title: gPSC4-PGCLC_Rep3

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

data_processing:
Clean reads were mapped to the Mus musculus mm10 reference genome using Bowtie2 (population_ or Hisat2 (a few cells_.
Reads were assigned and counted to genes using the RSEM.
The resulting matrix of read counts was then loaded into RStudio (R version 3.4.2), and DESeq2 were used to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet with FPKM

source_name: PGCLCs induction from gPSC4

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For the experiments by treatment with crotonic acid during induction, 7 mM crotonic acid (pH=7) was added into induction medium from 16D to 28D continuously; For the induced PGCLCs, ESCs or gSCs treated with 1%KSR, 1. ng/ml bFGF and 2ng/ml Activin A for 2 days can form EpiLCs, and further treated with 500 ng/ml BMP4, 100 ng/ml SCF, 50ng/ml EGF and 1000 IU mLif for 4 days to form PGCLCs.

value: PGCLCs induction from gPSC4


title: E12.5PGC_Rep2

status: Public on Mar 06 2019

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: mouse E12.5 primordial germ cell

tag: strain

tag: cell type

value: mouse E12.5 primordial germ cell


title: E12.5PGC_Rep3


title: pob3-Q308K3

city: Salt Lake City

first: Tim

last: Formosa

state: UT

address: 15 N Medical Dr East RM 4100

department: Biochemistry

country: USA

institute: University of Utah School of Medicine

library_source: genomic

data_processing:
Reads were aligned to the yeast genome version SacCer3 using Novocraft novoalign version 2.8, with adapter trimming, no multi-mapping, and filtered for a minimum mapping quality of 13.
Duplicate alignments were randomly sub-sampled to a level of 40% relative to non-duplicate reads using bam_partial_dedup, version 1.7, https://github.com/tjparnell/HCI-Scripts/tree/master/BamFile.
Fragment coverage was generated using bam2wig version 1.52 (https://github.com/tjparnell/biotoolbox) with an extension of 150 bp, skipping chrMito, depth normalized to Reads Per Million, and converted to bigWig format.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig files representing the nucleosome fragment coverage, normalized to Reads Per Million.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Whole yeast cells

growth_protocol: Cultures were grown to logarithmic phase in rich medium at 30° C and harvested by centrifugation.

extract_protocol:
Cells were subjected to cross-linking with formaldehyde (1%) for 20 min at room temperature. Glycine (final 0.2 M) was added to quench crosslinking and cells were washed with 1X Tris-buffered saline. Cell walls were removed with 500 U lyticase, 37° 20 minutes, or until >90% of cells are spheroplasted and collected by centrifugation.
Cells were lysed in MNase digestion buffer and 10 U MNase, then incubated at 37° for 15 minutes, and the reaction stopped, diluted, and crosslinks reversed by incubating 5 hours at 65°. DNA was precipitated with ethanol, then treated with RNase A, followed by Proteinase K digestion and purification on Qiagen Qiaquick columns.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina. Ligated samples were purified by electrophoresis through 1.5% agarose, excising the 270 bp mononocleosome band (150 bp + 120 bp adaptors), purified on a Qiagen gel extraction kit. Samples were then subjected to 50 bp single-end sequencing in an Illumina Hiseq2500 sequencer.

tag: culture conditions

value: Rich medium, 30°, log phase

tag: genotype


title: 1.5 µM PF-067446846, 1 hr, rep 3

city: Berkeley

first: Jamie

middle: HD

last: Cate

state: CA

address: 748 Stanley Hall

institute: University of California Berkeley

description:
JCNL006L_S12_L006
processed data file:
846_vs_Veh_Deseq_poststall.csv

data_processing:
library strategy: Ribo-seq
Illumina Casava1.7 software used for basecalling.
De-multiplexed reads were stripped of 3′ adapters with the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and aligned to the human ribosomal RNA sequences using Bowtie to remove ribosomal RNA-mapped reads.
Read not aligning to rRNA sequences were aligned to  UCSC/Gencodev24 known coding Canonical Transcripts of the Grch38 human reference genome using Bowtie.
Reads that mapped to more than 1 position of the reference transcriptome were filtered out.
Reads were mapped along the transcripts, an mRNA P site-offset was determined depending on the size of the fragment as 14 nt for fragment of 26 nucleotides or less, 15 nt for fragments of 27 to 29 nucleotides, and 16 nt for fragments of 30 nucleotides or more. Codon maps were then generated for the CDS of each transcript using custom Python scripts
DMax value was calculated for each transcript as the maximum difference between cumulative normalized reads in PF-06378503 or PF-06744846 treated and untreated (DMSO control) samples
For each sample, a Z-score transformation of the DMax values was calculated using the scale function in R and the DMax positions with a Z-score greater than or equal to 2 were considered putative stalled transcripts.
A differential expression analysis was then performed in R using DEseq for transcripts that had more than 30 counts mapping to CDS reads located 3’ of the DMax position, or 10 codons after the start codon for transcripts lacking a clear DMax value. Reads 10 codons before the end of the transcript were also omitted. Transcripts showing a log2 fold change and FDR adjusted p-value < 0.05 were considered significant.
Genome_build: Dec. 2013 Grch38(hg38)
Supplementary_files_format_and_content: .csv files containing the DEseq analysis

organism: Homo sapiens

growth_protocol: Overnight cultures of 7x10^5 Huh7 cells in 10 cm dishes

extract_protocol:
Rinsed with phosphate-buffered saline (PBS) containing cycloheximide (100 µg/mL) and triturated in lysis buffer (20 mM Tris-Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide, 1% Triton X-100 and 25 U/mL DNAse I, Promega). The lysates were aliquoted, flash frozen and stored at -80 °C until used for ribosome footprint library preparation.
Ribosomes and libraries were prepared as described in Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012;7: 1534–1550.

treatment_protocol: Treated with 1.5 µM PF-06744846, 1.5 µM PF-06378503, or 0.5% DMSO control for 1 hr, in biological triplicate

tag: cell line

tag: treatment

tag: molecule subtype

value: mRNA, ribosome protected fragments


title: WT_2

description:
WT_log2_f.bw
WT_log2_r.bw

data_processing:
Reads were aligned to the genome index using Novocraft Novoalign version 2.8.3. The index was built containing genomic sequence plus known splice junctions as was built using the USeq application MakeTranscriptome, version 8.8.8 (http://useq.sourceforge.net). Up to 10 multiple mappings were allowed.
Raw alignments were processed to convert splice alignments to genomic alignments using USeq SamTranscriptomeParser, version 9.1.3. One alignment was kept per read.
Stranded, spliced, read-depth normalized coverage was generated with bam2wig (BioToolBox, version 1.60, https://github.com/tjparnell/biotoolbox). The three replicates were depth-normalized to Reads Per Million (RPM) prior to taking a mean coverage.
Coverage files were converted to log2 scale by adding 1 to the RPM value and taking the log2 value using manipulate_wig (BioToolBox, version 1.60). Wig files were converted to bigWig.
Genome_build: SacCer3
Supplementary_files_format_and_content: BigWig files representing stranded, spliced, read-depth normalized mean coverage of three replicates.

growth_protocol: Cultures were grown to logarithmic phase in rich medium at 30° C and harvested by centrigugation.

extract_protocol:
RNA was extracted from cell pellets using an acid phenol procedure followed by pelleting in CsCl2, resuspension, ethanol precipitation, and purification by Qiagen Rneasy mini kit.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina, and subjected to 50 bp single-end sequencing in an Illumina Hiseq2500 sequencer.

value: WT


title: E12.5PGC_Rep1


title: 1.5 µM PF-06378503, 1 hr, rep 1

description:
JCNL012X_S8_L004
processed data file:
503_vs_Veh_Deseq_poststall.csv


title: H3-K56Q1


title: 1.5 µM PF-067446846, 1 hr, rep 2

description:
JCNL002D_S4_L002
processed data file:
846_vs_Veh_Deseq_poststall.csv


title: pob3-Q308K2


title: Fetal liver HSPC,infected with MLLT3-OE vector sample2

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

description:
M2
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
MLLT3_OE_4w_HSPC_2

data_processing:
Alignment: TopHat v2.0.14. parameters --no-coverage-search --library-type fr-firststrand -o
Coverage file: Genomecov, Bedtools, parameters -bg -split –ibam
Tags: Maketagdirectory
RPKM: analyzeRepeats.pl. parameters -rna hg19 -noadj or -rpkm -strand - -count exons -condenseGenes
DGE: getDiffExpression.pl
Genome_build: hg19
Supplementary_files_format_and_content: txt containing RPKM and DGE

source_name: human FL CD34+CD38-/lowCD90+GFP+

growth_protocol: Fetal Liver is mechanically disrupted. CD34+ cells cells are magnetically separated. The indicated phenotype are facs sorted.

extract_protocol:
Cells are FACS sorted in RLT and RNA is extracted using RNeasy Mini kit (Qiagen)
KAPA RNA HyperPrep Kit with RiboErase (HMR)

treatment_protocol: Cells are infected with CTR or MLLT3-OE virus and cultured on OP9M2 stroma

value: FL-HSPC

tag: genotype/variation

value: MLLT3 overexpression

tag: time


title: gPSC4-PGCLC_Rep2


title: gPSC4-PGCLC_Rep1


title: Fetal liver HSPC,infected with CTR FUGW vector sample2

description:
F2
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
CTR_4w_HSPC_2

value: control


title: 1.5 µM PF-06378503, 1 hr, rep 2

description:
JCNL004H_S8_L004
processed data file:
503_vs_Veh_Deseq_poststall.csv


title: pob3-Q308K1


title: 1.5 µM PF-067446846, 1 hr, rep 1

description:
JCNL010T_S4_L002
processed data file:
846_vs_Veh_Deseq_poststall.csv


title: Fetal liver HSPC,infected with CTR FUGW vector sample4

description:
F4
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
CTR_4w_HSPC_4


title: Fetal liver HSPC,infected with MLLT3-OE vector sample1

description:
M1
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
MLLT3_OE_4w_HSPC_1


title: Fetal liver HSPC,infected with CTR FUGW vector sample1

description:
F1
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
CTR_4w_HSPC_1


title: WT3


title: H3-K56Q3


title: Dpy30_KO_H3K4me2-A

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

data_processing:
bcl2fastq 1.8.4
ChIP-seq reads were mapped to sacCer3 S. cerevisiae genome assembly using BWA and parallel version of pBWA (0.5.9-r32-MPIpatch2).
Uniquely mapped reads were filtered (-q 1) and PCR duplicates (reads with same start and mapped to same strand) were removed using Samtools (rmdup).
Read lengths were computationally extended to 150-bp strand specifically and stored in Bam format.
Genome_build: sacCer3 S. cerevisiae
Supplementary_files_format_and_content: The Bam files were subject to coverage calculation using the bamCoverage utility of deepTools for a sliding window of 40 bp, normalized using RPKM parameters, and stored in BigWig format.

growth_protocol: Yeast cells were grown over night in rich medium. Reinoculated the overnight grown cluture in frech medium and grown untill mid log phase of culture (OD of 0.8-1.0).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library was prepared following " NEBnext Ultra DNA Libprep Kit" protocol

value: Mutant Dpy30_KO

tag: chip antibody

value: H3K4me2 (Diagenode, pAB-035-050)


title: Nuclear RNA-seq DIS3-AID Plus auxin rep 2

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

description: bigwig coverage file were generated for total read or for separate stranded reads

data_processing:
[RNA-seq] Adapters removed from sequencing nuclear RNA-seq reads using Trim Galore v0.4.4 (wrapper tool for Cutadapt v1.9.1).
[RNA-seq] Alignment of nuclear RNA-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
[RNA-seq] Properly mapped single end reads were extracted using samtools v1.4.1.
[RNA-seq] For stranded coverge analysis, sense and antisense reads were seperated using samtools v1.4.1.
[RNA-seq] Bigwig files of nuclear RNA-seq reads were generated from BAM files using the bamCoverage of Deeptools v3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig files of nuclear RNA-seq reads represent normalised read coverage (RPKM) over single bp windows across the genome.

molecule: nuclear RNA

source_name: HCT116 Nuclear RNA-seq DIS3-AID Sleeping Beauty(TIR1) plus auxin

growth_protocol: HCT116 cell lines were maintained in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
Nuclear RNA was extracted from isolated nuclei using Trizol reagent.
Nuclear RNA was depleted of ribosomal RNA using Illumina Ribo-Zero Gold (Illumina #MRZE706). Library was constructed using Illumina TruSeq® Stranded Total RNA (Illumina #20020596)

treatment_protocol: Auxin was added to cell media at a final concentration of 500 µM  1 h  prior to collection.

value: auxin treated Nuclear RNA

value: Nucleoplasmic RNA


title: ESC-PGCLC_Rep2

source_name: PGCLCs induction from ESC

value: PGCLCs induction from ESC


title: ESC-PGCLC_Rep3


title: Fetal liver HSPC, sample3

description:
FLd0_90_4
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
FL_HSPC_3

source_name: human FL CD34+CD38-/lowCD90+


title: Fetal liver HSPC, sample2

description:
FLd0_90_3
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
FL_HSPC_2


title: ESC-PGCLC_Rep1


title: WT2


title: WT1


title: Fetal liver HSPC, sample1

description:
FLd0_90_2
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
FL_HSPC_1


title: gPSC4-EpiLC_Rep3

source_name: gPSC4-EpiLC during PGCLCs induction

value: gPSC4-EpiLC during PGCLCs induction


title: Nuclear RNA-seq DIS3-AID Plus auxin rep 1

source_name: HCT116 Nuclear RNA-seq EXOSC10-AID Sleeping Beauty(TIR1) plus auxin


title: gPSC4-EpiLC_Rep2


title: Nuclear RNA-seq DIS3-AID Minus auxin rep 1

source_name: HCT116 Nuclear RNA-seq EXOSC10-AID Sleeping Beauty(TIR1) minus auxin

treatment_protocol: Control: Treated for 1 h with ethanol.

value: Control:auxin untreated Nuclear RNA


title: gPSC4-EpiLC_Rep1


title: Nuclear RNA-seq EXOSC10-AID Plus auxin rep 2


title: Nuclear RNA-seq DIS3-AID Minus auxin rep 2

source_name: HCT116 Nuclear RNA-seq DIS3-AID Sleeping Beauty(TIR1) minus auxin


title: Nuclear RNA-seq EXOSC10-AID Minus auxin rep 2


title: MCF-7Luc

type: RNA

city: Shinjyuku-ku

first: Shinobu

last: Ueda

address: 6-1-1, Shinjyuku

country: Japan

institute: Tokyo Medical University

hyb_protocol: Hybridized using the Human microRNA Microarray kit (Agilent Technologies, Santa Clara, CA, USA) according to version 1.5 of the ‘Protocol for use with Agilent microRNA microarrays’

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) .

data_processing: All scanned images were analyzed using the Agilent Feature Extraction software (v9.5.3.1).

source_name: MCF-7Luc  Adherent

label_protocol: 100 ng RNA labeled and hybridized using the Human microRNA Microarray kit (Agilent Technologies, Santa Clara, CA, USA) according to version 1.5 of the ‘Protocol for use with Agilent microRNA microarrays’.

growth_protocol: MCF-7, HCC70-luc (luciferase gene tranfected) , HCC1954-luc cells were cultured in RPMI1640 medium (Life Technology, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Cell Culture Tecnologies, Canada) and penicillin/streptomycin (Sigma, St. Louis, MO, USA). All cells were grown at 37°C in a humidified atmosphere containing 5% CO2. For Mammospheres, the adherent growing breast cancer cell lines were dissociated into single cells using trypsin/EDTA and 10,000 single cells per dish seeded in petri dish using serum-free DMEM/F12 (D8062, Sigma)medium supplemented with 1x B27 supplement (17504-044, Gibco), 20 ng/ml human epidermal growth factor EGF (354052, BD), 20 ng/ml human basic fibroblast growth factor FGF (100-18B, PEPROTECH INC.) and 4 mg/ml Heparin (H4784, Sigma). Cells were incubated in a 5% CO2 humidified atmosphere at 37°C.

extract_protocol: RNA was prepared using ISOGEN (Nippon Gene, Tokyo, Japan) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: tissue

value: breast cancer cell line

value: luciferase gene tranfected


title: MCF-7Luc_Sphere2

source_name: MCF-7Luc Sphere d6


title: ISL1old

city: beijing

first: guo

last: ting

address: 52 Fucheng Road, Haidian District

country: China

institute: Peking University Cancer Hospital & Institute, Beijing

data_processing:
Basecalls performed using CASAVA version 1.8
aligned to the GRCh38 genome assembly using Hisat2（version:2.0.4）
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample ...

source_name: SGC7901 cells

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The SGC7901 cells were transfected by ISL1 Lentivirus and blank lentivirus as control.

tag: passages

value: gastric cancer cell line

tag: shRNA

value: ISL1 expression lentivirus


title: HCC1954Luc_TumorSphere

source_name: HCC1954Luc Tumor primary sphere


title: Nuclear RNA-seq EXOSC10-AID Plus auxin rep 1


title: HCC1954Luc_Sphere2

source_name: HCC1954Luc Sphere d6


title: ESC-EpiLC_Rep2

source_name: ESC-EpiLC during PGCLCs induction

value: ESC-EpiLC during PGCLCs induction


title: ESC-EpiLC_Rep1


title: Nuclear RNA-seq EXOSC10-AID Minus auxin rep 1


title: gPSC4_Rep3

source_name: gPSC4 cell line for PGCLCs induction

value: gPSC4 cell line for PGCLCs induction


title: gPSC4_Rep2


title: ATAC-seq for MLLT3 in 4 wk cultured FL-HSPC with MLLT3-OEvector

description:
ATACseq_MLLT3OE
Tagmented DNA

data_processing:
Alignment: Bowtie2 v2.2.5
Coverage file: Samtools/1.3.1
Coverage file: Bamcoverage, Deeptools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig tracks for each of the samples

growth_protocol: Fetal Liver is mechanically disrupted. CD34+ cells and CD34- cells are magnetically separated. The indicated phenotype are facs sorted.  Infected cells are cultured on OP9M2 for 4 weeks.

extract_protocol:
Chromatin was tagmented and DNA extracted (Nextera DNA Library Prep Kit, Illumina) and incubated at 37oC for 30 minutes, (see methods)
Transposed DNA was column purified and used for library amplification with custom made adaptor primers using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs)

treatment_protocol: lentivirus infection with MLLT3 overexpression or empty vector

value: 4 wk cultured FL-HSPC


title: ATAC-seq for MLLT3 in FL-Erythroblasts, sample2

description:
ATACseq_FL_Ery_2
Tagmented DNA

source_name: human FL CD34-CD71+CD235a+

value: FL-Erythroblasts


title: ESC-EpiLC_Rep3


title: ATAC-seq for MLLT3 in FL-Erythroblasts, sample1

description:
ATACseq_FL_Ery_1
Tagmented DNA


title: gPSC4_Rep1


title: HCC70Luc_Sphere2

source_name: HCC70Luc Sphere d7


title: HCC70Luc

source_name: HCC70Luc Adherent


title: HCC1954Luc

source_name: HCC1954Luc Adherent


title: HCC70Luc_Sphere_Tax10nM

source_name: HCC70Luc Sphere taxol 10 nM d7


title: ATAC-seq for MLLT3 in FL-HSPC, sample3

description:
ATACseq_FL_HSPC_3
Tagmented DNA

source_name: human FL CD34+CD38-/lowCD90+

value: FL-HSPC


title: ESC_Rep2

source_name: Female ES cell line for PGCLCs induction


title: Hippocampal Cells_with NGF_72h_rep2

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

hyb_protocol: Aliquots (750 ng) of Cy3-labeled cRNA targets were hybridized on SurePrint G3 Rat 8×60K Microarrays (Agilent Technologies). Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven)

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using Agilent 1-color Green Gene Expression Version 11.5 - FD 11.5 Default Protocol (protocol GE1_1105_Oct12 and Grid: 028279_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Hippocampal cells

label_protocol: Complementary RNAs (cRNAs) labeled with Cy3-CTP were synthesized from 1 μg of total RNA of each sample using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies), following the manufacturer's protocol.

growth_protocol: Hippocampal cultures were prepared from brain of embryos Wistar rats (Charles River) at embryonic day 17-18 (E17/E18), as previously reported (Campolongo et al., 2014). Briefly, hippocampus was dissected out in PBS and dissociated via trypsin treatment. Cells were plated at 1 × 106 cells on 3.5 cm diameter dishes precoated with poly-L-lysine.

extract_protocol: Total RNA was extracted with Trizol (Life Technologies, Monza, Italy) from four biological replicates (derived from the same litter) for each of the two experimental conditions examined: vehicle and Ngf treated HNs. RNA integrity was confirmed by using a RNA chip and a 2100 Bioanalyzer (Agilent Technologies), with the protocol outlined by the manufacturer.

treatment_protocol: After 2 days of culturing in neurobasal medium with 2% B-27 supplement (2 mM L-glutamine, 1% (50U/ml) antibiotic penicillin/streptomycin), half of the medium was changed every 3-4 days. Ngf treatment (100 ng/ml) for 72 h was performed from day 12 in vitro cultures in Neurobasal + 1% B27 fresh medium.

value: hippocampal neurons

value: Ngf (100 ng/ml) for 72h


title: ESC_Rep1

value: Female ES cell line for PGCLCs induction


title: Hippocampal Cells_without NGF_72h_rep4

value: vehicle control


title: ATAC-seq for MLLT3 in 4 wk cultured FL-HSPC with CTR vector

description:
ATACseq_CTR
Tagmented DNA

source_name: human FL CD34+CD38-/lowCD90+GFP+

value: control


title: ATAC-seq for MLLT3 in FL-HSPC, sample2

description:
ATACseq_FL_HSPC_2
Tagmented DNA


title: Hippocampal Cells_with NGF_72h_rep3


title: Hippocampal Cells_with NGF_72h_rep4


title: Hippocampal Cells_without NGF_72h_rep2


title: Hippocampal Cells_without NGF_72h_rep3


title: Hippocampal Cells_with NGF_72h_rep1


title: ATAC-seq for MLLT3 in FL-HSPC, sample1

description:
ATACseq_FL_HSPC_1
Tagmented DNA


title: ESC_Rep3


title: MEF_Rep2_1

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: DT40_SNS-seq

city: Berlin

first: Florian

last: Massip

address: Robert-Rössle-Straße 10

institute: Max Delbrueck Center for Molecular Medicin

data_processing:
Library strategy: SNS (Short nascent strands)-Seq
Reads were mapped using bowtie2. Reads with quality score smaller than 40 or reads mapping to unmapple regions of the genome were excluded.
Replication origins were called using the dedicated methods from (Picard et al., 2014, plosGenetics)  smaller threshold (500bp instead of 2 kb in the original method).
For each origin, the "SNS peak" is defined as the position for which the read accumulation profile is maximal. We computed this maximum on a smoothed read accumulation profile using a Gaussian kernel transformation with a bandwidth of sqrt(500).
Genome_build: gal5
Supplementary_files_format_and_content: bed format file with 5 columns presenting (in that order): chromosome, start, end, position of the SNS peak and strength of the origin (defined as the number of SNS reads mapping in the origin)

organism: Gallus gallus

source_name: DT40 chicken cell line

extract_protocol:
SNS were double-stranded by random priming with the Klenow exo-polymerase (# EP0421, Thermo Fisher Scientific) and random primers (#48190011, ThermoFisher Scientific). Adjacent strands were then ligated with Taq DNA Ligase (M0208L, Biolabs). RNA primers were hydrolysed for 30 min at 37oC with 2.5 M NaOH. The reaction was then neutralized with 2.5 M acetic acid, and SNS were purified by phenol chloroform extraction and recovered after ethanol precipitation and resuspension in TE buffer. SNS molecules were quantified with the QBit dsDNA HS assay kit (Q32854, Thermo Fisher Scientific) and 225 ng of double-stranded material was used for fragmentation using a Covaris apparatus with a 50-μl microTUBE-50 AFA Fiber screw-cap tune (PN 520166, Covaris) and a M220 Holder XTU (PN500488, Covaris). We used a soni- cation programme with 75 W peak incident power, 10% duty factor and 200 cycles per burst running at 4o C for 195 s to obtain molecules with a size of approximately 180 bp.
The library was constructed with the NEBNext©UltraTM II DNA Library Prep Kit for Illumina©(NEB#E7645S) following the manufacturer’s instructions with some minor modifications. For the adaptor ligation, undiluted adaptor and no size selection were used. The library amplification
The library amplification was performed using NEBNext ©Multiplex Oligos for Illumina©(NEB #E7335S) with NEBNext index 4 primer (#E7314A) and the NEBNext Universal PCR Primer (#E6861A) with three PCR cycles. Library purification was performed with the SPRIselect Reagent kit (Beckman coulter #B23317), and the final elution step was reduced to 20 μl of 0.1X TE. The mean size of the library molecules determined on an Agilent Bioanalyser High Sensitivity DNA chip (5067- 4626, Agilent technologies) was 550 bp. Sequencing was performed on a NextSeq 500 Illumina sequencer with a High Output 150 cycles flow cell (paired-end reads of 75 bp) according to standard procedures. A total of 246,14 M clusters were generated and provided 492,28 M of reads. All Illumina sequencing runs were performed at the GENOM’IC facility of the Cochin Institute.

treatment_protocol: Short nascent strands were purified as previously described (Prioleau et al. 2003). We pooled fractions 15 to 20 containing single-stranded DNA molecules with a size between 1.5 to 2.5 kb in size. We used 500 U of a custom-made λ-exonuclease (ThermoFisher Scientific (50 U.ml−1 )) for each preparation. For the genome-wide mapping of origins, six SNS preparations were obtained independently from 10^8 cells each and then pooled.

value: derived from a bursal lymphoma


title: normal tissue, total thyroidectomy,  replicate 4

city: Changsha, China

first: Xia

last: Fada

address: NO. 87, Xiangya Road

institute: Central South university

description: microRNA expression profile

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: normal thyroid  tissue_liquid nitrogen snap-frozen immediately

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: para-tumor normal thyroid tissue

tag: pathologic diagnosis

value: normal thyroid tissue without tumor cell invasion

tag: gender

value: female

tag: age

tag: t stage (cm)

value: normal tissue

tag: n stage

tag: m stage


title: normal tissue, total thyroidectomy,  replicate 3

description: microRNA expression profile


title: normal tissue, total thyroidectomy,  replicate 5

description: microRNA expression profile


title: normal tissue, total thyroidectomy,  replicate 1

description: microRNA expression profile

value: male


title: thyroid tumor, total thyroidectomy,  replicate 4

description: microRNA expression profile

source_name: thyroid tumor tissue_liquid nitrogen snap-frozen immediately

value: thyroid tumor tissue

value: papillary thyroid carcinoma


title: thyroid tumor, total thyroidectomy,  replicate 5

description: microRNA expression profile


title: normal tissue, total thyroidectomy,  replicate 2

description: microRNA expression profile


title: thyroid tumor, total thyroidectomy,  replicate 2

description: microRNA expression profile


title: thyroid tumor, total thyroidectomy,  replicate 3

description: microRNA expression profile


title: Set1_KO_spk_me1_RC07-42

data_processing:
bcl2fastq 2.17.1.14
reads were first aligned to sacCer3 reference and then to sPombe reference genomes
Percentage of reads aligned per sample per genome was documented in a tabular format
Genome_build: sacCer3 S. cerevisiae
Genome_build: S. Pombe
Supplementary_files_format_and_content: genome_coverage.xlsx; spreadsheet describing the genome coverage of sevaral species; rows are the samples and columns are the species plus additional information

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: S. cerevisiae mutant set1_KO+WT S. pombe

growth_protocol: Cells were grown over night in rich medium. Reinoculated the overnight grown cluture in frech medium and grown untill mid log phase of culture (OD of 0.8-1.0).

treatment_protocol: 2:1 ratio of Saccharomyces cerevisiae and  Schizosaccharomyces pombe were mixed.

tag: strain background

value: mutant set1_KO

value: H3K4me1 (Diagenode, pAB-037-050)


title: Sdc1_pMut_and_Yjr_KO_spk_me1-RC07-38

source_name: S. cerevisiae mutant sdc1*+ yjr_KO+ WT S.pombe

value: mutant sdc1*+ yjr_KO+ WT S.pombe


title: Set1_KO_spk_me1_RC07-41


title: Yjr_KO_spk_Me1_RC07-36

source_name: S. cerevisiae mutant Yjr_KO+WT S. pombe

value: mutant Yjr_KO


title: Hippocampal Cells_without NGF_72h_rep1

value: hippocampal neurons


title: male rep1

city: Irvine

first: Ali

last: Mortazavi

address: 2300 E biological science 3

institute: University of California Irvine

data_processing:
Unstranded, paired-end 43 bp RNA-seq reads for each worm were mapped to the S. carpocapsae genome using Bowtie 1.0.0 with the following options: -X 1500 -a -m 200 --S -- seedlen 25 -n 2 --offrate 1 -p 64 -v 3  (Langmead et al. 2009). After Bowtie, gene expression was quantified with RSEM with the following options: rsem-calculate-expression -- bam -- paired-end. Gene expression for S. carpocapsae were performed as previously described (Lu et al. 2017) and reported in Transcripts Per Million (TPM). We used counts for differential gene expression analysis.
The Transcript per million (TPM) generated by rsem-calculate-expression for S. carpocapsae samples were normalized according to groups using the R package limma (Ritchie et al., 2015) because samples were collected, processed and sequenced in different batches.
Genome_build: steinernemacarpocapsae.denovo.transcriptome.fa.gz
Supplementary_files_format_and_content: TPM

organism: Steinernema carpocapsae

source_name: activated in lawn of Xenorhabdus nematophila

growth_protocol: As described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.

extract_protocol:
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
PolyA RNA  unstranded, paired-end, read_length= 43 bp, as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.

treatment_protocol: No treatments. IJs were cultured with Xenorhabdus nematophila  and collected at the respective times.

tag: strain

value: ALL

tag: genotype

value: wild type

tag: developmental stage

value: adults

value: whole body

tag: time point


title: female rep2


title: female rep1


title: female rep3


title: 48hr rep3

value: late post-activation


title: male rep3


title: Yjr_KO_spk_Me1_RC07-35

tag: genotype/variation


title: sdc1_pMut_spk_me1-RC07-34

source_name: S. cerevisiae mutant sdc1*+WT S. pombe

value: mutant sdc1*


title: 36hr rep3


title: male rep2


title: 36hr rep2


title: sdc1_pMut_spk_me1-RC07-33


title: WT_AR2_spk_me1-RC07-32

source_name: S. cerevisiae WT+WT S. pombe

value: WT


title: thyroid tumor, total thyroidectomy,  replicate 1

description: microRNA expression profile


title: 24hr rep3


title: 48hr rep2


title: Fetal liver HSPC,infected with CTR FUGW vector sample3

description:
F3
MLLT3OE4w_6s_d0_3s_exoRpkmSt.txt
diffOE4w_6s_paired_edgeR.txt
CTR_4w_HSPC_3

tag: cell type

value: FL-HSPC

value: control

tag: time


title: WT_AR2_spk_me1-RC07-31

tag: chip antibody


title: WT_DS1_spk_me1-RC07-30


title: 24hr rep2

tag: tissue


title: mpm target3 rep 3

city: Los Alamos

first: Migun

last: Shakya

state: NM

address: Bikini atoll road

institute: Los Alamos National Lab

description:
Meropenem at two minimum bactericidal doses was applied as stress factor to increase the population of persister cells. Exponential growth popularions was treated with Mpm for 3h
mpmp022T

data_processing:
All steps processed using PiReT version 0.3.2 (https://github.com/mshakya/piret)
Supplementary_files_format_and_content: gene_count.tsv: output of featurecount that shows read counts of each gene
Supplementary_files_format_and_content: gene_count_FPM.csv: FPM calculated for each gene using DESeq2

organism: Burkholderia thailandensis

growth_protocol: B. thailandensis E264 were maintained on LB-Miller agar plates at room temperature. To test antibiotic sensitivity and metabolic activity, cultures initiated from single colonies were grown overnight in 5ml LB-Miller broth (Fisher Scientific) at 37◦C with agitation. Mid-log cultures from overnight stationary cultures were diluted 100-fold in fresh media and incubated at 37◦C with agitation at 120 rpm for 2-4 hours until OD600 0.2-0.3.

extract_protocol:
Bacterial pelets were treated with1,000 U lysozyme for 15min at 37◦C prior to dissolving cells in TRIzol reagent, and total RNA isolated using the miRNeasy Mini kit (QIAGEN).
Total RNA was depleted of ribosomal RNA using the Ribo-Zero Gram-Negative Bacteria kit (Illumina, Cat. #MRZGN126). cDNA libraries were generated with ScriptSeq v2 Library Preparation Kit (Illumina, Cat. #SSV21106), titrated with the Qubit dsDNA HS Assay (ThermoFisher Scientific, Cat. #Q32854), and  sequenced on the Illumina Mi-Seq platform, generating paired-end 151 bp reads

treatment_protocol: For isolation of  bacteria with low PMF we treated mid-log phase B. thailandensis (OD600 0.2-0.3) with 1µg/ml DiBAC4 for 30 min, washed bacteria twice in dye-free LB, and resuspended in fresh LB broth at OD600 ~0.1. Persisters were sorted using a blue laser (ex 488 nm and 530/30 emission) with the Aria BD FACS instrument. For isolation of persister stimulated by antibiotic treatment, 1x MBC meropenem at the mid-log phase (OD600 0.3) for 4h.

tag: group

value: treated with Mpm for 3h


title: 24hr rep1


title: mpm target3 rep 2

description:
Meropenem at two minimum bactericidal doses was applied as stress factor to increase the population of persister cells. Exponential growth popularions was treated with Mpm for 3h
mpm019T


title: 48hr rep1


title: 15hr rep3

value: early post-activation


title: Sdc1_pMut_and_Yjr_KO_spk_me1-RC07-37


title: Set1_KO_spk_me2_RC07-28

value: H3K4me2 (Diagenode, pAB-035-050)


title: mpm target3 rep 1

description:
Meropenem at two minimum bactericidal doses was applied as stress factor to increase the population of persister cells. Exponential growth popularions was treated with Mpm for 3h
mpm018T


title: 15hr rep2


title: mpm control3 rep 3

description:
Meropenem at two minimum bactericidal doses was applied as stress factor to increase the population of persister cells. Controls were B.thailandensis cells in the exponential growth phase NOT treated with Mpm
mpm017C

value: control NOT treated with Mpm


title: 15hr rep1


title: Set1_KO_spk_me2_RC07-27

value: mutant set1_KO


title: mpm control3 rep 2

description:
Meropenem at two minimum bactericidal doses was applied as stress factor to increase the population of persister cells. Controls were B.thailandensis cells in the exponential growth phase NOT treated with Mpm
mpm016C


title: Sdc1_pMut_and_Yjr_KO_spk_me2-RC07-24

value: mutant sdc1*+ yjr_KO+ WT S.pombe


title: 12hr rep3


title: 12hr rep2


title: Sdc1_pMut_and_Yjr_KO_spk_me2-RC07-23


title: mpm control3 rep 1

description:
Meropenem at two minimum bactericidal doses was applied as stress factor to increase the population of persister cells. Controls were B.thailandensis cells in the exponential growth phase NOT treated with Mpm
mpm015C


title: 36hr rep1


title: Yjr_KO_spk_Me2_RC07-22

value: mutant Yjr_KO


title: low PMF target1 rep 3

description:
Assay for low proton motive force (PMF): Target persister populations with low PMF have High florescence intensity. Mid-log phase B. thailandensis population (OD600 0.2-0.3) was treated with 1µg/ml DiBAC4 and was sorted using a blue laser (ex 488 nm and 530/30 emission) for High fluorescent intensity
lowPMF006T


title: WT_DS1_spk_me1-RC07-29

value: H3K4me1 (Diagenode, pAB-037-050)


title: Yjr_KO_spk_Me2_RC07-21


title: 12hr rep1

value: ALL


title: 9hr rep2

value: wild type


title: Wt_AR2_spk_me2-RC07-18


title: sdc1_pMut_spk_me2-RC07-19


title: low PMF target1 rep 1

description:
Assay for low proton motive force (PMF): Target persister populations with low PMF have High florescence intensity. Mid-log phase B. thailandensis population (OD600 0.2-0.3) was treated with 1µg/ml DiBAC4 and was sorted using a blue laser (ex 488 nm and 530/30 emission) for High fluorescent intensity
lowPMF002T


title: low PMF control1 rep 2

description:
Assay for low proton motive force (PMF): Control populations with normal PMF have LOW florescence intensity. Mid-log phase B. thailandensis population (OD600 0.2-0.3) was treated with 1µg/ml DiBAC4 and was sorted using a blue laser (ex 488 nm and 530/30 emission) for LOW fluorescent intensity
lowPMF003C

value: Control populations with normal PMF


title: low PMF target1 rep 2

description:
Assay for low proton motive force (PMF): Target persister populations with low PMF have High florescence intensity. Mid-log phase B. thailandensis population (OD600 0.2-0.3) was treated with 1µg/ml DiBAC4 and was sorted using a blue laser (ex 488 nm and 530/30 emission) for High fluorescent intensity
lowPMF004T


title: low PMF control1 rep 3

description:
Assay for low proton motive force (PMF): Control populations with normal PMF have LOW florescence intensity. Mid-log phase B. thailandensis population (OD600 0.2-0.3) was treated with 1µg/ml DiBAC4 and was sorted using a blue laser (ex 488 nm and 530/30 emission) for LOW fluorescent intensity
lowPMF005C


title: WT_AR2_spk_me2-RC07-17


title: 9hr rep1

value: whole body


title: 6hr rep3


title: WT_DS1_spk_me2-RC07-16


title: low PMF control1 rep 1

description:
Assay for low proton motive force (PMF): Control populations with normal PMF have LOW florescence intensity. Mid-log phase B. thailandensis population (OD600 0.2-0.3) was treated with 1µg/ml DiBAC4 and was sorted using a blue laser (ex 488 nm and 530/30 emission) for LOW fluorescent intensity
lowPMF001C


title: 6hr rep2


title: 3hr rep3


title: WT_DS1_spk_me2-RC07-15


title: 6hr rep1


title: aged target2 rep 2

description:
Total RNA was isolated from 200 coloni forming units grown on LB-agar Miller for 21 days
aged011T

value: grown on LB-agar Miller for 21 days


title: aged control2 rep 3

description:
Total RNA was isolated from 50 coloni forming units grown on LB-agar Miller for 1 day
aged013C

value: grown on LB-agar Miller for 1 day


title: Set1_KO_spk_me3_RC07-13

value: H3K4me3 (Abcam, ab8580)


title: 3hr rep2


title: Sdc1_pMut_and_YjrKO_spk_me3-RC07-10


title: aged target2 rep 1

description:
Total RNA was isolated from 200 coloni forming units grown on LB-agar Miller for 21 days
aged010T


title: sdc1_pMut_spk_me2-RC07-20

value: mutant sdc1*


title: aged control2 rep 2

description:
Total RNA was isolated from 50 coloni forming units grown on LB-agar Miller for 1 day
aged008C


title: 9hr rep3


title: naïve rep2

source_name: not activated Infective Juvenile(IJ)

value: Infective Juvenile (IJ)

value: naïve


title: Sdc1_pMut_and_YjrKO_spk_me3-RC07-9


title: aged control2 rep 1

description:
Total RNA was isolated from 50 coloni forming units grown on LB-agar Miller for 1 day
aged007C


title: Yjrko_KO_spk_Me3-RC07-8


title: gPSC16

source_name: gPSC cell line derived from GCs

value: gPSC cell line derived from GCs


title: Yjrko_KO_spk_Me3-RC07-7


title: static_BMEC

city: Nashville

first: Ethan

last: Lippmann

state: TN

address: 2400 Highland Ave, Room 303

department: Chemical and Biomolecular Engineering

institute: Vanderbilt University

data_processing:
Sequences were aligned to the human transcriptome using HISAT2 (version 1.2.0-OSX_x86_64). A list of known splice sites was generated using the UCSC Table Browser and hisat2_extract_splice_sites.py.
Alignments were assembled using StringTie (version 1.3.4d.OSX_x86_64).
FPKM values were extracted using Ballgown.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file contains transcript coverage and FPKM values for both samples.

source_name: IMR90-4 iPSC-derived blood-brain barrier endothelium

growth_protocol: iPSC-derived blood-brain barrier endothelium was seeded into channels in gelatin hydrogels.

extract_protocol:
Endothelium was removed from channels using trypsin, and total RNA was isolated using Direct-zol RNA MiniPrep Plus Kit (Zymo Research) with DNase I treatment following manufacturer's instructions. Samples were submitted to Vanderbilt Technologies for Advanced Genomics (VANTAGE) for library preparation.
cDNA libraries were prepared using a stranded mRNA (poly-A-selected) kit.

treatment_protocol: Brain endothelium was cultured for 1 day under static conditions or 14 days under perfused conditions.

tag: culture condition

value: static

tag: days in channel


title: Set1_KO_spk_me3_RC07-14


title: sdc1_pMut_spk_me3-RC07-6


title: gPSC11

data_processing:
Clean reads were mapped to the Mus musculus mm10 reference genome using Bowtie2 (population_ or Hisat2 (a few cells_.
Reads were assigned and counted to genes using the RSEM.
The resulting matrix of read counts was then loaded into RStudio (R version 3.4.2), and DESeq2 were used to identify differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet with FPKM


title: C9_r3

city: Wuhan P.R. China

first: Bin

last: Zhu

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

data_processing:
150bp paired-end reads were generated via Illumina HiSeqTM 3000
The clean reads were directly aligned to the reference genome of Brassica napus using Hisat software (version 0.1.6), with a strict mismatch tolerance according to the follow criterion: specifying -L, 0, -0.15.
The genes were assembled with Cufflinks according to a reference-guided method.
The differentially expressed genes between three different samples were computed on RNA-seq data by using CuffDiff2.
Genome_build: Brassica_napus.annotation_v5.gff3
Supplementary_files_format_and_content: See linked Excel tables; The gene_id used in the study is universal and can be avialable at the link http://www.genoscope.cns.fr/brassicanapus/data/, a genome brower for Brassica napus.

organism: Brassica rapa

source_name: Young Leaf

growth_protocol: All of the samples were established in green house for transcriptomic analyses.

extract_protocol:
Using TRIzol reagent (Invitrogen, Life Technologies) according the manufacturer’s protocol, total RNA was extracted from two biological replicates (three plants per replicate) for each genotype.
NanoDrop ND 1000 (NanoDrop technologies) was used to initially calculate the quality and quantity of the extracted RNA, and then the RNA Integrity Number (RIN) value was assessed by Agilent Technologies 2100 Bioanalyzer (Agilent). Only when the value of RIN was higher than 8, the RNA was used to prepare the c-DNA library according to the TruSeq RNA Sample Prep v2 protocol

value: Leaf

tag: development

value: The newly expanded third leaves without petioles

value: adding a C9 chromosome


title: AR2_spk_me3-RC07-4

value: WT


title: sdc1_pMut_spk_me3-RC07-5


title: C9_r2


title: C9_r1


title: C8_r3

value: adding a C8 chromosome


title: gPSC4

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: DS1_spk_me3-RC07-2


title: DS1_spk_me3-RC07-1


title: C8_r2


title: 3hr rep1

value: ALL

value: early post-activation


title: naïve rep1

value: wild type


title: perfused_BMEC

value: perfused


title: ES_2

source_name: Female ES cell line from the same strain


title: gPSC10


title: C7_r2

value: adding a C7 chromosome


title: C7_r3


title: aged target2 rep 3

description:
Total RNA was isolated from 200 coloni forming units grown on LB-agar Miller for 21 days
aged014T

value: grown on LB-agar Miller for 21 days


title: C7_r1


title: C6_r2

value: adding a C6 chromosome


title: 16D_XEN__2

source_name: 16D reprogramming cells

value: 16D reprogramming cells


title: AR2_spk_me3-RC07-3

value: H3K4me3 (Abcam, ab8580)


title: 16D_XEN__1


title: C5_r3

value: adding a C5 chromosome


title: MEF_Rep1

value: mouse embryonic fibroblasts


title: C5_r1


title: GC_2

source_name: mouse granulosa cells

value: mouse granulosa cells


title: GC_1


title: 28D+CA_2

source_name: 28D reprogramming cells with CA

value: 28D reprogramming cells with CA


title: C5_r2

value: Leaf

value: The newly expanded third leaves without petioles


title: 28D+CA_1


title: C4_r3

value: adding a C4 chromosome


title: C8_r1

value: adding a C8 chromosome


title: 28D_2

source_name: 28D reprogramming cells

value: 28D reprogramming cells


title: C4_r2


title: RNA Old-liver-1

city: Ya'an

first: Jianning

last: Chen

state: Sichuan

address: 46, Xinkang Road

institute: Sichuan Agricultural University

description:
domestic pig
mRNA_tpm.txt/lncRNA_tpm.txt/circRNA_tpm.txt

data_processing:
Illumina HiSeq 4000 was used to sequence the lncRNA libraries and 150 bp paired-end reads were obtained, and Illumina MiSeq platform was used to sequence the small RNA library preparations, and 50 bp single-end reads were produced.
Clean reads were obtained from raw data after removing the adapter, ploy-N and low quality reads. Clean reads were aligned to the Ensemble (Susscrofa 10.2) using TopHat2 (v2.0.14) with default parameters.
Mapped reads of each sample were assembled by using the StringTie (v1.2.3) software.
Coding Potential Calculator (CPC) (0.9) and Pfam Scan (v1.5) were used to examine the transcript coding potential.
LncRNA, mRNA, and circRNA, expression levels of transcripts per million (TPMs) were obtained using Salmon (v0.6.0)
Software mirdeep2 (v2.0.0.5) was used to identify the potential miRNA and to predict novel miRNA.
miRNA expression levels of transcripts per million (TPMs) were obtained using Salmon (v0.6.0)
Genome_build: Suscrofa.10.2 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

organism: Sus scrofa

source_name: Liver tissue

extract_protocol:
TRIzol Reagent (Invitrogen, CA, USA) was used to extract the total RNA, and subsequently treated with DNase and purified by using an RNeasy Mini Kit (Qiagen, CA, U.S.A.)
RNA samples were prepared by using about 5 µg RNA per sample. LncRNA sequencing libraries were generated by using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® ((New England Biolabs Ipswich, Massachusetts, USA) according the manufacturer’s provided information and library qualities were analyzed by the Agilent Bioanalyzer 2100 system. Small RNA library was prepared by using a total of 5 μg of RNA per sample as an input material. In order to generate sequencing libraries, NEBNext® Multiplex Small RNA sequencing Library Prep Set for Illumina® ((New England Biolabs Ipswich, Massachusetts, USA) was used by following the manufacturer’s provided information and to attribute sequences to each sample index codes were added. An Agilent Bioanalyzer 2100 system was used to test the library quality

tag: development stage

value: Old

value: Liver

tag: age

value: 8 years after birth


title: RNA Old-liver-2


title: C6_r1


title: RNA Young-liver-2

value: Yong

value: 180 days after birth


title: C3_r3

value: adding a C3 chromosome


title: gPSC15

value: gPSC cell line derived from GCs


title: C3_r2


title: C3_r1


title: C2_r3

value: adding a C2 chromosome


title: C2_r2


title: C2_r1


title: RNA Young-liver-1


title: C6_r3

value: adding a C6 chromosome


title: Bacteroides thetaiotaomicron VPI-5482_media_2h

city: Aberdeen

first: Imke

last: Mulder

address: Cornhill Road

institute: 4D Pharma Research Ltd

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
61090_532

hyb_protocol: Hybridization was performed following the NimbleGen Systems Inc. standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed following the NimbleGen Systems Inc. standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Bacteroides thetaiotaomicron VPI-5482

source_name: Bacteroides thetaiotaomicron VPI-5491

label_protocol: Labeling was performed using the One-Color DNA labeling Kit (Roche NimbleGen Inc) following manufacturers instructions.

growth_protocol: Caco2 cells were seeded in 35mm dishes in 10% FBS/4mM L-glutamine/1xAntibiotic-Antimycotic/DMEM media and grown at 5% CO2/37oC for 6 days. Cells were washed twice with Hank's Balanced Salt Solution and synchronised in serum and antibiotic free media for 24 hours before treatment.

extract_protocol: Bacterial culture was removed and RNA was prepared using Nucleospin II RNA Extraction Kit and reverse transcribed to cDNA using SuperScript II both following manufacturers instructions.

treatment_protocol: Synchronised cells were treated with flagellin of Salmonella enteritidis (10ng/well), phorbol-12-myristate-13-acetate (150ng/well) or interleukin 1 (10ng/well). Bacteroides thetaiotaomicron was added at 10^9 CFU/mL and incubated for 2 hours.

tag: treatment

value: Media

tag: incubation


title: C1_r3

value: adding a C1 chromosome


title: LCMV_CD206pos_MHCIIneg_1

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: CD206+ MHC-II- Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 1

hyb_protocol: Labeled cRNA were hybridized to these arrays according to the manufacturer’s guidelines (Affymetrix) in blinded interleaved fashion.

scan_protocol: The Scanner 3000 (Affymetrix) was used in conjunction with Affymetrix AGCC software (v4.0) to generate one .CEL file per hybridized cRNA.

data_processing: The Expression Console (Affymetrix) was used to generate 29,129 RMA normalized transcript expression values per .CEL file.

label: biotin

label_protocol: Total RNA was labeled on a sample-by-sample basis according to the manufacturer’s guidelines for use with the Mouse Clariom S Array (Affymetrix).

growth_protocol: C57BL/6J (B6) were purchased from The Jackson Laboratory (Bar Harbor, ME).  All mice in this study were handled in accordance with the guidelines set forth by the NIH Animal Care and Use Committee.

extract_protocol: CD206+ MHC-II+ or CD206+ MHC-II- macrophages were isolated from PBS or LCMV-infected mice at day 30 post-infection using a Beckman Astrios Cell Sorter. Macrophages were sorted to >95% purity based on the following markers: 7-AAD− Thy1.2−CD45.2+ CD11b+ Gr1− F4/80+ CD206+ and IAb/IEb +. FACS-sorted cells were collected in TRIzol (Invitrogen), and total RNA was extracted using PureLink RNA Micro kits (Life Technologies) per the manufacturer’s instructions.

treatment_protocol: To induce subacute meningitis, adult mice at 6–8 weeks of age were infected intracerebrally (i.c.) with 1,5 × 104 plaque-forming units of r3LCMV. Survival was monitored daily. Stocks were prepared by a single passage on BHK-21 cells, and viral titers were determined by plaque formation on Vero cells.

value: macrophages of the meninges

tag: condition

value: LCMV-infected

tag: markers

value: CD206+ MHC-II-


title: Bacteroides thetaiotaomicron VPI-5482_0h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
59915_532

source_name: Bacteroides thetaiotaomicron VPI-5490

value: No treatment


title: LCMV_CD206pos_MHCIIneg_3

description: CD206+ MHC-II- Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 3


title: LCMV_CD206pos_MHCIIpos_4

description: CD206+ MHC-II+ Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 4

value: CD206+ MHC-II+


title: LCMV_CD206pos_MHCIIneg_4

description: CD206+ MHC-II- Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 4


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_Fla_2h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
59865_532

source_name: Bacteroides thetaiotaomicron VPI-5489

value: Caco-2 and flagellin of Salmonella enteritidis


title: LCMV_CD206pos_MHCIIneg_2

description: CD206+ MHC-II- Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 2


title: C1_r2

value: Leaf

value: The newly expanded third leaves without petioles

tag: genotype


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_SE_2h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
59382_532

source_name: Bacteroides thetaiotaomicron VPI-5487

value: Caco-2 and Salmonella enteritidis


title: LCMV_CD206pos_MHCIIpos_1

description: CD206+ MHC-II+ Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 1


title: PBS_CD206pos_MHCIIneg_2

description: CD206+ MHC-II- Macrophages of the Meninges Post PBS Treatment - Biological Replicate 2

value: PBS-treated


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_2h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
59299_532

source_name: Bacteroides thetaiotaomicron VPI-5486


title: PBS_CD206pos_MHCIIneg_4

description: CD206+ MHC-II- Macrophages of the Meninges Post PBS Treatment - Biological Replicate 4


title: C1_r1


title: RBR_r2

value: normal


title: RBR_r1


title: RBR_r3


title: vector-36hpt

status: Public on Mar 05 2019

city: nanjing

first: zhao

last: yongxiang

address: NO.1,Weigang, Xuanwu District of Nanjing

institute: Nanjing Agricultural University

description: MARC-145 cells transfected with empty vector at 36pht

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
RNA-seq reads were aligned to the monkey genome assembly using Hisat2 version 2.0.5
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Ballgown version 2.8.4
Genome_build: chlSab2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Chlorocebus sabaeus

source_name: Kidney

extract_protocol:
Total RNA extraction from the transfected cells was performed using TRIzol by following the standard instructions (Invitrogen, CA). An amount of 2ug of total RNA were  performed twice Oligo(dT) selection using Poly(A) mRNA Magnetic Isolation Module (NEB).
After selection, mRNA was fragmented, and sequencing libraries were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

value: a monkey kidney cell line

tag: passages


title: vector-48hpt

description: MARC-145 cells transfected with empty vector at 48pht


title: PBS_CD206pos_MHCIIneg_3

description: CD206+ MHC-II- Macrophages of the Meninges Post PBS Treatment - Biological Replicate 3


title: C4_r1

value: adding a C4 chromosome


title: PBS_CD206pos_MHCIIneg_1

description: CD206+ MHC-II- Macrophages of the Meninges Post PBS Treatment - Biological Replicate 1


title: LCMV_CD206pos_MHCIIpos_3

description: CD206+ MHC-II+ Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 3


title: MAVS-48hpt

description: MARC-145 cells transfected with MAVS at 48pht


title: vector-24hpt

description: MARC-145 cells transfected with empty vector at 24pht


title: PBS_CD206pos_MHCIIpos_4

description: CD206+ MHC-II+ Macrophages of the Meninges Post PBS Treatment - Biological Replicate 4


title: ΔLMP1-MAVS-48hpt

description: MARC-145 cells transfected with ΔLMP1-MAVS at 48pht


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_SE_1h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
57435_532

source_name: Bacteroides thetaiotaomicron VPI-5483


title: MAVS-36hpt

description: MARC-145 cells transfected with MAVS at 36pht


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_PMA_1h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
57990_532

source_name: Bacteroides thetaiotaomicron VPI-5484


title: ΔLMP1-MAVS-36hpt

description: MARC-145 cells transfected with ΔLMP1-MAVS at 36pht


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_1h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
46159_532

source_name: Bacteroides thetaiotaomicron VPI-5482


title: PBS_CD206pos_MHCIIpos_1

description: CD206+ MHC-II+ Macrophages of the Meninges Post PBS Treatment - Biological Replicate 1


title: MAVS-24hpt

description: MARC-145 cells transfected with MAVS at 24pht


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_Fla_1h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
59131_532

source_name: Bacteroides thetaiotaomicron VPI-5485


title: PBS_CD206pos_MHCIIpos_3

description: CD206+ MHC-II+ Macrophages of the Meninges Post PBS Treatment - Biological Replicate 3


title: ΔLMP1-MAVS-24hpt

description: MARC-145 cells transfected with ΔLMP1-MAVS at 24pht


title: Leaf removed 6 h rep d

city: College Station

first: Scott

middle: Andrew

last: Finlayson

state: Texas

address: 370 Olsen Blvd

department: SOil and Crop Sciences

institute: Texas A&M University

description: LR 6 h - L6d (GE)

data_processing:
Reads were mapped to the Phytozome 3.1 sorghum genome sequence using CLC Genomics Workbench 8.5.1 giving an average of 28 M unique exon reads per sample.
A multi-group comparison was created and expression differences were assessed using CLC Genomics Workbench 8.5.1’s Extraction of Differential Gene Expression (EDGE) algorithm.
Genome_build: Phytozome 3.1 sorghum genome sequence
Supplementary_files_format_and_content: Processed data is in Excel (xlsx) format.  The data includes feature IDs,  EDGE test of Leaf Removed vs Intact Leaf samples at 1, 3 and 6 h, annotations, exon lengths, total and unique gene, exon and intron reads, and RPKM.

organism: Sorghum bicolor

source_name: Leaf removed 6 h_first axillary bud

growth_protocol: Seeds were sown singly in 50 mL conical centrifuge tubes modified with a drain hole and filled with LC1 soilless medium supplemented with 7.5g/L 20-20-20 Osmocote fertilizer.  Plants were grown in a growth chamber providing 575 mM m-2s-1 of PAR at a R:FR of 13.30 from t5 fluorescent lamps with a photoperiod of 16/8 light dark and 32/22oC day night temperatures.

extract_protocol:
RNA was extracted using Trizol, the extracted RNA was digested with DNAseI and purified using an RNAeasy kit.
Libraries were constructed with the Illumina TruSeq kit and 125 bp reads were obtained from an Illumina HiSeq 2500 sequencer.

treatment_protocol: Treatments began 7 days after sowing.  Plants were left intact, or leaf removal was conducted by peeling the entire coleoptile and first leaf from the culm to expose the axillary bud.  The dissection was easily accomplished with minimal handling and without touching the bud.  Axillary buds from the first leaf axil were harvested at 1, 3 and 6 h after leaf removal.  Four replicates of 15 buds were harvested.  The three highest quality replicates of each sample (by Bioanalyzer) were used for transcriptome analysis.

tag: cultivar

value: 7 days after sowing

value: 6h after leaf removal

value: First axillary bud


title: gPSC2

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

source_name: gPSC cell line derived from GCs

tag: strain

tag: cell type

value: gPSC cell line derived from GCs


title: Leaf removed 6 h rep b

description: LR 6 h - L6b (GE)


title: Leaf removed 3 h rep b

description: LR 3 h - L3b (GE)

source_name: Leaf removed 3 h_first axillary bud

value: 3h after leaf removal


title: Leaf removed 3 h rep c

description: LR 3 h - L3c (GE)


title: Leaf removed 3 h rep d

description: LR 3 h - L3d (GE)


title: Intact 6 h rep d

description: Con 6 h - C6d (GE)

source_name: Intact 6 h_first axillary bud

value: left intact


title: Leaf removed 6 h rep a

description: LR 6 h - L6a (GE)


title: Leaf removed 1 h rep c

description: LR 1 h - L1c (GE)

source_name: Leaf removed 1 h_first axillary bud

value: 1h after leaf removal


title: Intact 6 h rep c

description: Con 6 h - C6c (GE)


title: Leaf removed 1 h rep d

description: LR 1 h - L1d (GE)


title: Intact 1 h rep d

description: Con 1 h - C1d (GE)

source_name: Intact 1 h_first axillary bud


title: Intact 3 h rep a

description: Con 3 h - C3a (GE)

source_name: Intact 3 h_first axillary bud


title: Intact 1 h rep c

description: Con 1 h - C1c (GE)


title: Leaf removed 1 h rep b

description: LR 1 h - L1b (GE)


title: Intact 1 h rep b

description: Con 1 h - C1b (GE)


title: Intact 6 h rep a

description: Con 6 h - C6a (GE)


title: Intact 3 h rep c

description: Con 3 h - C3c (GE)


title: Intact 3 h rep b

description: Con 3 h - C3b (GE)


title: 28D_1

source_name: 28D reprogramming cells

value: 28D reprogramming cells


title: Bacteroides thetaiotaomicron VPI-5482_Caco-2_PMA_2h

description:
This sample is from wild-type Bacteroides thetaiotaomicron VPI-5482
59854_532

source_name: Bacteroides thetaiotaomicron VPI-5488


title: naïve rep3

source_name: not activated Infective Juvenile(IJ)

value: ALL

value: wild type

tag: developmental stage

value: Infective Juvenile (IJ)

value: whole body

tag: time point

value: naïve


title: AML_with_high_TET1 [S159]

city: Hangzhou

first: Jinghan

last: Wang

address: No.79 Qingchun Road, Hangzhou 310003 Zhejiang, People’s Republic of China

institute: Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, P.R. China

description: High TET1 expresser

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: Bone marrow blasts

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit (Cat # 217004，QIAGEN, GmbH, Germany), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Twenty four de novo AML samples were obtained from mononuclear cells isolated by Ficoll gradient centrifugation before patients recieved chemotherapy.

tag: Sex

value: Female


title: AML_with_high_TET1 [S11]

description: High TET1 expresser

value: Male


title: AML_with_high_TET1 [S45]

description: High TET1 expresser


title: AML_with_high_TET1 [S83]

description: High TET1 expresser


title: AML_with_high_TET1 [S29]

description: High TET1 expresser


title: AML_with_high_TET1 [S40]

description: High TET1 expresser


title: AML_with_high_TET1 [S51]

description: High TET1 expresser


title: AML_with_high_TET1 [S101]

description: High TET1 expresser


title: AML_with_high_TET1 [S127]

description: High TET1 expresser


title: AML_with_high_TET1 [S73]

description: High TET1 expresser


title: AML_with_high_TET1 [S163]

description: High TET1 expresser


title: AML_with_low_TET1 [S24]

description: Low TET1 expresser


title: AML_with_low_TET1 [S65]

description: Low TET1 expresser


title: AML_with_low_TET1 [S36]

description: Low TET1 expresser


title: ES_1

source_name: Female ES cell line from the same strain

treatment_protocol: For the experiments by treatment with crotonic acid during induction, 7 mM crotonic acid (pH=7) was added into induction medium from 16D to 28D continuously; For the induced PGCLCs, ESCs or gSCs treated with 1%KSR, 1. ng/ml bFGF and 2ng/ml Activin A for 2 days can form EpiLCs, and further treated with 500 ng/ml BMP4, 100 ng/ml SCF, 50ng/ml EGF and 1000 IU mLif for 4 days to form PGCLCs.


title: AML_with_low_TET1 [SS]

description: Low TET1 expresser


title: AML_with_low_TET1 [S151]

description: Low TET1 expresser


title: AML_with_low_TET1 [S84]

description: Low TET1 expresser


title: AML_with_low_TET1 [S62]

description: Low TET1 expresser


title: AML_with_low_TET1 [S172]

description: Low TET1 expresser


title: AML_with_low_TET1 [S80]

description: Low TET1 expresser


title: AML_with_low_TET1 [S141]

description: Low TET1 expresser


title: AML_with_low_TET1 [S81]

description: Low TET1 expresser


title: AML_with_low_TET1 [S34]

description: Low TET1 expresser


title: PBS_CD206pos_MHCIIpos_2

description: CD206+ MHC-II+ Macrophages of the Meninges Post PBS Treatment - Biological Replicate 2

value: macrophages of the meninges

value: PBS-treated

value: CD206+ MHC-II+


title: 73_OPTC_D00_6029: LAIV-Day-0

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Targeted RNA-Seq analysis completed in Illumina BaseSpace using TruSeq Targeted RNA version 1.0.1.
In summary, alignment using Smith-Waterman algorithm. Alignments that include more than 3 indels are filtered from alignment results.
Read 1 is evaluated against the reverse complement of the downstream locus-specific oligos (ULSO). Read 2 is evaluated against locus-specific oligos. If the start of a read matches a probe sequence with no more than 1 mismatch, the full length of the read is aligned against the amplicon target for that sequence. Alignments that include more than 3 indels are filtered from alignment results.
Differential expression analysis comprises three steps: depth of sequencing normalization, variance estimation, and p-value calculation.
Paired comparisons for RNA seq differential expression were completed using DESeq2 with non-default options for sharingMode =”fit-only” and fitType=”local”
Genome_build: Targeted RNA-Seq build Hg19
Supplementary_files_format_and_content: Targeted RNA-Seq inexcel format includes, Raw Mean counts, Normalized Mean Counts, Fold Change, Log2 Fold Change, p-value, and q-value.

source_name: Blood

extract_protocol:
Total RNA was isolated from PAXgene tubes using the PAXgene Blood RNA Kit following the manufacturer’s protocol. RNA Quality and quantity were assessed by Agilent Tapestation 2200 and Invitrogen Qubit 2.0 fluorometer.
50ng of Total RNA was used to perform a multiplexed gene expression profiling panel of 81 select targets using the TruSeq Targeted RNA Expression guide rev. C following the manufacturer’s protocol. In summary, the chemistry begins with reverse transcribing cDNA from purified total RNA. Two custom-designed oligonucleotide probes with adapter sequences hybridize up and downstream of the region of interest. An Extension-ligation reaction, following by amplification creates a new template strand. Templates are then PCR amplified to add indices, creating sequence-ready libraries. Final cDNA libraries quality and quantity were assessed following the previously discussed methods.

treatment_protocol: Whole human blood collected in Paxgene Tubes

tag: tissue

value: Blood

value: LAIV

tag: day


title: AML_with_high_TET1 [S104]

description: High TET1 expresser


title: 71_OPTC_D07_6008: IIV-Day-7

value: IIV


title: 72_OPTC_D00_5260: IIV-Day-0


title: LCMV_CD206pos_MHCIIpos_2

description: CD206+ MHC-II+ Macrophages of the Meninges Post LCMV Treatment - Biological Replicate 2

value: LCMV-infected


title: 70_OPTC_D00_6015: LAIV-Day-0


title: 67_OPTC_D00_6008: IIV-Day-0


title: 59_OPTC_D07_5295: LAIV-Day-7


title: 60_OPTC_D07_5258: IIV-Day-7


title: 58_OPTC_D07_6013: IIV-Day-7


title: 63_OPTC_D00_5295: LAIV-Day-0


title: 64_OPTC_D00_5258: IIV-Day-0


title: 54_OPTC_D07_6012: IIV-Day-7


title: 65_OPTC_D00_6019: IIV-Day-0


title: 61_OPTC_D00_6017: LAIV-Day-0


title: 55_OPTC_D00_5265: IIV-Day-0


title: 57_OPTC_D07_6017: LAIV-Day-7


title: 53_OPTC_D00_6016: LAIV-Day-0


title: 52_OPTC_D00_5257: IIV-Day-0


title: 51_OPTC_D07_5265: IIV-Day-7


title: 68_OPTC_D07_5260: IIV-Day-7


title: 69_OPTC_D07_6019: IIV-Day-7


title: 48_OPTC_D00_5089: IIV-Day-0


title: 47_OPTC_D07_5089: IIV-Day-7


title: 49_OPTC_D07_6016: LAIV-Day-7


title: 46_OPTC_D07_5086: LAIV-Day-7


title: 44_OPTC_D00_5070: LAIV-Day-0


title: 50_OPTC_D00_6012: IIV-Day-0


title: 66_OPTC_D07_6015: LAIV-Day-7


title: 42_OPTC_D07_5104: LAIV-Day-7


title: 41_OPTC_D00_5104: LAIV-Day-0


title: 43_OPTC_D07_5070: LAIV-Day-7


title: 40_OPTC_D07_5103: LAIV-Day-7


title: 56_OPTC_D07_5257: IIV-Day-7


title: Mature_Bap60-KD-MB_5

city: London

first: Jamie

middle: M

last: Kramer

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

country: Canada

institute: University of Western Ontario

data_processing:
Basecalls performed using RTA v2
RNA-Seq reads were trimmed using Prinseq-lite 0.20.4 quality aware trimming
Reads were aligned to the Drosophila genome using STAR 2.5.3a
Count tables were generated using HT-Seq Count v0.7.1 to count reads to genic features
Genome_build: BDGP release 6
Supplementary_files_format_and_content: processed data files are raw count tables in .txt format.

organism: Drosophila melanogaster

source_name: Mature-Bap60-KD MB

growth_protocol: Flies raised at 25°C and 70% humidity on standard agar growth medium

extract_protocol:
Mushroom body specific nuclei isolated using INTACT method (PMID:30158319), RNA extracted using Arcturus PicoPure RNA Isolation Kit (ThermoFisher: KIT0204)
RNA-Sequencing Library prepared using Nugen Ovation Universal RNA-Seq System for Drosophila  (Nugen: NU035032)

value: 1-5 days post-eclosion

value: male

tag: genotype/variation

tag: sample type

value: mushroom body nuclei


title: Mature_Bap60-KD-MB_3

tag: age


title: 62_OPTC_D00_6013: IIV-Day-0


title: 38_OPTC_D00_5099: LAIV-Day-0


title: Mature_Bap60-KD-MB_2


title: Mature_Bap60-KD-MB_4


title: 37_OPTC_D07_5099: LAIV-Day-7


title: Mature_Bap60-KD-MB_1


title: Mature_mCherry_4

source_name: Mature-mCherry


title: Mature_mCherry_3


title: Mature_mCherry_5


title: 45_OPTC_D00_5086: LAIV-Day-0


title: 35_OPTC_D00_5213: IIV-Day-0


title: Mature_mCherry_2


title: 34_OPTC_D00_5107: LAIV-Day-0


title: Juvenile_mCherry_3

source_name: Juvenile-mCherry

value: 0-3h post-eclosion


title: Juvenile_Bap60-KD-MB_1

source_name: Juvenile-Bap60-KD MB


title: 33_OPTC_D07_5107: LAIV-Day-7


title: Juvenile_Bap60-KD-MB_2


title: Mature_mCherry_1


title: 32_OPTC_D00_5212: IIV-Day-0


title: Juvenile_mCherry_2


title: 39_OPTC_D00_5103: LAIV-Day-0


title: 30_OPTC_D07_5201: IIV-Day-7


title: 31_OPTC_D07_5212: IIV-Day-7


title: Juvenile_mCherry_1


title: P7 Control biological replicate 3

city: Rochester

first: Xuhui

last: Dong

state: NY

address: 601 ELMWOOD AVE

institute: University of Rochester

data_processing:
alignment: Tophat 2
differentially expressed gene identification: Cufflinks
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with RPKM

source_name: RNA-Seq of Mus musculus: P7 control retina

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57BL/6J; 129S6 mixed background

value: retina

value: Postnatal day 7

value: control


title: P7 Control biological replicate 2


title: P7 Lhx4 Mutant biological replicate 2

source_name: RNA-Seq of Mus musculus: P7 Lhx4-null retina


title: 36_OPTC_D07_5213: IIV-Day-7


title: P7 Control biological replicate 1


title: 29_OPTC_D00_5201: IIV-Day-0


title: P7 Lhx4 Mutant biological replicate 3


title: 28_OPTC_D00_5110: IIV-Day-0


title: 27_OPTC_D07_5110: IIV-Day-7


title: A_S_05_21T_Cy3_vs_B_S_06_10T_Cy5

city: Hannover

first: Daniel

last: Sedding

address: Carl-Neubergstr. 1

department: Cardiology

institute: Hannover Medical School

hyb_protocol: Labeling, hybridization and scanning was performed by LC Sciences, LLC, Houston, Texas, USA)

data_processing: Data processing was performed by LC Sciences, LLC, Houston, Texas, USA)

source_name: S_05_21T_femoral artery, injured, 21 days

extract_protocol: miRNA was isolated using the PureLink miRNA Isolation kit according to the manufacturer's instructions (Thermo Fisher Scientific, MA, USA, Cat#K157001)

value: 12 weeks old

tag: gender

value: femoral artery

tag: treatment

value: injured

tag: time

value: 21 days

source_name: S_06_10T femoral artery, injured, 10 days

value: 10 days


title: 26_OPTC_D00_5111: IIV-Day-0

value: Blood


title: A_S_03_Control_Cy3_vs_B_S_04_21T_Cy5

scan_protocol: Labeling, hybridization and scanning was performed by LC Sciences, LLC, Houston, Texas, USA)

source_name: S_03_Control_femoral artery

source_name: S_04_21T_femoral artery, injured, 21 days


title: 25_OPTC_D07_5111: IIV-Day-7


title: P7 Lhx4 Mutant biological replicate 1


title: 24_OPTC_D00_5050: LAIV-Day-0

value: LAIV


title: 23_OPTC_D07_5069: LAIV-Day-7


title: 22_OPTC_D07_5064: IIV-Day-7

value: IIV


title: 21_OPTC_D07_5040: IIV-Day-7


title: 20_OPTC_D07_5066: IIV-Day-7


title: 19_OPTC_D07_5044: LAIV-Day-7


title: A_S_01_10T_Cy3_vs_B_S_02_Control_Cy5

source_name: S_01_10T_femoral artery, injured, 10 days

label_protocol: Labeling, hybridization and scanning was performed by LC Sciences, LLC, Houston, Texas, USA)

source_name: S_02_Control_femoral artery


title: 17_OPTC_D00_5040: IIV-Day-0


title: 18_OPTC_D00_5069: LAIV-Day-0


title: A_HepG2 TGF_day8_1

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw expression bead array data was exported from Genome Studio (version 2010.3, Illumina) into BRB-ArrayTools software (version 4.3.1, developed by Dr. Richard Simon and the BRB-ArrayTools Development Team). Data was normalized and annotated using the R/Bioconductor package “lumi”.

source_name: HepG2 TGF_day8

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Huh7 and HepG2 cells (American Type Culture Conditions) were cultured in DMEM medium (Gibco) at 37°C and 5% CO2, and were regularly tested for mycoplasma contamination (MycoAlert detection kit, Lonza).

extract_protocol: Total RNA was isolated using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions. RNA quantity and quality were assessed with a ND-8000 spectrophotometer and bioanalyzer. 500 ng of total RNA was used for each Human HT-12 Expression BeadChips (Illumina).

treatment_protocol: Cells were plated and allowed to adhere before adding medium containing 10ng/ml final of TGF-β1 (recombinant human, Peprotech).

tag: cell line

value: TGFb


title: C_HepG2 TGF_day8_3


title: F_HepG2 NEG_day8_1

source_name: HepG2 NEG_day8

value: Control


title: 5_Huh7 NEG_day8_2

source_name: Huh7 NEG_day8


title: D_HepG2 NEG_day8_3


title: 5_Huh7 NEG_day8_2_rep


title: 3_Huh7 TGF_day8_3

source_name: Huh7 TGF_day8


title: E_HepG2 NEG_day8_2


title: 1_Huh7 TGF_day8_1


title: 15_OPTC_D07_5050: LAIV-Day-7

source_name: Blood


title: 4_Huh7 NEG_day8_1


title: 146_OPTC_D00_6158: LAIV-Day-0


title: 145_OPTC_D07_6158: LAIV-Day-7


title: 144_OPTC_D07_6113: IIV-Day-7


title: 143_OPTC_D07_6109: LAIV-Day-7


title: B_HepG2 TGF_day8_2


title: 141_OPTC_D00_6151: IIV-Day-0


title: 140_OPTC_D00_6114: IIV-Day-0


title: 14_OPTC_D00_5066: IIV-Day-0


title: 16_OPTC_D00_5064: IIV-Day-0


title: sample24_Huh7_day8_TGF_3

type: genomic

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation HM450 Beadchip using standard Illumina protocol

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

data_processing: R/Bioconductor: color bias adjustment, followed by inter-sample quantile normalization, and probe bias correction with intra-array beta-mixture quantile normalization (BMIQ)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver cancer cell lines using desalting protocol

value: liver cancer cell line


title: sample21_Huh7_day8_neg_3


title: sample12_HEpG2_day8_TGF_3


title: sample17_Huh7_day4_TGF_2


title: sample18_Huh7_day4_TGF_3


title: 2_Huh7 TGF_day8_2


title: sample15_Huh7_day4_neg_3


title: sample23_Huh7_day8_TGF_2


title: sample8_HEpG2_day8_neg_2


title: sample22_Huh7_day8_TGF_1


title: sample19_Huh7_day8_neg_1


title: sample14_Huh7_day4_neg_2


title: 138_OPTC_D00_6154: IIV-Day-0


title: TS246

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

source_name: Human cord blood

extract_protocol: Genomic DNA was isolated using the DNeasy Blood & Tissue kit (Qiagen) as per manufacturer’s instructions. DNA was then purified and concentrated using the DNA Clean & Concentrator kit (Zymo Research).

tag: subject status

value: healthy child born via caesarian section

value: F

value: Human cord blood

tag: monocytes

tag: granulocytes

tag: nrbcs

tag: nk cells

tag: b cells

tag: cd4t cells

tag: cd8t cells


title: sample4_HEpG2_day4_TGF_1

tag: cell type


title: TS245

tag: Sex

tag: tissue


title: TS247


title: sample2_HEpG2_day4_neg_2


title: 136_OPTC_D00_6113: IIV-Day-0

tag: day


title: sample9_HEpG2_day8_neg_3


title: sample3_HEpG2_day4_neg_3


title: sample6_HEpG2_day4_TGF_3


title: sample11_HEpG2_day8_TGF_2


title: sample16_Huh7_day4_TGF_1


title: sample5_HEpG2_day4_TGF_2


title: sample7_HEpG2_day8_neg_1


title: sample13_Huh7_day4_neg_1


title: sample20_Huh7_day8_neg_2


title: 135_OPTC_D07_6109: LAIV-Day-0


title: 139_OPTC_D00_6111: IIV-Day-0


title: 134_OPTC_D07_6154: IIV-Day-7


title: sample1_HEpG2_day4_neg_1


title: TS241

value: M


title: 133_OPTC_D07_6116: LAIV-Day-7


title: TS244


title: 131_OPTC_D07_6151: IIV-Day-7


title: sample10_HEpG2_day8_TGF_1


title: TS242


title: TS237


title: TS243


title: 132_OPTC_D07_6155: IIV-Day-7


title: 130_OPTC_D07_6114: IIV-Day-7


title: TS240


title: TS239


title: TS234


title: cerebellum_oxbs_95

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

institute: University of Exeter Medical School

description: whole blood taken from sample 6842

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the final report files generated by Genome Studio (Illumina) software. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions. Pfilter function removed 15 samples and 38737 probes where 5% of sites had a detection p-value > 0.05

source_name: cerebellum

label_protocol: 1μg DNA from each sample was treated with sodium BS and OxBS in parallel using the true-methyl CEGX 96 kit (CEGX, Cambridge, UK) according to the manufacturer’s standard protocol

extract_protocol: Genomic DNA was extracted from frozen 100mg postmortem brain samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

tag: post-mortem diagnosis

value: Alzheimer's disease

tag: age at death

tag: braak stage

value: IV

tag: post-mortem interval(min)


title: cerebellum_bs_95

description: whole blood taken from sample 6841

tag: gender


title: cerebellum_oxbs_94

description: whole blood taken from sample 6892

value: I


title: 13_OPTC_D00_5044: LAIV-Day-0


title: cerebellum_bs_96

description: whole blood taken from sample 6851

value: VI


title: cerebellum_bs_93

description: whole blood taken from sample 6591

value: V


title: cerebellum_oxbs_96

description: whole blood taken from sample 6852


title: 129_OPTC_D07_6111: IIV-Day-7


title: 128_OPTC_D00_6156: IIV-Day-0


title: cerebellum_bs_94

description: whole blood taken from sample 6891


title: cerebellum_oxbs_93

description: whole blood taken from sample 6592


title: TS233

tag: subject status


title: 137_OPTC_D00_6116: LAIV-Day-0


title: cerebellum_bs_92

description: whole blood taken from sample 6581


title: 127_OPTC_D00_6152: IIV-Day-0


title: 124_OPTC_D07_6156: IIV-Day-7


title: 125_OPTC_D00_6112: IIV-Day-0


title: 126_OPTC_D00_6115: LAIV-Day-0


title: TS231

tag: monocytes


title: TS230

tag: granulocytes


title: TS236

tag: nrbcs


title: cerebellum_oxbs_91

description: whole blood taken from sample 6552


title: TS225

tag: nk cells


title: cerebellum_bs_89

description: whole blood taken from sample 6811


title: cerebellum_oxbs_89

description: whole blood taken from sample 6812


title: cerebellum_bs_91

description: whole blood taken from sample 6551


title: cerebellum_oxbs_92

description: whole blood taken from sample 6582


title: cerebellum_oxbs_90

description: whole blood taken from sample 6872

value: II


title: TS226

tag: b cells


title: 123_OPTC_D07_6152: IIV-Day-7


title: TS227

tag: cd4t cells


title: 121_OPTC_D07_6112: IIV-Day-7


title: cerebellum_oxbs_88

description: whole blood taken from sample 7252


title: cerebellum_bs_90

description: whole blood taken from sample 6871


title: cerebellum_bs_88

description: whole blood taken from sample 7251


title: cerebellum_bs_87

description: whole blood taken from sample 7221


title: TS223

tag: cd8t cells


title: cerebellum_oxbs_85

description: whole blood taken from sample 7202


title: cerebellum_oxbs_87

description: whole blood taken from sample 7222


title: 122_OPTC_D07_6115: LAIV-Day-7


title: TS228


title: TS235


title: cerebellum_bs_85

description: whole blood taken from sample 7201


title: cerebellum_oxbs_83

description: whole blood taken from sample 6722


title: 12_OPTC_D07_5039: LAIV-Day-7


title: 120_OPTC_D00_6035: IIV-Day-0


title: cerebellum_bs_83

description: whole blood taken from sample 6721


title: cerebellum_oxbs_82

description: whole blood taken from sample 6502


title: 119_OPTC_D00_6034: IIV-Day-0


title: TS224


title: cerebellum_oxbs_86

description: whole blood taken from sample 6522


title: 118_OPTC_D07_6034: IIV-Day-7


title: cerebellum_bs_86

description: whole blood taken from sample 6521


title: cerebellum_bs_78

description: whole blood taken from sample 6661


title: cerebellum_oxbs_80

description: whole blood taken from sample 6462


title: cerebellum_bs_80

description: whole blood taken from sample 6461


title: cerebellum_bs_82

description: whole blood taken from sample 6501


title: 117_OPTC_D07_6035: IIV-Day-7


title: cerebellum_oxbs_79

description: whole blood taken from sample 6692


title: cerebellum_bs_79

description: whole blood taken from sample 6691


title: 116_OPTC_D00_6033: LAIV-Day-0


title: cerebellum_oxbs_78

description: whole blood taken from sample 6662


title: cerebellum_bs_75

description: whole blood taken from sample 6651


title: 114_OPTC_D07_6036: LAIV-Day-7


title: TS232


title: cerebellum_oxbs_84

description: whole blood taken from sample 6432


title: cerebellum_oxbs_75

description: whole blood taken from sample 6652


title: 115_OPTC_D07_6033: LAIV-Day-7


title: 113_OPTC_D00_6036: LAIV-Day-0


title: cerebellum_bs_84

description: whole blood taken from sample 6431


title: 112_OPTC_D00_6032: LAIV-Day-0


title: cerebellum_oxbs_74

description: whole blood taken from sample 6402


title: 111_OPTC_D07_6032: LAIV-Day-7


title: cerebellum_bs_74

description: whole blood taken from sample 6401


title: cerebellum_oxbs_76

description: whole blood taken from sample 6422


title: cerebellum_bs_73

description: whole blood taken from sample 6621


title: cerebellum_oxbs_73

description: whole blood taken from sample 6622


title: cerebellum_bs_76

description: whole blood taken from sample 6421


title: 110_OPTC_D00_6037: IIV-Day-0


title: cerebellum_oxbs_67

description: whole blood taken from sample 6562


title: cerebellum_bs_67

description: whole blood taken from sample 6561


title: cerebellum_oxbs_71

description: whole blood taken from sample 6392


title: 11_OPTC_D07_5035: IIV-Day-7


title: cerebellum_bs_71

description: whole blood taken from sample 6391


title: cerebellum_oxbs_72

description: whole blood taken from sample 6312


title: cerebellum_oxbs_81

description: whole blood taken from sample 6332

value: III


title: cerebellum_bs_81

description: whole blood taken from sample 6331


title: 109_OPTC_D07_6037: IIV-Day-7

value: Blood


title: 108_OPTC_D00_6038: IIV-Day-0


title: 106_OPTC_D07_6039: IIV-Day-7


title: cerebellum_bs_72

description: whole blood taken from sample 6311


title: 105_OPTC_D00_6039: IIV-Day-0


title: cerebellum_bs_70

description: whole blood taken from sample 6541


title: cerebellum_bs_69

description: whole blood taken from sample 6531


title: cerebellum_bs_65

description: whole blood taken from sample 6291


title: cerebellum_bs_61

description: whole blood taken from sample 6511


title: cerebellum_oxbs_65

description: whole blood taken from sample 6292


title: 103_OPTC_D07_6040: IIV-Day-7


title: 104_OPTC_D00_6040: IIV-Day-0


title: cerebellum_oxbs_61

description: whole blood taken from sample 6512


title: cerebellum_oxbs_69

description: whole blood taken from sample 6532


title: cerebellum_oxbs_77

description: whole blood taken from sample 6232


title: cerebellum_bs_77

description: whole blood taken from sample 6231


title: cerebellum_bs_66

description: whole blood taken from sample 7341


title: 102_OPTC_D07_6043: LAIV-Day-7

value: LAIV


title: cerebellum_oxbs_66

description: whole blood taken from sample 7342


title: 10_OPTC_D07_5034: IIV-Day-7

value: IIV


title: cerebellum_oxbs_70

description: whole blood taken from sample 6542


title: 101_OPTC_D00_6043: LAIV-Day-0


title: 107_OPTC_D07_6038: IIV-Day-7


title: cerebellum_bs_63

description: whole blood taken from sample 7261


title: cerebellum_bs_68

description: whole blood taken from sample 6211


title: cerebellum_oxbs_63

description: whole blood taken from sample 7262


title: PGC-OGD

city: Tianjin

last: Han

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

description: processed data file: matrix.txt

data_processing:
Base-calling performed using Off-Line Basecaller software (OLB V1.8).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genome (GRCm38) using Hisat2 software (V2.1.0) with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: matrix.txt: Tab-delimited text file includes abundance measurements.

source_name: PGC-1α-overexpressed HT-22 cells with OGD treatment

growth_protocol: HT-22 cells were cultured in Eagle’s Minimum Essential Medium (10-009-CVR, Coring) containing 10% fetal bovine serum (FBS, Life Technologies, Vienna, Austria) and 1% penicillin/streptomycin (Life Technologies) in 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit (Illumina) was used with 1~2 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: PGC-1α-overexpressed HT-22 cells and control were subjected to the hypoxia incubator chamber (5% CO2 and 95% N2) and exposed to oxygen and glucose deprivation (OGD) treatment for 2 h in EMEM medium without serum/glucose. After that, HT-22 cells were cultured in normal medium at 37°C for 24 h.

tag: cell line

tag: cell type

value: Hippocampal neurons

tag: genotype/variation

value: PGC-1alpha overexpression

tag: treatment

value: Oxygen and glucose deprivation (OGD)


title: PGC-A

description: processed data file: matrix.txt

source_name: PGC-1α-overexpressed HT-22 cells


title: Ctrl

description: processed data file: matrix.txt

source_name: HT-22 cells

value: Wild type


title: Ctrl-OGD

description: processed data file: matrix.txt

source_name: HT-22 cells with OGD treatment


title: cerebellum_oxbs_68

description: whole blood taken from sample 6212

tag: post-mortem diagnosis


title: 099_OPTC_D07_6107: IIV-Day-7

tag: tissue

tag: day


title: cerebellum_oxbs_58

description: whole blood taken from sample 6472

value: F

tag: age at death

tag: braak stage

tag: post-mortem interval(min)


title: cerebellum_oxbs_54

description: whole blood taken from sample 6372

tag: gender


title: cerebellum_bs_58

description: whole blood taken from sample 6471


title: 096_OPTC_D00_6022: LAIV-Day-0


title: 098_OPTC_D00_6108: IIV-Day-0


title: 097_OPTC_D07_6108: IIV-Day-7


title: 095_OPTC_D00_6025: IIV-Day-0


title: 094_OPTC_D07_6028: IIV-Day-7


title: 100_OPTC_D00_6107: IIV-Day-0


title: cerebellum_bs_54

description: whole blood taken from sample 6371


title: cerebellum_bs_57

description: whole blood taken from sample 6052


title: cerebellum_oxbs_59

description: whole blood taken from sample 6091


title: cerebellum_oxbs_64

description: whole blood taken from sample 6051

value: Control


title: cerebellum_bs_64

description: whole blood taken from sample 6032


title: cerebellum_oxbs_62

description: whole blood taken from sample 6031

value: M


title: cerebellum_bs_59

description: whole blood taken from sample 8202

value: Alzheimer's disease


title: 093_OPTC_D00_6031: IIV-Day-0


title: cerebellum_oxbs_57

description: whole blood taken from sample 8201


title: cerebellum_bs_62

description: whole blood taken from sample 6022


title: iHepatocytes_7days_BeP_1uM_replicate 3

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

description:
21_BeP_1uM
Gene expression in iPSC-derived human treated with 1 μM BeP for 7 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray (G4858A-072363) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

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

growth_protocol: iPSC-derived human hepatocytes (iCell® Hepatocytes 2.0) were obtained from FUJIFILM Cellular Dynamics (Madison, WI).  iPSC-derived human hepatocytes were plated using Plating Medium (FUJIFILM Cellular Dynamics) on the collagen I-coated cell culture plates following the manufacturer’s recommendations. On the 4th day after initial plating, Plating Medium was replaced with Maintenance Medium.  The Maintenance Medium was changed every 2 days.

extract_protocol: Total RNA was extracted from iPSC-derived human hepatocytes using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: iPSC-derived human hepatocytes (on the 4th day after seeding) were treated with 0.2 µM AFB1 or AFB2, 1 µM B[a]P or B[e]P, or 20 µM methapyrilene for 7 consecutive days.

value: iPSC-derived human hepatocytes


title: cerebellum_oxbs_51

description: whole blood taken from sample 6021


title: 092_OPTC_D07_6022: LAIV-Day-7


title: iHepatocytes_7days_BeP_1uM_replicate 2

description:
20_BeP_1uM
Gene expression in iPSC-derived human treated with 1 μM BeP for 7 days


title: cerebellum_bs_51

description: whole blood taken from sample 5992


title: cerebellum_oxbs_53

description: whole blood taken from sample 5991


title: 091_OPTC_D07_6025: IIV-Day-7


title: iHepatocytes_7days_BeP_1uM_replicate 1

description:
19_BeP_1uM
Gene expression in iPSC-derived human treated with 1 μM BeP for 7 days


title: iHepatocytes_7days_control_replicate 6

description:
15_Control
Gene expression in control iPSC-derived human hepatocytes after 7 days of incubation

value: control


title: iHepatocytes_7days_AFB2_0-2uM_replicate 2

description:
17_AFB2_0-2uM
Gene expression in iPSC-derived human treated with 0.2 μM AFB2 for 7 days