title: ART Patient 01 ATACseq TEMRA CD4 T cells (2)

source_name: TEMRA CD4 T cells

tag: patient


title: xpo4-2 cpr5_2

status: Public on Jun 15 2020

type: SRA

city: Berkeley

first: Yangnan

last: Gu

state: CA

address: 371 Koshland Hall

department: Plant and Microbial Biology

country: USA

institute: University of California at Berkeley

library_source: transcriptomic

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Genome_build: TAIR 10
Supplementary_files_format_and_content: raw counts and normalized abundance measurements

molecule: total RNA

organism: Arabidopsis thaliana

source_name: xpo4-2 cpr5 double mutant_whole seedling

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 10-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: genotype

value: xpo4-2 cpr5 double mutant

tag: age

tag: tissue

value: whole seedlings


title: CG_C

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

country: China

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
Clean reads were obtained by removing contaminating reads, adapter sequences, poly-A tails and other artifacts.
Sequences reads were mapped to the G. biloba genome database downloaded from GigaDB using TopHat2 software with default parameters.
Gene abundances were quantified by RSEM, and the gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcriptper Million mapped reads) method.
Genome_build: GigaDB (http://gigadb.org/dataset/100209).
Supplementary_files_format_and_content: The tab-delimited text file include FPKM vaules of genes for each sample (gene_id, CG_A_fpkm, CG_B_fpkm,, CG_C_fpkm,, TG_A_fpkm,, TG_B_fpkm,, TG_C_fpkm)

organism: Ginkgo biloba

source_name: Control leaves

growth_protocol: The 5-years-old G. biloba trees (‘Fozhi’ cultivar) grown at the leaf-harvesting G. biloba nursery were used in this study, with sufficient light, well-drained and fertile soil, a fixed row spacing (0.6 m × 0.6 m).

extract_protocol:
The leaves of control and truncation treatment were used for RNA isolation. Total RNAs were extracted using TaKaRa MiniBEST plant RNA extraction kit (TaKaRa Bio Inc., Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 30 well-grown trees were cut into the short trunk at 85 cm height from the ground, and another 30  plants were regarded as control (without treatment).

tag: treatment

value: control leaves at leaf-harvesing stage

tag: organ

value: leaves


title: TG_B

source_name: Treatment leaves

value: truncation treatment (85 cm) leaves at leaf-harvesing stage


title: siUPF1 rep2

city: EDINBURGH

first: Kathryn

middle: Alexandra

last: Jackson-Jones

address: Institute of Genetics and Molecular Medicine, Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were pseudoaligned using kallisto v0.43.1 to kallisto index created by combining “all basic gene annotation” and “long non-coding RNA gene annotation” fasta files, downloaded from Gencode (www.gencodegenes.org/releases/current.html), Release 27 (GRCh38.p10). Kallisto was run with 100 bootstraps.
Differential gene expression was analysed using DESeq2 v1.14.1
Genome_build: hg38
Supplementary_files_format_and_content: kallisto output:  tab-delimited text files for each sample with RPKM values for each gene.

organism: Homo sapiens

source_name: HeLa cells

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Cat#NEB #E7103) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: samples were double depleted with siRNA pool against UPF1 or NBAS, or si-scr control

tag: cell line

value: HeLa

tag: knockdown


title: Activated-9hr-control-donor-207_S17

city: Cambridge

first: Ying-Lin Stefanie

last: Tan

state: MA

address: 1 Portland St

institute: Pfizer

data_processing:
UMI were generated using the QIASeq Tageted RNA Analysis Software
Reads were mapped to GRCh38 reference genome and alignment done using the STAR method.
Differential expression was calculated using the DESeq2 app in Illumina's Basespace Labs, according to the method described in Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. http://doi.org/10.1186/s13059-014-0550-8.
Genome_build: hg38

source_name: CD4+ T cells

growth_protocol: Primary human CD4+ T cells were isolated from frozen hPBMCs

extract_protocol:
RNA was extracted from frozen cell pellets using the Qiagen RNAeasy mini isolation kit, and 200ng RNA used in the construction of libraries.
Sequencing libraries were prepared using a Qiagen Targeted custom metabolic panel designed for the QiaSeq Target RNA kit, followed by Sw Illumina TruSeq Stranded mRNA Library Prep (cat.20020594) according to standard protocols.

treatment_protocol: Cells were activated for 24 hr in the presence of indicated treatment regimens, then washed and cell pellets flash frozen.

value: CD4+ T cells

tag: activation state

value: Activated

value: Water


title: ART Patient 01 ATACseq Naive CD4 T cells (2)

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

library_source: genomic

data_processing:
Reads were trimmed for adaptor sequence, then mapped to GRCh38 using bowtie2, duplicate fragments were then removed using Picard. Peaks were called using MACS2. For duplicated samples, peaks were merge using Bioconductor.
Genome_build: GRCh38
Supplementary_files_format_and_content: summits in BED

molecule: genomic DNA

source_name: Naive CD4 T cells

growth_protocol: Ex vivo PBMC from different patient cohorts were directed sorted and used for NGS.

extract_protocol:
DNA was treated with Tn5 and purified using Chip dna clean & concentrator
20,000 sorted cells were centrifuged at 1500 rpm for 10 min at 4°C in a pre-cooled fixed-angle centrifuge. All supernatant was removed and a modified transposase mixture (including 25 µl of 2x TD buffer, 1.5 µl of TDE1, 0.5 µl of 1% digitonin, 16.5 µl of PBS, 6.5 µl of nuclease-free water) was added to the cells and incubated in a heat block at 37°C for 30 min. Transposed DNA was purified using a ChIP DNA Clean & Concentrator Kit (Zymo Research #D5205) and eluted DNA fragments were used to amplify libraries.

treatment_protocol: There is no treatment for patient samples.

value: ART Patient 01

value: peripheral blood

tag: replicate

tag: cell type

value: Naive CD4 T cells


title: WT untreated rep3

city: Bloomington

first: David

middle: Peter

last: Giedroc

state: IN

address: 212 S. Hawthorne Drive

department: Chemistry

institute: Indiana University

description: geneCountsPrimary.xlsx

data_processing:
Demultiplexing of the reads was performed with bcl2fastq version 2.20.0 pipeline
Adapters and low quality bases were trimmed using Trimmomatic (version 0.36) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17
Reads were mapped to the transcriptome using Bowtie2 (version 2.3.4.3)
Reads mapped to transcripts were counted using Samtools (version version 1.9 ) and featureCounts (version 1.6.4)
R (version 3.6.0) and DESeq2 (version 1.24.0) were used to perform differential expresison analysis.
Genome_build: Acinetobacter_baumannii_atcc_17978.ASM1542v1.dna.chromosome.Chromosome.fa (ENSEMBL Release 43)
Supplementary_files_format_and_content: tab-delimited text file of raw count values for each Sample ...

organism: Acinetobacter baumannii

source_name: Exponentially grown cells

growth_protocol: Overnight cultures of A. baumannii 17978 were grown in LB medium overnight and used to inoculate 3mL LB medium at a 1:50 dilution and grown aerobically at 37°C with shaking at 200 rpm for 1 h. These cultures were then diluted 1:100 in fresh LB medium and grown under identical conditions until OD600=0.2.

extract_protocol:
Following growth and treatment, 10mL aliquots of cells were pelleted and resuspended in 1mL TriReagent (Molecular Research Center), then lysed with 0.1mm silica beads in a bead beater (MP Bio). RNA was extracted by adding 200 uL chloroform, mixing, and centrifuging. The aqueous layer was extracted and added to one volume of 70% ethanol. RNA purification was completeted using the RNeasy minikit (Qiagen).
First, the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. From each sample, 1ug of total RNA was used for ribosome RNA depletion with the Invitrogen™ RiboMinus™ Transcriptome Isolation Kit, bacteria.  After rRNA depletion, the libraries were prepared following the Illumina TruSeq Stranded mRNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads.

treatment_protocol: Sample 2 only

tag: strain


title: ChIP-seq_UTX_KO2_H3K36me3

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

data_processing:
ChIP-seq reads were aligned to the human GRCh38 reference genome (v33 from GENCODE) using Bowtie 2 (v.2.4.1) with default parameters. MACS (v.2.2.7.1) was used to call peaks (-g hs -q 0.01 -f BAM --fix-bimodal --extsize 200).
Genome_build: GRCh38

source_name: Human neurons from hESCs

growth_protocol: The human H9 (WA09) ESC line was obtained from Dr. Baoyang Hu at the Institute of Zoology, Chinese Academy of Sciences. H9 cells were cultured on Matrigel (BD, New Jersey, USA) using TeSR™-E8™ (STEMCELL Technologies, Vancouver, BC, Canada) and passaged with EDTA (100 μM). Neural differentiation of the H9 cells was initiated by the formation of embryoid bodies (EBs) as described previously with minor modifications (Jiang et al., 2013). Briefly, hESC colonies were dissociated with Accutase (BD, New Jersey, USA) and resuspended as single cells in E8 medium with 10μM Rock inhibitor （Y27632, Selleck, Shanghai, China）. To produce EBs from hESCs, hESCs medium was replaced with N2 medium（DMEMF/12, 1xN2, 1xNEAA) at day 3 and medium was changed every other day. To obtain NPCs derived from hESCs，the EBs were plated at day 7 on Matrigel-coated plates with 1μg/ml laminin (Life Technologies, Carlsbad, CA, USA) and cultured in N2 medium . NPCs in the form of rosettes were manually picked at day 14 and expanded as neurospheres in N2B27 medium (DMEM/F12, 1xN2, 1xB27, 0.2μM RA and 20ng/ml FGF2) until day 20. For neuronal differentiation, the dissociated NPCs at day 20 were plated onto poly-L-ornithine/laminin (50 μg/ml)-coated coverslips, and cultured in neuronal differentiation medium (DMEM/F12, 1xN2, 1xB27, 10ng/ml BDNF, 10ng/ml GDNF, 1mM dibutryrl-cyclic AMP and 200 nM ascorbic acid).

extract_protocol:
ChIP was performed according to published methods (Liu et al., 2010). Antibodies used were normal Rabbit IgG (Upstate, 12-370), rabbit H3K27me3 (Active Motif, 39155), rabbit H3K36me3 (Abcam, ab9050)
ChIP-seq libraries were from the d40 neurons. Chip sample QC was measured by BGISEQ-500.

treatment_protocol: We isolated hESCs-derived neurons at day 40 in culture. Total RNAs were extracted using TRIzol reagent, and sequenced on novaSeq 6000 system. ChIP was performed as described previously (Liu et al., 2010). ChIP-seq libraries were sequenced generating 50-bp single reads.

tag: passages

value: UTX-/-

tag: chip antibody

value: H3K36me3 (Abcam, ab9050)


title: Activated-6hr-control-donor-207_S13


title: xpo4-2 cpr5_1


title: ART Patient 01 ATACseq Naive CD4 T cells (1)


title: Activated-6hr-control-donor-44_S11


title: ChIP-seq_UTX_KO2_input

value: Normal Rabbit IgG (Upstate, 12-370)


title: ART Patient 01 ATACseq Effector memory CD4 T cells (2)

source_name: Effector memory CD4 T cells

value: Effector memory CD4 T cells


title: cpr5_2

source_name: cpr5 mutant_whole seedling

value: cpr5 mutant


title: cpr5_3


title: ChIP-seq_UTX_KO2_H3K27me3

value: H3K27me3 (Active Motif, 39155)


title: Activated-3hr-control-donor-207_S9


title: Activated-3hr-control-donor-44_S7


title: ART Patient 01 ATACseq Central memory CD4 T cells (2)

source_name: Central memory CD4 T cells

value: Central memory CD4 T cells


title: ChIP-seq_UTX_KO1_H3K27me3


title: KYSE150_siNC2 RNA-Seq

city: Los Angeles

first: Qian

last: Yang

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

data_processing:
ChIP-Seq pair-end 150bp reads were aligned to the hg19 reference genome using Bowtie2. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using STAR.
Adaptors were removed using Trim galore software. Each replicate, the raw reads were aligned to masked version of the reference human genome hg19.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

source_name: KYSE150_siNC2 RNA-Seq

growth_protocol: KYSE150 and TE5 cells are cultured in RPMI-1640 medium, media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL). The Anti-SREBF1 for ChIP-Seq is ProteinTech (lot: 14088-1-AP). The antibody number of KLF5 is sc-398409X from Santa Cruz company.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Total RNA was extracted by RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
Standard Illumina library preparation protocol

treatment_protocol: KYSE150 and TE5 cells knock-down SREBF1 with siRNA and negative control were generated by RNA deepsequencing, in triplicate, using Illumina GAIIx.

value: Esophageal Squamous cell carcinomas cell


title: ART Patient 01 ATACseq Central memory CD4 T cells (1)


title: cpr5_1

value: whole seedlings


title: xpo4-2_1

source_name: xpo4-2 mutant_whole seedling

value: xpo4-2 mutant


title: ART Patient 03 ATACseq Effector memory CD4 T cells (2)

value: ART Patient 03


title: xpo4-2_2


title: ΔbigR rep2

description: geneCountsPrimary.xlsx

tag: mutation

value: ΔbigR


title: ART Patient 01 ATACseq Effector memory CD4 T cells (1)


title: KYSE150_siNC1 RNA-Seq

source_name: KYSE150_siNC1 RNA-Seq


title: Col-0_3

source_name: wild type_whole seedling

value: wild type


title: KYSE150_siSREBF1_2 RNA-Seq

source_name: KYSE150_siSREBF1_2 RNA-Seq


title: ChIP-seq_UTX_KO1_input


title: ChIP-seq_WT_H3K27me3

value: Wild type


title: KYSE150_siSREBF1_1 RNA-Seq

source_name: KYSE150_siSREBF1_1 RNA-Seq


title: Col-0_2


title: si-eIF3e/si-ctrl replicate 1-2

type: RNA

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

description: Biological replicate 1 of 1 Cy3 vs 2 of 3 Atto

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and stored in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenPIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of  Cy3/Atto635 fluorescence signals were calculated for individual spots based on median fluorescence signal (background fluorescence subtraction).
3. Cy3 532/Atto635 ratios were normalized to Cy3 532/Atto635 values of tRNA standards (e.g. median Cy3 532/Atto635 ratios of the four tRNA standards E. coli tRNALys2, yeast tRNAAla5, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3 532/Atto635 ratios for individual blocks were averaged, representing final Cy3 532/Atto635 ratios; detailed protocol for  normalization using the dye control slide is published in: https://www.protocols.io/view/microarray-based-quantification-of-cellular-trnas-hfcb3iw or in : Dittmar KA, Mobley EM, Radek AJ, Pan T. (2004) Exploring the regulation of tRNA distribution on the genomic scale. J Mol Biol 12, 31-47

source_name: cultivated cells

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (4 pmol each; E. coli tRNALys2, E. coli tRNATyr2, yeast tRNAAla5, yeast tRNAPhe3) were added to 2 µg extracted total RNA prior to deacetylation.
2. For charging arrays total RNA was deacylated for 45 min at 37°C with 100 mM Tris-HCl (pH 9); For tRNA abundance arrays total RNA  was oxidized with periodate and thereafter treated for 45 min at 37°C with 100 mM Tris-HCl (pH 9) for tRNA deacetylation; tRNA standards were added prior teh deacyaltion step.
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 1h at RT in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol:
MCF-10a cells were cultured in DMEM/F12 medium with 0.5mg/mL hydrocortisone, 10µg/mL insulin, 20ng/mL EGF, 5% serum, 1X Pen/Strep, and incubate in 37℃ with 5% CO2.
Cell were grown independently for each biological experiment and checked frequently for mycoplasma contamination.

extract_protocol: Total RNA for total tRNA arrays was extracted using TriReagent (Sigma-Aldrich)  according to manufacturer's protocol

treatment_protocol: The cells were treated with 20nM si-control or si-eIF3e for 72h.

value: si-control

value: siRNA for eIF3e


title: ChIP-seq_UTX_KO1_H3K36me3


title: ChIP-seq_WT_input


title: si-eIF3e/si-ctrl replicate 1-1

description: Biological replicate 1 of 1 Cy3 vs 1 of 3 Atto


title: Col-0_1


title: si-eIF3e/si-ctrl replicate 2-3

description: Biological replicate 1 of 2 Cy3 vs 3 of 3 Atto


title: ChIP-seq_WT_H3K36me3


title: genomic DNA from 26R

status: Public on Jun 14 2020

type: genomic

city: New York

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

description: ADNP proband peripheral blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC Beadchip using standard Illumina protocol

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

data_processing: 862,927 probe sequences (50-mer oligonucleotides) were mapped to the reference human genome hg19 (NCBI37) using BSMAP, allowing up to 2 mismatches and 3 gaps, to retain uniquely mapped autosomal probes. We removed any probe that overlapped SNPs with MAF ≥5% identified by the 1000 Genomes Project within 5 bp upstream of the targeted CpG. Further, we removed probes with a detection p>0.01 in each individual. After filtering, we retained 820,167 autosomal probes, which were subjected to background correction, two color channel normalization and quantile normalization using the lumi package in R. The distributions of Infinium I and Infinium II probes were adjusted using BMIQ. Probes were then annotated based on their position relative to RefSeq genes using BEDTools v2.17. We defined promoter regions as ±2 kb from transcriptional start sites, gene body regions as transcription start to transcription end, and intergenic regions not annotated by the preceding categories. We also annotated individual CpG based on their overlap with CpG islands based on annotations in the UCSC genome browser, CpG shore (±2 kb of island), CpG shelf (±2 kb of shore), and CpG sea (regions outside the previous three categories).

label: Cy5 and Cy3

source_name: peripheral blood 26R

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using Gentra Puregene Blood Kit (Qiagen), Qiasymphony (Qiagen)  and the Masterpure DNA kit (Biozyme)

tag: gender

value: female

tag: sample type

value: peripheral blood

tag: disease state

value: ADNP proband

tag: disease state subtype

value: ADNP class 2


title: genomic DNA from 19A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 19A

tag: age


title: genomic DNA from 9A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 9A

value: male

value: ADNP class 1


title: genomic DNA from 25R

description: ADNP proband peripheral blood sample

source_name: peripheral blood 25R


title: genomic DNA from 18S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 18S


title: genomic DNA from 15A_sib

description: Control peripheral blood sample

source_name: peripheral blood 15A_sib

value: Control


title: genomic DNA from 30A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 30A


title: genomic DNA from 14S_sib1

description: Control peripheral blood sample

source_name: peripheral blood 14S_sib1


title: genomic DNA from 39A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 39A


title: genomic DNA from 24S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 24S


title: genomic DNA from 14S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 14S


title: genomic DNA from 15A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 15A


title: genomic DNA from 22S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 22S


title: genomic DNA from C19

description: Control peripheral blood sample

source_name: peripheral blood C19


title: genomic DNA from 23S_sib3

description: Control peripheral blood sample

source_name: peripheral blood 23S_sib3


title: genomic DNA from 24S_sib

description: Control peripheral blood sample

source_name: peripheral blood 24S_sib


title: genomic DNA from 1S_sib2

description: Control peripheral blood sample

source_name: peripheral blood 1S_sib2


title: genomic DNA from 43A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 43A


title: genomic DNA from 8A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 8A


title: genomic DNA from 23S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 23S


title: genomic DNA from 3S_sib

description: Control peripheral blood sample

source_name: peripheral blood 3S_sib


title: genomic DNA from 18S_sib

description: Control peripheral blood sample

source_name: peripheral blood 18S_sib


title: genomic DNA from 14S_sib2

description: Control peripheral blood sample

source_name: peripheral blood 14S_sib2


title: genomic DNA from 3S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 3S


title: genomic DNA from 23S_sib1

description: Control peripheral blood sample

source_name: peripheral blood 23S_sib1


title: genomic DNA from 22S_sib

description: Control peripheral blood sample

source_name: peripheral blood 22S_sib


title: genomic DNA from C18

description: Control peripheral blood sample

source_name: peripheral blood C18


title: genomic DNA from 1S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 1S


title: genomic DNA from 1S_sib1

description: Control peripheral blood sample

source_name: peripheral blood 1S_sib1


title: genomic DNA from 23S_sib2

description: Control peripheral blood sample

source_name: peripheral blood 23S_sib2


title: S-12

city: Wuerzburg

first: Susanne

last: Berger

address: Julius-von-Sachs-Platz 2

department: Pharmaceutical Biology

institute: Julius-von-Sachs-Institute

description: Gene expression, treatment 4 h 75 µM sulforaphane

hyb_protocol: hybridization was conducted as described in the Agilent one-color microarray-based gene expression analysis protocol

scan_protocol: Slides were scanned on the Agilent Microarray Scanner with extended dynamic range (XDR) at high resolution (5 μm)

data_processing:
Data sets were extracted by feature extraction software package (v11.5.1.1/ Agilent Technologies) using a standard protocol (GE1_1105_Oct12)
normalization was performed using the neqc function of the Limma package

source_name: 4 h 75 µM sulforaphane replicate 3

label_protocol: 200 ng total RNA were labeled using the one-color RNA spike-in kit (v5.0.1, 2006; Agilent)

growth_protocol: Col-0 seedlings were grown in MS medium with 3 % sucrose in 9 h light 15 h dark

extract_protocol: RNA extraction was performed using  Trizol (Invitrogen) and purified by NucleoSpin RNA clean up (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: 10 d old seedling were treated with 75 µM of sulforaphane, benzylisothiocyanate or prostaglandine A1 and harvested after 4 h

tag: tissue

value: seedling

tag: cultivar


title: M-3

description: Gene expression mock treated

source_name: 4 h mock (0,5% methanol) replicate 3


title: B-7

description: Gene expression, treatment 4 h 75 µM benzylisothiocyanate

source_name: 4 h 75 µM benzylisothiocyanate replicate 1


title: genomic DNA from 17S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 17S


title: genomic DNA from 12S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 12S


title: genomic DNA from 33S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 33S


title: B-9

description: Gene expression treatment 4 h 75 µM benzylisothiocyanate

source_name: 4 h 75 µM benzylisothiocyanate replicate 3


title: genomic DNA from 5S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 5S


title: PANC-1 Ctrl

city: Shanghai

first: Ling

last: Tian

state: Shanghai

address: No. 650, New Songjiang Road

department: Institute of Translational Medicine

institute: Shanghai General Hospital

description: rRNA depleted

data_processing:
Basecalls performed using CASAVA version 1.8
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36).
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results.
Gene expression values of the transcripts were computed by StringTie (version 1.3.3b). DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples.
Functional enrichment analyses including Gene Ontology (GO) was performed to identify which DEGs were significantly enriched in GO terms or metabolic pathways. GO terms with false discovery rate (q-value) <0.05 were considered as significantly altered.
Genome_build: Homo_sapiens.GRch38
Supplementary_files_format_and_content: .xls file includes raw reads, and normalized data (FKPM)

source_name: pancreatic cancer cell line PANC-1

growth_protocol: Pancreatic cell line PANC-1 was cultured with DMEM medium with 10% FBS. Pancreatic cell line SW1990 was cultured with 1640 medium  with 10% FBS.

extract_protocol:
Total RNA was extracted using the Trizol reagent (Life technology) according to the manufacturer's protocol.
A total amount of 2 μg RNA per sample was used for construction of the sequencing libraries with VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

treatment_protocol: 10Gy X-ray radiation was used to treat pancreatic cancer cell lines

value: Pancreatic cancer cell line

tag: passage

tag: treatment

value: unirradiated


title: genomic DNA from 17S_sib

description: Control peripheral blood sample

source_name: peripheral blood 17S_sib


title: P-4

description: Gene expression, treatment 4 h 75 µM prostaglandine A

source_name: 4 h 75 µM prostaglandine A replicate 1


title: genomic DNA from 40S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 40S


title: S-11

source_name: 4 h 75 µM sulforaphane replicate 2


title: SW1990 Rad

description: rRNA depleted

source_name: pancreatic cancer cell line SW1990

tag: cell line

value: irradiated


title: PANC-1 Rad

description: rRNA depleted


title: M-2

description: Gene expression mock treated

source_name: 4 h mock (0,5% methanol) replicate 2


title: Eso26_HNF4A Chip-seq

data_processing:
Single-end 49bp or pair-end 150bp reads were aligned to the hg19 reference genome using Bowtie. RNA-seq reads were trimmed for adaptor sequence, and then mapped to hg19 whole genome using Bowtie2. 4C-seq analysed using R package r3CSeq.
Adaptors were removed using Trim galore software. Each replicate, the raw reads were aligned to masked version of the reference human genome hg19 in 4C analysis.
PCR duplicate reads were removed using Picard MarkDuplicates in Chip-seq
Blacklist regions were removed using ENCODE blacklist file in Chip-seq
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

source_name: Eso26_HNF4A Chip-seq

growth_protocol: Eso26 cells are cultured in RPMI-1640 medium, media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL), and the Anti-HNF4A for ChIP-Seq is Abcam (lot: ab41898), Anti-GATA4-Flag for ChIP-Seq is Sigma (lot: F1804).

value: Esophageal Adenocarcinoma cell line

value: Anti-HNF4A  (Abcam; ab41898)


title: Eso26_GATA4-Flag Chip-seq

source_name: Eso26_GATA4-Flag Chip-seq

value: Anti-GATA4-Flag (Sigma; F1804)


title: genomic DNA from 34A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 34A


title: genomic DNA from C14

description: Control peripheral blood sample

source_name: peripheral blood C14


title: P-6

source_name: 4 h 75 µM prostaglandine A replicate 3


title: exosomal HCC mixed pool 2

city: Beijing

first: Jingyi

last: Cao

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
We first evaluated RNA-seq reads quality with FastQC (version 0.11.5). Then we removed adapters from the 3’ end of the reads by using cutadapt (version 1.16) with the parameter setting of: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
Next, trimmed reads were mapped to the human reference rRNA and removed rRNAs using Bowtie2 (version 2.2.9) with the following parameter setting: -norc, --sensitive-local, --no-unal.
The human genome sequence was downloaded from Ensembl (Homo sapiens GRCh38/hg38). The unmapped reads from the rRNA alignment step were sequentially aligned to human miRNAs, piRNAs, Y RNAs, srpRNAs, tRNAs, snoRNAs, snRNAs, vaultRNAs, lncRNAs, mRNAs and TUCP by using Bowtie2 with the following parameter setting: -norc, --sensitive-local, --no-unal.
We divided transcripts into 30bp bins with 15bp overlap and counted reads for each bin of each transcript. Raw read counts of each bin were counted by using featureCounts (Version 1.5.2). Differential expression analysis was done by Wilcoxon rank sum test and edgeR (Version 3.20.9)
Genome_build: hg38
Supplementary_files_format_and_content: tab-limited text file for raw counts

source_name: HCC exosome

extract_protocol:
We collected peripheral whole blood samples (5-10mL) from participant patients in K2EDTA tubes.  the blood cells were removed and the supernatant plasma was obtained. The plasma was then centrifuged at high speed of 14,000×g for 1 minute at 4°C, and the supernatant was got. Within 2 hours after blood sampling, we separated the plasma into 1mL centrifugation tubes and stored at -80°C. The cfRNA was isolated from plasma using ZYMO Quick-cfRNA Serum & Plasma kit (Catalog No. R1059) with a modified protocol.
We used NEBNext® Multiplex Small RNA Library Prep Set to construct the small RNA libraries and Illumina HiSeq X10 sequencing platform to sequence libraries

tag: subject status

value: hepatocellular carcinoma (HCC) patient

value: mixed

tag: tumor size


title: genomic DNA from C13

description: Control peripheral blood sample

source_name: peripheral blood C13


title: genomic DNA from C11

description: Control peripheral blood sample

source_name: peripheral blood C11


title: genomic DNA from 6S

description: ADNP proband peripheral blood sample

source_name: peripheral blood 6S


title: genomic DNA from C4

description: Control peripheral blood sample

source_name: peripheral blood C4


title: genomic DNA from C5

description: Control peripheral blood sample

source_name: peripheral blood C5


title: S-10

source_name: 4 h 75 µM sulforaphane replicate 1


title: genomic DNA from C12

description: Control peripheral blood sample

source_name: peripheral blood C12


title: genomic DNA from C10

description: Control peripheral blood sample

source_name: peripheral blood C10


title: genomic DNA from C1

description: Control peripheral blood sample

source_name: peripheral blood C1


title: Eso26-control2 RNA-seq

tag: cell type

tag: genotype/variation

value: control


title: genomic DNA from 12S_sib

description: Control peripheral blood sample

source_name: peripheral blood 12S_sib


title: genomic DNA from C17

description: Control peripheral blood sample

source_name: peripheral blood C17


title: genomic DNA from C16

description: Control peripheral blood sample

source_name: peripheral blood C16

value: female


title: M-1

description: Gene expression mock treated

source_name: 4 h mock (0,5% methanol) replicate 1


title: genomic DNA from C9

description: Control peripheral blood sample

source_name: peripheral blood C9

value: peripheral blood


title: Eso26-control1 RNA-seq


title: Sample_1498_202

data_processing:
Illumina adapter sequences were trimmed from all fragmented reads using TrimGalore (options –paired –illumina) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
All high-quality trimmed reads were mapped to UCSC Homo sapiens reference genome (build hg37) using default STAR v2.4.0 parameters.
Samtools was used to convert bamfiles to samfiles and featureCounts was used to quantify gene expression levels for each individual sample using default paired-end parameters.
Genome_build: hg37/hg19
Supplementary_files_format_and_content: Raw count data were generated with featureCounts and are provided as a separate matrix.

source_name: Leukocytes (PaxGene Tubes)

extract_protocol:
RNA was extracted and purified in accordance with the PAX gene RNA kit per manufacterer's instructions. Globin mRNA was depleted from samples using GLOBINclear - Human Kit (Life Technologies, USA).
RNA libraries were prepared for sequencing using stranded Illumina Tru-Seq protocols using the Illumina HiSeq 2000.

value: Peripheral blood

tag: group/diagnosis

value: Unaffected sibling

tag: batch

tag: rin

tag: family id


title: exosomal HCC mixed pool 1

tag: gender


title: Eso26-siHNF4AB2 RNA-seq

value: HNF4A knockdown


title: exosomal normal mixed pool 2

source_name: Normal exosome

value: healthy donor


title: Eso26-siHNF4AB1 RNA-seq


title: Sample_1498_201


title: exosomal normal mixed pool 1


title: 8-6d_S43_L007_R1_001

city: Carbondale

first: Bryan

middle: Manyasi

last: Musungu

state: IL

address: 1125 Lincoln Dr.

department: Plant Biology

institute: Southern Illinois University Carbondale

data_processing:
Reads were trimmed with CLC Genomics Work Bench
Reads were mapped with CLC Genomics Work bench
Unique read counts and RPKM were extracted from the abundance measurements
Genome_build: B73 RefGen_V3 5b+ and Aspergillus_flavus.JCVI-afl1-v2.0.35
Supplementary_files_format_and_content: RPKM and read counts

organism:
Zea mays
Aspergillus flavus

source_name: Kernel

growth_protocol: B73 was hand planted in Clayton NC.  At about 20 days after pollination, husks were pulled back and kernels were pin bar inoculated with 3357. Husks were placed back over the ear, secured with a rubber band, bagged and the bag was stapled around the stalk.  Kernels were harvested over time at 0h, 4h, 6h, 12h, 18h, 24h, 30h, 36h, 42h, 48h, 3d, 4d, 5d and 6d.  Each time course was harvested from a single plot. There were 8 plots (8 reps).

extract_protocol:
Eight kernels per ear were ground and used for RNA isolation. Approximately one hundred milligrams of ground tissue was homogenized (Virtis) in Saturated Phenol, pH 6.6 (Fisher) for 2 min. Samples were then dissolved in Tris EDTA buffer, pH 8.0 (ACROS Organics), purified with 5:1 Acid Phenol: Chloroform, pH 4.5 (Fisher), and precipitated with ice-cold 100% ethanol (ACROS Organics) overnight. Total RNA was purified again with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The quality and concentration of RNA was analyzed using an RNA Pico chip on an Agilent Bioanalyzer.
libraries for sequencing utilizing the NEBNext Ultra Directional RNA Library Prep Kit

treatment_protocol: A. flavus NRRL 3357, was grown on potato dextrose agar (PDA) and collected from plates by 0.05% (v/v) Triton X-100. The time course study was performed by pin bar inoculating one ear (per time point) of maize B73 with A. flavus NR3357 and harvesting at 0, 6, 12, 18, 24, 30, 36, 42, 48, 72, 96,120 and 144 hours post inoculation.

tag: strain

value: Kernel

value: Milk stage

value: innoculated with Aspergillus flavus

tag: timepoint


title: genomic DNA from C7

description: Control peripheral blood sample

source_name: peripheral blood C7

tag: sample type

tag: disease state

value: Control

tag: age

tag: disease state subtype


title: 7-6d_S21_L003_R1_001

tag: tissue

tag: treatment


title: genomic DNA from C2

description: Control peripheral blood sample

source_name: peripheral blood C2


title: Sample_1497_201

value: male


title: genomic DNA from C6

description: Control peripheral blood sample

source_name: peripheral blood C6


title: 6-6d_S35_L005_R1_001


title: chronic hepatitis B mixed pool 3

source_name: chronic hepatitis B patients plasma

tag: subject status

value: chronic hepatitis B patient


title: Sample_1488_202


title: 5_6d_S14_L002_R1_001


title: genomic DNA from 38A

description: ADNP proband peripheral blood sample

source_name: peripheral blood 38A

value: ADNP proband

value: ADNP class 2


title: 4-6d_S14_L002_R1_001


title: chronic hepatitis B mixed pool 2

tag: tumor size


title: Sample_1488_201

tag: cell type


title: 2-6d_S15_L003_R1_001


title: 1_6d_S33_L005_R1_001


title: 3-6d_S29_L005_R1_001


title: SW1990 Ctrl

description: rRNA depleted

source_name: pancreatic cancer cell line SW1990

value: Pancreatic cancer cell line

tag: cell line

tag: passage

value: unirradiated


title: genomic DNA from C15

description: Control peripheral blood sample

source_name: peripheral blood C15


title: Sample_1481_202

tag: group/diagnosis

tag: batch


title: 8-5d_S42_L007_R1_001


title: 7-5d_S20_L003_R1_001


title: P-5

source_name: 4 h 75 µM prostaglandine A replicate 2

value: seedling

tag: cultivar


title: Normal10

source_name: Normal plasma

tag: gender

value: M


title: 6-5d_S34_L005_R1_001

tag: strain


title: Sample_1480_202

tag: rin

tag: family id


title: Normal8

value: F


title: 4-5d_S13_L002_R1_001

tag: timepoint


title: chronic hepatitis B mixed pool 1

value: mixed

tag: age


title: Normal9


title: Sample_1480_201

value: Peripheral blood

value: female


title: 2-5d_S14_L003_R1_001


title: 3-5d_S28_L005_R1_001


title: Sample_1476_202


title: 1_5d_S32_L005_R1_001


title: 8-4d_S41_L007_R1_001


title: Sample_1481_201

value: Unaffected sibling


title: Normal6

value: healthy donor


title: Sample_1476_201


title: 6-4d_S33_L005_R1_001

value: Kernel

value: Milk stage


title: Sample_1451_204


title: Normal5


title: 5_4d_S12_L002_R1_001

value: innoculated with Aspergillus flavus


title: 4-4d_S12_L002_R1_001


title: genomic DNA from C3

description: Control peripheral blood sample

source_name: peripheral blood C3

tag: sample type

value: peripheral blood

tag: disease state

value: Control

tag: disease state subtype


title: Normal4

tag: subject status


title: 3-4d_S27_L005_R1_001

tag: tissue

tag: treatment


title: Sample_1451_203

tag: cell type


title: B-8

source_name: 4 h 75 µM benzylisothiocyanate replicate 2


title: 5_5d_S13_L002_R1_001


title: 2-4d_S13_L003_R1_001


title: Sample_1451_202

value: male


title: genomic DNA from C8

description: Control peripheral blood sample

source_name: peripheral blood C8


title: 1_4d_S31_L005_R1_001


title: Normal3

tag: tumor size


title: 8-3d_S40_L007_R1_001


title: Sample_1451_201

tag: group/diagnosis


title: 7-3d_S18_L003_R1_001


title: Normal1


title: 6-3d_S32_L005_R1_001


title: 5_3d_S11_L002_R1_001


title: Sample_1440_203

tag: batch


title: 4-3d_S11_L002_R1_001


title: HCC30

source_name: HCC plasma

value: hepatocellular carcinoma (HCC) patient


title: 3-3d_S26_L005_R1_001


title: 7-4d_S19_L003_R1_001


title: HCC29


title: 1_3d_S30_L005_R1_001


title: 2-3d_S12_L003_R1_001


title: Sample_1435_203


title: HCC28


title: 7-48h_S17_L003_R1_001


title: 8-48h_S39_L007_R1_001


title: Normal2


title: 6-48h_S31_L005_R1_001


title: Sample_1435_202


title: Sample_1498_203


title: HCC27


title: 4-48h_S10_L002_R1_001


title: 3-48h_S25_L005_R1_001


title: HCC26


title: HCC25


title: Sample_1411_202


title: 2-48h_S11_L003_R1_001


title: Sample_1411_203


title: Sample_1420_201


title: HCC24


title: 8-42h_S38_L007_R1_001


title: Sample_1440_202


title: Sample_1411_201


title: 7-42h_S16_L003_R1_001


title: HCC23


title: 6-42h_S30_L005_R1_001


title: 5_42h_S9_L002_R1_001


title: Sample_1409_203


title: 5_48h_S10_L002_R1_001


title: 4-42h_S9_L002_R1_001


title: Sample_1409_202


title: HCC21


title: 3-42h_S24_L005_R1_001


title: 1_42h_S28_L005_R1_001


title: 8-36h_S37_L007_R1_001


title: 2-42h_S10_L003_R1_001


title: HCC20


title: 1_48h_S29_L005_R1_001


title: Sample_1409_201


title: 6-36h_S29_L005_R1_001


title: Sample_1368_202


title: HCC19


title: 7-36h_S15_L003_R1_001


title: Sample_1368_201


title: 5_36h_S8_L002_R1_001


title: HCC18


title: 3-36h_S23_L005_R1_001


title: Sample_1360_201


title: 4-36h_S8_L002_R1_001


title: 2-36h_S9_L003_R1_001


title: HCC17


title: 1_36h_S27_L005_R1_001


title: HCC22


title: Sample_1349_202


title: HCC16


title: 7-30h_S50_L008_R1_001


title: Sample_1334_203


title: 6-30h_S28_L004_R1_001


title: 5_30h_S7_L001_R1_001


title: Sample_1334_202


title: HCC15


title: HCC14


title: Sample_1334_201


title: 2-30h_S8_L002_R1_001


title: HCC13


title: 8-24h_S35_L006_R1_001


title: Sample_1327_202


title: 1_30h_S26_L004_R1_001


title: HCC12


title: Sample_1327_201


title: 7-24h_S49_L008_R1_001


title: HCC11


title: 6-24h_S27_L004_R1_001


title: 5_24h_S6_L001_R1_001


title: 4-24h_S6_L001_R1_001


title: 8-30h_S36_L006_R1_001


title: 3-24h_S21_L004_R1_001


title: HCC10


title: 1_24h_S25_L004_R1_001


title: HCC9


title: 2-24h_S7_L002_R1_001


title: 3-30h_S22_L004_R1_001


title: 4-30h_S7_L001_R1_001


title: HCC8


title: 8-18h_S34_L006_R1_001


title: HCC7


title: 7-18h_S48_L008_R1_001


title: MCF7_UNT_rep3

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

description: Gene expression data from untreated MCF7 cells grew at the same time and kept in the same conditions as the treated ones

hyb_protocol: Labeled samples were hybridized to the Clariom_S_Human Genome Array (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions (Affymetrix; www.affymetrix.com/).

scan_protocol: The GeneArrays were scanned using the Affymetrix GeneChip Scanner (Affymetrix) using standard NASC protocols.

data_processing: Raw data from the microarrays was normalized at probe-level using RMA algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using command console.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 human breast carcinoma cells were cultured in RPMI medium without phenol red (Invitrogen) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and grown in T75 culture flasks at 37oC in a 5% CO2 atmosphere.

extract_protocol: Total cellular RNA was extracted from un-transfected cells, cells featuring knock-down and cells transfected with ON-TARGETplus Non-targeting Control siRNAs (Dharmacon) using TRIzol (Thermo Fisher Scientific) following the manufacturer's instructions.

treatment_protocol: To knock-down gene expression, MCF-7 cells were incubated for 48 hours with transfection media containing DharmaFect1 (Dharmacon) transfection reagent and ON-TARGET plus SMARTpool siRNA (Dharmacon) against STAG2. ON-TARGETplus Non-targeting siRNA (Dharmacon) was used as a negative control and siGLO controls (Dharmacon) for transfection optimisation experiments.

tag: cell line

tag: knockdown


title: 5_18h_S5_L001_R1_001

tag: strain


title: 4-18h_S5_L001_R1_001


title: 3-18h_S20_L004_R1_001


title: 2-18h_S6_L002_R1_001


title: HCC6

tag: gender


title: MCF7_UNT_rep2


title: HCC5


title: HCC4


title: 7-12h_S47_L008_R1_001


title: MCF7_STAG2_siRNA_rep3

description: Gene expression data from  MCF7 cells treated with 0.025 µm ON-TARGETplus Human STAG2 siRNA pool (Dharmacon)

value: STAG2 siRNA


title: MCF7_UNT_rep1


title: HCC2


title: 6-18h_S26_L004_R1_001


title: 4-12h_S4_L001_R1_001


title: 3-12h_S19_L004_R1_001


title: RNA-Seq ndt80pch2 rep2

city: Dortmund

first: Richard

last: Cardoso da Silva

state: North Rhine Westfallen

department: Mechanistic Cell Biology

institute: Max Planck Institute of Mol Physiol

description:
4h in SPO (ndt80Δ)
ndt80pch2_csv

data_processing:
Basecalls performed using (CLC Genomics Workbench 10)
Raw reads were firstly examined and quality trimmed using the FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were filtered and mapped to the S288c genome assembly R64 (sacCer3) using Hisat2 (Version 2.1.0), with default parameter settings. Analyses and quantification of transcripts was performed using the HTSeq (Version 0.9.1) and DESeq2 (2.11.40.6), respectively. Number of mapped reads and comparison of transcripts expression level were estimated using TPM (Transcripts Per Million fragments) values. The log2 fold changes of transcripts (TPM) was used to estimate differential expression levels. Transcripts with –log10 of P-value > 2 and log2 fold changes ≥ or ≤ 2.0 were considered as significantly differentially expressed
Genome_build: SacCer3
Supplementary_files_format_and_content: csv file (TPM)

organism: Saccharomyces cerevisiae

source_name: RNA-Seq ndt80pch2 rep2

growth_protocol: Cells were patched from glycerol stocks onto YPG plates and grown overnight. Patched cells were transferred to YPD and further grown overnight. Cells were cultured in liquid YPD at 23°C overnight and diluted at OD600 0.3 into pre-sporulation media (BYTA; phthalate-buffered yeast extract, tryptone and acetate). Cells were grown in BYTA for 16-18 hours at 30°C, washed twice in water and resuspended in sporulation media (0.3% KAc) at OD600 1.9 to induce meiosis. Sporulation cultures were grown at 30°C

extract_protocol:
110 mL of yeast undergoing meiosis at 4h (OD600 1.9) was harvested at 1000g for 5 min at 4C. Cells were washed with ice-cold TE buffer and mechanically lysed with glass beads. Samples were centrifuged for 2 min at full speed and transferred to a new microcentrifuge tube. 1mL of 70% ethanol was added to the homogenized lysate. Total RNA was then extracted and purified using the RNeasy RNA isolation Kit (Qiagen), including treatment with DNase. RNA was quantitated with Quantifluor (Promega). Enrichment of mRNA, library preparation and sequencing was performed by the Max Planck-Genome Centre, Cologne. Briefly, rRNA was depleted using the Ribo-zero rRNA removal kit (Epicentre). mRNA was enriched using oligo-dT beads (New England Biolabs).
Preparation of paired-end sequencing libraries was performed using the Illumina TruSeq ChIP library preparation kit Set-A (15034288),  according to the manufacturer’s guidelines. Ligation products were size-selected (250-300 bp) and purified from a 2% low-melting agarose gel using the MinElute Gel Extraction Kit (Qiagen). Ampure XP beads (Agilent) were used for cleanup steps and size selection. The final purified product was quantitated using Picogreen in a QuantiFluor dsDNA System (Promega). Paired-end sequencing (2 X 150bp) was performed on the Illumina HiSeq 3000 platform
and the cDNA library was prepared using the TrueSeq RNA sample preparation kit (Illumina) according to the manufacturer´s instructions. Samples were then sequenced on an Illumina HiSeq-3000 instrument.

value: cells undergoing meiosis in sporulation medium

tag: passages

value: 4h in SPO (ndt80delta)


title: Normal7


title: 2-12h_S5_L002_R1_001

tag: timepoint


title: 6-12h_S25_L004_R1_001

tag: age


title: HCC3


title: HCC1

value: M


title: MCF7_STAG2_siRNA_rep1


title: MCF7_STAG2_siRNA_rep2


title: 1_18h_S24_L004_R1_001


title: 8-12h_S33_L006_R1_001


title: MCF7_NONT_siRNA_rep2

description: Gene expression data from  MCF7 cells treated with 0.025 µm ON-TARGETplus Non-targeting siRNA

value: non-targeting siRNA


title: RNA-seq ndt80pch2 rep1

description:
4h in SPO (ndt80Δ)
ndt80pch2_csv

source_name: RNA-seq ndt80pch2 rep1


title: Rad B2

description: exosome-derived total RNA

data_processing:
Basecalls were performed using CASAVA version 1.8
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs
The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch
The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were filtered through Fold change. Ddifferentially expressed miRNA between two groups were filtered by Fold Change and P-value.
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx files include tag reads, and normalized data (TPM), etc.

source_name: pancreatic cancer cell-derived exosomes

growth_protocol: Pancreatic cell lines PANC-1, MIA PaCa-2 and BxPC-3 were cultured with DMEM medium (Dulbecco’s Modified Eagle Medium, HyClone) with 2% FBS (Fetal Bovirne Serum with exosome depleting). SW1990 was cultured with 1640 medium (Roswell Park Memorial Institute-1640, HyClone) with 2% FBS(Fetal Bovirne Serum with exosome depleting).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Life technology) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols, and ~150 bp PCR amplicons (corresponding to ~22nt miRNAs) were selected

treatment_protocol: 10Gy X-radiation treatment was used for generating dying tumor cells. Exosomes were purified from the conditioned media using differential ultracentrifugation. Centrifugation was performed at 300 g, 2,000 g and 10,000 g to remove the live cells, dead cells and cell debris, respectively. The supernant was further purified using 0.22um filters. The crude extract of exosomes was obtained by ultracentrifugation (100,000 g). And the pallet was washed using PBS to remove the contaminated protein.

value: pancreatic cancer cell lines

value: mixture of PANC-1, SW1990, BxPC-3, MIA PaCa-2

tag: cell compartment

value: exosome

value: irradiated


title: 7-6h_S46_L008_R1_001

source_name: Kernel


title: 8-6h_S32_L006_R1_001


title: 6-6h_S24_L004_R1_001


title: 1_12h_S23_L004_R1_001


title: Rad B1

description: exosome-derived total RNA


title: RNA-seq ndt80 rep2

description:
4h in SPO (ndt80Δ)
ndt80_csv

source_name: RNA-seq ndt80 rep2


title: 5_12h_S4_L001_R1_001


title: 5_6h_S3_L001_R1_001


title: RNA-seq ndt80 rep1

description:
4h in SPO (ndt80Δ)
ndt80_csv

source_name: RNA-seq ndt80 rep1


title: Ctrl A2

description: exosome-derived total RNA

value: unirradiated


title: MCF7_NONT_siRNA_rep1


title: 4-6h_S3_L001_R1_001

value: Kernel


title: 3-6h_S18_L004_R1_001

value: Milk stage


title: Ctrl A1

description: exosome-derived total RNA


title: 1_6h_S22_L004_R1_001

value: innoculated with Aspergillus flavus


title: 2-6h_S4_L002_R1_001


title: MCF7_NONT_siRNA_rep3


title: 7-4h_S45_L008_R1_001


title: 6-4h_S23_L004_R1_001


title: 5_4h_S2_L001_R1_001


title: Input xxChIP rep2

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

institute: University of Essex

description: Input xxChIP rep2

data_processing:
Genome_build: hg19
BED files with MUSIC-defined peaks

growth_protocol: The human myeloid leukemic cell line HL-60/S4 (ATCC, CRL-3306) was maintained in RPMI-1640 medium plus 10% FCS and 1% Pen/Strep/Glut.  Cells were grown in 6 ml of medium in T-25 flasks, generally split (1:6-1:12) 2-3 times/week.  For large scale preps, cells were grown in T-75 flasks with up to 30 ml media.  Cell concentrations were monitored using a hemocytometer. Rabbit polyclonal ChIP-Grade antibodies were obtained from Abcam: anti-histone H1.2 (ab4086) and anti-H1.5 (ab18208).  Both antibodies are directed against antigenic determinants within the N-terminal 1-100 aa residues.

extract_protocol:
For both single-fixation and double-fixation ChIP (xChIP and xxChIP, see Fig. 1), chromatin was disrupted with a Covaris Focused Ultrasonicator M220.  In xChIP, each frozen cell pellet (1 cryovial) was dispersed in 130 µl of Covaris Sonication Buffer (1 mM EDTA, 10 mM Tris [pH 7.6], 0.1 % SDS), followed by sonication (20 min, 200 cycles, 75 Watts, Duty Cycle 20%, 7oC).  The sonicates were centrifuged at 18,000xg, 10 min, 40C and the supernatants recovered.  SDS was reduced in the supernatants to ~0.003% and replaced with 0.05% Tween-20, employing repeated dilution with PBST (PBS+0.05% Tween-20) and centrifugal concentration using a Centricon YM-50.  Six centrifugations of ~1/2 dilutions with PBST at 1000xg, 10 min resulted in ~0.5 ml of the final retentate with reduced SDS.  IgG-free BSA (Sigma A3294) was added to a final BSA concentration of 5%.
All ChIP-Seq experiments were performed on undifferentiated HL-60/S4 cells that were fixed, permeabilized and stored in cryovials (containing ~107 cells/cryovial) in liquid Nitrogen.  Cells had been harvested from growth medium at ~106 cells/ml, centrifuged and washed with PBS, fixed in 1% HCHO/PBS for 10 min at RT, stopped with 0.125 M glycine for 5 min, washed with PBS, followed by PBS + 0.1 M PMSF.  The fixed cells were permeabilized for 10 min at 4oC in a lysis buffer containing 25 mM HEPES buffer (pH 7.8), 1 mM MgCl2, 10mM KCl, 0.1% NP40, 1 mM DTT and 0.5 mM PMSF.  Following centrifugation and removal of supernatants, cell pellets were frozen in residual lysis buffer at liquid Nitrogen temperature. For both single-fixation and double-fixation ChIP (xChIP and xxChIP, see Fig. 1), chromatin was disrupted with a Covaris Focused Ultrasonicator M220.  In xChIP, each frozen cell pellet (1 cryovial) was dispersed in 130 µl of Covaris Sonication Buffer (1 mM EDTA, 10 mM Tris [pH 7.6], 0.1 % SDS), followed by sonication (20 min, 200 cycles, 75 Watts, Duty Cycle 20%, 7oC).  The sonicates were centrifuged at 18,000xg, 10 min, 40C and the supernatants recovered.  SDS was reduced in the supernatants to ~0.003% and replaced with 0.05% Tween-20, employing repeated dilution with PBST (PBS+0.05% Tween-20) and centrifugal concentration using a Centricon YM-50.  Six centrifugations of ~1/2 dilutions with PBST at 1000xg, 10 min resulted in ~0.5 ml of the final retentate with reduced SDS.  IgG-free BSA (Sigma A3294) was added to a final BSA concentration of 5%. In xxChIP, the once-fixed frozen cell pellets were dispersed in a buffer reminiscent of the permeabilizing buffer used in immunostaining reactions (0.1% Triton X-100, 0.1 mM PMSF plus Sigma Protease Inhibitor Cocktail [P8340]) for 20 min at RT.  After PBS washes, the permeabilized cells were suspended in PBST+5% IgG-free BSA (PBSTB) and rotated for 90 min at RT.  To 300 µl aliquots containing ~6x107 cells, the primary antibody was added: 30 µl anti-histone H1.2 (1 mg/ml) or 60 µl anti-histone H1.5 (0.5 mg/ml).  The cells plus antibody were rotated for 4 hours at RT.  Following antibody incubation, the cells were washed several times with PBS to remove unbound antibody.  They were made 1% HCHO/PBS for the second fixation and rotated 2.5 minutes at RT.  Fixation was stopped with 0.125 M glycine for 5 min, cells washed with PBS and dispersed in 1.0 ml of Covaris Sonication Buffer (1 mM EDTA, 10 mM Tris [pH 7.6], 0.1 % SDS), followed by sonication at optimized conditions (40 min, 400 cycles, 75 Watts, Duty Cycle 26%, 7oC).  The sonication buffer was replaced with PBST, employing centrifugal concentration, as described above.
Library preparation was performed by the DKFZ sequencing facility following a standard Illumina protocol
Illumina NEBNext Ultra

tag: antibody

value: no antibody

tag: experiment

value: xxChIP, no treatment


title: Input xxChIP rep3

description: Input xxChIP rep3


title: 4-4h_S2_L001_R1_001


title: 2-4h_S3_L002_R1_001


title: 3-4h_S17_L004_R1_001


title: 1_4h_S21_L004_R1_001


title: 8-0h_S30_L006_R1_001

value: Control


title: Input xChIP rep1

description: Input xChIP rep1

value: xChIP, no treatment


title: Input xChIP rep2

description: Input xChIP rep2


title: Input xChIP rep3

description: Input xChIP rep3


title: 6-0h_S22_L004_R1_001


title: 5_0h_S1_L001_R1_001


title: 3-0h_S16_L004_R1_001


title: 4-0h_S1_L001_R1_001


title: 7-0h_S44_L008_R1_001


title: 2-0h_S2_L002_R1_001


title: 1_0h_S20_L004_R1_001


title: xxChIP H1.5 rep2

description:
xxChIP H1.5 rep2
XXChIP_H1.5.bed.tdf
XXChIP_H1.5.bed


title: 8-4h_S31_L006_R1_001


title: xxChIP H1.5 rep1

description:
xxChIP H1.5 rep1
XXChIP_H1.5.bed.tdf
XXChIP_H1.5.bed


title: xxChIP H1.2 rep3

description:
xxChIP H1.2 rep3
XXChIP_H1.2.bed.tdf
XXChIP_H1.2.bed


title: IV_AZ_if rep1

city: Dusseldorf

first: Anna

last: Sergeeva

address: Universitaetsstrasse 1

department: Institute of Botany

institute: Heinrich Heine University

data_processing:
Basecalls were performed and demultiplexed using bcl2fastq2.
Sequenced reads were trimmed for adapter sequence and masked for low-complexity or low-quality sequence, then mapped to theArabis_alpina.MPIPZ.V5 reference transcriptome using kallisto.
TSV files with TPM (transcripts per million) values were generated using kallisto.
Average insert length information was extracted from the command line output of kallisto.
Genome_build: Arabis_alpina.MPIPZ.V5
Supplementary_files_format_and_content: TSV files were generated using kallisto. Besides normalized TPM values they contain counts and length information.

organism: Arabis alpina

source_name: lateral stem

growth_protocol: Plants were grown on potting soil (Vermehrungssubstrat, Stender GmbH, Schermbeck, Germany) with a humidity of 70 % in a plant growth chamber (Percival Scientific, CLF Plant Climatics) under controlled long-day conditions (16 h light and 8 h dark, at 20 °C).

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer‘s instructions, including DNase I digestion via the RNase-Free DNase Set to remove traces of genomic DNA (Qiagen, Hilden, Germany).
Libraries were constructed with the Illumina TruSeq® Stranded mRNA Library Prep kit (Illumina Technologies). Double-stranded cDNA was purified for end repair, adaptor ligation, and DNA fragment enrichment.

tag: genotype

value: perpetual flowering 1-1 (pep1-1)

value: whole internode from the AZ in close proximity to the formed inflorescence of the lateral stem from 1st and 2nd node of the main axis

value: 30 weeks


title: IV_AZ_if rep2

tag: tissue


title: IV_AZ_if rep3


title: IV_AZ_si rep4

value: whole short internode from the AZ of the lateral stem from 1st and 2nd node of the main axis


title: Input xxChIP rep1

description: Input xxChIP rep1


title: xxChIP H1.2 rep2

description:
xxChIP H1.2 rep2
XXChIP_H1.2.bed.tdf
XXChIP_H1.2.bed


title: IV_AZ_si rep1


title: IV_AZ_si rep3


title: xxChIP H1.2 rep1

description:
xxChIP H1.2 rep1
XXChIP_H1.2.bed.tdf
XXChIP_H1.2.bed


title: IV_PZ rep3

value: whole 1st internode from the PZ of the lateral stem from 1st and 2nd node of the main axis


title: IV_PZ rep2


title: xxChIP H1.5 rep3

description:
xxChIP H1.5 rep3
XXChIP_H1.5.bed.tdf
XXChIP_H1.5.bed


title: xChIP H1.5 rep3

description:
xChIP H1.5 rep3
XChIP_H1.5.bed.tdf
XChIP_H1.5.bed


title: IV_PZ rep1


title: III_PZ rep3

value: 7 weeks


title: xChIP H1.5 rep2

description:
xChIP H1.5 rep2
XChIP_H1.5.bed.tdf
XChIP_H1.5.bed


title: III_PZ rep1


title: xChIP H1.5 rep1

description:
xChIP H1.5 rep1
XChIP_H1.5.bed.tdf
XChIP_H1.5.bed


title: TNseq dlon rep2

city: Amherst

first: Rilee

middle: D

last: Zeinert

address: 240 Thatcher Way

institute: UMass Amherst

data_processing:
Library strategy: Tn-seq
Base calling was done via Illumina Nextseq 500.
RNAseq: Reads were mapped to the Caulobacter NA1000 genome using BWA, sorted with Samtools and the resulting BAM files were used as input with bedtools map and a bedfile consisting of the all gene features to count the number of reads per gene
Tnseq:, single end 75 base reads were first demultiplexed by index, each library was concatenated and the molecular modifier added in the second PCR was clipped using Je (Girardot et al., 2016). Clipped reads were mapped to the Caulobacter crescentus NA1000 genome (NCBI Reference Sequence: NC_011916.1) using BWA (Li and Durbin, 2010), sorted with Samtools (Li et al., 2009). Duplicate transposon reads introduced by PCR were removed using Je (Girardot et al., 2016) and indexed with Samtools (Li et al., 2009). For ease of data visualization, the 5’ insertion sites of each transposon were converted to a wiggle file (.wig) and visualized using Integrative Genomics Viewer (IGV) (Robinson et al., 2011). Specific hits for each library were determined by calculating per position numbers of 5' sites for unique inserts across the entire genome using bedtools (Quinlan and Hall, 2010) genomecov, then counting the number of unique 5' insertions within the middle 80% of each gene using custom bedfiles with truncated ORFs and bedtools map. For statistical comparison, a quasi-likelihood F-test (glmQLFit) from the edgeR package in the Bioconductor suite (Robinson et al., 2009) was used to determine the false discovery rate adjusted p-values.
Genome_build: Caulobacter vibrioides NA1000
Supplementary_files_format_and_content: tab-delimited text files include counts for wt and dlon samples.
Supplementary_files_format_and_content: Wig files of insertion distributions for wt and dlon libraries for visualization.

organism: Caulobacter vibrioides NA1000

source_name: Bacterial cells

growth_protocol: Grown in PYE medium.

extract_protocol:
See methods for details. RNAseq was rRNA depleted with Ribozero from Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols. Tnseq was prepared by arbitrary priming and counting.

treatment_protocol: No special treatments.

tag: growth

value: exponential

value: outgrowth

value: Lon delete


title: II_PZ rep3

value: 5 weeks


title: xChIP H1.2 rep3

description:
xChIP H1.2 rep3
XChIP_H1.2.bed.tdf
XChIP_H1.2.bed


title: TNseq dlon rep1


title: IV_AZ_si rep2


title: HuFLT1_CD117lo HC_4

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

description: T1 human fetal liver

hyb_protocol: Biotinylated single stranded sense cDNA is then hybridized to GeneChip® HumanGene2.0ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the Fluidic Station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V21 was used for annotation.

source_name: First trimester (T1) human fetal liver

label_protocol: 2 ng of total RNA is reverse transcribed following the Ovation Pico System V2 (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

extract_protocol: RNeasy Plus Micro Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: CD34+CD38-CD45+CD117hi (HSC) and CD34+CD38-CD45+CD117lo (HC) populations were sorted from first trimester and second trimester fetal livers.

tag: source tissue

value: Liver

tag: developmental stage

value: First trimester

tag: cell population

value: Sorted CD117lo HC


title: HuFLT1_CD117hi HSC_4

description: T1 human fetal liver

value: Sorted CD117hi HSC


title: xChIP H1.2 rep2

description:
xChIP H1.2 rep2
XChIP_H1.2.bed.tdf
XChIP_H1.2.bed


title: II_PZ rep2


title: II_PZ rep1


title: HuFLT1_CD117lo HC_3

description: T1 human fetal liver


title: HuFLT2_CD117lo HC_2

description: T2 human fetal liver

source_name: Second trimester (T2) human fetal liver

value: Second trimester


title: TNseq WT rep1

value: wild type


title: I_PZ rep3

value: 4 weeks


title: HuFLT1_CD117hi HSC_3

description: T1 human fetal liver


title: RNAseq dlon rep2

data_processing:
Base calling was done via Illumina Nextseq 500.
RNAseq: Reads were mapped to the Caulobacter NA1000 genome using BWA, sorted with Samtools and the resulting BAM files were used as input with bedtools map and a bedfile consisting of the all gene features to count the number of reads per gene
Tnseq:, single end 75 base reads were first demultiplexed by index, each library was concatenated and the molecular modifier added in the second PCR was clipped using Je (Girardot et al., 2016). Clipped reads were mapped to the Caulobacter crescentus NA1000 genome (NCBI Reference Sequence: NC_011916.1) using BWA (Li and Durbin, 2010), sorted with Samtools (Li et al., 2009). Duplicate transposon reads introduced by PCR were removed using Je (Girardot et al., 2016) and indexed with Samtools (Li et al., 2009). For ease of data visualization, the 5’ insertion sites of each transposon were converted to a wiggle file (.wig) and visualized using Integrative Genomics Viewer (IGV) (Robinson et al., 2011). Specific hits for each library were determined by calculating per position numbers of 5' sites for unique inserts across the entire genome using bedtools (Quinlan and Hall, 2010) genomecov, then counting the number of unique 5' insertions within the middle 80% of each gene using custom bedfiles with truncated ORFs and bedtools map. For statistical comparison, a quasi-likelihood F-test (glmQLFit) from the edgeR package in the Bioconductor suite (Robinson et al., 2009) was used to determine the false discovery rate adjusted p-values.
Genome_build: Caulobacter vibrioides NA1000
Supplementary_files_format_and_content: tab-delimited text files include counts for wt and dlon samples.
Supplementary_files_format_and_content: Wig files of insertion distributions for wt and dlon libraries for visualization.


title: III_PZ rep2

value: perpetual flowering 1-1 (pep1-1)


title: siz1-2_BS

city: West Lafayette

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
MethylC-Seq： For data analysis, data were trimmed using trimmomatic with  parameter "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". Clean reads were mapped to Arabidopsis thaliana TAIR 10 genome using BSMAP with parameter "-m 0 -x 1000  -w 2", and python script of BSMAP was used to remove potential PCR duplicates and extract methylation ratios.
Genome_build: TAIR10
Supplementary_files_format_and_content: For MethylC-Seq: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

source_name: 14-day-old seedlings

growth_protocol: Seedlings were grown on 1/2 MS medium with 1% sucrose and 0.5% agar

extract_protocol: Genomic DNA was extracted from 14-day-old seedlings using the DNeasy Plant Maxi Kit (Qiagen, 68163) and sent to the Genomics Core Facilities of the PSC (Shanghai Center for Plant Stress Biology, Shanghai, China) for bisulfite treatment. Libraries were prepared for sequencing according to the manufacturer’s (Illumina) instructions and sequenced on an Illumina Hiseq 2500 platform.

value: siz1-2 mutant

value: seedlings


title: RNAseq dlon rep1


title: HuFLT1_CD117lo HC_2

description: T1 human fetal liver


title: RNAseq WT rep2


title: HuFLT2_CD117hi HSC_2

description: T2 human fetal liver


title: Asynchronous ESCs

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: Interphase

data_processing:
Basecalls performed using CASAVA 2.17
ATAC-seq data was processed using the nf-core atacseq pipeline version 1.1.0 (doi: 10.5281/zenodo.3529420)
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalised bigwig files were generated using BEDTools (version 2.27.1) and bedGraphToBigWig (version 4) by scaling to 1 million mapped reads

organism: Mus musculus

source_name: E14Tg2a mouse embryonic stem cells

growth_protocol: Gelatin, 15% FCS, 1000 U/ml LIF

extract_protocol: llumina Tagment DNA TDE1 Kit

tag: cell type

value: mouse embryonic stem cells (ESCs)

tag: sample type

value: Asynchronous ESCs


title: HuFLT1_CD117hi HSC_2

description: T1 human fetal liver


title: TNeq WT rep2


title: xChIP H1.2 rep1

description:
xChIP H1.2 rep1
XChIP_H1.2.bed.tdf
XChIP_H1.2.bed

tag: cell line

value: xChIP, no treatment


title: RNAseq WT rep1

tag: strain

value: exponential


title: Metaphase arrested ESCs

value: Metaphase arrested ESCs


title: 4C seq_HNF4A_promoter_bait2

source_name: 4C seq_HNF4A_promoter_bait

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Total RNA was extracted by RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
Standard Illumina library preparation protocol

value: Esophageal Adenocarcinoma cell line


title: 4C seq_HNF4A_promoter_bait1


title: I_PZ rep2

value: whole 1st internode from the PZ of the lateral stem from 1st and 2nd node of the main axis


title: MI 3 day rep 4

status: Public on Jun 13 2020

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads were mapped with BWA-ALN. Reads that mapped equally well to multiple loci in the reference genome were excluded
The first read of each readpair contains the cell barcode of the CELseq2 protocol and the UMI
The second read of each readpair was mapped to the reference genome
Per gene, all mapped reads containing the same cellular barcode and a different UMI in the first read were aggregated to obtain final readcounts
The cell barcodes that are used in the data are depicted in the tab names "Cellular Barcode"
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Readcounts of genes in cells are present in a matrix format, with rows being genes and columns being cells. Readcount tables are in .tsv format

molecule: polyA RNA

source_name: MI 3day

growth_protocol: Mouse were kept unde normal housing conditions

extract_protocol:
Single cardiac cells were collected according to a protocol of Gladka et al. (Circulation, 2018). cDNA preparation was performed using the SORT-seq protocol (Muraro et al., Cell Systems, 2016).  cDNA libraries were obtained by dispersion of the RT enzyme and second strand mixes with the Nanodrop II liquid handling platform (GC biotech).
Illumina sequencing libraries were prepared using the TruSeq small RNA primers (Illumina).

treatment_protocol: All mice underwent a myocardial infarct (MI) surgery. MI was performed by  permanent ligation of the left anterior descending (LAD) artery.

value: Cardiac (left ventricle - infarcted region)

tag: treatment

value: myocardial infarct (MI) surgery

value: 8 weeks

tag: Sex

value: Male


title: MI 3 day rep 3


title: MI 3 day rep 1


title: I_PZ rep1


title: MI 3 day rep 5


title: HuFLT1_CD117lo HC_1

description: T1 human fetal liver

value: Liver

value: First trimester

value: Sorted CD117lo HC


title: Flow-purified metaphase ESC chromosomes

description: Chromosomes

value: Flow-purified metaphase ESC chromosomes


title: e2240_mut_VSMC_PDGF_3

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to mm10 with hisat2 software then raw counts were computed with featureCounts for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes  REFSEQ isoform id,  raw counts and fpkm values for each transcript, in each sample

growth_protocol: Dermal fibroblasts (DF) and aortic vascular smooth muscle cells (VSMC) were isolated from two Stat1+/- mice (wt) and two Stat1-/- mice (mut) at 4-6 weeks of age. Cells were grown in DMEM + 10% fetal bovine serum (FBS), 2mM L-glutamine, and 2mM penicillin/streptomycin.

extract_protocol:
RNA was isolated using RNAeasy kit (Qiagen)
Illumina Truseq Stranded mRNA with Library Prep kit was used according to the manufacturers' protocol. Briefly, mature mRNA was enriched usingh beads coated with oligo‐dT homopolymers. The mRNA molecules were then chemically fragmented and the first strand of cDNA was generated using random primers. Following RNase digestion, the second strand of cDNA was generated replacing dTTP in the reaction mix with dUTP. Double stranded cDNA then underwent adenylation of 3' ends following ligation of Illumina‐specific adapter sequences. Subsequent PCR enrichment of ligated products further selected for those strands not incorporating dUTP, leading to strand‐specific sequencing libraries. Final libraries for each sample were assayed on the Agilent Tapestation for appropriate size and quantity. These libraries were then pooled in equimolar amounts as ascertained via fluorometric analyses.

treatment_protocol: At passage 2, the cells were serum-starved for 24 hours in DMEM + 0.05% FBS. Then cells were treated with 30ng/mL PDGF-BB for 1 hour, or left untreated.

tag: cell

value: VSMC (vascular smooth muscle)

value: PDGF-BB


title: e2242_wt_VSMC_PDGF_1


title: HuFLT2_CD117lo HC_1

description: T2 human fetal liver

value: Second trimester


title: e2234_mut_VSMC_PDGF_2


title: e2232_wt_VSMC_PDGF_0


title: HuFLT2_CD117hi HSC_1

description: T2 human fetal liver

value: Sorted CD117hi HSC


title: HuFLT1_CD117hi HSC_1

description: T1 human fetal liver


title: e2234_mut_VSMC_2

value: untreated


title: e2240_mut_VSMC_3


title: e2234_mut_DF_PDGF_2

value: DF (dermal fibroblasts)


title: e2232_wt_VSMC_0


title: e2242_wt_VSMC_1


title: e2242_wt_DF_PDGF_1


title: e2234_mut_DF_2


title: e2240_mut_DF_PDGF_3


title: e2232_wt_DF_PDGF_0


title: MI 3 day rep 2

tag: age


title: D0 Treg, D5/10/15 ex-Treg

city: Leuven

first: Susan

middle: M

last: Schlenner

address: Herestraat 49

department: Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

description: multiplexed sample

data_processing:
The raw data were processed thought BD Rhapsody pipeline. All steps in details are documented here: https://scomix.bd.com/hc/article_attachments/360048823252/23-21713-01_Rhapsody_Bioinfo_Handbook-ruo.pdf,
Briefly, the raw data were filtered from low quality reads based on average Phred score <20. R1 reads were used to determine the cell entity and molecule count. R2 reads were aligned to BD custom reference to define mRNA origin. Information about cell label, molecule and mRNA target was combined from R1 and R2. The molecule count was corrected by applying RSEC and DBEC correction for all genes that reached sequencing saturation >4. The residual cell labels were filtered based on cumulative number of mRNA reads in cells.
Genome_build: BD custom reference file
Supplementary_files_format_and_content: csv files generated by BD Rhapsody pipeline, expression matrix with molecule counts per gene/per cell index, sample tag call file with anotated name of sample per cell index

source_name: splenocytes + lymph nodes pooled

extract_protocol:
At day 5, day 10 and day 15 recipient mice were euthanized and spleen and lymp nodes were processed and FACS sorted for ex-Treg. As a control ex vivo Treg on day 0 were sorted from Foxp3YFP-Cre Rosa26 fl STOP fl RFP mice. Next, samples were stained using the with sample tag antibodies (BD Single-Cell Multiplexing Kit, BD biosciences). Afterwards, samples were pooled and stained using the following oligonucleotide-conjugated antibodies according to manufacturing instructions: anti CD25 (PC61), anti-CD44 (IM7), anti-CD62L (MEL-14), anti-GITR (DTA-1), anti-CD4 (RM4-5), anti TCR (H57-597), anti CD69 (H1.2F3), anti TIGIT (1G9), anti CD95 (Jo2), anti CD122 (TM 1β), anti Tim-3 (5D12), anti CCR7 (4B12), anti CD103 (M290), anti CD279 (J43), anti CD274 (MIH5), anti CD233 (C9B7W), anti CD71 (C2), anti CD278 (7E7G9), anti ITGB7 (M293), anti CD137 (1AH2), anti CD40 (3/23), anti CD3 (145-2C) from BD Biosciences. Single-cell capture and cDNA library preparation was performed using the BD Rhapsody Single-cell analysis system (BD Biosciences)
Library was constructed accordingly to BD's instruction (Doc ID: 214508 Rev 3.0). Briefly, captured mRNA were amplified with with a custom primer panel and with specific primer for the BD AbSeq and Sample tag antibodies. The Sample Tag and BD AbSeq PCR products were separated from the mRNA targeted PCR products by double-sided size selection with Agencourt® AMPure® XP magnetic beads. The BD AbSeq and Sample Tag PCR products underwent a separate index PCR from mRNA products with library index primers. BD Rhapsody™ mRNA targeted PCR products and Sample Tag PCR products underwent a second PCR amplification followed by an index PCR with library index primers.

treatment_protocol: Treg of Foxp3 YFP-Cre Rosa26 fl-STOP-fl RFP mice and naïve T cells of congenically disparated mice were sorted and adoptively transferred into Rag1-KO mice.

tag: strain name

value: Foxp3-YFP-Cre Rosa26 flSTOPfl RFP

tag: gender

value: male


title: e2232_wt_DF_0


title: e2242_wt_DF_1


title: e2240_mut_DF_3


title: T47D_Dose_HypoPolII_Veh_45mins_ChIP-seq

city: Chicago

first: Hari

last: Singhal

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

description: ChIP-seq

data_processing:
Chilin pipeline at CFCE, DFCI was used to perform RNA-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
The output from Bowtie2 (BAM files) was subjected to MACS14 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets.
genome build: HG19
BED files

source_name: T47D cells

growth_protocol: Cells were grown in DMEM supplemented with 8% fetal bovine serum (FBS) and 1% penicillin streptomycin.

extract_protocol:
ChIP-seq libraries were prepared using Kapa ChIP-seq kits.
Details of library preparation strategy are provided in the materials and methods section (ChIP and ChIP-seq) of the paper.

treatment_protocol:
Prior to experiments, cells were cultured for 48 hours in phenol red free media supplemented with 0.1% charcoal-stripped FBS and 1% penicillin streptomycin (steroid-deprived media). R5020 (PerkinElmer #NLP004005MG) dissolved in ethanol (vehicle) was used at a final concentration as mentioned in the manuscript.
Hormone-treated were harvested and ChIP was performed as per the directions provided in materials and method (ChIP and ChIP-sequencing)

tag: tissue type

value: T47D cells

tag: er/pr/her2 status

value: ER+ PR+

tag: drug treatment

value: Vehicle

tag: hormone exposure time

value: 45 mins

tag: protocol

value: ChIP-seq

tag: antibody

value: Anti-hypophosphorylated Pol II SC-56767 (Santa Cruz), 8WG16, Lot#K0711


title: T47D_Dose_HypoPolII_Low_45mins_ChIP-seq

description: ChIP-seq


title: T47D_Dose_HypoPolII_High_45mins_ChIP-seq

description: ChIP-seq


title: T47D_Dose_PR_KD68_Veh_45mins_ChIP-seq

description: ChIP-seq

value: anti-PR KD68 (Greene, Mol. End. 1988)


title: T47D_Dose_PR_KD68_High_45mins_ChIP-seq

description: ChIP-seq


title: T47D_Dose_PR_SC_High_45mins_ChIP-seq

description: ChIP-seq

value: Anti-PR SC-7208, Lot#B1115


title: T47D_Dose_PR_KD68_Low_45mins_ChIP-seq

description: ChIP-seq


title: T47D_Dose_Ser294_Low_45mins_ChIP-seq

description: ChIP-seq

value: anti-phospho-PR Ser294 (from Dean Edwards, Baylor College of Medicine)


title: T47D_Dose_PR_SC_Veh_45mins_ChIP-seq

description: ChIP-seq


title: T47D_Dose_PR_SC_Low_45mins_ChIP-seq

description: ChIP-seq


title: T47D_10nM_High_24h_RNA-seq 2

description:
mRNA-seq
Cuff_Counts_Patients15928M,16165M,6209M and T47D

data_processing:
VIPER pipeline at CFCE, DFCI was used to perform RNA-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using STAR.
Relative expression of transcripts were calculated by subjecting STAR output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
genome build: HG19
Fold induction relative to vehicle treatments is presented.

extract_protocol:
Hormone-treated cells were homogenized and total RNA was extracted using Qiagen RNAeasy kit
PolyA tail selection was performed on 250 ng of total RNA. RNA-seq libraries were prepared using NEBNext kit.
Details of library preparation strategy are provided in the materials and methods section (RNA expression and RNA-sequencing) of the paper.

treatment_protocol:
Prior to experiments, cells were cultured for 48 hours in phenol red free media supplemented with 0.1% charcoal-stripped FBS and 1% penicillin streptomycin (steroid-deprived media). R5020 (PerkinElmer #NLP004005MG) dissolved in ethanol (vehicle) was used at a final concentration as mentioned in the manuscript.
Patient tumor samples and all relevant clinical information were obtained from women undergoing breast surgeries at Burnside Private Hospital, Adelaide (approval numbers: H-065-2005; H-169-2011). The collected tissue samples were processed within an hour of surgeries and they were cultured via three-dimensional ex-vivo explant methodologies as previously described. Briefly, sliced pieces of tumors were incubated on gelatin sponges for 24 hours in regular RPMI media. Representative pieces of tumors were in parallel fixed in 4% formalin and subsequently immunohistochemistry was performed to assess the status of tumors for ER and PR protein. In parallel, apportioned tumors were treated with vehicle, 0.1nM, 1 nM or 10 nM R5020 for 24 hours prior to being subjected to RNA extraction. To study the transcriptome changes in response to hormone treatments, sequencing libraries were made from the RNA extracted from each of the treated tissue samples and next generation sequencing was performed.

value: 24 hours

value: Cell models and patient tumors RNA-seq


title: 1T47D_Vehicle_24h_RNA-seq 2


title: T47D_0.1nM_Low_24h_RNA-seq 2


title: T47D_Dose_Ser294_Veh_45mins_ChIP-seq

description: ChIP-seq


title: T47D_Dose_Ser294_High_45mins_ChIP-seq

description: ChIP-seq


title: T47D_0.1nM_Low_24h_RNA-seq 1


title: T47D_Vehicle_24h_RNA-seq 1

source_name: Patient tumor explant


title: Patient_6209M_R5020_10nM_High_24h_RNA-seq

value: Patient tumor explant

value: ER+ PR- HER2-


title: Patient_6209M_R5020_Vehicle_24h_RNA-seq


title: Patient_16165M_R5020_10nM_High_24h_RNA-seq


title: Patient_6209M_0.1nM_Low_24h_RNA-seq


title: Patient_6209M_R5020_1nM_Mid_24h_RNA-seq


title: Patient_15928M_R5020_10nM_High_24h_RNA-seq


title: Patient_16165M_Low_24h_RNA-seq


title: MCF7_10nM_High_24h_RNA-seq 2

description:
mRNA-seq
Cuff_Counts_Patients15832M,16094M,16099M and MCF7

source_name: MCF7 cells

value: MCF7 cells

value: ER+/PR+


title: Patient_15928M_R5020_0.1nM_Low_24h_RNA-seq


title: Patient_15928M_Vehicle_24h_RNA-seq


title: T47D_10nM_High_24h_RNA-seq 1


title: MCF7_0.1nM_Low_24h_RNA-seq 2


title: 1MCF7_0.1nM_Low_24h_RNA-seq


title: MCF7_10nM_High_24h_RNA-seq 1


title: MCF7_Vehicle_24h_RNA-seq 2


title: MCF7_Vehicle_24h_RNA-seq 1


title: Patient_16099M_Vehicle_24h_RNA-seq

value: ER+ PR+ HER2-


title: Patient_16099M_R5020_1nM_Mid_24h_RNA-seq


title: Patient_16099M_R5020_0.1nM_Low_24h_RNA-seq


title: Patient_16094M_R5020_0.1nM_Low_24h_RNA-seq


title: Patient_16094M_R5020_1nM_Mid_24h_RNA-seq


title: Patient_16094M_Vehicle_24h_RNA-seq


title: Patient_15832M_R5020_10nM_High_24h_RNA-seq


title: Patient_16099M_R5020_10nM_High_24h_RNA-seq


title: Patient_15928M_R5020_1nM_Mid_24h_RNA-seq


title: Patient_15832M_Vehicle_24h_RNA-seq


title: Patient_16094M_R5020_10nM_High_24h_RNA-seq


title: HFD islets exosomes_S02

city: Nanjing

first: Yi

last: Sun

address: Tianyuandong Road 818

institute: Nanjing medical university

description: exosome  miRNA

data_processing:
perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content of the clean data were calculated.
miRNA expression levels were estimated for each sample:1) sRNA were mapped back onto the precursor sequence.2) Readcount for each miRNA was obtained from the mapping results.
We used miRBase v21 annotation in our analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: abundance in xlsx format

source_name: exosomes

growth_protocol: Islets were isolated from normal control diet with 4% fat (NCD) or high-fat diet with 60% fat (HFD) mice and cultured in a serum-exosomes-free culture media for one week.

extract_protocol:
Total RNA was extracted from exosomes obtained by ultracentrifugating the collected cultivate supernatant
Sequencing libraries were generated using NEBNextR UltraTM small RNA Sample Library Prep Kit for IlluminaR(NEB, USA) following manufacturer’s recommendations

treatment_protocol: Cultivate supernatant was collected everyday.

tag: tissue

value: islets-derived exosomes

value: High fat diet (HFD)


title: NCD islets exosomes_S01

description: exosome  miRNA

value: normal chow diet (NCD)


title: Patient_15832M_R5020_1nM_Mid_24h_RNA-seq


title: Patient_15832M_R5020_0.1nM_Low_24h_RNA-seq


title: US84403582_252680610521_S01_GE1_107_Sep09_1_1_Naive_Young_Lung_day 0_19

city: Tokyo

first: Yoshihiro

last: Kawaoka

address: 4-6-1, Shirokanedai, Minato-ku

department: Department  of  Microbiology  and  Immunology

country: Japan

institute: University of Tokyo

hyb_protocol: hybridized  to  the   Rhesus  Macaque   Gene Expression    Microarray

scan_protocol: Specific antigen–antibody reactions were  visualized with  DAB staining  by  using  the  DAKO  Envision  system

data_processing: Statistical analysis was performed using the  LIMMA  package.  The  log2of  the  intensity  of  each  probe  was  background  corrected  and normalized   between   arrays   (using   the   quantile   method).   Duplicate   probes   were   averaged. Hierarchical  clustering  was  used  to  review  biological  replicate  quality.  One-way  or  two-way ANOVA were  constructed  and  the  moderated  t-statistic  was  calculated  to  determine  the  significance between  the  means.  The  duplicateCorrelation  function  was  used  to  control  for  multiple  samples from  the  same  animal.  All pvalues  were  Benjamini-Hochberg  (BH)  corrected  to  control  the  false discovery rate (FDR). Probes were considered differentially expressed (DE) if they had a fold change ≥ 2 and an FDR < 0.01.

organism: Macaca fascicularis

source_name: Lung

label_protocol: Total  RNA  was  extracted  from  lung  samples  and  blood  by  using  the  RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol. RNA was labeledwith Cy3 dye with the QuickAmplabelingkit(Agilent  Technologies)

growth_protocol: Aged (20–26 years) and young (2–3 years) female cynomolgus   macaques   (Macaca   fascicularis)   were   obtained from the   National   Institute   of Biomedical Innovation (NIBIO, Ibaraki, Japan),JapanLaboratoryAnimal Inc. (Tokyo, Japan)and SNBL, and    tested    to    ensure    that    they    were    serologically    negative    byneutralization    against A/Osaka/1365/2009   (H1N1pdm09),   A/Kawasaki/UTK-4/2009   (seasonal   H1N1),   A/Kawasaki/UTK-20/2008  (H3N2),  B/Tokyo/UT-E2/2008  (type  B),  and  A/duck/Hong  Kong/301/78  (H7N2)  viruses.  In this study

extract_protocol: Excised  macaque  tissues  were  preserved  in  10%  phosphate-buffered  formalin.  The  tissues  were  then  processed  for  paraffin embedding  and  cut  into  3-μm-thick  sections.  The  sections  of  each  tissue  sample  were  stained  using  a  standard hematoxylin and eosin procedure. Each serial section was processed  for  immunohistological staining  with  a  mouse  monoclonal  antibody  for  type  A  influenza  nucleoprotein  antigen (prepared  in our  laboratory)

treatment_protocol: macaques   were   intramuscularly anesthetized  with  ketamine  and  xylazine  or  medetomidine  and  inoculated  with  a  suspension containing 107plaque-forming units (pfu)/ml of Anhui/1through a combination of the intratracheal (4.5 ml), intranasal (0.5 ml per nostril), ocular (0.1 ml per eye) and oral (1 ml) routes, resulting in a total  infectious  dose  of  107.8pfu

value: lung

tag: lobe

value: Right Lower

tag: concentration (ng/ul)

tag: rin

value: Naive

tag: day

value: day 0

tag: death

value: No

value: Young

tag: animal number


title: US84403582_252680610521_S01_GE1_107_Sep09_1_3_Naive_Young_Lung_day 0_18

value: Left Upper

tag: strain


title: US84403582_252680610494_S01_GE1_107_Sep09_1_2_Naive_Young_Lung_day 0_19

tag: age


title: US84403582_252680610588_S01_GE1_107_Sep09_1_4_Naive_Young_Lung_day 0_18


title: IonXpress_014_rawlib

city: Shinanomachi,Shinjukuku

first: Shigeki

last: Ohta

state: Tokyo

institute: Keio University

data_processing:
AmpliSeq sequencing data of all samples was performed using Torrent Suite software version 4.2.1
Reads Per Million mapped reads (RPM) of the targeted genes is calculated using the ampliSeqRNA plugin
genome build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: shCtrl

growth_protocol: KnockOut™ DMEM/F-12 with StemPro® Neural Supplement

extract_protocol:
Fresh cell culture, RNeasy Mini Kit
For library preparation, a barcoded cDNA library is first generated with SuperScript® VILO™ cDNA Synthesis kit from 10 ng of total RNA. Then cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Amplified cDNA Libraries were evaluated for quality and quantified using Agilent Bioanalyzer High sensitivity chip. Libraries were then diluted to 100pM and pooled equally, with eight individual samples per pool. Pooled libraries were amplified using emulsion PCR on Ion Torrent OneTouch2 instruments (OT2) and enriched following manufactures instructions. Templated libraries were then sequenced on Ion Torrent Proton™ sequencing system, using Ion PI kit and chip V2.

treatment_protocol: Lentiviral expression of shControl RNA or shTPT1RNA in ES-derived Neural stem cells

tag: shRNA

value: shCtrl

tag: cell type

value: ES-derived neural stem cells (ES-NSCs)


title: IonXpress_015_rawlib


title: US84403582_252680610521_S01_GE1_107_Sep09_1_4_Naive_Young_Lung_day 0_19


title: US84403582_252680610520_S01_GE1_107_Sep09_1_3_Naive_Young_Lung_day 0_17


title: US84403582_252680610494_S01_GE1_107_Sep09_1_1_Naive_Young_Lung_day 0_18


title: US84403582_252680610589_S01_GE1_107_Sep09_1_2_Naive_Young_Lung_day 0_17


title: US84403582_252680610521_S01_GE1_107_Sep09_1_2_Naive_Young_Lung_day 0_17


title: US84403582_252680610464_S01_GE1_107_Sep09_1_4_Anhui1_Young_Lung_day 6_16

value: day 6


title: US84403582_252680610588_S01_GE1_107_Sep09_1_3_Naive_Young_Lung_day 0_17


title: US84403582_252680610511_S01_GE1_107_Sep09_1_4_Anhui1_Young_Lung_day 6_14


title: US84403582_252680610509_S01_GE1_107_Sep09_1_2_Anhui1_Young_Lung_day 6_16


title: US84403582_252680610512_S01_GE1_107_Sep09_1_2_Anhui1_Young_Lung_day 6_16


title: US84403582_252680610493_S01_GE1_107_Sep09_1_3_Naive_Young_Lung_day 0_19


title: US84403582_252680610462_S01_GE1_107_Sep09_1_2_Anhui1_Young_Lung_day 6_16


title: US84403582_252680610464_S01_GE1_107_Sep09_1_1_Anhui1_Young_Lung_day 3_13

value: day 3


title: US84403582_252680610512_S01_GE1_107_Sep09_1_1_Anhui1_Young_Lung_day 6_15


title: US84403582_252680610509_S01_GE1_107_Sep09_1_1_Anhui1_Young_Lung_day 6_15


title: US84403582_252680610508_S01_GE1_107_Sep09_1_4_Anhui1_Young_Lung_day 6_14


title: US84403582_252680610461_S01_GE1_107_Sep09_1_4_Anhui1_Young_Lung_day 6_14


title: US84403582_252680610464_S01_GE1_107_Sep09_1_2_Anhui1_Young_Lung_day 6_14


title: US84403582_252680610462_S01_GE1_107_Sep09_1_1_Anhui1_Young_Lung_day 6_15


title: US84403582_252680610511_S01_GE1_107_Sep09_1_3_Anhui1_Young_Lung_day 3_13


title: US84403582_252680610461_S01_GE1_107_Sep09_1_3_Anhui1_Young_Lung_day 3_13


title: US84403582_252680610520_S01_GE1_107_Sep09_1_4_Naive_Young_Lung_day 0_18


title: US84403582_252680610510_S01_GE1_107_Sep09_1_4_Anhui1_Young_Lung_day 6_15


title: Patient_16165M_R5020_0.1nM_Mid_24h_RNA-seq

tag: tissue type

value: Patient tumor explant

value: ER+ PR- HER2-

value: 24 hours

value: Cell models and patient tumors RNA-seq


title: US84403582_252680610511_S01_GE1_107_Sep09_1_2_Anhui1_Young_Lung_day 3_12


title: US84403582_252680610515_S01_GE1_107_Sep09_1_4_Anhui1_Young_Lung_day 3_11


title: US84403582_252680610586_S01_GE1_107_Sep09_1_4_Naive_Old_Lung_day 0_10

value: Old


title: US84403582_252680610463_S01_GE1_107_Sep09_1_3_Anhui1_Young_Lung_day 3_11


title: US84403582_252680610586_S01_GE1_107_Sep09_1_1_Naive_Old_Lung_day 0_10


title: US84403582_252680610523_S01_GE1_107_Sep09_1_2_Naive_Old_Lung_day 0_10


title: US84403582_252680610586_S01_GE1_107_Sep09_1_3_Naive_Old_Lung_day 0_9


title: US84403582_252680610515_S01_GE1_107_Sep09_1_3_Anhui1_Young_Lung_day 3_11


title: US84403582_252680610508_S01_GE1_107_Sep09_1_3_Anhui1_Young_Lung_day 3_13


title: US84403582_252680610461_S01_GE1_107_Sep09_1_2_Anhui1_Young_Lung_day 3_12


title: US84403582_252680610523_S01_GE1_107_Sep09_1_1_Naive_Old_Lung_day 0_9


title: US84403582_252680610522_S01_GE1_107_Sep09_1_3_Naive_Old_Lung_day 0_10


title: US84403582_252680610522_S01_GE1_107_Sep09_1_2_Naive_Old_Lung_day 0_9


title: US84403582_252680610470_S01_GE1_107_Sep09_1_2_Anhui1_Old_Lung_day 6_5


title: US84403582_252680610494_S01_GE1_107_Sep09_1_4_Naive_Old_Lung_day 0_9


title: US84403582_252680610522_S01_GE1_107_Sep09_1_1_Naive_Old_Lung_day 0_8


title: US84403582_252680610470_S01_GE1_107_Sep09_1_4_Anhui1_Old_Lung_day 3_7

value: Yes (3dpi, euthanasia)


title: US84403582_252680610467_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 3_7

value: lung


title: US84403582_252680610515_S01_GE1_107_Sep09_1_1_Anhui1_Old_Lung_day 3_7

value: Right Lower


title: US84403582_252680610522_S01_GE1_107_Sep09_1_4_Naive_Old_Lung_day 0_8

value: Naive


title: US84403582_252680610467_S01_GE1_107_Sep09_1_2_Anhui1_Old_Lung_day 6_6


title: US84403582_252680610586_S01_GE1_107_Sep09_1_2_Naive_Old_Lung_day 0_8

value: day 0


title: US84403582_252680610494_S01_GE1_107_Sep09_1_3_Naive_Old_Lung_day 0_8

value: No


title: US84403582_252680610518_S01_GE1_107_Sep09_1_4_Anhui1_Old_Lung_day 3_7


title: US84403582_252680610518_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 6_6


title: US84403582_252680610518_S01_GE1_107_Sep09_1_2_Anhui1_Old_Lung_day 6_5


title: US84403582_252680610470_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 6_6


title: US84403582_252680610495_S01_GE1_107_Sep09_1_4_Anhui1_Old_Lung_day 3_3


title: US84403582_252680610466_S01_GE1_107_Sep09_1_4_Anhui1_Old_Lung_day 4_4

value: day 4

value: Yes (4dpi)


title: US84403582_252680610517_S01_GE1_107_Sep09_1_4_Anhui1_Old_Lung_day 3_3

value: Left Upper


title: US84403582_252680610466_S01_GE1_107_Sep09_1_3_Anhui1_Old_Lung_day 3_3


title: US84403582_252680610518_S01_GE1_107_Sep09_1_1_Anhui1_Old_Lung_day 4_4