title: I1

city: Seoul

first: Sung-Yeon

last: Hwang

address: School of Biological Sciences, Seoul National University

country: South Korea

description:
Poly(A)+RNA
processed data file: M1_peaks.txt

data_processing:
For the analysis of MeRIP-seq, the adapters were trimmed using cutadapt (cutadapt -g TACAGTCCGACGATC -A TGGAATTCTCGGGTGCCAAGG). The 3′ and 5′ adapter sequences in the first and second read in a pair (due to the short insert size) were further trimmed and read pairs with either of the reads < 18 bp were discarded.
The remaining reads were then aligned to the combined human genome (hg19), and reporter L1 (pL1Hs) sequence using Spliced Transcripts Alignment to a Reference (STAR) and peak calling was performed with MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.txt: narrow peak (bed format)

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS, HyClone) and 1% (v/v) GlutaMAXI (Gibco).

extract_protocol:
48 h after transfection, total RNA was extracted using Trizol and then poly (A)+ RNA was purified using Poly (A) purist Mag kit (Invitrogen).
Poly (A)+ RNA was mixed with RNA fragmentation reagents (Invitrogen), and fragmented into 50-150 nt-long oligonucleotide by heating to 75°C for 5 min. Fragmented RNA was purified by ethanol precipitation. 6 μg of fragmented RNA was incubated with 4 μg of anti-m6A antibody (Merck, ABE572) in MeRIP buffer (50 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.1% NP-40) for 2 h on a rotating wheel at 4°C. After that, IP mixtures were mixed with Dynabead protein A (Invitrogen) and incubated overnight on a rotating wheel at 4°C. After five-times wash with MeRIP buffer, RNA was eluted twice by incubating for 1h on a rotating wheel at 4°C in elution buffer (6.7 mM m6A sodium salt and 200 unit/ml RNase inhibitor-containing MeRIP buffer). Eluted RNA was purified by ethanol precipitation. To generate cDNA library, RNA was dephosphorylated by CIP (Calf Intestinal alkaline phosphatase, NEB) and labeled with γ-32P-ATP using T4 polynucleotide kinase (Takara). RNA was run on 10% Urea-PAGE gel and purified from the excised gel corresponding to 50-150 nt-long RNA fragments. The extracted RNA was ligated to 3′ adapter by T4 RNA ligase 2, truncated KQ (NEB). RNA was then purified from free 3′ adapters by gel excision again. The 3′ adapter-ligated RNA was ligated to 5′ adapter by T4 RNA ligase 1 (NEB) and subsequently reverse transcribed by using SuperScript III reverse transcriptase (Invitrogen). cDNA library was amplified by PCR using Phusion HF polymerase (Thermo Fisher Scientific), separated by 6% acrylamide gel, and purified by gel excision.

treatment_protocol: HeLa cells were plated into two 100 mm dishes at 1.2 x 10e6 cells per each dish. 18 h later, cells were transfected 8 μg of pL1Hs per each dish using Lipefectamine 3000.

tag: cell line

value: HeLa

tag: transfected l1 expressing vector

tag: antibody


title: dilution_control_11

status: Public on Jan 09 2021

type: SRA

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

library_source: transcriptomic

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Only uniquely mapped reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
standard normalized count Fragments Per Kilobase of transcript per Million mapped reads (FPKM) except gene length in the formula is replaced with mapped length
Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Comma-separated (.csv) file include FPKM values for all the samples in the matrix form

molecule: total RNA

organism: Plasmodium falciparum

source_name: in vitro 3D7 strain culture

growth_protocol: P. falciparum 3D7 strain and subclone was maintained in RPMI 1640 medium (Gibco) supplemented with Albumax I (Gibco) (0.25%), hypoxanthine (Sigma) (0.1 mM), Sodium bicarbonate (Sigma) (2 g/L), and gentamicin (Gibco) (50 μg/L) in 2 % haematocrit at 37 oC on shaker.

extract_protocol:
Single cells were FACS sorted into lysis buffer directly. Total cell lysate was used for reverse transcription and cDNA amplification.
Illumina Nextera XT kit was used for library preparation according to the manufacturer's intructions.

tag: developmental stage

value: blood stage schizonts

tag: strain

value: 3D7 strain


title: dilution_control_14


title: BL03-D-4

city: Guangzhou

first: Li

middle: Bu

last: Su

address: No. 100, Xianlie Middle Road, Guangzhou, 510070, PR China

country: China

institute: Guangdong Institute of Microbiology

data_processing:
SeqPrep  (https://github.com/jstjohn/SeqPrep) used for basecalling
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads  ere separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
To identify DEGs (differential expression genes) between two different samples, the expression  level of each transcript was calculated according to the transcripts per million reads (TPM)  method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) [3] was used to quantify gene abundances
Supplementary_files_format_and_content: Excel file was genarated according to the transcripts per million reads (TPM) method to identify DEGs (differential expression genes) between two different samples

organism: Saccharomyces cerevisiae

growth_protocol: For cultivation, a single colony was picked up from a fresh YPD plate and transferred to a 5 mL YPD medium. After cultured at 200 rpm and 30°C, 1 mL seed culture was inoculated into a 250 mL shake-ﬂask with 50 mL YPD medium, or modified YPD medium (YPM) to an optical density (OD600) of about 0.05 and then incubated at 30 °C for 24 h.

extract_protocol:
Total RNA of different yeast cells was isolated after about 24 h cultivation using the HiPure Yeast RNA Kit (Magen, Guangzhou, China) according to the manufactur-er’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain type

tag: time


title: singlecell_112


title: dilution_control_17


title: dilution_control_15


title: 100cells_5


title: M1

institute: School of Biological Sciences, Seoul National University

organism: Homo sapiens

value: anti-m6A antibody (Merck, ABE572)


title: M2

description:
Poly(A)+RNA
processed data file: M2_peaks.txt


title: I2


title: 100cells_4


title: singlecell_99


title: singlecell_98


title: singlecell_97


title: 100cells_clone_2

value: 3D7 subclone


title: singlecell_clone_94


title: dilution_control_13


title: dilution_control_10


title: singlecell_96


title: 100cells_6


title: singlecell_clone_92


title: singlecell_clone_90


title: 100cells_clone_1


title: singlecell_92


title: singlecell_clone_95


title: singlecell_clone_89


title: singlecell_90


title: dilution_control_12


title: singlecell_clone_93


title: singlecell_95


title: singlecell_88


title: singlecell_clone_91


title: singlecell_94


title: singlecell_93


title: singlecell_84


title: singlecell_clone_97


title: singlecell_clone_96


title: singlecell_clone_88


title: singlecell_91


title: singlecell_89


title: singlecell_clone_80


title: singlecell_clone_86


title: singlecell_clone_84


title: singlecell_85


title: singlecell_clone_82


title: singlecell_83


title: singlecell_clone_83


title: singlecell_82


title: singlecell_clone_81


title: singlecell_87


title: Tspo mutant MA-10 cells rep2

city: Los Angeles

first: Vassilios

last: Papadopoulos

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences, School of

country: USA

institute: University of Southern California

data_processing:
Data analysis was performed using the RNA-Seq analysis pipeline  in the Genome Analysis ToolKit from the Center.
The RNA-Seq data was mapped to  mouse genome (NCBIM37), analyzed, presented using the SeqMonk software package (  http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/; Babraham Bioinformatics,  Cambridge, UK) and visualized in the UCSC Genome Browser (http://genome.ucsc.edu)  with a custom track
Genome_build: Mouse genome (NCBIM37)
Supplementary_files_format_and_content: Matrix table with normalized base counts for each exon of every gene and every sample

organism: Mus musculus

growth_protocol: MA-10 cells were maintained in Dulbecco’s modified Eagle medium/F-12 medium  (DMEM/F12; Gibco®, Thermo Fisher Scientific, Burlington, ON, Canada), supplemented  with 5% heat-inactivated fetal bovine serum and 2.5% horse serum. The MA-10-derived  wild-type subcell lines (Wt, previously G1) and the Tspo genome-edited subcell lines (Mut,  previously nG1) were created via CRISPR-Cas9 system, and all cells were grown in this medium  supplemented with 400 µg/mL of G418 (Roche Diagnostics, Indianapolis, IN, USA), 100  U/mL of penicillin, and 100 µg/mL of streptomycin in 5% CO2/air at 37 ◦C.

extract_protocol:
The cells used for total RNA extraction were cultured in 6-well plates to 80% confluence. Total RNA samples from Wt and Tspo mutant cells were extracted using TRIzol  reagent (Invitrogen; Thermo Fisher Scientific, Waltham, MA, USA)
The quantified RNA samples were used for NEBNext® (New  England Biolabs, Ipswich, MA, USA) rRNA-depleted (Human/Mouse/Rat) stranded  library preparation
To remove rRNA from the total RNAs

treatment_protocol: The expression of the  genes from both groups were affected by treatment with the cell permeable cAMP analog  dibutyryl-cAMP (dbcAMP) in Wt cells

tag: tissue

value: mouse Leydig tumor cells

tag: genotype

value: Tspo-/-


title: Wild-type MA-10 cells rep2

value: wild type


title: Wild-type MA-10 cells rep3


title: Wild-type MA-10 cells rep1


title: Tspo mutant MA-10 cells rep1


title: singlecell_clone_85


title: singlecell_clone_87


title: singlecell_86


title: siSCR_2

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

data_processing:
reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20).
reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis.
Reads were mapped onto the hg19 assembly of Homo sapiens genome using STAR version 2.5.3a. Gene expression quantiﬁcation was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 75 and “union” mode.
Only non-ambiguously assigned reads have been retained for further analyses. Read counts have been normalized across samples with the median-of-ratios method
Diﬀerential gene expression analysis was performed using the methodology implemented in the Bioconductor package DESeq2 version 1.16.1
P-values were adjusted for multiple testing by the method proposed by Benjamini and Hochberg
Deregulated genes were adjusted p-value <0.05.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file with matrix table with raw gene counts, RPKM values, log fold change expression values between siSCR and siGATA6 for every gene and every sample

extract_protocol:
total RNA was extracted using NucleoSpin RNAplus kit from Macherey-Nagel following manufacture instructions.
Total RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 8 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: cell type

value: mesenchymal-like melanoma cells

tag: tissue source

value: Skin

tag: genotype/variation

value: siSCR


title: siGATA6_2


title: siGATA6_1


title: singlecell_81


title: singlecell_79


title: singlecell_80


title: siSCR_1


title: Tspo mutant MA-10 cells rep3


title: singlecell_clone_78


title: singlecell_clone_77


title: singlecell_clone_76


title: singlecell_77


title: singlecell_clone_73


title: singlecell_78


title: singlecell_clone_79


title: singlecell_clone_71


title: singlecell_clone_74


title: singlecell_76


title: singlecell_75


title: V13_KB_8_rep2

type: RNA

city: Verona

first: Elodie

last: Vandelle

state: Verona

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

description: Gene expression in Psa V13 cells grown 8h in KB medium, replicate 2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) were 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 manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to Agilent-078853 8x60K custom microarray chip for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarray chips were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing using the Agilent DNA Microarray Scanner with one color scan settings for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to XDR Hi100%, XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid:078853_D_F_20151012) to substract the background and obtain spatially-detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Pseudomonas syringae pv. actinidiae

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 50 ng of RNA using the Low Input Quick Amp WT Labeling kit (Agilent Techonologies, Santa Clara, CA, USA) according to manufacturer's instructions for prokaryotic samples, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked using the NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA).

growth_protocol: Bacterial cells were cultured in liquid KB or hrp-inducing medium for 4 h or 8h at 28°C.

extract_protocol: Two ml of each bacterial suspension were centrifuged and total RNA was extracted from cell pellets using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, USA). Total RNA quantity, integrity and purity were controlled using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer Chip RNA 7500 serie II (Agilent).

treatment_protocol: no treatment

value: bacterial cells


title: singlecell_74


title: V13_HIM_8_rep1

description: Gene expression in Psa V13 cells grown 8h in hrp-inducing medium, replicate 1


title: V13_KB_8_rep3

description: Gene expression in Psa V13 cells grown 8h in KB medium, replicate 3


title: V13_HIM_8_rep2

description: Gene expression in Psa V13 cells grown 8h in hrp-inducing medium, replicate 2


title: V13_KB_8_rep1

description: Gene expression in Psa V13 cells grown 8h in KB medium, replicate 1


title: V13_KB_4_rep2

description: Gene expression in Psa V13 cells grown 4h in KB medium, replicate 2


title: V13_KB_4_rep3

description: Gene expression in Psa V13 cells grown 4h in KB medium, replicate 3


title: V13_HIM_8_rep3

description: Gene expression in Psa V13 cells grown 8h in hrp-inducing medium, replicate 3


title: singlecell_clone_72


title: Pto_KB_8_rep2

description: Gene expression in Pto DC3000 cells grown 8h in KB medium, replicate 2

organism: Pseudomonas syringae pv. tomato


title: V13_KB_4_rep1

description: Gene expression in Psa V13 cells grown 4h in KB medium, replicate 1


title: V13_HIM_4_rep2

description: Gene expression in Psa V13 cells grown 4h in hrp-inducing medium, replicate 2


title: V13_HIM_4_rep3

description: Gene expression in Psa V13 cells grown 4h in hrp-inducing medium, replicate 3


title: singlecell_73


title: V13_HIM_4_rep1

description: Gene expression in Psa V13 cells grown 4h in hrp-inducing medium, replicate 1


title: Pto_KB_4_rep2

description: Gene expression in Pto DC3000 cells grown 4h in KB medium, replicate 2


title: singlecell_72


title: singlecell_clone_75


title: singlecell_clone_70


title: Pto_KB_8_rep3

description: Gene expression in Pto DC3000 cells grown 8h in KB medium, replicate 3


title: singlecell_71


title: Pto_HIM_8_rep3

description: Gene expression in Pto DC3000 cells grown 8h in hrp-inducing medium, replicate 3


title: Pto_KB_8_rep1

description: Gene expression in Pto DC3000 cells grown 8h in KB medium, replicate 1


title: Pto_KB_4_rep3

description: Gene expression in Pto DC3000 cells grown 4h in KB medium, replicate 3


title: singlecell_68


title: singlecell_clone_66


title: singlecell_clone_69


title: singlecell_70


title: singlecell_clone_68


title: singlecell_clone_67


title: singlecell_65


title: Pto_HIM_8_rep1

description: Gene expression in Pto DC3000 cells grown 8h in hrp-inducing medium, replicate 1


title: Pto_KB_4_rep1

description: Gene expression in Pto DC3000 cells grown 4h in KB medium, replicate 1


title: singlecell_67


title: singlecell_clone_64


title: KN2_KB_8_rep3

description: Gene expression in Psa KN.2 cells grown 8h in KB medium, replicate 3


title: Pto_HIM_8_rep2

description: Gene expression in Pto DC3000 cells grown 8h in hrp-inducing medium, replicate 2


title: singlecell_clone_62


title: singlecell_64


title: singlecell_clone_65


title: singlecell_63


title: HEKa cells, FOXE1 siRNA2

city: Xi'an

first: Yan

last: Zheng

state: China

address: Xi'an Jiaotong University, No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi Province

institute: the second affiliated hospital of Xi'an Jiaotong University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Sequenced reads were trimmed for adaptor sequence. All the downstream analysis were based on the clean data with high quality. Hisat2 was chosen as the mapping toll and featureCounts v1.5.0-p3 was used to count the reads number mapped to each gene.
FKPM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Supplementary_files_format_and_content: FPKMs

source_name: skin

extract_protocol:
After 48 hours transfection, cell were harvested and lysed with TRIzol reagent. A total amount of 1 μg RNA per sample was uesd as input material for the RNA sample preparations
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEKa cells were transfected with 2 kinds of FOXE1-specific RNAis or control RNAi.

value: keratinocytes

tag: treatment

value: FOXE1 siRNA2


title: singlecell_clone_61


title: singlecell_66


title: Pto_HIM_4_rep3

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium, replicate 3


title: Open flower - ABAP1OE x WT

city: Rio de Janeiro

first: Adriana

middle: S

last: Hemerly

state: RJ

address: Bloco L, Subsolo, Salas 26,27 e 29 – CCS/UFRJ

department: Instituto de Bioquímica Médica Leopoldo de Meis

country: Brazil

institute: Universidade Federal do Rio de Janeiro

description: WT RNA from a pool of open flowers at stage 14 were used as control samples for comparison to ABAP1OE samples in the same developmental stage.

hyb_protocol: Hybridization of dye-labeled RNA were performed using Ambion SlideHyb Buffer #1 in 70mers (Operon) printed on poly-lysine or on Corning GAP slides (microarray platform deposited at NCBI-GEO under accession number GPL1077). Hybridization and washes procedures were done according to Wellmer et al., 2004.

scan_protocol: Hybridized arrays were scanned with an Axon 4000A scanner using the GenePix 3.1 analysis software (Axon Instruments, Foster City, CA) as described in Wellmer et al., 2004.

data_processing: Data were normalized to compensate for nonlinearity of intensity distributions and differences in probe labeling as described in Wellmer et al., 2004.

organism: Arabidopsis thaliana

source_name: Open flowers of ABAP1OE at stage 14

label_protocol: Labelling protocol was carried out according to Wellmer et al.(2004). 3-10 ug total RNA were primed with 1 uL T7dT primer (0.5 ug/ul) at 70°C for 10 min, then reversed transcribed at 37°C for 1 h in the presence of 1 uL SuperScript II RTase (Invitrogen) and 500 µM dNTP. Second strand was synthesized from first strand cDNA using DNA polymerase I and RNase H at 16oC  for 2h. cDNA was purified and in vitro transcribed using Megascript T7 kit containing 7.5 mM each ATP, CTP, GTP and UTP and 3.75 mM aminoallyl-UTP at 37oC for 6 hours. RNA were cleaned up using Qiagen RNeasy column. NHS-ester dyes (Cy3 and Cy5) were then directly coupled to 5-10 ug RNA in the modified bases in a simple chemical reaction containing 50 mM Na2CO3 pH 8.5 at room temperature for 1h in the dark. Dye-labeled RNA was fragmented before hybridization.

growth_protocol: Arabidopsis thaliana Col-0 and ABAP1OE plants (Col-0 background) were grown in a growth room at 23oC with a 16 h light/8 h dark cycle. Seeds were surface sterilized, groiwn in Murashige and Skoog agar After 7 days, in vitro plants were transferred to a mixture of soil:vermiculite  646 (2:1) and grown under the same conditions as described above.

extract_protocol: Total RNA was extracted using RNeasy RNA Isolation kit (Qiagen) with on column Dnase digestion, following manufacturer's instructions.

treatment_protocol: ABAP1OE plants were generated by Agrobacterium transformation of  a plasmid containing ABAP1 under the expression of the 35S CAMV promoter. Plasmid was constructed by PCR amplification of ABAP1 CDS and was transferred to a binary vector containing the CaMV 35S promoter and the zein terminator sequence with the selection marker eGFP in plants using Gateway Technology. For more details, see Masuda et al., 2008.

tag: ecotype

value: ABAP1 overexpressing (ABAP1OE)

value: Pool of ABAP1OE flowers

value: stage 14 of flower development (according to Smyth et al. 1990).

source_name: Open flowers of WT at stage 14

value: WT

value: Pool of WT flowers


title: Pto_HIM_4_rep2

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium, replicate 2


title: singlecell_clone_63

value: blood stage schizonts


title: Flower bud - ABAP1OE x WT

description: WT RNA from a pool of flower buds at stage 13 were used as control samples for comparison to ABAP1OE samples in the same developmental stage.

source_name: Flower buds of ABAP1OE at stage 13

value: Pool of ABAP1OE flower buds

value: stage 13 of flower development (according to Smyth et al. 1990).

source_name: Flower buds of WT at stage 13

value: Pool of WT flower buds


title: Silique - ABAP1OE x WT

description: WT RNA from a pool of siliques at stages 15/16 were used as control samples for comparison to ABAP1OE samples in the same developmental stage.

source_name: Siliques of ABAP1OE at stage 15/16

value: Pool of ABAP1OE siliques

value: stage 15/16 of flower development (according to Smyth et al. 1990).

source_name: Siliques of WT at stage 15/16

value: Pool of WT siliques


title: Pto_HIM_4_rep1

description: Gene expression in Pto DC3000 cells grown 4h in hrp-inducing medium, replicate 1


title: KN2_KB_4_rep3

description: Gene expression in Psa KN.2 cells grown 4h in KB medium, replicate 3


title: HEKa cells, FOXE1 siRNA1

value: FOXE1 siRNA1


title: singlecell_69

value: 3D7 strain


title: KN2_KB_8_rep2

description: Gene expression in Psa KN.2 cells grown 8h in KB medium, replicate 2

value: bacterial cells


title: anterior septal tissues - exome-HCM18

city: Boston

first: Bradley

last: Maron

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham & Women's Hospital

library_source: genomic

data_processing:
Library strategy: whole exome sequencing
Illumina HiSeq 2000 was used for sequencing and Illumina's CASAVA software package was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 and bowtie2 packages; GATK (Genome Analysis Toolkit) was used to generate VCF files
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample; Variant Call Format (VCF) files

molecule: genomic DNA

source_name: anterior septal tissues

extract_protocol: Not provided

tag: disease state

value: Hypertrophic cardiomyopathy (HCM)

value: anterior septal tissues derived from frozen hearts


title: KN2_KB_8_rep1

description: Gene expression in Psa KN.2 cells grown 8h in KB medium, replicate 1


title: anterior septal tissues - exome-HCM16


title: HEKa cells, RNAi control

value: keratinocytes

value: RNAi control


title: KN2_KB_4_rep2

description: Gene expression in Psa KN.2 cells grown 4h in KB medium, replicate 2


title: singlecell_clone_60

value: 3D7 subclone


title: singlecell_clone_59


title: KN2_HIM_8_rep1

description: Gene expression in Psa KN.2 cells grown 8h in hrp-inducing medium, replicate 1


title: singlecell_60


title: anterior septal tissues - exome-HCM17


title: singlecell_clone_58


title: KN2_HIM_8_rep2

description: Gene expression in Psa KN.2 cells grown 8h in hrp-inducing medium, replicate 2


title: singlecell_58


title: singlecell_clone_56


title: KN2_KB_4_rep1

description: Gene expression in Psa KN.2 cells grown 4h in KB medium, replicate 1


title: dilution_control_clone_10


title: singlecell_59


title: singlecell_clone_57


title: singlecell_57


title: anterior septal tissues - exome-HCM12


title: singlecell_clone_55


title: anterior septal tissues - exome-HCM15


title: anterior septal tissues - exome-HCM14


title: singlecell_62


title: anterior septal tissues - exome-HCM11


title: KN2_HIM_8_rep3

description: Gene expression in Psa KN.2 cells grown 8h in hrp-inducing medium, replicate 3


title: singlecell_clone_53


title: dilution_control_clone_9


title: singlecell_53


title: anterior septal tissues - exome-HCM13


title: KN2_HIM_4_rep1

description: Gene expression in Psa KN.2 cells grown 4h in hrp-inducing medium, replicate 1


title: KN2_HIM_4_rep3

description: Gene expression in Psa KN.2 cells grown 4h in hrp-inducing medium, replicate 3


title: singlecell_54


title: singlecell_52


title: KN2_HIM_4_rep2

description: Gene expression in Psa KN.2 cells grown 4h in hrp-inducing medium, replicate 2


title: J35_KB_8_rep2

description: Gene expression in Psa J35 cells grown 8h in KB medium, replicate 2


title: singlecell_55


title: singlecell_clone_54


title: J35_KB_8_rep3

description: Gene expression in Psa J35 cells grown 8h in KB medium, replicate 3


title: singlecell_clone_52


title: singlecell_56


title: anterior septal tissues - exome-HCM10


title: anterior septal tissues - exome-HCM9


title: singlecell_51


title: dilution_control_clone_8


title: J35_KB_4_rep3

description: Gene expression in Psa J35 cells grown 4h in KB medium, replicate 3


title: dilution_control_9


title: singlecell_clone_51


title: singlecell_50


title: dilution_control_8


title: anterior septal tissues - exome-HCM7


title: J35_KB_4_rep1

description: Gene expression in Psa J35 cells grown 4h in KB medium, replicate 1


title: anterior septal tissues - exome-HCM5


title: J35_KB_8_rep1

description: Gene expression in Psa J35 cells grown 8h in KB medium, replicate 1


title: anterior septal tissues - exome-HCM2


title: anterior septal tissues - exome-HCM8


title: dilution_control_clone_7


title: anterior septal tissues - exome-HCM6


title: J35_HIM_8_rep2

description: Gene expression in Psa J35 cells grown 8h in hrp-inducing medium, replicate 2


title: dilution_control_4


title: J35_HIM_4_rep3

description: Gene expression in Psa J35 cells grown 4h in hrp-inducing medium, replicate 3


title: J35_HIM_8_rep3

description: Gene expression in Psa J35 cells grown 8h in hrp-inducing medium, replicate 3


title: singlecell_clone_46


title: J35_HIM_8_rep1

description: Gene expression in Psa J35 cells grown 8h in hrp-inducing medium, replicate 1


title: singlecell_clone_50


title: dilution_control_6


title: singlecell_clone_49


title: anterior septal tissues - exome-HCM4


title: CRA_KB_8_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 8h in KB medium, replicate 2


title: anterior septal tissues - HCM16

data_processing:
Illumina HiSeq 2000 was used for sequencing and Illumina's CASAVA software package was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 and bowtie2 packages; GATK (Genome Analysis Toolkit) was used to generate VCF files
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample; Variant Call Format (VCF) files

extract_protocol: RNeasy Fibrous Tissue Mini Kit (Qiagen, #74704)


title: dilution_control_1


title: anterior septal tissues - exome-HCM3


title: dilution_control_5


title: singlecell_clone_48


title: singlecell_clone_45


title: 100cells_3


title: anterior septal tissues - exome-HCM1


title: singlecell_clone_47


title: anterior septal tissues - HCM17


title: J35_HIM_4_rep2

description: Gene expression in Psa J35 cells grown 4h in hrp-inducing medium, replicate 2


title: 100cells_2


title: CRA_KB_4_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in KB medium, replicate 3


title: anterior septal tissues - HCM14


title: dilution_control_7


title: dilution_control_3


title: J35_HIM_4_rep1

description: Gene expression in Psa J35 cells grown 4h in hrp-inducing medium, replicate 1


title: singlecell_clone_44


title: anterior septal tissues - HCM18


title: dilution_control_2


title: dilution_control_clone_6


title: CRA_KB_8_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 8h in KB medium, replicate 3


title: anterior septal tissues - HCM12


title: J35_KB_4_rep2

description: Gene expression in Psa J35 cells grown 4h in KB medium, replicate 2


title: singlecell_clone_42


title: dilution_control_clone_4


title: anterior septal tissues - HCM15


title: singlecell_47


title: CRA_KB_8_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 8h in KB medium, replicate 1


title: singlecell_clone_41


title: anterior septal tissues - HCM9


title: 100cells_1


title: CRA_KB_4_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in KB medium, replicate 2


title: anterior septal tissues - HCM13


title: singlecell_clone_43


title: singlecell_49


title: CRA_HIM_8_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 8h in hrp-inducing medium, replicate 2


title: dilution_control_clone_5


title: dilution_control_clone_2


title: singlecell_48


title: CRA_KB_4_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in KB medium, replicate 1


title: anterior septal tissues - HCM7


title: anterior septal tissues - HCM11


title: anterior septal tissues - HCM10


title: WT_GD6_S29_L003_R1_001 (WTG_4)

city: East Lansing

first: Dae Kwan

last: Ko

state: MI

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

data_processing:
RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Library (Illumina, San Diego, CA, USA) and sequenced in single-end mode on the Illumina HiSeq 4000 platform (50-nt) at Research Technology Support Facility Genomics Core at Michigan State University (RTSF-MSU). The quality of raw reads was evaluated using FastQC (version 0.11.5). Reads were cleaned for quality and adapters with Cutadapt (version 1.8.1) using a minimum base quality of 20 retaining reads with a minimum length of 30 nucleotides after trimming. Quality-filtered reads were aligned to the Col-0 reference genome (TAIR10) using Bowtie (version 2.2.4) and TopHat (version 2.0.14) with a 10 bp minimum intron length and 15,000 bp maximum intron length. Fragments per kilobase exon model per million mapped reads (FPKM) were calculated using TAIR10 gene model annotation with Cufflinks (version 1.3.0).
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files: the normalized expression values (FPKM)

source_name: WT_Ground_whole seedlings

growth_protocol: This experiment utilized 4 Biological Research In a Canister (BRIC) containing a total of 22 Petri Dish Fixation Unit (PDFU) hardware  to cultivate sterile dark grown seedlings germinated aboard the International Space Station (ISS) for a 14 day period. PDFU actuation chambers were loaded with tissue fixative (RNAlater; Invitrogen) to preserve samples at the conclusion of the experiment. An identical set of samples was prepared and grown on earth with a two-day offset at Kennedy Space Center (KSC) ISS Environmental Simulator (ISSES) to allow for data transmission and reproduction of incubation conditions experienced by flight samples in orbit. Petri dishes (60mm) were prepared with 6.7 ml of sterile ½ MS media supplemented with Gamborg’s B5 Vitamins, 0.5% Sucrose, 0.4% Phytagel, pH adjusted to 5.7.  In a sterile hood, seeds of wild-type and UPR mutant genotypes were surface sterilized with one wash of 70% ethanol, one wash of 50% bleach containing 0.5% Tween 20, and then nine additional washes with sterile double distilled H2O. After the final wash was removed, seeds were resuspended in 1.5 ml sterile water for wet plating using a 1 ml pipette equipped with sterile filter-tips. Each plate replicate contained 70-80 seeds evenly spaced in a grid pattern on the plate surface. Petri dish lids were closed by Parafilm wrap and individual plates were then double wrapped in sterile aluminum foil. Individually wrapped plates were grouped by BRIC configuration and wrapped together with two more layers of sterile foil prior to sample removal from the sterile hood. Plates were placed at 4°C until integration of samples into science hardware the following morning. Launch samples (i.e., seeds) were integrated into BRIC flight hardware in a sterile hood approximately 48 hours before the August 14th, 2017 launch of SpaceX-CRS12 spacecraft. Integrated science/hardware was kept at 4°C to maintain seed dormancy prior to packing in cold storage bags while being loaded onto Dragon capsule and during launch. After docking, samples were removed from cold storage bags by ISS astronauts, warmed to ambient ISS temperature, allowing seed germination and experiment initiation in the BRIC. After 14 days ISS astronauts actuated PDFUs, which were then incubated at room temperature for a further 3 hours before being transferred to the ISS -80 MELFI freezer. Samples were kept at approximately -80°C until BRICs were conditioned to -32°C in double cold bag storage and stowed in the Dragon capsule before undocking and atmospheric reentry on September 16th.  After returning to KSC, samples were stored at -80°C until de-integration of the flight and ground samples.

extract_protocol:
Flight and ground control experiments samples were preserved in RNAlater in situ, and kept at -80°C (see results section for experimental timeline). The Petri dishes were removed from packaging and thawed in groups of three to prevent excess exposure to room temperatures during sample collection. After removing most of the RNAlater from the plates, sterile forceps were used to transfer seedlings from the plates to microcentrifuge tubes containing two glass beads. Seedlings were then frozen in liquid nitrogen. Frozen samples were ground to a powder using a Retch Mixer Mill (Retch; Haan, Germany). RNA was extracted from tissues using a NucleoSpin RNA Plant Kit (Machery-Nagel) according to the manufacturer’s instructions including DNase Digestion. RNA yield was assessed via NanoDrop ND-1000 (Thermo Fisher Scientific; Waltham, USA), and sample integrity was analyzed via Agilent Bioanalyzer 2100 (Agilent, Santa Clara USA).
RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Library (Illumina, San Diego, CA, USA)

tag: ecotype background

value: WT

tag: condition

value: Ground

value: Whole seedlings


title: singlecell_46

value: blood stage schizonts


title: CRA_HIM_4_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium, replicate 1


title: singlecell_clone_40


title: anterior septal tissues - HCM6


title: singlecell_45


title: singlecell_42


title: WT_GD4_S39_L004_R1_001 (WTG_3)


title: anterior septal tissues - HCM8


title: singlecell_44


title: anterior septal tissues - HCM5


title: dilution_control_clone_1


title: anterior septal tissues - HCM4


title: CRA_HIM_8_rep1

description: Gene expression in Psa CRAFRU8.43 cells grown 8h in hrp-inducing medium, replicate 1


title: dilution_control_clone_3


title: singlecell_clone_37


title: singlecell_43


title: singlecell_40


title: WT_GB2_S18_L002_R1_001 (WTG_2)


title: WT_GA1_S19_L002_R1_001 (WTG_1)


title: CRA_HIM_4_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium, replicate 3


title: singlecell_clone_39


title: singlecell_clone_35


title: singlecell_41


title: singlecell_39


title: CRA_HIM_4_rep2

description: Gene expression in Psa CRAFRU8.43 cells grown 4h in hrp-inducing medium, replicate 2


title: anterior septal tissues - HCM1


title: anterior septal tissues - HCM3


title: anterior septal tissues - HCM2


title: singlecell_clone_36


title: singlecell_37


title: singlecell_clone_33


title: WT_FD6_S42_L004_R1_001 (WTF_5)

description:
WT_FD6_S42_L004_R1_001
used for initial quality controls, but not used for further data processing (keep only 4 biological replicates to be consistent with other genotypes)

source_name: WT_Space flight_whole seedlings

value: Space flight


title: WT_GC3_S28_L003_R1_001 (WTG_5)

description:
WT_GC3_S28_L003_R1_001
used for initial quality controls, but not used for further data processing (keep only 4 biological replicates to be consistent with other genotypes)


title: singlecell_clone_34


title: singlecell_clone_38


title: singlecell_36


title: anterior septal tissues - ctrl4

source_name: Left ventricular free wall tissue

value: Healthy control

value: Left ventricular free wall tissues derived from frozen hearts


title: singlecell_clone_32


title: singlecell_clone_31


title: singlecell_34


title: anterior septal tissues - ctrl2


title: singlecell_35


title: anterior septal tissues - ctrl5


title: singlecell_38


title: singlecell_33


title: singlecell_clone_29


title: singlecell_32


title: anterior septal tissues - ctrl1


title: WT_FC3_S9_L001_R1_001 (WTF_3)


title: singlecell_clone_28


title: Escherichia coli BW25113 (EF4 mutant) Tetra replicate 2 (RNA-Seq)

city: Beijing

first: Bin

last: Liu

state: Beijing

address: Hai Dian

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BW25113 whole genome using bowtie v2.2.9
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: BW25113 (Genbank accession number: CP009273.1)
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

organism: Escherichia coli BW25113

source_name: Escherichia coli BW25113 (EF4 mutant)

extract_protocol:
mRNA were extracted trizol reagents according to the manual.
The  libraries were prepared for sequencing using standard  protocols

value: EF4 mutant

value: Tetracycline


title: IRE1_GC4_S37_L004_R1_001 (ire1a ire1bG_3)

source_name: ire1a-4 ire1b-2_Ground_whole seedlings

value: ire1a-4 ire1b-2


title: IRE1_GD1_S31_L003_R1_001 (ire1a ire1bG_4)


title: Escherichia coli BW25113 Tetra replicate 2 (RNA-Seq)

source_name: Escherichia coli BW25113

value: wild type


title: singlecell_clone_27


title: singlecell_30

value: 3D7 strain


title: anterior septal tissues - ctrl3


title: singlecell_clone_26


title: WT_FB2_S11_L001_R1_001 (WTF_2)


title: singlecell_31


title: IRE1_GA6_S44_L004_R1_001 (ire1a ire1bG_1)


title: WT_FA1_S1_L001_R1_001 (WTF_1)


title: Escherichia coli BW25113 (EF4 mutant) replicate 2 (RNA-Seq)


title: singlecell_29


title: singlecell_61


title: Escherichia coli BW25113 replicate 2 (RNA-Seq)


title: IRE1_GB5_S23_L003_R1_001 (ire1a ire1bG_2)


title: singlecell_clone_30


title: IRE1_FD1_S12_L002_R1_001 (ire1a ire1bF_4)

source_name: ire1a-4 ire1b-2_Space flight_whole seedlings


title: singlecell_clone_25


title: WT_FD4_S41_L004_R1_001 (WTF_4)


title: singlecell_27


title: IRE1_FC4_S40_L004_R1_001 (ire1a ire1bF_3)


title: Escherichia coli BW25113 Tetra replicate 1 (RNA-Seq)


title: singlecell_28


title: singlecell_clone_22


title: singlecell_clone_24


title: CRA_HIM_8_rep3

description: Gene expression in Psa CRAFRU8.43 cells grown 8h in hrp-inducing medium, replicate 3

value: bacterial cells


title: 68_GD3_S24_L003_R1_001 (bzip28 bzip60G_4)

value: bzip28-2 bzip60-1


title: IRE1_FA6_S38_L004_R1_001 (ire1a ire1bF_1)


title: Escherichia coli BW25113 replicate 1 (RNA-Seq)


title: singlecell_25


title: 68_GC2_S26_L003_R1_001 (bzip28 bzip60G_5)

description:
68_GC2_S26_L003_R1_001
used for initial quality controls, but not used for further data processing (keep only 4 biological replicates to be consistent with other genotypes)


title: singlecell_clone_21


title: singlecell_clone_20


title: singlecell_24


title: 3-13

first: Yao

last: Ni

address: 54 South Xianlie Road

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
Illumina bcl2fastq (v2.19.1.403) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using HISAT2 v2.1.0 with default parameters
Mapped reads used the StringTie software and Ensembl GTF file(release 90) to obtain gene expression profiles,and then the differential expression analysis was executed via the DESeq2 package on R programmer
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and transcript in every sample
Differential expression analysis results by DESeq2

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMC were collected using Ficoll-Paque™ PREMIUM Media and SepMate™-50, RNeasy Mini Kit was used to extract the total RNA. rRNA was removed by Epicentre Ribo-zero rRNA Removal Kit. The DNA was cleaned by DNase and then captured and purified by magnet beads.
First-strand cDNA was synthesized and double-strand cDNA was obtained thereafter with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina.

tag: nationality

value: Chinese

tag: ethnicity

value: Han

tag: diesase status

value: proliferative vitreoretinopathy patient

value: peripheral blood mononuclear cells


title: 68_GB4_S32_L003_R1_001 (bzip28 bzip60G_3)

value: Ground


title: singlecell_clone_19

source_name: in vitro 3D7 strain culture

tag: developmental stage

value: 3D7 subclone


title: 3-16


title: singlecell_22

value: blood stage schizonts

tag: strain


title: singlecell_23


title: 3-15


title: Escherichia coli BW25113 (EF4 mutant) Tetra replicate 1 (RNA-Seq)


title: singlecell_21


title: IRE1_FB5_S6_L001_R1_001 (ire1a ire1bF_2)

value: Space flight

value: Whole seedlings


title: singlecell_clone_23


title: singlecell_clone_18


title: Escherichia coli BW25113 (EF4 mutant) replicate 1 (RNA-Seq)


title: 68_FD3_S16_L002_R1_001 (bzip28 bzip60F_5)

description:
68_FD3_S16_L002_R1_001
used for initial quality controls, but not used for further data processing (keep only 4 biological replicates to be consistent with other genotypes)

source_name: bzip28-2 bzip60-1_Space flight_whole seedlings


title: singlecell_20


title: singlecell_clone_16


title: 68_FC2_S8_L001_R1_001 (bzip28 bzip60F_4)


title: 3-11


title: singlecell_clone_17


title: 3-7


title: 68_GA3_S13_L002_R1_001 (bzip28 bzip60G_1)


title: singlecell_26


title: singlecell_19


title: singlecell_18


title: 68_GA4_S15_L002_R1_001 (bzip28 bzip60G_2)


title: 3-6


title: 68_FB4_S4_L001_R1_001 (bzip28 bzip60F_3)


title: 3-5


title: 3-8


title: singlecell_clone_13


title: 68_FA3_S5_L001_R1_001 (bzip28 bzip60F_1)


title: singlecell_17


title: singlecell_16


title: 3-4


title: singlecell_clone_11


title: 3-2


title: singlecell_15


title: 60_GC1_S25_L003_R1_001 (bzip60G_3)

source_name: bzip60-2_Ground_whole seedlings


title: singlecell_clone_15


title: singlecell_clone_14


title: singlecell_clone_12


title: singlecell_14


title: 60_GD2_S33_L003_R1_001 (bzip60G_4)


title: singlecell_13


title: singlecell_clone_9


title: singlecell_clone_10


title: 3-1


title: 1-13

value: idiopathic epiretinal membrane patient


title: singlecell_clone_8


title: 1-12


title: singlecell_12


title: 68_FA4_S34_L004_R1_001 (bzip28 bzip60F_2)


title: singlecell_11


title: 60_FD2_S14_L002_R1_001 (bzip60F_4)

source_name: bzip60-2_Space flight_whole seedlings


title: 1-11


title: 1-10


title: singlecell_clone_7


title: singlecell_9


title: 60_FA2_S3_L001_R1_001 (bzip60F_1)


title: 60_GB3_S20_L002_R1_001 (bzip60G_2)


title: 1-8


title: singlecell_clone_4


title: 28_GD5_S27_L003_R1_001 (bzip28G_4)

source_name: bzip28-2_Ground_whole seedlings


title: 60_GA2_S22_L002_R1_001 (bzip60G_1)


title: singlecell_7


title: singlecell_clone_2


title: singlecell_6


title: 1-7


title: 1-5


title: 28_GB1_S35_L004_R1_001 (bzip28G_2)


title: 28_GC5_S30_L003_R1_001 (bzip28G_3)


title: 60_FC1_S7_L001_R1_001 (bzip60F_3)


title: singlecell_10


title: singlecell_clone_1


title: 1-9


title: 60_FB3_S2_L001_R1_001 (bzip60F_2)


title: singlecell_clone_6


title: singlecell_8


title: 28_GA5_S43_L004_R1_001 (bzip28G_1)


title: 1-2


title: 1-3


title: singlecell_clone_5


title: 1-4


title: singlecell_4


title: singlecell_5


title: 28_FB1_S10_L001_R1_001 (bzip28F_2)

source_name: bzip28-2_Space flight_whole seedlings


title: 1-1


title: 28_FD5_S17_L002_R1_001 (bzip28F_4)


title: singlecell_2


title: RIP_rep3

status: Public on Jan 08 2021

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

country: Japan

institute: Kagoshima University

description: immunoprecipitated RNA

data_processing:
Quality check by FastQC
The sequences were mapped to Aspergillus kawachii IFO 4308 genomes using STAR software
The mapped reads were counted by featureCounts
FPKM were calculated by a perl script
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Aspergillus luchuensis

source_name: whole cell

extract_protocol:
Total RNA was extracted as follows. The conidia of A. kawachii control and Tet-S-nrdA strains were inoculated into YES medium with Dox and pre-cultured and then transferred to YES medium with or without Dox and further cultivated. After incubation, mycelia were collected and ground to a powder in the presence of liquid nitrogen. Total RNA was extracted using RNAiso Plus (Takara Bio) according to the manufacturer's protocol. Next, immunoprecipitated RNA was prepared as follows. The conidia of A. kawachii Tet-S-nrdA strain were inoculated into YES medium with Dox and pre-cultured and then transferred to medium with Dox and further cultivated. After incubation, mycelia were collected and ground to a powder in the presence of liquid nitrogen. The powdered mycelia was dissolved in the ice-cold nuclear extraction buffer (25 mM HEPES [pH 6.8], 1 M sorbitol, 250 μg/ml phenylmethylsulfonyl fluoride [PMSF], cOmplete [EDTA-free protease inhibitor cocktail, Roche, Basel, Switzerland]) and vigorously mixed using a vortexer. Cell debris was removed by filtration using miracloth, and then centrifuged. The supernatant was removed and the pellet was dissolved in the ice-cold nuclear solubilization buffer (25 mM HEPES [pH 6.8], 1 M sorbitol, 0.5% NP-40, 250 μg/ml phenylmethylsulfonyl fluoride [PMSF], cOmplete). After incubation, the debris was removed by centrifugation. The resultant supernatant was added 25 µl of protein A sepharose beads (50% slurry contained PBS buffer) (GE healthcare) and the resulting mixture was gently mixed for 1 h at 4°C using a rotator. The mixture was separated by centrifugation, and supernatant was mixed with anti-S-tag antibody (MBL) or normal rabbit IgG (MBL) cross-linked protein A sepharose. Then, these mixtures were gently mixed for 3 h at 4°C using a rotator. Immunoprecipitated RNA was purified using RiboCluster Profiler (MBL) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tet-S-nrdA


title: RIP_rep2

description: immunoprecipitated RNA


title: Dox_plus_rep3


title: singlecell_1


title: Dox_minus_rep3


title: Dox_plus_rep1


title: singlecell_3


title: RIP_rep1

description: immunoprecipitated RNA


title: Dox_minus_rep1


title: Control_rep3

value: ctrl


title: Dox_minus_rep2


title: Dox_plus_rep2


title: 28_FA5_S36_L004_R1_001 (bzip28F_1)


title: Control_rep1


title: 28_FC5_S21_L002_R1_001 (bzip28F_3)


title: ProliferativeVsSenescent Replicate 1

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

country: Canada

institute: University of Saskatchewan

hyb_protocol: Labelled cDNA hybridised using the to arrays (Op Human ReadyArray HS1200 from Operon/Microarray Inc.) for 16hours using Slidebooster (Advalytix). Arrays then washed in 2x SSC (+0.2 % SDS), 2x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min. Hybridization of the Cy3/Cy5 containing dendrimers were then performed followed by repetition of the washing steps prior todrying and scanning.

scan_protocol: Arrays images were imported into BlueFuse 3.2 software for analysis.

data_processing: Raw data was imported into the BioArray Software Environment (BASE) and normalized using the LOWESS algorithm. Intenity values were log tramsformed and comparision between dye-swapped Cy3/Cy5 samples performed. 4 Biological replciates were analyzed. Fold change values were calculted .

source_name: proliferative human normal diploid fibroblast

label_protocol: cDNAs were labeled using the 3DNA array 900 labeling kit (Genisphere) as per manufacturers instructions

growth_protocol: Proliferative fibroblasts were grown in 10% FBS/DMEM high glucose in 5% CO2.

extract_protocol: Trizol/MP24 fast RNA extraction kit (green) were used for extractions

treatment_protocol: replicatative senescence was induced by the serial passaging of cells beyond passage 35 and by population doubling times eceeding 500 hours

tag: tag

value: skin

source_name: Senescent human normal diploid fibroblast


title: ProliferativeVsSenescent Replicate 4


title: Control_rep2


title: ProliferativeVsSenescent Replicate 3


title: ProliferativeVsSenescent Replicate 2


title: FFCJD-22_FC

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

scan_protocol: 50-100 ng of RNA was analysed for the expression of 770 genes related to the innate immune system with the nCounter® Human Myeloid Innate Immunity Panel v2 utilizing the NanoString platform, using the CodeSet-Plus/Panel-Plus nCounter XT Gene Expression Assay.

data_processing: Raw data were quality checked in the nSolver software followed by normalization. Normalization factors were calculated based on 40 reference genes included in the myeloid innate immunity panel.

source_name: brain biopsy, fresh frozen

extract_protocol: Total RNA was isolated from ten 10-μm sections of FFPE samples using the Roche high pure RNA FFPE isolation kit.

tag: diagnosis

value: CJD

tag: brain region

value: FC

tag: subject

tag: gender

value: M

tag: codon 129

value: VV

tag: cjd subtype


title: FFCJD-20_FC

value: F

value: MM


title: FFCJD-22_CB

value: CB


title: FFCJD-20_CB


title: FFCT-48_FC

value: CT

value: MV


title: FFCT-54_FC


title: FFCT-54_CB


title: FFCT-47_FC


title: FFCJD-29_FC


title: FFCJD-35_FC


title: FFCJD-35_CB


title: FFCT-47_CB


title: FFCT-53_CB


title: FFCJD-13_FC


title: FFCJD-28_CB


title: FFCJD-29_CB


title: FFCJD-28_FC


title: FFCT-55_CB


title: FFCT-55_FC


title: FFCJD-19_FC


title: FFCJD-19_CB


title: FFCJD-13_CB


title: FFCT-48_CB


title: FFCT-53_FC


title: FFCJD-23_FC


title: FFCJD-23_CB


title: FFCT-46_FC


title: FFCJD-34_FC


title: FFCT-52_CB


title: FFCT-52_FC


title: FFCJD-18_CB


title: FFCJD-18_FC


title: FFCT-45_CB


title: FFCJD-10_FC


title: FFCT-46_CB


title: FFCT-45_FC


title: FFCJD-10_CB


title: FFCJD-14_CB


title: FFCT-50_FC


title: FFCJD-14_FC


title: FFCT-50_CB


title: FFCJD-15_CB


title: FFCT-44_FC


title: FFCT-44_CB


title: FFCJD-21_FC


title: FFCJD-21_CB


title: PrP Mutant 3

city: Edmonton

first: Niall

last: Pollock

state: Alberta

address: Department of Biological Sciences, CW 405, Biological Sciences Bldg.

institute: University of Alberta

data_processing:
RNA preparation and quality control handled by otogenetics. Sequences were trimmed to remove adapters and low quality bases at ends.
Trimmed sequences underwent the otogenetics RNA sequencing pipeline, briefly: Reads were aligned to zebrafish reference genome using TopHat and annotated using Cufflinks. Differential expression analysis was carried out using Cuffdiff to calculate and compare FPKM values.
Genome_build: GRCz10 (danRer10)
Supplementary_files_format_and_content: comma delimited .csv file with FPKM values for all 6 samples and every gene. Wild-type samples are listed as WT1, WT2 and WT3. Mutant samples (prp1 and prp2 knockouts) are listed as MT1, MT2 and MT3. Wild-type reads were identified in MT1 and MT2.

organism: Danio rerio

source_name: Whole larvae

extract_protocol:
Each sample consists of a pool of 50 zebrafish larvae. Pools were homogenised in TRIzol and sent to Otogenetics for RNA extraction and RNA-sequencing.
RNA Libraries were constructed using standard Illumina protocols

tag: genetic background

value: AB

tag: age

value: 3 days post fertlisation

tag: genotype


title: 883004_RNAseq

city: Columbus

first: Daniel

last: Stover

state: OH

address: Biomedical Research Tower, Room 512, 460 W. 12th Avenue

institute: Ohio State University Comprehensive Cancer Center

data_processing:
Samples with >10 million unique reads were included for further analyses
RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
Genome_build: Ensembl release 76
Supplementary_files_format_and_content: log2 normalized abundance data as a matrix table in a text file

source_name: Tumor biopsy

extract_protocol:
Pre-treatment biopsies were collected in RNAlater and total RNA was extracted.
Total RNA underwent whole transcriptome RNA sequencing (RNAseq) using RiboZero Gold rRNA depletion
All samples were sequenced on an Illumina HiSeq 3000 with single-end 50bp reads

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: N0 (clinically negative or biopsy negative)

value: Every 3 weeks

value: Never

value: RD


title: FFCJD-15_FC

value: CJD


title: PrP Mutant 2

description:
Small wild-type contamination present
Replicate_FPKM_Count.csv


title: Wild-Type 3

value: Wild-type


title: Wild-Type 1


title: PrP Mutant 1


title: 883005_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: 869003_RNAseq


title: 881003_RNAseq

value: N1-2 (biopsy positive)


title: 868011_RNAseq

value: pCR


title: 881002_RNAseq


title: 883003_RNAseq


title: 868009_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 881001_RNAseq


title: 867002_RNAseq


title: 867001_RNAseq


title: 869004_RNAseq


title: 869001_RNAseq


title: 869002_RNAseq


title: 869005_RNAseq


title: 868008_RNAseq


title: 868010_RNAseq


title: 880001_RNAseq


title: 868002_RNAseq

value: Current


title: 1-6

value: Chinese

value: Han

value: idiopathic epiretinal membrane patient

tag: cell type

value: peripheral blood mononuclear cells


title: 850003_RNAseq


title: 868007_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: 868001_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Every 3 weeks

value: Never


title: 842003_RNAseq

value: RD


title: 842001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: 862002_RNAseq


title: 865009_RNAseq


title: 862001_RNAseq

value: A


title: 840005_RNAseq

value: N1-2 (biopsy positive)


title: 850001_RNAseq

value: Former


title: 842004_RNAseq

value: pCR


title: 840001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 850004_RNAseq

value: Every 2 weeks


title: 827002_RNAseq


title: 827008_RNAseq


title: 827003_RNAseq


title: 847001_RNAseq


title: 844004_RNAseq


title: 840004_RNAseq


title: 840002_RNAseq


title: 841001_RNAseq


title: Wild-Type 2

value: AB

value: 3 days post fertlisation

value: Wild-type


title: 841002_RNAseq


title: 826002_RNAseq


title: 827001_RNAseq


title: 842002_RNAseq


title: 825015_RNAseq


title: 825013_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: 825012_RNAseq


title: 825009_RNAseq


title: 825011_RNAseq

value: B


title: 825010_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 827005_RNAseq


title: 827009_RNAseq


title: 825007_RNAseq

value: Every 3 weeks


title: 824009_RNAseq

value: Never


title: 827006_RNAseq


title: 824006_RNAseq

value: RD


title: 824007_RNAseq


title: 824010_RNAseq


title: 824005_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: 824004_RNAseq


title: 824003_RNAseq

value: A


title: 824008_RNAseq

value: N1-2 (biopsy positive)


title: 823014_RNAseq


title: 823013_RNAseq


title: 10X_liver

city: San Francisco

first: George

middle: Christopher

last: Hartoularos

address: 513 Parnassus Ave S965F

department: Graduate Division

institute: University of California, San Francisco

description: Droplet-based transcriptome

data_processing:
Fastq files generated from raw Illumina base calls using bcl2fastq v2.0, demultiplexed along the second combinatorial barcode.
Reads trimmed using Trim Galore v0.6.5 with parameters: -a AAAAAAAA --three_prime_clip_R1 1
Reads aligned using STAR v2.7.0a with parameters: --outFilterMatchNminOverLread 0.3 --outSAMstrandField intronMotif
Reads quality filtered using samtools v1.10 with parameters: view -bh -q 30 -F 4
Reads UMI deduplicated and split along the first combinatorial barcode using a custom python script.
Cell by gene matrix generated using a custom python script.
Genome_build: Merged GRCm38 GRCh38 genome
Supplementary_files_format_and_content: 10X_raw_feature_bc_matrix.h5: 10x-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: 10X_mouse_down_processed.h5ad: AnnData-formatted h5 file containing a matrix with downsampled, transformed counts from mouse cells of a liver slice.
Supplementary_files_format_and_content: L10C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L30C8.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L30C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L20C1.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: L20T.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a liver slice.
Supplementary_files_format_and_content: cell_line_raw_labeled.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a cell line mixture.
Supplementary_files_format_and_content: S10C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S20C2.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S20C1.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: S15C.h5ad: AnnData-formatted h5 file containing a matrix with raw counts from a spleen slice.
Supplementary_files_format_and_content: liver_all_raw_labeled.loom: Loom file containing a matrix with raw counts and cell labels from multiple liver slices.
Supplementary_files_format_and_content: spleen_all_raw_labeled.h5ad: AnnData-formatted h5 file containing a matrix with raw counts and cell labels from multiple spleen slices.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: mouse liver injected with MC38 and with HEK293t spike in

growth_protocol: MC38 cell line was cultured in complete cell culture medium (RPMI 1640 with GlutaMAX, penicillin, streptomycin, sodium pyruvate, HEPES, NEAA, and 10% fetal bovine serum).

extract_protocol:
Cell lysis and amplification.
In-situ reverse transcription on spatially barcoded microwell array. Pooling cells off array and FACS sorting for secondary indexing. Cell lysis, reverse transcription template switching and barcoded cDNA amplification. cDNA tagmentation amplification with primers containing short-read sequencing adapters (Illumina).
Combinatorial indexing for single cell barcoding. Initial barcoding step provides 2-dimensional spatial index.

treatment_protocol: MC38 tumor cells (5x10^5 cells) were injected directly into liver or spleen of a C57BL/6 mouse. 10 days post tumor inoculation, mice were sacrificed and harvested. Organs were fixed in dithiobis (succinimidyl propionate) (DSP) and cryopreserved.

tag: mouse strain

tag: mouse organ

value: Liver

tag: injection

tag: human cell line


title: spleen_slice_S20C1

description:
S20C1
Combinatorially-indexed transcriptome
spleen_all_raw_labeled.h5ad

source_name: mouse spleen injected with MC38 and with HEK293t spike in

value: Spleen


title: spleen_slice_S20C2

description:
S20C2
Combinatorially-indexed transcriptome
spleen_all_raw_labeled.h5ad


title: 823011_RNAseq

value: pCR


title: 823012_RNAseq


title: spleen_slice_S15C

description:
S15C
Combinatorially-indexed transcriptome
spleen_all_raw_labeled.h5ad


title: spleen_slice_S10C

description:
S10C
Combinatorially-indexed transcriptome
spleen_all_raw_labeled.h5ad


title: singlecell_clone_3

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

institute: Nanyang Technological University

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Only uniquely mapped reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
standard normalized count Fragments Per Kilobase of transcript per Million mapped reads (FPKM) except gene length in the formula is replaced with mapped length
Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Comma-separated (.csv) file include FPKM values for all the samples in the matrix form

extract_protocol:
Single cells were FACS sorted into lysis buffer directly. Total cell lysate was used for reverse transcription and cDNA amplification.
Illumina Nextera XT kit was used for library preparation according to the manufacturer's intructions.

tag: developmental stage

value: blood stage schizonts

value: 3D7 subclone


title: 825008_RNAseq


title: 823009_RNAseq

value: Every 2 weeks


title: 823010_RNAseq


title: 823007_RNAseq


title: 823006_RNAseq


title: 823008_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: liver_slice_L20T

description:
L20T
Combinatorially-indexed transcriptome
liver_all_raw_labeled.loom


title: liver_slice_L20C1

description:
L20C1
Combinatorially-indexed transcriptome
liver_all_raw_labeled.loom


title: liver_slice_L10C

description:
L10C
Combinatorially-indexed transcriptome
liver_all_raw_labeled.loom


title: liver_slice_L30C8

description:
L30C8
Combinatorially-indexed transcriptome
liver_all_raw_labeled.loom


title: 823004_RNAseq


title: 823003_RNAseq


title: 823002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: 822003_RNAseq


title: 822002_RNAseq

value: B


title: 822001_RNAseq


title: whole embryo RNA-line sj461_rep2

city: St. Louis

first: Aaron

last: Johnson

state: MO

address: 600 S Euclid

institute: Washington University School of Medicine in St. Louis

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (v2.4)
Trimmed reads were aligned using STAR (v2.5.4b) to the Drosophila reference genome BDGP6 with Ensemble Gene Annotation (v95)
Variants for each line were called using aligned reads with the bcftools (v1.9) mpileup function followed by the bcftools call function
Low quality variants were filtered using bcftools filter. Variants not found in both replicates from a line were discarded. Variants present in any complementary lines were discarded.
Remaining variants were mapped to genes and prioritized using VEP (ensembl.org /Tools/VEP)
Genome_build: BDGP6
Supplementary_files_format_and_content: Excel files have a QUAL score for each variant

organism: Drosophila melanogaster

source_name: whole embryo RNA

growth_protocol: Adult flies were allowed to lay on grape agar plates for 3hr at 25C. The plates were then changed and aged for 7hr to stage the embryos. Embryos were dechorionated and placed on ice.

extract_protocol:
Total RNA was extracted from whole embryos using the Qiagen RNeasy kit.
cDNA libraries were constructed by Novogene

treatment_protocol: Homozygous embryos were identified and collected by hand using a 'green balancer' under a fluorescent dissecting microscope.

value: Stage 12

tag: tissue

value: embryo

tag: line


title: whole embryo RNA-line sj461_rep1_1


title: whole embryo RNA-line sj287_rep2_1


title: whole embryo RNA-line sj287_rep1_2


title: whole embryo RNA-line sj287_rep1_1


title: 821021_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Never


title: whole embryo RNA-line sj440_rep2_2


title: liver_slice_L30C

description:
L30C
Combinatorially-indexed transcriptome
liver_all_raw_labeled.loom


title: 821020_RNAseq

value: RD


title: 821019_RNAseq

value: Every 3 weeks

value: Unknown


title: whole embryo RNA-line sj440_rep1


title: 821018_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: N1-2 (biopsy positive)


title: whole embryo RNA-line sj266_rep2


title: 821017_RNAseq


title: whole embryo RNA-line sj266_rep1


title: 823001_RNAseq


title: whole embryo RNA-line sj287_rep2_2


title: whole embryo RNA-line sj461_rep1_2


title: whole embryo RNA-line sj340_rep1


title: whole embryo RNA-line sj154_rep2_1


title: 821011_RNAseq

value: pCR


title: 821010_RNAseq


title: 821013_RNAseq


title: 821009_RNAseq


title: whole embryo RNA-line sj154_rep1_2


title: whole embryo RNA-line sj340_rep2


title: whole embryo RNA-line sj154_rep2_2


title: whole embryo RNA-line sj154_rep1_1


title: 821005_RNAseq


title: whole embryo RNA-line sj440_rep2_1


title: 821002_RNAseq


title: 821003_RNAseq


title: 4-hFOB-SMAD1-IP-BMP2-N1-INPUT

city: Berlin

first: Maria

last: Reichenbach

address: Thielallee 63

department: Institute for Chemistry and Biochemistry

country: Germany

institute: Freie Universität Berlin

description: INPUT

data_processing:
Sequencing data quality was assessed prior to processing using FastQC (version 0.11.8).
Quality trimming and adapter clipping were performed using cutadapt (v.2.4) with the following parameters: minimum length = 25, minimum quality = 20, overlap = 5), followed by a quality assessment using FastQC.
Trimmed reads of enriched and input samples were aligned to GRCm38 using bwa mem and sorted using samtools v.1.10.
We used bamstats to monitor the alignment statistics. Duplicate reads were removed using GATK4/Picard MarcDuplicates (v.4.1.4.1).
Reads with a mapping quality of below 15 were filtered using samtools view. Genome wide bigWig coverage files were created using bamCoverage 3.4.3 without data normalization and with CPM normalization for enriched and input samples.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig

source_name: hFOB 1.10, ATCC CRL-11372

growth_protocol: hFOBs (ATCC® CRL-11372™) were cultured in a 1:1 mixture of Dulbeccos’ Modified Eagle’s Medium and Ham’s F12 Medium with 2.5 mM L-glutamine and 8.1 mg/l Phenol Red supplemented with 10% Fetal Calf Serum and antibiotics (100 U/ml Penicillin and 0.1 mg/ml Streptomycin and 0.3 mg/ml G418). The cells were grown at a permissive temperature of 33.5°C in a 5% CO2 humidified atmosphere until confluent.

extract_protocol:
Cells were fixed in 1% formaldehyde and quenched by adding glycine 125 mM for 5 min at 4 °C. After this, cells were harvested and lysed according to the protocol described by Lee et al. and chromatin was sheared by sonication using the Bioruptor ultrasonicator (Diagenode). Sheared chromatin was immunoprecipitated using 10 μg of total SMAD1 antibody (Cell Signaling, #9743) or the normal rabbit IgG antibody (Cell Signaling, #2729) as a control, followed by incubation with protein G magnetic beads (Invitrogen). Eluted DNA was purified using DNA purification buffers and spin columns kit, according to the manufacturer's instructions (Cell Signaling).
NEBNext Ultra II DNA library preparation kit was used according to manufacturer's instruction.

treatment_protocol: Cells were grown to confluence and then starved in 0% FCS for 3 h and stimulated with BMP-2 (5nM) for 90 min.

value: human fetal osteoblastic cell line

tag: cell line

value: hFOB 1.10, ATCC CRL-11372

tag: treatment

value: 5nM BMP2

tag: chip antibody

tag: experiment


title: 820013_RNAseq


title: 3-hFOB-SMAD1-IP-BMP2-N1-INPUT

description: INPUT


title: hFOB-SMAD1-IP-with-BMP2-N2

description: ChIP


title: hFOB-SMAD1-IP-with-BMP2-N1

description: ChIP


title: 820012_RNAseq


title: 820011_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 820010_RNAseq


title: 820009_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: 821014_RNAseq

value: Every 2 weeks


title: 820008_RNAseq


title: 821012_RNAseq


title: 820005_RNAseq


title: 820006_RNAseq


title: 820007_RNAseq


title: 821006_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 770003_RNAseq

value: Never


title: 820003_RNAseq


title: 770005_RNAseq

value: RD


title: 770004_RNAseq

value: Every 3 weeks


title: CRISPRa-hESC gene expression library

city: Singapore

first: John

middle: F.

last: Ouyang

address: 8 College Road, Level 8 CVMD

institute: Duke-NUS Medical School

description:
single-cell
polyA RNA

data_processing:
To distinguish the protospacer and scaffold present in the gRNA, we inspected different regions within the paired-end sequencing reads in the gRNA library (Supplementary Figure S2b). In read 2, we expect the read to begin with the 10x template switching oligo (TSO) sequence (30 nt), followed by a G nucleotide, the protospacer (20nt) and then the backbone. In read 1, we expect the read to contain the 10X cell barcode and UMI (28nt in total), followed by the capture sequence (22nt) and finally the backbone. Thus, we computationally searched the four following regions to determine the protospacer-scaffold combination. We first searched region 1 (position 32-51) and region 2 (position 52 to 71) in read 2 to identify the protospacer and backbone respectively. Second, we scanned region 4 (position 29-50) and region 3 (position 51 to 70) in read 1 to identify the capture sequence and capture sequence position respectively. Each region was also scanned 1nt upstream and downstream to account for frame shifts. We then used a quality control filtering criterion of allowing for (i) a maximum of one mismatch/ deletion/ insertion, i.e. a Levenshtein distance of 1, in each of the four regions and (ii) a maximum of total two mismatches/ deletions/ insertions across all four regions. This was performed using the stringdistmatrix function in the stringdist R package (v0.9.6). We also removed reads that do not contain cell barcodes of single cells passing the gene expression quality control (see details in the next section). Overall, this resulted in 33,910,609 reads remaining, which is then collapsed to 7,129,656 UMIs.
For the GEX library, alignment to the hg38 genome (GRCh38, Cell Ranger reference version  2020-A) and unique molecular identifier (UMI) counting were performed using Cell Ranger  (v4.0.0), specifying the expected number of cells to be 11500. The filtered_feature_bc_matrix  generated was used as the starting gene expression matrix for downstream quality control,  preprocessing and analysis.
Genome_build: hg38
Supplementary_files_format_and_content: count matrix for gene expression and CRISPR gRNA capture

source_name: hESC-CRISPRa-GEX

growth_protocol: The inducible dCas9-VPR AAVS1 knock-in H1 cells (Clone 4K) were seeded at 1.5 x 104 cells/cm2 on Geltrex coated 6 wells plate 2 days prior to lentivirus transduction in mTeSR TM1, supplemented with 10 μM Y-27632 for the first day.

extract_protocol:
Cells were lifted using Accutase (Gibco) and resuspended in FACS buffer (1X Dulbecco's  phosphate-buffer saline (DPBS; Lonza) supplemented with 0.1% (w/v) Bovine Serum Albumin (BSA; Sigma Aldrich) and 2.5mM EDTA (Invitrogen)). Cells were stained with Propidium Iodide (PI; 1:500; Sigma Aldrich) prior to sorting using the FACSAriaTM III cell sorter (BD Biosciences). Cells expressing gRNA of interest were defined as live/ PI- and GFP+. Control population was defined as live/ PI- . 30,000 cells per sample (10 samples) were sorted into FACS buffer for downstream processing for scRNA-seq.
Single cell capture, RNA-seq library construction and sequencing were carried out using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 with Feature Barcoding technology (10X Genomics)
single-cell RNA sequencing

treatment_protocol: For transduction, gRNA of 8 unique scaffolds but containing the same protospacer sequence (SOX17, ASCL1 or SCRAM) were delivered to individual wells by lentivirus. A total MOI of 2.4 (MOI of ~0.3 per virus) was pooled in mTeSR TM1 containing 8 μg/ml Polybrene (Sigma Aldrich) and 2 μg/ml Doxycycline (Sigma Aldrich). Virus infected cells were maintained at 37°C with 5% CO2 with daily media change and harvested 0- (non-infected), 3-, 5- or 7-days post transduction.

value: hESC


title: 766001_RNAseq


title: 763005_RNAseq

value: Current


title: 770001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: 764002_RNAseq

value: pCR


title: 771001_RNAseq

value: N1-2 (biopsy positive)


title: CRISPRa-hESC CRISPR gRNA capture library

description:
single-cell
CRISPR gRNA

source_name: hESC-CRISPRa-CRISPR


title: 763004_RNAseq


title: 767003_RNAseq


title: 820002_RNAseq


title: F13d28-75P

city: Tulln

first: Bertrand

last: Grenier

address: Technopark 1

department: Research Center

country: Austria

institute: BIOMIN

data_processing:
Adapter removal and quality trimming with bbduk (bbmap - v38.22)
Alignment with STAR (v2.6.1d). Resulting BAM files are sorted by coordinates.
Quantification with HTSeq-counts (v0.11.2)
Normalization, differential gene expression analysis with DESeq2(v1.22.2)
Genome_build: Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa
Supplementary_files_format_and_content: Count matrix with raw counts for every gene for every sample
Supplementary_files_format_and_content: Raw count matrix is normalized by the DESeq2's Relative Log Expression (RLE) method and then used for downstream analysis

organism: Sus scrofa

extract_protocol:
Approximately 30 mg of ileal or liver tissues were disrupted via a bead-beating step, and the total RNA was extracted and purified with the RNeasy Mini Kit including DNase digestion on column (Qiagen, Germany)
Construction of RNA sequencing libraries was done with the Illumina stranded TruSeq RNA library including poly(A) enrichment.

treatment_protocol: After cutting, rinsing with sterile saline water the ileum, small pieces were transferred into 1 mL of RNAlater (Ambion Inc., USA), stored overnight at 4 °C, and transferred to -80°C until transcriptomics analysis. The same procedure was applied for the liver with cleaned small pieces transferred into 1 mL of RNAlater, and stored the same way as for the ileum samples.

value: Phytogenics

value: Ileum


title: 767001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Former


title: 764003_RNAseq


title: 760002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: F13d28-80C

value: Control


title: 762002_RNAseq

value: B


title: F13d28-134P


title: F13d28-138P


title: F13d28-92C


title: 747011_RNAseq

value: C

value: Every 2 weeks


title: 747008_RNAseq

value: Never

value: RD


title: F13d28-71C


title: 763003_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Every 3 weeks


title: F13d28-95P


title: 747003_RNAseq


title: 745011_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Current


title: 745007_RNAseq

value: pCR


title: F13d28-110C


title: 763001_RNAseq

value: N1-2 (biopsy positive)


title: 744002_RNAseq

value: A


title: F13d28-107P

value: Phytogenics

value: Ileum


title: PLOOP_137_2

value: Phytogenics Feed Additive and Oxidized Oil; PFA_OO

value: Liver


title: 745002_RNAseq


title: 745010_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: 745006_RNAseq

value: B

value: Former


title: 745005_RNAseq

value: Every 2 weeks


title: 745003_RNAseq

value: Never


title: 740008_RNAseq


title: 744001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: RD


title: 740009_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)


title: PigLiv_00P_79


title: PigLiv_00P_126


title: 740005_RNAseq

value: Every 3 weeks

value: pCR


title: PigLiv_00P_98


title: PLOOP_77_2


title: 740006_RNAseq

value: N1-2 (biopsy positive)


title: PLOO_130_2

value: Oxidized Oil; OO


title: 740003_RNAseq


title: 747002_RNAseq


title: 721004_RNAseq


title: F13d28-100C

value: Control

value: Ileum


title: 721002_RNAseq

value: A


title: PigLiv_00P_105

value: Phytogenics Feed Additive and Oxidized Oil; PFA_OO

value: Liver


title: 744004_RNAseq

value: Current


title: 706012_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Every 2 weeks


title: 721001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Never


title: PigLiv_00_99


title: 706008_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)

value: Former


title: 740002_RNAseq

value: N1-2 (biopsy positive)

value: pCR


title: 706007_RNAseq


title: 704005_RNAseq

value: Every 3 weeks

value: RD


title: 704004_RNAseq


title: PLOO_88_2

value: Oxidized Oil; OO


title: 706003_RNAseq


title: PigLiv_00_74


title: 706006_RNAseq

value: A


title: 706002_RNAseq


title: 702011_RNAseq


title: 702009_RNAseq


title: 702012_RNAseq


title: 702007_RNAseq


title: PigLiv_P_138

value: Phytogenics Feed Additive ; PFA

value: Liver


title: PLP_134_2


title: 702004_RNAseq

value: Current


title: PigLiv_P_107


title: 702005_RNAseq


title: 702003_RNAseq


title: PLP_95_2


title: PigLiv_00_102


title: PLOO_97_1


title: 702001_RNAseq


title: 706005_RNAseq


title: 655001_RNAseq


title: PLP_75_2


title: 653006_RNAseq


title: PigLiv_P_67


title: 653005_RNAseq


title: 653002_RNAseq


title: PigLiv_C_110

value: Control; CTR


title: 653001_RNAseq


title: PigLiv_C_92


title: 652001_RNAseq


title: 651002_RNAseq


title: PLC_85_1


title: 651001_RNAseq


title: 593002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Every 2 weeks


title: 652008_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Never


title: 702002_RNAseq


title: 584004_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N0 (clinically negative or biopsy negative)


title: PLC_80_1


title: 584003_RNAseq

value: N1-2 (biopsy positive)

value: Former

value: pCR


title: 584002_RNAseq


title: 593001_RNAseq

value: RD


title: PigLiv_C_71


title: 581004_RNAseq

value: A


title: 575002_RNAseq

value: Every 3 weeks


title: 581001_RNAseq


title: 575001_RNAseq


title: PigLiv_C_100

value: Liver


title: 581005_RNAseq


title: 584001_RNAseq


title: 652004_RNAseq

value: Unknown


title: 652003_RNAseq


title: 581002_RNAseq


title: cKO_dDG_Input_rep1

city: New York

first: Eric

middle: F

last: Schmidt

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
FASTQC 0.11.4 was used to assess the quality of reads and Trim Galor 0.4.1 wasused to trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.4.2a using defaul settings.
SAMtools v0.1.19-444 was used for indexing and removal of duplicates.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Differential expression was calculated by DESeq2 v1.4.5 using default settings.
Genome_build: mm10
Supplementary_files_format_and_content: CSV format; Data output from DESeq2 on all genes for each sample in the analysis including: ensemblID, chromosome, gene symbol, chromosome, strand, txStart position, txEnd position, description, transcriptID, normalized counts for each sample, baseMean, log2FoldChange (IP/input), lfcSE, stat, pvalue, pad, UCSC ID, RefSeq ID, EntrezGene ID.

source_name: Whole cortex input RNA pooled from two mice with transgenic expression of EGFPL10a

extract_protocol:
Ventral dentate gyrus was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol. Total RNA from "input" samples was purified from the pre-IP tissue homogentates using the Agilent Nanoprep kit.
15 ng total RNA from TRAP IP or input was amplified using the NuGEN Ovation RNA-Seq System V2 and libraries were prepared from 10 ug amplified RNA using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocols.

treatment_protocol: For TRAP, Drd3-Cre KI198 mice were crossed to Rosa26-fsTRAP mice to express EGFP-L10a transgene in granule cell in granule cell layer and mossy cells in hilus of the dentate gyrus. For cKOs, Drd3-Cre KI198::Htr4-Floxed mice were crossed to Rosa26-fsTRAP::Htr4-Floxed mice. TRAP was performed in adult (8-12 week old) animals.

tag: strain

tag: brain region

value: Dorsal Dentate Gyrus

value: Granule Cells/Mossy Cells

value: Conditional Htr4 Knockout

tag: rna

value: Whole tissue input


title: 574002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Every 2 weeks


title: 573002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: Never


title: 574003_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N1-2 (biopsy positive)


title: 573003_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Current

value: pCR


title: 573004_RNAseq

value: Every 3 weeks


title: WT_dDG_Input_rep2

value: Drd3-Cre KI198::Rosa26-fsTRAP

value: Wildtype


title: 574005_RNAseq

value: C

value: Unknown

value: RD


title: 573001_RNAseq

value: A


title: cKO_dDG_Input_rep2

value: Dorsal Dentate Gyrus

value: Granule Cells/Mossy Cells

value: Conditional Htr4 Knockout

value: Whole tissue input


title: 567001_RNAseq

value: Every 2 weeks

value: Former


title: WT_dDG_Input_rep1


title: 566001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B

value: N1-2 (biopsy positive)

value: Never


title: 564001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: Every 3 weeks


title: cKO_vDG_Input_rep2

description:
cKO_vDG_TRAP_IPvInput.csv
vDG_cKOvWT_Input.csv

value: Ventral Dentate Gyrus


title: 564002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: N0 (clinically negative or biopsy negative)

value: Current


title: 569001_RNAseq

value: A

value: RD


title: cKO_vDG_Input_rep1

value: Granule Cells/Mossy Cells

value: Conditional Htr4 Knockout


title: 558002_RNAseq

value: pCR


title: 560003_RNAseq

value: Every 2 weeks


title: 560002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2


title: 560004_RNAseq

value: B


title: 557004_RNAseq


title: WT_vDG_Input_rep3

description:
WT_vDG_TRAP_IPvInput.csv
vDG_cKOvWT_Input.csv

value: Drd3-Cre KI198::Rosa26-fsTRAP

value: Wildtype

value: Whole tissue input


title: cKO_vDG_TRAP_IP_rep2

description:
cKO_vDG_TRAP_IPvInput.csv
vDG_cKOvWT_IP.csv

source_name: TRAP IP RNA of pooled vDG from three mice with transgenic expression of EGFPL10a

value: TRAP IP


title: 574001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N1-2 (biopsy positive)


title: WT_dDG_Input_rep3

value: Dorsal Dentate Gyrus


title: 557002_RNAseq

value: Every 3 weeks

value: Former


title: cKO_vDG_TRAP_IP_rep1

value: Ventral Dentate Gyrus


title: 557001_RNAseq

value: A

value: Current

value: RD


title: 556003_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: N0 (clinically negative or biopsy negative)

value: Unknown


title: 555007_RNAseq

value: Never

value: pCR


title: WT_vDG_Input_rep2

value: Drd3-Cre KI198::Rosa26-fsTRAP

value: Granule Cells/Mossy Cells

value: Wildtype

value: Whole tissue input


title: 556002_RNAseq


title: 555008_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: WT_vDG_Input_rep1


title: WT_vDG_TRAP_IP_rep3

description:
WT_vDG_TRAP_IPvInput.csv
vDG_cKOvWT_IP.csv

value: TRAP IP


title: 555005_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: N1-2 (biopsy positive)

value: Every 3 weeks


title: 555006_RNAseq

value: A

value: RD


title: 555003_RNAseq

value: Current


title: 555002_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 516001_RNAseq

value: Former


title: WT_vDG_TRAP_IP_rep2

value: Ventral Dentate Gyrus


title: 514007_RNAseq

value: Never


title: 514002_RNAseq

value: pCR


title: WT_vDG_TRAP_IP_rep1

value: Drd3-Cre KI198::Rosa26-fsTRAP

value: Granule Cells/Mossy Cells


title: sgStat1 [ACTGAGCG_TAAGGCTC]

first: Michael

last: Wheeler

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Reads were aligned against the GRCm38 mouse transcriptome using kallisto (v0.46.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: abundance.tsv: count file; abundance.h5: count table for downstream analysis, same as abundance.tsv.

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on CD11b-low, CD45+, Ly6c-low.
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: strain background

tag: genotype/variation

tag: Sex

value: F

tag: age

value: 12-13 weeks

tag: tissue/cell type

value: CNS/CD11b-low, CD45+, Ly6c-low


title: sgStat1 [TAGCGCTC_TAAGGCTC]


title: 514001_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: 512010_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 512007_RNAseq

value: Every 3 weeks


title: 512006_RNAseq

value: N1-2 (biopsy positive)

value: Unknown


title: 512009_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: RD


title: 512005_RNAseq

value: Current


title: sgStat1 [ATGCGCAG_TAAGGCTC]


title: sgStat1 [TACGCTGC_TAAGGCTC]


title: 512004_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Never

value: pCR


title: 512003_RNAseq


title: 508006_RNAseq


title: 512001_RNAseq


title: 512002_RNAseq


title: 508005_RNAseq

value: Every 2 weeks


title: 509001_RNAseq


title: sgIfngr2 [GGAGCTAC_TAAGGCTC]

value: F

value: 12-13 weeks


title: sgIfngr2 [ACTCGCTA_TAAGGCTC]

value: CNS/CD11b-low, CD45+, Ly6c-low


title: sgIfngr2 [CGGAGCCT_TAAGGCTC]


title: sgIfngr2 [GCGTAGTA_TAAGGCTC]


title: sgIfngr1 [TCGACGTC_ATAGCCTT]


title: 508003_RNAseq


title: 508004_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: 508001_RNAseq


title: 508002_RNAseq


title: sgIfngr1 [TGCAGCTA_ATAGCCTT]


title: 507003_RNAseq


title: 507001_RNAseq


title: sgIfngr1 [CGATCAGT_ATAGCCTT]


title: 555004_RNAseq


title: 502002_RNAseq


title: 502003_RNAseq


title: 502004_RNAseq


title: sgTnfsf10 [ACTGAGCG_ATAGCCTT]


title: 502001_RNAseq


title: sgTnfsf10 [TAGCGCTC_ATAGCCTT]


title: 501006_RNAseq


title: sgIfngr1 [CCTAAGAC_ATAGCCTT]


title: 501003_RNAseq


title: 500005_RNAseq


title: 501004_RNAseq


title: sgTnfsf10 [ATGCGCAG_ATAGCCTT]


title: 500003_RNAseq


title: 500001_RNAseq


title: 500002_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 451006_RNAseq

value: N1-2 (biopsy positive)

value: Every 3 weeks


title: sgScrmbl [CGGAGCCT_ATAGCCTT]

source_name: sgScrmbl

value: sgScrmbl


title: 451004_RNAseq


title: sgScrmbl [GCGTAGTA_ATAGCCTT]


title: 453001_RNAseq

value: Former


title: 451003_RNAseq

value: RD


title: 408014_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A


title: sgScrmbl [TACGCTGC_ATAGCCTT]


title: 408013_RNAseq

value: Never


title: SgStat1 ACTCGCTA_ATAGCCTT

data_processing:
Reads were aligned against the GRCm38 mouse transcriptome using kallisto (v0.46.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: run_info.json: Alignment QC; abundance.tsv: count file compatible with Excel; abundance.h5: count table for downstream analysis, same as abundance.tsv.

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to Smart-seq 2 protocol as described (Picelli et al., 2014)


title: 408008_RNAseq

value: N0 (clinically negative or biopsy negative)


title: 408011_RNAseq

value: pCR


title: SgStat1 TCGACGTC_CTTAATAG

value: F


title: 408010_RNAseq


title: 408012_RNAseq


title: SgStat1 CGATCAGT_CTTAATAG

value: 12-13 weeks


title: SgStat1 TGCAGCTA_CTTAATAG


title: 408009_RNAseq


title: 408007_RNAseq


title: SgIfngr2 CCTAAGAC_CTTAATAG


title: 451007_RNAseq


title: 408006_RNAseq


title: 404001_RNAseq


title: 408001_RNAseq


title: SgIfngr2 ACTGAGCG_CTTAATAG


title: 403008_RNAseq

value: Every 2 weeks


title: sgScrmbl [GGAGCTAC_ATAGCCTT]

value: CNS/CD11b-low, CD45+, Ly6c-low


title: SgIfngr2 TAGCGCTC_CTTAATAG


title: 403006_RNAseq

value: Current


title: 403002_RNAseq


title: SgIfngr1 TACGCTGC_CTTAATAG


title: 402005_RNAseq

value: Unknown


title: 402006_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: SgIfngr1 CGGAGCCT_CTTAATAG


title: 403001_RNAseq

value: N1-2 (biopsy positive)


title: 300006_RNAseq


title: 401001_RNAseq


title: 408005_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C

value: Every 3 weeks


title: 301001_RNAseq


title: 402004_RNAseq

value: RD


title: 300005_RNAseq


title: SgIfngr1 GCGTAGTA_CTTAATAG


title: 300004_RNAseq


title: 300003_RNAseq

value: Former


title: SgTnfsf10 ACTCGCTA_CTTAATAG


title: SgTnfsf10 TCGACGTC_TCTTACGC


title: SgTnfsf10 TGCAGCTA_TCTTACGC


title: SgIfngr2 ATGCGCAG_CTTAATAG


title: 300002_RNAseq

value: Never


title: 270001_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: N0 (clinically negative or biopsy negative)


title: SgScrmbl CCTAAGAC_TCTTACGC

source_name: SgScrmbl

value: F

value: 12-13 weeks


title: SgScrmbl ACTGAGCG_TCTTACGC


title: SgIfngr1 GGAGCTAC_CTTAATAG


title: 230001_RNAseq

value: Every 2 weeks


title: 221007_RNAseq


title: 221008_RNAseq

value: pCR


title: LampKD [TCCTGAGC_ATAGAGAG]

data_processing:
The sample is aligned to GRCm38 transcriptome using Kallisto (v0.46.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Kallisto alignment/quantification software output including txt format with transcripts ID and abundance.

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al. 2014).

value: WT C57Bl/6

value: Female

tag: cell type

value: Astrocytes

tag: sg

tag: disease state

value: Induced EAE


title: 221004_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: B


title: SgScrmbl TAGCGCTC_TCTTACGC


title: 221003_RNAseq

value: PBO FOR VELIPARIB 50 MG BID + PBO FOR CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: C


title: 408002_RNAseq

value: N1-2 (biopsy positive)

value: Every 3 weeks

value: Former

value: RD


title: 300001_RNAseq

value: Current


title: 221006_RNAseq

value: N0 (clinically negative or biopsy negative)

value: Never


title: 221005_RNAseq

value: Every 2 weeks


title: 220005_RNAseq

value: VELIPARIB 50 MG BID + CARBOPLATIN AUC 6 + PACLITAXEL 80 MG/M^2

value: A

value: pCR


title: Scr [TAAGGCGA_ATAGAGAG]

value: WT C57Bl/6

value: Female

value: 12-13 weeks

value: Astrocytes

value: sgScrmbl


title: LampKD [TAGGCATG_ATAGAGAG]

value: Induced EAE


title: 220006_RNAseq