 1 mismatch (mm1), as single-end reads allowing 0 mismatches (mm0) and as paired-end reads allowing 1 mismatch using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25.   For CUT&RUN samples, R1 and R2 reads were mapped 2 ways: as single-end reads allowing 1 mismatch (mm1) and as single-end reads allowing 0 mismatches (mm0).  For all samples, reads per transcript or gene body were counted using htseq and a gtf file specifying transcript/gene body (union of all exons) or SNP locations per transcript/gene body.
To determine RPKM for all reads that mapped to a transcript or gene body,  only the first mate (R1) of paired-end Illumina reads that mapped allowing 1 mismatch was used. RPKM was calculated by first scaling total reads used to 1 million, then dividing by transcript length in kb (union of all exons).   To determine allele-specific transcript and gene body reads, both mates of paired-end reads were mapped as single-end reads from which only SNP-containing reads were used for further SNP analysis. Reads that emanated from the sperm allele (N2 background) were SNP-containing reads that mapped to the N2 genome when allowing 0 mismatches. Reads that emanated from the oocyte allele (CB4856 background) were SNP-containing reads that mapped to the N2 genome when allowing 1 mismatch but not 0 mismatches. RPSM (reads per SNP per million) was calculated by scaling total SNP-containing reads to 1 million, then dividing transcript or gene body SNP-containing reads (reads per million) by the number of SNP locations in the transcript or gene body (per SNP).  To perform differential gene expression analysis, reads that were mapped paired-end using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25 were used to calculate significantly misexpressed genes using the differential analysis program DESeq2 (1.22.2).
Assembly: ce10
Supplementary files format and content: RNAseq_rawCounts.matrix.txt and CRseq_rawCounts.matrix.txt  are matrices containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file. Counts were generated using HTseq from 1) R1 and R2 reads mapped as pairs for downstream differential expression analysis, 2) from R1 reads mapped as single end reads for RPKM calculations or 3) R1 and R2 reads mapped as single end reads and filtered for reads overalpping SNPs between Bristol (N2) and Hawaii (CB4856) genomes. RNAseq_DEGs_RPKM_RSPM.matrix.txt is a matrix containing log2 fold changes and adjusted p values generated with DESeq as well as transcript reads per kilobase per million (RPKM) and gamete-specific transcript reads per SNP per million SNPs (RSPM). CRseq_zscores.matrix.txt is a matrix containing H3K27me3 and H3K36me3 zscores calculated over exons and gamete-specific zscores.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: distal half of hermaphrodite germline

growth_protocol: All strains were maintained on nematode growth medium (NGM) agar plates seeded with a lawn of Escherichia coli OP50 and maintained at 20˚C except for fem-2 containing strains, which were maintained at 15˚C. To generate females, fem-2 containing strains were raised at 25˚C until they developed to the L4 stage

extract_protocol:
For germline collections, worms were selected at the L4 stage and allowed to develop 1 day at 20˚C to reach the 1st day of adulthood. Worms were decapitated to extrude the germlines. The distal halves of the germlines were collected by cutting the germline at the bend and transferring to ice-cold TRIzol reagent to reach a total of 30-50 germlines. Biological replicates of germlines in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation.  2-4 biological replicates were collected for each genotype.   For L1 collections, gravid mothers were allowed to lay eggs overnight at 20˚C. The next day, late-stage embryos along with some bacteria were transferred to 50 uL drops of S Basal on gelatin chrom alum-coated slides. After 2 hours at room temperature, newly hatched L1 larvae were transferred to ice-cold TRIzol. This process of transferring embryos to S basal, incubating 2 hours, and transferring newly hatched L1 larvae to TRizol was repeated throughout the day to reach a final collection of ~100 newly hatched larvae per replicate. Biological replicates of L1 larvae in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation. 3 biological replicates were collected for each genotype.
Libraries were prepared according to manufacturer's instructions.  For transcript analysis, RNA was polyA-selected (NEB #E7490) and libraries prepared (NEB #E7530). For CUT&RUN library preparation, DNA associated with H3K27me3 and H3K36me3 was collected via CUT&RUN method (Skene and Henikoff 2017; Skene et al. 2018) and libraries prepared (Tecan Genomics #0344NB-32).

tag: mother genotype

value: fem-2(b245ts) (CB4856 background)

tag: father genotype

value: mes-3(bn35); him-8(e1489) (N2 background)

tag: molecule subtype

value: DNA associated with H3K27me3


title: covid-19_lung_cov22

city: Karimnagar

first: Abhilash

last: Dasari

state: Telangana

address: H.No:8-4-652/3/1/1, Hanuman Nagar, Karimnagar

department: Biochemical engineering and biotechnology

country: India

institute: IIT Delhi

data_processing:
Quality test is performed using FastQC (version 0.11.9)
Using Trimmomatic (version 0.39) adaptor content and low quality bases are removed.
star aligner (version 2.7.8a) is used to align the reads.
Feature counts subreads package (version 2.0.1) is used to estimate the expression values of genes
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read values for each Sample ...
Supplementary_files_format_and_content: Matrix table with compiled raw counts of all samples in csv file

organism: Homo sapiens

source_name: Dead covid-19 patient lung

growth_protocol: Samples are extracted from  the parenchyma region of human lungs, these tissues are not grown invitro.

extract_protocol:
Lung tissue was harvested from the parenchyma region using standard protocol for histology and snap frozen within two hours for RNA extraction is done.
Total RNA was extracted from lung tissue using the Maxwell automated instrument and the Maxwell® RSC Viral Total Nucleic Acid Purification Kit (Promega)

treatment_protocol: samples are extracted from  the parenchyma region of human lungs, we haven't performed any specific treatment on extracted samples

value: lung tissue

tag: gender

value: Female

tag: disease state


title: FN ribDKO rep1

city: Ube-shi

first: Kensuke

last: Shibata

state: Yamaguchi

address: 1-1 Minami-Kogushi 1-chome

country: Japan

institute: Yamaguchi univeristy

description: Sample 4

data_processing:
Illumina RTA3 software used for basecalling.
Quality trimming and adapter clipping were performed using fastp v0.20.1 with parameters -3 -q 15 -n 0 -t 1 -l 50 -w 8.
Trimmed reads were mapped to transcripts in the reference Francisella tularensis subsp. novicida U112 chromosome (NZ_CP009633.1) using Bowtie2 aligner within RSEM v1.3.1 (Robinson et al., 2009). RSEM performed the estimation of the abundance of genes and isoforms and  generated raw counts.
The EdgeR v3.32.1 software program (Li et al., 2011) was used to normalize and detect the differentially expressed genes (DEGs).
Genome_build: NZ_CP009633.1
Supplementary_files_format_and_content: tab-delimited text file includes normalized count values for each sample.

source_name: Francisella novicida U112 mutant of ribD gene replicate 1

growth_protocol: Francisella strains were cultured  to exponential phase at 37 °C in a  brain heart infusion broth (Becton, Dickinson and Company, Franklin Lakes, NJ) supplemented with cysteine.

extract_protocol:
After the culture of Francisella strains in the growth media, cell pellets were harvested using NucleoSpin RNA (Takara Bio, Cat#740955). After removal of rRNA using Illumina Ribo-Zero Plus rRNA Depletion Kit(Cat#20037135), TruSeq Stranded mRNA Library Prep Kit(Cat#20020595) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mutant of ribD gene


title: RNAseq_him8_male_germline_rep1

description:
RNAseq_rawCounts.matrix.txt
RNAseq_DEGs_RPKM_RSPM.matrix.txt

data_processing:
Libraries sequenced on the NovaSeq platform were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries sequenced on the NextSeq platform were sequenced and demultiplexed at UC Santa Cruz.
Illumina reads longer than 50 bp were trimmed to 50 bp. 50 bp reads were mapped to the Bristol (N2) genome version WS220 using tophat2 (v2.1.1) with bowtie2 (2.3.5.1).
For RNA-seq samples, R1 and R2 reads were mapped 3 ways: as single-end reads allowing 1 mismatch (mm1), as single-end reads allowing 0 mismatches (mm0) and as paired-end reads allowing 1 mismatch using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25.   For CUT&RUN samples, R1 and R2 reads were mapped 2 ways: as single-end reads allowing 1 mismatch (mm1) and as single-end reads allowing 0 mismatches (mm0).  For all samples, reads per transcript or gene body were counted using htseq and a gtf file specifying transcript/gene body (union of all exons) or SNP locations per transcript/gene body.
To determine RPKM for all reads that mapped to a transcript or gene body,  only the first mate (R1) of paired-end Illumina reads that mapped allowing 1 mismatch was used. RPKM was calculated by first scaling total reads used to 1 million, then dividing by transcript length in kb (union of all exons).   To determine allele-specific transcript and gene body reads, both mates of paired-end reads were mapped as single-end reads from which only SNP-containing reads were used for further SNP analysis. Reads that emanated from the sperm allele (N2 background) were SNP-containing reads that mapped to the N2 genome when allowing 0 mismatches. Reads that emanated from the oocyte allele (CB4856 background) were SNP-containing reads that mapped to the N2 genome when allowing 1 mismatch but not 0 mismatches. RPSM (reads per SNP per million) was calculated by scaling total SNP-containing reads to 1 million, then dividing transcript or gene body SNP-containing reads (reads per million) by the number of SNP locations in the transcript or gene body (per SNP).  To perform differential gene expression analysis, reads that were mapped paired-end using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25 were used to calculate significantly misexpressed genes using the differential analysis program DESeq2 (1.22.2).
Assembly: ce10
Supplementary files format and content: RNAseq_rawCounts.matrix.txt and CRseq_rawCounts.matrix.txt  are matrices containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file. Counts were generated using HTseq from 1) R1 and R2 reads mapped as pairs for downstream differential expression analysis, 2) from R1 reads mapped as single end reads for RPKM calculations or 3) R1 and R2 reads mapped as single end reads and filtered for reads overalpping SNPs between Bristol (N2) and Hawaii (CB4856) genomes. RNAseq_DEGs_RPKM_RSPM.matrix.txt is a matrix containing log2 fold changes and adjusted p values generated with DESeq as well as transcript reads per kilobase per million (RPKM) and gamete-specific transcript reads per SNP per million SNPs (RSPM). CRseq_zscores.matrix.txt is a matrix containing H3K27me3 and H3K36me3 zscores calculated over exons and gamete-specific zscores.

molecule: polyA RNA

source_name: distal half of male germline

value: no father


title: Knockout Rep 2


title: RNAseq_F2_K27me3_GMpGPm_hermaphrodite_germline_rep3


title: Wildtype Rep 3

value: Wildtype


title: FN rep2

description: Sample 2

organism: Francisella tularensis subsp. novicida U112

source_name: Francisella novicida U112 wild-type replicate 2

value: wild-type


title: covid-19_lung_cov6


title: RNAseq_F2_K27me3_GMpGPm_hermaphrodite_germline_rep2


title: Heterozygous Rep 2


title: covid-19_lung_cov21


title: covid-19_lung_cov30

value: Male


title: Wildtype Rep 2


title: FN rep1

description: Sample 1

source_name: Francisella novicida U112 wild-type replicate 1


title: RNAseq_F2_K27me3_GMpGPm_hermaphrodite_germline_rep1


title: covid-19_lung_cov27


title: Knockout Rep 1


title: RNAseq_F1_K27me3_MpPp_hermaphrodite_germline_rep3


title: covid-19_lung_cov26


title: Heterozygous Rep 1


title: RNAseq_F1_K27me3_MpPp_hermaphrodite_germline_rep2


title: RNAseq_F1_K27me3_MpPp_hermaphrodite_germline_rep1


title: covid-19_lung_cov20


title: RNAseq_F1_K27me3_MpPm_hermaphrodite_germline_rep2


title: RNAseq_F1_K27me3_MpPm_hermaphrodite_germline_rep3


title: covid-19_lung_cov23


title: E2_C1-2

city: Omaha

first: Shyamal

middle: K.

last: Roy

state: NE

address: 984515 Nebraska Medical Center

department: Ob/Gyn

institute: University of Nebraska Medical Center

data_processing:
Alignment to mm10 was performed by Tophat2 and read counts were obtained by Htseq-Count.
Differential expression analysis was performed by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Text files with read counts per gene

source_name: Embryonic ovary

growth_protocol: Mouse ovaries, collected on E16, were cultured in phenol red-free α-MEM containing penicillin, streptomycin and amphotericin B and modified ITS+ (0.1 μg/ml insulin, and 1.25 μg/ml transferrin, 1.25 μg/ml selenium, and 10.7 μg/ml linoleic acid) on a tissue culture insert with 3 µm high density pores.

extract_protocol:
Total-RNA was extracted with Qiagen micro kit according to the manufacturer's instruction.
RNA samples with RIN value over 9 were used for making sequencing libraries with Illumina True-Seq RNA Sample Preparation V2 kit.

treatment_protocol: Ovaries were cultured for 24 hours with either vehicle or recombinant human BMP2 (50ng/ml) or estradiol-17β (3.67µM).

value: E16+24hours culture

value: WT

value: Ovarian cells

value: Ovary


title: Wildtype Rep 1

value: CD71+Ter119+ Splenocytes

value: 4 weeks

value: Spleen


title: E2_C1-3


title: FN rep3

description: Sample 3

source_name: Francisella novicida U112 wild-type replicate 3


title: E2_C1-1


title: RNAseq_F1_K27me3_MpPm_hermaphrodite_germline_rep1

value: fem-2(b245ts) (CB4856 background)


title: covid-19_lung_cov16


title: C_C1-3


title: C_C1-2


title: covid-19_lung_cov8


title: C_C1-1


title: covid-19_lung_cov40


title: covid-19_lung_cov19


title: RNAseq_K27me3_MpPp_male_germline_rep2

value: mes-3(bn35)/hT2-GFP; him-8(e1489) (N2 background)


title: B2_C1-3


title: BA_2_4w: 6-BA_2.0 mg/L_4 w

city: Shenzhen

first: Zhicai

last: Wang

state: guangdong province

address: N.889, wangtong RD, Luohu district

country: China

institute: Orchid conservation and research center of Shenzhen

data_processing:
The raw fastq format reads obtained from the sequencing were purified by filtering out low-quality reads.
The clean reads were mapped against the primary CDS from the D. catenatum genome database (accession code: JSDN00000000, URL: http://www.ncbi.nlm.nih.gov/bioproject/262478) for quantification of the gene abundance as read counts using Hisat2 (version 2.0.6) software.
The expression levels of genes were presented as the fragments per kilobase per million map reads (FPKM) using Cufflinks (version 2.2.2) software.
EdgeR was used to compare differently expressed genes (DEGs) between groups.
Pheatmap was used to generate heatmaps of DEGs.
Genome_build: Accession code: JSDN00000000, URL: http://www.ncbi.nlm.nih.gov/bioproject/262478

organism: Dendrobium catenatum

source_name: seedlings

growth_protocol: D. catenatum seeds were germinated on half-strength Murashige and Skoog (MS) medium with 3.0% sucrose, 0.4% agar, and 20.0% potato (pH=5.8). Materials were grown in a greenhouse at a temperature of 25 ± 2℃ with a 12/12 h light/dark cycle (40 μmol/m -2 /S -1) and 60-70% relative humidity.

extract_protocol:
Total RNA was isolated from phytohormone treated D. catenatum plantlets using the Plant RNA Isolation Mini Kit (BioTeke, Beijing, China) according to the manufacturer’s recommendation.
DNA contamination was removed with recombinant RNase-free DNase I (TaKaRa, Tokyo, Japan) and then mRNA was enriched with Oligo(dT) magnetic beads (Thermo Fisher Scientific, MA, USA). The purified mRNA was cut into small pieces using fragmentation buffer and reverse-transcribed to produce the cDNA library using mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA) as instructed by the manufacturer.

treatment_protocol: Nine months-old plantlets were transferred onto mediums supplemented with varied concentrations of 6-BA (0, 0.5, 1.0, and 2.0 mg/L) and sampled at different time points (2w and 4w).

value: young leaves,stems and shoots

tag: Stage

value: 9-month old

tag: treatment

tag: rna-seq number

value: the second RNA-seq

tag: treating time


title: KF62_melanoma lesion from patient p8

type: RNA

city: Milano

first: Chiara

last: Gargiuli

address: via Amadeo

department: Dept. of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

description: FFPE lesion of a melanoma patient

hyb_protocol: Hybridization was performed according to manufacturer’s standard protocols.

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 scanner

data_processing: Raw CEL files were imported in R and pre-processed using the robust multi-array average method implemented in the oligo Bioconductor package

label: biotin

source_name: FFPE specimen of a melanoma patient

label_protocol: RNA was labeled and processed according to manufacturer’s recommended protocols.

extract_protocol: RNA was extracted using the QIAGEN miRNeasy FFPE mini kit

tag: Sex

value: female

tag: patient id

tag: tissue type

value: melanoma tumor

tag: therapy status

value: post

tag: therapeutic response

value: long responder

tag: metastatic site

value: lymph node


title: covid-19_lung_cov18

tag: tissue

value: lung tissue

value: Female


title: EY29_melanoma lesion from patient p8

description: FFPE lesion of a melanoma patient

value: pre

value: subcutaneous


title: covid-19_lung_cov2

value: Male


title: BA_1_4w: 6-BA_1.0 mg/L_4 w

value: 4 weeks


title: BA_0_5_4w: 6-BA_0.5 mg/L_4 w


title: RNAseq_K27me3_MpPp_male_germline_rep1

tag: genotype


title: RNAseq_K27me3_MpPm_male_germline_rep4

tag: mother genotype

value: mes-3(bn35); him-8(e1489) (N2 background)


title: RNAseq_K27me3_MpPp_male_germline_rep4

value: fem-2(b245ts) (CB4856 background)

tag: father genotype


title: EY30_melanoma lesion from patient p8

description: FFPE lesion of a melanoma patient


title: BA_0_4w: 6-BA_0 mg/L_4 w

value: Distilled water


title: B2_C1-2

tag: age

value: E16+24hours culture

value: WT

tag: strain

tag: cell type

value: Ovarian cells

value: Ovary


title: B2_C1-1


title: RNAseq_K27me3_MpPp_male_germline_rep3

value: mes-3(bn35)/hT2-GFP; him-8(e1489) (N2 background)


title: Normal_lung_21N

source_name: normal human lung

tag: gender

tag: disease state

value: normal


title: PD3plus -treated with 24 mM oxamate

city: Jerusalem

first: Eli

last: Pikarsky

address: Ein Karem

department: The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University-Hadassah Medical School

data_processing:
Raw reads were created with bcl2fastq, v2.18.0.12, then processed to remove bad quality and adapter bases with cutadapt, v1.18, using parameters -q32,32, -O 1, --match-read-wildcards and -m 15. Processed reads were further filtered by fastq_quality_filter, FASTX v0.0.14, with parameters -q 20 and -p 90.
Processed reads were aligned to the mouse genome with tophat, v2.1.1, using parameters -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 18, --read-realign-edit-dist 3, --no-coverage-search, --library-type fr-firststrand, and gene annotations from Ensembl release 99.
Counts per gene were calculated with htseq-count, v0.6.0, using -s 'reverse' and masking for short genes (e.g. miRNAs).
Statistical testing was done with DESeq2, v1.22.2, taking genes with at least 10 counts and incorporating the date of preparation as a batch factor in the model.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file with a single header row, followed by a row for each gene. Columns A-K have general gene information, L-W have raw counts for each sample, X-AI have normalized counts for each sample, AJ is the average expression (baseMean), then 5 columns for each comparison with the output of DESeq2 results.

source_name: isolated and cultured cells

extract_protocol:
RNA was isolated using Qiagen mini kit
Libraries were prepared with poly-A capturing and the KAPA Stranded mRNA-Seq Kit

value: cultured germ cells

tag: developmental stage

value: Pachytene/Diplotene

tag: treatment

value: Treated with 24 mM oxamate, 48 hrs


title: Normal_lung_17N

value: lung tissue

value: Female


title: RNAseq_K27me3_MpPm_male_germline_rep3


title: BA_2_2w: 6-BA_2.0 mg/L_2 w

value: young leaves,stems and shoots

tag: Stage

value: 9-month old

tag: rna-seq number

value: the second RNA-seq

tag: treating time

value: 2 weeks


title: RNAseq_K27me3_MpPm_male_germline_rep2

value: fem-2(b245ts) (CB4856 background)

value: mes-3(bn35); him-8(e1489) (N2 background)


title: covid-19_lung_cov11

value: Male


title: BA_1_2w: 6-BA_1.0 mg/L_2 w


title: Normal_lung_7N


title: PD2plus-treated with 24 mM oxamate


title: PD1plus-treated with 24 mM oxamate


title: Normal_lung_19N


title: RNAseq_K27me3_MpPm_male_germline_rep1


title: FB89_melanoma lesion from patient p8

description: FFPE lesion of a melanoma patient

tag: Sex

value: female

tag: patient id

tag: tissue type

value: melanoma tumor

tag: therapy status

value: post

value: long responder

value: abdominal


title: BA_0_5_2w: 6-BA_0.5 mg/L_2 w

tag: tissue


title: RNAseq_K27me3_MpPp_hermaphrodite_germline_rep1

tag: genotype

tag: mother genotype

value: mes-3(bn35)/hT2-GFP; him-8(e1489) (N2 background)


title: RNAseq_K27me3_MpPp_hermaphrodite_germline_rep2

tag: father genotype


title: PD3-nontreated

tag: strain

value: cultured germ cells

value: Pachytene/Diplotene

value: Untreated


title: PD2-nontreated

tag: cell type


title: Normal_lung_N9

value: lung tissue

tag: gender

value: normal


title: BA_0_2w: 6-BA_0 mg/L_2 w

value: young leaves,stems and shoots

value: 9-month old

value: Distilled water


title: D2: 0.1 mg/L NAA + 1.0 mg/L 6-BA_3w_rep2

treatment_protocol: Two month-old uniform plantlets were sub-cultured on a medium described above, supplemented with distilled water (sample A), 0.1 mg/L NAA (sample B), 1.0 mg/L 6-BA (sample C), and 0.1 mg/L NAA + 1.0 mg/L 6-BA (sample D), two biological replicates for each treatment. The plantlets were sampled after three weeks of cultivation.

value: 2-month old

value: 0.1 mg/L NAA + 1.0 mg/L 6-BA

value: the first RNA-seq

value: 3 weeks


title: Normal_lung_N7

value: Female

tag: disease state


title: RNAseq_K27me3_MpPm_hermaphrodite_germline_rep2

value: fem-2(b245ts) (CB4856 background)

value: mes-3(bn35); him-8(e1489) (N2 background)


title: LZ3plus-treated with 0.3 mM octyl-L2HG

tag: developmental stage

value: Leptotene/Zygotene

value: Treated with 0.3 mM octyl-L2HG-6 days


title: Normal_lung_N6


title: PD1-nontreated

value: cultured germ cells

tag: treatment


title: Normal_lung_N10

value: Male


title: RNAseq_K27me3_MpPm_hermaphrodite_germline_rep1


title: C1: 1.0 mg/L 6-BA_3w_rep1

tag: Stage


title: Alk-YS, 2

city: Gothenburg

first: Ruth

last: Palmer

address: Medicinaregatan 9A, Shalgrenska Academy

department: Medical Biochemistry & Cell Biology

country: Sweden

institute: Gothenburg University

data_processing:
mapping hisat2 v2.0.5 --dta --phred33
quantification FeatureCounts v1.5.0-p3 Default
Differential Analysis DESeq2 v1.20.0 padj<=0.05
Assembly: ensembl_drosophila_melanogaster_bdgp6_gca_000001215_4
Supplementary files format and content: Excel, FPKM & log2FC

organism: Drosophila melanogaster

source_name: 3rd instar larval CNS

growth_protocol: Drosophila melanogaster strains were maintained on a standard fly food.

extract_protocol:
3rd instar larvae (40 - 45) were collected and quickly washed in water to remove food leftovers and yeast. Larvae were placed in ice-cold PBS of a depression well. Fine forceps were used to dissect the larval CNS. Once the larval CNS was exposed, it was dissected out using forceps, and the intact CNS were collected in an Eppendorf tube containing 250 μl of ice-cold solution (equal volume of both RNA free PBS and RNALater solution from Invitrogen) for a maximum of one hour. Afterwards, the tubes containing the CNS were centrifuged at 2000 rpm for 5 minutes at 4 °C and removed the supernatant. 500 μl fresh RNALater solution was added to the CNS and were stored at -80°C. Once the CNS collection for 3 biological replicates per genotype was obtained, RNA-extraction was carried out according to the manufacturer’s protocol (Promega ReliaPrepTM RNA Tissue Miniprep System, REF-Z6111). Total RNA was measured using NanoDrop OneC (Thermo Scientific) for its concentration and RNA-integrity was checked on the gel electrophoresis. 4-6 µg of total RNA/biological replicate was shipped to Novogene Co. Ltd (UK) for sequencing.
cDNA

treatment_protocol: No treatment

value: 3rd instar larval CNS

value: Mutant


title: B2: 0.1 mg/L NAA_3w_rep2

value: 0.1 mg/L NAA

tag: rna-seq number


title: Normal_lung_4N

value: lung tissue

value: normal


title: Normal_lung_N11


title: Alk-YS, 3


title: LZ2plus-treated with 0.3 mM octyl-L2HG


title: scRNAseq_H9_KOSR_day8 shCtrl

city: Santa Barbara

first: Dasol

last: Han

state: California

address: University of California Santa Barbara

institute: University of California Santa Barbara

data_processing:
The Cell Ranger toolkit (version 3.1.0) provided by 10X Genomics was applied for scRNA-seq data to align reads and generate the gene-cell unique molecular identifier (UMI) matrix, using the reference genome GRCh37. LTR7/HERVH unit (named as ERV as prefix) were added in the genome annotation file using cellranger mkref command.
The expression matrices were imported into Seurat V3.0 R package (https://satijalab.org/seurat).
All samples were integrated into one Seurat object by "IntegrateData" Seurat function.
Processed data file "GRCh37_LTR7HERVH_integrated_count_matrix.csv" is the count matrix extracted from the integrated Seurat object which is used for entire downstream analysis.
Genome_build: GRCh37, LTR7/HERVH annotated
Supplementary_files_format_and_content: CSV, raw count matrix of integrated Seurat object

source_name: H9 hESCs

growth_protocol: H9 hESCs were culutred on matrigel-coated tissu culture plates with mTeSR1 or TeSR-E8 media and passaged every 4-5 days depending on confluency using either Accutase or ReLeSR.

extract_protocol:
Cells were harvested and dissociated into single cells using Accutase, and then 4,000 live cells per sample were loaded onto a Chromium Controller (10X Genomics) using Chromium Next GEM Chip G Single Cell Kit (1000127).
We followed 10x genomics protocol using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (cat 1000121). The libraries from all four samples were multiplexed together and sequenced on an Illumina NovaSeq (Paired-end 150).

treatment_protocol: H9 cells were transduced with lentiviral vectors expressing control (GFP) or ZBTB12 shRNA (shA, see manuscript). Puromycin (1μg/ml) was added to the media from 24 hr post transduction. Day 0 samples were harvested at 48 hr post transfection. For day 8 samples, cells were treated with spontenous differentiation medium (10% Knockout serum replacement, 1X MEM nonessential amino acid solution and 0.1 mM β-mercaptoethanol in DMEM/F12) for eight days, with media refreshment every other days.

tag: cell line

value: H9 hESCs (WiCell)

tag: passage

tag: shRNA

value: pLKO.1 GFP shRNA (Addgene #30323)

value: spontaneous differentiation induced for 8 days (see materials and methods)

tag: barcode appendix


title: D1: 0.1 mg/L NAA + 1.0 mg/L 6-BA_3w_rep1

value: young leaves,stems and shoots

value: 2-month old

value: 0.1 mg/L NAA + 1.0 mg/L 6-BA

value: the first RNA-seq

tag: treating time


title: w1118, 3

value: Control


title: LZ3-nontreated

value: Leptotene/Zygotene

value: Untreated


title: LZ2-nontreated

value: cultured germ cells


title: scRNAseq_H9_KOSR_day8 shZBTB12

value: pLKO.1 ZBTB12 shRNA (Sigma TRCN0000164972)


title: Alk-YS, 1

value: 3rd instar larval CNS


title: scRNAseq_H9_mTeSR1_day0 shZBTB12

value: no treatment (cultured in mTeSR1)


title: w1118, 1


title: C2: 1.0 mg/L 6-BA_3w_rep2

tag: tissue

value: 3 weeks


title: B1: 0.1 mg/L NAA_3w_rep1

value: 0.1 mg/L NAA


title: w1118, 2

tag: genotype


title: LZ1-nontreated


title: A2: Ctrl_3 w_rep2

value: Distilled water


title: LZ1plus-treated with 0.3 mM octyl-L2HG

value: Treated with 0.3 mM octyl-L2HG-6 days


title: scRNAseq_H9_mTeSR1_day0 shCtrl

value: H9 hESCs (WiCell)

value: pLKO.1 GFP shRNA (Addgene #30323)


title: A1: Ctrl_3 w_rep1

value: young leaves,stems and shoots


title: UAMS-1 codYccpA, 6h, sample 2

status: Public on May 30 2022

first: MARAT

last: SADYKOV

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

data_processing:
CLC Genomics Workbench version 21.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to the annotated reference genome Staphylococcus aureus strain: UAMS-1(GCA_000788115.1) from NCBI using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Staphylococcus aureus strain: UAMS-1(GCA_000788115.1)
Supplementary files format and content: Excel file that includes Name, Chromosome, Expression n value, TPM, RPKM, Gene Length, Unique gene reads, Total gene reads. The second excel files contains a compiled spreadsheet of all samples with the values used to genereate figures.

organism: Staphylococcus aureus

growth_protocol: grown in tryptic soy broth (TSB) (BD Biosciences) supplemented with 0.25% glucose (Sigma-Aldrich).   Bacterial cultures were inoculated to an optical density at 600 nm (OD600) of 0.05 from overnight cultures, incubated at 37°C, and aerated at 250 rpm with a flask to medium ratio of 10:1. Bacterial growth was assessed by measuring the OD600. The OD600 for stationary-phase cultures was measured following dilution of cultures in TSB to remain within the linear range of a spectrophotometer.  Antibiotics were purchased from Thermo Fisher Scientific and were used at the following concentrations: erythromycin at 5 μg/ml, chloramphenicol at 10 μg/ml, and tetracycline at 10 μg/ml.

extract_protocol:
Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete
Libraries were generated using 100 ng of total RNA from each sample and the Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete (Tecan Genomics, Inc. 900) following the recommended procedure

value: Bacteria

value: CodYCcpA mutant

tag: time

value: 6 hours


title: UAMS-1 codYccpA, 6h, sample 3


title: UAMS-1 codY, 6h, sample 2

value: CodY mutant


title: UAMS-1 ccpA, 6h, sample 3

value: CcpA mutant


title: UAMS-1 WT, 6h, sample 2

value: WT


title: UAMS-1 codYccpA, 6h, sample 1


title: UAMS-1 ccpA, 6h, sample 2


title: UAMS-1 codYccpA, 3h, sample 3

value: 3 hours


title: UAMS-1 WT, 6h, sample 3


title: UAMS-1 ccpA, 6h, sample 1


title: UAMS-1 codYccpA, 3h, sample 1


title: UAMS-1 codYccpA, 3h, sample 2


title: UAMS-1 codY, 3h, sample 3


title: UAMS-1 ccpA, 3h, sample 3


title: UAMS-1 ccpA, 3h, sample 2


title: UAMS-1 codY, 3h, sample 1


title: UAMS-1 codY, 3h, sample 2


title: UAMS-1 WT, 3h, sample 2


title: UAMS-1 WT, 3h, sample 3


title: UAMS-1 WT, 3h, sample 1


title: UAMS-1 WT, 6h, sample 1


title: UAMS-1 codY, 6h, sample 1


title: UAMS-1 codY, 6h, sample 3


title: Human_paraffin-embedded_placental_tissue_Sample 87

city: Ann Arbor

first: Ashley

last: Hesson

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

data_processing:
An index of the hg38 reference genome was created and sequences were aligned to this index using the Rsubread package from the Bioconductor suite in R (Vienna, Austria)
The alignment files were subsequently summarized and associated with their respective features and meta-data.  Initial quality control was performed in MultiQC.
Read count extraction and normalization were performed using the Bioconductor suite and DESeq2 package in R
Assembly: hg38
Supplementary files format and content: counts

source_name: placenta

extract_protocol:
Placenta samples were formalin-fixed and paraffin-embedded; five 20-micron sections of each placenta sample were subjected to RNA extraction using the RNAstormTM kit (Cell Data Sciences, Fremont, CA, USA) as per the manufacturer’s instructions.
Total RNA was processed for high-throughput sequencing using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Greenland, NH, USA). Following mRNA generation, fragmentation, and cDNA synthesis, adaptor barcodes were ligated and final cDNA libraries were amplified by PCR and assessed for quality and concentration.

value: placenta

tag: gestational age

value: Preterm

value: Preeclampsia


title: Human_paraffin-embedded_placental_tissue_Sample 83

value: Term


title: Human_paraffin-embedded_placental_tissue_Sample 78


title: Human_paraffin-embedded_placental_tissue_Sample 69


title: Human_paraffin-embedded_placental_tissue_Sample 76


title: UAMS-1 ccpA, 3h, sample 1


title: Human_paraffin-embedded_placental_tissue_Sample 81


title: Human_paraffin-embedded_placental_tissue_Sample 85


title: Human_paraffin-embedded_placental_tissue_Sample 63


title: Human_paraffin-embedded_placental_tissue_Sample 66


title: Human_paraffin-embedded_placental_tissue_Sample 57


title: Human_paraffin-embedded_placental_tissue_Sample 56


title: Human_paraffin-embedded_placental_tissue_Sample 48


title: Human_paraffin-embedded_placental_tissue_Sample 42


title: Human_paraffin-embedded_placental_tissue_Sample 38


title: Human_paraffin-embedded_placental_tissue_Sample 40


title: Human_paraffin-embedded_placental_tissue_Sample 52


title: Human_paraffin-embedded_placental_tissue_Sample 50


title: Human_paraffin-embedded_placental_tissue_Sample 43


title: Human_paraffin-embedded_placental_tissue_Sample 41


title: Human_paraffin-embedded_placental_tissue_Sample 39


title: Human_paraffin-embedded_placental_tissue_Sample 64


title: Human_paraffin-embedded_placental_tissue_Sample 74


title: Human_paraffin-embedded_placental_tissue_Sample 36


title: Human_paraffin-embedded_placental_tissue_Sample 32


title: Human_paraffin-embedded_placental_tissue_Sample 55


title: Human_paraffin-embedded_placental_tissue_Sample 37


title: Human_paraffin-embedded_placental_tissue_Sample 35


title: Human_paraffin-embedded_placental_tissue_Sample 30


title: Human_paraffin-embedded_placental_tissue_Sample 34


title: TG1

city: Changsha

first: Liang

last: Tang

address: No 1501, Leifeng road

institute: Changsha Medical University

description: Gene expression after treated with TG hippocampal tissue

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.Genespring (version 14.8,Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “Detected” were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

organism: Mus

source_name: hippocampal tissue, treated with TG, replicate 1

label_protocol: RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: General anesthesia was performed by intraperitoneal injection of 0.2% pentasorbital sodium (0.1 ml/10g). The hippocampus was isolated from brain tissues and were stored at -80℃

extract_protocol: Trizol (Invitrogen, USA) was used to extract total RNA from the hippocampus of 3 mice in each group. DNAse I treatment to remove DNA contamination.

treatment_protocol: The Aβ25-35-induced AD model mice and the intervention of TG were conducted according to our previous study. The AD+TG group (0.25 mg/10 g.d, 1 mg/ml TG), and AD model group (0.5 ml/d, 0.9% NS) were selected to perform the micro-array analysis.

value: hippocampal tissue

value: male


title: Human_paraffin-embedded_placental_tissue_Sample 29


title: CK3

description: Gene expression after treated with NS hippocampal tissue

source_name: hippocampal tissue, treated with NS, replicate 3


title: Human_paraffin-embedded_placental_tissue_Sample 26


title: Human_paraffin-embedded_placental_tissue_Sample 27


title: TG2

source_name: hippocampal tissue, treated with TG, replicate 2


title: Human_paraffin-embedded_placental_tissue_Sample 10

value: Control


title: Human_paraffin-embedded_placental_tissue_Sample 13


title: Human_paraffin-embedded_placental_tissue_Sample 8


title: Human_paraffin-embedded_placental_tissue_Sample 20


title: Human_paraffin-embedded_placental_tissue_Sample 25


title: CK1

source_name: hippocampal tissue, treated with NS, replicate 1


title: Human_paraffin-embedded_placental_tissue_Sample 14


title: Human_paraffin-embedded_placental_tissue_Sample 9


title: Human_paraffin-embedded_placental_tissue_Sample 12


title: Human_paraffin-embedded_placental_tissue_Sample 18


title: Human_paraffin-embedded_placental_tissue_Sample 28


title: CK2

source_name: hippocampal tissue, treated with NS, replicate 2


title: Human_paraffin-embedded_placental_tissue_Sample 7


title: TG3

source_name: hippocampal tissue, treated with TG, replicate 3


title: Human_paraffin-embedded_placental_tissue_Sample 6


title: Human_paraffin-embedded_placental_tissue_Sample 5


title: Human_paraffin-embedded_placental_tissue_Sample 4


title: H1_AD_0h_rep3

city: New York

last: Yan

email: linda.lee2@mssm.edu, nan.yang1@mssm.edu

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Mount Sinai

data_processing:
All data processing steps were completed using the ENCODE ATAC-seq pipeline v1.4.2. Adapter trimming performed with cutadapt.
Genomic alignment to hg38 performed using Bowtie2
Removal of mitochondrial reads and duplicate alignments
Peak calling and reproducibility analysis using MACS2 and IDR, respectively (Idr threshold 0.05)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Peak files (.narrowpeak) contain the called peaks from MACS2

source_name: WA01 (H1 ES)

growth_protocol: hES or hiPS cell–derived neurons were routinely generated by overexpression of the transcription factors Ngn2 (Glu neurons) or Ascl1 and Dlx2 (GABA neurons). On day 1, medium was replaced by N2 media(1x N2 supplement, 1X NEAA in DMEM-F12 media) containing 2 mg/ml Doxycycline to induce TetO expression. Selection of transduced cells was achieved with N2 media containing antibiotics for 2 or 3 days, and media was replaced with N2 media containing 4 μM Cytosine β-D-arabinofuranoside hydrochloride for 2 or 3 days to inhibit cell proliferation. Induced neurons were dissociated using Accutase and replated with mouse glial cells on Geltrex-coated plates. The media used for plating was a 1:1 mix of Neurobasal medium supplemented with B27, Glutamax containing 1% FBS and glial plating media(1x Glutamax , 2mg/ml Glucose and 5% FBS) containing 2 μM Thiazovivin(TV) and 2 mg/ml Doxycycline. TV was removed from media the following day. Half of the media was changed every 2-3 days and replaced with fresh Neurobasal medium supplemented with B27, Glutamax containing 1% FBS. 7 days later, the media was replaced by Neurobasal A, B27, Glutamax containing 1% FBS and half of it was replaced every 4 days. Mature neurons were co-cultured with mouse glial cells on day in vitro 35 (DIV35) for various experiments.

extract_protocol:
75,000 DIV35 neurons were washed once with 50μl cold PBS and resuspended in 50μl cold Lysis Buffer (48.5μl Resuspension Buffer (10mM Tris-HCl pH7.5, 10mM NaCl, 3mM MgCl2 in nuclease-free water), 0.1% NP-40 (Sigma/Roche 11332473001), 0.1% Tween-20, 0.01% Digitonin (EMD Millipore 300410)). The resuspension was incubated for 3 mins on ice and then 1ml of Wash Buffer (990μl Resuspension Buffer, 0.1% Tween-20) was added. Samples were centrifuged at 500g for 10 mins at 4ºC to collect the nuclei. The nuclei were then resuspended in 50μl Transposition Reaction mix (25 μl 2xTD Buffer (from Illumina Tagment DNA Enzyme and Buffer kit (Illumina 20034211)), 16.5μl 1xPBS, 0.1% Tween-20, 0.01% Digitonin, 2.5μl Tagment DNA Enzyme 1 (from Illumina Tagment DNA Enzyme and Buffer kit), up to 50μl nuclease-free water) and incubated at 37ºC for 30 mins at 1000rpm. DNA was then isolated using Qiagen MinElute Reaction Cleanup kit (Qiagen 28206) following manufacturer’s instructions.
The eluted ATAC DNA was amplified by PCR as previously described. Briefly, the samples were initially amplified for 5 cycles and then qPCR was performed for each sample. The relative fluorescence (Rn) was plotted against the cycle number and the additional number of cycles to perform was determined by the cycle in which the Rn reached one-third of the maximum fluorescence intensity. After PCR amplification, libraries were purified using Qiagen MinElute PCR Purification kit and eluted in 20 μl of Elution Buffer. Libraries were sent to Genewiz for sequencing using HiSeq.

treatment_protocol: Prior to depolarization, medium was replaced with serum free Neurobasal A/B27/Glutamax for 3 days. The neuronal culture was then silenced using 1μM of Tetrodotoxin citrate (TTX) (Labome 1069/1) and 100μM of DL-2-amino-5-phosphopentnoic acid (DL-AP5) (Abcam ab120271) for 12-16h. The neurons were then depolarized by adding depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl and 10 mM HEPES directly into the media to a final concentration of 30% of the total culture media. Neurons were collected at different time points after depolarization for experiments.

value: WA01 (H1 ES)

value: induced GABAergic neurons

value: depolarization

tag: timepoint (minutes)


title: H1_AD_45min_rep3

tag: cell type


title: H1_AD_90min_rep2


title: H1_AD_0h_rep2


title: H1_AD_90min_rep3


title: H1_AD_45min_rep2


title: H1_AD_90min_rep1


title: H1_AD_45min_rep1


title: H1_AD_0h_rep1


title: Human_paraffin-embedded_placental_tissue_Sample 3


title: Human_paraffin-embedded_placental_tissue_Sample 2


title: H1_Ngn2_45min_rep3

value: induced glutamatergic neurons


title: control-treated BM-2

city: Daejeon

first: Da Yeon

last: Kim

state: Daejoen (30)

address: 141, Gajeong-ro, Yuseong-gu,

department: Genetic & Epigenetic Toxicology Research Group

country: South Korea

institute: Korea Institute of Toxicology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: bone marrow

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Male 6 weeks old C57BL/6 mice were oral gavage administrated for 28 days, then harvest the bone marrow cells at day29.

value: bone marrow

value: RBC lysed bone marrow cells

tag: strain

value: wild type

tag: Sex

value: sterile water

value: 28 days

tag: age

value: 6 weeks old


title: AR-treated BM-3

tag: treatment

value: Asari Radix et Rhizoma


title: H1_Ngn2_45min_rep2


title: control-treated BM-3


title: H1_Ngn2_0h_rep2


title: control-treated BM-1


title: H1_Ngn2_0h_rep3


title: N4701

city: Crawley

first: Erica

middle: Louise

last: Parker

state: WA

address: 35 Stirling Highway

country: Australia

institute: University of Western Australia

data_processing:
Read quality was assessed using FastQC
Reads were aligned to HG19 using HISAT
Alignment quality was assessed using SAMStat
Quantification and normalisation of read counts was performed using summariseOverlaps (GenomicAlignments package) and voom (limma package), both from Bioconductor
Assembly: HG19
Supplementary files format and content: Matrix table with each row representing a different sample, and each column representing a gene (expressed as raw gene counts) and relevant clinical variables variables. NOTE: 75 observations of 47975 variables. Data will be lost if csv file of this size (many columns) is opened in MS Excel. Please open in R or other statistical program.

source_name: Peripheral blood mononuclear cell

extract_protocol:
PBMC isolated from peripheral blood sample on day of collection, and stored in RNAprotect (Qiaged, Germany) at -80C. RNA extraction was completed using modified protocol for the RNeasy MinElute Clean-up kit (Qiagen, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject gender

value: M

tag: subject age

tag: disease state

value: HIV non-infected

tag: month since screening

tag: hiv treatment

value: not applicable


title: H1_Ngn2_90min_rep2

tag: cell line


title: AR-treated BM-2


title: H1_Ngn2_90min_rep1


title: AR-treated BM-1


title: N4601

value: F


title: N4501


title: H1_Ngn2_45min_rep1


title: H1_Ngn2_0h_rep1


title: H1_Ngn2_90min_rep3


title: N4401


title: N3801


title: N4301


title: N3701


title: N4001


title: N3401


title: N4101


title: N3501


title: N3601


title: N3301


title: N3901


title: N3101


title: N3201


title: N3001.


title: N2901


title: G114_G08_80_THP-1_exp3_Inulin-chicory

city: Wageningen

first: Coen

last: Govers

address: Bornse Weilanden 9

country: Netherlands

institute: Wageningen Food & Biobased Research

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm using the Affymetrix® Expression Console™ Software.

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Inulin-chicory for 6 hours, biological replicate 3

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: ATTC derived THP-1 cells were cultured in RPMI-1640 medium (Gibco) supplemented with 10% heat inactivated FBS (Hyclone Perbio) and Pen/Strep (Invitrogen, ThermoFischer ) and used within passage numbers 20 and 40. For assays cells were set to differentiate at 1x10^6/ml and 500ul/well in a 24-well flat-bottom TCT plate and incubated with 100 ng/ml phorbol 12-myristate 13-acetate (Sigma) for 48 hours. Subsequently, cells were washed 3 times and set to rest in 500 ul of medium for 48 hours.

extract_protocol: Total RNA was prepared from the THP-1 macrophages using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Compounds have been resuspended, aliquoted and lyophilized prior to the experiment. Resuspending the compounds in medium before addition to macrophages was performed at 37 degrees celcius while rotating for 30 minutes. THP-1 macrophages were stimulated for 6 hours with 500 ul medium or medium with 500 ug/ml compounds or 11.85 pg/ml LPS.

value: macrophage

value: male

tag: patient age

value: 1 year infant

tag: tumor origin

value: acute monocytic leukemia

value: Inulin-chicory 500 ug/ml

tag: passage number

value: passage 20-40

tag: days of differentiation on tranwells

value: 4 day differentiated


title: G114_G04_76_THP-1_exp2_GOS

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with GOS for 6 hours, biological replicate 2

value: GOS 500 ug/ml


title: G114_G06_78_THP-1_exp3_LPS

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with LPS for 6 hours, biological replicate 3

value: LPS 11.85 pg/ml


title: N2801


title: G114_G02_74_THP-1_exp2_Sugar beet pectin

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Sugar beet pectin for 6 hours, biological replicate 2

value: Sugar beet pectin 500 ug/ml


title: G114_G10_82_THP-1_exp3_Sugar beet pectin

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Sugar beet pectin for 6 hours, biological replicate 3


title: G114_G09_81_THP-1_exp3_Resistant starch corn

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Resistant starch corn for 6 hours, biological replicate 3

value: Resistant starch corn 500 ug/ml


title: G114_G12_84_THP-1_exp3_GOS

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with GOS for 6 hours, biological replicate 3


title: G114_G03_75_THP-1_exp2_Beta-glucan oat med. visc.

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Beta-glucan oat medium viscocity for 6 hours, biological replicate 2

value: beta-glucan oat medium viscosity 500 ug/ml


title: G114_G07_79_THP-1_exp3_Novelose

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Novelose for 6 hours, biological replicate 3

value: Novelose 500 ug/ml


title: G114_G11_83_THP-1_exp3_Beta-glucan oat med. visc.

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Beta-glucan oat medium viscocity for 6 hours, biological replicate 3


title: N2701


title: G114_G05_77_THP-1_exp3_medium

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with medium for 6 hours, biological replicate 3

value: medium


title: N2601

value: M

value: HIV non-infected


title: G114_F11_71_THP-1_exp2_Novelose

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Novelose for 6 hours, biological replicate 2


title: N2501

value: F

value: not applicable


title: N2301


title: G114_F12_72_THP-1_exp2_Inulin-chicory

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Inulin-chicory for 6 hours, biological replicate 2

value: macrophage

value: male


title: N2401


title: G114_F10_70_THP-1_exp2_LPS

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with LPS for 6 hours, biological replicate 2

value: 1 year infant

value: acute monocytic leukemia


title: G114_F09_69_THP-1_exp2_medium

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with medium for 6 hours, biological replicate 2

value: passage 20-40


title: G114_G01_73_THP-1_exp2_Resistant starch corn

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Resistant starch corn for 6 hours, biological replicate 2

value: 4 day differentiated


title: G114_F08_68_THP-1_exp1_GOS

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with GOS for 6 hours, biological replicate 1

value: GOS 500 ug/ml


title: N2201

source_name: Peripheral blood mononuclear cell


title: G114_F07_67_THP-1_exp1_Beta-glucan oat med. visc.

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Beta-glucan oat medium viscocity for 6 hours, biological replicate 1


title: G114_F04_64_THP-1_exp1_Inulin-chicory

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Inulin-chicory for 6 hours, biological replicate 1

value: Inulin-chicory 500 ug/ml


title: G114_F06_66_THP-1_exp1_Sugar beet pectin

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Sugar beet pectin for 6 hours, biological replicate 1

value: Sugar beet pectin 500 ug/ml


title: G114_F05_65_THP-1_exp1_Resistant starch corn

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Resistant starch corn for 6 hours, biological replicate 1

value: Resistant starch corn 500 ug/ml


title: N2101


title: N1901


title: N2001


title: G114_F03_63_THP-1_exp1_Novelose

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with Novelose for 6 hours, biological replicate 1


title: N1801


title: N1601


title: N1701


title: G114_F01_61_THP-1_exp1_medium

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with medium for 6 hours, biological replicate 1


title: G114_E09_57_Caco_exp3_LPS

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with LPS for 6 hours, biological replicate 3

growth_protocol: ATCC derived Caco-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco-Invitrogen, Bleiswijk, The Netherlands) with 4.5 g/L glucose, 0.58 g/L glutamine, no pyruvate, supplemented with 10% heat inactivated FBS (Hyclone Perbio, Etten-Leur, The Netherlands) and used with passage numbers between 30 and 60. For transwell assays, 0.33x105 cells were grown on ThinCert transwells with 33.6 mm2 membranes and 0.4 μm pores in 24-well suspension culture plates. Cells were grown for 21 days at 5% CO2 and 37°C and apical (150 μl) and basolateral (700 μl) medium were replaced three times per week.

extract_protocol: Total RNA was prepared from the Caco-2 cells using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Compounds have been resuspended, aliquoted and lyophilized prior to the experiment. Resuspending the compounds in medium before addition to macrophages was performed at 37 degrees celcius while rotating for 30 minutes. Dietary fibres and LPS were diluted in DMEM+10%FBS medium to a concentration of 500 ug/ml and 11.85 pg/ml, respectively. The cell medium was replaced the day before the exposure experiments. Medium was removed from the apical and basal compartments and diluted samples were added in to the apical compartment while fresh DMEM+10%FBS medium was added to the basal compartment. In each experiment, the samples were exposed to Caco-2 cells in triplicate and three independent exposure experiments were performed (=3 independent biological replicates). After 6h incubation, the Caco-2 cells were lysed with 200 μL TRIzol and the triplicates in each experiment were pooled for RNA isolation.

value: LPS 11.85 pg/ml

value: Caucasian colon adenocarcinoma


title: PNT1A cells placed in the thyroid location of quasi-humanoid phantom [thyroid rep2]

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Human Gene 2.1 ST ArrayStrip (20 h, 292 48 °C)

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: PNT1A cells were cultured and irradiated in T-25 Nunc™ culture flasks (Ther-moFisher Scientific, MA, USA). The flasks were filled with room temperature PBS (Biowest, France) directly before irradiation to ensure homogenous dose distribution during delivery. Cells were irradiated in the quasi-humanoid phantom described above. The culture flasks were placed in the water container in the phantom at a depth of 11 cm in five locations (distance from axial plane in cm) to simulate the following organs: prostate (PTV, central beam axis (CAX)); intestine (15 cm); lung (35 cm); thyroid (52 cm ); and brain (74 cm). The cells in the prostate were irradiated to a total dose of 70 Gy (10 Gy delivered seven times, consecutively) in approximately 50 min. In parallel, sham-irradiated cells were cultured, filled with PBS, and kept at room temperature (they were not exposed to radiation). After irradiation, the cells were handled as described in sections 2.5, 2.6, and 2.7. The experiment was performed in at least three biological replicates

extract_protocol: Total RNA was isolated from the PNT1A cells which were collected one hour after irradiation, plated on a 6-well plate and cultured in full medium for 24 h. After that the total RNA was isolated, using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) and Direct-zol™ RNA MiniPrep Kit (Zymo Research, CA, USA), according to the manufac-turer’s instructions. The concentration and purity of isolated RNA were determined by gel electrophoresis and spectrophotometry, using DeNovix DS-11 (DeNovix, DE, USA) to measure absorbance at 260, 230, and 280 nm. The first-strand cDNA was synthesised from 1 µg of the isolated RNA using iScript™ RT-qPCR cDNA Synthesis Kit (Bio-Rad, CA, USA), following the manufacturer’s instructions. The cDNA was then diluted ten times in nuclease-free water.

treatment_protocol: The PNT1A cells were placed and irradiated in a quasi-humanoid phantom under conditions similar to those of real-life radiotherapy. The phantom was made with water-equivalent poly(methyl methacrylate) (PMMA) slices in the coronal plane to simulate the torso, head, and neck. The slices included natural cork and gypsum inhomogeneities in the lung and head locations to simulate lung tissue and bones, respectively. The layer for cell irradiation was equipped with a water container to allow for the placement of five flasks with the cells.  A radiation treatment plan was created for the T-25 culture flask containing PNT1A cells in the prostate location, which was delineated as the gross tumour volume (GTV). The flask was considered the clinical target volume (CTV). To create the planning target volume (PTV), a margin of 3 mm was added around the CTV, following the usual clinical practice to ensure that the PTV received the prescribed dose. The other four flasks were placed in the water containers in the following locations at various distances from the axial plane: intestine (transverse colon) (15 cm from the axial plane; lung (35 cm); thyroid (52 cm); and brain (74 cm). Figure 1 shows the VMAT plan for these organs at risk.  We used a 6 MV photon beam with a flattening filter to deliver the total dose of 70 Gy to the cells in the prostate, delivered in seven consecutive fractions of 10 Gy each (the highest fraction dose delivered for prostate SBRT). This approach is known as dose scaling (see AAPM Report 158). The 10 Gy SBRT fraction was used for planning (instead of 2 Gy, which is used for conventional fractionations, to a total dose of 70 Gy) because we wanted to assure the same scheme of collimator leaves’ movement (a different scheme is used for different doses per fraction during arc therapies). Treatment plans were prepared for the RapidArc VMAT technique using three co-planar arcs, with the first, second, and third arcs delivered, respectively, counterclockwise (gantry angles from 140° to 220°), clockwise (181° to 179°), and counterclockwise (179° to 181°), and with a 0.5 cm multi-leaf collimator  By scaling the dose to 70 Gy (in target) in a single delivery, we were able to obtain more reliable measurements of the out-of-field doses using Gafchromic EBT3 films (dynamic dose range: 0.01 Gy to 20 Gy, optimum 0.2 Gy to 10 Gy), especially for locations as far away as the thyroid and brain. This approach also allowed us to compare the biological effects induced by this radiation delivery method, especially for the different out-of-field locations. The radiation doses to these “organs” (in the phantom) were due to scattered radiation, thus the term “nontarget dose” was equivalent to “out-of-field” dose.  A 6 MV beam was delivered with a TrueBeam linear accelerator (Varian Medical Systems, CA, USA). Optimisation and calculations were performed in the Eclipse Treatment Planning System, v. 15.6 (Varian Medical Systems, CA, USA), using the anisotropic analytical algorithm.  Before irradiation, dosimetry pre-verification was performed, using the electronic portal imaging device system and the gamma evaluation method (γ passing rate ≥ 95%, 3%/2 mm, a 10% threshold, global normalisation).

value: PNT1A human cell line

value: Human post pubertal prostate normal, immortalised with SV40


title: PNT1A cells placed in the brain location of quasi-humanoid phantom [brain rep1]


title: PNT1A cells placed in the thyroid location of quasi-humanoid phantom [thyroid rep1]


title: PNT1A cells placed in the lung location of quasi-humanoid phantom [lung rep3]


title: G114_E06_54_Caco_exp3_GOS

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with GOS for 6 hours, biological replicate 3


title: PNT1A cells placed in the intestine location of quasi-humanoid phantom [intestine rep2]


title: PNT1A cells placed in the intestine location of quasi-humanoid phantom [intestine rep3]


title: G114_E05_53_Caco_exp3_Beta-glucan oat med. visc.

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Beta-glucan oat medium viscosity for 6 hours, biological replicate 3

value: Beta-glucan oat medium viscosity 500 ug/ml


title: PNT1A cells placed in the lung location of quasi-humanoid phantom [lung rep2]


title: PNT1A cells placed in the brain location of quasi-humanoid phantom [brain rep2]


title: PNT1A cells placed in the brain location of quasi-humanoid phantom [brain rep3]


title: PNT1A cells placed in the lung location of quasi-humanoid phantom [lung rep1]


title: G114_E03_51_Caco_exp3_Resistant starch corn

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Resistant starch corn for 6 hours, biological replicate 3


title: PNT1A cells placed in the prostate location of quasi-humanoid phantom [axis rep1]


title: G114_F02_62_THP-1_exp1_LPS

source_name: 2 days PMA, 2 days rest differentiated THP-1 macrophages incubated with LPS for 6 hours, biological replicate 1


title: G114_E04_52_Caco_exp3_Sugar beet pectin

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Sugar beet pectin for 6 hours, biological replicate 3


title: PNT1A untreated cells  [control rep3]

source_name: PNT1A untreated cells

value: untreated cells


title: G114_E01_49_Caco_exp3_Novelose

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Novelose for 6 hours, biological replicate 3

value: Novelose 500 ug/ml


title: PNT1A cells placed in the intestine location of quasi-humanoid phantom [intestine rep1]


title: N1501

value: F

value: HIV non-infected

value: not applicable


title: N1401


title: N1101

value: M


title: N1201


title: PNT1A cells placed in the thyroid location of quasi-humanoid phantom [thyroid rep3]


title: PNT1A cells placed in the prostate location of quasi-humanoid phantom [axis rep2]


title: ST1022-2-17A020373F_L3

city: Shanghai

first: Jiahao

state: Shanghai

address: Yueyang road

department: Bioinformatisc core

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

data_processing:
Trim adapters and low-quality bases using TrimGalore version 0.6.5 with the following setting: default
Genome alignment using STAR version 2.6.1d with the following setting: outFilterMultimapNmax (20), alignSJoverhangMin (8), alignSJDBoverhangMin (1), outFilterMismatchNmax (999), outFilterMismatchNoverReadLmax (0.04), alignIntronMin (20), alignIntronMax (1000000), alignMatesGapMax (1000000), twopassMode (Basic)
Transcript quantification using  kallisto version 0.46.1 with the following setting: bootstrap-samples (100)
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include counts, TPM values for each Sample

source_name: Placenta

extract_protocol:
 Within 15 min after delivery, 5 ml of neonatal umbilical cord blood was collected using two PAXGenRNA sampling tubes (2.5 ml/tube), and collected samples were were stored at -80 ℃. The placental tissues were collected from both the maternal and fetal side. Specifically, using a clean scalpel, one full-thick placental tissue was incised 5 cm from the perimeter of the placenta (a size of about 1×1×2 cm, including maternal and fetal side). Then, the tissues were rinsed with phosphate buffer (PBS) or normal saline until no visible blood and stored at -80 ℃ in a cryopreservation tube. DNA or RNA was extracted after homogenizing the tissues together.
RRBS and RNAseq library construction protocol -- Genomic DNA of placenta and umbilical cord blood specimens were extracted by using the TIANamp genomic DNA kit (Cat. No. DP304-02, TIANGEN Biotech CO. LTD., Beijing, China) per the manufacture’s recommendations. 50-300 ng of purified genomic DNA was utilized to generate RRBS libraries as previously described (https://www.nature.com/articles/s41594-018-0046-4). Indexed RRBS libraries were pooled accordingly and sequenced in a NovaSeq 6000 sequencer (Illumina, USA) with 100-base paired-end reads. Similarly, total RNAs were isolated using a miRNeasy Mini kit (QIAGEN, Germany) according to the manufacture’s recommendations. We used the Ribo-off rRNA depletion kit (Cat. No. N406-01, Vazyme Biotech Co. Ltd, Nanjing, China) to remove ribosomal RNA from total RNAs following the manufacturer’s instructions. To generate RNA-seq libraries, 10-100 ng rRNA-depleted RNAs were utilized by using the VAHTS total RNA-seq (H/M/R) library prep kit for Illumina (Cat. No. NR603-01, Vazyme Biotech Co. Ltd, Nanjing, China) per the manufacturer’s instructions. We sequenced the RNA-seq libraries in the NovoSeq 6000 sequencer with 100-base paired-end reads. The sequencing data volume of a single sample is around 8 gigabases (Gb) and the average sequencing depth of the target region of the enzyme digestion fragment is > 30×, the coverage proportion of CpG region is > 40%, and the total data volume is 100 Gb. Similarly, transcriptome profile for each placenta and umbilical cord blood sample was also conducted. VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® based on Ribo-zero method was used to constructed transcriptome RNA library and high-throughput sequencing was performed subsequently. 10 Gb volume of transcriptome data for each sample was necessary.

tag: group

value: GDM


title: ST1022-2-17A031052_L3

source_name: Umbilical cord blood


title: N0901

source_name: Peripheral blood mononuclear cell


title: ST1022-2-17A031044F_L3


title: ST1022-2-17A020345F_L3

value: Control


title: PNT1A untreated cells  [control rep1]


title: N1001


title: G114_E02_50_Caco_exp3_Inulin-chicory

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Inulin-chicory for 6 hours, biological replicate 3

value: male


title: ST1022-2-17A031059_L3


title: PNT1A untreated cells  [control rep2]


title: PNT1A cells placed in the prostate location of quasi-humanoid phantom [axis rep3]


title: G114_D05_41_Caco_exp3_medium

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with medium for 6 hours, biological replicate 3

value: medium


title: 17A031068F_S27_L001


title: N0801


title: N1301


title: G114_D01_37_Caco_exp2_LPS

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with LPS for 6 hours, biological replicate 2


title: N0701


title: 17A031068_S24_L004


title: 17A031067F_S26_L001


title: ST1022-2-17A020346_L3


title: 17A031062F_S25_L001


title: 17A031067_S23_L004


title: 17A031062_S22_L004


title: N0501


title: 17A031061_S21_L004


title: 17A031060F_S23_L001


title: 17A031061F_S24_L001


title: N0401


title: G114_C07_31_Caco_exp2_Resistant starch corn

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Resistant starch corn for 6 hours, biological replicate 2


title: 17A031059F_S26_L004


title: G114_C09_33_Caco_exp2_Beta-glucan oat med. visc.

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Beta-glucan oat medium viscosity for 6 hours, biological replicate 2


title: 17A031058F_S22_L001


title: G114_C10_34_Caco_exp2_GOS

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with GOS for 6 hours, biological replicate 2

value: GOS 500 ug/ml


title: G114_C08_32_Caco_exp2_Sugar beet pectin

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Sugar beet pectin for 6 hours, biological replicate 2

value: Sugar beet pectin 500 ug/ml


title: G114_C05_29_Caco_exp2_Novelose

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Novelose for 6 hours, biological replicate 2


title: N0201


title: N0301


title: G114_C06_30_Caco_exp2_Inulin-chicory

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Inulin-chicory for 6 hours, biological replicate 2

value: Inulin-chicory 500 ug/ml


title: N0101


title: G114_B09_21_Caco_exp2_medium

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with medium for 6 hours, biological replicate 2

value: Caucasian colon adenocarcinoma


title: 17A031056F_S20_L001


title: N0601


title: 17A031057_S18_L004


title: 17A031056_S17_L004


title: 17A031054F_S19_L001


title: A5001

value: HIV infected

value: untreated


title: 17A031060_S20_L004


title: G114_B02_14_Caco_exp1_GOS

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with GOS for 6 hours, biological replicate 1


title: G114_B05_17_Caco_exp1_LPS

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with LPS for 6 hours, biological replicate 1

value: LPS 11.85 pg/ml


title: 17A031054_S16_L004


title: 17A031057F_S21_L001


title: 17A031058_S19_L004


title: 17A031053F_S18_L001


title: A4901


title: A4501


title: 17A031053_S15_L004


title: A4401


title: G114_B01_13_Caco_exp1_Beta-glucan oat med. visc.

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Beta-glucan oat medium viscosity for 6 hours, biological replicate 1

value: Beta-glucan oat medium viscosity 500 ug/ml


title: 17A031052F_S25_L004


title: ST1022-2-17A020373_L3


title: 17A031051F_S17_L001


title: 17A031050F_S16_L001


title: A4301


title: 17A031051_S14_L004


title: A4201


title: 17A031050_S13_L004


title: G114_A11_11_Caco_exp1_Resistant starch corn

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Resistant starch corn for 6 hours, biological replicate 1

value: Resistant starch corn 500 ug/ml


title: 17A031049_S12_L004


title: 17A031049F_S15_L001

source_name: Placenta


title: 17A031048F_S14_L001


title: A4101

value: F


title: 17A031048_S11_L004

source_name: Umbilical cord blood


title: G114_A09_09_Caco_exp1_Novelose

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Novelose for 6 hours, biological replicate 1

value: Novelose 500 ug/ml


title: G114_A10_10_Caco_exp1_Inulin-chicory

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Inulin-chicory for 6 hours, biological replicate 1


title: 17A031047F_S13_L001


title: G114_A12_12_Caco_exp1_Sugar beet pectin

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with Sugar beet pectin for 6 hours, biological replicate 1


title: TCL1_M4_Tregs_A

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

description: Treg from leukemic mice

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Mouse Reference genome (GRCm38).
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Spleens were removed, gently dissociated on ice, and cells were antibody-stained (anti-CD44-PE-Cy7 and anti-CD69-PE) and sorted by FACS (Aria III). RNA was harvested using RNeasy Micro Kit. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 100 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols

value: Regulatory T cells

tag: phenotype

value: Foxp3EGFP subset CD44low CD69+ LAG3high

value: leukemic


title: TCL1_M2_Tregs_B

description: Treg from leukemic mice

tag: cell type

value: Foxp3EGFP subset CD44high CD69+ LAG3high


title: 17A031047_S10_L004

value: Control


title: A3801

source_name: Peripheral blood mononuclear cell


title: A3301


title: TCL1_M1_Tregs_B

description: Treg from leukemic mice

tag: strain


title: TCL1_M4_Tregs_B

description: Treg from leukemic mice


title: TCL1_M1_Tregs_A

description: Treg from leukemic mice


title: 17A031043F_S43_L004


title: 17A031042F_S42_L004


title: 17A031046_S9_L004


title: 17A031044_S8_L004

value: GDM


title: CTRL_M4_Treg

description: Treg from healthy control mice

value: healthy


title: 17A031042_S22_L004


title: G114_A01_01_Caco_exp1_medium

description: 21 days differentiated Caco-2 cells

source_name: 21 days differentiated Caco-2 cells incubated with medium for 6 hours, biological replicate 1

tag: Sex

value: male

value: medium


title: 17A031043F_S8_L001


title: A3101

value: M


title: A2501

value: HIV infected


title: 17A031046F_S12_L001


title: 17A020374F_S41_L004


title: 17A020374_S21_L004


title: CTRL_M2_Treg

description: Treg from healthy control mice


title: TCL1_M2_Tregs_A

description: Treg from leukemic mice


title: CTRL_M3_Treg

description: Treg from healthy control mice


title: A1901

value: untreated


title: 17A020371_S20_L004


title: A2001


title: 17A020371F_S40_L004


title: 17A020370F_S11_L001


title: 17A020370_S27_L004


title: A3201


title: A1501


title: A3701


title: A1801


title: 17A020369_S26_L004


title: 17A020368_S19_L004


title: 17A020368F_S39_L004


title: A1401


title: 17A031043_S23_L004


title: 17A020367_S18_L004


title: EW3,control,Day8

city: Wuhan

first: Yuchen

last: Chen

address: Donghu road 115

institute: Wuhan University

data_processing:
The raw signal data were basecalled using the ONT Albacore software package with default parameters.
The reads were aligned to FlyBase genome annotation version r6.39 using minimap2 and Samtools to filter out Drosophila reads.
The final reads were bridged using Flye (v2.6) and racon (1.22) and annotated using Karken2 and Bracken.
Library strategy: DNA-seq

organism: insect gut metagenome

source_name: total guts from Drosophila melanogaster

growth_protocol: All flies were grown on the food containing 5.5 g agar, 65 g sucrose, 25 g dry yeast, 65 g cornmeal, 4 mL propionic acid, and 1.25 g Methylparaben (dissolved in 95% ethanol) per liter under standard laboratory conditions

extract_protocol:
gDNA was extracted using fecal DNA extacting kit (Tiangen Company, Beijing, China). 1.0ug of total gDNA was used for the construction of sequencing libraries.
DNA libraries were constructed using the Oxford Nanopore Technologies (ONT) LSK109 library preparation kits following the manufacturer's instructions and were sequenced on single R9.4 flow cells on the Oxford Nanopore PromethION.

treatment_protocol: Virgin progenies were maintained at 18_x0001_C for 6-8 days and then switched to 29_x0001_C to induce transgenes for 8 days.Whole midguts of 8 days old flies were maintained as intact tissues to prevent bacterial leakage, the crops and Malpighian tubules of fly guts were removed.

tag: tissue

value: total guts from Drosophila melanogaster

tag: model

value: control fly

tag: genotype

value: esg-GAL4, UAS-GFP, tub-GAL80TS /+


title: EY1,control,Day8

value: yki3SA tumor-bearing fly

value: esg-GAL4, UAS-GFP, tub-GAL80TS /+; UAS-yki3SA/+


title: EW2,control,Day8


title: A1301

tag: subject gender

value: F

tag: subject age


title: EY3,control,Day8


title: 17A020366F_S9_L001


title: A1101

tag: disease state

tag: month since screening


title: 17A020366_S25_L004


title: 17A020369F_S10_L001


title: 17A020365F_S37_L004


title: 17A020366F_S44_L004


title: EW1,control,Day8


title: A0901

tag: hiv treatment


title: 17A020365_S17_L004


title: 17A020364F_S36_L004


title: A0801


title: 17A020364_S16_L004


title: 17A020363F_S35_L004


title: EY2,control,Day8


title: 17A020367F_S38_L004


title: VSMCs AD

city: Taizhou,  Zhejiang Province

first: Cheng

last: Xu

address: Department of Cardiology, Taizhou Hospital, Wenzhou Medical University, 150 Ximen Street, Linhai 317000, P.R. China

institute: Taizhou Hospital Affiliated to Wenzhou Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Mouse aortic vascular tissue

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Male

value: Mouse aortic vascular tissue

tag: treatment

value: Mice were infused for 7 days with angiotensin II (Ang II ) (2500ng/kg/min)

tag: age

value: 7 month old

value: vascular smooth muscle cells


title: 17A020361F_S34_L004

value: GDM


title: A0701


title: VSMCs Con

description: 10x Genomics

value: Mice were infused for 7 days with saline


title: 17A020363_S15_L004


title: A0601


title: R745A_cmt3_7.fq.gz

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

description: Columbia-0 background with cmt3-11 mutation and R745A-FLAG transgene

data_processing:
1x50 bp bisulfite reads were aligned to the TAIR10 genome using the BSMAP program (Xi Y, Li W,. BMC Bioinformatics. 2009) using a QC trim score >= 33, -n 0 mapping type  and filtering for less than 5 n using 4% or less overall read mismatch. Aligned reads were converted to bisulfite methylation values via methratio.py (from BSMAP).  Methylation ratios at each cytosine were converted to bedGraph files using awk and to bigWig files using the UCSC executable script "bedGraphToBigWig".
Genome_build: TAIR10
Supplementary_files_format_and_content: Methratio output files were converted to bedGraphs via custom awk scripts and bedGraph files were converted to BigWig files via UCSC;s "bedGraphToWig" executable script.

organism: Arabidopsis thaliana

source_name: 10-day-old seedling

growth_protocol: Plants were grown on 1/2X MS agar (0.7%) for 10 days under long day conditions (16hrs light/8hrs dark). After 10 days of growth, whole seedlings were harvested and frozen in liquid nitrogen for DNA extraction for sequencing.

extract_protocol:
DNA extracted via CTAB method
Bisulfite-seq libraries were prepated as Pignatta, D. et al Bio-Protocols 2015.

treatment_protocol: (See Growth)

tag: ecotype


title: 17A020361_S14_L004

last: Wang


title: H466A_cmt3_4.fq.gz

description: Columbia-0 background with cmt3-11 mutation and H466A-FLAG transgene


title: 17A020344_S13_L004

value: Control


title: 17A020344F_S33_L004


title: A0401

value: M


title: H466A_cmt3_2.fq.gz

value: cmt3-11 mutation and H466A-FLAG transgene


title: 17A020343F_S32_L004


title: Col0.fq.gz

description: Columbia-0 background

value: wildtype


title: CMT3_cmt3_4.fq.gz

description: Columbia-0 background with cmt3-11 mutation and CMT3-FLAG transgene


title: 17A020343_S12_L004


title: MDA-MB-231 F2 [231-F2P3]

city: Washington

first: Jerry

last: Xiao

state: DC

address: 3900 Reservoir Rd NW, PCS Bldg, Room GR10C

department: Tumor Biology

institute: Georgetown University

description:
RNA sample of cultured, serially derived cell line
X.home.zubenlab.CTC.Project.STAR_alignments.231.F2P3.Resub_Aligned.out.bam

data_processing:
Base-calling was performed by Genewiz.
adapter were trimmed using cutadapt v2.6 -a CTGTCTCTTATA -A CTGTCTCTTATA -j 23 -q 30 -m 40
Reads were aligned to the human genome (Star Genecode v32) using STAR aligner v2.7.3a --runThreadN 23 --outSAMtype BAM Unsorted
reads were counted using feature counts in R annot.inbuilt='hg38' isPairedEnd = TRUE nthreads=23
Differential Expression was calculated using DESeq2 in R
Genome_build: GRCH38.p13
Supplementary_files_format_and_content: raw and normalized gene counts (CSV) created from DESeq2

source_name: MDA-MB-231 F2 Cell Line

growth_protocol: MDA-MB-231 cells were grown in M-2D conditions. MDA-MB-231 F1 and F2 subpopulations were serially derived from the ZTM model and propagated in vitro in M-2D conditions.

extract_protocol:
RNA was extracted using NEB Total RNA Miniprept Kit (#T2010)  kit following manufacturer protocol.
Clonetech SMARTer kit was used for conversion to cDNA from ulta-low input RNA. NEBNextUltra DNA library prep kit was then used to finish the library construction. Library contstructions were done through a third-party company, Genewiz. Libraries were read using an Illumina HiSeq 2x150 PE HO configuration.
Genewiz was consulted for the construction and preparation of all libraries.

tag: cell line

value: MDA-MB-231 F2

value: Triple Negative Breast Cancer cell line


title: 17A020342F_S31_L004

tag: group


title: cmt3.fq.gz

description: Columbia-0 background with cmt3-11 mutation

value: cmt3-11 mutation


title: A0301

value: HIV infected

value: untreated


title: 17A020340_S9_L004


title: 17A020345_S24_L004


title: 17A020340F_S29_L004


title: 17A020342_S11_L004


title: A0201

value: F


title: 17A020341_S10_L004


title: 17A020341F_S30_L004


title: MDA-MB-231 F1 [231-F1P2]

description:
RNA sample of cultured, serially derived cell line
X.home.zubenlab.CTC.Project.STAR_alignments.231.F1P2.Resub_Aligned.out.bam

source_name: MDA-MB-231 F1 Cell Line

value: MDA-MB-231 F1


title: A0501


title: 17A020338F_S28_L004


title: MDA-MB-231 Parental P18 [231-1-1]

description:
RNA sample of cultured cell line
X.home.zubenlab.CTC.Project.STAR_alignments.231.1.1_Aligned.out.bam

source_name: MDA-MB-231 Cell Line


title: 17A031068-M

data_processing:
Trim adapters and low-quality bases using TrimGalore version 0.6.5 with the following setting: default
Genome alignment using BSMAP version 2.90 with the following setting: -q 20 -f 5 -p 8 -r 0 -v 0.05 -s 16 -S 1 -n 0
Sorting bam file using  sambamba version 0.7.1
Extracting CpG site methylation information using MethylDackel version 0.5.0
Assembly: hg19
Supplementary files format and content: Tab-delimited text files including methylated counts and total counts for each CpG site


title: 17A031062-M


title: 17A020346F_S27_L004


title: 17A020338_S8_L004


title: 500621

city: Camperdown

first: Dario

last: Strbenac

state: NSW

address: City Road

department: School of Mathematics and Statistics

institute: University of Sydney

hyb_protocol: A thermal cycler is pre-heated to 67  C. Tagset and RNA samples are removed from a freezer and thawed at room temperature. The tubes are inverted to mix and then briefly spun down. A hybridization master mix is created by adding 70  L of hybridization buffer and 7  L of the Probe A working pool directly to the tube containing the Tagset. The solution is inverted several times to mix and spun down. 7 L of the Probe B working pool is added to the master mix. 8  L of master mix is added to each of the 12 strip tubes then 7  L of RNA sample is added to each tube. Strip tubes are inverted several times and flicked to increase mixing. The tunes are briefly spun and immediately placed in the pre-heated 67  C thermal cycler, incubated for 16 hours and then ramped down to 4  C.

scan_protocol: A high-density scan (encompassing 600 fields of view) was performed.

data_processing: Raw values.

label: Fluorescent barcode

source_name: melanoma patient

label_protocol: Batches of 12 separate samples at one time were prepared according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from 20 to 30mg of fresh frozen tissue. Tissue samples were homogenized using a high-speed agitation polytron blender (Kinematica, Luzern, Switzerland) in the presence of Trizol. The RNA was isolated and purified with an RNeasy purification kit (Qiagen RNeasy purification kit; Qiagen) with DNAse I digestion on the column. The quality of the RNA preparations was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA). RNA integrity scores were more than 8 for all the samples analysed.

value: Male

tag: age at banking (years)

tag: stage at banking

value: III

tag: time since metastasis (months)

tag: recurrence-free survival (months)

tag: recurrence-free category

value: melanoma


title: 17A031061-MF


title: 500401

tag: Sex

value: Poor

tag: tissue


title: 17A031061-M


title: 85272


title: 17A031068-MF

value: GDM


title: MDA-MB-231 Parental P15 [231-P15]

description:
RNA sample of cultured cell line
X.home.zubenlab.CTC.Project.STAR_alignments.231.P15.Resub_Aligned.out.bam

tag: cell type


title: 17A031067-M


title: 85178

value: Female


title: 17A031060-M


title: 17A031067-MF


title: AGS1_C

city: Lanzhou

first: Yehua

last: Li

state: Gansu

address: 967-Anning Road

department: College of Life Science

institute: Northwest Normal University

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequence reads were trimmed for adaptor sequence/reads containing N/low-quality sequence with Qphred<=20
Trimmed sequence reads were mapped to GRCh38/hg38 using HISAT2 genomic benchwork
Read count extraction and normalization were performed using HISAT2 genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Stomach

growth_protocol: AGS-1 and HGC-27 cells maintained in RPMI-1640 medium (Gibco, United States) containing 10% fetal bovine serum (Gibco, United States) and 1% penicillin/streptomycin at 37 °C in a humidified atmosphere containing 95% air and 5% CO2

extract_protocol:
Cells were collected directly into TRIzol and RNA was extracted using a QIAGEN RNeasy Mini Kit
10 ng of high-quality RNA (RNA integrity number, RIN > 8) was used to produce cDNA libraries using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s instructions

treatment_protocol: Isorhamnetinwere were used for treatment at 50μM for 24h

value: Stomach

value: AGS

value: Gastric adenocarcinoma cell

tag: genotype

value: WT


title: AGS1_I

value: isorhamnetin 50μM 24h


title: HGC27_I

value: Gastric carcinoma cell


title: HGC27_C


title: 46568


title: 56111


title: 17A031060-MF


title: 46330


title: 17A031058-MF


title: 45631 Replicate 2

value: Good


title: 17A031059-M


title: 17A031062-MF

value: Control


title: 45631 Replicate 1